bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases
Authors: Junqueira Alves Chrystian , Yotoko Karla , Zou Hongyan , Friedel Roland H. 
Published: February 2019

AbstractThe transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.
Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species
Authors: Nowicki Marcin , Zhao Yichen , Boggess Sarah L. , Fluess Helge , Payá-Milans Miriam , Staton Margaret E. , Houston Logan C. , Hadziabdic Denita , Trigiano Robert N. 
Published: February 2019

AbstractTaraxacum kok-saghyz (TKS) carries great potential as alternative natural rubber source. To better inform future breeding efforts with TKS and gain a deeper understanding of its genetic diversity, we utilized de novo sequencing to generate novel genomic simple sequence repeats markers (gSSRs). We utilized 25 gSSRs on a collection of genomic DNA (gDNA) samples from germplasm bank, and two gDNA samples from historical herbarium specimens. PCR coupled with capillary electrophoresis and an array of population genetics tools were employed to analyze the dataset of our study as well as a dataset of the recently published genic SSRs (eSSRs) generated on the same germplasm. Our results using both gSSRs and eSSRs revealed that TKS has low- to- moderate genetic diversity with most of it partitioned to the individuals and individuals within populations, whereas the species lacked population structure. Nineteen of the 25 gSSR markers cross-amplified to other Taraxacum spp. collected from Southeastern United States and identified as T. officinale by ITS sequencing. We used a subset of 14 gSSRs to estimate the genetic diversity of the T. officinale gDNA collection. In contrast to the obligatory outcrossing TKS, T. officinale presented evidence for population structure and clonal reproduction, which agreed with the species biology. We mapped the molecular markers sequences from this study and several others to the well-annotated sunflower genome. Our gSSRs present a functional tool for the biodiversity analyses in Taraxacum, but also in the related genera, as well as in the closely related tribes of the Asteraceae.
Impact of HIV-ART on the restoration of Th17 and Treg cells in blood and female genital mucosa
Authors: Caruso María Paula , Falivene Juliana , Holgado María Pía , Zurita Diego Hernán , Laufer Natalia , Castro Carina , Nico Ángeles , Maeto Cynthia , Salido Jimena , Pérez Héctor , Salomón Horacio , Cahn Pedro , Sued Omar , Fink Valeria , Turk Gabriela , Gherardi María Magdalena 
Published: February 2019

AbstractThe aim of this study was to evaluate the effectiveness of antiretroviral treatment (ART) on the proportion and functions of Th17 and Treg cells in peripheral blood and female genital tract (FGT) respectively. To this aim, samples from 41 HIV-neg, 33 HIV+ ART-naïve and 32 HIV+ ART+ subjects were obtained. In peripheral blood, altered Th17 and Th17/Treg proportions were normalized in HIV+ ART+, but certain abnormal Treg and activated T-cell proportions were still observed. In FGT, abnormal patterns of secretion for Th17-related cytokines were observed in cervical mononuclear cells (CMCs) from HIV+ women, even in those from HIV+ ART+, compared to the HIV-neg group. Moreover, these altered patterns of secretion were associated with diminished levels of CXCL5 and CXCL1 chemokines and with an immunoregulatory skew in the CCL17/CCL20 ratio in ectocervix samples of these women. Finally, ART did not restore proportions of Th17-precursor cells with gut-homing potential in PBMCs, and positive correlations between these cells and the levels of IL-17F and IL-21 production by CMCs may suggest that a better homing of these cells to the intestine could also imply a better restoration of these cells in the female genital tract. These results indicate that antiretroviral treatment did not restore Th17-related immune functions completely at the female mucosal level.
The neural correlates of integrated aesthetics between moral and facial beauty
Authors: Luo Qiuling , Yu Mengxia , Li You , Mo Lei 
Published: February 2019

