bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasticity in Triticeae centromere DNA sequences: a wheat × tall wheatgrass (decaploid) model
Authors: Zhao Jing , Hao Weiwei , Tang Caiguo , Yao Han , Li Baochun , Zheng Qi , Li Zhensheng , Zhang Xueyong 
Published: July 2019

SummaryCentromeres mediate chromosome attachment to microtubules and maintain the integrity of chromosomes for proper segregation of the sister chromatids during cell division. Advances in the assembly of Triticeae genome sequences combined with the capacity to recover hybrid species derived from very distantly related species provides potential experimental systems for linking retrotransposon amplification and repositioning of centromeres via non‐mendelian inheritance in partial amphiploid breeds. The decaploid tall wheatgrass (Thinopyrum ponticum) is one of the most successfully used perennial species in wheat breeding for generating translocation lines with valuable agronomic traits. We found that wheat centromere retrotransposons CRW and Quinta widely occur within the tall wheatgrass genome. In addition, one of the genome donors to Th. ponticum, Pseudoroegneria stipifolia (StSt), has been shown to have Abigail and a satellite repeat, CentSt. We also found two other centromeric retrotransposons, Abia and CL135 in Th. ponticum by ChIP‐seq. Examination of partial amphiploid lines that were generated in the 1970s demonstrated extensive modification in centromere sequences using CentSt, Abigail and Abia as probes. We also detected that St‐genome chromosomes were more enriched with Abigail and CentSt, whereas E‐genome chromosomes were enriched with CRW and Quinta in tall wheatgrass and its closer relatives. It can be concluded that bursts of transposition of retrotransposons and repositioning of centromeres via non‐mendelian segregation are common in partial amphiploids derived from interspecific hybrids. Practically speaking, our study reveals that the existence of homologous centromere functional sequences in both a donor and its receptor can substantially contribute to the successful transfer of alien genes into crop species.Open Research Badges

This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/sra/SRR9089557; https://www.ncbi.nlm.nih.gov/sra/SRR9089558; https://www.ncbi.nlm.nih.gov/sra/SRR9089559; https://www.ncbi.nlm.nih.gov/sra/SRR9089560; https://www.ncbi.nlm.nih.gov/sra/SRR9089561; https://www.ncbi.nlm.nih.gov/sra/SRR9089562; https://www.ncbi.nlm.nih.gov/sra/SRR9089563; https://www.ncbi.nlm.nih.gov/sra/SRR9089564; https://www.ncbi.nlm.nih.gov/nuccore/MK999394; https://www.ncbi.nlm.nih.gov/nuccore/MK999395; https://www.ncbi.nlm.nih.gov/nuccore/MK999396
The volatility of world trade in the 21st century: Whose fault is it anyway?
Authors: Bennett Federico , Lederman Daniel , Pienknagura Samuel , Rojas Diego 
Published: July 2019

AbstractThis paper explores the drivers of the volatility of international trade. It decomposes trade growth into six components that have gained attention in the literature and studies their contribution to overall volatility. It yields three main findings. First, trade volatility in the 1990–2015 period is mostly explained by a common factor, changes in the gravity‐related characteristics of a country's trading partners and country‐specific factors. Product composition and the identity of trading partners appear to be less important in explaining volatility. Second, the pre‐2009 decline in volatility and the post‐2009 increase in volatility appear to be driven by different factors. The former is mostly explained by a decline in the variance of country‐specific factors; the latter appears to be driven by an increase in the volatility of common factors. Third, diversification is a likely force behind the steady decline in the volatility stemming from country‐specific factors, especially in developing countries.
Machine learning for prediction of sudden cardiac death in heart failure patients with low left ventricular ejection fraction: study protocol for a retroprospective multicentre registry in China
Authors: Meng Fanqi , Zhang Zhihua , Hou Xiaofeng , Qian Zhiyong , Wang Yao , Chen Yanhong , Wang Yilian , Zhou Ye , Chen Zhen , Zhang Xiwen , Yang Jing , Zhang Jinlong , Guo Jianghong , Li Kebei , Chen Lu , Zhuang Ruijuan , Jiang Hai , Zhou Weihua , Tang Shaowen , Wei Yongyue , Zou Jiangang 
Published: July 2019

