bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zebrafish type I collagen mutants faithfully recapitulate human type I collagenopathies
Authors: Gistelinck Charlotte , Kwon Ronald Y. , Malfait Fransiska , Symoens Sofie , Harris Matthew P. , Henke Katrin , Hawkins Michael B. , Fisher Shannon , Sips Patrick , Guillemyn Brecht , Bek Jan Willem , Vermassen Petra , De Saffel Hanna , Witten Paul Eckhard , Weis MaryAnn , De Paepe Anne , Eyre David R. , Willaert Andy , Coucke Paul J. 
Published: August 2018

Significance
Type I collagenopathies are a heterogenous group of connective tissue disorders, caused by genetic defects in type I collagen. Inherent to these disorders is a large clinical variability, of which the underlying molecular basis remains undefined. By systematically analyzing skeletal phenotypes in a large set of type I collagen zebrafish mutants, we show that zebrafish models are able to both genocopy and phenocopy different forms of human type I collagenopathies, arguing for a similar pathogenetic basis. This study illustrates the future potential of zebrafish as a tool to further dissect the molecular basis of phenotypic variability in human type I collagenopathies, to improve diagnostic strategies as well as promote the discovery of new targetable pathways for pharmacological intervention of these disorders.
A data-driven computational model on the effects of immigration policies
Authors: Simon Miranda , Schwartz Cassilde , Hudson David , Johnson Shane D. 
Published: August 2018

SignificanceWould more restrictive immigration policies stop individuals from migrating? We present an agent-based computational model, calibrated using original survey and experimental data, which represents an important step in estimating the “substitution effect” whereby migrants reorient toward unauthorized channels due to changes in policy. We find that government-imposed restrictions on migrants can decrease total migration. However, some restrictions are highly ineffective while others decrease legal migration only at the cost of driving migrants into unauthorized channels. Restrictions on students and high-skilled workers are least effective in reducing migration, and restrictions on family-based visas are especially counterproductive in diverting migrants to back channels. We also find that increasing enforcement would not effectively eliminate the diversion to unauthorized channels.
In vitro single-cell dissection revealing the interior structure of cable bacteria
Authors: Jiang Zaixing , Zhang Shuai , Klausen Lasse Hyldgaard , Song Jie , Li Qiang , Wang Zegao , Stokke Bjørn Torger , Huang Yudong , Besenbacher Flemming , Nielsen Lars Peter , Dong Mingdong 
Published: August 2018

Significance
Cable bacteria were recently discovered as the facilitators of electron transfer over centimeter distances in marine sediments. In this work, we explore the unique structure of the cable bacteria, using atomic force microscopy-based single-cell in vitro dissection. We identify different types of bacterial cell–cell junctions and continuous dimeric strings hidden under the outer membrane that pass through the cell junctions. The strings seem to serve an important function in maintaining the integrity of individual cable bacteria cells as a united filament. On the basis of our findings, we propose a model for the division and growth of the cable bacteria, which illustrate the possible structural requirements for the formation of centimeter-length filaments in the recently discovered cable bacteria.
Constructing the Czech nation
Authors: Batistová Anna , Carpentier Nico 
Published: August 2018

Abstract
The article’s objective is to analyse the discursive construction of the Czech nation in three cultural magazines, produced by
Czech exiles in London during WWII. The theoretical backbone for this analysis is provided by Laclau and Mouffe’s (1985) discourse theory, which in turn supports a discourse-theoretical re-reading of the
literature on the nation, first in general and then in relation to the Czech nation. These three theoretical components support an
analysis of 650 selected contributions in 36 issues of the three main cultural journals of the Czech London exile:
Obzor [Horizon], Kulturní zápisník [Cultural Notebook] and Review. This
discourse-theoretical analysis shows the presence, particularity and contingency of a series of internal nodal points (temporal,
spatial, linguistic, cultural and popular), in combination with the external nodal point of diversity in relation to outgroups. In
the conclusion, the political nature of this construction, which we label the politics of poetry, is emphasized.
Notions of “money” and “house” in the language consciousness of Russians and the Japanese
Authors: Palkin Alexei D. 
Published: August 2018

AbstractCross-cultural research is crucially important in the modern globalized world where different cultural notions clash and interact. This article sheds light on the notions “money” and “house”, which represent attitudes to property, in the perception of Russians and the Japanese. The research method is an association experiment that allows to explain the grounds for mutual understanding or possible misunderstanding in the instances of interethnic contacts. Analysis of association fields formed on the basis of two Russian and one Japanese sampling shows that modern Japanese tend to perceive money as beneficial, while modern Russians tend to perceive it as something evil and related to governance. 21st-century Japanese respondents and 21st-century Russian respondents proved to be more work-oriented than their early 1990s Russian counterparts. Regardless of cultural differences, both Russians and the Japanese admitted their need of money as an indispensable element of modern life. A house is understood in both cultures as a place to live in, but 1990s Russians found it less cozy and comfortable than 21st-century Russians and the Japanese.
Nutrient Production and Micronutrient Gaps: Evidence from an Agriculture‐Nutrition Randomized Control Trial
Authors: Dillon Andrew , Arsenault Joanne , Olney Deanna 
Published: August 2018

