bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis of potential key genes and pathways in neonatal necrotizing enterocolitis
Authors: Liu Xuexiu , Zhang Xianhong , Li Luquan , Wang Jianhui , Chen Yanhan , Wu Liping 
Published: September 2022

Abstract
Objective
To detect differentially expressed genes in patients with neonatal necrotizing enterocolitis (NEC) by bioinformatics methods and to provide new ideas and research directions for the prevention, early diagnosis and treatment of NEC.
Methods
Gene chip data were downloaded from the Gene Expression Omnibus database. The genes that were differentially expressed in NEC compared with normal intestinal tissues were screened with GEO2R. The functions, pathway enrichment and protein interactions of these genes were analyzed with DAVID and STRING. Then, the core network genes and significant protein interaction modules were detected using Cytoscape software.
Results
Overall, a total of 236 differentially expressed genes were detected, including 225 upregulated genes and 11 downregulated genes, and GO and KEGG enrichment analyses were performed. The results indicated that the upregulated differentially expressed genes were related to the dimerization activity of proteins, while the downregulated differentially expressed genes were related to the activity of cholesterol transporters. KEGG enrichment analysis revealed that the differentially expressed genes were significantly concentrated in metabolism and fat digestion and absorption pathways. Through STRING analysis, 9 key genes in the protein network interaction map were identified: EPCAM, CDH1, CFTR, IL-6, APOB, APOC3, APOA4, SLC2A and NR1H4.
Conclusion
Metabolic pathways and biological processes may play important roles in the development of NEC. The screening of possible core targets by bioinformatics is helpful in clarifying the pathogenesis of NEC at the gene level and in providing references for further research.
Palmitic acid inhibits vascular smooth muscle cell switch to synthetic phenotype through upregulation of miR-22 expression
Authors: Hu Yanchao , Fan Yajie , Zhang Chunyan , Wang Congxia 
Published: September 2022

Abstract
Background
Vascular smooth muscle cell (VSMC) phenotype switch to a dedifferentiated, synthetic phenotype has been shown to play a vital role in many vascular diseases. Mounting evidence has shown that fatty acid metabolism is highly associated with vascular diseases. However, how fatty acids regulate VSMC phenotype is poorly understood. Here, we aimed to examine the effects of palmitic acid (PA), the most common saturated fatty acid in circulation, on VSMC phenotype and the underlying mechanism.
Methods
The effect of the PA on VSMC was measured by live/dead and EdU assays, as well as flow cytometry. Migration ability of VSMCs was determined by transwell assay. The underlying targets of miR-22 was predicted using bioinformatics online tools, and comfirmed by luciferase reporter assay. The RNA and protein expression of certain gene or protein was detected by qRT-PCR and western blot, respectively.
Results
We found that PA inhibited VSMC switch to synthetic phenotype, as manifested by inhibiting VSMC proliferation, migration, and synthesis. PA upregulated miR-22 in VSMCs, and miR-22 mimics exerted similar effects as PA treatment, inhibiting VSMC switch to synthetic phenotype. Inhibition of miR-22 using miR-22 inhibitor blocked the effects of PA on VSMC phenotype modulation, suggesting that PA modulated VSMC phenotype through upregulation of miR-22 expression. In addition, we found that ecotropic virus integration site 1 protein homolog (EVI1) was the target of miR-22 in regulation of VSMC phenotype. Overexpression of miR-22 or/and PA treatment attenuated the inhibitive effect of EVI1 on synthetic phenotype switch of VSMCs.
Conclusions
These findings suggested that PA inhibits VSMC switch to synthetic phenotype through upregulation of miR-22 thereby inhibiting EVI1, and correcting the dysregulation of miR-22/EVI1 or PA metabolism is a potential treatment to vascular diseases.
Injectable long acting antiretroviral for HIV treatment and prevention: Perspectives of potential users
Authors: Slama Laurence , Porcher Raphael , Linard Françoise , Chakvetadze Catherine , Cros Agnès , Carillon Séverine , Gallardo Lucille , Viard Jean-Paul , Molina Jean-Michel 
Published: September 2022

Abstract
Background :

The use of long acting injectable (LAA) antiretroviral drugs may be an alternative option for HIV treatment and prevention. Our study focused on patient perspectives to understand which individuals, among people with HIV (PWH) and pre-exposure prophylaxis (PrEP) users, would constitute the preferential target for such treatments in terms of expectations, tolerability, adherence and quality of life.

