bluuebunny/crossref_metadata_2025_split huggingface dataset:
Granulometry analysis of Ngrayong sandstone, Tempuran Area, Rembang Zone, North East Java Basin
Authors: Min Htun Myo , Sapto Surjono Sugeng , Setyowiyoto Jarot 
Published: March 2020

Abstract
The study area is located near Tempuran Village, Rembang Zone, North-East Java. Ngrayong sandstone is a famous reservoir in north-east Java, mainly composed of sandstones which are exposed along east-west trending along the southern flank of Pakel Anticline. Eighteen samples from four different facies from eight outcrops conducted for granulometry analysis. The objective of this paper is to predict the reservoir potential base on granulometry analysis especially grain size and sorting. The study area is still needs to confirm about reservoir quality. Ngrayong Formation consists of laminated to thin bedded sandstone facies, thick bedded to massive sandstone facies, calcareous sandstone facies and cross-bedded sandstone facies. According to the analytical results, sandstone facies are composed of very fine to fine, poorly sorted to very well sorted sandstones. Base on the results of analyzed samples, Ngrayong sandstone have good porosity and permeability, thus Tempuran area can be considered as a prospective reservoir.
Relation between gross domestic product (GDP) and poverty population in East Kalimantan Province from 2013 - 2017
Authors: Putra A U , Putro H R V , Budiman L S , Adlina L , Putri R F 
Published: March 2020

Abstract
Gross Domestic Product (GDP) is one of the important factors to determine the economic conditions of an area in a certain period. This study uses GDP according to the business field based on constant prices in 2010. The purpose of this study, first is to determine trends of GDP and the percentage of the poverty population. Second, is to find out the relationship between GDP to poverty in East Kalimantan. The method used in this study is spatial method to find out the distribution and temporal trends. For determine the relationship, this research used simple regression calculations. The results of the study show that: (1) From 2013 to 2017 the tendency of GDP in East Kalimantan Province was increasing and the most dominant GDP contributor sector was the mining sector. (2) The trend in the percentage of the poverty population in East Kalimantan Province from 2013 to 2017 is fluctuating. (3) Simple regression calculations indicate that there is a relationship between GDP and poverty in Bontang City, Kutai Barat Regency, and Penajam Paser Utara Regency.
MPTherm: database for membrane protein thermodynamics for understanding folding and stability
Authors: Kulandaisamy A , Sakthivel R , Gromiha M Michael 
Published: March 2020

Abstract
The functions of membrane proteins (MPs) are attributed to their structure and stability. Factors influencing the stability of MPs differ from globular proteins due to the presence of membrane spanning regions. Thermodynamic data of MPs aid to understand the relationship among their structure, stability and function. Although a wealth of experimental data on thermodynamics of MPs are reported in the literature, there is no database available explicitly for MPs. In this work, we have developed a database for MP thermodynamics, MPTherm, which contains more than 7000 thermodynamic data from about 320 MPs. Each entry contains protein sequence and structural information, membrane topology, experimental conditions, thermodynamic parameters such as melting temperature, free energy, enthalpy etc. and literature information. MPTherm assists users to retrieve the data by using different search and display options. We have also provided the sequence and structure visualization as well as cross-links to UniProt and PDB databases. MPTherm database is freely available at http://www.iitm.ac.in/bioinfo/mptherm/. It is implemented in HTML, PHP, MySQL and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Opera. MPTherm would serve as an effective resource for understanding the stability of MPs, development of prediction tools and identifying drug targets for diseases associated with MPs.
Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers
Authors: Wei Ran , Li Pengcheng , He Funan , Wei Gang , Zhou Zhan , Su Zhixi , Ni Ting 
Published: March 2020

