bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold tolerance in rice plants is partially controlled by root responses
Authors: Rativa Angie Geraldine Sierra , Junior Artur Teixeira de Araújo , Friedrich Daniele da Silva , Gastmann Rodrigo , Lamb Thainá Inês , Vargas Igor de , Silva Alexsander dos Santos , Pozzebon-Silva Ândrea , Adamski Janete Mariza , Fett Janette Palma , Ricachenevsky Felipe Klein , Sperotto Raul Antonio 
Published: January 2020

AbstractRice (Oryza sativaL.) ssp.indicais the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H2O2accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genesSRC2(defense),root architecture associated 1(growth),ACC oxidase,ethylene-responsive transcription factor, andcytokinin-O-glucosyltransferase 2(hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.
A neural correlate of visual discomfort from flicker
Authors: Gentile Carlyn Patterson , Aguirre Geoffrey K. 
Published: January 2020

AbstractThe theory of “visual stress” holds that visual discomfort results from overactivation of the visual cortex. Despite general acceptance, there is a paucity of empirical data that confirm this relationship, particularly for discomfort from visual flicker. We examined the association between neural response and visual discomfort using flickering light of different temporal frequencies that separately targeted the magnocellular, parvocellular, and koniocellular post-receptoral pathways. Given prior work that has shown larger cortical responses to flickering light in people with migraine, we examined 10 headache free people and 10 migraineurs with visual aura. The stimulus was a uniform field, 50 degrees in diameter, that modulated with high-contrast flicker between 1.625 and 30 Hz. We asked subjects to rate their visual discomfort while we recorded steady state visually evoked potentials (ssVEP) from primary visual cortex. The peak temporal sensitivity ssVEP amplitude varied by post-receptoral pathway, and was consistent with the known properties of these visual channels. Notably, there was a direct, linear relationship between the amplitude of neural response to a stimulus and the degree of visual discomfort it evoked. No substantive differences between the migraine and control groups was found. These data link increased visual cortical activation with the experience of visual discomfort.
Hydropathy patterning complements charge patterning to describe conformational preferences of disordered proteins
Authors: Zheng Wenwei , Dignon Gregory , Brown Matthew , Kim Young C. , Mittal Jeetain 
Published: January 2020

AbstractUnderstanding the conformational ensemble of an intrinsically disordered protein (IDP) is of great interest due to its relevance to critical intracellular functions and diseases. It is now well established that the polymer scaling behavior can provide a great deal of information about the conformational properties as well as liquid-liquid phase separation of an IDP. It is, therefore, extremely desirable to be able to predict an IDP’s scaling behavior from the protein sequence itself. The work in this direction so far has focused on highly charged proteins and how charge patterning can perturb their structural properties. As naturally occurring IDPs are composed of a significant fraction of uncharged amino acids, the rules based on charge content and patterning are only partially helpful in solving the problem. Here, we propose a new order parameter, sequence hydropathy decoration (SHD), which can provide a near quantitative understanding of scaling and structural properties of IDPs devoid of charged residues. We combine this with a charge patterning parameter, sequence charge decoration (SCD), to obtain a general equation, parameterized from extensive coarse-grained simulation data, for predicting protein dimensions from the sequence. We finally test this equation against available experimental data and find a semi-quantitative match in predicting the scaling behavior. We also provide guidance on how to extend this approach to experimental data, which should be feasible in the near future.Graphical TOC Entry
Heterozygous mutation of Sonic Hedgehog receptor (Ptch) drives cerebellar overgrowth and sex-specifically alters hippocampal and cortical layer structure, activity, and social behavior in female mice
Authors: Jackson Thomas W. , Bendfeldt Gabriel A. , Beam Kelby A. , Rock Kylie D. , Belcher Scott M. 
Published: January 2020

