bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iatrogenic thermal burn after hot water immersion for weever fish sting treatment: a case report
Authors: Abdul Jalil Khairun Izlinda , Qayyum Muhammad Tayyab 
Published: September 2020

Introduction: Lesser weever fish are saltwater fish that are found on the Mediterranean and European coasts, over sandy and muddy seabed areas, typically around the summer season. These bottom dwellers have envenoming dorsal spines that sting when stepped on. Severe pain is the main symptom. Initial treatment involves wound irrigation, removal of spines if they are visible and immediate hot water immersion (HWI). Tetanus prophylaxis, leg elevation and analgesia are recommended after pain subsides. HWI treatment is described as immersion of the affected area in hot, but not scalding, water to tolerance (upper limit 45 °C) for 30–90 min or until there is significant pain relief. While HWI is an effective therapy for the pain control of marine envenomation, it presents a potential risk of thermal burn injury in the untrained or unsupervised. Here, we present a case of an iatrogenic thermal burn after HWI for the treatment of a weever fish sting. Case report: A 16-year-old girl was referred to our outpatient department with a superficial dermal thickness burn to her big toe 12 days after accidental stepping on a lesser weever fish. She reported receiving HWI treatment at the scene of the injury. She was treated with dressing, oral antibiotics and leg elevation. This healed with no sequalae at nine-month follow-up. Conclusion: Thermal burn injury can occur after HWI treatment. Providers should be aware and diligent while the patient needs to be educated in the potential risks. Lay Abstract 5, e, s Stings from lesser weever fish occur mostly in the summer months. These bottom dweller saltwater fish are found in the Mediterranean and European coasts, over sandy and muddy seabed areas; it releases venom from its dorsal spine when stepped on. Severe pain is the main symptom. Recommended first aid includes wound irrigation, removal of spines if they are visible and immediate hot water immersion (HWI) treatment. HWI means immersion of the affected part into hot, but not scalding, water (upper limit 45 °C) for 30–90 min or until pain is alleviated. In an ideal situation, the water temperature should be checked with a thermometer. However, in practice, where no thermometer is available, the water must be tested before immersion. It is advised to ensure that the water should be no hotter than the first aider can stand or the highest temperature tolerable by the patient. However, HWI treatment has a potential risk of burn injury. Here we describe a case of a 16-year-old patient who sustained burn injury after HWI therapy received after a sting by a weever fish. The patient was treated with dressings and the wound healed without requiring surgical intervention. Here, we like to highlight that although HWI is effective in treating stings from marine animals, both the provider and the patient need to be aware of potential burn injury associated with this treatment.
Cross-polarization dynamics and conformational study of variously sized cellulose crystallites using solid-state 13C NMR
Authors: Daicho Kazuho , Fujisawa Shuji , Kobayashi Kayoko , Saito Tsuguyuki , Ashida Jun 
Published: September 2020

AbstractCellulose forms crystalline fibrils, via biosynthesis, that can be just a few nanometers wide. The crystallinity is a structural factor related to material performance. Recently, many routes to isolate these fibrils as nanocellulose have been developed, and there exist various types of nanocellulose with different crystallinities. Quantitative assessment of the crystallinity of nanocellulose is thus essential to advance knowledge in the high performance and functionality of such materials. Solid-state 13C cross-polarization/magic-angle spinning (CP/MAS) nuclear magnetic resonance (NMR) spectroscopy is a strong tool to investigate the structural features and dynamics of solid cellulose. The crystallinity is often evaluated by using the NMR signal ratio of the C4 crystalline and noncrystalline regions as a crystallinity index (CI) value. To calculate the CI value, it is necessary to examine the dependence of the contact time (CT) for CP on the signal intensity and set the optimum CT at a maximum of the signal intensity. However, the dependence has not been investigated for evaluation of the CI value of various cellulose samples with different crystal sizes. Here, we optimized the CT for evaluation of the CI value of cellulose with different crystal sizes. The error in the CI at the optimized CT was ~ 3%. At the optimized CT, the structural change after surface modification by TEMPO-oxidation was also analyzed from the NMR spectra of the C6 region. The relationship between the CI value and the degree of oxidation shows that it is possible to evaluate the degree of oxidation from the NMR spectra irrespective of the crystallinity of cellulose. Furthermore, the C4-based CI value was linearly correlated with the C6-based trans-gauche (tg) ratio, which is approximated by a function, CI = 0.9 tg ratio.
Effects and interaction of different interior material treatment and personal preference on psychological and physiological responses in living environment
Authors: Sun Minkai , Nakashima Taisuke , Yoshimura Yuri , Honden Akiyoshi , Nakagawa Toshinori , Saijo Hiromi , Watanabe Yuichiro , Ajimi Tsuyoshi , Yasunari Shinji , Yamada Yuki , Nagano Jun , Okamoto Tsuyoshi , Ishikawa Hiroya , Ohnuki Koichiro , Fujimoto Noboru , Shimizu Kuniyoshi 
Published: September 2020

