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1.
  • Pulit, S. L., et al. (författare)
  • Atrial fibrillation genetic risk differentiates cardioembolic stroke from other stroke subtypes
  • 2018
  • Ingår i: Neurology-Genetics. - : Ovid Technologies (Wolters Kluwer Health). - 2376-7839. ; 4:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective We sought to assess whether genetic risk factors for atrial fibrillation (AF) can explain cardioembolic stroke risk. We evaluated genetic correlations between a previous genetic study of AF and AF in the presence of cardioembolic stroke using genome-wide genotypes from the Stroke Genetics Network (N = 3,190 AF cases, 3,000 cardioembolic stroke cases, and 28,026 referents). We tested whether a previously validated AF polygenic risk score (PRS) associated with cardioembolic and other stroke subtypes after accounting for AF clinical risk factors. We observed a strong correlation between previously reported genetic risk for AF, AF in the presence of stroke, and cardioembolic stroke (Pearson r = 0.77 and 0.76, respectively, across SNPs with p < 4.4 x 10(-4) in the previous AF meta-analysis). An AF PRS, adjusted for clinical AF risk factors, was associated with cardioembolic stroke (odds ratio [OR] per SD = 1.40, p = 1.45 x 10(-48)), explaining similar to 20% of the heritable component of cardioembolic stroke risk. The AF PRS was also associated with stroke of undetermined cause (OR per SD = 1.07,p = 0.004), but no other primary stroke subtypes (all p > 0.1). Genetic risk of AF is associated with cardioembolic stroke, independent of clinical risk factors. Studies are warranted to determine whether AF genetic risk can serve as a biomarker for strokes caused by AF.
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3.
  • Marini, S., et al. (författare)
  • Association of Apolipoprotein E With Intracerebral Hemorrhage Risk by Race/Ethnicity A Meta-analysis
  • 2019
  • Ingår i: Jama Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 76:4, s. 480-491
  • Tidskriftsartikel (refereegranskat)abstract
    • IMPORTANCE Genetic studies of intracerebral hemorrhage (ICH) have focused mainly on white participants, but genetic risk may vary or could be concealed by differing nongenetic coexposures in nonwhite populations. Transethnic analysis of risk may clarify the role of genetics in ICH risk across populations. OBJECTIVE To evaluate associations between established differences in ICH risk by race/ethnicity and the variability in the risks of apolipoprotein E (APOE) epsilon 4 alleles, the most potent genetic risk factor for ICH. DESIGN, SETTING, AND PARTICIPANTS This case-control study of primary ICH meta-analyzed the association of APOE allele status on ICH risk, applying a 2-stage clustering approach based on race/ethnicity and stratified by a contributing study. A propensity score analysis was used to model the association of APOE with the burden of hypertension across race/ethnic groups. Primary ICH cases and controls were collected from 3 hospital- and population-based studies in the United States and 8 in European sites in the International Stroke Genetic Consortium. Participants were enrolled from January 1, 1999, to December 31, 2017. Participants with secondary causes of ICH were excluded from enrollment. Controls were regionally matched within each participating study. MAIN OUTCOMES AND MEASURES Clinical variables were systematically obtained from structured interviews within each site. APOE genotype was centrally determined for all studies. RESULTS In total, 13 124 participants (7153 [54.5%] male with a median [interquartile range] age of 66 [56-76] years) were included. In white participants, APOE epsilon 2 (odds ratio [OR], 1.49; 95% CI, 1.24-1.80; P < .001) and APOE epsilon 4 (OR, 1.51; 95% CI, 1.23-1.85; P < .001) were associated with lobar ICH risk; however, within self-identified Hispanic and black participants, no associations were found. After propensity score matching for hypertension burden, APOE epsilon 4 was associated with lobar ICH risk among Hispanic (OR, 1.14; 95% CI, 1.03-1.28; P = .01) but not in black (OR, 1.02; 95% CI, 0.98-1.07; P = .25) participants. APOE epsilon 2 and epsilon 4 did not show an association with nonlobar ICH risk in any race/ethnicity. CONCLUSIONS AND RELEVANCE APOE epsilon 4 and epsilon 2 alleles appear to affect lobar ICH risk variably by race/ethnicity, associations that are confirmed in white individuals but can be shown in Hispanic individuals only when the excess burden of hypertension is propensity score-matched; further studies are needed to explore the interactions between APOE alleles and environmental exposures that vary by race/ethnicity in representative populations at risk for ICH.
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4.
  • Shellock, R. J., et al. (författare)
  • Building leaders for the UN Ocean Science Decade : a guide to supporting early career women researchers within academic marine research institutions
  • 2023
  • Ingår i: ICES Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 80:1, s. 56-75
  • Tidskriftsartikel (refereegranskat)abstract
    • Diverse and inclusive marine research is paramount to addressing ocean sustainability challenges in the 21st century, as envisioned by the UN Decade of Ocean Science for Sustainable Development. Despite increasing efforts to diversify ocean science, women continue to face barriers at various stages of their career, which inhibits their progression to leadership within academic institutions. In this perspective, we draw on the collective experiences of thirty-four global women leaders, bolstered by a narrative review, to identify practical strategies and actions that will help empower early career women researchers to become the leaders of tomorrow. We propose five strategies: (i) create a more inclusive culture, (ii) ensure early and equitable career development opportunities for women ECRs, (iii) ensure equitable access to funding for women ECRs, (iv) offer mentoring opportunities and, (v) create flexible, family-friendly environments. Transformational, meaningful, and lasting change will only be achieved through commitment and collaborative action across various scales and by multiple stakeholders. 
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5.
  • Anderson, Christopher D., et al. (författare)
  • Genetic variants in CETP increase risk of intracerebral hemorrhage
  • 2016
  • Ingår i: Annals of Neurology. - : Wiley. - 1531-8249 .- 0364-5134. ; 80:5, s. 730-740
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: In observational epidemiologic studies, higher plasma high-density lipoprotein cholesterol (HDL-C) has been associated with increased risk of intracerebral hemorrhage (ICH). DNA sequence variants that decrease cholesteryl ester transfer protein (CETP) gene activity increase plasma HDL-C; as such, medicines that inhibit CETP and raise HDL-C are in clinical development. Here, we test the hypothesis that CETP DNA sequence variants associated with higher HDL-C also increase risk for ICH.METHODS: We performed 2 candidate-gene analyses of CETP. First, we tested individual CETP variants in a discovery cohort of 1,149 ICH cases and 1,238 controls from 3 studies, followed by replication in 1,625 cases and 1,845 controls from 5 studies. Second, we constructed a genetic risk score comprised of 7 independent variants at the CETP locus and tested this score for association with HDL-C as well as ICH risk.RESULTS: Twelve variants within CETP demonstrated nominal association with ICH, with the strongest association at the rs173539 locus (odds ratio [OR] = 1.25, standard error [SE] = 0.06, p = 6.0 × 10(-4) ) with no heterogeneity across studies (I(2) = 0%). This association was replicated in patients of European ancestry (p = 0.03). A genetic score of CETP variants found to increase HDL-C by ∼2.85mg/dl in the Global Lipids Genetics Consortium was strongly associated with ICH risk (OR = 1.86, SE = 0.13, p = 1.39 × 10(-6) ).INTERPRETATION: Genetic variants in CETP associated with increased HDL-C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL-raising strategies, further exploration of potential adverse cerebrovascular outcomes may be warranted. Ann Neurol 2016;80:730-740.
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6.
  • Gron, K. L., et al. (författare)
  • The association of fatigue, comorbidity burden, disease activity, disability and gross domestic product in patients with rheumatoid arthritis. : Results from 34 countries participating in the Quest-RA programme
  • 2014
  • Ingår i: Clinical and Experimental Rheumatology. - 0392-856X .- 1593-098X. ; 32:6, s. 869-877
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective The aim is to assess the prevalence of comorbidities and to further analyse to which degree fatigue can be explained by comorbidity burden, disease activity, disability and gross domestic product (GDP) in patients with rheumatoid arthritis (RA). Methods Nine thousands eight hundred seventy-four patients from 34 countries, 16 with high GDP (>24.000 US dollars [USD] per capita) and 18 low-GDP countries (<24.000 USD) participated in the Quantitative Standard monitoring of Patients with RA (QUEST-RA) study. The prevalence of 31 comorbid conditions, fatigue (0-10 cm visual analogue scale [VAS] [10 worst]), disease activity in 28 joints (DAS28), and physical disability (Health Assessment Questionnaire score MAW) were assessed. Univariate and multivariate linear regression analyses were performed to assess the association between fatigue and comorbidities, disease activity, disability and GDP. Results Overall, patients reported a median of 2 comorbid conditions of which hypertension (31.5%), osteoporosis (17.6%), osteoarthritis (15.5%) and hyperlipidaemia (14.2%) were the most prevalent. The majority of comorbidities were more common in high-GDP countries. The median fatigue score was 4.4 (4.8 in low-GDP countries and 3.8 in high-GDP countries, p<0.001). In low-GDP countries 25.4% of the patients had a high level of fatigue (>6.6) compared with 23.0% in high-GDP countries (p<0.001). In univariate analysis, fatigue increased with increasing number of comorbidities, disease activity and disability in both high- and low-GDP countries. In multivariate analysis of all countries, these 3 variables explained 29.4% of the variability, whereas GDP was not significant. Conclusion Fatigue is a widespread problem associated with high comorbidity burden, disease activity and disability regardless of GDP.
