bluuebunny/crossref_metadata_2025_split huggingface dataset:
A subclass of the IS1202family of bacterial insertion sequences targets XerCD recombination sites
Authors: Siguier Patricia , Rousseau Philippe , Cornet François , Chandler Michael 
Published: December 2022

AbstractIS1202, originally isolated fromStreptococcus pneumoniain the mid-1990s had been previously tagged as an emerging IS family in ISfinder. While searching for plasmid-associated Xer recombinase recombination sites (xrs) inAcinetobacter baumannii, we observed that some insertion sequences related to IS1202were repeatedly found abutting these sites in a number of plasmids. The plasmids often carried repeatedxrsthought to form a new type of mobile genetic element (MGE) which uses the chromosomally-encoded XerCD recombinase for mobility. The MGE (xrscassette) consist ofxrsflanking one or a small number of genes often including different clinically important carbapenemase-encodingbla-OXA. The IS1202-related IS are inserted with their left, transposase proximal extremity, IRL, five base pairs fromxrsand include a characteristic 5bp flanking target duplication. Further searches revealed that many different plasmid- and chromosome-bornexrscan be targeted and that IS1202-xrscombinations are not limited toAcinetobacter baumanniibut occur in other bacteria.In addition to 28 IS1202group ISs in ISfinder and a number which had been subsequently submitted, we undertook a survey of the NCBI (February 2020) and identified 138 additional IS1202-related IS. These could be divided into 3 principal subgroups based on their transposase sequences and on the length of the DR generated on insertion: subgroup IS120227-28bp DR); ISTde1(15-17bp); and ISAba32(5-6bp). Members of each group which lacked DR were also found. But since other examples of most of these were subsequently identified having DR, those lacking DR may have been generated by intra-replicon recombination. Only members of the group which generate 5bp DR were found to targetxrs. These were not only identified in plasmids but also occurred at some individualxrssites,dif, located at the chromosome replication terminus and involved in post-replication chromosome segregation. Further analysis showed the presence of subgroup-specific indels in their transposases which may be responsible for the differences in their behavior.We propose that this collection of IS be classed as a new insertion sequence family: the IS1202family composed of at three subfamilies, only one of which specifically targets plasmid-bornexrs. We discuss the implications ofxrstargeting for gene mobility.
The Neurophysiological Modality Effect in Native and Second Language Processing: An ERP Study
Authors: Gallagher Daniel , Yano Masataka , Ohta Shinri 
Published: December 2022

ABSTRACTExperimental psychology has long discussed the modality effect, whereby the stimulus modality significantly affects retention of the information presented. In neurolinguistics, however, the effect of stimulus modality on language processing has gained little attention. We conducted a multi-modal event-related potential (ERP) experiment on both native and non-native Spanish speakers to investigate the possibility of a neurophysiological modality effect in language processing. Using morphosyntactically violated and orthographically/phonologically violated stimuli, we elicited a robust N400 and P600 in native speakers. We showed that the N400 has consistent features across modalities, while the P600 has modality-specific features. Specifically, the auditory evoked P600 was characterized by a more gradual slope and a later peak than the visual evoked P600. We discuss this in detail along with other modality effects observed post sensory perception. Among second language (L2) learner groups, those with higher proficiency exhibited more nativelike neurophysiological responses in both modalities when compared to those with lower proficiency. We additionally observed fewer modality-specific differences in low proficiency learners than in higher proficiency learners suggesting that modality-specific specialization in language processing comes with increased proficiency. We further discuss the question of modality-specific differences in the process of neurophysiological nativization, whereby L2 learners’ ERPs become increasingly on nativelike.
Population size shapes the evolution of lifespan
Authors: Bagic Martin , Valenzano Dario Riccardo 
Published: December 2022

