bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crimp: fast and scalable cluster relabeling based on impurity minimization
Authors: Lautenschlager Ulrich 
Published: March 2022

MotivationTo analyze population structure based on multilocus geno-type data, a variety of popular tools perform model-based clustering, as-signing individuals to a prespecified number of ancestral populations. Since such methods often involve stochastic components, it is a common practice to perform multiple replicate analyses based on the same input data and parameter settings. Their results are typically affected by the label-switching phenomenon, which complicates their comparison and summary. Available tools allow to mitigate this problem, but leave room for improvements, in particular, regarding large input datasets.ResultsIn this work, I present Crimp, a lightweight command-line tool, which offers a relatively fast and scalable heuristic to align clusters across multiple replicate clusterings consisting of the same number of clusters. For small problem sizes, an exact algorithm can be used as alternative. Additional features include row-specific weights, input and output files similar to those of CLUMPP (Jakobsson & Rosenberg, 2007), and the evaluation of a given solution in terms of either CLUMPP’s and its own objective functions. Benchmark analyses show that Crimp, especially when applied to larger datasets, tends to outperform alternative tools considering runtime requirements and various quality measures.AvailabilityCrimp’s source code along with precompiled binaries for Linux and Windows, usage guidelines and benchmark code are freely available at https://github.com/ulilautenschlager/crimp.Contactulrich.lautenschlager@ur.de
Neural activity in the anterior cingulate cortex is required for effort-based decision making
Authors: Kashay Adrienne Q. , Cheung Jovian Y. , Vaknalli Rahil N. , Delaney Molly J. , Navarro Michael B. , Junaidi Christabelle , Veenker Faith , Neuwirth Morgan E. , Gabriel Christopher J. , DeNardo Laura A. , Wilke Scott A. 
Published: March 2022

ABSTRACTAdaptive decision making requires the evaluation of cost-benefit tradeoffs to guide action selection. Effort-based decision making (EBD) involves weighing predicted gains against effort costs and is disrupted in several neuropsychiatric disorders. The anterior cingulate cortex (ACC) is postulated to control effort-based choice via its role in encoding the value of overcoming effort costs in rodent EBD assays. However, temporally precise methods of manipulating neural activity have rarely been applied to EBD. We developed and validated a mouse version of the barrier T-maze EBD task, in which action selection is spatiotemporally segregated from surmounting an effortful obstacle and effort is minimally confounded with time cost. Optogenetic silencing of ACC excitatory neurons during action selection, rapidly and reversibly impaired preference to exert greater effort for a larger reward, when a less effortful alternative was available. Detailed analysis of mouse choice trajectories revealed that silencing ACC disrupts kinematics, especially prior to high effort choices. However, there were no effects on overall mobility or tendency to exert effort in non-choice assays. These findings establish causality between ACC neural activity and effortful action selection during spatial cost-benefit decision making.SIGNIFICANCE STATEMENTDisturbances in evaluating effort-based costs during decision making occur in depression, schizophrenia, addiction and Parkinson’s disease. Precisely resolving the function of prefrontal brain regions in mediating these processes will reveal key loci of dysfunction and potential therapeutic intervention in these disorders.
Marked regional glial heterogeneity in the human white matter of the central nervous system
Authors: Seeker Luise A. , Bestard-Cuche Nadine , Jäkel Sarah , Kazakou Nina-Lydia , Bøstrand Sunniva M. K. , Kilpatrick Alastair M. , Van Bruggen David , Kabbe Mukund , Pohl Fabio Baldivia , Moslehi Zahra , Henderson Neil C. , Vallejos Catalina A. , Manno Gioele La , Castelo-Branco Gonçalo , Williams Anna 
Published: March 2022

