bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structuring of water molecules near a copper surface
Authors: Andryushchenko V A , Boyko E V 
Published: December 2020

Abstract
Using the molecular dynamics method, the structuring of water molecules near copper surfaces at various temperatures is studied. Samples with crystallographic orientations of 100 and 111 are considered at temperatures from 300 K to 350 K. It is found that the planes of water molecules in the near-surface region with the size is about six angstroms are oriented mainly parallel to the copper surface. However, the character of the structuring of water molecules near the copper surface weakly depends on the considered crystallographic orientations and temperatures.
How can digital building information modelling (BIM) facilitate climate transition in cities?
Authors: Andersson Réka , Eidenskog Maria 
Published: December 2020

Abstract
Digitalization of the construction industry is considered important in combating climate change through more efficient use of resources and better control of energy calculations. Digital modelling of buildings is argued to make building’s energy use more efficient through better energy management. However, research regarding the use of the promising digital tool Building Information Modelling (BIM) has shown that BIM creates unclear roles, division of responsibilities and that cultural barriers between professional groups can be a problem. This paper focuses on how the work with BIM is organized and what conditions are needed to create effective workflows with BIM. The methodology consists of a literature study of digitalization processes in the construction industry and workshops with different professionals. Workshops as a research method provides an exploratory way to understand complex issues, as well as knowledge processes, in relation to digital tools. The co-productive format of the workshops facilitates conversations where different professional groups meet and share experiences of working with BIM. The study shows that several requirements needs to be met to fully make use of the BIM potential. Communication between different professions, knowledge transfer over project boarders, different standards and competence, both within and in relation to the clients, are important components when working with BIM. There is a need for interdisciplinary work practices which are complicated by the project organizational form most used in construction industry. For BIM to be utilized as a tool to combat climate change in cities through effective resource planning, the organizational settings and workflows needs to be interdisciplinary and communication between departments, clients and professions must be standardized while still flexible.
Investigating the Efficacy of Genetic, Environmental, and Multifactorial Risk Information When Communicating Obesity Risk to Parents of Young Children
Authors: Persky Susan , Yaremych Haley E , Goldring Megan R , Ferrer Rebecca A , Rose Margaret K , Hollister Brittany M 
Published: December 2020

Abstract

Background
Effectively communicating with parents about children’s obesity risk is of critical importance for preventive medicine and public health.

Purpose
The current study investigates the efficacy of communications focused on two primary causes of obesity: genes and environment.

Methods
We compared parental feeding responses to messages focused on (i) genetics alone, (ii) family environment alone, (iii) genetics–family environment interaction (G × FE), and (iv) no causal message. We also examined whether parental guilt mediates the effect of message type on feeding. Our sample consisted of 190 parents, half mothers and half fathers, of children 3–7 years old. After receiving one of the four types of messages, parents chose foods for their child using the Virtual Reality Buffet measure. Parents responded to questionnaires in the lab and at 1-week follow-up.

Results
In the VR Buffet, parents did not feed their children differently in message provision conditions versus control. There were, however, differences among message provision conditions wherein mothers who received any genetic information chose higher-calorie meals in the VR Buffet. At 1-week follow-up, parents who received information about genetics alone reported feeding their child more junk food and fatty meat on self-report food frequency assessments; there were no such differences for sugary beverages, sugary foods, or fast foods. Parental guilt was typically higher for participants who received family environment information alone but did not mediate the relation between information provision and feeding outcomes.

Conclusions
While none of the messages improved feeding above the control condition, GxFE messages were associated with a better overall profile of outcomes. As such, it may be beneficial for messaging for parents about children’s obesity risk to include content that reflects the complexity of genetic and environmental contributions to obesity risk.
Targeting the Opioid Receptors: A Promising Therapeutic Avenue for Treatment in “Heavy Drinking Smokers”
Authors: Domi Ana , Barbier Estelle , Adermark Louise , Domi Esi 
Published: December 2020

Abstract

Aims
Despite a general decline in tobacco use in the last decades, the prevalence of tobacco smoking in individuals with alcohol use disorder (AUD) remains substantial (45–50%). Importantly, the co-use of both substances potentiates the adverse effects, making it a significant public health problem. Substantial evidence suggests that AUD and Tobacco use disorder (TUD) may share common mechanisms. Targeting these mechanisms may therefore provide more effective therapy. Numerous studies describe a potential role of the endogenous opioid system in both AUD and TUD. Reviewing this literature, we aim to evaluate the efficacy of molecules that target the opioid system as promising therapeutic interventions for treating alcohol and tobacco co-use disorders.

