bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein multiple alignments: sequence-based versus structure-based programs
Authors: Carpentier Mathilde , Chomilier Jacques 
Published: April 2019

AbstractMotivationMultiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures.ResultsWe compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs.Availability and implementationAll data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/.Supplementary informationSupplementary data are available at Bioinformatics online.
Functional Parcellation of Human Brain Precuneus Using Density-Based Clustering
Authors: Luo Zhiguo , Zeng Ling-Li , Qin Jian , Hou Chenping , Shen Hui , Hu Dewen 
Published: April 2019

Abstract
The human precuneus is involved in many high-level cognitive functions, which strongly suggests the existence of biologically meaningful subdivisions. However, the functional parcellation of the precuneus needs much to be investigated. In this study, we developed an eigen clustering (EIC) approach for the parcellation using precuneus–cortical functional connectivity from fMRI data of the Human Connectome Project. The EIC approach is robust to noise and can automatically determine the cluster number. It is consistently demonstrated that the human precuneus can be subdivided into six symmetrical and connected parcels. The anterior and posterior precuneus participate in sensorimotor and visual functions, respectively. The central precuneus with four subregions indicates a media role in the interaction of the default mode, dorsal attention, and frontoparietal control networks. The EIC-based functional parcellation is free of the spatial distance constraint and is more functionally coherent than parcellation using typical clustering algorithms. The precuneus subregions had high accordance with cortical morphology and revealed good functional segregation and integration characteristics in functional task-evoked activations. This study may shed new light on the human precuneus function at a delicate level and offer an alternative scheme for human brain parcellation.
The Democratic Case for a Written Constitution
Authors: King Jeff 
Published: April 2019

Abstract
Written constitutions have often been viewed as a bridle for unchecked political majoritarianism, as a restraint on government, and hence as a limiting device rather than form of democratic political expression. Breaking with that tradition, this article sets out a democratic case for a written constitution and contrasts it with the rights-based and clarity-based cases. It then proceeds to show why the case against written constitutions – which is broadly located in a conservative critique, an anti-rationalist critique and an anti-judicialisation critique – is misguided. Nevertheless, a democratic case for a written constitution necessarily raises challenging questions about how the constitution would be enacted, and how rigidly entrenched it should be. In relation to the former, the author argues for a constituent assembly consisting of party and direct citizen representation. As for the latter, he defends a model of entrenchment that permits amendment through a simple majoritarian parliamentary procedure in conjunction with a referendum, and, most controversially, a provision requiring a new constitutional convention about once in a generation. This is the type of democratic constitution, in the author’s view, that accommodates the need for the United Kingdom constitutional order to take both rights and democracy seriously.
The polarity protein Scrib limits atherosclerosis development in mice
Authors: Schürmann Christoph , Dienst Franziska L , Pálfi Katalin , Vasconez Andrea E , Oo James A , Wang ShengPeng , Buchmann Giulia K , Offermanns Stefan , van de Sluis Bart , Leisegang Matthias S , Günther Stefan , Humbert Patrick O , Lee Eunjee , Zhu Jun , Weigert Andreas , Mathoor Praveen , Wittig Ilka , Kruse Christoph , Brandes Ralf P 
Published: April 2019

Abstract

Aims
The protein Scrib (Scribble 1) is known to control apico-basal polarity in epithelial cells. The role of polarity proteins in the vascular system remains poorly characterized; however, we previously reported that Scrib maintains the endothelial phenotype and directed migration. On this basis, we hypothesized that Scrib has anti-atherosclerotic functions.

Methods and results
Tamoxifen-induced Scrib-knockout mice were crossed with ApoE−/− knockout mice and spontaneous atherosclerosis under high-fat diet (HFD), as well as accelerated atherosclerosis in response to partial carotid artery ligation and HFD, was induced. Deletion of Scrib resulted in increased atherosclerosis development in both models. Mechanistically, flow- as well as acetylcholine-induced endothelium-dependent relaxation and AKT phosphorylation was reduced by deletion of Scrib, whereas vascular permeability and leucocyte extravasation were increased after Scrib knockout. Scrib immune pull down in primary carotid endothelial cells and mass spectrometry identified Arhgef7 (Rho Guanine Nucleotide Exchange Factor 7, βPix) as interaction partner. Scrib or Arhgef7 down-regulation by siRNA reduced the endothelial barrier function in human umbilical vein endothelial cells. Gene expression analysis from murine samples and from human biobank material of carotid endarterectomies indicated that loss of Scrib resulted in endothelial dedifferentiation with a decreased expression of endothelial signature genes.

