bluuebunny/crossref_metadata_2025_split huggingface dataset:
The representative structure of graphene oxide nanoflakes from machine learning
Authors: Motevalli Benyamin , Parker Amanda J , Sun Baichuan , Barnard Amanda S 
Published: December 2019

Abstract
In this paper we revisit the structure of graphene oxide, and determine the pure and truly representative structures for graphene nanoflakes using machine learning. Using 20 396 random configurations relaxed at the electronic structure level, we observe the presence of hydroxyl, ether, double bonds, aliphatic (cyclohexane) disruption, defects and significant out-of-plane distortions that go beyond the Lerf–Klinowski model. Based on an diverse list of 224 chemical, structural and topological features we identify 25 archetypal ‘pure’ graphene oxide structures which capture all of the complexity and diversity of the entire data set; and three prototypes that are the truly representative averages in 224-dimensional space. Together these 28 structures, which are shown to be largely robust against changes in thermochemical conditions modeled using ab initio thermodynamics, can be downloaded and used collectively as a small data set for with a fraction of the computational cost in future work, or independently as an exemplar of graphene oxide with the required oxidation.
Female need for paternal care shapes variation in extra-pair paternity in a cooperative breeder
Authors: Cousseau Laurence , Van de Loock Dries , Githiru Mwangi , Vangestel Carl , Lens Luc 
Published: December 2019

AbstractSocially monogamous females regularly mate with males outside the pair bond. The prevailing explanation for this behavior is that females gain genetic benefits resulting from increased fitness of extra-pair offspring. Furthermore, because of the risk of reduced paternal care in response to cuckoldry, females are expected to seek extra-pair copulations when they can rear offspring with little help from their social partner (“constrained female” hypothesis). We tested these hypotheses and analyzed variation in paternal care in the Afrotropical, facultative cooperative breeding placid greenbul (Phyllastrephus placidus). Overall, approximately 50% of the offspring resulted from extra-pair (and extra-group) mating. Identified extra-pair males were in most cases neighboring dominant males, yet never within-group subordinates. As predicted by the constrained female hypothesis, the occurrence of extra-pair paternity (EPP) increased with the number of cooperative helpers (and not with total group size). However, dominant males did not adjust their food provisioning rates in response to EPP. Although extra-pair males were more strongly related to the dominant female and less heterozygous than the latter’s social mate, this did not result in more inbred extra-pair offspring, likely because identified extra-pair males were not representative of the extra-pair male population. While earlier studies on EPP mainly focused on male genetic quality, results from this study provide evidence that female’s social context may affect extra-pair strategies too.
‘In His Passionate Way’: Emotion, Race and Gender in Cases of Partner Murder in England and Wales, 1900–39
Authors: Seal Lizzie , Neale Alexa 
Published: December 2019

AbstractThis article examines 10 capital cases of men of colour sentenced to death in England and Wales for intimate murders of white British women during 1900–39. It argues that such cases enable analysis of the prevailing emotional norms of this era and the ways in which these were shaped by race, gender and class. Perceptions of intimate relationships as legitimate or illegitimate—judgments about who should feel what about whom—‘is’ related to understandings of citizenship. In revealing the emotional norms at play in cases of murder, it is possible to illustrate how the criminal justice system governed through emotion.
Spatial Attentional Selection Modulates Early Visual Stimulus Processing Independently of Visual Alpha Modulations
Authors: Gundlach C , Moratti S , Forschack N , Müller M M 
Published: December 2019