AbstractIntegrated agriculture nutrition programs can increase the quantity and quality of nutritious foods through multiple pathways. Increased household production increases the availability of own produced food for consumption, as well as income for food purchases. Increased knowledge of nutrition introduced through a behavior change communication strategy can change food preferences and shift purchasing decisions towards nutritious foods. In a randomized control trial, we demonstrate that an integrated agriculture‐nutrition program in Burkina Faso improved the quality of diets by reducing household macro and micronutrient consumption gaps. We estimate production and consumption nutrient gaps for households in our sample by comparing reported consumption or production of nutrients relative to recommended daily allowances for households. Differences between actual nutrient consumption and production values and the recommended daily allowances provide an estimate of the nutrient gaps (surplus or deficit) within the household. We find that the integrated agriculture‐nutrition program reduced consumption nutrient gaps in treatment households. We also investigate whether the production or nutrition knowledge pathways explain the consumption nutrient gap treatment effects. Though crop choice led to a diversified household production of nutritious foods in treatment villages on the extensive production margin, increased household production of nutrients does not explain the improvements in diet quality due to limited treatment effects for the estimated production nutrient gaps at the intensive production margin. Consumption expenditures in treatment villages did increase purchases of nutritious foods, suggesting that the behavior change communication strategy is effective at not only increasing nutrition knowledge, but also in affecting consumer preferences.
Breast cancer prognosis signature: linking risk stratification to disease subtypes
Authors: Yu Fulong , Quan Fei , Xu Jinyuan , Zhang Yan , Xie Yi , Zhang Jingyu , Lan Yujia , Yuan Huating , Zhang Hongyi , Cheng Shujun , Xiao Yun , Li Xia 
Published: August 2018

AbstractBreast cancer is a very complex and heterogeneous disease with variable molecular mechanisms of carcinogenesis and clinical behaviors. The identification of prognostic risk factors may enable effective diagnosis and treatment of breast cancer. In particular, numerous gene-expression-based prognostic signatures were developed and some of them have already been applied into clinical trials and practice. In this study, we summarized several representative gene-expression-based signatures with significant prognostic value and separately assessed their ability of prognosis prediction in their originally targeted populations of breast cancer. Notably, many of the collected signatures were originally designed to predict the outcomes of estrogen receptor positive (ER+) patients or the whole breast cancer cohort; there are no typical signatures used for the prognostic prediction in a specific population of patients with the intrinsic subtype. We thus attempted to identify subtype-specific prognostic signatures via a computational framework for analyzing multi-omics profiles and patient survival. For both the discovery and an independent data set, we confirmed that subtype-specific signature is a strong and significant independent prognostic factor in the corresponding cohort. These results indicate that the subtype-specific prognostic signature has a much higher resolution in the risk stratification, which may lead to improved therapies and precision medicine for patients with breast cancer.
Comparative Network Reconstruction using mixed integer programming
Authors: Bosdriesz Evert , Prahallad Anirudh , Klinger Bertram , Sieber Anja , Bosma Astrid , Bernards René , Blüthgen Nils , Wessels Lodewyk F A 
Published: August 2018

Abstract

Motivation
Signal-transduction networks are often aberrated in cancer cells, and new anti-cancer drugs that specifically target oncogenes involved in signaling show great clinical promise. However, the effectiveness of such targeted treatments is often hampered by innate or acquired resistance due to feedbacks, crosstalks or network adaptations in response to drug treatment. A quantitative understanding of these signaling networks and how they differ between cells with different oncogenic mutations or between sensitive and resistant cells can help in addressing this problem.

Results
Here, we present Comparative Network Reconstruction (CNR), a computational method to reconstruct signaling networks based on possibly incomplete perturbation data, and to identify which edges differ quantitatively between two or more signaling networks. Prior knowledge about network topology is not required but can straightforwardly be incorporated. We extensively tested our approach using simulated data and applied it to perturbation data from a BRAF mutant, PTPN11 KO cell line that developed resistance to BRAF inhibition. Comparing the reconstructed networks of sensitive and resistant cells suggests that the resistance mechanism involves re-establishing wild-type MAPK signaling, possibly through an alternative RAF-isoform.

Availability and implementation
CNR is available as a python module at https://github.com/NKI-CCB/cnr. Additionally, code to reproduce all figures is available at https://github.com/NKI-CCB/CNR-analyses.

