bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promoting a gender-affirming environment in research: implications for research nurses
Authors: Thangthaeng Nopporn , Hillard Mallory A , Cayford Melody , Barrett Sophia , Ducar Dallas , Larkin Mary E 
Published: April 2022

Background: Approximately 25 million people around the world identify as transgender, and the numbers are growing. While visibility of transgender communities has increased, significant healthcare disparities remain. Transgender individuals report being less inclined to share their sex assigned at birth due to fear of stigmatization and mistrust of the medical community. The mistrust and inequity experienced by transgender individuals are not limited to clinical care and may extend to clinical research as well. Aim and method: The aim of this paper is to start a conversation about barriers to participating in research and the role of research staff, specifically the Clinical Research Nurse, in promoting engagement of transgender individuals in clinical research trials. Discussion and conclusions: A discussion of safety considerations, data integrity, and implications for data management is included. Because disparities may result in large part from lack of education and knowledge on best practices for providing care for this population, recommendations for fostering a culture of competence and gender-affirming care among research professionals featuring the role of the research nurse will be discussed.
Insulin Titration Guidelines for Patients With Type 1 Diabetes: It Is About Time!
Authors: Walsh John , Roberts Ruth , Bailey Timothy S. , Heinemann Lutz 
Published: April 2022

Purpose: A proposal that an Insulin Advisory Committee develop insulin titration guidelines 100 years after its discovery. Findings: Glucose control metrics remain poor despite significant advances in diabetes technology. Summary: A century after the introduction of insulin, health care providers and patients with type 1 diabetes have worldwide access to a variety of insulin delivery devices (IDDs), glucose monitors, bolus calculators (BCs), continuous glucose monitors (CGMs), and automated insulin delivery (AID) systems. However, these advances have not enabled most patients to achieve today’s clear A1c and time-in-range goals. Much of this failure arises from the lack of clear insulin titration guidelines for determining appropriate insulin doses. The lack of dosing clarity results in local physicians, clinics, and individual patients managing insulin titrations as they see fit, creating significant inefficiencies for reaching recommended glycemic goals. This review (1) details the widespread problems generated by nonphysiological dose settings in today’s BCs, insulin pumps, and AID systems; (2) presents a method to develop and implement optimized total daily doses of insulin to correct the most common problem of hyperglycemia; (3) discusses using large device databases to provide clear insulin titration guidelines that optimize BC settings from an optimized total daily dose (TDD) of insulin for patients with T1D; and (4) recommends the formation of an Insulin Advisory Committee to clarify the steps to take toward universal insulin titration guidelines, optimized BC settings, and a systematic logic for their use in insulin delivery devices.
‘More collaborative and open’: As systemic psychotherapists become more familiar with videoconferencing, are the advantages of the medium becoming more apparent? A focus group study with UK systemic practitioners
Authors: Burbach Frank R. , Stiles Katie M. , Brown Katherine , Allen Victoria M. E. , Mc Kenny Richard 
Published: April 2022

Three semi-structured online focus group interviews were conducted with 17 systemic psychotherapists in the UK 1 year after the transition to videoconferencing therapy (or ‘teletherapy’) prompted by the COVID-19 pandemic. Thematic analysis identified 23 themes within 10 superordinate themes including Advantages of working online; Changes to the therapeutic relationship; Comparison to in-person therapy; Using therapeutic techniques online; Disadvantages of working online; Adapting to the affordances and constraints of technology. Whilst experiences were mildly positive overall, participants responded with almost twice as many positive comments as negative ones and described themselves as likely to continue working online. This study explores the advantages of online delivery which were described in the focus groups and posits that these digital affordances will lead to the development of more collaborative and invitational approaches.
Genome Editing Technology and Its Application to Metabolic Engineering in Rice
Authors: Sukegawa Satoru , Toki Seiichi , Saika Hiroaki 
Published: April 2022

