tbuckley/cabot-search huggingface dataset:
Psychology's Replication Crisis and Clinical Psychological Science
Authors: Jennifer L. Tackett, Cassandra M. Brandes, Kevin M. King, Kristian E. Markon
Journal: Annual Review of Clinical Psychology (2019)

Despite psychological scientists’ increasing interest in replicability, open science, research transparency, and the improvement of methods and practices, the clinical psychology community has been slow to engage. This has been shifting more recently, and with this review, we hope to facilitate this emerging dialogue. We begin by examining some potential areas of weakness in clinical psychology in terms of methods, practices, and evidentiary base. We then discuss a select overview of solutions, tools, and current concerns of the reform movement from a clinical psychological science perspective. We examine areas of clinical science expertise (e.g., implementation science) that should be leveraged to inform open science and reform efforts. Finally, we reiterate the call to clinical psychologists to increase their efforts toward reform that can further improve the credibility of clinical psychological science.
Perioperative Therapy in Renal Cell Carcinoma: What Do We Know, What Have We Learned, What's Next?
Authors: Naomi B. Haas, Robert G. Uzzo
Journal: Journal of Clinical Oncology (2018)

Recent adjuvant vascular endothelial growth factor tyrosine kinase inhibitor trials in resected high-risk renal cell carcinoma that compared sunitinib, sorafenib, pazopanib, and axitinib with placebo controls have demonstrated mixed impact on disease-free survival, no improvement in overall survival, and, thus, controversy. Here, we discuss the results and conduct of these trials to provide new insight into the goals and strategies of treating resected renal cell cancer that is at high risk for recurrence. The potential for leveraging what we have learned from these trials to conduct successful contemporary adjuvant and perioperative immune checkpoint inhibition trials and future adjuvant trial design is discussed.
Surgery in Cervical Cancer
Authors: Amanda N. Fader
Journal: New England Journal of Medicine (2018)

Cervical cancer is the fourth most frequently diagnosed cancer and the fourth leading cause of cancer-related death in women worldwide.1 For early-stage disease, surgical removal of the uterus remains the primary treatment and has the greatest effect on long-term survival. However, abdominal ("open") radical hysterectomy is associated with complications, including a risk of lymphedema in the legs and bladder and sexual dysfunction.2 Recently, a greater emphasis on reducing surgical morbidity has led to the development of minimally invasive techniques. Despite a paucity of randomized trials, retrospective data suggesting superior surgical and similar oncologic results led to widespread acceptance of minimally . . .
Letter to Editor: Using Proper Methods to Identify Patients With Cirrhosis in Administrative Databases Is Crucial to Correctly Predict Outcomes
Authors: Abdel Aziz Shaheen, Mark G. Swain
Journal: Hepatology (2018)

Potential conflict of interest: Dr. Swain advises and received grants from Gilead, Intercept, Allergan, and Novartis. He is on the speakers' bureau for Abbott. He received grants from CymaBay, GSK, and Genkyotex. To the Editor: We would like to congratulate Mumtaz et al.1 for their important study attempting to develop and validate a risk score to predict 30‐day hospital readmission in patients with decompensated cirrhosis using the US nationwide readmission database (NRD). Identifying patients with cirrhosis at high risk for readmission is critical for developing processes to effectively address this problem. However, flaws in patient identification challenge the utility of the risk score outlined in this study. Specifically, the authors failed to discuss their observed high readmission rates in the context of published data from the large multistate study by Tapper et al.2 The NRD consists of patient data from multiple state inpatient databases (SID). Tapper et al. used SID data from five large geographically diverse states to describe 12.9% to 24.2% 30‐day readmission rates in patients with 1‐3 cirrhosis decompensation features, respectively. In contrast, Mumtaz et al. report a baseline 30‐day readmission rate of 27%—an unexpected significant difference in readmission rates, given that the NRD is based on SID. This variation could be due to the case definition of decompensated cirrhosis. Specifically, the authors defined decompensated cirrhosis as the presence of cirrhosis plus any of the following: ascites, hepatic encephalopathy, variceal bleeding, or spontaneous bacterial peritonitis. However, in reviewing their coding, the International Classification of Disease Ninth Edition (ICD‐9) clinical modification codes 348.30, 348.39, and 780.97 were included, which describe general encephalopathy or altered mental status. The authors cite two studies to support the use of these codes. However, no study has in fact validated these codes in patients with cirrhosis. Similarly, the authors used nonvalidated codes for coagulopathy. There are important studies describing the validity of ICD‐9 codes to identify patients with cirrhosis.3 The use of well‐validated codes to identify patients with cirrhosis in administrative databases is critical for accuracy of conclusions made from using the data. We re‐extracted the cohort of patients with cirrhosis from the NRD 2013 (n = 14,325,172) using the authors' codes and methodology (cirrhosis plus at least one decompensation condition) and identified 107,317 patients with decompensated cirrhosis, compared with 175,761 patients used for the authors' analysis. Therefore, it is very likely that other nonvalidated decompensation features such as coagulopathy were included in their case definition. An additional concern is the inclusion of patients with cirrhosis who were readmitted for non‐cirrhosis‐related conditions, such as epilepsy or pneumonia, which would increase readmission rates.
Two novel reassortant high pathogenic H7N9 viruses isolated in Southern China in fifth wave shows internal genomic diversity and high virulence in chickens and ducks
Authors: Lihong He, Dong Liu, Jiao Hu, Lei Shi, Jiao Liu, Tianyu Cai, Liwei Shi, Han Gu, Jiangyan Zhao, Xiaoquan Wang, Min Gu, Shunlin Hu, Xiaowen Liu, Zenglei Hu, Xiufan Liu
Journal: Journal of Infection (2018)
Reconstructing the Human Renal Vascular–Tubular Unit In Vitro
Authors: Samuel G. Rayner, Kiet T. Phong, Jun Xue, Daniel Lih, Stuart J. Shankland, Edward J. Kelly, Jonathan Himmelfarb, Ying Zheng
Journal: Advanced Healthcare Materials (2018)