ABSTRACTThe myelinated white matter tracts of the central nervous system (CNS) are essential for fast transmission of electrical impulses and are commonly affected in neurodegenerative diseases. However, these often uniquely human diseases differentially affect white matter regions, at various ages and between males and females, and we hypothesised that this is secondary to physiological variation in white matter glia with region, age and sex. Using single nucleus RNA sequencing of healthy human post-mortem samples, we find marked glial heterogeneity with tissue region (primary motor cortex, cerebellum, cervical spinal cord), with tissue-specific cell populations of oligodendrocyte precursor cells and astrocytes, and a spinal cord-enriched oligodendrocyte type that appears human-specific. Spinal cord microglia but not astrocytes show a more activated phenotype compared to brain. These regional effects, with additional differentially expressed genes with age and sex in all glial lineages, help explain pathological patterns of disease – essential knowledge for therapeutic strategies.
The genomics and physiology of abiotic stressors associated with global elevation gradients inArabidopsis thaliana
Authors: Gamba Diana , Lorts Claire , Haile Asnake , Sahay Seema , Lopez Lua , Xia Tian , Takou Margarita , Kulesza Evelyn , Elango Dinakaran , Kerby Jeffrey , Yifru Mistire , Bulafu Collins E. , Wondimu Tigist , Glowacka Katarzyna , Lasky Jesse R. 
Published: March 2022

AbstractPhenotypic and genetic diversity inArabidopsis thalianamay be associated with adaptation along its wide elevational range. We took a multi-regional view of elevational adaptation and in a diverse panel of ecotypes measured plant responses to high elevation stressors: low partial CO2pressure, high light, and night freezing. We conducted genome-wide association studies (GWAS) and found evidence of contrasting locally adaptive clines between regions. Western Mediterranean ecotypes showed low δ13C/early flowering at low elevations to high δ13C/late flowering at high elevations, while Asian ecotypes showed the opposite pattern. We mapped different candidate genes for each region, and trait-associated SNPs often showed elevational clines likely maintained by selection. Antioxidants and pigmentation showed regional differentiation but rarely elevational clines. GWAS for antioxidants identified an ascorbate transporterPHT4;4(AT4G00370), which we show alters non-photochemical quenching kinetics under high light and may be involved in local adaptation to Moroccan mountains. The low-antioxidantPHT4;4GWAS allele was associated with lowerPHT4;4expression and this haplotype was characterized by binding sites of a transcription factor family, DOF, involved in light response. Our results highlight how physiological and genomic elevational clines in different regions can be unique, underlining the complexity of local adaptation in widely distributed species.
Influenza infection in ferrets with SARS-CoV-2 infection history
Authors: de Melo Caroline Vilas Boas , Peters Florence , van Dijken Harry , Lenz Stefanie , van de Ven Koen , Wijsman Lisa , Gommersbach Angéla , Schouten Tanja , van Kasteren Puck B. , Judith van den Brand , de Jonge Jørgen 
Published: March 2022

