bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public Health Learning Agenda for Systems Change Toolkit: National Pilot Evaluation Results
Authors: Welter Christina , Davis Sarah , Elnicki Jill , Kulik Phoebe K. G. , Lloyd Laura M. , Tenney Martha , Todd Barrett Karla , Rose Barbara , Walter Cassidy 
Published: October 2022

ABSTRACT

Context:
There have been multiple calls in the United States for public health workforce development approaches that expand practitioner skill sets to respond to profound inequities and improve population health more effectively. However, most workforce models address individual competencies that instead focus on collective approaches to systems change.

Program:
In response to this opportunity, the HRSA-funded Regional Public Health Training Centers (PHTCs) and the University of Illinois Chicago Policy, Practice, and Prevention Research Center (P3RC) released Creating a Learning Agenda for Systems Change: A Toolkit for Building an Adaptive Public Health Workforce (the Toolkit) in December 2020. We later supplemented the Toolkit with additional learning activities to launch the Learning Agenda Toolkit Pilot Test (Toolkit Pilot).

Implementation:
From June to August 2021, 24 diverse teams piloted the Toolkit. Teams completed a multistep process simulating the development of a learning agenda aimed at addressing community health issues and impacting systems change.

Evaluation:
We conducted an evaluation process to assess the usability and impact of the Toolkit Pilot to inform its improvement and future implementation. An evaluation subcommittee analyzed worksheets completed by the Pilot Teams that are aligned to the Learning Agenda steps and conducted and analyzed 12 key informant interviews using concepts from the Toolkit Pilot Logic Model.

Findings and Discussion:
Evaluation results suggest that most Pilot Teams found that the Toolkit Pilot offered a step-by-step process toward a clear vision that produced a concrete product on how to address community challenges through learning and systems change. Pilot Teams noted that the Toolkit Pilot provided exposure to and a unique focus on systems thinking; however, prior knowledge of systems thinking and systems change was important. Building readiness for systems change and having more time, resources, and technical assistance would be needed for future versions of the Learning Agenda Toolkit.
68Ga-FAPI-04 Versus 18F-FDG PET/CT in Detection of Epithelioid Malignant Pleural Mesothelioma
Authors: Dong Aisheng , Zhao Bo , Cheng Chao , Zuo Changjing 
Published: October 2022

Abstract
We describe 68Ga-FAPI (fibroblast activation protein inhibitor)-04 and 18F-FDG PET/CT findings in a case with epithelioid malignant pleural mesothelioma. Compared with 18F-FDG PET/CT, 68Ga-FAPI-04 PET/CT more clearly showed the pleural tumors and lymph node metastases and detected more pleural lesions because the tumors showed higher 68Ga-FAPI-04 activity. This case indicates that 68Ga-FAPI-04 PET/CT may be a promising new tool in evaluation of malignant pleural mesothelioma, which needs further investigation.
Nasal Tube Securement
Authors: McNeely Heidi L. , Quackenbush Debra , Bothwell Samantha , Banks Ashley , Brinton John T. 
Published: October 2022

Abstract

Purpose
The aim of this study was to compare accidental dislodgement rates of nasal gastric tubes secured with standard methods or a nasal tube securement device in pediatric patients.

Design
A randomized controlled trial was conducted.

Methods
Participants (n = 43) were randomized into standard securement or nasal tube securement device using block randomization to control for age and diagnosis. Surveys were collected from staff and caregivers on device ease of use and satisfaction.

Results
There were a similar number of tube dislodgements for patients in the nasal tube securement device group (n = 6) and the standard practice group (n = 7). The median hospital length of stay was higher for the standard practice group (13 days vs. 9 days).

Conclusion
Use of the nasal tube securement device did not significantly decrease the rate of tube dislodgements compared with standard practice.

Clinical Relevance to Rehabilitation Nursing
The study provides information for pediatric rehabilitation nurses in choosing securement options for nasal gastric tubes.
Application of Skin-stretching Device for Closing Scalp Defect
Authors: Zhang Qingtao , Xu Lei , Liu Yang , Tang Xiaoyong , Wang Jia , Deng Yongbing , Chen Peng 
Published: October 2022

Background:
The scalp defect was a clinical common constructive challenge. This research verified the efficacy of the skin-stretching device in the treatment of scalp defect and assessed the associated complications.