Abstract
The capacity-limited human brain is constantly confronted with a huge amount of sensory information. Selective attention is needed for biasing neural processing towards relevant information and consequently allows meaningful interaction with the environment. Activity in the alpha-band has been proposed to be related to top-down modulation of neural inhibition and could thus represent a viable candidate to control the priority of stimulus processing. It is, however, unknown whether modulations in the alpha-band directly relate to changes in the sensory gain control of the early visual cortex. Here, we used a spatial cueing paradigm while simultaneously measuring ongoing alpha-band oscillations and steady-state visual evoked potentials (SSVEPs) as a marker of continuous early sensory processing in the human visual cortex. Thereby, the effects of spatial attention for both of these signals and their potential interactions were assessed. As expected, spatial attention modulated both alpha-band and SSVEP responses. However, their modulations were independent of each other and the corresponding activity profiles differed across task demands. Thus, our results challenge the view that modulations of alpha-band activity represent a mechanism that directly alters or controls sensory gain. The potential role of alpha-band oscillations beyond sensory processing will be discussed in light of the present results.
The Natural History of BK Polyomavirus and the Host Immune Response After Stem Cell Transplantation
Authors: Laskin Benjamin L , Denburg Michelle R , Furth Susan L , Moatz Taylor , Altrich Michelle , Kleiboeker Steve , Lutzko Carolyn , Zhu Xiang , Blackard Jason T , Jodele Sonata , Lane Adam , Wallace Gregory , Dandoy Christopher E , Lake Kelly , Duell Alexandra , Litts Bridget , Seif Alix E , Olson Timothy , Bunin Nancy , Davies Stella M 
Published: December 2019

Abstract

Background
BK polyomavirus (BKPyV) is associated with symptomatic hemorrhagic cystitis after hematopoietic cell transplantation (HCT). Little is known about the host immune response, effectiveness of antiviral treatment, or impact of asymptomatic replication on long-term kidney function.

Methods
In children and young adults undergoing allogeneic HCT, we quantified BKPyV viruria and viremia (pre-HCT and at Months 1–4, 8, 12, and 24 post-HCT) and tested associations of peak viremia ≥10 000 or viruria ≥109 copies/mL with estimated kidney function (glomerular filtration rate, eGFR) and overall survival at 2 years posttransplant. We examined the factors associated with viral clearance by Month 4, including BKPyV-specific T cells by enzyme-linked immune absorbent spot at Month 3 and cidofovir use.

Results
We prospectively enrolled 193 participants (median age 10 years) and found that 18% had viremia ≥10 000 copies/mL and 45% had viruria ≥109 copies/mL in the first 3 months post-HCT. Among the 147 participants without cystitis (asymptomatic), 58 (40%) had any viremia. In the entire cohort and asymptomatic subset, having viremia ≥10 000 copies/mL was associated with a lower creatinine/cystatin C eGFR at 2 years post-HCT. Viremia ≥10 000 copies/mL was associated with a higher risk of death (adjusted hazard ratio, 2.2; 95% confidence interval, 1.1–4.2). Clearing viremia was associated with detectable BKPyV-specific T cells and having viremia &lt;10 000 copies/mL, but not cidofovir exposure.

Conclusions
Screening for BKPyV viremia after HCT identifies asymptomatic patients at risk for kidney disease and reduced survival. These data suggest potential changes to clinical practice, including prospective monitoring for BKPyV viremia to test virus-specific T cells to prevent or treat BKPyV replication.
From Correspondence to Computers: A Theory of Mediated Presence in History
Authors: Bourdon Jérôme 
Published: December 2019

AbstractThis article proposes a theory of mediated presence, defined as the sense of presence— despite physical absence—made possible by technology. Pushing the boundaries of media, the theory integrates various notions of presence at a distance: telepresence in telecommunications and computer-mediated communication, liveness in broadcasting and on the Internet, and the epistolary presence of antiquity. Theoretically, it adopts a social constructivist approach to long-term communication history, with an emphasis on technological breakdowns. The core discussion addresses three criteria for a historical, comparative analysis of mediated presence: dissemination versus dialogue, transmission-reception time lags, and levels of disembodiment. Refuting axiological and technology-centered views of history, the article concludes that increased technological options for presence at a distance have remained essentially ambivalent for users who vacillate between the need for distance and the search for connection.
Microbial indicators are better predictors of wheat yield and quality than N fertilization
Authors: Yergeau Étienne , Quiza Liliana , Tremblay Julien 
Published: December 2019

