bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome resequencing reveals the evolutionary history of garlic reproduction traits
Authors: Wang Haiping , Shemesh-Mayer Einat , Zhang Jiangjiang , Gao Song , Zeng Zheng , Yang Zemao , Zhang Xueyu , Jia Huixia , Wang Yanzhou , Song Jiangping , Zhang Xiaohui , Yang Wenlong , He Qiaoyun , Sherman Amir , Li Lin , Kamenetsky Rina , Liu Touming 
Published: October 2023

Abstract
The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.
Red light induces salicylic acid accumulation by activating CaHY5 to enhance pepper resistance against Phytophthora capsici
Authors: Yang Youxin , Li Yu , Guang Yelan , Lin Jinhui , Zhou Yong , Yu Ting , Ding Fei , Wang Yanfeng , Chen Jinyin , Zhou Yanhong , Dang Fengfeng 
Published: October 2023

Abstract
Pepper (Capsicum annuum L.) is frequently challenged by various pathogens, among which Phytophthora capsici is the most devastating to pepper production. Red light signal acts as a positive induction of plant resistance against multiple pathogens. However, little is known about how the red light signal affects pepper resistance to P. capsici infection (PCI). Here, we report that red light regulates salicylic acid (SA) accumulation by activating elongated hypocotyl5 (CaHY5), a basic leucine zipper (bZIP) transcription factor, thereby decreasing pepper susceptibility to PCI. Exogenous SA treatment reduced pepper susceptibility to PCI, while silencing of CaPHYB (a red light photoreceptor) increased its susceptibility. PCI significantly induced CaHY5 expression, and silencing of CaHY5 reduced SA accumulation, accompanied by decreases in the expression levels of phenylalanine ammonia-lyase 3 (CaPAL3), CaPAL7, pathogenesis-related 1 (CaPR1), and CaPR1L, which finally resulted in higher susceptibility of pepper to PCI. Moreover, CaHY5 was found to activate the expression of CaPAL3 and CaPAL7, which are essential for SA biosynthesis, by directly binding to their promoters. Further analysis revealed that exogenous SA treatment could restore the resistance of CaHY5­silenced pepper plants to PCI. Collectively, this study reveals a critical mechanism through which red light induces SA accumulation by regulating CaHY5­mediated CaPAL3 and CaPAL7 expression, leading to enhanced resistance to PCI. Moreover, red light-induced CaHY5 regulates pepper resistance to PCI, which may have implications for PCI control in protected vegetable production.
Persons ‘never treated’ in mass drug administration for lymphatic filariasis: identifying programmatic and research needs from a series of research review meetings 2020–2021
Authors: Brady Molly A , Toubali Emily , Baker Margaret , Long Elizabeth , Worrell Caitlin , Ramaiah Kapa , Graves Patricia , Hollingsworth T Deirdre , Kelly-Hope Louise , Stukel Diana , Tripathi Bhupendra , Means Arianna Rubin , Matendechero Sultani Hadley , Krentel Alison 
Published: October 2023

Abstract
As neglected tropical disease programs rely on participation in rounds of mass drug administration (MDA), there is concern that individuals who have never been treated could contribute to ongoing transmission, posing a barrier to elimination. Previous research has suggested that the size and characteristics of the never-treated population may be important but have not been sufficiently explored. To address this critical knowledge gap, four meetings were held from December 2020 to May 2021 to compile expert knowledge on never treatment in lymphatic filariasis (LF) MDA programs. The meetings explored four questions: the number and proportion of people never treated, their sociodemographic characteristics, their infection status and the reasons why they were not treated. Meeting discussions noted key issues requiring further exploration, including how to standardize measurement of the never treated, adapt and use existing tools to capture never-treated data and ensure representation of never-treated people in data collection. Recognizing that patterns of never treatment are situation specific, participants noted measurement should be quick, inexpensive and focused on local solutions. Furthermore, programs should use existing data to generate mathematical models to understand what levels of never treatment may compromise LF elimination goals or trigger programmatic action.
Scalable and interpretable alternative to chart review for phenotype evaluation using standardized structured data from electronic health records
Authors: Ostropolets Anna , Hripcsak George , Husain Syed A , Richter Lauren R , Spotnitz Matthew , Elhussein Ahmed , Ryan Patrick B 
Published: October 2023

