bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Vaccine Acceptance Among Health Care Workers in the United States
Authors: Shekhar Rahul , Sheikh Abu Baker , Upadhyay Shubhra , Singh Mriganka , Kottewar Saket , Mir Hamza , Barrett Eileen , Pal Suman 
Published: January 2021

ABSTRACTBackgroundAcceptance of the COVID-19 vaccine will play a major role in combating the pandemic. Healthcare workers (HCWs) are amongst the first group to receive vaccination, so it is important to consider their attitudes about COVID-19 vaccination to better address barriers to widespread vaccination acceptance.MethodsWe conducted a cross sectional study to assess the attitude of HCWs toward COVID-19 vaccination. Data was collected between October 7th and November 9th, 2020. We received 4080 responses out of which 3479 were complete responses and were included in final analysis.Results36% of respondents were willing to take the vaccine as soon as it became available while 56% were not sure or would wait to review more data. Vaccine acceptance increased with increasing age, education, and income level. Lower acceptance was noted in females (31%), Black (10%), Latinx (30%) and Conservative/Republican (21%) HCWs, and those working in a rural setting (26%). Direct medical care providers had higher vaccine acceptance (49%). Safety (69%), effectiveness (69%) and speed of development/approval (74%) were noted as the most common concerns regarding COVID-19 vaccination in our survey.ConclusionImmediate acceptance of a COVID-19 vaccine is low, with the majority of HCWs choosing to wait to review more data before deciding on personal vaccination. Overall attitudes toward vaccination were positive but specific concerns regarding COVID-19 vaccine are prevalent. Differences in vaccine acceptance were noted between individual and group characteristics which should be addressed to avoid exacerbating health inequities.
Colour Ambiguity in Real Scenes and the Role of Perceptual Organisation
Authors: Werner Annette , Schmidt Alisa , Hilmers Julian , Boborzi Lukas , Weigold Manuela 
Published: January 2021

AbstractIn this study we show a reproduction of the dress-ambiguity phenomenon in a real scene and we report quantitative measurements of the corresponding colour perceptions. The original, real dress, known from #thedress-illusion, was illuminated by combined short- and longwavelength broadband lights from two slide projectors. Test subjects viewing the dress reported to perceive the dress’ fabric and lace colours as blue & black, white & gold or light blue & brown; their corresponding perceptual matches were distributed along the blue/yellow cardinal axis, and exhibited a variability comparable to the ambiguity of the dress photograph. It is particularly noteworthy that the colour ambiguity emerged despite explicit knowledge of the observers about the direction of the light source. Manipulating the background of the real dress (change in chromaticity and luminance, or masking) revealed significant differences between the perceptual groups regarding lightness and colour of the dress. Our findings suggest that observer specific differences in the perceptual organisation of the visual scene are responsible for the colour ambiguity observed for the real dress; in particular, we conclude that colour computations of white & gold viewers focused onto the local region of the dress, whereas the colour processes of blue & black and light-blue & brown viewers were strongly influenced by contextual computations including the background. Our segmentation hypothesis extends existing explanations for the dress’ ambiguity and proposes image based (in the case of the real scene) and high level (in the case of the photograph) neural processes which control the spatial reach of contextual colour computations. The relation between the ambiguity in our real scene and the dress photograph is discussed.
Small mitochondrial protein NERCLIN regulates cardiolipin homeostasis and mitochondrial ultrastructure
Authors: Konovalova Svetlana , Torregrosa-Muñumer Rubén , Manjunath Pooja , Baral Sundar , Liu Xiaonan , Holopainen Minna , Kvist Jouni , Rajendran Jayasimman , Yang Yang , Varjosalo Markku , Käkelä Reijo , Somerharju Pentti , Tyynismaa Henna 
Published: January 2021

