bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of lignocellulose degradation in microorganisms
Authors: Gurovic María Soledad Vela , Viceconte Fatima Regina , Bidegain Maximiliano Andres , Dietrich Julián 
Published: March 2023

AbstractMicrobial strategies for biomass deconstruction involve an incredible repertoire of enzymatic, structural, and regulatory proteins. From carbohydrate active enzymes to cellulosomes, bacteria, yeast, and filamentous fungi adapt their functional machinery to grow from alternative carbon sources such as lignocellulose and survive starvation. In that context, microbes must be able to sense, bind, degrade, and utilize lignin, cellulose, and hemicelluloses. Nature has developed specialized protein modules, RNA structures, and regulatory systems operating at a genomic, transcription, and translation level. This review briefly summarizes the main regulatory pathways involved in lignocellulose microbial degradation, including carbon catabolite repression; anti-sigma factors; regulatory RNA elements such as small RNAs, antisense RNA, RNA-binding proteins, and selective RNA processing and stabilization; and transcriptional regulators and unfolded protein response. Interplay with global regulators controlling pH response and nitrogen utilization is also revised.
Effects of low-energy diet supplemented with betaine on growth performance, nutrient digestibility, and serum metabolomic profiles in growing pigs
Authors: Fu Runqi , Liang Chan , Chen Daiwen , Tian Gang , Zheng Ping , He Jun , Yu Jie , Mao Xiangbing , Gu Zhemin , Yang Wenwu , Yu Bing 
Published: March 2023

AbstractTwo experiments were carried out to evaluate the effects of betaine (BET) supplementation in diets with reduced net energy (NE) levels on growth performance, nutrient digestibility, and serum metabolomic profiles in growing pigs. In experiment 1, 24 growing pigs (initial body weight, BW, 30.83 ± 2.50 kg) were allotted to one of the four treatments (six replications with 1 pig per pen) in a 2 × 2 factorial arrangement, including two dietary NE levels (2475 [N-NE] or 2395 [R80-NE] kcal/kg) and two BET doses (0 or 1500 mg/kg). In experiment 2, 72 growing pigs were used in a 2 × 3 factorial arrangement, including three dietary NE levels (2475 [N-NE], 2415 [R60-NE], or 2355 [R120-NE] kcal/kg) and two BET doses (0 or 1500 mg/kg). Pigs with initial BW of 31.44 ± 1.65 kg were divided to one of the six treatments (six replications with 2 pigs per pen). In experiment 1, lowing NE concentrations increased average daily feed intake (ADFI) by 10.69% in pigs fed the diet without BET (P &gt; 0.05). BET significantly increased ADFI in N-NE diet (P &lt; 0.05) but had no influence on ADFI in R80-NE diet (P &gt; 0.05). BET enhanced the apparent digestibility of crude protein (CP), dry matter (DM), organic matter (OM), gross energy (GE), and ether extract (EE) in R80-NE diet (P &lt; 0.05). In experiment 2, lowing NE concentrations enhanced ADFI (P &gt; 0.05) and decreased average daily gain (ADG; P &lt; 0.05). The reduction in feed intake by BET was further enhanced as NE concentrations decreased from 2415 to 2355 kcal/kg (P &lt; 0.10). BET reversed the elevation of serum triglyceride, alkaline phosphatase, aspartate aminotransferase, and alanine aminotransferase levels caused by R120-NE diet (P &lt; 0.05). The concentrations of cholecystokinin and glucagon-like peptide 1 were increased by BET in pigs fed the R120-NE diet (P &lt; 0.05). Serum metabolomics reveals that lowing dietary NE concentrations affected mainly amino acid biosynthetic pathways (P &lt; 0.05). BET supplementation in R120-NE diet up-regulated serum BET levels and down-regulated homocysteine, DL-carnitine, and four amino acid secondary metabolites (P &lt; 0.05). In conclusion, lowing dietary NE contents reduced the growth performance and caused metabolic abnormalities in growing pigs. However, BET decreased feed intake to a certain extent and improved the metabolic health of pigs fed the low-NE diets, which may be related to the dual regulation of amino acid metabolism and the secretion of appetite related hormones by BET.
Traction-related complications in hip arthroscopy for 26 years. A systematic review
Authors: Arriaza Carlos R , Navarrete Carlos Andrés , Palos Jaime , Suarez-Ahedo Carlos 
Published: March 2023

