bluuebunny/crossref_metadata_2025 huggingface dataset:
Overview of the Special Issue on the Development of Disaster Statistics Part 2
Authors: Sasaki Daisuke ,   International Research Institute of Disaster Science (IRIDeS), Tohoku University 468-1-S302 Aoba, Aramaki, Aoba, Sendai, Miyagi 980-0845, Japan, Ono Yuichi
Published: October 2019

A year has passed since the first special issue on the development of disaster statistics was published in the Journal of Disaster Research. The attempt to improve and utilize disaster statistics throughout the world is still in progress, although it is steadily moving forward. Under such circumstances, the Global Centre for Disaster Statistics (GCDS) at Tohoku University has also made advances in this area. The Centre participates in the Sendai Framework Voluntary Commitments (SFVC) launched by the United Nations Office for Disaster Risk Reduction (UNDRR). This second special issue on the development of disaster statistics aims to publish the research results from the latest studies related to this topic. For the SFVC, the GCDS has committed to publishing this special issue of the Journal of Disaster Research towards the development of disaster statistics as for academic contributions. In addition, the publication of the special issue itself has a positive impact on the acceleration of research activity at the GCDS. In this issue, there seems to be two main categories of research questions; namely “development of the existing disciplined-based research,” and “analyzing various issues by means of questionnaire surveys.” Under the umbrella of the development of the existing disciplined-based research by means of disaster statistics, two disciplines are covered: river engineering, and international studies. The large number of studies based on questionnaire surveys acts as an excellent reminder of the effectiveness of a questionnaire survey when adopted as a methodology of disaster statistics. The guest editors hope that this second special issue on the development of disaster statistics would also contribute to the literature of disaster statistics and accelerate their development.
Exploratory Analysis of the Relationship Between Livelihood Disruptions and Displacement Intentions Following a Volcanic Eruption: A Case from the 2014 Mt. Kelud Eruption
Authors: Jibiki Yasuhito , Pelupessy Dicky , Iuchi Kanako ,   Next Generation Volcano Researcher Development Program, Tohoku University 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan,   Faculty of Psychology, Universitas Indonesia, Jawa Barat, Indonesia,   International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
Published: October 2019

The current study explores the possible relationship between livelihood disruptions and displacement intentions in the short and long term, following a volcanic eruption. Previous studies in a similar context suggest that livestock breeding and farming remain important to the affected population in terms of livelihood maintenance, even when eruptions severely interrupt these activities. Other research findings suggest people consider eruptions opportunities to improve income through increased crop cultivations. Previous studies have concluded that people prefer to return to agricultural and farming activities, even if eruptions significantly disturb them. Little research, however, quantitatively addresses the impact of eruptions on income or explores the relationship between livelihood disruption and relocation intention. To understand this relationship, we conducted a questionnaire survey of villagers in the Kediri and Blitar districts of Indonesia who received an evacuation order during the 2014 Mt. Kelud eruption. We collected and analyzed the data from 440 valid responses. One of our major findings supports earlier research findings vis-à-vis the association between agricultural losses and villagers’ decisions to relocate in the long term. Our data suggest that villagers with no relocation intention had experienced larger agricultural losses, thus suggesting that agricultural losses do not constitute a large factor affecting relocation intention. Likewise, we found there to be no statistically significant relationship between livestock damages/losses and displacement intentions. These findings suggest the importance of further research into causal relationships among economic loss, farming damages and losses, and displacement intentions.
PENGEMBANGAN MODUL MATAKULIAH STATISTIKA YANG TERINTEGRASI DENGAN MICROSOFT EXCEL DAN SPSS MENGGUNAKAN PENDEKATAN KECERDASAN LINGUISTIK
Authors: Febrinita Filda , Puspitasari Wahyu Dwi , Kirom Sabitul
Published: October 2019