Abstract

Objectives
Chart review as the current gold standard for phenotype evaluation cannot support observational research on electronic health records and claims data sources at scale. We aimed to evaluate the ability of structured data to support efficient and interpretable phenotype evaluation as an alternative to chart review.

Materials and Methods
We developed Knowledge-Enhanced Electronic Profile Review (KEEPER) as a phenotype evaluation tool that extracts patient’s structured data elements relevant to a phenotype and presents them in a standardized fashion following clinical reasoning principles. We evaluated its performance (interrater agreement, intermethod agreement, accuracy, and review time) compared to manual chart review for 4 conditions using randomized 2-period, 2-sequence crossover design.

Results
Case ascertainment with KEEPER was twice as fast compared to manual chart review. 88.1% of the patients were classified concordantly using charts and KEEPER, but agreement varied depending on the condition. Missing data and differences in interpretation accounted for most of the discrepancies. Pairs of clinicians agreed in case ascertainment in 91.2% of the cases when using KEEPER compared to 76.3% when using charts. Patient classification aligned with the gold standard in 88.1% and 86.9% of the cases respectively.

Conclusion
Structured data can be used for efficient and interpretable phenotype evaluation if they are limited to relevant subset and organized according to the clinical reasoning principles. A system that implements these principles can achieve noninferior performance compared to chart review at a fraction of time.
Information displays for automated surveillance algorithms of in-hospital patient deterioration: a scoping review
Authors: Wan Yik-Ki Jacob , Wright Melanie C , McFarland Mary M , Dishman Deniz , Nies Mary A , Rush Adriana , Madaras-Kelly Karl , Jeppesen Amanda , Del Fiol Guilherme 
Published: October 2023

Abstract

Objective
Surveillance algorithms that predict patient decompensation are increasingly integrated with clinical workflows to help identify patients at risk of in-hospital deterioration. This scoping review aimed to identify the design features of the information displays, the types of algorithm that drive the display, and the effect of these displays on process and patient outcomes.

Materials and methods
The scoping review followed Arksey and O’Malley’s framework. Five databases were searched with dates between January 1, 2009 and January 26, 2022. Inclusion criteria were: participants—clinicians in inpatient settings; concepts—intervention as deterioration information displays that leveraged automated AI algorithms; comparison as usual care or alternative displays; outcomes as clinical, workflow process, and usability outcomes; and context as simulated or real-world in-hospital settings in any country. Screening, full-text review, and data extraction were reviewed independently by 2 researchers in each step. Display categories were identified inductively through consensus.

Results
Of 14 575 articles, 64 were included in the review, describing 61 unique displays. Forty-one displays were designed for specific deteriorations (eg, sepsis), 24 provided simple alerts (ie, text-based prompts without relevant patient data), 48 leveraged well-accepted score-based algorithms, and 47 included nurses as the target users. Only 1 out of the 10 randomized controlled trials reported a significant effect on the primary outcome.

Conclusions
Despite significant advancements in surveillance algorithms, most information displays continue to leverage well-understood, well-accepted score-based algorithms. Users’ trust, algorithmic transparency, and workflow integration are significant hurdles to adopting new algorithms into effective decision support tools.
Cryoablation Therapy for Early-Stage Breast Cancer: Evidence and Rationale
Authors: Thai Janice N , Sevrukov Alexander B , Ward Robert C , Monticciolo Debra L 
Published: October 2023