Conclusions
By maintaining a quiescent endothelial phenotype, the polarity protein Scrib elicits anti-atherosclerotic functions.
The Sources of Growth in a Technologically Progressive Economy: The United States, 1899–1941
Authors: Bakker Gerben , Crafts Nicholas , Woltjer Pieter 
Published: April 2019

Abstract
We develop new aggregate total factor productivity (TFP) growth estimates for the USA between 1899 and 1941, and sectoral estimates at the most disaggregated level so far, 38 industries. We include hard-to-measure services, and a refined measure of sectoral labour quality growth. The resulting data set supersedes Kendrick (1961), showing TFP growth lower than previously thought, broadly based across industries, and strongly variant intertemporally. The four ‘great inventions’ that Gordon (2016) highlighted were important but less dominant in TFP growth than their predecessors in the British industrial revolution. The findings also make it unlikely the 1930s had the twentieth century's highest TFP growth.
Determinants of non-participation in colon examination following positive stool sample in colorectal cancer screening
Authors: Deding Ulrik , Henig Anna Sharon , Hindersson Peter , Torp-Pedersen Christian , Bøggild Henrik 
Published: April 2019

Abstract

Background
Social inequalities has been shown for participation in colorectal cancer screening and recently in the initial stool sample blood test. If these differences persist at follow-up colon examination after a positive stool test, it would suggest that social inequality in screening may be greater than the inequality observed in initial stool sample blood test.

Methods
All data were derived from national registers. Using logistic regression analyses, odds of non-participation for follow-up colon examination were estimated based on age group, educational level, income quartile, immigration status and marital status in men and in women, who had participated in initial stool sample test for blood with a positive result.

Results
Among 20 849 men and 16 565 women invited for follow-up colonoscopy in the period 2014–15, 10.63 and 11.37%, respectively, did not attend. In men, odds of non-participation were higher in the eldest, those with lower income and lower educational level, in immigrants and in singles. Odds ratio (OR) in males of highest income quartile was 0.54 [95% confidence interval (CI) 0.46; 0.63] compared with lowest income quartile. In women, the differences were not as large. OR in females of highest income quartile was 0.73 (95% CI 0.61; 0.87) compared with lowest income quartile.

Conclusion
Sociodemographic differences in odds of non-participation exist in follow-up colon examination in the Danish colorectal cancer screening. Differences were evident in all subgroups of the male population. The same patterns were seen in women. Social inequalities in participation for follow-up colon examination can increase overall social inequality and consequently, lead to health disparities.
China vs the WHO: a behavioural norm conflict in the SARS crisis
Authors: Kreuder-Sonnen Christian 
Published: April 2019

Abstract
This article studies a conflict over two competing norms in which the actors demonstrated incompatible positions not through arguments, but through actions. During the SARS crisis, China and the World Health Organization (WHO) entered a norm conflict over the precedence of sovereignty or global health security. Both resorted to behavioural, not discursive contestation: while the WHO practically but not rhetorically challenged the sovereignty norm by acting according to the norm of global health security, China—without openly acknowledging it—contravened the basic principles of global health security by acting according to the overlapping sovereignty norm. Why and with what consequences do actors choose to contest norms through actions rather than words? The article accounts for the resort to behavioural contestation by pointing to the strategic advantages it offers for furthering a contentious norm understanding without facing the social costs of making it explicit. It furthermore highlights that behavioural contestation may feed back into and change the odds of discursive contestation as its practical effects provide rhetorical resources to (de-)legitimate one or the other position. The propositions are illustrated in the interactions of China and the WHO during the SARS crisis and the subsequent norm development. This article forms part of the special section of the May 2019 issue of International Affairs on ‘The dynamics of dissent’, guest-edited by Anette Stimmer and Lea Wisken.
Farmer monitoring reveals the effect of tidal height on mortality risk of oysters during a herpesvirus outbreak
Authors: Pernet Fabrice , Gachelin Sonia , Stanisière Jean-Yves , Petton Bruno , Fleury Elodie , Mazurié Joseph 
Published: April 2019

