bluuebunny/crossref_metadata_2025_split huggingface dataset:
Form-Finding with and without Cable Reinforced Thomsen Surface in Tensioned Fabric Structure
Authors: Yee HM , Abdul Hadi MN 
Published: March 2019

Abstract
Tensioned Fabric Structure (TFS) is structure that is composed of tensioned fabric as structural members. The form of Thomsen surface applied in TFS has been developed in this study because the form of Thomsen surface has not been studied by others researcher. The objective of this study is to determine initial equilibrium shape in Thomsen form and cable reinforced of Thomsen surface in TFS with variable u=v=0.8 using nonlinear analysis method. The surface of Thomsen surface, u=v=0.8 shows the least square error of total warp and fill stress deviation is less than 0.01. From the result, initial equilibrium shape in Thomsen form and cable reinforced of Thomsen surface, u=v=0.8 is corresponding to equal tension surface. In conclusion, Thomsen form and cable reinforced of Thomsen surface with variable u=v=0.8 will provide an alternative shape for designer to be considered for adopted in tensioned fabric structure.
Investigation of Isospin Conservation Effects on Pre-Equilibrium Nuclear Reactions for Some Nuclei
Authors: Shafik Shafik S. , Alattabi Hadi D. , Kadhim Masar A. 
Published: March 2019

Abstract
The pre-equilibrium emission spectra have been studied and calculated using the exciton model. The calculations took different reactions (nucleon – nucleon, nucleon – cluster, cluster – nucleon) at low and high incident energies to investigate and study the influence of adding the isospin conservation effects into the nuclear level density on the energy spectra. The isospin conservation effect added to the state density showed no significance variation for mixed and conserved isospin calculations for all reactions at different incident energies. The results were obtained by depending on the PRECO-2006 code of C. Kalbach.
phylostratr: a framework for phylostratigraphy
Authors: Arendsee Zebulun , Li Jing , Singh Urminder , Seetharam Arun , Dorman Karin , Wurtele Eve Syrkin 
Published: March 2019

Abstract

Motivation
The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene’s phylostratum.

Results
We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae.

Availability and implementation
Source code available at https://github.com/arendsee/phylostratr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data
Authors: Li Hongjian , Peng Jiangjun , Sidorov Pavel , Leung Yee , Leung Kwong-Sak , Wong Man-Hon , Lu Gang , Ballester Pedro J 
Published: March 2019

AbstractMotivationStudies have shown that the accuracy of random forest (RF)-based scoring functions (SFs), such as RF-Score-v3, increases with more training samples, whereas that of classical SFs, such as X-Score, does not. Nevertheless, the impact of the similarity between training and test samples on this matter has not been studied in a systematic manner. It is therefore unclear how these SFs would perform when only trained on protein-ligand complexes that are highly dissimilar or highly similar to the test set. It is also unclear whether SFs based on machine learning algorithms other than RF can also improve accuracy with increasing training set size and to what extent they learn from dissimilar or similar training complexes.ResultsWe present a systematic study to investigate how the accuracy of classical and machine-learning SFs varies with protein-ligand complex similarities between training and test sets. We considered three types of similarity metrics, based on the comparison of either protein structures, protein sequences or ligand structures. Regardless of the similarity metric, we found that incorporating a larger proportion of similar complexes to the training set did not make classical SFs more accurate. In contrast, RF-Score-v3 was able to outperform X-Score even when trained on just 32% of the most dissimilar complexes, showing that its superior performance owes considerably to learning from dissimilar training complexes to those in the test set. In addition, we generated the first SF employing Extreme Gradient Boosting (XGBoost), XGB-Score, and observed that it also improves with training set size while outperforming the rest of SFs. Given the continuous growth of training datasets, the development of machine-learning SFs has become very appealing.Availability and implementationhttps://github.com/HongjianLi/MLSFSupplementary informationSupplementary data are available at Bioinformatics online.
GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology
Authors: Belcastro Vincenzo , Cano Stephane , Marescotti Diego , Acali Stefano , Poussin Carine , Gonzalez-Suarez Ignacio , Martin Florian , Bonjour Filipe , Ivanov Nikolai V , Peitsch Manuel C , Hoeng Julia 
Published: March 2019

AbstractSummaryGladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the ‘tcpl’ core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate PDF reports for quality control and data processing.Availability and implementationGladiaTOX R package (bioconductor). Also available via: git clone https://github.com/philipmorrisintl/GladiaTOX.git.Supplementary informationSupplementary data are available at Bioinformatics online.
onlineFDR: an R package to control the false discovery rate for growing data repositories
Authors: Robertson David S , Wildenhain Jan , Javanmard Adel , Karp Natasha A 
Published: March 2019

Abstract

Summary
In many areas of biological research, hypotheses are tested in a sequential manner, without having access to future P-values or even the number of hypotheses to be tested. A key setting where this online hypothesis testing occurs is in the context of publicly available data repositories, where the family of hypotheses to be tested is continually growing as new data is accumulated over time. Recently, Javanmard and Montanari proposed the first procedures that control the FDR for online hypothesis testing. We present an R package, onlineFDR, which implements these procedures and provides wrapper functions to apply them to a historic dataset or a growing data repository.

Availability and implementation
The R package is freely available through Bioconductor (http://www.bioconductor.org/packages/onlineFDR).

Supplementary information
Supplementary data are available at Bioinformatics online.
Emergency valve surgery improves clinical results in patients with infective endocarditis complicated with acute cerebral infarction: analysis using propensity score matching†
Authors: Samura Takaaki , Yoshioka Daisuke , Toda Koichi , Sakaniwa Ryoto , Yokoyama Junya , Suzuki Kota , Miyagawa Shigeru , Yoshikawa Yasushi , Hata Hiroki , Takano Hiroshi , Matsumiya Goro , Monta Osamu , Sakaguchi Taichi , Fukuda Hirotsugu ,   Oscar Study Group, Sawa Yoshiki 
Published: March 2019

Abstract

OBJECTIVES
To date, the optimal timing for patients with infective endocarditis (IE) with acute cerebral infarction (CI) to undergo valve surgery is unknown. Although some previous studies have reported that early valve surgery for IE patients within 1 or 2 weeks after CI could be performed safely, an initial strategy has not been identified because of the unmatched cohorts in previous studies. This study aimed to assess the feasibility and safety of early surgery within a few days after cerebral infarction by using propensity score matching.

METHODS
Between 2009 and 2017, 585 patients underwent valve surgery for patients with active IE at 14 institutions. Among these, 152 had preoperative acute CI. Early surgery was defined as surgery within 3 days after the diagnosis of CI. Of these 152 patients, 67 underwent early valve surgery (early group), whereas 85 underwent delayed valve surgery (delayed group). Of the patients, 45 in each group were analysed using propensity score matching. The primary outcome was in-hospital death after valve surgery, and secondary outcomes included neurological complications. We compared the clinical results of these matched patients.

RESULTS
Hospital mortality was lower in the early group (2% vs 16%, P = 0.058). The rate of postoperative intracranial haemorrhage in the early and delayed groups was 4% in both groups. The postoperative modified Rankin scale was not significantly different [early group: 0 (0–2); delayed group: 0 (0–2)]. Incidence of neurological deterioration did not differ significantly between the groups. The survival rates after the first discharge at 1, 3 and 5 years after valve operation were 100%, 97% and 97% in the early group and 91%, 83% and 80% in the delayed group, respectively (P = 0.029).