Methods:
The clinical data of 12 patients with scalp defect treated with skin-stretching device from January 2020 to January 2021 were collected. We used EASApprox skin-stretching device for the treatment of scalp defect. We described a detailed reconstruction procedure for this treatment. We collected the site, distance from wound edge and other characteristics of the wound, and recorded the number of stretching cycles, operation time, closed state, healing time, and observed postoperative complications and wound healing status.

Results:
In this research, the scalp defect was mainly caused by pressure ulcer, and mainly located in the parietooccipital site. The average distance from wound edge was 3.2 cm, the average stretching cycles was 4.2 times during the operation, and the average operation time was 43.5 minutes. Ten patients were directly sutured after stretching, and 2 patients underwent first-stage stretching to reduce the wound. The average time of wound healing was 13.5 days. Postoperative follow-up of 3 months, no patients had wound tear, necrosis, 1 patient suffered from wound exudation and infection due to poor nutrition. Skin function and final scar was acceptable.

Conclusion:
The treatment of skin-stretching device was effective for scalp defect and has the advantages of convenient operation, acceptable functional results, without severe complications. In addition to traditional treatment, this was a promising treatment. However, more clinical and preclinical research of the skin-stretching device were required.
Gender-Affirming Facial Feminization Surgery at a Public, Safety-Net Hospital: A Single-Center Early Experience
Authors: Alcon Andre , Badiee Ryan K. , Barnes Laura L. , Pardo Seth T. , Zevin Barry , Pomerantz Jason H. 
Published: October 2022

Background:
Facial feminization surgery (FFS) remains inaccessible to many transgender patients. Zuckerberg San Francisco General Hospital (ZSFG) was among the first public, safety-net hospitals to perform FFS. The purpose of this study is to examine the postoperative outcomes of patients who underwent FFS at ZSFG and describe barriers to providing FFS in a public hospital setting.

Methods:
A retrospective review identified patients who underwent FFS at ZSFG. Demographic data, comorbidity profiles, postoperative outcomes, and hospital utilization data were collected from the medical records. FACE-Q modules (scored 0–100) were used to survey patient satisfaction at least 1 year postoperatively.

Results:
Seventeen patients underwent comprehensive FFS surgery at ZSFG. The median age was 41 years [interquartile range (IQR): 38–55], median body mass index was 26.4 (IQR: 24.1–31.3). Patients underwent a median of 9 procedures, the most common of which included frontal cranioplasty (n=13, 77%), open brow lift (n=13, 77%), rhinoplasty (n=12, 71%), and mandible contouring (n=12, 71%). There were no complications, readmissions, or reoperations within 30 days. Patients reported high satisfaction with the surgical outcome (median: 87, IQR: 87–100), excellent postoperative psychological functioning (median: 100, IQR: 88–100), and low levels of appearance-related distress (median: 3, IQR: 0–35). An estimated 243 operating room hours and 51 inpatient bed days were required to cover all FFS procedures.

Conclusions:
Performing FFS in a public, safety-net hospital was associated with zero postoperative complications, few revision procedures, and excellent patient satisfaction. Limited operating room hours and inpatient availability represented barriers to providing FFS in this setting.
Generalized habitual tendencies in alcohol dependent rats
Authors: Giannone Francesco , Hach Arian , Chrószcz Magda , Friske Marion M. , Meinhardt Marcus , Spanagel Rainer , Sommer Wolfgang H. , Hansson Anita C. 
Published: October 2022