Methods
We provide a synthesis of the current epidemiological knowledge of alcohol and tobacco co-use disorders. We evaluate clinical and preclinical research that focuses on the regulation of the endogenous opioid system in alcohol, nicotine, and their interactions.

Results
The epidemiological data confirm that smoking stimulates heavy drinking and facilitates alcohol craving. Pharmacological findings suggest that treatments that are efficacious in the dual addiction provide a beneficial treatment outcome in comorbid AUD and TUD. In this regard, MOP, DOP and NOP-receptor antagonists show promising results, while the findings prompt caution when considering KOP-receptor antagonists as a treatment option in alcohol and tobacco co-use disorders.

Conclusions
Existing literature suggests a role of the opioid system in sustaining the high comorbidity rates of AUD and TUD. Molecules targeting opioid receptors may therefore represent promising therapeutic interventions in ‘heavy drinking smokers.’
Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction
Authors: Wang Wei , Liu Wei 
Published: December 2020

AbstractMotivationAccurately predicting the risk of cancer patients is a central challenge for clinical cancer research. For high-dimensional gene expression data, Cox proportional hazard model with the least absolute shrinkage and selection operator for variable selection (Lasso-Cox) is one of the most popular feature selection and risk prediction algorithms. However, the Lasso-Cox model treats all genes equally, ignoring the biological characteristics of the genes themselves. This often encounters the problem of poor prognostic performance on independent datasets.ResultsHere, we propose a Reweighted Lasso-Cox (RLasso-Cox) model to ameliorate this problem by integrating gene interaction information. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. We used random walk to evaluate the topological weight of genes, and then highlighted topologically important genes to improve the generalization ability of the RLasso-Cox model. Experiments on datasets of three cancer types showed that the RLasso-Cox model improves the prognostic accuracy and robustness compared with the Lasso-Cox model and several existing network-based methods. More importantly, the RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.Availability and implementationhttp://bioconductor.org/packages/devel/bioc/html/RLassoCox.htmlSupplementary informationSupplementary data are available at Bioinformatics online.
From matte banded to glossy black: structures underlying colour change in the caudal lures of southern death adders (Acanthophis antarcticus,Reptilia: Elapidae)
Authors: Crowe-Riddell Jenna M , Dix Stacey , Pieterman Ludo , Nankivell James H , Ford Matthew , Ludington Alastair J , Simões Bruno F , Dunstan Nathan , Partridge Julian C , Sanders Kate L , Allen Luke 
Published: December 2020

AbstractMany ambush-foraging snakes move their tails to entice prey within striking range (‘caudal luring’). During ontogeny, the conspicuous hues of caudal lures change to match the cryptic patterning of the body/head. This coincides with decreased luring behaviour and reflects the trade-off between prey acquisition and camouflage as the snake grows. Australo-Papuan death adders (Acanthophis, Elapidae) are unique in that both juveniles and adults use caudal luring, but ontogenetic colour change has not been investigated. We examined the spectral reflectance, microstructure and pigmentation of caudal skin in wild-sourced and captive bred Acanthophis antarcticus ranging in body size (snout-vent length 116–674 mm; mass 3–832 g; N = 33) to test whether colour properties change as snakes grow. We found that lure colour is distinct from the cryptic body skin across the life history, and changes from a matte banding pattern (grey/black) in neonates/juveniles, to uniform and glossy black with a yellow ventral stripe in larger snakes. These colour changes are caused by increases in dermal pigmentation and a transition to a smooth, interlocking epidermal microstructure. To understand the selection pressures that might be driving ontogenetic colour change in this species, further studies should test how different prey types respond to distinct lure morphologies.
Impact of COVID-19 outbreak on esophageal cancer surgery in Northern Italy: lessons learned from a multicentric snapshot
Authors: Rebecchi Fabrizio , Arolfo Simone , Ugliono Elettra , Morino Mario , Asti Emanuele , Bonavina Luigi , Borghi Felice , Coratti Andrea , Cossu Andrea , De Manzoni Giovanni , De Pascale Stefano , Ferrari Giovanni Carlo , Fumagalli Romario Uberto , Giacopuzzi Simone , Gualtierotti Monica , Guglielmetti Massimo , Merigliano Stefano , Pallabazzer Giovanni , Parise Paolo , Peri Andrea , Pietrabissa Andrea , Rosati Riccardo , Santi Stefano , Tribuzi Angela , Valmasoni Michele , Viganò Jacopo , Weindelmayer Jacopo 
Published: December 2020

