bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the influence of carbon black on the rheology and electromechanical properties of ethylene butene copolymer
Authors: Hamid Yasin , Svoboda Petr 
Published: December 2020

Abstract
In this scientific article, the potential of producing a highly capable sensor by the addition of electric conductive carbon black (CB) to polymer composite was studied, and the effects of various carbon black content on ethylene-butene copolymer (EBC) on rheological and electromechanical were investigated. Electric conductive composites have many attempts at producing original material in technology as a sensor. The amount of (0, 4.07, 6.31, 8.71, and 11.28) volume % of CB was introduced to EBC using Brabender, mixed, and homogenized for 5 min at 180 °C. The dynamic mechanical analysis (DMA) and electromechanical test show that the addition of CB to the EBC would increase the viscosity, modulus, while electric resistance significantly decreased and changed greatly with elongation. The modulus increased from 8.9 to 15 MPa by increase of from 15 to 25 wt% of CB while the gauge factor decreases for about five times by increasing the CB from 15 to 25 wt% under 5 N force. These works demonstrate the possibility of producing strain sensors using a cheap and versatile technique, with potential health and electromechanical sensors.
Modelling the effect of nanofiller’s shape and alignment on the dielectric strength and permittivity of polyethylene nanocomposite insulation
Authors: Safdar Adnan , Amin Salman 
Published: December 2020

Abstract
Solid insulation defects are a major cause of power failures. Incorporation of micro and nanoparticles in the solid insulation materials has proven its advantage. It has been reported that nanocomposites are far superior in terms of insulation to microcomposites because of larger interphase area between nanofillers and polymer in nanocomposites. In addition to that nature, size, shape, concentration and alignment of nanofillers affect the properties of resulting nanocomposite insulation. A lot of work has reported the effect of nanofiller’s nature, size and concentration but very little is reported on the effect of filler’s shape and alignment on the insulation and dielectric properties. In this paper nanocomposite dielectrics with nanofillers of various shapes and alignment are modelled by varying their permittivity using finite element method. To characterize the effect of various shapes and orientation electric field intensity and energy density models are computed. Simulations are performed using AC/DC module of COMSOL Multiphysics. The results revealed that shape and alignment of nanofillers are the two key factors in tuning the breakdown strength and permittivity of nanocomposite dielectrics for their applications in insulation as well as high voltage capacitors.
SVIM-asm: structural variant detection from haploid and diploid genome assemblies
Authors: Heller David , Vingron Martin 
Published: December 2020

Abstract

Motivation
With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes.

Results
We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual.

Availability and implementation
SVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/svim-asm.

Supplementary information
Supplementary data are available at Bioinformatics online.
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides
Authors: Borrman Tyler , Pierce Brian G , Vreven Thom , Baker Brian M , Weng Zhiping 
Published: December 2020

Abstract

Motivation
The binding of T-cell receptors (TCRs) to their target peptide MHC (pMHC) ligands initializes the cell-mediated immune response. In autoimmune diseases such as multiple sclerosis, the TCR erroneously recognizes self-peptides as foreign and activates an immune response against healthy cells. Such responses can be triggered by cross-recognition of the autoreactive TCR with foreign peptides. Hence, it would be desirable to identify such foreign-antigen triggers to provide a mechanistic understanding of autoimmune diseases. However, the large sequence space of foreign antigens presents an obstacle in the identification of cross-reactive peptides.

Results
Here, we present an in silico modeling and scoring method which exploits the structural properties of TCR-pMHC complexes to predict the binding of cross-reactive peptides. We analyzed three mouse TCRs and one human TCR isolated from a patient with multiple sclerosis. Cross-reactive peptides for these TCRs were previously identified via yeast display coupled with deep sequencing, providing a robust dataset for evaluating our method. Modeling query peptides in their associated TCR-pMHC crystal structures, our method accurately selected the top binding peptides from sets containing more than a hundred thousand unique peptides.

Availability and implementation
Analyses were performed using custom Python and R scripts available at https://github.com/weng-lab/antigen-predict.