AbstractHabitual responses and ultimately compulsive behavior are thought to be at the core of addiction including alcohol use disorder (AUD). Little is known whether the habitization concerns exclusively the response towards alcohol or generalizes to other daily activities. Here, we address this question in a well-established animal model of AUD – the postdependent rat model – by testing habitual responses towards a sweet palatable reward in two striatal learning paradigms: spatial navigation and reward conditioning. For the spatial navigation task, alcohol-dependent and control rats were tested on a sequential decision-making test after short and prolonged T-Maze training; for the reward conditioning task, rats were trained under a random interval schedule for a short and prolonged period and tested in a satiety devaluation test at each time point. Another cohort of alcohol-naive rats was trained and tested on both paradigms under DREADD (designer receptors exclusively activated by designer drugs)-mediated inactivation of the dorsomedial striatum (DMS) which controls goal-directed behavior. Our results show that alcohol-dependent rats displayed increased habitual behavior to obtain saccharin reward on both paradigms, with overall more habitual choices after prolonged training on the spatial navigation task, and increased habitual responses already after short training on the reward conditioning task. Finally, DREADD-mediated inactivation of the DMS increased habitual behavior in non-dependent rats on both paradigms. Our results provide evidence that a history of alcohol dependence produces a bias towards habitual responding that generalizes to a natural reward in rats. Similarly, a habitual bias was induced in non-dependent rats after inactivation of the DMS, thus confirming the critical role of this region in maintaining goal-directed behavior and suggesting its diminished control in AUD.
The investigation on metabolites, genes and open chromatins involved in colored leaves ofEucommia ulmoides‘Ziye’
Authors: Long Li , Qianqian Shi , Wenjing Yao 
Published: October 2022

SUMMARYEucommia ulmoidesOliver ‘Ziye’ has unique purple-red leaves, which contain a variety of flavonoids, so it has high ornamental and medicinal value. However, the categories of flavonoids and molecular mechanism of specific accumulation of flavonoids in ‘Ziye’ leaves is still unclear. Here, differences in metabolic level, gene expression level, chromatin accessibility and cis-regulatory elements were compared between ‘Ziye’ and ‘Huazhong 1’ with green leaf color by metabolome profiling, RNA-seq, and ATAC-seq. A total of 205 flavonoids were identified from these two varieties using ultraperformance liquid chromatography–mass spectrometry (UPLC-MS). The accumulation of most delphinidin, cyaniding, quercetin, myricetin, and isorhamnetin derivatives peaked in old leaves of ‘Ziye’. Single-molecule long-read sequencing indicated that genes in the phenylpropanoid biosynthesis and flavonoid biosynthetic pathway, as well as many transcription factors including MYB, ERF, and WRKY were highly expressed in ‘Ziye’ leaves. ATAC-seq revealed the presence of cell preferentially enriched peaks, which annotated to 6114 genes. Analysis of the genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF-binding motifs, highlighting sets of TFs such as MYB, ERF, and WRKY that are probably important for color formation of ‘Ziye’ cell. Interestingly, the TFs within each of these cell type-enriched sets also showed evidence of extensively co-regulating each other. Our work demonstrated how chromatin accessibility and TF expression level influenced the expression of flavonoid biosynthesis associated genes, resulted in flavonoids accumulation in ‘Ziye’ leaf. Our results could lay a foundation for further studies of gene expression and functional genomics inE. ulmoides.
Benchmarking Automated Cell Type Annotation Tools for Single-cell ATAC-seq Data
Authors: Wang Yuge , Sun Xingzhi , Zhao Hongyu 
Published: October 2022

AbstractAs single-cell chromatin accessibility profiling methods advance, scATAC-seq has become ever more important in the study of candidate regulatory genomic regions and their roles underlying developmental, evolutionary and disease processes. At the same time, cell type annotation is critical in understanding the cellular composition of complex tissues and identifying potential novel cell types. However, most existing methods that can perform automated cell type annotation are designed to transfer labels from an annotated scRNA-seq data set to another scRNA-seq data set, and it is not clear whether these methods are adaptable to annotate scATAC-seq data. Several methods have been recently proposed for label transfer from scRNA-seq data to scATAC-seq data, but there is a lack of benchmarking study on the performance of these methods. Here, we evaluated the performance of five scATAC-seq annotation methods on both their classification accuracy and scalability using publicly available single-cell datasets from mouse and human tissues including brain, lung, kidney, PBMC and BMMC. Using the BMMC data as basis, we further investigated the performance of these methods across different data sizes, mislabeling rates, sequencing depths and the number of cell types unique to scATAC-seq. Bridge integration, which is the only method that requires additional multimodal data and does not need gene activity calculation, was overall the best method and robust to changes in data size, mislabeling rate and sequencing depth. Conos was the most time and memory efficient method but performed the worst in terms of prediction accuracy. scJoint tended to assign cells to similar cell types and performed relatively poorly for complex datasets with deep annotations but performed better for datasets only with major label annotations. The performance of scGCN and Seurat v3 was moderate, but scGCN was the most time-consuming method and had the most similar performance to random classifiers for cell types unique to scATAC-seq.
Comprehensive Physical Exam versus Lung Ultrasound for Dyspneic Patients in the Emergency Department
Authors: Secko Michael , Cheng Yuwen , Raj Sonika , Goradia Eshani , Reardon Lindsay , Thode Henry C. , Singer Adam J. 
Published: October 2022

