bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fertility restorer gene CaRf and PepperSNP50K provide a promising breeding system for hybrid pepper
Authors: Tang Bingqian , Yang Huiping , Yin Qinbiao , Miao Wu , Lei Yuting , Cui Qingzhi , Cheng Jiawen , Zhang Xinhao , Chen Ying , Du Juan , Xie Lingling , Tang Shunxue , Wang Meiqi , Li Jiayue , Cao Mingyue , Chen Li , Xie Fangling , Li Xiumin , Zhu Fan , Wang Zhongyi , Xiong Cheng , Dai Xiongze , Zou Xuexiao , Liu Feng 
Published: October 2024

Abstract
Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene encodes a mitochondria-targeted pentatricopeptide repeat protein, validated through the induction of male sterility upon its silencing in hybrid F1 plants. To enhance pepper breeding efficiency, 176 important pepper breeding parent materials were resequenced, and a PepperSNP50K liquid-phase breeding chip was developed, comprising 51 172 markers. Integration of CaRf functional characterization and PepperSNP50K facilitated the development of a high-quality red pepper hybrid. These findings provide significant insights and practical strategies for advancing molecular-designed breeding in peppers.
Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member
Authors: Wang Liying , Yin Zhipeng , Yan Wei , Hao Jialong , Tian Fei , Shi Jianbo 
Published: October 2024

Abstract
Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labeling with carbon dioxide–fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.
Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation
Authors: Lee Sungeun , Hazard Christina , Nicol Graeme W 
Published: October 2024

Abstract
Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173 kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.
The number of patient scheduled hours resulting in a 40-hour work week by physician specialty and setting: a cross-sectional study using electronic health record event log data
Authors: Sinsky Christine A , Rotenstein Lisa , Holmgren A Jay , Apathy Nate C 
Published: October 2024

Abstract

Objective
To quantify how many patient scheduled hours would result in a 40-h work week (PSH40) for ambulatory physicians and to determine how PSH40 varies by specialty and practice type.

Methods
We calculated PSH40 for 186 188 ambulatory physicians across 395 organizations from November 2021 through April 2022 stratified by specialty.

Results
Median PSH40 for the sample was 33.2 h (IQR: 28.7-36.5). PSH40 was lowest in infectious disease (26.2, IQR: 21.6-31.1), geriatrics (27.2, IQR: 21.5-32.0) and hematology (28.6, IQR: 23.6-32.6) and highest in plastic surgery (35.7, IQR: 32.8-37.7), pain medicine (35.8, IQR: 32.6-37.9) and sports medicine (36.0, IQR: 33.3-38.1).

Discussion
Health system leaders and physicians will benefit from data driven and transparent discussions about work hour expectations. The PSH40 measure can also be used to quantify the impact of variations in the clinical care environment on the in-person ambulatory patient care time available to physicians.

Conclusions
PSH40 is a novel measure that can be generated from vendor-derived metrics and used by operational leaders to inform work expectations. It can also support research into the impact of changes in the care environment on physicians’ workload and capacity.
Designing and testing clinical simulations of an early warning system for implementation in acute care settings
Authors: Kang Min-Jeoung , Rossetti Sarah C , Lowenthal Graham , Knaplund Christopher , Zhou Li , Schnock Kumiko O , Cato Kenrick D , Dykes Patricia C 
Published: October 2024

Abstract

Objectives
Conducting simulation testing with end-users is essential for facilitating successful implementation of new health information technologies. This study designed a standardized simulation testing process with a system prototype prior to implementation to help study teams identify the system’s interpretability and feasibility from the end-user perspective and to effectively integrate new innovations into real-world clinical settings and workflows.

Materials and Methods
A clinical simulation model was developed to test a new Clinical Decision Support (CDS) system outside of the clinical environment while maintaining high fidelity. A web-based CDS prototype, the “CONCERN Smart Application,” which leverages clinical data to measure and express a patient’s risk of deterioration on a 3-level scale (“low,” “moderate,” or “high”), and audiovisual-integrated materials, were used to lead simulation sessions.

Results
A total of 6 simulation sessions with 17 nurses were held to investigate how nurses interact with the CONCERN Smart application and how it influences their critical thinking, and clinical responses. Four themes were extracted from the simulation debriefing sessions and used to inform implementation strategies. The strategies include how the CDS should be improved for practical real-world use.