ABSTRACT
The primary aim of the study is to determine the rate of traction-related complications in hip arthroscopy (HA) including perineal compression and distraction injuries, and the secondary objective is to report the incidence of complications in HA found on the studies selected by a systematic review. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were used for data extraction from the PubMed and Cochrane databases obtained in February 2022. Reviewers extracted the title, author, date of publication, number of hips treated and number of complications describing the affected area, nerve and soft tissue injury related to traction. Studies on postless HA and HA combined with other procedures were excluded. Twenty-six years of HA literature was found in the search that included 35 studies and 8126 hips (89% Level IV) that reported the complications found during the procedure and described complications related to traction. A total of 623 hips (7.7%) had some sort of complications during HA, and complications related to traction were in 227 hips (36%). Injuries caused specifically by the perineal compression were in 144 hips (23%) that included the pudendal nerve and soft tissue injury of the groin area. Complications caused by the distraction were in 83 hips (13%) that included sciatic and peroneal nerve injury, numbness or pain of ankle and foot. HA complications occurred in 7.7% of hips treated, which is found in this systematic review. One-third of the complications are related to traction, 23% are caused by perineal compression and 13% are caused by distraction.
Monoclonal Antibodies for COVID-19 in Children: Case Series Should be Just the Start
Authors: Teoh Zheyi , Willis Zachary I 
Published: March 2023

Abstract
Two new articles describe the use and implementation of monoclonal antibodies to treat COVID-19 in children. While these studies provide valuable guidance for pediatric clinicians, more studies of monoclonal antibodies and other COVID-19 therapies in children are needed.
Marsupialization and peripheral ostectomy for the management of large odontogenic keratocyst: a case report
Authors: Khalil Ali , Albash Ziad , Sleman Nadim , Sayegh Wadie 
Published: March 2023

AbstractOdontogenic keratocyst has been of particular interest due to its distinctive behavior and its tendency to frequently recurrence and the diversity of treatment methods. Researchers have differed over the past decades about the nature of this lesion, sometimes it was classified as a cyst and sometimes it was classified as a tumor because of its specific histopathologic features, high recurrence rate and aggressive behavior. We discuss a case of a large odontogenic keratocyst (OKC) that was treated by marsupialization followed by peripheral ostectomy. Based on our findings, we conclude that the marsupialization followed by peripheral ostectomy was a conservative and effective option for the management of large OKC.
Assessing the spin–orbit obliquity of low-mass planets in the breaking the chain formation model: a story of misalignment
Authors: Esteves Leandro , Izidoro André , Winter Othon C , Bitsch Bertram , Isella Andrea 
Published: March 2023

ABSTRACT
The spin–orbit obliquity of a planetary system constraints its formation history. A large obliquity may either indicate a primordial misalignment between the star and its gaseous disc or reflect the effect of different mechanisms tilting planetary systems after formation. Observations and statistical analysis suggest that system of planets with sizes between 1 and 4 R⊕ has a wide range of obliquities (∼0–30○), and that single- and multiplanet transiting have statistically indistinguishable obliquity distributions. Here, we revisit the ‘breaking the chains’ formation model with focus in understanding the origin of spin–orbit obliquities. This model suggests that super-Earths and mini-Neptunes migrate close to their host stars via planet–disc gravitational interactions, forming chain of planets locked in mean-motion resonances. After gas-disc dispersal, about 90–99 per cent of these planetary systems experience dynamical instabilities, which spread the systems out. Using synthetic transit observations, we show that if planets are born in discs where the disc angular momentum is virtually aligned with the star’s rotation spin, their final obliquity distributions peak at ∼5° or less, and the obliquity distributions of single- and multiplanet transiting systems are statistically distinct. By treating the star-disc alignment as a free-parameter, we show that the obliquity distributions of single- and multiplanet transiting systems only become statistically indistinguishable if planets are assumed to form in primordially misaligned natal discs with a tilt’ distribution peaking at ≳10–20°. We discuss the origin of these misalignments in the context of star formation and potential implications of this scenario for formation models.
The connection between stellar mass, age, and quenching time-scale in massive quiescent galaxies atz≃ 1
Authors: Hamadouche M L , Carnall A C , McLure R J , Dunlop J S , Begley R , Cullen F , McLeod D J , Donnan C T , Stanton T M 
Published: March 2023

