bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient Governance in a Patient-Powered Research Network for Adult Rheumatologic Conditions
Authors: Nowell W. Benjamin , Curtis Jeffrey R. , Crow-Hercher Rachelle 
Published: August 2018

Background:
Patient-Powered Research Networks (PPRNs) are a unique type of patient-powered patient registry for patient-centered outcomes research requiring that stakeholder engagement play a key role in governance (eg, research guidance and decision making). The purpose of this report is to describe the governance structure of a newly formed PPRN and the activities undertaken prelaunch and postlaunch to evaluate and improve the engagement of patient stakeholders in governance.

Methods:
During the 18-month start-up period of ArthritisPower, a PPRN for adult rheumatologic conditions, 12 members of the patient body of the PPRN governance completed a 12-item preassessment and postassessment based on the Patient-Centered Outcomes Research Institute (PCORI) Engagement Rubric. The assessment was intended to measure Patient Governor (PG) perceptions of their engagement in governance within the first 3 months of their involvement at an in-person orientation. Six months later, the PG Chair initiated a mid-year evaluation with the same group to identify areas for improvement. Semistructured phone interviews were conducted with 11 PGs who were asked to rate and explain their perceptions about their participation in PPRN governance, the progress of the PPRN toward conducting research, the support they receive from staff, and the support they receive from other PGs. Results were compiled and interpreted by the Chair with help from the coprincipal investigator.

Results:
Preassessment/postassessments indicated that PGs understood their governance role and decision-making authority after in-person orientation and felt that major PPRN decisions were being made with their input. Feedback and scores from the PG-led mid-year evaluation coalesced around 3 themes: a preference for receiving news and updates via email to allow more discussion and decision making during conference calls, a desire for guidance about how best to help advance the PPRN toward the conduct of research, and a need to communicate with each other as a group outside of monthly conference calls. Suggested activities to support patient engagement in PPRN governance include communicating clear expectations, providing well-prepared tools for engagement, and conducting regular assessments.

Conclusions:
Members of an online patient community are willing to share their expertise to participate in and shape research governance and bring both their professional and lived health experience to the development and improvement of PPRN governance structure. A patient-initiated and patient-led evaluation of governance communication procedures within the PPRN provided more specific recommendations for improvement than did an investigator-led preevaluation/postevaluation based on the PCORI Engagement Rubric.
Additive Interactions Between Gender and Bullying Victimization on Depressive Symptoms and Suicidality
Authors: Pontes Nancy M.H. , Ayres Cynthia G. , Pontes Manuel C.F. 
Published: August 2018

Background
Bullying victimization is common among adolescents and increases the likelihood of depressive symptoms and suicidality. Two previous meta-analyses have shown that these relationships do not significantly vary by gender.

Objectives
This research investigated whether there are significant positive additive interactions between bullying victimization and female gender on depressive symptoms, suicidal ideation, suicide attempts, and suicide attempts that required treatment.

Methods
For this research, analyses of pooled data from the 2011, 2013, and 2015 Youth Risk Behavior Survey (N = 44,632) were performed to estimate measures of additive interaction, as well as measures of multiplicative interaction in order to examine whether the relationship between bullying victimization and depressive symptoms or suicidality significantly varied by gender.

Results
Measures of additive interaction show that the magnitude of the relationship between bullying victimization and depressive symptoms or suicidality is significantly greater among female than male individuals. In contrast, measures of multiplicative interaction indicate that the magnitude of the relationship between bullying and depressive symptoms or suicidality is not significantly greater among female than male individuals.

Discussion
Measures of additive interaction are relevant for nursing and population health research. Future research should further explore how and why bullying victimization appears to more profoundly affect female individuals more than male individuals and how to mitigate it.
Knowledge of Pelvic Floor Disorders in Obstetrics
Authors: Mckay Elishia R. , Lundsberg Lisbet S. , Miller Devin T. , Draper Ashley , Chao Jamie , Yeh Judy , Rangi Sabrina , Torres Priscilla , Stoltzman Michelle , Guess Marsha K. 
Published: August 2018

Objectives
The aim of this study was to investigate knowledge and demographic factors associated with a lack of knowledge proficiency about urinary incontinence (UI) and pelvic organ prolapse (POP) among pregnant and postpartum women.

Methods
This was a cross-sectional survey of women receiving antepartum and postpartum care at 9 Connecticut sites. Knowledge was assessed using the validated Prolapse and Incontinence Knowledge Questionnaire. Lack of knowledge proficiency was defined as less than 80% and less than 50% correct responses on the Prolapse and Incontinence Knowledge Questionnaire UI and POP subscales. Logistic regression was used to evaluate unadjusted and adjusted odds ratios (ORs) and 95% confidence intervals (CIs). P < 0.05 was considered statistically significant.

