bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conducting Health Research in Carceral Systems: Considerations and Recommendations
Authors: Neher Taylor L. , Udochi Aisha L. , Wilson Kayla A. , Guillory Devin M. , Zaller Nickolas D. , Zielinski Melissa J. 
Published: January 2020

Although the number of people incarcerated in the United States has grown dramatically, research on how incarceration affects individuals and the communities they return to has lagged behind. This may be because of the unique challenges of doing research within carceral systems and the relatively small number of investigators who are competent to undertake these efforts. We provide a primer for investigators with limited experience conducting research in carceral settings and highlight considerations and recommendations that may aid those conducting health research with incarcerated persons. We follow this with an illustrative case example exemplifying how the considerations apply to recent health research that our team conducted on mental illness prevalence in a large regional jail. Understanding how to effectively conduct research with criminal justice populations and systems is the first step in beginning to understand the effects of mass incarceration as a driver of health disparities and health inequity.
Negative Police Encounters and Police Avoidance as Pathways to Depressive Symptoms Among US Black Men, 2015–2016
Authors: Bowleg Lisa , Maria del Río-González Ana , Mbaba Mary , Boone Cheriko A. , Holt Sidney L. 
Published: January 2020

Objectives. To examine negative police encounters and police avoidance as mediators of incarceration history and depressive symptoms among US Black men and to assess the role of unemployment as a moderator of these associations. Methods. Data were derived from the quantitative phase of Menhood, a 2015–2016 study based in Washington, DC. Participants were 891 Black men, 18 to 44 years of age, who completed computer surveys. We used moderated mediation to test the study’s conceptual model. Results. The results showed significant indirect effects of incarceration history on depressive symptoms via negative police encounters and police avoidance. Unemployment moderated the indirect effect via police avoidance. Participants with a history of incarceration who were unemployed reported significantly higher police avoidance and, in turn, higher depressive symptoms. Moderation of unemployment on the indirect effect via negative police encounters was not significant. Conclusions. There is a critical need to broaden research on the health impact of mass incarceration to include other aspects of criminal justice involvement (e.g., negative police encounters and police avoidance) that negatively affect Black men’s mental health.
Plasma HER2ECD a promising test for patient prognosis and prediction of response in HER2 positive breast cancer: Results of a randomized study - SAKK 22/99.
Authors: Eppenberger-Castori Serenella , Klingbiel Dirk , Ruhstaller Thomas , Dietrich Daniel , Rufle Daniel Alexander , Rothgiesser Karin , Pagani Olivia , Thürlimann Beat 
Published: January 2020

Abstract
Background: The HER2 extracellular domain shed in blood (HER2ECD) is reported to rise and fall in parallel with HER2+ breast cancer behavior. In this study, we evaluated the clinical relevance of plasma HER2ECD values in patients with metastatic breast cancer treated in the SAKK22/99 trial comparing trastuzumab monotherapy followed by trastuzumab-chemotherapy combination at progression versus upfront combination therapy. Methods : Quantitative assessment of plasma HER2ECD was performed in 133 patients at baseline; after 2-24 hours; at 3 weeks; at first response evaluation (8-9 weeks); and at tumor progression. Associations with tumor characteristics, disease course and trial treatment were evaluated.Results: Baseline HER2ECD levels were stable within 24 hours after the first trastuzumab injection. These plasma values correlated positively with the HER2 gene ratio (rs=0.39, P<0.001) and HER2 protein expression levels (rs=0.36, P<0.001) but not with ER/PR status of the primary tumor. HER2ECD baseline levels were positively associated with the presence of visceral disease (P=0.05) and poor patients’ outcome (Cox-regression: P=0.009). Patients with high baseline levels (>35ng/ml) had the worst overall survival (P=0.03) if treated with upfront combination therapy. Conversely, patients with low HER2ECD baseline values (<15ng/ml) had longer time to progression on combined trastuzumab-chemotherapy when first treated with trastuzumab monotherapy (P=0.02). Monitoring HER2ECD levels during the course of the trial revealed significant time (P=0.001) and time-treatment arm interactions (P=0.0007). Under upfront trastuzumab alone, the HER2ECD levels remained stable until just before disease progression. In patients responding to combination treatment HER2ECD levels decreased to >20%. Conclusions: Plasma HER2ECD levels in patients with metastatic breast cancer reflect HER2 disease status. This robust biomarker might help identifying patients without visceral disease profiting from a sequential treatment’s modality. Monitoring HER2ECD levels during trastuzumab monotherapy could help defining the optimal time to introduce chemotherapy.
Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)
Authors: Wu Peipei , Cogill Steven , Qiu Yijian , Li Zhigang , Zhou Man , Hu Qian , Chang Zhihui , Noorai Rooksana E. , Xia Xiaoxia , Saski Christopher , Raymer Paul , Luo Hong 
Published: January 2020