ABSTRACTWe present a spectrophotometric study of a mass-complete sample of quiescent galaxies at 1.0 &lt; z &lt; 1.3 with $\mathrm{log_{10}}(M_{\star }/\mathrm{{\rm M}_{\odot }}) \ge 10.3$ drawn from the VANDELS survey, exploring the relationship between stellar mass, age, and star-formation history. Within our sample of 114 galaxies, we derive a stellar–mass versus stellar–age relation with a slope of $1.20^{+0.28}_{-0.27}$ Gyr per decade in stellar mass. When combined with recent literature results, we find evidence that the slope of this relation remains consistent over the redshift interval 0 &lt; z &lt; 4. The galaxies within the VANDELS quiescent sample display a wide range of star-formation histories, with a mean quenching time-scale of 1.4 ± 0.1 Gyr. We also find a large scatter in the quenching time-scales of the VANDELS quiescent galaxies, in agreement with previous evidence that galaxies at z ∼ 1 cease star formation via multiple mechanisms. We then focus on the oldest galaxies in our sample, finding that the number density of galaxies that quenched before z = 3 with stellar masses $\mathrm{log_{10}}(M_{\star }/\mathrm{{\rm M}_{\odot }}) \ge 10.6$ is $1.12_{-0.72}^{+1.47} \times 10^{-5} \ \mathrm{Mpc}^{-3}$. Although uncertain, this estimate is in good agreement with the latest observational results at 3 &lt; z &lt; 4, tentatively suggesting that neither rejuvenation nor merger events are playing a major role in the evolution of the oldest massive quiescent galaxies within the redshift interval 1 &lt; z &lt; 3.
Spatially resolved observations of outflows in the radio loud AGN of UGC 8782
Authors: Riffel Rogemar A , Riffel Rogério , Bianchin Marina , Storchi-Bergmann Thaisa , Souza-Oliveira Gabriel Luan , Zakamska Nadia L 
Published: March 2023

ABSTRACTWe use optical integral field spectroscopy (IFU) to study the gas emission structure and kinematics in the inner 3.4 × 4.9 kpc2 region of the galaxy UGC 8782 (3C 293), host of a radio loud active galactic nucleus (AGN). The observations were performed with the Gemini-North multi-object spectrograph (GMOS)-IFU on the Gemini North telescope, resulting in a spatial resolution of ∼725 pc at the distance of the galaxy. While the stars present ordered rotation following the orientation of the large-scale disc, the gas shows a disturbed kinematics. The emission-line profiles present two kinematic components: a narrow (σ ≲ 200 km s−1) component associated with the gas in the disc of the galaxy and a broad (σ ≳ 200 km s−1) component produced by gas outflows. Emission-line ratio diagrams indicate that the gas in the disc is excited by the AGN radiation field, while the emission of the outflow includes additional contribution of shock excitation due to the interaction of the radio jet with the environment gas. Deviations from pure rotation, of up to 30 km s−1, are observed in the disc component and likely produced by a previous merger event. The broad component is blueshifted by ∼150–500 km s−1 relative to the systemic velocity of the galaxy in all locations. We construct radial profiles of the mass outflow rate and kinetic power of the ionized gas outflows, which have the maximum values at ∼1 kpc from the nucleus with peak values of $\dot{M}_{\rm out,\Delta R} = 0.5\pm 0.1$ M⊙ yr−1 and $\dot{K}_{\rm out,\Delta R} = (6.8\pm 1.1)\times 10^{41}$ erg s−1. The kinetic coupling efficiency of these outflows are in the range of 1–3 per cent, indicating that they could be powerful enough to affect the star formation in the host galaxy as predicted by theoretical simulations.
Efficient exploration of reionization parameters for the upcoming 21 cm observations using a photon-conserving seminumerical model SCRIPT
Authors: Maity Barun , Choudhury Tirthankar Roy 
Published: March 2023

