bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of pesticides in European water and relationship for public health: A protocol for systematic review and meta-analysis
Authors: Valera Manuel Serrano , Vela Nuria , Piuvezam Grasiela , Mateo-Ramírez Francisco , Fernandes Pimenta Isaac Davidson Santiago , Martínez-Alcalá Isabel 
Published: February 2023

AbstractBackgroundThere is currently a growing interest in the so-called emerging pollutants, such as pesticides, pharmaceuticals, personal hygiene care products, drugs, etc., whose presence in natural ecosystems is not necessarily recent, but the development in latest years of new and more sensitive methods of analysis have allowed their detection. They can be present in the natural environment, in food, and in many products of everyday origin, which suggests that human exposure is massive and universal. These contaminants correspond, in most cases, to unregulated substances, which may be candidates for future regulations, depending on research on their potential health effects and monitoring data regarding their prevalence. Therefore, the study of this type of substances is becoming one of the priority lines of research of the main agencies dedicated to the protection of public and environmental health, such as the World Health Organization (WHO), the United States Environmental Protection Agency (USEPA) or the European Union (EU). In this sense, it is of vital importance to know the nature and quantity of this type of contaminants, to establish preventive mechanisms that minimize their presence in the environment, including, of course, aquatic systems, with special requirements for water human consumption.MethodsThis systematic review and meta-analyzes protocol is conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA) statement guidelines and the Cochrane Handbook of Systematic Reviews of Interventions. The papers should include monitoring studies carried out in pesticides polluted waters in Europe. Prevalence studies of emerging contaminants (pesticides) in water resources (watersheds, aquifers, river, marine and springs), waste waters (influent and effluent) and drinking water should be included. Therefore, the comprehensive search strategy will be conducted in the following databases: PubMed, Scopus, Web of Science, EMBASE, ScienceDirect. Two independent reviewers will conduct all study selection procedures, data extraction, and methodological evaluation, and disagreements will be referred to a third reviewer. RevMan 5.3 software will be used to gather data and perform the meta-analysis if possible.DiscussionThis systematic review should provide evidence on the presence of pesticides in European waters in order to establish preventive mechanisms that minimize their presence in the environment.Dissemination and ethicsThe findings of this scoping review will be disseminated in print, at conferences, or via peer-reviewed journals. Ethical approval is not necessary as this paper does not involve patient data.Systematic review registrationPROSPERO CRD42022348332.
Evolution of horn length and lifting strength in the Japanese rhinoceros beetleTrypoxylus dichotomus
Authors: Weber Jesse N. , Kojima Wataru , Boisseau Romain , Niimi Teruyuki , Morita Shinichi , Shigenobu Shuji , Gotoh Hiroki , Araya Kunio , Lin Chung-Ping , Thomas-Bulle Camille , Allen Cerisse E. , Tong Wenfei , Lavine Laura Corley , Swanson Brook O. , Emlen Douglas J. 
Published: February 2023

AbstractRhinoceros beetle (Trypoxylus dichotomus) males have pitchfork-shaped head horns, which they use to pry rival males from the trunks of trees. In the largest males these horns can be three times the length of horns in the two closest sister species. Because this weapon functions as a lever, longer horns should lift with less force than shorter horns (the ‘paradox of the weakening combatant’) unless other elements of the weapon system (e.g., input lever length, muscle mass) evolve to compensate. We used next-generation sequencing approaches to consolidate 23 sample locations into 8 genetically distinguishable populations, reconstructing their historical relationships and providing a comprehensive picture of the evolution of this horn lever system. We show that head horns likely increased in length independently in the Northern and Southern lineages. In both instances this resulted in weaker lifting forces, but this mechanical disadvantage was later ameliorated, to some extent and in some locations, by subsequent reductions to horn length, changes in muscle size, or by an increase in input lever length (head height). Our results reveal an exciting geographic mosaic of differences in weapon size, weapon force, and in the extent and nature of mechanical compensation. Reconstructing the evolution of this weapon system offers critical insights towards meaningfully linking mating system dynamics, selection patterns, and diversity in sexually selected traits.
Microbiome compositions and fecal metabolite concentrations predict post-operative infection in liver transplant recipients
Authors: Lehmann Christopher J , Dylla Nicholas P , Odenwald Matthew , Nayak Ravi , Khalid Maryam , Boissiere Jaye , Cantoral Jackelyn , Adler Emerald , Stutz Matthew R , Cruz Mark Dela , Moran Angelica , Lin Huaiying , Sundararajan Anitha , Sidebottom Ashley M. , Pamer Eric G , Aronsohn Andrew , Fung John , Baker Talia B , Kacha Aalok 
Published: February 2023