ABSTRACTIn view of their key roles in many soil- and plant-related processes, we hypothesized that soil microorganisms could play a larger role in determining wheat baking quality than nitrogen fertilization. A field experiment was conducted under bread wheat production conditions, where different fertilization treatments, ranging from 0–120 kg/ha NH4NO3, were applied. Soil samples were taken in May, June and July. Functional genes in the nitrogen cycle were quantified and amplicons of the 16S rRNA gene and the ITS region were sequenced. Wheat yields were measured, and the grain baking quality was analysed for each plot. Fertilisation did not significantly influence the yields and the grain quality. Many bacterial and fungal Amplicon Sequence Variants showed significant positive or negative correlations with yield and grain baking quality parameters. Among the functional gene quantified, the archaeal amoA showed strong negative correlations with the wheat yields and many grain and flour quality parameters. Regression models were able to explain up to 81% of the variability in grain quality based on the microbial data from the May sampling. A better understanding of the microbiology of wheat fields could lead to an optimized management of the N fertilization to maximize yields and grain quality.
Castelnuovo–Mumford Regularity up to Symmetry
Authors: Le Dinh Van , Nagel Uwe , Nguyen Hop D , Römer Tim 
Published: December 2019

AbstractWe study the asymptotic behavior of the Castelnuovo–Mumford regularity along chains of graded ideals in increasingly larger polynomial rings that are invariant under the action of symmetric groups. A linear upper bound for the regularity of such ideals is established. We conjecture that their regularity grows eventually precisely linearly. We establish this conjecture in several cases, most notably when the ideals are Artinian or squarefree monomial.
Genetic influence of ABCG2, UGT1A1 and NR1I2 on dolutegravir plasma pharmacokinetics
Authors: Elliot Emilie R , Neary Megan , Else Laura , Khoo Saye , Moyle Graeme , Carr Daniel F , Wang Xinzhu , Mcclure Myra , Boffito Marta , Owen Andrew 
Published: December 2019

AbstractObjectivesDolutegravir has replaced efavirenz as first-line treatment in universal HIV guidelines. We sought to ascertain the contributory effect of SNPs in four key genes linked to dolutegravir disposition (UGT1A1, ABCG2, CYP3A and NR1I2) on plasma dolutegravir pharmacokinetics.MethodsPaired pharmacogenetic/pharmacokinetic data from 93 subjects were analysed for association using multivariate linear regression.ResultsCo-occurring UGT1*28 and NR1I2 c.63396C&gt;T homozygosity was associated with a 79% increase in AUC0–24 (P = 0.001; 27% if analysed individually), whilst combined ABCG2 c.421C&gt;A and NR1I2 c.63396C&gt;T variants were associated with a 43% increase in Cmax (P = 0.002) and a 39% increase in AUC0–24 (P = 0.002). When analysed individually, homozygosity for the NR1I2 c.63396C&gt;T variant alleles was associated with a 28% increase in Cmax (P = 0.033) and homozygosity for the ABCG2 c.421C&gt;A variant alleles was associated with a 28% increase in Cmax (P = 0.047). The UGT1A1*28 (rs8175347) poor metabolizer status (*28/*28; *28/*37; *37/*37) was individually associated with a 27% increase in AUC0–24 (P = 0.020). The combination of UGT1A1*28 poor metabolizer and UGT1A1*6 intermediate metabolizer statuses correlated with a 43% increase in AUC0–24 (P = 0.023).ConclusionsThis study showed a pharmacogenetic association between dolutegravir pharmacokinetics and variants in the ABCG2, UGT1A1 and NR1I2 genes, particularly when combined. Further research is warranted to confirm these associations in population-specific studies and to investigate their putative relationship with dolutegravir pharmacodynamics.
Developing and Sustaining an Effective and Resilient Oncology Careforce: Opportunities for Action
Authors: Takvorian Samuel U , Balogh Erin , Nass Sharyl , Valentin Virginia L , Hoffman-Hogg Lori , Oyer Randall A , Carlson Robert W , Meropol Neal J , Sheldon Lisa Kennedy , Shulman Lawrence N 
Published: December 2019

Abstract
Advances in cancer care have led to improved survival, which, coupled with demographic trends, have contributed to rapid growth in the number of patients needing cancer care services. However, with increasing caseload, care complexity, and administrative burden, the current workforce is ill equipped to meet these burgeoning new demands. These trends have contributed to clinician burnout, compounding a widening workforce shortage. Moreover, family caregivers, who have unique knowledge of patient preferences, symptoms, and goals of care, are infrequently appreciated and supported as integral members of the oncology “careforce.” A crisis is looming, which will hinder access to timely, high-quality cancer care if left unchecked. Stemming from the proceedings of a 2019 workshop convened by the National Cancer Policy Forum of the National Academies of Sciences, Engineering, and Medicine, this commentary characterizes the factors contributing to an increasingly strained oncology careforce and presents multilevel strategies to improve its efficiency, effectiveness, and resilience. Together, these will enable today’s oncology careforce to provide high-quality care to more patients while improving the patient, caregiver, and clinician experience.
Toward an Aggregate, Implicit, and Dynamic Model of Norm Formation: Capturing Large-Scale Media Representations of Dynamic Descriptive Norms Through Automated and Crowdsourced Content Analysis
Authors: Liu Jiaying , Siegel Leeann , Gibson Laura A , Kim Yoonsang , Binns Steven , Emery Sherry , Hornik Robert C 
Published: December 2019