Modul merupakan salah satu bahan ajar yang dapat digunakan untuk membantu mencapai tujuan pembelajaran. Berdasarkan hasil observasi dan wawancara dengan dosen pengajar statistika dan mahasiswa prodi teknik informatika, dosen masih menggunakan bahan ajar berupa buku teks. Penyajian materi pada buku teks terkadang masih sulit dipahami mahasiswa. Namun, untuk mendapatkan buku teks yang lebih bagus pun, membutuhkan biaya yang relatif mahal. Oleh karena itu, perlu adanya bahan ajar yang memaparkan materi dengan jelas dan mudah dimengerti sehingga memudahkan mahasiswa dalam mempelajari statistika. Berdasarkan hal tersebut, dilakukanlah penelitian pengembangan yang bertujuan untuk menghasilkan modul matakuliah statistika yang terintegrasi dengan Excel dan SPSS menggunakan pendekatan kecerdasan linguistik, yang memenuhi kriteria valid, praktis dan efektif. Prosedur pengembangan produk mengikuti model pengembangan 4-D dari Thiagarajan tetapi pada penelitian ini tahapan yang digunakan adalah pendefinisian (define), perancangan (design), dan pengembangan (develop). Hasil penelitian menunjukkan nilai dari validasi ahli adalah 2,4 sehingga modul memenuhi kriteria valid. Hasil observasi keterlaksanaan modul adalah 2,54 sehingga modul memenuhi kriteria praktis. Sedangkan untuk nilai tes akhir, 78% mahasiswa memperoleh nilai 75 ke atas. Selain itu, 61,6% mahasiswa menyatakan setuju dan 34,9% mahasiswa menyatakan sangat setuju terhadap penggunaan modul dalam pembelajaran. Tercapainya ketuntasan belajar dan adanya respon positif tersebut menunjukkan bahwa modul memenuhi kriteria afektif.  Berdasarkan hasil penelitian secara keseluruhan, dapat disimpulkan bahwa modul yang dikembangkan telah memenuhi kriteria valid, praktis dan efektif.
Gene EBNA3C: Type of Infection by EBV (EBV1 and EBV2) Correlation With Clinical and Biochemical Parameters (AST, ALT and GGT) in Individuals With Infectious Mononucleosis in the Metropolitan Area of Belém, Pará, 2005-2016
Authors: Monteiro Talita Antonia Furtado , Costa Iran Barros , Costa Igor Brasil , Corrêa Thais Letícia dos Santos , Coelho Beatriz Monteiro Rodrigues , Polaro Alessandra Alves , Silva Amanda Emanuelle Santos da , Ramos Francisco Lúzio de Paula , Filho Arnaldo Jorge Martins , Monteiro Jose Luiz Furtado , Sousa Rita Catarina Medeiros
Published: October 2019

Background: Two types of Epstein Barr virus (EBV1 and 2) have been shown to infect humans. This study aimed to detect the types of EBV that cause infectious mononucleosis and correlate these viral types with clinical parameters in the metropolitan region of Belém from 2005 to 2016.Methods: A total of 76 cases of infectious mononucleosis (IM) were processed at the Instituto Evandro Chagas, Ananindeua, Brazil. PCR was used to analyze the EBNA 3C region for the recognition of EBV types. Biochemical testing (aspartate aminotransferase (AST), alanine aminotransferase (ALT) and gamma-glutamyl transferase (GGT) was performed by the COBAS INTEGRA clinical biochemistry PLUS 400 / ROCHE automatic analyzer. The data were evaluated using the Statistical Package for Social Science - SPSS 17.0 and GraphPadPrism 7.0 for Windows.Results: EBV1 infection was observed in 71.1% (54/76) of individuals, among whom those > 14 years constituted 66.7% (36/54); the average age was 23 years, and the number of women infected was higher (61.1% [33/54]) than that of men 38.9%[21/54]). The symptoms/clinical signs observed in infection by EBV1 were cervical lymphadenopathy in 64.8% (35/54), fever in 63% (34/54), headache and arthralgia in 20.3% (11/54), and exanthema in 18.5% (10/54). Infection by EBV2 was observed in only 17.1% (13/76) of cases. Coinfections by EBV1 and EBV2, most frequently showing symptoms of fever and cervical lymphadenopathy, occurred in 66.7% (6/9) and 55.6% (5/9) of individuals. Alterations to AST were confirmed in 14.8% (8/54), EBV2 of cases in 7.7% (1/13) in EBV1 infection. Conclusions: EBV1 was predominant in 71% of clinical cases of infectious mononucleosis. The correlation of biochemical parameters in infection by EBV1, EBV2, and coinfections by EBV1/2 revealed a statistically significant difference in mean changes of EBV1 in individuals older than 14 years.
Clinical approaches to cultural diversity in mental health care and specificities of French transcultural consultations: A narrative review.
Authors: CARRERA LAURA CARBALLEIRA , Lévesque-Daniel Sarah , Radjack Rahmeth , Moro Marie Rose , Lachal Jonathan
Published: October 2019