ABSTRACTBackgroundLiver transplantation (LT) is associated with postoperative infections caused by antibiotic-resistant bacterial pathogens that reside in the intestine. An intact intestinal microbiome suppresses expansion of enteric pathogens, however patients with severe liver disease often have reduced microbiome diversity and increased density of antibiotic-resistantEnterococcusandEnterobacteralesspecies. (1–4) Experimental models have demonstrated that metabolites produced by the intestinal microbiome, including short chain fatty acids (SCFAs), secondary bile acids and indole compounds, enhance host epithelial and immune defenses against enteric pathogens.(5–10) Microbiome derived metabolites likely contribute to resistance against infectious diseases in LT patients, however, this remains uninvestigated.MethodsWe prospectively enrolled 107 liver transplant candidates and determined peri-transplant fecal microbiome compositions including relative and absolute fecal metabolite concentrations.ResultsFecal microbiomes in LT recipients ranged from highly diverse to complete loss of diversity resulting in expansion ofEnterococcusand/orEnterobacteralesspecies that were associated with postoperative infection. Gas chromatographic (GC-) and liquid chromatographic (LC-) Mass spectrometric analyses revealed decreased concentrations of SCFAs, secondary bile acids, and indole compounds in fecal samples with low microbiome diversity and associated expansion ofEnterococcusandEnterobacteralespopulations.ConclusionFecal metabolite abundances accurately predicted LT patients with reduced microbial diversity and those who developed postoperative infection.
Re-weightingMC1R, ASIPandIRF4risk variants optimises polygenic risk scores for keratinocyte cancer stratification in solid organ transplant recipients
Authors: Seviiri Mathias , Law Matthew H. , Olsen Catherine M. , Whiteman David C. , Green Adele C. , MacGregor Stuart 
Published: February 2023

ABSTRACTIntroductionSolid organ transplant recipients (SOTRs) are at much higher risk of developing squamous cell carcinoma (SCC) and basal cell carcinoma (BCC), compared to the general population. Previous studies have derived genetics-based predictors (polygenic risk scores, PRS) of SCC and BCC risk in SOTRs by assuming that genetic risk variants act in the same way in the general population as in SOTRs, but this assumption has not been fully tested.ObjectiveTo investigate whether known genetic risk variants for SCC and BCC have different effect sizes in SOTRs versus in non-transplantees, and if a re-weighted PRS would improve risk prediction.MethodsWe conducted genome-wide association studies for SCC and BCC separately in the non-transplant general population and in SOTRs, and compared the risks associated with selected common genetic variants for KC risk in SOTR vs non-transplant individuals from the UK Biobank. For regions with an increased log odds ratio in SOTRs, PRSs including these weights were validated in the QSkin study, and applied to the Australian STAR SOTR cohort.ResultsEffect sizes for functional variants in MC1R (rs1805007),ASIP(rs6059655), andIRF4(rs12203592) were much more strongly associated with the risk of KC in SOTRs than in non-transplantees. The proportional increase in the effect sizes ranged from 1.9-fold for rs6059655 and BCC risk (SOTRs log (OR)=0.49, 95%CI=0.00-0.98 vs log (OR)=0.26, 95%CI=0.24-0.30 in non-transplantees) to as high as 4.8-fold for rs1805007 and SCC risk (SOTR log (OR)=0.88, 95% CI=0.41-1.35 vs log (OR)=0.18, 95% CI=0.12-0.24 in non-transplantees). PRS with SOTR derived weights for these SNPs showed improved SCC/BCC risk stratification in the STAR Cohort, with the optimised PRS reclassifying 19% of SCC cases vs 8% using the standard PRS, and 18% of BCC cases vs 12% using the standard PRS.ConclusionEffect sizes for SCC and BCC risk for genetic variants in theMC1R, ASIP and IRF4genes are elevated in SOTRs, and correctly weighting these variants improves risk stratification based on polygenic risk.
The timing of transcription of RpoS-dependent genes varies across multiple stresses inEscherichia coliK-12
Authors: Adams Josephine , Hoang Johnson , Petroni Emily , Ashby Ethan , Hardin Johanna , Stoebel Daniel M. 
Published: February 2023

