bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining Generalizability of Nutrient-Based Food Patterns and Their Cross-Sectional Associations with Cardiometabolic Health for Hispanic/Latino Adults in the US: Results from the National Health and Nutrition Examination Survey (NHANES) and the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Authors: Varela Jeanette J , Mattei Josiemer , Sotres-Alvarez Daniela , Mossavar-Rahmani Yasmin , McClain Amanda C , Maldonado Luis E , Daviglus Martha L , Stephenson Briana J.K. 
Published: May 2023

AbstractBackgroundEthnicity, cultural background, and geographic location differ significantly amongst the US Hispanic/Latino population. These characteristic differences can greatly define measured diet and its relationship with cardiometabolic disease, thus influencing generalizability of results.ObjectiveWe aimed to examine dietary patterns of Hispanic/Latino adults and their association with cardiometabolic risk factors (high cholesterol, hypertension, obesity, diabetes) across two representative studies with differing sampling strategies.MethodsData were collected from Mexican or Other Hispanic adult participants from 2007-2012 National Health and Nutrition Examination Survey (NHANES, n=3,209) and 2007-2011 Hispanic Community Health Survey/Study of Latinos (HCHS/SOL, n=13,059). Nutrient-based food patterns (NBFPs) were derived using factor analysis on nutrient intake data estimated from 24-hour dietary recalls and interpreted using common foods prominent in these nutrients. Cross-sectional association between NBFPs (quintiles) and cardiometabolic risk factors, defined by clinical measures and self-report, were estimated using survey-weighted logistic regression.ResultsFive NBFPs were identified in both studies: (1) meats, (2) grains/legumes, (3) fruits/vegetables, (4) dairy, and (5) fats/oils. Association to cardiometabolic risk factors differed by NBFP and study. In HCHS/SOL, persons in the highest quintile of meats NBFP had higher odds of diabetes (OR=1.43, 95%CI: 1.10, 1.86) and obesity (OR=1.36, 95%CI: 1.14, 1.63). Those in the lowest quintile of grains/legumes NBFP (OR=1.22, 95%CI: 1.02, 1.47) and the highest quintile of fats/oils (OR=1.26, 95%CI: 1.03, 1.53) also had higher odds of obesity. In NHANES, NBFPs associated with higher odds of diabetes included those in the lowest quintile of dairy (OR=1.66, 95%CI: 1.01, 2.72) and highest quintile of grains/legumes (OR=2.10, 95%CI: 1.26, 3.50). Persons in the fourth quintile of meats (OR=0.68, 95%CI: 0.47, 0.99) had lower odds of cholesterol.ConclusionDiet-disease relationships among Hispanic/Latino adults vary according to two representative studies. These differences have research and practical implications when generalizing inferences on heterogeneous underrepresented populations.
Structural and biochemical characterisation of the N-Carbamoyl-β-Alanine Amidohydrolase fromRhizobium radiobacterMDC 8606
Authors: Paloyan Ani , Sargsyan Armen , Karapetyan Mariam D. , Hambardzumyan Artur , Kocharov Sergey , Panosyan Henry , Dyukova Karine , Kinosyan Marina , Krüger Anna , Piergentili Cecilia , Stanley Will A. , Baslé Arnaud , Marles-Wright Jon , Antranikian Garabed 
Published: May 2023

