Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Bioinformatics
Title: Wham: Identifying Structural Variants of Biological Consequence
Abstract: Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
Extracted statement — deposits: Wham
Research field: Bioinformatics
Title: Wham: Identifying Structural Variants of Biological Consequence
Abstract: Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
Extracted statement — uses: Wham
Research field: Bioinformatics
Title: ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
Abstract: The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis. Time-lapse microscopic imaging of transgenic embryos expressing fluorescent reporters is the method of choice for tracking morphogenetic changes and establishing cell lineages and fate maps in vivo. However, the manual steps involved in curating thousands of putative cell segmentations have been a major bottleneck in the application of these technologies especially for cell membranes. Segmentation of cell membranes while more difficult than nuclear segmentation is necessary for quantifying the relations between changes in cell morphology and morphogenesis. We present a novel and fully automated method to first reconstruct membrane signals and then segment out cells from 3D membrane images even in dense tissues. The approach has three stages: 1) detection of local membrane planes, 2) voting to fill structural gaps, and 3) region segmentation. We demonstrate the superior performance of the algorithms quantitatively on time-lapse confocal and two-photon images of zebrafish neuroectoderm and paraxial mesoderm by comparing its results with those derived from human inspection. We also compared with synthetic microscopic images generated by simulating the process of imaging with fluorescent reporters under varying conditions of noise. Both the over-segmentation and under-segmentation percentages of our method are around 5%. The volume overlap of individual cells, compared to expert manual segmentation, is consistently over 84%. By using our software (ACME) to study somite formation, we were able to segment touching cells with high accuracy and reliably quantify changes in morphogenetic parameters such as cell shape and size, and the arrangement of epithelial and mesenchymal cells. Our software has been developed and tested on Windows, Mac, and Linux platforms and is available publicly under an open source BSD license (https://github.com/krm15/ACME).
Extracted statement — uses: Windows
Research field: Bioinformatics
Title: Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
Abstract: Nonribosomally and ribosomally synthesized bioactive peptides constitute a source of molecules of great biomedical importance, including antibiotics such as penicillin, immunosuppressants such as cyclosporine, and cytostatics such as bleomycin. Recently, an innovative mass-spectrometry-based strategy, peptidogenomics, has been pioneered to effectively mine microbial strains for novel peptidic metabolites. Even though mass-spectrometric peptide detection can be performed quite fast, true high-throughput natural product discovery approaches have still been limited by the inability to rapidly match the identified tandem mass spectra to the gene clusters responsible for the biosynthesis of the corresponding compounds. With Pep2Path, we introduce a software package to fully automate the peptidogenomics approach through the rapid Bayesian probabilistic matching of mass spectra to their corresponding biosynthetic gene clusters. Detailed benchmarking of the method shows that the approach is powerful enough to correctly identify gene clusters even in data sets that consist of hundreds of genomes, which also makes it possible to match compounds from unsequenced organisms to closely related biosynthetic gene clusters in other genomes. Applying Pep2Path to a data set of compounds without known biosynthesis routes, we were able to identify candidate gene clusters for the biosynthesis of five important compounds. Notably, one of these clusters was detected in a genome from a different subphylum of Proteobacteria than that in which the molecule had first been identified. All in all, our approach paves the way towards high-throughput discovery of novel peptidic natural products. Pep2Path is freely available from http://pep2path.sourceforge.net/, implemented in Python, licensed under the GNU General Public License v3 and supported on MS Windows, Linux and Mac OS X.