Abstract
Background: Seashore paspalum (Paspalum vaginatum), a halophytic warm-seasoned perennial grass, is tolerant of many environmental stresses, especially salt stress. To investigate molecular mechanisms underlying salinity tolerance in seashore paspalum, physiological characteristics and global transcription profiles of highly (Supreme) and moderately (Parish) salinity-tolerant cultivars under normal and salt stressed conditions were analyzed.Results: Physiological characterization comparing highly (Supreme) and moderately (Parish) salinity-tolerant cultivars revealed that Supreme’s higher salinity tolerance is associated with higher Na+ and Ca2+ accumulation under normal conditions and further increase of Na+ under salt-treated conditions (400 mM NaCl), possibly by vacuolar sequestration. Moreover, K+ retention under salt treatment occurs in both cultivars, suggesting that it may be a conserved mechanism for prevention of Na+ toxicity. We sequenced the transcriptome of the two cultivars under both normal and salt-treated conditions (400 mM NaCl) using RNA-seq. De novo assembly of about 153 million high-quality reads and identification of Open Reading Frames (ORFs) uncovered a total of 82,608 non-redundant unigenes, of which 3,250 genes were identified as transcription factors (TFs). Gene Ontology (GO) annotation revealed the presence of genes involved in diverse cellular processes in seashore paspalum’s transcriptome. Differential expression analysis identified a total of 828 and 2,222 genes that are responsive to high salinity for Supreme and Parish, respectively. “Oxidation-reduction process” and “nucleic acid binding” are significantly enriched GOs among differentially expressed genes in both cultivars under salt treatment. Interestingly, compared to Parish, a number of salt stress induced transcription factors are enriched and show higher abundance in Supreme under normal conditions, possibly due to enhanced Ca2+ signaling transduction out of Na+ accumulation, which may be another contributor to Supreme’s higher salinity tolerance.Conclusion: Physiological and genomics analyses of seashore paspalum reveal major molecular underpinnings contributing to plant response to salt stress in this halophytic warm-seasoned perennial grass. The data obtained provide valuable molecular resources for functional studies and developing strategies to engineer plant salinity tolerance.
Feasibility and Evaluation of a Large-Scale External Validation Approach for Patient-Level Prediction in an International Data Network: Validation of models predicting stroke in female patients newly diagnosed with atrial fibrillation.
Authors: Reps Jenna Marie , Williams Ross , You Seng Chan , Falconer Thomas , Minty Evan , Callahan Alison , Ryan Patrick B , Park Rae Woong , Rijnbeek Peter 
Published: January 2020