ABSTRACTObjectiveOverreliance on technology has led to dwindling physical exam (PE) skills. We compared the diagnostic accuracy of a structured lung physical examination (L-PE) to structured lung ultrasound (LUS) in ED patients with undifferentiated dyspnea. We also examined the change in differential diagnosis and degree of certainty based on order and type of examMethodsThis was a prospective, randomized, crossover study of a convenience sample of adult ED patients with undifferentiated dyspnea. Comprehensive L-PE and LUS were performed in random order followed by the other exam. An adjudication committee determined the final diagnosis based on all available data and served as the criterion standard. Primary outcome was diagnostic accuracy. A sample of 86 patients had 80% power to detect a 25% difference in diagnostic accuracy.ResultsA total of 102 patients were enrolled. Similar accuracies were found between L-PE and LUS for both COPD [75% (95% CI 65-83) vs. 76% (95% CI 67-84)] and asthma [87% (95% CI 79-93) vs. 87% (95 CI 79-93)]. LUS [81% (95 CI 72-88)] was slightly more accurate compared to L-PE [72% (95 CI 62-80)] for diagnosis of pneumonia but not statistically significant. For patients presenting with pulmonary edema, LUS was slightly [76% (95 CI 66-84)] more accurate than L-PE [73% (95 CI 63-81)], but not statistically significant. Finally, for detecting pleural effusions, L-PE [96% (95 CI 90-99)] was more accurate than LUS [82% (95 CI 73-89)].ConclusionsThe diagnostic accuracies of comprehensive lung physical examination and focused lung ultrasound were generally similar in ED patients with dyspnea and should be used concurrently to maximize diagnostic accuracy.
Molecular and genetic mechanisms conferring dissolution of dioecy inDiospyros oleiferaCheng
Authors: Sun Peng , Nishiyama Soichiro , Li Huawei , Mai Yini , Han Weijuan , Suo Yujing , Liang Chengzhi , Du Huilong , Diao Songfeng , Wang Yiru , Yuan Jiaying , Zhang Yue , Tao Ryutaro , Li Fangdong , Fu Jianmin 
Published: October 2022

AbstractDioecy, a sexual system of single-sex (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sex individuals. Here, we report potential molecular and genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions ofDiospyros oleifera. All co-sexD. oleiferaplants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant geneOGI, implying that genetic factors control gynoecia development in genetically maleD. oleifera. In both single- and co-sex plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and aDUF247gene cluster strongly associated with the monoecious phenotype, as well as several regions that may contribute to andromonoecy. Collectively, our findings imply stable breakdown of the dioecious system inD. oleifera, presumably a result of the genomic features of the sex-linked region.
MAMBA: a model-driven, constraint-based multiomic integration method
Authors: Ugidos Manuel , Nuño-Cabanes Carme , Tarazona Sonia , Ferrer Alberto , Nielsen Lars Keld , Rodríguez-Navarro Susana , Marín de Mas Igor , Conesa Ana 
Published: October 2022