ABSTRACTCardiolipin (CL) is an essential phospholipid for mitochondrial structure and function. Here we present a small mitochondrial protein, NERCLIN, as a negative regulator of CL homeostasis and mitochondrial ultrastructure. Primate-specific NERCLIN is expressed ubiquitously fromGRPEL2locus on a tightly regulated low level, but induced by heat stress. NERCLIN overexpression severely disrupts mitochondrial cristae structure and induces mitochondrial fragmentation. Proximity labeling suggested interactions of NERCLIN with CL synthesis and prohibitin complexes on the matrix side of the inner mitochondrial membrane. Lipid analysis indicated that NERCLIN regulates mitochondrial CL content. The regulation may occur directly through interaction with PTPMT1, a proximal partner on the CL synthesis pathway, as its product phosphatidylglycerol was also reduced by NERCLIN. We propose that NERCLIN contributes to stress-induced adaptation of mitochondrial dynamics and turnover by regulating the mitochondrial CL content. Our findings add NERCLIN to the group of recently identified small mitochondrial proteins with important regulatory functions.
A stochastic model of homeostasis: the roles of noise and nuclear positioning in deciding cell fate
Authors: Jangid Amit , Selvarajan Suriya , Ramaswamy Ram 
Published: January 2021

AbstractWe study a population based cellular model starting from a single stem cell which stochastically divides to give rise to either daughter stem cells or differentiated daughter cells. There are three main components in the model: nucleus position, gene-regulatory network, and stochastic segregation of transcription factors in daughter cells. We study the proportion of self-renewal and differentiated cell lines as a function of the nucleus position, which in turn decides the plane of cleavage. Both nuclear position and noise play an important role in determining the stem cell genealogies and these results can be compared with a Markov model that ignores nucleus position. We have observed long and short genealogies from model simulation which compares well with experimental results from neuroblast and B-cell division. Symmetric cellular divisions were observed when the nucleus is apical, while asymmetric division occurs when the nucleus is towards the base. The number of clones decreases as a function of time in this model, although the average clone size increases.
SERS uncovers the link between conformation of cytochromecheme and mitochondrial membrane potential
Authors: Brazhe Nadezda A. , Nikelshparg Evelina I. , Baizhumanov Adil A. , Grivennikova Vera G. , Semenova Anna A. , Novikov Sergey M. , Volkov Valentyn S. , Arsenin Aleksey V , Yakubovsky Dmitry I. , Evlyukhin Andrey B. , Bochkova Zhanna V. , Goodilin Eugene A. , Maksimov Georgy V. , Sosnovtseva Olga , Rubin Andrey B. 
Published: January 2021

ABSTRACTThe balance between the mitochondrial respiratory chain activity and the cell’s needs in ATP ensures optimal cellular function. Cytochromecis an essential component of the electron transport chain (ETC), which regulates ETC activity, oxygen consumption, ATP synthesis and can initiate apoptosis. The impact of conformational changes in cytochromecon its function is not understood for lack of access to these changes in intact mitochondria. We have developed a novel sensor that uses unique properties of label-free surface-enhanced Raman spectroscopy (SERS) to identify conformational changes in heme of cytochromecand to elucidate their role in functioning mitochondria. We verify that molecule bond vibrations assessed by SERS is a reliable indicator of the heme conformation during changes in the inner mitochondrial membrane potential and ETC activity. We have found that cytochromecheme reversibly switches between planar and ruffled conformations in response to the inner mitochondrial membrane potential and H+concentration in the intermembrane space to regulate the efficiency of the mitochondrial respiratory chain, thus, adjusting the mitochondrial respiration to the cell’s consumption of ATP and the overall activity. The ability of the proposed SERS-based sensor to track mitochondrial function opens wide perspectives on cell bioenergetics.For Table of Contents Only
In vitropectate lyase activity and carbon uptake assays and whole genome sequencing ofBacillus amyloliquefacienssubsp.plantarumstrains for a pectin defective pathway
Authors: Hassan Mohammad K. 
Published: January 2021

