bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-scale habitat selection limits trade-offs between foraging and temperature in a grassland bird
Authors: Londe David W , Elmore R Dwayne , Davis Craig A , Fuhlendorf Samuel D , Hovick Torre J , Luttbeg Barney , Rutledge Jimmy 
Published: February 2021

AbstractMany species are frequently faced with the decision about how to balance the use of thermal refuge against access to food resources. We evaluated the habitat use of female greater prairie chickens (Tympanuchus cupido) to assess the potential for trade-offs between thermal conditions and food resources during the habitat selection process. Our objectives were to 1) compare near-ground temperatures, invertebrate availability, and vegetation characteristics at sites used by greater prairie chickens to conditions at random landscape locations in various time since fire patches and 2) assess changes in conditions at used sites throughout the day to determine if selection for resources changes relative to ambient conditions, resulting in trade-offs between foraging sites and thermal refuge. We found that greater prairie chickens primarily used patches 0–12 months postfire that had relatively high abundances and biomasses of invertebrates compared to other time since fire patches. Greater prairie chickens further modified their selection at relatively fine spatial scales within these food-rich patches to select for areas with cooler temperatures during the hottest part of the day. The use of thermal refuge did not appear to influence the access to food resources as invertebrate abundance and biomass at used sites were consistent throughout the day. Our results show that food resources and thermal cover influences habitat selection for greater prairie chickens, but there was little evidence for trade-offs during the habitat selection process. Consideration of spatial and temporal scales is critical for evaluating trade-offs in habitat selection for animals and this research provides insights into the decision-making process by prairie chickens.
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Authors: Rougny Adrien , Touré Vasundra , Albanese John , Waltemath Dagmar , Shirshov Denis , Sorokin Anatoly , Bader Gary D , Blinov Michael L , Mazein Alexander 
Published: February 2021

Abstract
A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction
Authors: Ji Beihong , He Xibing , Zhai Jingchen , Zhang Yuzhao , Man Viet Hoang , Wang Junmei 
Published: February 2021

Abstract
Structure-based virtual screenings (SBVSs) play an important role in drug discovery projects. However, it is still a challenge to accurately predict the binding affinity of an arbitrary molecule binds to a drug target and prioritize top ligands from an SBVS. In this study, we developed a novel method, using ligand-residue interaction profiles (IPs) to construct machine learning (ML)-based prediction models, to significantly improve the screening performance in SBVSs. Such a kind of the prediction model is called an IP scoring function (IP-SF). We systematically investigated how to improve the performance of IP-SFs from many perspectives, including the sampling methods before interaction energy calculation and different ML algorithms. Using six drug targets with each having hundreds of known ligands, we conducted a critical evaluation on the developed IP-SFs. The IP-SFs employing a gradient boosting decision tree (GBDT) algorithm in conjunction with the MIN + GB simulation protocol achieved the best overall performance. Its scoring power, ranking power and screening power significantly outperformed the Glide SF. First, compared with Glide, the average values of mean absolute error and root mean square error of GBDT/MIN + GB decreased about 38 and 36%, respectively. Second, the mean values of squared correlation coefficient and predictive index increased about 225 and 73%, respectively. Third, more encouragingly, the average value of the areas under the curve of receiver operating characteristic for six targets by GBDT, 0.87, is significantly better than that by Glide, which is only 0.71. Thus, we expected IP-SFs to have broad and promising applications in SBVSs.
Provoking a Cultural Shift in Data Quality
Authors: McCord Sarah E , Webb Nicholas P , Van Zee Justin W , Burnett Sarah H , Christensen Erica M , Courtright Ericha M , Laney Christine M , Lunch Claire , Maxwell Connie , Karl Jason W , Slaughter Amalia , Stauffer Nelson G , Tweedie Craig 
Published: February 2021

