bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progenitor B-1 B-cell acute lymphoblastic leukemia is associated with collaborative mutations in 3 critical pathways
Authors: Gough Sheryl M. , Goldberg Liat , Pineda Marbin , Walker Robert L. , Zhu Yuelin J. , Bilke Sven , Chung Yang Jo , Dufraine Joseph , Kundu Subhadip , Jacoby Elad , Fry Terry J. , Fischer Susanna , Panzer-Grümayer Renate , Meltzer Paul S. , Aplan Peter D. 
Published: October 2019

Key Points
An NUP98-PHF23 fusion collaborates with acquired Bcor and Jak/Stat mutations to produce a pro–B-1 ALL. Gene expression profile of murine pro–B-1 ALL resembles that of a subset of human ALL, suggesting some human ALLs arise from pro–B-1 B cells.
Standard measures for sickle cell disease research: the PhenX Toolkit sickle cell disease collections
Authors: Eckman James R. , Hassell Kathryn L. , Huggins Wayne , Werner Ellen M. , Klings Elizabeth S. , Adams Robert J. , Panepinto Julie A. , Hamilton Carol M. 
Published: October 2019

Key PointsThe PhenX Toolkit recommends standard SCD measures for use in clinical, epidemiologic, and genomic studies. Widespread use of PhenX measures will accelerate translational research to elucidate the etiology, epidemiology, and progression of SCD.
Thromboembolic event rate in patients exposed to anti-inhibitor coagulant complex: a meta-analysis of 40-year published data
Authors: Rota Matteo , Cortesi Paolo A. , Crea Roberto , Gringeri Alessandro , Mantovani Lorenzo G. 
Published: October 2019

Key PointsAICC has been used since 1977 to control bleeding in patients with hemophilia with inhibitors. AICC is associated with a low incidence of TEEs, especially when administered prophylactically.
Prothrombin conversion is accelerated in the antiphospholipid syndrome and insensitive to thrombomodulin
Authors: Kremers Romy M. W. , Zuily Stéphane , Kelchtermans Hilde , Peters Tessa C. , Bloemen Saartje , Regnault Véronique , Hemker H. Coenraad , de Groot Philip G. , Wahl Denis , de Laat Bas 
Published: October 2019

Key PointsThe rate of prothrombin conversion is elevated in APS patients, causing a hemostatic imbalance. TG and prothrombin conversion are higher in APS patients with prior thrombosis than in patients without thrombosis.
Defining autoimmune hemolytic anemia: a systematic review of the terminology used for diagnosis and treatment
Authors: Hill Quentin A. , Hill Anita , Berentsen Sigbjørn 
Published: October 2019

AbstractThe terminology applied to autoimmune hemolytic anemia (AIHA) seems inconsistent. We aimed to evaluate the consistency of definitions used for diagnosis and treatment. In this systematic review of literature from January 2006 to December 2015, we assessed heterogeneity in the definition of AIHA and its subtypes, refractory disease, disease phase, severity, criteria for treatment response, and response durability. A Medline search for anemia, hemolytic, autoimmune was supplemented with keyword searches. Main exclusions were conference abstracts, animal and non-English studies, and studies with &lt;10 cases. Of 1371 articles retrieved, 1209 were excluded based on titles and abstracts. Two authors independently reviewed 10% and 16% of abstracts and full papers, respectively. After full-paper review, 84 studies were included. AIHA was most frequently (32 [52%] of 61) defined as hemolytic anemia with positive direct antiglobulin test (DAT) and exclusion of alternatives, but 10 of 32 also recognized DAT-negative AIHA. A lower threshold for diagnosis of DAT-negative AIHA was observed in literature on chronic lymphocytic leukemia. Definitions of anemia, hemolysis, and exclusion criteria showed substantial variation. Definitions of primary/secondary cold agglutinin disease/syndrome were not consistent. Forty-three studies provided criteria for treatment response, and other than studies from 1 center, these were almost entirely unique. Other criteria were rarely defined. Only 7, 0, 3, 2, 2, and 3 studies offered definitions of warm AIHA, paroxysmal cold hemoglobinuria, mixed AIHA, AIHA severity, disease phase, and refractory AIHA, respectively. Marked heterogeneity in the time period sampled indicates the need to standardize AIHA terminology.
Characteristics and treatment regimens across ERS SHARP severe asthma registries
Authors: van Bragt Job J.M.H. , Adcock Ian M. , Bel Elisabeth H.D. , Braunstahl Gert-Jan , ten Brinke Anneke , Busby John , Canonica Giorgio W. , Cao Hui , Chung Kian Fan , Csoma Zsuzsanna , Dahlén Barbro , Davin Elizabeth , Hansen Susanne , Heffler Enrico , Horvath Ildiko , Korn Stephanie , Kots Maxim , Kuna Piotr , Kwon Namhee , Louis Renaud , Plaza Vicente , Porsbjerg Celeste , Ramos-Barbon David , Richards Levi B. , Škrgat Sabina , Sont Jacob K. , Vijverberg Susanne J.H. , Weersink Els J.M. , Yasinska Valentyna , Wagers Scott S. , Djukanovic Ratko , Maitland-van der Zee Anke H. 
Published: October 2019