CONCLUSIONS
Early valve surgery for patients with IE within 3 days after a CI measuring <2 cm in size improved clinical results without increasing the incidence of postoperative neurological complications.
Parent and child perceptions of gambling promotions in Australian sport
Authors: David Jennifer L , Thomas Samantha L , Randle Melanie , Pitt Hannah , Daube Mike 
Published: March 2019

AbstractGambling is recognized as a significant public health problem. However, there is little research exploring community attitudes towards gambling and the development of advocacy initiatives. Engaging adults and young people in advocacy efforts is recognized as being beneficial to the successful implementation of harm prevention and reduction strategies. This study explored the attitudes of young people and their parents towards the alignment of gambling with sport, and the strategies they perceive could be used to prevent and reduce gambling related harm. Using a Constructivist Grounded Theory approach, 30 family groups from Melbourne, Australia participated in semi-structured interviews. Parents and young people were asked about gambling and its promotion, alignment with sporting codes, the potential impact on young people and strategies that may prevent or reduce gambling harm. Thematic analysis was undertaken to interpret the data. The sample comprised 29 parents, one grandparent and 48 young people. Themes emerging from the data related to the use of imagery and appeal strategies in advertisements, the normalization of betting in advertisements and the alignment of betting with sport. Parents and young people also identified a number of potential gambling harm prevention and reduction initiatives. Parents and young people were able to describe a range of strategies used by gambling companies to promote their products, understand the potential impact of these strategies, and recommend strategies to reduce harm. Given this level of understanding there is clearly an opportunity to engage young people and stakeholders in advocacy initiatives aimed at reducing and preventing gambling harm.
Unmasking herd protection by an oral cholera vaccine in a cluster-randomized trial
Authors: Ali Mohammad , Qadri Firdausi , Kim Deok Ryun , Islam Taufiqul , Im Justin , Ahmmed Faisal , Chon Yun , Islam Khan Ashraful , Zaman Khalequ , Marks Florian , Clemens John D 
Published: March 2019

AbstractBackgroundSeveral studies have shown that inactivated, whole-cell oral cholera vaccines (OCVs) confer both direct protection on vaccinees and herd protection on populations. Because our earlier cluster-randomized effectiveness trial (CRT) in urban Bangladesh failed to detect OCV herd protection, we reanalysed the trial to assess whether herd effects were masked in our original analysis.MethodsA total of 267 270 persons were randomized to 90 approximately equal-sized clusters. In 60 clusters persons aged 1 year and older were eligible to receive OCV and in 30 clusters persons received no intervention and served as controls. We analysed OCV protection against severely dehydrating cholera for the entire clusters, as in our original analysis, and for subclusters consisting of residents of innermost households. We hypothesized that if OCV herd protection was attenuated by cholera transmission into the clusters from the outside in this densely populated setting, herd protection would be most evident in the innermost households.ResultsDuring 2 years of follow-up of all residents of the clusters, total protection (protection of OCV recipients relative to control residents) was 58% [95% confidence interval (CI): 43%, 70%; P<0.0001], indirect protection (protection of non-OCV recipients in OCV clusters relative to control participants) was 16% (95% CI: –20%, 41%; P=0.35) and overall OCV protection (protection of all residents in the OCV clusters relative to control residents) was 46% (95% CI: 30%, 59%; P<0.0001). Analyses of the inner 75% and 50% households of the clusters showed similar findings. However, total protection was 75% (95% CI: 50%, 87%, P<0.0001), indirect protection 52% (95% CI: –9%, 79%; P=0.08) and overall protection 72% (95% CI: 49%, 84%; P<0.0001) for the innermost 25% households.ConclusionConsistent with past studies, substantial OCV herd protective effects were identified, but were unmasked only by analysing innermost households of the clusters. Caution is needed in defining clusters for analysis of vaccine herd effects in CRTs of vaccines.
Adaptive optimal transport
Authors: Essid Montacer , Laefer Debra F , Tabak Esteban G 
Published: March 2019

