bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the architecture of hazelnut (Corylus avellana) Tonda di Giffoni over two successive years
Authors: Grisafi Francesca , Tombesi Sergio , Farinelli Daniela , Costes Evelyne , Durand Jean-Baptiste , Boudon Frédéric 
Published: May 2024

Abstract
Hazelnut (Corylus avellana) cultivation is increasing worldwide. A 3D model of its structure could improve managerial techniques such as pruning. This study aims to analyse, over two successive years, hazelnut architectural development to implement a functional structural plant model. One hundred and four one-year-old shoots of own-rooted hazelnut trees were selected and analysed in winter 2020 and 2021. Exploratory analyses, generalized linear models and multinomial regression models were used to describe the architectural processes. The existence of sylleptic shoots on hazelnut one-year-old shoots, characterized by the presence of the male inflorescence on apical position, was detected. Along proleptic shoots, the branching pattern was described by (i) blind nodes located in the proximal part (ii) sylleptic shoots and mixed buds in the median part (iii) vegetative buds in the distal part. Apical bud died during the growing season, suggesting that Tonda di Giffoni has a sympodial branching. The models revealed dependencies among buds located at the same node, in the case of proleptic shoots. Especially, the probability of a bud bursting depended on both its type (i.e. mixed or vegetative) and the presence of other buds, either mixed or vegetative. Based on these local models and on a flow diagram, which defines the steps that led to the construction of hazelnut tree architecture, the first functional–structural plant model of hazelnut tree architecture was built. Further experiments will be needed and should be repeated over the following years to extend this study towards the juvenile phase and tree architecture over time.
Practice patterns and survival outcomes for muscle-invasive bladder cancer: real-life experience in a general population setting
Authors: Plouvier Sandrine D , Marcq Gautier , Vankemmel Olivier , Colin Pierre , Bonnal Jean-Louis , Leroy Xavier , Saint Fabien , Pasquier David 
Published: May 2024

Abstract
Bladder cancer (BC) is a common malignancy in Europe and North America. Among BCs, muscle-invasive BCs (MIBCs) are distinguished, as they require aggressive treatment due to their spreading potential and poor prognosis. Despite its clinical relevance, little information on MIBC in a general population setting is available. This study aims to report practice patterns and survival outcomes for MIBC patients in a general population setting. MIBCs among BC incidence in 2011 and 2012 recorded in a French population-based cancer registry (810 000 inhabitants) were included in the study. Data were extracted from the medical files. Individual, tumour-related characteristics and initial management including diagnostic tools, multidisciplinary team meeting (MDT) assessment, and treatment delivered were described. Cystectomy, chemoradiation, radiotherapy, and chemotherapy were considered as specific treatments. Matching between MDT decision and the treatment provided was detailed. Management practices were discussed according to the guideline’s recommendations. Overall survival (using the Kaplan–Meier method) and net survival (using the Pohar-Perme estimator) were calculated. Among 538 incident BC cases, 147 (27.3%) were MIBCs. Diagnostic practices displayed a relevant locoregional assessment of BC. Almost all cases (n = 136, 92.5%) were assessed during an uro-oncological MDT with a median time from diagnosis of 18 days (first quartile:12-third quartile:32). Discrepancies appeared between MDT decisions and treatments delivered: 71 out of 86 subjects received the recommended cystectomy or chemoradiation (with or without neoadjuvant chemotherapy); 6 out of 11 had the recommended radio- or chemotherapy; and 9 patients did not undergo any specific treatment despite the MDT decision. Cystectomy was the most common treatment performed; the time to surgery appeared consistent with the guideline’s recommendations. Forty people only received supportive care. Still, the 5-year overall and net survival was poor, with 19% (13–26) and 22% (14–31), respectively. The 5-year net survival was 35% (23–48) for people who underwent curative-intent treatments. MIBC management remains challenging even for cases assessed during an MDT. Many people did not undergo any specific treatment. Prognosis was poor even when curative-intent therapies were delivered. Efforts to reduce exposure to risk factors such as tobacco smoking and occupational exposures must be maintained.
Clustering techniques performance comparison for predicting the battery state of charge: A hybrid model approach
Authors: Ordás María Teresa , del Blanco David Yeregui Marcos , Aveleira-Mata José , Zayas-Gato Francisco , Jove Esteban , Casteleiro-Roca José-Luis , Quintián Héctor , Luis Calvo-Rolle José , Alaiz-Moreton Héctor 
Published: May 2024

