bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numeracy and Understanding of Quantitative Aspects of Predictive Models: A Pilot Study
Authors: Weissman Gary , Yadav Kuldeep , Madden Vanessa , Courtright Katherine , Hart Joanna , Asch David , Schapira Marilyn , Halpern Scott 
Published: August 2018

Background The assessment of user preferences for performance characteristics of patient-oriented clinical prediction models is lacking. It is unknown if complex statistical aspects of prediction models are readily understandable by a general audience.
Objective A pilot study was conducted among nonclinical audiences to determine the feasibility of interpreting statistical concepts that describe the performance of prediction models.
Methods We conducted a cross-sectional electronic survey using the Amazon Mechanical Turk platform. The survey instrument included educational modules about predictive models, sensitivity, specificity, and confidence intervals (CIs). Follow-up questions tested participants' abilities to interpret these characteristics with both verbatim and gist knowledge. Objective and subjective numeracy were assessed using previously validated instruments. We also tested understanding of these concepts when embedded in a sample discrete choice experiment task to establish feasibility for future elicitation of preferences using a discrete choice experiment design. Multivariable linear regression was used to identify factors associated with correct interpretation of statistical concepts.
Results Among 534 respondents who answered all nine questions, the mean correct responses was 95.9% (95% CI, 93.8–97.4) for sensitivity, 93.1% (95% CI, 90.5–95.0) for specificity, and 86.6% (95% CI, 83.3–89.3) for CIs. Verbatim interpretation was high for all concepts, but significantly higher than gist only for CIs (p < 0.001). Scores on each discrete choice experiment tasks were slightly lower in each category. Both objective and subjective numeracy were positively associated with an increased proportion of correct responses (p < 0.001).
Conclusion These results suggest that a nonclinical audience can interpret quantitative performance measures of predictive models with very high accuracy. Future development of patient-facing clinical prediction models can feasibly incorporate patient preferences for model features into their development.
Psychosoziale und berufliche Folgen der Depression
Authors: Lang A. , Hamann J. , Brieger P. 
Published: August 2018

ZusammenfassungDepressionen gehören zu den häufigsten Formen psychischer Erkrankungen in unserer Gesellschaft und gehen mit einer hohen Krankheitslast einher. Für die Betroffenen führt dies zu Beeinträchtigungen in allen Aspekten ihrer Lebensführung. Auf psychosozialer Ebene äußert sich dies u. a. in familiären Schwierigkeiten sowie einer Verarmung der sozialen Situation. Auf beruflicher Ebene kommt es zu Einbußen in der Leistungsfähigkeit bis hin zur Arbeitsunfähigkeit und Frühverrentung. Die Wiederherstellung der psychosozialen sowie beruflichen Leistungsfähigkeit gilt daher als wichtiges Ziel der Behandlung. Den psychosozialen Beeinträchtigungen kann mit unterschiedlichen psychotherapeutischen Interventionen entgegengewirkt werden. Der Klärung der beruflichen Perspektiven und der Rückkehr an den Arbeitsplatz wird jedoch in der Versorgung noch zu wenig Beachtung geschenkt. Dies sollte stärker in den Fokus gesetzt werden, um die verschiedenen Möglichkeiten zur Unterstützung der beruflichen Wiedereingliederung ausschöpfen zu können.
Economic shifts in agricultural production and trade due to climate change
Authors: Porfirio Luciana L. , Newth David , Finnigan John J. , Cai Yiyong 
Published: August 2018

AbstractIn addition to expanding agricultural land area and intensifying crop yields, increasing the global trade of agricultural products is one mechanism that humanity has adopted to meet the nutritional demands of a growing population. However, climate change will affect the distribution of agricultural production and, therefore, food supply and global markets. Here we quantify the structural changes in the global agricultural trade network under the two contrasting greenhouse gas emissions scenarios by coupling seven Global Gridded Crop Models and five Earth System Models to a global dynamic economic model. Our results suggest that global trade patterns of agricultural commodities may be significantly different from today’s reality with or without carbon mitigation. More specifically, the agricultural trade network becomes more centralised under the high CO2 emissions scenario, with a few regions dominating the markets. Under the carbon mitigation scenario, the trade network is more distributed and more regions are involved as either importers or exporters. Theoretically, the more distributed the structure of a network, the less vulnerable the system is to climatic or institutional shocks. Mitigating CO2 emissions has the co-benefit of creating a more stable agricultural trade system that may be better able to reduce food insecurity.
Admissible sequences of positive operators
Authors: Kaftal Victor , Larson David 
Published: August 2018

