bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synaptotagmin 7 docks synaptic vesicles to support facilitation and Doc2α-triggered asynchronous release
Authors: Wu Zhenyong , Kusick Grant F. , Berns Manon M. M. , Raychaudhuri Sumana , Itoh Kie , Walter Alexander M. , Chapman Edwin R. , Watanabe Shigeki 
Published: May 2022

AbstractDespite decades of intense study, the molecular basis of asynchronous neurotransmitter release remains enigmatic. Synaptotagmin (syt) 7 and Doc2 have both been proposed as Ca2+sensors that trigger this mode of exocytosis, but conflicting findings have led to controversy. Here, we demonstrate that at excitatory mouse hippocampal synapses, Doc2α is the major Ca2+sensor for asynchronous release, while syt7 supports this process through activity-dependent docking of synaptic vesicles. In synapses lacking Doc2α, asynchronous release after single action potentials is strongly reduced, while deleting syt7 has no effect. However, in the absence of syt7, docked vesicles cannot be replenished on millisecond timescales. Consequently, both synchronous and asynchronous release depress from the second pulse onward during repetitive activity. By contrast, synapses lacking Doc2α have normal activity-dependent docking, but continue to exhibit decreased asynchronous release after multiple stimuli. Moreover, disruption of both Ca2+sensors is non-additive. These findings result in a new model whereby syt7 drives activity-dependent docking, thus providing synaptic vesicles for synchronous (syt1) and asynchronous (Doc2 and other unidentified sensors) release during ongoing transmission.
Does fatigue influence joint-specific work and ground force production during the first steps of maximal accelerative running?
Authors: Vial Shayne , Wilkie Jodie Cochrane , Turner Mitchell , Scanlan Mark , Blazevich Anthony J. 
Published: May 2022

ABSTRACTThe rate of initial acceleration during the first steps of a maximal-effort (sprint) run often determines success or failure in prey capture and predator evasion, and is a vital factor of success in many modern sports. However, accelerative events are commonly performed after having already run considerable distances, and the associated fatigue should impair muscle force production and thus reduce acceleration rate. Despite this, the effects of running-induced fatigue on our ability to accelerate as well as the running technique used to achieve it has been incompletely studied. We recorded 3-D kinematics and ground reaction forces during the first three steps of the acceleration phase from a standing start before and after performing a high-speed, multi-directional, fatiguing run-walk protocol in well-trained running athletes who were habituated to accelerative sprinting. We found that the athletes were able to maintain their rate of initial acceleration despite changing running technique, which was associated with use of a more upright posture, longer ground contact time, increased vertical ground reaction impulse, decreased hip flexion and extension velocities, and a shift in peak joint moments, power, and positive work from the hip to the knee joint; no changes were detected in ankle joint function. Thus, a compensatory increase in knee joint function alleviated the reduction in hip flexor-extensor capacity. These acute adaptations may indicate that the hip extensors (gluteal and hamstring muscle groups) were more susceptible to fatigue than the ankle and knee musculature, and may thus be a primary target for interventions promoting fatigue resistance.
Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory
Authors: Katriel Guy , Mahanaymi Udi , Koutschan Christoph , Zeilberger Doron , Steel Mike , Snir Sagi 
Published: May 2022

AbstractThe genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analysing the point mutations of standard markers is too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics events provide far richer information. The synteny index (SI) between a pair of genomes combines gene order and gene content information, allowing the comparison of genomes of unequal gene content, together with order considerations of their common genes. Recently, genome dynamics has been modelled as a continuous-time Markov process, and gene distance in the genome as a birth–death–immigration process. Nevertheless, due to complexities arising in this setting such as overlapping neighbourhoods and other confounding factors, no precise and provably consistent estimators could be derived.Here, we extend this modelling approach by using techniques from birth–death theory to derive explicit expressions of the system’s probabilistic dynamics in the form of rational functions of the model parameters. This, in turn, allows us to infer analytically the expected distances between organisms based on a transformation of their SI. Despite the complexity of the expressions obtained, we establish additivity of this estimated evolutionary distance (a desirable property yielding phylogenetic consistency).Applying the new measure in simulation studies shows that it attains very accurate results in realistic settings and even under model extensions. In the real-data realm, we applied the new formulation to unique data structure that we constructed - the ordered orthology DB - based on a new version of the EggNOG database, to construct a tree with more than 4.5K taxa. The resulted tree was compared it with a NCBI taxonomy for these organisms. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes flaws found in previous approaches.
Predicting past and future SARS-CoV-2-related sick leave using discrete time Markov modelling
Authors: Lei Jiayao , Clements Mark , Elfström Miriam , Lundgren Kalle Conneryd , Dillner Joakim 
Published: May 2022

