bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical note: ShinyAnimalCV: open-source cloud-based web application for object detection, segmentation, and three-dimensional visualization of animals using computer vision
Authors: Wang Jin , Hu Yu , Xiang Lirong , Morota Gota , Brooks Samantha A , Wickens Carissa L , Miller-Cushon Emily K , Yu Haipeng 
Published: December 2023

Abstract
Computer vision (CV), a non-intrusive and cost-effective technology, has furthered the development of precision livestock farming by enabling optimized decision-making through timely and individualized animal care. The availability of affordable two- and three-dimensional camera sensors, combined with various machine learning and deep learning algorithms, has provided a valuable opportunity to improve livestock production systems. However, despite the availability of various CV tools in the public domain, applying these tools to animal data can be challenging, often requiring users to have programming and data analysis skills, as well as access to computing resources. Moreover, the rapid expansion of precision livestock farming is creating a growing need to educate and train animal science students in CV. This presents educators with the challenge of efficiently demonstrating the complex algorithms involved in CV. Thus, the objective of this study was to develop ShinyAnimalCV, an open-source cloud-based web application designed to facilitate CV teaching in animal science. This application provides a user-friendly interface for performing CV tasks, including object segmentation, detection, three-dimensional surface visualization, and extraction of two- and three-dimensional morphological features. Nine pre-trained CV models using top-view animal data are included in the application. ShinyAnimalCV has been deployed online using cloud computing platforms. The source code of ShinyAnimalCV is available on GitHub, along with detailed documentation on training CV models using custom data and deploying ShinyAnimalCV locally to allow users to fully leverage the capabilities of the application. ShinyAnimalCV can help to support the teaching of CV, thereby laying the groundwork to promote the adoption of CV in the animal science community.
XMM-Newton-discovered Fast X-ray Transients: host galaxies and limits on contemporaneous detections of optical counterparts
Authors: Eappachen D , Jonker P G , Quirola-Vásquez J , Sánchez D Mata , Inkenhaag A , Levan A J , Fraser M , Torres M A P , Bauer F E , Chrimes A A , Stern D , Graham M J , Smartt S J , Smith K W , Ravasio M E , Zabludoff A I , Yue M , Stoppa F , Malesani D B , Stone N C , Wen S 
Published: December 2023

ABSTRACT
Extragalactic fast X-ray transients (FXTs) are a class of soft (0.3–10 keV) X-ray transients lasting a few hundred seconds to several hours. Several progenitor mechanisms have been suggested to produce FXTs, including supernova shock breakouts, binary neutron star mergers, or tidal disruptions involving an intermediate-mass black hole and a white dwarf. We present detailed host studies, including spectroscopic observations of the host galaxies of seven XMM-Newton-discovered FXTs. The candidate hosts lie at redshifts 0.0928 &lt;z &lt; 0.645 implying peak X-ray luminosities of 1043 erg s−1&lt;LX &lt; 1045 erg s−1 and physical offsets of 1 kpc &lt; rproj &lt; 22 kpc. These observations increase the number of FXTs with a spectroscopic redshift measurement by a factor of 2, although we note that one event is re-identified as a Galactic flare star. We infer host star formation rates and stellar masses by fitting the combined spectroscopic and archival photometric data. We also report on a contemporaneous optical counterpart search to the FXTs in Pan-STARRS and ATLAS by performing forced photometry at the position of the FXTs. We do not find any counterpart in our search. Given our constraints, including peak X-ray luminosities, optical limits, and host properties, we find that XRT 110 621 is consistent with an supernova shock breakout (SN SBO) event. Spectroscopic redshifts of likely host galaxies for four events imply peak X-ray luminosities that are too high to be consistent with SN SBOs, but we are unable to discard either the binary neutron star or white dwarf–intermediate-mass black hole tidal disruption event scenarios for these FXTs.
Atomic diffusion and mixing in old stars – VIII. Chemical abundance variations in the globular cluster M4 (NGC 6121)
Authors: Nordlander T , Gruyters P , Richard O , Korn A J 
Published: December 2023

