bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental influences on placental programming and offspring outcomes following maternal immune activation
Authors: Núñez Estevez Karen J. , Rondón-Ortiz Alejandro N. , Nguyen Jenny Q.T. , Kentner Amanda C. 
Published: August 2019

AbstractAdverse experiences during pregnancy induce placental programming, affecting the fetus and its developmental trajectory. However, the influence of ‘positive’ maternal experiences on the placenta and fetus remain unclear. In animal models of early life stress, environmental enrichment (EE) has ameliorated and even prevented associated impairments in brain and behavior. Here, using a maternal immune activation (MIA) model in rats, we test whether EE attenuates maternal, placental and/or fetal responses to an inflammatory challenge, thereby offering a mechanism by which fetal programming may be prevented. Moreover, we evaluate life-long EE exposure on offspring development and examine a constellation of genes and epigenetic writers that may protect against MIA challenges. In our model, maternal plasma corticosterone and interleukin-1β were elevated 3 h after MIA, validating the maternal inflammatory response. Evidence for developmental programming was demonstrated by a simultaneous decrease in the placental enzymes Hsd11b2 and Hsd11b2/Hsd11b1, suggesting disturbances in glucocorticoid metabolism. Reductions of Hsd11b2 in response to challenge is thought to result in excess glucocorticoid exposure to the fetus and altered glucocorticoid receptor expression, increasing susceptibility to behavioral impairments later in life. The placental, but not maternal, glucocorticoid implications of MIA were attenuated by EE. There were also sustained changes in epigenetic writers in both placenta and fetal brain as a consequence of environmental experience and sex. Following MIA, both male and female juvenile animals were impaired in social discrimination ability. Life-long EE mitigated these impairments, in addition to the sex specific MIA associated disruptions in central Fkbp5 and Oprm1. These data provide the first evidence that EE protects placental functioning during stressor exposure, underscoring the importance of addressing maternal health and well-being throughout pregnancy. Future work must evaluate critical periods of EE use to determine if postnatal EE experience is necessary, or if prenatal exposure alone is sufficient to confer protection.
Herpes simplex virus-1 pUL56 degrades GOPC to alter the plasma membrane proteome
Authors: Soh Timothy K. , Davies Colin T. R. , Muenzner Julia , Connor Viv , Bouton Clément R. , Barrow Henry G. , Smith Cameron , Emmott Edward , Antrobus Robin , Graham Stephen C. , Weekes Michael P. , Crump Colin M. 
Published: August 2019

SummaryHerpesviruses are ubiquitous in the human population and they extensively remodel the cellular environment during infection. Multiplexed quantitative proteomic analysis over a whole time-course of herpes simplex virus (HSV)-1 infection was used to characterize changes in the host-cell proteome and to probe the kinetics of viral protein production. Several host-cell proteins were targeted for rapid degradation by HSV-1, including the cellular trafficking factor GOPC. We identify that the poorly-characterized HSV-1 protein pUL56 binds directly to GOPC, stimulating its ubiquitination and proteasomal degradation. Plasma membrane profiling revealed that pUL56 mediates specific changes to the surface proteome of infected cells, including loss of IL18 receptor and Toll-like receptor 2, and delivery of Toll-like receptor 2 to the cell-surface requires GOPC. Our study highlights an unanticipated and efficient mechanism whereby a single virus protein targets a cellular trafficking factor to modify the abundance of multiple signaling molecules at the surface of infected cells.
Absence of pathogenic Short Tandem Repeat expansions in Systemic Lupus Erythematosus disease-associated genes
Authors: Lee Audrey , Cho Vicky , Andrews T. Daniel 
Published: August 2019

