bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaining experience in the provider role: Exploration of a novel simulation intervention to prepare nurse practitioner students to detect and manage skin cancer
Authors: Powers Kelly , Shue-McGuffin Katherine D. 
Published: January 2024

ABSTRACT

Background:
The high prevalence and negative outcomes associated with skin cancer demand effective strategies to prepare nurse practitioner students to detect cancerous lesions and manage patient care. However, few studies have examined dermatologic simulations to prepare nurse practitioner students to detect and manage skin cancer.

Purpose:
An exploratory–descriptive qualitative approach was used to examine nurse practitioner students' experiences with simulations involving standardized patients wearing three-dimensional (3-D) prosthetic skin lesions, perceptions of ability to apply the simulations to clinical practice, and preferences for learning dermatologic care.

Methodology:
A convenience sample of 39 nurse practitioner students participated in simulations with standardized patients wearing 3-D skin lesions. Focus groups were conducted following simulation participation, and thematic analysis was performed by two researchers.

Results:
Four themes emerged: Simulation provides a safe place to practice, Dermatology should be an integral part of education, Realism makes a difference, and Improved confidence and preparation for practice.

Conclusions:
Simulations with standardized patients wearing 3-D skin lesion prosthetics provided students the opportunity to assess, diagnose, and manage the care of patients with cancerous skin lesions. Participants valued the realistic practice with dermatologic care and reported improved confidence and preparation for practice.

Implications:
Faculty can use simulations to provide experiential learning about the provider role in general and as it pertains to skin cancer care. Attention to realism is important to aid in building students' confidence and preparation for practice.
Establishment of Nomogram for Prediction of Hearing Preservation after Retrosigmoid Approach in Patients with Vestibular Schwannoma
Authors: Lu Qi , Guo Xiaoyan , Kou Ting , Chen Jiyue , Shen Weidong 
Published: January 2024

Objective
To derive and validate a prognostic nomogram for the prediction of hearing preservation (HP) after retrosigmoid approach (RSA) in patients with vestibular schwannoma (VS) and further assist in clinical decision-making.

Study Design
Retrospective study.

Setting
Tertiary referral center.

Patients
A total of 111 patients diagnosed with VS with serviceable hearing from January 2013 to March 2023.

Interventions
All patients underwent surgery via RSA, and hearing outcomes were reviewed 2 weeks postoperatively.

Main Outcome Measures
Preoperative and postoperative hearing were analyzed and stratified according to the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS).

Results
In multivariate analysis of the primary group, preoperative hearing, tumor size, and tumor origin were significantly related to postoperative HP (p = 0.029, p = 0.043, and p = 0.018, respectively). Factors derived from the multivariate analysis were all assembled into the nomogram. The receiver operating characteristic (ROC) curves showed good predictive accuracy of the nomogram model in both primary and validation groups with area under the ROC curve (AUC) values of 0.802 and 0.797, respectively.

Conclusion
Independent predictors of postoperative HP in patients with VS were selected to create the nomogram. The nomogram was able to stratify patients into different risk groups and assist in clinical decision making.
A Comparison of State-Specific Pediatric Emergency Medical Facility Recognition Programs, 2020
Authors: Boggs Krislyn M. , Voligny Emma , Auerbach Marc , Espinola Janice A. , Samuels-Kalow Margaret E. , Sullivan Ashley F. , Camargo Carlos A. 
Published: January 2024

Objectives
Prior research suggests that the presence of state-specific pediatric emergency medical facility recognition programs (PFRPs) is associated with high emergency department (ED) pediatric readiness. The PFRPs aim to improve the quality of pediatric emergency care, but individual state programs differ. We aimed to describe the variation in PFRP characteristics and verification requirements and to describe the availability of pediatric emergency care coordinators (PECCs) in states with PFRPs.

Methods
In mid-2020, we collected information about each PFRP from 3 sources: the state Emergency Medical Services for Children (EMSC) website, the EMSC Innovation and Improvement Center website, or via communication with the state's EMSC program manager. For each state with a PFRP, we documented program characteristics, including program start date, number of tiers, whether participation was required/optional, and requirements for verification.

