bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of thers3856806Polymorphism in thePPARGGene with Type 2 Diabetes Mellitus: A Meta-Analysis of 11,811 Individuals
Authors: Tiongco Raphael Enrique , Basilio Henry , Camacho Dharleen Ryanne , Ellorin Willie Mae , Sico Clarisse Arianne , Arceo Engracia 
Published: October 2022

AbstractThis study investigated the role of the rs3856806 single nucleotide variant (SNV) on the peroxisome proliferator-activated receptor γ with the development of type 2 diabetes mellitus (T2DM) by conducting a meta-analysis. Relevant studies were searched in PubMed and were selected according to the inclusion criteria. Data were extracted and subjected to analysis using Review Manager 5.4.1. Pooled odds ratios (OR) and 95% confidence intervals (CI) were computed to measure the association of the SNV with T2DM development. Nine studies published in English were retrieved up to October 1, 2021. Homogeneity (I2 = 3%, P = .41) was achieved for the allelic model with significant outcomes (OR: 0.82; 95% CI: 0.76-0.89; P &lt; .00001). Genotypic models also yielded significant associations for the co-dominant, dominant, and recessive models. All genotypic analysis showed homogeneity (I2 = 0-31%, P = .17-0.76) of the pooled outcomes. Our findings suggest that carrying the T allele of the rs3856806 SNV significantly decreases the risk of acquiring T2DM. However, further studies are necessary to support our claims.
Platelet MicroRNA-484 as a Novel Diagnostic Biomarker for Acute Coronary Syndrome
Authors: Masoodi Khabar Parisa , Ghydari Mohamad Esmail , Vazifeh Shiran Nader , Shirazy Mohammadreza , Hamidpour Mohsen 
Published: October 2022

Abstract

Objective
Platelet microRNAs (miRs) have been indicated as a diagnostic biomarker in various diseases, including acute coronary syndrome (ACS). This study aimed to investigate the expression of miR-223-5p, miR-126-5p, miR-484, and miR-130a-3p in individuals with coronary artery disease (CAD).

Methods
Forty subjects with CAD and 13 healthy individuals were under study. The expression of miR-223-5p, miR-126-5p, miR-484, and miR-130a-3p was measured in platelets by quantitative reverse transcription–polymerase chain reaction. The relationship between miRNA expression and various parameters of the subjects was analyzed using analysis of variance and Spearman and t-tests.

Results
The miR-484 expression was significantly upregulated in the ACS subjects (P = .0097). Moreover, miR-484 had diagnostic value for screening subjects with unstable angina vs controls (area under the curve [AUC] = 0.978, 95% confidence interval [CI] 0.92–1, P = .0006) and NSTEMI patients versus controls (AUC = 0.910, 95% CI 0.74–1, P = .005).

Conclusion
The results of this study indicate that the upregulated expression of miR-484 in ACS patients might be used as a diagnostic biomarker in ACS.
Transient Osteoporosis of the Hip: A Case Report of a U.S. Soldier
Authors: Dichiera Robert , Yim Duke 
Published: October 2022

ABSTRACT
Transient osteoporosis of the hip is described as an uncommon, self-limiting condition that typically affects middle-aged men and pregnant women in their third trimester. Transient osteoporosis most commonly affects the hip, but cases have been described in the knee, ankle, and foot. Symptoms include pain, limited range of motion, and antalgic gait. A greater level of awareness of transient osteoporosis of the hip as a differential diagnosis for hip pain will obviate unnecessary, inefficient, or unproductive interventions and treatments. Transient osteoporosis of the hip is a self-limiting disease process that requires only symptomatic treatment such as basic analgesia, physical therapy, and activity modification. On average, recovery is seen within 6-12 months.
Binary black hole merger rates in AGN discs versus nuclear star clusters: loud beats quiet
Authors: Ford K E Saavik , McKernan Barry 
Published: October 2022