Abstract
Media content can shape people’s descriptive norm perceptions by presenting either population-level prevalence information or descriptions of individuals’ behaviors. Supervised machine learning and crowdsourcing can be combined to answer new, theoretical questions about the ways in which normative perceptions form and evolve through repeated, incidental exposure to normative mentions emanating from the media environment. Applying these methods, this study describes tobacco and e-cigarette norm prevalence and trends over 37 months through an examination of a census of 135,764 long-form media texts, 12,262 popular YouTube videos, and 75,322,911 tweets. Long-form texts mentioned tobacco population norms (4–5%) proportionately less often than e-cigarette population norms (20%). Individual use norms were common across sources, particularly YouTube (tobacco long-form: 34%; Twitter: 33%; YouTube: 88%; e-cigarette long form: 17%; Twitter: 16%; YouTube: 96%). The capacity to capture aggregated prevalence and temporal dynamics of normative media content permits asking population-level media effects questions that would otherwise be infeasible to address.
Military Realism and Doctrinal Innovation in Kennedy's Army: A New Perspective on Military Innovation
Authors: Campbell Peter 
Published: December 2019

AbstractThis article introduces a new theory of military innovation, military realism, which argues that senior military leaders spearhead major changes in military doctrine when existing doctrinal mission priorities and theories of victory do not address the most dangerous threats. What I call the military realist perspective drives this doctrinal innovation. Through a case study of change and continuity in US Army doctrine under President Kennedy, this article challenges bureaucratic, military cultural, and civilian realist theories of military innovation. Military realism provides a powerful explanation of a hard case, while the other theories struggle with what should be an easy case.
Risky Business: Foreign Direct Investment and the Economic Consequences of Electoral Violence
Authors: Doctor Austin C , Bagwell Stephen 
Published: December 2019

AbstractWhile the social and political consequences of electoral violence are widely discussed in the literature, less is known about the economic repercussions of electoral violence. Our study investigates this dynamic, asking how episodes of electoral violence affect existing levels of foreign direct investment. We argue that, when managing their investments in foreign markets, multinational firms weigh the expected gains of the investment with the probability that the host country experiences significant lapses in political stability. Electoral violence signals a greater risk of this undesirable outcome and, thus, increases the probability that firms divest in favor of more favorable investment environments. Using firm-level data, we investigate the investment behavior of seventy-seven multinational firms in twenty-five Sub-Saharan African countries from 1995 to 2008 with a series of logistic regression models. Directly modeling the choices that firms make with respect to yearly changes in investment, we demonstrate that firms are more likely to divest following events of electoral violence in a host country. This study carries important implications for our understanding of how electoral violence may undermine the economic stability of emerging economies.
Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles
Authors: Lauria Andrea , Peirone Serena , Giudice Marco Del , Priante Francesca , Rajan Prabhakar , Caselle Michele , Oliviero Salvatore , Cereda Matteo 
Published: December 2019