AbstractAlcohol consumption is a critical risk factor for multiple types of cancer. A genome can be attacked and acquire numerous somatic mutations in the environment of alcohol exposure. Mutational signature has the capacity illustrating the complex somatic mutation patterns in cancer genome. Recent studies have discovered distinct mutational signatures associating with alcohol consumption in liver and esophageal cancers. However, their prevalence among diverse cancers, impact of genetic background and origin of alcohol-induced mutational signatures remain unclear. By a comprehensive bioinformatics analysis on somatic mutations from patients of four cancer types with drinking information, we identified nine mutational signatures (signatures B–J), among which signature J (similar to COSMIC signature 16) was distinctive to alcohol drinking. Signature J was associated with HNSC, ESCA and LIHC but not PAAD. Interestingly, patients with mutated allele rs1229984 in ADH1B had lower level of signature J while mutated allele rs671 in ALDH2 exhibited higher signature J abundance, suggesting acetaldehyde is one cause of signature J. Intriguingly, somatic mutations of three potential cancer driver genes (TP53, CUL3 and NSD1) were found the critical contributors for increased mutational load of signature J in alcohol consumption patients. Furthermore, signature J was enriched with early accumulated clonal mutations compared to mutations derived from late tumor growth. This study systematically characterized alcohol-related mutational signature and indicated mechanistic insights into the prevalence, origin and gene–environment interaction regarding the risk oncogenic mutations associated with alcohol intake.
Inbreeding and competition, but not abiotic stresses, increase fluctuating asymmetry ofMimulus guttatusflowers
Authors: Sandner Tobias M 
Published: March 2020

AbstractGenetic and environmental disturbances are expected to increase developmental instability, which may result in higher fluctuating asymmetry (FA), i.e. small random deviations from symmetry. Plant leaves often do not show this pattern, possibly due to high phenotypic plasticity of leaf shape and low adaptive significance of leaf symmetry. In contrast, symmetry in many animal traits but also in flower shape is considered to be under selection, and FA in such traits may better reflect developmental instability. Using geometric morphometrics, I analysed the symmetry of flowers of inbred and outbred Mimulus guttatus (Phrymaceae) plants grown under five stress treatments with and without grass competition. Flower FA was not increased by abiotic stress, but by inbreeding and competition. As inbreeding and competition affected different principal components of flower FA, different mechanisms may be involved in their effects on FA. FA decreased with individual biomass particularly in selfed offspring, which suggests that inbreeding increased FA particularly when growth was limited by environmental or genetic constraints. Increased flower FA of inbred offspring may explain increased flower handling time and reduced pollinator preference for inbred plants in other M. guttatus studies, and could thus have important consequences for plant demography and plant–pollinator interactions.
Conditionally reprogrammed macaque endocervical cells retain steroid receptor expression and produce mucus
Authors: Han Leo , Andrews Walker , Wong Karsten , Jensen Jeffrey T 
Published: March 2020

AbstractCervical mucus produced by the endocervix plays an essential role as a hormonally induced regulator of female fertility. Cervical mucus fluctuates in both physical characteristics and in sperm penetrability in response to estrogens and progestogens. However, the mechanisms by which steroid hormones change mucus remains poorly understood. Current in vitro models have limited capability to study these questions as primary endocervical cells possess limited expansion potential, and immortalized cells lose in vivo characteristics such as steroid sensitivity. Here we overcome these limitations by establishing an in vitro primary endocervical cell culture model using conditionally reprogrammed cells (CRCs). CRC culture utilizes a Rho-kinase inhibitor and a fibroblast feeder layer to expand proliferative potential of epithelial cell types that have normally short in vitro life spans. In our studies, we produce CRC cultures using primary endocervical cells from adult female rhesus macaques (Macaca mulatta). We demonstrate that primary endocervical cells from the nonhuman primate can be robustly expanded using a CRC method, while retaining steroid receptor expression. Moreover, when removed from CRC conditions and switched to differentiation conditions, these cells are able to differentiate and produce mucus including MUC5B, the most prevalent mucin of the endocervix. We conclude that this method provides a promising in vitro platform for conducting mechanistic studies of cervical mucus regulation as well as for screening new therapeutic targets for fertility regulation and diseases of the endocervix.
Orthonasal, but not Retronasal Olfaction Is Specifically Impaired in Parkinson’s Disease
Authors: Aubry-Lafontaine Emilie , Tremblay Cécilia , Durand-Martel Pascali , Dupré Nicolas , Frasnelli Johannes 
Published: March 2020

