Miracle-dz/UniFAR-FTUs huggingface dataset:
Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.

Untargeted metabolomics can detect more than 10 000 peaks in a single LC-MS run. The correspondence between these peaks and metabolites, however, remains unclear. Here, we introduce a Peak Annotation and Verification Engine (PAVE) for annotating untargeted microbial metabolomics data. The workflow involves growing cells in 13C and 15N isotope-labeled media to identify peaks from biological compounds and their carbon and nitrogen atom counts. Improved deisotoping and deadducting are enabled by algorithms that integrate positive mode, negative mode, and labeling data. To distinguish metabolites and their fragments, PAVE experimentally measures the response of each peak to weak in-source collision induced dissociation, which increases the peak intensity for fragments while decreasing it for their parent ions. The molecular formulas of the putative metabolites are then assigned based on database searching using both m/ z and C/N atom counts. Application of this procedure to Saccharomyces cerevisiae and Escherichia coli revealed that more than 80% of peaks do not label, i.e., are environmental contaminants. More than 70% of the biological peaks are isotopic variants, adducts, fragments, or mass spectrometry artifacts yielding ∼2000 apparent metabolites across the two organisms. About 650 match to a known metabolite formula based on m/ z and C/N atom counts, with 220 assigned structures based on MS/MS and/or retention time to match to authenticated standards. Thus, PAVE enables systematic annotation of LC-MS metabolomics data with only ∼4% of peaks annotated as apparent metabolites.
portal The Virtual Kidney : an eScience interface and Grid

References l.html#ref-list-1 http://rsta.royalsocietypublishing. org/content/367/1896/2141.ful This article cites 33 articles, 4 of which can be accessed free Subject collections (22 articles) computer modelling and simulation  (51 articles) computational biology  collections Articles on similar topics can be found in the following Email alerting service here in the box at the top right-hand corner of the article or click Receive free email alerts when new articles cite this article sign up
Evaluation of Quality of Life after Implantation of Light or Standard Polypropylene Hernia Meshes

Introduction: The present pilot study evaluates the quality of life of Bulgarian patients after a conventional hernia operation in which light or standard polypropylene hernia meshes were used. Materials and methods: Sixty-eight patients planned for recovery of primary or recurrent open hernia with implanted standard or lightweight polypropylene meshes were included in the study. Patients’ data were collected prospectively for a 5-month period (October 2017 - February 2018) on the basis of the case histories. The patients were interviewed using the EQ5D questionnaire and a visual analogue scale. Follow-up of each patient’s results was performed up to a year after surgery. Results: Three months after the operation, the patients reported only the presence of pain. On average, 24.5% of patients experienced mild pain and 20.3% - severe pain. In the standard mesh group, on average, the mild pain was 7.69%, swelling 3.84%, and foreign body sensation - 15.38% one year after the surgery. In the light mesh group the reported mild pain was 6.69%, pulling without pain - 13.33%, and foreign body sensation - 6.69%. There was no statistically significant difference in the pain level according to the used mesh, but in the group with implanted standard meshes, the reported problems prevailed. At the end of the survey period, the average score was 84.39±13.67. Conclusions: Hernia operation reduces pain 1 year after the procedure. The intensity of chronic pain one year after the surgery is relatively similar for both light and standard meshes in conventional inguinal hernia repair. The differences in the overall quality of life are insignificant in the long run. An individualized choice, based on the patients’ characteristics and safety of meshes, should be done by the healthcare specialists.
Zircon and apatite thermochronology of the Nankai Trough accretionary prism and trench, Japan: Sediment transport in an active and collisional margin setting