Abstract
Ecological studies require quality data to describe the nature of ecological processes and to advance understanding of ecosystem change. Increasing access to big data has magnified both the burden and the complexity of ensuring quality data. The costs of errors in ecology include low use of data, increased time spent cleaning data, and poor reproducibility that can result in a misunderstanding of ecosystem processes and dynamics, all of which can erode the efficacy of and trust in ecological research. Although conceptual and technological advances have improved ecological data access and management, a cultural shift is needed to embed data quality as a cultural practice. We present a comprehensive data quality framework to evoke this cultural shift. The data quality framework flexibly supports different collaboration models, supports all types of ecological data, and can be used to describe data quality within both short- and long-term ecological studies.
‘Private Family Arrangements’ for Children in Ireland: The Informal Grey Space In-Between State Care and the Family Home
Authors: Burns Kenneth , O’Mahony Conor , Brennan Rebekah 
Published: February 2021

Abstract
The literature on alternative care focuses overwhelmingly on formal, court-ordered placements; voluntary care placements are discussed less frequently. Least attention of all has been given to informal kinship care placements, where a child is cared for by relatives but is not formally in the legal care of state authorities. In Ireland, these placements, when facilitated by state authorities in lieu of a care order or voluntary care agreement, are known by professionals as ‘private family arrangements’. This article explores evidence which shows that the use of such arrangements is motivated partly by a concern for subsidiarity, and partly by necessity: they provide a source of placements in cases where regulatory requirements and a lack of resources would otherwise make the placement challenging or impossible. However, this strategy carries significant risks. Private family arrangements receive less support and oversight from state authorities than formal care placements, and family members providing care under this model have no legal rights or responsibilities in respect of the child(ren). This places the child(ren) in a precarious position and raises concerns regarding a lack of equity of care. The article will illustrate the impact of these concerns and make recommendations for reform.
Impact of Anti–PD-1 and Anti–CTLA-4 on the Human Immunodeficiency Virus (HIV) Reservoir in People Living With HIV With Cancer on Antiretroviral Therapy: The AIDS Malignancy Consortium 095 Study
Authors: Rasmussen Thomas A , Rajdev Lakshmi , Rhodes Ajantha , Dantanarayana Ashanti , Tennakoon Surekha , Chea Socheata , Spelman Tim , Lensing Shelly , Rutishauser Rachel , Bakkour Sonia , Busch Michael , Siliciano Janet D , Siliciano Robert F , Einstein Mark H , Dittmer Dirk P , Chiao Elizabeth , Deeks Steven G , Durand Christine , Lewin Sharon R 
Published: February 2021

Abstract

Background
Antibodies to programmed cell death 1 (PD-1) and cytotoxic T-lymphocyte–associated protein 4 (CTLA-4) may perturb human immunodeficiency virus (HIV) persistence during antiretroviral therapy (ART) by reversing HIV latency and/or boosting HIV-specific immunity, leading to clearance of infected cells. We tested this hypothesis in a clinical trial of anti–PD-1 alone or in combination with anti–CTLA-4 in people living with HIV (PLWH) and cancer.

Methods
This was a substudy of the AIDS Malignancy Consortium 095 Study. ART-suppressed PLWH with advanced malignancies were assigned to nivolumab (anti–PD-1) with or without ipilimumab (anti–CTLA-4). In samples obtained preinfusion and 1 and 7 days after the first and fourth doses of immune checkpoint blockade (ICB), we quantified cell-associated unspliced (CA-US) HIV RNA and HIV DNA. Plasma HIV RNA was quantified during the first treatment cycle. Quantitative viral outgrowth assay (QVOA) to estimate the frequency of replication-competent HIV was performed before and after ICB for participants with samples available.

Results
Of 40 participants, 33 received nivolumab and 7 nivolumab plus ipilimumab. Whereas CA-US HIV RNA did not change with nivolumab monotherapy, we detected a median 1.44-fold increase (interquartile range, 1.16–1.89) after the first dose of nivolumab and ipilimumab combination therapy (P = .031). There was no decrease in the frequency of cells containing replication-competent HIV, but in the 2 individuals on combination ICB for whom we had longitudinal QVOA, we detected decreases of 97% and 64% compared to baseline.

Conclusions
Anti–PD-1 alone showed no effect on HIV latency or the latent HIV reservoir, but the combination of anti–PD-1 and anti–CTL-4 induced a modest increase in CA-US HIV RNA and may potentially eliminate cells containing replication-competent HIV.