AbstractThe pectin lyase activity of 59Bacillus amyloliquefaciens subsp. plantarum (Bap)strains was testedin vitroon Pectate Agar (PA) and Tris-Spizizen Salts (TSS) medium. Bap strains were cultured on TSA medium and washed three times with sterile water before the inoculation on PA media. Higher and lower pectate lyase activity were observed in six (AP193, AP203, AP299, AP80, AP102, and AP52) and four (AP 194, AP214, AP215, and AP305)Bapstrains compared to other Bap strains. A total of 12 Bap strains (AP67, AP71, AP77, AP78, AP85, AP102, AP108, AP135, AP143, AP189, AP192, and AP193) grew vigorously on TSS medium. A total of sixBapstrains (AP194, AP204, AP214, AP216, AP219, and HD73) had lower growth compared to otherBapstrains. Pectin (1%) were used forin vitroPA and TSS medium. Pectate lyase and utilization activity were not found inBacillus thuringiensissubsp.kurstakistrain HD73 compared toBapstrains. A draft genome sequence for strains AP194 and AP214 that were negative for pectin utilization were generated using an Illumina MiSeq. RAST analysis revealed that the pectin-associated gene altronate hydrolase(uxaA)absent in AP 214 strain. Multiple amino acid alignments ofexuTanduxuBgene sequence showed dissimilarities among AP194, AP214, and referenceBapstrains.
Aberrant Dynamic Functional Connectivity of Default Mode Network in Schizophrenia and Links to Symptom Severity
Authors: Sendi Mohammad S.E. , Zendehrouh Elaheh , Ellis Charles A. , Liang Zhijia , Fu Zening , Mathalon Daniel H. , Ford Judith M. , Preda Adrian , van Erp Theo G. M. , Miller Robyn. L , Pearlson Godfrey D. , Turner Jessica A. , Calhoun Vince D. 
Published: January 2021

AbstractBackgroundSchizophrenia affects around 1% of the global population. Functional connectivity extracted from resting-state functional magnetic resonance imaging (rs-fMRI) has previously been used to study schizophrenia and has great potential to provide novel insights into the disorder. Some studies have shown abnormal functional connectivity in the default mode network of individuals with schizophrenia, and more recent studies have shown abnormal dynamic functional connectivity (dFC) in individuals with schizophrenia. However, DMN dFC and the link between abnormal DMN dFC and symptom severity have not been well characterized.MethodResting-state fMRI data from subjects with schizophrenia (SZ) and healthy controls (HC) across two datasets were analyzed independently. We captured seven maximally independent subnodes in the DMN by applying group independent component analysis and estimated dFC between subnode time courses using a sliding window approach. A clustering method separated the dFCs into five reoccurring brain states. A feature selection method modeled the difference between SZs and HCs using the state-specific FC features. Finally, we used the transition probability of a hidden Markov model to characterize the link between symptom severity and dFC in SZ subjects.ResultsWe found decreases in the connectivity of the anterior cingulate cortex (ACC) and increases in the connectivity between the precuneus (PCu) and the posterior cingulate cortex (PCC) (i.e., PCu/PCC) of SZ subjects. In SZ, the transition probability from a state with weaker PCu/PCC and stronger ACC connectivity to a state with stronger PCu/PCC and weaker ACC connectivity increased with symptom severity.ConclusionsTo our knowledge, this was the first study to investigate DMN dFC and its link to schizophrenia symptom severity. We identified reproducible neural states in a data-driven manner and demonstrated that the strength of connectivity within those states differed between SZs and HCs. Additionally, we identified a relationship between SZ symptom severity and the dynamics of DMN functional connectivity. We validated our results across two datasets. These results support the potential of dFC for use as a biomarker of schizophrenia and shed new light upon the relationship between schizophrenia and DMN dynamics.
6-gingerol interferes with amyloid-beta (Aβ) peptide aggregation
Authors: Berntsson Elina , Paul Suman , Sholts Sabrina B. , Jarvet Jüri , Barth Andreas , Gräslund Astrid , Wärmländer Sebastian K. T. S. 
Published: January 2021

AbstractAlzheimer’s disease (AD) is the most prevalent age-related cause of dementia. AD affects millions of people worldwide, and to date there is no cure. The pathological hallmark of AD brains is deposition of amyloid plaques, which mainly consist of amyloid-β (Aβ) peptides, commonly 40 or 42 residues long, that have aggregated into amyloid fibrils. Intermediate aggregates in the form of soluble Aβ oligomers appear to be highly neurotoxic. Cell and animal studies have previously demonstrated positive effects of the molecule 6-gingerol on AD pathology. Gingerols are the main active constituents of the ginger root, which in many cultures is a traditional nutritional supplement for memory enhancement. Here, we use biophysical experiments to characterizein vitrointeractions between 6-gingerol and Aβ40peptides. Our experiments with atomic force microscopy imaging, and nuclear magnetic resonance and Thioflavin-T fluorescence spectroscopy, show that the hydrophobic 6-gingerol molecule interferes with formation of Aβ40aggregates, but does not interact with Aβ40monomers. Thus, together with its favourable toxicity profile, 6-gingerol appears to display many of the desired properties of an anti-AD compound.
Testosterone induces a conditioned place preference to the nest of a monogamous mouse under field conditions
Authors: Petric Radmila , Kalcounis-Rueppell Matina C. , Marler Catherine A. 
Published: January 2021

