bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification and analyses of tomato (Solanum lycopersicum L.) high-affinity nitrate transporter 2 (NRT2) family genes and their responses to drought and salinity
Authors: Akbudak M. Aydın , Filiz Ertugrul , Çetin Durmuş 
Published: December 2021

AbstractHigh-affinity nitrate transporter 2 (NRT2) proteins have vital roles in nitrate (NO3-) uptake and translocation in plants. The gene families coding NRT2 proteins have been identified and functionally characterized in many plant species. However, no systematic identification of NRT2 family members have been reported in tomato (Solanum lycopersicum). There is also little known about their expression profiles under environmental stresses. Accordingly, the present study aimed to identify NRT2 gene family in the tomato genome; then, investigate them in detail through bioinformatics, physiological and expression analyses. As a result, four novel NRT2 genes were identified in the tomato genome, all of which contain the same domain belonging to the Major Facilitator Superfamily (PF07690). The co-expression network of SlNRT genes revealed that they were co-expressed with several other genes in many different molecular pathways including transport, photosynthesis, fatty acid metabolism and amino acid catabolism. Programming many crucial physiological and metabolic pathways, various numbers of phosphorylation sites were predicted in the NRT2 proteins.
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
Authors: Toh H. , Yang C. , Formenti G. , Raja K. , Yan L. , Tracey A. , Chow W. , Howe K. , Bergeron L.A. , Zhang G. , Haase B. , Mountcastle J. , Fedrigo O. , Fogg J. , Kirilenko B. , Munegowda C. , Hiller M. , Jain A. , Kihara D. , Rhie A. , Phillippy A.M. , Swanson S. , Jiang P. , Clegg D.O. , Jarvis E.D. , Thomson J.A. , Stewart R. , Chaisson M.J.P. , Bukhman Y.V. 
Published: December 2021

AbstractThe Nile rat (Avicanthis niloticus) is an important animal model for biomedical research, including the study of diurnal rhythms and type 2 diabetes. Here, we report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3,613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including those that affect genes associated with type 2 diabetes and metabolic dysfunctions. These include 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. Our findings reflect the exceptional level of genomic detail present in this assembly, which will greatly expand the potential of the Nile rat as a model organism for genetic studies.
People with nicotine use-disorder exhibit more prefrontal activity during preparatory control but reduced anterior cingulate activity during reactive control
Authors: Kalhan Shivam , Evelyn Chen Li Peng , Garrido Marta I. , Hester Robert 
Published: December 2021

AbstractReduced inhibitory control and a hypersensitivity to reward are key deficits in drug-dependents, however, they tend to be studied in isolation. Here we seek to understand the neural processes underlying control over reward and how this is different in people with a nicotine use disorder (pNUD). A novel variant of the monetary incentive delay task was performed by pNUD (n = 20) and non-smokers (n = 20), where we added a stop-signal component such that participants had to inhibit prepotent responses to earn a larger monetary reward. Brain activity was recorded using functional magnetic resonance imaging (fMRI). We estimated stop signal reaction times (SSRT), an indicator of impulsivity, and correlated these with brain activity. Inhibitory accuracy scores did not differ between the control group and pNUD. However, pNUD had slower SSRTs, suggesting that they may find it harder to inhibit responses. Brain data revealed that pNUD had greater preparatory control activity in the middle frontal gyrus and inferior frontal gyrus prior to successful inhibitions over reward. In contrast, non-smokers had greater reactive control associated with more activity in the anterior cingulate cortex during these successful inhibitions. SSRT-brain activity correlations revealed that pNUD engaged more control related prefrontal brain regions when SSRTs are slower. Overall, whilst the inhibition accuracy scores were similar between groups, differential neural processes and strategies were used to successfully inhibit a prepotent response. The findings suggest that increasing preparatory control in pNUD may be one possible treatment target in order to increase inhibitory control over reward.
Boosting serotonin increases information gathering by reducing subjective cognitive costs
Authors: Michely Jochen , Martin Ingrid M. , Dolan Raymond J. , Hauser Tobias U. 
Published: December 2021

