bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of clinical staging for T2N0 oesophageal cancer: systematic review and meta-analysis
Authors: Wolfson Paul , Ho Kai Man Alexander , Bassett Paul , Haidry Rehan , Olivo Alessandro , Lovat Laurence , Sami Sarmed S 
Published: February 2021

Summary
Oesophageal cancer is the sixth commonest cause of overall cancer mortality. Clinical staging utilizes multiple imaging modalities to guide treatment and prognostication. T2N0 oesophageal cancer is a treatment threshold for neoadjuvant therapy. Data on accuracy of current clinical staging tests for this disease subgroup are conflicting. We performed a meta-analysis of all primary studies comparing clinical staging accuracy using multiple imaging modalities (index test) to histopathological staging following oesophagectomy (reference standard) in T2N0 oesophageal cancer. Patients that underwent neoadjuvant therapy were excluded. Electronic databases (MEDLINE, Embase, Cochrane Library) were searched up to September 2019. The primary outcome was diagnostic accuracy of combined T&N clinical staging. Publication date, first recruitment date, number of centers, sample size and geographical location main histological subtype were evaluated as potential sources of heterogeneity. The search strategy identified 1,199 studies. Twenty studies containing 5,213 patients met the inclusion criteria. Combined T&N staging accuracy was 19% (95% CI, 15–24); T staging accuracy was 29% (95% CI, 24–35); percentage of patients with T downstaging was 41% (95% CI, 33–50); percentage of patients with T upstaging was 28% (95% CI, 24–32) and percentage of patients with N upstaging was 34% (95% CI, 30–39). Significant sources of heterogeneity included the number of centers, sample size and study region. T2N0 oesophageal cancer staging remains inaccurate. A significant proportion of patients were downstaged (could have received endotherapy) or upstaged (should have received neoadjuvant chemotherapy). These findings were largely unchanged over the past two decades highlighting an urgent need for more accurate staging tests for this subgroup of patients.
State-of-the-art intra-procedural imaging for the mitral and tricuspid PASCAL Repair System
Authors: Hahn Rebecca T , Kodali Susheel K 
Published: February 2021

Abstract
Advanced intra-procedural imaging techniques have been integral to technical and procedural success transcatheter devices. A novel leaflet approximation therapy, the PASCAL Transcatheter Valve Repair System (Edwards Lifesciences, Irvine, CA, USA) has demonstrated high procedural success, acceptable safety, and significant clinical improvement in patients with severe mitral and tricuspid regurgitation and has CE mark approval in Europe with pivotal trials underway in the USA. This review outlines the pre-procedural imaging views and advanced transoesophageal imaging protocols both mitral and tricuspid valve device implantation.
Myocardial work in Stage 1 and 2 hypertensive patients
Authors: Jaglan Akshar , Roemer Sarah , Perez Moreno Ana Cristina , Khandheria Bijoy K 
Published: February 2021

Abstract

Aims
Myocardial work (MW) is a novel parameter that can be used in a clinical setting to assess left ventricular (LV) pressures and deformation. We sought to distinguish patterns of global MW index in hypertensive vs. non-hypertensive patients and to look at differences between categories of hypertension.

Methods and results
Sixty-five hypertensive patients (mean age 65 ± 13 years; 30 male) and 15 controls (mean age 38 ± 12 years; 7 male) underwent transthoracic echocardiography at rest. Hypertensive patients were subdivided into Stage 1 (n = 32) and Stage 2 (n = 33) hypertension based on 2017 American College of Cardiology guidelines. Exclusion criteria were suboptimal image quality for myocardial deformation analysis, reduced ejection fraction, valvular heart disease, intracardiac shunt, and arrhythmia. Global work index (GWI), global constructive work (GCW), global wasted work (GWW), and global work efficiency were estimated from LV pressure–strain loops utilizing proprietary software from speckle-tracking echocardiography. LV systolic and diastolic pressures were estimated using non-invasive brachial artery cuff pressure. Global longitudinal strain and LV ejection fraction were preserved between the groups with no statistically significant difference, whereas there was a statically significant difference between the control and two hypertension groups in GWI (P = 0.01), GCW (P &lt; 0.001), and GWW (P &lt; 0.001).

