bluuebunny/crossref_metadata_2025_split huggingface dataset:
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking
Authors: Ambrosetti Francesco , Olsen Tobias Hegelund , Olimpieri Pier Paolo , Jiménez-García Brian , Milanetti Edoardo , Marcatilli Paolo , Bonvin Alexandre M J J 
Published: July 2020

Abstract

Motivation
Monoclonal antibodies are essential tools in the contemporary therapeutic armory. Understanding how these recognize their antigen is a fundamental step in their rational design and engineering. The rising amount of publicly available data is catalyzing the development of computational approaches able to offer valuable, faster and cheaper alternatives to classical experimental methodologies used for the study of antibody–antigen complexes.

Results
Here, we present proABC-2, an update of the original random-forest antibody paratope predictor, based on a convolutional neural network algorithm. We also demonstrate how the predictions can be fruitfully used to drive the docking in HADDOCK.

Availability and implementation
The proABC-2 server is freely available at: https://wenmr.science.uu.nl/proabc2/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Selection of side of ovulation by intraovarianism in Bos taurus heifers†
Authors: Ginther O J 
Published: July 2020

Abstract
Intraovarianism refers to mechanisms within an ovary that affect the local follicle and luteal dynamics and is well-represented in heifers by greater frequency of ovulation from the right ovary (RO) than the left ovary (LO). On average, the RO has more 6-mm follicles than the LO before one follicle is selected to deviate in diameter and become the future ovulatory follicle. Therefore, the ovulatory follicle is more frequently selected from the RO. More follicles in the RO likely develop before birth as indicated by greater weight of the RO with more 0.3- to 4.8-mm follicles in recently born calves. It has been proposed that differences in intraovarianism between sides are a consequence of differences between sides in the inherent intraovarian angioarchitecture. The frequency of the pair of ovulations at the beginning and end of 900 interovulatory intervals (IOI) was lowest for the left/left (LL) pair (16%) and higher and similar among the RR, LR, and RL pairs (28% each). The lower frequency of LO ovulation was entirely a function of the LL pair as indicated by the lower frequency of the LL than RR pairs without a difference among the RR, LR, and RL pairs. Ovulations from the opposite sides at the beginning and end of an IOI (LR and RL pairs) would not have contributed to a difference in ovulation frequency between LO and RO. In conclusion, the greater frequency of RO (56%) than LO (44%) ovulation was mathematically and functionally a direct consequence of the low frequency of the LL pair of ovulations.
Hydroxychloroquine for Early Treatment of Adults With Mild Coronavirus Disease 2019: A Randomized, Controlled Trial
Authors: Mitjà Oriol , Corbacho-Monné Marc , Ubals Maria , Tebé Cristian , Peñafiel Judith , Tobias Aurelio , Ballana Ester , Alemany Andrea , Riera-Martí Núria , Pérez Carla A , Suñer Clara , Laporte Pep , Admella Pol , Mitjà Jordi , Clua Mireia , Bertran Laia , Sarquella Maria , Gavilán Sergi , Ara Jordi , Argimon Josep M , Casabona Jordi , Cuatrecasas Gabriel , Cañadas Paz , Elizalde-Torrent Aleix , Fabregat Robert , Farré Magí , Forcada Anna , Flores-Mateo Gemma , Muntada Esteve , Nadal Núria , Narejos Silvia , Nieto Aroa , Prat Nuria , Puig Jordi , Quiñones Carles , Reyes-Ureña Juliana , Ramírez-Viaplana Ferran , Ruiz Lidia , Riveira-Muñoz Eva , Sierra Alba , Velasco César , Vivanco-Hidalgo Rosa Maria , Sentís Alexis , G-Beiras Camila , Clotet Bonaventura , Vall-Mayans Martí 
Published: July 2020

Abstract

Background
No effective treatments for coronavirus disease 2019 (COVID-19) exist. We aimed to determine whether early treatment with hydroxychloroquine (HCQ) would be efficacious for outpatients with COVID-19.

Methods
Multicenter open-label, randomized, controlled trial conducted in Catalonia, Spain, between 17 March and 26 May 2020. Patients recently diagnosed with &lt;5-day of symptom onset were assigned to receive HCQ (800 mg on day 1 followed by 400 mg once daily for 6 days) or usual care. Outcomes were reduction of viral load in nasopharyngeal swabs up to 7 days after treatment start, disease progression up to 28 days, and time to complete resolution of symptoms. Adverse events were assessed up to 28 days.