AbstractNon-pharmaceutical interventions (NPIs) to contain the SARS-CoV-2 pandemic drastically reduced human-to-human interactions, decreasing the circulation of other respiratory viruses as well. As a consequence, influenza virus circulation – normally responsible for 3-5 million hospitalizations per year globally – was significantly reduced. With downscaling the NPI countermeasures, there is a concern for increased influenza disease, particularly in individuals suffering from post-acute effects of SARS-CoV-2 infection. To investigate this possibility, we performed a sequential influenza H1N1 infection 4 weeks after an initial SARS-CoV-2 infection in the ferret model. Upon H1N1 infection, ferrets that were previously infected with SARS-CoV-2 showed an increased tendency to develop clinical symptoms compared to the control H1N1 infected animals. Histopathological analysis indicated only a slight increase for type II pneumocyte hyperplasia and bronchitis. The effects of the sequential infection thus appeared minor. However, ferrets were infected with B.1.351-SARS-CoV-2, the beta variant of concern, which replicated poorly in our model. The histopathology of the respiratory organs was mostly resolved 4 weeks after SARS-CoV-2 infection, with only reminiscent histopathological features in the upper respiratory tract. Nevertheless, SARS-CoV-2 specific cellular and humoral responses were observed, confirming an established infection. Thus, there may likely be a SARS-CoV-2 variant-dependent effect on the severity of disease upon a sequential influenza infection as we observed mild effects upon a mild infection. It, however, remains to be determined what the impact is of more virulent SARS-CoV-2 variants.ImportanceDuring the COVID-19 pandemic, the use of face masks, social distancing and isolation were not only effective in decreasing the circulation of SARS-CoV-2, but also in reducing other respiratory viruses such as influenza. With less restrictions, influenza is slowly returning. In the meantime, people still suffering from long-COVID, could be more vulnerable to an influenza virus infection and develop more severe influenza disease. This study provides directions to the effect of a previous SARS-CoV-2 exposure on influenza disease severity in the ferret model. This model is highly valuable to test sequential infections under controlled settings for translation to humans. We could not induce clear long-term COVID-19 effects as SARS-CoV-2 infection in ferrets was mild. However, we still observed a slight increase in influenza disease severity compared to ferrets that had not encountered SARS-CoV-2 before. It may therefore be advisable to include long-COVID patients as a risk group for influenza vaccination.
Does contrast-enhancement improve visualisation of lenticulostriate arteries in cerebral small vessel disease using time-of-flight magnetic resonance angiography at 7 Tesla?
Authors: Osuafor Christopher N. , Rua Catarina , Mackinnon Andrew D. , Egle Marco , Benjamin Philip , Tozer Daniel J. , Rodgers Christopher T. , Markus Hugh S. 
Published: March 2022

AbstractBackground And Purpose7 Tesla-field-strength (7T) Magnetic Resonance Imaging (MRI) allows the small perforating arteries in the brain to be visualised, and this modality may allow visualisation of the arterial pathology in cerebral small vessel disease (cSVD). Most studies have used standard Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA). Whether the use of contrast enhancement improves perforating artery visualisation at 7T remains unclear.Materials And MethodsIn a prospective study, we compared standard ToF MRA with contrast-enhanced (CE) ToF MRA at 7T for the visualisation of the lenticulostriate arteries (LSAs). Ten patients with symptomatic lacunar stroke were recruited (mean age, SD, 64±9.9 years). Visualisation was assessed using a visual rating scale administered by two independent expert readers and length of the LSAs visible.ResultsVisualisation of the LSAs was improved with CE ToF MRA. The mean Visibility and Sharpness Score was higher for CE ToF MRA over standard ToF MRA (2.55±0.64 vs 1.75±0.68; P=0.0008). The mean length of LSA visualised was significantly longer with CE ToF MRA compared to standard ToF MRA (24.4±4.5 vs 21.9±4.0 mm; P=0.01).ConclusionCE ToF MRA offers improved visualisation of the LSAs over standard ToF MRA. The addition of contrast may improve the ability to visualise cerebral small vessel disease arterial pathology.
Microglial Piezo1 senses Aβ fibrils stiffness to restrict Alzheimer’s disease
Authors: Hu Jin , Zhu Hongrui , Yang Qihua , Shen Huidan , Chai Guolin , Zhang Boxin , Chen Shaoxuan , Chen Qiang , Cai Zhiyu , Li Xuewen , Hong Fan , Li Hongda , Hou Lichao , Mo Wei 
Published: March 2022

SummaryThe pathology of Alzheimer’s disease (AD) is associated with the extracellular amyloid-β (Aβ) plaques that perturb the mechanical properties of brain tissue. Microglia sense and integrate biochemical cues in their local microenvironment, intimate linking with AD progress. However, neither the microglial mechanosensing pathway nor its impact on AD pathogenesis is well studied. Here, we showed that the mechanosensitive ion channel Piezo1 is increased in microglia upon stiffness stimuli of Aβ fibrils. The upregulation of Piezo1 in Aβ plaque-associated microglia was observed in AD mouse models and human patients. Microglia lacking Piezo1 disturbed microglial clustering, phagocytosis, and compaction of Aβ plaques, resulting in the exacerbation of Aβ and neurodegenerative pathologies in AD. Conversely, pharmacological activation of Piezo1 ameliorated brain Aβ burden and cognitive impairment in the 5×FAD mouse. Together, our results reveal Piezo1, as a mechanosensor of Aβ fibrils stiffness in microglia, could represent a promising therapeutic target for AD.
Genetics of Fertility Restoration in A1 Cytoplasmic Genetic Male Sterility (CGMS) Systems in Sorghum (Sorghum bicolor L. Moench)
Authors: Narkhede Gopal W , Mehtre Shivaji P , Ingle Krishnananda P , Romana Kirandeep Kaur , Vinutha KS , Deshpande Santosh P 
Published: March 2022

