bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macrophage NCOR1 protects from atherosclerosis by repressing a pro-atherogenic PPARγ signature
Authors: Oppi Sara , Nusser-Stein Stefanie , Blyszczuk Przemyslaw , Wang Xu , Jomard Anne , Marzolla Vincenzo , Yang Kangmin , Velagapudi Srividya , Ward Liam J , Yuan Xi-Ming , Geiger Martin A , Guillaumon Ana T , Othman Alaa , Hornemann Thorsten , Rancic Zoran , Ryu Dongryeol , Oosterveer Maaike H , Osto Elena , Lüscher Thomas F , Stein Sokrates 
Published: September 2019

Abstract

Aims
Nuclear receptors and their cofactors regulate key pathophysiological processes in atherosclerosis development. The transcriptional activity of these nuclear receptors is controlled by the nuclear receptor corepressors (NCOR), scaffolding proteins that form the basis of large corepressor complexes. Studies with primary macrophages demonstrated that the deletion of Ncor1 increases the expression of atherosclerotic molecules. However, the role of nuclear receptor corepressors in atherogenesis is unknown.

Methods and results
We generated myeloid cell-specific Ncor1 knockout mice and crossbred them with low-density lipoprotein receptor (Ldlr) knockouts to study the role of macrophage NCOR1 in atherosclerosis. We demonstrate that myeloid cell-specific deletion of nuclear receptor corepressor 1 (NCOR1) aggravates atherosclerosis development in mice. Macrophage Ncor1-deficiency leads to increased foam cell formation, enhanced expression of pro-inflammatory cytokines, and atherosclerotic lesions characterized by larger necrotic cores and thinner fibrous caps. The immunometabolic effects of NCOR1 are mediated via suppression of peroxisome proliferator-activated receptor gamma (PPARγ) target genes in mouse and human macrophages, which lead to an enhanced expression of the CD36 scavenger receptor and subsequent increase in oxidized low-density lipoprotein uptake in the absence of NCOR1. Interestingly, in human atherosclerotic plaques, the expression of NCOR1 is reduced whereas the PPARγ signature is increased, and this signature is more pronounced in ruptured compared with non-ruptured carotid plaques.

Conclusions
Our findings show that macrophage NCOR1 blocks the pro-atherogenic functions of PPARγ in atherosclerosis and suggest that stabilizing the NCOR1–PPARγ binding could be a promising strategy to block the pro-atherogenic functions of plaque macrophages and lesion progression in atherosclerotic patients.
Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment
Authors: Yoon Jaewoo , Maharjan Sailesh , Choi Hyukjae 
Published: September 2019

ABSTRACT
Polyphasic taxonomic analysis was performed on a novel marine bacterium, designated as strain YJ057T, isolated from marine sediment collected in the Republic of Korea. The strain was Gram-negative, beige-colored, facultatively anaerobic, coccoid or ovoid-shaped and nonmotile. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that this novel marine isolate belongs to the family Rhodobacteraceae of the class Alphaproteobacteria, and has the greatest (96.2%) sequence similarity to Paracoccus aestuariivivens GHD-30T. Major (&gt;10%) fatty acids of strain YJ057T were C16:0 and C18:1 ω7c, G+C content in the genomic DNA of the strain was 63.6 mol% and the sole respiratory quinone was ubiquinone Q-10. It had phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified components (three aminolipids, a glycolipid, a phospholipid and two lipids). As per the distinct phylogenetic position and combination of phenotypic and genotypic traits, the strain is considered a novel species of the genus Paracoccus, and the name Paracoccus ravus sp. nov. is proposed.
Maternal and neonatal outcome of asymptomatic bacteriuria at term pregnancy
Authors: Perlitz Yuri , Saffoury Enas , Shabso Nora , Labai Aminat , Namatiyof Jennifer Fathy , Nitzan Orna , Ben-Shlomo Izhar , Azrad Maya , Ben-Ami Moshe , Peretz Avi 
Published: September 2019

ABSTRACT

Objectives
Guidelines recommend antibiotic treatment for every episode of asymptomatic bacteriuria throughout pregnancy in order to reduce maternal and fetal complications. We evaluated intra- and post-partum, as well as puerperal maternal and neonatal outcomes of an untreated group of pregnant women with asymptomatic bacteriuria at term.