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7.
  • Hagag, Naglaa M., et al. (författare)
  • Isolation of a Novel Reassortant Highly Pathogenic Avian Influenza (H5N2) Virus in Egypt
  • 2019
  • Ingår i: Viruses. - : MDPI. - 1999-4915. ; 11:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Highly pathogenic avian influenza (HPAI) H5N1 and H5N8 have become endemic among domestic poultry in Egypt since 2006 and 2016, respectively. In parallel, the low pathogenic avian influenza H9N2 virus has been endemic since 2010. Despite the continuous circulation of these subtypes for several years, no natural reassortant has been detected so far among the domestic poultry population in Egypt. In this study, the HPAI (H5N2) virus was isolated from a commercial duck farm, giving evidence of the emergence of the first natural reassortment event in domestic poultry in Egypt. The virus was derived as a result of genetic reassortment between avian influenza viruses of H5N8 and H9N2 subtypes circulating in Egypt. The exchange of the neuraminidase segment and high number of acquired mutations might be associated with an alteration in the biological propensities of this virus.
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8.
  • Krys, K, et al. (författare)
  • Happiness Maximization Is a WEIRD Way of Living
  • 2024
  • Ingår i: Perspectives on psychological science : a journal of the Association for Psychological Science. - 1745-6924. ; , s. 17456916231208367-
  • Tidskriftsartikel (refereegranskat)
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9.
  • Alsoghier, H. M., et al. (författare)
  • NMR spectroscopic investigation of benzothiazolylacetonitrile azo dyes : CR7 substitution effect and semiempirical study
  • 2021
  • Ingår i: RESULTS IN CHEMISTRY. - : Elsevier. - 2211-7156. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Ebead et al. had reported in the synthesis and the UV-Visible solvatochromism combined with semiempirical calculations to study the tautomerism of 1,3-benzothiazol-2-ylacetonitrile azo dyes [1]. In this study, 1,3-ben zothiazol-2-ylacetonitrile azo dyes (1-6) have been resynthesized, one and two dimensional H-1 and C-13 NMR, as well as absorption and emission spectra, were collected and interpreted. The obtained results were used to clarify the tautomerization phenomenon of these dyes. Predominantly, these dyes exist in Z-hydrazone form reinforced through intramolecular hydrogen bonding in deuterated chloroform. Substituents (R) in carbon7 (CR7) are the key player of the changes in H-1 and C-13 NMR chemical shifts, also in the absorption and emission wavelengths of benzothiazole azo dyes. Also, the relative photoluminescence quantum yields (PL QY) of these dyes (1-6) were estimated and related to the nature of substituents. Finally, PM6 semiempirical calculations were employed to confirm the preferred geometric structure and experimental NMR, absorption, and emission results.
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10.
  • Leard, Lorriana E., et al. (författare)
  • Consensus document for the selection of lung transplant candidates: An update from the International Society for Heart and Lung Transplantation
  • 2021
  • Ingår i: Journal of Heart and Lung Transplantation. - : Elsevier BV. - 1053-2498 .- 1557-3117. ; 40, s. 1349-1379
  • Tidskriftsartikel (refereegranskat)abstract
    • Tens of thousands of patients with advanced lung diseases may be eligible to be considered as potential candidates for lung transplant around the world each year. The timing of referral, evaluation, determination of candidacy, and listing of candidates continues to pose challenges and even ethical dilemmas. To address these challenges, the International Society for Heart and Lung Transplantation appointed an international group of members to review the literature, to consider recent advances in the management of advanced lung diseases, and to update prior consensus documents on the selection of lung transplant candidates. The purpose of this updated consensus document is to assist providers throughout the world who are caring for patients with pulmonary disease to identify potential candidates for lung transplant, to optimize the timing of the referral of these patients to lung transplant centers, and to provide transplant centers with a framework for evaluating and selecting candidates. In addition to addressing general considerations and providing disease specific recommendations for referral and listing, this updated consensus document includes an ethical framework, a recognition of the variability in acceptance of risk between transplant centers, and establishes a system to account for how a combination of risk factors may be taken into consideration in candidate selection for lung transplantation.
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11.
  • Mosaad, Zienab, et al. (författare)
  • Emergence of Highly Pathogenic Avian Influenza A Virus (H5N1) of Clade 2.3.4.4b in Egypt, 2021-2022
  • 2023
  • Ingår i: Pathogens. - : MDPI. - 2076-0817. ; 12:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Wild migratory birds have the capability to spread avian influenza virus (AIV) over long distances as well as transmit the virus to domestic birds. In this study, swab and tissue samples were obtained from 190 migratory birds during close surveillance in Egypt in response to the recent outbreaks of the highly pathogenic avian influenza (HPAI) H5N1 virus. The collected samples were tested for a variety of AIV subtypes (H5N1, H9N2, H5N8, and H6N2) as well as other pathogens such as NDV, IBV, ILT, IBDV, and WNV. Among all of the tested samples, the HPAI H5N1 virus was found in six samples; the other samples were found to be negative for all of the tested pathogens. The Egyptian HPAI H5N1 strains shared genetic traits with the HPAI H5N1 strains that are currently being reported in Europe, North America, Asia, and Africa in 2021-2022. Whole genome sequencing revealed markers associated with mammalian adaption and virulence traits among different gene segments, similar to those found in HPAI H5N1 strains detected in Europe and Africa. The detection of the HPAI H5N1 strain of clade 2.3.4.4b in wild birds in Egypt underlines the risk of the introduction of this strain into the local poultry population. Hence, there is reason to be vigilant and continue epidemiological and molecular monitoring of the AIV in close proximity to the domestic-wild bird interface.
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12.
  • Biffi, Alessandro, et al. (författare)
  • APOE genotype and extent of bleeding and outcome in lobar intracerebral haemorrhage: a genetic association study
  • 2011
  • Ingår i: Lancet Neurology. - 1474-4465. ; 10:8, s. 702-709
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Carriers of APOE epsilon 2 and epsilon 4 have an increased risk of intracerebral haemorrhage (ICH) in lobar regions, presumably because of the effects of these gene variants on risk of cerebral amyloid angiopathy. We aimed to assess whether these variants also associate with severity of ICH, in terms of haematoma volume at presentation and subsequent outcome. Methods We investigated the association of APOE epsilon 2 and epsilon 4 with ICH volume and outcomes in patients with primary ICH in three phases: a discovery phase of 865 individuals of European ancestry from the Genetics of Cerebral Hemorrhage on Anticoagulation study, and replication phases of 946 Europeans (replication 1) and 214 African-Americans (replication 2) from an additional six studies. We also assessed the association of APOE variants with ICH volume and outcomes in meta-analyses of results from all three phases, and the association of APOE epsilon 4 with mortality in a further meta-analysis including data from previous reports. Admission ICH volume was quantified on CT scan. We assessed functional outcome (modified Rankin scale score 3-6) and mortality at 90 days. We used linear regression to establish the effect of genotype on haematoma volume and logistic regression to assess the effect on outcome from ICH. Findings For patients with lobar ICH, carriers of the APOE epsilon 2 allele had larger ICH volumes than did non-carriers in the discovery phase (p=2. 5x10(-5)), in both replication phases (p=0.008 in Europeans and p=0.016 in African-Americans), and in the meta-analysis (p=3.2x10(-8)). In the meta-analysis, each copy of APOE epsilon 2 increased haematoma size by a mean of 5.3 mL (95% CI 4.7-5.9; p=0.004). Carriers of APOE epsilon 2 had increased mortality (odds ratio [OR] 1.50, 95% CI 1.23-1.82; p=2.45x10(-5)) and poorer functional outcomes (modified Rankin scale score 3-6; 1-52, 1.25-1.85; p=1.74x10(-5)) compared with non-carriers after lobar ICH. APOE epsilon 4 was not associated with lobar ICH volume, functional outcome, or mortality in the discovery phase, replication phases, or meta-analysis of these three phases; in our further meta-analysis of 2194 patients, this variant did not increase risk of mortality (1.08,0.86-1.36; p=0.52). APOE allele variants were not associated with deep ICH volume, functional outcome, or mortality. Interpretation Vasculopathic changes associated with the APOE epsilon 2 allele might have a role in the severity and clinical course of lobar ICH. Screening of patients who have ICH to identify the epsilon 2 variant might allow identification of those at increased risk of mortality and poor functional outcomes.