Supplementary information
Supplementary data are available at Bioinformatics online.
A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia
Authors: Li Miaoxin , Jiang Lin , Mak Timothy Shin Heng , Kwan Johnny Sheung Him , Xue Chao , Chen Peikai , Leung Henry Chi-Ming , Cui Liqian , Li Tao , Sham Pak Chung 
Published: August 2018

Abstract

Motivation
It remains challenging to unravel new susceptibility genes of complex diseases and the mechanisms in genome-wide association studies. There are at least two difficulties, isolation of the genuine susceptibility genes from many indirectly associated genes and functional validation of these genes.

Results
We first proposed a novel conditional gene-based association test which can use only summary statistics to isolate independently associated genes of a disease. Applying this method, we detected 185 genes of independent association with schizophrenia. We then designed an in-silico experiment based on expression/co-expression to systematically validate pathogenic potential of these genes. We found that genes of independent association with schizophrenia formed more co-expression pairs in normal post-natal but not pre-natal human brain regions than expected. Interestingly, no co-expression enrichment was found in the brain regions of schizophrenia patients. The genes with independent association also had more significant P-values for differential expression between schizophrenia patients and controls in the brain regions. In contrast, indirectly associated genes or associated genes by other widely-used gene-based tests had no such differential expression and co-expression patterns. In summary, this conditional gene-based association test is effective for isolating directly associated genes from indirectly associated genes, and the results insightfully suggest that common variants might contribute to schizophrenia largely by distorting expression and co-expression in post-natal brains.

Availability and implementation
The conditional gene-based association test has been implemented in a platform ‘KGG’ in Java and is publicly available at http://grass.cgs.hku.hk/limx/kgg/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Police Education in the USA
Authors: Cordner Gary 
Published: August 2018

Abstract
Higher education for police has a 100-year history in the USA. Initially, it incorporated both ‘education’ and much of what is now considered ‘training’, out of necessity because police occupational training had yet to be widely implemented. Since the 1960s, though, separate police training institutions and systems have been established throughout the country. In conjunction with this bifurcation of education and training, the dominant higher education model for police became ‘criminal justice’. Over the last 40 years, criminal justice has become a very popular field of study in American colleges and universities, curricula have broadened to include a wide variety of crime and justice topics, and faculty academic credentials have risen to meet and exceed higher education standards. In the process, however, policing has become a smaller and smaller part of the criminal justice educational enterprise. Today, what passes for police education in the USA has very little police in it.
Effects of sodium metabisulfite additives on nursery pig growth
Authors: Shawk Dwight J , Dritz Steve S , Goodband Robert D , Tokach Mike D , Woodworth Jason C , DeRouchey Joel M 
Published: August 2018

Abstract
Sodium metabisulfite (SMB)-based feed additive efficacy was evaluated in three nursery pig growth experiments where pigs were fed diets containing low deoxynivalenol (&lt;1.5 mg/kg; DON) concentrations. Pigs were weaned at approximately 22 d of age and randomly allotted to pens with one pen of 27 gilts and one pen of 27 barrows per feeder; thus, feeder was the experimental unit. In experiment 1, a total of 2,268 pigs were used in a 35-d trial with 21 feeders per treatment. Experimental treatments included a control diet or the control with 0.50% SMB-based Product 1 (Defusion; Provimi, Brookville, OH) fed in phase 1 and 0.25% fed in phases 2 and 3, then all pigs were fed a control diet for the last week of the study. Pigs fed Product 1 had greater (P &lt; 0.05) ADG, ADFI, and G:F compared with pigs fed the control diet from days 0 to 28. However, from days 28 to 35, the opposite response was observed with pigs fed the control diet having greater ADG and G:F than pigs previously fed Product 1. Despite this response, pigs fed Product 1 were heavier (P &lt; 0.05) on day 35 than control-fed pigs. In experiment 2, a total of 4,320 pigs were used in a 42-d trial. Pigs were fed a control diet or diets with SMB-based either Product 1 or Product 2 (NutriQuest, Mason City, IA) at different concentrations and durations. Among the various treatments, Product 1 or Product 2 concentrations ranged from 0.50% initially to 0.25%, 0.15%, or none the last week of the study. Overall, pigs fed either of the additives at the highest concentrations and for the longest period of time had greater (P &lt; 0.05) ADG and ADFI compared with pigs fed the control diet, with those fed lower concentrations or shorter durations being intermediate. In experiment 3, a total of 2,808 pigs were used in a 28-d trial with 13 feeders per treatment. All pigs were fed a common diet for 7 d after weaning. Pigs were then fed either a control diet (without any SMB-containing product) or a diet containing Product 1 (0.50% and 0.25% from days 0 to 21 and 21 to 28, respectively) or SMB (0.50% and 0.25% from days 0 to 21 and 21 to 28, respectively) or 0.25% SMB from days 0 to 28. Overall, pigs fed Product 1 or high-SMB diets had greater (P &lt; 0.05) ADG compared with pigs fed low-SMB or control diets. In conclusion, results of these experiments indicate that in diets with low DON concentrations, these SMB-based products increased ADG compared with control diets.
Discovering an Anatomic Variant of the Palmaris Profundus during Open Carpal Tunnel Release
Authors: Van Demark Robert E. , Anderson Matthew C. , List Jeb T. , Hayes Meredith , Hayes Matthew , Woodard David 
Published: August 2018