Clinical Trials Registration
NCT02408861.
The Impact of State Mask-Wearing Requirements on the Growth of Coronavirus Disease 2019 Cases, Hospitalizations, and Deaths in the United States
Authors: Rebeiro Peter F , Aronoff David M , Smith M Kevin 
Published: February 2021

Abstract
In ecologic analyses of US states, piecewise multivariable models showed lower case-rate slopes after implementation of mask requirements: −1.0% (95% confidence interval, −1.34% to −.57%) and −0.44% (−.86% to −.03%) per 100 000 per day in early- and late-adopter states, respectively, compared with never-adopter states. Our findings support statewide mask requirements to mitigate transmission of coronavirus disease 2019.
Battering Review Spam Through Ensemble Learning in Imbalanced Datasets
Authors: Khurshid Faisal , Zhu Yan , Hu Jie , Ahmad Muqeet , Ahmad Mushtaq 
Published: February 2021

Abstract
Nowadays, people’s buying or availing services decisions are subject to online available reviews/opinions. The authenticity of these reviews/opinions is dubious, as there exist many fake reviews posted to attain monetary benefits by promoting their own or demoting the competitor’s products or services known as review spam. Although the number of spam is relatively less than that of normal reviews in real-life, this class imbalance is a critical concern in review spam detection. The performance degrades when the classifier skew towards the majority class. Moreover, efficient feature selection is essentially needed for this issue. The purpose of this study is to develop a framework based on different effective feature selection along with data balancing techniques. Validation results show that our proposed framework commendably copes up with the review spam issue and a higher precision on the real-life dataset. Further, we tested the sensitivity of our proposed framework using both parametric and non-parametric tests and found it significant.
From organic and inorganic phosphates to valvular and vascular calcifications
Authors: Bäck Magnus , Michel Jean-Baptiste 
Published: February 2021

AbstractCalcification of the arterial wall and valves is an important part of the pathophysiological process of peripheral and coronary atherosclerosis, aortic stenosis, ageing, diabetes, and chronic kidney disease. This review aims to better understand how extracellular phosphates and their ability to be retained as calcium phosphates on the extracellular matrix initiate the mineralization process of arteries and valves. In this context, the physiological process of bone mineralization remains a human model for pathological soft tissue mineralization. Soluble (ionized) calcium precipitation occurs on extracellular phosphates; either with inorganic or on exposed organic phosphates. Organic phosphates are classified as either structural (phospholipids, nucleic acids) or energetic (corresponding to phosphoryl transfer activities). Extracellular phosphates promote a phenotypic shift in vascular smooth muscle and valvular interstitial cells towards an osteoblast gene expression pattern, which provokes the active phase of mineralization. A line of defense systems protects arterial and valvular tissue calcifications. Given the major roles of phosphate in soft tissue calcification, phosphate mimetics, and/or prevention of phosphate dissipation represent novel potential therapeutic approaches for arterial and valvular calcification.
Electrophysiological and Behavioral Responses of Dasychira baibarana (Lepidoptera: Lymantriidae) to Tea Plant Volatiles
Authors: Magsi Fida Hussain , Luo Zongxiu , Zhao Yingjie , Li Zhaoqun , Cai Xiaoming , Bian Lei , Chen Zongmao 
Published: February 2021