IntroductionLeft ventricular ejection fraction (LVEF) ≤35%, as current significant implantable cardioverter-defibrillator (ICD) indication for primary prevention of sudden cardiac death (SCD) in heart failure (HF) patients, has been widely recognised to be inefficient. Improvement of patient selection for low LVEF (≤35%) is needed to optimise deployment of ICD. Most of the existing prediction models are not appropriate to identify ICD candidates at high risk of SCD in HF patients with low LVEF. Compared with traditional statistical analysis, machine learning (ML) can employ computer algorithms to identify patterns in large datasets, analyse rules automatically and build both linear and non-linear models in order to make data-driven predictions. This study is aimed to develop and validate new models using ML to improve the prediction of SCD in HF patients with low LVEF.Methods and analysisWe will conduct a retroprospective, multicentre, observational registry of Chinese HF patients with low LVEF. The HF patients with LVEF ≤35% after optimised medication at least 3 months will be enrolled in this study. The primary endpoints are all-cause death and SCD. The secondary endpoints are malignant arrhythmia, sudden cardiac arrest, cardiopulmonary resuscitation and rehospitalisation due to HF. The baseline demographic, clinical, biological, electrophysiological, social and psychological variables will be collected. Both ML and traditional multivariable Cox proportional hazards regression models will be developed and compared in the prediction of SCD. Moreover, the ML model will be validated in a prospective study.Ethics and disseminationThe study protocol has been approved by the Ethics Committee of the First Affiliated Hospital of Nanjing Medical University (2017-SR-06). All results of this study will be published in international peer-reviewed journals and presented at relevant conferences.Trial registration numberChiCTR-POC-17011842; Pre-results.
Impact of audit and feedback with action implementation toolbox on improving ICU pain management: cluster-randomised controlled trial
Authors: Roos-Blom Marie-José , Gude Wouter T , de Jonge Evert , Spijkstra Jan Jaap , van der Veer Sabine N , Peek Niels , Dongelmans Dave A , de Keizer Nicolette F 
Published: July 2019

BackgroundAudit and feedback (A&F) enjoys widespread use, but often achieves only marginal improvements in care. Providing recipients of A&F with suggested actions to overcome barriers (action implementation toolbox) may increase effectiveness.ObjectiveTo assess the impact of adding an action implementation toolbox to an electronic A&F intervention targeting quality of pain management in intensive care units (ICUs).Trial designTwo-armed cluster-randomised controlled trial. Randomisation was computer generated, with allocation concealment by a researcher, unaffiliated with the study. Investigators were not blinded to the group assignment of an ICU.ParticipantsTwenty-one Dutch ICUs and patients eligible for pain measurement.InterventionsFeedback-only versus feedback with action implementation toolbox.OutcomeProportion of patient-shift observations where pain management was adequate; composed by two process (measuring pain at least once per patient in each shift; re-measuring unacceptable pain scores within 1 hour) and two outcome indicators (acceptable pain scores; unacceptable pain scores normalised within 1 hour).Results21 ICUs (feedback-onlyn=11;feedback-with-toolboxn=10) with a total of 253 530 patient-shift observations were analysed. We found absolute improvement on adequate pain management in thefeedback-with-toolboxgroup (14.8%; 95% CI 14.0% to 15.5%) and thefeedback-onlygroup (4.8%; 95% CI 4.2% to 5.5%). Improvement was limited to the two process indicators. Thefeedback-with-toolboxgroup achieved larger effects than thefeedback-onlygroup both on the composite adequate pain management (p<0.05) and on measuring pain each shift (p<0.001). No important adverse effects have occurred.ConclusionFeedback with toolbox improved the number of shifts where patients received adequate pain management compared with feedback alone, but only in process and not outcome indicators.Trial registration numberNCT02922101.
Flow diagnostics for naturally fractured reservoirs
Authors: Spooner Victoria , Geiger Sebastian , Arnold Dan 
Published: July 2019

Reliable production forecasting for fractured carbonate reservoirs is a challenge. Natural fractures, adverse wettability and complex matrix heterogeneity are all uncertain and can all negatively impact upon recovery. Ideally, we should consider different reservoir concepts encapsulated in a large ensemble of reservoir models to quantify the impact of these and other geological uncertainties on reservoir performance. However, the computational cost of considering many scenarios can be significant, especially for dual porosity/permeability models, rendering robust uncertainty quantification impractical for most asset teams.
Flow diagnostics provide a complement to full-physics simulations for comparing models. Flow diagnostics approximate the dynamic response of the reservoir in seconds. In this paper we describe the extension of flow diagnostics to dual porosity models for naturally fractured reservoirs. Our new diagnostic tools link the advective time of flight in the fractures to the transfer from the matrix, identifying regions where transfer and flux are not in balance leading to poor matrix oil sweep and early breakthrough. Our new diagnostics tools have been applied to a real field case and are shown to compare well with full-physics simulation results.

