bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution towards minimum ovule size? Ovule size variations and the relative sizes of ovules to seeds
Authors: Itagaki Tomoyuki , Mochizuki Jun , Aoyagi Blue Yuta , Ito Masaya , Sakai Satoki 
Published: February 2019

AbstractBackground and AimsIs there selection minimizing the costs of ovule production? Such selection should lead to a smaller ovule size in relation to seed size and, at the same time, smaller variation in ovule size within plants, the latter because the minimum structures and resources for functioning of ovules should be the same among ovules. Additionally, within species, ovule size should not depend on the plant’s resource status.MethodsTo confirm these predictions, we examined ovule and seed production for a variety of species.Key ResultsAmong the 27 species studied, we found a significant negative dependence of the species mean of the coefficient of variation for plant ovule size on the ratio of the mean species seed size/mean species ovule size. Thus, the smaller the ovule size as compared with seed size, the smaller the degree of variation in ovule size. Among the 49 species studied, only two species showed significant positive dependence of mean ovule size on plant size. Although larger plants should have greater resources for ovule production, selection has not enhanced the production of large ovules in most species.ConclusionsThese results suggest that there is selection minimizing the costs of ovule production.
Transnational Literacies as Social Remittances: The Role of Language Ideologies in Shaping Migrants’ Online Literacies
Authors: Capstick Tony 
Published: February 2019

Abstract
It is now twenty years since the term ‘social remittances’ was taken up to capture the notion that migration involves the circulation of ideas, practices, identities, and social capital between destination and origin countries, in addition to the more tangible circulation of money. In a similar vein, a social theory of literacy sees practices not as observable units of behaviour but rather as social processes which connect people. To identify how literacy practices can be seen as social remittances, I identify how Usman, the key respondent in this study, goes about describing his first six months in the UK by tracing the meaning-making trajectories in our interviews together. I then explore the language and literacy choices that his family and friends make on Facebook as they remit ideas, beliefs, and practices in their transnational literacies. I examine how these practices are shaped by beliefs about language. The article seeks to understand the relationship between migrants’ literacy practices before and after their migrations and how these practices remit ideas and beliefs which maintain transnational migration.
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
Authors: Orellana Laura , Gustavsson Johan , Bergh Cathrine , Yoluk Ozge , Lindahl Erik 
Published: February 2019

Abstract

Summary
Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships.

Availability and implementation
eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using association signal annotations to boost similarity network fusion
Authors: Ruan Peifeng , Wang Ya , Shen Ronglai , Wang Shuang 
Published: February 2019

Abstract

Motivation
Recent technology developments have made it possible to generate various kinds of omics data, which provides opportunities to better solve problems such as disease subtyping or disease mapping using more comprehensive omics data jointly. Among many developed data-integration methods, the similarity network fusion (SNF) method has shown a great potential to identify new disease subtypes through separating similar subjects using multi-omics data. SNF effectively fuses similarity networks with pairwise patient similarity measures from different types of omics data into one fused network using both shared and complementary information across multiple types of omics data.

Results
In this article, we proposed an association-signal-annotation boosted similarity network fusion (ab-SNF) method, adding feature-level association signal annotations as weights aiming to up-weight signal features and down-weight noise features when constructing subject similarity networks to boost the performance in disease subtyping. In various simulation studies, the proposed ab-SNF outperforms the original SNF approach without weights. Most importantly, the improvement in the subtyping performance due to association-signal-annotation weights is amplified in the integration process. Applications to somatic mutation data, DNA methylation data and gene expression data of three cancer types from The Cancer Genome Atlas project suggest that the proposed ab-SNF method consistently identifies new subtypes in each cancer that more accurately predict patient survival and are more biologically meaningful.