Little is known about the characteristics and treatments of patients with severe asthma across Europe, but both are likely to vary. This is the first study in the European Respiratory Society Severe Heterogeneous Asthma Research collaboration, Patient-centred (SHARP) Clinical Research Collaboration and it is designed to explore these variations. Therefore, we aimed to compare characteristics of patients in European severe asthma registries and treatments before starting biologicals.This was a cross-sectional retrospective analysis of aggregated data from 11 national severe asthma registries that joined SHARP with established patient databases.Analysis of data from 3236 patients showed many differences in characteristics and lifestyle factors. Current smokers ranged from 0% (Poland and Sweden) to 9.5% (Belgium), mean body mass index ranged from 26.2 (Italy) to 30.6 kg·m−2(the UK) and the largest difference in mean pre-bronchodilator forced expiratory volume in 1 s % predicted was 20.9% (the NetherlandsversusHungary). Before starting biologicals patients were treated differently between countries: mean inhaled corticosteroid dose ranged from 700 to 1335 µg·day−1between those from SloveniaversusPoland when starting anti-interleukin (IL)-5 antibody and from 772 to 1344 µg·day−1in those starting anti-IgE (SloveniaversusSpain). Maintenance oral corticosteroid use ranged from 21.0% (Belgium) to 63.0% (Sweden) and from 9.1% (Denmark) to 56.1% (the UK) in patients starting anti-IL-5 and anti-IgE, respectively.The severe asthmatic population in Europe is heterogeneous and differs in both clinical characteristics and treatment, often appearing not to comply with the current European Respiratory Society/American Thoracic Society guidelines definition of severe asthma. Treatment regimens before starting biologicals were different from inclusion criteria in clinical trials and varied between countries.
LncRNA AB209371 up-regulated Survivin gene by down-regulating miR-203 in ovarian carcinoma
Authors: Zheng Zi-Hui , Wu Dong-Mei , Fan Shao-Hua , Wen Xin , Han Xin-Rui , Wang Shan , Wang Yong-Jian , Zhang Zi-Feng , Shan Qun , Li Meng-Qiu , Hu Bin , Zheng Yuan-Lin , Lu Jun 
Published: October 2019

Abstract
AB209371 gene has been characterized as an oncogenic lncRNA in liver cancer. However, its involvement in ovarian carcinoma (OC) is unknown. In the present study, we analyzed the roles of AB209371 in OC. We found that AB209371 gene and Survivin gene were up-regulated in OC and positively correlated with OC development. AB209371 over-expression led to up-regulated Survivin in OC cells, while Survivin over-expression failed to affect AB209371. In addition, AB209371 over-expression led to down-regulated miR-203. However, miR-203 over-expression failed to affect AB209371, but down-regulated the expression of Survivin. In addition, over-expressions of AB209371 and Survivin resulted in the increased proliferation rate of OC cells. Over-expression MiR-203 played the opposite role and attenuated the effects of AB209371 over-expression. Therefore, AB209371 may down-regulate miR-203 to up-regulate Survivin, thereby promoting OC cell proliferation. Our study provided novel insights into the pathogenesis of OC.
Combinatorial treatment of acute myocardial infarction using stem cells and their derived exosomes resulted in improved heart performance
Authors: Huang Peisen , Wang Li , Li Qing , Xu Jun , Xu Junyan , Xiong Yuyan , Chen Guihao , Qian Haiyan , Jin Chen , Yu Yuan , Liu Jiandong , Qian Li , Yang Yuejin 
Published: October 2019

