bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological monitoring using Collembola metabarcoding with extremely low bycatch amplification
Authors: Pedro Pedro M. , Cullen Laury , Prado Fabiana , Uezu Alexandre , Piper Ross , Faria Christiana M.A. , Knogge Christoph , Pepe Razzolini Maria Tereza , Paiva Marcela B. , Dropa Milena , Silva Miriam , Rech Tatiane Cristina , Püttker Thomas 
Published: May 2023

AbstractCollembola are used widely to monitor soil health and functional parameters. Recent developments in high throughput sequencing (especially metabarcoding) have substantially increased their potential for these ends. Collembola are especially amenable to metabarcoding because of their small size, high abundance, and ubiquity in most habitat types. However, most Collembola sampling protocols collect a substantial and highly varied bycatch that can be a considerable impediment to metabarcoding, especially because of data lost to non-target species. We designed a primer set amplifying the D2 expansion segment of ribosomal DNA that is highly conserved across Collembola and successfully excludes from amplification nearly all other invertebrate taxa. We tested the diagnostic power of the primer set by clearly distinguishing Collembola communities between forest sites with differing habitat qualities in São Paulo State, Brazil. The oligos successfully amplified targets from all Collembola orders previously encountered in the sampling locations, with no non-target amplification, and also excluded the closely related Protura and Diplura. Alpha diversity (OTU count) and phylogenetic diversity was significantly higher in high quality habitats. Moreover, the beta diversity indices successfully differentiated high and low-quality habitats. This new addition to the biomonitoring toolbox greatly increases the accessibility of Collembola metabarcoding for various types of habitat assessments.
Climatic niche differentiation between native and non-native ranges is widespread in Ponto-Caspian amphipods
Authors: Šidagytė-Copilas Eglė , Copilaș-Ciocianu Denis 
Published: May 2023

AbstractNiche conservatism posits that a species’ non-native populations establish in areas that match the native environmental conditions. Although the Ponto-Caspian region is a major source of inland aquatic alien species, the extent to which their climatic niches diverged between the invasive and native ranges remains poorly understood.Using an n-dimensional hypervolume approach, we quantified climatic niche overlap and inferred patterns of niche differentiation (shift, contraction, or expansion) among native and invaded ranges for 12 widespread Ponto-Caspian amphipod species (six genera in three families).Our results show that all investigated species experience substantially different climatic conditions in the invaded range. The invasive niche either contracted (five species), shifted (four species), expanded and shifted (two species), or shifted and contracted (one species) relative to the native niche.We conclude that although the focal taxa share a common geographic origin and evolutionary history, they exhibit disparate patterns of climatic niche change outside the native range. The niche conservatism hypothesis receives mixed support given that half of the studied species underwent niche shifts/expansion. Furthermore, congeners exhibited both identical and contrasting patterns of niche differentiation, suggesting a limited phylogenetic effect.The uncovered diversity of niche dynamics among closely related species indicates that each has a unique potential for invasiveness and long-term persistence. This has important implications for predicting invasion risk and refining management strategies.
Generation and characterization of aDkk4-Creknock-in mouse line
Authors: Khatif Houda , Bazzi Hisham 
Published: May 2023

AbstractEctodermal appendages in mammals, such as teeth, mammary glands, sweat glands and hair follicles, are generated during embryogenesis through a series of mesenchymal-epithelial interactions. Canonical Wnt signaling and its inhibitors are implicated in the early steps of ectodermal appendage development and patterning. To study the activation dynamics of the Wnt target and inhibitorDickkopf4(Dkk4) in ectodermal appendages, we used CRSIPR/Cas9 to generate aDkk4-Creknock-in mouse (Mus musculus) line, where theCrerecombinase cDNA replaces the expression of endogenousDkk4. UsingCrereporters, theDkk4-Creactivity was evident at the prospective sites of ectodermal appendages, overlapping with theDkk4mRNA expression. Unexpectedly, a predominantly mesenchymal cell population in the embryo posterior also showedDkk4-Creactivity. Lineage-tracing suggested that these cells are likely derived from a fewDkk4-Cre-expressing cells in the epiblast at early gastrulation. Finally, our analyses ofDkk4-Cre-expressing cells in developing hair follicle epithelial placodes revealed intra- and inter-placodal cellular heterogeneity, supporting emerging data on the positional and transcriptional variability in placodes. Collectively, we propose the newDkk4-Creknock-in mouse line as a suitable model to study Wnt and DKK4 inhibitor dynamics in early mouse development and ectodermal appendage morphogenesis.
Tight junctions regulate lumen morphology via hydrostatic pressure and junctional tension
Authors: Mukenhirn Markus , Wang Chen-Ho , Guyomar Tristan , Bovyn Matthew J. , Staddon Michael F. , Maraspini Riccardo , Lu Linjie , Martin-Lemaitre Cecilie , Sano Masaki , Hiraiwa Tetsuya , Riveline Daniel , Honigmann Alf 
Published: May 2023

