bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia
Authors: Wang Ran , Zheng Xubin , Wang Jun , Wan Shibiao , Song Fangda , Wong Man Hon , Leung Kwong Sak , Cheng Lixin 
Published: January 2022

AbstractThe advances in single-cell RNA sequencing (scRNA-seq) technologies enable the characterization of transcriptomic profiles at the cellular level and demonstrate great promise in bulk sample analysis thereby offering opportunities to transfer gene signature from scRNA-seq to bulk data. However, the gene expression signatures identified from single cells are typically inapplicable to bulk RNA-seq data due to the profiling differences of distinct sequencing technologies. Here, we propose single-cell pair-wise gene expression (scPAGE), a novel method to develop single-cell gene pair signatures (scGPSs) that were beneficial to bulk RNA-seq classification to transfer knowledge across platforms. PAGE was adopted to tackle the challenge of profiling differences. We applied the method to acute myeloid leukemia (AML) and identified the scGPS from mouse scRNA-seq that allowed discriminating between AML and control cells. The scGPS was validated in bulk RNA-seq datasets and demonstrated better performance (average area under the curve [AUC] = 0.96) than the conventional gene expression strategies (average AUC$\le$ 0.88) suggesting its potential in disclosing the molecular mechanism of AML. The scGPS also outperformed its bulk counterpart, which highlighted the benefit of gene signature transfer. Furthermore, we confirmed the utility of scPAGE in sepsis as an example of other disease scenarios. scPAGE leveraged the advantages of single-cell profiles to enhance the analysis of bulk samples revealing great potential of transferring knowledge from single-cell to bulk transcriptome studies.
Quantifying Environmental Mitigation of Aerosol Viral Load in a Controlled Chamber With Participants Diagnosed With Coronavirus Disease 2019
Authors: Parhizkar Hooman , Dietz Leslie , Olsen-Martinez Andreas , Horve Patrick F , Barnatan Liliana , Northcutt Dale , Van Den Wymelenberg Kevin G 
Published: January 2022

AbstractBackgroundSeveral studies indicate that coronavirus disease 2019 (COVID-19) is primarily transmitted within indoor spaces. Therefore, environmental characterization of severe acute respiratory syndrome coronavirus 2 viral load with respect to human activity, building parameters, and environmental mitigation strategies is critical to combat disease transmission.MethodsWe recruited 11 participants diagnosed with COVID-19 to individually occupy a controlled chamber and conduct specified physical activities under a range of environmental conditions; we collected human and environmental samples over a period of 3 days for each participant.ResultsHere we show that increased viral load, measured by lower RNA cycle threshold (CT) values, in nasal samples is associated with higher viral loads in environmental aerosols and on surfaces captured in both the near field (1.2 m) and far field (3.5 m). We also found that aerosol viral load in far field is correlated with the number of particles within the range of 1–2.5 µm. Furthermore, we found that increased ventilation and filtration significantly reduced aerosol and surface viral loads, while higher relative humidity resulted in lower aerosol and higher surface viral load, consistent with an increased rate of particle deposition at higher relative humidity. Data from near field aerosol trials with high expiratory activities suggest that respiratory particles of smaller sizes (0.3–1 µm) best characterize the variance of near field aerosol viral load.ConclusionsOur findings indicate that building operation practices such as ventilation, filtration, and humidification substantially reduce the environmental aerosol viral load and therefore inhalation dose, and should be prioritized to improve building health and safety.
A cross-sectional study of the practice types of US adult primary care physician specialists
Authors: Young Richard A , Wilkinson Elizabeth , Barreto Tyler W , Newton Rebecca L , Turebylu Akshaj , Bullock Dana 
Published: January 2022

Abstract

Background
Many physicians listed as primary care in databases such as the American Medical Association (AMA) Masterfile do not provide traditional ambulatory primary care.

Objective
To compare physicians listed in the AMA Masterfile as primary care physician (PCPs) specialists for adult patients with their actual practice type.

Methods
We conducted a cross-sectional study of the AMA Masterfile report for PCPs who care for adults (listed as family medicine, internal medicine, medicine-paediatrics, and geriatrics) in the summer and fall of 2018 (spring of 2019 for Hartford, CT) in the primary counties of 8 metropolitan areas across the United States. We searched multiple websites to determine the actual practice type of each physician in the study counties. We correlated the 2 datasets: the AMA Masterfile list vs the results of our searches.

Results
Family physicians were more likely to function as traditional ambulatory PCPs than internists [1,738/2,101 (82.7%) vs 1,241/2,025 (60.9%), P &lt; 0.001], and less likely to be hospitalists [83/2,101 (4.0%) vs 631/2,025 (31.0%), P &lt; 0.001]. Other practice types included urgent care [105 (5.0%) family physicians, 16 (0.8%) internists] and emergency medicine [49 (2.3%) family physicians, 20 (1.0%) internists]. The AMA Masterfile identified 4,892 practicing PCPs for adult patients in the study counties, of which 3,084 (63.0%) matched by location and ambulatory PCP practice type [3,695 (75.5%) for ambulatory PCP practice type only].