AbstractBiological aging results from the age-dependent change in the force of natural selection, which increases the probability of germline variants that limit survival to accumulate in genes acting predominantly in late life1. The evolutionary mechanisms underlying the accumulation of neutral mutations and antagonistically pleiotropic gene variants that cause biological aging have been analyzed to date under the assumption of infinitely large population size. However, even though population size importantly shapes genetic and phenotype variation via drift and selection2,3, we still have a limited understanding of how finite population size impacts the evolution of mortality at the population level. Here, we study the impact of population size on lifespan evolution under mutation accumulation and antagonistic pleiotropy. We found that larger population size leads to lower age-independent, as well as age-dependent mortality under mutation accumulation, due to more effective purifying selection against deleterious germline variants. Strikingly, large population size can lead to extended lifespan under antagonistic pleiotropy, due to more effective positive selection on gene variants increasing survival in early-life, while leading to increased post-maturation mortality. Our findings provide a comprehensive numerical framework for the two major evolutionary genetic theories of aging and reveal a fundamental and yet non-appreciated role for population size in the evolution of mortality trajectories.
Transcriptional and translational dynamics underlying heat shock response in the thermophilic CrenarchaeonSulfolobus acidocaldarius
Authors: Baes Rani , Grünberger Felix , dit Ruys Sébastien Pyr , Couturier Mohea , De Keulenaer Sarah , Skevin Sonja , Van Nieuwerburgh Filip , Vertommen Didier , Grohmann Dina , Ferreira-Cerca Sébastien , Peeters Eveline 
Published: December 2022

AbstractHigh-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. In this work, we set out to study heat shock response in the thermoacidophilic model crenarchaeonSulfolobus acidocaldarius, which thrives in volcanic hot springs and has an optimal growth temperature of 75°C. Pulse-labeling experiments demonstrated that a temperature shift to 86°C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and TMT-labeled mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by the more subtle reprogramming of the protein landscape. A limited correlation was observed in differential expression on the RNA and protein level, suggesting that there is a prevalence of post-transcriptional and post-translational regulation upon heat shock. Furthermore, based on the finding that promoter regions of heat shock regulon genes lack a conserved DNA-binding motif, we propose that heat-shock responsive transcription regulation is likely not to be accomplished by a classical transcription factor. Instead, in contrast to histone-harboring Euryarchaeota that have heat-shock transcription factors, it is hypothesized that Sulfolobales and other histone-lacking thermophilic archaea employ an evolutionary ancient mechanism relying on temperature-responsive changes in DNA organization and compaction, induced by the action of nucleoid-associated proteins.
The ins and outs of membrane bending by intrinsically disordered proteins
Authors: Yuan Feng , Lee Christopher T. , Sangani Arjun , Houser Justin R. , Wang Liping , Lafer Eileen M. , Rangamani Padmini , Stachowiak Jeanne C. 
Published: December 2022

AbstractMembrane curvature is essential to diverse cellular functions. While classically attributed to structured domains, recent work illustrates that intrinsically disordered proteins are also potent drivers of membrane bending. Specifically, repulsive interactions among disordered domains drive convex bending, while attractive interactions, which lead to liquid-like condensates, drive concave bending. How might disordered domains that contain both repulsive and attractive domains impact curvature? Here we examine chimeras that combine attractive and repulsive interactions. When the attractive domain was closer to the membrane, its condensation amplified steric pressure among repulsive domains, leading to convex curvature. In contrast, when the repulsive domain was closer to the membrane, attractive interactions dominated, resulting in concave curvature. Further, a transition from convex to concave curvature occurred with increasing ionic strength, which reduced repulsion while enhancing condensation. In agreement with a simple mechanical model, these results illustrate a set of design rules for membrane bending by disordered proteins.
Excellent repigmentation was observed in the treatment of refractory vitiligo with autologous cultured epithelium grafting: a real-world retrospective cohort study
Authors: Li Jian , Zeng Xuanhao , Chen Shujun , Tang Luyan , Zhang Qi , Lv Minzi , Uyama Taro , Wu Fuyue , Lian Weiling , Wang Jinqi , Lv Haozhen , Liu Yating , Wu Jinfeng , Xu Jinhua 
Published: December 2022