Supplementary information
Supplementary data are available at Bioinformatics online.
Notch1 is crucial for decidualization and maintaining the first pregnancy in the mouse†
Authors: Wu Yao , He Jia-Peng , Xie Juan , Wang Ke-zhi , Kang Jin-Wen , Fazleabas Asgerally T , Su Ren-Wei 
Published: December 2020

Abstract
The endometrium undergoes a pregnancy-delivery-repair cycle multiple times during the reproductive lifespan in females. Decidualization is one of the critical events for the success of this essential process. We have previously reported that Notch1 is essential for artificial decidualization in mice. However, in a natural pregnancy, the deletion of Notch1 (PgrCre/+Notch1f/f, or Notch1d/d) only affects female fertility in the first 30 days of a 6-month fertility test, but not the later stages. In the present study, we undertook a closer evaluation at the first pregnancy of these mice to attempt to understand this puzzling phenomenon. We observed a large number of pregnancy losses in Notch1d/d mice in their first pregnancy, which led to the subfertility observed in the first 30 days of the fertility test. We then demonstrated that the initial pregnancy loss is a consequence of impaired decidualization. Furthermore, we identified a group of genes that contribute to Notch1 regulated decidualization in a natural pregnancy. Gene ontogeny analysis showed that these differentially expressed genes in the natural pregnancy are involved in cell–cell and cell–matrix interactions, different from genes that have been previously identified from the artificial decidualization model, which contribute to cell proliferation and apoptosis. In summary, we determined that Notch1 is essential for normal decidualization in the mouse uterus only in the first pregnancy but not in subsequent ones.
Using the Past to Understand the Present: Coping with Natural and Anthropogenic Noise
Authors: Gomes Dylan G E , Francis Clinton D , Barber Jesse R 
Published: December 2020

ABSTRACT
Anthropogenic noise has received significant attention in recent years, and researchers have highlighted the ways in which animals might deal with these noise sources. However, much of our understanding of animal responses to this novel source of background acoustics lacks an evolutionary perspective. Natural sources of noise predate the origin of hearing organs in animals. Therefore, it is unlikely that animals have only recently evolved strategies to cope with anthropogenic noise de novo but, rather, already have preexisting coping mechanisms, because of countless generations of evolution within a naturally noisy world, on which contemporary selection is now likely acting. We review strategies to cope with natural sources of noise and suggest a more quantitative and mechanistic understanding of how particular characteristics of noise have shaped animal populations and communities in the past, enabling us to predict the effects that novel sources of noise will have on the future.
Anonymous Linkage Between College Students and Human Immunodeficiency Virus (HIV) Facilities: Systematic Evaluation of Urine Self-Collection for HIV Testing Initiative in China
Authors: Lv Yi , Li Guanqiao , Hu Maogui , Xu Chengdong , Lu Hongyan , Chen Lu , Xing Yan , Liang Shu , Ma Yanling , Liang Shujia , Zhuang Minghua , Li Yi , Huang Chun , Bai Yaqing , Jiang Yan , Zhang Linqi 
Published: December 2020

Abstract

Background
Identifying young individuals living with human immunodeficiency virus (HIV) who are unaware of their status is a major challenge for HIV control in China. To address this, an innovative, anonymous vending machine–based urine self-collection for HIV testing (USCT) program was implemented in 2016 in colleges across China.

Methods
From June 2016 to December 2019, 146 vending machines stocked with urine self-collection kits were distributed on 73 college campuses across 11 provinces of China. Urine samples were collected, delivered, and tested in an anonymous manner. We analyzed the returned rate, reactive rate (likelihood of HIV screening positive), testing effectiveness (the annual number of college students living with HIV screened by USCT or other testing methods), and the spatiotemporal relationship between USCT usage and student activity per college generated from the usage of a social networking application.

Results
Among the 5178 kits sold, 3109 (60%) samples were returned; of these, 2933 (94%) were eligible for testing. The HIV reactive rate was 2.3% (66 of 2933). The average effectiveness ratio among the 34 participating Beijing colleges was 0.39 (12:31) between USCT and conventional testing methods. A strong spatiotemporal correlation between USCT numbers and online student activity was observed during school semesters in Beijing.

Conclusions
USCT is a powerful complement to current interventions that target at-risk students and promote HIV testing. The social networking–based evaluation framework can be a guide in prioritizing at-risk target populations.
Panel kink threshold regression model with a covariate-dependent threshold
Authors: Yang Lixiong , Zhang Chunli , Lee Chingnun , Chen I-Po 
Published: December 2020

SummaryThis article extends the kink threshold regression model with a constant threshold to a panel data framework with a covariate-dependent threshold, where the threshold is modeled as a function of informative covariates. We suggest an estimator based on the within-group transformation and propose test statistics for kink threshold effect and threshold constancy. We establish the asymptotic joint normality of the slope and threshold estimators and derive the limiting distributions of the test statistics. Our asymptotic results show that the inclusion of a covariate-dependent threshold does not affect the asymptotic joint normality of the slope and threshold estimates in the kink threshold regression model. Monte Carlo simulations show that the finite-sample proprieties of the proposed estimator and test statistics are generally satisfactory.
Haplotyping the Potato Psyllid (Hemiptera: Triozidae) and the Associated Pathogenic Bacterium ‘Candidatus Liberibacter solanacearum’ in Non-crop Alternative Hosts in Southern Idaho
Authors: Dahan Jennifer , Wenninger Erik J , Thornton Michael , Corral César A Reyes , Olsen Nora , Karasev Alexander V 
Published: December 2020

