bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis
Authors: Tyagi Punit , Bhide Mangesh 
Published: November 2021

BackgroundIn the past decade, RNA sequencing and mass spectrometry based quantitative approaches are being used commonly to identify the differentially expressed biomarkers in different biological conditions. Data generated from these approaches come in different sizes (e.g., count matrix, normalized list of differentially expressed biomarkers, etc.) and shapes (e.g., sequences, spectral data, etc.). The list of differentially expressed biomarkers is used for functional interpretation and retrieve biological meaning, however, it requires moderate computational skills. Thus, researchers with no programming expertise find difficulty in data interpretation. Several bioinformatics tools are available to analyze such data; however, they are less flexible for performing the multiple steps of visualization and functional interpretation.ImplementationWe developed an easy-to-use Shiny based web application (named as OMnalysis) that provides users with a single platform to analyze and visualize the differentially expressed data. The OMnalysis accepts the data in tabular form from edgeR, DESeq2, MaxQuant Perseus, R packages, and other similar software, which typically contains the list of differentially expressed genes or proteins, log of the fold change, log of the count per million, thePvalue,q-value, etc. The key features of the OMnalysis are multiple image type visualization and their dimension customization options, seven multiple hypothesis testing correction methods to get more significant gene ontology, network topology-based pathway analysis, and multiple databases support (KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database PharmGKB and STRINGdb) for extensive pathway enrichment analysis. OMnalysis also fetches the literature information from PubMed to provide supportive evidence to the biomarkers identified in the analysis. In a nutshell, we present the OMnalysis as a well-organized user interface, supported by peer-reviewed R packages with updated databases for quick interpretation of the differential transcriptomics and proteomics data to biological meaning.AvailabilityThe OMnalysis codes are entirely written in R language and freely available athttps://github.com/Punit201016/OMnalysis. OMnalysis can also be accessed from -http://lbmi.uvlf.sk/omnalysis.html. OMnalysis is hosted on a Shiny server athttps://omnalysis.shinyapps.io/OMnalysis/. The minimum system requirements are: 4 gigabytes of RAM, i3 processor (or equivalent). It is compatible with any operating system (windows, Linux or Mac). The OMnalysis is heavily tested on Chrome web browsers; thus, Chrome is the preferred browser. OMnalysis works on Firefox and Safari.
Constraints as Perceived and Suggestions as Expressed by Sheep Rearing Farmers in Raichur District of Karnataka, India
Authors: Channappa . , Shashidhar K. K. , Goudappa S. B. , Hulagur Basavaraj , Sreedhara J. N. 
Published: November 2021

The study was conducted in purposively selected Raichur district of Karnataka. Highest number of sheep population criteria were used in selection of taluks and villages. A total of 120 respondents were selected from 06 selected villages of 2 taluks namely Lingasuguru and Raichur The quantitative and qualitative data were used to collected the information through interview schedule, The present study is highlighted different constraints and suggestion perceived by sheep rearing farmers during management practices simple statistical tools frequency and percentage are used in the study. In socio economic constraints the result found that majority (71.67%) poor knowledge and Ignorance on management practices followed literacy rate (62.05 %), It was found that a high majority (92.50%) unaware insurance services, poor credit facilities (87.50%), shrinkage of grazing land (76.67%) and cost of medicine (61.67%). Suggestion expressed by 69.17 per cent suggested on vaccination followed by keeping quality of buck (65.00%), increase number of veterinary hospital and staff (60.00%) and increase the community grazing land (37.50%), more than three-fourth of sheep farmers suggested discourage the middle man in market, strengthening the existing the animal market (72.50%) and develop new marketing channel (63.33%).
Comparative Evaluation of Cognitive Function among Indian Obese and Non-Obese Middle-Aged Subjects
Authors: Ranjeet Srivarsha , Sridevi G. , Preetha S. 
Published: November 2021