AbstractThe intertidal zone is characterized by a sharp vertical gradient of environmental stress, which structures species distribution and their interactions. Few studies, however, have examined the influence of tidal height on host–pathogen interactions. Here, we investigated how the tidal height influence outbreak of the Ostreid herpesvirus type 1 (OsHV-1) affecting the Pacific oyster. A volunteer network composed of 20 oyster growers monitored the survival of 28 batches of oysters during an epizootic event in Southern Brittany, France. Oysters were spat from wild collection or hatchery production. The sampling sites were spread over a 150-km2 area with a tidal height ranging from 0.98 to 2.90 m. Concomitantly, we followed survival of oyster spats in relation with OsHV-1 DNA detection at two sites and conducted risk analysis. We found that tidal height was associated with a lower risk of mortality. This effect was higher for hatchery than for wild oysters probably reflecting differences in health status. Our study opens perspectives for mitigation strategies based on tidal height and emphasizes the value of volunteer science in marine epidemiological studies.
Redo aortic root repair in patients with infective prosthetic endocarditis using xenopericardial solutions
Authors: Kondov Stoyan , Beyersdorf Friedhelm , Rylski Bartosz , Kreibich Maximilian , Dimov Aleksandar , Berger Tim , Siepe Matthias , Czerny Martin 
Published: April 2019

Abstract

OBJECTIVES
We describe a conceptual approach involving the use of self-made xenopericardial grafts in combination with biological aortic valve prostheses and in addition using a xenopericardial tubes for aortic valve reimplantation in patients with infective prosthetic endocarditis after aortic root repair or supracoronary ascending aortic replacement.

METHODS
The cohort comprised 7 consecutive patients with proven prosthetic infection either after aortic root replacement (n = 5), the David operation (n = 1) or supracoronary ascending aortic replacement (n = 1). The strategy consists of complete removal of the infected prosthetic material and orthotopic reconstruction using a bovine pericardial patch sewn as a tube according to the required aortic diameter.

RESULTS
In case of valve replacement, Edwards Magna Ease (n = 4 patients) and Edwards Inspiris (n = 2 patients) were used inside the xenopericardial tube. Five patients also required hemiarch and 1 patient required complete aortic arch replacement. Median length of stay in the intensive care unit and on the regular ward thereafter was 11 (6.5–13.5) days and 26.0 (14.5–32.5) days, respectively. All patients were successfully discharged. Median follow-up time was 7.6 (±2.1) months. Currently, all patients are not on antibiotic therapy and free from any signs of persisting or recurring infection. At the short-term follow-up, no structural valve deterioration, paravalvular insufficiency or graft calcification was found.

CONCLUSIONS
Using a self-made xenopericardial graft in combination with a biological aortic valve prosthesis for a Bio-Bentall and using a xenopericardial tube for a Bio-David operation is a safe and reproducible strategy and presents an off-the-shelf alternative to homografts. The short-term results of this approach are excellent. Further studies are needed to confirm mid- and long-term durability in larger cohorts.
The impact of violence on Venezuelan life expectancy and lifespan inequality
Authors: García Jenny , Aburto José Manuel 
Published: April 2019

Abstract

Background
Venezuela is one of the most violent countries in the world. According to the United Nations, homicide rates in the country increased from 32.9 to 61.9 per 100 000 people between 2000 and 2014. This upsurge coincided with a slowdown in life expectancy improvements. We estimate mortality trends and quantify the impact of violence-related deaths and other causes of death on life expectancy and lifespan inequality in Venezuela.

Methods
Life tables were computed with corrected age-specific mortality rates from 1996 to 2013. From these, changes in life expectancy and lifespan inequality were decomposed by age and cause of death using a continuous-change model. Lifespan inequality, or variation in age at death, is measured by the standard deviation of the age-at-death distribution.

