bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deterministic processes played more important roles than stochastic processes in driving community assembly of ectomycorrhizal fungal associated withPinus tabuliformis –an endemic Pinaceae species in China
Authors: Fan Yongjun , Yu Zhimin , Li Jinyan , Zhang Xuan , Li Min , Ma Jianjun , Wang Yonglong 
Published: July 2024

AbstractPinus tabuliformisrepresents a typical and essential woody ectomycorrhizae (EM) host plant growing in North China. EM fungi contribute to the host healthy and the stability of the forest ecosystem. However, EM fungal community associated with this tree is less documented. We examined EM fungal diversity and composition ofP. tabuliformisfrom three sites in Inner Mongolia, China by using Illumina MiSeq sequencing on the rDNA ITS2 region. Our results showed that a total of 105 EM fungal operational taxonomic units (OTUs) were identified from 15 composite root samples, and the dominant lineages were /suillus-rhizopogon, /tomentella-thelephora, /tricholoma, /amphinema-tylospora, /wilcoxina, /inocybeand /Sebacina. A high proportion of unique EM fungal OTUs were detected and some abundant OTUs preferred to exist in specific sites. EM fungal communities were significantly different among the sites, with soil, climatic and spatial variables being responsible for the community variations. The EM fungal community assembly was mainly governed by deterministic processes. These findings suggest that this endemic Pinaceae species in China also harbored a rich and distinctive EM fungal community and deterministic processes played more important roles than stochastic in shaping the symbiotic fungal community. Our study improves our understanding of EM fungal diversity and community structure from the perspective of a single host plant that has not been investigated exclusively before.
VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization
Authors: Yang Ziyue , Shan Yongtao , Liu Xue , Chen Guowei , Pan Yuanfei , Gou Qinyu , Zou Jie , Chang Zilong , Zeng Qiang , Yang Chunhui , Kong Jianbin , Sun Yanni , Li Shaochuan , Zhang Xu , Wu Wei Chen , Li Chunmei , Peng Hong , Holmes Edward C. , Guo Deyin , Shi Mang 
Published: July 2024

AbstractRNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase (RdRP) database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identity RNA viruses of all type, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.
Drivers of recovery and degradation of riverine benthic macroinvertebrate communities: A nationwide analysis of time series
Authors: Schürings Christian , Kaijser Willem , Gillmann Svenja , Peters Kristin , Kiesel Jens , Lorenz Armin W. , Hering Daniel 
Published: July 2024

AbstractIn response to the global freshwater biodiversity crisis this study examines the drivers, influencing recovery and degradation in riverine benthic macroinvertebrate communities across Germany. Utilizing the Asymmetric Response Concept (ARC), which posits that species tolerances to stressors, dispersal capacity, and biotic interactions are critical drivers in aquatic ecosystem recovery, we analyzed a comprehensive dataset from 1568 sites, sampled between 2004 and 2022. Our findings indicate that abiotic stress consistently influences ecological status in both recovery and degradation phases. Interspecific competition shows a stronger positive relationship with ecological status improvements during recovery phases than during degradation, underscoring its importance in the recovery process. Additionally, land use intensity has a nuanced impact: catchments with higher proportions of cropland and urban areas are more likely to recover, while forested catchments are more prone to degradation. This study supports the ARC and highlights the complex interplay of biotic and abiotic variables in shaping ecological outcomes, underscoring the importance of integrated management approaches in freshwater conservation and restoration efforts.
Reconstructing the phylogeny and evolutionary history of freshwater fishes (Nemacheilidae) across Eurasia since early Eocene
Authors: Šlechtová Vendula , Dvořák Tomáš , Freyhof Jörg , Kottelat Maurice , Levin Boris , Golubtsov Alexander , Šlechta Vlastimil , Bohlen Jörg 
Published: July 2024

AbstractEurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic era, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic era on the base of 471 specimens representing 279 species and 37 genera. Molecular phylogeny using 6 genes uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 million years ago. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.
Novel quantal analysis method reveals conservation of average excitatory synaptic charge across cortical pyramidal neurons of different sizes
Authors: Dervinis Martynas , Major Guy 
Published: July 2024

