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| 2. |
- Rahmani, V., et al.
(författare)
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Data reduction for X-ray serial crystallography using machine learning
- 2023
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 56, s. 200-213
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Tidskriftsartikel (refereegranskat)abstract
- Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the 'bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
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| 3. |
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| 4. |
- Gisladottir, Rosa S, et al.
(författare)
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Sequence Variants in TAAR5 and Other Loci Affect Human Odor Perception and Naming.
- 2020
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Ingår i: Current biology : CB. - : Elsevier BV. - 1879-0445 .- 0960-9822. ; 30:23
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Tidskriftsartikel (refereegranskat)abstract
- Olfactory receptor (OR) genes in humans form a special class characterized by unusually high DNA sequence diversity, which should give rise to differences in perception and behavior. In the largest genome-wide association study to date based on olfactory testing, we investigated odor perception and naming with smell tasks performed by 9,122 Icelanders, with replication in a separate sample of 2,204 individuals. We discovered an association between a low-frequency missense variant in TAAR5 and reduced intensity rating of fish odor containing trimethylamine (p.Ser95Pro, pcombined= 5.6× 10-15). We demonstrate that TAAR5 genotype affects aversion to fish odor, reflected by linguistic descriptions of the odor and pleasantness ratings. We also discovered common sequence variants in two canonical olfactory receptor loci that associate with increased intensity and naming of licorice odor (trans-anethole: lead variant p.Lys233Asn in OR6C70, pcombined= 8.8× 10-16 and pcombined= 1.4× 10-9) and enhanced naming of cinnamon (trans-cinnamaldehyde; intergenic variant rs317787-T, pcombined= 5.0× 10-17). Together, our results show that TAAR5 genotype variation influences human odor responses and highlight that sequence diversity in canonical OR genes can lead to enhanced olfactory ability, in contrast to the view that greater tolerance for mutations in the human OR repertoire leads to diminished function.
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| 5. |
- McLaughlin, K., et al.
(författare)
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Loss of tetraspanin-7 expression reduces pancreatic beta-cell exocytosis Ca2+ sensitivity but has limited effect on systemic metabolism
- 2022
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Ingår i: Diabetic Medicine. - : Wiley. - 0742-3071 .- 1464-5491. ; 39:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tetraspanin-7 (Tspan7) is an islet autoantigen involved in autoimmune type 1 diabetes and known to regulate beta-cell L-type Ca-2(+) channel activity. However, the role of Tspan7 in pancreatic beta-cell function is not yet fully understood. Methods: Histological analyses were conducted using immunostaining. Whole-body metabolism was tested using glucose tolerance test. Islet hormone secretion was quantified using static batch incubation or dynamic perifusion. beta-cell transmembrane currents, electrical activity and exocytosis were measured using whole-cell patch-clamping and capacitance measurements. Gene expression was studied using m RNA-sequencing and quantitative PCR. Results: Tspan7 is expressed in insulin-containing granules of pancreatic beta-cells and glucagon-producing alpha-cells. Tspan7 knockout mice (Tspan(gamma/-) mouse) exhibit reduced body weight and ad libitum plasma glucose but normal glucose tolerance. Tspan(gamma/- )islets have normal insulin content and glucose- or tolbutamide-stimulated insulin secretion. Depolarisation-triggered Ca2+ current was enhanced in Tspan(gamma/-) beta-cells, but beta-cell electrical activity and depolarisation-evoked exocytosis were unchanged suggesting that exocytosis was less sensitive to Ca2+. TSPAN7 knockdown (KD) in human pseudo-islets led to a significant reduction in insulin secretion stimulated by 20 mM Transcriptomic analyses show that TSPAN7 KD in human pseudo-islets correlated with changes in genes involved in hormone secretion, apoptosis and ER stress. Consistent with rodent beta-cells, exocytotic Ca2+ sensitivity was reduced in a human beta-cell line (EndoC-beta H1) following Tspan7 KD. Conclusion: Tspan7 is involved in the regulation of Ca2+-dependent exocytosis in beta-cells. Its function is more significant in human beta-cells than their rodent counterparts.
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| 6. |
- Nawaz, S., et al.
(författare)
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Explainable machine learning for diffraction patterns
- 2023
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Ingår i: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 56:5, s. 1494-1504
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Tidskriftsartikel (refereegranskat)abstract
- Serial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as 'hit' and 'miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad. 25, 655-670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a 'black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.