Abstract
Olfactory dysfunction (OD) in Parkinson’s disease (PD) appears several years before the presence of motor disturbance. Olfactory testing has the potential to serve as a tool for early detection of PD, but OD is not specific to PD as it affects up to 20% of the general population. Olfaction includes an orthonasal and a retronasal components; in some forms of OD, retronasal olfactory function is preserved. We aimed to evaluate whether combined testing components allows for discriminating between PD-related OD and non-Parkinsonian OD (NPOD). The objective of this study is to orthonasal and retronasal olfactory function in PD patients and compare them to a NPOD group and to healthy controls. We hypothesized that this combined testing allows to distinguish PD patients from both other groups. We included 32 PD patients, 25 NPOD patients, and 15 healthy controls. Both olfactory components were impaired in PD and NPOD patients, compared with controls; however, NPOD patients had significantly better orthonasal scores than PD patients. Furthermore, the ratio of retronasal/orthonasal score was higher in PD than in both other groups. In the NPOD group, orthonasal and retronasal scores were significantly correlated; no such correlation could be observed in PD patients. In summary, PD patients seem to rely on compensatory mechanisms for flavor perception. Combined orthonasal and retronasal olfactory testing may contribute to differentiate PD patients from patients with NPOD.
Handling, infectious agents and physiological condition influence survival and post-release behaviour in migratory adult coho salmon after experimental displacement
Authors: Chapman J M , Teffer A K , Bass A L , Hinch S G , Patterson D A , Miller K M , Cooke S J 
Published: March 2020

Abstract
For Pacific salmon captured and released by fisheries, post-release behaviour and survival may be influenced by their health and condition at time of capture. We sought to characterize the interactions between infectious agent burden, fish immune and stress physiology and fisheries stressors to investigate the potential for capture-mediated pathogen-induced mortality in adult coho salmon Oncorhynchus kisutch. We used radio-telemetry paired with high-throughput qPCR of non-lethal gill biopsies for infectious agents and host biomarkers from 200 tagged fish experimentally displaced and exposed to various experimental fisheries treatments (gill net entanglement, recreational angling and recreational angling with air exposure vs. non-sampled control). We characterized relationships among post-release behaviour and survival, infectious agent presence and loads, physiological parameters and transcription profiles of stress and immune genes. All infectious agents detected were endemic and in loads consistent with previous adult Pacific salmon monitoring. Individuals exposed to fisheries treatments were less likely to reach spawning habitat compared to controls, and handling duration independent of fisheries gear had a negative effect on survival. High infectious agent burden was associated with accelerated migration initiation post-release, revealing behavioural plasticity in response to deteriorating condition in this semelparous species. Prevalence and load of infectious agents increased post-migration as well as transcription signatures reflected changes in immune and stress profiles consistent with senescence. Results from this study further our understanding of factors associated with fisheries that increase risk of post-release mortality and characterize some physiological mechanisms that underpin migratory behaviour.
Molecular determinants of surface colonisation in diarrhoeagenicEscherichia coli(DEC): from bacterial adhesion to biofilm formation
Authors: Ageorges Valentin , Monteiro Ricardo , Leroy Sabine , Burgess Catherine M , Pizza Mariagrazia , Chaucheyras-durand Frédérique , Desvaux Mickaël 
Published: March 2020

ABSTRACTEscherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
Novel Prognostic Biomarkers of Mucosal Healing in Ulcerative Colitis Patients Treated With Anti-TNF: Neutrophil-to-Lymphocyte Ratio and Platelet-to-Lymphocyte Ratio
Authors: Bertani Lorenzo , Rossari Federico , Barberio Brigida , Demarzo Maria Giulia , Tapete Gherardo , Albano Eleonora , Baiano Svizzero Giovanni , Ceccarelli Linda , Mumolo Maria Gloria , Brombin Chiara , de Bortoli Nicola , Bellini Massimo , Marchi Santino , Bodini Giorgia , Savarino Edoardo , Costa Francesco 
Published: March 2020

Abstract

Background
Anti-tumor necrosis factor drugs (anti-TNFs) are widely used for the treatment of ulcerative colitis (UC). However, many patients experience loss of response during the first year of therapy. An early predictor of clinical remission and mucosal healing is needed. The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are markers of subclinical inflammation poorly evaluated in UC patients treated with anti-TNFs. The aim of this multicenter study was to evaluate whether NLR and PLR could be used as prognostic markers of anti-TNF treatment response.

Methods
Patients with UC who started anti-TNF treatment in monotherapy were evaluated. Patients with concomitant corticosteroid treatment ≥20 mg were excluded. We calculated NLR, PLR, and fecal calprotectin before treatment and after induction. The values of NLR and PLR were correlated with clinical remission and mucosal healing at the end of follow-up (54 weeks) using the Mann-Whitney U test and then multivariate analysis was conducted.

Results
Eighty-eight patients were included. Patients who reached mucosal healing after 54 weeks of therapy displayed lower levels of both baseline NLR and PLR (P = 0.0001 and P = 0.04, respectively); similar results were obtained at week 8 (P = 0.0001 and P = 0.001, respectively). Patients who presented with active ulcers at baseline endoscopic evaluation had higher baseline NLR and PLR values compared with those without detected ulcers (P = 0.002 and P = 0.0007, respectively).

Conclusions
BothNLR and PLR showed a promising role as early predictors of therapeutic response to anti-TNF therapy in UC patients. If confirmed in larger studies, classification and regression trees proposed in this article could be useful to guide clinical decisions regarding anti-TNF treatment.
Premobilization of CD133+ progenitors is associated with attenuated inflammation-induced pulmonary dysfunction following extracorporeal circulation in mice
Authors: Luo Dan , Liu Xinhao , Zhang Jie , Du Lei , Bai Lin , Luo Shuhua 
Published: March 2020

AbstractOBJECTIVESProgenitor cells mobilized by granulocyte colony-stimulating factor (G-CSF) have been shown to lessen acute kidney injury induced by extracorporeal circulation (ECC). Both acute kidney injury and lung injury are characterized by endothelial dysfunction. Our goal was to examine whether and how G-CSF-mobilized progenitors with endothelial capacity may help mitigate ECC-induced pulmonary dysfunction.METHODSG-CSF (10 μg/kg/day) was administered subcutaneously to C57BL/6 mice before or at the initiation of the ECC process, after which lung injury was assessed by measuring neutrophils in the fluid from bronchoalveolar lavage and determining the pathological score in lung tissue. CD133+ progenitors were isolated and injected into C57BL/6 mice before ECC in vivo. We incubated the CD133+ cells with pulmonary monocytes or neutrophils isolated from naïve mice in vitro.RESULTSPretreatment with G-CSF for 2 days significantly decreased the number of neutrophils in the bronchoalveolar lavage fluid, and the pathological score (P &lt; 0.01; n = 5) improved the PaO2/FiO2 ratio [193.4 ± 12.7 (ECC without G-CSF) vs 305.6 ± 22.6 mmHg (ECC with G-CSF); P = 0.03, n = 5] and suppressed neutrophil elastase and tumour necrosis factor-α levels in the circulation; we also observed increases in both circulating and pulmonary populations of CD133+ progenitors. Similar effects were observed in animals pretreated with CD133+ progenitors instead of G-CSF before ECC. The majority of CD133+/CD45− and CD133+/CD45+ progenitors were mobilized in the lung and in the circulation, respectively. Incubating CD133+ progenitors with neutrophils or pulmonary monocytes blocked lipopolysaccharide-induced release of inflammatory factors.CONCLUSIONSOur results suggest that pretreatment of G-CSF attenuates ECC-induced pulmonary dysfunction through inhibiting the inflammatory response in lung tissue and in the circulation with associated premobilization of CD133+ progenitors.
Citrullinated fibrinogen is a target of auto-antibodies in interstitial lung disease in mice with collagen-induced arthritis
Authors: Sato Tomomi , Satooka Hiroki , Ichioka Satoko , Maruo Yoshihiro , Hirata Takako 
Published: March 2020