Methods
This was a single center prospective cohort study. We enrolled women who came for labor or checkups, 37–42 weeks gestation, with singleton, vertex presentation. On admission, women gave a urine sample; we compared maternal, obstetric and neonatal data from the positive culture group to the negative culture.

Results
Among 248 pregnant women recruited, 205 negative and 32 positive urine cultures were collected. None of the women that participated in this study developed pyelonephritis during hospitalization or during the puerperium. No significant differences were detected between the two groups in terms of age, nulliparity, gestational age at delivery, length of hospitalization, birth type, intra- or post-partum fever, antibiotic treatment during labor or post-partum.

Conclusions
No increased maternal or neonatal adverse effects were observed in women with untreated ASB detected at term.
Interaction Between Physical Activity and Genes Related to Neurotrophin Signaling in Late-Life Cognitive Performance: The Cache County Study
Authors: Sanders Chelsea L , Rattinger Gail B , Deberard M Scott , Hammond Alexandra G , Wengreen Heidi , Kauwe John S K , Buhusi Mona , Tschanz Joann T 
Published: September 2019

AbstractResearch indicates that lifestyle and genetic factors influence the course of cognitive impairment in aging, but their interactions have not been well-examined. This study examined the relationship between physical activity and genotypes related to brain-derived neurotrophic factor (BDNF) in predicting cognitive performance in a sample of older adults with up to 12 years of follow-up. Physical activity levels (sedentary, light, and moderate/vigorous) were determined for the sample of 3,591 participants (57% female) without dementia. The genotypes examined included BDNF gene single nucleotide polymorphisms (SNPs) (rs6265 and rs56164415) and receptor gene SNPs (NTRK2 rs2289656 and NGFR rs2072446). Cognition was assessed triennially using the Modified Mini-Mental State Exam. Unadjusted linear mixed models indicated that sedentary (β = −5.05) and light (β = −2.41) groups performed worse than moderate–vigorous (p &lt; .001). Addition of interaction effects showed significant differences in rate of decline between activity levels, particularly among males (p = .006). A three-way interaction with sex, NGFR SNP rs2072446, and physical activity suggested that the C/C allele was associated with better cognitive performance among males engaging in light activity only (p = .004). Physical activity and sex, but not BDNF-related SNPs, predicted rate of cognitive decline in older adults, while NGFR rs2072446 may modify main effects.
Accelerometer-Measured Sleep Duration and Clinical Cardiovascular Risk Factor Scores in Older Women
Authors: Full Kelsie M , Malhotra Atul , Gallo Linda C , Kerr Jacqueline , Arredondo Elva M , Natarajan Loki , LaMonte Michael J , Stefanick Marcia L , Stone Katie L , LaCroix Andrea Z 
Published: September 2019

Abstract

Background
Evidence suggests that short and long sleep durations are potential lifestyle factors associated with cardiovascular disease (CVD). Research on sleep duration and CVD risk is limited by use of self-report sleep measures, homogeneous populations, and studies on individual CVD risk factors. For women, risk of CVD and inadequate sleep duration increases with age. We hypothesized that accelerometer-measured sleep duration was associated with 10-year predicted probability of future CVD risk in a cohort of aging women.

Methods
This cross-sectional analysis included 3,367 older women (mean age 78.9 years; 53.3% White), from the Objective Physical Activity and Cardiovascular Health Study, ancillary study to the Women’s Health Initiative. Women wore ActiGraph GT3X+ accelerometers on the hip for 24 hours/7 days. A 10-year predicted probability of future CVD risk, the Reynolds Risk Score (RRS), was computed using age, systolic blood pressure, high-sensitivity C-reactive protein (CRP), total and HDL cholesterol, diabetes mellitus status, smoking status, and family history of CVD. Average nightly sleep duration was derived from accelerometer data. Adjusted linear regression models investigated the association between sleep duration and RRS.

