bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic profiling of subtelomeric silencing factors in budding yeast
Authors: Juárez-Reyes Alejandro , Avelar-Rivas J Abraham , Hernandez-Valdes Jhonatan A , Hua Bo , Campos Sergio E , González James , González Alicia , Springer Michael , Mancera Eugenio , DeLuna Alexander 
Published: July 2023

Abstract
Subtelomeric gene silencing is the negative transcriptional regulation of genes located close to telomeres. This phenomenon occurs in a variety of eukaryotes with salient physiological implications, such as cell adherence, virulence, immune-system escape, and ageing. The process has been widely studied in the budding yeast Saccharomyces cerevisiae, where genes involved in this process have been identified mostly on a gene-by-gene basis. Here, we introduce a quantitative approach to study gene silencing, that couples the classical URA3 reporter with GFP monitoring, amenable to high-throughput flow cytometry analysis. This dual silencing reporter was integrated into several subtelomeric loci in the genome, where it showed a gradual range of silencing effects. By crossing strains with this dual reporter at the COS12 and YFR057W subtelomeric query loci with gene-deletion mutants, we carried out a large-scale forward screen for potential silencing factors. The approach was replicable and allowed accurate detection of expression changes. Results of our comprehensive screen suggest that the main players influencing subtelomeric silencing were previously known, but additional potential factors underlying chromatin conformation are involved. We validate and report the novel silencing factor LGE1, a protein with unknown molecular function required for histone H2B ubiquitination. Our strategy can be readily combined with other reporters and gene perturbation collections, making it a versatile tool to study gene silencing at a genome-wide scale.
The Health, Aging, and Body Composition (Health ABC) Study—Ground-Breaking Science for 25 Years and Counting
Authors: Newman Anne B , Visser Marjolein , Kritchevsky Stephen B , Simonsick Eleanor , Cawthon Peggy M , Harris Tamara B 
Published: July 2023

Abstract

Background
The Health, Aging, and Body Composition Study is a longitudinal cohort study that started just over 25 years ago. This ground-breaking study tested specific hypotheses about the importance of weight, body composition, and weight-related health conditions for incident functional limitation in older adults.

Methods
Narrative review with analysis of ancillary studies, career awards, publications, and citations.

Results
Key findings of the study demonstrated the importance of body composition as a whole, both fat and lean mass, in the disablement pathway. The quality of the muscle in terms of its strength and its composition was found to be a critical feature in defining sarcopenia. Dietary patterns and especially protein intake, social factors, and cognition were found to be critical elements for functional limitation and disability. The study is highly cited and its assessments have been widely adopted in both observational studies and clinical trials. Its impact continues as a platform for collaboration and career development.

Conclusions
The Health ABC provides a knowledge base for the prevention of disability and promotion of mobility in older adults.
Prognostic Value of Inflammatory Bowel Disease-associated Biomarkers in Patients With Immune Checkpoint Inhibitor Enterocolitis: A Retrospective Cohort Study
Authors: Kogan Lawrence , Townsend Matthew J , Raj Dhanya , Levy Alexander N , Giobbie-Hurder Anita , Grover Shilpa 
Published: July 2023

Lay Summary
In the emerging field of immune checkpoint inhibitor enterocolitis, biomarkers to predict disease course are lacking. Select genetic polymorphisms (ATG16L1T300A) and serum amyloid A warrant further study as potential biomarkers associated with severe ICI enterocolitis.
Optimization of fermentation, purification, and properties of blue pigment produced from Quambalaria cyanescens QY229
Authors: Zhu Liping , Huang Luwen , Xie Yajing , Zhang Tingxin , Jiang Zhaoxu , Yan Shigan , Zhang Zhiguo 
Published: July 2023

Abstract

Aim
Blue pigments have broad applications in foods, cosmetics, and clothing. However, natural blue pigments are rare. At present, the majority of blue pigments for sale are chemically synthetic. Owing to the safety risks of chemical pigments, it is an urgent demand to develop novel natural blue pigments.

Methods and Results
The fermentation medium and culture conditions of blue pigment produced by Quambalaria cyanescens QY229 were optimized by Plackett–Burman (PB) experimental design and response surface methodology (RSM) for the first time. The stability, bioactivity, and toxicity of the obtained blue pigment were studied after isolation and purification.