Abstract
Tea black tussock moth, Dasychira baibarana (Matsumura) (Lepidoptera: Lymantriidae), is a devastating pest species of the tea plant in China. Here, we evaluated the responses of D. baibarana to tea plant volatiles using gas chromatography coupled electroantennographic detection (GC–EAD), eleclectroantennography (EAG), and a Y-tube olfactometer. In total, 11 of 18 analyzed compounds elicited GC–EAD responses from test insects. GC–EAD bio-active compounds were further investigated using EAG and behavioral responses. In the EAG analysis, male moths had significantly greater responses to four compounds [(Z)-3-hexenyl butyrate, (Z)-3-hexen-1-ol, ocimene and benzyl alcohol] than female moths. For females, maximum EAG amplitudes, were recorded in response to linalool, (Z)-3-hexenyl hexanoate and (Z)-jasmone. In EAG and behavioral bio-assays, the responses of both sexes were dose independent. In behavioral bio-assays male moths responding significantly to (Z)-3-hexen-1-ol, ocimene, (Z)-3-hexenyl butyrate, linalool, benzyl alcohol, and (Z)-jasmone at various concentrations. For females, significant behavioral responses were observed to (Z)-3-hexenyl hexanoate, followed by (Z)-jasmone, linalool, ocimene, and benzyl alcohol. However, neither sex was sensitive to 4 of the 11 tested compounds, phenyethyl alcohol, phenylacetonitrile, (E)-nerolidol, and indole. The present results showed that tea plant volatiles influenced the behavior of D. baibarana moths, which will greatly contribute in developing eco-friendly control strategies for D. baibarana, through the application of a blend of compounds that showed significant EAG and behavioral responses or a blend combined with female-produced sex pheromones.
Economic burden of patients living with heart disease in the last years of life in Australia: a retrospective analysis using linked data
Authors: Kularatna Sanjeewa , Senanayake Sameera , Parsonage William , Jun Deokhoon , McPhail Steven 
Published: February 2021

AbstractAimsPeople living with heart disease are at elevated risk of hospitalization during the last years of their life. The aim of this study was to describe hospitalization-related usage patterns, and associated cost burden, for patients living with heart disease in the last 6 years of their life.Methods and resultsThe study was an observational cohort study, using routinely collected and linked data from hospital admission (HA), emergency department (ED) presentation and death registry data in Queensland, Australia. The study sample included 1000 randomly selected patients who died in 2017 due to any cause who had been living with heart disease for at least the prior 6 years. The two main outcomes of interest in this study were cost of HAs and cost of ED presentation in the last 6 years before death. Total cost was calculated as a sum of direct and overhead costs from each of the hospital presentations. The mean HA per patient in the sixth year, second year, and last year prior to death was 5.3, 6.6, and 7.5, respectively, with a similar pattern observed for ED presentations. The associated costs per patient from HA followed a similar trajectory increasing gradually from $17 711 in the sixth year to $26 658 in the second last year prior to death. A similar pattern was observed for ED presentation costs.ConclusionThe large increase cost in the last year of life was primarily attributable to higher treatment cost per HA at end of life.
Impacts of stage 1 palliation and pre-Glenn pulmonary artery pressure on long-term outcomes after Fontan operation
Authors: Kido Takashi , Burri Melchior , Mayr Benedikt , Strbad Martina , Cleuziou Julie , Hager Alfred , Hörer Jürgen , Ono Masamichi 
Published: February 2021

Abstract

OBJECTIVES
The present study was aiming to determine whether high mean pulmonary artery pressure before bidirectional cavopulmonary shunt is a risk factor for late adverse events in patients with low pulmonary artery pressure before total cavopulmonary connection (TCPC).

METHODS
We retrospectively reviewed the medical records of all patients undergoing both bidirectional cavopulmonary shunt and TCPC with available cardiac catheterization data.

RESULTS
A total of 316 patients were included in this study. The patients were divided into 4 groups according to mean pulmonary pressure: those with pre-Glenn &lt;16 mmHg and pre-Fontan &lt;10 mmHg (Group LL, n = 124), those with pre-Glenn ≥16 mmHg and pre-Fontan &lt;10 mmHg (Group HL, n = 61), those with pre-Glenn &lt;16 mmHg and pre-Fontan ≥10 mmHg (Group LH, n = 66) and those with pre-Glenn ≥16 mmHg and pre-Fontan ≥10 mmHg (Group HH, n = 65). Group HL showed significantly higher rate of adverse events after TCPC than Group LL (P = 0.02). In univariate linear analysis, a history of atrial septectomy at stage 1 palliation was associated with low pre-Glenn mean pulmonary artery pressure (Coefficient B −1.38, 95% confidence interval −2.53 to −0.24; P = 0.02), while pulmonary artery banding was a significant risk factor for elevated pre-Fontan mean pulmonary artery pressure (Coefficient B 1.68, 95% confidence interval 0.81 to 2.56, P &lt; 0.001).