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| 7. |
- Salimi, L., et al.
(författare)
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Synergies in exosomes and autophagy pathways for cellular homeostasis and metastasis of tumor cells
- 2020
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Ingår i: Cell and Bioscience. - : Springer Science and Business Media LLC. - 2045-3701. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Eukaryotic cells demonstrate two tightly linked vesicular transport systems, comprising intracellular vesicle transport and extracellular vesicle transport system. Intracellular transport vesicles can translocate biomolecules between compartments inside the cell, for example, proteins from the rough endoplasmic reticulum to the Golgi apparatus. Whereas, the secreted vesicles so-called extracellular vesicles facilitate the transport of biomolecules, for example, nucleic acids, proteins and lipids between cells. Vesicles can be formed during the process of endocytosis or/and autophagy and not only act as mediators of intra- and inter-cellular communication but also represent pathological conditions of cells or tissues. Methods In this review, we searched articles in PubMed, published between 2000 and 2020, with following terms: autophagy, autophagocytosis, transport vesicles, lysosomes, endosomes, exocytosis, exosomes, alone or in different combinations. The biological functions that were selected based on relevancy to our topic include cellular homeostasis and tumorigenesis. Results The searched literature shows that there is a high degree of synergies between exosome biogenesis and autophagy, which encompass endocytosis and endosomes, lysosomes, exocytosis and exosomes, autophagocytosis, autophagosomes and amphisomes. These transport systems not only maintain cellular homeostasis but also operate synergically against fluctuations in the external and internal environment such as during tumorigenesis and metastasis. Additionally, exosomal and autophagic proteins may serve as cancer diagnosis approaches. Conclusion Exosomal and autophagy pathways play pivotal roles in homeostasis and metastasis of tumor cells. Understanding the crosstalk between endomembrane organelles and vesicular trafficking may expand our insight into cooperative functions of exosomal and autophagy pathways during disease progression and may help to develop effective therapies against lysosomal diseases including cancers and beyond.
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| 8. |
- Skuladottir, AT, et al.
(författare)
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A genome-wide meta-analysis identifies 50 genetic loci associated with carpal tunnel syndrome
- 2022
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 1598-
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Tidskriftsartikel (refereegranskat)abstract
- Carpal tunnel syndrome (CTS) is the most common entrapment neuropathy and has a largely unknown underlying biology. In a genome-wide association study of CTS (48,843 cases and 1,190,837 controls), we found 53 sequence variants at 50 loci associated with the syndrome. The most significant association is with a missense variant (p.Glu366Lys) in SERPINA1 that protects against CTS (P = 2.9 × 10−24, OR = 0.76). Through various functional analyses, we conclude that at least 22 genes mediate CTS risk and highlight the role of 19 CTS variants in the biology of the extracellular matrix. We show that the genetic component to the risk is higher in bilateral/recurrent/persistent cases than nonrecurrent/nonpersistent cases. Anthropometric traits including height and BMI are genetically correlated with CTS, in addition to early hormonal-replacement therapy, osteoarthritis, and restlessness. Our findings suggest that the components of the extracellular matrix play a key role in the pathogenesis of CTS.
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| 9. |
- Skuladottir, AT, et al.
(författare)
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A genome-wide meta-analysis uncovers six sequence variants conferring risk of vertigo
- 2021
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 4:1, s. 1148-
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Tidskriftsartikel (refereegranskat)abstract
- Vertigo is the leading symptom of vestibular disorders and a major risk factor for falls. In a genome-wide association study of vertigo (Ncases = 48,072, Ncontrols = 894,541), we uncovered an association with six common sequence variants in individuals of European ancestry, including missense variants in ZNF91, OTOG, OTOGL, and TECTA, and a cis-eQTL for ARMC9. The association of variants in ZNF91, OTOGL, and OTOP1 was driven by an association with benign paroxysmal positional vertigo. Using previous reports of sequence variants associating with age-related hearing impairment and motion sickness, we found eight additional variants that associate with vertigo. Although disorders of the auditory and the vestibular system may co-occur, none of the six genome-wide significant vertigo variants were associated with hearing loss and only one was associated with age-related hearing impairment. Our results uncovered sequence variants associating with vertigo in a genome-wide association study and implicated genes with known roles in inner ear development, maintenance, and disease.
