Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Information Retrieval Models on Quran dataset in Cross-Language Information Retrieval systems

English is an international language used for communication worldwide but still many cannot read, write, understand, or communicate in English. On the other hand, the World Wide Web has unlimited resources of information in different languages which English native find challenging to understand. To avoid such barriers, Cross-Language Information Retrieval (CLIR) systems are proposed, which refers to document retrieval tasks across different languages. This work focuses on the performance evaluation of different Information Retrieval (IR) models in CLIR system using Quran dataset. Furthermore, this work also investigated the length of query and query expansion models for effective retrieval. The results show that different length of queries has an impact on the performance of the retrieval methods in terms of effectiveness. Hence, after comprehensive experiments, an appropriate length of query for Arabic CLIR system is suggested along with the best query expansion and retrieval model.
Fast and robust active neuron segmentation in two-photon calcium imaging using spatiotemporal deep learning

Significance Two-photon calcium imaging is a standard technique of neuroscience laboratories that records neural activity from individual neurons over large populations in awake-behaving animals. Automatic and accurate identification of behaviorally relevant neurons from these recordings is a critical step toward complete mapping of brain activity. To this end, we present a fast deep learning framework which significantly outperforms previous methods and is the first to be as accurate as human experts in segmenting active and overlapping neurons. Such neuron detection performance is crucial for precise quantification of population-level and single-cell–level neural coding statistics, which will aid neuroscientists to temporally synchronize dynamic behavioral or neural stimulus to the subjects’ neural activity, opening the door for unprecedented accelerated progress in neuroscientific experiments. Calcium imaging records large-scale neuronal activity with cellular resolution in vivo. Automated, fast, and reliable active neuron segmentation is a critical step in the analysis workflow of utilizing neuronal signals in real-time behavioral studies for discovery of neuronal coding properties. Here, to exploit the full spatiotemporal information in two-photon calcium imaging movies, we propose a 3D convolutional neural network to identify and segment active neurons. By utilizing a variety of two-photon microscopy datasets, we show that our method outperforms state-of-the-art techniques and is on a par with manual segmentation. Furthermore, we demonstrate that the network trained on data recorded at a specific cortical layer can be used to accurately segment active neurons from another layer with different neuron density. Finally, our work documents significant tabulation flaws in one of the most cited and active online scientific challenges in neuron segmentation. As our computationally fast method is an invaluable tool for a large spectrum of real-time optogenetic experiments, we have made our open-source software and carefully annotated dataset freely available online.
Testing for Hardy–Weinberg equilibrium in structured populations using genotype or low‐depth next generation sequencing data

Testing for deviations from Hardy–Weinberg equilibrium (HWE) is a common practice for quality control in genetic studies. Variable sites violating HWE may be identified as technical errors in the sequencing or genotyping process, or they may be of particular evolutionary interest. Large‐scale genetic studies based on next‐generation sequencing (NGS) methods have become more prevalent as cost is decreasing but these methods are still associated with statistical uncertainty. The large‐scale studies usually consist of samples from diverse ancestries that make the existence of some degree of population structure almost inevitable. Precautions are therefore needed when analysing these data set, as population structure causes deviations from HWE. Here we propose a method that takes population structure into account in the testing for HWE, such that other factors causing deviations from HWE can be detected. We show the effectiveness of PCAngsd in low‐depth NGS data, as well as in genotype data, for both simulated and real data set, where the use of genotype likelihoods enables us to model the uncertainty.
Review: Clinical, neuropathological and genetic features of Lewy body dementias

Lewy body dementias are the second most common neurodegenerative dementias after Alzheimer's disease and include dementia with Lewy bodies and Parkinson's disease dementia. They share similar clinical and neuropathological features but differ in the time of dementia and parkinsonism onset. Although Lewy bodies are their main pathological hallmark, several studies have shown the emerging importance of Alzheimer's disease pathology. Clinical amyloid‐β imaging using Pittsburgh Compound B (PiB) supports neuropathological studies which found that amyloid‐β pathology is more common in dementia with Lewy bodies than in Parkinson's disease dementia. Nevertheless, other co‐occurring pathologies, such as cerebral amyloid angiopathy, TDP‐43 pathology and synaptic pathology may also influence the development of neurodegeneration and dementia. Recent genetic studies demonstrated an important role of APOE genotype and other genes such as GBA and SNCA which seem to be involved in the pathophysiology of Lewy body dementias. The aim of this article is to review the main clinical, neuropathological and genetic aspects of dementia with Lewy bodies and Parkinson's disease dementia. This is particularly relevant as future management for these two conditions may differ.
PON1 hypermethylation and PON3 hypomethylation are associated with risk of cerebral infarction.