ABSTRACT
Variations in chemical abundances with evolutionary phase have been identified among stars in globular and open clusters with a wide range of metallicities. In the metal-poor clusters, these variations compare well with predictions from stellar structure and evolution models considering the internal diffusive motions of atoms and ions, collectively known as atomic diffusion, when moderated by an additional mixing process with a fine-tuned efficiency. We present here an investigation of these effects in the Galactic globular cluster NGC 6121 (M4) ([Fe/H] = −1.13) through a detailed chemical abundance analysis of 86 stars using high-resolution ESO Very Large Telescope (VLT) Fibre Large Array Multi Element Spectrograph (FLAMES) spectroscopy. The stars range from the main-sequence turnoff point (TOP) to the red giant branch (RGB) just above the bump. We identify C-N-O and Mg-Al-Si abundance anticorrelations, and confirm the presence of a bimodal population differing by 1 dex in nitrogen abundance. The composition of the second-generation stars imply pollution from both massive (20–40 $\rm M_{\odot }$) and asymptotic giant branch stars. We find evolutionary variations in chemical abundances between the TOP and RGB, which are robust to uncertainties in stellar parameters and modelling assumptions. The variations are weak, but match predictions well when employing efficient additional mixing. Without correcting for Galactic production of lithium, we derive an initial lithium abundance 2.63 ± 0.10, which is marginally lower than the predicted primordial big-bang nucleosynthesis value.
Ascertainment Bias in the Genomic Test of Positive Selection on Regulatory Sequences
Authors: Jiang Daohan , Zhang Jianzhi 
Published: December 2023

AbstractEvolution of gene expression mediated by cis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptive cis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former at n sites, one can predict the TF-binding affinities of many n-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of 3 TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here, we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
Abrogation of the G2/M checkpoint as a chemosensitization approach for alkylating agents
Authors: Lang Fengchao , Cornwell James A , Kaur Karambir , Elmogazy Omar , Zhang Wei , Zhang Meili , Song Hua , Sun Zhonghe , Wu Xiaolin , Aladjem Mirit I , Aregger Michael , Cappell Steven D , Yang Chunzhang 
Published: December 2023

Abstract

Background
The cell cycle is tightly regulated by checkpoints, which play a vital role in controlling its progression and timing. Cancer cells exploit the G2/M checkpoint, which serves as a resistance mechanism against genotoxic anticancer treatments, allowing for DNA repair prior to cell division. Manipulating cell cycle timing has emerged as a potential strategy to augment the effectiveness of DNA damage-based therapies.

Methods
In this study, we conducted a forward genome-wide CRISPR/Cas9 screening with repeated exposure to the alkylating agent temozolomide (TMZ) to investigate the mechanisms underlying tumor cell survival under genotoxic stress.

Results
Our findings revealed that canonical DNA repair pathways, including the Ataxia–telangiectasia mutated (ATM)/Fanconi and mismatch repair, determine cell fate under genotoxic stress. Notably, we identified the critical role of PKMYT1, in ensuring cell survival. Depletion of PKMYT1 led to overwhelming TMZ-induced cytotoxicity in cancer cells. Isobologram analysis demonstrated potent drug synergy between alkylating agents and a Myt1 kinase inhibitor, RP-6306. Mechanistically, inhibiting Myt1 forced G2/M-arrested cells into an unscheduled transition to the mitotic phase without complete resolution of DNA damage. This forced entry into mitosis, along with persistent DNA damage, resulted in severe mitotic abnormalities. Ultimately, these aberrations led to mitotic exit with substantial apoptosis. Preclinical animal studies demonstrated that the combination regimen involving TMZ and RP-6306 prolonged the overall survival of glioma-bearing mice.

