bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic insights into the critically endangered King Island scrubtit
Authors: Crates Ross , von Takach Brenton , Young Catherine M , Stojanovic Dejan , Neaves Linda E , Murphy Liam , Gautschi Daniel , Hogg Carolyn J , Heinsohn Robert , Bell Phil , Farquharson Katherine A 
Published: May 2024

Abstract
Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of &lt;100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.
Effects of vitamin D supplementation on a deep learning–based mammographic evaluation in SWOG S0812
Authors: McGuinness Julia E , Anderson Garnet L , Mutasa Simukayi , Hershman Dawn L , Terry Mary Beth , Tehranifar Parisa , Lew Danika L , Yee Monica , Brown Eric A , Kairouz Sebastien S , Kuwajerwala Nafisa , Bevers Therese B , Doster John E , Zarwan Corrine , Kruper Laura , Minasian Lori M , Ford Leslie , Arun Banu , Neuhouser Marian L , Goodman Gary E , Brown Powel H , Ha Richard , Crew Katherine D 
Published: May 2024

Abstract
Deep learning–based mammographic evaluations could noninvasively assess response to breast cancer chemoprevention. We evaluated change in a convolutional neural network–based breast cancer risk model applied to mammograms among women enrolled in SWOG S0812, which randomly assigned 208 premenopausal high-risk women to receive oral vitamin D3 20 000 IU weekly or placebo for 12 months. We applied the convolutional neural network model to mammograms collected at baseline (n = 109), 12 months (n = 97), and 24 months (n = 67) and compared changes in convolutional neural network-based risk score between treatment groups. Change in convolutional neural network-based risk score was not statistically significantly different between vitamin D and placebo groups at 12 months (0.005 vs 0.002, P = .875) or at 24 months (0.020 vs 0.001, P = .563). The findings are consistent with the primary analysis of S0812, which did not demonstrate statistically significant changes in mammographic density with vitamin D supplementation compared with placebo. There is an ongoing need to evaluate biomarkers of response to novel breast cancer chemopreventive agents.
Harnessing controlled-environment systems for enhanced production of medicinal plants
Authors: Dsouza Ajwal , Dixon Mike , Shukla Mukund , Graham Thomas 
Published: May 2024

Abstract
Medicinal plants are valued for their contributions to human health. However, the growing demand for medicinal plants and the concerns regarding their quality and sustainability have prompted the reassessment of conventional production practices. Controlled-environment cropping systems, such as vertical farms, offer a transformative approach to production of medicinal plants. By enabling precise control over environmental factors, such as light, carbon dioxide, temperature, humidity, nutrients, and airflow, controlled environments can improve the consistency, concentration, and yield of bioactive phytochemicals in medicinal plants. This review explores the potential of controlled-environment systems for enhancing production of medicinal plants. First, we describe how controlled environments can overcome the limitations of conventional production in improving the quality of medicinal plants. Next, we propose strategies based on plant physiology to manipulate environmental conditions for enhancing the levels of bioactive compounds in plants. These strategies include improving photosynthetic carbon assimilation, light spectrum signalling, purposeful stress elicitation, and chronoculture. We describe the underlying mechanisms and practical applications of these strategies. Finally, we highlight the major knowledge gaps and challenges that limit the application of controlled environments, and discuss future research directions.
The wall-associated receptor-like kinase CsWAKL01, positively regulated by the transcription factor CsWRKY53, confers resistance to citrus bacterial canker via regulation of phytohormone signaling
Authors: Yu Qiyuan , He Houzheng , Xian Baohang , Zhang Chenxi , Zhong Xin , Liu Yiqi , Zhang Miao , Li Man , He Yongrui , Chen Shanchun , Li Qiang 
Published: May 2024