Methods :

The study consisted in one self-administrated questionnaire. Data collected included lifestyle issues, medical history, perceived benefits and inconveniences of LAA. Groups were compared using Wilcoxon rank tests or Fisher‘s exact test.

Results :

In 2018, 100 PWH and 100 PrEP users were enrolled. Overall, 74% of PWH and 89% of PrEP users expressed interest for LAA with a significantly higher rate for PrEP users (p = 0.001). No characteristics were associated with acceptance of LAA in both groups in term of demographics, lifestyle or comorbidities. Further studies should be conducted to better characterize targeted individuals.

Conclusion:

PWH and PrEP users expressed a high level of interest in LAA, since a large majority seems to be in favor of this new approach.
Occurrence of variants of unknown clinical significance in genetic testing for hereditary breast and ovarian cancer syndrome and Lynch syndrome - A Literature review and analytical observational retrospective cohort study
Authors: Adam Felicia , Fluri Muriel , Scherz Amina , Rabaglio Manuela 
Published: September 2022

Abstract
Background and purpose
Over the last decade, the implementation of multigene panels for hereditary tumor syndrome has increased at our institution (Inselspital, University Hospital Berne, Switzerland). The aim of this study was to determine the prevalence of variants of unknown significance (VUS) in patients with suspected Lynch syndrome (LS) and suspected hereditary breast and ovarian cancer syndrome, the latter in connection with the trend toward ordering larger gene panels.
Results
Retrospectively collected data from 1057 patients at our institution showed at least one VUS in 126 different cases (11.9%). In patients undergoing genetic testing for BRCA1/2, the prevalence of VUS was 6%. When < 10 additional genes were tested in addition to BRCA1/2, the prevalence increased to 13.8%, and 31.8% for > 10 additional genes, respectively. The gen most frequently affected with a VUS was ATM. 6% of our patients who were tested for Lynch syndrome had a VUS result in either MLH1, MSH2 or MSH6.
Conclusions
Our data demonstrate that panel testing statistically significantly increases VUS rates due to variants in non-BRCA genes. Good genetic counseling before and after obtaining results is therefore particularly important when conducting multigene panels to minimize patient uncertainty due to VUS results.
On the Use of Mega Constellation Services in Space
Authors: Capez Gabriel Maiolini , Caceres Mauricio , Bridges Christopher , Frey Stefan , Armellin Roberto , Garello Roberto , Bargellini Pier 
Published: September 2022

Abstract
Mega-constellations are being deployed to offer innovative services to Earth's users. Our work shows how they can provide seamless connectivity to LEO spacecrafts too, and transform them into highly responsive nodes of a space-to-space network characterized by high throughput, low latency, and low cost. For realizing the new mega-constellation services in space paradigm, we present a complete design of the LEO space terminal. By focusing on existing mega-constellations, we derive the service performance under realistic scenarios, and compare it with existing services like Ground Station Networks and Data Relay Systems. All the results show that the new approach can be potentially disruptive for the space ecosystem, by transforming each satellite into a 24/7 available node of a high performance space network, thus enabling a myriad of innovative applications.
Involvement of ACACA (acetyl-CoA carboxylase α) in the lung pre-metastatic niche formation in breast cancer by senescence phenotypic conversion in fibroblasts
Authors: Huang Yung-Chi , Hou Ming-Feng , Tsai Ying-Ming , Pan Yi-Chung , Tsai Pei-Hung , Lin Yi-Shiuan , Chang Chao-Yuan , Tsai Eing-Mei , Hsu Ya-Ling 
Published: September 2022