Summary:
A 46-year-old female presented after 3 years of steadily increasing numbness in her hands bilaterally with worse symptoms in her right hand. She reported nighttime paresthesia and exacerbation of her symptoms while writing, typing, and driving. Tinel’s and carpal tunnel compression test were positive bilaterally. During the right hand carpal tunnel release, a layer of synovium was present deep to the carpal ligament with a tendinous portion running midline longitudinally along the median nerve. This layer was an anomalous palmaris profundus (PP) tendon within the carpal tunnel, which inserted distally in the palmar fascia. The PP tendon was freed and released. The PP is a rare muscle variation of the forearm and wrist, and although it has no function, it has been reported as a cause of median nerve compression at the wrist. More commonly, it is an incidental finding during carpal tunnel surgery. Because of its close association with the median nerve, it can cause confusion when encountered during carpal tunnel surgery. Clinicians should be aware of this rare finding, which may be present during carpal tunnel surgery. We present a case, with intraoperative photographs, of a PP tendon that was encountered during a carpal tunnel release.
How different governance models may impact physician–hospital alignment
Authors: Burns Lawton R. , Alexander Jeffrey A. , Andersen Ronald M. 
Published: August 2018

Background:
Hospitals utilize three ideal type models for governing relationships with their physicians: the traditional medical staff, strategic alliances, and employment. Little is known about how these models impact physician alignment.

Purpose:
The study compares the level of physician–hospital alignment across the three models.

Approach:
We used survey data from 1,895 physicians in all three models across 34 hospitals in eight systems to measure several dimensions of alignment. We used logistic equations to predict survey nonresponse and differential physician selection into the alliance and employment models. Controlling for these selection effects, we then used multiple regression to estimate the effects of alliance and employment models on alignment.

Results:
Physicians in employment models express greater alignment with their hospital on several dimensions, compared to physicians in alliances and the traditional medical staff. There were no differences in physician alignment between the latter two models.

Conclusions:
Employment models promote greater alignment on some (but not all) dimensions, controlling for physician selection. The impact of employment on alignment is not large, however.

Practice Implications:
Hospitals and accountable care organizations that rely on employment may achieve higher physician alignment compared to the other two models. It is not clear that the gain in alignment is worth the cost of employment. Given the small impact of employment on alignment, it is also clear that they are not identical. Hospitals may need to go beyond structural models of integration to achieve alignment with their physicians.
Multimodal Imaging of Retired Professional Contact Sport Athletes Does Not Provide Evidence of Structural and Functional Brain Damage
Authors: Zivadinov Robert , Polak Paul , Schweser Ferdinand , Bergsland Niels , Hagemeier Jesper , Dwyer Michael G. , Ramasamy Deepa P. , Baker John G. , Leddy John J. , Willer Barry S. 
Published: August 2018

Background:
Long-term consequences of playing professional football and hockey on brain function and structural neuronal integrity are unknown.

Objectives:
To investigate multimodal metabolic and structural brain magnetic resonance imaging (MRI) differences in retired professional contact sport athletes compared with noncontact sport athletes.

Methods:
Twenty-one male contact sport athletes and 21 age-matched noncontact sport athletes were scanned on a 3 tesla (3T) MRI using a multimodal imaging approach. The MRI outcomes included presence, number, and volume of focal white matter signal abnormalities, volumes of global and regional tissue-specific brain structures, diffusion-tensor imaging tract-based spatial statistics measures of mean diffusivity and fractional anisotropy, quantitative susceptibility mapping of deep gray matter, presence, number, and volume of cerebral microbleeds, MR spectroscopy N-acetyl-aspartate, glutamate, and glutamine concentrations relative to creatine and phosphor creatine of the corpus callosum, and perfusion-weighted imaging mean transit time, cerebral blood flow, and cerebral blood volume outcomes. Subjects were also classified as having mild cognitive impairment.

Results:
No significant differences were found for structural or functional MRI measures between contact sport athletes and noncontact sport athletes.

Conclusions:
This multimodal imaging study did not show any microstructural, metabolic brain tissue injury differences in retired contact versus non-contact sport athletes.