Abstract
Citrus bacterial canker (CBC) is a disease that poses a major threat to global citrus production and is caused by infection with Xanthomonas citri subsp. citri (Xcc). Wall-associated receptor-like kinase (WAKL) proteins play an important role in shaping plant resistance to various bacterial and fungal pathogens. In a previous report, CsWAKL01 was identified as a candidate Xcc-inducible gene found to be up-regulated in CBC-resistant citrus plants. However, the functional role of CsWAKL01 and the mechanisms whereby it may influence resistance to CBC have yet to be clarified. Here, CsWAKL01 was found to localize to the plasma membrane, and the overexpression of the corresponding gene in transgenic sweet oranges resulted in pronounced enhancement of CBC resistance, whereas its knockdown had the opposite effect. Mechanistically, the effect of CsWAKL01 was linked to its ability to reprogram jasmonic acid, salicylic acid, and abscisic acid signaling activity. CsWRKY53 was further identified as a transcription factor capable of directly binding to the CsWAKL01 promoter and inducing its transcriptional up-regulation. CsWRKY53 silencing conferred greater CBC susceptibility to infected plants. Overall, these data support a model wherein CsWRKY53 functions as a positive regulator of CsWAKL01 to enhance resistance to CBC via the reprogramming of phytohormone signaling. Together these results offer new insights into the mechanisms whereby WAKLs shape phytopathogen resistance while underscoring the potential value of targeting the CsWRKY53–CsWAKL01 axis when seeking to breed CBC-resistant citrus plant varieties.
Spatial multi-omics characterizes GPR35-relevant lipid metabolism signatures across liver zonation in MASLD
Authors: Otkur Wuxiyar , Zhang Yiran , Li Yirong , Bao Wenjun , Feng Tingze , Wu Bo , Ma Yaolu , Shi Jing , Wang Li , Pei Shaojun , Wang Wen , Wang Jixia , Zhao Yaopeng , Liu Yanfang , Li Xiuling , Xia Tian , Wang Fangjun , Chen Di , Liang Xinmiao , Piao Hai-long 
Published: May 2024

Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic disease that can progress to metabolic dysfunction-associated steatohepatitis (MASH), cirrhosis, and cancer. The zonal distribution of biomolecules in the liver is implicated in mediating the disease progression. Recently, G-protein-coupled receptor 35 (GPR35) has been highlighted to play a role in MASLD, but the precise mechanism is not fully understood, particularly, in a liver-zonal manner. Here, we aimed to identify spatially distributed specific genes and metabolites in different liver zonation that are regulated by GPR35 in MASLD, by combining lipid metabolomics, spatial transcriptomics (ST), and spatial metabolomics (SM). We found that GPR35 influenced lipid accumulation, inflammatory and metabolism-related factors in specific regions, notably affecting the anti-inflammation factor ELF4 (E74 like E-twenty six (ETS) transcription factor 4), lipid homeostasis key factor CIDEA (cell death-inducing DNA fragmentation factor alpha (DFFA)-like effector A), and the injury response-related genes SAA1/2/3 (serum amyloid A1/2/3), thereby impacting MASLD progression. Furthermore, SM elucidated specific metabolite distributions across different liver regions, such as C10H11N4O7P (3ʹ,5ʹ-cyclic inosine monophosphate (3ʹ,5ʹ-IMP)) for the central vein, and this metabolite significantly decreased in the liver zones of GPR35-deficient mice during MASLD progression. Taken together, GPR35 regulates hepatocyte damage repair, controls inflammation, and prevents MASLD progression by influencing phospholipid homeostasis and gene expression in a zonal manner.
The Neurologic Examination (What We Localize)
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter offers general comments on the neurologic examination and provides specific and comprehensive instructions for performing the exam. It discusses the presentation of the exam, including fine points of terminology. It explains how to interpret abnormal exam findings. It concludes with a section on how to modify the neuro exam in certain circumstances, specifically a screening exam, examining a patient in a video interaction, examining patients with altered level of consciousness, and examining patients with inconsistent or anomalous findings.
Seizures
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter defines seizures and epilepsy and presents the clinical features of common seizure types and epilepsy syndromes. It discusses the pathophysiology and diagnostic approach, including electroencephalography (EEG). It explains the approaches to management principles, including antiseizure medications (ASMs) and when to start them, ablative surgery, vagus nerve stimulation, deep brain stimulation, responsive stimulation, and ketogenic diet. It discusses lifestyle restrictions (especially driving), status epilepticus and issues related to pregnancy.
Sleep Disorders
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter begins with an explanation of sleep physiology and the tests used in diagnosing sleep disorders. This is followed by detailed discussion of the clinical manifestations, pathophysiology, and approach to diagnosis and management of major sleep disorders: insufficient sleep syndrome, obstructive sleep apnea, central sleep apnea, narcolepsy, psychophysiologic insomnia, delayed sleep-wake phase disorder, advanced sleep-wake phase disorder, night terrors, sleepwalking, sleep talking, confusional arousals, enuresis, periodic limb movements, seizures, rapid eye movement (REM) sleep behavior disorder, and nightmares.
Multifocal Central Nervous System Disorders
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter covers multifocal CNS disorders, including focal conditions with multifocal propagation as well as intrinsically multifocal conditions. It offers a detailed discussion of the clinical manifestations, pathophysiology, and approach to diagnosis and management of metastases to the brain or spinal cord, paraneoplastic syndromes, CNS abscesses, infective endocarditis, human immunodeficiency virus (HIV), neurosyphilis, Lyme disease, tuberculosis, Herpes simplex virus, Varicella zoster virus, COVID-19, anthrax, smallpox, botulism, multiple sclerosis (MS), neuromyelitis optica spectrum disorders (NMOSD), myelin oligodendrocyte glycoprotein (MOG) antibody disease (MOGAD), systemic lupus erythematosus, rheumatoid arthritis, sarcoidosis, and coagulation disorders. The chapter concludes with a brief discussion of functional disorders and the confusion surrounding what causes them and the terminology that should be used.
Headache
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter begins by distinguishing primary from secondary headaches. It then discusses the pathophysiology of migraine, which is presumed to be similar to the mechanisms underlying other types of headache. It then offers a detailed discussion of the clinical manifestations and approach to diagnosis and management of bacterial meningitis and subarachnoid hemorrhage, the two most urgent causes of secondary headache. It then provides a detailed discussion of the clinical manifestations and approach to diagnosis and management of other causes of secondary headache: viral meningitis or encephalitis, fungal or tuberculous meningitis, mass lesions, giant cell arteritis, idiopathic intracranial hypertension (IIH), spontaneous intracranial hypotension (SIH), cerebral venous dissection, arterial dissection, reversible cerebral vasoconstriction syndrome (RCVS), sinus disease, temporomandibular disorders, and post-concussion syndrome. It then presents a discussion of the clinical manifestations and treatment of primary headache disorders: migraine/tension, trigeminal neuralgia, glossopharyngeal neuralgia, cluster headache, trigeminal autonomic cephalalgias, primary stabbing headache, and persistent idiopathic facial pain.
Visual Symptoms
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter begins with an overview of the visual system and an approach to visual symptoms. It next considers causes of monocular vision loss, particularly optic neuritis in young individuals and—in older individuals—retinal artery occlusion and ischemic optic neuropathy. It next discusses the three main causes of episodic monocular vision loss: migraine, TIA, and increased intracranial pressure. This is followed by a brief discussion of persistent binocular vision loss. Finally, there is a discussion of diplopia, particularly lesions of cranial nerves III, IV, or VI or of the medial longitudinal fasciculus (MLF).
Back Pain and Neck Pain
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter begins with a discussion of the causes of neck or back pain that require urgent surgical intervention: metastasis, abscess, or other causes of spinal cord compression. It then presents the other, less urgent reasons to consider surgery. It then discusses specific conditions: musculoskeletal pain, intervertebral disc herniation, and spinal stenosis.
Incontinence
Authors: Gelb Douglas J. 
Published: May 2024