Results
A total of 293 patients were eligible for intention-to-treat analysis: 157 in the control arm and 136 in the intervention arm. The mean age was 41.6 years (SD, 12.6), mean viral load at baseline was 7.90 log10 copies/mL (SD, 1.82), and median time from symptom onset to randomization was 3 days. No differences were found in the mean reduction of viral load at day 3 (−1.41 vs −1.41 log10 copies/mL in the control and intervention arm, respectively) or at day 7 (−3.37 vs −3.44). Treatment did not reduce risk of hospitalization (7.1% control vs 5.9% intervention) nor shorten the time to complete resolution of symptoms (12 days, control vs 10 days, intervention). No relevant adverse events were reported.

Conclusions
In patients with mild COVID-19, no benefit was observed with HCQ beyond the usual care.
Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group
Authors: Godsey James H , Silvestro Angela , Barrett J Carl , Bramlett Kelli , Chudova Darya , Deras Ina , Dickey Jennifer , Hicks James , Johann Donald J , Leary Rebecca , Lee Jerry S H , McMullen Joe , McShane Lisa , Nakamura Katherine , Richardson Aaron O , Ryder Matthew , Simmons John , Tanzella Kelli , Yee Laura , Leiman Lauren C 
Published: July 2020

AbstractLiquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC’s Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors’ presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.
Dual Targeted Therapy: A Possible Option for the Management of Refractory Inflammatory Bowel Disease
Authors: Privitera Giuseppe , Onali Sara , Pugliese Daniela , Renna Sara , Savarino Edoardo , Viola Anna , Ribaldone Davide Giuseppe , Buda Andrea , Bezzio Cristina , Fiorino Gionata , Fantini Massimo Claudio , Scaldaferri Franco , Guidi Luisa , Danese Silvio , Gasbarrini Antonio , Orlando Ambrogio , Armuzzi Alessandro 
Published: July 2020

Abstract

Background and Aims
Dual targeted therapy [DTT] has been proposed as a novel therapeutic strategy for the management of complicated patients with inflammatory bowel diseases [IBD]. Our aim here was to investigate the safety and effectiveness of this approach in a real-life setting.

Methods
We retrospectively extracted data from IBD patients receiving DTT in Italian IBD referral centres. Baseline characteristics, clinical activity of intestinal and extra-intestinal disease, and C-reactive protein levels were recorded. All adverse events were reported. Clinical effectiveness, biochemical remission and safety of DTT were investigated.

Results
Sixteen patients were identified; indications for DTT were: ‘active IBD’ or ‘active EIM’ despite ongoing biological therapy. The most commonly used DTT were: vedolizumab + ustekinumab [three patients] and vedolizumab + adalimumab [three patients]. Clinical response of intestinal or extra-intestinal symptoms, according to the indication for DTT, was reported by all patients by the end of the induction. Four patients discontinued DTT during follow-up. Three patients experienced an adverse event; no serious adverse event was reported.

Conclusions
DTT seems to be an effective and safe treatment and may represent an appealing therapeutic strategy for the management of complicated IBD patients.
Point-of-Care Ultrasound in Inflammatory Bowel Disease
Authors: Allocca Mariangela , Furfaro Federica , Fiorino Gionata , Peyrin-Biroulet Laurent , Danese Silvio 
Published: July 2020

Abstract
Inflammatory bowel diseases [IBD], including Crohn’s disease [CD] and ulcerative colitis [UC], are chronic, relapsing and destructive inflammatory disorders of the gastrointestinal tract which can lead to organ damage and impair quality of life. A ‘treat-to-target’ strategy based on activity and severity of disease and response to treatment with close monitoring of intestinal inflammation is recommended. Ileocolonoscopy [CS] is considered the first-line procedure for the assessment of IBD, and magnetic resonance enterography [MRE] is the current standard for assessing the small bowel and complications in CD, and has been proposed as an alternative procedure to CS in the evaluation of both ileo-colonic CD and UC. As that both CS and MRE are invasive and expensive procedures and unappealing to patients, they are unfeasible as frequent and repetitive tools for the monitoring of disease activity. Bowel ultrasound [US] represents a well-tolerated, non-invasive and cost-effective modality to manage IBD patients in clinical practice. Compared to CS and MRE, bowel US has been shown to have the same level of accuracy in assessing and monitoring disease activity and severity of both CD and UC. It can be performed at the point-of-care and therefore allow for real-time clinical decision-making. Point-of-care ultrasound [POCUS] is suggested as the stethoscope of the future and is gaining interest and diffusion in the medical field because it can be used for the bedside examination of patients. The aim of this review is to discuss point-of-care bowel ultrasound [POCBUS] in the management of patients with IBD.
The impact of coronavirus disease 2019 on the practice of thoracic oncology surgery: a survey of members of the European Society of Thoracic Surgeons (ESTS)
Authors: Depypere Lieven P , Daddi Niccolò , Gooseman Michael R , Batirel Hasan F , Brunelli Alessandro 
Published: July 2020

Abstract

OBJECTIVES
There is widespread acknowledgement that coronavirus disease 2019 (COVID-19) has disrupted surgical services. The European Society of Thoracic Surgeons (ESTS) sent out a survey to assess what impact the COVID-19 pandemic has had on the practice of thoracic oncology surgery.