AbstractN-Carbamoyl-β-Alanine Amidohydrolase (CβAA) constitute one of the most important groups of industrially relevant enzymes used in production of optically pure amino acids and derivatives. In this study, a N-carbamoyl-β-alanine amidohydrolase encoding gene fromRhizobium radiobacterMDC 8606 was cloned and overexpressed inEscherichia coli. The purified recombinant enzyme (RrCβAA) showed a specific activity of 14 U/mg using N-carbamoyl-β-alanine as a substrate with an optimum activity of 55°C at pH 8.0. In this work, we report also the first prokaryotic N-carbamoyl-β-alanine amidohydrolases structure at a resolution of 2.0 Å. A discontinuous catalytic domain and a dimerization domain attached through a flexible hinge region at the domain interface has been revealed. We have found that the ligand is interacting with a conserved glutamic acid (Glu131), histidine (H385) and arginine (Arg291) residues. Studies let us to explain the preference on the enzyme for linear carbamoyl substrates as large carbamoyl substrates cannot fit in the active site of the enzyme. This work envisages the use of RrCβAA from theRhizobium radiobacterMDC 8606 for the industrial production of L-α-, L-β-, and L-γ – amino acids. The structural analysis provides new insights on enzyme–substrate interaction, which shed light on engineering of N-carbamoyl-β-alanine amidohydrolases for high catalytic activity and broad substrate specificity.
Human Smc5/6 recognises transcription-generated positive DNA supercoils
Authors: Diman Aurélie , Panis Gaël , Castrogiovanni Cédric , Prados Julien , Baechler Bastien , Strubin Michel 
Published: May 2023

SummaryBeyond its essential roles in ensuring faithful chromosome segregation and genomic stability, the human Smc5/6 complex acts as an antiviral factor. It binds to and impedes the transcription of extrachromosomal DNA templates; an ability which is lost upon chromosomal DNA integration. How the complex distinguishes among different DNA templates is unknown. Here we show that, in human cells, Smc5/6 preferentially binds to circular rather than linear extrachromosomal DNA. We further show that this binding is unlikely due to differences in the chromatin composition. Instead, the transcriptional process, per se, and more specifically the accumulation of DNA secondary structures known to be substrates for topoisomerases, is responsible for Smc5/6 recruitment. Those findings, in conjunction with our genome-wide Smc5/6 binding analysis showing that Smc5/6 localizes at few but highly transcribe chromosome loci, reveal a previously unforeseen role of Smc5/6 in DNA topology management during transcription.
Anterior forebrain pathway in parrots is necessary for producing learned vocalizations with individual signatures
Authors: Zhao Zhilei , Teoh Han Kheng , Carpenter Julie , Nemon Frieda , Kardon Brian , Cohen Itai , Goldberg Jesse H. 
Published: May 2023

SummaryParrots have enormous vocal imitation capacities and produce individually unique vocal signatures. Like songbirds, parrots have a nucleated neural song system with distinct anterior (AFP) and posterior forebrain pathways (PFP). To test if song systems of parrots and songbirds, which diverged over 50 million years ago, have a similar functional organization, we first established a neuroscience-compatible call-and-response behavioral paradigm to elicit learned contact calls in budgerigars (Melopsittacus undulatus). Using variational autoencoder-based machine learning methods, we show that contact calls within affiliated groups converge but that individuals maintain unique acoustic features, or vocal signatures, even after call convergence. Next, we transiently inactivated the outputs of AFP to test if learned vocalizations can be produced by the PFP alone. As in songbirds, AFP inactivation had an immediate effect on vocalizations, consistent with a premotor role. But in contrast to songbirds, where the isolated PFP is sufficient to produce stereotyped and acoustically normal vocalizations, isolation of the budgerigar PFP caused a degradation of call acoustic structure, stereotypy, and individual uniqueness. Thus the contribution of AFP and the capacity of isolated PFP to produce learned vocalizations have diverged substantially between songbirds and parrots, likely driven by their distinct behavioral ecology and neural connectivity.
Structural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development
Authors: Carmona-Rosas Gabriel , Li Jingxian , Smith Jayson J. , Cheng Shouqiang , Baltrusaitis Elana , Nawrocka Wioletta I. , Zhao Minglei , Kratsios Paschalis , Araç Demet , Özkan Engin 
Published: May 2023