Abstract
Batteries are a fundamental storage component due to its various applications in mobility, renewable energies and consumer electronics among others. Regardless of the battery typology, one key variable from a user’s perspective is the remaining energy in the battery. It is usually presented as the percentage of remaining energy compared to the total energy that can be stored and is labeled State Of Charge (SOC). This work addresses the development of a hybrid model based on a Lithium Iron Phosphate (LiFePO4) power cell, due to its broad implementation. The proposed model calculates the SOC, by means of voltage and electric current as inputs and the latter as the output. Therefore, four models based on k-Means, Agglomerative Clustering, Gaussian Mixture and Spectral Clustering techniques have been tested in order to obtain an optimal solution.
Prevalence of anal cytology screening among persons with HIV and lack of access to high-resolution anoscopy at HIV care facilities
Authors: Rim Sun Hee , Beer Linda , Saraiya Mona , Tie Yunfeng , Yuan Xin , Weiser John 
Published: May 2024

Abstract

Background
People with HIV at highest risk of anal cancer include gay, bisexual, and other men who have sex with men and transgender women aged 35 years or older as well as other people with HIV aged 45 years or older. Identifying and treating precancerous lesions can reduce anal cancer incidence in these groups. We assessed the prevalence of anal cytology and access to high-resolution anoscopy among people with HIV overall and in those individuals at highest risk.

Methods
Data were obtained from the Centers for Disease Control and Prevention’s Medical Monitoring Project, a population-based survey of people with HIV aged 18 years and older, and a supplemental Medical Monitoring Project facility survey. We report weighted percentages of people with HIV receiving anal cytology during the past 12 months, access to high-resolution anoscopy, and characteristics of HIV care facilities by availability of high-resolution anoscopy.

Results
Overall, 4.8% (95% confidence interval [CI] = 3.4% to 6.1%) of people with HIV had undergone anal cytology in the prior 12 months. Only 7.7% (95% CI = 5.1% to 10.6%) of gay, bisexual, and other men who have sex with men as well as transgender women 35 years of age or older and 1.9% (95% CI = 0.9% to 2.9%) of all other people with HIV aged 45 years and older had anal cytology. Prevalence was statistically significantly low among people with HIV with the following characteristics: non-Hispanic or Latino, Black or African American, high school education or less, heterosexual orientation, and living in southern Medical Monitoring Project states. Among people with HIV, 32.8% (95% CI = 28.0% to 37.7%) had no access to high-resolution anoscopy on-site or through referral at their care facility; 22.2% (95% CI = 19.5% to 24.9%) had on-site access; 45.0% (95% CI = 41.5% to 48.5%) had high-resolution anoscopy available through referral. Most facilities that received Ryan White HIV/AIDS Program funding, cared for more than 1000 people with HIV, or provided on-site colposcopy also provided high-resolution anoscopy on-site or through referral.

Conclusions
Rates of anal cytology and access to high-resolution anoscopy were low among people with HIV, including those individuals at highest risk of anal cancer. Our data may inform large-scale implementation of anal cancer prevention efforts.
Temporal logics for compartmental models
Authors: Machado Vitor , Benevides Mario 
Published: May 2024

Abstract
This paper introduces two logic frameworks for the study of SIR (Susceptible-Infected-Recovered) and SIRS compartmental epidemic models, one based on Linear Temporal Logic and the other on Computation Tree Logic. We provide a short literature overview on compartmental models and other related works using logics, and then define our logics with their respective axiomatizations, and demonstrate their soundness and completeness proofs.
Functional Divergence in Orthologous Transcription Factors: Insights from AtCBF2/3/1 and OsDREB1C
Authors: Deng Deyin , Guo Yixin , Guo Liangyu , Li Chengyang , Nie Yuqi , Wang Shuo , Wu Wenwu 
Published: May 2024