AbstractGenome editing technology can be used for gene engineering in many organisms. A target metabolite can be fortified by the knockout and modification of target genes encoding enzymes involved in catabolic and biosynthesis pathways, respectively, via genome editing technology. Genome editing is also applied to genes encoding proteins other than enzymes, such as chaperones and transporters. There are many reports of such metabolic engineering using genome editing technology in rice. Genome editing is used not only for site-directed mutagenesis such as the substitution of a single base in a target gene but also for random mutagenesis at a targeted region. The latter enables the creation of novel genetic alleles in a target gene. Recently, genome editing technology has been applied to random mutagenesis in a targeted gene and its promoter region in rice, enabling the screening of plants with a desirable trait from these mutants. Moreover, the expression level of a target gene can be artificially regulated by a combination of genome editing tools such as catalytically inactivated Cas protein with transcription activator or repressor. This approach could be useful for metabolic engineering, although expression cassettes for inactivated Cas fused to a transcriptional activator or repressor should be stably transformed into the rice genome. Thus, the rapid development of genome editing technology has been expanding the scope of molecular breeding including metabolic engineering. In this paper, we review the current status of genome editing technology and its application to metabolic engineering in rice.
Supervised promoter recognition: a benchmark framework
Authors: Perez Martell Raul I. , Ziesel Alison , Jabbari Hosna , Stege Ulrike 
Published: April 2022

Abstract
Motivation
Deep learning has become a prevalent method in identifying genomic regulatory sequences such as promoters. In a number of recent papers, the performance of deep learning models has continually been reported as an improvement over alternatives for sequence-based promoter recognition. However, the performance improvements in these models do not account for the different datasets that models are evaluated on. The lack of a consensus dataset and procedure for benchmarking purposes has made the comparison of each model’s true performance difficult to assess.

Results
We present a framework called Supervised Promoter Recognition Framework (‘SUPR REF’) capable of streamlining the complete process of training, validating, testing, and comparing promoter recognition models in a systematic manner. SUPR REF includes the creation of biologically relevant benchmark datasets to be used in the evaluation process of deep learning promoter recognition models. We showcase this framework by comparing the models’ performances on alternative datasets, and properly evaluate previously published models on new benchmark datasets. Our results show that the reliability of deep learning ab initio promoter recognition models on eukaryotic genomic sequences is still not at a sufficient level, as overall performance is still low. These results originate from a subset of promoters, the well-known RNA Polymerase II core promoters. Furthermore, given the observational nature of these data, cross-validation results from small promoter datasets need to be interpreted with caution.
Predict the role of lncRNA in kidney aging based on RNA sequencing
Authors: Li Jie , Gao Fanfan , Wei Limin , Chen Lei , Qu Ning , Zeng Lu , Luo Yulong , Huang Xinmei , Jiang Hongli 
Published: April 2022

Abstract
Background
Long noncoding RNAs (lncRNAs) are involved in physiological and pathological processes. However, no studies have been conducted on the relationship between lncRNAs and renal aging.

Results
First, we evaluated the histopathology of young (3-month-old) and old (24-month-old) C57BL/6J mouse kidneys. Masson trichrome staining and PAS staining showed interstitial collagen deposition and fibrosis, mesangial matrix expansion, a thicker basement membrane and renal interstitial fibrosis in old mouse kidneys. Senescence-associated β-galactosidase (SA-β-gal)-positive areas in the kidneys of old mice were significantly elevated compared to those of young mice. Then, we analyzed the differential expression of lncRNAs and mRNAs in the kidneys of young and old mouse kidneys by RNA-seq analysis. 42 known and 179 novel differentially expressed lncRNAs and 702 differential mRNAs were detected in the mouse kidney. Next, we focused on the differentially expressed mRNAs and lncRNAs by RNA-seq. GO and KEGG analyses were performed based on differentially expressed mRNAs between young and old mouse kidneys. Transregulation based on RIsearch and the correlation coefficient of mRNA-lncRNA were also calculated. The mRNA-lncRNA network was constructed by choosing a Spearman correlation coefficient > 0.9 or <-0.9. GO and KEGG pathway enrichment analyses revealed that differentially expressed mRNAs participated in aging-related pathways. A total of 10 lncRNAs and trans-regulated mRNAs were constructed. Finally, we validated the role of lncRNA Gm43360 by CCK-8, flow cytometry, western blot and SA-β-gal staining. The expression level of Adra1a was positively correlated and Csnk1a1 was negatively correlated with lncRNA Gm43360. The cell counting kit-8 (CCK-8) results showed that lncRNA Gm43360 promoted cell viability. LncRNA Gm43360 increased the percentage of S phase cells and decreased the percentage of G1 phase cells compared with the negative control. LncRNA Gm43360 decreased the expression of p53, p21 and SA-β-gal.