A scalar sequence

ξ
\xi

is said to be admissible for a positive operator

A
A

if

A
=
∑

ξ
j

P
j

A= \sum \xi _jP_j

for some rank-one projections

P
j

P_j

, or, equivalently, if diag

ξ
\xi

is the diagonal of

V
A

V
∗

VAV^*

for some partial isometry

V
V

having as domain the closure of the range of

A
A

. The main result of this paper is that if

A
A

is the sum of infinitely many projections (converging in the strong operator topology) and

ξ
\xi

is a nonsummable sequence in

[
0
,
1
]

[0,1]

that satisfies the Kadison condition that requires that either

∑
{

ξ
i

∣

ξ
i

≤

1
2

}
+
∑
{
(
1
−

ξ
i

)
∣

ξ
i

>

1
2

}
=
∞

\sum \{\xi _i \mid \xi _i\le \frac {1}{2}\}+ \sum \{(1-\xi _i) \mid \xi _i> \frac {1}{2}\} = \infty

or the difference

∑
{

ξ
i

∣

ξ
i

≤

1
2

}
−
∑
{
(
1
−

ξ
i

)
∣

ξ
i

>

1
2

}

\sum \{\xi _i \mid \xi _i\le \frac {1}{2}\}- \sum \{(1-\xi _i) \mid \xi _i> \frac {1}{2}\}

is an integer, then

ξ
\xi

is admissible for

A
A

. This result extends Kadison’s carpenter’s theorem and provides an independent proof of it.
FastSpar: rapid and scalable correlation estimation for compositional data
Authors: Watts Stephen C , Ritchie Scott C , Inouye Michael , Holt Kathryn E 
Published: August 2018

AbstractSummaryA common goal of microbiome studies is the elucidation of community composition and member interactions using counts of taxonomic units extracted from sequence data. Inference of interaction networks from sparse and compositional data requires specialized statistical approaches. A popular solution is SparCC, however its performance limits the calculation of interaction networks for very high-dimensional datasets. Here we introduce FastSpar, an efficient and parallelizable implementation of the SparCC algorithm which rapidly infers correlation networks and calculates P-values using an unbiased estimator. We further demonstrate that FastSpar reduces network inference wall time by 2–3 orders of magnitude compared to SparCC.Availability and implementationFastSpar source code, precompiled binaries and platform packages are freely available on GitHub: github.com/scwatts/FastSparSupplementary informationSupplementary data are available at Bioinformatics online.
PlayMolecule BindScope: large scale CNN-based virtual screening on the web
Authors: Skalic Miha , Martínez-Rosell Gerard , Jiménez José , De Fabritiis Gianni 
Published: August 2018

AbstractSummaryVirtual screening pipelines are one of the most popular used tools in structure-based drug discovery, since they can can reduce both time and cost associated with experimental assays. Recent advances in deep learning methodologies have shown that these outperform classical scoring functions at discriminating binder protein-ligand complexes. Here, we present BindScope, a web application for large-scale active-inactive classification of compounds based on deep convolutional neural networks. Performance is on a pair with current state-of-the-art pipelines. Users can screen on the order of hundreds of compounds at once and interactively visualize the results.Availability and implementationBindScope is available as part of the PlayMolecule.org web application suite.Supplementary informationSupplementary data are available at Bioinformatics online.
Comparative analysis of methods for evaluation of protein models against native structures
Authors: Olechnovič Kliment , Monastyrskyy Bohdan , Kryshtafovych Andriy , Venclovas Česlovas 
Published: August 2018

Abstract

Motivation
Measuring discrepancies between protein models and native structures is at the heart of development of protein structure prediction methods and comparison of their performance. A number of different evaluation methods have been developed; however, their comprehensive and unbiased comparison has not been performed.