Results
Surveys from 399 diverse pregnant and postpartum women were analyzed. Three quarters showed a lack of knowledge proficiency about UI and POP (74.2%, 70.6%). After adjustment, increased odds of lacking UI knowledge proficiency were associated with primiparity versus nulliparity (OR, 4.73; 95% CI, 2.24–9.98), Hispanic versus white race (OR, 2.72; 95% CI, 1.18–6.01), and having a high school diploma/General Education Development/less (OR, 3.17; 95% CI, 1.34–7.48) or some college (OR, 2.55; 95% CI, 1.08–6.01) versus bachelor’s degree; greater lack of POP knowledge proficiency was associated with having a high school diploma/General Education Development versus bachelor’s degree (OR, 2.11; 95% CI, 1.05–4.26) and never seeing a urologist/urogynecologist versus those who had (OR, 0.30; 95% CI, 0.12–0.77). Women working in a medical field versus those who did not demonstrated decreased odds of lacking UI and POP knowledge proficiency (ORs, 0.26 [95% CI, 0.13–0.52] and 0.38 [95% CI, 0.21–0.70]).

Conclusions
Pregnant and postpartum women lack knowledge about UI and POP. Preconceptional counseling provides an opportunity for educational intervention.
Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation
Authors: Esin Alexander , Ellis Tom , Warnecke Tobias 
Published: August 2018

AbstractHorizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillusspp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. These zones encompass and connect classically defined genomic islands. Analyzing topological and strand biases of recent and older transfer events, we show that restrictions on entry are rapidly enforced by selection and that restrictive and permissive zones have existed in their current locations for long periods of evolution. The largest zone, characterized by a high influx of metabolic genes, is centred on the terminus. The other two zones flank a narrow non-permissive zone around the origin of replication and extend to delimit the first third of the chromosome – the part of the chromosome that is confined to the forespore during early spore formation. Horizontal transfers into this area are biased towards functions classically controlled by the forespore-specific sigma factor σF: signal transduction, transcription, and particularly membrane biogenesis. Similar enrichment patterns are present in spore-forming but absent in non-spore-forming Bacilli. Our results suggest that the topology of HGT in Geobacillus, and Bacilli more generally, reflects constraints imposed by chromosomal organization for fast and sporulation, as asymmetric chromosomal entrapment in the forespore during early spore formation restricts where HGT-driven innovation in sporulation can occur.
Modified TCA/acetone precipitation of plant proteins for proteomic analysis
Authors: Niu Liangjie , Zhang Hang , Wu Zhaokun , Wang Yibo , Liu Hui , Wu Xiaolin , Wang Wei 
Published: August 2018

AbstractProtein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.
Age and genetic background determine hybrid male sterility in house mice
Authors: Widmayer Samuel J. , Aylor David L. 
Published: August 2018

AbstractHybrid male sterility (HMS) is a unique type of reproductive isolation commonly observed between house mouse (Mus musculus) subspecies in the wild and in laboratory crosses. We identified hybrids that display three distinct trajectories of fertility despite having identical genotypes at the major HMS gene Prdm9 and the X Chromosome. In each case, we crossed female PWK/PhJ mice representative of the M.m.musculus subspecies to males from classical inbred strains representative of M.m.domesticus: 129S1/SvImJ, A/J, C57BL/6J, and DBA/2J. PWK129S1 males are always sterile, while PWKDBA2 males escape HMS. In addition, we observe age-dependent sterility in PWKB6 and PWKAJ males. These males are fertile between 15 and 35 weeks with moderate penetrance. These results point to multiple segregating HMS modifier alleles, some of which have an age-dependent mode of action. Age-dependent mechanisms could have broad implications for the maintenance of reproductive barriers in nature.Author SummaryTwo subspecies of house mice show partial reproductive barriers in nature, and may be in the process of speciation. We used mice derived from each subspecies to replicate hybrid male sterility (HMS) in laboratory mice. Two major genetic factors are well established as playing a role in mouse HMS, but the number of additional factors and their mechanisms are unknown. We characterized reproductive trait variation in a set of hybrid male mice that were specifically designed to eliminate the effects of known genetic factors. We discovered that age played an important role in fertility of some hybrids. These hybrid males showed a delayed onset of fertility, then became fertile for only a few weeks. Across all hybrids males in our study, we observed three distinct trajectories of fertility: complete fertility, complete sterility, and age-dependent fertility. These results point to two or more critical HMS variants with large enough effects to completely restore fertility. This study advances our understanding of the genetic architecture and biological mechanisms of reproductive isolation in mice.
Inter-species differences in response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
Authors: Ward Michelle C. , Gilad Yoav 
Published: August 2018