Abstract
Despite traditional beliefs of orthologous genes maintaining similar functions across species, growing evidence points to their potential for functional divergence. C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are critical in cold acclimation, with their overexpression enhancing stress tolerance but often constraining plant growth. In contrast, a recent study unveiled a distinctive role of rice OsDREB1C in elevating nitrogen use efficiency (NUE), photosynthesis, and grain yield, implying functional divergence within the CBF/DREB1 orthologs across species. Here, we delve into divergent molecular mechanisms of OsDREB1C and AtCBF2/3/1 by exploring their evolutionary trajectories across rice and Arabidopsis genomes, regulatomes, and transcriptomes. Evolutionary scrutiny shows discrete clades for OsDREB1C and AtCBF2/3/1, with the Poaceae-specific DREB1C clade mediated by a transposon event. Genome-wide binding profiles highlight OsDREB1C's preference for GCCGAC compared to AtCBF2/3/1's preference for A/GCCGAC, a distinction determined by R12 in the OsDREB1C AP2/ERF domain. Cross-species multiomic analyses reveal shared gene orthogroups (OGs) and underscore numerous specific OGs uniquely bound and regulated by OsDREB1C, implicated in NUE, photosynthesis, and early flowering, or by AtCBF2/3/1, engaged in hormone and stress responses. This divergence arises from gene gains/losses (∼16.7% to 25.6%) and expression reprogramming (∼62.3% to 66.2%) of OsDREB1C- and AtCBF2/3/1-regulated OGs during the extensive evolution following the rice–Arabidopsis split. Our findings illustrate the regulatory evolution of OsDREB1C and AtCBF2/3/1 at a genomic scale, providing insights on the functional divergence of orthologous transcription factors following gene duplications across species.
LncRNA SNHG3 discriminates rheumatoid arthritis from healthy individuals and regulates inflammatory response and oxidative stress via modulating miR-128-3p
Authors: Li Kejun , Liu Wei , Zhao Xueru , Lin Weiyi , Zhou Wenhui , Zhang Qi 
Published: May 2024

ABSTRACT

Objectives
This study evaluated the expression and significance of SNHG3 in rheumatoid arthritis (RA), aiming to explore a biomarker and regulator for RA.

Methods
The expression of SNHG3 in serum and synovial tissue was compared between RA patients and healthy individuals using polymerase chain reaction (PCR). The RA animal models were induced by the Porcine Type II collagen in Wistar rats and validated by the foot volume and arthritis index score. The human fibroblast-like synoviocytes were treated with lipopolysaccharide (LPS) to mimic the injury during RA onset, and the cell growth was assessed by cell counting kit-8 (CCK8) assay.

Results
SNHG3 was significantly downregulated in the serum and synovial tissue of RA patients compared with healthy individuals. Downregulated SNHG3 could discriminate RA patients from healthy individuals with high sensitivity (0.875) and specificity (0.844). Porcine Type II collagen induced increasing foot volume and arthritis index scores of rats, and SNHG3 was downregulated in RA rats. In LPS-induced human fibroblast-like synoviocytes, SNHG3 negatively regulated miR-128-3p, and the alleviated effect of SNHG3 overexpression on cellular inflammation and oxidative stress was reversed by miR-128-3p upregulation.

Conclusions
Serum SNHG3 was considered a potential diagnostic biomarker for RA from healthy individuals. SNHG3 regulated inflammatory response and oxidative stress by negatively modulating miR-128-3p.
Designer TALEs enable discovery of cell death-inducer genes
Authors: Roeschlin Roxana A , Azad Sepideh M , Grove René P , Chuan Ana , García Lucila , Niñoles Regina , Uviedo Facundo , Villalobos Liara , Massimino Maria E , Marano María R , Boch Jens , Gadea José 
Published: May 2024

