bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling In-patients with Chronic Non-Communicable Diseases Using Parametric Shared Frailty Models
Authors: Hunde Belachew Melese 
Published: October 2019

Abstract
Background Non-communicable diseases, known as chronic diseases, are not contagious in their nature. They progress slowly in affecting the health of a person. They are the leading causes of death in all continents except Africa, but current projections indicated that by 2025 the largest increases in the non-communicable diseases deaths will occur in Africa. In Ethiopian about 34% of patients suffered from chronic non communicable diseases and there is a gap of estimating the time-to-death of these patients to manage the diseases progression in earlier. Thus, this study was aimed in estimating the survival outcome (death times) of the retrospective follow-up studies of registered inpatients for three years in three hospitals of Oromiya National Regional State, Ethiopia. Methods To describe the prediction and diseases progression of non-communicable diseases, different types of parametric frailty models were compared. Hospitals of the patients were considered as the unobserved variable in the models. The Exponential, Weibull and log-logistic as baseline hazard functions and the gamma and inverse Gaussian for the frailty distributions were checked for their performance using both AIC criteria and Likelihood ratio test. Results On average death times of chronic diseases was 12 days with the maximum of 40 days. Of 646 chronic non-communicable hospitalized patients about 41.5% were died. The log-logistic model with inverse Gaussian frailty has the minimum AIC and LRT value among the models compared. The hospital of the patient has a significant effect in modeling time-to-death of chronic diseases datasets. Conclusion The log-logistic with inverse Gaussian frailty model fitted better than other distributions for the chronic diseases data sets. Therefore, considering the hospital as random effects has a significant impact on time-to-death for NCDs patients and therefore, it is recommendable to include frailty to act as covariates for capturing any dependency under clustered time-to-event methods.
Analysis of TP53 gene mutations demonstrates that aflatoxin is a risk factor for hepatocellular carcinoma in Guatemala
Authors: Privado Christian Alvarez , Ortiz Jeremy , Bendfeldt-Avila Giovanna , Xie Yi , Wang Mingyi , Wu Dongjing , Higson Herbert , Lee Elisa , Teshome Kedest , Barnoya Joaquin , Kleiner David E. , Groopman John , Orozco Roberto , McGlynn Katherine A , Gharzouzi Eduardo , Dean Michael 
Published: October 2019

Abstract
Background Guatemala has the highest incidence of hepatocellular carcinoma (HCC), the dominant type of liver cancer, in the Western Hemisphere. The major risk factors in Guatemala are not well-characterized, but the prevalence of hepatitis B (HBV) and hepatitis C virus (HCV) appear to be low, while the prevalence of aflatoxin (AFB 1 ) exposure appears to be high. To examine whether AFB 1 could be a risk factor for HCC in Guatemala, this study examined the frequency of the AFB 1 -signature mutation in the TP53 gene (R249S) as well as other somatic mutations.Methods Ninety-one formalin-fixed, paraffin-embedded (FFPE) HCC tissues were obtained from three hospitals in Guatemala City. An additional, eighteen tumor tissues preserved in RNAlater were also obtained. Targeted sequencing of TP53 was successfully performed in 89 of the FFPE samples, and a panel of 245 genes were sequenced in the RNAlater samples.Results Overall, 47% of HCCs had a TP53 mutation. The AFB 1 -signature R249S mutation was present in 24%. Among the RNAlater samples, 44% had any TP53 mutation and 33% had the R249S mutation. Other somatic mutations were identified in known HCC driver genes such as ARID1A , ARID2 , and CTNNB1 .Conclusions The presence of the TP53 R249S mutation indicates that AFB 1 is a risk factor for HCC in Guatemala. The proportion of HBV positive tumors was low, suggesting that AFB 1 is associated with HCC in the absence of concomitant HBV infection. To decrease the risk of HCC in Guatemala, AFB 1 abatements efforts are warranted.
Metabolic profiling of liver in C57BL/6 mice with DSS-induced inﬂammatory bowel disease by untargeted metabolomics analysis
Authors: Xin Zhongquan , Zhai Zhenya , Long Hongrong , Zhang Fan , Ni Xiaojun , Deng Jinping , Yi Lunzhao , Deng Baichuan 
Published: October 2019