AbstractDespite anatomical similarities, there appear to be differences in susceptibility to cardiovascular disease between primates. For example, humans are prone to ischemia-induced myocardial infarction unlike chimpanzees, which tend to suffer from fibrotic disease. However, it is challenging to determine the relative contributions of genetic and environmental effects to complex disease phenotypes within and between primates. The ability to differentiate cardiomyocytes from induced pluripotent stem cells (iPSCs), now allows for direct inter-species comparisons of the gene regulatory response to disease-relevant perturbations. A consequence of ischemia is oxygen deprivation. Therefore, in order to understand human-specific regulatory adaptations in the heart, and to potentially gain insight into the evolution of disease susceptibility and resistance, we developed a model of hypoxia in human and chimpanzee cardiomyocytes. We differentiated eight human and seven chimpanzee iPSC lines into cardiomyocytes under normoxic conditions, and subjected these cells to 6 hours of hypoxia, followed by 6 or 24 hours of re-oxygenation. We collected genome-wide gene expression data as well as measurements of cellular stress at each time-point. The overall cellular and transcriptional response to hypoxic stress is generally conserved across species. Supporting the functional importance of precise regulatory response to hypoxia, we found that genes that respond to hypoxic stress in both species are depleted for association with expression quantitative trait loci (eQTLs) in the heart, and cardiovascular-related genes. We also identified hundereds of inter-species regulatory differences in our study. In particular, RASD1, which is associated with coronary artery disease, is up-regulated specifically in humans following hypoxia.
Detecting Large Indels Using Optical Map Data
Authors: Fan Xian , Xu Jie , Nakhleh Luay 
Published: August 2018

AbstractOptical Maps (OM) provide reads that are very long, and thus can be used to detect large indels not detectable by the shorter reads provided by sequence-based technologies such as Illumina and PacBio. Two existing tools for detecting large indels from OM data are BioNano Solve and OMSV. However, these two tools may miss indels with weak signals. We propose a local-assembly based approach, OMIndel, to detect large indels with OM data. The results of applying OMIndel to empirical data demonstrate that it is able to detect indels with weak signal. Furthermore, compared with the other two OM-based methods, OMIndel has a lower false discovery rate. We also investigated the indels that can only be detected by OM but not Illumina, PacBio or 10X, and we found that they mostly fall into two categories: complex events or indels on repetitive regions. This implies that adding the OM data to sequence-based technologies can provide significant progress towards a more complete characterization of structural variants (SVs). The algorithm has been implemented in Perl and is publicly available onhttps://bitbucket.org/xianfan/optmethod.
Descriptions of four new species ofMinyomerusHorn, 1876 sec. Jansen & Franz, 2018 (Coleoptera: Curculionidae), with notes on their distribution and phylogeny
Authors: Jansen M. Andrew , Franz Nico M. 
Published: August 2018

ABSTRACTThis contribution adopts the taxonomic concept approach, including the use oftaxonomic concept labels(name sec. [according to] source) and Region Connection Calculus (RCC-5) articulations and alignments. Prior to this study, the broad-nosed weevil genusMinyomerusHorn, 1876 sec. Jansen & Franz, 2015 (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) contained 17 species distributed throughout the desert and plains regions of North America. In this review ofMinyomerussec. Jansen & Franz, 2018, we describe the following four species as new to science:Minyomerus ampullaceussec. Jansen & Franz, 2018 (henceforth: [JF2018]),new species,Minyomerus franko[JF2018],new species,Minyomerus sculptilis[JF2018],new species, andMinyomerus tylotos[JF2018],new species. The four new species are added to, and integrated with, the preceding revision, and an updated key and phylogeny ofMinyomerus[JF2018] are presented. A cladistic analysis using 52 morphological characters of 26 terminal taxa (5/21 outgroup/ingroup) yielded a single most-parsimonious cladogram (Length = 99 steps, Consistency Index = 60, Retention Index = 80). The analysis reaffirms the monophyly ofMinyomerus[JF2018] with eight unreversed synapomorphies. The species-group placements, possible biogeographic origins, and natural history of the new species are discussed in detail.
More than black and white: complex relationships involving serine proteases regulate the Toll pathway and the melanization response inDrosophila
Authors: Dudzic J.P. , Hanson M.A. , latsenko I. , Kondo S. , Lemaitre B. 
Published: August 2018