Objective Paraoxonase (PON) family genes are closely related to the etiology and prognosis of cerebral infarction. This study explored the association of the promoter methylation of PON family genes (PON1, PON2 and PON3) with the risk of cerebral infarction. Materials and Methods In this study, 152 patients with confirmed cerebral infarction were selected as the case group, and 152 healthy controls were selected as the control group. The quantitative methylation-specific PCR (qMSP) was used to determine the promoter methylation levels of PON1, PON2 and PON3 genes. The methylation level was expressed as a methylation reference percentage (PMR). Results Our results indicated that PON1 methylation was significantly higher in the case group than in the control group (P = 0.0001). On the contrary, PON3 methylation was significantly lower in the case group than in the control group(P = 0.002). In addition, we found that PON2 gene had a very low level of methylation in both case and control groups (PMR = 0). Subgroup analysis showed that PON1 and PON3 methylation were associated with cerebral infarction only in males (PON1, P = 0.0002; PON3, P = 0.007). Interestingly, the methylation levels of PON1 and PON3 were correlated with each other (case: r = 0.418, P = 0.0001; control: r = 0.3, P = 0.0002). Further multiple regression analysis suggested that elevated methylation levels of PON3 were a protective factor for cerebral infarction [OR (95% CI) = 0.979 (0.96, 0.999), β = -0.021,P = 0.035)], high- density lipoprotein (HDL) and uric acid (UA) also were protective factors for cerebral infarction [HDL, OR (95% CI) = 0.01 (0.003, 0.033), P < 0.0001); UA, OR (95% CI) = 0.995 (0.991, 0.998), P = 0.003)]. The ROC curve analysis found that the combination of PON3, HDL, and UA had a good predictive power for cerebral infarction (AUC=0.878, 95% CI=0.839-0.918, sensitivity 73.7%, specificity 89.7%, P < 0.0001). Conclusion PON1 and PON3 promoter methylation levels in peripheral blood were closely related. PON1 and PON3 methylation were associated with the risk of cerebral infarction in men. PON3 promoter methylation combined with HDL and UA could be used as potential biomarkers for the diagnosis of cerebral infarction.
Abnormal maturation of the resting‐state peak alpha frequency in children with autism spectrum disorder

Age‐related changes in resting‐state (RS) neural rhythms in typically developing children (TDC) but not children with autism spectrum disorder (ASD) suggest that RS measures may be of clinical use in ASD only for certain ages. The study examined this issue via assessing RS peak alpha frequency (PAF), a measure previous studies, have indicated as abnormal in ASD. RS magnetoencephalographic (MEG) data were obtained from 141 TDC (6.13–17.70 years) and 204 ASD (6.07–17.93 years). A source model with 15 regional sources projected the raw MEG surface data into brain source space. PAF was identified in each participant from the source showing the largest amplitude alpha activity (7‐13 Hz). Given sex differences in PAF in TDC (females > males) and relatively few females in both groups, group comparisons were conducted examining only male TDC (N = 121) and ASD (N = 183). Regressions showed significant group slope differences, with an age‐related increase in PAF in TDC (R2 = 0.32) but not ASD (R2 = 0.01). Analyses examining male children below or above 10‐years‐old (median split) indicated group effects only in the younger TDC (8.90 Hz) and ASD (9.84 Hz; Cohen's d = 1.05). In the older ASD, a higher nonverbal IQ was associated with a higher PAF. In the younger TDC, a faster speed of processing was associated with a higher PAF. PAF as a marker for ASD depends on age, with a RS alpha marker of more interest in younger versus older children with ASD. Associations between PAF and cognitive ability were also found to be age and group specific.
Increased Water Content in Periventricular Caps in Patients without Acute Hydrocephalus