AbstractLatrophilins/ADGRLs are conserved adhesion-type G protein-coupled receptors associated with early embryonic morphogenesis defects, lethality, and sterility across multiple model organisms. However, their mechanistic roles in embryogenesis and the identity of their binding ligands remain unknown. Here, we identified a cell-surface receptor, TOL-1, the sole Toll-like receptor inC. elegans, as a novel ligand for theC. elegansLatrophilin, LAT-1. The extracellular lectin domain of LAT-1 directly binds to the second leucine-rich repeat domain of TOL-1. The highresolution crystal structure and the cryo-EM density map of the LAT-1–TOL-1 ectodomain complex reveal a previously-unobserved mode of one-to-one interaction enabled by a large interface. CRISPR/Cas9-mediated mutation of key interface residues selectively disrupted the endogenous LAT-1–TOL-1 interaction inC. elegans,leading to partial sterility, lethality, and malformed embryos. Thus, TOL-1 binding to LAT-1 represents a receptor-ligand axis essential for animal morphogenesis.
Biosynthesis of gibberellin-related compounds modulates far-red light responses in the liverwortMarchantia polymorpha
Authors: Sun Rui , Okabe Maiko , Miyazaki Sho , Ishida Toshiaki , Mashiguchi Kiyoshi , Inoue Keisuke , Yoshitake Yoshihiro , Yamaoka Shohei , Nishihama Ryuichi , Kawaide Hiroshi , Nakajima Masatoshi , Yamaguchi Shinjiro , Kohchi Takayuki 
Published: May 2023

ABSTRACTThe phytohormone gibberellins (GAs) are key regulators of growth, development and environmental responses in angiosperms. From an evolutionary perspective, all major steps of GA biosynthesis are conserved among vascular plants, while GA biosynthetic intermediates such asent-kaurenoic acid (KA) are also produced by bryophytes. Here we show that in the liverwortMarchantia polymorpha, KA and GA12are synthesized by evolutionarily conserved enzymes, which are required for developmental responses to far-red light (FR). Under FR-enriched conditions, mutants of various biosynthesis enzymes consistently altered thallus growth allometry, delayed the initiation of gametogenesis, and affected the morphology of gamete-bearing structures (gametangiophores). By chemical treatments and LC-MS/MS analyses, we confirmed these phenotypes were caused by deficiency of some GA-related compounds derived from KA, but not bioactive GAs from vascular plants. Transcriptome analysis showed that FR enrichment induced the up-regulation of genes related to stress responses and secondary metabolism inM. polymorpha, which was largely dependent on the biosynthesis of GA-related compounds. Due to the lack of the canonical GA receptors in bryophytes, we hypothesize that GA-related compounds are commonly synthesized in land plants but co-opted independently to regulate responses to light quality change in different lineages during the past 450 million years of evolution.
A Method for Monitoring the Effective Air Change Rate for Respiratory Aerosols Using Real-Time Tracers
Authors: Pathak Saurabh , Kottapalli Kalyan , Santarpia Joshua L. , Botham Aaron D. , Molyneux Sam D. , Balarashti Jamie 
Published: May 2023

AbstractVentilation is one of the most critical components in a layered approach toward reducing the spread of airborne infectious diseases in indoor spaces. However, building ventilation systems act together with natural ventilation, local filtration systems and other aerosol removal processes to remove infectious aerosols from an occupied space. Airflow-based determinations of ACH do not account for the full range of aerosol removal processes; however understanding the effective aerosol removal rate is critical to providing airborne infection control.In this study, we investigated the relationship between the calculated air change rate of a space (i.e. volumetric airflow based) and the effective air change rate for aerosol particle removal within the breathing zone based on direct measurements of the rate of change in tracer particle concentrations at representative occupant locations in a room. Further, we examined positional effects under well mixed and non-well mixed conditions.Our results demonstrate that tracer particles combined with real-time sensors can be used to make rapid, accurate measurements of the effective air change rate (eACH) for respiratory aerosols within the breathing zone of non-well mixed rooms. We used two experimental test beds for these analyses. First, numerical simulation (computational fluid dynamic simulation, CFD) was conducted to visualize airflow and particle removal paths within a realistic large room. Here, simulated sensors were placed in concentric zones around a nebulizer providing test-particle releases. This CFD model allowed a direct comparison of the differences between eACH and airflow ACH values under varying levels of mixing and airflow, in a fully controlled system.We then recapitulated this system in physical space to validate the CFD results under real-world conditions that include all mechanisms of particle removal that contribute to true aerosol clearance rates, including deposition and leakage. Here, we measured eACH using the decay of DNA tracer aerosols nebulized and monitored in real-time. We find that a standard sampling time of 15 minutes from the end of nebulization is sufficient to produce an accurate eACH value under non-well mixed conditions. The availability of a rapid direct test for eACH will enable empirical optimization of a wide range of ventilation and filtration mechanisms to reach and maintain target aerosol clearance rates that deliver reliable airborne infection control in typical indoor environments.
Geometric approach for non pharmaceutical interventions in epidemiology
Authors: Evain Laurent , Loeb Jean-Jacques 
Published: May 2023