Abstract
This chapter begins with a brief discussion of the components of the nervous system that are involved in bladder and bowel control. It then considers non-neurologic causes of incontinence. It then discusses neurologic causes of incontinence, distinguishing the clinical features that are typical of incontinence due to PNS lesions from the features that suggest a CNS lesion.
Star-formation activity of low-mass galaxies at the peak epoch of galaxy formation probed by deep narrow-band imaging
Authors: Daikuhara Kazuki , Kodama Tadayuki , Pérez-Martínez Jose M , Shimakawa Rhythm , Suzuki Tomoko L , Tadaki Ken-ichi , Koyama Yusei , Tanaka Ichi 
Published: May 2024

ABSTRACT
Low-mass galaxies at high redshifts are the building blocks of more massive galaxies at later times and are thus key populations for understanding galaxy formation and evolution. We have made deep narrow-band observations for two protoclusters and the general field in COSMOS at z ∼ 2. In a clumpy young protocluster, USS1558−003, at z = 2.53, we find many star-forming galaxies well above the star-forming main sequence of field galaxies at the low-mass end ($M_{\star }/\mathrm{{\rm M}_{\odot }}\lt 10^{8.9}$). This suggests that some environmental effects may be at work in low-mass galaxies in high-density regions to enhance their star-formation activities. In the core of this protocluster, we also find enhanced star-formation activity of middle-mass galaxies ($10^{8.9} \lt M_{\star }/\mathrm{{\rm M}_{\odot }} \lt 10^{10.2}$) while such trends are not observed in a more mature protocluster, PKS1138−262 at z = 2.16. We expect these activities to be mainly due to galaxy mergers/interactions and differences in the amount of cold gas accretion. As one piece of evidence, we show that the star-formation activity within individual galaxies in the protoclusters is more centrally concentrated than those in the field. This is probably due to enhanced interactions between galaxies in the protocluster, which can reduce the angular momentum of the gas, drive the gas towards the galaxy centre, and lead to a central starburst.
Probing intracluster dynamics and evolution of globular clusters through cataclysmic variable populations
Authors: Oh Kwangmin , Hong Jongsuk , Hui C Y , Kim Sangin , Giersz Mirek 
Published: May 2024