Availability and implementation
The R package abSNF is freely available for downloading from https://github.com/pfruan/abSNF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Niche conservatism predominates in adaptive radiation: comparing the diversification of Hawaiian arthropods using ecological niche modelling
Authors: Hiller Anna E , Koo Michelle S , Goodman Kari R , Shaw Kerry L , O’Grady Patrick M , Gillespie Rosemary G 
Published: February 2019

Abstract
The role of the environmental niche in fostering ecological divergence during adaptive radiation remains enigmatic. In this study, we examine the interplay between environmental niche divergence and conservatism in the context of adaptive radiation on oceanic islands, by characterizing the niche breadth of four Hawaiian arthropod radiations: Tetragnatha spiders (Tetragnathidae Latreille, 1804), Laupala crickets (Gryllidae Otte, 1994), a clade of Drosophila flies (Drosophilidae Fallén, 1823) and Nesosydne planthoppers (Delphacidae Kirkaldy, 1907). We assembled occurrence datasets for the four lineages, modelled their distributions and quantified niche overlap. All four groups occupy the islands in distinct ways, highlighting the contrasting axes of diversification for different lineages. Laupala and Nesosydne have opposite environmental niche extents (broad and narrow, respectively), whereas Tetragnatha and Drosophila share relatively intermediate tolerances. Temperature constrains the distributions of all four radiations. Tests of phylogenetic signal suggest that, for Tetragnatha and Drosophila, closely related species exhibit similar environmental niches; thus, diversification is associated with niche conservatism. Sister species comparisons also show that populations often retain similar environmental tolerances, although exceptions do occur. Results imply that diversification does not occur through ecological speciation; instead, adaptive radiation occurs largely within a single environment.
‘So, Why Am I Here?’ Ambiguous Practices of Protection, Treatment and Punishment in Danish Secure Institutions for Youth
Authors: Henriksen Ann-Karina , Prieur Annick 
Published: February 2019

Abstract
This article explores how a nexus of punishment, treatment and protection creates unique mechanisms of control in secure institutions for young people. It is based on a study in Danish secure institutions, which accommodate young people confined on legal and welfare grounds. In these hybrid institutions, protection, treatment and punishment merge in ambiguous and contradictory practices that are experienced as unjust or even harmful by the young people and possibly breach the UN Convention of the Child. These practices are explored through a Foucauldian theorization highlighting the disciplinary practices unique to the confinement of minors. The article contributes to wider debates on the treatment–punishment nexus, Nordic exceptionalism and criminal justice for youth in an era of neoliberal penal-welfarism.
Understanding the Differential Effects of Land Uses On Crime: An Examination Across Philadelphia Neighbourhoods
Authors: Wo James C 
Published: February 2019

Abstract
Although criminology presumes that the physical structural qualities of neighbourhoods have important consequences for crime, there is a dearth of research to test the effects of different land uses on crime rates. Using data on a sample of Philadelphia census blocks, I compute the percentage of the block area classified into seven land use categories, and I use Poisson models to test the localized and broader spatial impact of each of these land uses on crime, controlling for key sociodemographic characteristics. The results show that to effectively understand the interplay between physical structure and crime rates, researchers should disaggregate nonresidential land uses, account for the surrounding environment in which neighbourhoods are situated and analyse a specific form of moderation.
Prevalence of Chagas Disease Among Family Members of Previously Diagnosed Patients in Los Angeles, California
Authors: Hernandez Salvador , Forsyth Colin J , Flores Carmen A , Meymandi Sheba K 
Published: February 2019

Abstract
Chagas disease (CD) in the United States is severely underdiagnosed, due to an absence of systematic screening as part of routine healthcare. We screened 189 relatives of 86 existing patients and found a CD prevalence of 7.4%. Screening close relatives of previously diagnosed individuals can effectively identify new CD cases.
The Impact of Improved Water, Sanitation, and Hygiene on Oral Rotavirus Vaccine Immunogenicity in Zimbabwean Infants: Substudy of a Cluster-randomized Trial
Authors: Church James A , Rukobo Sandra , Govha Margaret , Lee Benjamin , Carmolli Marya P , Chasekwa Bernard , Ntozini Robert , Mutasa Kuda , McNeal Monica M , Majo Florence D , Tavengwa Naume V , Moulton Lawrence H , Humphrey Jean H , Kirkpatrick Beth D , Prendergast Andrew J 
Published: February 2019

Abstract

Background
Oral vaccines have lower efficacy in developing compared to developed countries. Poor water, sanitation, and hygiene (WASH) may contribute to reduced oral vaccine immunogenicity.