Thematic collection:
This article is part of the Naturally Fractured Reservoirs collection available at:
https://www.lyellcollection.org/cc/naturally-fractured-reservoirs
Mapeo del proceso clínico de pacientes con ideación suicida activa que consultan en el Centro de Salud Familiar “San Alberto Hurtado” en Chile
Authors: Gómez Cannobbio Constanza , González Gutiérrez Constanza , Hasbún Zegpi Catalina , Santander Barría María Jesús , Beca Jofré Paulina , Bittner Salgado Marcela , Rojas González Pamela 
Published: July 2019

Introducción: el suicidio es un fenómeno complejo y prevalente. En Chile, los centros de atención primaria pesquisan pacientes con ideación suicida activa y los derivan a centros terciarios, pero el proceso es complejo y poco fluido.El objetivo de este trabajo fue mapear el proceso clínico que siguen los pacientes con ideación suicida activa derivados desde el Centro de Salud Familiar Áncora San Alberto Hurtado en Santiago, Chile. Métodos: se realizaron reuniones con los principales protagonistas y se recolectaron protocolos de manejo. Se graficaron los procesos clínicos según la edad del paciente, identificando nudos, brechas y quiebres. Resultados: los pacientes menores de 15 años son derivados al servicio de urgencia pediátrica en el Complejo Asistencial Dr. Sótero del Río, donde son evaluados por un psiquiatra infanto-juvenil, quien determina si son dados de alta para continuar seguimiento en el nivel secundario o son hospitalizados. Los pacientes mayores de 15 años son referidos al servicio de urgencia psiquiátrica del Complejo Asistencial Barros Luco Trudeau para ser evaluados por un psiquiatra, quien evalúa si requieren seguimiento a nivel secundario u hospitalización. En este último caso, son derivados nuevamente al Hospital Sótero del Río. Se identificaron nudos, brechas y quiebres que dificultan la atención y seguimiento de los pacientes. Conclusión: existen condiciones que afectan el proceso clínico de pacientes con ideación suicida activa derivados desde un centro de atención primaria, y es fundamental reparar las dificultades identificadas para ofrecer a la población una atención en salud mental eficiente.
Serum Urate, Genetic Variation, and Prostate Cancer Risk: Atherosclerosis Risk in Communities (ARIC) Study
Authors: Wang Anqi , Barber John R. , Tin Adrienne , De Marzo Angelo M. , Kottgen Anna , Joshu Corinne E. , Platz Elizabeth A. 
Published: July 2019

Abstract

Background:
Evidence is mounting that intraprostatic inflammation influences prostate cancer development. Uric acid crystals depositing in the prostate could result in injury and inflammation, increasing prostate cancer risk.

Methods:
Included were 6,574 men ages 45–64 years who enrolled in the Atherosclerosis Risk in Communities study in 1987 to 1989. We used Cox proportional hazards regression to estimate the association of serum urate concentration alone and to improve accuracy, jointly with a genetic risk score (GRS, N = 4,983) derived from variants predictive of urate concentration, with prostate cancer (N = 813) risk.

Results:
Serum urate concentration or joint categories of urate concentration and GRS were not associated with prostate cancer risk (Ptrend for quartiles = 0.3). Results were generally similar by race and after excluding users of medications that influence uric acid.

Conclusions:
Serum urate alone and with a urate-associated GRS were not associated with prostate cancer risk.