ABSTRACT
Dynamical interactions in globular clusters (GCs) significantly impact the formation and evolution of binary sources, including cataclysmic variables (CVs). This study investigates the connection between dynamical states of GCs and X-ray luminosity (Lx) distributions of CV populations through both simulations and actual observations. Utilizing a Monte Carlo simulation tool, mocca, we categorize the simulated GCs into three different evolutionary stages which are referred to as Classes I/II/III. Significant differences are found in the Lx distributions of the CVs among these three Classes. In observational aspects, we have analysed 179 CV candidates in 18 GCs observed by the Chandra X-ray Observatory. By dividing these GCs into three Families of different dynamical ages, namely Families I/II/III, the Lx distributions of the CV candidates also show significant differences among these three Families. Both simulations and observational results suggest that CVs in more dynamically evolved clusters (Class/Family III) exhibit brighter X-ray emission. This highlights the influence of the dynamical status of a GC on the properties of its hosted compact binaries. Similar to blue stragglers, CV populations can serve as tracers of a GC’s dynamical history. Our findings provide insights for understanding the interplay between intracluster dynamics and the evolution of compact binaries in GCs.
The ALPINE-ALMA [C ii] survey: characterization of spatial offsets in main-sequence galaxies at z ∼ 4–6
Authors: Killi Meghana , Ginolfi Michele , Popping Gergö , Watson Darach , Zamorani Giovanni , Lemaux Brian C , Fujimoto Seiji , Faisst Andreas , Bethermin Matthieu , Romano Michael , Fudamoto Yoshinobu , Bardelli Sandro , Boquien Médéric , Carniani Stefano , Dessauges-Zavadsky Miroslava , Gruppioni Carlotta , Hathi Nimish , Ibar Eduardo , Jones Gareth C , Koekemoer Anton M , Langan Ivanna , Méndez-Hernández Hugo , Sugahara Yuma , Vallini Livia , Vergani Daniela 
Published: May 2024

ABSTRACT
The morphology of galaxies is shaped by stellar activity, feedback, gas and dust properties, and interactions with surroundings, and can therefore provide insight into these processes. In this paper, we study the spatial offsets between stellar and interstellar medium emission in a sample of 54 main-sequence star-forming galaxies at z ∼ 4–6 observed with the Atacama Large Millimeter/submillimeter Array (ALMA), and drawn from the ALMA Large Program to INvestigate C+ at Early times (ALPINE). We find no significant spatial offset for the majority (∼70 per cent) of galaxies in the sample among any combination of [C ii], far-infrared continuum, optical, and ultraviolet emission. However, a fraction of the sample (∼30 per cent) shows offsets larger than the median by more than 3σ significance (compared to the uncertainty on the offsets), especially between [C ii] and ultraviolet emission. We find that these significant offsets are of the order of ∼0.5–0.7 arcsec, corresponding to ∼3.5–4.5 kiloparsecs. The offsets could be caused by a complex dust geometry, strong feedback from stars and active galactic nuclei, large-scale gas inflow and outflow, or a combination of these phenomena. However, our current analysis does not definitively constrain the origin. Future, higher resolution ALMA and JWST observations may help resolve the ambiguity. Regardless, since there exist at least some galaxies that display such large offsets, galaxy models and spectral energy distribution fitting codes cannot assume co-spatial emission in all main-sequence galaxies, and must take into account that the observed emission across wavelengths may be spatially segregated.
A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis
Authors: Takada Hiraku , Paternoga Helge , Fujiwara Keigo , Nakamoto Jose A , Park Esther N , Dimitrova-Paternoga Lyudmila , Beckert Bertrand , Saarma Merilin , Tenson Tanel , Buskirk Allen R , Atkinson Gemma C , Chiba Shinobu , Wilson Daniel N , Hauryliuk Vasili 
Published: May 2024

Abstract
Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.
The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model
Authors: Ouyang Zhangyi , Liu Feng , Li Wanying , Wang Junting , Chen Bijia , Zheng Yang , Li Yaru , Tao Huan , Xu Xiang , Li Cheng , Cong Yuwen , Li Hao , Bo Xiaochen , Chen Hebing 
Published: May 2024

Abstract
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.