AbstractBackgroundPrediction of SARS-CoV-2-induced sick leave among healthcare workers (HCWs) is essential for being able to plan the healthcare response to the epidemic.MethodsDuring first wave of the SARS-Cov-2 epidemic (April 23rd to June 24th, 2020), the HCWs in the greater Stockholm region in Sweden were invited to a study of past or present SARS-CoV-2 infection. We develop a discrete time Markov model using a cohort of 9449 healthcare workers (HCWs) who had complete data on SARS-CoV-2 RNA and antibodies as well as sick leave data for the calendar year 2020. The one-week and standardized longer term transition probabilities of sick leave and the ratios of the standardized probabilities for the baseline covariate distribution were compared with the referent period (an independent period when there were no SARS-CoV-2 infections) in relation to PCR results, serology results and gender.ResultsThe one-week probabilities of transitioning from healthy to partial sick leave or full sick leave during the outbreak as compared to after the outbreak were highest for healthy HCWs testing positive for large amounts of virus (3.69, (95% confidence interval, CI: 2.44-5.59) and 6.67 (95% CI: 1.58-28.13), respectively). The proportion of all sick leaves attributed to COVID-19 during outbreak was at most 55% (95% CI: 50%-59%).ConclusionsA robust Markov model enabled use of simple SARS-CoV-2 testing data for quantifying past and future COVID-related sick leave among HCWs, which can serve as a basis for planning of healthcare during outbreaks.
Will The Grass Be Greener On The Other Side Of Climate Change?
Authors: Morris Craig D , Kirkman Kevin P , Zacharias Pete JK 
Published: May 2022

ABSTRACTIncreasing atmospheric [CO2] is stimulating photosynthesis and plant production, increasing the demand for nitrogen relative to soil supply with declining global foliar nitrogen concentrations as a consequence. The effect of such oligotrophication on the forage quality of sweetveld, mixedveld, and sourveld grasslands in South Africa, which support livestock production and native ungulates, are unknown. Soil characteristics and the herbage quality of an abundant grass are described from baseline historical (mid 1980s) data collected across a sweet-mixed-sour grassland gradient in KwaZulu-Natal. Sourveld occurred on the most acidic, dystrophic soils and exhibited a pronounced decline in leaf N, digestibility, and other macronutrients during winter, in sharp contrast to sweetveld, on nutrient-rich soils, where forage quality varied little seasonally. In a carbon enriched, warmer, and most likely drier future climate, we predict that forage quality will be little altered in sweetveld where soil nutrients and temperature are not limiting but that sourveld could become ‘sourer’ because soil nutrients will be inadequate to match higher plant production promoted by elevated [CO2] and warmer and longer growing seasons. Reassessing historical data and seasonal and spatial monitoring of forage quality will enable past and future impacts of climate change on grassland forage quality to be assessed.SignificanceGrassland forage quality will likely decline with elevated [CO2] and warming, particularly in sourveld.Climate change could deepen and widen the sourveld winter forage bottleneck, necessitating greater supplementary feeding of livestock.
Exceptional yield vesicle packaged recombinant protein production from E. coli
Authors: Eastwood Tara A. , Baker Karen , Streather Bree R. , Allen Nyasha , Wang Lin , Botchway Stanley W. , Brown Ian R. , Hiscock Jennifer R. , Lennon Christopher , Mulvihill Daniel P. 
Published: May 2022

SummaryWe describe a novel system that exports diverse recombinant proteins in extracellular vesicles from E. coli. The vesicles not only compartmentalise toxic, insoluble and disulphide bond containing proteins in a soluble and functional form (e.g. DNaseI, nanobodies and IgG-fusions), but the continued release of the inducible vesicle packaged proteins into the media supports continuous isolation of protein from active culture within a micro-environment allowing stable long-term storage. This technology results in unprecedented yields of vesicle packaged functional proteins for efficient downstream processing for a wide range of applications from discovery science to applied biotechnology and medicine.
A revised phylogenetic classification forViola(Violaceae)
Authors: Marcussen Thomas , Ballard Harvey E. , Danihelka Jiří , Flores Ana R. , Nicola Marcela V. , Watson John M. 
Published: May 2022