AbstractCoronavirus Disease-19 (COVID-19) outbreak has significantly burdened healthcare systems worldwide, leading to reorganization of healthcare services and reallocation of resources. The Italian Society for Study of Esophageal Diseases (SISME) conducted a national survey to evaluate changes in esophageal cancer management in a region severely struck by COVID-19 pandemic. A web-based questionnaire (26 items) was sent to 12 SISME units. Short-term outcomes of esophageal resections performed during the lockdown were compared with those achieved in the same period of 2019. Six (50%) centers had significant restrictions in their activity. However, overall number of resections did not decrease compared to 2019, while a higher rate of open esophageal resections was observed (40 vs. 21.7%; P = 0.034). Surgery was delayed in 24 (36.9%) patients in 6 (50%) centers, mostly due to shortage of anesthesiologists, and occupation of intensive care unit beds from intubated COVID-19 patients. Indications for neoadjuvant chemo (radio) therapy were extended in 14% of patients. Separate COVID-19 hospital pathways were active in 11 (91.7%) units. COVID-19 screening protocols included nasopharyngeal swab in 91.7%, chest computed tomography scan in 8.3% and selective use of lung ultrasound in 75% of units. Postoperative interstitial pneumonia occurred in 1 (1.5%) patient. Recovery from COVID-19 pandemic was characterized by screening of patients in all units, and follow-up outpatient visits in only 33% of units. This survey shows that clinical strategies differed considerably among the 12 SISME centers. Evidence-based guidelines are needed to support the surgical esophageal community and to standardize clinical practice in case of further pandemics.
Similar outcomes with manual contact force ablation catheters and traditional catheters in the treatment of outflow tract premature ventricular complexes
Authors: Ábrahám Pál , Ambrus Mercédesz , Herczeg Szilvia , Szegedi Nándor , Nagy Klaudia Vivien , Salló Zoltán , Osztheimer István , Széplaki Gábor , Tahin Tamás , Merkely Béla , Gellér László 
Published: December 2020

Abstract

Aims
Unlike in atrial fibrillation ablation, there is a lack of appropriately sized and properly designed studies regarding outflow tract (OT) premature ventricular complex (PVC) ablation outcomes with contact force sensing (CFS) catheters. We aimed to compare the acute success-, complication-, and long-term recurrence rates of manual CFS catheters with traditional irrigated catheters (T) in OT PVC ablation.

Methods and results
Single-centre, propensity-matched data of 75–75 patients ablated for right-sided OT (RVOT) or left-sided OT (LVOT) PVCs in 2015–17 with CFS or T catheters were compared. Acute success rate, peri-procedural complications, post-procedural daily PVC burden, and long-term recurrence rates were compared on intention-to-treat basis. Acute success rate equalled 80% in both groups, with no difference in force values in the CFS group comparing successful or failed cases [12.0 (8.75–17.0) vs. 16.0 (10.25–22.25) g, P = 0.21]. There were three cases of pseudo-aneurysm and one cardiac tamponade. PVC burden fell significantly from baseline 22 (15–30)% to 2 (0–10)% (P &lt; 0.0001), with no difference between catheter types [CFS: 1 (0–7)% vs. T: 4 (1–12) %; P = 0.21]. There was no significant difference in recurrence-free survival of CFS and T catheters (58 vs. 59%, P = 0.29) during 12 months of follow-up, respectively. Recurrence in the CFS group did not differ either by the force exerted below or above the median value of 12 g (P = 0.66).