Background: Obesity has become one of the common problems encountered by people of the present day. This condition is often accompanied by cardiovascular problems like hypertension, hyperlipidemia, is chemic heart disease. Also, that the relationship between obesity and cognitive impairment plays an important role in the development of neurodegenerative disorders. But reports on the association between obesity and working memory lack scientific evidence. So, the present study planned to assess the influence of obesity on cognitive functions and compare among obese and non - obese individuals.
Objective: This study evaluated the changes in cognitive functions comparative between samples of obese and non-obese individuals from India.
Methods: Based on the Body Mass Index (BMI), the participants were classified into 2 groups. Cognitive screening was done using MINI MENTAL STATE EXAMINATION and the parameters like level of orientation, registration, recall, language, copy art skills were analyzed and scores were calculated. The data was statistically analyzed using SPSS version 23 and the independent sample t test was used to analyze the differences in cognitive functions.
Results: The study reported that there was statistically significant decline in language, recall and copy art skills in obese individuals compared to non-obese group.
Conclusion: The study concluded an innovative finding that obesity is associated with impaired cognitive performance pertaining to recall, language and copy art and overall decreased MMSE scores indicating that accelerated cognitive decline and neurodegenerative pathologies such as dementia in later life is influenced by changes in body weight. Interventions that target mid-life obesity may be helpful in reducing the cognitive risks associated with obesity.
Comparison of Lymph Node Involvement in Carcinomas during Precovid and Covid Era
Authors: Manasvi P. , Gowtham V. Rishi 
Published: November 2021

Background: This is a clinicopathological study comparing the involvement of lymph nodes in various carcinomas before and during the COVID-19 period. During the pandemic the access to healthcare and timely detection and intervention of carcinomas were severely affected. This delay in treatment has led to the progression of malignancies and metastasis to lymph nodes.
Methods: A retrospective study was conducted of 40 patients (20 from 2019 and 20 from 2021) with carcinomas who were treated by surgical excision of tumour combined with lymph node resection. Histopathological examination of the nodes was done to detect malignant metastasis and the average node positivity rate was calculated.
Results: Lymph node metastasis was observed in 10 patients in 2019 (50%) and 16 patients in 2021 (80%). The average node positivity rate is significantly higher in 2021 than in 2019, in 2019 it is 31% and in 2021 it is 43%. Lymph node metastasis is expected to increase by 43% in 2021.
Conclusion: In the Covid-19 pandemic, a significant decrease and delay of patients presenting to the OPD for neoplasms, resulting in a delay in the diagnosis and treatment of advanced-stage neoplasms that manifest as metastases in the regional lymph nodes. Surgeons need to be vigilant and extensively explore the all draining affected lymph nodes and resect them.
Prevalence of Malignancy in Solitary Thyroid Nodule-A Retrospective Study
Authors: Kavya A. , Prabu K. R. Manoj 
Published: November 2021

Background: Solitary thyroid nodule is defined as discrete mass palpable in an otherwise apparently normal thyroid gland. Solitary nodule is the common presentation of thyroid disorders.
Objective: This study aimed to look into the prevalence of malignancy in clinico-radiologically detected solitary thyroid nodule and to correlate the findings in pre-operative fine needle aspiration cytology(FNAC) and post-operative histopathological examination(HPE).
Materials and Methods: A retrospective study was carried out in our Institute for a period of 6 months using the data obtained between 2018-2020 of patients who were clinically and radiologically diagnosed as solitary thyroid nodule in the Department of General Surgery.
Results: Out of 30 cases of clinically detected solitary thyroid nodule 7(23.3%)cases was found to be malignant. The mean age of presentation was 41.2 years with male female ratio of 1:9. 25(83.3%)cases was reported as benign nodules according to pre-operative FNAC out of these 2(6.6%)cases turned out to be malignant on post-operative histopathological examination.
Conclusion: It is concluded that from the present study the prevalence of malignancy in clinically detected solitary thyroid nodule is 23.3%. FNAC being sensitive, cost effective and reliable tool in the preoperative assessment of solitary thyroid nodules and HPE in post operative evaluation of clinical specimen both playing a vital role in management of solitary thyroid nodule thus helping in early diagnosis and proper surgical intervention.
Effect of Sustained Isometric and Isotonic Exercises on Blood Pressure and Heart Rate Variability – A Comparative Study
Authors: Harshini S. Sneha , Sridevi G. , Preetha S. 
Published: November 2021