AbstractThe genusViola(Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then known 400 species were distributed among 14 sections and numerous unranked groups. Here we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species ofViola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We subdivide the 658 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus ofViola(subg.Neoandinium, a replacement name for the illegitimate subg.Andinium), six new sections (sect.Abyssinium, sect.Himalayum, sect.Melvio, sect.Nematocaulon, sect.Spathulidium, sect.Xanthidium), and seven new subsections (subsect.Australasiaticae, subsect.Bulbosae, subsect.Clausenianae, subsect.Cleistogamae, subsect.Dispares, subsect.Formosanae, subsect.Pseudorupestres). Evolution within the genus is discussed in light of biogeography, fossil record, morphology, and particular traits.Violais among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps forViolaconcern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent.Violahas also never been subject to comprehensive anatomical study. Study on seed anatomy and morphology is required to understand the fossil record of the genus.
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
Authors: Ezzamouri Bouchra , Rosario Dorines , Bidkori Gholamreza , Lee Sunjae , Uhlen Mathias , Shoaie Saeed 
Published: May 2022

AbstractThe human gut microbiome has been associated with several metabolic disorders including type 2 diabetes. Understanding metabolic changes in the gut microbiome is important to elucidate the role of gut bacteria in regulating host metabolism. Here, we used available metagenomics data from a metformin study, together with genome-scale metabolic modelling of the key bacteria in individual and community-level to investigate the mechanistic role of the gut microbiome in response to metformin. Individual modelling predicted that species that are increased after metformin treatment have higher growth rates in comparison to species that are decreased after metformin treatment. Gut microbial enrichment analysis showed prior to metformin treatment pathways related to the hypoglycemic effect were enriched. Our observations highlight how the key bacterial species after metformin treatment have commensal and competing behavior, and how their cellular metabolism changes due to different nutritional environment. Integrating different diets showed there were specific microbial alterations between different diets. These results show the importance of the nutritional environment and how the dietary guidelines may improve drug efficiency through the gut microbiota.
A retrospective molecular investigation of selected pigeon viruses between 2018-2021 in Turkey
Authors: Sahindokuyucu Ismail , Yazici Zafer , Barry Gerald 
Published: May 2022

AbstractA recent first detection of pigeon aviadenovirus-1 and pigeon circovirus co-infection associated with Young Pigeon Disease Syndrome (YPDS) in a pigeon flock in Turkey, prompted a study focused on documenting the distribution of Pigeon aviadenovirus (PiAdV-1 and PiAdV-2), Pigeon circovirus (PiCV), Columbid alphaherpesvirus 1 (pigeon herpesvirus (PiHV)) and Fowl aviadenovirus (FAdV) in the country. These viruses were selected as they are associated with severe disease in pigeons across the world. A total of 192 cloacal swabs were collected from young (<1 year old) pigeons from 16 different private pigeon flocks across Turkey, between 2018 and 2021 as part of routine diagnostic sampling. PiCV genetic material was the most frequently detected 4/16 (25%), PiAdV-1 and CoHV-1 DNA were both found in one flock each, while neither PiAdV-2 and FAdV were detected in any of the studied pigeon flocks. PiCV and PiHV genetic material were both detected in the same pigeon flock’s cloacal samples as a co-infection with the identification of PiHV being a first in Turkey.
Synapses learn to utilize pre-synaptic noise for the prediction of postsynaptic dynamics
Authors: Kappel David , Tetzlaff Christian 
Published: May 2022