CONCLUSIONS
High mean pulmonary artery pressure before bidirectional cavopulmoary shunt (≥16mmHg) remains a significant risk factor for adverse events after TCPC even though mean pulmonary artery pressure decreased below 10 mmHg before TCPC.
Surgical therapy of infective endocarditis following interventional or surgical pulmonary valve replacement
Authors: Gierlinger Gregor , Sames-Dolzer Eva , Kreuzer Michaela , Mair Roland , Zierer Andreas , Mair Rudolf 
Published: February 2021

Abstract

OBJECTIVES
Percutaneous pulmonary valve prostheses and right ventricle-to-pulmonary artery conduits are at risk for infective endocarditis (IE). In children and adults with a congenital heart disease, a pulmonary valve implant is frequently necessary. Prosthetic valve endocarditis is a conservatively barely manageable, serious life-threatening condition. We investigated the results of surgical pulmonary valve replacements in patients with IE.

METHODS
A total of 20 patients with congenital heart disease with the definite diagnosis of IE between March 2013 and July 2020 were included in this single institutional, retrospective review. Infected conduits were 11 Melody, 5 Contegra, 3 homografts and 1 Matrix P Plus. All of the infected prosthetic material was removed from the right ventricular outflow tract up to the pulmonary bifurcation. Pulmonary homografts were implanted after pulmonary root resection as right ventricle-to-pulmonary artery conduits.

RESULTS
All patients survived and were discharged infection-free. The mean time from the conduit implant to the operation for IE was 4.9 years [95% confidence interval (CI), 3.0–6.9]. The median intensive care unit stay was 3.0 days (95% CI, 2.0–4.7), and the median hospital time was 25.0 days (95% CI, 19.2–42.0). Median follow-up time was 204.5 days (range 30 days to 5 years) without death or recurrent endocarditis.

CONCLUSIONS
The surgical treatment of IE of percutaneous pulmonary valve prostheses and right ventricle-to-pulmonary artery conduits is a safe and effective therapeutic concept. Early surgical referral of patients with suspicion of IE should be pursued to avoid sequelae such as right ventricular failure, septic emboli, intracardiac expansion and antibiotic resistance.
Reporting, interpretation, and extrapolation issues (SPIN) in abstracts of orthodontic meta-analyses published from 2000 to 2020
Authors: Makou Olga , Eliades Theodore , Koletsi Despina 
Published: February 2021

Summary

Aim
To assess the prevalence of and identify factors associated with SPIN in abstracts of orthodontic meta-analyses.

Materials and methods
Electronic search was performed within the contents of five orthodontic journals and the Cochrane Database of Systematic Reviews (CDSR) to identify meta-analyses of studies involving humans, from 1 January 2000 until 31 August 2020. Inclusion of SPIN in the abstract of meta-analyses, defined as misleading reporting, misleading interpretation, and inappropriate extrapolation of the findings, was documented. Extent of SPIN and associations with journal and year of publication, type of study, number of authors, continent of authorship, methodologist involvement, funding, and significance of the primary outcome were investigated.

Results
One hundred and nine meta-analyses were identified, with the highest proportion being published in the European Journal of Orthodontics (EJO: 31/109; 28.4%). Inclusion of SPIN, in at least one domain, was recorded in nearly half (53/109; 48.6%) of the studies, of which 30 (56.6%) included 2 or more domains of SPIN. Meta-analyses of observational studies presented 1.66 times higher risk for including SPIN in their abstracts compared with interventional ones [95% confidence intervals (CIs): 1.14, 2.40; P = 0.007], after adjusting for a number of predictors. Studies with a large number of authors (≥6) presented 1.76 times higher risk of SPIN (≥6 versus 1–3: 95% CIs: 1.04, 2.97; Wald test, P = 0.021), conditional on the pre-defined predictors.

Conclusions
Flaws in the reporting and interpretation of the findings of abstracts of meta-analyses, as framed by inclusion of SPIN are persistent in orthodontic research, being more prevalent in meta-analyses of observational studies. Consistent, multidirectional efforts should be endorsed to improve the quality of the disseminated research findings.