AbstractShort tandem repeat (STR) expansions have been shown to be pathogenic in human neurological diseases, such as Huntington disease. Yet, the potential role of STRs in non-neurological diseases has yet to be fully investigated. In this study, the potential role of STR expansions in the pathogenesis of systemic lupus erythematosus (SLE) was investigated using patient genomic data and two computational tools, HipSTR and exSTRa. The length variability of STRs in 76 SLE-associated genes was compared using exome data from 271 SLE affected individuals and 158 of their unaffected relatives. We conclude that no large STR expansions associated with SLE were present in these affected individuals within the 76 genes investigated. Lack of evidence does not negate a pathogenic role for STR expansions in SLE, yet given the number of individuals included in this study, we expect that this is not a common source of pathogenesis in SLE.Significance statementThe increasing availability and decreasing cost of sequencing genomes lends itself to computational analysis, extracting information to aid diagnosis, guide treatment or discover disease mechanisms and new treatments. Computational tools have been developed to look for various types of mutations, including short tandem repeats (STRs), which has been shown to cause diseases such as Huntington disease. Limited research on the possible role of STR expansions in systemic lupus erythematosus (SLE) has been done. Here we use computational tools to compare the length of STRs in 76 SLE-associated genes in patients and their unaffected relatives. Our results did not identify any large STR expansions associated with SLE, and further research is required to gain a better understanding of this complex disease.
Assessment of human diploid genome assembly with 10x Linked-Reads data
Authors: Zhang Lu , Zhou Xin , Weng Ziming , Sidow Arend 
Published: August 2019

AbstractBackgroundProducing cost-effective haplotype-resolved personal genomes remains challenging. 10x Linked-Read sequencing, with its high base quality and long-range information, has been demonstrated to facilitate de novo assembly of human genomes and variant detection. In this study, we investigate in depth how the parameter space of 10x library preparation and sequencing affects assembly quality, on the basis of both simulated and real libraries.FindingsWe prepared and sequenced eight 10x libraries with a diverse set of parameters from standard cell lines NA12878 and NA24385 and performed whole genome assembly on the data. We also developed the simulator LRTK-SIM to follow the workflow of 10x data generation and produce realistic simulated Linked-Read data sets. We found that assembly quality could be improved by increasing the total sequencing coverage (C) and keeping physical coverage of DNA fragments (CF) or read coverage per fragment (CR) within broad ranges. The optimal physical coverage was between 332X and 823X and assembly quality worsened if it increased to greater than 1,000X for a given C. Long DNA fragments could significantly extend phase blocks, but decreased contig contiguity. The optimal length-weighted fragment length (WμFL) was around 50 – 150kb. When broadly optimal parameters were used for library preparation and sequencing, ca. 80% of the genome was assembled in a diploid state.ConclusionThe Linked-Read libraries we generated and the parameter space we identified provide theoretical considerations and practical guidelines for personal genome assemblies based on 10x Linked-Read sequencing.
Direct detection of mRNA expression in microbial cells by fluorescencein situhybridization using RNase H-assisted rolling circle amplification
Authors: Takahashi Hirokazu , Horio Kyohei , Kato Setsu , Kobori Toshiro , Watanabe Kenshi , Aki Tsunehiro , Nakashimada Yutaka , Okamura Yoshiko 
Published: August 2019

ABSTRACTMeta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescencein situhybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both gram-negative and gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.
High Fat Diet-Induced Obesity Negatively Affects Whole Bone Bending Strength but not Cortical Structure in the Femur
Authors: Hanne Nicholas J. , Steward Andrew J. , Cox Jason M. , Easter Elizabeth D. , Thornburg Hannah L. , Sessions Marci R. , Pinnamaraju Sriharsha V. , Cole Jacqueline H. 
Published: August 2019