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13.
  • Gau, Rémi, et al. (författare)
  • Brainhack : Developing a culture of open, inclusive, community-driven neuroscience
  • 2021
  • Ingår i: Neuron. - : Elsevier. - 0896-6273 .- 1097-4199. ; 109:11, s. 1769-1775
  • Tidskriftsartikel (refereegranskat)abstract
    • Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.
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14.
  • Woo, Daniel, et al. (författare)
  • Meta-Analysis of Genome-Wide Association Studies Identifies 1q22 as a Susceptibility Locus for Intracerebral Hemorrhage.
  • 2014
  • Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297. ; 94:4, s. 511-521
  • Tidskriftsartikel (refereegranskat)abstract
    • Intracerebral hemorrhage (ICH) is the stroke subtype with the worst prognosis and has no established acute treatment. ICH is classified as lobar or nonlobar based on the location of ruptured blood vessels within the brain. These different locations also signal different underlying vascular pathologies. Heritability estimates indicate a substantial genetic contribution to risk of ICH in both locations. We report a genome-wide association study of this condition that meta-analyzed data from six studies that enrolled individuals of European ancestry. Case subjects were ascertained by neurologists blinded to genotype data and classified as lobar or nonlobar based on brain computed tomography. ICH-free control subjects were sampled from ambulatory clinics or random digit dialing. Replication of signals identified in the discovery cohort with p < 1 × 10(-6) was pursued in an independent multiethnic sample utilizing both direct and genome-wide genotyping. The discovery phase included a case cohort of 1,545 individuals (664 lobar and 881 nonlobar cases) and a control cohort of 1,481 individuals and identified two susceptibility loci: for lobar ICH, chromosomal region 12q21.1 (rs11179580, odds ratio [OR] = 1.56, p = 7.0 × 10(-8)); and for nonlobar ICH, chromosomal region 1q22 (rs2984613, OR = 1.44, p = 1.6 × 10(-8)). The replication included a case cohort of 1,681 individuals (484 lobar and 1,194 nonlobar cases) and a control cohort of 2,261 individuals and corroborated the association for 1q22 (p = 6.5 × 10(-4); meta-analysis p = 2.2 × 10(-10)) but not for 12q21.1 (p = 0.55; meta-analysis p = 2.6 × 10(-5)). These results demonstrate biological heterogeneity across ICH subtypes and highlight the importance of ascertaining ICH cases accordingly.
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15.
  • Zanaty, Ali M., et al. (författare)
  • Avian influenza virus surveillance in migratory birds in Egypt revealed a novel reassortant H6N2 subtype
  • 2019
  • Ingår i: Avian Research. - : Elsevier BV. - 2053-7166. ; 10:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundAvian influenza viruses (AIVs) have been identified from more than 100 different species of wild birds around the globe. Wild migratory birds can act as potential spreaders for AIVs to domestic birds between different countries. Egypt is situated on important migratory flyways for wild birds between different continents. While much is known about circulation of zoonotic potential H5N1 and H9N2 AIVs in domestic poultry in Egypt, little is known about the pivotal role of migratory birds in the maintenance and transmission of the viruses in Egypt.MethodsTargeted AIV surveillance has been conducted in 2017 in different wetlands areas in Northern and Eastern Egypt.ResultsAIV of subtype H5 was detected in two bird species. In addition, a novel reassortant strain of the H6N2 subtype was identified which reveals the continuous risk of new influenza virus(es) introduction into Egypt. This novel virus possesses a reassortant pattern originating from different AIV gene pools.ConclusionsIntervention control strategies should be performed to minimize the possible contact of domestic birds with wild birds to lower the risk of virus transmission at this interface. In addition, constant monitoring of AIVs in migratory birds is essential in the early detection of influenza virus introduction into Egypt.
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16.
  • Amer, Fatma, et al. (författare)
  • Temporal Dynamics of Influenza A(H5N1) Subtype before and after the Emergence of H5N8
  • 2021
  • Ingår i: Viruses. - : MDPI. - 1999-4915. ; 13:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Highly pathogenic avian influenza (HPAI) viruses continue to circulate worldwide, causing numerous outbreaks among bird species and severe public health concerns. H5N1 and H5N8 are the two most fundamental HPAI subtypes detected in birds in the last two decades. The two viruses may compete with each other while sharing the same host population and, thus, suppress the spread of one of the viruses. In this study, we performed a statistical analysis to investigate the temporal correlation of the HPAI H5N1 and HPAI H5N8 subtypes using globally reported data in 2015-2020. This was joined with an in-depth analysis using data generated via our national surveillance program in Egypt. A total of 6412 outbreaks were reported worldwide during this period, with 39% (2529) as H5N1 and 61% (3883) as H5N8. In Egypt, 65% of positive cases were found in backyards, while only 12% were found in farms and 23% in live bird markets. Overall, our findings depict a trade-off between the number of positive H5N1 and H5N8 samples around early 2017, which is suggestive of the potential replacement between the two subtypes. Further research is still required to elucidate the underpinning mechanisms of this competitive dynamic. This, in turn, will implicate the design of effective strategies for disease control.
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17.
  • Bayha, Luca, et al. (författare)
  • Observing the emergence of a quantum phase transition shell by shell
  • 2020
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7835, s. 583-587
  • Tidskriftsartikel (refereegranskat)abstract
    • Many-body physics describes phenomena that cannot be understood by looking only at the constituents of a system1. Striking examples are broken symmetry, phase transitions and collective excitations2. To understand how such collective behaviour emerges as a system is gradually assembled from individual particles has been a goal in atomic, nuclear and solid-state physics for decades3–6. Here we observe the few-body precursor of a quantum phase transition from a normal to a superfluid phase. The transition is signalled by the softening of the mode associated with amplitude vibrations of the order parameter, usually referred to as a Higgs mode7. We achieve fine control over ultracold fermions confined to two-dimensional harmonic potentials and prepare closed-shell configurations of 2, 6 and 12 fermionic atoms in the ground state with high fidelity. Spectroscopy is then performed on our mesoscopic system while tuning the pair energy from zero to a value larger than the shell spacing. Using full atom counting statistics, we find the lowest resonance to consist of coherently excited pairs only. The distinct non-monotonic interaction dependence of this many-body excitation, combined with comparison with numerical calculations allows us to identify it as the precursor of the Higgs mode. Our atomic simulator provides a way to study the emergence of collective phenomena and the thermodynamic limit, particle by particle.
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18.
  • Devan, William J., et al. (författare)
  • Heritability Estimates Identify a Substantial Genetic Contribution to Risk and Outcome of Intracerebral Hemorrhage
  • 2013
  • Ingår i: Stroke: a journal of cerebral circulation. - 1524-4628. ; 44:6, s. 1578-1583
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Purpose-Previous studies suggest that genetic variation plays a substantial role in occurrence and evolution of intracerebral hemorrhage (ICH). Genetic contribution to disease can be determined by calculating heritability using family-based data, but such an approach is impractical for ICH because of lack of large pedigree-based studies. However, a novel analytic tool based on genome-wide data allows heritability estimation from unrelated subjects. We sought to apply this method to provide heritability estimates for ICH risk, severity, and outcome. Methods-We analyzed genome-wide genotype data for 791 ICH cases and 876 controls, and determined heritability as the proportion of variation in phenotype attributable to captured genetic variants. Contribution to heritability was separately estimated for the APOE (encoding apolipoprotein E) gene, an established genetic risk factor, and for the rest of the genome. Analyzed phenotypes included ICH risk, admission hematoma volume, and 90-day mortality. Results-ICH risk heritability was estimated at 29% (SE, 11%) for non-APOE loci and at 15% (SE, 10%) for APOE. Heritability for 90-day ICH mortality was 41% for non-APOE loci and 10% (SE, 9%) for APOE. Genetic influence on hematoma volume was also substantial: admission volume heritability was estimated at 60% (SE, 70%) for non-APOE loci and at 12% (SE, 4%) for APOE. Conclusions-Genetic variation plays a substantial role in ICH risk, outcome, and hematoma volume. Previously reported risk variants account for only a portion of inherited genetic influence on ICH pathophysiology, pointing to additional loci yet to be identified.
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19.
  • El-Saadony, Mohamed T., et al. (författare)
  • Impacts of turmeric and its principal bioactive curcumin on human health: pharmaceutical, medicinal, and food applications : a comprehensive review
  • 2023
  • Ingår i: Frontiers in Nutrition. - : Frontiers Media S.A.. - 2296-861X. ; 9
  • Forskningsöversikt (refereegranskat)abstract
    • The yellow polyphenolic pigment known as curcumin, originating from the rhizome of the turmeric plant Curcuma longa L., has been utilized for ages in ancient medicine, as well as in cooking and food coloring. Recently, the biological activities of turmeric and curcumin have been thoroughly investigated. The studies mainly focused on their antioxidant, antitumor, anti-inflammatory, neuroprotective, hepatoprotective, and cardioprotective impacts. This review seeks to provide an in-depth, detailed discussion of curcumin usage within the food processing industries and its effect on health support and disease prevention. Curcumin’s bioavailability, bio-efficacy, and bio-safety characteristics, as well as its side effects and quality standards, are also discussed. Finally, curcumin’s multifaceted uses, food appeal enhancement, agro-industrial techniques counteracting its instability and low bioavailability, nanotechnology and focused drug delivery systems to increase its bioavailability, and prospective clinical use tactics are all discussed.