AbstractSurgical intervention is considered as the mainstream therapy for refractory vitiligo. In this study, we developed a modified autologous cultured epithelial grafting (ACEG) technique for the surgical treatment of vitiligo. A total of 726 patients with vitiligo treated with ACEG were enrolled from January 2015 to June 2019 in China. Patient characteristics, such as sex, age, clinical type, lesion sites, course of the disease, and disease stable period, were recorded. In 2118 skin lesions from 726 patients who received ACEG, total efficacy rate was 82.81% (1754/2118).However, the repigmentation rate of the ACEG was 64.87%, which was higher than that of conventional surgical interventions (52.69%). Patients with segmental vitiligo, skin lesions in the lower limbs, aged 18 years or below, and a stable period of over 3 years might have a good response to ACEG. Single-cell RNA sequencing was performed to observe different cell compositions in the skin before and after ACEG. The number of melanocytes increased by 50% after transplantation. In addition, there was a significant increase in hair follicle outer root sheath-derived keratinocytes in ACEG, and the numbers of these cells in the repigmentation sites 1 year after ACEG were still higher than those in the skin lesions. Therefore, ACEG is a promising therapeutic agent for refractory vitiligo. Age, clinical type, lesion site, and lesion stable period before surgery have significant impacts on repigmentation in ACEG. ACEG can increase the number of melanocytes and KRT6C+ keratinocytes in skin lesions, thereby restoring a skin microenvironment suitable for melanocyte survival.One sentence summaryAutologous cultured epithelial grafting (ACEG) technique is a promising therapy for refractory vitiligo.
Effect of insulin insufficiency on ultrastructure and function in skeletal muscle
Authors: Kopecky Chantal , Haug Michael , Reischl Barbara , Deshpande Nandan , Manandhar Bikash , King Thomas W. , Lee Victoria , Wilkins Marc R , Morris Margaret , Polly Patsie , Friedrich Oliver , Rye Kerry-Anne , Cochran Blake J 
Published: December 2022

AbstractBackgroundDecreased insulin availability and high blood glucose levels, the hallmark features of poorly controlled diabetes, drive disease progression and are associated with decreased skeletal muscle mass. We have shown that mice with β-cell dysfunction and normal insulin sensitivity have decreased skeletal muscle mass. This project asks how insulin deficiency impacts on the structure and function of the remaining skeletal muscle in these animals.MethodsSkeletal muscle function was determined by measuring exercise capacity and specific muscle strength prior to and after insulin supplementation for 28 days in 12-week-old mice with conditional β-cell deletion of the ATP binding cassette transporters ABCA1 and ABCG1 (β-DKO mice).Abca1andAbcg1floxed (fl/fl) mice were used as controls. RNAseq was used to quantify changes in transcripts in soleus and extensor digitorum longus muscles. Skeletal muscle and mitochondrial morphology were assessed by transmission electron microscopy. Myofibrillar Ca2+sensitivity and maximum isometric single muscle fibre force were assessed usingMyoRobotbiomechatronics technology.ResultsRNA transcripts were significantly altered in β-DKO mice compared to fl/fl controls (32 in extensor digitorum longus and 412 in soleus). Exercise capacity and muscle strength were significantly decreased in β-DKO mice compared to fl/fl controls (p=0.012), and a loss of structural integrity was also observed in skeletal muscle from the β-DKO mice. Supplementation of β-DKO mice with insulin restored muscle integrity, strength and expression of 13 and 16 of the dysregulated transcripts in and extensor digitorum longus and soleus muscles, respectively.ConclusionsInsulin insufficiency due to β-cell dysfunction perturbs the structure and function of skeletal muscle. These adverse effects are rectified by insulin supplementation.
The phosphoinositide signature guides the final step of plant cytokinesis
Authors: Lebecq Alexis , Fangain Aurélie , Gascon Elsa , Goldy Camila , Belcram Katia , Pastuglia Martine , Bouchez David , Caillaud Marie-Cécile 
Published: December 2022