AbstractSynapses in the brain are highly noisy, which leads to a large trial-by-trial variability. Given how costly synapses are in terms of energy consumption these high levels of noise are surprising. Here we propose that synapses use their noise to represent uncertainties about the activity of the post-synaptic neuron. To show this we utilize the free-energy principle (FEP), a well-established theoretical framework to describe the ability of organisms to self-organize and survive in uncertain environments. This principle provides insights on multiple scales, from high-level behavioral functions such as attention or foraging, to the dynamics of single microcircuits in the brain, suggesting that the FEP can be used to describe all levels of brain function. The synapse-centric account of the FEP that is pursued here, suggests that synapses form an internal model of the somatic membrane dynamics, being updated by a synaptic learning rule that resembles experimentally well-established LTP/LTD mechanisms. This approach entails that a synapse utilizes noisy processes like stochastic synaptic release to also encode its uncertainty about the state of the somatic potential. Although each synapse strives for predicting the somatic dynamics of its neuron, we show that the emergent dynamics of many synapses in a neuronal network resolve different learning problems such as pattern classification or closed-loop control in a dynamic environment. Hereby, synapses coordinate their noise processes to represent and utilize uncertainties on the network level in behaviorally ambiguous situations.
Anatomical and Palynological Investigation within flora of Family Asteraceae
Authors: Shahzad Asim , Iqbal Shahid , Kayani Sadaf , Shafiq Tayyab , Zafar Muhammad , Naeem Muhammad , Yasmin Humaira 
Published: May 2022

ABSTRACTA comprehensive microscopic investigation of the leaf epidermis, as well as anatomical and palynological research of selected Asteraceae species from the flora of Havali (Kahutta) Azad Jammu and Kashmir (AJK) Pakistan, was carried out. This study includes 11 plant species comprising of Senecio jacobea, Leucanthemum vulgare, Halianthus annuus, Erigeron bonariensis, Achillea millifolium, Halianthus Linnaeus, Taraxacum officinale, Anaphalius nepalensis, Erigeron Canadensis, and Tagetes erecta. All the species studied were amphistomatic, with four different forms of stomata i.e tetracytic, anomocytic, anisocytic, and tricytic. The main stomatal type was tetracytic, followed by anomocytic. The abaxial epidermis has a higher stomatal density than the adaxial epidermis. Highest stomatal density was present Tagetes erecta while lowest is present in Conyza canadensis. In lower epidermis stomatal index was higher in Taraxacum officinale followed by Halianthus annuus and Tagetes erecta while in upper epidermis highest index was shown by Halianthus annuus. For this study species of family Acteraceae were properly collected. Furthermore, variation in pollen can be seen. List of palynomorph which includes family name, botanical name, local name, English name, flower colour, season and pollen description for the logical arrangement of these species. The logical ordering of these species was guided by dust characteristics such as form and pollen morphology. Palynological data has been found to be too big for taxonomists to calculate and make appropriate observations on their findings.
Dual RNA-seq reveals a type 6 secretion system-dependent blockage of TNF-α signaling and BicA as a Burkholderia pseudomallei virulence factor important during gastrointestinal infection
Authors: Sanchez-Villamil Javier I. , Tapia Daniel , Khakum Nittaya , Widen Steven G. , Torres Alfredo G. 
Published: May 2022

AbstractMelioidosis is a disease caused by the Gram-negative bacillus Burkholderia pseudomallei (Bpm), commonly found in soil and water of endemic areas. Naturally acquired human melioidosis infections can result from either exposure through percutaneous inoculation, inhalation, or ingestion of soil-contaminated food or water. Our prior studies recognized Bpm as an effective enteric pathogen, capable of establishing acute or chronic gastrointestinal infections following oral inoculation. However, the specific mechanisms and virulence factors involved in the pathogenesis of Bpm during intestinal infection are unknown. In our current study, we standardized an in vitro intestinal infection model using primary intestinal epithelial cells (IECs) and demonstrated that Bpm requires a functional T6SS for full virulence. Further, we performed dual RNA-seq analysis on Bpm-infected IECs to evaluate differentially expressed host and bacterial genes in the presence or absence of a T6SS. Our results showed a dysregulation in the TNF-α signaling via NF-κB pathway in the absence of the T6SS, with some of the genes involved in inflammatory processes and cell death also affected. Analysis of the bacterial transcriptome identified virulence factors and regulatory proteins playing a role during infection, with association to the T6SS. By using a Bpm transposon mutant library and isogenic mutants, we showed that deletion of the bicA gene, encoding a putative T3SS/T6SS regulator, ablated intracellular survival and plaque formation by Bpm and impacted survival and virulence when using murine models of acute and chronic gastrointestinal infection. Overall, these results highlight the importance of the type 6 secretion system in the gastrointestinal pathogenesis of Bpm.
A revisit to universal single-copy genes in bacterial genomes
Authors: Wang Saidi , Ventolero Minerva , Hu Haiyan , Li Xiaoman 
Published: May 2022

AbstractUniversal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated bacterial RefSeq genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study shed new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.