Results
Overall, we identified 17 states with active PFRPs. Five states had only 1 tier or level of recognition whereas the others had multiple. All programs did require presence of a PECC for verification. However, some PRFPs with multiple verification tiers did not require presence of a PECC to achieve each level of verification. In states with PFRPs, EDs with higher total visit volumes, a separate pediatric ED area, located in the Northeast, and earlier program start date were all more likely to have a PECC.

Conclusions
There is variation in state PFRPs, although all prioritize the presence of a PECC. We encourage further research on the effect of different aspects of PFRPs on patient outcomes.
Gender-Affirming Mastectomy: Psychosocial and Surgical Outcomes in Transgender Adults
Authors: Bertrand AA , DeLong Michael R , McCleary Sean P , Nahabet Edward H , Slack Ginger C , DaLio Andrew L , Weimer Amy K , Kwan Lorna , Bernacki Jessica , Rudkin George H ,   the Plastic Surgery Research Group
Published: January 2024

BACKGROUND:
Limited literature exists examining the effects of gender-affirming mastectomy on transmasculine and nonbinary patients that is prospective and uses validated survey instruments.

STUDY DESIGN:
The psychosocial functioning of transmasculine and nonbinary patients was compared between patients who underwent gender-affirming mastectomy and those who had not yet undergone surgery. Participants were enrolled in a single-site, combined study of surgical and psychosocial outcomes, including a cross-sectional cohort of preoperative and postoperative patients, as well as separate prospective cohort. Participants completed the BREAST-Q psychosocial and sexual well-being modules, the BODY-Q satisfaction with chest and nipples modules, the Body Image Quality of Life Inventory, the Transgender Congruence Scale, the Patient Health Questionnaire-9, and the Generalized Anxiety Disorder-7 scale before and after surgery. We also examined how patient demographic factors correlated with postoperative surgical and psychosocial outcomes.

RESULTS:
A total of 111 transmasculine and nonbinary patients 18 to 63 years of age (mean ± SD 26.5 ± 8) underwent mastectomy and were included in the study. All were included in the cross-sectional cohort, and 20 were enrolled in the prospective cohort. More than one-third (34.2%) of patients were nonbinary. After surgery, psychosocial and sexual well-being, satisfaction, body image–related quality of life, and gender congruence were increased (p < 0.001) in both cohorts, and depression (p < 0.009 cross-sectional), and anxiety (p < 0.001 cross-sectional) were decreased. The most common adverse event was hypertrophic scarring, which occurred in 41 (36.9%) participants.

CONCLUSIONS:
In this study of transmasculine and nonbinary adults, gender-affirming mastectomy was followed by substantial improvements in psychosocial functioning.
Evaluating the effect and mechanism of Yiqi Huayu Jiedu decoction combined with FLOT regimen neoadjuvant chemotherapy for the patients with locally advanced gastric cancer: protocol for a prospective, double-arm, randomized controlled clinical trial
Authors: Zou Kun , Zhang Pei-Chan , Luo Chun-Yang , Wang Rui , Xu Shuo , Xiang Chun-Jie , Huan Xiang-Kun , Yao Wen-Chao , Li Xiu-Yuan , Zhang Jun-Feng , Liu Shen-Lin , Wu Zhen-Feng 
Published: January 2024