ABSTRACT
Galactic nuclei are promising sites for stellar origin black hole (BH) mergers, as part of merger hierarchies in deep potential wells. We show that binary black hole (BBH) merger rates in active galactic nuclei (AGNs) should always exceed merger rates in quiescent galactic nuclei (nuclear star clusters, NSCs) around supermassive black holes (SMBHs) without accretion discs. This is primarily due to average binary lifetimes in AGNs that are significantly shorter than those in NSCs. The lifetime difference comes from rapid hardening of BBHs in AGNs, such that their semimajor axes are smaller than the hard–soft boundary of their parent NSC; this contrasts with the large average lifetime to merger for BBHs in NSCs around SMBHs, due to binary ionization mechanisms. Secondarily, merger rates in AGNs are enhanced by gas-driven binary formation mechanisms. Formation of new BHs in AGN discs is a minor contributor to the rate differences. With the gravitational wave detection of several BBHs with at least one progenitor in the upper mass gap, and signatures of dynamical formation channels in the χeff distribution, we argue that AGNs could contribute $\sim 25{\!-\!}80{{\ \rm per\ cent}}$ of the LIGO–Virgo measured rate of $\sim 24\, \rm {Gpc}^{-3} \rm {yr}^{-1}$.
TRAPUM upper limits on pulsed radio emission for SMC X-ray pulsar J0058−7218
Authors: Carli E , Levin L , Stappers B W , Barr E D , Breton R P , Buchner S , Burgay M , Kramer M , Padmanabh P V , Possenti A , Venkatraman Krishnan V , Behrend J , Champion D J , Chen W , Men Y P 
Published: October 2022

ABSTRACT
The TRAPUM collaboration has used the MeerKAT telescope to conduct a search for pulsed radio emission from the young Small Magellanic Cloud pulsar J0058−7218 located in the supernova remnant IKT 16, following its discovery in X-rays with XMM–Newton. We report no significant detection of dispersed, pulsed radio emission from this source in three 2-h L-band observations using the core dishes of MeerKAT, setting an upper limit of 7.0 $\mu$Jy on its mean flux density at 1284 MHz. This is nearly seven times deeper than previous radio searches for this pulsar in Parkes L-band observations. This suggests that the radio emission of PSR J0058−7218 is not beamed towards Earth or that PSR J0058−7218 is similar to a handful of Pulsar Wind Nebulae systems that have a very low radio efficiency, such as PSR B0540−6919, the Large Magellanic Cloud Crab pulsar analogue. We have also searched for bright, dispersed, single radio pulses and found no candidates above a fluence of 93 mJy ms at 1284 MHz.
Velocity profiles of matter and biased tracers around voids
Authors: Massara Elena , Percival Will J , Dalal Neal , Nadathur Seshadri , Radinović Slađana , Winther Hans A , Woodfinden Alex 
Published: October 2022

ABSTRACT
The velocity profile of galaxies around voids is a key ingredient for redshift space distortion (RSD) measurements made using the void–galaxy correlation function. In this paper, we use simulations to test whether the velocity profile of the tracers used to find the voids matches the velocity profile of the dark matter around these voids. A mismatch is expected and found in the inner part of voids, where tracers are very sparse. We discuss how this difference is caused by a selection effect where the void centre positions are correlated to the particular realization of the sparse tracers and their spatial distribution. In turn, this then affects the RSD void–galaxy correlation analysis. We show this by evaluating the Jacobian of the real to redshift space mapping using the tracer or matter velocity profile. Differences of the order of 20 per cent in the velocity profile translate into differences of the order of few per cent in the Jacobian. This small discrepancy propagates to the monopole and quadrupole of the void–tracer correlation function, producing modifications of comparable magnitude to those from changes in fσ8 at the level of the statistical uncertainties from current analyses.
Standard self-confinement and extrinsic turbulence models for cosmic ray transport are fundamentally incompatible with observations
Authors: Hopkins Philip F , Squire Jonathan , Butsky Iryna S , Ji Suoqing 
Published: October 2022