SummaryFormation of fluid filled lumen by epithelial tissues is a fundamental process for organ development. How epithelial cells regulate the hydraulic and cortical forces to control lumen morphology is not completely understood. Here, we quantified the mechanical role of tight junctions in lumen formation using genetically modified MDCKII cysts. We found that the paracellular ion barrier formed by claudin receptors is not required for hydraulic inflation of lumen. However, depletion of the zonula occludens scaffold resulted in lumen collapse and folding of apical membranes. Combining quantitative measurements and perturbations of hydrostatic lumen pressure and junctional tension with modelling, we were able to predict lumen morphologies from the pressure-tension force balance. We found that in MDCK tissue the tight junction promotes formation of spherical lumen by decreasing cortical tension via inhibition of myosin. In addition, we found that the apical surface area of cells is largely uncoupled from lumen volume changes, suggesting that excess apical area contributes to lumen opening in the low-pressure regime. Overall, our findings provide a mechanical understanding of how epithelial cells use tight junctions to modulate tissue and lumen shape.
Grazing of the free-living filamentous brown seaweed,Pilayella littoralis, by the amphipodGammarus tigrinis
Authors: Miller Steven L. , Wilce Robert T. 
Published: May 2023

AbstractPilayella littoralisis a common brown alga with a cosmopolitan distribution. A distinct form of the alga is found free-living in Nahant Bay, Massachusetts. Characteristics that distinguish the free-living form include radial branching that results in a ball-like morphology, reproduction by fragmentation of filaments rather than by spores, and year-round persistence of the population. The amphipodGammarus tigrinisis frequently found within the floating drifts ofP. littoralis. We conducted gut content analyses to document thatG. tigrinisconsumesP. littoralis. Culture studies revealed that ingestedP. littoraliscould survive and grow from fecal pellets produced byG. tigrinis. In addition, inefficient grazing produces vegetative fragments (propagules) that can increase numbers within the free-living population. δ13C values for the amphipods andP. littoralisaveraged -17.4 o/oo and -17.7 o/oo, respectively, suggesting thatG. tigrinisacquires most of its carbon fromP. littoralis.
NMA1982 is a Novel Phosphatase and Potential Virulence Factor inNeisseria meningitidis
Authors: Wu Shuangding , Coureuil Mathieu , Nassif Xavier , Tautz Lutz 
Published: May 2023

AbstractProtein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase fromNeisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine phosphatase. Importantly, we show that NMA1982 is secreted byN. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential forN. meningitidissurvival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
Mechanistic target of rapamycin (mTOR) pathway in Sertoli cells regulates age-dependent changes in sperm DNA methylation
Authors: Amir Saira , Arowolo Olatunbosun , Mironova Ekaterina , McGaunn Joseph , Oluwayiose Oladele , Sergeyev Oleg , Pilsner J. Richard , Suvorov Alexander 
Published: May 2023

AbstractOver the past several decades, a trend toward delayed childbirth has led to increases in parental age at the time of conception. Sperm epigenome undergoes age-dependent changes increasing risks of adverse conditions in offspring conceived by fathers of advanced age. The mechanism(s) linking paternal age with epigenetic changes in sperm remain unknown. The sperm epigenome is shaped in a compartment protected by the blood-testes barrier (BTB) known to deteriorate with age. Permeability of the BTB is regulated by the balance of two mTOR complexes in Sertoli cells where mTOR complex 1 (mTORC1) promotes the opening of the BTB and mTOR complex 2 (mTORC2) promotes its integrity. We hypothesized that this balance is also responsible for age-dependent changes in the sperm epigenome. To test this hypothesis, we analyzed reproductive outcomes, including sperm DNA methylation in transgenic mice with Sertoli cell-specific suppression of mTORC1 (Raptor KO) or mTORC2 (Rictor KO). mTORC2 suppression accelerated aging of the sperm DNA methylome and resulted in a reproductive phenotype concordant with older age, including decreased testes weight and sperm counts, and increased percent of morphologically abnormal spermatozoa and mitochondrial DNA copy number. Suppression of mTORC1 resulted in the shift of DNA methylome in sperm opposite to the shift associated with physiological aging – sperm DNA methylome rejuvenation, and mild changes in sperm parameters. These results demonstrate for the first time that the balance of mTOR complexes in Sertoli cells regulates the rate of sperm epigenetic aging. Thus, mTOR pathway in Sertoli cells may be used as a novel target of therapeutic interventions to rejuvenate the sperm epigenome in advanced-age fathers.Ethics statementAll procedures followed the guidelines of the National Institutes of Health Guide for the Care and Use of Laboratory Animals and the approval for this study was received from the Institutional Animal Care and Use Committee at University of Massachusetts, Amherst.
Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability
Authors: Lear Bo P. , Thompson Elizabeth A.N. , Rodriguez Kendra , Arndt Zachary P. , Khullar Saniya , Klosa Payton C. , Lu Ryan J. , Morrow Christopher S. , Risgaard Ryan , Peterson Ella R. , Teefy Brian B. , Bhattacharyya Anita , Sousa Andre M.M. , Wang Daifeng , Benayoun Bérénice A. , Moore Darcie L. 
Published: May 2023