Abstract Engineered human kidney‐on‐a‐chip platforms show tremendous promise for disease modeling and drug screening. Outstanding challenges exist, however, in reconstructing the complex architecture, cellular make‐up, and matrix composition necessary for the proper modeling of kidney function. Herein, the first fully tunable human kidney‐on‐a‐chip platform is reported that allows the reconstruction of the native architecture of the renal endothelial–epithelial exchange interface using entirely cell‐remodelable matrix and patient‐derived kidney cells. This platform consists of a double‐layer human renal vascular–tubular unit (hRVTU) enabled by a thin collagen membrane that replicates the kidney exchange interface. It is shown that endothelial and epithelial cells lining their respective lumens remodel the membrane in culture into a ≈1 µm thick exchange interface composed of native basement membrane proteins. This interface displays sufficient mechanical integrity for media flow and blood perfusion. As a proof of principle, it is demonstrated that the hRVTU performs kidney‐specific functions including reabsorption of albumin and glucose from the epithelial channel. By incorporating multiple cell populations from single donors, it is demonstrated that the hRVTU may have utility for future precision medicine applications. The success of the system provides new opportunities for the next generation of organ‐on‐a‐chip models.
Recent developments and highlights in allergen immunotherapy
Authors: Oliver Pfaar, Hongfei Lou, Yuan Zhang, Ludger Klimek, Luo Zhang
Journal: Allergy (2018)

Allergen immunotherapy (AIT) is the only disease-modifying treatment option for patients with IgE-mediated inhalant allergies. Though used in clinical practice for more than 100 years, most innovations in AIT efficacy and safety have been developed in the last two decades. This expert review aimed to highlight the recent progress in AIT for both application routes, the sublingual (SLIT) and subcutaneous (SCIT) forms. As such, it covers recent aspects regarding efficacy and safety in clinical trials and real-life data and outlines new concepts in consensus and position papers as well as in guidelines for AIT. Potential clinical and nonclinical biomarkers are discussed. This review also focuses on potential future perspectives in AIT, such as alternative application routes, immune-modulating adjuvants, and recombinant vaccines. In conclusion, this state of the art review provides a comprehensive overview of AIT and highlights unmet needs for the future.
Primary Hepatic Neuroendocrine Tumor
Authors: Xia Bai, Xia Zhang, Xuemei Wang
Journal: Clinical Nuclear Medicine (2018)

A 53-year-old man with tentative diagnosis of likely hepatocellular carcinoma underwent FDG PET/CT, which showed intense activity in both right lobe and caudate lobe of the liver. However, pathology examination from biopsy showed neuroendocrine tumor. He received transarterial chemoembolization and systemic chemotherapy. Posttherapy follow-up FDG PET/CT revealed no abnormal FDG activity in the liver.
Abstract 16563: Genetic and Pharmacological Inactivation of ANGPTL3 is Associated With Reduced Atherosclerotic Cardiovascular Disease
Authors: Frederick E Dewey, Viktoria Gusarova, Colm O’Dushlaine, Omri Gottesman, Cristopher V Van Hout, Shannon Bruse, Joseph B Leader, Michael F Murray, Marylyn D Ritchie, H. Lester Kirchner, David H Ledbetter, Lukas Habegger, An Zhao, Weiping Shao, John Overton, Jeffrey Reid, Neil Stahl, Andrew Murphy, Poulabi Banerjee, Scott Mellis, William J Sasiela, David J Carey, Anita M van den Hoek, Hans M Princen, Ingrid B Borecki, Alan R Shuldiner, George D Yancopoulos, Jesper Gromada, Aris Baras
Journal: Circulation (2016)