AbstractFacial beauty and moral beauty have been suggested to be two significant forms of social aesthetics. However, it remains unknown the extent to which there are neural underpinnings of the integration of these two forms of beauty. In the present study, participants were asked to make general aesthetic judgments of facial portraits and moral descriptions while collecting fMRI data. The facial portrait and moral description were randomly paired. Neurally, the appreciation of facial beauty and moral beauty recruited a common network involving the middle occipital gyrus (MOG) and medial orbitofrontal cortex (mOFC). The activities of the mOFC varied across aesthetic conditions, while the MOG was specifically activated in the most beautiful condition. In addition, there was a bilateral insular cortex response to ugliness specifically in the congruent aesthetic conditions, while SMA was selectively responsive to the most ugly condition. Activity associated with aesthetic conflict between facial and moral aesthetic information was limited to the medial prefrontal cortex (mPFC), with enhanced response to the incongruent condition compared to the congruent condition. These findings provide novel neural evidence for the integrated aesthetics of social beauty and suggest that integrated aesthetics is a more complex cognitive process than aesthetics restricted to a single modality.
Increase of glandular epithelial cell clusters by an external volume expansion device promotes adipose tissue regeneration by recruiting macrophages
Authors: Chen Xihang , He Yunfan , Xu Anqi , Deng Zilong , Feng Jingwei , Lu Feng , Yuan Yi 
Published: February 2019

Abstract
Background: There is a clinical need for the use of engineered adipose tissue in place of surgical reconstruction. We previously found that the external volume expansion (EVE) device increased special cell clusters in well-vascularized connective stroma during adipose regeneration. However, the origin of these cell clusters and their role in adipose tissue regeneration remain unknown. Aim: In the present study, we evaluated EVE in the construction of expanded prefabricated adipose tissue (EPAT) in a rat model. Methods: Rats were randomized into an EVE suction group and a control group, with 24 rats in each group. The structure and origin of the special cell clusters were determined by hematoxylin and eosin staining, and immunohistochemistry; their role in adipose tissue regeneration was investigated by immunohistochemistry and Western blot analyses. Results: Special cell clusters began to increase at week 1 with a peak at week 4, and then receded from weeks 8 to 12. Clusters were identified as glandular epithelial cells as determined by their gland-like structure and expression of specific markers. The cell clusters induced significant infiltration of macrophage antigen-2 (Mac-2) positive macrophages by secreting monocyte chemoattractant protein-1 (MCP-1) at the early stage of suction. Subsequently, these infiltrated macrophages expressed massive vascular endothelial growth factor (VEGF) to promoted angiogenesis. Conclusion: EVE generated glandular epithelial cell clusters, which recruited macrophages to promote angiogenesis and subsequent adipose tissue regeneration. These findings shed light on the mechanisms underlying the effects of EVE devices on adipose tissue regeneration.
Human G protein-coupled receptor 30 is N-glycosylated and N-terminal domain asparagine 44 is required for receptor structure and activity
Authors: Gonzalez de Valdivia Ernesto , Sandén Caroline , Kahn Robin , Olde Björn , Leeb-Lundberg L.M. Fredrik 
Published: February 2019