AbstractAlthough body mass index is positively associated with bone mineral density, suggesting obesity is protective against fracture, elderly obese individuals experience greater fracture risk at certain sites than non-obese peers, suggesting bone structural or material changes contribute to fragility. Diet-induced obesity rodent studies have reported detrimental changes to bone microstructure and some apparent-level material properties, but tissue-level material changes are not well understood. Because adipose tissue is highly vascularized, and bone remodeling depends critically on functional vascular supply, concurrent effects on osteovascular perfusion and structure may provide insight about obesity-related bone fragility. This study aimed to determine the effects of obesity on both tissue-level bone properties and osteovascular properties that could negatively impact bone strength. Five-week-old male C57Bl/6J mice were fed either high fat diet (HFD) or control fat diet (CFD) for 17 weeks and received daily treadmill exercise or remained sedentary for eight weeks at ages 14-22 weeks. HFD negatively affected femur bending strength, with 18% lower yield load than CFD. Although HFD negatively altered cancellous microstructure in the distal femur, with 32% lower bone volume fraction than CFD, it did not affect cortical bone geometry in the femoral metaphysis or diaphysis. HFD caused increased carbonate substitution but had no effect on other composition metrics or apparent- or tissue-level material properties in the femoral diaphysis. Exercise did not affect bone strength or microstructure but increased endosteal mineralizing surface in the tibial diaphysis, mineral crystallinity and mineral-to-matrix ratio in the femur, and blood supply to the proximal tibial metaphysis. HFD did not affect blood supply in the tibia or 2D osteovascular structure in the distal femoral metaphysis, indicating that HFD negatively affects cancellous bone without affecting osteovasculature. This study reveals that HFD negatively affected cancellous microstructure without affecting osteovascular structure, and whole-bone strength without altering cortical geometry or material properties.
Ischemic Stroke Reduces Bone Perfusion and Alters Osteovascular Structure
Authors: Hanne Nicholas J. , Steward Andrew J. , Geeroms Carla , Easter Elizabeth D. , Thornburg Hannah L. , Kerckhofs Greet , Parac-Vogt Tatjana , Sheng Huaxin , Cole Jacqueline H. 
Published: August 2019

AbstractRationaleStroke patients lose bone mass and experience fracture at an elevated rate. Although functional intraosseous vasculature is necessary for skeletal maintenance, the effect of stroke on osteovasculature is unknown.ObjectiveTo characterize changes to osteovascular function, structure, and composition following mild-to-moderate-severity ischemic stroke in mice, both with and without exercise therapy.Methods and ResultsTwelve-week-old male mice (n=27) received either a stroke (middle cerebral artery occlusion) or sham procedure, followed by four weeks of daily treadmill or sedentary activity. Intraosseous perfusion, measured weekly in the proximal tibial metaphysis, was reduced by stroke for two weeks. In the second week of recovery, exercise nearly restored perfusion to sham levels, and perfusion tended to be lower in the stroke-affected limb. At the conclusion of the study, osteovascular structure was assessed with contrast-enhanced computed tomography in the distal femoral metaphysis. Stroke significantly increased osteovascular volume and branching but reduced the relative number of blood vessels close to bone surfaces (6-22 µm away) and increased the relative number more than 52 µm away. These differences in vessel proximity to bone were driven by changes in the stroke-exercise group, indicating compounded effects of stroke and exercise. Exercise, but not stroke, nearly reduced the amount of osteogenic Type H blood vessels in the proximal tibial metaphysis, quantified with immunofluorescence microscopy.ConclusionsThis study is the first to examine the effects of stroke on osteovasculature. Stroke increased the amount of osteovasculature, but since blood vessels close to bone are associated with bone remodeling, the shift in osteovascular structure could play a role in bone loss following stroke. The exercise-induced reduction in the amount of Type H vessels and the stroke-exercise effect on osteovascular structure suggest moderate aerobic activity may have detrimental effects on bone remodeling during early stroke recovery.
Synchrony and complexity in state-related EEG networks: an application of spectral graph theory
Authors: Ghaderi Amir Hossein , Baltaretu Bianca R. , Andevari Masood Nemati , Bharmauria Vishal , Balci Fuat 
Published: August 2019