BACKGROUND AND PURPOSE: Periventricular caps are a common finding on MR imaging and are believed to reflect focally increased interstitial water content due to dysfunctional transependymal transportation rather than ischemic-gliotic changes. We compared the quantitative water content of periventricular caps and microvascular white matter lesions, hypothesizing that periventricular caps associated with increased interstitial fluid content display higher water content than white matter lesions and are therefore differentiable from microvascular white matter lesions by measurement of the water content. MATERIALS AND METHODS: In a prospective study, we compared the water content of periventricular caps and white matter lesions in 50 patients using a quantitative multiple-echo, gradient-echo MR imaging water-mapping sequence. RESULTS: The water content of periventricular caps was significantly higher than that of white matter lesions (P = .002). Compared with normal white matter, the mean water content of periventricular caps was 17% ± 5% higher and the mean water content of white matter lesions was 11% ± 4% higher. Receiver operating characteristic analysis revealed that areas in which water content was 15% higher compared with normal white matter correspond to periventricular caps rather than white matter lesions, with a specificity of 93% and a sensitivity of 60% (P < .001). There was no significant correlation between the water content of periventricular caps and whole-brain volume (P = .275), white matter volume (P = .243), gray matter volume (P = .548), lateral ventricle volume (P = .800), white matter lesion volume (P = .081), periventricular cap volume (P = .081), and age (P = .224). CONCLUSIONS: Quantitative MR imaging allows differentiation between periventricular caps and white matter lesions. Water content quantification of T2-hyperintense lesions may be a useful additional tool for the characterization and differentiation of T2-hyperintense diseases.
Utility of Complementary Magnetic Resonance Plaque Imaging and Contrast‐Enhanced Ultrasound to Detect Carotid Vulnerable Plaques

Background We aimed to improve the assessment quality of plaque vulnerability with combined use of magnetic resonance imaging and contrast‐enhanced ultrasound (CEUS). Methods and Results We prospectively enrolled 71 patients with internal carotid artery stenosis who underwent carotid endarterectomy and performed preoperative CEUS and magnetic resonance plaque imaging. We distinguished high–signal‐intensity plaques (HIPs) and non‐HIPs based on magnetization‐prepared rapid acquisition with gradient echo images. We graded them according to the CEUS contrast effect and compared the CEUS images with the carotid endarterectomy specimens. Among the 70 plaques, except 1 carotid endarterectomy tissue sample failure, 59 were classified as HIPs (43 symptomatic) and 11 were classified as non‐HIPs (5 symptomatic). Although the magnetization‐prepared rapid acquisition with gradient echo findings alone had no significant correlation with symptoms (P=0.07), concomitant use of magnetization‐prepared rapid acquisition with gradient echo and CEUS findings did show a significant correlation (P<0.0001). CEUS showed that all 5 symptomatic non‐HIPs had a high‐contrast effect. These 5 plaques were histopathologically confirmed as vulnerable, with extensive neovascularization but only a small amount of intraplaque hemorrhage. Conclusions Complementary use of magnetic resonance imaging and CEUS to detect intraplaque hemorrhage and neovascularization in plaques can be useful for evaluating plaque vulnerability, consistent with the destabilization process associated with neovessel formation and subsequent intraplaque hemorrhage.
Diet-dependent acid load - the missing link between an animal protein-rich diet and non-alcoholic fatty liver disease?