Abstract
Zebra chip, is a potato disease associated with the bacterium ‘Candidatus Liberibacter solanacearum’ (Lso) and vectored by the potato psyllid, Bactericera cockerelli Šulc. Potato psyllids are native to North America, where four haplotypes have been described. They are able to colonize a wide range of solanaceous species, crops, and weeds. The epidemiology of zebra chip disease is still poorly understood and might involve the different haplotypes of psyllids as well as two haplotypes of Lso. As several perennial weeds have been recognized as potential host for potato psyllids and Lso, a yearly monitoring of several patches of bittersweet nightshade (Solanum dulcamara) and field bindweed (Convolvulus arvensis) located in the potato-growing region of southern Idaho was conducted from 2013 to 2017, to gain insight into psyllid dynamics in non-potato hosts and Lso presence in the fields. Potato psyllids caught on each host were individually tested for Lso, and a subset were haplotyped based on the CO1 gene, along with the haplotyping of Lso in positive samples. On bittersweet nightshade, the Northwestern haplotype was numerically dominant, with around 2.7% of psyllids found to be carrying either Lso haplotype A or B, suggesting a limited role in zebra chip persistence, which has infected Idaho fields at a low occurrence since the 2012 outbreak. Field bindweed was found to be a transient, non-overwintering host for potato psyllid of Northwestern, Western and Central haplotypes late in the season, suggesting minor, if any, role in persistence of Lso and field infestation by potato psyllids.
Acute, Exercise-Induced Alterations in Cytokines and Chemokines in the Blood Distinguish Physically Active and Sedentary Aging
Authors: MacNeil Lauren G , Tarnopolsky Mark A , Crane Justin D 
Published: December 2020

Abstract
Aging results in a chronic, proinflammatory state which can promote and exacerbate age-associated diseases. In contrast, physical activity in older adults improves whole body health, protects against disease, and reduces inflammation, but the elderly are less active making it difficult to disentangle the effects of aging from a sedentary lifestyle. To interrogate this interaction, we analyzed peripheral blood collected at rest and postexercise from 68 healthy younger and older donors that were either physically active aerobic exercisers or chronically sedentary. Subjects were profiled for 44 low-abundance cytokines, chemokines, and growth factors in peripheral blood. At rest, we found that regular physical activity had no impact on the age-related elevation in circulating IL-18, eotaxin, GRO, IL-8, IP-10, PDGF-AA, or RANTES. Similarly, there was no impact of physical activity on the age-related reduction in VEGF, EGF, or IL-12 (p70). However, older exercisers had lower resting plasma fractalkine, IL-3, IL-6, and TNF-α compared to sedentary older adults. In contrast to our resting characterization, blood responses following acute exercise produced more striking difference between groups. Physically active younger and older subjects increased over 50% of the analyzed factors in their blood which resulted in both unique and overlapping exercise signatures. However, sedentary individuals, particularly the elderly, had few detectable changes in response to exercise. Overall, we show that long-term physical activity has a limited effect on age-associated changes in basal cytokines and chemokines in the healthy elderly, yet physically active individuals exhibit a broader induction of factors postexercise irrespective of age.
Attempts at Redress Through the Lens of Social Identity: Housing, Land and Property of the Displaced in Cyprus
Authors: de Waardt Mijke , Georgiou Dora , Celal Evren 
Published: December 2020

Abstract
Transitional justice measures, particularly reparations, have started to address housing, land and property (HLP) issues in relation to internally displaced persons (IDPs), but HLP grievances have not decreased. Because it is difficult to meaningfully engage IDPs in reparations and redress, contextualized approaches are suggested for remedies to become effective. We propose a lens of social identity theory (SIT) to illuminate the potential for HLP attempts for redress to be expanded to groups in intractable conflict. Based on research in Cyprus, we argue that SIT enables the scrutiny of whether and how legal decisions and administrative remedy mechanisms meaningfully relate to IDPs’ notions of victimhood and (in)justice. We show that attempts for redress may act to maintain competitive narratives and exclusionary social identities in Cyprus. An inclusive victimhood narrative may shift categories available for an intergroup social identity for Cypriots, making it more likely for actual progress on the HLP issue.
On the behavior of 1-Laplacian ratio cuts on nearly rectangular domains
Authors: Hamilton Wesley , Marzuola Jeremy L , Wu Hau-tieng 
Published: December 2020