Abstract
Interstitial lung disease (ILD) is a very common and lethal complication of rheumatoid arthritis (RA), yet its pathogenesis is not well understood, in part due to the lack of adequate animal models. Although collagen-induced arthritis (CIA) is the most widely used animal model for RA, the lung involvement occurring in this model has scarcely been studied. To evaluate the suitability of CIA as a model for RA-associated ILD (RA-ILD), we immunized DBA/1 mice with bovine type II collagen and characterized lung disease in this model. Histologic analyses revealed patchy interstitial infiltration of inflammatory cells in the peripheral regions of the lung, notably in the subpleural region, in mice with CIA. This pattern resembled usual interstitial pneumonia in humans, which is the most prevalent pattern in RA-ILD. Among infiltrates in the lung, CD11bhi macrophages of the M2 phenotype were most prominently increased. IgG and C3 were deposited in the subpleural region where inflammatory cells infiltrated. The sera from CIA mice contained auto-antibodies against citrullinated proteins, which are specific and predictive markers for RA. Protein citrullination was enhanced in the lung of CIA mice compared with naive mice, and citrullinated fibrinogen was primarily targeted by these auto-antibodies. The elevation of auto-antibodies against citrullinated proteins and their deposition in the lung with patchy subpleural preponderance suggest that CIA can serve as a model to study the pathogenesis of RA-ILD.
Problems with the problem list: challenges of transparency in an era of patient curation
Authors: Porter Amy S , O’Callaghan Jolene , Englund Kristin A , Lorenz Robert R , Kodish Eric 
Published: March 2020

Abstract
In recent years, the OpenNotes movement and other changes in healthcare have driven institutions to make medical records increasingly transparent. As patients have begun to question and request changes to their Problem Lists, clinicians have come to face the ever more frequent challenge of discerning which changes to make and which to refuse. Now clinicians and patients together choose the list of problems that represent the patient’s current state of health and illness. As the physician’s role slides closer to consultant and the medical paternalism of the twentieth century falls further into the background of our technology-infused present, who holds the power of delineating a patient’s clinical identity? This paper examines the ethical and practical dimensions of this question and proposes a research agenda that aims to answer it. Such explorations are essential to ensuring that the physician remains relevant to patient’s notions of health, illness, intervention, and healing.
Discovery of a retrogradely rotating neutron star in the X-ray pulsar GX 301–2
Authors: Mönkkönen Juhani , Doroshenko Victor , Tsygankov Sergey S , Nabizadeh Armin , Abolmasov Pavel , Poutanen Juri 
Published: March 2020

ABSTRACT
We report on the analysis of the spin evolution of a slow X-ray pulsar GX 301–2 along the orbit using long-term monitoring by Fermi/Gamma-ray Burst Monitor. Based on the observationally confirmed accretion scenario and an analytical model for the accretion of angular momentum, we demonstrate that in this system, the neutron star spins retrogradely, that is, in a direction opposite to the orbital motion. This first-of-a-kind discovery of such a system proves the principal possibility of retrograde rotation in accreting systems with suitable accretion torque, and might have profound consequences for our understanding of the spin evolution of X-ray pulsars, estimates of their initial spin periods, and the ultimate result of their evolution.