AbstractAn adaptive, adversarial methodology is developed for the optimal transport problem between two distributions $\mu $ and $\nu $, known only through a finite set of independent samples $(x_i)_{i=1..n}$ and $(y_j)_{j=1..m}$. The methodology automatically creates features that adapt to the data, thus avoiding reliance on a priori knowledge of the distributions underlying the data. Specifically, instead of a discrete point-by-point assignment, the new procedure seeks an optimal map $T(x)$ defined for all $x$, minimizing the Kullback–Leibler divergence between $(T(x_i))$ and the target $(y_j)$. The relative entropy is given a sample-based, variational characterization, thereby creating an adversarial setting: as one player seeks to push forward one distribution to the other, the second player develops features that focus on those areas where the two distributions fail to match. The procedure solves local problems that seek the optimal transfer between consecutive, intermediate distributions between $\mu $ and $\nu $. As a result, maps of arbitrary complexity can be built by composing the simple maps used for each local problem. Displaced interpolation is used to guarantee global from local optimality. The procedure is illustrated through synthetic examples in one and two dimensions.
Analysis of a fractal ultrasonic transducer with a range of piezoelectric length scales
Authors: Algehyne Ebrahem A , Mulholland Anthony J 
Published: March 2019

Abstract
The transmission and reception sensitivities of most piezoelectric ultrasonic transducers are enhanced by their geometrical structures. This structure is normally a regular, periodic one with one principal length scale, which, due to the resonant nature of the devices, determines the central operating frequency. There is engineering interest in building wide-bandwidth devices, and so it follows that, in their design, resonators that have a range of length scales should be used. This paper describes a mathematical model of a fractal ultrasound transducer whose piezoelectric components span a range of length scales. There have been many previous studies of wave propagation in the Sierpinski gasket but this paper is the first to study its complement. This is a critically important mathematical development as the complement is formed from a broad distribution of triangle sizes, whereas the Sierpinski gasket is formed from triangles of equal size. Within this structure, the electrical and mechanical fields fluctuate in tune with the time-dependent displacement of these substructures. A new set of basis functions is developed that allow us to express this displacement as part of a finite element methodology. A renormalization approach is then used to develop a recursion scheme that analytically describes the key components from the discrete matrices that arise. Expressions for the transducer’s operational characteristics are then derived and analysed as a function of the driving frequency. It transpires that the fractal device has a significantly higher reception sensitivity (18 dB) and a significantly wider bandwidth (3 MHz) than an equivalent Euclidean (standard) device.
Rapid Disappearance of Poliovirus Type 2 (PV2) Immunity in Young Children Following Withdrawal of Oral PV2-Containing Vaccine in Vietnam
Authors: Huyen Dang Thi Thanh , Mach Ondrej , Thanh Trung Nguyen , Thai Pham Quang , Thang Ho Vinh , Weldon William C , Oberste M Steven , Jeyaseelan Visalakshi , Sutter Roland W , Anh Dang Duc 
Published: March 2019

AbstractBackgroundDue to global shortage of inactivated poliovirus vaccine and withdrawal of oral vaccine containing poliovirus type 2 (PV2), a PV2-containing vaccine was not used in Vietnam May 2016 to October 2018. We assessed the population immunity gap to PV2.MethodsA cross-sectional survey in children aged 1–18 months was carried out in January 2018. One blood sample per child was analyzed for presence of poliovirus neutralizing antibodies. In children with detectable anti-PV2 antibodies, a second sample was analyzed 4 months later to distinguish between passive (maternally derived) and active (induced by secondary transmission or vaccination) immunity.ResultsSera were obtained from 1106/1110 children. Seroprevalence of PV2 antibodies was 87/368 (23.6%) at age 1–7 months, 27/471 (5.7%) at 8–15 months, and 19/267 (7.1%) at 16–18 months. Seroprevalence declined with age in the 1–7 months group; in the 8–18 months group there was no significant change with age. Four months later, 11/87 (14%), 9/27 (32%), and 12/19 (37%) remained seropositive in 1–7, 8–15, and 16–18 months age groups, respectively.ConclusionsWe found declining immunity to PV2, suggesting Vietnam is at risk for an outbreak of type 2 vaccine-derived poliovirus following virus importation or new emergence.
Supplemental Screening for Women with Dense Breasts: What Do Practicing Radiologists Recommend?
Authors: Singer Tisha , Lourenco Ana P , Baird Grayson L , Mainiero Martha B 
Published: March 2019

