bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI-based breast cancer radiogenomics using RNA profiling: association with subtypes in a single-center prospective study
Authors: Park Ah Young , Han Mi-Ryung , Seo Bo Kyoung , Ju Hye-Yeon , Son Gil Soo , Lee Hye Yoon , Chang Young Woo , Choi Jungyoon , Cho Kyu Ran , Song Sung Eun , Woo Ok Hee , Park Hyun Soo 
Published: June 2023

Abstract
Background
There are few prospective studies on the correlations between MRI features and whole RNA-sequencing data in breast cancer according to molecular subtypes. The purpose of our study was to explore the association between genetic profiles and MRI phenotypes of breast cancer and to identify imaging markers that influences the prognosis and treatment according to subtypes.

Methods
From June 2017 to August 2018, MRIs of 95 women with invasive breast cancer were prospectively analyzed, using the breast imaging-reporting and data system and texture analysis. Whole RNA obtained from surgical specimens was analyzed using next-generation sequencing. The association between MRI features and gene expression profiles was analyzed in the entire tumor and subtypes. Gene networks, enriched functions, and canonical pathways were analyzed using Ingenuity Pathway Analysis. The P value for differential expression was obtained using a parametric F test comparing nested linear models and adjusted for multiple testing by reporting Q value.

Results
In 95 participants (mean age, 53 years ± 11 [standard deviation]), mass lesion type was associated with upregulation of CCL3L1 (sevenfold) and irregular mass shape was associated with downregulation of MIR421 (sixfold). In estrogen receptor-positive cancer with mass lesion type, CCL3L1 (21-fold), SNHG12 (11-fold), and MIR206 (sevenfold) were upregulated, and MIR597 (265-fold), MIR126 (12-fold), and SOX17 (fivefold) were downregulated. In triple-negative breast cancer with increased standard deviation of texture analysis on precontrast T1-weighted imaging, CLEC3A (23-fold), SRGN (13-fold), HSPG2 (sevenfold), KMT2D (fivefold), and VMP1 (fivefold) were upregulated, and IGLC2 (73-fold) and PRDX4 (sevenfold) were downregulated (all, P < 0.05 and Q < 0.1). Gene network and functional analysis showed that mass type estrogen receptor-positive cancers were associated with cell growth, anti-estrogen resistance, and poor survival.

Conclusion
MRI characteristics are associated with the different expressions of genes related to metastasis, anti-drug resistance, and prognosis, depending on the molecular subtypes of breast cancer.
Meta-research on pragmatism of randomized trials: rationale and design of the PragMeta database
Authors: Hirt Julian , Janiaud Perrine , Düblin Pascal , Hemkens Lars G. 
Published: June 2023

Abstract
Background
Pragmatic trials provide decision-oriented, real-world evidence that is highly applicable and generalizable. The interest in real-world evidence is fueled by the assumption that effects in the “real-world” are different to effects obtained under artificial, controlled, research conditions as often used for traditional explanatory trials. However, it is unknown which features of pragmatism, generalizability, and applicability would be responsible for such differences. There is a need to provide empirical evidence and promote meta-research to answer these fundamental questions on the pragmatism of randomized trials and real-world evidence. Here, we describe the rationale and design of the PragMeta database which pursues this goal (www.PragMeta.org).

Methods
PragMeta is a non-commercial, open data platform and infrastructure to facilitate research on pragmatic trials. It collects and shares data from published randomized trials that either have a specific design feature or other characteristic related to pragmatism or they form clusters of trials addressing the same research question but having different aspects of pragmatism. This lays the foundation to determine the relationship of various features of pragmatism, generalizability, and applicability with intervention effects or other trial characteristics.
The database contains trial data actively collected for PragMeta but also allows to import and link existing datasets of trials collected for other purposes, forming a large-scale meta-database. PragMeta captures data on (1) trial and design characteristics (e.g., sample size, population, intervention/comparison, outcome, longitudinal structure, blinding), (2) effects estimates, and (3) various determinants of pragmatism (e.g., the use of routinely collected data) and ratings from established tools used to determine pragmatism (e.g., the PRagmatic–Explanatory Continuum Indicator Summary 2; PRECIS-2).
PragMeta is continuously provided online, inviting the meta-research community to collaborate, contribute, and/or use the database. As of April 2023, PragMeta contains data from > 700 trials, mostly with assessments on pragmatism.