Extracted statement — uses: Windows
Research field: Bioinformatics
Title: Women’s autonomy and men's involvement in child care and feeding as predictors of infant and young child anthropometric indices in coffee farming households of Jimma Zone, South West of Ethiopia
Abstract: Background Most of child mortality and under nutrition in developing world were attributed to suboptimal childcare and feeding, which needs detailed investigation beyond the proximal factors. This study was conducted with the aim of assessing associations of women’s autonomy and men’s involvement with child anthropometric indices in cash crop livelihood areas of South West Ethiopia. Methods Multi-stage stratified sampling was used to select 749 farming households living in three coffee producing sub-districts of Jimma zone, Ethiopia. Domains of women’s Autonomy were measured by a tool adapted from demographic health survey. A model for determination of paternal involvement in childcare was employed. Caring practices were assessed through the WHO Infant and young child feeding practice core indicators. Length and weight measurements were taken in duplicate using standard techniques. Data were analyzed using SPSS for windows version 21. A multivariable linear regression was used to predict weight for height Z-scores and length for age Z-scores after adjusting for various factors. Results The mean (sd) scores of weight for age (WAZ), height for age (HAZ), weight for height (WHZ) and BMI for age (BAZ) was -0.52(1.26), -0.73(1.43), -0.13(1.34) and -0.1(1.39) respectively. The results of multi variable linear regression analyses showed that WHZ scores of children of mothers who had autonomy of conducting big purchase were higher by 0.42 compared to children's whose mothers had not. In addition, a child whose father was involved in childcare and feeding had higher HAZ score by 0.1. Regarding age, as for every month increase in age of child, a 0.04 point decrease in HAZ score and a 0.01 point decrease in WHZ were noted. Similarly, a child living in food insecure households had lower HAZ score by 0.29 compared to child of food secured households. As family size increased by a person a WHZ score of a child is decreased by 0.08. WHZ and HAZ scores of male child was found lower by 0.25 and 0.38 respectively compared to a female child of same age. Conclusion Women’s autonomy and men’s involvement appeared in tandem with better child anthropometric outcomes. Nutrition interventions in such setting should integrate enhancing women’s autonomy over resource and men’s involvement in childcare and feeding, in addition to food security measures.
Extracted statement — uses: windows
Research field: Bioinformatics
Title: Exploiting syntax when detecting protein names in text
Abstract: This paper presents work on a method to detect names of proteins in running text. Our system - Yapex - uses a combination of lexical and syntactic knowledge, heuristic filters and a local dynamic dictionary. The syntactic information given by a general-purpose off-the-shelf parser supports the correct identification of the boundaries of protein names, and the local dynamic dictionary finds protein names in positions incompletely analysed by the parser. We present the different steps involved in our approach to protein tagging, and show how combinations of them influence recall and precision. We evaluate the system on a corpus of MEDLINE abstracts and compare it with the KeX system (Fukuda et al., 1998) along four different notions of correctness.
Extracted statement — model: Yapex
Research field: Bioinformatics
Title: Future directions in meditation research: Recommendations for expanding the field of contemplative science
Abstract: The science of meditation has grown tremendously in the last two decades. Most studies have focused on evaluating the clinical effectiveness of mindfulness-based interventions, neural and other physiological correlates of meditation, and individual cognitive and emotional aspects of meditation. Far less research has been conducted on more challenging domains to measure, such as group and relational, transpersonal and mystical, and difficult aspects of meditation; anomalous or extraordinary phenomena related to meditation; and post-conventional stages of development associated with meditation. However, these components of meditation may be crucial to people’s psychological and spiritual development, could represent important mediators and/or mechanisms by which meditation confers benefits, and could themselves be important outcomes of meditation practices. In addition, since large numbers of novices are being introduced to meditation, it is helpful to investigate experiences they may encounter that are not well understood. Over the last four years, a task force of meditation researchers and teachers met regularly to develop recommendations for expanding the current meditation research field to include these important yet often neglected topics. These meetings led to a cross-sectional online survey to investigate the prevalence of a wide range of experiences in 1120 meditators. Results show that the majority of respondents report having had many of these anomalous and extraordinary experiences. While some of the topics are potentially controversial, they can be subjected to rigorous scientific investigation. These arenas represent largely uncharted scientific terrain and provide excellent opportunities for both new and experienced researchers. We provide suggestions for future directions, with accompanying online materials to encourage such research.