Abstract

Background
Bone marrow mesenchymal stem cells (MSCs) are among the most common cell types to be used and studied for cardiac regeneration. Low survival rate and difficult retention of delivered MSCs in infarcted heart remain as major challenges in the field. Co-delivery of stem cell-derived exosomes (Exo) is expected to improve the recruitment and survival of transplanted MSCs.

Methods
Exo was isolated from MSCs and delivered to an acute myocardial infarction (AMI) rat heart through intramyocardial injection with or without intravenous infusion of atrovastatin-pretreated MSCs on day 1, day 3, or day 7 after infarction. Echocardiography was performed to evaluate cardiac function. Histological analysis and ELISA test were performed to assess angiogenesis, SDF-1, and inflammatory factor expression in the infarct border zone. The anti-apoptosis effect of Exo on MSCs was evaluated using flow cytometry and Hoechst 33342 staining assay.

Results
We found that intramyocardial delivery of Exo followed by MSC transplantation (in brief, Exo+MSC treatment) into MI hearts further improved cardiac function, reduced infarct size, and increased neovascularization when compared to controls treated with Exo or MSCs alone. Of note, comparing the three co-transplanting groups, intramyocardially injecting Exo 30 min after AMI combined with MSCs transplantation at day 3 after AMI achieved the highest improvement in heart function. The observed enhanced heart function is likely due to an improved microenvironment via Exo injection, which is exemplified as reduced inflammatory responses and better MSC recruitment and retention. Furthermore, we demonstrated that pre-transplantation injection of Exo enhanced survival of MSCs and reduced their apoptosis both in vitro and in vivo.

Conclusions
Combinatorial delivery of exosomes and stem cells in a sequential manner effectively reduces scar size and restores heart function after AMI. This approach may represent as an alternative promising strategy for stem cell-based heart repair and therapy.
Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes
Authors: Zhang Shu , Zhang Yong-Jie 
Published: October 2019

Abstract
Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungus Tolypocladium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16 fungi of different phyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.
Investigating effect of Helicobacter pylori treatment on improvement of non-alcoholic fatty liver parameters: a randomized trial
Authors: Kazemifar Amir Mohammad , Shafikhani Ali Akbar , HajiNoormohammadi Elaheh , Azarion Zahra , Hajiaghamohammadi Aliakbar 
Published: October 2019

Abstract

Background and objective
The correlation between the eradication of Helicobacter pylori (HP) and non-alcoholic fatty liver disease (NAFLD) is a controversial one. The aim of this study is to investigate the effect of Helicobacter pylori treatment on liver function tests and lipid profiles and to compare its effects with exercise therapy and diet alone.

Method
This was a double-blind randomized clinical trial conducted at Qazvin University of Medical Sciences. One hundred patients with NAFLD having a positive test for urea breath testing were randomly assigned into one of the intervention and comparison groups. The diet and physical activity program were given to two groups of patients for 8 weeks, three sessions per week. In addition to the above therapy, the patients in the intervention group also received HP treatment for 2weeks. The data corresponding to anthropometric and clinical features before and after the intervention were collected in both groups and compared using appropriate statistical methods.

Results
After the treatment interventions, the variables of weight, BMI, blood glucose, triglyceride, AST, ALT, total cholesterol, and LDL-C were significantly decreased in both groups (p < .05). In the between-group comparisons, only ALT was significantly lower in the intervention group (HP) (p < .05).

Conclusion
Findings of this study showed that the eradication of Helicobacter pylori could significantly improve the ALT index, but it had no additional effect on changes in metabolic indicators.