Discussion and Conclusions
Standardized simulation testing procedures identified and informed the necessary CDS improvements, the enhancements needed for real-world use, and the training requirements to effectively prepare end-users for system go-live.
How Low Socioeconomic Status Hinders Organ Donation: An Extended Self Account
Authors: Vieites Yan , Mittal Chiraag 
Published: October 2024

Abstract
Past studies find that lower socioeconomic status (SES) individuals are less likely to donate organs. Building on the extended self literature, we propose that this effect occurs in part because the body is more central to the sense of self of lower-SES individuals. We test our predictions across seven studies (N = 8,782) conducted in different countries (United States and Brazil) with qualitative, observational, and experimental data in controlled and field settings. Results show that lower-SES individuals ascribe a greater weight to their bodies in forming their self-concept, which reduces their willingness to donate organs. Consistent with this rationale, socioeconomic disparities in organ donation are attenuated when (a) conceptions of selfhood prioritize non-physical aspects (e.g., the mind) over physical aspects (e.g., the body), and (b) appeals emphasize organ donation as a means to extend one’s sense of self (e.g., “let yourselves live through others”). Overall, this research documents an unexplored psychological barrier to organ donation and provides insights into how donation rates can be increased among lower-SES individuals.
Is There a “Best” Way for Patients to Participate in Pharmacovigilance?
Authors: Due Austin 
Published: October 2024

Abstract
The underreporting of suspected adverse drug reactions hinders pharmacovigilance. Solutions to underreporting are oftentimes directed at clinicians and healthcare professionals. However, given the recent rise of public inclusion in medical science, solutions may soon begin more actively involving patients. I aim to offer an evaluative framework for future possible proposals that would engage patients with the aim of mitigating underreporting. The framework may also have value in evaluating current reporting practices. The offered framework is composed of three criteria that are bioethical, social-epistemic, and pragmatic: (i) patients should not be exposed to undue harms, for example, nocebo effects; (ii) data should be collected, analyzed, and communicated while prioritizing pharmacovigilance’s aims, that is, free from industry bias; and (iii) proposals should account for existing and foreseeable pragmatic constraints like clinician “buy in” and existing reporting infrastructure. Proposals to engage patients in pharmacovigilance that fulfil or address these criteria are preferable to those that do not.
The heat shock response in plants: new insights into modes of perception, signaling, and the contribution of hormones
Authors: Dündar Gönül , Ramirez Veronica E , Poppenberger Brigitte 
Published: October 2024

Abstract
Plants have evolved specific temperature preferences, and shifts above this range cause heat stress with detrimental effects such as physiological disruptions, metabolic imbalances, and growth arrest. To reduce damage, plants utilize the heat shock response (HSR), signaling cascades that activate heat shock factors (HSFs), transcription factors that control the heat stress-responsive transcriptome for activation of protective measures. While the core HSR is well studied, we still know relatively little about heat stress perception and signal integration or crosstalk with other pathways. In the last few years, however, significant progress has been made in this area, which is summarized here. It has emerged that the plant hormones brassinosteroids (BRs) and abscisic acid (ABA) contribute to heat stress tolerance by impacting the modes of activity of HSFs. Also, we began to understand that heat stress is sensed in different cellular compartments and that events in the nucleus, such as nuclear condensate formation via liquid–liquid phase separation, play a key role. In the future, it will be important to explore how these multilayered perception and signaling modes are utilized to understand how environmental context and developmental stage determine the outcome of heat stress effects on plant growth and development.
Prognostic Value of ISS and TRISS Scores in Tunisian Terrorism Victims
Authors: Bahrini Khadija , Horchani Houcine , Boughariou Sana , Rebai Aicha , Zakraoui Mohamed , Naas Imen , Gharsallah Hedi , Labbene Iheb , Ferjani Mustapha , Sallemi Walid , Hajjej Zied , Shimi Maha , Fourati Hazem , Romdhani Chihebeddine 
Published: October 2024

ABSTRACT

Introduction
Injuries caused by terrorism attacks are one of the urgent problems of the society and the health system. In this work, we aimed to assess the injury severity score (ISS) and trauma injury severity score (TRISS) in Tunisian military combatants injured during terrorism attacks.

Materials and Methods
A total of 153 victims of terrorism admitted to the Military Hospital of Tunis between January 2012 and January 2017 were included. Among them, 107 survived and 46 died (43 victims died at the terrorist attack scene and 3 died in the hospital). All dead patients were autopsied. Injury severity scores and TRISSs were then calculated by 2 professors in the anesthesia-resuscitation department, and the agreement level was assessed using the Bland and Altman curve.

Results
We obtained a strong agreement between the 2 experts when assessing the TRISS and ISS. Using the Bland and Altman curve, an agreement between the 2 experts was obtained between 0 to 40 and 60 to 75 for the ISS and between 0 to 25 and 75 to 100 for the TRISS. Moreover, we detected a high level of ISS and TRISS, especially in deceased victims compared to survivors (P &lt;.001). To predict mortality, we revealed by the receiver operating characteristic curve high sensitivity and specificity (more than 90%) before day 28 of hospital stay as well as for ISS and TRISS. Regarding the mechanism of injury, patients injured by gunshot have higher ISSs and TRISSs than those injured by explosion (P &lt; .001).

