bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing wildfire spread modelling by building a gridded fuel moisture content product with machine learning
Authors: McCandless Tyler C , Kosovic Branko , Petzke William 
Published: July 2020

Abstract
Wildland fire decision support systems require accurate predictions of wildland fire spread. Fuel moisture content (FMC) is one of the important parameters controlling the rate of spread of wildland fire. However, dead FMC measurements are provided by a relatively sparse network of remote automatic weather stations (RAWS), while live FMC is relatively infrequently measured manually. We developed a high resolution, gridded, real-time FMC data sets that did not previously exist for assimilation into operational wildland fire prediction systems based on ML. We used surface observations of live and dead FMC to train machine learning models to estimate FMC based on satellite observations. Moderate Resolution Imaging Spectrometer Terra and Aqua reflectances are used to predict the live and dead FMC measured by the Wildland Fire Assessment System and RAWS). We evaluate multiple machine learning methods including multiple linear regression, random forests (RFs), gradient boosted regression and artificial neural networks. The models are trained to learn the relationships between the satellite reflectances, surface weather and soil moisture observations and FMC. After training on data corresponding to the temporally and spatially nearest grid points to the irregularly spaced surface FMC observations, the machine learning models could be applied to all grid cells for a gridded product over the Conterminous United States (CONUS). The results show generally that the rule-based approaches have the lowest errors likely due to the sharp decision boundaries among the predictors, and the RF approach that utilizes bagging to avoid over-fitting has the lowest error on the test dataset. The errors are typically between 25%−33% the typical variability of the FMC data, which indicate the skill of the RF in estimating the FMC based on satellite data and surface characteristics. The FMC gridded product based on the RF runs operationally daily over CONUS and can be assimilated into WRF-Fire for more accurate wildland fire spread predictions.
Deprescribing in older people approaching end-of-life: development and validation of STOPPFrail version 2
Authors: Curtin Denis , Gallagher Paul , O’Mahony Denis 
Published: July 2020

Abstract

Background
Screening Tool of Older Persons Prescriptions in Frail adults with limited life expectancy (STOPPFrail) criteria were developed in 2017 to assist physicians with deprescribing decisions in older people approaching end-of-life. Updating was required to make the tool more practical, patient-centred and complete.

Methods
a thorough literature review was conducted to, first, devise a practical method for identifying older people who are likely to be approaching end-of-life, and second, reassess and update the existing deprescribing criteria. An eight-member panel with a wide-ranging experience in geriatric pharmacotherapy reviewed a new draft of STOPPFrail and were invited to propose new deprescribing criteria. STOPPFrail version 2 was then validated using Delphi consensus methodology.

Results
STOPPFrail version 2 emphasises the importance of shared decision-making in the deprescribing process. A new method for identifying older people who are likely to be approaching end-of-life is included along with 25 deprescribing criteria. Guidance relating to the deprescribing of antihypertensive therapies, anti-anginal medications and vitamin D preparations comprises the new criteria.

Conclusions
STOPPFrail criteria have been updated to assist physicians in efforts to reduce drug-related morbidity and burden for their frailest older patients. Version 2 is based on an up-to-date literature review and consensus validation by a panel of experts.
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
Authors: Sadeqi Azer Erfan , Rashidi Mehrabadi Farid , Malikić Salem , Li Xuan Cindy , Bartok Osnat , Litchfield Kevin , Levy Ronen , Samuels Yardena , Schäffer Alejandro A , Gertz E Michael , Day Chi-Ping , Pérez-Guijarro Eva , Marie Kerrie , Lee Maxwell P , Merlino Glenn , Ergun Funda , Sahinalp S Cenk 
Published: July 2020

Abstract

Motivation
Recent advances in single-cell sequencing (SCS) offer an unprecedented insight into tumor emergence and evolution. Principled approaches to tumor phylogeny reconstruction via SCS data are typically based on general computational methods for solving an integer linear program, or a constraint satisfaction program, which, although guaranteeing convergence to the most likely solution, are very slow. Others based on Monte Carlo Markov Chain or alternative heuristics not only offer no such guarantee, but also are not faster in practice. As a result, novel methods that can scale up to handle the size and noise characteristics of emerging SCS data are highly desirable to fully utilize this technology.