Conclusions
LncRNA Gm43360 may play a protective role in kidney aging.
Phylogenetic position of Bopyroides hippolytes, with comments on the rearrangement of the mitochondrial genome in isopods (Isopoda: Epicaridea: Bopyridae)
Authors: Wu Ruiwen , Guo Rongxiu , Xi Qianqian , Paulay Gustav , An Jianmei 
Published: April 2022

Abstract
Background
Classification of parasitic bopyrids has traditionally been based on morphological characteristics, but phylogenetic relationships have remained elusive due to limited information provided by morphological data and tendency for loss of morphological features as a result of parasitic lifestyle. Subfamily Argeiinae was separated from Bopyrinae based on morphological evidence, although the assignment of all genera has not been phylogenetically evaluated. Bopyroides hippolytes has been traditionally classified in Bopyrinae, but divergent morphological characters make this assignment questionable. To investigate the relationship of bopyrines, we sequenced the complete mitochondrial genome of B. hippolytes and four mitochondrial genes of two other Bopyrinae.

Results
The phylogenetic trees based on separate and combined cox1and 18S sequence data recovered Bopyridae as robustly monophyletic, but Bopyrinae as polyphyletic. Bopyroides hippolytes was a close sister to Argeia pugettensis, type species to Argeiinae. Mitochondrial phylogenomics also suggested that B. hippolytes was close to Argeiinae. We also found a novel gene order in B. hippolytes compared to other isopods.

Conclusions
Bopyroides hippolytes should be excluded from the Bopyrinae and has a close affinity with Argeia pugettensis based on molecular and morphological data. The conserved syntenic blocks of mitochondrial gene order have distinctive characteristics at a subordinal level and may be helpful for understanding the higher taxonomic level relationships of Isopoda.
Response of soil microbial community structure and function to different altitudes in arid valley in Panzhihua, China
Authors: Zhang Runji , Tian Xianrui , Xiang Quanju , Penttinen Petri , Gu Yunfu 
Published: April 2022

Abstract
Background
Altitude affects biodiversity and physic-chemical properties of soil, providing natural sites for studying species distribution and the response of biota to environmental changes. We sampled soil at three altitudes in an arid valley, determined the physic-chemical characteristics and microbial community composition in the soils, identified differentially abundant taxa and the relationships between community composition and environmental factors.

Results
The low, medium and high altitudes were roughly separated based on the physic-chemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents. The contents of organic and microbial biomass C, total and available N and available P, and the richness and diversity of the microbial communities were lowest in the medium altitude. The relative abundances of phyla Proteobacteria, Gemmatimonadetes, Actinobacteria and Acidobacteria were high at all altitudes. The differentially abundant amplified sequence variants (ASVs) were mostly assigned to Proteobacteria and Acidobacteria. The highest number of ASVs characterizing altitude were detected in the high altitude. However, the predicted functions of the communities were overlapping, suggesting that the contribution of the communities to soil processes changed relatively little along the altitude gradient.