AbstractBackgroundNeoadjuvant chemotherapy plays a vital role in the treatment of advanced gastric cancer, however, optimizing its effectiveness remains an important research focus. Traditional Chinese medicine (TCM), a promising adjunctive therapy, has shown enhanced clinical outcomes when combined with postoperative adjuvant chemotherapy. Therefore, this study is designed to evaluate the clinical efficacy of Yiqi Huayu Jiedu decoction combined with neoadjuvant chemotherapy FLOT in the treatment of advanced gastric cancer.MethodsThis study is a prospective, double-arm, randomized controlled trial. It involves a total of 260 patients diagnosed with advanced gastric cancer, who will be randomly assigned to two groups - a TCM treatment group and a control group, each comprising 130 patients. All patients will receive standard FLOT chemotherapy, and patients in the TCM treatment group will additionally receive traditional Chinese medicine treatment with Yiqi Huayu Jiedu decoction. After four cycles of chemotherapy, gastric cancer D2 radical surgery will be performed. The primary objective is to evaluate the postoperative pathological response rate of the tumor. The secondary objectives include evaluating the perioperative nutritional status, the efficacy of traditional Chinese medicine syndrome, and adverse events associated with both chemotherapy and surgery.DiscussionCurrently, no trials have investigated the impact of traditional Chinese medicine in combination with neoadjuvant chemotherapy on the preoperative treatment in patients with advanced gastric cancer.Accordingly, it is imperative to conduct this prospective study to evaluate the clinical efficacy and safety of this regimen, meanwhile providing high-level clinical evidence for traditional Chinese medicine combined with neoadjuvant chemotherapy and introducing an innovative regimen for preoperative comprehensive treatment of gastric cancer.Trial registrationChiCTR2300072742
Hurdles to Horizontal Gene Transfer: Synonymous variation determines antibiotic resistance phenotype across species
Authors: Finnegan Michael , Rose Caroline J , Hamet Jeanne , Prat Benjamin , Bedhomme Stéphanie 
Published: January 2024

AbstractEvidence that synonymous mutations and synonymous gene variants have fitness effects have accumulated recently. Since horizontal gene transfer represents a change in the genome of expression of the transferred gene, we hypothesized that the codon usage preferences of a horizontally transferred gene could determine the conferred fitness advantage or disadvantage, condition the immediate success of the transfer and in the longer term orient transfers.To test this hypothesis, we characterized resistance levels of synonymous variants of a gentamicin resistance gene, inserted into a broad-host range plasmid and transformed into three different bacterial speciesEscherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa.We revealed a strong species effect, explained in part by differences in plasmid copy number between host species. Importantly, the relative levels of resistance conferred by each synonymous variant were not conserved across species, indicating that these phenotypic effects are due to differing compatibility between the transferred variants and the receiver bacterial genomes. This species-variant interaction confirms that the codon composition of a gene can be a determinant of post-horizontal gene transfer success. However, the similarity in codon usage between the synonymous variants and the host genome only explained the phenotypic differences between variants in one species,P. aeruginosa. Further investigations of the effects of local codon usage, translation bottlenecks and internal Shine-Dalgarno sequences did not reveal common universal mechanisms across our three bacterial species and point to multiple paths leading from the synonymous sequence to phenotype and a species-specific sensitivity to these different paths.
The MKK3 MAPK cascade integrates temperature and after-ripening signals to modulate seed germination
Authors: Otani Masahiko , Tojo Ryo , Regnard Sarah , Zheng Lipeng , Hoshi Takumi , Ohmori Suzuha , Tachibana Natsuki , Sano Tomohiro , Koshimizu Shizuka , Ichimura Kazuya , Colcombet Jean , Kawakami Naoto 
Published: January 2024

AbstractTemperature is a major environmental cue for seed germination. The permissive temperature range for germination is narrow in dormant seeds and expands during after-ripening. Quantitative trait loci analyses of pre-harvest sprouting in cereals have revealed that MKK3, a mitogen-activated protein kinase (MAPK) cascade protein, is a negative regulator of grain dormancy. Here we show that the MAPKKK19/20-MKK3-MPK1/2/7/14 cascade modulates germination temperature range in Arabidopsis seeds by elevating germinability of the seeds at sub- and supra-optimal temperatures. The expression ofMAPKKK19andMAPKKK20is regulated by an unidentified temperature sensing and signaling mechanism the sensitivity of which is modulated during after-ripening of the seeds, and MPK7 is activated at the permissive temperature for germination regulated by expression levels ofMAPKKK19/20. Activation of the MKK3 cascade represses abscisic acid (ABA) biosynthesis enzyme gene expression, and induces expression of ABA catabolic enzyme and gibberellic acid biosynthesis enzyme genes, resulting in expansion of the germinable temperature range. Our data demonstrate that the MKK3 cascade integrates temperature and after-ripening signals to germination processes including phytohormone metabolism.
PTF-Vāc:Ab-initiodiscovery of plant transcription factors binding sites using explainable and generative deep co-learning encoders-decoders
Authors: Gupta Sagar , Jyoti  , Bhati Umesh , Kesarwani Veerbhan , Sharma Akanksha , Shankar Ravi 
Published: January 2024