Abstract
Objective: To demonstrate how the Observational Healthcare Data Science and Informatics (OHDSI) collaborative network and standardization can be utilized to scale-up external validation of patient-level prediction models by enabling validation across a large number of heterogeneous observational healthcare datasets.Materials & Methods: Five previously published prognostic models (ATRIA, CHADS2, CHADS2VASC, Q-Stroke and Framingham) that predict future risk of stroke in patients with atrial fibrillation were replicated using the OHDSI frameworks. A network study was run that enabled the five models to be externally validated across nine observational healthcare datasets spanning three countries and five independent sites. Results: The five existing models were able to be integrated into the OHDSI framework for patient-level prediction and they obtained mean c-statistics ranging between 0.57-0.63 across the 6 databases with sufficient data to predict stroke within 1 year of initial atrial fibrillation diagnosis for females with atrial fibrillation. This was comparable with existing validation studies. The validation network study was run across nine datasets within 60 days once the models were replicated. An R package for the study was published at https://github.com/OHDSI/StudyProtocolSandbox/tree/master/ExistingStrokeRiskExternalValidation.Discussion: This study demonstrates the ability to scale up external validation of patient-level prediction models using a collaboration of researchers and a data standardization that enable models to be readily shared across data sites. External validation is necessary to understand the transportability or reproducibility of a prediction model, but without collaborative approaches it can take three or more years for a model to be validated by one independent researcher. Conclusion : In this paper we show it is possible to both scale-up and speed-up external validation by showing how validation can be done across multiple databases in less than 2 months. We recommend that researchers developing new prediction models use the OHDSI network to externally validate their models.
Reliability and correlation of mixture cell correction in methylomic and transcriptomic blood data
Authors: Chaumette Boris , Kebir Oussama , Dion Patrick A. , Rouleau Guy A. , Krebs Marie-Odile 
Published: January 2020

Abstract
Objectives : The number of DNA methylome and RNA transcriptome studies is growing, but investigators have to consider the cell type composition of tissues used. In blood samples, the data reflect the picture of a mixture of different cells. Specialized algorithms can address the cell-type heterogeneity issue. We tested if these corrections are correlated between two heterogeneous datasets. Results : We used methylome and transcriptome datasets derived from a cohort of ten individuals whose blood was sampled at two different timepoints. We examined how the cell composition derived from these omics correlated with each other using “CIBERSORT” for the transcriptome and “EstimateCellCounts function” for the methylome. The correlation coefficients between the two omic datasets ranged from 0.45 to 0.81 but correlations were minimal between two different timepoints. Our results suggest that a posteriori correction of a mixture of cells present in blood samples is reliable. Using an omic dataset to correct a second dataset for relative fractions of cells appears to be applicable, but only when the samples are simultaneously collected. This could be beneficial when there are difficulties to control the cell types in the second dataset, even when the sample size is limited.
Disease characteristics and treatment patterns of Chinese patients with metastatic colorectal cancer: a retrospective study using medical records from China
Authors: Xu Ruihua , Wang Wei , Zhu Bo , Lin Xiaoyan , Ma Dong , Zhu Lingjun , Zhao Qingchuan , Nie Yongzhan , Cai Xiaohong , Li Qi , Fang Weijia , Li Hongyan , Wang Ning , Chen Yun , Peng Cike , Fang Honghao , Shen Lin 
Published: January 2020

Abstract
Background: Colorectal cancer (CRC) is the third most prevalent cancer in China but few large-scale studies were conducted to understand CRC patients. The current study is aimed to gain a real-world perspectives of CRC patients in China. Methods: Using electronic medical records of sampled patients between 2011 and 2016 from 12 hospitals in China, a retrospective cohort study was conducted to describe demographics and disease prognosis of CRC patients, and examine treatment sequences among metastatic CRC (mCRC) patients. Descriptive, comparative and survival analyses were conducted. Results: Among mCRC patients (3,878/8,136, 48%), the fluorouracil, leucovorin, and oxaliplatin (FOLFOX) and other oxaliplatin-based regimens were the most widely-used first-line treatment (42%). Fluorouracil, leucovorin, irinotecan (FOLFIRI) and other irinotecan-based regimens dominated the second-line (40%). There was no a dominated regimen for the third-line. The proportion of patients receiving chemotherapy with targeted biologics increased from less than 20% for the first- and second- lines to 34% for the third-line (p<0.001). The most common sequence from first- to second-line was from FOLFOX and other oxaliplatin-based regimens to FOLFIRI and other irinotecan-based regimens (286/1,200, 24%).Conclusions: Our findings reflected a lack of consensus on the choice of third-line therapy and limited available options in China. It is evident o continue promoting early CRC diagnosis and to increase the accessibility of treatment options for mCRC patients. As the only nationwide large-scale study among CRC and mCRC patients before more biologics became available in China, our results can also be used as the baseline to assess treatment pattern changes before and after more third-line treatment were approved and covered into the National Health Insurance Plan in China between 2017 - 2018.
Comparative analysis of retrograde intrarenal surgery and modified Ultra-mini percutaneous nephrolithotomy in management of lower pole renal stones (1.5-3.5 cm)
Authors: Li Zhuohang , Lai Cong , Shah Arvind K. , Xie Weibin , Liu Cheng , Huang Li , Li Kuiqing , Yu Hao , Xu Kewei 
Published: January 2020

