bluuebunny/crossref_metadata_2025_split huggingface dataset:
gcPathogen: a comprehensive genomic resource of human pathogens for public health
Authors: Guo Chongye , Chen Qi , Fan Guomei , Sun Yan , Nie Jingyi , Shen Zhihong , Meng Zhen , Zhou Yuanchun , Li Shiwen , Wang Shuai , Ma Juncai , Sun Qinglan , Wu Linhuan 
Published: October 2023

Abstract
Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive ‘one-stop shop’ that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.
AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging
Authors: Huang Kexin , Liu Xi , Zhang Zhaocan , Wang Tiangang , Xu Haixia , Li Qingxuan , Jia Yuhao , Huang Liyu , Kim Pora , Zhou Xiaobo 
Published: October 2023

Abstract
Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, proteins, metabolites, mitochondrial genes, microbiotas and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. AgeAnnoMO not only facilitates a deeper and more generalizable understanding of aging mechanisms, but also provides potential insights of the specificity across tissues and species in aging process, which is important to develop the effective anti-aging interventions for diverse populations. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology and identifying the targetable biomarkers for aging research.
Retained primary teeth: A clinical complaint not to be dismissed
Authors: Leung Christy W M , Leung Ting Fan 
Published: October 2023

Abstract
Retained primary teeth (RPT) may be an isolated finding, or one associated with other clinical complaints. In order to achieve timely and accurate diagnosis, it is helpful for paediatricians to perform thorough work-up for these patients. The article aims at providing an overview of the inborn medical causes that may be related to children with RPT, as well as their corresponding investigation and treatment modalities.
E3 ligases MAC3A and MAC3B ubiquitinate UBIQUITIN-SPECIFIC PROTEASE14 to regulate organ size in Arabidopsis
Authors: Guo Xiaopeng , Zhang Xin , Jiang Shan , Qiao Xin , Meng Bolun , Wang Xiaohang , Wang Yanan , Yang Kaihuan , Zhang Yilan , Li Na , Chen Tianyan , Kang Yiyang , Yao Mengyi , Zhang Xuan , Wang Xinru , Zhang Erling , Li Junhua , Yan Dawei , Hu Zhubing , Botella José Ramón , Song Chun-Peng , Li Yunhai , Guo Siyi 
Published: October 2023

Abstract
The molecular mechanisms controlling organ size during plant development ultimately influence crop yield. However, a deep understanding of these mechanisms is still lacking. UBIQUITIN-SPECIFIC PROTEASE14 (UBP14), encoded by DA3, is an essential factor determining organ size in Arabidopsis (Arabidopsis thaliana). Here, we identified two suppressors of the da3-1 mutant phenotype, namely SUPPRESSOR OF da3-1 1 and 2 (SUD1 and SUD2), which encode the E3 ligases MOS4-ASSOCIATED COMPLEX 3A (MAC3A) and MAC3B, respectively. The mac3a-1 and mac3b-1 mutations partially suppressed the high ploidy level and organ size phenotypes observed in the da3-1 mutant. Biochemical analysis showed that MAC3A and MAC3B physically interacted with and ubiquitinated UBP14/DA3 to modulate its stability. We previously reported that UBP14/DA3 acts upstream of the B-type cyclin-dependent kinase CDKB1;1 and maintains its stability to inhibit endoreduplication and cell growth. In this work, MAC3A and MAC3B were found to promote the degradation of CDKB1;1 by ubiquitinating UBP14/DA3. Genetic analysis suggests that MAC3A and MAC3B act in a common pathway with UBP14/DA3 to control endoreduplication and organ size. Thus, our findings define a regulatory module, MAC3A/MAC3B-UBP14-CDKB1;1, that plays a critical role in determining organ size and endoreduplication in Arabidopsis.
Maize GOLDEN2-LIKE proteins enhance drought tolerance in rice by promoting stomatal closure
Authors: Li Xia , Li Jing , Wei Shaobo , Gao Yuan , Pei Hongcui , Geng Rudan , Lu Zefu , Wang Peng , Zhou Wenbin 
Published: October 2023