The Nankai accretionary complex is the most recent addition to the accretionary complexes of southwest Japan and has preserved a record of sediment flux to the trench during its construction. In this study, we use U‐Pb zircon and fission track analysis of both zircons and apatites from sediments taken from the forearc and trench of the Nankai Trough, as well as rivers from southwest Japan to examine the exhumation history of the margin since the Middle Miocene. Modern rivers show a flux dominated by erosion of the Mesozoic‐Eocene Shimanto and Sanbagawa accretionary complexes. Only the Fuji River, draining the collision zone between the Izu and Honshu arcs, is unique in showing much faster exhumation. Sediment from the Izu‐Honshu collision is not found 350–500 km along the margin offshore Kyushu indicating limited along‐strike sediment transport. Sediment deposited since 2 Ma on the midtrench slope offshore the Muroto Peninsula of Shikoku (ODP Site 1176) and on the lower slope trenchward of the Kumano Basin (IODP Sites C0006E and C00007E) shares the dominant source in the Shimanto and Sanbagawa complexes seen in the modern rivers. Prior to 5 Ma, additional sediment was being sourced from further north in more slowly exhumed terrains, ~350 km from the trench axis. Around 9.4 Ma, U‐Pb zircon ages of ~1800 Ma indicate enhanced erosion from the North China Craton, exposed in northern Honshu. In the middle Miocene, at ~15.4 Ma, the sediment was being derived from a much wider area including the Yangtze Craton (U‐Pb ages ~800 Ma). We suggest that this enhanced catchment may have reflected the influence of the Yangtze River in supplying into the Shikoku Basin prior to rifting of the Okinawa Trough at 10 Ma and migration of the Palau‐Kyushu Ridge to form a barrier to transport. The restriction of Nankai Trough provenance to Mesozoic source partly reflects continued uplift of the Shimanto and Sanbagawa complexes since the Middle Miocene.
Effect of fluid velocity on model‐estimated rates of radial solute diffusion in a cylindrical macropore column

Solute transfer between regions of high and low permeability will limit rates of aquifer remediation in the field and can also affect solute transport through laboratory columns. Transport in systems with such rate limitations is often modeled by assuming that advective transport occurs only in the high‐permeability region (mobile domain) and that solute movement within the lower‐permeability region (immobile domain) is via diffusion only. The validity of such models was explored by experimentally observing the influence of pore water velocity on the apparent rates of transfer within a geometrically well defined, two‐domain system. Tritiated water tracer (3H2O) experiments were conducted in a 7‐cm soil column with a central cylindrical zone of highly permeable material surrounded by an annulus of relatively impermeable finer‐grained sediment. Experimental pore water velocities spanned over two orders of magnitude and included “long” and “short” solute input pulse lengths. The breakthrough data were interpreted using a first‐order mass transfer model (FOM) and a Fickian pore‐diffusion model (PDM). As expected, the rate parameters fitted to the PDM were less sensitive to pore water velocity than those estimated using the FOM. Nonetheless, parameters for the PDM exhibited a negative correlation with pore water velocity. Reestimated parameters from experiments of Young and Ball (1998) showed similar scaling. The velocity dependency indicates deficiencies in inherent model assumptions of both the FOM and the PDM. For the PDM, reasons for the velocity dependency may include mass transfer limitations in the mobile domain and/or heterogeneity of diffusion rates within the immobile domain.
PENERAPAN METODE PASSIVE SAMPLER UNTUK ANALISA NO2 UDARA AMBIEN DI BEBERAPA LOKASI DI JAKARTA DAN SEKITARNYA

Analisa polutan udara ambien seperti NO2, SO2, O3 dan lain-lain dengan menggunakan Metode Passive Sampler telah banyak digunakan di negara-negara maju seperti Jepang, Thailand, China, USA. Sedangkan di Indonesia, metode ini masih belum dikenal luas. Metode ini memiliki banyak kelebihan dibanding dengan metode lain, antara lain mudah dibawa dan mempunyai tingkat mobilitas yang tinggi, dapat digunakan untuk menganalisa udara pada kondisi cuaca yang berbeda dll. Dalam paper ini, penulis bekerja sama dengan Universitas Tokushima, Jepang telah mencoba menerapkan metode Passive Sampler yang dikembangkan oleh Yanagisawa(1) untuk menganalisa konsentrasi NO2 dalam udara ambien di beberapa lokasi di Jakarta dan sekitarnya dari bulan Januari 1997 sampai Agustus 1997. Hasil analisa menunjukkan bahwa kandungan NO2 udara ambien di wilayah Jakarta dan sekitarnya belum melebihi nilai ambang batas yang ditentukan.
Telehealth Before and During the COVID-19 Pandemic: Analysis of Health Care Workers' Opinions