ABSTRACTOne of the most promising probes to constrain the reionization history of the universe is the power spectrum of neutral hydrogen 21 cm emission fluctuations. The corresponding analyses require computationally efficient modelling of reionization, usually achieved through seminumerical simulations. We investigate the capability of one such seminumerical code, SCRIPT, to constrain the reionization parameters. Our study involves creating a mock data set corresponding to the upcoming SKA-Low, followed by a Bayesian inference method to constrain the model parameters. In particular, we explore in detail whether the inferred parameters are unbiased with respect to the inputs used for the mock and also if the inferences are insensitive to the resolution of the simulation. We find that the model is successful on both fronts. We also develop a simple template model of reionization that can mimic the complex physical processes like inhomogeneous recombinations and radiative feedback and show that it can recover the global reionization history reliably with a moderate computational cost. However, such simple models are not suitable for constraining the properties of the ionizing sources. Our results are relevant for constraining reionization using high-quality data expected in the future telescopes.
Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution
Authors: Bernard Charles , Li Yanyan , Lopez Philippe , Bapteste Eric 
Published: March 2023

AbstractGram-positive Firmicutes bacteria and their mobile genetic elements (plasmids and bacteriophages) encode peptide-based quorum-sensing systems (QSSs) that orchestrate behavioral transitions as a function of population densities. In their simplest form, termed “RRNPP”, these QSSs are composed of two adjacent genes: a communication propeptide and its cognate intracellular receptor. RRNPP QSSs notably regulate social/competitive behaviors such as virulence or biofilm formation in bacteria, conjugation in plasmids, or lysogeny in temperate bacteriophages. However, the genetic diversity and the prevalence of these communication systems, together with the breadth of behaviors they control, remain largely underappreciated. To better assess the impact of density dependency on microbial community dynamics and evolution, we developed the RRNPP_detector software, which predicts known and novel RRNPP QSSs in chromosomes, plasmids, and bacteriophages of Firmicutes. Applying RRNPP_detector against available complete genomes of viruses and Firmicutes, we identified a rich repertoire of RRNPP QSSs from 11 already known subfamilies and 21 novel high-confidence candidate subfamilies distributed across a vast diversity of taxa. The analysis of high-confidence RRNPP subfamilies notably revealed 14 subfamilies shared between chromosomes/plasmids/phages, 181 plasmids and 82 phages encoding multiple communication systems, phage-encoded QSSs predicted to dynamically modulate bacterial behaviors, and 196 candidate biosynthetic gene clusters under density-dependent regulation. Overall, our work enhances the field of quorum-sensing research and reveals novel insights into the coevolution of gram-positive bacteria and their mobile genetic elements.
Rye: genetic ancestry inference at biobank scale
Authors: Conley Andrew B , Rishishwar Lavanya , Ahmad Maria , Sharma Shivam , Norris Emily T , Jordan I King , Mariño-Ramírez Leonardo 
Published: March 2023