Results
We carried out a comparative analysis of several popular model assessment methods (RMSD, TM-score, GDT, QCS, CAD-score, LDDT, SphereGrinder and RPF) to reveal their relative strengths and weaknesses. The analysis, performed on a large and diverse model set derived in the course of three latest community-wide CASP experiments (CASP10–12), had two major directions. First, we looked at general differences between the scores by analyzing distribution, correspondence and correlation of their values as well as differences in selecting best models. Second, we examined the score differences taking into account various structural properties of models (stereochemistry, hydrogen bonds, packing of domains and chain fragments, missing residues, protein length and secondary structure). Our results provide a solid basis for an informed selection of the most appropriate score or combination of scores depending on the task at hand.

Supplementary information
Supplementary data are available at Bioinformatics online.
Enhancing social values, identity and wellbeing: the impact of participatory working with housing association tenants
Authors: Lambourne Thomas , Jenkins Suzanne 
Published: August 2018

Abstract
Community engagement is now embedded in the work of housing associations and local authorities in the UK, as a way of enhancing community development and involvement. This research takes as its focus a housing association based in Merthyr Tydfil, Wales; a town that has experienced deindustrialization, peripheralization, and as a result, some of the UK’s highest levels of socio-economic deprivation. The importance of participatory working outside of a regulatory agenda and boundary is explored, to evaluate the role of tenant participation in building more effective community development practices. The data is gathered through an ethnographic methodology, working with tenants on facilitated projects to explore the impact of TP on tenants. It draws on two distinctive tenant initiatives: a cooking group and a tenant ‘youth forum’. The research finds that through these methods of engagement, a number of positive outcomes can be identified across the tenant body, namely (i) the forging and embedding of social values, (ii) empowering tenant groups and sustaining community identity and (iii) enhancing tenant wellbeing.
Altered White Matter Organization in the TUBB3 E410K Syndrome
Authors: Grant P Ellen , Im Kiho , Ahtam Banu , Laurentys Cynthia T , Chan Wai-Man , Brainard Maya , Chew Sheena , Drottar Marie , Robson Caroline D , Drmic Irene , Engle Elizabeth C 
Published: August 2018

AbstractSeven unrelated individuals (four pediatric, three adults) with the TUBB3 E410K syndrome, harboring identical de novo heterozygous TUBB3 c.1228 G>A mutations, underwent neuropsychological testing and neuroimaging. Despite the absence of cortical malformations, they have intellectual and social disabilities. To search for potential etiologies for these deficits, we compared their brain's structural and white matter organization to 22 controls using structural and diffusion magnetic resonance imaging. Diffusion images were processed to calculate fractional anisotropy (FA) and perform tract reconstructions. Cortical parcellation-based network analysis and gyral topology-based FA analyses were performed. Major interhemispheric, projection and intrahemispheric tracts were manually segmented. Subjects had decreased corpus callosum volume and decreased network efficiency. While only pediatric subjects had diffuse decreases in FA predominantly affecting mid- and long-range tracts, only adult subjects had white matter volume loss associated with decreased cortical surface area. All subjects showed aberrant corticospinal tract trajectory and bilateral absence of the dorsal language network long segment. Furthermore, pediatric subjects had more tracts with decreased FA compared with controls than did adult subjects. These findings define a TUBB3 E410K neuroimaging endophenotype and lead to the hypothesis that the age-related changes are due to microscopic intrahemispheric misguided axons that are pruned during maturation.
Genetic Variability of Melipona subnitida (Hymenoptera: Apidae) in Introduced and Native Populations
Authors: de Souza Flaviane Santos , Costa Maria Angélica Pereira de Carvalho , de Oliveira Eddy José Francisco , Ribeiro Márcia de Fátima , Souza Bruno de Almeida , Araújo Edilson Divino , Imperatriz-Fonseca Vera L , de Carvalho Carlos Alfredo Lopes 
Published: August 2018