AbstractVarious non pharmaceutical interventions have been settled to minimise the burden of the COVID-19 outbreak. We build a framework to analyse the dynamics of non pharmaceutical interventions, to distinguish between mitigations measures leading to objective scientific improvements and mitigations based on both political and scientific considerations. We analyse two possible strategies within this framework. Namely, we consider mitigations driven by the limited resources of the health system and mitigations where a constant set of measures is applied at different moments. We describe the optimal interventions for these scenarios. Our approach involves sir differential systems, it is qualitative and geometrical rather than computational. Along with the analysis of these scenarios, we collect several results that may be useful on their own, in particular on the ground when the variables are not known in real time.
Rme-6 integrates EGFR trafficking and signalling to regulate ERK1/2 signalosome dynamics
Authors: Alshahrani Fahad , Zhu Zhou , Ferreira Filipe , McComb Alasdair , Maib Hannes , Pruzina Sara , Robinson Darren , Murray David , Smythe Elizabeth 
Published: May 2023

AbstractEpidermal growth factor receptor (EGFR) signalling results in a variety of cell behaviours, including cell proliferation, migration and apoptosis, which depend on cell context. Here we have explored how the Rab5GEF, Rme-6, regulates EGFR signalling by modulating endocytic flux. We demonstrate that Rme-6, which acts early in the endocytic pathway, regulates EGFR trafficking through an endocytic compartment that is competent for ERK1/2 signalling. While overexpression of Rme-6 results in enhanced ERK1/2 nuclear localisation and c-Fos activation, loss of Rme-6 results in aberrant ERK1/2 signalling with increased cytoplasmic ERK1/2 phosphorylation (Thr202/Tyr204) but decreased ERK1/2 nuclear translocation and c-Fos activation, the latter leading to decreased cell proliferation. Phosphorylation of ERK1/2 by protein kinase 2 (CK2) is required for its nuclear translocation and our data support a model whereby Rme-6 provides a scaffold for a population of CK2 which is required for efficient nuclear translocation of ERK1/2. Rme-6 is itself a substrate for CK2 on Thr642 and Ser996 and phosphorylation on these sites can activate its Rab5GEF activity and endocytic trafficking of EGFR. Together our results indicate that Rme-6 co-ordinates EGFR trafficking and signalling to regulate the assembly and disassembly of an ERK1/2 signalosome.Summary statementHere we demonstrate how Rme-6, a Rab5GEF, co-ordinates trafficking and signalling of EGFR on the early endocytic pathway to ensure appropriate regulation of downstream ERK1/2 signalling.
Post-translational regulation of photosynthetic activity via the TOR kinase in plants
Authors: D’Alessandro Stefano , Velay Florent , Lebrun Régine , Mehrez Marwa , Romand Shanna , Saadouni Rim , Forzani Céline , Citerne Sylvie , Montané Marie-Hélène , Robaglia Christophe , Menand Benoît , Meyer Christian , Field Ben 
Published: May 2023