AbstractSerotonin is implicated in the valuation of aversive costs, such as delay or physical effort. However, its role in governing sensitivity to cognitive effort, for example deliberation costs during information gathering, is unclear. We show that week-long treatment with a serotonergic antidepressant enhances a willingness to gather information when trying to maximize reward. Using computational modelling, we show this arises from a diminished sensitivity to subjective deliberation costs during the sampling process. This result is consistent with the notion that serotonin alleviates sensitivity to aversive costs in a domain-general fashion, with implications for its potential contribution to a positive impact on motivational deficits in psychiatric disorders.
D-amphetamine maintenance therapy reduces cocaine use in female rats
Authors: Ndiaye Ndeye Aissatou , Allain Florence , Samaha Anne-Noël 
Published: December 2021

AbstractCurrently, there are no approved medications to treat cocaine addiction. In this context, d-amphetamine maintenance therapy is a promising pharmacological strategy to reduce cocaine use. In both male rats and human cocaine users, d-amphetamine treatment reduces cocaine taking and seeking. However, this has not been examined systematically in female animals, even though cocaine addiction afflicts both women and men, and the sexes can differ in their response to cocaine. Here, we determined how d-amphetamine maintenance therapy during cocaine self-administration influences cocaine use in female rats. In experiment 1, two groups of female rats received 14 intermittent access (IntA) cocaine self-administration sessions. One group received concomitant d-amphetamine maintenance treatment (COC + A rats; 5 mg/kg/day, via minipump), the other group did not (COC rats). After discontinuing d-amphetamine treatment, we measured responding for cocaine under a progressive ratio schedule, responding under extinction and cocaine-primed reinstatement of drug seeking. In experiment 2, we assessed the effects of d-amphetamine maintenance on these measures in already cocaine-experienced rats. To this end, rats first received 14 IntA cocaine self-administration sessions without d-amphetamine. They then received 14 more sessions now either with (COC/COC + A rats) or without (COC/COC rats) concomitant d-amphetamine treatment. In both experiments, d-amphetamine treatment did not influence cocaine-primed reinstatement of cocaine seeking. However, after d-amphetamine treatment, rats responded less for cocaine both under progressive ratio and extinction conditions. Thus, d-amphetamine treatment can both prevent and reverse increases in the motivation to take and seek cocaine in female animals.
Escape Steering by Cholecystokinin Peptidergic Signaling
Authors: Chen Lili , Liu Yuting , Su Pan , Hung Wesley , Li Haiwen , Wang Ya , Yue Zhongpu , Ge Minghai , Wu Zhengxing , Zhang Yan , Fei Peng , Chen Li-Ming , Tao Louis , Mao Heng , Zhen Mei , Gao Shangbang 
Published: December 2021

AbstractEscape is an evolutionarily conserved and essential avoidance response. Considered to be innate, most studies on escape responses focused on hard-wired circuits. We report here that peptidergic signaling is an integral and necessary component of the Caenorhabditis elegans escape circuit. Combining genetic screening, electrophysiology and calcium imaging, we reveal that a neuropeptide NLP-18 and its cholecystokinin receptor CKR-1 enable the escape circuit to execute a full omega (Ω) turn, the last motor step where the animal robustly steers away from its original trajectory. We demonstrate in vivo and in vitro that CKR-1 is a Gαq protein coupled receptor for NLP-18. in vivo, NLP-18 is mainly secreted by the gustatory sensory neuron (ASI) to activate CKR-1 in the head motor neuron (SMD) and the turn-initiating interneuron (AIB). Removal of NLP-18, removal of CKR-1, or specific knockdown of CKR-1 in SMD or AIB neurons lead to shallower turns hence less robust escape steering. Consistently, elevation of head motor neuron (SMD)’s Ca2+ transients during escape steering is attenuated upon the removal of NLP-18 or CKR-1. in vitro, synthetic NLP-18 directly evokes CKR-1-dependent currents in oocytes and CKR-1-dependent Ca2+ transients in SMD. Thus, cholecystokinin signaling modulates an escape circuit to generate robust escape steering.
Improved Transcriptome Assembly Using a Hybrid of Long and Short Reads with StringTie
Authors: Shumate Alaina , Wong Brandon , Pertea Geo , Pertea Mihaela 
Published: December 2021