Background: Cultural context substantially affects the experience and clinical expression of psychiatric diseases, while cultural factors limit both access to and effectiveness of care, especially for migrant families requiring specific types of services. In France, Transcultural Psychotherapy is an original method conceived for therapy for immigrant families facing issues that cannot be solved in standard psychotherapy. We reviewed the international literature on child and adult mental health services to compare the different models of care and uncover the specificities of the French model.
Methods: Systematic electronic search of databases (PubMed and PsycINFO), manual search of archives of journals dealing with transcultural psychiatry, and consultations with international experts, to identify all papers describing clinical models devoted to mental health care for migrants, published between January 1990 and October 2018. Narrative synthesis of the included articles.
Results: The study included 28 papers. The specificities of mental health services for migrant families are linked to the host country's migration patterns and citizenship model. In English-speaking countries, specialized services for ethnic minorities offer ethnic matching of the therapist and patient. In Canada, indirect transcultural consultation services have existed since the late 1990s. Australia emphasizes the networking of consultation services and professional training in cultural competence, while the Nordic countries (Sweden, Finland, Norway, and Denmark) focus management on trauma. In France, psychotherapy services, with flexible numbers of therapists involved according to the situation, have existed since 1990.
Discussion: Most initiatives place emphasis on training and supervision, in an indirect approach not specifically focused on the patient, or offer cultural matching of patient and therapist. The French transcultural approach, on the contrary, makes the family's culture and its cultural diversity an integral part of the therapy process. Although this approach appears clinically effective, constraints linked to the size of the therapist group limit its generalization to all situations and impose the need for alternative forms of care.
DTIRF: Predicting Drug-Target Interactions Based on Improved Rotation Forest from Drug Molecular Structure and Protein Sequence
Authors: wang lei , You Zhu-Hong , Li Li-Ping , Yan Xin , Zhang Wei , Wang Hai-Feng
Published: October 2019

Background: The identification and prediction of Drug-Target Interaction (DTI) is the basis for screening drug candidates, which plays a vital role in the development of innovative drugs. However, due to the time-consuming and high cost constraints of biological experimental methods, traditional drug target identification technologies are often difficult to develop on a large scale. Therefore, in silico methods are urgently needed to predict drug-target interactions in a genome-wide manner.

Results: In this article, we design a new in silico approach, named DTIRF, to predict the DTI combine feature weighted Rotation Forest (FwRF) classifier with protein amino acids information. More specifically, we first use Position-Specific Score Matrix (PSSM) to numerically convert protein sequences and utilize Pseudo Position-Specific Score Matrix (PsePSSM) to extract their features. Then a unified digital descriptor is formed by combining molecular fingerprints representing drug information. Finally, the feature weighted rotation forest is applied to implement on Enzyme, Ion Channel, GPCR, and Nuclear Receptor data sets. The results of the five-fold cross-validation experiment show that the prediction accuracy of this approach reaches 91.68%, 88.11%, 84.72% and 78.33% on four benchmark data sets, respectively. To further validate the performance of the DTIRF, we compare it with other excellent methods and Support Vector Machine (SVM) model. In addition, 7 of the 10 highest predictive scores in predicting novel DTIs were validated by relevant databases.

Conclusions: The experimental results of cross-validation indicated that DTIRF is feasible in predicting the relationship among drugs and target, and can provide help for the discovery of new candidate drugs.
Seed-Biopriming of Durum Wheat with Diazotrophic Plant Browth Promoting Bacteria (PGPB) Enhanced Tolerance to Fusarium Head Blight (FHB) and Salinity Stress
Authors: Brahim Adel Hadj , Jlidi Mouna , Daoud Lobna , Ben-Ali Manel , Akremi Asmahen , Hmani Houda , Feto Naser Aliye , Ben-Ali Mamdouh
Published: October 2019