Abstract
G protein-coupled receptor 30 (GPR30), or G protein-coupled estrogen receptor (GPER), is a G protein-coupled receptor (GPCR) that is currently attracting considerable attention in breast cancer and cardiometabolic regulation. The receptor was reported to be a novel membrane estrogen receptor mediating rapid non-genomic responses. However, questions remain about both the cognate ligand and the subcellular localization of receptor activity. Here, we used human embryonic kidney (HEK) 293 (HEK293) cells ectopically expressing N-terminally FLAG-tagged human GPR30 and three unique antibodies (Ab) specifically targetting the receptor N-terminal domain (N-domain) to investigate the role of N-glycosylation in receptor maturation and activity, the latter assayed by constitutive receptor-stimulated extracellular-regulated protein kinase (ERK) 1/2 (ERK1/2) activity. GPR30 expression was complex with receptor species spanning from approximately 40 kDa to higher molecular masses and localized in the endoplasmatic reticulum (ER), the plasma membrane (PM), and endocytic vesicles. The receptor contains three conserved asparagines, Asn25, Asn32, and Asn44, in consensus N-glycosylation motifs, all in the N-domain, and PNGase F treatment showed that at least one of them is N-glycosylated. Mutating Asn44 to isoleucine inactivated the receptor, yielding a unique receptor species at approximately 20 kDa that was recognized by Ab only in a denatured state. On the other hand, mutating Asn25 or Asn32 either individually or in combination, or truncating successively N-domain residues 1–42, had no significant effect either on receptor structure, maturation, or activity. Thus, Asn44 in the GPR30 N-domain is required for receptor structure and activity, whereas N-domain residues 1–42, including specifically Asn25 and Asn32, do not play any major structural or functional role(s).
Gas flow around a planet embedded in a protoplanetary disc
Authors: Kuwahara Ayumu , Kurokawa Hiroyuki , Ida Shigeru 
Published: February 2019

Context. The ubiquity of short-period super-Earths remains a mystery in planet formation, as these planets are expected to become gas giants via runaway gas accretion within the lifetime of a protoplanetary disc. The cores of super-Earths should form in the late stage of disc evolution to avoid runaway gas accretion.
Aims. The three-dimensional structure of the gas flow around a planet is thought to influence the accretion of both gas and solid materials. In particular, the outflow in the midplane region may prevent the accretion of solid materials and delay the formation of the super-Earth cores. However, it is not yet understood how the nature of the flow field and outflow speed change as a function of the planetary mass. In this study, we investigate the dependence of gas flow around a planet embedded in a protoplanetary disc on the planetary mass.
Methods. Assuming an isothermal, inviscid gas disc, we perform three-dimensional hydrodynamical simulations on the spherical polar grid, which has a planet located at its centre.
Results. We find that gas enters the Bondi or Hill sphere at high latitudes and exits through the midplane region of the disc regardless of the assumed dimensionless planetary mass m = RBondi∕H, where RBondi and H are the Bondi radius of the planet and disc scale height, respectively. The altitude from where gas predominantly enters the envelope varies with planetary mass. The outflow speed can be expressed as |uout| = √3/2mcs (RBondi ≤ RHill) or |uout| = √3/2(m/3)1/3cs (RBondi ≥ RHill), where cs is the isothermal sound speed and RHill is the Hill radius. The outflow around a planet may reduce the accretion of dust and pebbles onto the planet when m ≳ √St, where S t is the Stokes number.
Conclusions. Our results suggest that the flow around proto-cores of super-Earths may delay their growth and consequently help them to avoid runaway gas accretion within the lifetime of the gas disc.
Defizite in der Gesundheitskompetenz stationär behandelter Patienten – eine Querschnittstudie
Authors: Gundling Felix , Parasiris Paris , Bunz Anna-Lena , Sohn Maximilian , Haller Bernhard , Schepp Wolfgang , Mühling Tobias 
Published: February 2019