Abstract
Purpose: Impairment of metabolism is strongly associated with the development of cancer. However, the role of metabolic reprogramming in the remodeling of pre-metastatic niche (PMN), a key step in metastasis, is still unknown. We aimed to investigate the metabolic alternation of lung PMN.
Methods: We assessed the transcriptomes and lipidomics of lung of MMTV-PyVT mice by microarray and liquid chromatography-tandem mass spectrometry before lung metastasis. The validation of protein expressions was performed by immunoblot and immunohistochemistry. The lung fibroblasts were isolated from mice and co-cultured with breast cancer to identify the influence of cancer on the change of lung fibroblasts.
Results: We demonstrated changes in the lipid profile and several lipid metabolism genes in the lungs of breast cancer-bearing MMTV-PyVT mice before cancer spread. The expression of ACACA (acetyl-CoA carboxylase) was downregulated in the lung fibroblasts, which contributed to changes in acetylation of protein’s lysine residues and the synthesis of fatty acid. The downregulation of ACACA in lung fibroblasts triggered a senescent and inflammatory phenotypic shift of lung fibroblasts in both in vivo and in vitro models. The senescence-associated secretory phenotype of lung fibroblasts enabled the recruitment of immunosuppressive granulocytic myeloid-derived suppressor cells into the lungs through the production of CXCL1 in the lungs. Knock-in of ACACA prevented lung metastasis in the MMTV-PyVT mouse model, further supporting that ACACA was involved in the remodeling of the lung PMN.
Conclusion: These data revealed a mechanism by which ACACA downregulation directs the formation of an immunosuppressive lung PMN in breast cancer.
A method to analyze the food-water-energy nexus for data-sparse cities: A comparison of green roofs in São José dos Campos, Brazil and Johannesburg, South Africa
Authors: Meng Fanxin , Yuan Qiuling , Bellezoni Rodrigo , de Oliveira José Puppim , Hu Yuanchao , Jing Rui , Liu Gengyuan , Yang Zhifeng , Seto Karen 
Published: September 2022

Abstract
Green roofs have gained relevance in urban sustainability and affect the urban food-water-energy nexus in cities in many different ways. However, it remains unknown regarding systemically quantifying the trade-offs of green roofs on urban food-water-energy nexus. Most city-scale research is restricted to a silo lens (e.g., life cycle impacts and food-water-energy related benefits) while research focusing on green roof’s multiple trade-offs occurs at smaller scales (e.g., neighborhood). Here we developed a generalizable integrated methodology framework for data-sparse cities to analyze the food-water-energy nexus of green roofs from an urban system perspective and tested the framework in two global south cities, São José dos Campos, Brazil and Johannesburg, South Africa. We find São José dos Campos could reach its total self-sufficiency of vegetables in prospect by green roof farming, whereas its life cycle energy consumption would achieve 45% of urban energy demand in the worst scenario. Fueled by the scheme of rainwater substitution, 96% of the life cycle water consumption in São José dos Campos rushed to the infrastructure stage from the operation stage. Johannesburg had potential to satisfy 73% of urban vegetable self-sufficiency and contribute 8% to the city’s alternative water supply goal by rainwater harvesting. Local food supplies are cardinal drivers of trans-boundary water footprints beyond the cities of both São José dos Campos and Johannesburg. We highlight the necessity to balance the trade-offs of green roofs orienting urban food-water-energy goals and call for opportunities for green roof practice in cities.
Physician Perspectives on Chronic Pain Management: Barriers, Needs, and the Use of eHealth in the COVID-19 Era
Authors: Kaseweter Kimberley , Nazemi Mark , Gregoire Nina , Louw W. Francois , Walsh Zach , Holtzman Susan 
Published: September 2022