Conclusions
Injury severity scores and TRISSs showed a high reliability to predict the mortality rate in Tunisian victims of terrorism.
Analytical strong line diagnostics and their redshift evolution
Authors: Yang Shengqi , Lidz Adam , Benson Andrew , Chauhan Swathya Singh , Smith Aaron , Li Hui 
Published: October 2024

ABSTRACT
The JWST is allowing new measurements of gas-phase metallicities in galaxies between cosmic noon and cosmic dawn. The most robust approach uses luminosity ratios between the excited auroral transition, [O iii] 4364 Å, and the lower [O iii] 5008 Å/4960 Å lines to determine the gas temperature. The ratio of the luminosities in the latter transitions to those in hydrogen Balmer series lines then yield relatively clean metallicity estimates. In the absence of detection of the [O iii] auroral line, the ratios of various [O iii], [O ii], [N ii], and Balmer lines are used to determine metallicities. Here, we present a refined approach for extracting metallicities from these ‘strong line diagnostics’. Our method exploits empirical correlations between the temperature of O iii/O ii regions and gas-phase metallicity. We then show, from first principles, how to extract metallicities and break degeneracies in these estimates using traditional strong line diagnostics, R2, R3, R23, and O3O2 and N2O2. We show that these ratios depend also on volume correction factors, that is, on accounting for the fraction of the volume of H ii regions that are in O iii and O ii, but that these can be determined self-consistently along with the metallicities. We quantify the success of our method using metallicities derived from galaxies with auroral line determinations and show that it generally works better than previous empirical approaches. The scatter in the observed line ratios and redshift evolution are largely explained by O3O2 variations. We provide publicly available routines for extracting metallicities from strong line diagnostics using our methodology.
The mystery of water in the atmosphere of τ Boötis b continues: Insights from revisiting archival CRIRES observations
Authors: Panwar Vatsal , Brogi Matteo , Gandhi Siddharth , Cegla Heather , Lafarga Marina 
Published: October 2024

ABSTRACT
The chemical abundances of gas-giant exoplanet atmospheres hold clues to the formation and evolution pathways that sculpt the exoplanet population. Recent ground-based high-resolution spectroscopic observations of the non-transiting hot Jupiter $\tau$ Boötis b from different instruments have resulted in a tension on the presence of water vapour in the planet’s atmosphere, which impact the planet’s inferred C/O and metallicity. To investigate this, we revisit the archival CRIRES observations of the planet’s day-side in the wavelength range 2.28–2.33 $\mu$m. We re-analyse them using the latest methods for correcting stellar and telluric systematics, and free- and equilibrium-chemistry Bayesian atmospheric retrieval. We find that a spurious detection of CH$_4$ can arise from inadequate telluric correction. We confirm the detection of CO and constrain its abundance to be near solar $\log _{10}(\mathrm{CO})$ = –3.44$^{+1.63}_{-0.85}$ volume mixing ratios (VMR). We find a marginal evidence for H$_{2}$O with $\log _{10}(\mathrm{H_{2}O})$ = –5.13$^{+1.22}_{-6.37}$ VMR. This translates to super solar C/O (0.95$^{+0.06}_{-0.31}$), marginally sub-solar metallicity (–0.21 $^{+1.66}_{-0.87}$). Due to the relatively large uncertainty on H$_{2}$O abundance, we cannot confidently resolve the tension on the presence of H$_{2}$O and the super-solar atmospheric metallicity of $\tau$ Boötis b. We recommend further observations of $\tau$ Boötis b in the wavelength ranges simultaneously covering CO and $\mathrm{H_{2}O}$ to confirm the peculiar case of the planet’s super-solar C/O and metallicity.
The rate of extreme coronal line emitting galaxies in the Sloan Digital Sky Survey and their relation to tidal disruption events
Authors: Callow J , Graur O , Clark P , Palmese A , Aguilar J , Ahlen S , BenZvi S , Brooks D , Claybaugh T , de la Macorra A , Doel P , Forero-Romero J E , Gaztañaga E , Gontcho A Gontcho S , Lambert A , Landriau M , Manera M , Meisner A , Miquel R , Moustakas J , Nie J , Poppett C , Prada F , Rezaie M , Rossi G , Sanchez E , Silber J , Tarlé G , Weaver B A , Zhou Z 
Published: October 2024