Results
Results suggested a U-shaped relationship between sleep duration and RRS, with both short and long sleep associated with higher RRS (p &lt; .001). The association remained significant after adjustments for race/ethnicity, education, lifestyle factors, and health status indicators.

Conclusion
In older women, actigraphy-ascertained sleep duration was associated with a 10-year predicted probability of future CVD risk. This study supports sleep duration as a modifiable risk factor for CVD in older women.
High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
Authors: Stroehlein Andreas J , Korhonen Pasi K , Chong Teik Min , Lim Yan Lue , Chan Kok Gan , Webster Bonnie , Rollinson David , Brindley Paul J , Gasser Robin B , Young Neil D 
Published: September 2019

Abstract

Background
Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting &gt;100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation.

Findings
Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available.

Conclusions
We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.
A constant-Q model for general viscoelastic media
Authors: Wang Yanghua 
Published: September 2019

SUMMARY
When seismic waves propagate through viscoelastic media, the viscoelastic response can be presented as a fractional-order derivative of the strain. This fractional order $\beta $ controlling the degree of viscoelasticity of subsurface media is referred to as the viscoelastic parameter. However, the viscoelasticity is conventionally quantified by the quality factor Q, and there is a gap between the viscoelastic parameter $\beta $ and the Q factor. Here this paper bridges the gap by establishing a relationship between these two parameters. An exact Q model is derived analytically based on the viscoelastic parameter $\beta $. Since the exact Q model is frequency dependent, a constant-Q model which is frequency independent is proposed under a small-dissipation assumption. This constant-Q model is applicable to seismic data with a narrow frequency band and is consistent with Kolsky's attenuation model. Furthermore, an inverse function of the constant-Q model is presented for evaluating the viscoelastic parameter $\beta $ from any given Q factor. Thus, the viscoelastic parameter $\beta $ has an intuitive physical meaning that is directly linked to the Q factor.
Inversions of time-domain spectral induced polarization data using stretched exponential
Authors: Kang Seogi , Oldenburg Douglas W 
Published: September 2019

SUMMARY
We provide a two-stage approach to extract spectral induced polarization (SIP) information from time-domain IP data. In the first stage we invert dc data to recover the background conductivity. In the second, we solve a linear inverse problem and invert all time channels simultaneously to recover the IP parameters. The IP decay curves are represented by a stretched exponential (SE) rather than the traditional Cole–Cole model, and we find that defining the parameters in terms of their logarithmic values is advantageous. To demonstrate the capability of our simultaneous SIP inversion we use synthetic data simulating a porphyry mineral deposit. The challenge is to image a mineral body that is hosted within an alteration halo having the same chargeability but a different time constant. For a 2-D problem, we were able to distinguish the body using our simultaneous inversion but we were not successful in using a sequential (or conventional) SIP inversion approach. For the 3-D problem we recovered 3-D distributions of the SIP parameters and used those to construct a 3-D rock model having four rock units. Three chargeable units were distinguished. The compact mineralization zone, having a large time constant, was distinguished from the circular alteration halo that had a small time constant. Finally, to promote the use of the SIP technique, and to have further development of SIP inversion, all examples presented in this paper are available in our open source resources (https://github.com/simpeg-research/kang-2018-spectral-inducedpolarization).
Evaluating the accuracy of hybrid finite element/particle-in-cell methods for modelling incompressible Stokes flow
Authors: Gassmöller Rene , Lokavarapu Harsha , Bangerth Wolfgang , Puckett Elbridge Gerry 
Published: September 2019