Abstract
Background: Inﬂammatory bowel disease (IBD) is a systemic disease that frequently causes liver damage. However, the metabolic mechanism of liver disorder induced by IBD is still unclear. This study aimed to revile metabolic profiles of liver in mice which induced inﬂammatory bowel disease by dextran sulfate sodium (DSS) and treated by cecropin A and gentamicin . Methods: In this study, IBD mold mice were established, C57BL/6 mice were given water containing 2.5% dextran sulfate sodium (DSS) for 5 days. Subsequently, the mice were treated via intraperitoneally injected with saline, 15 mg/kg cecropin A, 5 mg/kg gentamicin for 3 days, respectively. The liver in IBD mold mice or treated by cecropin A and gentamicin, were performed metabolomics analysis through UPLC–Orbitrap–MS/MS. Database integration analysis software was used to identify metabolites of liver. Multivariate analysis, including principal component analysis (PCA), hierarchical cluster analysis (HCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA). Furthermore, metabolic pathway analysis was performed using MetaboAnalyst 4.0. Results: A total of 133 metabolites were identified in liver of mice and 20 key metabolites were considered as potential biomarkers were identified between the control and IBD group. There are 4 key metabolic pathways include bile acid metabolism, arachidonic acid metabolism, amino acid and protein metabolism, and steroid hormone biosynthesis in liver was disturbed by IBD, and we also found that those pathways were reversed when mice were treated by cecropin A and gentamicin. Conclusion: The results indicated that those differential metabolites and metabolic pathways changed in liver were likely to be caused by IBD. The further study shall be carried out to explore the mechanism of liver disorder induced by IBD.
Relationship between monocyte-to-lymphocyte ratio and coronary plaque vulnerability in patients with acute coronary syndrome: an optical coherence tomography study
Authors: Zhang Ting-yu , Zhao Qi , Liu Ze-sen , Zhang Chao-yi , Yang Jie , Meng Kang 
Published: October 2019

Abstract
Background The importance of monocyte-to-lymphocyte ratio (MLR) has been indicated in the initiation and progression of coronary artery disease (CAD). However, few previous researches demonstrated the relationship between MLR and plaque vulnerability. We aimed to investigate coronary plaque vulnerability in patients with acute coronary syndrome (ACS) by optical coherence tomography (OCT). Methods A total of 72 ACS patients who underwent coronary angiography and OCT test in Beijing Anzhen hospital were included in this retrospective study. The plaque vulnerability and plaque morphology were assessed by OCT. Results The coronary plaque in high MLR group exhibited more vulnerable features, characterizing as thinner thickness of fibrous cap (FCT)(112.37 ± 60.24 vs 153.49 ± 73.29 μm, P = 0.013), greater maximum lipid core angle (167.36 ± 62.33 vs 138.79 ± 56.37°, P = 0.010) and longer lipid plaque length (6.34 ± 3.12 vs 4.50 ± 2.21mm, P = 0.041). A prominently negative liner relation was found between MLR and FCT (R = 0.225, P < 0.005). Meanwhile, the incidence of OCT-detected thin cap fibro-atheroma (TCFA) (44.7% vs 18.4%, P = 0.014) and plaque rupture (36.8% vs 13.2%, P = 0.017) were higher in high MLR group. Most importantly, multivariable logistic regression analysis showed MLR level was related to the presence of TCFA (OR:3.316，95%：1.448-7.593，P = 0.005). MLR level could differentiate TCFA with a sensitivity of 72.0% and a specificity of 66.1%. Conclusion Circulating MLR level has potential value in identifying the presence of vulnerable plaque in patients with ACS. MLR, as a non- invasive biomarker of inflammation, may be valuable in revealing plaque vulnerability. Key words Monocyte-to-lymphocyte ratio, Optical coherence tomography, Plaque vulnerability
Inter- and intra-patient circadian variabilities in eight urinary modified nucleosides excretion in patients with metastatic colorectal cancer
Authors: Dulong Sandrine , Qi Huang , Fabio Innominato Pasquale , Abdoulaye Karaboue , Mohamed Bouchahda , Alain Pruvost , Frédéric Théodoro , Luigi Agrofoglio , René Adam , Barbel Finkenstädt , Francis Lévi 
Published: October 2019