ABSTRACT
High-ionization iron coronal lines (CLs) are a rare phenomenon observed in galaxy and quasi-stellar object spectra that are thought to be created by high-energy emission from active galactic nuclei and certain types of transients. In cases known as extreme coronal line emitting galaxies (ECLEs), these CLs are strong and fade away on a time-scale of years. The most likely progenitors of these variable CLs are tidal disruption events (TDEs), which produce sufficient high-energy emission to create and sustain the CLs over these time-scales. To test the possible connection between ECLEs and TDEs, we present the most complete variable ECLE rate calculation to date and compare the results to TDE rates from the literature. To achieve this, we search for ECLEs in the Sloan Digital Sky Survey (SDSS). We detect sufficiently strong CLs in 16 galaxies, more than doubling the number previously found in SDSS. Using follow-up spectra from the Dark Energy Spectroscopic Instrument and Gemini Multi-Object Spectrograph, Wide-field Infrared Survey Explorer mid-infrared observations, and Liverpool Telescope optical photometry, we find that none of the nine new ECLEs evolve in a manner consistent with that of the five previously discovered variable ECLEs. Using this sample of five variable ECLEs, we calculate the galaxy-normalized rate of variable ECLEs in SDSS to be $R_\mathrm{G}=3.6~^{+2.6}_{-1.8}~(\mathrm{statistical})~^{+5.1}_{-0.0}~(\mathrm{systematic})\times 10^{-6}~\mathrm{galaxy}^{-1}~\mathrm{yr}^{-1}$. The mass-normalized rate is $R_\mathrm{M}=3.1~^{+2.3}_{-1.5}~(\mathrm{statistical})~^{+4.4}_{-0.0}~(\mathrm{systematic})\times 10^{-17}~\mathrm{M_\odot ^{-1}}~\mathrm{yr}^{-1}$ and the volumetric rate is $R_\mathrm{V}=7~^{+20}_{-5}~(\mathrm{statistical})~^{+10}_{-0.0}~(\mathrm{systematic})\times 10^{-9}~\mathrm{Mpc}^{-3}~\mathrm{yr}^{-1}$. Our rates are one to two orders of magnitude lower than TDE rates from the literature, which suggests that only 10–40 per cent of all TDEs produce variable ECLEs. Additional uncertainties in the rates arising from the structure of the interstellar medium have yet to be included.
Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations
Authors: Srivastava Yoshita , Akinyemi Olayinka , Rohe Tiana C , Pritchett Elizabeth M , Baker Cameron D , Sharma Akshara , Jenkins Jermaine L , Mathews David H , Wedekind Joseph E 
Published: October 2024

Abstract
Riboswitches are structured RNAs that sense small molecules to control expression. Prequeuosine1 (preQ1)-sensing riboswitches comprise three classes (I, II and III) that adopt distinct folds. Despite this difference, class II and III riboswitches each use 10 identical nucleotides to bind the preQ1 metabolite. Previous class II studies showed high sensitivity to binding-pocket mutations, which reduced preQ1 affinity and impaired function. Here, we introduced four equivalent mutations into a class III riboswitch, which maintained remarkably tight preQ1 binding. Co-crystal structures of each class III mutant showed compensatory interactions that preserve the fold. Chemical modification analysis revealed localized RNA flexibility changes for each mutant, but molecular dynamics (MD) simulations suggested that each mutation was not overtly destabilizing. Although impaired, class III mutants retained tangible gene-regulatory activity in bacteria compared to equivalent preQ1-II variants; mutations in the preQ1-pocket floor were tolerated better than wall mutations. Principal component analysis of MD trajectories suggested that the most functionally deleterious wall mutation samples different motions compared to wildtype. Overall, the results reveal that formation of compensatory interactions depends on the context of mutations within the overall fold and that functionally deleterious mutations can alter long-range correlated motions that link the riboswitch binding pocket with distal gene-regulatory sequences.
Massively parallel reporter assays identify enhancer elements in oesophageal Adenocarcinoma
Authors: Yang Shen-Hsi , Ahmed Ibrahim , Li Yaoyong , Bleaney Christopher W , Sharrocks Andrew D 
Published: October 2024

Abstract
Cancer is a disease underpinned by aberrant gene expression. Enhancers are regulatory elements that play a major role in transcriptional control and changes in active enhancer function are likely critical in the pathogenesis of oesophageal adenocarcinoma (OAC). Here, we utilise STARR-seq to profile the genome-wide enhancer landscape in OAC and identify hundreds of high-confidence enhancer elements. These regions are enriched in enhancer-associated chromatin marks, are actively transcribed and exhibit high levels of associated gene activity in OAC cells. These characteristics are maintained in human patient samples, demonstrating their disease relevance. This relevance is further underlined by their responsiveness to oncogenic ERBB2 inhibition and increased activity compared to the pre-cancerous Barrett's state. Mechanistically, these enhancers are linked to the core OAC transcriptional network and in particular KLF5 binding is associated with high level activity, providing further support for a role of this transcription factor in defining the OAC transcriptome. Our results therefore uncover a set of enhancer elements with physiological significance, that widen our understanding of the molecular alterations in OAC and point to mechanisms through which response to targeted therapy may occur.