Introduction: Isometric exercises are contractions of a particular muscle which doesn’t noticeably change length and the affected joint doesn’t move [1]. Isotonic exercises involve contracting muscle shortens against a constant weight, as when lifting as weight [2,3]. These two different types of exercise have profound changes in the body affecting the respiratory and cardiovascular systems [4]. Studies comparing the effectiveness of isotonic and isometric exercises on blood pressure and heart rate variability (HRV) were scanty [5].
Objective: The present study planned to investigate and compare the efficacy of isometric as well as isotonic exercises on changes in blood pressure, heart rate and HRV.
Materials and methods: 10 normal healthy subjects in the age group 17-20 years of both genders participated in the study. All the subjects were assessed under three different conditions: Resting state, After isotonic exercises (20 repetitions of straight leg raise) and After isometric exercises 2 mins of sustained abdominal exercises). After each procedure, blood pressure and heart rate variability were calculated.
Results: Isometric exercises cause reduction of systolic and diastolic blood pressure, mean arterial pressure while pulse rate increases significantly. Isotonic exercises increase the systolic and diastolic blood pressure and mean arterial pressure significantly. The result is statistically significant with p<0.050.
Conclusion: Thus it can be concluded an innovative finding that isometric exercise causes profound decline in blood pressure and increased heart rate variability thus showing a negative impact on cardiovascular health. So it can be concluded that isotonic exercise improves the circulation and supports the cardiovascular system and strengthens the muscle, improves bone density and boosts cardiac function
Knowledge, Attitude, and Practices towards Needle Stick Injuries among Students and Staff in a Tertiary Medical Centre in Chennai, Tamil Nadu, India
Authors: Aswin P. S. , Vikrannth V. 
Published: November 2021

Background: Needle stick injuries are one of the greatest fears that revolves around the health care workers all over the world, and the majority of them are avoidable by following proper precautionary methods in handling the devices. Even though, by following the precautionary methods, a few accidents may happen a few times and thus resulting in a needle stick injury. The aim of our study was to assess the knowledge, attitude and practices towards Needle stick injuries among students and staff in a tertiary medical centre in Chennai, Tamil Nadu , India
Objectives: To assess the knowledge, attitude, practices about needle stick injuries among students and staff in a tertiary medical centre in Chennai, Tamil Nadu, India.
Materials and Methods: This descriptive cross-sectional study was conducted in Saveetha Medical College and Hospital.
Our study included students and staff of the institution, irrespective of their age and sex. Data collection was carried out using a standardized questionnaire.
Results: 62.1% of the participants know the last universal precaution guidelines of needle stick injuries management. 83.3% are fully vaccinated with anti-HBV.70.9% always use gloves when deal with needles. 14.3% had Needle stick Injury. 40.9% strongly believe that needle stick injury can be prevented. Since adequate awareness is created by the institution, participants in this study have higher knowledge, attitude and practices when compared to reference studies.
Multi‐Color Au/Ag Nanoparticles for Multiplexed Lateral Flow Assay Based on Spatial Separation and Color Co‐Localization
Authors: Zhang Yi , Yu Yue , Ying Jackie Y. 
Published: November 2021

AbstractPaper or membrane‐based lateral flow assay (LFA) is a well‐established platform widely used in point‐of‐care diagnostics. The multiplexing on LFA platform is mainly realized by spatially separating test lines along the test strip, and it has limited multiplexing capability due to space restriction. In this report, a new strategy for multiplexing on LFA platform is presented. In addition to spatial separation, morphology and composition‐controlled Au/Ag nanoparticles of three primary colors are also employed to add another parameter for multiplexing. The co‐localization of primary particles would result in an array of secondary colors as an indication of various target combinations. This two‐parameter multiplexing strategy significantly improves the multiplexing capability of LFA, and extends the applicability of LFA to more complicated analysis. Using the proposed two‐parameter multiplexing LFA, all 32 combinations of two protein and three DNA targets are successfully identified. Subtyping of three herpes viruses is also performed by amplifying the viral DNA with loop‐mediated isothermal amplification, and detecting the amplicons using the two‐parameter multiplexing LFA.
Ionic Crosslinking‐Induced Nanochannels: Nanophase Separation for Ion Transport Promotion
Authors: Chen Weipeng , Dong Tiandu , Xiang Yun , Qian Yongchao , Zhao Xiaolu , Xin Weiwen , Kong Xiang‐Yu , Jiang Lei , Wen Liping 
Published: November 2021