Conclusions
We provide an updated estimate using a unique methodology to estimate how to correct the AMA Masterfile for PCPs who actually provide traditional ambulatory primary care to adult patients.
Challenging the Surge of Inflammatory Bowel Disease: The Role of the China Crohn’s and Colitis Foundation in the Healthcare Landscape of Inflammatory Bowel Disease
Authors: Peng Lishan , Hu Shurong , Yu Qiao , Chen Yan 
Published: January 2022

Abstract
Inflammatory bowel disease (IBD) is a chronic and lifelong disease, and patients must ultimately learn to live with and manage the condition. With advances in diagnostics and treatment in IBD, healthcare professionals (HCPs) and patients are now concerned with both quality of care (QOC) and quality of life (QOL). The China Crohn’s and Colitis Foundation (CCCF) is committed to improving the QOC and QOL for IBD patients by garnering social resources. This paper details how CCCF has worked for better IBD management over the past 5 years. The foundation has 4 main projects: education programs for IBD HCPs and patients, support activities, public awareness and advocacy, and research programs. CCCF is an increasingly influential public welfare organization providing advocacy for IBD patients in China. The foundation is now entering the next stage of its development in pursuing professional operations and helping to solve the social problems experienced by IBD patients. The CCCF ultimately plans to pioneer reforms in China’s medical system and hopefully provide a successful example of IBD advocacy for developing countries to emulate.
Patriarchy is a Judge: Young Feminists and LGBTQ+ Activists Performing Transitional Justice in Chile
Authors: Hiner Hillary , Badilla Manuela , López Ana , Zúñiga-Fajuri Alejandra , Hatibovic Fuad 
Published: January 2022

ABSTRACT
In recent years many articles have discussed transitional justice in Chile with respect to the Pinochet dictatorship, and some of these have had a gendered perspective. In this article we seek to build upon this research, but touching upon recent human rights violations and political sexual violence that took place in Chile during the 18-O Uprising (October 2019 to January 2020). Key in our argument is that young feminists and sexual dissidents have been crucial in re-conceptualizing and making visible the Piñera government’s human rights abuses, both appealing to previous human rights and feminist discourses and practices, as well as inventing new, creative ways of expressing their claims for transitional justice and reparations, like the ‘Rapist in Your Path’ performance. We will use discussion groups and interviews with young feminists and LGBTQ+ people, as well as a revision of relevant national and international human rights reports, to make our argument.
Fiscal Responses to Foreign Aid: Does the Permanence of Aid Matter?
Authors: Abdelwahed Loujaina 
Published: January 2022

AbstractThis paper shows that failing to distinguish between permanent (low frequency) and temporary (high frequency) aid results in misleading estimates of the fiscal responses to aid. I focus on foreign grants received by sub-Saharan Africa over the period 1990–2016, and I separately identify the fiscal responses to permanent and temporary foreign aid. Permanent and temporary aid generates fiscal responses that are meaningfully different on the components of expenditure and domestic borrowing. Temporary aid is associated with fiscal adjustments, such as lower domestic borrowing and increasing recurrent expenditure, while permanent aid is associated with higher public investments. Results provide important policy implications regarding the macroeconomic effects of foreign aid and the design of aid programs to developing countries.
Hoop-like role of the cytosolic interface helix in Vibrio PomA, an ion-conducting membrane protein, in the bacterial flagellar motor
Authors: Nishikino Tatsuro , Sagara Yugo , Terashima Hiroyuki , Homma Michio , Kojima Seiji 
Published: January 2022

Abstract
Vibrio has a polar flagellum driven by sodium ions for swimming. The force-generating stator unit consists of PomA and PomB. PomA contains four transmembrane regions and a cytoplasmic domain of approximately 100 residues, which interacts with the rotor protein, FliG, to be important for the force generation of rotation. The 3D structure of the stator shows that the cytosolic interface (CI) helix of PomA is located parallel to the inner membrane. In this study, we investigated the function of CI helix and its role as stator. Systematic proline mutagenesis showed that residues K64, F66 and M67 were important for this function. The mutant stators did not assemble around the rotor. Moreover, the growth defect caused by PomB plug deletion was suppressed by these mutations. We speculate that the mutations affect the structure of the helices extending from TM3 and TM4 and reduce the structural stability of the stator complex. This study suggests that the helices parallel to the inner membrane play important roles in various processes, such as the hoop-like function in securing the stability of the stator complex and the ion conduction pathway, which may lead to the elucidation of the ion permeation and assembly mechanism of the stator.
Diptera (Dryomyzidae, Fanniidae, Muscidae, Piophilidae) Associated With Pig Carcasses in a Forest Habitat of Poland: Sex-Related Patterns of Visitation and Effectiveness of Sampling Methods
Authors: Bajerlein Daria , Jarmusz Mateusz , Gregor Aleksandra , Grzywacz Andrzej 
Published: January 2022