Conclusion
Both types of catheters can effectively reduce OT PVC burden with minimal serious complication rates. Ablation with CFS or T catheters gives similar acute- and long-term results.
Economic Depreciation of In-Woods Forestry Equipment in the US South
Authors: McConnell T Eric 
Published: December 2020

Abstract
Forestry machines sold at auctions across the southern United States covering the years 2005 to 2019 (n = 640) were compiled into three equipment categories—rubber-tired feller bunchers, grapple skidders, and trailer-mounted loaders—with inflationary effects removed. The data were discounted by a reliability function derived from a two-parameter Weibull distribution, which defined the probability of future operability at machine hours h and a wrecking value based on each machine’s specified worth as scrap. These adjusted salvage values were then transformed using the Box-Cox normal method. Age affected all fellers and certain manufacturers of skidders and loaders. A significant annual use effect was revealed for fellers and skidders. Interactions of age and use with horsepower revealed that machine size influenced buyers’ feller and skidder purchasing decisions. Manufacturer intercept and slope shifters pointed to potential brand recognition by buyers. Perceived quality differences between manufacturers, however, were not revealed. Depreciation occurred at ever-increasing rates over machine lifetime.
The Relationship of Accelerometer-Assessed Standing Time With and Without Ambulation and Mortality: The WHI OPACH Study
Authors: Jain Purva , Bellettiere John , Glass Nicole , LaMonte Michael J , Di Chongzhi , Wild Robert A , Evenson Kelly R , LaCroix Andrea Z 
Published: December 2020

Abstract

Background
Self-reported time spent standing has been associated with lower risk of mortality. No previous studies have examined this association using device-measured standing.

Method
This was a prospective cohort study of 5878 older (median age = 80 years), racial/ethnically diverse, community-dwelling women in the WHI Objective Physical Activity and Cardiovascular Health Study (OPACH). Women wore accelerometers for 1 week and were followed for mortality. The study applied previously validated machine learning algorithms to ActiGraph GT3X+ accelerometer data to separately measure time spent standing with and without ambulation. Cox proportional hazards models were used to estimate mortality risk adjusting for potential confounders. Effect modification by age, body mass index, moderate-to-vigorous physical activity, sedentary time, physical functioning, and race/ethnicity was evaluated.

Results
There were 691 deaths during 26 649 person-years of follow-up through March 31, 2018 (mean follow-up = 4.8 years). In fully adjusted models, all-cause mortality risk was lower among those with more standing without ambulation (quartile [Q] 4 vs Q1 HR = 0.63; 95% CI = 0.49–0.81, p-trend = .003) and more standing with ambulation (Q4 vs Q1 HR = 0.50; 95% CI = 0.35–0.71, p-trend &lt; .001). Associations of standing with ambulation and mortality were stronger among women with above-median sedentary time (HR = 0.51; 95% CI = 0.38–0.68) compared to women with below-median sedentary time (HR = 0.80; 95% CI = 0.59–1.07; p-interaction = .02).

Conclusions
In this prospective study among older women, higher levels of accelerometer-measured standing were associated with lower risks of all-cause mortality. Standing is an achievable approach to interrupting prolonged sedentary time, and if not contraindicated, is a safe and feasible behavior that appears to benefit health in older ages.
Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix
Authors: Bedő Justin , Di Stefano Leon , Papenfuss Anthony T 
Published: December 2020

Abstract

Motivation
A challenge for computational biologists is to make our analyses reproducible—i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers.

Results
We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees.

Availability and Implementation
BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).
The Patterns of Use of Medications for Inflammatory Bowel Disease During Pregnancy in the US and Sweden Are Changing
Authors: Bröms Gabriella , Friedman Sonia , Kim Seoyoung C , Wood Mollie E , Hernandez-Diaz Sonia , Brill Gregory , Bateman Brian T , Huybrechts Krista F , Desai Rishi J 
Published: December 2020