METHODS
All ESTS members were invited (13–20 April 2020) to complete an online questionnaire of 26 questions, designed by the ESTS learning affairs committee.

RESULTS
The response rate was 23.0% and the completeness rate was 91.2%. The number of treated COVID-positive cases per hospital varied from fewer than 20 cases (30.6%) to more than 200 cases (22.7%) per hospital. Most hospitals (89.1%) postponed surgical procedures. All hospitals performed patient screening with a nasopharyngeal swab, but only 6.7% routinely tested health care workers. A total of 20% of respondents reported that multidisciplinary meetings were completely cancelled and 66%, that multidisciplinary decisions were not different from normal practice. Trends were recognized in prioritizing surgical patients based on age (younger than 70), type of surgery (lobectomy or less), size of tumour (T1–2) and lymph node involvement (N1). Sixty-three percent of respondents reported that surgeons were involved in daily care of COVID-19-positive patients. Fifty-three percent mentioned that full personal protective equipment was available to them when treating a COVID-19-positive patient.

CONCLUSIONS
The COVID-19 pandemic has created issues for the safety of health care workers, and surgeons have been forced to change their routine practice. However, there was no consensus about surgical priorities in lung cancer patients, demonstrating the need for the production of specific guidelines.
Why? – Successful Pseudomonas aeruginosa clones with a focus on clone C
Authors: Lee Changhan , Klockgether Jens , Fischer Sebastian , Trcek Janja , Tümmler Burkhard , Römling Ute 
Published: July 2020

ABSTRACT
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
Crises of commemoration: Cold War, decolonization and the bungled 1954 D-Day commemoration
Authors: Smith Andrew W M 
Published: July 2020

Abstract
In 1954, international dignitaries and veterans joined the commemoration of the Allied landings on the beaches of Normandy, though not everything went according to plan. For the French organizers, chief among them Gaullist deputy Raymond Triboulet, the event was intended to communicate a unifying, pro-Allied message amid a turbulent political climate. By June 1954, France had recently suffered a decisive defeat at Dien Bien Phu and was politically gripped by the divisive prospect of a European Defence Community. In debates over these crises, war memories surfaced and France’s experience of the Occupation and Liberation enflamed passions. For many who attended the Normandy ceremony in 1954, the missteps of organizers created tension and upset, endangering Allied participation in the Paris Liberation ceremonies to follow. This moment of disjuncture illuminates how currents of memory, international diplomacy, decolonization and broader Cold War tensions all intersected and influenced each other on the Normandy beaches.
Intercohort Variations in the Education–Health Gradient: Sociohistorical Changes in Early-Life Selection Mechanisms in the United States
Authors: Bhatta Tirth R 
Published: July 2020

Abstract

Objectives
Most prior studies on cohort-specific changes in the education gradient relative to health treat the distribution of education within a particular cohort as a “starting place” for understanding later-life health disparities. This premise has obfuscated the role that sociohistorical changes in early-life selection mechanisms play in the widening of education-based inequalities in functional limitations across birth cohorts.

Methods
Drawing from the Health and Retirement Survey (1992–2016; n = 20,920), this study employs inverse probability weight (IPW) to account for early-life selection mechanisms that are likely to affect both educational attainment and functional limitations. IPW-adjusted generalized linear mixed-effects models were used to estimate the total effect of education on functional limitations across birth cohorts (born 1924–1959).

Results
A significant linear decline in the negative effects of childhood socioeconomic disadvantage on education (β = 0.005, p &lt; .01) over the birth year was documented. By contrast, the same variable’s negative effect on functional health increased significantly (β = 0.006, p &lt; .001) across cohorts. Adjustment for childhood socioeconomic status did yield narrower education-based inequalities in functional limitations, but the difference between IPW-adjusted and unadjusted results was not statistically significant. The pattern of significant widening of education-based inequalities (β = −0.05, p &lt; .001) in functional limitations across birth cohorts was maintained.