AbstractSonic hedgehog (SHH) signaling is essential for the differentiation and migration of early stem cell populations during cerebellar development. Dysregulation of SHH-signaling can result in cerebellar overgrowth and the formation of the brain tumor medulloblastoma. Treatment for medulloblastoma is extremely aggressive and patients suffer life-long side effects including behavioral deficits. Considering that other behavioral disorders including autism spectrum disorders, holoprosencephaly, and basal cell nevus syndrome are known to present with cerebellar abnormalities, it is proposed that some behavioral abnormalities could be inherent to the medulloblastoma sequalae rather than treatment. Using a haploinsufficient SHH receptor knockout mouse model (Ptch1+/-), a partner preference task was used to explore activity, social behavior and neuroanatomical changes resulting from dysregulated SHH signaling. Compared to wild-type,Ptch1+/-females displayed increased activity by traveling a greater distance in both open-field and partner preference tasks. Social behavior was also sex-specifically modified inPtch1+/-females that interacted more with both novel and familiar animals in the partner preference task compared to same-sex wild-type controls. Haploinsufficency of PTCH resulted in cerebellar overgrowth in lobules IV/V and IX of both sexes, and female-specific decreases in hippocampal size and isocortical layer thickness. Taken together, neuroanatomical changes related to deficient SHH signaling may alter social behavior.
A Synergism Between Dimethyl Trisulfide And Methyl Thiolacetate In Attracting Carrion-Frequenting Beetles Demonstrated By Use Of A Chemically-Supplemented Minimal Trap
Authors: Trumbo Stephen T. , Dicapua John A. 
Published: January 2020

AbstractMicrobially-derived volatile organic compounds recruit insects to carrion, shaping community assembly and ecological succession. The importance of individual volatiles and interactions between volatiles are difficult to assess in the field because of (1) the myriad compounds from decomposing animals, and (2) the likelihood that complex component blends are important for the final approach to carrion. On the assumption that searching insects may use simpler volatile cues to orient at a distance, we employed a chemically-supplemented minimal trap that uses test chemicals to attract from a distance and a minimal carrion bait to induce trap entry. Traps supplemented with dimethyl trisulfide (DMTS) attracted more individuals than controls, while traps supplemented only with methyl thiolacetate (MeSAc) did not. Traps supplemented with both chemicals, however, attracted statistically greater numbers of adult silphids (Necrophila americanaandOiceoptoma noveboracense), and the histeridEuspilotus assimilisthan the combined totals of DMTS-only and MeSAc-only traps, demonstrating a synergism. The attraction ofNecrophila americanalarvae to traps left in the field for less than 24 h suggests that this species sometimes moves between carrion sources; a follow-up experiment in the laboratory demonstrated that larvae have the ability to feed on non-carrion insects and to survive without food while moving between carcasses. The use of such species for forensic applications requires caution.
Finding A Fresh Carcass: Bacterially-Derived Volatiles And Burying Beetle Search Success
Authors: Trumbo Stephen T. , Steiger Sandra 
Published: January 2020

AbstractWhen burying beetles first emerge as adults, they search for well-rotted carcasses with fly maggots on which to feed. After attaining reproductive competence, they switch their search and respond to a small, fresh carcass to prepare for their brood. Because the cues used to locate a feeding versus a breeding resource both originate from carrion, the beetles must respond to subtle changes in volatiles during decomposition. We investigated cues used to locate a fresh carcass in the field by (1) a general subtractive method, applying an antibacterial or antifungal to reduce volatiles, and (2) a specific additive method, placing chemicals near a fresh carcass. Five sulfur-containing compounds were studied: dimethyl sulfide (DMS), dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS), methyl thiolacetate (MeSAc) and methyl thiocyanate (MeSCN). For the sulfides, we predicted that DMS would be the most attractive and DMTS the least attractive because of differences in the timing of peak production. We made noa prioripredictions for MeSAc and MeSCN. Antibacterial treatment of a carcass aged for 48 h resulted in a 59% decrease in beetles discovering the resource. The addition of MsSAc had no effect on discovery of a fresh carcass, while DMS and DMDS had a limited ability to attract breeding beetles. The chemical that was least well known, MeSCN, had a remarkable effect, increasing beetle numbers by 200-800% on a fresh carcass and almost guaranteeing discovery. DMTS, which is known to attract a variety of carrion insects, was the only compound to significantly reduce beetle presence at a fresh carcass. A laboratory experiment demonstrated that DMTS does not directly inhibit breeding, suggesting that DMTS deters breeding beetles while they fly.
SCANNER: A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data
Authors: Cai Guoshuai , Xiao Feifei 
Published: January 2020