Methods
We conducted a cluster-randomized 2 × 2 factorial trial in rural Zimbabwe. Pregnant women and their infants were eligible if they lived in clusters randomized to (1) standard of care (52 clusters); (2) improved infant feeding (53 clusters); (3) WASH: ventilated improved pit latrine, 2 hand-washing stations, liquid soap, chlorine, infant play space, and hygiene counseling (53 clusters); or (4) feeding plus WASH (53 clusters). This substudy compared oral rotavirus vaccine (RVV) seroconversion (primary outcome), and seropositivity and geometric mean titer (GMT) (secondary outcomes), in WASH vs non-WASH infants by intention-to-treat analysis.

Results
We included 801 infants with documented RVV receipt and postvaccine titer measurements (329 from 84 WASH clusters; 472 from 102 non-WASH clusters); 328 infants with prevaccination titers were included in the primary outcome. Thirty-three of 109 (30.3%) infants in the WASH group seroconverted following rotavirus vaccination, compared to 43 of 219 (19.6%) in the non-WASH group (absolute difference, 10.6% [95% confidence interval {CI}, .54%–20.7%]; P = .031). In the WASH vs non-WASH groups, 90 of 329 (27.4%) vs 107 of 472 (22.7%) were seropositive postvaccination (absolute difference, 4.7% [95% CI, –1.4% to 10.8%]; P = .130), and antirotavirus GMT was 18.4 (95% CI, 15.6–21.7) U/mL vs 14.9 (95% CI, 13.2–16.8) U/mL (P = .072).

Conclusions
Improvements in household WASH led to modest but significant increases in seroconversion to RVV in rural Zimbabwean infants.

Clinical Trials Registration
NCT01824940.
A Dose-finding Study of a Wild-type Influenza A(H3N2) Virus in a Healthy Volunteer Human Challenge Model
Authors: Han Alison , Czajkowski Lindsay M , Donaldson Amanda , Baus Holly Ann , Reed Susan M , Athota Rani S , Bristol Tyler , Rosas Luz Angela , Cervantes-Medina Adriana , Taubenberger Jeffery K , Memoli Matthew J 
Published: February 2019

AbstractBackgroundThe development of vaccines and therapeutics has relied on healthy volunteer influenza challenge studies. A validated human infection model with wild-type A(H1N1)pdm09 was reported previously. Our objective was to characterize a wild-type influenza A/Bethesda/MM1/H3N2 challenge virus in healthy volunteers.MethodsParticipants received a single dose of a cell-based, reverse-genetics, Good Manufacturing Practices–produced wild-type influenza A(H3N2)2011 virus intranasally and were isolated at the National Institutes of Health Clinical Center for ≥9 days. Dose escalation was performed from 104 to 107 TCID50 (50% tissue culture infectious dose). Viral shedding and clinical disease were evaluated daily.ResultsOf 37 participants challenged, 16 (43%) had viral shedding and 27 (73%) developed symptoms, with 12 (32%) participants experiencing mild to moderate influenza disease (MMID), defined as shedding and symptoms. Only participants receiving 106 and 107 TCID50 experienced MMID at 44% and 40%, respectively. Symptom severity peaked on day 3, whereas most viral shedding occurred 1–2 days after challenge. Only 10 (29%) participants had a ≥4-fold rise in hemagglutination inhibition antibody titer after challenge.ConclusionsThe A/Bethesda/MM1/H3N2 challenge virus safely induced MMID in healthy volunteers, but caused less MMID than the A(H1N1)pdm09 challenge virus even at the highest dose. There was less detection of shedding though the incidence of symptoms was similar to A(H1N1)pdm09. Fewer serum anti-hemagglutinin (HA) antibody responses with less MMID indicate that preexisting immunity factors other than anti-HA antibody may limit shedding in healthy volunteers. This A/Bethesda/MM1/H3N2 challenge virus can be utilized in future studies to further explore pathogenesis and immunity and to evaluate vaccine candidates.Clinical Trials RegistrationNCT02594189
Changes in Otitis Media Episodes and Pressure Equalization Tube Insertions Among Young Children Following Introduction of the 13-Valent Pneumococcal Conjugate Vaccine: A Birth Cohort–based Study
Authors: Wiese Andrew D , Huang Xiang , Yu Chang , Mitchel Edward F , Kyaw Moe H , Griffin Marie R , Grijalva Carlos G 
Published: February 2019

Abstract

Background
The impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on the occurrence of first and subsequent otitis media (OM) episodes in early childhood is unclear. We compared the risk of OM episodes among children age <2 years before and after PCV13 introduction, accounting for the dependence between OM episodes.