Abstract
Recent advances in breast cancer research and treatment propel a paradigm shift toward less aggressive and less invasive treatment for some early-stage breast cancer. Select patients with small, low-risk tumors may benefit from a less aggressive approach with de-escalated local therapy. Cryoablation of breast cancer is an emerging nonsurgical treatment alternative to breast-conserving surgery. Advantages of cryoablation over surgery include the use of local anesthesia, faster recovery, improved cosmesis, and cost savings. Proper patient selection and meticulous technique are keys to achieving successful clinical outcomes. The best candidates for cryoablation have unifocal invasive ductal carcinoma tumors that are low grade, hormone receptor positive, and ≤1.5 cm in size. In this review, we outline the current evidence, patient selection criteria, procedural technique, pre- and postablation imaging, and the advantages and limitations of cryoablation therapy.
Multi-threshold remote sensing image segmentation with improved ant colony optimizer with salp foraging
Authors: Qian Yunlou , Tu Jiaqing , Luo Gang , Sha Ce , Heidari Ali Asghar , Chen Huiling 
Published: October 2023

Abstract
Remote sensing images can provide direct and accurate feedback on urban surface morphology and geographic conditions. They can be used as an auxiliary means to collect data for current geospatial information systems, which are also widely used in city public safety. Therefore, it is necessary to research remote sensing images. Therefore, we adopt the multi-threshold image segmentation method in this paper to segment the remote sensing images for research. We first introduce salp foraging behavior into the continuous ant colony optimization algorithm (ACOR) and construct a novel ACOR version based on salp foraging (SSACO). The original algorithm’s convergence and ability to avoid hitting local optima are enhanced by salp foraging behavior. In order to illustrate this key benefit, SSACO is first tested against 14 fundamental algorithms using 30 benchmark test functions in IEEE CEC2017. Then, SSACO is compared with 14 other algorithms. The experimental results are examined from various angles, and the findings convincingly demonstrate the main power of SSACO. We performed segmentation comparison studies based on 12 remote sensing images between SSACO segmentation techniques and several peer segmentation approaches to demonstrate the benefits of SSACO in remote sensing image segmentation. Peak signal-to-noise ratio, structural similarity index, and feature similarity index evaluation of the segmentation results demonstrated the benefits of the SSACO-based segmentation approach. SSACO is an excellent optimizer since it seeks to serve as a guide and a point of reference for using remote sensing image algorithms in urban public safety.
Prognosis and risk prediction of bone impaction grafting through femoral head–neck fenestration: a retrospective cohort study
Authors: Chen Hao , He Shuai , Xi Hongzhong , Xue Peng , Sun Guangquan , Du Bin , Liu Xin 
Published: October 2023

ABSTRACT
The bone impaction grafting through femoral head–neck fenestration was a favorable hip preservation procedure but without prognosis estimation. This study retrospectively reviewed 79 patients’ clinical data (114 hips) with osteonecrosis of the femoral head (ONFH) who underwent this procedure from June 2009 to June 2019. By the end of June 2022, the median survival time of the hip was (74.13 ± 44.88) months, and the success rate of hip preservation was 68.42%. Lateral reserved angle (LPA) and combined reserved angle (CPA) had statistically significant differences (P &lt; 0.001) both in univariate analysis and a multivariate logistic regression model. The multivariate logistic regression model of area under curve (AUC) area of the receiver operating characteristic (ROC) curve was 0.931(sensitivity = 95.00%, specificity = 88.40%, log-rank test: P &lt; 0.01), and the calibration curve indicated good prediction accuracy. The ROC analysis and Cox proportional hazards regression model revealed that the cutoff point of LPA was 50.95° (sensitivity = 95.00%, specificity = 72.09%, log-rank test: P &lt; 0.05) and the cutoff point of CPA was 90.51° (sensitivity = 90.00%, specificity = 90.70%, log-rank test: P &lt; 0.05). A nomogram plot to predict the risk of failure (C-index = 0.873, 95% CI: 0.785 to 0.961) and nomograms for predicting the survival probability at 1, 2 or 3 years whose calibration curves showed excellent prediction accuracy were available for the clinician. Preserved angles (PAs) are valuable in the prediction of prognosis in surgical treatment. The bone impaction grafting through femoral head–neck fenestration can achieve better clinical efficacy, especially for patients with LPA &gt;50.95° and CPA &gt;90.51°.
Chronic traumatic encephalopathy-neuropathologic change in a routine neuropathology service: 7-year follow-up
Authors: Del Bigio Marc R , Krawitz Sherry , Sinha Namita 
Published: October 2023