Extracted statement — uses: Excel
Research field: Bioinformatics
Title: Ecological Genetics of Chinese Rhesus Macaque in Response to Mountain Building: All Things Are Not Equal
Abstract: Background Pliocene uplifting of the Qinghai-Tibetan Plateau (QTP) and Quaternary glaciation may have impacted the Asian biota more than any other events. Little is documented with respect to how the geological and climatological events influenced speciation as well as spatial and genetic structuring, especially in vertebrate endotherms. Macaca mulatta is the most widely distributed non-human primate. It may be the most suitable model to test hypotheses regarding the genetic consequences of orogenesis on an endotherm. Methodology and Principal Findings Using a large dataset of maternally inherited mitochondrial DNA gene sequences and nuclear microsatellite DNA data, we discovered two maternal super-haplogroups exist, one in western China and the other in eastern China. M. mulatta formed around 2.31 Ma (1.51–3.15, 95%), and divergence of the two major matrilines was estimated at 1.15 Ma (0.78–1.55, 95%). The western super-haplogroup exhibits significant geographic structure. In contrast, the eastern super-haplogroup has far greater haplotypic variability with little structure based on analyses of six variable microsatellite loci using Structure and Geneland. Analysis using Migrate detected greater gene flow from WEST to EAST than vice versa. We did not detect signals of bottlenecking in most populations. Conclusions Analyses of the nuclear and mitochondrial datasets obtained large differences in genetic patterns for M. mulatta. The difference likely reflects inheritance mechanisms of the maternally inherited mtDNA genome versus nuclear biparentally inherited STRs and male-mediated gene flow. Dramatic environmental changes may be responsible for shaping the matrilineal history of macaques. The timing of events, the formation of M. mulatta, and the divergence of the super-haplogroups, corresponds to both the uplifting of the QTP and Quaternary climatic oscillations. Orogenesis likely drove divergence of western populations in China, and Pleistocene glaciations are likely responsible for genetic structuring in the eastern super-haplogroup via geographic isolation and secondary contact.
Extracted statement — uses: migrate
Research field: Biophysics
Title: Adaptive behaviour and learning in slime moulds: the role of oscillations
Abstract: The slime mould Physarum polycephalum, an aneural organism, uses information from previous experiences to adjust its behaviour, but the mechanisms by which this is accomplished remain unknown. This article examines the possible role of oscillations in learning and memory in slime moulds. Slime moulds share surprising similarities with the network of synaptic connections in animal brains. First, their topology derives from a network of interconnected, vein-like tubes in which signalling molecules are transported. Second, network motility, which generates slime mould behaviour, is driven by distinct oscillations that organize into spatio-temporal wave patterns. Likewise, neural activity in the brain is organized in a variety of oscillations characterized by different frequencies. Interestingly, the oscillating networks of slime moulds are not precursors of nervous systems but, rather, an alternative architecture. Here, we argue that comparable information-processing operations can be realized on different architectures sharing similar oscillatory properties. After describing learning abilities and oscillatory activities of P. polycephalum, we explore the relation between network oscillations and learning, and evaluate the organism's global architecture with respect to information-processing potential. We hypothesize that, as in the brain, modulation of spontaneous oscillations may sustain learning in slime mould. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
Extracted statement — Has information processing paradigm: Oscillations
Research field: Chemistry
Title: Preparation of Polycrystalline TiO2 Photocatalysts Impregnated with Various Transition Metal Ions: Characterization and Photocatalytic Activity for the Degradation of 4-Nitrophenol
Abstract: A set of polycrystalline TiO2 photocatalysts loaded with various ions of transition metals (Co, Cr, Cu, Fe, Mo, V, and W) were prepared by using the wet impregnation method. The samples were characterized by using some bulk and surface techniques, namely X-ray diffraction, BET specific surface area determination, scanning electron microscopy, point of zero charge determination, and femtosecond pump−probe diffuse reflectance spectroscopy (PP-DRS). The samples were employed as catalysts for 4-nitrophenol photodegradation in aqueous suspension, used as a probe reaction. The characterization results have confirmed the difficulty to find a straightforward correlation between photoactivity and single specific properties of the powders. Diffuse reflectance measurements showed a slight shift in the band gap transition to longer wavelengths and an extension of the absorption in the visible region for almost all the doped samples. SEM observation and EDX measurements indicated a similar morphology for all the parti...