OBJECTIVE Our group recently showed that animal protein was independently associated with non-alcoholic fatty liver disease (NAFLD). We hypothesize that this may be explained by a high diet-dependent acid load (DAL). METHODS This cross-sectional study is embedded in a prospective population-based cohort. We estimated DAL-proxies via food-frequency questionnaires using potential renal acid load (PRAL; using dietary protein, phosphorus, potassium, calcium, and magnesium intake), net endogenous acid production (NEAP; using protein and potassium intake), and animal-protein-to-potassium-ratio (A:P). We defined NAFLD using ultrasound after excluding secondary steatogenic causes. We used logistic regression models -adjusted for socio-demographic, lifestyle, and metabolic traits- on categorized (Q1-Q4) and continuous DAL-proxies (allowing for non-linearity) and NAFLD. RESULTS We included 3882 participants of which 1337 had NAFLD. All DAL-proxies were higher, meaning more acidic, in individuals with NAFLD (PRAL: -2.9 vs -5.5mEq/day; NEAP: 37.0 vs 35.1mEq/day, and AP:13.3 vs 12.4; all P<0.001). The highest quartile of DAL-proxies was associated with NAFLD independent of socio-demographic and lifestyle confounders, but significance dissipated after correction for metabolic confounders and multiple testing. However, the P-value for non-linearity was significant in all DAL-proxies (P<0.001). Natural cubic splines performed better with than without DAL-proxies in the fully adjusted model (all P≤0.038). The highest probability of NAFLD was found for an acidic diet. CONCLUSIONS This study showed an independent non-linear association between an acidic diet and NAFLD. Further studies with acid-base biomarkers are needed, but our findings might provide a mechanistic explanation for the harmful association between an animal protein-rich diet and NAFLD.
Cytomegalovirus cholestasis in an immunocompetent host.

Primary infection or reactivation of cytomegalovirus (CMV) can induce in immunocompromised patients a severe disease depending on the type of immuno-suppression, and can affect multiple organs. On the other hand, the infection is benign and mostly asymptomatic in immunocompetent individuals who do not require antiviral treatment. Rare cases of primary infection have been documented. In this article, we report the case of a 21-year-old immunocompetent female patient with CMV cholestatic jaundice. The diagnosis was retained on all clinico-pathologic data after eliminating the autoimmune, surgical and other infectious causes. Resolution of cholestasis has been observed with ganciclovir.
Defects in intervertebral disc and spine during development, degeneration, and pain: New research directions for disc regeneration and therapy

Intervertebral discs are cartilaginous joints present between vertebrae. The centers of the intervertebral discs consist of a gelatinous nucleus pulposus derived from the embryonic notochord. With age or injury, intervertebral discs may degenerate, causing neurological symptoms including back pain, which affects millions of people worldwide. Back pain is a multifactorial disorder, and disc degeneration is one of the primary contributing factors. Recent studies in mice have identified the key molecules involved in the formation of intervertebral discs. Several of these key molecules including sonic hedgehog and Brachyury are not only expressed by notochord during development, but are also expressed by neonatal mouse nucleus pulposus cells, and are crucial for postnatal disc maintenance. These findings suggest that intrinsic signals in each disc may maintain the nucleus pulposus microenvironment. However, since expression of these developmental signals declines with age and degeneration, disc degeneration may be related to the loss of these intrinsic signals. In addition, findings from mouse and other mammalian models have identified similarities between the patterning capabilities of the embryonic notochord and young nucleus pulposus cells, suggesting that mouse is a suitable model system to understand disc development and aging. Future research aimed at understanding the upstream regulators of these developmental signals and the modes by which they regulate disc growth and maintenance will likely provide mechanistic insights into disc growth and aging. Further, such findings will likely provide insights relevant to the development of effective therapies for treatment of back pain and reversing the disc degenerative process.
Draft Genome Sequence of Halotolerant Bacterium Chromohalobacter salexigens ANJ207, Isolated from Salt Crystal Deposits in Pipelines

Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. ABSTRACT Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. The genome was determined to have 3.66 Mb represented in 13 scaffolds, with a total of 3,406 genes predicted.
Serum Sodium and Pulse Pressure in SPRINT.