SUMMARY
Combining finite element methods for the incompressible Stokes equations with particle-in-cell methods is an important technique in computational geodynamics that has been widely applied in mantle convection, lithosphere dynamics and crustal-scale modelling. In these applications, particles are used to transport along properties of the medium such as the temperature, chemical compositions or other material properties; the particle methods are therefore used to reduce the advection equation to an ordinary differential equation for each particle, resulting in a problem that is simpler to solve than the original equation for which stabilization techniques are necessary to avoid oscillations.
On the other hand, replacing field-based descriptions by quantities only defined at the locations of particles introduces numerical errors. These errors have previously been investigated, but a complete understanding from both the theoretical and practical sides was so far lacking. In addition, we are not aware of systematic guidance regarding the question of how many particles one needs to choose per mesh cell to achieve a certain accuracy.
In this paper we modify two existing instantaneous benchmarks and present two new analytic benchmarks for time-dependent incompressible Stokes flow in order to compare the convergence rate and accuracy of various combinations of finite elements, particle advection and particle interpolation methods. Using these benchmarks, we find that in order to retain the optimal accuracy of the finite element formulation, one needs to use a sufficiently accurate particle interpolation algorithm. Additionally, we observe and explain that for our higher-order finite-element methods it is necessary to increase the number of particles per cell as the mesh resolution increases (i.e. as the grid cell size decreases) to avoid a reduction in convergence order.
Our methods and results allow designing new particle-in-cell methods with specific convergence rates, and also provide guidance for the choice of common building blocks and parameters such as the number of particles per cell. In addition, our new time-dependent benchmark provides a simple test that can be used to compare different implementations, algorithms and for the assessment of new numerical methods for particle interpolation and advection. We provide a reference implementation of this benchmark in aspect (the ‘Advanced Solver for Problems in Earth’s ConvecTion’), an open source code for geodynamic modelling.
Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens
Authors: Pluvinage Benjamin , Massel Patricia M , Burak Kristyn , Boraston Alisdair B 
Published: September 2019

AbstractThe opportunistic pathogen Clostridium perfringens possesses the ability to colonize the protective mucin layer in the gastrointestinal tract. To assist this, the C. perfringens genome contains a battery of genes encoding glycoside hydrolases (GHs) that are likely active on mucin glycans, including four genes encoding family 84 GHs: CpGH84A (NagH), CpGH84B (NagI), CpGH84C (NagJ) and CpGH84D (NagK). To probe the potential advantage gained by the expansion of GH84 enzymes in C. perfringens, we undertook the structural and functional characterization of the CpGH84 catalytic modules. Here, we show that these four CpGH84 catalytic modules act as β-N-acetyl-D-glucosaminidases able to hydrolyze N- and O-glycan motifs. CpGH84A and CpGH84D displayed a substrate specificity restricted to terminal β-1,2- and β-1,6-linked N-acetyl-D-glucosamine (GlcNAc). CpGH84B and CpGH84C appear more promiscuous with activity on terminal β-1,2-, β-1,3- and β-1,6-linked GlcNAc; both possess some activity toward β-1,4-linked GlcNAc, but this is dependent upon which monosaccharide it is linked to. Furthermore, all the CpGH84s have different optimum pHs ranging from 5.2 to 7.0. Consistent with their β-N-acetyl-D-glucosaminidase activities, the structures of the four catalytic modules revealed similar folds with a catalytic site including a conserved −1 subsite that binds GlcNAc. However, nonconserved residues in the vicinity of the +1 subsite suggest different accommodation of the sugar preceding the terminal GlcNAc, resulting in subtly different substrate specificities. This structure–function comparison of the four GH84 catalytic modules from C. perfringens reveals their different biochemical properties, which may relate to how they are deployed in the bacterium’s niche in the host.
Phenome-wide investigation of health outcomes associated with genetic predisposition to loneliness
Authors: Abdellaoui Abdel , Sanchez-Roige Sandra , Sealock Julia , Treur Jorien L , Dennis Jessica , Fontanillas Pierre , Elson Sarah ,   The 23andme Research Team, Nivard Michel G , Ip Hill Fung , van der Zee Matthijs , Baselmans Bart M L , Hottenga Jouke Jan , Willemsen Gonneke , Mosing Miriam , Lu Yi , Pedersen Nancy L , Denys Damiaan , Amin Najaf , M van Duijn Cornelia , Szilagyi Ingrid , Tiemeier Henning , Neumann Alexander , Verweij Karin J H , Cacioppo Stephanie , Cacioppo John T , Davis Lea K , Palmer Abraham A , Boomsma Dorret I 
Published: September 2019