ABSTRACT
Models for cosmic ray (CR) dynamics fundamentally depend on the rate of CR scattering from magnetic fluctuations. In the ISM, for CRs with energies ∼MeV-TeV, these fluctuations are usually attributed either to ‘extrinsic turbulence’ (ET) – a cascade from larger scales – or ‘self-confinement’ (SC) – self-generated fluctuations from CR streaming. Using simple analytic arguments and detailed ‘live’ numerical CR transport calculations in galaxy simulations, we show that both of these, in standard form, cannot explain even basic qualitative features of observed CR spectra. For ET, any spectrum that obeys critical balance or features realistic anisotropy, or any spectrum that accounts for finite damping below the dissipation scale, predicts qualitatively incorrect spectral shapes and scalings of B/C and other species. Even if somehow one ignored both anisotropy and damping, observationally required scattering rates disagree with ET predictions by orders of magnitude. For SC, the dependence of driving on CR energy density means that it is nearly impossible to recover observed CR spectral shapes and scalings, and again there is an orders-of-magnitude normalization problem. But more severely, SC solutions with super-Alfvénic streaming are unstable. In live simulations, they revert to either arbitrarily rapid CR escape with zero secondary production, or to bottleneck solutions with far-too-strong CR confinement and secondary production. Resolving these fundamental issues without discarding basic plasma processes requires invoking different drivers for scattering fluctuations. These must act on a broad range of scales with a power spectrum obeying several specific (but plausible) constraints.
Martes martes(Carnivora: Mustelidae)
Authors: Monakhov Vladimir 
Published: October 2022

AbstractMartes martes (Linnaeus, 1758), commonly called the European pine marten, is a small predator widespread in western Eurasia. In almost all its geographic distribution, it is autochthonous. It is as a secondary consumer but, a predator with omnivorous traits. Martes martes inhabits forests with varied tree compositions, but in recent decades, it has spread to forest-steppe and agricultural areas. It is hunted in some areas, mainly in winter. In some countries during the 20th century, it experienced significant declines in numbers, but at present, it is “Least Concern” (LC) on the International Union for the Conservation of Nature’s Red List of Threatened Species.
Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei
Authors: Lindahl Paul A , Vali Shaik Waseem 
Published: October 2022

Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems’ level is underdeveloped as doing so would require considering the entire iron content of the cell—the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
MiMeDB: the Human Microbial Metabolome Database
Authors: Wishart David S , Oler Eponine , Peters Harrison , Guo AnChi , Girod Sagan , Han Scott , Saha Sukanta , Lui Vicki W , LeVatte Marcia , Gautam Vasuk , Kaddurah-Daouk Rima , Karu Naama 
Published: October 2022

Abstract
The Human Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, multi-omic, microbiome resource that connects: (i) microbes to microbial genomes; (ii) microbial genomes to microbial metabolites; (iii) microbial metabolites to the human exposome and (iv) all of these ‘omes’ to human health. MiMeDB was established to consolidate the growing body of data connecting the human microbiome and the chemicals it produces to both health and disease. MiMeDB contains detailed taxonomic, microbiological and body-site location data on most known human microbes (bacteria and fungi). This microbial data is linked to extensive genomic and proteomic sequence data that is closely coupled to colourful interactive chromosomal maps. The database also houses detailed information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that ultimately lead to the observed microbial metabolites in humans. Additional, extensively referenced data about the known or presumptive health effects, measured biosample concentrations and human protein targets for these compounds is provided. All of this information is housed in richly annotated, highly interactive, visually pleasing database that has been designed to be easy to search, easy to browse and easy to navigate. Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases. We believe that MiMeDB represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.
PDBspheres: a method for finding 3D similarities in local regions in proteins
Authors: Zemla Adam T , Allen Jonathan E , Kirshner Dan , Lightstone Felice C 
Published: October 2022

Abstract
We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains &gt;2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.
Prediction of response to lomustine-based chemotherapy in glioma patients at recurrence using MRI and FET PET
Authors: Wollring Michael M , Werner Jan-Michael , Bauer Elena K , Tscherpel Caroline , Ceccon Garry S , Lohmann Philipp , Stoffels Gabriele , Kabbasch Christoph , Goldbrunner Roland , Fink Gereon R , Langen Karl-Josef , Galldiks Norbert 
Published: October 2022

Abstract

Background
We evaluated O-(2-[18F]fluoroethyl)-l-tyrosine (FET) PET and MRI for early response assessment in recurrent glioma patients treated with lomustine-based chemotherapy.

Methods
Thirty-six adult patients with WHO CNS grade 3 or 4 gliomas (glioblastoma, 69%) at recurrence (median number of recurrences, 1; range, 1–3) were retrospectively identified. Besides MRI, serial FET PET scans were performed at baseline and early after chemotherapy initiation (not later than two cycles). Tumor-to-brain ratios (TBR), metabolic tumor volumes (MTV), the occurrence of new distant hotspots with a mean TBR &gt;1.6 at follow-up, and the dynamic parameter time-to-peak were derived from all FET PET scans. PET parameter thresholds were defined using ROC analyses to predict PFS of ≥6 months and OS of ≥12 months. MRI response assessment was based on RANO criteria. The predictive values of FET PET parameters and RANO criteria were subsequently evaluated using univariate and multivariate survival estimates.