ABSTRACTPlant cytokinesis, which fundamentally differs from that in animals, involves de novo assembly of a plasma membrane precursor named the cell plate. How the transition from the cell plate to a plasma membrane occurs at the end of the plant cytokinesis remains poorly understood. Here, we describe with unprecedented spatiotemporal precision, the acquisition of plasma membrane identity upon cytokinesis through the lateral patterning of phosphatidylinositol 4,5-bisphosphate PI(4,5)P2at the newly formed cell plate membrane. We show that during late cytokinesis, opposing polarity domains are formed along the cell plate. Exclusion of PI(4,5)P2from the leading edge of the cell plate is controlled by SAC9, a putative phosphoinositide phosphatase. SAC9 colocalizes with MAP65-3, a key regulator of the cytokinesis, at the cell plate leading zone and regulates its function. In thesac9-3mutant, the polar distribution of PI(4,5)P2at the cell plate is altered, leading to de-novo recruitment of the cytokinesis apparatus and to formation of an additional, ectopic cell plate insertion site. We proposed that PI(4,5)P2acts as a polar cue to spatially separate the expansion and maturation domains of the forming cell plate during the final steps of cytokinesis.One Sentence SummaryThe phosphoinositide PI(4,5)P2acts as an hallmark to guide the final step of plant cell division.
Application of computational data modeling to a large-scale population cohort assists the discovery of specific nutrients that influence beneficial human gut bacteriaFaecalibacterium prausnitzii
Authors: Dogra Shaillay Kumar , Dardinier Adrien , Mainardi Fabio , Siegwald Léa , Bartova Simona , Roy Caroline le , Chou Chieh Jason 
Published: December 2022

ABSTRACTFaecalibacterium prausnitzii(F. prausnitzii) is a bacterial taxon of the human gut with anti-inflammatory properties and negative associations with chronic inflammatory conditions.F. prausnitziimay be one of key species contributing to the effects of healthy eating habits, and yet little is known about the nutrients that enhance the growth ofF. prausnitziiother than simple sugars and fibers. Here we combined dietary and microbiome data from the American Gut Project (AGP) to identify nutrients that may be linked to the relative abundance ofF. prausnitzii. Using a machine learning approach in combination with univariate analyses, we identified that sugar alcohols, carbocyclic sugar and vitamins may contribute toF. prausnitziigrowth. We next explored the effects of these nutrients on the growth of twoF. prausnitziistrainsin vitroand observed strain dependent growth patterns on the nutrient tested. In the context of a complex community usingin vitrofermentation, none of the tested nutrients and nutrient combinations exerted a significant growth-promoting effect onF. prausnitziidue to high variability in batch responses. A positive association betweenF. prausnitziiand butyrate concentrations was observed. Future nutritional studies aiming to increase relative abundance ofF. prausnitziishould explore a personalized approach accounting for strain-level genetic variations and community-level microbiome composition.
Numerical investigation of the dynamics of a rigid spherical particle in a vortical cross-slot flow at moderate inertia
Authors: Kechagidis Konstantinos , Owen Benjamin , Guillou Lionel , Tse Henry , Di Carlo Dino , Krüger Timm 
Published: December 2022

AbstractThe study of flow and particle dynamics in microfluidic cross-slot channels is of high relevance for lab-on-a-chip applications. In this work we investigate the dynamics of a rigid spherical particle in a cross-slot junction for a channel height-to-width ratio of 0.6 and at a Reynolds number of 120 for which a steady vortex exists in the junction area. Using an in-house immersed- boundary-lattice-Boltzmann code, we analyse the effect of the entry position of the particle in the junction and the particle size on the dynamics and trajectory shape of the particle. We find that the dynamics of the particle depends strongly on its lateral entry position in the junction and weakly on its vertical entry position; particles that enter close to the centre show trajectory oscillations. Larger particles have longer residence times in the junction and tend to oscillate less due to their confinement. Our work contributes to the understanding of the particle dynamics in intersecting flows and enables the design of optimised geometries for cytometry and particle manipulation.
Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques
Authors: Rahmberg Andrew R. , Wu Chuanfeng , Shin Taehoon , Hong So Gun , Pei Luxin , Hickman Heather D. , Dunbar Cynthia E. , Brenchley Jason M. 
Published: December 2022