Results
We introduce PhISCS-BnB (phylogeny inference using SCS via branch and bound), a branch and bound algorithm to compute the most likely perfect phylogeny on an input genotype matrix extracted from an SCS dataset. PhISCS-BnB not only offers an optimality guarantee, but is also 10–100 times faster than the best available methods on simulated tumor SCS data. We also applied PhISCS-BnB on a recently published large melanoma dataset derived from the sublineages of a cell line involving 20 clones with 2367 mutations, which returned the optimal tumor phylogeny in &lt;4 h. The resulting phylogeny agrees with and extends the published results by providing a more detailed picture on the clonal evolution of the tumor.

Availability and implementation
https://github.com/algo-cancer/PhISCS-BnB.

Supplementary information
Supplementary data are available at Bioinformatics online.
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
Authors: Comte Nicolas , Morel Benoit , Hasić Damir , Guéguen Laurent , Boussau Bastien , Daubin Vincent , Penel Simon , Scornavacca Celine , Gouy Manolo , Stamatakis Alexandros , Tannier Eric , Parsons David P 
Published: July 2020

Abstract

Motivation
Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists.

Results
We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview.

Availability and implementation
Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/.
Sweeping the flies away: evidence from a fruit fly eradication program
Authors: Salazar Lina , Aramburu Julian , Agurto Marcos , Maffioli Alessandro , Fahsbender Jossie 
Published: July 2020

Abstract
This article evaluates the short-term impacts of a fruit fly integrated pest management program in Peru. Exploiting arbitrary variation in the program’s intervention borders, we use a geographical regression discontinuity design to identify the program’s effects on agricultural outcomes. Pre-treatment balance tests show that producer and farm-level pre-treatment characteristics evolve smoothly at the intervention border. Results indicate that farmers within treated areas improved pest knowledge and are more likely to implement prevention and control practices. Also, they increased fruit production and sales. Our findings are confirmed by placebo tests and are robust to alternative regression discontinuity bandwidths and polynomials.
Oesophageal Probe Evaluation in Radiofrequency Ablation of Atrial Fibrillation (OPERA): results from a prospective randomized trial
Authors: Schoene Katharina , Arya Arash , Grashoff Friederike , Knopp Helge , Weber Alexander , Lerche Matthias , König Sebastian , Hilbert Sebastian , Kircher Simon , Bertagnolli Livio , Dinov Borislav , Hindricks Gerhard , Halm Ulrich , Zachäus Markus , Sommer Philipp 
Published: July 2020

Abstract

Aims
The aim of the study was to determine the incidence of oesophageal lesions after radiofrequency ablation (RFA) of atrial fibrillation (AF) with or without the use of oesophageal temperature probes.

Methods and results
Two hundred patients were prospectively randomized into two groups: the OPERA+ group underwent RFA using oesophageal probes (SensiTherm™); the OPERA− group received RFA using fixed energy levels of 25 W at the posterior wall without an oesophageal probe. All patients underwent post-interventional endoscopy and Holter-electrocardiogram after 6 months. (Clinical.Trials.gov: NCT03246594). One hundred patients were randomized in OPERA+ and 100 patients in OPERA−. The drop-out rate was 10%. In total, 18/180 (10%) patients developed endoscopically diagnosed oesophageal lesions (EDEL). There was no difference between the groups with 10/90 (11%) EDEL in OPERA+ vs. 8/90 (9%) in OPERA− (P = 0.62). Despite the higher power delivered at the posterior wall in OPERA+ [28 ± 4 vs. 25 ± 2 W (P = 0.001)], the average EDEL size was equal [5.7 ± 2.6 vs. 4.5 ± 1.7 mm (P = 0.38)]. The peak temperature did not correlate with EDEL size. During follow-up, no patient died. Only one patient in OPERA− required a specific therapy for treatment of the lesion. Cumulative AF recurrence after 6 (3–13) months was 28/87 (32%) vs. 34/88 (39%), P = 0.541.