AbstractMotivationIn recent years, efficient scRNA-seq methods have been developed, enabling the transcriptome profiling of single cells massively in parallel. Meanwhile, its high dimensionality brought challenges in data modeling, analysis, visualization and interpretation. Available analysis tools require extensive knowledge and training of data properties, statistical modeling and computational skills. It is challenging for biologists to efficiently view, browse and interpret the data.ResultsHere we developed SCANNER, as a public webserver resource to equip the biologists and bioinformatician to share and analyze scRNA-seq data in a comprehensive and collaborative manner. It is effort-less and host-free without requirement on software setup or coding skills, and enables a user-friendly way to compare the activation status of gene sets on single cell basis. Also, it is equipped with multiple data interfaces for easy data sharing and currently provide a database for studying the smoking effect on single cell gene expression in lung. Using SCANNER, we have identified larger proportions of cancer-associated fibroblasts cells and activeness of fibroblast growth related genes in melanoma tissues in females compared to males. Moreover, we foundACE2is mainly expressed in pneumocytes, secretory cells and ciliated cells with disparity in gene expression by smoking behavior.Availability and implementationSCANNER is available athttps://www.thecailab.com/scanner/.Supplementary informationSupplementary data are available online.ContactGCAI@mailbox.sc.eduorXIAOF@mailbox.sc.ecuKey PointsSCANNER provides a new web server resource for promoting scRNA-seq data analysisSCANNER enables comprehensive and dynamic analysis and visualization, novel functional annotation and activeness inference, online databases and easy data sharing.SCANNER bridges the data analysis and the biological experiment units.
Recombinant protein production and purification of SiiD, SiiE and SiiF - components of the SPI4-encoded type I secretion system fromSalmonellaTyphimurium
Authors: Klingl Stefan , Kordes Sina , Schmid Benedikt , Gerlach Roman G. , Hensel Michael , Muller Yves A. 
Published: January 2020

AbstractIn humans,Salmonella entericainfections are responsible for a pleiotropy of medical conditions. These include intestinal inflammation and typhoid fever. The initial contact betweenSalmonellaand polarized epithelial cells is established by the SPI4-encoded type I secretion system (T1SS), which secrets SiiE, a giant non-fimbrial adhesin. We have recombinantly produced various domains of this T1SS fromSalmonella entericaserovar Typhimurium inEscherichia colifor further experimental characterization. We purified three variants of SiiD, the periplasmic adapter protein spanning the space between the inner and outer membrane, two variants of the SiiE N-terminal region and the N-terminal domain of the SiiF ATP-binding cassette (ABC) transporter. In all three proteins, at least one variant yielded high amounts of pure soluble protein. Proper folding and cooperative unfolding were investigated by circular dichroism (CD) spectroscopy. Secondary structure content estimations from CD spectra were in good agreement with the values derived from SiiD and SiiF homology models or, in case of the SiiE N-terminal region, a secondary structure prediction. For one SiiD variant, protein crystals could be obtained that diffracted X-rays to approximately 4 Å resolution.
Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment
Authors: Rubin Jonathan D. , Stanley Jacob T. , Sigauke Rutendo F. , Levandowski Cecilia B. , Maas Zachary L. , Westfall Jessica , Taatjes Dylan J. , Dowell Robin D. 
Published: January 2020

1AbstractDetecting differential activation of transcription factors (TFs) in response to perturbation provides insight into cellular processes. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional motif enrichment within a list of ranked regions of interest (ROIs). As ROIs are typically inferred from the data, we also introducemuMerge, a statistically principled method of generating a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data that informs on transcriptional regulation including nascent (eg. PRO-Seq), CAGE, ChIP-Seq, and accessibility (e.g. ATAC-Seq). TFEA not only identifies the key regulators responding to a perturbation, but also temporally unravels regulatory networks with time series data. Consequently, TFEA serves as a hypothesis-generating tool that provides an easy, rigorous, and cost-effective means to broadly assess TF activity yielding new biological insights.
MISTR: A conserved MItochondrial STress Response network revealed by signatures of evolutionary conflict
Authors: Sorouri Mahsa , Chang Tyron , Jesudhasan Palmy , Pinkham Chelsea , Elde Nels C. , Hancks Dustin C. 
Published: January 2020

ABSTRACTHost-pathogen conflicts leave genetic signatures of variation in homologous host genes. Using these “molecular scars” as a guide, we discovered a vertebrate-specificMItochondrialSTressResponse circuit (MISTR). MISTR proteins are associated with electron transport chain factors and activated by stress signals such as interferon-gamma and hypoxia. Upon stress, ultraconserved miRNAs downregulate MISTR1 followed by replacement with paralogs MISTRAntiViral (MISTRAV) or MISTRHypoxia (MISTRH), depending on the insult. While cells lacking MISTR1 are more sensitive to apoptotic triggers, cells lacking MISTRAV or expressing the poxvirus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes forMISTR1andMISTRAVindicate ancient and ongoing conflicts with pathogens. MISTR proteins are also found in plants, yeasts, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.
Preservation of cognition in hypertension-treated South Indian rural population
Authors: Rajkumar Radhika , Merciline Alex Divya , Muthukrishnan Suresh Kumar , Subhashree Murali , Duraimurugan Muniswamy , JanakiDevi Velmurugan , Datta Manjula , Subramaniam Jamuna R. 
Published: January 2020