AbstractDiscovery of transcription factors (TFs) binding sites (TFBS) and their motifs in plants pose significant challenges due to high cross-species variability. The interaction between TFs and their binding sites is highly specific and context dependent. Most of the existing TFBS finding tools are not accurate enough to discover these binding sites in plants. They fail to capture the cross-species variability, interdependence between TF structure and its TFBS, and context specificity of binding. Since they are coupled to predefined TF specific model/matrix, they are highly vulnerable towards the volume and quality of data provided to build the motifs. All these software make a presumption that the user input would be specific to any particular TF which renders them of very limited uses. This all makes them hardly of any use for purposes like genomic annotations of newly sequenced species. Here, we report an explainable Deep Encoders-Decoders generative system, PTF-Vāc, founded on a universal model of deep co-learning on variability in binding sites and TF structure, PTFSpot, making it completely free from the bottlenecks mentioned above. It has successfully decoupled the process of TFBS discovery from the prior step of motif finding and requirement of TF specific motif models. Due to the universal model for TF:DNA interactions as its guide, it can discover the binding motifs in total independence from data volume, species and TF specific models. PTF-Vāc can accurately detect even the binding motifs for never seen before TF families and species, and can be used to define credible motifs from its TFBS report.
Predicting protein functions using positive-unlabeled ranking with ontology-based priors
Authors: Zhapa-Camacho Fernando , Tang Zhenwei , Kulmanov Maxat , Hoehndorf Robert 
Published: January 2024

AbstractAutomated protein function prediction is a crucial and widely studied problem in bioinformatics. Computationally, protein function is a multilabel classification problem where only positive samples are defined and there is a large number of unlabeled annotations. Most existing methods rely on the assumption that the unlabeled set of protein function annotations are negatives, inducing thefalse negativeissue, where potential positive samples are trained as negatives. We introduce a novel approach named PU-GO, wherein we address function prediction as a positive-unlabeled ranking problem. We apply empirical risk minimization, i.e., we minimize the classification risk of a classifier where class priors are obtained from the Gene Ontology hierarchical structure. We show that our approach is more robust than other state-of-the-art methods on similarity-based and time-based benchmark datasets. Data and code are available athttps://github.com/bio-ontology-research-group/PU-GO.
Mitochondrial DNA analysis in ayu (Plecoglossus altivelis) raises a urgent conservation need for its southernmost population
Authors: Ha Linh Manh , Tran Hau Duc , Takeshima Hirohiko , Iguchi Kei’ichiro 
Published: January 2024