AbstractJapanese cedar (Cryptomeria japonica) wood is widely used as a traditional construction material in Japan. The relationship between an individual’s perceived comfort level and a preference for Japanese cedar wood interiors is of interest. We compared volunteers’ physiological responses and subjective evaluations of wooden dwelling spaces with different wood materials: planed Japanese cedar lumber, or printed grain resin sheet overlay boards. Eighty-three subjects were asked to stay in each room for 30 min. We evaluated salivary stress markers, blood pressure, the profile of mood states-brief form (POMS), and a questionnaire that used the semantic differential method to evaluate the subjects’ feeling state for both rooms. The concentrations of the volatile organic compounds in both rooms were also quantified after the experiment. The results demonstrated that the subjects’ evaluation of each room was highly dependent on their preference; each room was evaluated more positively by subjects who preferred it. Although the subjects’ feelings were also influenced by their preference, the room with Japanese cedar did not elicit negative feelings, even from the subjects who disliked it. The subjects’ physiological responses were totally independent of their preferences. Their blood pressure decreased in the Japanese cedar room, and their salivary alpha-amylase activity was repressed in both rooms. These results indicated that the subjective evaluations were influenced in part by the subjects’ preferences, while their physiological responses were not affected. Regardless of which room the subjects preferred, the Japanese cedar room reduced the subjects’ blood pressure compared to the room with artificial materials.
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature
Authors: Ivanisenko Timofey V. , Saik Olga V. , Demenkov Pavel S. , Ivanisenko Nikita V. , Savostianov Alexander N. , Ivanisenko Vladimir A. 
Published: September 2020

Abstract
Background
The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products. Previously, we developed the Associative Network Discovery System (ANDSystem), which also implements such a cycle. However, the drawback of these systems is dependence on the employed ontologies describing the subject area, which limits their functionality in searching information based on user-specified queries.

Results
The ANDDigest system is a new web-based module of the ANDSystem tool, permitting searching within PubMed by using dictionaries from the ANDSystem tool and sets of user-defined keywords. ANDDigest allows performing the search based on complex queries simultaneously, taking into account many types of objects from the ANDSystem’s ontology. The system has a user-friendly interface, providing sorting, visualization, and filtering of the found information, including mapping of mentioned objects in text, linking to external databases, sorting of data by publication date, citations number, journal H-indices, etc. The system provides data on trends for identified entities based on dynamics of interest according to the frequency of their mentions in PubMed by years.

Conclusions
The main feature of ANDDigest is its functionality, serving as a specialized search for information about multiple associative relationships of objects from the ANDSystem’s ontology vocabularies, taking into account user-specified keywords. The tool can be applied to the interpretation of experimental genetics data, the search for associations between molecular genetics objects, and the preparation of scientific and analytical reviews. It is presently available at https://anddigest.sysbio.ru/.
Review of medical image recognition technologies to detect melanomas using neural networks
Authors: Efimenko Mila , Ignatev Alexander , Koshechkin Konstantin 
Published: September 2020

Abstract
Background
Melanoma is one of the most aggressive types of cancer that has become a world-class problem. According to the World Health Organization estimates, 132,000 cases of the disease and 66,000 deaths from malignant melanoma and other forms of skin cancer are reported annually worldwide (https://apps.who.int/gho/data/?theme=main) and those numbers continue to grow. In our opinion, due to the increasing incidence of the disease, it is necessary to find new, easy to use and sensitive methods for the early diagnosis of melanoma in a large number of people around the world. Over the last decade, neural networks show highly sensitive, specific, and accurate results.

Objective
This study presents a review of PubMed papers including requests «melanoma neural network» and «melanoma neural network dermatoscopy». We review recent researches and discuss their opportunities acceptable in clinical practice.

Methods
We searched the PubMed database for systematic reviews and original research papers on the requests «melanoma neural network» and «melanoma neural network dermatoscopy» published in English. Only papers that reported results, progress and outcomes are included in this review.

Results
We found 11 papers that match our requests that observed convolutional and deep-learning neural networks combined with fuzzy clustering or World Cup Optimization algorithms in analyzing dermatoscopic images. All of them require an ABCD (asymmetry, border, color, and differential structures) algorithm and its derivates (in combination with ABCD algorithm or separately). Also, they require a large dataset of dermatoscopic images and optimized estimation parameters to provide high specificity, accuracy and sensitivity.

Conclusions
According to the analyzed papers, neural networks show higher specificity, accuracy and sensitivity than dermatologists. Neural networks are able to evaluate features that might be unavailable to the naked human eye. Despite that, we need more datasets to confirm those statements. Nowadays machine learning becomes a helpful tool in early diagnosing skin diseases, especially melanoma.
The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion
Authors: Polyanovsky Valery , Lifanov Alexander , Esipova Natalia , Tumanyan Vladimir 
Published: September 2020

Abstract
Background
The alignment of character sequences is important in bioinformatics. The quality of this procedure is determined by the substitution matrix and parameters of the insertion-deletion penalty function. These matrices are derived from sequence alignment and thus reflect the evolutionary process. Currently, in addition to evolutionary matrices, a large number of different background matrices have been obtained. To make an optimal choice of the substitution matrix and the penalty parameters, we conducted a numerical experiment using a representative sample of existing matrices of various types and origins.