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| 10. |
- Alibakhshikenari, Mohammad, et al.
(författare)
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Broadband 3-D shared aperture high isolation nine-element antenna array for on-demand millimeter-wave 5G applications
- 2022
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Ingår i: Optik (Stuttgart). - : Elsevier BV. - 0030-4026 .- 1618-1336. ; 267
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Tidskriftsartikel (refereegranskat)abstract
- The paper presents the results of a novel 3-D shared aperture 3 x 3 matrix antenna-array for 26 GHz band 5 G wireless networks. Radiation elements constituting the array are hexagonal-shaped patches that are elevated above the common dielectric substrate by 3.35 mm and excited through a metallic rod of 0.4 mm diameter. The rod protrudes through the substrate of 0.8 mm thickness. It is shown that by isolating each radiating element in the array with a wall suppresses unwanted electromagnetic (EM) wave interactions, resulting in improvement in the antenna's impedance matching and radiation characteristics. Moreover, the results show that by embedding hexagonalshaped slots in the patches improve the antenna's gain and radiation efficiency performance. The subwavelength length slots in the patches essentially transform the radiating elements to exhibit metasurface characteristics when the array is illuminated by EM-waves. The proposed array structure has an average gain and radiation efficiency of 20 dBi and 93%, respectively, across 24.0-28.4 GHz. The isolation between its radiation elements is greater than 22 dB. Compared to the unslotted array the improvement in isolation between radiating elements is greater than 11 dB, and the gain and efficiency are better than 10.5 dBi, and 25%, respectively. The compact array has a fractional bandwidth of 16% and a form factor of 20 x 20 x 3.35 mm(3).
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| 11. |
- Farnocchia, Davide, et al.
(författare)
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International Asteroid Warning Network Timing Campaign: 2019 XS
- 2022
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Ingår i: The Planetary Science Journal. - : Institute of Physics Publishing (IOPP). - 2632-3338. ; 3:7
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Tidskriftsartikel (refereegranskat)abstract
- As part of the International Asteroid Warning Network's observational exercises, we conducted a campaign to observe near-Earth asteroid 2019 XS around its close approach to Earth on 2021 November 9. The goal of the campaign was to characterize errors in the observation times reported to the Minor Planet Center, which become an increasingly important consideration as astrometric accuracy improves and more fast-moving asteroids are observed. As part of the exercise, a total of 957 astrometric observations of 2019 XS during the encounter were reported and subsequently were analyzed to obtain the corresponding residuals. While the timing errors are typically smaller than 1 s, the reported times appear to be negatively biased, i.e., they are generally earlier than they should be. We also compared the observer-provided position uncertainty with the cross-track residuals, which are independent of timing errors. A large fraction of the estimated uncertainties appear to be optimistic, especially when <0 2. We compiled individual reports for each observer to help identify and remove the root cause of any possible timing error and improve the uncertainty quantification process. We suggest possible sources of timing errors and describe a simple procedure to derive reliable, conservative position uncertainties.
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| 12. |
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| 13. |
- Karwen, T., et al.
(författare)
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Platelet-derived lipids promote insulin secretion of pancreatic beta cells
- 2023
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Ingår i: Embo Molecular Medicine. - 1757-4676. ; 15:9
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Tidskriftsartikel (refereegranskat)abstract
- Hyperreactive platelets are commonly observed in diabetic patients indicating a potential link between glucose homeostasis and platelet reactivity. This raises the possibility that platelets may play a role in the regulation of metabolism. Pancreatic beta cells are the central regulators of systemic glucose homeostasis. Here, we show that factor(s) derived from beta cells stimulate platelet activity and platelets selectively localize to the vascular endothelium of pancreatic islets. Both depletion of platelets and ablation of major platelet adhesion or activation pathways consistently resulted in impaired glucose tolerance and decreased circulating insulin levels. Furthermore, we found platelet-derived lipid classes to promote insulin secretion and identified 20-Hydroxyeicosatetraenoic acid (20-HETE) as the main factor promoting beta cells function. Finally, we demonstrate that the levels of platelet-derived 20-HETE decline with age and that this parallels with reduced impact of platelets on beta cell function. Our findings identify an unexpected function of platelets in the regulation of insulin secretion and glucose metabolism, which promotes metabolic fitness in young individuals.
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| 14. |
- Khalid, M., et al.