Conclusion
This first randomized study demonstrates that intraoesophageal temperature monitoring using the SensiTherm™ probe does not affect the probability of developing EDEL. The peak temperature measured by the thermoprobe seems not to correlate with the incidence of EDEL. Empiric energy reduction at the posterior wall did not affect the efficacy of the procedure.
Arrhythmic burden in patients with new-onset persistent left bundle branch block after transcatheter aortic valve replacement: 2-year results of the MARE study
Authors: Muntané-Carol Guillem , Urena Marina , Nombela-Franco Luis , Amat-Santos Ignacio , Kleiman Neal , Munoz-Garcia Antonio , Atienza Felipe , Serra Vicenç , Deyell Marc W , Veiga-Fernandez Gabriela , Masson Jean-Bernard , Canadas-Godoy Victoria , Himbert Dominique , Castrodeza Javier , Elizaga Jaime , Francisco Pascual Jaume , Webb John G , de la Torre Hernandez Jose M , Asmarats Lluis , Pelletier-Beaumont Emilie , Philippon Francois , Rodés-Cabau Josep 
Published: July 2020

Abstract

Aims
We determined the incidence and type of arrhythmias at 2-year follow-up in patients with new-onset persistent left bundle branch block (LBBB) following transcatheter aortic valve replacement (TAVR).

Methods and results
Multicentre prospective study including 103 consecutive patients with new-onset persistent LBBB post-TAVR (SAPIEN XT/3: 53; CoreValve/Evolut R: 50). An implantable cardiac monitor (Reveal XT, Reveal Linq) was implanted before hospital discharge and patients had continuous monitoring for up to 2 years. Arrhythmic events were adjudicated in a central core lab. 1836 new arrhythmic events (tachyarrhythmias: 1655 and bradyarrhythmias: 181) occurred at 2 years. Of these, 283 (15%) occurred beyond 1 year (tachyarrhythmias 212, bradyarrhythmias 71) in 33 (36%) patients, without differences between valve type. Most late (&gt;1 year) arrhythmic events were asymptomatic (94%) and led to a treatment change in 17 (19%) patients. A total of 71 late bradyarrhythmias [high-degree atrioventricular block (HAVB): 3, severe bradycardia: 68] were detected in 17 (21%) patients. At 2 years, 18 (17%) patients had received a permanent pacemaker (PPM) or implantable cardiac-defibrillator. PPM implantation due to HAVB predominated in the early phase post-TAVR, with only 1 HAVB event requiring PPM implantation after 1 year.

Conclusion
Patients with new-onset LBBB post-TAVR exhibited a very high burden of arrhythmic events within the 2 years post-procedure. While new tachyarrhythmic events were homogeneously distributed over time, the vast majority of new HAVB episodes leading to PPM implantation occurred early after the procedure. These results should help to guide the management of this challenging group of patients. (clinicaltrials.gov: NCT02153307)
Prospective use of ablation index for the ablation of right ventricle outflow tract premature ventricular contractions: a proof of concept study
Authors: Gasperetti Alessio , Sicuso Rita , Dello Russo Antonio , Zucchelli Giulio , Saguner Ardan Muammer , Notarstefano Pasquale , Soldati Ezio , Bongiorni Maria Grazia , Della Rocca Domenico Giovanni , Mohanty Sanghamitra , Carbucicchio Corrado , Duru Firat , Di Biase Luigi , Natale Andrea , Tondo Claudio , Casella Michela 
Published: July 2020

Abstract

Aims
Radiofrequency catheter ablation (RFCA) represents an effective option for idiopathic premature ventricular contractions (PVCs) treatment. Ablation Index (AI) is a novel ablation marker incorporating RF power, contact force, and time of delivery into a single weighted formula. Data regarding AI-guided PVCs RFCA are currently lacking. Aim of the study was to compare AI-guided and standard RFCA outcomes in patients with PVCs originating from the right ventricle outflow tract (RVOT).