Trial registration
Registration number: IRCT2015042020951N2
Name of trial registry: The study of treatment of Helicobacter pylori in improvement of non-alcoholic fatty liver disease
The date of registration: 2015-05-12
Where the full trial protocol can be accessed: https://fa.irct.ir/trial/18489
Noncurated Data Lead to Misinterpretation of Treatment Outcomes in Patients With Prostate Cancer After Salvage or Palliative Radiotherapy
Authors: Rutzner Sandra , Ganslandt Thomas , Fietkau Rainer , Prokosch Hans-Ulrich , Lubgan Dorota 
Published: October 2019

PURPOSE Clinical data warehouses (cDWHs) and cancer registry databases have enabled researchers to conduct clinical analytics with structured electronic health record data. However, these secondary electronic health record sources are often limited in scope because they do not capture the clinical information needed to understand complex clinical questions. Thus, we evaluated the effect of additional curation of data. MATERIALS AND METHODS Clinical data sets of 149 patients with prostate cancer with biochemical recurrence after radical prostatectomy treated with salvage or palliative radiotherapy between 2008 and 2017 from our institutional cDWH and Gießener Tumor Documentation System (GTDS) were linked (data warehouse [DWH] population) for analyzing treatment outcomes. The linked data sets were manually curated (manual postprocessing [MPP], eg, incorporate data from established urologists). The primary outcomes were the impact on data quality of treatment outcomes and the time spent on data curation. RESULTS We obtained significantly more information on disease progression and patient survival (nonsignificant) when using curated data; the biochemical progression-free survival rate at 5 years for the DWH and DWH plus MPP populations was 63% v 30% ( P ≤ .001) and the overall survival rate was 84% v 81% ( P = .479), respectively. The median deviation of completeness and the median concordance of clinical data values were 21.47% (range, 55.38%-100%) and 95.00% (range, 63.40%-100%), respectively. We spent 121 hours, 42 minutes on data curation, with most time required for laboratory values, accounting, for a total of 45 hours, 20 minutes (37.26%). CONCLUSION Our analysis indicates that time-to-event outcomes for patients with prostate cancer cannot be extracted using secondary data sources (cDWH plus GTDS) only. Outcomes data differed between the electronic data (DWH) and the second manual extraction (DWH plus MPP) because of a lack of follow-up data. When using such unique database resources, only baseline characteristics can reliably be extracted.
Understanding the Value of International Research Networks: An Evaluation of the International Cancer Screening Network of the US National Cancer Institute
Authors: Vogel Amanda L. , Puricelli Perin Douglas M. , Lu Ya-Ling , Taplin Stephen H. 
Published: October 2019

PURPOSE International research networks have the potential to accelerate scientific progress via knowledge sharing and collaboration. In 2018, the US National Cancer Institute evaluated the International Cancer Screening Network (ICSN), in operation since 1988. METHODS ICSN hosts a biennial scientific meeting and scientific working groups. A survey was fielded to 665 ICSN participants, and a bibliometric analysis was conducted for ICSN publications. RESULTS A total of 243 individuals completed the survey (36.5%). They reported that participating in the ICSN helped advance their knowledge of cancer screening research (75.7%), policy development (56%), and implementation (47.7%). Approximately three-quarters agreed that ICSN facilitated knowledge sharing and networking among researchers and implementers (79.9%) and those working on different continents (74.0%) and cancer sites (73.7%). More than half reported that participating helped them form new collaborations in screening implementation (58.0%) or research (57.6%). Most agreed that ICSN helped to advance screening research and evaluation (75.4%), effective screening practices (71.2%), and screening policies (60.9%). Many reported that participating informed advances in their own research (68.7%) and screening implementation (50.2%) and policies (49.4%) in their settings. Approximately two-thirds agreed that ICSN helped advance career development among current experts (66.6%) and train the next generation (62.2%). Half (51.4%) reported that participating advanced their own careers. The 20 ICSN publications included 75 coauthors. They were cited in 589 publications with more than 2,000 coauthors. CONCLUSION Findings provide evidence of the influence of ICSN on international knowledge dissemination, collaboration, and advances in cancer screening research, implementation, and policies and highlight the potential value of longstanding international research networks.
A small bioactive glycoside inhibits epsilon toxin and prevents cell death
Authors: Shivappagowdar Abhishek , Pati Soumya , Narayana Chintam , Ayana Rajagopal , Kaushik Himani , Sah Raj , Garg Swati , Khanna Ashish , Kumari Jyoti , Garg Lalit , Sagar Ram , Singh Shailja 
Published: October 2019