BACKGROUND High dietary sodium intake may induce a small, yet physiologically relevant rise in serum sodium concentration, which associates with increased systolic blood pressure. Cellular data suggest that this association is mediated by increased endothelial cell stiffness. We hypothesized that higher serum sodium levels were associated with greater arterial stiffness in participants in the Systolic Blood Pressure Intervention Trial (SPRINT). METHODS Multivariable linear regression was used to examine the association between baseline serum sodium level and (i) pulse pressure (PP; n = 8,813; a surrogate measure of arterial stiffness) and (ii) carotid-femoral pulse wave velocity (CFPWV; n = 591 in an ancillary study to SPRINT). RESULTS Baseline mean ± SD age was 68 ± 9 years and serum sodium level was 140 ± 2 mmol/L. In the PP analysis, higher serum sodium was associated with increased baseline PP in the fully adjusted model (tertile 3 [≥141 mmol] vs. tertile 2 [139-140 mmol]; β = 0.87, 95% CI = 0.32 to 1.43). Results were similar in those with and without chronic kidney disease. In the ancillary study, higher baseline serum sodium was not associated with increased baseline CFPWV in the fully adjusted model (β = 0.35, 95% CI = -0.14 to 0.84). CONCLUSIONS Among adults at high risk for cardiovascular events but free from diabetes, higher serum sodium was independently associated with baseline arterial stiffness in SPRINT, as measured by PP, but not by CFPWV. These results suggest that high serum sodium may be a marker of risk for increased PP, a surrogate index of arterial stiffness.
Reporting quality in systematic reviews of in vitro studies: a systematic review

Abstract Background: Systematic reviews (SRs) and/or meta-analyses of in vitro research have an important role in establishing the foundation for clinical studies. In this study, we aimed to evaluate the reporting quality of SRs of in vitro studies using the PRISMA checklist. Method: Four databases were searched including PubMed, Virtual Health Library (VHL), Web of Science (ISI) and Scopus. The search was limited from 2006 to 2016 to include all SRs and/or meta-analyses (MAs) of pure in vitro studies. The evaluation of reporting quality was done using the PRISMA checklist. Results: Out of 7702 search results, 65 SRs were included and evaluated with the PRISMA checklist. Overall, the mean overall quality score of reported items of the PRISMA checklist was 68%. We have noticed an increasing pattern in the numbers of published SRs of in vitro studies over the last 10 years. In contrast, the reporting quality was not significantly improved over the same period (p = .363). There was a positive but not significant correlation between the overall quality score and the journal impact factor of the included studies. Conclusions: The adherence of SRs of in vitro studies to the PRISMA guidelines was poor. Therefore, we believe that using reporting guidelines and journals paying attention to this fact will improve the quality of SRs of in vitro studies.
Against Intuitive Horribleness

Testimony by disabled people concerning the relationship between their experiences and overall well-being has long been an object of social scientific and humanistic study. Often discussed in terms of “the disability paradox,” these studies contrast the intuitive horribleness of certain impaired states against the testimonial evidence suggesting that people in such states do not in fact experience their lives as horrible. Explanations for why such testimonial evidence is suspect range from claims about adaptive preferences to issues of qualitative research methodology. In this paper, I argue that the problem lies not with the evidence, but the intuitions in question. Using the disability paradox as a case study, I further argue against the use of the concept of intuitive horribleness in social epistemology. I contend that testimonial and hermeneutical injustices are baked into most deployments of the concept, and even if one were to justify its use in select cases, it should be accompanied with prima facie suspicion. In conclusion, I discuss the implications of this analysis for the literature on transformative experience and also for the stakes of multi-cultural, historically informed philosophical analyses more generally.
3D X-Y-T Space Path Planning for Autonomous Mobile Robots Considering Dynamic Constraints

An autonomous mobile robot in a human living space should be able to not only realize collision-free motion but also give way to humans depending on the situation. Although various reactive obstacle avoidance methods have been proposed, it is difficult to achieve such motion. On the other hand, 3D X-Y-T space path planning, which takes into account the motion of both the robot and the human in a look-ahead time horizon, is effective. This paper proposes a real-time obstacle avoidance method for an autonomous mobile robot that considers the robots dynamic constraints, the personal space, and human directional area based on grid-based 3D X-Y-T space path planning. The proposed method generates collision-free motion in which the robot can yield to humans. To verify the effectiveness of the proposed method, various experiments in which the humans position and velocity were estimated using laser range finders were carried out.