Methods and results
Consecutive patients undergoing AI-guided RFCA of RVOT idiopathic PVCs were prospectively enrolled. Radiofrequency catheter ablation was performed following per-protocol target cut-offs of AI, depending on targeted area (RVOT free wall AI cut-off: 590; RVOT septum AI cut-off: 610). A multi-centre cohort of propensity-matched (age, sex, ejection fraction, and PVC site) patients undergoing standard PVCs RFCA was used as a comparator. Sixty AI-guided patients (44.2 ± 18.0 years old, 58% male, left ventricular ejection fraction 56.2 ± 3.8%) were enrolled; 34 (57%) were ablated in RVOT septum and 26 (43%) patients in the RVOT free wall area. Propensity match with 60 non-AI-guided patients was performed. Acute outcomes and complications resulted comparable. At 6 months, arrhythmic recurrence was more common in non-AI-guided patients whether in general (28% vs. 7% P = 0.003) or by ablated area (RVOT free wall: 27% vs. 4%, P = 0.06; RVOT septum 29% vs. 9% P = 0.05). Ablation Index guidance was associated with improved survival from arrhythmic recurrence [overall odds ratio 6.61 (1.95–22.35), P = 0.001; RVOT septum 5.99 (1.21–29.65), P = 0.028; RVOT free wall 11.86 (1.12–124.78), P = 0.039].

Conclusion
Ablation Index-guidance in idiopathic PVCs ablation was associated with better arrhythmic outcomes at 6 months of follow-up.
Long-term cardiometabolic disease risk in women with PCOS: a systematic review and meta-analysis
Authors: Wekker V , van Dammen L , Koning A , Heida K Y , Painter R C , Limpens J , Laven J S E , Roeters van Lennep J E , Roseboom T J , Hoek A 
Published: July 2020

Abstract

BACKGROUND
Polycystic ovary syndrome (PCOS) is associated with cardiometabolic disease, but recent systematic reviews and meta-analyses of longitudinal studies that quantify these associations are lacking.

OBJECTIVE AND RATIONALE
Is PCOS a risk factor for cardiometabolic disease?

SEARCH METHODS
We searched from inception to September 2019 in MEDLINE and EMBASE using controlled terms (e.g. MESH) and text words for PCOS and cardiometabolic outcomes, including cardiovascular disease (CVD), stroke, myocardial infarction, hypertension (HT), type 2 diabetes (T2D), metabolic syndrome and dyslipidaemia. Cohort studies and case–control studies comparing the prevalence of T2D, HT, fatal or non-fatal CVD and/or lipid concentrations of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TGs) between women with and without PCOS of ≥18 years of age were eligible for this systematic review and meta-analysis. Studies were eligible regardless of the degree to which they adjusted for confounders including obesity. Articles had to be written in English, German or Dutch. Intervention studies, animal studies, conference abstracts, studies with a follow-up duration less than 3 years and studies with less than 10 PCOS cases were excluded. Study selection, quality assessment (Newcastle–Ottawa Scale) and data extraction were performed by two independent researchers.

OUTCOMES
Of the 5971 identified records, 23 cohort studies were included in the current systematic review. Women with PCOS had increased risks of HT (risk ratio (RR): 1.75, 95% CI 1.42 to 2.15), T2D (RR: 3.00, 95% CI 2.56 to 3.51), a higher serum concentration of TC (mean difference (MD): 7.14 95% CI 1.58 to 12.70 mg/dl), a lower serum concentration of HDL-C (MD: −2.45 95% CI −4.51 to −0.38 mg/dl) and increased risks of non-fatal cerebrovascular disease events (RR: 1.41, 95% CI 1.02 to 1.94) compared to women without PCOS. No differences were found for LDL-C (MD: 3.32 95% CI −4.11 to 10.75 mg/dl), TG (MD 18.53 95% CI −0.58 to 37.64 mg/dl) or coronary disease events (RR: 1.78, 95% CI 0.99 to 3.23). No meta-analyses could be performed for fatal CVD events due to the paucity of mortality data.