Abstract

Background：To compare the safety and efficacy of retrograde intrarenal surgery (RIRS) and modified Ultra-mini percutaneous nephrolithotomy (UMP) in semi-supine combined lithotomy position for the management of 1.5-3.5 cm lower pole renal stones (LPSs). Methods: A total of 63 patients with 1.5-3.5 cm LPSs who underwent RIRS (n= 33) or modified UMP (n= 30) in diameter between January 2017 and January 2019 were analyzed retrospectively. Modified UMP was performed in semi-supine combined lithotomy position and a 9.5/11.5 F ureteral access sheath (UAS) was inserted during the procedure in order to maintain low pelvic pressure and to facilitate the removal of stone fragments. Base-line parameters, stone characteristics, illness condition, operation time, postoperative hemoglobin (Hb) drop, postoperative creatinine (Cr) elevation, length of hospital stay, length of postoperative hospital stay, stone-free rate (SFR) and complications were compared between the two groups. Results: There were no significant differences between the two groups in base-line parameters, stone characteristics and illness condition. The mean operating time of RIRS group was longer than UMP group (95.61 ± 21.9 vs. 55.0 ± 16.1 min, p< 0.001). The mean postoperative Hb drop was less in RIRS group (7.42 ± 4.7 vs. 15.70 ± 9.8 g/L, p< 0.001). The length of hospital stay and postoperative hospital stay for RIRS were shorter than UMP (4.76 ± 1.1 vs. 5.83 ± 0.8 d, p< 0.001, 2.97 ± 0.9 vs. 4.07 ± 0.9 d, p< 0.001). The Early SFR was higher in UMP group (54.5 vs. 80.0%, p< 0.050) while SFR at 1-month and 3-months postoperatively was similar in both groups (p= 0.504, p= 0.675). There were no significant differences between the two groups in complications (p= 0.228). Conclusion：For patients with 1.5-3.5 cm LPSs, both modified UMP and RIRS are safe and viable. The modified UMP technique was used in this study, application semi-supine combined lithotomy position and the retention of UAS can improve the surgical efficiency and maintain low pressure perfusion in the kidney, which resulted in superior treatment efficacy. Therefore, we highly recommend this technique for LPSs with heavy stone burdens.
Reactivity and reproducibility of accelerometer-based sedentary behavior and physical activity in two measurement periods: Results of a feasibility randomized-controlled study
Authors: Ullrich Antje , Baumann Sophie , Voigt Lisa , John Ulrich , Ulbricht Sabina 
Published: January 2020

Abstract

Background: The aims of the study were to investigate measurement reactivity in sedentary behavior (SB), physical activity (PA), and accelerometer wear time in two measurement periods, to examine the reproducibility of these outcomes and to quantify measurement reactivity as a confounder for the reproducibility of SB and PA data.Methods: A total of 136 participants (65% women, mean age = 54.6 years, study period 02/2015 to 08/2016) received 7-day accelerometry at baseline and after 12 months. Latent growth models were used to identify measurement reactivity in each period. Intraclass correlations (ICC) were calculated to examine the reproducibility using two-level mixed-effects linear regression analyses. Results: At both measurement periods, participants increased time spent in SB (b=2.4 min/d; b=3.8 min/d), reduced time spent in light PA (b=2.0 min/day; b=3.2 min/d), but did not change moderate-to-vigorous PA. Participants reduced accelerometer wear time (b=5.2 min/d) only at baseline. The ICC coefficients ranged from 0.42 (95% CI=0.32-0.53) for accelerometer wear time to 0.74 (95% CI=0.68-0.79) for SB. In none of the regression models, a reactivity indicator was identified as a confounder for the reproducibility of SB and PA data.Conclusions: The results show that measurement reactivity differentially influences SB and PA in two measurement periods. Although 7-day accelerometry seems to be a reproducible measure of SB and PA, our findings highlight the importance of accelerometer wear time as a crucial confounder when using accelerometry in monitoring SB and PA, planning interventions, and analyzing SB and PA data.Clinical trial registration number: NCT02990039 (retrospectively registered); December 12, 2016
Library preparation and MiSeq sequencing for the genotyping-by-sequencing of the Huntington disease HTT exon one trinucleotide repeat and the quantification of somatic mosaicism
Authors: Ciosi Marc , Cumming Sarah A. , Alshammari Asma M. , Symeonidi Efthymia , Herzyk Pawel , McGuinness David , Galbraith Julie , Hamilton Graham , Monckton Darren G. 
Published: January 2020