AbstractBackgroundPopulation-level data spanning different countries describing oral and parenteral treatment in pregnant women with inflammatory bowel disease (IBD) are scarce. We studied treatment with sulfasalazine/5-aminosalicylates, corticosteroids, thiopurines/immunomodulators, and tumor necrosis factor (TNF)-inhibitors in the United States (Optum Clinformatics Data Mart and the Medicaid Analytics Extract [MAX]) and in the Swedish national health registers.MethodsWe identified 2975 pregnant women in Optum (2004–2013), 3219 women in MAX (2001–2013), and 1713 women in Sweden (2006–2015) with a recorded diagnosis of IBD. We assessed patterns of use for each drug class according to filled prescriptions, assessing frequency of treatment continuation in those that were treated in the prepregnancy period.ResultsThe proportion of women with Crohn’s disease and ulcerative colitis on any treatment during pregnancy was 56.1% and 56.3% in Optum, 47.5% and 49.3% in MAX, and 61.3% and 64.7% in Sweden, respectively, and remained stable over time. Sulfasalazine/5-aminosalicylates was the most commonly used treatment in Crohn’s disease, ranging from 25.1% in MAX to 31.8% in Optum, and in ulcerative colitis, ranging from 34.9% in MAX to 53.6% in Sweden. From 2006 to 2012, the TNF-inhibitor use increased from 5.0% to 15.5% in Optum, from 3.6% to 8.5% in MAX, and from 0.7% to 8.3% in Sweden. Continuing TNF-inhibitor treatment throughout pregnancy was more common in Optum (55.8%) and in MAX (43.0%) than in Sweden (11.8%).ConclusionsIn this population-based study from 2 countries, the proportion of women with IBD treatment in pregnancy remained relatively constant. TNF-inhibitor use increased substantially in both countries.
Early Changes in Serum Albumin Predict Clinical and Endoscopic Outcomes in Patients With Ulcerative Colitis Starting Anti-TNF Treatment
Authors: Lee Sun-Ho , Walshe Margaret , Oh Eun Hye , Hwang Sung Wook , Park Sang Hyoung , Yang Dong-Hoon , Byeon Jeong-Sik , Myung Seung-Jae , Yang Suk-Kyun , Greener Tomer , Weizman Adam V , Silverberg Mark S , Ye Byong Duk 
Published: December 2020

Abstract

Background
Up to 60% of patients with ulcerative colitis (UC) ultimately fail anti-tumor necrosis factor (TNF) treatment. We aimed to investigate early predictive markers of clinical and endoscopic outcomes in patients with UC who were anti-TNF-naïve commencing anti-TNF treatment, with particular focus on changes in albumin and C-reactive protein levels in the first 2 weeks of treatment.

Methods
We retrospectively investigated 210 patients with UC who started infliximab or adalimumab between 2009 and 2016 (male, 62.4%; median age at diagnosis, 37.9 years [interquartile range, 25.5–48.9 years]; median follow-up duration, 3.3 years [1.9–5.0 years]). Logistic and Cox proportional-hazards regressions were performed to identify variables associated with primary nonresponse (PNR), endoscopic outcomes, time-to-colectomy, and anti-TNF failure.

Results
Forty-one patients (19.5%) experienced PNR; week 0/week 2 ratio serum albumin was associated with PNR (adjusted odds ratio [aOR], 1.8; 95% confidence interval [CI], 1.1–2.9, per interquartile range increase). Week 0/week 2 ratio albumin was also associated with endoscopic response (aOR, 0.28; 95% CI, 0.31–0.82) and endoscopic remission (aOR, 0.61; 95% CI, 0.39–0.96) at weeks 8 to 14, time-to-colectomy (adjusted hazard ratio, 2.12; 95% CI, 1.29–3.49) and time-to-anti-TNF failure (adjusted hazard ratio, 1.54; 95% CI, 1.22–1.96), regardless of age, disease severity, or in-patient status. Association with time-to-colectomy and anti-TNF failure was externally validated in an independent cohort of inpatients with UC starting infliximab.

Conclusions
Change in serum albumin within the first 2 weeks of anti-TNF treatment is predictive of PNR, endoscopic outcomes, time-to-colectomy, and anti-TNF failure in patients with UC. Timely access to this biomarker enables early identification of patients with UC at risk of anti-TNF failure and may guide early optimization of anti-TNF treatment to improve disease outcomes.