Introduction: Loss of function (LoF) variants in ANGPTL3 have been associated with low plasma low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) and triglycer...
Epidermal electronics for noninvasive, wireless, quantitative assessment of ventricular shunt function in patients with hydrocephalus
Authors: Siddharth R. Krishnan, Tyler R. Ray, Amit B. Ayer, Yinji Ma, Philipp Gutruf, KunHyuck Lee, Jong Yoon Lee, Chen Wei, Xue Feng, Barry Ng, Zachary A. Abecassis, Nikhil Murthy, Izabela Stankiewicz, Juliet Freudman, Julia Stillman, Natalie Kim, Grace Young, Camille Goudeseune, John Ciraldo, Matthew Tate, Yonggang Huang, Matthew Potts, John A. Rogers
Journal: Science Translational Medicine (2018)

A soft, wearable sensor noninvasively and wirelessly detects ventricular catheter shunt malfunction in patients with hydrocephalus.
Accuracy, Safety, and Reliability of Novel Phase I Designs—Response
Authors: Heng Zhou, Ying Yuan, Lei Nie
Journal: Clinical Cancer Research (2018)

We appreciate that Drs. Wages and Braun agree with us on the importance of studying the within-trial behavior of phase I methods, which is one of the primary objectives of our article and the reason why we proposed and investigated the rationality of dose assignments in various phase I methods ([1][
Nrf2 regulates CD4+ T cell–induced acute graft-versus-host disease in mice
Authors: Jennifer J. Tsai, Enrico Velardi, Yusuke Shono, Kimon V. Argyropoulos, Amanda M. Holland, Odette M. Smith, Nury L. Yim, Uttam K. Rao, Fabiana M. Kreines, Sophie R. Lieberman, Lauren F. Young, Amina Lazrak, Salma Youssef, Ya-Yuan Fu, Chen Liu, Cecilia Lezcano, George F. Murphy, Il-Kang Na, Robert R. Jenq, Alan M. Hanash, Jarrod A. Dudakov, Marcel R. M. van den Brink
Journal: Blood (2018)
Long Non-coding RNA ECRAR Triggers Post-natal Myocardial Regeneration by Activating ERK1/2 Signaling
Authors: Yanmei Chen, Xinzhong Li, Bing Li, He Wang, MengSha Li, Senlin Huang, Yili Sun, Guojun Chen, Xiaoyun Si, Chixiong Huang, Wangjun Liao, Yulin Liao, Jianping Bin
Journal: Molecular Therapy (2018)