AbstractThe cause of Cytoplasmic Genetic Male Sterility (CGMS) is specific nuclear and mitochondrial interactions. Almost all commercial sorghum hybrids were developed using the A1 cytoplasmic genetic male sterility system. Understanding the inheritance of fertility restoration in sorghum for A1 cytoplasm, for example, can improve the selection efficiency of restorer lines for increased seed production. In a cross of male sterile line 296A with A1 cytoplasm and restorer lines comprised of a set of Recombinant Inbred Lines (RILs), the inheritance pattern of fertility restoration of sorghum was studied. The F1 hybrid was completely fertile, revealing the dominant nature of fertility restoration, which is controlled by one or two major genes with modifiers. In this study, the genetics of fertility restoration of the A1 cytoplasmic nuclear male sterility system (CGMS) in sorghum were investigated in segregating F2 and BC1 populations of A1 cytoplasm crosses. Fertility restoration was governed by a monogenic inheritance (3F:1S) mechanism represented by a single dominant gene responsible for fertility restoration in all of the crosses studied.
Successor-like representation guides the prediction of future events in human visual cortex and hippocampus
Authors: Ekman Matthias , Kusch Sarah , de Lange Floris P. 
Published: March 2022

AbstractHuman agents build models of their environment, which enable them to anticipate and plan upcoming events. However, little is known about the properties of such predictive models. Recently, it has been proposed that hippocampal representations take the form of a predictive map-like structure, the so-called successor representation. Here we used human fMRI to probe whether activity in the early visual cortex (V1) and hippocampus adhere to the postulated properties of the successor representation after visual sequence learning. Participants were exposed to an arbitrary spatiotemporal sequence consisting of four items (A-B-C-D). We found that after repeated exposure to the sequence, merely presenting single sequence items (e.g., - B - -) resulted in V1 activation at the successor locations of the full sequence (e.g., C-D), but not at the predecessor locations (e.g., A). This highlights that visual representations are skewed toward future states, in line with the successor representation. Similar results were also found in the hippocampus. Moreover, the hippocampus developed a tuning profile that showed sensitivity to the temporal distance in sequence-space, with fading representations for sequence events in the more distant past and future. V1, in contrast, showed a tuning profile that was only sensitive to spatial distance in stimulus-space. Together, these results provide empirical evidence for the proposition that both visual and hippocampal cortex represent a predictive map of the visual world akin to the successor representation.
The gender gap in academic career achievements and the mediation effect of work-family conflict and partner support
Authors: Zheng Xiang , Yuan Haimiao , Ni Chaoqun 
Published: March 2022

AbstractParenthood has long been associated with gender disparities in academia. Yet, the underlying mechanism of how parenting is associated with career achievement gaps of academics remains unclear. Using data from a large-scale survey distributed to 7,764 scholars and their publication profiles from the Web of Science database, we analyze the gender differences in parenthood, academic achievements, and the mediation effect of work-family conflict and partner support in these gender gaps. Our results suggest that gender gaps in academic achievements are in fact “parenthood gaps”. Specifically, we found significant gender gaps exist in all measures of objective and subjective career achievements of academics in the parent group but not in the non-parent group. Additionally, mothers are more likely than fathers to experience higher levels of work-family conflict, and receive lower levels of partner support, contributing significantly to the gender gaps in objective and subjective career achievements for the parent group. Findings from this study identify the forms and the impact of parenthood on gender disparities in career achievements of academics and shed light on possible interventions and actions for mitigating gender inequalities in academia.
Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus
Authors: Horta Maria Augusta , Steenwyk Jacob , Mead Matthew E. , dos Santos Luciano H. Braz , Zhao Shu , Gibbons John G. , Marcet-Houben Marina , Gabaldón Toni , Rokas Antonis , Goldman Gustavo H. 
Published: March 2022

AbstractAspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanCore genome of A. fumigatus constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical vs. environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates.ImportanceAspergillus fumigatus is a cosmopolitan species of fungi responsible for thousands of cases of invasive disease. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.
Long-term cellular cargo tracking reveals intricate trafficking through active cytoskeletal networks
Authors: Park Jin-Sung , Lee Il-Buem , Moon Hyeon-Min , Hong Seok-Cheol , Cho Minhaeng 
Published: March 2022

AbstractA eukaryotic cell is a microscopic world within which efficient material transport is essential. To examine cargo transport in a crowded cellular environment, we tracked unlabeled cargos in directional motion in a massively parallel fashion using the interferometric scattering microscopy. Our label-free, cargo-tracing method revealed not only dynamic cargo transportation but also the fine architecture of the actively used cytoskeletal highways and the long-term evolution of the associated traffic at sub-diffraction resolution via a myriad of molecular strokes. Cargos experience a traffic jam, but they have an effective strategy to circumvent it: moving together in tandem or migrating collectively. All taken together, a cell is an incredibly complex and busy space where the principle and practice in transportation intriguingly parallel those of our macroscopic world.
International comparison of the impact of the pandemic and vaccination measures adopted on children and adolescent population
Authors: Rajmil Luis , Pinzón-Segura María-Camila , Yaw Appiah Seth Christopher , Ekpenyong Bernadine , González Fernando , Gündoğdu Zuhal , Oncel Selim , Çakıcı Özlem 
Published: March 2022

AbstractBackgroundThe objectives of this study were to compare the cumulative incidence, hospitalizations and mortality, by country and age group, in child and young people (CYP) from the beginning of the pandemic to January 2022, and to describe the differences and similarities and justification in the measures adopted in relation to CYP vaccination against SARS-CoV-2.MethodsA descriptive quantitative summary of the available data on the impact of the COVID-19 on children and adolescents (<18y) from 7 countries (Chile, Colombia, Paraguay, Nigeria, Ghana, Spain) or regions (Kocaeli, Turkey), based on official published data was performed. Outcome measures were: available data on incidence, admission to hospital and to intensive care units (ICU), and deaths, by country or region; vaccination plans, including age, type of vaccine and official justification about the proposal.ResultsAll countries analyzed data showed variable incidence rate, and relatively low ICU hospitalizations and deaths. Vaccines used and age at starting were also variable, i.e. starting at 3-5y in some Latin American countries, while in other countries proposal starts at 15y old. Almost all justifications were based on the idea to promote collective protection, and that vaccination is important as it -directly and indirectly-protect the rest of the population.ConclusionsThe results reinforce the idea of the urgent need to prioritize globally and equitably distribution of vaccines in the population at greatest risk, and to apply the precautionary principle in CYP before deciding to massively vaccinate it.What is knownThe child population has less severe infections and seems to transmit the infection less than the adult population.Published data from the Randomized Clinical Trials (RCT) of vaccines in minors presented short follow-up than in the adult population and basically studied the incidence of infection as the main endpointWhat this study addsMortality in the child population due to COVID-19 since the start of the pandemic has been low in all the countries analyzedThe vaccines used as well as the vaccination guidelines shows high variability in these countriesThe results of the study reinforce the need to establish global and equitable mechanisms for the distribution of vaccines and prioritize the population at greatest risk, such as older people.In the child population, it is necessary to apply the precautionary principle before establishing massive vaccination plans