Background The use of bioinoculants based on plant growth-promoting bacteria (PGPB) to promote plant growth under biotic and abiotic stresses is in full expansion. To our knowledge much work has not been, thus far, done on seed-biopriming of durum wheat for tolerance to biotic and abiotic stresses. In the present work, we report detailed account of the effectiveness a potent bacterial strain with proven plant growth-promoting ability and antimicrobial activity. The isolate was selected following screening of several bacterial strains isolated from halophytes that grow in a coastal saline soil in Tunisia for their role in enhancing durum wheat tolerance to both salinity stress and head blight disease.Results Accordingly, Bacillus strains MA9, MA14, MA17 and MA19 were found to have PGPB characteristics as they produced indole-3-acetic acid, siderophores and lytic enzymes, fixed free atmospheric nitrogen, and solubilized inorganic phosphate, in vitro . The in vivo study that involved in planta inoculation assays under control (25 mM NaCl) and stress (125 mM NaCl) conditions indicated that all PGPB strains significantly ( P < 0.05) increased the total plant length, dry weight, root area, seed weight, nitrogen, protein and total mineral content. On the other hand, strain MA17 reduced Fusarium Head Blight (FHB) disease incidence in wheat explants by 64.5%, showing that the strain has antifungal activity as was also displayed by in vitro inhibition study.Conclusions Both in vitro and in vivo studies showed that MA9, MA14 MA9, MA14, MA17 and MA19 strains were able to play the PGPB role. Yet, biopriming with Bacillus strain MA17 offered the highest bioprotection against FHB, plant growth promotion, and salinity tolerance. Hence, the MA17 strain should further be evaluated under field condition and formulated for commercial production. Besides, the strain could further be evaluated for its potential role in bioprotection and growth promotion of other crop plants. We believe, the strain has potential to significantly contribute to wheat production in the arid and semi-arid region, especially the salt affected Middle Eastern Region, besides its potential role in improving wheat production under biotic and abiotic stresses in other parts of the world.
Peer support programs for people experiencing suicidality – A systematic scoping review of current literature
Authors: SCHLICHTHORST MARISA , Ozols Ingrid , Reifels Lennart , Morgan Amy
Published: October 2019

Background Peer-led support models have gained increasing popularity in mental healthcare. Yet little is known about the types of peer support programs that exist in suicide prevention and whether these are effective in improving the health and wellbeing of people at risk of suicide.Method We conducted a systematic scoping review, involving a search of three academic (Medline, PsycINFO, Embase), and selected grey literature databases (Google Scholar, WHO Clinical Trials Registry) for publications between 2000 and 2019. We also contacted suicide prevention experts and relevant internet sites to identify peer support programs that exist but have not been evaluated. The screening of records followed a systematic two-stage process in alignment with PRISMA guidelines.Results We identified 8 records accounting for 7 programs focused on peer-led support programs in suicide prevention. These programs employed a range of different designs and included a variety of settings (schools, communities, rural and online). Only 4 of these 7 programs contained data on the effectiveness of the program, and this evaluation data was descriptive on all accounts but showed promising results. With the small number of eligible programs in this review our findings are limited and must be interpreted with caution.Conclusions Despite the increased focus of policymakers on the importance of peer support programs in suicide prevention, our scoping review confirms an evidence gap in research knowledge regarding design, implementation, and effectiveness of programs. More rigour is required in reporting peer support initiatives to clarify the underlying definition of peer support and to enhance our understanding of the types of current peer support programs available to those experiencing suicidality. Further, we need formal and high-quality evaluations of peer support suicide prevention programs to better understand their effectiveness on participant health across different settings and delivery modalities and to allow for comprehensive systematic reviews and meta-analysis in future.
Endoscopic transforaminal lumbar discectomy in the treatment of multilevel disc herniations
Authors: Yan Denglu , Zhang Zaiheng , Zhang Zhi
Published: October 2019

Background There were no studies in literature of multiple level lumbar disc herniation treatment by endoscopic procedures. The purpose of this study was to evaluate the efficacy of endoscopic treatment multiple level lumbar disc herniation by compare to the one level disc herniation. Methods A total of 267 patients of lumbar disc herniation who had endoscopic surgery were categorized into three different groups depending on the level number of endoscopic procedures. 78 cases had one level procedure (OL group), 54 cases had couple level procedures (CL group), and 35 cases had triple level procedures (TL group). Endoscopic discectomy procedures was performed and the clinical outcomes were recorded. Results There was no intraoperative death in this series. The hospital day were no significant difference among three groups. The operational time and blood loss were biggest in triple levels procedures and lest in one level procedure. When take into the influence the numbers of disc herniation, there were no significant difference per level among three groups. The pain index and ODI score were better than preoperational in all patients, and there were no significant difference among three groups. The disk and foramen height, and lumbar lordosis were no significant difference compare to preoperative in all patients, and there were no significant difference among three groups. All patients achieved pain free accomplished all surgery procedures, no infection, and no dural tear of cerebrospinal fluid leakage complication. Conclusions Endoscopic lumbar discectomy was effective and safe procedures in the treatment of multilevel lumbar disc herniation.
Modeling In-patients with Chronic Non-Communicable Diseases Using Parametric Shared Frailty Models
Authors: Hunde Belachew Melese
Published: October 2019