Zusammenfassung
Einleitung Systematische Untersuchungen zum objektiven Verständnis von Patienten bezüglich häufiger medizinischer Begriffe in Deutschland sind selten.
Methodik 196 Patienten (38 % weiblich, 62 % männlich) in stationären Fachabteilungen an einem kommunalen Krankenhaus wurden mittels eines zuvor entwickelten Fragebogens untersucht. Dieser enthielt 43 Fragen zu häufig im Alltag vorkommenden medizinischen Fachbegriffen. Untersucht wurden der subjektive und objektive Bekanntheitsgrad. Zusätzlich wurde eine Assoziation mit verschiedenen potenziellen Einflussfaktoren (u. a. Ausbildung, Versicherungsstatus, Konsum bestimmter Informationsmedien) durchgeführt.
Ergebnisse Durchgehend gaben mehr Patienten an, die Bedeutung medizinischer Begriffe zu kennen, als dies bei objektiver Überprüfung der Fall war. Die Assoziation des medizinischen Kenntnisstandes mit verschiedenen Einflussfaktoren ergab, dass Frauen häufiger über korrektes medizinisches Wissen verfügten als Männer (51,1 vs. 47,2 %, p = 0,12). Das Lebensalter war negativ mit dem medizinischen Kenntnisstand korreliert (p < 0,001). Die Länge der Schulbildung war mit einem besseren medizinischen Kenntnisstand assoziiert (p < 0,001). Privat versicherte Patienten waren besser medizinisch gebildet als gesetzlich Versicherte (p = 0,001). Männliche Patienten mit eher mentaler Arbeit hatten einen besseren Kenntnisstand als solche mit körperlicher Arbeit (51,1 vs. 41,8 %; p = 0,002). Zeitungs- und Fernsehkonsum sowie Anzahl der Arztkontakte waren nicht mit einer Verbesserung des medizinischen Kenntnisstandes vergesellschaftet.
Fazit Ein hoher Bekanntheitsgrad medizinischer Begriffe kann Ärzte im Anamnesegespräch dazu verleiten, das Verständnis dieser Begriffe auch von Seiten des Patienten stillschweigend vorauszusetzen. Ärzte sollten daher durch aktives Nachfragen das Verständnis beim Patienten sicherstellen. Zukünftige Erhebungen zur Gesundheitskompetenz auf Patientenseite sollten diese Divergenz zwischen subjektiver Einschätzung und objektivem Wissen berücksichtigen.
Empowering Patients during Hospitalization: Perspectives on Inpatient Portal Use
Authors: McAlearney Ann , Fareed Naleef , Gaughan Alice , MacEwan Sarah , Volney Jaclyn , Sieck Cynthia 
Published: February 2019

Background Patients have demonstrated an eagerness to use portals to access their health information and connect with care providers. While outpatient portals have been extensively studied, there is a recognized need for research that examines inpatient portals.
Objective We conducted this study to improve our understanding about the role of a portal in the context of inpatient care. Our study focused on a large sample of the general adult inpatient population and obtained perspectives from both patients and care team members about inpatient portal use.
Methods We interviewed patients (n = 120) who used an inpatient portal during their hospitalization at 15 days or 6 months after discharge to learn about their portal use. We also interviewed care team members (n = 331) 4 weeks, 6 months, and 12 months after inpatient portal implementation to collect information about their ongoing perspectives about patients' use of the portal.
Results The perspectives of patients and care team members generally converged on their views of the inpatient portal. Three features—(1) ordering meals, (2) looking up health information, and (3) viewing the care team—were most commonly used; the secure messaging feature was less commonly used and of some concern to care team members. The inpatient portal benefited patients in four main ways: (1) promoted independence, (2) reduced anxiety, (3) informed families, and (4) increased empowerment.
Conclusion Inpatient portals are recognized as a tool that can enhance the delivery of patient-centered care. In addition to empowering patients by increasing their sense of control, inpatient portals can support family members and caregivers throughout the hospital stay. Given the consistency of perspectives about portal use across patients and care team members, our findings suggest that inpatient portals may facilitate shifts in organizational culture that increase the patient centeredness of care and improve patient experience in the hospital context.
A Novel Treatment for Massive Hemorrhage after Maternal Trauma in Pregnancy
Authors: Gonzalez Maritza , Wei Ruth , Hatch Kenneth , Gries Lynn , Hill Meghan 
Published: February 2019