AbstractHumans are social animals that experience intense suffering when they perceive a lack of social connection. Modern societies are experiencing an epidemic of loneliness. Although the experience of loneliness is universally human, some people report experiencing greater loneliness than others. Loneliness is more strongly associated with mortality than obesity, emphasizing the need to understand the nature of the relationship between loneliness and health. Although it is intuitive that circumstantial factors such as marital status and age influence loneliness, there is also compelling evidence of a genetic predisposition toward loneliness. To better understand the genetic architecture of loneliness and its relationship with associated outcomes, we extended the genome-wide association study meta-analysis of loneliness to 511 280 subjects, and detect 19 significant genetic variants from 16 loci, including four novel loci, as well as 58 significantly associated genes. We investigated the genetic overlap with a wide range of physical and mental health traits by computing genetic correlations and by building loneliness polygenic scores in an independent sample of 18 498 individuals with EHR data to conduct a PheWAS with. A genetic predisposition toward loneliness was associated with cardiovascular, psychiatric, and metabolic disorders and triglycerides and high-density lipoproteins. Mendelian randomization analyses showed evidence of a causal, increasing, the effect of both BMI and body fat on loneliness. Our results provide a framework for future studies of the genetic basis of loneliness and its relationship to mental and physical health.
Intrathecal AAVrh10 corrects biochemical and histological hallmarks of mucopolysaccharidosis VII mice and improves behavior and survival
Authors: Pagès G , Giménez-Llort L , García-Lareu B , Ariza L , Navarro M , Casas C , Chillón M , Bosch A 
Published: September 2019

AbstractMucopolysaccharidosis (MPS) type VII is a lysosomal storage disease caused by ß-glucuronidase deficiency, prompting glycosaminoglycan accumulation in enlarged vesicles, leading to peripheral and neuronal dysfunction. Here, we present a gene therapy strategy using lumbar puncture of AAVrh10 encoding human β-glucuronidase (AAVrh10-GUSB) to adult MPS VII mice. This minimally invasive technique efficiently delivers the recombinant vector to the cerebrospinal fluid (CSF) with a single intrathecal injection. We show that AAVrh10 delivery to the CSF allows global, stable transduction of CNS structures. In addition, drainage of AAVrh10-GUSB from the CSF to the bloodstream resulted in the transduction of somatic organs such as liver, which provided a systemic β-glucuronidase source sufficient to achieve serum enzyme activity comparable to wild type mice. ß-glucuronidase levels were enough to correct biochemical and histopathological hallmarks of the disease in the CNS and somatic organs at short and long term. Moreover, the progression of the bone pathology was also reduced. Importantly, the biochemical correction led to a significant improvement in the physical, cognitive and emotional characteristics of MPS VII mice, and doubling their life span. Our strategy may have implications for gene therapy in patients with lysosomal storage diseases.
Sexuality and Gender Identity in Transitional Societies: Peacebuilding and Counterhegemonic Politics
Authors: Ashe Fidelma 
Published: September 2019

Abstract∞
This article contributes to a developing field of scholarship that has been concerned with exploring the impacts of conflict and its transformation on sexual and gender minorities. Drawing on extant analysis, the article explores the marginalization of issues pertaining to sexuality and gender in international law and peace agreements. It then moves on to an assessment of the effects of the integration of sexual orientation and gender identity equality provisions into a limited number of peace agreements. The article contends that attempts to implement and extend sexual orientation and gender identity (SOGI) equality provisions in peace agreements in meaningful ways typically become cast as justifiable, residual or reprehensible by agonistic groups at local levels during transition. It claims that this fracturing of standpoints on SOGI equality can strengthen counterhegemonic articulations of sexual and gender minorities’ identities that provoke radical versions of peacebuilding.