| 11. |
- Abbara, Aula, et al.
(författare)
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Weaponisation of water
- 2022
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Ingår i: The Lancet. - : Elsevier. - 0140-6736 .- 1474-547X. ; 400:10367, s. 1925-1925
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Tidskriftsartikel (refereegranskat)
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| 12. |
- Abbara, Aula, et al.
(författare)
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Weaponizing water as an instrument of war in Syria: Impact on diarrhoeal disease in Idlib and Aleppo governorates, 2011–2019
- 2021
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Ingår i: International Journal of Infectious Diseases. - : Elsevier. - 1201-9712 .- 1878-3511. ; 108, s. 202-208
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Investigate the weaponization of water during the Syrian conflict and the correlation of attacks on water, sanitation, and hygiene (WASH) infrastructure in Idlib and Aleppo governorates with trends in waterborne diseases reported by Early Warning and Response surveillance systems.Methods: We reviewed literature and databases to obtain information on attacks on WASH in Aleppo and Idlib governorates between 2011 and 2019. We plotted weekly trends in waterborne diseases from two surveillance systems operational in Aleppo and Idlib governorates between 2015 and early 2020.Results: The literature review noted several attacks on water and related infrastructure in both governorates, suggesting that WASH infrastructure was weaponized by state and non-state actors. Most interference with WASH in the Aleppo governorate occurred before 2019 and in the Idlib governorate in the summer of 2020. Other acute diarrhea represented >90% of cases of diarrhea; children under 5 years contributed 50% of cases. There was substantial evidence (p < 0.001) of an overall upward trend in cases of diarrheal disease.Conclusions: Though no direct correlation can be drawn between the weaponization of WASH and the burden of waterborne infections due to multiple confounders, this research introduces important concepts on attacks on WASH and their potential impacts on waterborne diseases.
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| 13. |
- Abbasi, Ahtisham Fazeel, et al.
(författare)
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Deep learning architectures for the prediction of YY1-mediated chromatin loops
- 2023
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Ingår i: Bioinformatics research and applications. - : Springer. - 9789819970735 - 9789819970742 ; , s. 72-84
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Konferensbidrag (refereegranskat)abstract
- YY1-mediated chromatin loops play substantial roles in basic biological processes like gene regulation, cell differentiation, and DNA replication. YY1-mediated chromatin loop prediction is important to understand diverse types of biological processes which may lead to the development of new therapeutics for neurological disorders and cancers. Existing deep learning predictors are capable to predict YY1-mediated chromatin loops in two different cell lines however, they showed limited performance for the prediction of YY1-mediated loops in the same cell lines and suffer significant performance deterioration in cross cell line setting. To provide computational predictors capable of performing large-scale analyses of YY1-mediated loop prediction across multiple cell lines, this paper presents two novel deep learning predictors. The two proposed predictors make use of Word2vec, one hot encoding for sequence representation and long short-term memory, and a convolution neural network along with a gradient flow strategy similar to DenseNet architectures. Both of the predictors are evaluated on two different benchmark datasets of two cell lines HCT116 and K562. Overall the proposed predictors outperform existing DEEPYY1 predictor with an average maximum margin of 4.65%, 7.45% in terms of AUROC, and accuracy, across both of the datases over the independent test sets and 5.1%, 3.2% over 5-fold validation. In terms of cross-cell evaluation, the proposed predictors boast maximum performance enhancements of up to 9.5% and 27.1% in terms of AUROC over HCT116 and K562 datasets.
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| 14. |
- Abdel-Aziz, Mahmoud I., et al.
(författare)
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A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes
- 2022
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Ingår i: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 59:1
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Tidskriftsartikel (refereegranskat)abstract
- A multi-omics approach revealed the underlying biological pathways in the microbiome-driven severe asthma phenotypes. This may help to elucidate new leads for treatment development, particularly for the therapeutically challenging neutrophilic asthma.
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| 15. |
- Abdel-Shafi, Seham, et al.