Abstract
Background : Modified nucleosides reflect nucleic acids turnover, and are eliminated into the urine. They can serve as non-invasive biomarkers for monitoring tumour dynamics, and treatment responses. Methods : 8 modified nucleosides were determined by LC-HRMS in urine voids collected in three linical trials recorded on NCT01693848, NCT01693861 and NCT01693835 by a total of 39 patients. The patients’ circadian timing system was studied by wrist actimetry. Rhythms parameters were estimated using Hidden Markov model (HMM) for telemetric activity data and cosinor analysis for urinary nucleosides excretion. Results : Pseudouridine, was ~ 10-fold larger than those of 1-methylguanosine, 1-methyladenosine, or 4-acetylcytidine, and ~100 fold larger than those of adenosine and cytidine. In St 1, a significant increase in the overnight urinary excretion of 1-methylguanosine was associated with prolonged 4-year survival in patients with R1 resection for liver metastases. In St 2, a significant increase in one nucleoside excretion after chemotherapy was associated with that in plasma carcinoembryonic antigen 1-2 months later, and poor survival. In St3, ten fractionated urines were collected over 2-days. Circadian and/or 12-h rhythms were found in up to 48.3% of the patients for pseudouridine. Rhythm amplitudes were significantly associated with rest-activity circadian parameters. Conclusion : Urinary excretion dynamics of modified nucleosides appeared useful for tracking early responses to surgical or medical treatments, and for characterizing circadian control of cellular proliferation in colorectal cancer patients.
Innovative Technologies Can Improve Understanding of Microbial Nitrogen Dynamics in Agricultural Soils
Authors: Cloutier Mara Lee , Bhowmik Arnab , Bell Terrence H. , Bruns Mary Ann 
Published: October 2019

Core Ideas
Innovative technologies improve metadata quality for soil N cycle omics studies.
Microfluidics and automated sensing enhance tracking of N cycle intermediates and products.
Model microfabricated systems offer greater control of microbial habitat conditions.
Multiple approaches can achieve parallel quantification of N cycling genes.
Insights from small‐scale studies can inform field‐scale management to reduce N losses.
Roughly half of all nitrogen (N) added to soils is not incorporated by crops and is lost to the environment, but our ability to reduce N loss from soils is hampered by an inadequate grasp of microbial processes affecting N retention and mobility. High‐throughput sequencing (HTS) of microbial DNA is enabling fundamental insights into N cycling microorganisms and their metabolisms. This commentary describes six emerging technologies that could be combined with HTS to enable real‐time collection of metadata on N transformations, intermediates, and products to link soil properties, microbial processes, and the fate of N. These technologies include microdialysis and microfluidics, automated sensing, microfabrication of model soils, parallel quantification of N functional genes, sorting active cells, and stable isotope probing. Use of integrated technologies applied initially under controlled conditions at small scales can lead to identification of soil conditions and field‐scale management practices that promote better N conservation and delivery to agricultural crops.
Evaluating Selection of a Quantitative Trait: Snow Mold Tolerance in Winter Wheat
Authors: Kruse Erika B. , Esvelt Klos Kathy L. , Marshall Juliet M. , Murray Timothy D. , Ward Brian P. , Carter Arron H. 
Published: October 2019

Core Ideas
Six quantitative trait loci for snow mold tolerance were detected in a winter wheat recombinant inbred line population.
Marker‐assisted selection to incorporate QTL is unlikely to help breed for highly quantitative traits.
Genomic selection could replace initial phenotyping for quantitative traits.
Selection for snow mold tolerance (SMT) in winter wheat (Triticum aestivum L.) is complicated by the influence of numerous quantitative trait loci (QTL) and of environmental conditions. The goals of this study were to identify QTL for SMT, determine the effectiveness of marker‐assisted selection (MAS), and model the effectiveness of genomic prediction for SMT. Quantitative trait loci analysis of a recombinant inbred line (RIL) subpopulation, derived from a cross between Xerpha and Münstertaler, detected six unique QTL. Progeny from the same cross were advanced by MAS and compared with the unselected subpopulation to evaluate the efficacy of MAS. No significant difference was found between the SMT means (p = 0.41). Similarly, genomic selection had very poor accuracy (−0.07) in the Xerpha–Münstertaler (XM) RIL subpopulation. This contrasts with the apparent effectiveness of genomic selection (0.65) in a Finch–Eltan RIL population, also evaluated for SMT. The failure of selection tools to improve SMT in the XM population is likely due to the challenges of rating a quantitative trait that requires highly specific environmental conditions for phenotype development.
High Temperature Reduces the Viability of Pollen from Upland Cotton in China
Authors: Zhou Heng , Hu Qirui , Zhang Chaojun , Hu Shaoxin , Chen Quanzhan , Tang Canming 
Published: October 2019