AbstractIn chemical synapses of the central nervous system (CNS), information is transmitted via the presynaptic release of a vesicle (or ‘quantum’) of neurotransmitter, which elicits a postsynaptic electrical response with an amplitude termed the ‘quantal size’. Measuring amplitudes of miniature postsynaptic currents (mPSCs) or potentials (mPSPs) at the cell soma is generally thought to offer a technically straightforward way to estimate quantal sizes, as each of these miniature responses (minis) is generally thought to be elicited by the spontaneous release of a single neurotransmitter vesicle. However, in large highly-branched neurons, a somatically recorded mini is typically massively attenuated compared with at its input site, and a significant fraction are indistinguishable from (or cancelled out by) background noise fluctuations. Here, using a new software package called ‘minis’, we describe a novel quantal analysis method that estimates the ‘electrical size’ of the synapse by comparing events detected in somatic recordings from the same neuron of (a)realminis and (b) background noise (minis blocked pharmacologically) withsimulatedminis added by a genetic algorithm. The estimated minis’ distributions reveal a striking inverse dependence of mean excitatory mPSP amplitude on total cell capacitance (proportional to cell size, more exactly, extracellular membrane surface area) suggesting that, in rats at least, the average charge (ca. 30 fC) injected by excitatory synapses is conserved across neocortical pyramidal neurons of different sizes.
Force monitoring reveals single trial dynamics of motor control in a stop signal task
Authors: Ramawat Surabhi , Marc Isabel B , Di Bello Fabio , Bardella Giampiero , Ferraina Stefano , Pani Pierpaolo , Brunamonti Emiliano 
Published: July 2024

ABSTRACTThe Stop Signal Task (SST) has been the benchmark for studying the behavioral and physiological basis of movement generation and inhibition. In our study, we extended the scope beyond physiological findings related to muscle activity, focusing our analysis on the initial biomechanical state of the effector. By incorporating a force sensitive resistor (FSR), we continuously monitored the force applied by the effector (here the index finger) during a button release version of the SST. This modified task design allowed us to examine both the baseline force before the relevant Go signal was presented and during the covert state of movement preparation. Notably, variations in force over time in response to the Go signal revealed differences across trials where movement was either generated or successfully inhibited, depending on the amount of force during the baseline period. Specifically, higher baseline force was associated with a delayed movement generation, which simultaneously slowed down the force release, facilitating successful inhibition when requested. Our results highlight the influence of biomechanical variables in movement control, which should be accounted for by the models developed for investigating the physiology of this ability.NEW & NOTEWORTHYMovement involves changing the position of anatomical effectors, like a finger. The initial biomechanical state of an effector impacts movement generation and inhibition. Using the Stop-Signal task, we studied these factors by measuring the force applied to a mouse button before movement onset. Higher initial force delayed movement generation and slowed force release, aiding movement inhibition. This research links behavioral models of action-stopping with movement biomechanics, highlighting the effector’s initial state importance.
Modeling immunoglobulin light chain amyloidosis inCaenorhabditis elegans
Authors: Romeo Margherita , Barzago Maria Monica , Corbelli Alessandro , Maglioni Silvia , Ventura Natascia , Natale Carmina , Conz Andrea , Salmona Mario , Palladini Giovanni , Nuvolone Mario , Fiordaliso Fabio , Merlini Giampaolo , Diomede Luisa 
Published: July 2024

AbstractCardiomyopathy determines the prognosis of patients with immunoglobulin light chain (AL) amyloidosis, a rare systemic disease caused by the misfolding and deposition of monoclonal light chains (LCs). The reasons underlining their cardiac tropism remain unknown, and an animal model recapitulating the main pathological features of AL amyloidosis is instrumental. Taking advantage of the similarities between the vertebrate heart andC. elegans’ pharynx, we developed a new transgenic nematode expressing a human amyloidogenic λ LC whose sequence was deduced from a patient suffering from AL amyloidosis with cardiac involvement (MNH). Strains expressing a non-amyloidogenic LC (MNM) or the empty vector only (MNV) were generated as controls. At variance with controls, LCs expressed in the body-wall muscle of MNH worms formed native soluble dimeric assemblies, which were secreted and reached different organs, including the pharynx. Noteworthy, MNH worms exerted a pharyngeal impairment resembling cardiac functional impairment occurring in patients with AL, accompanied by increased radical oxygen species production and tissue ultrastructural damage. This new animal model can allow the elucidation of the mechanisms underlying the cardiac-specific tropism occurring in AL amyloidosis, providing innovative insights into the pathophysiology.
Probing tau citrullination in Alzheimer’s disease brains and mouse models of tauopathy
Authors: Liang Huimin , Hunt Jerry B. , Ma Chao , Kovalenko Andrii , Calahatian John , Pedersen Cecelie , Lui Haiying , Li Junyan , Serrano Malina , Blazier Danielle , Watler Mallory , Rocha-Rangel Patricia , Saunders Christopher , Blair Laura J. , Breydo Leonid , Nash Kevin , Quadri Zainuddin , Kraemer Brian , Nelson Peter , Norris Christopher , Abner Erin L. , Uversky Vladimir N. , Chaput Dale , Selenica Maj-Linda B. , Lee Daniel C. 
Published: July 2024