Conclusions
Collectively, our findings highlight the potential of targeting cell cycle timing through Myt1 inhibition as an effective strategy to enhance the efficacy of current standard cancer therapies, potentially leading to improved disease outcomes.
Breaking Barriers: A Single-Center Real-World Experience With Recruitment and Administration of COVID-19 Monoclonal Antibodies and Opportunities for Improvement
Authors: Brenner Sara , Knee Alexander , Salvador Douglas , Housman Erica , Fernandez Gladys , Paez Armando 
Published: December 2023

Abstract
We conducted a retrospective exploratory study evaluating factors associated with selection to receive and infusion with coronavirus disease 2019 monoclonal antibodies. While priority was given to high-risk patients, patients with increased Social Vulnerability Index scores were less likely to present for infusion, raising concern that social factors created barriers to treatment.
Evaluating the Impact of Source-specific Order Sets for Sepsis on Empiric Antibiotic Selection in the Emergency Department
Authors: Menendez Alvarado Lourdes R , Margulis Landayan Alice , Morell Jason , Wasielewski Anthony S , Zhang Zhenwei , Levine Richard , Gauthier Timothy P 
Published: December 2023

Abstract
This retrospective cohort study found that implementing source-specific antibiotic order sets for sepsis in the emergency department increased appropriate empiric antibiotic selection from 51% to 74% (P = .01).
Targeted A-to-G base editing in the organellar genomes of Arabidopsis with monomeric programmable deaminases
Authors: Zhou Chang , Okuno Miki , Nakazato Issei , Tsutsumi Nobuhiro , Arimura Shin-ichi 
Published: December 2023

Abstract
Plastids and mitochondria are 2 intracellular organelles containing DNA-encoding partial but essential components for their roles, photosynthesis, and respiration. Precise base editing in both plastid and mitochondrial genomes would benefit their gene functional analysis and crop breeding. Targeted base editing in organellar genomes relies on a protein-based genome-editing system that uses the TALE-DNA recognition motif with deaminases. This is because the efficient delivery of guide RNA for clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems into organelles is currently impossible. Since TALE-based base editors used in organellar genomes are usually dimeric types, in this study, we used targeted A-to-G base editing in Arabidopsis (Arabidopsis thaliana) plastid and mitochondrial genomes with monomeric TALE-based deaminase for easier assembling of vectors. As a result, inheritable targeted A-to-G base editing of adenosine triphosphatase subunit 6-2 (atp6-2) in plant mitochondrial genomes and of 16S ribosomal RNA (16S rRNA) in plastid genomes of Arabidopsis was successfully induced by monomeric TALE-based adenine deaminase (AD) without off-target mutations. The monomeric TALE-based adenine deaminases also demonstrated a preference for editing the 8th T on the same strand from the recognition end. Phenotypic analysis showed that A-to-G conversion at 1139A of plastid 16S rRNA conferred substantial spectinomycin resistance in Arabidopsis, but not the other 2 potential-resistant mutations at 1131T and 1137T, predicted from the previous bacterial data. Our study demonstrated the feasibility of monomeric TALE-based ADs in plant organelles and their potential contribution to the functional analyses of plant organelles with easier assembling.
Localized measurements of water potential reveal large loss of conductance in living tissues of maize leaves
Authors: Jain Piyush , Huber Annika E , Rockwell Fulton E , Sen Sabyasachi , Holbrook Noel Michele , Stroock Abraham D 
Published: December 2023

Abstract
The water status of the living tissue in leaves between the xylem and stomata (outside xylem zone (OXZ) plays a critical role in plant function and global mass and energy balance but has remained largely inaccessible. We resolve the local water relations of OXZ tissue using a nanogel reporter of water potential (ψ), AquaDust, that enables an in situ, nondestructive measurement of both ψ of xylem and highly localized ψ at the terminus of transpiration in the OXZ. Working in maize (Zea mays L.), these localized measurements reveal gradients in the OXZ that are several folds larger than those based on conventional methods and values of ψ in the mesophyll apoplast well below the macroscopic turgor loss potential. We find a strong loss of hydraulic conductance in both the bundle sheath and the mesophyll with decreasing xylem potential but not with evaporative demand. Our measurements suggest the OXZ plays an active role in regulating the transpiration path, and our methods provide the means to study this phenomenon.
Therapeutic Effects of Hematopoietic Stem Cell Derived From Gene-Edited Mice on β654-Thalassemia
Authors: Lu Dan , Gong Xiuli , Guo Xinbing , Chen Yanwen , Zhu Yiwen , Fang Yudan , Cai Qin , Xu Miao , Yang Hua , Li Dali , Zeng Yitao , Zeng Fanyi 
Published: December 2023