Conclusions
PragMeta will inform a better understanding of pragmatism and the generation and interpretation of real-world evidence.
Autism-associated gene shank3 is necessary for social contagion in zebrafish
Authors: Kareklas Kyriacos , Teles Magda C. , Dreosti Elena , Oliveira Rui F. 
Published: June 2023

AbstractBackgroundAnimal models enable targeting autism-associated genes, such as theshank3gene, to assess their impact on behavioural phenotypes. However, this is often limited to simple behaviours relevant for social interaction. Social contagion is a complex phenotype forming the basis of human empathic behaviour and involves attention to the behaviour of others for recognizing and sharing their emotional or affective state. Thus, it is a form of social communication, which constitutes the most common developmental impairment across autism spectrum disorders (ASD).MethodsHere we describe the development of a zebrafish model that identifies the neurocognitive mechanisms by whichshank3mutation drives deficits in social contagion. We used a CRISPR-Cas9 technique to generate mutations to theshank3agene, a zebrafish paralogue found to present greater orthology and functional conservation relative to the human gene. Mutants were first compared to wild types during a two-phase protocol that involves the observation of two conflicting states, distress and neutral, and the later recall and discrimination of others when no longer presenting such differences. Then, the whole-brain expression of different neuroplasticity markers was compared between genotypes and their contribution to cluster-specific phenotypic variation was assessed.ResultsTheshank3mutation markedly reduced social contagion via deficits in attention contributing to difficulties in recognising affective states. Also, the mutation changed the expression of neuronal plasticity genes. However, only downregulated neuroligins clustered withshank3aexpression under a combined synaptogenesis component that contributed specifically to variation in attention.LimitationsWhile zebrafish are extremely useful in identifying the role ofshank3mutations to composite social behaviour, they are unlikely to represent the full complexity of socio-cognitive and communication deficits presented by human ASD pathology. Moreover, zebrafish cannot represent the scaling up of these deficits to higher-order empathic and prosocial phenotypes seen in humans.ConclusionsWe demonstrate a causal link between the zebrafish orthologue of an ASD-associated gene and the attentional control of affect recognition and consequent social contagion. This models autistic affect-communication pathology in zebrafish and reveals a genetic attention-deficit mechanism, addressing the ongoing debate for such mechanisms accounting for emotion recognition difficulties in autistic individuals.
Interleukin-22 facilitates the interferon-λ-mediated production of tripartite motif protein 25 to inhibit replication of duck viral hepatitis A virus type 1
Authors: An Hao , Liu Yumei , Shu Ming , Chen Junhao 
Published: June 2023

AbstractThe innate immune system provides a defense against invading pathogens by inducing various interferon (IFN)-stimulated genes (ISGs). We recently reported that tripartite motif protein 25 (TRIM25), an important ISG, was highly upregulated in duck embryo hepatocyte cells (DEFs) after infection with duck viral hepatitis A virus type 1 (DHAV-1). However, the mechanism of upregulation of TRIM25 remains unknown. Here we reported that interleukin-22 (IL-22), whose expression was highly facilitated in DEFs and various organs of 1-day-old ducklings after DHAV-1 infection, highly enhanced the IFN-λ-induced production of TRIM25. The treatment with IL-22 neutralizing antibody or the overexpression of IL-22 highly suppressed or facilitated TRIM25 expression, respectively. The phosphorylation of signal transducer and activator of transcription 3 (STAT3) was crucial for the process of IL-22 enhancing IFN-λ-induced TRIM25 production, which was suppressed by WP1066, a novel inhibitor of STAT3 phosphorylation. The overexpression of TRIM25 in DEFs resulted in a high production of IFNs and reduced DHAV-1 replication, whereas the attenuated expression of IFNs and facilitated replication of DHAV-1 were observed in the RNAi group, implying that TRIM25 defended the organism against DHAV-1 propagation by inducing the production of IFNs. In summary, we reported that IL-22 activated the phosphorylation of STAT3 to enhance the IFN-λ-mediated TRIM25 expression and provide a defense against DHAV-1 by inducing IFN production.
Effect of e-health interventions on HIV prevention: a protocol of systematic review and meta-analysis
Authors: Wang Lei , Yan Xiang-yu , Mei Lin , Jia Zhong-wei , Hao Rui-gang , Xu Ji-hong , Zhang Bo 
Published: June 2023

Abstract
Background
Global epidemiological data indicates that despite implementation of multiple interventions and significant financial investment, the HIV/AIDS epidemic remained inadequately controlled as of 2020. E-health presents a novel approach in delivering health information and health care and has gained popularity in HIV prevention worldwide. However, evidence on the effectiveness of e-health interventions on HIV prevention among diverse populations remains inadequate. Our study aims to systematically evaluate the effectiveness of varying e-health interventions on HIV prevention, with the objective of providing data support and guidance for the development of future e-health HIV intervention strategies.