Conclusion
The results showed that the optimal fermentation parameters were 34.61 g·L−1 of peptone concentration, 31.67°C of growing temperature, and 72.33 mL of medium volume in a 250-mL flask, and the yield of blue pigment reached 348.2 ± 7.1 U·mL−1. QY229 blue pigment is stable to light, heat, pH, most metal ions, and additives, and has certain antioxidant and inhibitory activity of α-glucosidase in vitro. QY229 blue pigment at concentrations of 0–1.25 mg·mL−1 was nontoxic to Caenorhabditis elegans in an acute toxicity trial.
Payer reimbursement practices and incentives for improving interpretation of germline genetic testing
Authors: Deverka Patricia , Geary Janis , Mathews Charles , Cohen Matan , Hooker Gillian , Majumder Mary , Skvarkova Zuzana , Cook-Deegan Robert 
Published: July 2023

Abstract
Germline genetic testing for inherited cancer risk has shifted to multi-gene panel tests (MGPTs). While MGPTs detect more pathogenic variants, they also detect more variants of uncertain significance (VUSs) that increase the possibility of harms such as unnecessary surgery. Data sharing by laboratories is critical to addressing the VUS problem. However, barriers to sharing and an absence of incentives have limited laboratory contributions to the ClinVar database. Payers can play a crucial role in the expansion of knowledge and effectiveness of genetic testing. Current policies affecting MGPT reimbursement are complex and create perverse incentives. Trends in utilization and coverage for private payers and Medicare illustrate opportunities and challenges for data sharing to close knowledge gaps and improve clinical utility. Policy options include making data sharing (i) a condition of payment, and (ii) a metric of laboratory quality in payment contracts, yielding preferred coverage or enhanced reimbursement. Mandating data sharing sufficient to verify interpretations and resolve discordance among labs under Medicare and federal health programs is an option for the US Congress. Such policies can reduce the current waste of valuable data needed for precision oncology and improved patient outcomes, enabling a learning health system.
Disparities in breast cancer among patients with disabilities: care gaps, accessibility, and best practices
Authors: Keegan Grace , Rizzo John-Ross , Joseph Kathie-Ann 
Published: July 2023

Abstract
Pronounced disparities exist in detecting and treating breast cancer in women with disabilities, leading to cancer detection at advanced stages. This paper provides an overview of disparities for women with disabilities related to breast cancer screening and care, primarily focusing on clinically significant mobility disabilities. Current care gaps include screening barriers related to accessibility and inequitable treatment options, with race and ethnicity, socioeconomic status, geographic location, and disability severity factors mediating the disparities for this population. The reasons for these disparities are myriad and stem from both system-level deficiencies and individual-level clinician bias. Although structural changes are warranted, individual healthcare professionals must also be incorporated into the requisite change. Intersectionality is critical to disparities and inequities and should be central to any discussion of strategies for improving care for people with disabilities, many of whom have intersectional identities. Efforts to reduce screening rate disparities for breast cancer in women with mobility-related disabilities should start with improving accessibility through removing structural barriers, establishing comprehensive accessibility standards, and addressing healthcare professional bias. Future interventional studies are needed to implement and assess the value of programs to improve breast cancer screening rates in women with disabilities. Increasing the representation of women with disabilities in clinical trials may provide another avenue for reducing treatment disparities because these trials often provide breakthrough treatment to women with cancer diagnosed at later stages. Ultimately, attention to the specific needs of patients with disabilities should be improved across the United States to promote inclusive and effective cancer screening and treatment.
Cutting off the King’s Head: Rethinking Authority in International Law
Authors: Zarbiyev Fuad 
Published: July 2023

Abstract
The renewed attention to the concept of authority in the literature of international law and international relations has allowed to gain a better understanding of the phenomenon of authority in international affairs. But even recent works remain focused on ‘authority figures’ in the form of persons, offices and institutions. Building on an approach proposed by Kim Scheppele and Karol Soltan, this article frames authority as a matter of attractiveness in a choice situation, showing a way to go beyond the dominant actor-focused conception of authority. What it proposes, in particular, is to revisit the existing understanding of authority by shifting the focus from authority figures to authoritative resources. The practice of authority assertions and authority contestations in international law shows that rather than being ‘agent-centered’, claims and challenges to authority primarily turn around attributes that pass for ‘authoritative resources’ in the relevant contexts.
Digital inequality in disconnection practices: voluntary nonuse during COVID-19
Authors: Nguyen Minh Hao , Hargittai Eszter 
Published: July 2023