ABSTRACT
Clostridium perfringens epsilon toxin (Etx) is categorized as the third most lethal bioterrorism agent by the Centers for Disease Control and Prevention (CDC), with no therapeutic counter measures available for humans. Here, we have developed a high-affinity inhibitory compound by synthesizing and evaluating the structure activity relationship (SAR) of a library of diverse glycosides (numbered 1-12). SAR of glycoside-Etx heptamers revealed exceptionally strong H-bond interactions of glycoside-4 with a druggable pocket in the oligomerization and β-hairpin region of Etx. Analysis of its structure suggested that glycoside-4 might self-aggregate to form a robust micelle-like supra-molecular complex due to its linear side-chain architecture, which was authenticated by fluorescence spectroscopy. Further, this micelle hinders the Etx monomer-monomer interaction required for oligomerization, validated by both surface plasmon resonance (SPR) and immunoblotting. This phenomenon in turn leads to blockage of pore formation. Downstream evaluation revealed that glycoside-4 effectively blocked cell death of Etx-treated cultured primary cells and maintained cellular homeostasis via disrupting oligomerization, blocking pore formation, restoring calcium homeostasis, stabilizing the mitochondrial membrane and impairing high mobility group box 1 (HMGB1) translocation from nucleus to cytoplasm. Furthermore, a single dosage of glycoside-4 protected the Etx-challenged mice and restored normal function to multiple organs. This work reports for the first time a potent, nontoxic glycoside with strong ability to occlude toxin lethality, representing it as a bio-arm therapeutic against Etx-based biological threat.
An open invitation to join the Pediatric Proton/Photon Consortium Registry to standardize data collection in pediatric radiation oncology
Authors: Lawell Miranda P. , Indelicato Daniel J , Paulino Arnold C , Hartsell William , Laack Nadia N. , Ermoian Ralph P. , Perentesis John P. , Vatner Ralph , Perkins Stephanie , Mangona Victor S. , Hill-Kayser Christine E. , Wolden Suzanne L. , Kwok Young , Chang John Han-Chih , Wilkinson J. Ben , MacEwan Iain , Chang Andrew L. , Eaton Bree R. , Ladra Matthew M. , Gallotto Sara L. , Weyman Elizabeth A. , Bajaj Benjamin V.M. , Baliga Sujith , Yeap Beow Y. , Berrington de Gonzalez Amy , Yock Torunn I. 
Published: October 2019

Objective:
The Pediatric Proton/Photon Consortium Registry (PPCR) is a comprehensive data registry composed of pediatric patients treated with radiation. It was established to expedite outcomes-based research. The attributes which allow the PPCR to be a successful collaboration are reviewed.

Methods and materials:
Current eligibility criteria are radiotherapy patients &lt; 22 years treated at one of the 15 US participating institutions. Detailed health and treatment data are collected about the disease presentation and treatment exposures, and annually thereafter, in REDCap (Research Electronic Data Capture). DICOM (Digital Imaging and Communications in Medicine) imaging and radiation plans are collected through MIM/MIMcloud. An optional patient-reported quality-of-life (PedsQL) study is administered at 10 sites.

Results:
Accrual started October 2012 with 2,775 participants enrolled as of 25 July 2019. Most patients, 62.0%, were treated for central nervous system (CNS) tumors, the most common of which are medulloblastoma (n = 349), ependymoma (n = 309), and glial/astrocytoma tumors (n = 279). The most common non-CNS diagnoses are rhabdomyosarcoma (n = 284), Ewing’s sarcoma (n = 153), and neuroblastoma (n = 130). While the majority of participants are US residents, 18.7% come from 36 other countries. Over 685 patients participate in the PedsQL study.

Conclusions:
The PPCR is a valuable research platform capable of answering countless research questions that will ultimately improve patient care. Centers outside of the USA are invited to participate directly or may engage with the PPCR to align data collection strategies to facilitate large-scale international research.

Advances in knowledge:
For investigators looking to carry out research in a large pediatric oncology cohort or interested in registry work, this paper provides an updated overview of the PPCR.