AbstractShort-read RNA sequencing and long-read RNA sequencing each have their strengths and weaknesses for transcriptome assembly. While short reads are highly accurate, they are unable to span multiple exons. Long-read technology can capture full-length transcripts, but its high error rate often leads to mis-identified splice sites, and its low throughput makes quantification difficult. Here we present a new release of StringTie that performs hybrid-read assembly. By taking advantage of the strengths of both long and short reads, hybrid-read assembly with StringTie is more accurate than long-read only or short-read only assembly, and on some datasets it can more than double the number of correctly assembled transcripts, while obtaining substantially higher precision than the long-read data assembly alone. Here we demonstrate the improved accuracy on simulated data and real data from Arabidopsis thaliana, Mus musculus, and human. We also show that hybrid-read assembly is more accurate than correcting long reads prior to assembly while also being substantially faster. StringTie is freely available as open source software at https://github.com/gpertea/stringtie.
Improving Lab Culture through Self-Assessment: A Case Study
Authors: Hernandez Soleil , Mumme Raymond , Court Laurence , Basha Daniel El , Gay Skylar , Marquez Barbara , Xiao Yao , Huang Kai , Baroudi Hana , Cao Wenhua , Cardenas Carlos , Douglas Raphael , Duryea Jack , Kaffey Zaphanlene , Mann Deborah , Nealon Kelly , Netheron Tucker , Nguyen Callistus , Oh Kyuhak , Olanrewaju Adenike , Sjogreen Carlos , Rhee DJ , Yang Jinzhong , Yu Cenji , Zhang Lifei , Zhao Yao , Ziyaee Hamid , Gronberg Mary 
Published: December 2021

AbstractPurposeMotivated by perceived dissatisfaction within our lab’s changed working environment brought about by the COVID-19 pandemic, we performed a self-assessment of our lab culture through anonymous surveys and live sessions.MethodsIn Survey 1, we asked each lab member to identify and rank up to 10 values that are important for a healthy lab environment. They were then asked to rate how well the lab embodied those values at two time points: before the COVID-19 pandemic while working onsite, and at the time of the survey while working remotely (10 months into the pandemic). In a series of live group sessions, we reviewed relevant literature and the survey results to finalize ten themes. We then reflected on each theme and proposed action items to address any deficiencies. Finally, we conducted Survey 2 after the self-assessment to judge the group’s finalized themes, implemented changes, and overall satisfaction with the assessment process.ResultsThemes identified were attitude, accountability, teamwork/collaboration, communication, diversity/inclusion, emotional intelligence, integrity, training, well-being, and adaptability in crisis-management. All lab members liked the self-assessment process and felt their voices were heard. On average, there was a 12% increase in satisfaction across all themes from the start to end of the lab assessment.ConclusionWe successfully assessed the culture of our lab and subsequently improved lab member satisfaction. The success of this team project suggests that other scientific labs could benefit from similar interactive self-assessments.
HBV enveloped particle secretion is positively regulated by GRP78 through direct interaction with preS1
Authors: Shi Yueyuan , Jin Xin , Wu Shuang , Liu Junye , Zhang Hongpeng , Cai Xuefei , Yang Yuan , Zhang Xiang , Wei Jie , Peng Hui , Luo Miao , Zhou Hua , Zhou Huihao , Huang Ailong , Wang Deqiang 
Published: December 2021