Methods
We identified consecutive annual (July–June) cohorts of Tennessee Medicaid–enrolled children (2006–2014) from birth through age 2 years. We identified OM episodes using coded diagnoses (we classified diagnoses <21 days apart as the same episode). We modeled adjusted hazard ratios (aHRs) for OM comparing 7-valent pneumococcal conjugate vaccine (PCV7)–era (2006–2010) and PCV13-era (2011–2014) birth cohorts, accounting for risk factors and dependence between first and subsequent episodes. Secondary analyses examined pressure equalization tube (PET) insertions and compared the risk of recurrent OM (≥3 episodes in 6 months or ≥4 episodes in 12 months) between PCV7- and PCV13-era birth cohorts.

Results
We observed 618 968 OM episodes and 24 875 PET insertions among 368 063 children. OM and PET insertion rates increased during the PCV7 years and declined after PCV13 introduction. OM and PET insertion risks were lower in the 2013–2014 cohort compared with the 2009–2010 cohort (aHRs [95% confidence interval], 0.92 [.91–.93] and 0.76 [.72–.80], respectively). PCV13 introduction was associated with declines in the risk of first, subsequent, and recurrent OM.

Conclusions
The transition from PCV7 to PCV13 was associated with a decline of OM among children aged <2 years due to a reduction in the risk of both the first and subsequent OM episodes.
High-risk Human Papilloma Virus Testing Improves Diagnostic Performance to Predict Moderate- to High-grade Anal Intraepithelial Neoplasia in Human Immunodeficiency Virus–infected Men Who Have Sex With Men in Low-to-Absent Cytological Abnormalities
Authors: Viciana Pompeyo , Milanés-Guisado Yusnelkis , Fontillón María , Domínguez Castaño Ana , Sotomayor César , Espinosa Nuria , López-Cortés Luis F , Neukam Karin 
Published: February 2019

AbstractBackgroundScreening methods for anal squamous intraepithelial lesions (SILs) are suboptimal. We aimed to determine the diagnostic performance of a composite endpoint comprising anal liquid-based cytology (aLBC) and high-risk human papillomavirus (HR-HPV) testing to predict histological high-grade SILs (hHSILs).MethodsFrom the SeVIHanal cohort, human immunodeficiency virus (HIV)–infected men who have sex with men (MSM) who had an aLBC with concomitant HR-HPV testing were included. hHSILs were determined by high-resolution anoscopy (HRA)–guided biopsy.ResultsA total of 705 visits obtained from 426 patients were included. The prevalence of HR-HPV among aLBC results were 51.9% (133/215) normal, 87.9% (20/232) low-grade SILs (LSILs), and 90.9% (149/164) high-grade SILs; P (linear association) < .001. Low prevalence of hHSILs was only observed for the composite aLBC/HR-HPV testing endpoint “normal/noHR-HPV” (10%) and “LSIL/noHR-HPV” (4%). The prognostic values (95% confidence interval) for HR-HPV to predict hHSILs in normal cytology were positive predictive value (PPV), 29.3% (25.6%–33.3%); negative predictive value (NPV), 90.2% (82.8%–94.7%); sensitivity, 83% (69.2%–92.4%); and specificity, 44.1% (36.4%–51.9%). Corresponding figures for cytologic LSILs were PPV, 39.2% (37.4%–41.1%); NPV, 96.4% (78.9%–99.5%); sensitivity, 98.8% (93.3%–99.9%); and specificity, 17.9% (12.1%–24.9%). A positive interaction and a synergistic effect for the composite endpoint were observed (relative excess risk = 1.50, attributable proportion of histological results to interaction = 0.17, synergy index = 1.24).ConclusionsHRA should not be indicated in the setting of LSILs/noHR-HPV following aLBC-based screening. In contrast, HIV-infected MSM with normal aLBC/HR-HPV infection should be considered for HRA.Clinical Trials RegistrationNCT03713229.
Signals, Educational Decision-Making, and Inequality
Authors: Holm Anders , Hjorth-Trolle Anders , Jæger Mads Meier 
Published: February 2019