AbstractChloroplasts are the powerhouse of the plant cell, yet they are resource-intensive and will cause photooxidative damage if their activity overshoots the demands of growth. The adjustment of chloroplast activity to match growth is therefore vital for stress acclimation. Here we identify a novel post-translational mechanism linking the conserved eukaryotic TOR kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origin that regulates chloroplast activity, and photosynthesis in particular. We show that RelA SpoT Homologue 3 (RSH3), a nuclear-encoded chloroplastic enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific N-terminal region (NTR) which is hyper-phosphorylated in a TOR-dependent manner. Downregulation of TOR activity reduces NTR phosphorylation, enhances ppGpp synthesis by RSH3, and causes a ppGpp-dependent decrease in photosynthetic capacity. Altogether we demonstrate that the TOR-RSH3 signaling axis is a novel and direct post-translational mechanism that allows chloroplast activity to be matched with plant growth, setting a new precedent for the regulation of organellar function by TOR.One sentence summaryThe TOR kinase post-translationally controls guanosine tetraphosphate signaling to regulate plant photosynthetic activity.
Acute joint inflammation induces a sharp increase in the number of synovial fluid EVs and modifies their phospholipid profile
Authors: Varela Laura , van de Lest Chris H.A. , Boere Janneke , Libregts Sten F.W.M. , Lozano–Andres Estefania , van Weeren P. René , Wauben Marca H.M. 
Published: May 2023

ABSTRACTInflammation is the hallmark of most joint disorders. However, the precise regulation of induction, perpetuation, and resolution of joint inflammation is not entirely understood. Since extracellular vesicles (EVs) are critical for intercellular communication, we aim to unveil their role in these processes. Here, we investigated the EVs’ dynamics and phospholipidome profile from synovial fluid (SF) of healthy equine joints and from horses with lipopolysaccharide (LPS)–induced synovitis. LPS injection triggered a sharp increase of SF–EVs at 5–8hr post–injection, which started to decline at 24h post–injection. Importantly, we identified significant changes in the lipid profile of SF–EVs after synovitis induction. Compared to healthy joint–derived SF–EVs (0h), SF–EVs collected at 5, 24, and 48h post–LPS injection were strongly increased in hexosylceramides. At the same time, phosphatidylserine, phosphatidylcholine, and sphingomyelin were decreased in SF–EVs at 5h and 24h post–LPS injection. Based on the lipid changes during acute inflammation, we composed specific lipid profiles associated with healthy and inflammatory state–derived SF–EVs. The sharp increase in SF–EVs during acute synovitis and the correlation of specific lipids with either healthy or inflamed states–derived SF–EVs are findings of potential interest for unveiling the role of SF–EVs in joint inflammation, as well as for the identification of EV–biomarkers of joint inflammation.
Formal learning and organizational performance: the interplay of goal setting and flexible learning practices in attaining goal congruence
Authors: Madhavan Vandana , Venugopalan Murale 
Published: May 2023

PurposeEmployee training and learning have transformed over the years. The movement from classroom training to the blended format represents the magnitude of this evolution. This has placed much attention on self-regulated learning. This study aimed to understand the individual and organizational mechanisms that sustain the formal learning process in organizations. It explored the goals the organizations and employees strive to achieve by investing in learning. Through this, the authors investigated how technology assistance makes learning more goal-oriented, despite the possibility of different goals for different stakeholders. They also examined how person-job fit can be achieved in employee training.Design/methodology/approachThe study adopted a grounded theory-based inductive approach using a qualitative inquiry that used in-depth interviews of employees working in the Indian IT/ITES sector. This sector is knowledge-intensive and engages in constant skill development. A content analysis of the interview transcripts unraveled the most relevant themes from the participants' discussion.FindingsIndividual learners use dimensions of self-regulated learning to set and achieve goals such as better performance and career development. On the other hand, organizations use learning support mechanisms such as better access and flexibility to direct employee learning behavior to achieve organizational goals. Focusing on goal congruence leads to better achievement of results. Goal congruence also implies good person-organization fit.Originality/valueThis research established how aligning individual and organizational mechanisms can help achieve training goals that ultimately contribute to organizational performance. The study differentiated itself by investigating training goal setting and goal achievement at two levels – organizational and individual – using a qualitative approach. It also showed how goal congruence is vital in improving organizational performance and how technology-enabled training practices rely on self-regulated learning and help achieve goal congruence.