Methods
A systematic search of electronic English databases, including MEDLINE through PubMed, Embase, Scopus, and Web of Science, along with three Chinese databases, including National Knowledge Infrastructure (CNKI), Chinese Wanfang Digital Periodicals (WANFANG), and Chinese Science and Technology Periodicals (VIP) database, will be conducted for the period of 1 January 1980 to 31 December 2022. Additionally, gray literature and unpublished trials in trial registers will be searched. Studies aimed at HIV prevention through e-health interventions, with full-text publications available in either English or Chinese, will be included. Study types will be limited to RCT, cluster RCT, and quasi-experiment study. The risk of bias in individual studies will be assessed following the guideline highlighted by the Cochrane Handbook for Systematic Reviews of Interventions. The outcomes will cover cognitive, behavioral, psychological, management, and biological measures of individuals involved in e-health interventions. The quality of evidence will be assessed by the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach. Ultimately, a systematic review with meta-analysis will be conducted to compare the effectiveness of e-health interventions among diverse populations.

Discussion
This systematic review seeks to establish novel insights into the effectiveness of e-health interventions in diverse populations worldwide. It will inform the design and use of e-health interventions to optimize HIV-related strategies.

Systematic review registration
PROSPERO CRD42022295909.
Drug use patterns and related factors among female sex workers in Iran in 2019–2020: results from Integrated Bio-Behavioral Surveillance-III (IBBS-III)
Authors: Zareie Bushra , Rasouli Mohammad Aziz , Gouya Mohammad Mehdi , Akbarpour Samaneh , Hadavandsiri Fatemeh , Rezaei Elham , Moradi Yousef , Soltani Ali , Moradi Ghobad 
Published: June 2023

Abstract
Introduction
Drug use is highly prevalent among female sex workers (FSWs). Some forms of drug use, such as injecting drug users (IDU), put them at greater risks for HIV and blood born disease (BBD). In this study, the pattern of drug use and its related factors among Iranian FSWs were investigated.

Materials and methods
This cross-sectional study was performed based on the data of the integrated bio-behavioral surveillance-III (IBBS-III) on FSWs in 8 cities of Iran using the respondent-driven sampling (RDS) method conducting in 2019–2020. Of the 1515 FSWs participating in the IBBS-III study, 1,480 answered questions about drug use. To calculate the prevalence of drug use lifetime and in the past month, weighted analysis was used. Univariate and multivariate logistic regression was used to investigate the factors related to drug use.

Results
The prevalence of lifetime drug use and the prevalence of current drug use (single and poly drug use) among FSWs were estimated to be 29.3% and 18.86%, respectively. According to multivariate regression analysis, the odds ratio (odds) of lifetime drug use showed a statistically significant association with lower education (AOR = 1.18; 95% CI: 1.07–1.3), being a direct sex worker (AOR = 1.77; 95% CI: 1.21–2.61), working in team houses or hangouts (AOR = 1.51; 95% CI: 1.10–2.06), a history of intentional abortion (AOR = 1.41; 95% CI: 1.07–1.87), condom use in the last sex (AOR = 1.61; 95% CI: 1.19–2.17), a history of imprisonment (AOR = 3.05; 95% CI: 2.25–4.14), HIV positive tests (AOR = 8.24; 95% CI: 1.66–40.9), alcohol use (AOR = 1.69; 95% CI: 1.29–2.29), and finding sexual clients in places such as parties, shopping malls, streets, and hotels, or by friends (AOR = 1.46; 95% CI: 1.01–2.12).

Conclusion
Given that drug use among FSWs is about 14 times higher than that of the Iranian general population, it is imperative that drug reduction programs be integrated into service packages. Specifically, prevention programs should be prioritized for occasional drug users within this population as they are at a greater risk of developing drug use issues compared to the general population.
Second malignant tumors and non-tumor causes of death for patients with localized and regional kidney cancer after diagnosis
Authors: Yang Luchen , Wu Xiaotian , Zhou Jing , Song Pan , Liu Zhenghuan , Chen Junhao , Dong Qiang 
Published: June 2023

Abstract
Background
To evaluate the second malignant tumors (SMTs) and non-tumor causes of death among patients diagnosed with localized and regional kidney cancer.