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21.
  • Falcone, Guido J., et al. (författare)
  • Burden of Risk Alleles for Hypertension Increases Risk of Intracerebral Hemorrhage
  • 2012
  • Ingår i: Stroke: a journal of cerebral circulation. - 1524-4628. ; 43:11, s. 2877-2883
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Purpose-Genetic variation influences risk of intracerebral hemorrhage (ICH). Hypertension (HTN) is a potent risk factor for ICH and several common genetic variants (single nucleotide polymorphisms [SNPs]) associated with blood pressure levels have been identified. We sought to determine whether the cumulative burden of blood pressure-related SNPs is associated with risk of ICH and pre-ICH diagnosis of HTN. Methods-We conducted a prospective multicenter case-control study in 2272 subjects of European ancestry (1025 cases and 1247 control subjects). Thirty-nine SNPs reported to be associated with blood pressure levels were identified from the National Human Genome Research Institute genomewide association study catalog. Single-SNP association analyses were performed for the outcomes ICH and pre-ICH HTN. Subsequently, weighted and unweighted genetic risk scores were constructed using these SNPs and entered as the independent variable in logistic regression models with ICH and pre-ICH HTN as the dependent variables. Results-No single SNP was associated with either ICH or pre-ICH HTN. The blood pressure-based unweighted genetic risk score was associated with risk of ICH (OR, 1.11; 95% CI, 1.02-1.21; P=0.01) and the subset of ICH in deep regions (OR, 1.18; 95% CI, 1.07-1.30; P=0.001), but not with the subset of lobar ICH. The score was associated with a history of HTN among control subjects (OR, 1.17; 95% CI, 1.04-1.31; P=0.009) and ICH cases (OR, 1.15; 95% CI, 1.01-1.31; P=0.04). Similar results were obtained when using a weighted score. Conclusion-Increasing numbers of high blood pressure-related alleles are associated with increased risk of deep ICH as well as with clinically identified HTN. (Stroke. 2012; 43: 2877-2883.)
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22.
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23.
  • Khan, N. A., et al. (författare)
  • Patient's global assessment of disease activity and patient's assessment of general health for rheumatoid arthritis activity assessment : Are they equivalent?
  • 2012
  • Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 71:12, s. 1942-1949
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives: To assess (A) determinants of patient's global assessment of disease activity (PTGL) and patient's assessment of general health (GH) scores of rheumatoid arthritis (RA) patients; (B) whether they are equivalent as individual variables; and (C) whether they may be used interchangeably in calculating common RA activity assessment composite indices. Methods: Data of 7023 patients from 30 countries in the Quantitative Standard Monitoring of Patients with RA (QUEST-RA) was analysed. PTGL and GH determinants were assessed by mixed-effects analyses of covariance models. PTGL and GH equivalence was determined by Bland-Altman 95% limits of agreement (BALOA) and Lin's coefficient of concordance (LCC). Concordance between PTGL and GH based Disease Activity Score 28(DAS28), Clinical Disease Activity Index (CDAI) and Routine Assessment of Patient Index Data 3 (RAPID3) indices were calculated using LCC, and the level of agreement in classifying RA activity in four states (remission, low, moderate, high) using κ statistics. Results: Significant differences in relative and absolute contribution of RA and non-RA related variables in PTGL and GH ratings were noted. LCC of 0.64 and BALOA of -4.41 to 4.54 showed that PTGL and GH are not equivalent. There was excellent concordance (LCC 0.95-0.99) for PTGL and GH based DAS28, CDAI and RAPID3 indices, and >80% absolute agreement (κ statistics 0.75-0.84) in RA activity state classification for all three indices. Conclusions: PTGL and GH ratings differ in their determinants. Although they are individually not equivalent, they may be used interchangeably for calculating composite indices for RA activity assessment.
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24.
  • Marini, Sandro, et al. (författare)
  • 17p12 Influences Hematoma Volume and Outcome in Spontaneous Intracerebral Hemorrhage
  • 2018
  • Ingår i: Stroke. - 0039-2499. ; 49:7, s. 1618-1625
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Purpose-Hematoma volume is an important determinant of clinical outcome in spontaneous intracerebral hemorrhage (ICH). We performed a genome-wide association study (GWAS) of hematoma volume with the aim of identifying novel biological pathways involved in the pathophysiology of primary brain injury in ICH. Methods-We conducted a 2-stage (discovery and replication) case-only genome-wide association study in patients with ICH of European ancestry. We utilized the admission head computed tomography to calculate hematoma volume via semiautomated computer-Assisted technique. After quality control and imputation, 7 million genetic variants were available for association testing with ICH volume, which was performed separately in lobar and nonlobar ICH cases using linear regression. Signals with P<5×10- 8 were pursued in replication and tested for association with admission Glasgow coma scale and 3-month post-ICH dichotomized (0-2 versus 3-6) modified Rankin Scale using ordinal and logistic regression, respectively. Results-The discovery phase included 394 ICH cases (228 lobar and 166 nonlobar) and identified 2 susceptibility loci: A genomic region on 22q13 encompassing PARVB (top single-nucleotide polymorphism rs9614326: β, 1.84; SE, 0.32; P=4.4×10-8) for lobar ICH volume and an intergenic region overlying numerous copy number variants on 17p12 (top single-nucleotide polymorphism rs11655160: β, 0.95; SE, 0.17; P=4.3×10-8) for nonlobar ICH volume. The replication included 240 ICH cases (71 lobar and 169 nonlobar) and corroborated the association for 17p12 (P=0.04; meta-Analysis P=2.5×10-9; heterogeneity, P=0.16) but not for 22q13 (P=0.49). In multivariable analysis, rs11655160 was also associated with lower admission Glasgow coma scale (odds ratio, 0.17; P=0.004) and increased risk of poor 3-month modified Rankin Scale (odds ratio, 1.94; P=0.045). Conclusions-We identified 17p12 as a novel susceptibility risk locus for hematoma volume, clinical severity, and functional outcome in nonlobar ICH. Replication in other ethnicities and follow-up translational studies are needed to elucidate the mechanism mediating the observed association.
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25.
  • Rannikmaee, Kristiina, et al. (författare)
  • Common variation in COL4A1/COL4A2 is associated with sporadic cerebral small vessel disease
  • 2015
  • Ingår i: Neurology. - 1526-632X. ; 84:9, s. 918-926
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives:We hypothesized that common variants in the collagen genes COL4A1/COL4A2 are associated with sporadic forms of cerebral small vessel disease.Methods:We conducted meta-analyses of existing genotype data among individuals of European ancestry to determine associations of 1,070 common single nucleotide polymorphisms (SNPs) in the COL4A1/COL4A2 genomic region with the following: intracerebral hemorrhage and its subtypes (deep, lobar) (1,545 cases, 1,485 controls); ischemic stroke and its subtypes (cardioembolic, large vessel disease, lacunar) (12,389 cases, 62,004 controls); and white matter hyperintensities (2,733 individuals with ischemic stroke and 9,361 from population-based cohorts with brain MRI data). We calculated a statistical significance threshold that accounted for multiple testing and linkage disequilibrium between SNPs (p < 0.000084).Results:Three intronic SNPs in COL4A2 were significantly associated with deep intracerebral hemorrhage (lead SNP odds ratio [OR] 1.29, 95% confidence interval [CI] 1.14-1.46, p = 0.00003; r(2) > 0.9 between SNPs). Although SNPs associated with deep intracerebral hemorrhage did not reach our significance threshold for association with lacunar ischemic stroke (lead SNP OR 1.10, 95% CI 1.03-1.18, p = 0.0073), and with white matter hyperintensity volume in symptomatic ischemic stroke patients (lead SNP OR 1.07, 95% CI 1.01-1.13, p = 0.016), the direction of association was the same. There was no convincing evidence of association with white matter hyperintensities in population-based studies or with non-small vessel disease cerebrovascular phenotypes.Conclusions:Our results indicate an association between common variation in the COL4A2 gene and symptomatic small vessel disease, particularly deep intracerebral hemorrhage. These findings merit replication studies, including in ethnic groups of non-European ancestry.
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26.