ABSTRACTHepatitis B virus (HBV) infection is a common cause of liver diseases worldwide. Existing drugs do not effectively eliminate HBV from infected hepatocytes; thus, novel curative therapies are needed. Enveloped-particle secretion is a key but poorly studied aspect of the viral life cycle. Here, we report that GRP78 positively regulates HBV enveloped-particle secretion. GRP78 is the specific target of preS1 binding; HBV can upregulate GRP78 in liver cell lines and sera from chronic hepatitis B patients. GRP78 promoted intact HBV-particle secretion in liver cell lines and an HBV transgenic-mouse model. Some peptides screened from preS1 via phage display could inhibit viral-particle secretion by interacting with GRP78 via hydrogen bonds and hydrophobic interactions, thereby disturbing the interaction with HBV particles. These results provide insight into enveloped-particle secretion in the HBV life cycle. GRP78 might be a potential target for HBV-infection treatment via restricting GRP78–preS1 interactions to block viral-particle secretion.IMPORTANCEHBV is a major human pathogen. The virus More than 250 million n individuals globally are chronically infected with HBV and can result in the infected personsabout 800,000 die for HBV-related disease annually. The mature HBV enveloped particles containing HBs and the relaxed circular (RC) DNA genome could secreted extracellularly as virions. And these enveloped virions serves as the infectious HBV particles for initiating a complete life cycle of the virus. Here, we show the GRP78 is the specific target of preS1 binding, and it could positive regulate HBV enveloped particle secretion in cell and HBV transgenic mice model. Furthermore, several peptides screened from preS1 and Phage screening could inhibit viral particle secretion by interacting with GRP78 and disturbing its interaction with HBV, and then block the life cycle of the virus. This has important implications for our understanding of the mechanisms of antivirals that target intact HBV particles secretion.
Effect of growth forms of bamboo on the mycorrhizal and fluorescent pseudomonas population
Authors: Das Solomon , Singh Y. P. , Negi Yogesh K. , Shrivastav P. C. 
Published: December 2021

AbstractBamboo, also called as the poor man’s timber, is one of the fastest growing giant grass species. Having shallow root system and fast growth rate, the dependability of the plant on the rhizospheric microbial web cannot be denied. The study was conducted to explore the population and seasonal variations of indigenous mycorrhizal fungi as well as the functional diversity of plant growth promoting bacteria, especially fluorescent pseudomonas from the different growth forms of Dendrocalamus strictus, the most commonly present bamboo species in Indian sub-continent. In a past study, it was established that the growth forms of D. strictus which developed over time in their respective locations, were genetically varied. The present research further explores the variations in their respective rhizospheric microbes and looks for the role of plant selection phenomenon. Considerable variation in mycorrhizal structures and in the functional diversity of fluorescent pseudomonas was registered. It seems probable that selection pressure of nutrient deficient condition has created a condition that promoted occurrence of high numbers of P solubilisers which, in turn, boosted the mycorrhizal as well as bamboo growth.
Oligogenic risk model for Gilles de la Tourette syndrome reveals a genetic continuum of tic disorders
Authors: Borczyk Malgorzata , Fichna Jakub P , Piechota Marcin , Gołda Sławomir , Zięba Mateusz , Hoinkis Dzesika , Cięszczyk Paweł , Korostyński Michal , Janik Piotr , Żekanowski Cezary 
Published: December 2021