Methods
Patients diagnosed with kidney cancer between 2000 and 2017 in the Surveillance, Epidemiology, and End Results (SEER) program database were identified. All causes of death for patients during the follow-up and standardized mortality ratio (SMR) were analyzed.

Result
113,734 patients with localized kidney cancer with 30,390 cases of death were analyzed. 60.4% of the death cases were due to non-tumor caused and 23.6% were second malignant tumors (SMTs). Main SMTs included cancers of lung and bronchus [n = 1,283, SMR: 1.00 (0.95–1.06)] and pancreas [n = 393, SMR: 1.27 (1.15–1.41)]. Causes of death for non-tumor mainly included heart diseases [n = 6,161, SMR: 1.25 (1.21–1.28)] and chronic obstructive pulmonary disease (COPD) [n = 1,185, SMR: 0.99 (0.94–1.05)]. 14,437 of 29,602 patients with regional kidney cancer died. 14.6% of all deaths were due to SMTs and 23.6% due to non-tumor causes. Main SMTs contained bladder cancer [n = 371, SMR: 10.90 (9.81–12.06)] and lung and bronchus cancer [n = 346, SMR: 1.21 (1.08–1.34)]. The main non-tumor death was heart disease [n = 1,424, SMR: 1.26 (1.2–1.33)]. When stratified by pathological types, patients with clear cell renal cell carcinoma (RCC) did not have increased mortality risks of bladder cancer and lung cancer but patients with non-clear cell RCC did.

Conclusion
SMTs and non-tumor diseases including lung and bronchus cancer, bladder cancer, pancreas cancer, diseases of heart, COPD, and cerebrovascular diseases are the leading causes of death besides kidney cancer and should be paid more attention during patients’ survival period.
Comparison of the cytokine adsorption ability in continuous renal replacement therapy using polyethyleneimine-coated polyacrylonitrile (AN69ST) or polymethylmethacrylate (PMMA) hemofilters: a pilot single-center open-label randomized control trial
Authors: Nakamura Yoshihiko , Hatomoto Hiroki , Yamasaki Shintaro , Yamauchi Kazuya , Kiyomi Fumiaki , Hoshino Kota , Kawano Yasumasa , Nakano Takafumi , Hasegawa Takehiro , Ishikura Hiroyasu 
Published: June 2023

Abstract
Background
Sepsis occurs as a result of dysregulated host response to infection. However, cytokine adsorption therapy may restore the balance of proinflammatory and anti-inflammatory mediator responses in patients with sepsis. This study aimed to determine the cytokine adsorption ability of two different types of continuous renal replacement therapy (CRRT) hemofilters for polyethyleneimine-coated polyacrylonitrile (AN69ST) (surface-treated) and polymethylmethacrylate (PMMA) CRRT.

Methods
We performed a randomized controlled trial among sepsis patients undergoing CRRT, who were randomly assigned (1:1) to receive either AN69ST or PMMA-CRRT. The primary outcome was cytokine clearance of hemofilter adsorption (CHA). The secondary endpoints were the intensive care unit (ICU) and 28-day mortalities.

Results
We randomly selected 52 patients. Primary outcome data were available for 26 patients each in the AN69ST-CRRT and PMMA-CRRT arms. The CHA of high-mobility group box 1, tumor necrosis factor, interleukin (IL)-8, monokine induced by interferon-γ, and macrophage inflammatory protein were significantly higher in the AN69ST-CRRT group than in the PMMA-CRRT group (P < 0.001, P < 0.01, P < 0.001, P < 0.001 and P < 0.001, respectively). In contrast, the CHA of IL-6 was significantly higher in the PMMA-CRRT group than in the AN69ST-CRRT group (P < 0.001). In addition, the 28-day mortality was not significantly different between the two groups (50% in AN69ST-CRRT vs. 30.8% in PMMA-CRRT, P = 0.26).