Abstract
Drought has become one of the most severe abiotic stresses experienced in agricultural production across the world. Plants respond to water deficit via stomatal movements in the leaves, which are mainly regulated by abscisic acid (ABA). A previous study from our lab showed that constitutive expression of maize (Zea mays L.) GOLDEN2-LIKE (GLK) transcription factors in rice (Oryza sativa L.) can improve stomatal conductance and plant photosynthetic capacity under field conditions. In the present study, we uncovered a function of ZmGLK regulation of stomatal movement in rice during drought stress. We found that elevated drought tolerance in rice plants overexpressing ZmGLK1 or GOLDEN2 (ZmG2) was conferred by rapid ABA-mediated stomatal closure. Comparative analysis of RNA-sequencing (RNA-seq) data from the rice leaves and DNA affinity purification sequencing (DAP-seq) results obtained in vitro revealed that ZmGLKs played roles in regulating ABA-related and stress-responsive pathways. Four upregulated genes closely functioning in abiotic stress tolerance with strong binding peaks in the DAP-seq data were identified as putative target genes of ZmGLK1 and ZmG2 in rice. These results demonstrated that maize GLKs play an important role in regulating stomatal movements to coordinate photosynthesis and stress tolerance. This trait is a valuable target for breeding drought-tolerant crop plants without compromising photosynthetic capacity.
Returns to Scale from Labor Specialization: Evidence from Asset Management Mergers
Authors: Luo Mancy , Manconi Alberto , Schumacher David 
Published: October 2023

Abstract
We study human capital synergies in asset management mergers that stem from the improved ability to assign fund managers to more specialized tasks in larger firms. More specialized task assignment allows rotated managers to focus on their investment expertise and leads to incremental $54 million of value added per deal per year on average. The effects are concentrated in mergers that lead to a large increase in firm size and in funds whose management appears less specialized prior to the merger. Our results provide direct evidence on the role of firms in the assignment of tasks to fund managers. (JEL G23, J24, G34)
Image analysis to automatically classify anemia based on Famacha score in sheep using ocular conjunctiva images
Authors: Freitas Luara A , Ferreira Rafael E P , Savegnago Rodrigo P , Dórea João R R , Stafuzza Nedenia B , Rosa Guilherme J M , Paz Claudia C P 
Published: October 2023

AbstractHaemonchus contortus is the most pathogenic blood-feeding parasitic in sheep, causing anemia and consequently changes in the color of the ocular conjunctiva, from the deep red of healthy sheep to shades of pink to practically white of non-healthy sheep. In this context, the Famacha method has been created for detecting sheep unable to cope with the infection by H. contortus, through visual assessment of ocular conjunctiva coloration. Thus, the objectives of this study were (1) to extract ocular conjunctiva image features to automatically classify Famacha score and compare two classification models (multinomial logistic regression—MLR and random forest—RF) and (2) to evaluate the applicability of the best classification model on three sheep farms. The dataset consisted of 1,156 ocular conjunctiva images from 422 animals. RF model was used to segment the images, i.e., to select the pixels that belong to the ocular conjunctiva. After segmentation, the quantiles (1%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 99%) of color intensity in each image channel (red, blue, and green) were determined and used as explanatory variables in the classification models, and the Famacha scores 1 (non-anemic) to 5 (severely anemic) were the target classes to be predicted (scores 1 to 5, with 162, 255, 443, 266, and 30 images, respectively). For objective 1, the performance metrics (precision and sensitivity) were obtained using MLR and RF models considering data from all farms randomly split. For objective 2, a leave-one-farm-out cross-validation technique was used to assess prediction quality across three farms (farms A, B, and C, with 726, 205, and 225 images, respectively). The RF provided the best performances in predicting anemic animals, as indicated by the high values of sensitivity for Famacha score 3 (80.9%), 4 (46.2%), and 5 (60%) compared to the MLR model. The precision of the RF was 72.7% for Famacha score 1 and 62.5% for Famacha score 2. These results indicate that is possible to successfully predict Famacha score, especially for scores 2 to 4, in sheep via image analysis and RF model using ocular conjunctiva images collected in farm conditions. As expected, model validation excluding entire farms in cross-validation presented a lower prediction quality. Nonetheless, this setup is closer to reality because the developed models are supposed to be used across farms, including new ones, and with different environments and management conditions.
Permissive Hypotension Has No Deleterious Impact on Fluid Balance or Kidney Function
Authors: Lavillegrand Jean-Rémi , Blum Laurene , Morin Alexandra , Urbina Tomas , Gabarre Paul , Bonny Vincent , Baudel Jean-Luc , Guidet Bertrand , Maury Eric , Ait-Oufella Hafid 
Published: October 2023