AbstractTo characterize differences between different state-related brain networks, statistical graph theory approaches have been employed to identify informative, topological properties. However, dynamical properties have been studied little in this regard. Our goal here was to introduce spectral graph theory as a reliable approach to determine dynamic properties of functional brain networks and to find how topological versus dynamical features differentiate between such networks. To this goal, 45 participants performed no task with eyes open (EO) or closed (EC) while electroencephalography data were recorded. These data were used to create weighted adjacency matrices for each condition (rest state EO and rest state EC). Then, using the spectral graph theory approach and Shannon entropy, we identified dynamical properties for weighted graphs, and we compared these features with topological aspects of graphs. The results showed that spectral graph theory can distinguish different state-dependent neural networks with different synchronies. On the other hand, correlation analysis indicated that although dynamical and topological properties of random networks are completely independent, these network features can be related in the case of brain generated graphs. In conclusion, the spectral graph theory approach can be used to make inferences about various state-related brain networks, for healthy and clinical populations.Author SummeryBy considering functional communications across different brain regions, a complex network is achieved that is known as functional brain network. Topologically, this network is constructed by different nodes (activity of brain regions or signals over recording electrodes) and different edges (similarity, correlation or phase difference between nodes). Paths, clusters, hubs, and centrality of nodes are examples of topological properties of these networks. However, synchrony and stability of functional brain networks can not be revealed by consideration of topological properties. Alternatively, spectral graph theory (SGT) can demonstrate the dynamic, synchrony and stability of graphs. But this approach has been studied little in brain network analysis. Here, we employed SGT, as well as topological methods, to investigate which approaches are more reliable to find differences between distinct state-related brain networks. On the other hand, we investigated correlations between topology and dynamic in different type of networks (brain generated and random networks). We found that SGT measures can clearly distinguish between distinct state-related brain networks and it can reveal synchrony and complexity of these networks. Also, results show that although dynamic and topology of random-generated graph are completely independent, these properties exhibit several correlations in the case of functional brain networks.
Reconstructing the invasion route of DNA transposons using extant population samples
Authors: Weilguny Lukas , Vlachos Christos , Selvaraju Divya , Kofler Robert 
Published: August 2019

AbstractReconstructing invasion routes of transposable elements (TEs), so far, required capturing an ongoing invasion with population samples from different geographic regions and time points. Here, we propose a more accessible approach. Abundantly occurring internal deletions of DNA transposons allow to trace the direction as well as the path of an invasion, even hundreds of generations after the spread of a TE. We validated this hypothesis with computer simulations and by accurately reproducing the route of the P-element invasion inDrosophila melanogaster. Finally, we used our method to shed light on the controversial hobo invasion inD. melanogaster. Our approach solely requires sequenced samples from extant populations and sequences of TEs of interest. Hence, DNA transposons in a wide range of model and non-model organisms may be analyzed. Our approach will further our understanding of TE dynamics, migration patterns, and the ecology of species.
Influence of inclined Lorentz forces through a porous media on squeezing Cu-H2o nanofluid in the presence of heat source/sink
Authors: Mousavisani Seyedmohammad , Khalesi Javad , Golbaharan Hossein , Sepehr Mohammad , Ganji D.D. 
Published: August 2019

Purpose
The purpose of this paper is to find the approximate solutions of unsteady squeezing nanofluid flow and heat transfer between two parallel plates in the presence of variable heat source, viscous dissipation and inclined magnetic field using collocation method (CM).

Design/methodology/approach
The partial governing equations are reduced to nonlinear ordinary differential equations by using appropriate transformations and then are solved analytically by using the CM.

Findings
It is observed that the enhancing values of aligned angle of the magnetic causes a reduction in temperature distribution. It is also seen that the effect of nanoparticle volume fraction is significant on the temperature but negligible on the velocity profile.