Conclusion
Non-invasive MW analysis allows better understanding of LV response under conditions of increased afterload. MW is an advanced assessment of LV systolic function in hypertension patients, giving a closer look at the relationship between LV pressure and contractility in settings of increased load dependency than LV ejection fraction and global longitudinal strain.
Use of sepsis-related diagnostic criteria in primary care: a survey among general practitioners
Authors: Mulders Merijn C F , Loots Feike J , van Nieuwenhoven Joey , ter Maaten Jan C , Bouma Hjalmar R 
Published: February 2021

Abstract

Background
Use of sepsis-criteria in hospital settings is effective in realizing early recognition, adequate treatment and reduction of sepsis-associated morbidity and mortality. Whether general practitioners (GPs) use these diagnostic criteria is unknown.

Objective
To gauge the knowledge and use of various diagnostic criteria. To determine which parameters GPs associate with an increased likelihood of sepsis.

Methods
Two thousand five hundred and sixty GPs were invited and 229 agreed to participate in a survey, reached out to through e-mail and WhatsApp groups. The survey consisted of two parts: the first part aimed to obtain information about the GP, training and knowledge about sepsis recognition, and the second part tested specific knowledge using six realistic cases.

Results
Two hundred and six questionnaires, representing a response rate of 8.1%, were eligible for analysis. Gut feeling (98.1%) was the most used diagnostic method, while systemic inflammatory response syndrome (37.9%), quick Sequential Organ Failure Assessment (qSOFA) (7.8%) and UK Sepsis Trust criteria (UKSTc) (1.5%) were used by the minority of the GPs. Few of the responding GPs had heard of either the qSOFA (27.7%) or the UKSTc (11.7%). Recognition of sepsis varied greatly between GPs. GPs most strongly associated the individual signs of the qSOFA (mental status, systolic blood pressure, capillary refill time and respiratory rate) with diagnosing sepsis in the test cases.

Conclusions
GPs mostly use gut feeling to diagnose sepsis and are frequently not familiar with the ‘sepsis-criteria’ used in hospital settings, although clinical reasoning was mostly in line with the qSOFA score. In order to improve sepsis recognition in primary care, GPs should be educated in the use of available screening tools.
Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water
Authors: Rahlff Janina , Stolle Christian , Giebel Helge-Ansgar , Mustaffa Nur Ili Hamizah , Wurl Oliver , P. R. Herlemann Daniel 
Published: February 2021

ABSTRACT
The occurrence of foams at oceans’ surfaces is patchy and generally short-lived, but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here, we investigated how marine foams differ from the sea-surface microlayer (SML), a &lt;1-mm-thick layer at the air–sea interface, and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed distinctive foam bacterial communities compared with SML and underlying water, with high abundance of Gammaproteobacteria. Typical SML dwellers such as Pseudoalteromonas and Vibrio were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports the previous assumption that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air–sea exchange processes in the ocean.
Effects of Sample Plot Size and Prediction Models on Diameter Distribution Recovery
Authors: Bankston Josh B , Sabatia Charles O , Poudel Krishna P 
Published: February 2021

Abstract
Distribution of tree diameters in a stand is characterized using models that predict diameter moments and/or percentiles in conjunction with a mathematical system to recover the parameters of an assumed statistical distribution. Studies have compared Weibull diameter distribution recovery systems but arrived at different conclusions regarding the best approach for recovering a stand’s diameter distribution from predicted stand-level statistics. We assessed the effects of sample plot size and diameter moments/percentiles prediction models on the accuracy of three approaches used in recovering Weibull distribution parameters—method of moments, percentile method, and moments-percentile hybrid method. Data from five plot sizes, four of which were virtually created from existing larger plots, from unthinned loblolly pine (Pinus taeda) plantations, were used to fit moments/percentile prediction models and to evaluate the accuracy of the diameter distribution recovered using three approaches. Both plot size and prediction model form affected the accuracy of the recovery approaches as indicated by the changes in their ranking from one plot size to another for the same model form. The method of moments approach ranked best when the evaluation error index did not account for tree stumpage value, but the moments-percentile hybrid approach ranked best when stumpage value was considered.
Mutation of a major CG methylase alters genome-wide lncRNA expression in rice
Authors: Li Juzuo , Li Ning , Zhu Ling , Zhang Zhibin , Li Xiaochong , Wang Jinbin , Xun Hongwei , Zhao Jing , Wang Xiaofei , Wang Tianya , Wang Hongyan , Liu Bao , Li Yu , Gong Lei 
Published: February 2021