WIDER IMPLICATIONS
Women with PCOS are at increased risk of cardiometabolic disease. This review quantifies this risk, which is important for clinicians to inform patients and to take into account in the cardiovascular risk assessment of women with PCOS. Future clinical trials are needed to assess the ability of cardiometabolic screening and management in women with PCOS to reduce future CVD morbidity.
Outcomes of patients diagnosed with COVID-19 in the early postoperative period following cardiac surgery
Authors: Yates Martin T , Balmforth Damian , Lopez-Marco Ana , Uppal Rakesh , Oo Aung Y 
Published: July 2020

Abstract
The coronavirus 2019 (COVID-19) pandemic has disrupted patient care across the NHS. Following the suspension of elective surgery, priority was placed in providing urgent and emergency surgery for patients with no alternative treatment. We aim to assess the outcomes of patients undergoing cardiac surgery who have COVID-19 infection diagnosed in the early postoperative period. We identified 9 patients who developed COVID-19 infection following cardiac surgery. These patients had a significant length of hospital stay and extremely poor outcomes with mortality of 44%. In conclusion, the outcome of cardiac surgical patients who contracted COVID-19 infection perioperatively is extremely poor. In order to offer cardiac surgery, units must implement rigorous protocols aimed at maintaining a COVID-19 protective environment to minimize additional life-threatening complications related to this virus infection.
Design of a partially premixed burner for biogas-fired wall-mounted boiler
Authors: Sun Mengxiao , Huang Xiaomei , Zhao Yi , Zhang Pengyuan , Zhou Yang 
Published: July 2020

Abstract
Biogas is deemed as one of the most promising renewable fuels emerging in the past several decades. At present, biogas is mainly applied to cooking for substituting fossil fuels. However, biogas is rarely reported to be used for space heating. In this paper, we designed a biogas-fired partially premixed burner for gas-fired wall-mounted boilers, which has the heat input of 25 kW and can be used for space heating and water heater tank heating. The reference gas was assumed as 60% of methane (CH4) and 40% of CO2, and the burner port area was designed as 4744.5 mm2 according to the calculation. Then, experiments were conducted to study the performance of this burner. Jet diameters were modified in order to investigate their effects on heat input, primary air ratio and flame stability of the burner. The results indicate that the burner shows superior performance when the jet diameter is 2.0 mm. Meanwhile, the primary air ratio (${\alpha}^{\prime }$) satisfies the design requirement. Moreover, a gas-fired wall-mounted boiler with this burner was examined to investigate the influence of different biogas composition on exhaust emissions and thermal efficiency. The results show that the concentration of CO in the flue gas meets the national standard when CH4 varied from 40% to 60% in the biogas. However, the thermal efficiency of the biogas-fired wall-mounted boiler reduces greatly with the increase of CH4 percentage.
A Chronic Murine Disease Model of Coccidioidomycosis Using Coccidioides posadasii, Strain 1038
Authors: Shubitz Lisa F , Powell Daniel A , Butkiewicz Christine D , Lewis M Lourdes , Trinh Hien T , Frelinger Jeffrey A , Orbach Marc J , Galgiani John N 
Published: July 2020

Abstract
Murine infections with most Coccidioides spp. strains are lethal by 3 weeks, limiting the study of immune responses. Coccidioides posadasii, strain 1038 (Cp1038), while slowly lethal, resulted in protracted survival of C57BL/6 (B6) mice. In resistant (B6D2)F1/J mice, lung fungal burdens stabilized by week 4 without progression through week 16, better modeling human coccidioidal infections after their immunologic control. Immunodeficient tumor necrosis factor (Tnf) α knockout (KO) and interferon (Ifn) γ receptor 1 (Ifn-γr1) KO mice survived a median of 22.5 and 34 days, compared with 70 days in B6 mice (P = .001 and P &lt; .01, respectively), though 14-day lung fungal burden studies showed little difference between Ifn-γr1 KO and B6 mice. B6 mice showed peak concentrations of key inflammatory lung cytokines, including interleukin 6, 23, and 17A, Tnf-α, and Ifn-γ, only after 4 weeks of infection. The slower progression in B6 and the acquired fungal burden stability in B6D2 mice after Cp1038 infection greatly increases the array of possible immunologic studies.