AbstractHeterogeneity is a fundamental feature of complex phenotypes. So far, genomic screenings have profiled thousands of samples providing insights into the transcriptome of the cell. However, disentangling the heterogeneity of these transcriptomic Big Data to identify defective biological processes remains challenging. Here we present GSECA, a method exploiting the bimodal behavior of RNA-sequencing gene expression profiles to identify altered gene sets in heterogeneous patient cohorts. Using simulated and experimental RNA-sequencing data sets, we show that GSECA provides higher performances than other available algorithms in detecting truly altered biological processes in large cohorts. Applied to 5941 samples from 14 different cancer types, GSECA correctly identified the alteration of the PI3K/AKT signaling pathway driven by the somatic loss of PTEN and verified the emerging role of PTEN in modulating immune-related processes. In particular, we showed that, in prostate cancer, PTEN loss appears to establish an immunosuppressive tumor microenvironment through the activation of STAT3, and low PTEN expression levels have a detrimental impact on patient disease-free survival. GSECA is available at https://github.com/matteocereda/GSECA.
Molecular subgrouping of atypical teratoid/rhabdoid tumors—a reinvestigation and current consensus
Authors: Ho Ben , Johann Pascal D , Grabovska Yura , De Dieu Andrianteranagna Mamy Jean , Yao Fupan , Frühwald Michael , Hasselblatt Martin , Bourdeaut Franck , Williamson Daniel , Huang Annie , Kool Marcel 
Published: December 2019

Abstract

Background
Atypical teratoid/rhabdoid tumors (ATRTs) are known to exhibit molecular and clinical heterogeneity even though SMARCB1 inactivation is the sole recurrent genetic event present in nearly all cases. Indeed, recent studies demonstrated 3 molecular subgroups of ATRTs that are genetically, epigenetically, and clinically distinct. As these studies included different numbers of tumors, various subgrouping techniques, and naming, an international working group sought to align previous findings and to reach a consensus on nomenclature and clinicopathological significance of ATRT subgroups.

Methods
We integrated various methods to perform a meta-analysis on published and unpublished DNA methylation and gene expression datasets of ATRTs and associated clinicopathological data.

Results
In concordance with previous studies, the analyses identified 3 main molecular subgroups of ATRTs, for which a consensus was reached to name them ATRT-TYR, ATRT-SHH, and ATRT-MYC. The ATRT-SHH subgroup exhibited further heterogeneity, segregating further into 2 subtypes associated with a predominant supratentorial (ATRT-SHH-1) or infratentorial (ATRT-SHH-2) location. For each ATRT subgroup we provide an overview of its main molecular and clinical characteristics, including SMARCB1 alterations and pathway activation.

Conclusions
The introduction of a common classification, characterization, and nomenclature of ATRT subgroups will facilitate future research and serve as a common ground for subgrouping patient samples and ATRT models, which will aid in refining subgroup-based therapies for ATRT patients.
Emergence and Evolution of High-Level Cephalosporin-Resistant Salmonella Goldcoast in Northern Taiwan
Authors: Feng Ye , Chang Yi-Jung , Fang Szu-Hsuan , Su Lin-Hui , Li Hsin-Chieh , Yang Hsin-Ping , Yu Min-Jia , Chiu Cheng-Hsun 
Published: December 2019

Abstract

Background
Nontyphoidal Salmonella (NTS) is an important foodborne pathogen worldwide. We investigated a 2018 outbreak of highly antimicrobial-resistant Salmonella enterica serotype Goldcoast in northern Taiwan.

Methods
We collected 30 clinical isolates and 2 meat isolates from this outbreak in New Taipei and Taoyuan, Taiwan in 2018. The clinical manifestations and the treatment of the patients were reviewed. To trace the source, we examined NTS isolated from food samples collected from the markets in northern Taiwan. All of the isolates along with an additional human isolate from China were sequenced and compared with the sequences of Salmonella Goldcoast reported by other countries.

Results
The outbreak involved 14 pediatric patients (&lt;5 years old) and 16 adults (36 to 83 years old). Nine patients with invasive or severe disease required carbapenem treatment. The MIC90 of ceftriaxone and ciprofloxacin for the outbreak isolates was &gt;256 μg/mL and 1 μg/mL, respectively, and a conjugative 278-kilobase plasmid harboring blaCTX-M-55 and qnrS1 contributed towards the resistance. Whole-genome sequencing revealed a clonal relationship among the outbreak isolates and the 2 collected from the retail meats. The outbreak clone was phylogenetically close to that of Salmonella Goldcoast reported in the United Kingdom, Poland, and China, whereas similar resistance plasmids were found in China and Cambodia.

Conclusions
The clinical spectrum of the high-level cephalosporin-resistant Salmonella Goldcoast is similar to that of other NTS serotypes, but severe cases required carbapenem treatment. The study confirmed the emergence of a highly antimicrobial-resistant clone of Salmonella Goldcoast, highlighting the importance of surveillance for food safety.