Extracted statement — chemical doping method: impregnation
Research field: Chemistry
Title: Synthesis and Characterization of Nitrogen-Doped TiO2 Nanophotocatalyst with High Visible Light Activity
Abstract: Nitrogen-doped TiO2 nanocatalysts with a homogeneous anatase structure were successfully synthesized through a microemulsion−hydrothermal method by using some organic compounds such as triethylamine, urea, thiourea, and hydrazine hydrate. Analysis by Raman and X-ray photoemission spectroscopy indicated that nitrogen was doped effectively and most nitrogen dopants might be present in the chemical environment of Ti−O−N and O−Ti−N. A shift of the absorption edge to a lower energy and a stronger absorption in the visible light region were observed. The results of photodegradation or the organic pollutant rhodamine B in the visible light irradiation (λ > 420 nm) suggested that the TiO2 photocatalysts after nitrogen doping were greatly improved compared with the undoped TiO2 photocatalysts and Degussa P-25; especially the nitrogen-doped TiO2 using triathylamine as the nitrogen source showed the highest photocatalytic activity, which also showed a higher efficiency for photodecomposition of 2,4-dichlorophenol. T...
Extracted statement — chemical doping method: microemulsion
Research field: Chemistry
Title: Improved photocatalytic activity of Sn 4+ doped TiO 2 nanoparticulate films prepared by plasma-enhanced chemical vapor deposition
Abstract: Sn4+ ion doped TiO2 (TiO2–Sn4+) nanoparticulate films with a doping ratio of about 7∶100 [(Sn)∶(Ti)] were prepared by the plasma-enhanced chemical vapor deposition (PCVD) method. The doping mode (lattice Ti substituted by Sn4+ ions) and the doping energy level of Sn4+ were determined by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), surface photovoltage spectroscopy (SPS) and electric field induced surface photovoltage spectroscopy (EFISPS). It is found that the introduction of a doping energy level of Sn4+ ions is profitable to the separation of photogenerated carriers under both UV and visible light excitation. Characterization of the films with XRD and SPS indicates that after doping by Sn, more surface defects are present on the surface. Consequently, the photocatalytic activity for photodegradation of phenol in the presence of the TiO2–Sn4+ film is higher than that of the pure TiO2 film under both UV and visible light irradiation.
Extracted statement — doping elements: Sn4+
Research field: Coating and Surface Technology
Title: Clay-Based Nanocomposite Coating for Flexible Optoelectronics Applying Commercial Polymers
Abstract: Transparency, flexibility, and especially ultralow oxygen (OTR) and water vapor (WVTR) transmission rates are the key issues to be addressed for packaging of flexible organic photovoltaics and organic light-emitting diodes. Concomitant optimization of all essential features is still a big challenge. Here we present a thin (1.5 μm), highly transparent, and at the same time flexible nanocomposite coating with an exceptionally low OTR and WVTR (1.0 × 10(-2) cm(3) m(-2) day(-1) bar(-1) and <0.05 g m(-2) day(-1) at 50% RH, respectively). A commercially available polyurethane (Desmodur N 3600 and Desmophen 670 BA, Bayer MaterialScience AG) was filled with a delaminated synthetic layered silicate exhibiting huge aspect ratios of about 25,000. Functional films were prepared by simple doctor-blading a suspension of the matrix and the organophilized clay. This preparation procedure is technically benign, is easy to scale up, and may readily be applied for encapsulation of sensitive flexible electronics.
Extracted statement — Polymer material: Polyurethane
Research field: Coating and Surface Technology
Title: Large Scale Self-Assembly of Smectic Nanocomposite Films by Doctor Blading versus Spray Coating: Impact of Crystal Quality on Barrier Properties
Abstract: Flexible transparent barrier films are required in various fields of application ranging from flexible, transparent food packaging to display encapsulation. Environmentally friendly, waterborne polymer–clay nanocomposites would be preferred but fail to meet in particular requirements for ultra high water vapor barriers. Here we show that self-assembly of nanocomposite films into one-dimensional crystalline (smectic) polymer–clay domains is a so-far overlooked key-factor capable of suppressing water vapor diffusivity despite appreciable swelling at elevated temperatures and relative humidity (R.H.). Moreover, barrier performance was shown to improve with quality of the crystalline order. In this respect, spray coating is superior to doctor blading because it yields significantly better ordered structures. For spray-coated waterborne nanocomposite films (21.4 μm) ultra high barrier specifications are met at 23 °C and 50% R.H. with oxygen transmission rates (OTR) < 0.0005 cm3 m–2 day–1 bar–1 and water vapor ...
Extracted statement — Solvent: water