Abstract
β-thalassemia is an inherited blood disease caused by reduced or inadequate β-globin synthesis due to β-globin gene mutation. Our previous study developed a gene-edited mice model (β654-ER mice) by CRISPR/Cas9-mediated genome editing, targeting both the βIVS2-654 (C &gt; T) mutation site and the 3ʹ splicing acceptor site at 579 and corrected abnormal β-globin mRNA splicing in the β654-thalassemia mice. Herein, we further explored the therapeutic effect of the hematopoietic stem cells (HSCs) from β654-ER mice on β-thalassemia by consecutive HSC transplantation. The results indicated that HSC transplantation derived from gene-edited mice can significantly improve the survival rate of mice after lethal radiation doses and effectively achieve hematopoietic reconstruction and long-term hematopoiesis. Clinical symptoms, including hematologic parameters and tissue pathology of transplanted recipients, were significantly improved compared to the non-transplanted β654 mice. The therapeutic effect of gene-edited HSC transplantation demonstrated no significant difference in hematological parameters and tissue pathology compared with wild-type mouse-derived HSCs. Our data revealed that HSC transplantation from gene-edited mice completely recovered the β-thalassemia phenotype. Our study systematically investigated the therapeutic effect of HSCs derived from β654-ER mice on β-thalassemia and further confirmed the efficacy of our gene-editing approach. Altogether, it provided a reference and primary experimental data for the clinical usage of such gene-edited HSCs in the future.
Ten years of using key characteristics of human carcinogens to organize and evaluate mechanistic evidence in IARC Monographs on the identification of carcinogenic hazards to humans: Patterns and associations
Authors: Rusyn Ivan , Wright Fred A 
Published: December 2023

Abstract
Systematic review and evaluation of mechanistic evidence using the Key Characteristics approach was proposed by the International Agency for Research on Cancer (IARC) in 2012 and used by the IARC Monographs Working Groups since 2015. Key Characteristics are 10 features of agents known to cause cancer in humans. From 2015 to 2022, a total of 19 Monographs (73 agents combined) used Key Characteristics for cancer hazard classification. We hypothesized that a retrospective analysis of applications of the Key Characteristics approach to cancer hazard classification using heterogenous mechanistic data on diverse agents would be informative for systematic reviews in decision-making. We extracted information on the conclusions, data types, and the role mechanistic data played in the cancer hazard classification from each Monograph. Statistical analyses identified patterns in the use of Key Characteristics, as well as trends and correlations among Key Characteristics, data types, and ultimate decisions. Despite gaps in data for many agents and Key Characteristics, several significant results emerged. Mechanistic data from in vivo animal, in vitro animal, and in vitro human studies were most impactful in concluding that an agent could cause cancer via a Key Characteristic. To exclude the involvement of a Key Characteristic, data from large-scale systematic in vitro testing programs such as ToxCast, were most informative. Overall, increased availability of systemized data streams, such as human in vitro data, would provide the basis for more confident and informed conclusions about both positive and negative associations and inform expert judgments on cancer hazard.
Parking choice behaviour analysis of rural residents based on the latent variable random forest model
Authors: Zhu Minqing , Zhao Bo , Cui Hongjun , Yao Sheng , Xu Feng 
Published: December 2023