AbstractTauopathies, which include Alzheimer’s disease (AD) share a common defining factor, namely misfolded tau protein. However, the “upstream” etiology and downstream clinical manifestations of tauopathies are quite diverse. Tau deposition elicits different pathological phenotypes and outcomes depending on the tau strain and regional susceptibility. Posttranslational modifications (PTM) can alter tau structure, function, networks, and its pathological sequalae. We uncovered a novel PTM of tau, named citrullination, caused by peptidyl arginine deiminase (PAD) enzymes. PAD induced citrullination irreversibly converts arginine residues to citrulline, producing net loss of positive charge, elimination of pi-pi interactions, and increased hydrophobicity. We observed increased PAD2 and PAD4 in Alzheimer’s disease (AD) brain and that they both can citrullinate tau. Tau can become citrullinated by PADs at all 14 arginine residues throughout the N-terminal domain (N-term), proline-rich domain (PR), microtubule binding repeat domain (MBR), and C-terminal domain (C-term) on full length tau (2N4R). Citrullination of tau impacts fibrillization and oligomerization rates in aggregation assays. Utilizing a panel of novel citrullinated tau (citR tau) antibodies, we identified citrullination of tauin vitro, several animal models of tauopathies, and Alzheimer’s disease (AD). CitR tau increased with Braak stage and was enriched in AD brains with higher phospho-tau burden. This work provides a new area of tau biology that signifies further consideration in the emerging spectrum of tauopathies and its clinical understanding.
Representation of visual uniformity in the lateral prefrontal cortex
Authors: Ge Yijun , Taschereau-Dumouchel Vincent , Lin Qi , Moharramipour Ali , Sun Zhouyuan , Lau Hakwan 
Published: July 2024

AbstractVisual illusions tend to have early visual cortical correlates. However, this general trend may not apply to our subjective impression of a detailed and uniform visual world, which may be considered illusory given the paucity of peripheral processing. Using a psychophysically calibrated visual illusion, we assessed the patterns of hemodynamic activity in the human brain that distinguished between the illusory percept of uniformity in the periphery (i.e., Gabor patches having identical orientations) from the accurate perception of incoherence. We identified voxel patterns in the lateral prefrontal cortex that predicted perceived uniformity, which could also generalize to scene uniformity in naturalistic movies. Because similar representations of visual uniformity can also be found in the intermediate and late layers of a feedforward convolutional neural network, the perception of uniformity may involve high-level coding of abstract properties of the entire scene as a whole, that is distinct from the filling-in of specific details in early visual areas.
A pumpless and tubeless microfluidic device enables extendedin vitrodevelopment ofCryptosporidium parvum
Authors: Gunasekera Samantha , Thierry Benjamin , Cheah Edward , King Brendon , Monis Paul , Carr Jillian M. , Chopra Abha , Watson Mark , O’Dea Mark , Ryan Una 
Published: July 2024

AbstractThe enteric parasiteCryptosporidiumremains a treatment challenge for drinking water utilities globally due to its resistance to chlorine disinfection. However, the lack of anin vitroculture system forCryptosporidiumthat is both cost-effective and reliable remains a key bottleneck inCryptosporidiumresearch. Here we report that the microfluidic culture of HCT-8 cells under fluid shear stress enables the extended development ofCryptosporidium parvum. Specifically, the growth ofC. parvumin a user-friendly pumpless microfluidic device was assessed using immunofluorescence assays, scanning electron microscopy and quantitative PCR, which revealed that development peaked at six days post-infection but continued for ten days in total. Oocysts produced within the microfluidic device were infective to fresh HCT-8 monolayers, however these oocysts were only present at low levels. We anticipate that such microfluidic approaches will facilitate a wide range ofin vitrostudies onCryptosporidiumand may have the potential to be further developed as a routine infectivity assessment tool for the water industry.
Influence of Information Access on Organ Donation: A Questionnaire-Based Cross-Sectional Study
Authors: Costaguta Guillermo A. , Romero Andrea , Costaguta Alejandro C. 
Published: July 2024