  • Anderson, Christopher D., et al. (författare)
  • Common Variants Within Oxidative Phosphorylation Genes Influence Risk of Ischemic Stroke and Intracerebral Hemorrhage
  • 2013
  • Ingår i: Stroke: a journal of cerebral circulation. - 1524-4628. ; 44:3, s. 612-619
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Purpose-Previous studies demonstrated association between mitochondrial DNA variants and ischemic stroke (IS). We investigated whether variants within a larger set of oxidative phosphorylation (OXPHOS) genes encoded by both autosomal and mitochondrial DNA were associated with risk of IS and, based on our results, extended our investigation to intracerebral hemorrhage (ICH). Methods-This association study used a discovery cohort of 1643 individuals, a validation cohort of 2432 individuals for IS, and an extension cohort of 1476 individuals for ICH. Gene-set enrichment analysis was performed on all structural OXPHOS genes, as well as genes contributing to individual respiratory complexes. Gene-sets passing gene-set enrichment analysis were tested by constructing genetic scores using common variants residing within each gene. Associations between each variant and IS that emerged in the discovery cohort were examined in validation and extension cohorts. Results-IS was associated with genetic risk scores in OXPHOS as a whole (odds ratio [OR], 1.17; P=0.008) and complex I (OR, 1.06; P=0.050). Among IS subtypes, small vessel stroke showed association with OXPHOS (OR, 1.16; P=0.007), complex I (OR, 1.13; P=0.027), and complex IV (OR, 1.14; P=0.018). To further explore this small vessel association, we extended our analysis to ICH, revealing association between deep hemispheric ICH and complex IV (OR, 1.08; P=0.008). Conclusions-This pathway analysis demonstrates association between common genetic variants within OXPHOS genes and stroke. The associations for small vessel stroke and deep ICH suggest that genetic variation in OXPHOS influences small vessel pathobiology. Further studies are needed to identify culprit genetic variants and assess their functional consequences. (Stroke. 2013;44:612-619.)
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27.
  • Ashry, Noha M., et al. (författare)
  • Evaluation of graphene oxide, chitosan and their complex as antibacterial agents and anticancer apoptotic effect on HeLa cell line
  • 2022
  • Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Cancer and bacterial infection are the most serious problems threatening people's lives worldwide. However, the overuse of antibiotics as antibacterial and anticancer treatments can cause side effects and lead to drug-resistant bacteria. Therefore, developing natural materials with excellent antibacterial and anticancer activity is of great importance. In this study, different concentrations of chitosan (CS), graphene oxide (GO), and graphene oxide-chitosan composite (GO-CS) were tested to inhibit the bacterial growth of gram-positive (Bacillus cereus MG257494.1) and gram-negative (Pseudomonas aeruginosa PAO1). Moreover, we used the most efficient natural antibacterial material as an anticancer treatment. The zeta potential is a vital factor for antibacterial and anticancer mechanism, at pH 3–7, the zeta potential of chitosan was positive while at pH 7–12 were negative, however, the zeta potential for GO was negative at all pH values, which (p < 0.05) increased in the GO-CS composite. Chitosan concentrations (0.2 and 1.5%) exhibited antibacterial activity against BC with inhibition zone diameters of 4 and 12 mm, respectively, and against PAO1 with 2 and 10 mm, respectively. Treating BC and PAO1 with GO:CS (1:2) and GO:CS (1:1) gave a larger (p < 0.05) inhibition zone diameter. The viability and proliferation of HeLa cells treated with chitosan were significantly decreased (p < 0.05) from 95.3% at 0% to 12.93%, 10.33%, and 5.93% at 0.2%, 0.4%, and 0.60% concentrations of chitosan, respectively. Furthermore, CS treatment increased the activity of the P53 protein, which serves as a tumor suppressor. This study suggests that chitosan is effective as an antibacterial and may be useful for cancer treatment.
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28.
  • Biffi, Alessandro, et al. (författare)
  • Variants at APOE Influence Risk of Deep and Lobar Intracerebral Hemorrhage
  • 2010
  • Ingår i: Annals of Neurology. - : Wiley. - 1531-8249 .- 0364-5134. ; 68:6, s. 934-943
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective: Prior studies investigating the association between APOE alleles epsilon 2/epsilon 4 and risk of intracerebral hemorrhage (ICH) have been inconsistent and limited to small sample sizes, and did not account for confounding by population stratification or determine which genetic risk model was best applied. Methods: We performed a large-scale genetic association study of 2189 ICH cases and 4041 controls from 7 cohorts, which were analyzed using additive models for epsilon 2 and epsilon 4. Results were subsequently meta-analyzed using a random effects model. A proportion of the individuals (322 cases, 357 controls) had available genome-wide data to adjust for population stratification. Results: Alleles epsilon 2 and epsilon 4 were associated with lobar ICH at genome-wide significance levels (odds ratio [OR] = 1.82, 95% confidence interval [CI] = 1.50-2.23, p = 6.6 x 10(-10); and OR = 2.20, 95%CI = 1.85-2.63, p = 2.4 x 10(-11), respectively). Restriction of analysis to definite/probable cerebral amyloid angiopathy ICH uncovered a stronger effect. Allele epsilon 4 was also associated with increased risk for deep ICH (OR = 1.21, 95% CI = 1.08-1.36, p = 2.6 x 10(-4)). Risk prediction evaluation identified the additive model as best for describing the effect of APOE genotypes. Interpretation: APOE epsilon 2 and epsilon 4 are independent risk factors for lobar ICH, consistent with their known associations with amyloid biology. In addition, we present preliminary findings on a novel association between APOE epsilon 4 and deep ICH. Finally, we demonstrate that an additive model for these APOE variants is superior to other forms of genetic risk modeling previously applied. ANN NEUROL 2010;68:934-943
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29.
  • Falcone, Guido J., et al. (författare)
  • Genetically Elevated LDL Associates with Lower Risk of Intracerebral Hemorrhage
  • 2020
  • Ingår i: Annals of Neurology. - : Wiley. - 0364-5134 .- 1531-8249. ; 88:1, s. 56-66
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective: Observational studies point to an inverse correlation between low-density lipoprotein (LDL) cholesterol levels and risk of intracerebral hemorrhage (ICH), but it remains unclear whether this association is causal. We tested the hypothesis that genetically elevated LDL is associated with reduced risk of ICH. Methods: We constructed one polygenic risk score (PRS) per lipid trait (total cholesterol, LDL, high-density lipoprotein [HDL], and triglycerides) using independent genomewide significant single nucleotide polymorphisms (SNPs) for each trait. We used data from 316,428 individuals enrolled in the UK Biobank to estimate the effect of each PRS on its corresponding trait, and data from 1,286 ICH cases and 1,261 matched controls to estimate the effect of each PRS on ICH risk. We used these estimates to conduct Mendelian Randomization (MR) analyses. Results: We identified 410, 339, 393, and 317 lipid-related SNPs for total cholesterol, LDL, HDL, and triglycerides, respectively. All four PRSs were strongly associated with their corresponding trait (all p < 1.00 × 10-100). While one SD increase in the PRSs for total cholesterol (odds ratio [OR] = 0.92; 95% confidence interval [CI] = 0.85–0.99; p = 0.03) and LDL cholesterol (OR = 0.88; 95% CI = 0.81–0.95; p = 0.002) were inversely associated with ICH risk, no significant associations were found for HDL and triglycerides (both p > 0.05). MR analyses indicated that 1mmol/L (38.67mg/dL) increase of genetically instrumented total and LDL cholesterol were associated with 23% (OR = 0.77; 95% CI = 0.65–0.98; p = 0.03) and 41% lower risks of ICH (OR = 0.59; 95% CI = 0.42–0.82; p = 0.002), respectively. Interpretation: Genetically elevated LDL levels were associated with lower risk of ICH, providing support for a potential causal role of LDL cholesterol in ICH. ANN NEUROL 2020.
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30.
  • Selim, Mahmoud, et al. (författare)
  • Safe Reinforcement Learning using Data-Driven Predictive Control
  • 2022
  • Ingår i: 2022 5TH INTERNATIONAL CONFERENCE ON COMMUNICATIONS, SIGNAL PROCESSING, AND THEIR APPLICATIONS (ICCSPA). - : Institute of Electrical and Electronics Engineers (IEEE).
  • Konferensbidrag (refereegranskat)abstract
    • Reinforcement learning (RL) algorithms can achieve state-of-the-art performance in decision-making and continuous control tasks. However, applying RL algorithms on safety-critical systems still needs to be well justified due to the exploration nature of many RL algorithms, especially when the model of the robot and the environment are unknown. To address this challenge, we propose a data-driven safety layer that acts as a filter for unsafe actions. The safety layer uses a data-driven predictive controller to enforce safety guarantees for RL policies during training and after deployment. The RL agent proposes an action that is verified by computing the data-driven reachability analysis. If there is an intersection between the reachable set of the robot using the proposed action, we call the data-driven predictive controller to find the closest safe action to the proposed unsafe action. The safety layer penalizes the RL agent if the proposed action is unsafe and replaces it with the closest safe one. In the simulation, we show that our method outperforms state-of-the-art safe RL methods on the robotics navigation problem for a Turtlebot 3 in Gazebo and a quadrotor in Unreal Engine 4 (UE4).