AbstractGilles de la Tourette syndrome (GTS) and other Tic Disorders (TDs) have a substantial genetic component with their heritability estimated at between 60 and 80%. Here we propose an oligogenic risk model of TDs using whole-genome sequencing (WGS) data from a group of Polish GTS patients, their families, and control samples (n = 278). The model is based on the overrepresentation of coding and non-coding genetic variants in and in the vicinity of genes selected from a set of 84 genes previously indicated as putatively associated with GTS. In the discovery phase, based on a variant burden test between unrelated GTS cases (n = 37) and a database of local allele frequencies 10 genes were selected for the model (CHADL,DRD2,MAOA,PCDH10,HTR2A,SLITRK5,SORCS3,KCNQ5,CDH9,andCHD8). Variants in these genes (n = 7654) with a median minor allele frequency in the non-Finnish European population of 0.02 were integrated into an additive classifier. This risk model was then applied to healthy and GTS-affected individuals from 23 families and 100 unrelated healthy samples from the Polish population (AUC-ROC=0.62, p=0.02). Application of the oligogenic model to a group of patients with other tic disorders revealed a continuous increase of the oligogenic score with healthy individuals with the lowest mean, then patients with other tic disorders, then GTS patients, and finally with severe GTS cases with the highest oligogenic score. Results were also overlapped with Psychiatric Genomics Consortium (PGC) GWAS data and we found no significant overlap between the common variant signal and our oligogenic model (p=0.21). Therefore obtained results were compared with the polygenic risk score built from the PGC GWAS data, which revealed a significant contribution of common variant background in severe GTS cases. Overall, we leveraged WGS data to construct a GTS/TDs risk model based on variants that may cooperatively contribute to the etiology of these disorders. This study provides evidence that typical and severe adult GTS as well as other tic disorders may exist on a single spectrum in terms of their genetic background.
Population Optimally Immunized after Accounting for Type-Specific COVID-19 Vaccine Waning Intervals: State-Level Prevalence and Trends
Authors: Pathak Elizabeth B. , Salemi Jason L. 
Published: December 2021

ABSTRACTBACKGROUNDCOVID-19 vaccines exhibit real-world waning effectiveness against SARS-CoV-2 infection within the first 3-6 months after a completed series. Consequently, the main metric tracked by the CDC (percent “fully vaccinated,” with no adjustment for booster status) has become insufficiently informative.METHODSWe analyzed CDC daily vaccination data to quantify COVID-19 immunization status for 4 mutually-exclusive groups: (1) not immunized; (2) partially immunized (people who received the 1st dose of a 2-dose series); (3) immunized with waning immunity (previously immunized people whose booster dose is overdue); and (4) optimally immunized (people who: (a) received the Janssen vaccine <2 months ago or completed an mRNA vaccine series <6 months ago, or (b) received the Janssen vaccine >2 months ago or completed an mRNA vaccine series >6 months ago and received a booster dose.)RESULTSThe proportion of the total US population who were optimally immunized against COVID-19 fell from a high of 45.3% on July 17 to 29.4% on November 30. During November, the majority of states experienced a worsening trend in the percent of the total population who were overdue for a booster dose, including the 4 largest states, with percentage point increases of 3.5 in New York, 3.4 in California, 2.3 in Texas and 1.7 in Florida.CONCLUSIONSOur proposed classification scheme accounts for type-specific vaccine waning intervals, provides an accurate assessment of progress toward national immunization goals, and reveals the urgent need for additional public health mitigation strategies to successfully combat the COVID-19 pandemic in the United States.
Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults respectively, with both subclades exhibiting extensive genetic diversity
Authors: Howson-Wells Hannah C. , Tsoleridis Theocharis , Zainuddin Izzah , Tarr Alexander W. , Irving William L. , Ball Jonathan K. , Berry Louise , Clark Gemma , McClure C. Patrick 
Published: December 2021

AbstractEnterovirus D68 (EV-D68) has been recently identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-D68 in 194 known EV positive samples from late 2018, UK. EV-D68 was detected in 83 (58%) of the 143 EV positive samples. Sequencing and phylogenetic analysis revealed an extensive genetic diversity, split between subclades B3 (n=50) and D1 (n=33), suggesting epidemiologically unrelated infections. B3 predominated in children and younger adults, and D1 in older adults and the elderly (p=0.0009). Clinical presentation indicated causation or exacerbation of respiratory distress in 91.4% of EV-D68-positive individuals, principally: cough (75.3%), shortness of breath (56.8%), coryza (48.1%), wheeze (46.9%), supplemental oxygen required (46.9%) and fever (38.9%). Clinical features were not distinguished by subclade. Two cases of AFM were observed, one with EV-D68 detectable in the cerebrospinal fluid, otherwise neurological symptoms were rarely reported (n=4).