AbstractMacrophages are critical orchestrators of tissue immunity, from the initiation and resolution of antimicrobial immune responses to the subsequent repair of damaged tissue. Murine studies have demonstrated that tissue-resident macrophages are comprised of a mixture of yolk sac-derived cells that populate the tissue before birth and hematopoietic-derived replacements that are recruited in adult tissues both at steady-state and in increased numbers in response to tissue damage or infection. While resident macrophages in some murine tissues are readily turned over and replaced, other tissues primarily retain their original, yolk sac-derived complement of macrophages. How this translates to species that are constantly under immunologic challenge, such as humans, is unknown. To understand the ontogeny and longevity of tissue-resident macrophages in nonhuman primates (NHPs), we employ a model of autologous HSPC transplantation with HSPCs genetically modified to express individual bar-coded markers allowing for subsequent analysis of clonal differentiation of leukocyte subsets. We study the contribution of HSPC to tissue-macrophages and their clonotypic profiles relative to leukocyte subsets across tissues and peripheral blood. We also use in vivo bromodeoxyuracil infusions to monitor tissue macrophage turnover in NHPs at steady state. We find that, in all anatomic sites we studied, HSPC contribute to tissue-resident macrophage populations. Their clonotypic profile is dynamic and overlaps significantly with the clonal hierarchy of contemporaneous monocytes in peripheral blood. Moreover, we find evidence of tissue-macrophage turnover at steady state in otherwise unmanipulated NHPs. These data demonstrate the life span of tissue-resident macrophages can be limited and they can be replenished from HSPCs. Thus, in primates not all yolk-sac derived tissue-macrophages survive for the duration of the host’s life.
Corruption, quality of institutions and growth
Authors: Beyaert Arielle , García-Solanes José , Lopez-Gomez Laura 
Published: December 2022

Purpose
This paper aims to apply regression-tree analysis to capture the nonlinear effects of corruption on economic growth. Using data of 103 countries for the period 1996–2017, the authors endogenously detect two distinct areas in corruption quality in which the members share the same model of economic growth.

Design/methodology/approach
The authors apply regression tree analysis to capture the nonlinearity of the influences. This methodology allows us to split endogenously the whole sample of countries and characterize the different ways through which corruption impacts economic growth in each group of countries.

Findings
The traditional determinants of economic growth have different impacts on countries depending on their level of corruption, which, in turn, confirms the parameter heterogeneity of the Solow model found in other strands of the literature.

Originality/value
The authors apply a new approach to a worldwide sample obtaining novel results.
Project monitoring and evaluation to engage stakeholders of international development projects for community impact
Authors: Amin Humera , Scheepers Helana , Malik Mohsin 
Published: December 2022

PurposeThis paper aims to examine the role of project monitoring and evaluation (M&E) in international development (ID) project stakeholders' relationships. This study draws on agency theory to examine the specific role M&E plays in improving ID project impact.Design/methodology/approachQualitative data comprising of in-depth interviews were collected from ID project stakeholders such as project donors, implementing partners and steering committee members.FindingsResults of the study show that project M&E activities can serve multiple purposes including the collection of data for the assessment of inputs, outputs, outcomes and impact. This information is shared with stakeholders to assist in evidence-based decision-making to improve project impact on community. This study shows that M&E activities strengthen the relationship between stakeholders by involving multiple stakeholders at different stages of ID projects to identify community needs and to demonstrate the positive community impact. Agency issues such as goal incongruence, information asymmetry and risk-sharing affect the relationship between the stakeholders. Investing in different M&E activities can reduce these issues, ultimately leading to a positive impact at the community level.Originality/valueThere has been limited research that explores the principal-agent relationship between project stakeholders of ID projects through the lens of agency theory. The role of M&E to collect project data and address agency issues between project stakeholders to improve project impact is the novel contribution of this paper.