Abstract
To follow our 2016 study of chronic traumatic encephalopathy neuropathologic change (CTE-NC) in our forensic autopsy service, we prospectively screened all cases with clinical histories of multiple concussions, persistent post-head injury symptoms, or ≥3 hospital investigations for head injuries from 2016 to 2022 inclusive using hyperphosphorylated tau (p-tau) immunostaining. The cases had routine brain sampling plus 4-6 additional lateral hemisphere samples. When “pathognomonic” CTE-NC lesions were identified, additional p-tau immunostaining was done for CTE-NC staging. Of ∼1100 adult brains aged 18–65 years examined, 85 were screened, and 16 were positive for CTE-NC (2 women, 14 men, ages 35–61 years, median 47 years). Alcohol abuse was documented in 14 of 16 (8 in combination with other substances); 5 had developmental brain anomalies (2 presumed genetic, 3 from acquired perinatal insults). Widespread p-tau deposits (high CTE-NC) were found in 7 of 16. Old brain contusions were present in 9 of 16, but CTE-NC did not colocalize. Of particular interest were (1) a man with FGFR3 mutation/hypochondroplasia and life-long head banging, (2) a woman with cerebral palsy and life-long head banging, and (3) a man with bilateral peri-Sylvian polymicrogyria, alcohol abuse, and multiple head injuries. Thus, CTE-NC occurs in association with repeated head trauma outside contact sports. Substance abuse is a common determinant of risk behavior. The utility of diagnosing mild-/low-stage CTE-NC in this population remains to be determined.
Correlates of Longitudinal Trajectories of Depressive Symptoms in Adolescents With Traumatic Brain Injuries
Authors: Shen Jiabin , Wang Yan 
Published: October 2023

Abstract

Objective
Depression poses a significant threat to the health and well-being of adolescents with traumatic brain injury. Existing research has limitations in longitudinal follow-up period, consideration of sample heterogeneity, and outcome measurement modeling. This study aimed to address these gaps by applying the second-order growth mixture model (SO-GMM) to examine the 10-year post-injury depression trajectories in adolescents with TBI.

Methods
A total of 1,989 adolescents with TBI 16–21 years old from the Traumatic Brain Injury Model System National Data Bank were analyzed up to 10 years post-injury. Depressive symptoms were measured by Patient Health Questionnaire-9. Covariates included age, sex, race/ethnicity, employment, Functional Independence Measure Cognition, TBI severity, pre-injury disability, and substance use. Longitudinal measurement invariance was tested at the configural, metric, and scalar levels before SO-GMM was fit. Logistic regression was conducted for disparities in depression trajectories by covariates.

Results
A 2-class SO-GMM was identified with a low-stable group (85% of the sample) and a high-increasing group (15% of the sample) on depression levels. Older age, being a Native American, and having Hispanic origin was associated with a higher likelihood of being in the high-increasing class (odds ratios [ORs] = 1.165–4.989 and 1.609, respectively), while patients with higher education and being male were less likely to be in the high-increasing class (ORs = 0.735 and 0.557, respectively).