(författare)
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Isolation and characterization of antibacterial conglutinins from Lupine seeds
- 2023
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Ingår i: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 28:1
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Tidskriftsartikel (refereegranskat)abstract
- The main target of this work is to discover new protein fractions from natural resources with high antibacterial action. The 7S and 11S globulin fractions, as well as the basic subunit (BS), were isolated from lupine seeds (Lupinus termis), chemically characterized, and screened for antibacterial activity against seven pathogenic bacteria. SDS-PAGE revealed molecular weights ranging from 55 to 75 kDa for 7S globulin, 20–37 kD for 11S globulin, and 20 kD for the BS. 11S globulin and the BS migrated faster on Urea-PAGE toward the cathode compared to 7S globulin. FTIR and NMR showed different spectral patterns between the 7S and 11S globulins but similar ones between 11S globulin and the BS. The MICs of the BS were in the range of 0.05–2 μg/mL against Listeria monocytogenes, Klebsiella oxytoca, Proteus mirabilis, Staphylococcus aureus, Listeria ivanovii, Salmonella typhimurium, and Pseudomonas aeruginosa compared to higher values for 11S globulin. The BS surpassed 11S globulin in antibacterial action, while 7S globulin showed no effect. The MICs of 11S globulin and the BS represented only 5% and 2.5% of the specific antibiotic against L. monocytogenes, respectively. Scanning electron microscopy (SEM) demonstrated different signs of cellular deformation and decay in the protein-treated bacteria, probably due to interaction with the bacterial cell wall and membranes. 11S globulin and the BS can be nominated as effective food biopreservatives.
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| 16. |
- Abdel-Shafi, Seham, et al.
(författare)
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The Association between icaA and icaB Genes, Antibiotic Resistance and Biofilm Formation in Clinical Isolates of Staphylococci spp.
- 2022
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Ingår i: Antibiotics. - : MDPI. - 0066-4774 .- 2079-6382. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Sixty-six (66) Staphylococcus bacterial isolates were withdrawn from separate clinical samples of hospitalized patients with various clinical infections. Conventional bacteriological tests identified the species of all isolates, and standard microbiological techniques differentiated them into CoPS or CoNS. Their biofilm development was followed by an analysis via the MTP (microtiter tissue culture plates) technique, and we then investigated the presence/absence of icaA and icaB, which were qualified in the top-30 potent biofilm-forming isolates. Thirteen isolates (46.7%) showed the presence of one gene, six (20%) isolates exhibited the two genes, while ten (33.3%) had neither of them. The formation of staphylococci biofilms in the absence of ica genes may be related to the presence of other biofilm formation ica-independent mechanisms. CoPS was the most abundant species among the total population. S. aureus was the sole representative of CoPS, while S. epidermidis was the most abundant form of CoNS. Antibiotic resistance was developing against the most frequently used antimicrobial drugs, while vancomycin was the least-resisted drug. The totality of the strong and medium-strength film-forming isolates represented the majority proportion (80%) of the total investigated clinical samples. The biochemical pattern CoPS is associated with antibiotic resistance and biofilm formation and can be an alarming indicator of potential antibiotic resistance.
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| 17. |
- Abdellah, Tebani, et al.
(författare)
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies andimmune cell profiling, complementedwith gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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| 18. |
- AbdelMageed, Manar, et al.
(författare)
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Clinical significance of stem cell biomarkers epcam, lgr5 and lgr4 mrna levels in lymph nodes of colon cancer patients
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- The significance of cancer stem cells (CSCs) in initiation and progression of colon cancer (CC) has been established. In this study, we investigated the utility of measuring mRNA expression levels of CSC markers EpCAM, LGR5 and LGR4 for predicting survival outcome in surgically treated CC patients. Expression levels were determined in 5 CC cell lines, 66 primary CC tumors and 382 regional lymph nodes of 121 CC patients. Prognostic relevance was determined using Kaplan‐Meier survival and Cox regression analyses. CC patients with lymph nodes expressing high levels of EpCAM, LGR5 or LGR4 (higher than a clinical cutoff of 0.07, 0.06 and 2.558 mRNA cop-ies/18S rRNA unit, respectively) had a decreased mean survival time of 32 months for EpCAM and 42 months for both LGR5 and LGR4 at a 12‐year follow‐up (p = 0.022, p = 0.005 and p = 0.011, respec-tively). Additional patients at risk for recurrence were detected when LGR5 was combined with the biomarkers CXCL17 or CEA plus CXCL16. In conclusion, the study underscores LGR5 as a particularly useful prognostic biomarker and illustrates the strength of combining biomarkers detecting different subpopulations of cancer cells and/or cells in the tumor microenvironment for predicting recurrence.
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| 19. |
- Abdelmalek, George, et al.