Discussion
This study underscores the role that sociohistorical changes in early-life selection mechanisms play in modifying patterns of education-based inequalities in health across cohorts.
Positive semidefinite penalty method for quadratically constrained quadratic programming
Authors: Gu Ran , Du Qiang , Yuan Ya-xiang 
Published: July 2020

Abstract
Quadratically constrained quadratic programming (QCQP) appears widely in engineering applications such as wireless communications and networking and multiuser detection with examples like the MAXCUT problem and boolean optimization. A general QCQP problem is NP-hard. We propose a penalty formulation for the QCQP problem based on semidefinite relaxation. Under suitable assumptions we show that the optimal solutions of the penalty problem are the same as those of the original QCQP problem if the penalty parameter is sufficiently large. Then, to solve the penalty problem, we present a proximal point algorithm and an update rule for the penalty parameter. Numerically, we test our algorithm on two well-studied QCQP problems. The results show that our proposed algorithm is very effective in finding high-quality solutions.
Sequential implementation of the EQUIPPED geriatric medication safety program as a learning health system
Authors: Vandenberg Ann E , Kegler Michelle , Hastings S Nicole , Hwang Ula , Wu Daniel , Stevens Melissa B , Clevenger Carolyn , Eucker Stephanie , Genes Nick , Huang Wennie , Ikpe-Ekpo Edidiong , Nassisi Denise , Previll Laura , Rodriguez Sandra , Sanon Martine , Schlientz David , Vigliotti Debbie , Vaughan Camille P 
Published: July 2020

Abstract

Objectives
To present the three-site EQUIPPED academic health system research collaborative, which engaged in sequential implementation of the EQUIPPED medication safety program, as a learning health system; to understand how the organizations worked together to build resources for program scale-up.

Design
Following the Replicating Effective Programs framework, we analyzed content from implementation teams’ focus groups, local and cross-site meeting minutes and sites’ organizational profiles to develop an implementation package.

Setting
Three academic emergency departments that each implemented EQUIPPED over three successive years.

Participants
Implementation team members at each site participating in focus groups (n = 18), local meetings during implementation years, and cross-site meetings during all years of the projects.

Intervention(s)
EQUIPPED provides Emergency Department providers with clinical decision support (education, order sets, and feedback) to reduce prescribing of potentially inappropriate medications to adults aged 65 years and older who received a prescription at time of discharge.

Main Outcome Measure(s)
Implementation process components assembled through successive implementation.

Results
Each site had clinical and environmental characteristics to be addressed in implementing the EQUIPPED program. We identified 10 process elements and describe lessons for each. Lessons guided the compilation of the EQUIPPED intervention package or toolkit, including the EQUIPPED logic model.

Conclusions
Our academic health system research collaborative addressing medication safety through sequential implementation is a learning health system that can serve as a model for other quality improvement projects with multiple sites. The network produced an implementation package that can be vetted, piloted, evaluated, and finalized for large-scale dissemination in community-based settings.
Large variability in feeding behavior among crossbred growing cattle
Authors: Kelly David N , Sleator Roy D , Murphy Craig P , Conroy Stephen B , Judge Michelle M , Berry Donagh P 
Published: July 2020

Abstract
The purpose of this study was to define an extensive suite of feeding behavior traits in growing crossbred cattle and to investigate their phenotypic inter-relationships as well as relationships with other performance and efficiency traits. Time-series feeding behavior data, as well as feed intake and liveweight records, were available for 624 growing crossbred cattle, of which 445 were steers and 179 were heifers. Feeding behavior repeatability estimates were calculated using linear mixed models. Additionally, partial Spearman correlations were estimated among 14 feeding behavior traits, as well as between feeding behavior with both performance and feed efficiency traits, using residuals retained from linear mixed models. The marginal contribution of several feeding behavior traits to the variability in metabolizable energy intake (MEI) was also determined. Repeatability estimates of 0.57, 0.36, and 0.48 were calculated for the number of feed events per day, the total time spent feeding per day, and the feeding rate, respectively. Cattle that ate more frequently each day, ate at a faster rate and consumed less energy in each visit to the feed bunk. More efficient cattle fed less often per day and fed for a shorter duration per day; they also had a slower feeding rate and fed for longer in each visit to the feed bunk. Moreover, heavier cattle fed for a longer duration per day had a faster feeding rate, but fed less often per day; heavier animals also fed first in the pen after the fresh feed was offered. The number of feed events per day and feeding time per day together explained an additional 13.4 percentage points of the variability in MEI above that already explained by all of growth rate, liveweight, and backfat depth. The results from the present study suggest that several repeatable time-series-related feeding behavior traits, that are less resource intensive to measure, may have a role as useful predictor traits of important but relatively difficult to record traits, such as feed intake and efficiency.