Conclusions
This study examined the disparities in depression among two distinct longitudinal groups of adolescents with TBI 10 years post-injury. Findings of the study are informative for intervention development to improve long-term mental health in adolescents with TBI.
Awake minimally invasive parafascicular approach to a language eloquent brain tumour—surgical video
Authors: Sangha Miljyot S , Rajwani Kapil M , Price Sally-Ann , Wren Hilary , Pescador Ana M , Gullan Richard , Ashkan Keyoumars , Vergani Francesco , Bhangoo Ranjeev , Lavrador Jose P 
Published: October 2023

Abstract
Deep-seated brain tumours are surgically challenging to access. When planning approaches to these lesions, it is important to take into account eloquent cortical areas, grey matter nuclei, and subcortical white matter tracts. Traditionally, access to deep-seated lesions would require brain retraction; however, this is associated with secondary brain damage, which may impair neurological function. A trans-sulcal minimally invasive parafascicular approach allows gentle splitting of brain fibres and is thought to splay rather than sever white matter tracts. This is particularly important when approaching medially located, language-eloquent tumours, which lack brain surface expression. This video describes a minimally invasive approach to a deep-seated, language-eloquent brain tumour. We utilized preoperative cortical and subcortical planning to define a safe surgical corridor. We then demonstrate using intraoperative neuro-monitoring and mapping of the motor and language functions to define the boundaries of surgical resection. We find trans-sulcal minimally invasive parafascicular approach to be a safe and effective technique when approaching language-eloquent lesions medial to the main language subcortical networks.
Are You my Rabbi? Yitz Greenberg’s Intellectual Biography in Kuhnian Terms
Authors: Schramm Netta 
Published: October 2023

Abstract
This article considers Rabbi Yitz Greenberg’s version of open orthodoxy and its development. Greenberg initially framed his theological journey as a “paradigm shift.” Archival materials from “before” and “during” this theological breakdown are discussed, and a fine-tuning of Greenberg’s narrative is suggested. The article demonstrates how overemphasizing what changed in Greenberg’s views misses the structural continuities in his writings across the decades. Finally, three shifts or “transgressions” are discussed: religious feminism, openness towards world religions, and denominational pluralism. The reception of these shifts is described as a function of a Kuhnian-inspired linguistic incommensurability. However, the Kuhn model, which describes winning and losing camps, is called into question.
Deubiquitination module is critical for oxidative stress response and biofilm formation in Candida glabrata
Authors: Huang Yue-Han , Lee Yi-Hang , Lin Chi-Jan , Hsu Li-Hang , Chen Ying-Lien 
Published: October 2023

Abstract
Candidiasis is one of the most important fungal diseases and generally refers to diseases of the skin or mucosal tissues caused by Candida species. Candida glabrata is an opportunistic human fungal pathogen. Infection with C. glabrata has significantly increased due to innate antifungal drug tolerance and the ability to adhere to mucocutaneous surfaces. Spt-Ada-Gcn5 acetyltransferase complex contains two different post-translational modifications, histone acetylation (HAT) module and deubiquitination (DUB) module, which are decisive in gene regulation and highly conserved in eukaryotes. Previous research in our laboratory found that the HAT module ADA2 could regulate C. glabrata oxidative stress tolerance, drug tolerance, cell wall integrity, and virulence. However, the roles of the DUB module that is comprised of UBP8, SGF11, SGF73, and SUS1 genes in those phenotypes are not yet understood. In this study, we found that DUB module genes UBP8, SGF11, and SUS1, but not SGF73 positively regulate histone H2B DUB. Furthermore, ubp8, sgf11, and sus1 mutants exhibited decreased biofilm formation and sensitivity to cell wall-perturbing agent sodium dodecyl sulfate and antifungal drug amphotericin B. In addition, the sgf73 mutant showed increased biofilm formation but was susceptible to oxidative stresses, antifungal drugs, and cell wall perturbing agents. The ubp8, sgf11, and sus1 mutants showed marginal hypovirulence, whereas the sgf73 mutant exhibited virulence similar to the wild type in a murine systemic infection model. In conclusion, the C. glabrata DUB module plays distinct roles in H2B ubiquitination, oxidative stress response, biofilm formation, cell wall integrity, and drug tolerance, but exhibits minor roles in virulence.