Abstract
The pervasiveness of digital media renders people constantly connected. Digital inequality theory tends to focus on how socio-digital factors link to technology access, skills, uses, and opportunities derived from such use. It is not clear, however, whether this theoretical lens applies to a time of heightened connection when privilege may also explain intended disconnection. Drawing on data from 1,551 U.S. adults surveyed during the pandemic, we find that younger age, higher education, frequent Internet use, less dependable access, and better skills are related to partaking in voluntary nonuse (e.g., having technology-free moments, switching off the Internet). As digital disconnection emerges from a place of socio-digital privilege as well as disadvantage, in a society of technology abundance, new inequalities arise around who has the freedom to use it in moderation rather than use it at all. Our study extends theoretical notions from digital inequality to the realm of voluntary digital nonuse.
Popliteal endarterectomy at the leg level with venous enlargement patch: about 14 cases
Authors: Channane Hamid , Shaporov A , Sandica A , Atay S , Snopok I , Frunza T , Viebahn R 
Published: July 2023

Abstract
The incidence of lesions of the popliteal artery below the knee constitutes one of the greatest problems in revascularization of the lower limb. Firstly, this segment constitutes the departure of the leg tripod, decisive crossroads for a subsequent endovascular intervention. On the other hand, it constitutes a fairly used relay point in the event of an indication for a pedal bypass. It is assumed that the performance of a popliteal endarterectomy with an enlargement by medial approach in patients with a localized lesion at this level constitutes an effective therapeutic approach and can facilitate any gesture of crural bypass or endovascular dilation later. We present a retrospective review of all patients who underwent popliteal endarterectomy with venous patch plasty for localized popliteal disease in our institution over the past 3 years.
Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis
Authors: Chien Pei-Shan , Chen Pin-Hua , Lee Cheng-Ruei , Chiou Tzyy-Jen 
Published: July 2023

Abstract
Genome-wide association study (GWAS) has improved our understanding of complex traits, but challenges exist in distinguishing causation versus association caused by linkage disequilibrium. Instead, transcriptome-wide association studies (TWAS) detect direct associations between expression levels and phenotypic variations, providing an opportunity to better prioritize candidate genes. To assess the feasibility of TWAS, we investigated the association between transcriptomes, genomes, and various traits in Arabidopsis, including flowering time. The associated genes formerly known to regulate growth allometry or metabolite production were first identified by TWAS. Next, for flowering time, six TWAS-newly identified genes were functionally validated. Analysis of the expression quantitative trait locus (eQTL) further revealed a trans-regulatory hotspot affecting the expression of several TWAS-identified genes. The hotspot covers the FRIGIDA (FRI) gene body, which possesses multiple haplotypes differentially affecting the expression of downstream genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). We also revealed multiple independent paths towards the loss of function of FRI in natural accessions. Altogether, this study demonstrates the potential of combining TWAS with eQTL analysis to identify important regulatory modules of FRI-FLC-SOC1 for quantitative traits in natural populations.
On the minimum spin period of accreting pulsars
Authors: Çıkıntoğlu Sercan , Ekşi K Yavuz 
Published: July 2023

ABSTRACT
The distribution of the spin frequencies of neutron stars in low-mass X-ray binaries exhibits a cut-off at 730 Hz, below the break-up frequency (mass-shedding limit) of neutron stars. The absence of submillisecond pulsars presents a problem, given that these systems are older than the spin-up time-scale. We examine models of the disc–magnetosphere interaction near torque equilibrium balanced by the torque due to gravitational wave emission. We note that field lines penetrating the disc beyond the inner radius reduce the maximum rotation frequency of the star, a result well known since the seminal work of Ghosh & Lamb. We show that the polar cap area corresponds to about half the neutron star surface area at the cut-off frequency if the inner radius is slightly smaller than the corotation radius. We then include the change in the moment of inertia of the star due to the accretion of mass and find that this effect further reduces the maximum rotation frequency of the star. Finally, we include the torque due to gravitational wave emission and calculate its contribution to the torque equilibrium. Our results suggest that all three processes are significant at the cut-off frequency, and that all of them must be considered in addressing the absence of submillisecond pulsars.
Dynamical effects of magnetic opacity in neutron star accretion columns
Authors: Sheng Xin , Zhang Lizhong , Blaes Omer , Jiang Yan-Fei 
Published: July 2023