AbstractThe melanization response is a rapid and important defense mechanism in arthropods. Melanin is produced around wound sites and invading microorganisms by phenoloxidases (POs), which need to be activated by the sequential activation of an extracellular serine protease (SP) cascade.Drosophila melanogasterhas been a useful genetic model for dissecting insect immune signaling, but understanding these proteolytic cascades has been complicated by the large number of SP genes, possibly with redundant function. Taking advantage of recently-generated null and compound mutants, we re-investigated the role of SPs involved in the melanization response inD. melanogasterand discovered phenotypes previously concealed in single mutant analysis. We found that two of them, Hayan and Sp7, can activate the melanization response in two different manners: Hayan is required in the local blackening of wound sites, while Sp7 regulates an alternate melanization reaction responsible for the clearance of septic infections withStaphylococcus aureus. We present evidence that both Sp7 and Hayan regulate the Toll NF-kB pathway. Sp7 is regulated by canonical Toll signaling downstream of PGRP-SA, ModSP, and Grass, leading to control of septic infections via a Sp7-dependent melanization response. Additionally, we found that Hayan and the Toll-regulating SP Psh are the result of a recent gene duplication. Using genetic manipulations, we reveal the hidden role for Hayan, alongside Psh, in propagating Toll signaling downstream of pattern recognition receptors. Thus, we describe the existence of two pathways leading to the melanization response and reveal previously unknown dynamics in the activation of the Toll pathway.
Inner lumen proteins stabilize doublet microtubules in cilia/flagella
Authors: Owa Mikito , Uchihashi Takayuki , Yanagisawa Haruaki , Yamano Takashi , Iguchi Hiro , Fukuzawa Hideya , Wakabayashi Ken-ichi , Ando Toshio , Kikkawa Masahide 
Published: August 2018

AbstractMotile cilia are microtubule-based organelles that play important roles in most eukaryotes. Although it is known that microtubules in cilia are sufficiently stable to withstand their beating motion, it remains unknown how they are stabilized while serving as tracks for axonemal dynein and intraflagellar transport. To address this question, we identified a new class of microtubule-associated proteins, named FAP45 and FAP52, inChlamydomonas. These proteins are conserved among eukaryotes with motile cilia. Using cryo-electron tomography (cryo-ET) and high-speed atomic force microscopy (HS-AFM), we established that lack of these proteins leads to a loss of inner protrusions in B-tubules and less stable microtubules. These inner protrusions are located near the inner junctions of doublet microtubules and lack of FAP45, FAP52, and FAP20 results in detachment of the B-tubule from the A-tubule, as well as flagellar shortening. These results demonstrated that FAP45 and FAP52 bind to the inside of microtubules and stabilize ciliary axonemes.
MicroRNA-27a is a key modulator of cholesterol biosynthesis
Authors: Khan Abrar A. , Agarwal Heena , Reddy S. Santosh , Arige Vikas , Gupta Vinayak , Kalyani Ananthamohan , Barthwal Manoj K. , Mahapatra Nitish R. 
Published: August 2018

ABSTRACTHypercholesterolemia is a strong predictor of cardiovascular diseases. 3-Hydroxy-3-methylglutaryl-coenzyme A reductase gene (Hmgcr) coding for the rate-limiting enzyme in the cholesterol biosynthesis pathway is a crucial regulator of plasma cholesterol levels. However, the post-transcriptional regulation of Hmgcr remains poorly understood. The main objective of this study was to explore the role of miRNAs in the regulation ofHmgcrexpression. Systematicin silico predictionsand experimental analyses reveal that miR-27a specifically interacts with theHmgcr3’-untranslated region in murine and human hepatocytes. Moreover, our data shows thatHmgcrexpression is inversely correlated with miR-27a levels in various cultured cell lines, human and rodent tissues. Actinomycin D chase assays and relevant experiments demonstrate that miR-27a regulates Hmgcr by translational attenuation followed by mRNA degradation. Early Growth Response 1 (Egr1) regulates miR-27a expression under basal and cholesterol-modulated conditions. miR-27a augmentation via tail-vein injection of miR-27a mimic in high cholesterol diet-fedApoe−/−mice shows down-regulation of hepatic Hmgcr and plasma cholesterol levels. Pathway and gene expression analyses show that miR-27a also targets several other genes (apart fromHmgcr) in cholesterol biosynthesis pathway. Taken together, miR-27a emerges as a key regulator of cholesterol biosynthesis and has therapeutic potential for clinical management of hypercholesterolemia.