AbstractChange in diet, life style and increased life expectancy has led to the dramatic escalation in old age related complication like cognitive decline leading to dementia. Cardiovascular diseases (CVD) are huge risk factors for dementia, including Alzheimer disease (AD). Hypertension is very well known to cause cognitive impairment. Control of CVD could provide protection against dementia. Earlier, in the mouse model of AD, reserpine, an antihypertensive and antipsychotic drug could elicit improvement in the working memory in AD model mice and enhance the same in normal mice. Hence, Cognitive protection in the patients on chronic antihypertensive drug which contains reserpine was evaluated. Cognition in a cohort (in the South Indian rural population) of hypertensive patients (majority age group – 50-70 years) who have been chronically treated with a combinatorial drug, (adelphane/adelphane esidrex-Novaritis, Switzerland) consisting of reserpine and hydrazine for years was compared with controls without hypertension. The cohorts were age, sex, socio-economic, education background matched. Cognition was scored using the Tamil version of: Addenbrooke’s Cognitive Examination-III (T-ACEIII) and Tamil-Montreal Cognitive Assessment (T-MoCA) scales. The composite T-ACEIII score of control and treated groups were 53.6 and 53.2, respectively. T-MoCA scores (Control-15.1 and Treated-14.7) did not show much alteration. Further, the mean scores of the control and treated groups’ individual components of cognition in ACE, namely, Attention, Memory, Fluency, Language and visuospatial – cognitive skills also did not reveal significant difference. Thus, controlling blood pressure or hypertension with chronic antihypertensive medication like adelphane/adelphane esirdex (reserpine containing drugs) has retained normal cognition in both genders.
An individualized risk prediction model for new-onset, progression and regression of chronic kidney disease in a retrospective cohort of patients with type 2 diabetes under primary care in Hong Kong
Authors: Yang Lin , Chu Tsun Kit , Lian Jinxiao , Lo Cheuk Wai , Zhao Shi , He Daihai , Qin Jing , Liang Jun 
Published: January 2020

AbstractObjectivesThis study is aimed to develop and validate a prediction model for multi-state transitions across different stages of chronic kidney disease in patients with type 2 diabetes mellitus under primary care.SettingWe retrieved the anonymized electronic health records of a population based retrospective cohort in Hong Kong.ParticipantsA total of 26,197 patients were included in the analysis.Primary and secondary outcome measuresThe new-onset, progression, and regression of chronic kidney disease were defined by the transitions of four stages that were classified by combining glomerular filtration rate and urine albumin-to-creatinine ratio. We applied a multi-scale multi-state Poisson regression model to estimate the rates of the stage transitions by integrating the baseline demographic characteristics, routine laboratory test results and clinical data from electronic health records.ResultsDuring the mean follow-up time of 1.7 years, there were 2,935 patients newly diagnosed with chronic kidney disease, 1,443 progressed to the next stage and 1,971 regressed into an earlier stage. The models achieved the best performance in predicting the new-onset and progression with the predictors of sex, age, body mass index, systolic blood pressure, diastolic blood pressure, serum creatinine, HbA1c, total cholesterol, LDL, HDL, triglycerides and drug prescriptions.ConclusionsThis study demonstrated that individual risks of new-onset and progression of chronic kidney disease can be predicted from the routine physical and laboratory test results. The individualized prediction curves developed from this study could potentially be applied to routine clinical practices, to facilitate clinical decision making, risk communications with patients and early interventions.Article summaryStrengths of this studyEarly predictions for chronic kidney disease progression and timely intervention is critical for clinical management of patients with diabetes.We successfully developed a multi-scale multi-state Poisson regression models that achieved the satisfactory performance in predicting the new-onset and progression of chronic kidney diseases.The model incorporates the predictors of demographic characteristics, routine laboratory test results and clinical data from electronic health records.The individualized prediction curves could potentially be applied to facilitate clinical decision making, risk communications with patients and early interventions of CKD progression.Limitations of this studyThe cohort has a relatively short follow-up period and the retrospective study design might suffer from report bias and selection bias.