Background Trauma in pregnancy can lead to life-threatening hemorrhage. Conventional treatments of hemorrhage include medical and surgical management. However, if these measures fail uterine compression is an option to control bleeding. We present a case where this management was employed.
Case A patient presented at 36 weeks of gestation with multiple injuries after a motor vehicle collision and experienced disseminated intravascular coagulation (DIC). The use of a Bakri balloon in combination with external compression with Coban, a sterile self-adherent bandage, after delivery temporized her bleeding and allowed her to become stable for further management.
Conclusion When other measures fail and a hysterectomy is considered unsafe, the combination of internal and external uterine compression is an option.
An Approximation of the Steady Gravity Wave Induced by Mountainous Topography*
Authors: Xu Peng-Cheng , Zuo Qun-Jie , Gao Shou-Ting 
Published: February 2019

AbstractAn approximation of the orography gravity wave, which is induced by mountainous topography, is considered in this study. By assuming that the horizontal wind is a linear function with respect to the height, the approximating equation for the orography gravity waves is obtained. Four topography functions are considered in this study and the orography gravity wave are obtained. The dynamics of the orography gravity wave is then discussed by considering the effect of the surface topography and background horizontal wind.
Gsmodutils: a python based framework for test-driven genome scale metabolic model development
Authors: Gilbert James , Pearcy Nicole , Norman Rupert , Millat Thomas , Winzer Klaus , King John , Hodgman Charlie , Minton Nigel , Twycross Jamie 
Published: February 2019

Abstract

Motivation
Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include thousands of reactions and metabolites, with many crucial pathways that only become activated in specific simulation settings. However, despite their widespread use, power and the availability of tools to aid with the construction and analysis of large scale models, little methodology is suggested for their continued management. For example, when genome annotations are updated or new understanding regarding behaviour is discovered, models often need to be altered to reflect this. This is quickly becoming an issue for industrial systems and synthetic biotechnology applications, which require good quality reusable models integral to the design, build, test and learn cycle.

Results
As part of an ongoing effort to improve genome scale metabolic analysis, we have developed a test-driven development methodology for the continuous integration of validation data from different sources. Contributing to the open source technology based around COBRApy, we have developed the gsmodutils modelling framework placing an emphasis on test-driven design of models through defined test cases. Crucially, different conditions are configurable allowing users to examine how different designs or curation impact a wide range of system behaviours, minimizing error between model versions.

Availability and implementation
The software framework described within this paper is open source and freely available from http://github.com/SBRCNottingham/gsmodutils.

Supplementary information
Supplementary data are available at Bioinformatics online.
refineD: improved protein structure refinement using machine learning based restrained relaxation
Authors: Bhattacharya Debswapna 
Published: February 2019

AbstractMotivationProtein structure refinement aims to bring moderately accurate template-based protein models closer to the native state through conformational sampling. However, guiding the sampling towards the native state by effectively using restraints remains a major issue in structure refinement.ResultsHere, we develop a machine learning based restrained relaxation protocol that uses deep discriminative learning based binary classifiers to predict multi-resolution probabilistic restraints from the starting structure and subsequently converts these restraints to be integrated into Rosetta all-atom energy function as additional scoring terms during structure refinement. We use four restraint resolutions as adopted in GDT-HA (0.5, 1, 2 and 4 Å), centered on the Cα atom of each residue that are predicted by ensemble of four deep discriminative classifiers trained using combinations of sequence and structure-derived features as well as several energy terms from Rosetta centroid scoring function. The proposed method, refineD, has been found to produce consistent and substantial structural refinement through the use of cumulative and non-cumulative restraints on 150 benchmarking targets. refineD outperforms unrestrained relaxation strategy or relaxation that is restrained to starting structures using the FastRelax application of Rosetta or atomic-level energy minimization based ModRefiner method as well as molecular dynamics (MD) simulation based FG-MD protocol. Furthermore, by adjusting restraint resolutions, the method addresses the tradeoff that exists between degree and consistency of refinement. These results demonstrate a promising new avenue for improving accuracy of template-based protein models by effectively guiding conformational sampling during structure refinement through the use of machine learning based restraints.Availability and implementationhttp://watson.cse.eng.auburn.edu/refineD/.Supplementary informationSupplementary data are available at Bioinformatics online.