The viability of pollen grains from upland cotton (Gossypium hirsutum L.) has an important influence on fertilization and fiber yield and quality, and high temperature adversely affects cotton pollen grain development. However, the effects of high temperature on the vigor of pollen grains and cultivars having pollen grains resistant to high temperature in different regions have not been reported. The purpose of this study was to evaluate how high temperatures influence the viability of pollen from upland cotton and determine the high‐temperature risk to pollen vigor in upland cotton cultivars in major cotton‐producing regions in China. In this study, pollen grain germination was performed in vitro by culturing pollen grains in medium to detect cotton pollen grain viability. Pollen germination rates decreased significantly when the maximum daily temperature was ≥35°C for three consecutive days. The resistance of pollen vigor to high temperatures significantly differed among cultivars. According to the average annual number of days with temperatures ≥35°C from June to August in the main cotton‐producing areas in China within a 10‐yr period, the risk of high temperature affecting pollen vigor can be divided into five levels. Seventeen cultivars (lines) resistant to high temperatures were selected from 206 upland cotton cultivars, and four simple sequence repeat (SSR) markers were found to be associated with pollen germination rates under high temperature. This study clarified the degree of high‐temperature risk in major cotton‐producing areas in China and provided guidance for the selection of suitable heat‐resistant cultivars.Core Ideas

Pollen germination rates decreased significantly when the maximum daily temperature was ≥35°C for three consecutive days.
The heat resistance index was calculated to evaluate the differences in the heat resistance among the different cultivars.
Resistance of pollen vigor to high temperature significantly differed among cultivars.
Four simple sequence repeat markers associated with pollen germination rates under high temperature were identified.
Relative Permeability Measurements during the Exsolution and Dissolution of Hydrogen Gas Produced by the Hydrolysis of Sodium Borohydride
Authors: Mohammed Obai , Mumford Kevin G. , Sleep Brent E. 
Published: October 2019

Core Ideas
Aqueous relative permeability experiments followed gas exsolution and trapping.
Hydrogen gas was produced by the reaction of sodium borohydride and water.
Internal drainage, external drainage and imbibition, and dissolution were compared.
Trapped gas saturations were higher following internal drainage.
Aqueous relative permeability was similar for internal and external displacement.
The presence of trapped gas in otherwise water‐saturated porous media has a substantial effect on water flow, which is important to a wide variety of subsurface applications including groundwater remediation, CO2 sequestration, and the release of greenhouse gases associated with oil and gas development. Trapped gases can be created by external drainage and imbibition, where fluids invade from system boundaries, or by internal drainage (exsolution), where gas is produced at nucleation sites within a porous medium. A series of laboratory experiments were conducted in thin flow cells, in which H2 gas was produced by the reaction of sodium borohydride and water to produce a range of trapped gas saturations. Aqueous relative permeability was measured following H2 exsolution and during dissolution and compared with measurements in the presence of air trapped by external drainage and imbibition. The results showed that gas saturations higher than those produced by external displacement remained trapped (immobile) when produced by exsolution but that aqueous relative permeability was similar at the same gas saturations. The results of this study suggest that traditional aqueous relative permeability relationships based on external drainage may be suitable to describe the effects of internal drainage in uniform, loosely packed sands. However, additional investigation across a wider range of porous media and at higher gas saturations is required.
A new emerald occurrence from Kruta Balka, Western Peri-Azovian region, Ukraine: Implications for understanding the crystal chemistry of emerald
Authors: Franz Gerhard , Vyshnevskyi Oleksii , Taran Michail , Khomenko Vladimir , Wiedenbeck Michael , Schiperski Ferry , Nissen Jörg 
Published: October 2019