OBJECTIVES:
Mean arterial hypotension between 55 and 65 mm Hg could be tolerated safely in the absence of tissue hypoperfusion, but the consequences on fluid balance and kidney function remain unknown.

DESIGN:
During a 1-year period, we retrospectively collected data of consecutive septic patients admitted for sepsis with a mean arterial pressure (MAP) less than 65 mm Hg despite fluid resuscitation.

SETTING:
Medical 18-bed ICU in a tertiary teaching hospital.

PATIENTS:
Septic patients with a MAP less than 65 mm Hg despite initial resuscitation.

INTERVENTIONS:
In our ICU, MAP between 55 and 65 mm Hg was tolerated in the absence of peripheral hypoperfusion (permissive hypotension) or corrected using norepinephrine (septic shock group) when peripheral tissue hypoperfusion was present.

MEASUREMENTS AND MAIN RESULTS:
Ninety-four consecutive septic patients were included, 15 in the permissive hypotension group and 79 in the septic shock group. Median age was 66 years (57–77 yr) and 42% were women. The main sources of infection were respiratory (45%) and abdominal (18%). Severity was more important in septic shock group with higher Sequential Organ Failure Assessment score (7 [5–10] vs. 4 [1–6]; p < 0.0001), more frequent organ support therapy and ultimately higher mortality (38 vs. 0%; p < 0.01). The total volume of crystalloids infused before ICU admission was not different between groups (1930 ± 250 vs. 1850 ± 150 mL; p = 0.40). Within the 6 first hours of ICU stay, patients in the permissive hypotension group received less fluids (530 ± 170 vs. 1100 ± 110 mL; p = 0.03) and had higher urinary output (1.4 mL [0.88–2.34 mL] vs. 0.47 mL/kg/hr [0.08–1.25 mL/kg/hr]; p < 0.001). In addition, kidney injury evaluated using KDIGO score was lower in the permissive hypotension group at 48 hours (0 hr [0–1 hr] vs. 1 hr [0–2 hr]; p < 0.05).

CONCLUSIONS:
In septic patients without clinical peripheral hypoperfusion, mean arterial hypotension between 55 and 65 mm Hg could be tolerated safely without vasopressor infusion and was not associated with excessive fluid administration or kidney damage.
The STING-IRF3 Signaling Pathway, Mediated by Endoplasmic Reticulum Stress, Contributes to Impaired Myocardial Autophagic Flux After Ischemia/Reperfusion
Authors: Li Yuanbin , Lin Hui , Tang Hao , Zhu Ke , Zhou Zhangfu , Zeng Zhaohui , Pan Bin , Chen Zhuang 
Published: October 2023