Background: The COVID-19 pandemic and the lockdowns for controlling the spread of infection have led to a surge in telehealth adoption by many health care organizations. It is unclear how this pandemic has impacted health professionals’ view about telehealth. The analysis of textual data, such as comments posted on a discussion forum, can uncover information that may not be captured by a structured survey. Objective: This study aims to examine the opinions of health care workers about telehealth services during the time frame of March 2013-December 2020. Methods: Comments about telehealth posted by health care workers from at least 46 countries were collected from an online discussion forum dedicated to health professionals. The analysis included the computation of sentiment scores from the textual data and the use of structural topic modeling to identify the topics of discussions as well as the factors that may be associated with the prevalence of these topics. Results: The analysis of the comments revealed positive opinions about the perceived benefits of telehealth services before and during the pandemic, especially the ability to reach patients who cannot come to the health facility for diverse reasons. However, opinions about these benefits were less positive during the pandemic compared to the prepandemic period. Specific issues raised during the pandemic included technical difficulties encountered during telehealth sessions and the inability to perform certain care routines through telehealth platforms. Although comments on the quality of care provided through telehealth were associated with a negative sentiment score overall, the average score was less negative during the pandemic compared to the prepandemic period, signaling a shift in opinion about the quality of telehealth services. In addition, the analysis uncovered obstacles to the adoption of telehealth, including the absence of adequate legal dispositions for telehealth services and issues regarding the payment of these services by health insurance organizations. Conclusions: Enhancing the adoption of telehealth services beyond the pandemic requires addressing issues related to the quality of care, payment of services, and legal dispositions for delivering these services.
Data Augmentation for Deep Neural Network Acoustic Modeling

This paper investigates data augmentation for deep neural network acoustic modeling based on label-preserving transformations to deal with data sparsity. Two data augmentation approaches, vocal tract length perturbation (VTLP) and stochastic feature mapping (SFM), are investigated for both deep neural networks (DNNs) and convolutional neural networks (CNNs). The approaches are focused on increasing speaker and speech variations of the limited training data such that the acoustic models trained with the augmented data are more robust to such variations. In addition, a two-stage data augmentation scheme based on a stacked architecture is proposed to combine VTLP and SFM as complementary approaches. Experiments are conducted on Assamese and Haitian Creole, two development languages of the IARPA Babel program, and improved performance on automatic speech recognition (ASR) and keyword search (KWS) is reported.
Random placement models explain species richness and dissimilarity of frog assemblages within Atlantic Forest fragments.

1. Understanding the effects of random versus niche-based processes on biodiversity patterns is a central theme in ecology, and an important tool for predicting effects of habitat loss and fragmentation on biodiversity. We investigated the predictive power of random processes to explain species richness and species dissimilarity of amphibian assemblages in a fragmented tropical landscape of the Atlantic Forest of South America. 2. We analyzed a large database of amphibian abundance and occupancy, sampled in 21 forest fragments ranging in size from 1.9 to 619 ha. We compared observed species richness and species dissimilarity with the outcomes of two null (random placement) models: 1- the traditional Coleman's area-based model and 2 - an abundance-based model (based on the number of individuals observed in each fragment). We applied these models for all species combined, and separately for forest-dependent and habitat-generalist species. 3. The abundance-based model fitted the observed species richness data better than the area-based model for all species, forest-dependent species, and generalist species. The area-based and the abundance-based models were also able to significantly explain species dissimilarity for all species and for generalists, but not for forest dependent species. 4. The traditional area-based model assigned too many individuals to large fragments, thus failing to accurately explain species richness within patches across the landscape. 5. Although niche-based processes may be important to structuring the regional pool of species in fragmented landscapes, our results suggest that part of the variation in species richness and species dissimilarity can be successfully explained by random placement models, especially for generalist species. Evaluating which factors cause variation in the number of individuals among patches should be a focus in future studies aiming to understand biodiversity patterns in fragmented landscapes.
Sperm divergence in a passerine contact zone: indication of reinforcement