AbstractWe investigated emerald, the bright-green gem variety of beryl, from a new locality at Kruta Balka, Ukraine, and compare its chemical characteristics with those of emeralds from selected occurrences worldwide (Austria, Australia, Colombia, South Africa, Russia) to clarify the types and amounts of substitutions as well as the factors controlling such substitutions. For selected crystals, Be and Li were determined by secondary ion mass spectrometry, which showed that the generally assumed value of 3 Be atoms per formula unit (apfu) is valid; only some samples such as the emerald from Kruta Balka deviate from this value (2.944 Be apfu). An important substitution in emerald (expressed as an exchange vector with the additive component Al2Be3Si6O18) is (Mg,Fe2+)NaAl–1☐–1, leading to a hypothetical end-member NaAl(Mg,Fe2+)[Be3Si6O18] called femag-beryl with Na occupying a vacancy position (☐) in the structural channels of beryl. Based on both our results and data from the literature, emeralds worldwide can be characterized based on the amount of femag-substitution. Other minor substitutions in Li-bearing emerald include the exchange vectors LiNa2Al–1☐–2 and LiNaBe–1☐–1, where the former is unique to the Kruta Balka emeralds. Rarely, some Li can also be situated at a channel site, based on stoichiometric considerations. Both Cr- and V-distribution can be very heterogeneous in individual crystals, as shown in the samples from Kruta Balka, Madagascar, and Zimbabwe. Nevertheless, taking average values available for emerald occurrences, the Cr/(Cr+V) ratio (Cr#) in combination with the Mg/(Mg+Fe) ratio (Mg#) and the amount of femag-substitution allows emerald occurrences to be characterized. The “ultramafic” schist-type emeralds with high Cr# and Mg# come from occur-rences where the Fe-Mg-Cr-V component is controlled by the presence of ultramafic meta-igneous rocks. Emeralds with highly variable Mg# come from “sedimentary” localities, where the Fe-Mg-Cr-V component is controlled by metamorphosed sediments such as black shales and carbonates. A “transitional” group has both metasediments and ultramafic rocks as country rocks. Most “ultramafic” schist type occurrences are characterized by a high amount of femag-component, whereas those from the “sedimentary” and “transitional” groups have low femag contents. Growth conditions derived from the zoning pattern—combined replacement, sector, and oscillatory zoning—in the Kruta Balka emeralds indicate disequilibrium growth from a fluid along with late-stage Na-infiltration. Inclusions in Kruta Balka emeralds (zircon with up to 11 wt% Hf, tourmaline, albite, Sc-bearing apatite) point to a pegmatitic origin.
A method to estimate the pre-eruptive water content of basalts: Application to the Wudalianchi–Erkeshan–Keluo volcanic field, Northeastern China
Authors: Di Yankun , Tian Wei , Chen Mimi , Li Zefeng , Chu Zhuyin , Liang Ju 
Published: October 2019

AbstractWater plays an important role in the generation and evolution of volcanic systems. However, the direct measurement of the pre-eruption water content of subaerial volcanic rocks is difficult, because of the degassing during magma ascent. In this study, we developed a method to calculate the pre-eruption water content of the basalts from the Cenozoic Wudalianchi–Erkeshan–Keluo (WEK) potassic volcanic field, Northeastern China, and investigated their mantle source. A water-insensitive clinopyroxene–melt thermobarometer and a water-sensitive silica activity thermobarometer were applied to these basalts. Two pressure-temperature (P-T) paths of the ascending magma were calculated using these two independent thermobarometers, with a similar P-T slope but clear offset. By adjusting the water content used in the calculation, the difference between the two P-T paths was minimized, and the water content of the WEK melts was estimated to be 4.5 ± 1.2 wt% at a pressure range of 10.1–13.5 kbar, corresponding to depths of 37–47 km. Degassing modeling shows that during the magma ascent from below the Moho to near the surface, CO2 was predominantly degassed, while the melt H2O content kept stable. Significant H2O degassing occurred until the magma ascended to 5–2 kbar. The silica activity P–T estimates of the most primary WEK samples suggest that the magmas were generated by the melting of convective mantle, which was probably facilitated by a wet upwelling plume from the mantle transition zone. The high water content found in the WEK basalts is similar to the recent reports on Phanerozoic intraplate large igneous provinces (LIPs) and supports the presence of hydrated deep mantle reservoirs as one possible source of the LIPs.