Impact:
It is unlikely that circulating urate concentration influences prostate cancer development.
Mechanisms of Innate and Acquired Resistance to Anti-EGFR Therapy: A Review of Current Knowledge with a Focus on Rechallenge Therapies
Authors: Parseghian Christine M. , Napolitano Stefania , Loree Jonathan M. , Kopetz Scott 
Published: July 2019

AbstractInnate and acquired resistance to anti-EGFR therapy (EGFRi) is a major limitation in the treatment of metastatic colorectal cancer (mCRC). Although RAS genes are the most commonly mutated innate and acquired oncogenes in cancer, there are a number of other mechanisms that limit the effectiveness of EGFRi. Patients with innate resistance have been found to contain BRAFV600E mutations, and possibly MET, MEK, PIK3CA, PTEN, and HER2 alterations. Meanwhile, BRAFV600E mutations may also be involved in acquired resistance to EGFRi, in addition to EGFR ectodomain mutations, MET alterations, and possibly HER2 amplification. In addition, paracrine effects and cell-fate mechanisms of resistance are being increasingly described as contributing to acquired resistance. Utilization of circulating tumor DNA has been paramount in monitoring the dynamic nature of acquired resistance and has helped to guide treatment decisions, particularly in the EGFRi rechallenge setting. Herein, we provide an in-depth review of EGFRi-resistance mechanisms and describe the current therapeutic landscape in the hopes of identifying effective rechallenge strategies.
Mismatch Repair–Proficient Colorectal Cancer: Finding the Right TiME to Respond
Authors: Willis Jason A. , Overman Michael J. , Vilar Eduardo 
Published: July 2019

Abstract
New approaches are required for addressing the important and unmet need to expand the benefits of checkpoint blockade to patients with mismatch repair proficient colorectal cancer. Systematic profiling of the tumor immune microenvironment provides insights into potential mechanisms of resistance, predictive biomarkers, and novel combinatorial strategies for overcoming resistance.
See related article by Llosa et al., p. 5250
Predictive Potential of Head and Neck Squamous Cell Carcinoma Organoids
Authors: Hill Sarah J. , D'Andrea Alan D. 
Published: July 2019

Abstract

Summary:
In this issue of Cancer Discovery, Driehuis and colleagues establish culture conditions for the rapid, efficient, and long-term expansion of healthy human oral mucosa and head and neck squamous cell carcinoma (HNSCC) tumor organoids. The HNSCC tumor organoids provide a functional platform for analyzing tumor cell phenotype, tumorigenic potential, and drug and radiotherapy response, and they have a potential role in clinical decision-making.
See related article by Driehuis et al., p. 852.
Lymphoma Chemotherapy: Hungry Macrophages Strike the Final Blow
Authors: Duval Florent , De Palma Michele 
Published: July 2019

Abstract

Summary:
Macrophages modulate tumor response to chemotherapy; in this issue, Lossos and colleagues show that high-dose alkylating agents instigate a synthetic lethal program in lymphoma cells that is independent of DNA damage and involves recruitment and priming of macrophages for antibody-mediated tumor phagocytosis. These findings implicate chemotherapy-elicited macrophages as critical effectors of lymphoma clearance during biological therapy.
See related article by Lossos et al., p. 944.
Recharacterizing Tumor-Infiltrating Lymphocytes by Single-Cell RNA Sequencing
Authors: Zhang Lei , Zhang Zemin 
Published: July 2019

Abstract
T cells are central players in cancer immunotherapy. Despite much concentrated effort on the study of tumor-infiltrating lymphocytes (TIL), such as T cells, a series of fundamental properties that include heterogeneity, clonal expansion, migration, and functional state transition remain elusive. Advances of single-cell sequencing have enabled the detailed characterization of immune cells in tumors and have vastly improved our understanding of less-defined cell subsets. Here, we discuss the current strategies for uncovering the heterogeneity of TILs, and how the deep transcriptome coupled with T-cell receptor analysis enhances the understanding of detailed properties of T-cell subsets. We further discuss the identification of novel T-cell markers with therapeutic or prognosis potentials, and highlight distinct T-cell properties among different cancer indications.
Arterial Remodeling and Dysfunction in the ZSF1 Rat Model of Heart Failure With Preserved Ejection Fraction
Authors: Leite Sara , Cerqueira Rui J. , Ibarrola Jaime , Fontoura Dulce , Fernández-Celis Amaya , Zannad Faiez , Falcão-Pires Inês , Paulus Walter J. , Leite-Moreira Adelino F. , Rossignol Patrick , López-Andrés Natalia , Lourenço André P. 
Published: July 2019

Background:
The interplay between the stiffened heart and vessels has long been viewed as a core mechanism in heart failure with preserved ejection fraction, but the incremental vascular molecular remodeling mechanisms from systemic arterial hypertension to heart failure with preserved ejection fraction remain poorly investigated. Our aim was to characterize central arterial remodeling and dysfunction in ZSF1 obese rats and to compare it with hypertensive ZSF1 lean and healthy Wistar-Kyoto controls.