4 Postcopulatory sexual selection may promote evolutionary diversification in sperm form, but 5 the contribution of between-species divergence in sperm morphology to the origin of 6 reproductive isolation and speciation remains little understood. To assess the possible role of 7 sperm diversification in reproductive isolation, we studied sperm morphology in two closely 8 related bird species, the common nightingale (Luscinia megarhynchos) and the thrush 9 nightingale (L. luscinia), that hybridize in a secondary contact zone spanning Central and 10 Eastern Europe. We found: (1) striking divergence between the species in total sperm length, 11 accompanied by a difference in the length of the mitochondrial sperm component; (2) greater 12 divergence between species in sperm morphology in sympatry than in allopatry, with evidence 13 for character displacement in sperm head length detected in L. megarhynchos; (3) interspecific 14 hybrids showing sperm with a length intermediate between the parental species, but no 15 evidence for decreased sperm quality (the proportion of abnormal spermatozoa in ejaculates). 16 Our results demonstrate that divergence in sperm morphology between the two nightingale 17 species does not result in intrinsic postzygotic isolation, but may contribute to postcopulatory 18 prezygotic isolation. This isolation could be strengthened in sympatry by reinforcement. 19
Prediction of Incident Diabetes Mellitus in Middle-aged Adults

Methods: We estimated the 7-year risk of T2DM in middle-aged participants who had an oral glucose tolerance test at baseline. There were 160 cases of new T2DM, and regression models were used to predict new T2DM, starting with characteristics known to the subject (personal model, ie, age, sex, parental history of diabetes, and body mass index [calculated as the weight in kilograms divided by height in meters squared]), adding simple clinical measurements that included metabolic syndrome traits (simple clinical model), and, finally, assessing complex clinical models that included (1) 2-hour post–oral glucose tolerance test glucose, fasting insulin, and C-reactive protein levels; (2) the Gutt insulin sensitivity index; or (3) the homeostasis model insulin resistance and the homeostasis model insulin resistance -cell sensitivity indexes. Discrimination was assessed with area under the receiver operating characteristic curves (AROCs). Results: The personal model variables, except sex, were statisticallysignificantpredictorsofT2DM(AROC,0.72). In the simple clinical model, parental history of diabetes andobesityremainedsignificantpredictors,alongwithhypertension, low levels of high-density lipoprotein cholesterol,elevatedtriglyceridelevels,andimpairedfastingglucose findings but not a large waist circumference (AROC, 0.85). Complex clinical models showed no further improvement in model discriminations (AROC, 0.8500.854)andwerenotsuperiortothesimpleclinicalmodel. Conclusion: Parental diabetes, obesity, and metabolic syndrometraitseffectivelypredictT2DMriskinamiddleaged white population sample and were used to develop a simple T2DM prediction algorithm to estimate risk of new T2DM during a 7-year follow-up interval. Arch Intern Med. 2007;167:1068-1074
Altered Structural Connectivity in Neonates at Genetic Risk for Schizophrenia: a Combined Study Using Morphological and White Matter Networks