AbstractInjury to adult mammalian central nervous system (CNS) axons results in limited regeneration. Rodent studies have revealed a developmental switch in CNS axon regenerative ability, yet whether this is conserved in humans is unknown. Using human fibroblasts from 8 gestational-weeks to 72 years-old, we performed direct reprogramming to transdifferentiate fibroblasts into induced neurons (Fib-iNs), avoiding pluripotency which restores cells to an embryonic state. We found that early gestational Fib-iNs grew longer neurites than all other ages, mirroring the developmental switch in regenerative ability in rodents. RNA-sequencing and screening revealed ARID1A as a developmentally-regulated modifier of neurite growth in human neurons. These data suggest that age-specific epigenetic changes may drive the intrinsic loss of neurite growth ability in human CNS neurons during development.One-Sentence Summary:Directly-reprogrammed human neurons demonstrate a developmental decrease in neurite growth ability.
The transcription factor bZIP11 acts antagonistically with trehalose 6-phosphate to inhibit shoot branching
Authors: Hellens A. M. , Kreisz P. , Humphreys J. L. , Feil R. , Lunn J.E. , Dröge-Laser W. , Beveridge C. A. , Fichtner F. , Weiste C. , Barbier F. F. 
Published: May 2023

AbstractThe ontogenetic regulation of shoot branching allows plants to adjust their architecture in accordance with the environment. This process is due to the regulation of axillary bud outgrowth into branches, which can be induced by increasing sugar availability to the buds through decapitation of the shoot tip. Different sugar signalling components have been identified in the induction of shoot branching. However, the molecular components that maintain bud dormancy in response to sugar starvation remain largely unknown. Here, we show at the genetic level that basic leucine zipper 11 (bZIP11), a transcription factor that plays important roles in response to sugar starvation in plants, inhibits shoot branching inArabidopsis thaliana. Physiology experiments demonstrated that bZIP11 protein levels are decreased by decapitation. Molecular and genetic evidence suggests that bZIP11 acts in a negative feedback loop with trehalose 6-phosphate (Tre6P), a sugar signal that promotes shoot branching. Our data also suggest that the central energy sensor SUCROSE NON-FERMENTING 1 RELATED KINASE1 (SnRK1), alleviates the inhibitory effect of Tre6P on bZIP11 protein accumulation and inhibits shoot branching. Altogether, these data provide a working model that involves bZIP11, Tre6P and SnRK1 in the regulation of shoot branching.
A Standardized Antiviral Pipeline for Human Norovirus in Human Intestinal Enteroids Demonstrates No Antiviral Activity of Nitazoxanide
Authors: Lewis Miranda A. , Cortés-Penfield Nicolás W. , Ettayebi Khalil , Patil Ketki , Kaur Gurpreet , Neill Frederick H. , Atmar Robert L. , Ramani Sasirekha , Estes Mary K. 
Published: May 2023

AbstractHuman noroviruses (HuNoVs) are the leading cause of acute gastroenteritis. In immunocompetent hosts, symptoms usually resolve within three days; however, in immunocompromised persons, HuNoV infection can become persistent, debilitating, and sometimes life-threatening. There are no licensed therapeutics for HuNoV due to a near half-century delay in its cultivation. Treatment for chronic HuNoV infection in immunosuppressed patients anecdotally includes nitazoxanide, a broad-spectrum antimicrobial licensed for treatment of parasite-induced gastroenteritis. Despite its off-label use for chronic HuNoV infection, nitazoxanide has not been clearly demonstrated to be an effective treatment. In this study, we established a standardized pipeline for antiviral testing using multiple human small intestinal enteroid (HIE) lines representing different intestinal segments and evaluated whether nitazoxanide inhibits replication of 5 HuNoV strainsin vitro. Nitazoxanide did not exhibit high selective antiviral activity against any HuNoV strains tested, indicating it is not an effective antiviral for norovirus infection. HIEs are further demonstrated as a model to serve as a pre-clinical platform to test antivirals against human noroviruses to treat gastrointestinal disease.
Differential functional coupling in Gp130-JAK complexes expands the plasticity of the interleukin-6 signaling axis
Authors: McFarlane Alison , Bellón Junel Sotolongo , Meyer Thomas , Pohler Elizabeth , Piehler Jacob , Moraga Ignacio 
Published: May 2023