Abstract
Background
Chronic pain is a highly prevalent and disabling condition which is often undertreated and poorly managed in the community. The emergence of COVID-19 has further complicated pain care, with an increased prevalence of chronic pain and mental health comorbidities, and burnout among physicians. While the pandemic has led to a dramatic increase in virtual health care visits, the uptake of a broader range of eHealth technologies remains unclear. The present study sought to better understand physicians’ current needs and barriers in providing effective pain care within the context of COVID-19, as well as gauge current use, interest, and ongoing barriers to eHealth implementation.
Methods
A total of 100 practicing physicians in British Columbia, Canada, completed a brief online survey.
Results
The sample was comprised of physicians practicing in rural and urban areas (rural = 48%, urban = 42%; both = 10%), with the majority (72%) working in family practice. The most prominent perceived barriers to providing chronic pain care were a lack of interdisciplinary treatment and allied health care for patients, challenges related to opioid prescribing and management, and a lack of time to manage the complexities of chronic pain. Moreover, despite expressing considerable interest in eHealth for chronic pain management (82%), low adoption rates were observed for several technologies. Specifically, only a small percentage of the sample reported using eHealth for the collection of intake data (21%), patient-reported outcomes (14%), and remote patient monitoring (26%). The most common perceived barriers to implementation were cost, complexity, and unfamiliarity with available options.
Conclusions
Findings provide insight into physicians’ ongoing needs and barriers in providing effective pain management during the COVID-19 pandemic. Despite the potential for eHealth technologies to help address barriers in pain care, and strong interest from physicians, enhanced useability, education and training, and funding are likely required to achieve successful implementation of a broader range of eHealth technologies in the future.
Keratin 17 is a prognostic biomarker in endometrial carcinoma and correlates with immune invasion
Authors: Zhang HanBin , Deng JinMan , Li Hao , Wang XinXin , Yang QiuHong , Shao YingYing 
Published: September 2022

Abstract
Background：Keratin 17 expression has been detected in some carcinoma types, although its function in endometrial carcinoma remains unclear. According to the Cancer Genome Atlas (TCGA) data library, we aimed to demonstrate the correlation between Keratin 17 and endometrial carcinoma.
Methods：We analyzed the relationship between clinicopathologic characteristics and Keratin 17 expression using Kruskal-Wallis test, Wilcoxon signed-rank test, and Logistic regression. Based on the receiver operating characteristic (ROC) curve and Area Under the Curve (AUC) score, the binary classifier value for Keratin 17 was derived. Kaplan-Meier method and Cox regression analysis were used to assess the prognosis factors. The Keratin 17 Gene set enrichment analysis (GSEA) and immune invasion analysis were used to determine its important functions.
Results：Keratin17 expression was associated with the clinical classification of endometrial carcinoma (P=0.002), Histological type (P<0.001). The Keratin 17 ROC curve showed strong diagnostic and prognostic capabilities (AUC=0.789). High Keratin 17 expression indicated a poorer overall survival (OS) (P=0.018). According to immune invasion analysis, the expression of Keratin 17 is associated with some types of immune invasive cells.
Conclusions：Keratin 17 expression is strongly associated with poor survival and immune invasion of endometrial carcinoma, and may represent a promising biomarker for endometrial cancer.
Evaluation of Staffordshire, Stoke on Trent Allied Health Professionals preceptorship programmes: a mixed method UK study
Authors: Salt Emma , Jackman Karen , O'Brien Anne 
Published: September 2022