AbstractTransient increases in testosterone (T-pulses) occur after social interactions in males of various vertebrate species, but the functions of T-pulses are poorly understood. Under laboratory conditions, the rewarding nature of T-pulses induces conditioned place preferences (CPPs), but what are the effects in a complex field environment? We present the first evidence that T-pulses administered to males at their nest site in the wild increased time spent at the nest regardless of pup presence in the monogamous, biparental, and territorial California mouse (Peromyscus californicus). Female partners of the T-males, in turn, spent less time at the nest. Independent of treatment, mice produced more ultrasonic vocalizations (USVs) when alone, but T-mice produced more USVs than controls. T-males produced USVs with a smaller bandwidth that likely traveled farther. Our combined results provide compelling evidence that T-pulses can significantly shift the behavioral focus and location of individuals in a complex field setting.
A field-wide assessment of differential expression profiling by high throughput sequencing reveals widespread bias
Authors: Päll Taavi , Luidalepp Hannes , Tenson Tanel , Maiväli Ülo 
Published: January 2021

AbstractHere we assess inferential quality in the field of differential expression profiling by high throughput sequencing, based on analysis of datasets submitted 2008-2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p values, the distribution of which can indicate the validity of assumptions behind the test. Moreover, from a well-behaved p value setπ0, the fraction of genes that are not differentially expressed, can be estimated. We found that only 25% of experiments resulted in theoretically expected p value histogram shapes, although there is a marked improvement over time. Uniform p value histogram shapes, indicative of < 100 true effects, were extremely few. Furthermore, although many HT-seq workflows assume that most genes are not differentially expressed we found 37% of experiments to haveπ0-s of less than 0.5, as if most genes changed their expression level. Restricting our analysis to studies involving cancer or transcription factors, expected to lead to real changes in expression of many genes, did not result in meaningfully different distributions ofπ0-s. Both the fractions of different p value histogram types and theπ0values are strongly associated with the differential expression analysis program used by the original authors. While we could double the proportion of theoretically expected p value distributions by removing low-count features from analysis, this treatment did not remove the association with the analysis program. Taken together, our results indicate widespread bias in differential expression profiling field.
Positive and Neutral Updating Reconsolidate Aversive Episodic Memories via Different Routes
Authors: Wang Jingyi , Chen Boxuan , Sha Manqi , Gu Yiran , Wu Haitao , Forcato Cecilia , Qin Shaozheng 
Published: January 2021

AbstractAversive memories are long-lasting and prone to have adverse effects on our emotional wellbeing and mental health. Yet, how to remedy the maladaptive effects of aversive memories remains elusive. Using memory reactivation and emotional updating manipulations, we investigated how positive and neutral emotion updates aversive memories for reconsolidation in humans. We found that positive updating after reactivation was equivalent to neutral updating in altering true memories of the aversive story, but introduced more false memory. Moreover, an additional 12 hours of sleep reconsolidation did not further enlarge true memory differences, but attenuated the effect of reactivation and updating on false memory. Interestingly, the neutral rather than the positive updating reduced the emotional arousal of the aversive memory 24 hours later. Our findings provide novel insights into real-world therapeutic applications regarding how updating with positive and neutral emotion may reshape aversive memories, especially when taking wake- and sleep-filled reconsolidation into account.
DenovoProfiling: a webserver for de novo generated molecule library profiling
Authors: Liu Zhihong , Du Jiewen , Liu Bingdong , Cui Zongbin , Fang Jiansong , Xie Liwei 
Published: January 2021