ABSTRACTCytokines dimerize/oligomerize surface receptors to activate signaling. While cytokine receptors preferentially bind only one member of the JAK family, ancestral cytokine receptors, such as Gp130, promiscuously recruit different JAKs to elicit their activities. Here, we have explored how the identity of JAKs in Gp130 signaling complexes can regulate functional outcomes. Using a synthetic biology approach, we show that Gp130 bound to different JAKs propagates distinct STAT activation profiles. While Gp130-JAK1 complexes activated both, STAT1 and STAT3 very potently, Gp130-JAK2 complexes exhibited a clear preference for STAT3 activation. Gp130-TYK2 complexes triggered overall weaker signaling but with diminished STAT specificity. The three JAKs competed for binding to Gp130 and led to differential activation of phospho-Tyr in the Gp130 intracellular domain. JAK1, JAK2 and to a lower extent TYK2 bound with comparable affinities to Gp130, and in response to IL-6 stimulation efficiently drove Gp130 dimerization. However, the three JAKs differentially affected Gp130 surface expression, identifying JAK-dependent receptor trafficking as a critical determinant of signaling plasticity. Our results provide new mechanistic insights into how differential functional coupling in Gp130-JAK complexes translates into unique signaling signatures that likely contribute to its large functional diversity.
Fed-ComBat: A Generalized Federated Framework for Batch Effect Harmonization in Collaborative Studies
Authors: Silva Santiago , Oxtoby Neil , Altmann Andre , Lorenzi Marco 
Published: May 2023

AbstractIn neuroimaging research, the utilization of multi-centric analyses is crucial for obtaining sufficient sample sizes and representative clinical populations. Data harmonization techniques are typically part of the pipeline in multi-centric studies to address systematic biases and ensure the comparability of the data. However, most multi-centric studies require centralized data, which may result in exposing individual patient information. This poses a significant challenge in data governance, leading to the implementation of regulations such as the GDPR and the CCPA, which attempt to address these concerns but also hinder data access for researchers. Federated learning offers a privacy-preserving alternative approach in machine learning, enabling models to be collaboratively trained on decentralized data without the need for data centralization or sharing.In this paper, we present Fed-ComBat, a federated framework for batch effect harmonization on decentralized data. Fed-ComBat extends existing centralized linear methods, such as ComBat and distributed as d-ComBat, and nonlinear approaches like ComBat-GAM in accounting for potentially nonlinear and multivariate covariate effects. By doing so, Fed-ComBat enables the preservation of nonlinear covariate effects without requiring centralization of data and without prior knowledge of which variables should be considered nonlinear or their interactions, differentiating it from ComBat-GAM. We assessed Fed-ComBat and existing approaches on simulated data and multiple cohorts comprising healthy controls (CN) and subjects with various disorders such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and autism spectrum disorder (ASD).Results indicate that Fed-ComBat outperforms centralized ComBat in the presence of nonlinear effects and is comparable to centralized methods such as ComBat-GAM. Using synthetic data, Fed-ComBat is able to better reconstruct the target unbiased function by 35% (RMSE = 0.5952) with respect to d-ComBat (RMSE = 0.9162) and 12% with respect to our proposal to federate ComBat-GAM, d-ComBat-GAM (RMSE= 0.6751) and exhibits comparable results on MRI-derived phenotypes to centralized methods as ComBat-GAM without the need of prior knowledge on potential nonlinearities.
Product innovation research over the past 60 years: a bibliometric analysis of intellectual structure and emergent trends
Authors: Aboelmaged Mohamed , Bani-Melhem Shaker , Al-Hawari Mohd Ahmad , Ali Imran 
Published: May 2023

PurposeLiterature on product innovation (PI) has witnessed tremendous growth over the past 60 years. Yet, there has been a dearth of a comprehensive review of the extant PI research maintaining the breadth and depth of the topic. To seal this gap, this paper aims to explore the intellectual foundations and emergent trends in 2,588 research papers on PI from 1962 to 2022.Design/methodology/approachThe paper adopts a bibliometric analysis approach via visualization maps of prolific contributions, co-citation, co-occurrence and thematic networks.FindingsEmerging streams, frontiers and hotspots in PI research are revealed and a knowledge graph is developed. The review provides a broad spectrum of opportunities that enrich imminent research to better inform business decisions.Practical implicationsThe review addresses 20 research questions associated with barely examined areas in PI research that require further analysis in imminent research.Originality/valueTo the best of the authors' knowledge, this is the first review that comprehensively synthesizes the intersected knowledge base of PI research using bibliometric analysis of a vast number of documents within a long time span.