AbstractCharge‐governed ion transport is crucial to numerous industries, and the advanced membrane is the essential component. In nature, the efficient and selective ion transport is mainly governed by the charged ion channels located in cell membrane, indicating the architecture with functional differentiation. Inspired by this architecture, a membrane by ionic crosslinking sulfonated poly(arylene ether ketone) and imidazolium‐functionalized poly(arylene ether sulfone) is designed and fabricated to make full use of the charges. This ionic crosslinking is designed to realize nanophase separation to aggregate the ion pathways in the membrane, which results in excellent ion selectivity and high ion conductivity. With the excellent ion transport behavior, ionic crosslinking membrane shows great potential in osmotic energy conversion, which maximum power density can be up to 16.72 W m−2. This design of ionic crosslinking‐induced nanophase separation offers a roadmap for ion transport promotion.
Imidodiphosphoric Acids Catalysed Asymmetric Functionaliza‐tion with Thiols: Access to Oxindole Derived ɑ‐Chiral Thioethers
Authors: Qin Xiangshuo , Jiang Guofeng , Gao Jigang , Zhang Heng , Sun Dongyang , Zhang Guangliang , Zheng Liangyu , Zhang Suoqin 
Published: November 2021

AbstractChiral imidodiphosphoric acid‐catalysed asymmetric functionalization of 3‐hydroxy bisindoles was established. Sulfur‐containing groups could be successfully introduced into isatin frameworks using commercially available thiols. The transformation was compatible with substrates bearing distinct substituents, both aromatic and aliphatic thiols were amenable to afford the desired products. A total of 41 reactions furnished various chiral 3‐thiooxindoles in 23%–99% yield, with 72%–99% enantioselectivity.magnified image
Intrinsically Disordered Tardigrade Proteins Self‐Assemble into Fibrous Gels in Response to Environmental Stress
Authors: Malki Anas , Teulon Jean‐Marie , Camacho‐Zarco Aldo R. , Chen Shu‐wen W. , Adamski Wiktor , Maurin Damien , Salvi Nicola , Pellequer Jean‐Luc , Blackledge Martin 
Published: November 2021

AbstractTardigrades are remarkable for their ability to survive harsh stress conditions as diverse as extreme temperature and desiccation. The molecular mechanisms that confer this unusual resistance to physical stress remain unknown. Recently, tardigrade‐unique intrinsically disordered proteins have been shown to play an essential role in tardigrade anhydrobiosis. Here, we characterize the conformational and physical behaviour of CAHS‐8 from Hypsibius exemplaris. NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini. Upon concentration, the protein is shown to successively form oligomers, long fibres, and finally gels constituted of fibres in a strongly temperature‐dependent manner. The helical domain forms the core of the fibrillar structure, with the disordered termini remaining highly dynamic within the gel. Soluble proteins can be encapsulated within cavities in the gel, maintaining their functional form. The ability to reversibly form fibrous gels may be associated with the enhanced protective properties of these proteins.
Dynamic Optical Visualization of Proton Transport Pathways at Water–Solid Interfaces
Authors: Yang Jinmei , Lu Yuxian , Jin Lei , Zhao Chunxiao , Chen Yuang , Xu Yang , Chen Fanfan , Feng Jiandong 
Published: November 2021