Abstract
Transcription activator-like effectors (TALEs) in plant-pathogenic Xanthomonas bacteria activate expression of plant genes and support infection or cause a resistance response. PthA4AT is a TALE with a particularly short DNA-binding domain harboring only 7.5 repeats which triggers cell death in Nicotiana benthamiana; however, the genetic basis for this remains unknown. To identify possible target genes of PthA4AT that mediate cell death in N. benthamiana, we exploited the modularity of TALEs to stepwise enhance their specificity and reduce potential target sites. Substitutions of individual repeats suggested that PthA4AT-dependent cell death is sequence specific. Stepwise addition of repeats to the C-terminal or N-terminal end of the repeat region narrowed the sequence requirements in promoters of target genes. Transcriptome profiling and in silico target prediction allowed the isolation of two cell death inducer genes, which encode a patatin-like protein and a bifunctional monodehydroascorbate reductase/carbonic anhydrase protein. These two proteins are not linked to known TALE-dependent resistance genes. Our results show that the aberrant expression of different endogenous plant genes can cause a cell death reaction, which supports the hypothesis that TALE-dependent executor resistance genes can originate from various plant processes. Our strategy further demonstrates the use of TALEs to scan genomes for genes triggering cell death and other relevant phenotypes.
Crowding in Private Quality: The Equilibrium Effects of Public Spending in Education
Authors: Andrabi Tahir , Bau Natalie , Das Jishnu , Karachiwalla Naureen , Ijaz Khwaja Asim 
Published: May 2024

Abstract
We estimate the equilibrium effects of a public school grant program administered through school councils in Pakistani villages with multiple public and private schools and clearly defined catchment boundaries. The program was randomized at the village level, allowing us to estimate its causal impact on the market. Four years after the start of the program, test scores were 0.2 standard deviations higher in public schools. We find evidence of an education multiplier: test scores in private schools were also 0.2 standard deviations higher in treated markets. Consistent with standard models of product differentiation, the education multiplier is greater for those private schools that faced a greater threat to their market power. Accounting for private sector responses increases the program’s cost-effectiveness by 85% and affects how a policy maker would target spending. Given that markets with several public and private schools are now pervasive in low- and middle-income countries, prudent policy requires us to account for private sector responses to public policy, both in policies’ design and evaluation.
The Genetic Architecture of Arabidopsis thaliana in Response to Native Non-Pathogenic Bacterial Species Revealed by Genome-Wide Association Mapping in Field Conditions
Authors: Ramírez-Sánchez Daniela , Duflos Rémi , Gibelin-Viala Chrystel , Zamar Rémy , Vailleau Fabienne , Roux Fabrice 
Published: May 2024

Non-pathogenic bacteria can substantially contribute to plant health by mobilizing and supplying nutrients, providing protection against pathogens, and alleviating abiotic stresses. However, the number of genome-wide association studies reporting the genetic architecture of the response to individual members of the beneficial microbiota remains limited. In this study, we established a genome-wide association study under field conditions to estimate the level of genetic variation and the underlying genetic architecture among 162 accessions of Arabidopsis thaliana originating from 54 natural populations in the southwest of France in response to 13 strains of seven of the most abundant and prevalent non-pathogenic bacterial species isolated from the leaf compartment of A. thaliana in the same geographical region. Using a high-throughput phenotyping methodology to score vegetative growth-related traits, extensive genetic variation was detected among A. thaliana accessions in response to these leaf bacteria, at both the species and strain levels. The presence of crossing reaction norms between each strain and the mock treatment indicates that declaring a strain as a plant growth-promoting bacterium is highly dependent on the host genotype tested. In line with the strong genotype-by-genotype interactions, we detected a complex and highly flexible genetic architecture between the 13 strains. Finally, the candidate genes underlying the quantitative trait loci revealed significant enrichment in several biological pathways, including cell, secondary metabolism, signaling, and transport. Altogether, plant innate immunity appears as a significant source of natural genetic variation in plant–microbiota interactions and opens new avenues for better understanding the ecologically relevant molecular dialog during plant–microbiota interactions. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Artificial Intelligence in Dermatology: A Systematic Review of Its Applications in Melanoma and Keratinocyte Carcinoma Diagnosis
Authors: Jairath Neil , Pahalyants Vartan , Shah Rohan , Weed Jason , Carucci John A. , Criscito Maressa C. 
Published: May 2024

BACKGROUND
Limited access to dermatologic care may pose an obstacle to the early detection and intervention of cutaneous malignancies. The role of artificial intelligence (AI) in skin cancer diagnosis may alleviate potential care gaps.

OBJECTIVE
The aim of this systematic review was to offer an in-depth exploration of published AI algorithms trained on dermoscopic and macroscopic clinical images for the diagnosis of melanoma, basal cell carcinoma, and cutaneous squamous cell carcinoma (cSCC).

METHODS
Adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, a systematic review was conducted on peer-reviewed articles published between January 1, 2000, and January 26, 2023.