Conclusion
AN69ST and PMMA membranes have different cytokine CHA in patients with sepsis. Therefore, these two hemofilters may have to be used depending on the target cytokine.
Trial registration number: This study was registered in the University Hospital Medical Information Network on November 1, 2017 (Trial No: UMIN000029450, https://center6.umin.ac.jp).
Group dynamic assessment vs. computerized dynamic assessment: impacts on L2 listening development, L2 students’ perfectionism, foreign language anxiety, and intrinsic motivation
Authors: Ahmed Abdel-Al Ibrahim Khaled , Karimi Ali Reza , Abdelrasheed Nasser Said Gomaa , Shatalebi Vida 
Published: June 2023

AbstractDynamic assessment is heavily based on Vygotskian socio-cultural theory and in recent years researchers have shown interest in the theory as a way to facilitate learning. This study attempted to examine the comparative effect of group dynamic assessment (GDA) and computerized dynamic assessment (CDA) on listening development, L2 learners’ perfectionism, anxiety, and intrinsic motivation. To this end, 91 intermediate learners of English were selected based on convenience sampling and were divided into 3 groups: a GDA, a CDA, and a control group (CG). After implementing the treatment, the tests conducted and the data gathered. The results of one-way ANOVA showed that both GDA and CDA were facilitative of listening development with a large effect size (effect size = .516), and the difference between them was nonsignificant (p> 0.05). The results further showed that both GDA and CDA could ameliorate perfectionism with a moderate effect size (effect size = .332), decrease anxiety with a small effect size (.218), and increase intrinsic motivation among L2 learners with a small effect size (effect size = .228). The findings can have implications for language practitioners, and materials developers. The implications of the study are discussed.
Indications for zygomatic implants: a systematic review
Authors: Polido Waldemar D. , Machado-Fernandez Agustin , Lin Wei-Shao , Aghaloo Tara 
Published: June 2023

Abstract
Purpose
The purpose of this systematic review was to assess the evidence regarding the indications for placement of zygomatic implants to rehabilitate edentulous maxillae.

Material and methods
A focused question using the PIO format was developed, questioning “in patients in need of an implant-supported rehabilitation of the edentulous maxillae, what are the indications for the use of zygomatic implants’’. The primary information analyzed and collected was a clear description of the indication for the use of zygomatic implants.

Results
A total of 1266 records were identified through database searching. The full-text review was conducted for 117 papers, and 10 were selected to be included in this review. Zygomatic implant indications were extreme bone atrophy or deficiency secondary to different factors. The quad zygoma concept (two zygomatic implants bilaterally placed and splinted) was applied to 107 patients, the classic zygoma concept (one zygomatic implant bilaterally placed and splinted to standard anterior implants) was used in 88 patients, and the unilateral concept (one zygomatic implant on one side, splinted with one or more conventional implants) was employed in 14 patients.

Conclusions
The main indication for the use of zygomatic implants was considered extreme maxillary bone atrophy, resulting from many factors. The clear definition of what was considered “extreme bone atrophy” is not uniquely defined in each paper. Further studies are needed to develop clear indications for zygomatic implants.

Graphic Abstract
Mixed acinar-neuroendocrine carcinoma of the pancreas with positive for microsatellite instability: a case report and review of the literature
Authors: Yoshino Kenji , Kasai Yosuke , Kurosawa Manabu , Itami Atsushi , Takaori Kyoichi 
Published: June 2023

Abstract
Background
Mixed acinar-neuroendocrine carcinoma (MANEC) of the pancreas is a rare tumor. We report a case of successful surgical resection of expansively growing MANEC of the pancreas with microsatellite instability (MSI)-high.

Case presentation
The patient was an asymptomatic 65-year-old male. A computed tomography (CT) scan for a follow-up after treatment of pneumonia incidentally revealed a hypoenhancing 12-cm expansively growing tumor in the pancreatic body. An endoscopic ultrasound-guided fine-needle aspiration of the tumor suggested the diagnosis of MANEC. We performed distal pancreatectomy with combined resection of the spleen, left adrenal gland, transverse colon, small bowel, and stomach. The intraoperative findings showed that the tumor was capsular and was in contact with the SMA, SMV, and CA; however, obvious infiltration of these vessels was not observed..Pathological findings indicated MANEC with MSI-high. Among mismatch repair (MMR) gene proteins, PMS2 was lost and MLH1, MSH2, and MSH6 were retained. The tumor recurred 5 months after surgery. The patient was treated with gemcitabine plus nab-paclitaxel followed by pembrolizumab, which did not show objective response.

Discussion
This is the first report investigating MSI and MMR in MANEC. Standard chemotherapy has not been established for MANEC. Detection of MSI-high is essential since PD-1 monoclonal antibodies for MSI-high cases might be one of the good treatment options. Herein, we discuss the various cytomorphologic and clinical features of MANEC and present a brief review of the literatures.

Conclusions
The accumulation of data from additional cases is necessary to further evaluate this type of carcinoma and provide a standardized optimal therapy for MANEC.