Abstract
Biobank projects are generating genomic data for many thousands of individuals. Computational methods are needed to handle these massive data sets, including genetic ancestry (GA) inference tools. Current methods for GA inference do not scale to biobank-size genomic datasets. We present Rye—a new algorithm for GA inference at biobank scale. We compared the accuracy and runtime performance of Rye to the widely used RFMix, ADMIXTURE and iAdmix programs and applied it to a dataset of 488221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis of genomic variant samples from ancestral reference populations and query individuals. The algorithm's accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares regression. Rye produces highly accurate GA estimates for three-way admixed populations—African, European and Native American—compared to RFMix and ADMIXTURE (${R}^2 = \ 0.998 - 1.00$), and shows 50× runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at both continental and subcontinental levels. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.
Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity
Authors: Rostain William , Grebert Theophile , Vyhovskyi Danylo , Pizarro Paula Thiel , Tshinsele-Van Bellingen Gatwa , Cui Lun , Bikard David 
Published: March 2023

Abstract
Genetic tools derived from the Cas9 RNA-guided nuclease are providing essential capabilities to study and engineer bacteria. While the importance of off-target effects was noted early in Cas9’s application to mammalian cells, off-target cleavage by Cas9 in bacterial genomes is easily avoided due to their smaller size. Despite this, several studies have reported experimental setups in which Cas9 expression was toxic, even when using the catalytic dead variant of Cas9 (dCas9). Specifically, dCas9 was shown to be toxic when in complex with guide RNAs sharing specific PAM (protospacer adjacent motif)-proximal sequence motifs. Here, we demonstrate that this toxicity is caused by off-target binding of Cas9 to the promoter of essential genes, with silencing of off-target genes occurring with as little as 4 nt of identity in the PAM-proximal sequence. Screens performed in various strains of Escherichia coli and other enterobacteria show that the nature of toxic guide RNAs changes together with the evolution of sequences at off-target positions. These results highlight the potential for Cas9 to bind to hundreds of off-target positions in bacterial genomes, leading to undesired effects. This phenomenon must be considered in the design and interpretation of CRISPR–Cas experiments in bacteria.
Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers
Authors: Patel Parasvi S , Algouneh Arash , Krishnan Rehna , Reynolds John J , Nixon Kevin C J , Hao Jun , Lee Jihoon , Feng Yue , Fozil Chehronai , Stanic Mia , Yerlici Talya , Su Peiran , Soares Fraser , Liedtke Elisabeth , Prive Gil , Baider Gary D , Pujana Miquel Angel , Mekhail Karim , He Housheng Hansen , Hakem Anne , Stewart Grant S , Hakem Razqallah 
Published: March 2023

Abstract
BRCA1 mutations are associated with increased breast and ovarian cancer risk. BRCA1-mutant tumors are high-grade, recurrent, and often become resistant to standard therapies. Herein, we performed a targeted CRISPR-Cas9 screen and identified MEPCE, a methylphosphate capping enzyme, as a synthetic lethal interactor of BRCA1. Mechanistically, we demonstrate that depletion of MEPCE in a BRCA1-deficient setting led to dysregulated RNA polymerase II (RNAPII) promoter-proximal pausing, R-loop accumulation, and replication stress, contributing to transcription-replication collisions. These collisions compromise genomic integrity resulting in loss of viability of BRCA1-deficient cells. We also extend these findings to another RNAPII-regulating factor, PAF1. This study identifies a new class of synthetic lethal partners of BRCA1 that exploit the RNAPII pausing regulation and highlight the untapped potential of transcription-replication collision-inducing factors as unique potential therapeutic targets for treating cancers associated with BRCA1 mutations.
Short tandem repeats are important contributors to silencer elements in T cells
Authors: Hussain Saadat , Sadouni Nori , van Essen Dominic , Dao Lan T M , Ferré Quentin , Charbonnier Guillaume , Torres Magali , Gallardo Frederic , Lecellier Charles-Henri , Sexton Tom , Saccani Simona , Spicuglia Salvatore 
Published: March 2023

AbstractThe action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
Authors: Padroni Giacomo , Bikaki Maria , Novakovic Mihajlo , Wolter Antje C , Rüdisser Simon H , Gossert Alvar D , Leitner Alexander , Allain Frederic H-T 
Published: March 2023

AbstractThe pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further fragment expansion and drug development.