AbstractWith the advances of deep learning techniques, various architectures for molecular generation have been proposed for de novo drug design. Successful cases from academia and industrial demonstrated that the deep learning based de novo molecular design could efficiently accelerate the drug discovery process. The flourish of the de novo molecular generation methods and applications created great demand for the visualization and functional profiling for the de novo generated molecules. The rising of publicly available chemogenomic databases lays good foundations and create good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a web server dedicated for de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification & visualization, (2) chemical space, (3) scaffold analysis, (4) molecular alignment, (5) target & pathways, and (6) drugs mapping. DenovoProfiling could provide structural identification, chemical space exploration, drugs mapping, and targets & pathways. The comprehensive annotated information could give user a clear picture of their de novo library and could provide guidance in the further selection of candidates for synthesis and biological confirmation. DenovoProfiling is freely available athttp://denovoprofiling.xielab.net.
The engineered peptide construct NCAM1-Aβ inhibits aggregation of the human prion protein (PrP)
Authors: Gielnik Maciej , Zhukova Lilia , Zhukov Igor , Gräslund Astrid , Kozak Maciej , Wärmländer Sebastian K.T.S. 
Published: January 2021

AbstractIn prion diseases, the prion protein (PrP) becomes misfolded and forms fibrillar aggregates, which are resistant to proteinase degradation and become responsible for prion infectivity and pathology. So far, no drug or treatment procedures have been approved for prion disease treatment. We have previously shown that engineered cell-penetrating peptide constructs can reduce the amount of prion aggregates in infected cells. The molecular mechanisms underlying this effect are however unknown. Here, we use atomic force microscopy (AFM) imaging to show that the aggregation of the human PrP protein can be inhibited by equimolar amounts of the 25 residues long engineered peptide construct NCAM1-Aβ.
An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis
Authors: Lee Sanghwa , Zhu Ling , Huq Enamul 
Published: January 2021

AbstractPlant growth and development are acutely sensitive to high ambient temperature ascribable in part to climate change. However, the mechanism of high ambient temperature signaling is not well defined. Here, we show that HECATEs (HEC1 and HEC2), two helix-loop-helix transcription factors, inhibit thermomorphogenesis. While the expression ofHEC1andHEC2is increased and HEC2 protein is stabilized at high ambient temperature,hec1hec2double mutant showed exaggerated thermomorphogenesis. Analyses of the four major PIF (PIF1, PIF3, PIF4 and PIF5) mutants and overexpression lines showed that they all contribute to promote thermomorphogenesis. Furthermore, genetic analysis showed thatpifQis epistatic tohec1hec2. HECs and PIFs oppositely control the expression of many genes in response to high ambient temperature. HEC2 interacts with PIF4 both in yeast andin vivo. In the absence of HECs, PIF4 binding to its own promoter as well as the target gene promoters was enhanced, indicating that HECs control PIF4 activity via heterodimerization. Overall, these data suggest that PIF4-HEC forms an autoregulatory composite negative feedback loop that controls growth genes to modulate thermomorphogenesis.
Quantifying the regulatory role of individual transcription factors inEscherichia coli
Authors: Guharajan Sunil , Chhabra Shivani , Parisutham Vinuselvi , Brewster Robert C. 
Published: January 2021

AbstractGene regulation often results from the action of multiple transcription factors (TFs) acting at a promoter, with a net regulation that depends on both the direct interactions of TFs with RNA polymerase (RNAP) and the indirect interactions with each other. Here we measure the fundamental regulatory interactions of TFs inE. coliby designing synthetic target genes that isolate the individual TFs regulatory effect. Using a thermodynamic model, the direct regulatory impact of the TF on RNAP is decoupled from TF occupancy and interpreted as acting through two mechanisms: (de)stabilization of RNAP and (de)acceleration of transcription initiation. We find the contributions of each mechanism depends on TF identity and binding location; for the set of TFs profiled, regulation immediately downstream of the promoter is insensitive to TF identity, yet these same TFs regulate by distinct mechanisms upstream of the promoter. Strikingly, we observe two fundamental regulatory paradigms with these two mechanisms acting coherently, to rein-force the observed regulatory role (activation or repression), or incoherently, where the TF regulates two distinct steps with opposing effect. This insight provides critical information on the scope of TF-RNAP regulation allowing for a stronger approach to characterize the endogenous regulatory function of TFs.