ABSTRACTIntroductionOrgan transplantation is the sole effective treatment for end-stage organ diseases. However, the availability of donor organs remains insufficient. This shortage is driven by several factors, with access to accurate information being the key determinant of an individual’s willingness to donate organs.MethodsA cross-sectional study based on anonymous surveys conducted from January to December 2019, categorizing participants into healthcare professionals and non-healthcare individuals. Data included willingness to donate organs, reasons for refusal, age, education level, and understanding of brain death. Statistical significance was set at p<0.05.ResultsA total of 408 participants were included: 203 in the healthcare sector and 205 in the non-healthcare sector. Among healthcare professionals, 90% were willing to donate organs compared to 43% in the non-healthcare group (p<0.001). Non-healthcare respondents refused due to the fear of being alive during organ removal (74%), concerns about reduced emergency care (21%), and religious beliefs (5%). Despite these concerns, 88% acknowledged that organ donation saves lives and 95% recognized the gap between organ supply and demand. No significant differences in education levels were found between donors and non-donors, but healthcare professionals had a significantly better understanding of brain death (p<0.001). All respondents indicated that they would accept a donated organ, if needed.ConclusionHealthcare professionals are more inclined to be organ donors than are those outside the field. Misunderstandings among non-healthcare individuals contributed to higher refusal rates. Tailored awareness campaigns and educational programs could rectify these misconceptions, potentially improving donation rates and mitigating organ shortage crises.
Tall women with breast cancer have poorer survival than short women
Authors: Lehrer Steven , Rheinstein Peter H. 
Published: July 2024

AbstractBackgroundTall women are more likely to develop breast cancer (BC). High Mobility Group AT-Hook 1(HMGA1), an oncofetal protein, plays a role in the progression of breast cancer. Non-coding sequences proximal to HMGA1 contain variants associated with 4.83 cm taller height. In the current study, we used UK Biobank data to examine the relationship of HMGA1 to height, risk, and prognosis of women with breast cancer.MethodsOur analysis included all subjects with invasive BC that occurred either before or after participant enrollment and were recorded in the UK Biobank database using self-reported data and the International Classification of Diseases (ICD10, ICD9). We divided the subjects into three previously described three height groups: Short (< 155 cm), Medium (155 cm to 175 cm), Tall (> 175 cm). We analyzed the HMGA1 SNP rs41269028, a single nucleotide intron variant, C > T, minor allele frequency 0.044. SNP rs41269028 was previously evaluated in subjects with diabetes.ResultsHeight of 9583 women with BC homozygous for the HMGA1 SNP rs41269028 major allele was 162.29 cm ± 6.18. Height of 944 women with BC who were carriers or homozygotes (CT + TT) of the minor allele T was 162.88 cm ± 6.001. This difference was significant (p = 0.005). The effect of height group on survival was significant (p = 0.032, log rank test). Tall women had the poorest survival. The effect of HMGA1 SNP rs41269028 genotype on BC risk (p = 0.602) and survival (p = 0.439, log rank test) was insignificant.ConclusionWe conclude that HMGA1 influences height, but we were unable to demonstrate that HMGA1 is related to increased incidence or poor prognosis of tall women with breast cancer. We did find that tall women with breast cancer have poorer survival than short women. Our finding that tall women have a worse prognosis is important because it could help the oncologist decide, along with other prognostic factors, whether adjuvant therapy is warranted.
Scoping review of Japanese encephalitis virus transmission models
Authors: Laidlow Troy A. , Johnston Erin S. , Zadoks Ruth N. , Walsh Michael , Viana Mafalda , Wiley Kerrie E. , Singh Balbir B. , Baldini Francesco , Dhanze Himani , Webb Cameron , Brookes Victoria J. 
Published: July 2024

AbstractJapanese encephalitis virus (JEV) causes approximately 100,000 clinical cases and 25,000 deaths annually worldwide, mainly in South-East Asia and the Western Pacific and mostly in children. JEV is transmitted from competent hosts to humans through the bite of mosquitoes, and the abiotic environment, such as seasonal rainfall, influences transmission. Transmission models have an important role in understanding disease dynamics and developing prevention and control strategies to limit the impact of infectious diseases. Our goal was to investigate how transmission models capture JEV infection dynamics and their role in predicting and controlling infection. This was achieved by identifying published JEV transmission models, describing their features, and identifying their limitations, to guide future modelling. A PRISMA-ScR guided scoping review of peer-reviewed JEV transmission models was conducted. Databases searched included PubMed, ProQuest, Scopus, Web of Science and Google Scholar. Of 881 full text papers available in English, 29 were eligible for data extraction. Publication year ranged from 1975 to 2023. The median number of host populations represented in each model was 3 (range: 1–8; usually humans, mosquitoes and pigs). Most (72% [n=21]) models were deterministic, using ordinary differential equations to describe transmission. Ten models were applied (representing a real JEV transmission setting) and validated with field data, while the remaining 19 models were theoretical. In the applied models, data from only a small proportion of countries in South-East Asia and the Western Pacific were used. Limitations included gaps in knowledge of local JEV epidemiology, vector attributes and the impact of prevention and control strategies, along with a lack of model validation with field data. The lack and limitations of models highlight that further research to understand JEV epidemiology is needed and that there is opportunity to develop and implement applied models to improve control strategies for at-risk populations of animals and humans.