Abstract
This study aimed to determine whether endoplasmic reticulum (ER) stress is involved in impaired autophagy after myocardial ischemia/reperfusion (M-I/R) and elucidate the underlying mechanisms. The expression levels of stimulator of interferon gene (STING) and interferon regulatory transcription factor 3 (IRF3) phosphorylation increased in M-I/R heart tissues and hypoxia-treated/reoxygenation-treated H9c2 cells. The ER stress inhibitor 4-phenylbutyric acid (4-PBA) significantly suppressed the stimulation of STING-IRF3 transcription and alleviated cardiac dysfunction caused by M-I/R injury. In addition, 4-PBA reversed ischemia-induced/reperfusion-induced autophagic flux dysfunction, as demonstrated by a decrease in p62 and LC3 levels. Similarly, the protective effect of STING deficiency on myocardial cell damage was achieved by the recovery of autophagic flux. Conversely, the protective effect of 4-PBA against hypoxia/reoxygenation injury in cardiomyocytes was offset by STING overexpression, wherein the activated STING-IRF3 pathway promoted the expression of Rubicon (a negatively-regulated autophagic molecule) by binding to the Rubicon promoter. Rubicon ablation effectively counteracts the adverse effects of STING overexpression in cardiomyocytes. The data showed that STING-IRF3 signaling of ER stress receptors is particularly important in the progression of physiological M-I/R caused by the inhibition of autophagic flow in vivo and in vitro.
CTRP3 inhibits myocardial fibrosis through the P2X7R-NLRP3 inflammasome pathway in SHR rats
Authors: Liu Na , Gong Zhaowei , Li Yang , Xu Yang , Guo Yutong , Chen Wenjia , Sun Xue , Yin Xinhua , Liu Wenxiu 
Published: October 2023

Background and purpose:
Reducing hypertensive myocardial fibrosis is the fundamental approach to preventing hypertensive ventricular remodelling. C1q/TNF-related protein-3 (CTRP3) is closely associated with hypertension. However, the role and mechanism of CTRP3 in hypertensive myocardial fibrosis are unclear. In this study, we aimed to explore the effect of CTRP3 on hypertensive myocardial fibrosis and the potential mechanism.

Methods and results:
WKY and SHR rats were employed, blood pressure, body weight, heart weight, H/BW were measured, and fibrotic-related proteins, CTRP3 and Collagen I were tested in myocardium at 12 and 20 weeks by immunohistochemical staining and Western blotting, respectively. The results showed that compared with the WKY, SBP, DBP, mean arterial pressure and heart rate (HR) were all significantly increased in SHR at 12 and 20 weeks, while heart weight and H/BW were only increased at 20 weeks. Meanwhile, CTRP3 decreased, while Collagen I increased significantly in the SHR rat myocardium at 20 weeks, which compared to the WKY. Moreover, the expression of α-SMA increased from 12 weeks, Collagen I/III and MMP2/9 increased and TIMP-2 decreased until 20 weeks. In order to explore the function and mechanism of CTRP3 in hypertensive fibrosis, Angiotensin II (Ang II) was used to induce hypertension in primary neonatal rat cardiac fibroblasts in vitro. CTRP3 significantly inhibited the Ang II induced activation of fibrotic proteins, purinergic 2X7 receptor (P2X7R)-NLRP3 inflammasome pathway. The P2X7R agonist BzATP significantly exacerbated Ang II-induced NLRP3 inflammasome activation, which was decreased by the P2X7R antagonists A43079, CTRP3 and MCC950.

Conclusion:
CTRP3 expression was decreased in the myocardium of SHR rats, and exogenous CTRP3 inhibited Ang II-induced fibrosis in cardiac fibroblasts by regulating the P2X7R-NLRP3 inflammasome pathway, suggesting that CTRP3 is a potential drug for alleviating myocardial fibrosis in hypertensive conditions.
Contribution Factors of Effective Lens Position, Tilt, and Decentration during Flanged Scleral Fixation of Intraocular Lens: A Model Eye Study
Authors: Park Chang-Hyun , Moon Kun , Kim Jessica S , Shim Kyu Young , Jun Jong Hwa 
Published: October 2023

Abstract

Purpose:
We aimed to elucidate the factors related to effective lens position (ELP), tilt, and decentration of scleral fixed intraocular lenses (IOLs) with a flanged haptic technique in an artificial eye model using anterior segment optical coherence tomography (AS-OCT).