Results
From 1996 to 2013 in Venezuela, female life expectancy rose 3.57 [95% confidence interval (CI): 3.08–4.09] years [from 75.79 (75.98–76.10) to 79.36 (78.97–79.68)], and lifespan inequality fell 1.03 (–2.96 to 1.26) years [from 18.44 (18.01–19.00) to 17.41 (17.30–18.27)]. Male life expectancy increased 1.64 (1.09–2.25) years [from 69.36 (68.89–59.70) to 71.00 (70.53–71.39)], but lifespan inequality increased 0.95 (–0.80 to 2.89) years [from 20.70 (20.24–21.08) to 21.65 (21.34–22.12)]. If violence-related death rates had not risen over this period, male life expectancy would have increased an additional 1.55 years, and lifespan inequality would have declined slightly (–0.31 years).

Conclusions
As increases in violence-related deaths among young men (ages 15–39) have slowed gains in male life expectancy and increased lifespan inequality, Venezuelan males face more uncertainty about their age at death. There is an urgent need for more accurate mortality estimates in Venezuela.
The well-to-wheel analysis of hydrogen enriched compressed natural gas for heavy-duty vehicles using life cycle approach to a fuel cycle
Authors: Gupta Pralhad , Zhuge Weilin , Luo Sijie , Ma Fanhua 
Published: April 2019

Abstract
Increasing urban air pollution, greenhouse gases, and declining fossil energy sources are the three major problems of transportation sector which drive the use of alternative vehicular fuels to prevent energy shortage, reduce oil dependency and decrease tailpipe emissions including air pollutants and greenhouse gas emissions. This research work focused on life cycle analysis of HCNG® heavy-duty vehicle in which 20% gaseous hydrogen blended with compressed natural gas has been investigated in terms of net energy ratio, GHG value, and cost-effectiveness over a scale of ‘per MJ energy output’ in two fuel options, i.e. 0%HCNG and 20%HCNG for an entire well-to-wheel cycle. An engineering economic approach has been used to evaluate cost-effectiveness ratio of CNG and 20%HCNG pathways derived from fuel economy improvement. It has been shown that at pump-to-wheel stage, 7% reduction in fuel consumption can be achieved together with 11% reduction in GHGs, 7% reduction in energy consumption at operation and 7% reduction in total costs (RMB/MJ) for 20%HCNG compared with CNG. Rank (1 means ‘best and 10 means ‘worst’) showed that renewable-based hydrogen pathways such as solar, wind and biomass showed dual benefits of lower energy consumption and lower GHG emissions whereas grid electricity-to-hydrogen displayed the worst case in both scenarios. Usually, biomass-based HCNG pathways may have higher net energy ratio, but the sources are cleaner, and renewable in nature. The energy efficiency of fossil-based pathways such as natural gas, coal, etc., is higher than biomass gasification pathway.
Dietary Factors in Prevention of PediatricEscherichia coliInfection: A Model Using Domestic Piglets
Authors: Liu Yanhong , Ji Peng 
Published: April 2019