ABSTRACT
We present relativistic radiation magnetohydrodynamic simulations of supercritical neutron star accretion columns in Cartesian geometry, including temperature-dependent polarization-averaged Rosseland mean opacities accounting for classical electron scattering in a magnetic field. Just as in our previous pure Thomson scattering simulations, vertical oscillations of the accretion shock and horizontally propagating entropy waves (photon bubbles) are present in all our simulations. However, at high magnetic fields ≳1012 G, the magnetic opacities produce significant differences in the overall structure and dynamics of the column. At fixed accretion rate, increasing the magnetic field strength results in a shorter accretion column, despite the fact that the overall opacity within the column is larger. Moreover, the vertical oscillation amplitude of the column is reduced. Increasing the accretion rate at high magnetic fields restores the height of the column. However, a new, slower instability takes place at these field strengths because they are in a regime where the opacity increases with temperature. This instability causes both the average height of the column and the oscillation amplitude to substantially increase on a time-scale of ∼10 ms. We provide physical explanations for these results, and discuss their implications for the observed properties of these columns, including mixed fan-beam/pencil-beam emission patterns caused by the oscillations.
Time-varying Na iD absorption in ILRTs as a probe of circumstellar material
Authors: Byrne R A , Fraser M , Cai Y-Z , Reguitti A , Valerin G 
Published: July 2023

ABSTRACTIntermediate-luminosity red transients (ILRTs) are a class of observed transient posited to arise from the production of an electron-capture supernova from a super-asymptotic giant branch star within a dusty cocoon. In this paper, we present a systematic analysis of narrow Na i D absorption as a means of probing the circumstellar environment of these events. We find a wide diversity of evolution in ILRTs in terms of line strength, time-scale, and shape. We present a simple toy model designed to predict this evolution as arising from ejecta from a central supernova passing through a circumstellar environment wherein Na ii is recombining to Na i over time. We find that while our toy model can qualitatively explain the evolution of a number of ILRTs, the majority of our sample undergoes evolution more complex than predicted. The success of using the Na i D doublet as a diagnostic tool for studying circumstellar material will rely on the availability of regular high-resolution spectral observations of multiple ILRTs, and more detailed spectral modelling will be required to produce models capable of explaining the diverse range of behaviours exhibited by ILRTs. In addition, the strength of the Na i D absorption feature has been used as a means of estimating the extinction of sources, and we suggest that the variability visible in ILRTs would prevent such methods from being used for this class of transient, and any others showing evidence of variability.
Multiple Origins and Genomic Basis of Complex Traits in Sighthounds
Authors: Li Wu-Lue , Liu Yan-Hu , Li Jin-Xiu , Ding Meng-Ting , Adeola Adeniyi C , Isakova Jainagul , Aldashev Almaz A , Peng Min-Sheng , Huang Xuezhen , Xie Guoli , Chen Xi , Yang Wei-Kang , Zhou Wei-Wei , Ghanatsaman Zeinab Amiri , Olaogun Sunday C , Sanke Oscar J , Dawuda Philip M , Hytönen Marjo K , Lohi Hannes , Esmailizadeh Ali , Poyarkov Andrey D , Savolainen Peter , Wang Guo-Dong , Zhang Ya-Ping 
Published: July 2023

Abstract
Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in “regulation of release of sequestered calcium ion into cytosol” (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T &gt; C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T &gt; A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.
Change in volumetric tumor growth rate after cytotoxic therapy is predictive of overall survival in recurrent glioblastoma
Authors: Oshima Sonoko , Hagiwara Akifumi , Raymond Catalina , Wang Chencai , Cho Nicholas S , Lu Jianwen , Eldred Blaine S C , Nghiemphu Phioanh L , Lai Albert , Telesca Donatello , Salamon Noriko , Cloughesy Timothy F , Ellingson Benjamin M 
Published: July 2023

AbstractBackgroundAlterations in tumor growth rate (TGR) in recurrent glioblastoma (rGBM) after treatment may be useful for identifying therapeutic activity. The aim of this study was to assess the impact of volumetric TGR alterations on overall survival (OS) in rGBM treated with chemotherapy with or without radiation therapy (RT).MethodsSixty-one rGBM patients treated with chemotherapy with or without concomitant radiation therapy (RT) at 1st or 2nd recurrence were retrospectively examined. Pre- and post-treatment contrast enhancing volumes were computed. Patients were considered “responders” if they reached progression-free survival at 6 months (PFS6) and showed a decrease in TGR after treatment and “non-responders” if they didn’t reach PFS6 or if TGR increased.ResultsStratification by PFS6 and based on TGR resulted in significant differences in OS both for all patients and for patients without RT (P &lt; 0.05). A decrease of TGR (P = 0.009), smaller baseline tumor volume (P = 0.02), O6-methylguanine-DNA methyltransferase promoter methylation (P = 0.048) and fewer number of recurrences (P = 0.048) were significantly associated with longer OS after controlling for age, sex and concomitant RT.ConclusionA decrease in TGR in patients with PFS6, along with smaller baseline tumor volume, were associated with a significantly longer OS in rGBM treated with chemotherapy with or without radiation. Importantly, all patients that exhibited PFS6 also showed a measurable decrease in TGR.