AbstractThe alternative sigma factor RpoS regulates transcription of over 1000 genes inEscherichia coliin response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of RpoS for the temporal patterns of expression of RpoS-regulated genes have not been described. We measured RpoS levels at various times during the entry to stationary phase, or in response to high osmolarity or low temperature, and found that the time required to reach maximum levels varied by several hours. We quantified the transcriptome across these stresses using RNA-seq. The number of differentially expressed genes differed among stresses, with 1379 DE genes identified in stationary phase, 633 in high osmolarity, and 302 in cold shock. To quantify the timing of gene expression, we fit sigmoid or double sigmoid models to differentially expressed genes in each stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS. The timing of individual gene’s expression was not correlated across stresses. Taken together, our results demonstrateE. coliactivates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response to each stress.ImportanceBacteria adapt to changing environments by altering the transcription of their genes. Specific proteins can regulate these changes. This study explored how a single protein called RpoS controls how many genes change expression during adaptation to three stresses. We found that: 1) RpoS is responsible for activating different genes in different stresses; 2) that during a stress, the timing of gene activation depends on the what stress it is, and; 3) that how much RpoS a gene needs in order to be activated can predict when that gene will be activated during the stress of stationary phase.
Amino acid substitutions in norovirus VP1 dictate cell tropism via an attachment process dependent on membrane mobility
Authors: Mills Jake T. , Minogue Susanna C. , Snowden Joseph S. , Arden Wynter K.C. , Rowlands David J. , Stonehouse Nicola J. , Wobus Christiane E. , Herod Morgan R. 
Published: February 2023

AbstractViruses interact with receptors on the cell surface to initiate and co-ordinate infection. The distribution of receptors on host cells can be a key determinant of viral tropism and host infection. Unravelling the complex nature of virus-receptor interactions is, therefore, of fundamental importance to understanding viral pathogenesis. Noroviruses are non-enveloped, icosahedral, positive-sense RNA viruses of global importance to human health, with no approved vaccine or antiviral agent available. Here we use murine norovirus as a model for the study of molecular mechanisms of virus-receptor interactions. We show that variation at a single amino acid residue in the major viral capsid protein had a key impact on the interaction between virus and receptor. This variation did not affect virion production or virus growth kinetics, but a specific amino acid was rapidly selected through evolution experiments, and significantly improved cellular attachment when infecting immune cells in suspension. However, reducing plasma membrane mobility counteracted this phenotype, providing insight into for the role of membrane fluidity and receptor recruitment in norovirus cellular attachment. When the infectivity of a panel of recombinant viruses with single amino acid variations was comparedin vivo, there were significant differences in the distribution of viruses in a murine model, demonstrating a role in cellular tropismin vivo. Overall, these results highlight the importance of lipid rafts and virus-induced receptor recruitment in viral infection, as well as how capsid evolution can greatly influence cellular tropism, within-host spread and pathogenicity.ImportanceAll viruses initiate infection by utilising receptors to attach to target host cells. These virus-receptor interactions can therefore dictate viral replication and pathogenesis. Understanding the nature of virus-receptor interactions could also be important to developing novel therapies. Noroviruses are non-enveloped icosahedral viruses of medical importance. They are a common cause of acute gastroenteritis with no approved vaccine or therapy and are a tractable model for studying fundamental virus biology. In this study, we utilise the murine norovirus model system to show that variation in a single amino acid of the major capsid protein can alone can affect viral infectivity through improved attachment to suspension cells. Reducing plasma membrane mobility reduced infectivity, providing an insight into the importance of membrane mobility for receptor recruitment. Furthermore, variation at this site was able to change viral distribution in a murine model, illustrating how in-host capsid evolution can influence viral infectivity and immune evasion.
Host and transmission route ofEnterocytozoon hepatopenaei(EHP) from dragonfly to shrimp
Authors: Kumar Dewangan Naresh , Pang Jianhu , Zhao Caiyuan , Cao Changsheng , Yin Bin , Weng Shaoping , He Jianguo 
Published: February 2023