Methods and Results:
Twenty-week-old male ZSF1 obese (n=9), lean (n=9), and Wistar-Kyoto rats (n=9) underwent left ventricular pressure-volume loop evaluation and synchronous acquisition of ascending aortic flow and pressure. Aortic rings underwent functional evaluation, histology, and molecular biology studies. Although mean arterial pressure, characteristic aortic impedance, and reactivity to phenylephrine were similarly increased in hypertensive ZSF1 lean and obese, only ZSF1 obese showed impaired relaxation and upward-shifted end-diastolic pressure-volume relationships despite preserved systolic function indexes, denoting heart failure with preserved ejection fraction. ZSF1 obese phenotype further showed decreased aortic compliance, increased wave reflection, and impaired direct NO donor and endothelial-mediated vasodilation which were accompanied on structural and molecular grounds by aortic media thickening, higher collagen content and collagen/elastin ratio, increased fibronectin and α-5 integrin protein expression and upregulated TGF (transforming growth factor)-β and CTGF (connective tissue growth factor) levels.

Conclusions:
Functional, molecular, and structural disturbances of central vessels and their potentially underlying pathways were newly characterized in experimental heart failure with preserved ejection fraction rendering the ZSF1 obese rat model suitable for preclinical testing.
Modern Muslim Subjectivities: Religion and Multiple Modernities within Islam
Authors: Jung Dietrich 
Published: July 2019

AbstractThis article presents the overarching theoretical framework and some tentative findings of the Modern Muslim Subjectivities Project (MMSP). It discusses some of its conceptual tools and presents strategies for studying the role of religion in modern Muslim subjectivity formation. The core rationale of this research program is to explore the role of religious traditions in the construction of modern forms of Muslim subjectivity and social order. It investigates the ways in which Muslims have imagined specifically Islamic modernities in combination with non-religious and globally relevant cultural scripts. In criticizing the alleged Western origin and secular nature of modernity, the MMSP aims at making original contributions both to conceptual discussions of modernity in the study of religions and to our knowledge of modern Muslim societies.
Daily Ritual, Mission, and the Transformation of the Self: the Case of Tablighi Jamaat
Authors: Pieri Zacharias 
Published: July 2019

AbstractTablighi Jamaat (TJ) is Islam’s largest movement, with estimates of up to 80 million Muslims taking part in its activities. Having originated on the Indian subcontinent, TJ has expanded to have a strong presence across the globe. Traditionally, TJ is known for bringing lapsed Muslims back to a stricter understanding of Islam and the recommendation that its male (and to an increasing extent also its female) members spend a certain portion of time each year working on the “path of Allah” — that is, on missionary activities. Tablighi leaders are conscious that participation in the movement impacts not only those who are the targets of missionary activity but also those who are doing the missionizing, having a powerful effect upon the formation of selfhoods. TJ also emphasizes the importance of imitating the Prophet Muhammad, and members are encouraged to ritualize every aspect of their life in accordance with the Prophet’s example. The ritualization of everyday practices, a focus on purity and mission, combined with textual (re)interpretation, contribute to individual and collective identity construction among members of TJ. For TJ, the formation of modern Muslim selfhoods is of vital importance, as they believe that an identity centered on an authentic form of Islam can protect Muslims in a fast-changing world.
An Islamic University in the West and the Question of Modern Authenticity
Authors: Sinclair Kirstine 
Published: July 2019

AbstractThe aim of this article is to discuss how Islamic universities in the West facilitate and condition the formation of modern Muslim subjectivities in minority contexts, with an emphasis on the institutions as providers of guidelines for good, Muslim minority life. This is done through a case study of Cambridge Muslim College in the UK. Its values and aims are explored through interviews with the founder and dean, faculty members and students, and through participatory observation. Cambridge Muslim College sees itself as a mediator between Islamic traditions and modern Muslims in the West, and as responsible for engaging in the development of both Muslim minorities and the wider society within which it operates. The questions guiding the study are the following: What role do Islamic universities play in shaping modern Muslim subjectivities in the West? How does Cambridge Muslim College combine understandings of authenticity with preparing their students for professional careers in Britain? The study shows that the understanding of authenticity that is encouraged by college dean Shaykh Abdal Hakim provides an important tool for the students as they strive to form meaningful selves and careers in contemporary Britain. Thus, references to authentic Islam is used to support the development of both working and moral modern subjects.