Abstract

Objective
To evaluate radiologists’ supplemental screening recommendations for women with dense breasts, at average, intermediate, or high risk of breast cancer, and to determine if there are differences between their recommendations for their patients, their friends and family, and themselves.

Methods
This is an anonymous survey of Society of Breast Imaging (SBI) members. Demographics, knowledge of breast density as a risk factor, and recommendations for screening with digital breast tomosynthesis (DBT), ultrasound (US), and magnetic resonance imaging (MRI) in women with dense breasts, at average, intermediate, or high- risk of breast cancer were assessed. The likelihood of their recommending the screening test for their patients, their family and friends, and themselves was assessed on a Likert scale from 0 to 4 (0 = “not at all likely” to 4 = “extremely likely”).

Results
There were 295 responses: 67% were women, and breast imaging comprised 95% of their practice. Among participants, 53% correctly answered the question on relative risk of breast cancer when comparing extremely dense versus fatty breasts, and 57% when comparing heterogeneously dense versus scattered breasts. US is recommended at a relatively low rate (1.0–1.4 on the 0–4 scale), regardless of risk. DBT is recommended at a relatively high rate (2.5–3.0 on the 0–4 scale), regardless of risk status. MR is recommended mainly for those at high risk (3.6 on the 0–4 scale). Radiologists were more likely to recommend additional imaging for themselves than for their patients and their family and friends.

Conclusion
For women with dense breasts, radiologists are “somewhat likely” to recommend US and “likely” to “very likely” to recommend DBT regardless of risk group. They are “very likely” to recommend MRI for high-risk groups.
Distribution of a New Invasive Species, Sipha maydis (Heteroptera: Aphididae), on Cereals and Wild Grasses in the Southern Plains and Rocky Mountain States
Authors: Puterka Gary J , Hammon Robert W , Franklin Melissa , Mornhinweg Dolores W , Springer Tim , Armstrong Scott , Brown Mike J 
Published: March 2019

AbstractSipha maydis Passerini (Heteroptera: Aphididae) is a cereal pest with an extensive geographical range that includes countries in Europe, Asia, Africa, and South America. Reports of S. maydis in the United States have been infrequent since it was first detected in California, 2007. Two studies, focused (NW CO) and multistate (OK, TX, NM, CO, UT, WY), were conducted to determine the distribution and host range of S. maydis in the Rocky Mountain and Southern Plains states over a 3-yr period, 2015–2017. In 2015, focused sampling in NW Colorado found S. maydis at 59% of the 37 sites, primarily on wheat. Sipha maydis did not survive extreme winter temperatures from late December 2015 to early January 2016 that ranged from −9.0 to −20.9°C over a 9-d period, which resulted in no aphids detected in 2016. In the multistate study, S. maydis occurred in 14.6% of 96 sites sampled in 2015, 8% of 123 sites in 2016, and 9% of 85 sites in 2017 at wide range of altitudes from 1,359 to 2,645 m. Sipha maydis occurred mainly in NW and SW Colorado and NE New Mexico along with a few sites in NE Colorado, SE Utah, and SE Wyoming. This aphid mainly infested wheat followed by a variety of eight wild grass species. No parasites, predators, sexual morphs, or significant plant damage occurred at the sites. Sipha maydis utilized 14 hosts in the United States including 8 new host records, which expands its host range to 52 plant species worldwide. Sipha maydis may be of concern to wheat, barley, and sorghum production in the United States if its populations continue to increase.