Reactivating post-natal myocardial regeneration potential may be a feasible strategy to regenerate the injured adult heart. Long non-coding RNAs (lncRNAs) have been implicated in regulating cellular differentiation, but whether they can elicit a regenerative response in the post-natal heart remains unknown. In this study, by characterizing the lncRNA transcriptome in human hearts during the fetal-to-adult transition, we found that 3,092 lncRNAs were differentially expressed, and we further identified a novel upregulated fetal lncRNA that we called endogenous cardiac regeneration-associated regulator (ECRAR), which promoted DNA synthesis, mitosis, and cytokinesis in post-natal day 7 and adult rat cardiomyocytes (CMs). Overexpression of ECRAR markedly stimulated myocardial regeneration and induced recovery of cardiac function after myocardial infarction (MI). Knockdown of ECRAR inhibited post-natal day 1 CM proliferation and prevented post-MI recovery. ECRAR was transcriptionally upregulated by E2F transcription factor 1 (E2F1). In addition, ECRAR directly bound to and promoted the phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), resulting in downstream targets of cyclin D1 and cyclin E1 activation, which, in turn, activated E2F1. The E2F1-ECRAR-ERK1/2 signaling formed a positive feedback loop to drive cell cycle progression, and, therefore, it promoted CM proliferation. These findings indicated that our newly discovered ECRAR may be a valuable therapeutic target for heart failure.
Multidrug-resistant bacterial infections in patients with decompensated cirrhosis and with acute-on-chronic liver failure in Europe
Authors: Javier Fernández, Verónica Prado, Jonel Trebicka, Alex Amoros, Thierry Gustot, Reiner Wiest, Carme Deulofeu, Elisabet Garcia, Juan Acevedo, Valentin Fuhrmann, François Durand, Cristina Sánchez, Maria Papp, Paolo Caraceni, Victor Vargas, Rafael Bañares, Salvatore Piano, Martin Janicko, Agustin Albillos, Carlo Alessandria, German Soriano, Tania M. Welzel, Wim Laleman, Alexander Gerbes, Andrea De Gottardi, Manuela Merli, Minneke Coenraad, Faouzi Saliba, Marco Pavesi, Rajiv Jalan, Pere Ginès, Paolo Angeli, Vicente Arroyo
Journal: Journal of Hepatology (2018)
Prognostic importance of lymph node (LN) yield after curative resection of gastroenteropancreatic neuroendocrinetumours (GEP NETs)
Authors: J. Chiramel, R. Almond, A.E. Slagter, A. Khan, K.H.J. Lim, B. Chakrabarty, A. Minicozzi, A. Lamarca, W. Mansoor, R. Hubner, J.W. Valle, M.G. McNamara
Journal: Annals of Oncology (2018)
Synergy between FLT3-ITD and p53 Haploinsufficiency or Loss in the Development of Acute Myeloid Leukemia
Authors: Zengkai Pan, Min Yang, Kezhi Huang, Guntram Buesche, Gudrun Göhring, Michaela Scherr, Matthias Gaestel, Matthias Eder, Julia Skokowa, Jianfeng Zhou, Karl Welte, Li-Gen Liu, Arnold Ganser, Zhixiong Li
Journal: Blood (2018)
Visualizing the dynamics of histone variants in the S-phase nucleus
Authors: Stella Maxouri, Stavros Taraviras, Zoi Lygerou
Journal: Genome biology (2018)

Histone variants constitute a fundamental feature of the epigenome. However, their dynamics during normal and challenged DNA replication and their distribution in the three-dimensional space of the nucleus remain poorly characterized. A recent study employed stochastic optical reconstruction microscopy (STORM) to obtain a high-resolution view of the spatial distribution of H3 histone variants in the nucleus and related this to the timing of DNA replication.
Genetically inspired prognostic scoring system (GIPSS) outperforms dynamic international prognostic scoring system (DIPSS) in myelofibrosis patients
Authors: Andrew T. Kuykendall, Chetasi Talati, Eric Padron, Kendra Sweet, David Sallman, Alan F. List, Jeffrey E. Lancet, Rami S. Komrokji
Journal: American Journal of Hematology (2018)

Abstract A genetically inspired prognostic scoring system (GIPSS) that stratifies primary myelofibrosis (PMF) patients by genetic variants alone was recently proposed. While non‐inferior to the dynamic international prognostic scoring system (DIPSS), the lack of overlapping prognostic variables between the models leads to increased risk for disagreement between two valid prognostic models and presents a challenging clinical situation. In an external cohort of 266 molecularly annotated myelofibrosis (MF) patients, we demonstrated that the GIPSS model significantly differentiated between four risk groups (low, int‐1, int‐2, high) with median OS that was not reached, not reached, 60.5 and 28.9 months, respectively. High‐risk patients had significantly inferior leukemia‐free survival (LFS) ( P &lt; 0.0001). We identified a cohort of prognostically ambiguous patients ( n = 39) in which GIPSS and DIPSS models differed by ≥2 risk groups. Among these patients, a similar proportion were up‐staged by DIPSS ( n = 19) and GIPSS ( n = 20). Patients upstaged by GIPSS (genetically high‐risk) had a trend toward inferior OS compared with patients upstaged by DIPSS (clinically high‐risk) ( P = .08) and significantly worse LFS ( P = .04). Patients deemed intermediate‐2 and high‐risk by GIPSS who underwent allogeneic transplant had improved OS compared with those that did not ( P = .04). GIPSS is a valid disease‐specific prognostic system and outperforms DIPSS in patients where the two models disagree. Additionally, while GIPSS was developed for PMF; the current study shows, however, that the contemporary genetic model performs equally well for both primary and secondary myelofibrosis.
Abstract 14993: Does Pregnancy Increase the Risk of Deterioration of Homograft Valves? A Systematic Review and Meta-analysis
Authors: Jerson Munoz-Mendoza, Veronica Pinto Miranda, Leonardo Tamariz, Mario Garcia
Journal: Circulation (2015)