Abstract
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2−/−) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2−/− due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5′-upstream genomic regions of lncRNAs in OsMET1-2−/−. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
Implementation of dCas9-mediated CRISPRi in the fission yeast Schizosaccharomyces pombe
Authors: Ishikawa Ken , Soejima Saeko , Masuda Fumie , Saitoh Shigeaki 
Published: February 2021

Abstract
Controllable and reversible transcriptional repression is an essential method to study gene functions. A systematic knock-down method using catalytically inactive Cas9 (dCas9) was originally established in bacteria. dCas9 forms a ribonucleoprotein with a small guide RNA and uses it to recognize a specific DNA sequence via Watson-Crick base-pairing. When specifically bound to a targeted DNA, dCas9 impairs RNA polymerase activity and represses transcription of that target gene. This technology, CRISPRi, has been implemented in several organisms, but not in Schizosaccharomyces pombe using dCas9. Here, we provide a plasmid that expresses dCas9 and sgRNA in fission yeast. With this plasmid, CRISPRi repressed endogenous gene transcription by as much as 87%. This transcriptional repression method is controllable, reversible, and efficient enough to alter cellular phenotypes. Here, we offer a CRISPRi method to choose proper targeting sequences for transcriptional repression in fission yeast. Implementation of CRISPRi will help to reveal gene functions and to develop tools based on dCas9 technology in S. pombe.
A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout
Authors: Gao Guangtu , Magadan Susana , Waldbieser Geoffrey C , Youngblood Ramey C , Wheeler Paul A , Scheffler Brian E , Thorgaard Gary H , Palti Yniv 
Published: February 2021

Abstract
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is shown through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.
Using WhatsApp messenger for health systems research: a scoping review of available literature
Authors: Manji Karima , Hanefeld Johanna , Vearey Jo , Walls Helen , de Gruchy Thea 
Published: February 2021

Abstract
Globally, the use of mobile phones for improving access to healthcare and conducting health research has gained traction in recent years as rates of ownership increase, particularly in low- and middle-income countries (LMICs). Mobile instant messaging applications, including WhatsApp Messenger, provide new and affordable opportunities for health research across time and place, potentially addressing the challenges of maintaining contact and participation involved in research with migrant and mobile populations, for example. However, little is known about the opportunities and challenges associated with the use of WhatsApp as a tool for health research. To inform our study, we conducted a scoping review of published health research that uses WhatsApp as a data collection tool. A key reason for focusing on WhatsApp is the ability to retain contact with participants when they cross international borders. Five key public health databases were searched for articles containing the words &#x02018;WhatsApp&#x02019; and &#x02018;health research&#x02019; in their titles and abstracts. We identified 69 articles, 16 of which met our inclusion criteria for review. We extracted data pertaining to the characteristics of the research. Across the 16 studies&#x02014;11 of which were based in LMICs&#x02014;WhatsApp was primarily used in one of two ways. In the eight quantitative studies identified, seven used WhatsApp to send hyperlinks to online surveys. With one exception, the eight studies that employed a qualitative (n&#x02009;&#x0003D;&#x02009;6) or mixed-method (n&#x02009;&#x0003D;&#x02009;2) design analysed the WhatsApp content generated through a WhatsApp-based programmatic intervention. We found a lack of attention paid to research ethics across the studies, which is concerning given the controversies WhatsApp has faced with regard to data protection in relation to end-to-end encryption. We provide recommendations to address these issues for researchers considering using WhatsApp as a data collection tool over time and place.
Impact of a prolonged COVID-19 lockdown on patterns of admission, mortality and performance indicators in a cardiovascular intensive care unit
Authors: Szarfer Jorge Luis , Puente Luciana , Bono Leandro , Estrella María Laura , Doppler Eugenia , Napoli Llobera Mariano , Arce María Patricia , Borri Karina Alejandra , Fiandesio Mariana Elisa , Ferraris Marta Josefina , Gagliardi Juan 
Published: February 2021