AbstractEnterocytozoon hepatopenaei(EHP) is a shrimp pathogen that causes huge economic losses. In the present study, the hosts of EHP were investigated using polymerase chain reaction (PCR) in an aquaculture farm located in Maoming, China. EHP was detected inLitopenaeus vannamei,Penaeus monodon, crab, false mussel, and three dragonfly species (Anax parthenope,Pantala flavescens, andIschnura senegalensis). In the histopathological examination using hematoxylin–eosin staining, EHP spores were found in nymphs and adult dragonflies naturally infected with EHP that were collected from the shrimp farm. Fluorescence in situ hybridization results showed a positive signal for EHP infection in the fat body of dragonfly nymphs. Immature and mature microsporidian spores and late sporogonial plasmodium were observed in the cytoplasm of dragonfly nymphs using transmission electron microscopy. The transmission of EHP from shrimp to dragonfly nymphs was confirmed via cohabitation challenge experiments in which EHP-free dragonfly nymphs were cohabited with EHP-infected shrimp, and the transmission of EHP from dragonfly nymphs to shrimp was demonstrated via the cohabitation of EHP-infected dragonfly nymphs with EHP-free shrimp and oral administration challenge experiments. This study confirms that dragonflies can act as natural EHP hosts, and a novel EHP horizontal transmission route exists between dragonflies and shrimp.Author summaryTo the authors’ knowledge, this study presents the first report of microsporidia (EHP) infecting both crustaceans and insects (A. parthenope,P. flavescens, andI. senegalensis). The horizontal transmission of EHP between dragonfly nymphs and shrimp was confirmed through cohabitation and oral administration challenge experiments. EHP has become a globally significant threat to shrimp aquaculture. The findings of the present study will help to design prevention strategies, such as the use of nets to prevent dragonflies from entering shrimp ponds.
A cleaved METTL3 potentiates the METTL3-WTAP interaction and breast cancer progression
Authors: Yan Chaojun , Xiong Jingjing , Zhou Zirui , Li Qifang , Gao Chuan , Zhang Mengyao , Yu Liya , Li Jinpeng , Hu Ming-Ming , Zhang Chen-Song , Cai Cheguo , Zhang Haojian , Zhang Jing 
Published: February 2023

AbstractN6-methyladenosine (m6A) methylation of RNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers andWilms’ tumor 1-associated protein(WTAP), contributes to breast tumorigenesis, but the underlying regulatory mechanisms remain elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3). We find that METTL3a is required for the METTL3-WTAP interaction, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is essential for the METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A deposition, and METTL3a mediates mTOR activation via m6A-mediated suppression of TMEM127 expression. Moreover, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component of MTC, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.
Elasticity of Whole Blood Clots Measured via Volume Controlled Cavity Expansion
Authors: Varner Hannah , Sugerman Gabriella P. , Rausch Manuel K. , Cohen Tal 
Published: February 2023