Results
After treatment initiation, the median follow-up time was 11 months (range, 3–71 months). Relative changes of TBR, MTV, and RANO criteria predicted a significantly longer PFS (all P ≤ .002) and OS (all P ≤ .045). At follow-up, the occurrence of new distant hotspots (n ≥ 1) predicted a worse outcome, with significantly shorter PFS (P = .005) and OS (P &lt; .001). Time-to-peak changes did not predict a significantly longer survival. Multivariate survival analyses revealed that new distant hotspots at follow-up FET PET were most potent in predicting non-response (P &lt; .001; HR, 8.578).

Conclusions
Data suggest that FET PET provides complementary information to RANO criteria for response evaluation of lomustine-based chemotherapy early after treatment initiation.
Law, Coercion and Folk Intuitions
Authors: Miotto Lucas , Almeida Guilherme F C F , Struchiner Noel 
Published: October 2022

Abstract
In discussing whether legal systems are necessarily coercive, legal philosophers usually appeal to thought experiments involving angels or other morally driven beings who need no coercion to organise their social lives. Such appeals have invited criticism. Critics have not only challenged the relevance of such thought experiments to our understanding of legal systems; they have also argued that, contrary to the intuitions of most legal philosophers, the ‘man on the Clapham Omnibus’ would not hold that there is law in a society of angels because the view that law is necessarily coercive ‘enjoys widespread support among laypersons’. This is obviously an empirical claim. Critics, however, never systematically polled the ‘man on the Clapham Omnibus’. We boarded that bus. This article discusses findings from five empirical studies on the relationship between law and coercion.
Black Patients with Metastatic Castrate-Resistant Prostate Cancer Have a Shorter Time Interval Between PSA and Clinical Progression on Novel Hormonal Therapies plus Avelumab
Authors: Hawkins Charlotte (Manogue) , Barata Pedro C , Cotogno Patrick , Davis Gaynelle , Jaeger Ellen , Ledet Elisa , Miller Patrick , Lewis Brian , Sartor Oliver , Layton Jodi 
Published: October 2022

AbstractBackgroundBlack men are at higher risk for prostate cancer death. Previous studies showed a benefit of different therapies, including immune-based therapy, for Black men with metastatic prostate cancer. We sought to explore the efficacy of the PD-L1 inhibitor avelumab in Black men with metastatic castrate-resistant prostate cancer (mCRPC) progressing after abiraterone or enzalutamide.MethodsThis pilot phase II study enrolled self-identified Black patients who developed mCRPC on next-generation hormonal therapies (NHTs) abiraterone acetate or enzalutamide (NCT03770455). Enrolled patients received avelumab 10mg/kg IV every 2 weeks while remaining on the same NHTs. The primary endpoint of our study was ≥ 50% reduction in prostate specific antigen (PSA) at ≥8 weeks.ResultsA total of eight patients were enrolled. The median duration on NHTs prior to enrollment was 364 days (95% CI, 260.9-467.1). The median time to initiate avelumab was 8 days (3-14). With a median follow-up of 196 days, no patients achieved the primary endpoint. The median time to PSA progression was 35 days (95 CI%, 0-94.8) and the median time to radiographic and/or clinical progression was 44 days (95 CI%, 0-118.5). The study was closed prematurely due to safety concerns related to the rapid clinical progression observed in the patients enrolled on study.ConclusionIn conclusion, the addition of avelumab to NHT did not demonstrate clinical activity in Black men with new mCRPC. The unexpected short interval between PSA and radiographic and/or clinical progression observed in this study has potential clinical implications.ClinicalTrials.gov Identifier: NCT03770455 (IND number 139559).
Plant biomechanics and resilience to environmental changes are controlled by specific lignin chemistries in each vascular cell type and morphotype
Authors: Ménard Delphine , Blaschek Leonard , Kriechbaum Konstantin , Lee Cheng Choo , Serk Henrik , Zhu Chuantao , Lyubartsev Alexander , Nuoendagula  , Bacsik Zoltán , Bergström Lennart , Mathew Aji , Kajita Shinya , Pesquet Edouard 
Published: October 2022

Abstract
The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.