AbstractBackgroundThe effects of an early and prolonged lockdown during the coronavirus disease 2019 (COVID-19) pandemic on cardiovascular intensive care units (CICUs) are not well established.ObjectivesThis study analyses patterns of admission, mortality and performance indicators in a CICU before and during the Argentine lockdown in the COVID-19 pandemic.MethodsThis is a retrospective observational cross-sectional study of all consecutive patients aged 18 years or more admitted to the cardiac intensive care unit at a high-volume reference hospital in Buenos Aires, Argentina, comparing hospitalization rates, primary causes of admission, inpatient utilization indicators, pharmacy supplies’ expenditures and in-hospital mortality between 5 March and 31 July 2020, with two corresponding control periods in 2019 and 2018.ResultsWe included 722 female patients [mean age of 61.6 (SD 15.5) years; 237 (32.8%)]. Overall hospitalizations dropped 53.2% (95%CI: 45.3, 61.0%), from 295.5 patients/year over the periods 2018/2019 to 137 patients in 2020. Cardiovascular disease–related admissions dropped 59.9%, while admission for non-cardiac causes doubled its prevalence from 9.6% over the periods 2018/2019 to 22.6% in the study period (P &lt; 0.001).In the period 2020, the bed occupancy rate fell from 82.2% to 77.4%, and the bed turnover rate dropped 50% from 7.88 to 3.91 monthly discharges/bed. The average length of stay doubled from 3.26 to 6.75 days, and the turnover interval increased from 3.8 to 8.39 days in 2020.Pharmacy supplies’ expenditures per discharge increased 134% along with a rise in antibiotics usage from 6.5 to 11.4 vials/ampoules per discharge (P &lt; 0.02).Overall mortality increased from 7% (n = 41) to 13.9% (n = 19) (P = 0.008) at the expense of non-cardiac-related admissions (3.6–19.4%, P = 0.01).ConclusionsThis study found a significant reduction in overall and cardiovascular disease–related causes of admission to the cardiac intensive care unit, worse performance indicators and increased in-hospital mortality along the first 5 months of the early and long-lasting COVID-19 lockdown in Argentina. These results highlight the need to foster public awareness concerning the risks of avoiding hospital attendance. Moreover, health systems should follow strict screening protocols to prevent potential biases in the admission of patients with critical conditions unrelated to the COVID-19 pandemic.
Uniform criteria for total hip replacement surgery in patients with hip osteoarthritis: a decision tool to guide treatment decisions
Authors: Atsma Femke , Molenkamp Olivier , Bouma Heinse , Bolder Stefan B , Groenewoud A Stef , Westert Gert P 
Published: February 2021

Abstract

Background
Uniform criteria for performing hip replacement surgery in hip osteoarthritis patients are currently lacking. As a result, variation in surgery and inappropriateness of care may occur. The aim of this study was to develop a consensus-based decision tool to support the decision-making process for hip replacement surgery.

Methods
Patients with a diagnosis of unilateral or bilateral osteoarthritis were included. Consensus rounds with orthopedic surgeons were organized to blindly reassess medical files and to decide whether surgery is indicated or not, based on all available pre-treatment information. We compared the outcomes obtained from the blind reassessment by the consensus group with the actual treatment. Furthermore, prediction models were fitted on the reassessment outcome to identify which set of clinical parameters would be most predictive and uniformly shared in the decision to operate.
Two prediction models were fitted, one model without radiologic outcomes and one model where radiologic outcomes were included.

Results
In total, 364 medical files of osteoarthritis patients were included and reassessed in the analyses. Key predictors in the prediction model without radiology were age, flexion, internal rotation and the Hip disability and Osteoarthritis Outcome Score–quality of life. The discriminative power was high (Area Under Receiver Operating Curve (AUC) = 0.86). Key predictors in the prediction model with radiology were age, internal rotation and Kellgren and Lawrence severity score (AUC = 0.94).

Conclusion
The study yielded a decision tool with uniform criteria for hip replacement surgery in osteoarthritis patients. The tool will guide the clinical decision-making process of physicians on whether to perform hip surgery and should be used together with information about patient preferences and social context.