AbstractEnterotoxigenic Escherichia coli (ETEC) is the major etiological agent causing acute watery diarrhea that is most frequently seen in young children in lower-income countries. The duration of diarrheal symptom may be shortened by antibiotic treatment, but ETEC is relative refractory to common antibiotics. Burgeoning evidence suggests bioactive components that naturally occur in human milk (e.g., lysozyme and oligosaccharides) and plants (e.g., nondigestible carbohydrates and phytochemicals) contain antimicrobial functions are promising preventive measures to control ETEC infection. Although the exact protective mechanisms may vary for each compound and are still not completely understood, they generally act to (1) competitively inhibit the binding of pathogenic bacteria and toxins to gut epithelium; (2) directly kill pathogens; and (3) stimulate and/or enhance host mucosal and systemic immune defense against pathogenic microorganisms. An appropriate ETEC-challenge animal model is critical to evaluate the effect and unveil the mechanism of bioactive compounds in prevention of enteric infection. Despite wide application in biomedical research, rodents do not usually manifest typical clinical signs of enteric infections. The remarkable differences in digestive physiology, immune response, and gut microbiota between rodents and human beings necessitate the use of alternative animal models. Pigs are closely related to humans in terms of genomes, physiology, anatomy of gastrointestinal tracts, digestive enzymes, components of immune system, and gut microbiota. Like human infants and young children, nursing and nursery piglets are more susceptible to ETEC infection and reproduce the clinical signs as observed in humans. Hence, the ETEC-challenge piglet represents a valuable translational model to study pathogenesis and evaluate dietary factors (e.g., milk bioactive compounds, nondigestible carbohydrates, and phytochemicals) as preventive measures for ETEC infection in pediatrics.
miR-145 improves metabolic inflammatory disease through multiple pathways
Authors: He Min , Wu Nan , Leong Man Cheong , Zhang Weiwei , Ye Zi , Li Rumei , Huang Jinyang , Zhang Zhaoyun , Li Lianxi , Yao Xiao , Zhou Wenbai , Liu Naijia , Yang Zhihong , Dong Xuehong , Li Yintao , Chen Lili , Li Qin , Wang Xuanchun , Wen Jie , Zhao Xiaolong , Lu Bin , Yang Yehong , Wang Qinghua , Hu Renming 
Published: April 2019

Abstract
Chronic inflammation plays a pivotal role in insulin resistance and type 2 diabetes, yet the mechanisms are not completely understood. Here, we demonstrated that serum LPS levels were significantly higher in newly diagnosed diabetic patients than in normal control. miR-145 level in peripheral blood mononuclear cells decreased in type 2 diabetics. LPS repressed the transcription of miR-143/145 cluster and decreased miR-145 levels. Attenuation of miR-145 activity by anti-miR-145 triggered liver inflammation and increased serum chemokines in C57BL/6 J mice. Conversely, lentivirus-mediated miR-145 overexpression inhibited macrophage infiltration, reduced body weight, and improved glucose metabolism in db/db mice. And miR-145 overexpression markedly reduced plaque size in the aorta in ApoE−/− mice. Both OPG and KLF5 were targets of miR-145. miR-145 repressed cell proliferation and induced apoptosis partially by targeting OPG and KLF5. miR-145 also suppressed NF-κB activation by targeting OPG and KLF5. Our findings provide an association of the environment with the progress of metabolic disorders. Increasing miR-145 may be a new potential therapeutic strategy in preventing and treating metabolic diseases such as type 2 diabetes and atherosclerosis.
Parenting Stress, Sleep, and Psychological Adjustment in Parents of Infants and Toddlers With Congenital Heart Disease
Authors: Bishop Meredith N , Gise Jensi E , Donati Matthew R , Shneider Caitlin E , Aylward Brandon S , Cohen Lindsey L 
Published: April 2019

AbstractObjectiveParents of children with chronic medical needs report increased parenting challenges, poor sleep, and maladjustment. The impact of parenting stress on both sleep and adjustment has yet to be evaluated for parents of infants and young children with congenital heart disease (CHD). We studied the relations among parenting stress, sleep, and adjustment in parents of infants and toddlers with CHD. We expected that sleep quality would mediate the relationship between parenting stress and adjustment.MethodsSixty-nine parents of infants and toddlers with CHD were evaluated on self-report measures of illness-related parenting stress (Pediatric Inventory for Parents), sleep (Pittsburgh Sleep Quality Index), and psychological adjustment (Brief Symptom Index-18).ResultsThe parents of infants and toddlers with CHD reported elevated levels of parenting stress, sleep problems, and maladjustment. The positive relationship between parenting stress and parent maladjustment was mediated by sleep quality.ConclusionsFindings suggest that parents of infants and toddlers with CHD report high parenting stress, poor sleep, and maladjustment. Analyses indicate the stress-adjustment relationship is mediated by quality of sleep. Given the multiple demands on parents of infants and children with CHD, it is important to attend to parents’ overall functioning and mental health. Our findings highlight targets for intervention to improve the well-being of parents of young children with CHD.