(författare)
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Intercostal nerve transfer for biceps reinnervation in obstetrical brachial plexus palsy : a preferred reporting items for systematic reviews and meta-analysis for individual patient data systematic review using individualized fusion and comparison to supraclavicular exploration and nerve grafting
- 2024
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Ingår i: Journal of Children's Orthopaedics. - : Sage Publications. - 1863-2521 .- 1863-2548. ; 18:1, s. 54-63
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Forskningsöversikt (refereegranskat)abstract
- Introduction: The objective of this study was to search existing literature on nerve reconstruction surgery in patients with obstetric brachial plexus palsy to determine whether treatment with supraclavicular exploration and nerve grafting produced better elbow flexion outcomes compared to intercostal nerve transfer.Methods: This study was a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis for Individual Patient Data guidelines. A systematic search was conducted using multiple databases. An ordinal regression model was used to analyze the effect of using supraclavicular exploration and nerve grafting or intercostal nerve on elbow flexion with the two scores measured: elbow flexion Medical Research Council scores and Toronto active movements scale scores for elbow flexion.Results: A final patient database from 6 published articles consisted of 83 supraclavicular exploration and nerve grafting patients (73 patients with Medical Research Council and 10 patients with Toronto score) and 7 published articles which consisted of 131 intercostal nerve patients (84 patients with Medical Research Council and 47 patients with Toronto scores). Patients who underwent supraclavicular exploration and nerve grafting presented with an average Medical Research Council score of 3.9 ± 0.72 and an average Toronto score of 6.2 ± 2.2. Patients who underwent intercostal nerve transfer presented with an average Medical Research Council score of 3.9 ± 0.71 and an average Toronto score of 6.4 ± 1.2. There was no statistical difference between supraclavicular exploration and nerve grafting and intercostal nerve transfer when utilizing Medical Research Council elbow flexion scores (ordinal regression: 0.3821, standard error: 0.4590, p = 0.2551) or Toronto Active Movement Scale score for elbow flexion (ordinal regression: 0.7154, standard error: 0.8487, p = 0.2188).Conclusion: Regardless of surgical intervention utilized (supraclavicular exploration and nerve grafting or intercostal nerve transfers), patients had excellent outcomes for elbow flexion following obstetric brachial plexus palsy when utilizing Medical Research Council or Toronto scores for elbow flexion. The difference between these scores was not statistically significant.Type of study/Level of evidence: Therapeutic Study: Investigating the Result of Treatment/level III.
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| 20. |
- Abdelrahim, Nada A., et al.
(författare)
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Human herpes virus type-6 is associated with central nervous system infections in children in Sudan
- 2022
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Ingår i: African Journal of Laboratory Medicine. - : AOSIS. - 2225-2002 .- 2225-2010. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Human herpes virus type-6 (HHV-6) is increasingly recognised as a febrile agent in children. However, less is known in sub-Saharan African countries, including Sudan.Objective: We investigated the involvement of HHV-6 in paediatric central nervous system (CNS) infections in Khartoum, Sudan.Methods: Febrile patients aged up to 15 years with suspected CNS infections at Omdurman Hospital for Children from 01 December 2009 to 01 August 2010 were included. Viral DNA was extracted from leftover cerebrospinal fluid (CSF) specimens and quantitatively amplified by real-time polymerase chain reaction (PCR) at Umeå University in Sweden.Results: Of 503 CSF specimens, 13 (2.6%) were positive for HHV-6 (33.0% [13/40 of cases with proven infectious meningitis]). The median thermal cycle threshold for all HHV-6-positive specimens was 38 (range: 31.9-40.8). The median number of virus copies was 281.3/PCR run (1 × 105 copies/mL CSF; range: 30-44 × 103 copies/PCR run [12 × 103 - 18 × 106 copies/mL CSF]). All positive patients presented with fever and vomiting; 86.0% had seizures. The male-to-female ratio was 1:1; 50.0% were toddlers, 42.0% infants and 8.0% teenagers. Most (83.0%) were admitted in the dry season and 17.0% in the rainy season. Cerebrospinal fluid leukocytosis was seen in 33.0%, CSF glucose levels were normal in 86.0% and low in 14.0%, and CSF protein levels were low in 14.0% and high in 43.0%.Conclusion: Among children in Sudan with CNS infections, HHV-6 is common. Studies on the existence and spread of HHV-6 chromosomal integration in this population are needed.
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