Originality/value
To the best of the authors’ knowledge, no research has been carried out considering the combined effects of inclined Lorentz forces and variable heat source on squeezing flow and heat transfer of nanofluid between the infinite parallel plates.
Nonlinear radiative flow of nanofluid in presence of gyrotactic microorganisms and magnetohydrodynamic
Authors: Hayat Tasawar , Bashir Zeenat , Qayyum Sumaira , Alsaedi Ahmed 
Published: August 2019

Purpose
This paper aims to explore the study of magnetohydrodynamic viscous fluid flow past on a stretching cylinder with nonlinear thermal radiation having gyrotactic microorganisms.

Design/methodology/approach
Appropriate transformations reduce the nonlinear partial differential equation to ordinary ones. Subsequent nonlinear equations are calculated to get convergent series solutions.

Findings
Fluid velocity declines for elevating values of magnetic field parameter. For larger values of curvature parameter near the cylinder temperature reduces.

Originality/value
To the best of the authors’ knowledge, magnetohydrodynamic boundary layer flow of viscous fluid by nonlinear stretching cylinder with nonlinear thermal radiation having gyrotatic microorganisms is not studied yet. The purpose is to study this.
Shared amenities’ impacts on condominium resale values
Authors: Tajima Kayo 
Published: August 2019

Purpose
This study aims to analyze whether and how condominium shared utilities and facilities (e.g. community spaces), of which buyers assume a share of the ownership upon acquisition of a residential unit, affect the condominium unit price over time.

Design/methodology/approach
The transaction price of each unit reflects the quality of the residential unit and the properties of the shared facilities. Based on the hedonic pricing method, this study assesses the impact of shared amenities on unit resale prices, using an original data set on condominium unit resale transactions and the status of housing characteristics for both condominium units and condominium buildings.

Findings
Results show that holding other conditions constant, a meeting room and an external space that can host events increase the unit resale price by approximately 7 and 16 per cent, respectively. Some community amenities such as a meeting room may increase its impact later in the condominium’s lifetime.

Research limitations/implications
Because of the proprietary nature of data, the analysis focuses on high-end condominium properties in central Tokyo. Although it is difficult to single out the shared amenities’ effects on condominium resale prices from potentially confounding factors, this study partially overcomes this issue by including explanatory geographical variables (e.g. ground heights).

Practical implications
The results suggest that a shared facility that hosts social interactions among residents significantly affects the resale market value of housing units and that their magnitudes may change over time.

Originality/value
To the best of the author’s knowledge, this study provides the first empirical evidence of the impacts of shared structures on condominium unit sales using micro-level transaction data in Japan.
Sustainability in Brazilian HEI: practices overview
Authors: Moura Manoela Maria Caron , Frankenberger Fernanda , Tortato Ubiratã 
Published: August 2019

Purpose
The purpose of this paper is to verify how Brazilian HEIs apply sustainability practices, as means to improve their effects towards society, making clear to the public, including current and future students, what the university is doing and how it is concerned with sustainability.

Design/methodology/approach
Based on the Brazilian Education Ministry evaluation, 123 HEIs were selected as sample for the study. The websites of these HEI were verified to check for sustainability practices.

Findings
In general, the HEI focuses on helping people who live around the campus with social projects, health and work preparation. Further practices areas are new forms of energy, selective collection and new standards of plastic consumption. HEI with higher evaluations from the Education Ministry focuses mainly on educational programs and projects to improve sustainability inside and outside the campus.

Research limitations/implications
With the methodology used, not all HEIs in Brazil were analyzed, which gives a great opportunity for further studies.

Practical implications
HEIs may use the findings of this research to develop their sustainability practices, either in the curriculum, projects, strategic plans or even organizational structure.

Social implications
Communities are positively supported by universities applying sustainability practices. Such support includes education, health, guidance and provision of services to the community, financial aid and social well-being.

Originality/value
Focusing on sustainability practices of HEI located in Brazil, the research finds, besides the practices, gaps in several of the researched universities.