AbstractWe propose a model of educational decision-making based on rational choice theory in which students use signals about academic ability to make inference about the costs and benefits of different educational options. Our model is simple, extends ideas from previous models, and has testable implications. We test our model using data on Danish monozygotic twins and find that (i) students who receive a positive signal about their academic ability have a higher likelihood of enrolling in and completing a college-bound track compared with those who do not; (ii) the effect of the signal is stronger for students from low socio-economic status (SES) backgrounds than for those from high-SES ones; and (iii) for low-SES students the effect is stronger on enrolment than on completion. Our results suggest that signals about academic ability affect educational decisions in general; they are more important for students who do not have a family ‘push’ to avoid downward social mobility; and they affect educational inequality by making low-SES students too optimistic about their likelihood of completing the college-bound track.
Dimension-Free L
p-Maximal Inequalities for Spherical Means in ℤm+1N
Authors: Greenblatt Jordan , Kolla Alexandra , Krause Ben 
Published: February 2019

Abstract
We extend the main result of Krause—the existence of dimension-free $L^p$-bounds, $p &gt; 1$, for the spherical maximal function in the hypercube, $\{0,1\}^N$—to all cyclic groups, $\mathbb{Z}_{m+1}^N, \ m \geq 1$. Our approach follows that of Krause, which grew out of the arguments of Harrow, Kolla, and Schulman, which were in turn motivated by the spectral technique developed by Nevo and Stein, and by Stein, in the context of pointwise ergodic theorems on general groups.
Semi-Uniform Domains and the A∞ Property for Harmonic Measure
Authors: Azzam Jonas 
Published: February 2019

Abstract
We study the properties of harmonic measure in semi-uniform domains. Aikawa and Hirata showed in [ 5] that, for John domains satisfying the capacity density condition (CDC), the doubling property for harmonic measure is equivalent to the domain being semi-uniform. Our 1st result removes the John condition by showing that any domain satisfying the CDC whose harmonic measure is doubling is semi-uniform. Next, we develop a substitute for some classical estimates on harmonic measure in nontangentially accessible domains that works in semi-uniform domains. We also show that semi-uniform domains with uniformly rectifiable boundary have big pieces of chord-arc subdomains. We cannot hope for big pieces of Lipschitz subdomains (as was shown for chord-arc domains by David and Jerison [ 19]) due to an example of Hrycak, which we review in the appendix. Finally, we combine these tools to study the $A_{\infty }$-property of harmonic measure. For a domain with Ahlfors–David regular boundary, it was shown by Hofmann and Martell that the $A_{\infty }$ property of harmonic measure implies uniform rectifiability of the boundary [ 25, 27]. Since $A_{\infty }$-weights are doubling, this also implies the domain is semi-uniform. Our final result shows that these two properties, semi-uniformity and uniformly rectifiable boundary, also imply the $A_{\infty }$ property for harmonic measure, thus classifying geometrically all domains for which this holds.
A high-fat diet aggravates osteonecrosis through a macrophage-derived IL-6 pathway
Authors: Zhou Zubin , Pan Chenhao , Wang Nan , Zhou Lihui , Shan Haojie , Gao Youshui , Yu Xiaowei 
Published: February 2019

Abstract
Inflammation plays an important role in osteonecrosis. Obesity, a risk factor for osteonecrosis, leads to a chronic inflammatory status. We hypothesized that inflammation mediated the effects of obesity on osteonecrosis and tested our hypothesis in a mouse model of osteonecrosis. We fed mice with a high-fat diet (HFD) for 12 weeks before osteonecrosis induction by methylprednisolone and examined bone structure and IL-6 expression. Then we investigated the effects of IL-6 deletion in mice with osteonecrosis on the HFD. Next, we isolated bone marrow cells and determined the cell types responsible for HFD-induced IL-6 secretion. Finally, we investigated the roles of macrophages and macrophage-driven IL-6 in HFD-mediated effects on osteonecrosis and osteogenesis of bone marrow stromal cells (BMSCs). The HFD lead to exacerbated destruction of the femoral head in mice with osteonecrosis and increased IL-6 expression in macrophages. Il-6 knockout or macrophage depletion suppressed the effects of the HFD on bone damage. When co-cultured with macrophages isolated from HFD-fed mice with osteonecrosis, BMSCs showed reduced viability and suppressed osteogenic differentiation. Our results suggest that macrophage-driven IL-6 bridges obesity and osteonecrosis and inhibition of IL-6 or depletion of macrophage may represent a therapeutic strategy for obesity-associated osteonecrosis.