Abstract
Aim: This study aimed to evaluate current preceptorship provision across AHP professions in the Staffordshire, Stoke on Trent (SSOT) region of England to improve consistency, share and optimise best practice.
Background: Preceptorship, defined as a period of structured transition from newly qualified to an independent practitioner, is thought to improve recruitment and retention of staff and ultimately improve patient care. During the COVID pandemic SSOT recognised a particular need to support newly qualified staff, and to evaluate existing AHP provision for recent graduates.
Methods: An explanatory sequential mixed methods design, utilising a cross sectional survey questionnaire and two subsequent focus groups, were used to explore existing AHP preceptorship in SSOT in 2021.
Following ethical approval respondents were recruited via professional networks who completed an online survey questionnaire. . Two subsequent focus groups enabled an in-depth exploration of survey results. Descriptive statistics summarised survey data and thematic analysis was used to describe focus group findings.
Results: SSOT AHPs (n=217; 26% preceptees; 47% preceptors) participated in the survey questionnaire and 20 in the focus groups. 57% of preceptees rated existing preceptorship programmes to be “somewhat or not effective”. Preceptors reported feeling unprepared for their role. Preceptees and preceptors reported that, post pandemic, most existing programs required revisions to be fit for purpose. Six pragmatic summary recommendations were made.
Conclusions: Allied Health Professions Preceptorship in SSOT was found to be inconsistent, poorly understood and inadequate. Revisions to SSOT preceptorship programs are planned to reflect changes in AHP practice since the COVID pandemic.
Optimal Measurement Structures for Contextuality Applications
Authors: Ramanathan Ravishankar , Liu Yuan , Horodecki Karol , Rosicka Monika , Horodecki Pawe{\l} 
Published: September 2022

Abstract
The Kochen-Specker (KS) theorem is a corner-stone result in the foundations of quantum mechanics describing the fundamental difference between quantum theory and classical non-contextual theories. Recently specific substructures termed $01$-gadgets were shown to exist within KS proofs that capture the essential contradiction of the theorem. Here, we show these gadgets and their generalizations provide an optimal toolbox for contextuality applications including (i) constructing classical channels exhibiting entanglement-assisted advantage in zero-error communication, (ii) identifying large separations between quantum theory and binary generalised probabilistic theories, and (iii) finding optimal tests for contextuality-based semi-device-independent randomness generation. Furthermore, we introduce and study a generalisation to definite prediction sets for more general logical propositions, that we term higher-order gadgets. We pinpoint the role these higher-order gadgets play in KS proofs by identifying these as induced subgraphs within KS graphs and showing how to construct proofs of state-independent contextuality using higher-order gadgets as building blocks. The constructions developed here may help in solving some of the remaining open problems regarding minimal proofs of the Kochen-Specker theorem.
Tailoring sexual health research practices to meet the needs of adolescent girls in low-and-middle-income countries: findings from Mexico
Authors: Servin Argentina E. , Macklin Ruth , Wilkerson Sara , Rocha-Jimenez Teresita , Rangel Gudelia M. , Fisher Celia B. , Alvarez-Hernandez Sabrina , O'Bryan Sophie 
Published: September 2022

Abstract
Background
Sexual and reproductive health (SRH) research is essential for the development of population-tailored evidence-based policies and programs that support sexual health among adolescent girls. However, various ethical challenges create barriers to girls’ participation in SRH research in low-and-middle-income countries (LMIC) such as Mexico where sexual health topics are considered a cultural taboo.
Methods
From February to September 2019, adolescent girls ages 16–20 (n = 30) who had participated in the Jovenes Sanos study in Mexico’s northern border city of Tijuana, Baja California (ClinicalTrials: NCT03660514) responded to in-depth interviews (IDs) on perceived risks and benefits of participating in studies addressing gender-based violence and HIV.
Results
Emergent themes pointed to the need to ensure consent and incentive procedures are tailored to the developmental level and experience of participants, the importance of the researcher-participant relationship, the potential for research to destigmatize SRH in LMICs and that research can serve as an opportunity to empower girls to express their sexual health medical needs in the future.
Conclusions
Listening to the voices of adolescent girls is a critical step in ensuring consent to SRH research is tailored to the developmental needs of participants and in developing best practices for creating researcher-participant relationships that empower girls’ reproductive choices.