AbstractProbing proton transport is of vital importance for understanding cellular transport, surface catalysis and fuel cells. Conventional proton transport measurements rely on the use of electrochemical conductivity and do not allow for the direct visualization of proton transport pathways. The development of novel experimental techniques to spatiotemporally resolve proton transport is in high demand. Here, building upon the general conversion of aqueous proton flux into spatially resolved fluorescence signals, we optically visualize proton transport through nanopores and along hydrophilic interfaces. We observed that the fluorescence intensity increased at negative voltage due to lateral transport. Thanks to the temporal resolution of optical imaging, our technique further empowers the analysis of proton transport dynamics.
Cascaded Nanozyme System with High Reaction Selectivity by Substrate Screening and Channeling in a Microfluidic Device**
Authors: Zhou Qing , Yang Hong , Chen Xinghua , Xu Yuan , Han Dan , Zhou Sisi , Liu Songqin , Shen Yanfei , Zhang Yuanjian 
Published: November 2021

AbstractSurpassing natural enzymes in cost, stability and mass production, nanozymes have attracted wide attention in fields from disease diagnosis to tumor therapy. However, nanozymes intrinsically have low reaction selectivity, which significantly restricts their applications. A general method is reported to address this challenge by following a biomimetic operation principle of substrates channeling and screening. Two oxidase‐ and peroxidase‐like nanozymes (i.e., emerging N‐doped carbon nanocages and Prussian blue nanoparticles), were cascaded as a proof of concept to improve the reaction selectivity in transforming the substrate into the targeted product by more than 2000 times. The cascaded nanozymes were also adopted to a spatially confined microfluidic device, leading to more than 100‐fold enhancement of the reaction efficiency due to signal amplification.
Enzymatic hydrolysis of bacterial cellulose in the presence of a non‐catalytic cerato‐platanin protein
Authors: Rovera Cesare , Luti Simone , Pazzagli Luigia , Heeley Ellen L. , Wan Chaoying , Romano Diego , Farris Stefano 
Published: November 2021

AbstractIn this work, the effect of an expansin‐like cerato‐platanin (CP) protein as a pre‐treatment for the enzymatic hydrolysis of bacterial cellulose (BC) is investigated. To this scope, cellulases from Trichoderma reesei are used as hydrolyzing agent using different enzyme/BC formulations. Turbidity experiments reveal that for the higher enzyme concentrations (formulations 0.5:1 and 1:1) the enzymatic hydrolysis of BC show similar hydrolysis kinetics and is not dependent of the CP. However, at higher BC concentrations (formulations 0.25:1 and 0.33:1), the hydrolysis of BC is hindered by the non‐catalytic protein, as confirmed by the lower content of cellobiose and glucose in the presence of CP. Light scattering experiments show that the addition of CP led to an increase of the BC particle size from (445–630 nm) to (890–1.26 μm) for the formulation 1:1, which is also corroborated by atomic force microscopy and transmission electron microscopy analyses. These results suggest that CP did not positively affect the hydrolysis of BC, in contrast to what was previously observed for plant‐derived cellulose. This work for the first time investigates the anomalous behavior of cerato platanin family members with regard to its loosening activity on the structure of bacterial cellulose.
Construction and analysis of the protein–protein interaction network for the detoxification enzymes of the silkworm, Bombyx mori
Authors: Xin ShangHong , Zhang WenJun 
Published: November 2021

AbstractDetoxification enzymes are necessary for insects to metabolize toxic substances and maintain physiological activities. Cytochromes P450 (CYPs), glutathione S‐transferases (GSTs), and carboxylesterase (CarEs) are the main detoxification enzymes in insects. In addition, UDP‐glucosyltransferase and ATP‐binding cassette transporter also participate in the process of material metabolism. This study collected proteins related to detoxification in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). And we performed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on these proteins to understand their biological function. We constructed the protein–protein interaction network for the silkworm's detoxification enzymes and analyzed the network's topological properties. We found that BGIBMGA014046‐TA, BGIBMGA003221‐TA, BGIBMGA011092‐TA, BGIBMGA000074‐TA, and LOC732976 are the essential proteins in the network. These proteins are primarily involved in the process of ribosome biogenesis and may be related to protein synthesis. We integrated GO, KEGG, and network analysis and found that ribosome‐associated protein and GSTs played a vital role in the detoxification process.