AbstractThe central-marginal hypothesis predicts that genetic diversity decreases and genetic differentiation increases toward the species distribution margin. We analyzed the mitochondrial DNA control region of ayu (Plecoglossus altivelis) collected from different localities, including central and marginal populations, to test the hypothesis. The results show that the ayu populations at southern marginal habitats (Tien Yen River in Vietnam and Yakugachi River in Amami-oshima Island) displayed low genetic diversity (Haplotype diversity,H= 0.52 and 0.67; Nucleotide diversity,Pi= 0.01 and 0.006, respectively) and significantly differed from the central populations (p< 0.001), consistent with the central-marginal hypothesis. However, ayu populations at the center of their distribution range (Shinano River in Honsyu and Hamoji River in Sado Island) and the northern marginal habitats (Yoichi River in Hokkaido and Aonae River in Okushiri Island) exhibited high genetic diversity (H= 1 for all rivers;Pi= 0.024–0.029). The genetic differences between the populations at the center and the northern marginal habitats were insignificant (p> 0.05). This study showed that in ayu, the central-marginal hypothesis is valid in the southern direction but not in the northern direction. Urgent conservation is needed for the genetically distinct population in the degraded southern habitat with severely low genetic diversity.
The impact of ligand-induced oligomer dissociation on enzyme diffusion, directly observed at the single-molecule level
Authors: Yancheva Yulia D. , Kaya Saniye G. , Belyy Alexander , Fraaije Marco W. , Tych Katarzyna M. 
Published: January 2024

ABSTRACTThe existence of the phenomenon of enhanced enzyme diffusion (EED) has been a topic of debate in recent literature. One proposed mechanism to explain the origin of EED is oligomeric enzyme dissociation. We use mass photometry (MP), a label-free single-molecule technique, to investigate the dependence of the oligomeric states of several enzymes on their ligands. The studied enzymes of interest are catalase, aldolase, alkaline phosphatase and vanillyl-alcohol oxidase (VAO). We compared the ratios of oligomeric states in the presence and absence of substrate as well as different substrate and inhibitor concentrations. Catalase and aldolase were found to dissociate into smaller oligomers in the presence of their substrates, independently of inhibition, while for alkaline phosphatase and VAO, different behaviors were observed. Thus, we have identified a possible mechanism which explains the previously observed diffusion enhancementin vitro. This enhancement may occur due to the dissociation of oligomers through ligand binding.
Possible roles of phytochemicals with bioactive properties in the prevention of and recovery from COVID-19
Authors: Koyama Sachiko , Shields Vonnie D.C. , Heinbockel Thomas , Joseph Paule V. , Adhikari Poonam , Kaur Rishemjit , Kumar Ritesh , Alizadeh Rafieh , Bhutani Surabhi , Calcinoni Orietta , Mucignat-Caretta Carla , Chen Jingguo , Cooper Keiland W. , Das Subha R. , Domínguez Paloma Rohlfs , Guàrdia Maria Dolors , Klyuchnikova Maria A. , Laktionova Tatiana K. , Mori Eri , Namjoo Zeinab , Nguyen Ha , Özdener Mehmet Hakan , Parsa Shima , Poyraz Elif Özdener , Strub Daniel Jan , Taghizadeh-Hesary Farzad , Ueha Rumi , Voznessenskaya Vera V. 
Published: January 2024

AbstractPurposeThere have been large geographical differences in the infection and death rates of COVID-19. Foods and beverages containing high amounts of phytochemicals with bioactive properties were suggested to prevent contracting, to limit the severity of, and to facilitate recovery from COVID-19. The goal of our study was to determine the correlation of the type of foods/beverages people consumed and the risk reduction of contracting COVID-19 and the recovery from COVID-19.MethodsWe developed an online survey that asked the participants whether they contracted COVID-19, their symptoms, time to recover, and their frequency of eating various types of foods/beverages. The survey was first developed in English and then translated into 10 different languages.ResultsThe participants who did not contract COVID-19 consumed vegetables, herbs/spices, and fermented foods/beverages significantly more than the participants who contracted COVID-19 and those who were not tested but became sick most likely from COVID-19. The geographic location of participants corresponded with the language of the survey, except for the English version, thus, nine out of the 10 language versions represented a country. Among the six countries (India, Iran, Italy, Japan, Russia, Spain) with over one hundred participants, we found that in India and Japan the people who contracted COVID-19 showed significantly shorter recovery time, and greater daily intake of vegetables, herbs/spices, and fermented foods/beverages was associated with faster recovery.ConclusionOur results suggest that phytochemical compounds included in the vegetables may have contributed in not only preventing contraction of COVID-19, but also accelerating their recovery. (249 words; EJN limit is 250 words)