Abstract
Melipona subnitida (Hymenoptera: Apidae) is a stingless bee native to Caatinga biome in Brazil, well adapted to hot and dry climate of that region and has been traditionally explored for honey production. Here, we evaluate the genetic structure of 173 colonies of M. subnitida in northeast Brazil by partially sequenced mitochondrial genes cytochrome oxidase I (COI) to compare an introduced population isolated for 30 yr into the Island of Fernando de Noronha (IFN) with the continental populations. We identified high haplotype diversity (0.8220) with 14 haplotypes on the continental populations, being three new ones, compared with the database GenBank. The haplotype H4 was present at the center of network, occurring in four localities on mainland and fixed as a single haplotype on IFN. We propose that the island populations originally introduced carried one haplotype (H4), even though IFN population is suffering pressure by island effect through changes on morphology. Studies on island populations could be a model to understand the dynamics of isolated populations and sustainable management of this biome to preserve M. subnitida.
The Discursive Governance of Forced-Migration Management: The Turkish Shift from Reticence to Activism in Asia
Authors: Korkut Umut 
Published: August 2018

AbstractThis article shows how similar humanitarian narratives of states can travel across different geographies in response to refugee crises. Empirically, it follows Turkey's position vis-à-vis the Syrian and Rohingya refugee crises. Considering Turkey's migration management practices, humanitarian activism narrative, and its political ambition to foster domestic and international audiences for this narrative, this article elaborates on how Turkey has become a humanitarian actor responding both to Syrian and the Rohingya crises. In both cases, the Turkish political discourses have been very resonant of each other, despite Syria and Myanmar being in different geographies and proximities to Turkey. The article also shows how Turkish politicians and the civil servants aspired to enhance visibility and credibility of Turkey as a humanitarian actor. Delineating Turkey's humanitarian narrative shows the role of political agency in forging sympathetic domestic and international audiences. Overall, the Turkish case presents how states operate migration regimes at the cusp of discourses and institutions affecting their forced migration management and humanitarian engagements.
A Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese
Authors: Chiang Charleston W K , Mangul Serghei , Robles Christopher , Sankararaman Sriram 
Published: August 2018

AbstractAs are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East–West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world’s largest ethnic group.
The Promise of Proton Therapy for Central Nervous System Malignancies
Authors: Vogel Jennifer , Carmona Ruben , Ainsley Christopher G , Lustig Robert A 
Published: August 2018

Abstract
Radiation therapy plays a significant role in management of benign and malignant diseases of the central nervous system. Patients may be at risk of acute and late toxicity from radiation therapy due to dose deposition in critical normal structures. In contrast to conventional photon delivery techniques, proton therapy is characterized by Bragg peak dose deposition which results in decreased exit dose beyond the target and greater sparing of normal structure which may reduce the rate of late toxicities from treatment. Dosimetric studies have demonstrated reduced dose to normal structures using proton therapy as compared to photon therapy. In addition, clinical studies are being reported demonstrating safety, feasibility, and low rates of acute toxicity. Technical challenges in proton therapy remain, including full understanding of depth of proton penetration and the biological activity in the distal Bragg peak. In addition, longer clinical follow-up is required to demonstrate reduction in late toxicities as compared to conventional photon-based radiation techniques. In this review, we summarize the current clinical literature and areas of active investigation in proton therapy for adult central nervous system malignancies.
No Association of Polymorphisms in Nav1.7 or Nerve Growth Factor Receptor Genes with Trigeminal Neuralgia
Authors: Costa Grazielle Mara Ferreira , Rocha Luiz Paulo C , Siqueira Silvia Regina Dowgan Tesseroli de , Moreira Paula Rocha , Almeida-Leite Camila Megale 
Published: August 2018