AbstractOur knowledge on many necrophilous dipterans was limited for a long time mainly due to taxonomic issues. Therefore, findings on the sex-related associations with pig carcasses in Dryomyzidae, Fanniidae, Muscidae, and Piophilidae are presented. Moreover, the effectiveness of pitfall traps and sweep nets in fly sampling were compared, since the correct method of collecting insects is critical for the development and application of entomological tools for forensic purposes. The trapped numbers of all species differed significantly in respect to both sexes. The sex ratios were strongly female-biased in most species of Muscidae and in Fanniidae. More females were also collected in Piophilidae, but the proportion of males was higher when compared to muscids. Within Dryomyzidae, the sex ratio differed according to species. Only Dryomyza flaveola (Fabricius, 1794) (Diptera: Dryomyzidae) and Muscina pascuorum (Meigen, 1826) (Diptera: Muscidae) had male-biased sex ratios. Differences in residency patterns between sexes in Stearibia nigriceps (Meigen, 1826) (Diptera: Piophilidae), Liopiophila varipes (Meigen, 1830) (Diptera: Piophilidae), and D. flaveola were statistically insignificant. All studied species were recorded for each sampling method. The effect of the sampling method on the number of individuals was statistically significant for all dipterans but Piophilidae. Pitfall traps outcompeted the aerial sweep net in representing Dryomyzidae and Muscidae, whereas both methods were almost equally effective in the collection of Piophilidae. A varied effectiveness of sampling methods was observed in Fanniidae. The sampling method significantly affected the determination of the appearance time of flies on carcasses, but the effect of species and sampling method was insignificant. Implications for forensic entomology are discussed.
Comparing compact object distributions from mass- and presupernova core structure-based prescriptions
Authors: Patton Rachel A , Sukhbold Tuguldur , Eldridge J J 
Published: January 2022

ABSTRACT
Binary population synthesis (BPS) employs prescriptions to predict final fates, explosion or implosion, and remnant masses based on one or two stellar parameters at the evolutionary cutoff imposed by the code, usually at or near central carbon ignition. In doing this, BPS disregards the integral role late-stage evolution plays in determining the final fate, remnant type, and remnant mass within the neutrino-driven explosion paradigm. To highlight differences between a popular prescription, which relies only on the core and final stellar mass and emerging methods, which rely on a star’s presupernova core structure, we generate a series of compact object distributions using three different methods for a sample population of single and binary stars computed in BPASS. The first method estimates remnant mass based on a star’s carbon–oxygen (CO) core mass and final total mass. The second method uses the presupernova core structure based on recent bare CO-core models combined with a parameterized explosion criterion to first determine final fate and remnant type, then remnant mass. The third method associates presupernova helium-core masses with remnant masses determined from public explosion models which rely implicitly on core structure. We find that the core-/final mass-based prescription favours lower mass remnants, including a large population of mass gap black holes, and predicts neutron star masses which span a wide range, whereas the structure-based prescriptions favour slightly higher mass remnants, mass gap black holes only as low as 3.5 M⊙, and predict NS mass distributions which cluster in a narrow range.
Reanalysis of c-type RR Lyrae variable BE Dor, period modulations and possible mechanism
Authors: Li L-J , Qian S-B , Zhu L-Y 
Published: January 2022

ABSTRACT
We reanalysed the c-type RR Lyrae star BE Dor (MACHO 5.4644.8, OGLE-LMC-RRLYR-06002) that had been discovered to show cyclic period changes. The photometric data of several sky surveys (DASCH, MACHO, OGLE, ASAS-SN, and TESS) were used for analyses. The O − C diagram and pulsation period obtained from Fourier analysis show significant period modulations in BE Dor. However, different from the previous viewpoint, the changes are quasi-periodic and abrupt. Therefore, the light-traveltime effect caused by the companion motion cannot explain the changes. Noting a same subtype star KIC 9453114 with similar phenomena has a high macroturbulent velocity, and the degree of O − C changes seem to be positively correlated with these velocities, we consider that the mechanism leading to period modulation should be caused by the interaction between turbulent convection and magnetic field activity in the ionization zone, i.e. the viewpoint of Stothers. It may not explain the general Blazhko effect but should explain such period modulations in BE Dor and those other c-type RR Lyrae stars. We hope our discoveries and viewpoints can provide some information and inspiration for relevant research.
Folic acid deficiency increases sensitivity to DNA damage by glucose and methylglyoxal
Authors: Donnellan Leigh , Simpson Bradley S , Dhillon Varinderpal S , Costabile Maurizio , Fenech Michael , Deo Permal 
Published: January 2022