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31.
  • van Kuilenburg, André B P, et al. (författare)
  • ß-ureidopropionase deficiency : phenotype, genotype and protein structural consequences in 16 patients
  • 2012
  • Ingår i: Biochimica et Biophysica Acta. - : Elsevier BV. - 0006-3002 .- 1878-2434. ; 1822:7, s. 1096-108
  • Tidskriftsartikel (refereegranskat)abstract
    • ß-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid to ß-alanine and ß-aminoisobutyric acid, ammonia and CO(2). To date, only five genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 11 newly identified ß-ureidopropionase deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological abnormalities (intellectual disabilities, seizures, abnormal tonus regulation, microcephaly, and malformations on neuro-imaging) and markedly elevated levels of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid in urine and plasma. Analysis of UPB1, encoding ß-ureidopropionase, showed 6 novel missense mutations and one novel splice-site mutation. Heterologous expression of the 6 mutant enzymes in Escherichia coli showed that all mutations yielded mutant ß-ureidopropionase proteins with significantly decreased activity. Analysis of a homology model of human ß-ureidopropionase generated using the crystal structure of the enzyme from Drosophila melanogaster indicated that the point mutations p.G235R, p.R236W and p.S264R lead to amino acid exchanges in the active site and therefore affect substrate binding and catalysis. The mutations L13S, R326Q and T359M resulted most likely in folding defects and oligomer assembly impairment. Two mutations were identified in several unrelated ß-ureidopropionase patients, indicating that ß-ureidopropionase deficiency may be more common than anticipated.
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32.
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33.
  • Adel, Amany, et al. (författare)
  • Genetic Variations among Different Variants of G1-like Avian Influenza H9N2 Viruses and Their Pathogenicity in Chickens
  • 2022
  • Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 14:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.
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34.
  • Aksoy, Selim, et al. (författare)
  • Algorithm Performance Contest
  • 2000
  • Ingår i: Proceedings. 15th International Conference on Pattern Recognition, 2000. - : IEEE. - 0769507506 ; , s. 870-876
  • Konferensbidrag (refereegranskat)abstract
    • This contest involved the running and evaluation of computer vision and pattern recognition techniques on different data sets with known groundwidth. The contest included three areas; binary shape recognition, symbol recognition and image flow estimation. A package was made available for each area. Each package contained either real images with manual groundtruth or programs to generate data sets of ideal as well as noisy images with known groundtruth. They also contained programs to evaluate the results of an algorithm according to the given groundtruth. These evaluation criteria included the generation of confusion matrices, computation of the misdetection and false alarm rates and other performance measures suitable for the problems. The paper summarizes the data generation for each area and experimental results for a total of six participating algorithms
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35.
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36.
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37.
  • Aljaradin, Mohammad, et al. (författare)
  • Evaluation of the Cover Effect in Mafraq Landfill –Jordan Using Hydrus-2d Simulation
  • 2011
  • Ingår i: IWWG. ; 13, s. 581-582
  • Konferensbidrag (refereegranskat)abstract
    • In this study, a two-dimensional numerical model for water flow and solute transport, Hydrus-2D, was used to investigate the impact of landfill cover thickness and the antecedent water content (Ө) of the soil beneath the landfill on the chloride percolation below the landfill. Series of simulation scenarios were performed using season varying climatic data during a 30-year period including two varying factors; thickness of landfill cover (0, 50, 100 cm) and the antecedent soil water content (0.12 and 0.20 m3m-3). The simulation results showed that maximum chloride concentration for different scenarios at all location within soil profile during the entire simulation period was less than the chloride concentration in the MSW leachate. In addition, as the landfill cover increased the concentration of chloride at a certain location decreased. Meanwhile, the time required to reach this location increased. The simulation results showed also that the impact of antecedent soil water content on chloride concentration reduction increase as the cover thickness increased. Based on the result, it was recommended to use a landfill cover to reduce the chloride concentration. Cover thickness of 50 cm is suitable in case of low antecedent soil water content.
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38.
  • Allanach, Benjamin C., et al. (författare)
  • Simple and statistically sound strategies for analysing physical theories
  • 2022
  • Ingår i: Reports on progress in physics (Print). - : Institute of Physics Publishing (IOPP). - 0034-4885 .- 1361-6633. ; 85:5
  • Forskningsöversikt (refereegranskat)abstract
    • Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both of these categories. These issues are often sidestepped with statistically unsound ad hoc methods, involving intersection of parameter intervals estimated by multiple experiments, and random or grid sampling of model parameters. Whilst these methods are easy to apply, they exhibit pathologies even in low-dimensional parameter spaces, and quickly become problematic to use and interpret in higher dimensions. In this article we give clear guidance for going beyond these procedures, suggesting where possible simple methods for performing statistically sound inference, and recommendations of readily-available software tools and standards that can assist in doing so. Our aim is to provide any physicists lacking comprehensive statistical training with recommendations for reaching correct scientific conclusions, with only a modest increase in analysis burden. Our examples can be reproduced with the code publicly available at Zenodo.
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39.
  • Arsov, Stefan, et al. (författare)
  • Does hepatitis C increase the accumulation of advanced glycation end products in haemodialysis patients?
  • 2010
  • Ingår i: Nephrology, Dialysis and Transplantation. - : Oxford Journals. - 0931-0509 .- 1460-2385. ; 25:3, s. 885-891
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Hepatitis C may cause increased levels of oxidative stress that contribute to accumulation of advanced glycation end products (AGEs), which increase the risk of cardiovascular disease (CVD). The aim of this study was to determine the influence of hepatitis C on AGE accumulation in haemodialysis patients. METHODS: AGE accumulation was measured by means of skin autofluorescence (AF) in 92 haemodialysis (HD) patients and 93 age-matched healthy controls. In the HD patients, CVD-related biochemical variables were also measured. The HD patients were tested for hepatitis C virus (HCV) antibodies and allocated to a HCV+ or HCV- group. RESULTS: Skin AF of the healthy subjects was lower than skin AF in the HD patients (3.13 +/- 0.95 vs 2.2 +/- 0.47; P < 0.001). We calculated the average increase of skin AF in the healthy subjects to be 0.017 arbitrary units per year, being 14 times lower than in HD patients with CVD only and 20 times lower than in HD patients suffering from combined CVD and diabetes mellitus (DM). Multivariate regression analysis showed that AGE accumulation in HD patients can be described by the independent effects of age, DM, CVD and HD vintage. Although inter-cellular adhesion molecule 1 and liver enzymes were elevated in HCV+ HD patients, levels of oxidative stress markers and skin AF were not significantly different between HCV+ and HCV- HD patients. CONCLUSIONS: AGE accumulation was higher in the HD patients than in the healthy controls. AGE accumulation did not differ in HCV+ and HCV- HD patients. This might be due to the fact that hepatitis C did not cause oxidative stress in our HD population. Independent markers of AGE accumulation were age, HD vintage, DM and CVD, but not hepatitis C.
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40.
  • Bali, Khaled M., et al. (författare)
  • Nutrient and salinity management for spinach production under sprinkler irrigation in the low desert region of California
  • 2021
  • Ingår i: Irrigation Science. - : Springer Science and Business Media LLC. - 0342-7188 .- 1432-1319. ; 39:6, s. 735-749
  • Tidskriftsartikel (refereegranskat)abstract
    • The efficiency of irrigation, as well as optimization of nutrients, affect spinach yield in all growth stages. In this study, the sensitivity of spinach (early and mature yields) to shallow saline groundwater and the effect of fertigation treatments on mature yield were experimentally investigated. The sprinkler irrigation experiments were conducted on 0.47 ha of silty clay soil at the University of California Desert Research and Extension Center (DREC) in Imperial Valley, California. Twelve beds in the experimental field were chosen randomly to investigate the effect of three fertigation treatments on spinach yield. Three rates of urea ammonium nitrate (UAN-32) fertilizer; T1: 200 kg ha−1 (150%), T2: 133.3 kg ha−1 (100%), and T3: 66.7 kg ha−1 (50%) in four replicates were applied. Soil samples to depths of up to 120 cm were collected at baby leaves and mature harvesting dates (17th October and 19th November 2019, respectively) for salinity measurements. Additionally, soil matric potential through the 120 cm soil depth was measured and groundwater levels in five observation wells were recorded during the growing season. Results showed that average soil salinity at baby leaves harvesting stage through the top 60 cm active root zone depth ranged from 0.61 to 1.48 dS m−1, which is lower than the spinach salinity threshold limit (2 dS m−1), while the average groundwater depth was 1.90 m with salinity ranging from 6.35 to 10.60 dS m−1. Correlation analysis showed that the baby spinach leaves yield was weakly correlated (r = 0.40) to the average soil salinity in the top 60 cm soil depth. Although groundwater and top 60 cm soil salinity showed an increase at the mature yield harvesting stage, the mature yield was weakly correlated to soil salinity (p = 0.116). As the UAN-32 rate increased, the mature spinach yield increased. The mature spinach yields were 17.31, 14.00, and 12.54 ton ha−1 for T1, T2, and T3 fertigation treatments, respectively. However, only a 10% reduction in yield occurred in T3 treatment corresponding to a 50% reduction in UAN-32 rate by 66.7 kg ha−1. Based on the results of this study, shallow saline groundwater has little impact on spinach yield. In addition, the 50% increase in UAN-32 rate had a significant impact on mature spinach yield. The 150% UAN-32 rate resulted in an increase in spinach yield and could be used in arid and semiarid regions with similar conditions to the Imperial Valley but additional measures to minimize the leaching of nitrate from the root zone and to reduce the load of nitrogen in drainage water are needed to minimize the potential negative impact of over-fertigation on the environment.