RESULTS AND DISCUSSION
Among the 232 studies in this review, the overall accuracy, sensitivity, and specificity of AI for tumor detection averaged 90%, 87%, and 91%, respectively. Model performance improved with time. Despite seemingly impressive performance, the paucity of external validation and limited representation of cSCC and skin of color in the data sets limits the generalizability of the current models. In addition, dermatologists coauthored only 12.9% of all studies included in the review. Moving forward, it is imperative to prioritize robustness in data reporting, inclusivity in data collection, and interdisciplinary collaboration to ensure the development of equitable and effective AI tools.
Plastin 3 expression in circulating tumor cells as a predictor of cancer status in patients with prostate cancer
Authors: Shih Meng-Hung , Cha Tai-Lung , Wu Sheng-Tang , Meng En , Tsao Chih-Wei , Kao Chien-Chang , Chen Chin-Li , Juho Yu-Ching , Ting Hui-Kung , Sun Guang-Huan , Chang Sun-Yran , Yu Dah-Shyong , Yang Ming-Hsin 
Published: May 2024

Abstract

Background
Prostate cancer (PCa) is the most common cancer among men worldwide. The aim of the study is to identify the role of plastin 3 (PLS3) expression in circulating tumor cells (CTCs) of early stage PCa.

Materials and Methods
CTCs were collected from 23 PCa patients based on cell surface markers targeting PCa by V-BioChip. Condition of Plastin 3 expression and correlations to the PCa were also analyzed.

Results
Of the 23 patients with PCa, total CTCs (CK+ or PLS3+) were found in 11 patients and PLS3+ CTCs were detected in 10 patients. When the cohort was stratified by risk group, 90% of the high-risk patients were found to have PLS3+ circulating tumor cells (9/10 patients). However, only 15.4% of low/intermediate-risk patients had PLS3+ circulating tumor cells (2/13 patients). The number of PLS3+ CTCs was higher in the high-risk group.

Conclusions
The expression of PLS3 in CTCs is associated with PCa risk. Further study of PLS3+ CTCs for prognosis prediction is required for clinical application in PCa patients.
In Silico Pharmacokinetics Evaluation of Forgiveness for Doravirine and Rilpivirine
Authors: Fromage Yeleen , Jamal Najwa , Codde Cyrielle , Monchaud Caroline , Labriffe Marc , Ponthier Laure , Marquet Pierre , Faucher Jean François , Woillard Jean-Baptiste 
Published: May 2024

Background:
This study aimed to evaluate the concentrations of rilpivirine (RLP) and doravirine (DOR) after 3 days-off using simulations from population pharmacokinetics models.

Methods:
The authors conducted a series of 500 sets of 10,000 Monte Carlo simulations to examine the steady-state conditions for 2 common dosage levels: 25 mg/d for RLP and 100 mg/d for DOR. These simulations were conducted under 2 scenarios: 1 without drug cessation and another after a 3-day break. The validity of the implementation was established through a comparison of median trough concentrations (C24h) with previously reported data. Subsequently, the proportion of simulated patients with C24h and C72h after 3 days-off (C72h/3do) that exceeded the inhibitory concentration 50 (IC50), 5.2 mcg/L for DOR and 20.5 mcg/L for RLP respectively, was calculated. The inhibitory quotient (IQ) was also computed, which was 6 times IC50 for DOR and 4.5 times IC50 for RLP. Finally, nomograms were constructed to estimate the probability of having C72h/3do > IC50 or > IQ for different ranges of C24h.

Results:
Simulated C24h median ± SD for RLP were 61.8 ± 0.4 mcg/L and for DOR 397 ± 0 mcg/L. For RLP, 99.3 ± 0.1% exceeded IC50 at C24h, 16.4 ± 0.4% at C72h/3do, and none surpassed the IQ threshold. In contrast, DOR had 100% ± 0% above IC50 at C24h, 93.6 ± 0.2% at C72h/3do, and 58.6 ± 0.5% exceeded the IQ.

Conclusions:
These findings suggest that treatment with DOR may offer a more forgiving therapeutic profile than RLP, given the larger proportion of patients achieving effective drug exposure with DOR. However, it is important to acknowledge a significant limitation of this study, namely, the assumption that drug concentration is a perfect surrogate for drug effectiveness.