Abstract
The $p$-Laplacian has attracted more and more attention in data analysis disciplines in the past decade. However, there is still a knowledge gap about its behavior, which limits its practical application. In this paper, we are interested in its iterative behavior in domains contained in two-dimensional Euclidean space. Given a connected set $\varOmega _0 \subset \mathbb{R}^2$, define a sequence of sets $(\varOmega _n)_{n=0}^{\infty }$ where $\varOmega _{n+1}$ is the subset of $\varOmega _n$ where the first eigenfunction of the (properly normalized) Neumann $p$-Laplacian $ -\varDelta ^{(p)} \phi = \lambda _1 |\phi |^{p-2} \phi $ is positive (or negative). For $p=1$, this is also referred to as the ratio cut of the domain. We conjecture that these sets converge to the set of rectangles with eccentricity bounded by 2 in the Gromov–Hausdorff distance as long as they have a certain distance to the boundary $\partial \varOmega _0$. We establish some aspects of this conjecture for $p=1$ where we prove that (1) the 1-Laplacian spectral cut of domains sufficiently close to rectangles is a circular arc that is closer to flat than the original domain (leading eventually to quadrilaterals) and (2) quadrilaterals close to a rectangle of aspect ratio $2$ stay close to quadrilaterals and move closer to rectangles in a suitable metric. We also discuss some numerical aspects and pose many open questions.
The Politicization of Objects: Meaning and Materiality in The U.S. Cannabis Market
Authors: Huff Aimee Dinnin , Humphreys Ashlee , Wilner Sarah J.S. 
Published: December 2020

AbstractIn this article, we theorize how marketplace objects and their properties facilitate market legitimacy. Adopting assemblage theory, we examine a politically contested market—the U.S. recreational cannabis market—using retail sales data, public opinion polls and surveys, mainstream media coverage, and interviews with producers and consumers. We find that objects convey meaning in the market by creating sensory or discursive alignment between new or contested products and products from existing, legitimate markets, and by creating sensory or discursive distancing between new products and products in existing, illegitimate markets. We further find that different types of consumers play different roles in the overall legitimation process because they perceive alignments and misalignments differently. We present a conceptual model that links object meaning with the market and broader, cultural, and societal levels, demonstrating how materiality contributes to the overall legitimation of a politically contested market.
Altering Planting Date to Manage Melanaphis sacchari (Hemiptera: Aphididae) Populations in Sweet Sorghum
Authors: Mercer Nathan H , Obrycki John J , Bessin Ricardo T 
Published: December 2020

Abstract
Melanaphis sacchari Zehntner is a new pest of sweet sorghum in the United States, with the potential to cause complete crop failure. In Kentucky, sweet sorghum is normally planted in early May and harvested in late August or September. Planting sweet sorghum earlier in the season may avoid damaging levels of M. sacchari that develop in late summer. In a 2-yr field study, three different planting dates separated by a month (April, May, and June) were tested for their effect on M. sacchari densities and sweet sorghum yield. April (early) planted sweet sorghum was grown in greenhouses and transplanted to the field. May (mid) and June (late) planted sweet sorghum were direct seeded in the field. Melanaphis sacchari population densities were evaluated weekly starting in June. Sweet sorghum was harvested at the onset of the hard dough stage. Plots were split into two subplots, insecticide or noninsecticide, in the second year to control for planting date effect on yield. Early-planted sweet sorghum had lower aphid densities, but had lower yield relative to mid-planting date, which had the highest yield. Insecticide drenches in 2019 reduced cumulative aphid days in mid-plantings and late plantings, but did not significantly affect yield within planting dates. Seeding sweet sorghum earlier can reduce M. sacchari densities; however, this method alone may not provide the highest yields. We documented that the recommended planting date (May) for Kentucky produced the highest yield.
The development of neutralizing antibodies against SARS-CoV-2 and their common features
Authors: Liu Liu Daisy , Lian Chaoyang , Yeap Leng-Siew , Meng Fei-Long 
Published: December 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide severe coronavirus disease 2019 (COVID-19) pandemic since December 2019. There is a great demand for effective therapies for the prevention and treatment of COVID-19. Developing therapeutic neutralizing antibodies (NAbs), which could block viral infection, is such a promising approach, as NAbs have been successfully applied to the treatment of other viral infections. The recent advances of antibody technology have greatly accelerated the discovery of SARS-CoV-2 NAbs, and many of which are now actively tested in clinical trials. Here, we review the approaches applied for SARS-CoV-2 NAb development, and discuss the emerging technologies underlining the antibody discovery. We further summarize the common features of these antibodies including the shared neutralizing epitopes and sequence features.