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

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

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

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

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

We 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

Water 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.
Constraints on non-isothermal diffusion modeling: An experimental analysis and error assessment using halogen diffusion in melts
Authors: Rout Smruti Sourav , Schmidt Burkhard C. , Wörner Gerhard
Published: October 2019

Diffusion chronometry on zoned crystals allows constraining duration of magmatic evolution and storage of crystals once temperatures are precisely known. However, non-isothermal diffusion is common in natural samples, and thus timescales may not be determined with confidence while assuming isothermal conditions. The “non-isothermal diffusion incremental step (NIDIS) model” (Petrone et al. 2016) is proposed for such cases for a non-isothermal diffusive analysis. We conducted diffusion experiments with stepwise temperature changes to analyze and test the model, evaluated the associated errors and improved the accuracy by suggesting an alternative algorithm to model diffusion times.

We used Cl and F (≤0.4 wt%) as the diffusing elements in nominally anhydrous (H2O ≤ 0.3 wt%) phonolitic melt with composition of Montana Blanca (Tenerife, Spain) in an experimental setup that successively generates multiple diffusive interfaces for different temperatures by adding glass blocks of different Cl and F concentrations. This compound set of two diffusion interfaces represents distinct compositional zones that diffusively interact at different temperatures, which can be taken as an equivalent to non-isothermal diffusion in zoned magmatic crystals. The starting temperature ranged from 975 to 1150 °C, and each set of experiments included a temperature change of 85–150 °C and a total duration of 8–12 h. The experiments were carried out in an internally heated pressure vessel equipped with a rapid quench device at 1 kbar pressure. Cl and F concentration profiles were obtained from the quenched samples by electron microprobe analysis. Although the estimated diffusion times from the NIDIS-model matched well with true experimental values, the errors on estimated timescales, due to errors in curve-fitting and uncertainty in temperature, were ±10–62% (1σ). The errors are much larger at 61–288% (1σ) when the uncertainty in diffusivity parameters is included. We discuss the efficiency and limitations of the model, assess the contribution from different sources of error, and their extent of propagation. A simpler alternative algorithm is proposed that reduces errors on the estimates of diffusion time to 10–32% (1σ) and 60–75% (1σ), with and without including uncertainty in diffusivity parameters, respectively. Using this new algorithm, we recalculated the individual diffusion times for the clinopyroxene crystals analyzed by Petrone et al. (2016) and obtained a significantly reduced error of 26–40% compared to the original error of 61–100%. We also analyzed a sanidine megacryst from Taapaca volcano (N. Chile) as a test case for non-isothermal modeling and obtained diffusion times of 1.5–9.4 ky, which is significantly different from isothermal analyses including a previous study on similar sample. In this analysis, the error estimated by our new method is reduced by 63–70%.
Incorporation of Mg in phase Egg, AlSiO3OH: Toward a new polymorph of phase H, MgSiH2O4, a carrier of water in the deep mantle
Authors: Bindi Luca , Bendeliani Aleksandra , Bobrov Andrey , Matrosova Ekaterina , Irifune Tetsuo
Published: October 2019

The crystal structure and chemical composition of a crystal of Mg-bearing phase Egg with a general formula M1−x3+Mx2+SiO4H1+x (M3+ = Al, Cr; M2+ = Mg, Fe), where x = 0.35, produced by subsolidus reaction at 24 GPa and 1400 °C of components of subducted oceanic slabs (peridotite, basalt, and sediment), was analyzed by electron microprobe and single-crystal X-ray diffraction. Neglecting the enlarged unit cell and the consequent expansion of the coordination polyhedra (as expected for Mg substitution for Al), the compound was found to be topologically identical to phase Egg, AlSiO3OH, space group P21/n, with lattice parameters a = 7.2681(8), b = 4.3723(5), c = 7.1229(7) Å, β = 99.123(8)°, V = 223.49(4) Å3, and Z = 4. Bond-valence considerations lead to hypothesize the presence of hydroxyl groups only, thereby excluding the presence of the molecular water that would be present in the hypothetical end-member MgSiO3·H2O. We thus demonstrate that phase Egg, considered as one of the main players in the water cycle of the mantle, can incorporate large amounts of Mg in its structure and that there exists a solid solution with a new hypothetical MgSiH2O4 end-member, according to the substitution Al3+ ↔ Mg2+ + H+. The new hypothetical MgSiH2O4 end-member would be a polymorph of phase H, a leading candidate for delivering significant water into the deepest part of the lower mantle.