a r t i c l e i n f o Keywords: High genetic risk Newborn infant Diffusion tensor imaging Schizophrenia Brain development Network analysis Recently, an increasing body of evidence suggests that developmental abnormalities related to schizophrenia may occur as early as the neonatal stage. Impairments of brain gray matter and wiring problems of axonal fibers are commonly suspected to be responsible for the disconnection hypothesis in schizophrenia adults, but significantly less is known in neonates. In this study, we investigated 26 neonates who were at genetic risk for schizophrenia and 26 demographically matched healthy neonates using both morphological and white matter networks to examine possible brain connectivity abnormalities. The results showed that both populations exhibited small-world network topology. Morphological network analysis indicated that the brain structural associations of the high-risk neonates tended to have globally lower efficiency, longer connection distance, and less number of hub nodes and edges with relatively higher betweenness. Subgroup analysis showed that male neonates were significantly disease-affected, while the female neonates were not. White matter network analysis, however, showed that the fiber networks were globally unaffected, although several subcortical–cortical connections had significantly less number of fibers in high-risk neonates. This study provides new lines of evidence in support of the disconnection hypothesis, reinforcing the notion that the genetic risk of schizophrenia induces alterations in both gray matter structural associations and white matter connectivity. Introduction Schizophrenia is a chronic, severe, and disabling mental disorder characterized by diverse clinical presentations, such as hallucinations, delusions, anhedonia, avolition and impaired cognitive functions (Schultz and Andreasen, 1999). It is commonly accepted that schizo-phrenia is not a result of regionally isolated pathologies, but is due to the alteration of interactions between two or more regions (Friston, 1998). However, the vast majority of studies on schizophrenia involved only adult subjects, and the impact of genetic risk of the illness on infants is still poorly understood. The symptoms of schizophrenia usually start to present at late adolescence and early adulthood, and persist for a lifetime in 1% of the population (Regier et al., 1993). Interestingly, our recent work suggested that the precursor of developmental disorder may occur as early as infancy (Gilmore et al., 2010). We found structural abnormalities, such as significantly larger intracranial, CSF, and lateral ventricular volumes, in (especially male) offspring of schizophrenic parents. No significant differences in diffusion properties, however, were reported for major white matter fiber bundles. Note …
Ieee Transactions on Visualization and Computer Graphics 1 Approximate Boolean Operations on Large Polyhedral Solids with Partial Mesh Reconstruction

—We present a new approach to compute the approximate Boolean operations of two freeform polygonal mesh solids efficiently with the help of Layered Depth Images (LDI). After applying the LDI sampling based membership classification, the most challenging part, a trimmed adaptive contouring algorithm, is developed to reconstruct the mesh surface from the LDI samples near the intersected regions and stitch it to the boundary of the retained surfaces. Our method of approximate Boolean operations holds the advantage of numerical robustness as the approach uses volumetric representation. However, unlike other methods based on volumetric representation, we do not damage the facets in non-intersected regions, thus preserving geometric details much better and speeding up the computation as well. We show that the proposed method can successfully compute the Boolean operations of freeform solids with a massive number of polygons in a few seconds.
Nonlinear adaptive control using networks of piecewise linear approximators

This paper presents a stable nonparametric adaptive control approach using a piecewise local linear approximator. The basic structure of the controller is based on the feedback linearizing control plus sliding control structure to ensure the global stability. As for distinctive features, the continuous piecewise linear approximator is newly introduced and a time varying activation region is defined for efficient self-organization of the approximator during operation. The feasibility of the piecewise linear adaptive control method is demonstrated by a computational simulation.
Expression pattern and putative function of EXL1 and homologous genes in Arabidopsis

The Arabidopsis EXORDIUM-LIKE1 (EXL1) gene (At1g35140) is required for adaptation to carbon (C)- and energy-limiting growth conditions. An exl1 loss of function mutant showed diminished biomass production in a low total irradiance growth regime, impaired survival during extended night, and impaired survival of anoxia stress. We show here additional expression data and discuss the putative roles of EXL1. We hypothesize that EXL1 suppresses brassinosteroid-dependent growth and controls C allocation in the cell. In-depth expression analysis of homologous genes suggests that the EXL2 (At5g64260) and EXL4 (At5g09440) genes play similar roles.