AbstractThe inclusion of omic data into constraint-based modeling (CBM) has improved metabolic network characterization of biological models. However, the integration of semi-quantitative metabolomic data into CBM remains challenging. Here, we present MAMBA (Metabolic Adjustment via Multiomic Blocks Aggregation), a CBM approach that enables the use of semi-quantitative metabolomic data together with a gene-centric omic data type (e.g. transcriptomics, ChIP-seq or chromatin accessibility data, among others), and the combination of different time points and conditions. MAMBA outperformed other methods in terms of metabolic network characterization and metabolite prediction accuracy. As a case study, we applied MAMBA to a yeast multiomic dataset with time series design where two different yeast strains where exposed to heat stress. MAMBA captured known biology of heat stress in yeast and identified novel affected metabolic pathways. MAMBA was implemented as an integer linear programming (ILP) problem to guarantee efficient computation, and coded for MATLAB (freely available at github.com/ConesaLab/MAMBA).
1H-MRS characterization of metabolic changes induced by photoperiod in the sheep brain: a promising eye into in-vivo adult neurogenesis?
Authors: Just Nathalie , Chevillard Pierre Marie , Batailler Martine , Dubois Jean-Philippe , Vaudin Pascal , Pillon Delphine , Migaud Martine 
Published: October 2022

ABSTRACTThe hypothalamus is a central structure of the mammalian brain, which controls physiological, endocrine and metabolic brain homeostasis. Despite this essential role, little is known about the normal and altered neurochemical changes occurring within the hypothalamic structures. Here, the metabolism of the hypothalamus of ewes was investigated at 3T using proton magnetic resonance spectroscopy (1H-MRS). We used the sensitivity of these animals to photoperiod i.e. the ratio of day to night length, to investigate the hypothalamic metabolic changes and their relationship to hypothalamic adult neurogenesis. A longitudinal study involving 4 ewes per timepoint was conducted at 4 time points (P01, P02, P03 and P04) during long days (LD) and 4 time points during short days (SD). Significant metabolic changes were found between LD and SD at all time points in particular for glutamate (Glu), glutamine, myo-inositol and total N-acetyl-Aspartate (NAA). During SD, glutamate and glutamine concentrations were significantly smaller at P01 compared to all other time points while significant neurochemical changes occurred during the entire LD period. Neurochemical changes relative to P01 remained stable during LD and SD except for Glu and Gln which increased between P01 and P02 during SD. Relative metabolic changes were significantly higher on average for NAA and Glu and significantly smaller on average for total choline during SD compared to LD, respectively, paralleling the average changes in the numbers of neural stem cells and glial and oligodendrocyte progenitors found by immunohistochemistry. Despite important differences between MRS and immunohistochemistry in terms of spatial resolution, both techniques suggest complementary findings that should contribute to a better characterization of the hypothalamus during photoperiodism and adult neurogenesis. We conclude that1H-MRS could be a promising non-invasive translational technique to investigate the existence of adult neurogenesis in-vivo in gyrencephalic brains.
Outer membrane β-barrel structure prediction through the lens of AlphaFold2
Authors: Topitsch Annika , Schwede Torsten , Pereira Joana 
Published: October 2022

AbstractMost proteins found in the outer membrane of Gram-negative bacteria share a common domain: the transmembrane β-barrel. These outer membrane β-barrels (OMBBs) occur in multiple sizes, and different families with a wide range of functions evolved independently by amplification from a pool of homologous ancestral ββ-hairpins. This is part of the reason why predicting their three-dimensional (3D) structure, especially by homology modeling, is a major challenge. Recently, DeepMind’s AlphaFold v2 (AF2) became the first structure prediction method to reach close-to-experimental atomic accuracy in CASP even for difficult targets. However, membrane proteins, especially OMBBs, were not abundant during its training, raising the question of how accurate the predictions are for these families. In this study, we assessed the performance of AF2 in the prediction of OMBBs of various topologies using an in-house-developed tool for the analysis of OMBB 3D structures,barrOs. In agreement with previous studies on other membrane protein classes, our results indicate that AF2 predicts OMBB structures at high accuracy independently of the use of templates, even for novel topologies absent from the training set. These results provide confidence on the models generated by AF2 and open the door to the structural elucidation of novel OMBB topologies identified in high-throughput OMBB annotation studies.