Introduction: A previous meta-analysis found that pregnancy increases the risk of structural valve deterioration (SVD) of bioprosthetic valves. However both homografts and xenografts were included indistinctly in the analysis. The purpose of this study is to conduct a meta-analysis to determine if pregnancy independently increases the risk of SVD in women recipient of homograft and xenograft valves. Methods: We searched MEDLINE, EMBASE, CINAHL, Web of Knowledge, and Cochrane Library databases for articles published from inception until May 2015. Only cohort and case control studies were included. We calculated the relative risk (RR) and the corresponding 95% confidence interval (CI) of having SVD by pregnancy status using the DeSirmonian-Laird method. Meta-regression examined the RR of SVD by age, number of pregnancies and time from valve replacement to delivery. Results: Our search strategy yielded 23 publications; nine studies met inclusion criteria. Two studies (75 women) were performed in recipients of homografts. They were divided in two groups according to their history of pregnancies, 22 who were pregnant at least once and 53 who never were pregnant. Eight studies (1071 women) assessed SVD in women recipient of xenografts, including 282 women who had been pregnant and 789 who never were pregnant. Twenty (26.6%) and 341 (31.8%) women recipients of homografts and xenografts respectively developed SVD. Among the recipients of xenografts, the RR of having SVD in pregnant women was 1.70; 95% CI 1.26-2.29; p&lt;0.01 (Figure), whereas it was 1.03 (95% CI 0.45-2.33; p&lt;0.01) in recipients of homografts. None of the factors evaluated in meta-regression in recipients of xenografts were statistically significant. Conclusion: Pregnancy does increase the risk of SVD in recipients of xenografts, but no homografts. Homografts would be a better option than xenografts in women of childbearing age non suitable for long-term anticoagulation.
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Authors: Philipp Drewe-Boss, Hans-Hermann Wessels, Uwe Ohler
Journal: Genome biology (2018)

CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein – RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays.
Abstract 19442: Molecular Crosstalk Between Necroptosis and Autophagy Signaling Pathways: Roles of p62 and p53
Authors: Koki Abe, Toshiyuki Yano, Makoto Ogasawara, Takayuki Miki, Masaya Tanno, Atsushi Kuno, Tetsuji Miura
Journal: Circulation (2017)

Purpose: Necroptosis, a programmed cell death, has been implicated in various pathological conditions including heart failure. Here we examined whether and how receptor-interacting protein kinase (...
Peritoneal Deciduoid Malignant Mesothelioma on 67Ga SPECT/CT
Authors: Yung-Chi Lai, Yu-Chin Wu, Chia-Hung Kao, Te-Chun Hsieh, Shung-Shung Sun
Journal: Clinical Nuclear Medicine (2018)

Malignant mesotheliomas may be classified into epithelioid (60%), sarcomatoid (20%), or mixed (20%) type microscopically. Malignant deciduoid mesothelioma, a rare phenotype of epithelioid mesothelioma, arises more commonly from the peritoneum of young women, but is also from the pleura of elderly people. In the current report, the authors describe an unusual case of peritoneal malignant epithelioid mesothelioma with rare deciduoid phenotype demonstrated with Ga SPECT/CT.
The global burden of disease attributable to alcohol and drug use in 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016
Authors: Louisa Degenhardt, Fiona Charlson, Alize Ferrari, Damian Santomauro, Holly Erskine, Ana Mantilla-Herrara, Harvey Whiteford, Janni Leung, Mohsen Naghavi, Max Griswold, Jürgen Rehm, Wayne Hall, Benn Sartorius, James Scott, Stein Emil Vollset, Ann Kristin Knudsen, Josep Maria Haro, George Patton, Jacek Kopec, Deborah Carvalho Malta, Roman Topor-Madry, John McGrath, Juanita Haagsma, Peter Allebeck, Michael Phillips, Joshua Salomon, Simon Hay, Kyle Foreman, Stephen Lim, Ali Mokdad, Mari Smith, Emmanuela Gakidou, Christopher Murray, Theo Vos
Journal: The Lancet Psychiatry (2018)

Alcohol and drug use can have negative consequences on the health, economy, productivity, and social aspects of communities. We aimed to use data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016 to calculate global and regional estimates of the prevalence of alcohol, amphetamine, cannabis, cocaine, and opioid dependence, and to estimate global disease burden attributable to alcohol and drug use between 1990 and 2016, and for 195 countries and territories within 21 regions, and within seven super-regions. We also aimed to examine the association between disease burden and Socio-demographic Index (SDI) quintiles.
Treatment of AL amyloidosis with bendamustine: a study of 122 patients
Authors: Paolo Milani, Stefan Schönland, Giampaolo Merlini, Christoph Kimmich, Andrea Foli, Tobias Dittrich, Marco Basset, Carsten Müller-Tidow, Tilmann Bochtler, Giovanni Palladini, Ute Hegenbart
Journal: Blood (2018)