AbstractMeasuring and understanding the mechanical properties of blood clots can provide insights into disease progression and the effectiveness of potential treatments. However, several limitations hinder the use of standard mechanical testing methods to measure the response of soft biological tissues, like blood clots. These tissues can be difficult to mount, and are inhomogeneous, irregular in shape, scarce, and valuable. To remedy this, we employ in this work Volume Controlled Cavity Expansion (VCCE), a technique that was recently developed, to measure local mechanical properties of soft materials in their natural environment. Through a highly controlled volume expansion of a water bubble at the tip of an injection needle, paired with simultaneous measurement of the resisting pressure, we obtain a local signature of whole blood clot mechanical response. Comparing this data with predictive theoretical models, we find that a 1-term Ogden model is sufficient to capture the nonlinear elastic response observed in our experiments and produces shear modulus values that are comparable to values reported in the literature. Moreover, we find that bovine whole blood stored at 4°C for greater than 2 days exhibits a statistically significant shift in the shear modulus from 2.53 ± 0.44 kPa on day 2 (N= 13) to 1.23 ± 0.18 kPa on day 3 (N= 14). In contrast to previously reported results, our samples did not exhibit viscoelastic rate sensitivity within strain rates ranging from 0.22 – 21.1 s−1. By surveying existing data on whole blood clots for comparison, we show that this technique provides highly repeatable and reliable results, hence we propose the more widespread adoption of VCCE as a path forward to building a better understanding of the mechanics of soft biological materials.Graphical AbstractHighlightsVolume controlled cavity expansion overcomes common obstacles to testing biological samplesWhole blood clot elasticity is well captured by the Ogden hyperelastic material modelShear modulus strain-rate sensitivity was not observed in clots for moderate rates
Truly dorsal: nonlinear integration of motion signals is required to account for the responses of pattern cells in rat visual cortex
Authors: Matteucci Giulio , Marotti Rosilari Bellacosa , Zattera Benedetta , Zoccolan Davide 
Published: February 2023

AbstractThe defining feature of advanced motion processing in the primate dorsal stream is the existence of pattern cells – specialized cortical neurons that integrate local motion signals into pattern-invariant representations of global direction. Pattern cells have also been reported in rodent visual cortex, but it is unknown whether the tuning of these neurons results from truly integrative, nonlinear mechanisms or trivially arises from linear receptive fields (RFs) with a peculiar geometry. Here we show that pattern cells in rat visual cortical areas V1 and LM process motion direction in a way that cannot be explained by the linear spatiotemporal structure of their RFs. Instead, their tuning properties are consistent with those of units in a state-of-the-art neural network model of the dorsal stream. This suggests that similar cortical processes underly motion representation in primates and rodents. The latter could thus serve as powerful model systems to unravel the underlying circuit-level mechanisms.
MotorNet: a Python toolbox for controlling differentiable biomechanical effectors with artificial neural networks
Authors: Codol Olivier , Michaels Jonathan A. , Kashefi Mehrdad , Pruszynski J. Andrew , Gribble Paul L. 
Published: February 2023

AbstractArtificial neural networks (ANNs) are a powerful class of computational models for unravelling neural mechanisms of brain function. However, for neural control of movement, they currently must be integrated with software simulating biomechanical effectors, leading to limiting impracticalities: (1) researchers must rely on two different platforms and (2) biomechanical effectors are not generally differentiable, constraining researchers to reinforcement learning algorithms despite the existence and potential biological relevance of faster training methods. To address these limitations, we developed MotorNet, an open-source Python toolbox for creating arbitrarily complex, differentiable, and biomechanically realistic effectors that can be trained on user-defined motor tasks using ANNs. MotorNet is designed to meet several goals: ease of installation, ease of use, a high-level user-friendly API, and a modular architecture to allow for flexibility in model building. MotorNet requires no dependencies outside Python, making it easy to get started with. For instance, it allows training ANNs on typically used motor control models such as a two joint, six muscle, planar arm within minutes on a typical desktop computer. MotorNet is built on PyTorch and therefore can implement any network architecture that is possible using the PyTorch framework. Consequently, it will immediately benefit from advances in artificial intelligence through PyTorch updates. Finally, it is open source, enabling users to create and share their own improvements, such as new effector and network architectures or custom task designs. MotorNet’s focus on higher order model and task design will alleviate overhead cost to initiate computational projects for new researchers by providing a standalone, ready-to-go framework, and speed up efforts of established computational teams by enabling a focus on concepts and ideas over implementation.