(författare)
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Genetic Risk of Autism Spectrum Disorder in a Pakistani Population
- 2020
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental and neuropsychiatric disorders in children characterized by impairment of communication and social interaction. Several genes with associated single nucleotide polymorphisms (SNPs) have been identified for ASD in different genetic association studies, meta-analyses, and genome-wide association studies (GWAS). However, associations between different SNPs and ASD vary from population to population. Four SNPs in genes CNTNAP2, EIF4E, ATP2B2, CACNA1C, and SNP rs4307059 (which is found between CDH9 and CDH10 genes) have been identified and reported as candidate risk factors for ASD. The aim of the present study was, for the first time, to assess the association of SNPs in these genes with ASD in the Pakistani population. PCR-based genotyping was performed using allele-specific primers in 93 ASD and 93 control Pakistani individuals. All genetic associations, genotype frequencies, and allele frequencies were computed as odds' ratios (ORs) using logistic regression with a threshold of p <= 0.01 to determine statistical significance. We found that the homozygous genotypes of mutant T alleles of CNTNAP2 and ATP2B2 were significantly associated with Pakistani ASD patients in unadjusted ORs (p < 0.01), but their significance score was lost in the adjusted model. Other SNPs such as rs4307059, rs17850950 of EIF4E, and rs1006737 of CACNA1C were not statistically significant. Based on this, we conclude that SNPs are not associated with, or are not the main cause of, autism in the Pakistani population, indicating the involvement of additional players, which need to be investigated in future studies in a large population size. One of the limitations of present study is its small sample size. However, this study, being the first on Pakistani ASD patients, may lay the foundations for future studies in larger samples.
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| 15. |
- Khattak, S, et al.
(författare)
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Knowledge, Attitude, and Perception of Cancer Patients towards COVID-19 in Pakistan: A Cross-Sectional Study
- 2022
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Ingår i: International journal of environmental research and public health. - : MDPI AG. - 1660-4601. ; 19:13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Cancer patients, being immunocompromised, are at higher risk of coronavirus disease (COVID-19). The current study determines cancer patients’ knowledge, attitude, perception, and impact of the COVID-19 pandemic. Method: A cross-sectional online survey was conducted in Pakistan from 1 April 2020 to 1 May 2020. The study respondents were cancer patients with ages equal to or greater than 18 years. Following a request for participation, the URL for the survey was distributed on numerous channels. Other social media platforms, including WeChat, WhatsApp, Facebook, Twitter, Instagram, Messenger, and LinkedIn, were used to increase cancer patient interaction. The questionnaire comprised five different sections such as: (1) sociodemographic information, (2) knowledge, (3) attitude, (4) perception, and (5) impact of COVID-19 on cancer patients. Descriptive medical statistics such as frequency, percentage, mean, and standard deviation were used to illustrate the demographic characteristics of the study participants. To compare mean knowledge scores with selected demographic variables, independent sample t-tests and one-way analysis of variance (ANOVA) were used, which are also practical methods in epidemiological, public health and medical research. The cut-off point for statistical significance was set at a p-value of 0.05. Results: More than 300 cancer patients were invited, of which 208 agreed to take part. The response rate was 69.33% (208/300). Gender, marital status, and employment status had a significant association with knowledge scores. Of the total recruited participants, 96% (n = 200) (p < 0.01) knew about COVID-19, and 90% were aware of general symptoms of COVID-19 disease, such as route of transmission and preventive measurements. In total, 94.5% (n = 197) (p < 0.01) were willing to accept isolation if they were infected with COVID-19, and 98% (n = 204) (p < 0.01) had reduced their use of public transportation. More than 90% (n = 188) (p < 0.01) of cancer patients were found to be practicing preventative measures such as using a face mask, keeping social distance, and avoiding handshaking and hugging. Around 94.4% (n = 196) (p < 0.01) of cancer patients had been impacted by, stopped or had changed cancer treatment during this pandemic, resulting in COVID-related anxiety and depression. Conclusion: The included cancer patients exhibited a good level of COVID-19 knowledge, awareness, positive attitude, and perception. Large-scale studies and efforts are needed to raise COVID-19 awareness among less educated and high-risk populations. The present survey indicates that mass-level effective health education initiatives are required for developing countries to improve and reduce the gap between KAP and COVID-19.
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| 16. |
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