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41.
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42.
  • Chung, Jaeyoon, et al. (författare)
  • Genome-wide association study of cerebral small vessel disease reveals established and novel loci
  • 2019
  • Ingår i: Brain : a journal of neurology. - : Oxford University Press (OUP). - 1460-2156. ; 142:10, s. 3176-3189
  • Tidskriftsartikel (refereegranskat)abstract
    • Intracerebral haemorrhage and small vessel ischaemic stroke (SVS) are the most acute manifestations of cerebral small vessel disease, with no established preventive approaches beyond hypertension management. Combined genome-wide association study (GWAS) of these two correlated diseases may improve statistical power to detect novel genetic factors for cerebral small vessel disease, elucidating underlying disease mechanisms that may form the basis for future treatments. Because intracerebral haemorrhage location is an adequate surrogate for distinct histopathological variants of cerebral small vessel disease (lobar for cerebral amyloid angiopathy and non-lobar for arteriolosclerosis), we performed GWAS of intracerebral haemorrhage by location in 1813 subjects (755 lobar and 1005 non-lobar) and 1711 stroke-free control subjects. Intracerebral haemorrhage GWAS results by location were meta-analysed with GWAS results for SVS from MEGASTROKE, using 'Multi-Trait Analysis of GWAS' (MTAG) to integrate summary data across traits and generate combined effect estimates. After combining intracerebral haemorrhage and SVS datasets, our sample size included 241 024 participants (6255 intracerebral haemorrhage or SVS cases and 233 058 control subjects). Genome-wide significant associations were observed for non-lobar intracerebral haemorrhage enhanced by SVS with rs2758605 [MTAG P-value (P) = 2.6 × 10-8] at 1q22; rs72932727 (P = 1.7 × 10-8) at 2q33; and rs9515201 (P = 5.3 × 10-10) at 13q34. In the GTEx gene expression library, rs2758605 (1q22), rs72932727 (2q33) and rs9515201 (13q34) are significant cis-eQTLs for PMF1 (P = 1 × 10-4 in tibial nerve), NBEAL1, FAM117B and CARF (P < 2.1 × 10-7 in arteries) and COL4A2 and COL4A1 (P < 0.01 in brain putamen), respectively. Leveraging S-PrediXcan for gene-based association testing with the predicted expression models in tissues related with nerve, artery, and non-lobar brain, we found that experiment-wide significant (P < 8.5 × 10-7) associations at three genes at 2q33 including NBEAL1, FAM117B and WDR12 and genome-wide significant associations at two genes including ICA1L at 2q33 and ZCCHC14 at 16q24. Brain cell-type specific expression profiling libraries reveal that SEMA4A, SLC25A44 and PMF1 at 1q22 and COL4A1 and COL4A2 at 13q34 were mainly expressed in endothelial cells, while the genes at 2q33 (FAM117B, CARF and NBEAL1) were expressed in various cell types including astrocytes, oligodendrocytes and neurons. Our cross-phenotype genetic study of intracerebral haemorrhage and SVS demonstrates novel genome-wide associations for non-lobar intracerebral haemorrhage at 2q33 and 13q34. Our replication of the 1q22 locus previous seen in traditional GWAS of intracerebral haemorrhage, as well as the rediscovery of 13q34, which had previously been reported in candidate gene studies with other cerebral small vessel disease-related traits strengthens the credibility of applying this novel genome-wide approach across intracerebral haemorrhage and SVS.
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43.
  • Eltarabily, Mohamed Galal, et al. (författare)
  • Comparative analysis of root growth modules in HYDRUS for SWC of rice under deficit drip irrigation
  • 2021
  • Ingår i: Water. - : MDPI AG. - 2073-4441. ; 13:14
  • Tidskriftsartikel (refereegranskat)abstract
    • Root distribution during rice cultivation is a governing factor that considerably affects soil water content (SWC) and root water uptake (RWU). In this study, the effects of activating root growth (using growth function) and assigning a constant average root depth (no growth during simulation) on SWC and RWU for rice cultivation under four deficit drip irrigation treatments (T90, T80, T70, and T60) were compared in the HYDRUS-2D/3D model version 3.03. A secondary objective was to investigate the effect of applied deficit irrigation treatments on grain yield, irrigation water use efficiency (IWUE), and growth traits of rice. The simulated DI system was designed to reflect a representative field experiment implemented in El-Fayoum Governorate, Egypt, during two successive seasons during 2017 and 2018. The deficit treatments (T90, T80, T70, and T60) used in the current study represent scenarios at which the first irrigation event was applied when the pre-irrigation average SWC within the upper 60 cm of soil depth was equal to 90%, 80%, 70%, and 60% of plant-available water, respectively. Simulation results showed that as water deficiency increased, SWC in the simulation domain decreased, and thereby, RWU decreased. The average SWC within the root zone during rice-growing season under different deficit treatments was slightly higher when activating root growth function than when considering constant average root depth. Cumulative RWU fluxes for the case of no growth were slightly higher than for the case of root growth function for T90, T80, and T70 accounting for 1289.50, 1179.30, and 1073.10 cm2, respectively. Average SWC during the growth season (24 h after the first irrigation event, mid-season, and 24 h after the last irrigation event) between the two cases of root growth was strongly correlated for T90, T80, T70, and T60, where r2 equaled 0.918, 0.902, 0.892, and 0.876, respectively. ANOVA test showed that there was no significant difference for SWC between treatments for the case of assigning root growth function while the difference in SWC among treatments was significant for the case of the constant average root depth, where p-values equaled 0.0893 and 0.0433, respectively. Experimental results showed that as water deficiency decreased, IWUE increased. IWUE equaled 1.65, 1.58, 1.31, and 1.21 kg m-3 for T90, T80, T70, and T60, respectively. Moreover, higher grain yield and growth traits of rice (plant height, tillers number plant-1, panicles length, panicle weight, and grain number panicles-1) were obtained corresponding to T90 as compared with other treatments. Activating the root growth module in HYDRUS simulations can lead to more precise simulation results for specific dates within different growth stages. Therefore, the root growth module is a powerful tool for accurately investigating the change in SWC during simulation. Users of older versions of HYDRUS-2D/3D (version 2.05 and earlier) should consider the limitations of these versions for irrigation scheduling.
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44.
  • Erfan, Ahmed M., et al. (författare)
  • Characterization of full genome sequences of chicken anemia viruses circulating in Egypt reveals distinct genetic diversity and evidence of recombination
  • 2018
  • Ingår i: Virus Research. - : ELSEVIER SCIENCE BV. - 0168-1702 .- 1872-7492. ; 251, s. 78-85
  • Tidskriftsartikel (refereegranskat)abstract
    • Chicken anemia virus (CAV) is one of the commercially important diseases of poultry worldwide. In Egypt, CAV has been reported to be a potential threat to the commercial poultry sectors. Hence, this study was aimed at isolation and full genomic analysis of CAVs circulating in chicken populations in different geographical location in Egypt. A total of 42 samples were collected from broiler chicken flocks in 9 governorates in Egypt from 12 to 42 days of age. The mortality rate observed among chickens was ranging from 3% to 22%. Nineteen out of 42 farms were found positive for the CAV genome by polymerase chain reaction (PCR). Full genome sequencing was conducted for 18 positive samples. Genetic analysis revealed a high similarity of > 99% in 11 viruses with the vaccine strain Del-Ros; while the other seven samples shared close similarity to CAV field strains isolated from China, Taiwan, and Brazil. The data also indicated Q139 and Q144 amino acids substitutions among the VP1 of Egyptian field strains, which are known to be important in virus replication and spread. Phylogenetic analysis of the sequenced viruses (n = 18) based on either the full gene nucleotide sequence or VP1 coding sequence, suggested the circulation of four distinct genotypes in Egypt designated as group A, B, C and D. Moreover, evidence of recombination was detected among four Egyptian CAVs located within group A. The findings of this study succeeded to elucidate the epidemiological and genetic features of CAVs circulating in Egypt, and underscores the important of CAVs surveillance.