Abstract
Type 2 diabetes (T2D) is associated with elevated frequencies of micronuclei (MNi) and other DNA damage biomarkers. Interestingly, individuals with T2D are more likely to be deficient in micronutrients (folic acid, pyridoxal-phosphate, cobalamin) that play key roles in one-carbon metabolism and maintaining genomic integrity. Furthermore, it has recently been shown that deficiencies in these nutrients, in particular folic acid leaves cells susceptible to glucose-induced DNA damage. Therefore, we sought to investigate if the B lymphoblastoid WIL2-NS cell line cultured under folic acid-deficient conditions was more sensitive to DNA damage induced by glucose, or the reactive glycolytic byproduct methylglyoxal (MGO) and subsequent advanced glycation endproduct formation. Here, we show that only WIL2-NS cultured under folic acid-deficient conditions (23 nmol/l) experience an increase in MNi frequency when exposed to high concentrations of glucose (45 mmol/l) or MGO (100 µmol/l). Furthermore, we showed aminoguanidine, a well-validated MGO and free radical scavenger was able to prevent further MNi formation in folic acid-deficient cells exposed to high glucose, which may be due to a reduction in MGO-induced oxidative stress. Interestingly, we also observed an increase in MGO and other dicarbonyl stress biomarkers in folic acid-deficient cells, irrespective of glucose concentrations. Overall, our evidence shows that folic acid-deficient WIL2-NS cells are more susceptible to glucose and/or MGO-induced MNi formation. These results suggest that individuals with T2D experiencing hyperglycemia and folic acid deficiency may be at higher risk of chromosomal instability.
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection
Authors: Rigden Daniel J , Fernández Xosé M 
Published: January 2022

AbstractThe 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.
The fork protection complex recruits FACT to reorganize nucleosomes during replication
Authors: Safaric Barbara , Chacin Erika , Scherr Matthias J , Rajappa Lional , Gebhardt Christian , Kurat Christoph F , Cordes Thorben , Duderstadt Karl E 
Published: January 2022

Abstract
Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.
Supramolecular CRISPR-OFF switches with host–guest chemistry
Authors: Xiong Wei , Liu Xingyu , Qi Qianqian , Ji Huimin , Liu Fengbo , Zhong Cheng , Liu Simin , Tian Tian , Zhou Xiang 
Published: January 2022

Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) technology is a powerful tool in biology and medicine. However, the safety and application of this technology is hampered by excessive activity of CRISPR machinery. It is particularly important to develop methods for switching off CRISPR activity in human cells. The current study demonstrates the concept of supramolecular CRISPR-OFF switches by employing host-guest chemistry. We demonstrate that the CRISPR systems show considerable tolerance to adamantoylation on guide RNAs (gRNAs), whereas supramolecular complexation tremendously affects the function of adamantoyl gRNAs. Host–guest chemistry is demonstrated to be novel and effective tools to reduce unwanted excessive activities of CRISPR complexes in human cells. This work indicates considerable potential of supramolecular strategy for controlling and enhancing CRISPR systems.
A Cas6-based RNA tracking platform functioning in a fluorescence-activation mode
Authors: Gao Feng , Zheng Ke , Li You-Bo , Jiang Feng , Han Chun-Yu 
Published: January 2022

Abstract
Given the fact that the localization of RNAs is closely associated with their functions, techniques developed for tracking the distribution of RNAs in live cells have greatly advanced the study of RNA biology. Recently, innovative application of fluorescent protein-labelled Cas9 and Cas13 into live-cell RNA tracking further enriches the toolbox. However, the Cas9/Cas13 platform, as well as the widely-used MS2-MCP technique, failed to solve the problem of high background noise. It was recently reported that CRISPR/Cas6 would exhibit allosteric alteration after interacting with the Cas6 binding site (CBS) on RNAs. Here, we exploited this feature and designed a Cas6-based switch platform for detecting target RNAs in vivo. Conjugating split-Venus fragments to both ends of the endoribonuclease-mutated Escherichia coli Cas6(dEcCas6) allowed ligand (CBS)-activated split-Venus complementation. We name this platform as Cas6 based Fluorescence Complementation (Cas6FC). In living cells, Cas6FC could detect target RNAs with nearly free background noise. Moreover, as minimal as one copy of CBS (29nt) tagged in an RNA of interest was able to turn on Cas6FC fluorescence, which greatly reduced the odds of potential alteration of conformation and localization of target RNAs. Thus, we developed a new RNA tracking platform inherently with high sensitivity and specificity.