Abstract
The imbalance of rural parking supply and demand has a great impact on traffic congestion and environmental pollution, which has attracted the attention of many scholars as well as policymakers. However, most of the current research on parking choice focuses on urban business and residential areas rather than on rural parking choice behaviour, and focuses on the analysis of observable factors, ignoring the internal relationship with potential variables. This study considers the heterogeneity of individuals and uses the random forest (RF) algorithm to construct a model of rural residents’ willingness to choose parking with both latent and explicit variables, to explore how much and in what ways individual characteristics and parking characteristics affect rural residents’ parking choices, and to explore parking planning programmes and strategies that are truly applicable to rural areas. The results of the study suggest that the safety and convenience of the parking environment are key factors influencing the parking choice behaviour of rural residents, and can greatly improve the predictive accuracy of the parking willingness model. Upon comparison, it is found that the application of the RF algorithm is also significantly better than the logit model in terms of prediction effect, indicating that there is a nonlinear effect among the factors influencing the parking choice behaviour of rural residents and that the RF model with the addition of latent variables provides a better explanatory ability for the study of the parking choice behaviour of rural residents.
Health disparities in gout
Authors: Helget Lindsay N. , Mikuls Ted R. 
Published: December 2023

Purpose of review
Gout, the most common type of inflammatory arthritis in the world, is characterized by painful episodes of arthritis linked by asymptomatic intercritical periods of hyperuricemia. Once characterized as a disease of wealthy white men, contemporary evidence demonstrates gout disproportionately afflicts racial/ethnic minorities, Indigenous populations and other underrepresented groups leading to significant health disparities.

Recent findings
Herein, we review the current literature reporting a higher incidence and prevalence of gout in racial/ethnic minorities and Indigenous populations, in addition to a growing gout burden reported in females. We also examine how these population are more likely to receive suboptimal treatment for flares and chronic phases of gout. Additionally, we examine biologic and social health determinants that may be contributing to these findings.

Summary
Racial/ethnic minorities, Indigenous populations, and females have experienced a disproportionate rise in the prevalence and incidence of gout in recent years, are more likely to seek acute medical care and are less likely to receive optimal long-term care for gout with urate lowering therapy. Mechanisms underpinning these findings appear to be multifactorial and include differences in social determinants of care and in some cases may be due to population differences in select biologic factors such as differences in age, sex, genetics.
Selective Laser Trabeculoplasty as a Substitute for Medications in Patients with Mild-to-moderate Glaucoma in the Brazilian Public Health System
Authors: Barbosa Leopoldo Ernesto Oiticica , Barboza Wilma Lelis , Guedes Ricardo Paletta , Pereira Clarissa dos Reis , Susanna Remo , Hatanaka Marcelo 
Published: December 2023

Précis:
Selective laser trabeculoplasty can be used as a substitute for medications in patients with mild-to-moderate glaucoma, reducing the cost of eye drop distribution in the Brazilian public health system.

Purpose:
To observe the effectiveness of selective laser trabeculoplasty (SLT) as a substitute for eye drops in patients with open angle glaucoma in the Brazilian Public Health System.

Materials and Methods:
SLT was performed bilaterally after medication washout. This is a prospective interventional study comparing intraocular pressure (IOP) when using eye drops at baseline (post-washout), and at 12-month follow-up after SLT. Medication was added if the target IOP was not achieved, following the Brazilian Public Health System eye drops protocol, based on medication costs. Absolute (without eye drops) and qualified (with eye drops) success were measured with IOP ≤ 21, IOP ≤ 18, IOP ≤ 15 and IOP ≤ 12 mm Hg. Besides IOP evolution, the ability to reduce IOP (in %), and eye drops reduction were evaluated.

Results:
Ninety-two eyes of 46 patients were included, 70 eyes with mild glaucoma and 22 with moderate glaucoma; the mean number of eye drops was 2.26±1.06 (82.6% were using a prostaglandin analogue), and post-washout IOP of 21.10±5.24 mm Hg. There was relative success at IOP ≤18 mm Hg, where the mild group had greater success than the moderate group (88.1% vs. 71.4%, P=0.824). The average IOP reductions were 23.04% and 25.74% at 6 and 12 months, respectively. The average number of eye drops was 1.02, with 1.1% using a prostaglandin analogue. Furthermore, 68.19% of the patients had a decrease in the quantity of eye drops used.

Conclusion:
SLT is effective in reducing IOP and replacing eye drops in patients in the Brazilian Public Health System. Moreover, there was a significant reduction in the use of prostaglandin analogues.