Conclusions
The low, medium and high altitudes were roughly separated based on the physicochemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents.
Electrocardiographic patterns predict the presence of collateral circulation and in-hospital mortality in acute total left main occlusion
Authors: Liu Chunwei , Yang Fan , Zhang Jingxia , Hu Yuecheng , Xiao Jianyong , Gao Mingdong , Wang Le , Li Ximing , Guo Zhigang , Cong Hongliang , Liu Yin 
Published: April 2022

AbstractBackgroundData on the clinical characteristics, electrocardiogram (ECG) findings and outcomes of patients with acute myocardial infarction (AMI) due to total unprotected left main (ULM) artery occlusion is limited.MethodsBetween 2009 and 2021, 44 patients with AMI due to total ULM occlusion underwent primary percutaneous coronary intervention (PCI) at our institution. The ECG, collateral circulation, clinical and procedural characteristics, and in-hospital mortality were retrospectively evaluated.ResultsTwenty five patients presented with shock and 18 patients had in-hospital mortality. Nineteen patients presented with ST-segment elevation myocardial infarction (STEMI), while 25 presented with non-ST-segment elevation myocardial infarction (NSTEMI). ST-segment elevation (STE) in I and STEMI were associated with the absence of collateral circulation, while STE in aVR was associated with its presence. In the NSTEMI group, patients with STE in both aVR and aVL showed more collateral filling of the left anterior descending coronary artery (LAD) territory, while patients with STE in aVR showed more collateral filling of the LAD and the left circumflex artery territory. Compared with total ULM occlusion, patients with partial ULM obstruction presented with more STE in aVR, less STE in aVR and aVL, and less STEMI. Shock, post-PCI TIMI 0–2 flow, non-STE in aVR, STEMI, and STE in I predicted in-hospital mortality. STEMI and the absence of collateral flow were significantly associated with shock.ConclusionsSTE in the precordial leads predicted the absence of collateral circulation while STE in aVR and STE in both aVR and aVL predicted different collateral filling territories in ULM occlusion. STE in I, non-STE in aVR, and STEMI predicted in-hospital mortality in these patients.
Multiparametric CMR imaging of myocardial structure and function changes in diabetic mini-pigs with preserved LV function: a preliminary study
Authors: Shao Guozhu , Cao Yukun , Cui Yue , Han Xiaoyu , Liu Jia , Li Yumin , Li Na , Shi Heshui 
Published: April 2022

Abstract
Background
The purpose of this study is to dynamically monitor the myocardial structure and function changes in diabetic mini-pigs by 1.5 T cardiac magnetic resonance.

Methods
Three male mini-pigs underwent cardiac magnet resonance (CMR) imaging, and histologic examination. T1-mapping was acquired at basal, mid and apical segments. CMR feature-tracking (CMR-FT) is used to quantify left ventricle global longitudinal (LVGLS), circumferential (LVGCS) and radial strain (LVGRS). Epicardial adipose tissue (EAT) was evaluated using a commercially available software.

Results
Left ventricular mass (LVM), myocardial native T1 value, extracellular volume (ECV) value and EAT were increased gradually after 6 months of modeling, while LVGLS decreased gradually after 6 months of modeling (LVM: 24.5 (23.4, 26.7) vs. 42.7 (41.4, 44.6) g/m2, p < 0.001; Native T1: 1005.5 (992.6, 1010.7) vs. 1028.7 (1015.5, 1035.6) ms, p = 0.041; EAT: 16.1 (14.5, 18.2) vs. 24.6 (20.8, 26.9) mL, p = 0.020; ECV: 21.4 (20.2, 23.9) vs. 28.9 (26.7, 30.3) %, p = 0.011; LVGLS: − 22.8 (− 21.4, − 23.9) vs. − 17.4 (− 17.2, − 19.2)%, p = 0.008). The diffuse myocardial interstitial fibrosis was found in histology samples.