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45.
  • Erfan, Ahmed M., et al. (författare)
  • Chicken anaemia virus enhances and prolongs subsequent avian influenza (H9N2) and infectious bronchitis viral infections
  • 2019
  • Ingår i: Veterinary Microbiology. - : ELSEVIER SCIENCE BV. - 0378-1135 .- 1873-2542. ; 230, s. 123-129
  • Tidskriftsartikel (refereegranskat)abstract
    • Immunosuppressive viral diseases have a great economic importance in the poultry industry due to the increased susceptibility to secondary infections. Chicken anaemia virus (CAV) is one of the major immunosuppressive diseases in chickens. In addition, low pathogenic avian influenza (LPAI) of subtype H9N2 and infectious bronchitis (IB) viruses are among the most frequently reported respiratory viral diseases in poultry worldwide. In the present study, specific pathogen free chickens were used to understand the impact of CAV on secondary infection with LPAI-H9N2 or 1B viruses. Clinical outcomes, viral shedding dynamics, and cytokine levels wereassessed. The results exhibit that chickens previously infected with CAV produceconsiderablyhigher titresof LPAI-H9N2 or IB viruses in the oropharyngeal swabs (P < 0.05), tracheas and kidneys. In addition, the immunologic effect of CAV provokedthe development of clinical signs of LPAI-H9N2 and IB virus infections. Moreover, results suggested that pre-infection with CAV directly correlated with elevated levels of IL-6 and IFN gamma. These findings underline the importance of CAV pre-infection on LPAI-H9N2 or IB infection in chickens, and indicate that co-circulation of CAV can contribute to the spread and evolution of LPAI H9N2 and IB viruses.
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46.
  • Hagag, Naglaa M., et al. (författare)
  • Molecular Epidemiology and Evolutionary Analysis of Avian Influenza A(H5) Viruses Circulating in Egypt, 2019-2021
  • 2022
  • Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 14:8
  • Tidskriftsartikel (refereegranskat)abstract
    • The highly pathogenic avian influenza (HPAI) H5N8 virus was first detected in Egypt in late 2016. Since then, the virus has spread rapidly among different poultry sectors, becoming the dominant HPAI H5 subtype reported in Egypt. Different genotypes of the HPAI H5N8 virus were reported in Egypt; however, the geographic patterns and molecular evolution of the Egyptian HPAI H5N8 viruses are still unclear. Here, extensive epidemiological surveillance was conducted, including more than half a million samples collected from different poultry sectors (farms/backyards/live bird markets) from all governorates in Egypt during 2019-2021. In addition, genetic characterization and evolutionary analyses were performed using 47 selected positive H5N8 isolates obtained during the same period. The result of the conducted surveillance showed that HPAI H5N8 viruses of clade 2.3.4.4b continue to circulate in different locations in Egypt, with an obvious seasonal pattern, and no further detection of the HPAI H5N1 virus of clade 2.2.1.2 was observed in the poultry population during 2019-2021. In addition, phylogenetic and Bayesian analyses revealed that two major genotypes (G5 and G6) of HPAI H5N8 viruses were continually expanding among the poultry sectors in Egypt. Notably, molecular dating analysis suggested that the Egyptian HPAI H5N8 virus is the potential ancestral viruses of the European H5N8 viruses of 2020-2021. In summary, the data of this study highlight the current epidemiology, diversity, and evolution of HPAI H5N8 viruses in Egypt and call for continuous monitoring of the genetic features of the avian influenza viruses in Egypt.
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47.
  • Hegazy, Mohamed-Elamir F., et al. (författare)
  • Cytotoxic Cembranoids from the Red Sea Soft Coral Sarcophyton glaucum
  • 2011
  • Ingår i: Natural Product Communications. - 1934-578X .- 1555-9475. ; 6:12, s. 1809-1812
  • Tidskriftsartikel (refereegranskat)abstract
    • One new cembrane diterpene, 2R,7R,8R-dihydroxydeepoxysarcophine (1), together with three known compounds, 7 alpha,8 beta-dihydroxydecpoxysarcophine (2), 7 beta-acetoxy-8 alpha-hydroxydeepoxysarcophine (3), and sarcophine (4), have been isolated from the Red Sea soft coral Sarcophyton glaucum. Their structures were determined using 1D and 2D NMR spectroscopy. 7 beta-Acetoxy-8 alpha-hydroxydeepoxysarcophine (3) exhibits cytotoxic activity against HepG2, HCT-116, and HeLa cells with IC(50) values of 3.6, 2.3, and 6.7 mu g/mL, respectively.
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48.
  • Hendaus, Mohamed A., et al. (författare)
  • Child abuse and neglect in a rapidly developing country : Parents' perspectives
  • 2020
  • Ingår i: Journal of Family Medicine and Primary Care. - : Wolters Kluwer. - 2249-4863 .- 2278-7135. ; 9:6, s. 3053-3059
  • Tidskriftsartikel (refereegranskat)abstract
    • Purpose: To identify parental awareness and knowledge regarding child abuse and neglect in the State of Qatar.Methods: A cross-sectional study using a questionnaire was conducted at Hamad Medical Corporation, the only tertiary pediatric hospital in the State of Qatar at the time of the study. Parents of children of all ages were offered a questionnaire that included demographic details, parental knowledge, and awareness of child abuse and neglect.Results: 300 questionnaires were completed (response rate = 95%). More than 70% of parents were older than 30 years of age, 60% of them were females, and 66% were college graduates. The majority of the participants stated their familiarity about child abuse, and 6% witnessed morbidity or mortality due to child abuse in the society. Despite the identified laws, only 50% of the parents were aware of laws restricting child abuse. In regards to children with special needs, only 16% of the participants agreed that disabled children are at a higher risk of abuse compared to healthy children, while 33% were neutral and 52% disagreed. In addition, one-fifth of the respondents stated that hitting is discipline, while 63% disagreed. Almost one-third of the respondents agreed that hitting hands and buttock or hitting with soft objects is acceptable form of discipline. Unexpectedly, one-quarter of participants stated that it is okay to hit a child as long as no damage incurs. As for verbal abuse, around one-third of parents stated that yelling is not a form of child abuse, and that yelling does not affect growth and development. Comparing both corporal and verbal abuse, approximately 70% of parents stated that yelling is less harmful than hitting. In terms of child neglect, around half of the respondents agreed with the statement "Leaving a child (<5 years) unattended at home is a form of neglect," while 42% were neutral. Finally, approximately 50% of the participants believed that it is okay to depend on nannies in assisting their children in eating and using the bathroom.Conclusion: Parents residing in the State of Qatar believe that they have a good knowledge regarding child abuse and neglect. However, this study shows many deficiencies in parental knowledge of child abuse and neglect. Parents' attitudes and perceptions are considered indispensable targets for community health intervention.
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49.
  • Herrick, Ariane L, et al. (författare)
  • Treatment outcome in early diffuse cutaneous systemic sclerosis : The European Scleroderma Observational Study (ESOS)
  • 2017
  • Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 76:7, s. 1207-1218
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives: The rarity of early diffuse cutaneous systemic sclerosis (dcSSc) makes randomised controlled trials very difficult. We aimed to use an observational approach to compare effectiveness of currently used treatment approaches. Methods: This was a prospective, observational cohort study of early dcSSc (within three years of onset of skin thickening). Clinicians selected one of four protocols for each patient: methotrexate, mycophenolate mofetil (MMF), cyclophosphamide or 'no immunosuppressant'. Patients were assessed three-monthly for up to 24 months. The primary outcome was the change in modified Rodnan skin score (mRSS). Confounding by indication at baseline was accounted for using inverse probability of treatment (IPT) weights. As a secondary outcome, an IPT-weighted Cox model was used to test for differences in survival. Results Of 326 patients recruited from 50 centres, 65 were prescribed methotrexate, 118 MMF, 87 cyclophosphamide and 56 no immunosuppressant. 276 (84.7%) patients completed 12 and 234 (71.7%) 24 months follow-up (or reached last visit date). There were statistically significant reductions in mRSS at 12 months in all groups: -4.0 (-5.2 to -2.7) units for methotrexate, -4.1 (-5.3 to -2.9) for MMF, -3.3 (-4.9 to -1.7) for cyclophosphamide and -2.2 (-4.0 to -0.3) for no immunosuppressant (p value for between-group differences=0.346). There were no statistically significant differences in survival between protocols before (p=0.389) or after weighting (p=0.440), but survival was poorest in the no immunosuppressant group (84.0%) at 24 months. Conclusions: These findings may support using immunosuppressants for early dcSSc but suggest that overall benefit is modest over 12 months and that better treatments are needed.
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50.
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