Abstract

Huntington disease \(HD) is an autosomal dominant neurodegenerative disorder caused by the expansion of a CAG repeat in the first exon of the _HTT_ gene. Affected individuals inherit more than 40 repeats and the CAG repeat is genetically unstable in both the germline and soma. Molecular diagnosis and genotyping of the CAG repeat is traditionally performed by estimation of PCR fragment size. However, this approach is complicated by the presence of an adjacent polymorphic CCG repeat and provides no information on the presence of variant repeats, flanking sequence variants or on the degree of somatic mosaicism. To overcome these limitations, we have developed an amplicon-sequencing protocol that allows the sequencing of hundreds of samples in a single MiSeq run. The composition of the _HTT_ exon one trinucleotide repeat locus can be determined from the MiSeq sequencing reads generated. With sufficient sequencing depth, such MiSeq data can also be used to quantify the degree of somatic mosaicism of the _HTT_ CAG repeat in the tissue analysed.
Dilation of the Cystic Duct Confluence in Laparoscopic Common Bile Duct Exploration and stone extraction for Patients with Secondary Choledocholithiasis
Authors: Yang Xiao-Bin , Xu An-Shu , Li Jian-Gang , Xu Yong-Ping , Xu De-Song , Fu Chao-Chun , Deng Da-Bo , Li Jie , Zhang Ma-Zhong 
Published: January 2020

Abstract
Objectives: Many options exist in the management of cholelithiasis and secondary choledocholithiasis. Among them, laparoscopic common bile duct exploration (LCBDE) with the choledocotomy followed by laparoscopic cholecystectomy has gained popularity. However, efforts should be made for minimally invasive or non-invasive to the common bile duct (CBD). For this purpose, we modified the surgical modality of laparoscopic transcystic approach by dilating the cystic duct confluence in CBD exploration (LTD-CBDE). Based on our preliminary experience, the aim of this work was to assess the feasibility, safety and effectivity of LTD-CBDE.Patients and methods: Sixty-eight patients were arbitrarily offered new LTD-CBDE technique from December 2015 to April 2018. During the surgery, we dilated the cystic duct confluence with separation forceps and/or the columnar dilation balloon. Subsequently, the CBD exploration and stone extraction were performed with choledochoscope. The entrance of CBD was covered with cystic duct stump wall and primarily closed at the end of surgery.Results: 49 females and 19 males with cholelithiasis and secondary choledocholithiasis were included. The mean age was 53 years old (18 to 72 yr). Of which, 62 cases (91.2%) were performed with LTD-CBDE techniques successfully, bile leakage was observed in 3 cases (4.4%). The mean operation time was 106 minutes and the mean hospital stay was 5.9 days. As for the other 6 patients, 3 cases were converted to open cholecystectomy due to severe fibrosis, unclear anatomical structure at the Calot’s triangle (n=2) and Mirizze syndrome (n=1); LCBDE were performed in 3 patients due to cystic duct atresia (n=2) and low level of the gallbladder duct into CBD (n=1). These patients had smooth postoperative course. None of the patients presented radiological evidence of retained CBD stone on the postoperative follow-up in 43/68 (40 cases used LTD-CBDE) patients one year later.Conclusion: The current work suggests that LTD-CBDE for the management of cholelithiasis and secondary choledocholithiasis is a feasible, safe and effective technique with a low rate of complications. It offers another alternative for surgeons to treat patients in similar scenarios. However, additional randomized, controlled study is further needed to demonstrate its efficacy, safety, and impact on CBD stenosis.