Conclusion
The progressive impairments in LV structure and myocardial deformation occurs in diabetic mini-pigs. T1 mapping and CMR-FT technology are promising to monitor abnormal changes of diabetic myocardium in the early stage of diabetic cardiomyopathy.
Comparing single and multiple imputation strategies for harmonizing substance use data across HIV-related cohort studies
Authors: Javanbakht Marjan , Lin Johnny , Ragsdale Amy , Kim Soyeon , Siminski Suzanne , Gorbach Pamina 
Published: April 2022

Abstract
Background
Although standardized measures to assess substance use are available, most studies use variations of these measures making it challenging to harmonize data across studies. The aim of this study was to evaluate the performance of different strategies to impute missing substance use data that may result as part of data harmonization procedures.

Methods
We used self-reported substance use data collected between August 2014 and June 2019 from 528 participants with 2,389 study visits in a cohort study of substance use and HIV. We selected a low (heroin), medium (methamphetamine), and high (cannabis) prevalence drug and set 10–50% of each substance to missing. The data amputation mimicked missingness that results from harmonization of disparate measures. We conducted Monte Carlo simulations to evaluate the comparative performance of single and multiple imputation (MI) methods using the relative mean bias, root mean square error (RMSE), and coverage probability of the 95% confidence interval for each imputed estimate.

Results
Without imputation (i.e., listwise deletion), estimates of substance use were biased, especially for low prevalence outcomes such as heroin. For instance, even when 10% of data were missing, the complete case analysis underestimated the prevalence of heroin by 33%. MI, even with as few as five imputations produced the least biased estimates, however, for a high prevalence outcome such as cannabis with low to moderate missingness, performance of single imputation strategies improved. For instance, in the case of cannabis, with 10% missingness, single imputation with regression performed just as well as multiple imputation resulting in minimal bias (relative mean bias of 0.06% and 0.07% respectively) and comparable performance (RMSE = 0.0102 for both and coverage of 95.8% and 96.2% respectively).

Conclusion
Our results from imputation of missing substance use data resulting from data harmonization indicate that MI provided the best performance across a range of conditions. Additionally, single imputation for substance use data performed comparably under scenarios where the prevalence of the outcome was high and missingness was low. These findings provide a practical application for the evaluation of several imputation strategies and helps to address missing data problem when combining data from individual studies.
|tPRiors |: a tool for prior elicitation and obtaining posterior distributions of true disease prevalence
Authors: Pateras Konstantinos , Kostoulas Polychronis 
Published: April 2022

Abstract
Background
Tests have false positive or false negative results, which, if not properly accounted for, may provide misleading apparent prevalence estimates based on the observed rate of positive tests and not the true disease prevalence estimates. Methods to estimate the true prevalence of disease, adjusting for the sensitivity and the specificity of the diagnostic tests are available and can be applied, though, such procedures can be cumbersome to researchers with or without a solid statistical background. This manuscript introduces a web-based application that integrates statistical methods for Bayesian inference of true disease prevalence based on prior elicitation for the accuracy of the diagnostic tests. This tool allows practitioners to simultaneously analyse and visualize results while using interactive sliders and output prior/posterior plots.

Methods - implementation
Three methods for prevalence prior elicitation and four core families of Bayesian methods have been combined and incorporated in this web tool. |tPRiors| user interface has been developed with R and Shiny and may be freely accessed on-line.

Results
|tPRiors| allows researchers to use preloaded data or upload their own datasets and perform analysis on either single or multiple population groups clusters, allowing, if needed, for excess zero prevalence. The final report is exported in raw parts either as.rdata or.png files and can be further analysed. We utilize a real multiple-population and a toy single-population dataset to demonstrate the robustness and capabilities of |tPRiors|.

Conclusions
We expect |tPRiors| to be helpful for researchers interested in true disease prevalence estimation and who are keen on accounting for prior information. |tPRiors| acts both as a statistical tool and a simplified step-by-step statistical framework that facilitates the use of complex Bayesian methods. The application of |tPRiors| is expected to aid standardization of practices in the field of Bayesian modelling on subject and multiple group-based true prevalence estimation.