Results
We tested both the classical evolutionary matrix series (PAM, Blosum, VTML, Pfasum); structural alignment based matrices, contact energy matrix, and matrix based on the properties of the genetic code. This study presents results for two test set types: first, we simulated sequences that reflect the divergent evolution; second, we performed tests on Balibase sequences. In both cases, we obtained the dependences of the alignment quality (Accuracy, Confidence) on the evolutionary distance between sequences and the evolutionary distance to which the substitution matrices correspond. Optimization of a combination of matrices and the penalty parameters was carried out for local and global alignment on the values of penalty function parameters.
Consequently, we found that the best alignment quality is achieved with matrices corresponding to the largest evolutionary distance. These matrices prove to be universal, i.e. suitable for aligning sequences separated by both large and small evolutionary distances. We analysed the correspondence of the correlation coefficients of matrices to the alignment quality. It was found that matrices showing high quality alignment have an above average correlation value, but the converse is not true.

Conclusions
This study showed that the best alignment quality is achieved with evolutionary matrices designed for long distances: Gonnet, VTML250, PAM250, MIQS, and Pfasum050. The same property is inherent in matrices not only of evolutionary origin, but also of another background corresponding to a large evolutionary distance. Therefore, matrices based on structural data show alignment quality close enough to its value for evolutionary matrices. This agrees with the idea that the spatial structure is more conservative than the protein sequence.
The speciation and adaptation of the polyploids: a case study of the Chinese Isoetes L. diploid-polyploid complex
Authors: Dai Xiaokang , Li Xiang , Huang Yuqian , Liu Xing 
Published: September 2020

AbstractBackgroundThe ChineseIsoetesL. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploidI. sinensisand its diploid parentsI. yunguiensisandI. taiwanensisis an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences.ResultsThere were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately:I. yunguiensiswith partial populations of theI. sinensisandI. taiwanensiswith the rest populations of theI. sinensis. The crow node of theI. sinensisallopolyploid system was 4.43 Ma (95% HPD: 2.77–6.97 Ma). The divergence time betweenI. sinensisandI. taiwanensiswas estimated to 0.65 Ma (95% HPD: 0.26–1.91 Ma). The narrower niche breadth inI.sinensisthan those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors.ConclusionsOur results elucidate thatI. yunguinensisandI. taiwanensiscontribute to the speciation ofI. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution ofI. sinensis. Additionally, niche novelty of the allopolyploid population ofI. sinensishas been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.
Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)
Authors: Yang Fan , Dong Fu-shuang , Hu Fang-hui , Liu Yong-wei , Chai Jian-fang , Zhao He , Lv Meng-yu , Zhou Shuo 
Published: September 2020

Abstract
Background
Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized.

Results
In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses.

Conclusions
This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.
MasterPATH: network analysis of functional genomics screening data
Authors: Rubanova Natalia , Pinna Guillaume , Kropp Jeremie , Campalans Anna , Radicella Juan Pablo , Polesskaya Anna , Harel-Bellan Annick , Morozova Nadya 
Published: September 2020

AbstractBackgroundFunctional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of genes potentially involved in biological processes of interest (so called hit list). Several computational methods exist to analyze and interpret such lists, the most widespread of which aim either at investigating of significantly enriched biological processes, or at extracting significantly represented subnetworks.ResultsHere we propose a novel network analysis method and corresponding computational software that employs the shortest path approach and centrality measure to discover members of molecular pathways leading to the studied phenotype, based on functional genomics screening data. The method works on integrated interactomes that consist of both directed and undirected networks – HIPPIE, SIGNOR, SignaLink, TFactS, KEGG, TransmiR, miRTarBase. The method finds nodes and short simple paths with significant high centrality in subnetworks induced by the hit genes and by so-called final implementers – the genes that are involved in molecular events responsible for final phenotypic realization of the biological processes of interest. We present the application of the method to the data from miRNA loss-of-function screen and transcriptome profiling of terminal human muscle differentiation process and to the gene loss-of-function screen exploring the genes that regulates human oxidative DNA damage recognition. The analysis highlighted the possible role of several known myogenesis regulatory miRNAs (miR-1, miR-125b, miR-216a) and their targets (AR, NR3C1, ARRB1, ITSN1, VAV3, TDGF1), as well as linked two major regulatory molecules of skeletal myogenesis, MYOD and SMAD3, to their previously known muscle-related targets (TGFB1, CDC42, CTCF) and also to a number of proteins such as C-KIT that have not been previously studied in the context of muscle differentiation. The analysis also showed the role of the interaction between H3 and SETDB1 proteins for oxidative DNA damage recognition.ConclusionThe current work provides a systematic methodology to discover members of molecular pathways in integrated networks using functional genomics screening data. It also offers a valuable instrument to explain the appearance of a set of genes, previously not associated with the process of interest, in the hit list of each particular functional genomics screening.