Methods:
Two bent 27-gauge needles were passed through a 1.0- or 2.0-mm scleral tunnel, 2.0 mm posterior to the limbus and 180° apart. Both haptics of a 3-piece IOL were docked with guide needles and externalized. Factors related to the IOL position were analyzed using AS-OCT and a stereomicroscope.

Results:
The 1.0-mm scleral tunnel induced a significantly longer ELP than the 2.0-mm tunnel and suture fixation (p<0.05 and p<0.01, respectively). Discrepancy in scleral tunnel length induced higher decentration of the optic to the opposite side of the haptic-embedded shorter tunnel and tilt perpendicular to the fixed axis than that in the scleral tunnel of the same length (p<0.001 and p<0.05, respectively). If the scleral fixation points of both haptics are not exactly 180° apart, the IOL may become decentered and tilted (p<0.01 and p<0.05, respectively).

Conclusion:
In the flanged haptic technique, the length, balance, and position of both scleral tunnels determine IOL ELP, tilt, and decentration.
Utility of Central 10 Degrees Visual Field Test With Size V Stimulus in End-Stage Glaucoma
Authors: Hwang Young Hoon 
Published: October 2023

Précis:
In end-stage glaucoma, the central 10-degree visual field test with a size V stimulus provided useful information, including the number of points with detectable retinal sensitivity threshold values and retinal sensitivity threshold values.

Purpose:
The purpose of this study was to evaluate the clinical utility of the central 10-degree visual field test with a size V stimulus in end-stage glaucoma.

Materials and Methods:
A total of 73 eyes with end-stage glaucoma (visual field limited to a radius of <10 degrees from fixation) were included. Central 10 degrees visual field tests were performed using both size III and V stimuli. Reliability indices, test duration, number of points with detectable retinal sensitivity threshold values, and retinal sensitivity threshold values at 4 central points, 4 quadrants, and 3 clusters (papillomacular area, superior half, and inferior half) were compared between the test results using size III and V stimuli.

Results:
When the size V stimulus was used, the mean test duration increased from 7.8 to 13.3 minutes (P < 0.001), the mean number of test points with detectable retinal sensitivity threshold values in total area increased from 19.0 to 37.3 (P < 0.001), and the mean retinal sensitivity threshold values in total area increased from 3.9 to 9.3 dB (P < 0.001) compared with the test results with the size III stimulus. Significant increase in the visual field parameters was found in all quadrants and clusters (P < 0.001), and a greater increase was associated with better visual acuity and greater mean deviation of the visual field (P < 0.05).

Conclusions:
The central 10-degree visual field test with a size V stimulus provided more information than the test with a size III stimulus in end-stage glaucoma.
Habituation to pain: self-report, electroencephalography, and functional magnetic resonance imaging in healthy individuals. A scoping review and future recommendations
Authors: van der Miesen Maite M. , Joosten Elbert A. , Kaas Amanda L. , Linden David E.J. , Peters Judith C. , Vossen Catherine J. 
Published: October 2023

Abstract
Habituation to pain is a fundamental learning process and important adaption. Yet, a comprehensive review of the current state of the field is lacking. Through a systematic search, 63 studies were included. Results address habituation to pain in healthy individuals based on self-report, electroencephalography, or functional magnetic resonance imaging. Our findings indicate a large variety in methods, experimental settings, and contexts, making habituation a ubiquitous phenomenon. Habituation to pain based on self-report studies shows a large influence of expectations, as well as the presence of individual differences. Furthermore, widespread neural effects, with sometimes opposing effects in self-report measures, are noted. Electroencephalography studies showed habituation of the N2-P2 amplitude, whereas functional magnetic resonance imaging studies showed decreasing activity during painful repeated stimulation in several identified brain areas (cingulate cortex and somatosensory cortices). Important considerations for the use of terminology, methodology, statistics, and individual differences are discussed. This review will aid our understanding of habituation to pain in healthy individuals and may lead the way to improving methods and designs for personalized treatment approaches in chronic pain patients.