AbstractObjectiveTrigeminal neuralgia is defined as a sudden severe shock-like pain within the distribution of the trigeminal nerve. Pain is a subjective experience that is influenced by gender, culture, environment, psychological traits, and genes. Sodium channels and nerve growth factor play important roles in the transmission of nociceptive signals and pain. The aim of this study was to investigate the occurrence of Nav1.7 sodium channel and nerve growth factor receptor TrkA gene polymorphisms (SCN9A/rs6746030 and NTRK1/rs633, respectively) in trigeminal neuralgia patients.MethodsNinety-six subjects from pain specialty centers in the southeastern region of Brazil were divided into 2 groups: 48 with classical trigeminal neuralgia diagnosis and 48 controls. Pain was evaluated using the visual analog scale and multidimensional McGill Pain Questionnaire. Genomic DNA was obtained from oral swabs in all individuals and was analyzed by real-time polymerase chain reaction.ResultsNo association was observed between evaluated polymorphisms and trigeminal neuralgia. For allele analyses, patients and controls had similar frequencies for both genes. Genotype distribution or allele frequencies of polymorphisms analyzed here did not correlate to pain scores.ConclusionsAlthough no association of evaluated polymorphisms and trigeminal neuralgia diagnosis or pain severity was observed, our data do not exclude the possibility that other genotypes affecting the expression of Nav1.7 or TrkA are associated with the disease. Further studies should investigate distinct genetic polymorphisms and epigenetic factors that may be important in expression of these molecules.
Newest lipoglycopeptides for the management of acute bacterial skin and skin structure infections
Authors: Bell Allison M. , King S. Travis , Barber Katie E. , Adcock Kim G. , Wagner Jamie L. , Stover Kayla R. 
Published: August 2018

Abstract:
Acute bacterial skin and skin structure infections (ABSSSIs) are some of the most commonly encountered infections worldwide. Hospitalizations as a result of ABSSSIs are associated with high mortality. This article discusses the role of oritavancin and dalbavancin, the two newest lipoglycopeptides, in the context of the other available I.V. infusion standard therapy options.
Characteristics and Outcomes of Young Children Hospitalized With Laboratory-confirmed Influenza or Respiratory Syncytial Virus in Ontario, Canada, 2009–2014
Authors: Buchan Sarah A. , Chung Hannah , Karnauchow Timothy , McNally J. Dayre , Campitelli Michael A. , Gubbay Jonathan B. , Katz Kevin , McGeer Allison J. , Richardson David C. , Richardson Susan E. , Simor Andrew , Smieja Marek , Zahariadis George , Tran Dat , Crowcroft Natasha S. , Rosella Laura C. , Kwong Jeffrey C. 
Published: August 2018

Background:
Respiratory illnesses are a major contributor to pediatric hospitalizations, with influenza and respiratory syncytial virus (RSV) causing substantial morbidity and cost each season. We compared the characteristics and outcomes of children 0–59 months of age who were hospitalized with laboratory-confirmed influenza or RSV between 2009 and 2014 in Ontario, Canada.

Methods:
We included hospitalized children who were tested for influenza A, influenza B and RSV and were positive for a single virus. We characterized individuals by their demographics and healthcare utilization patterns and compared their hospital outcomes, in-hospital cost and postdischarge healthcare use by virus type and by presence of underlying comorbidities.

Results:
We identified and analyzed 7659 hospitalizations during which a specimen tested positive for influenza or RSV. Children with RSV were the youngest whereas children with influenza B were the oldest [median ages 6 months (interquartile range: 2–17 months) and 25 months (interquartile range: 10–45 months), respectively]. Complex chronic conditions were more prevalent among children with all influenza (sub)types than RSV (31%–34% versus 20%). In-hospital outcomes were similar by virus type, but in children with comorbidities, postdischarge outcomes varied. We observed no differences in in-hospital cost between viruses or by presence of comorbidities [overall median cost: $4150 Canadian dollars (interquartile range: $3710–$4948)].

Conclusions:
Influenza and RSV account for large numbers of pediatric hospitalizations. RSV and influenza were similar in terms of severity and cost in hospitalized children. Influenza vaccination should be promoted in pregnant women and young children, and a vaccine against RSV would mitigate the high burden of RSV.