bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.
Authors: Souza Valeria , Vazquez-Rosas-Landa Mirna , Ponce-Soto Gabriel Yaxal , Aguirre-Liguori Jonás A. , Thakur Shalabh , Scheinvar Enrique , Barrera-Redondo Josué , Ibarra-Laclette Enrique , Guttman David S. , Eguiarte Luis E. 
Published: October 2019

Abstract
Background In bacteria, pan-genomes are the result of the evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size ( N e ) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.
Characterisation of multiple heavy metal resistance loci in the genome of the novel species Cupriavidus neocaledonicus STM 6070, a nickel- and zinc-tolerant Mimosa pudica microsymbiont isolated from mining site soil
Authors: Klonowska Agnieszka , Moulin Lionel , Ardley Julie , Braun Florence , Gollagher Margaret , Zandberg Jaco Daniel , Marinova Dora , Huntemann Marcel , Reddy T.B.K. , Varghese Neha , Woyke Tanja , Ivanova Natalia , Seshadri Rekha , Kyrpides Nikos , Reeve Wayne 
Published: October 2019

Abstract
Background
Cupriavidus strain STM 6070 was isolated from nickel-rich mine roadside soil near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.
Results
The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6,118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica -nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to five symbiotic and three non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.
Conclusions
STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica -nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences
Authors: McGrath J. Mitchell , Galewski Paul J. 
Published: October 2019

Abstract
Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet). Crop improvement and management activities are segregated by crop type, preserving unique genome diversity and differentiation, with occasional introgressions between diverged lineages for specific traits. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including table, leaf (chard), fodder, and sugar beet. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between populations based on identity-by-state and shared genetic variation among lineages. Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history inferences for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between the table and chard groups, perhaps the result of less intensive selection for their end use.
Clinical significance and therapeutic implication of CD200 in pancreatic cancer
Authors: Kinoshita Shoichi , Sho Masayuki , Akahori Takahiro , Nishiwada Satoshi , Nagai Minako , Migita Kazuhiro , Obara Shinsaku , Ouji-Sageshima Noriko , Ito Toshihiro , Ikeda Naoya 
Published: October 2019

Abstract
Background

CD200, a negative T cell regulator as well as a cancer stem cell marker, is a significant prognostic factor and potential therapeutic target in specific cancers. However, the clinical significance of CD200 is unknown in pancreatic ductal adenocarcinoma (PDAC).

Methods

CD200 was evaluated in 220 resected PDAC patients. Surgery was performed with or without neoadjuvant chemotherapy (NACRT), and adjuvant therapy was administered with systemic therapy or systemic therapy added with hepatic arterial infusion (HAI) therapy. We investigated the clinicopathological outcomes associated with CD200, in relation to the administered multimodal treatment. We further evaluated the impact of the immunological and cancer stem cell properties associated with CD200.

Results

NACRT patients had a lower average age, lower lymph node metastasis, higher negative surgical margins, and higher HAI administration rate, compared to upfront surgery (US) patients. NACRT was associated with better OS, and higher CD200 expression (66.4% vs. 32.2%, P<0.001) compared to US. CD200 was an independent poor prognostic factor in NACRT (hazard ratio 2.51; 95% confidence interval 1.35-4.66; P = 0.004), but not in US patients. In NACRT patients, the hepatic recurrence rate was relatively high in CD200+ cases despite HAI therapy. CD200 was associated with significantly lower CD4+, CD8+, and CD45RO+ tumor-infiltrating lymphocyte levels. Furthermore, the correlation of CD200 with pancreatic cancer stem cell markers CD44/CD24/ESA was stronger in irradiated human pancreatic cancer cells.

Conclusions

Our data highlight novel roles for CD200 in immune evasion as well as therapy resistance in pancreatic cancer.
Prognostic significance of preoperative plasma fibrinogen levels in primary gastrointestinal stromal tumours: a retrospective cohort study
Authors: Song Shibo , Cao Xianglong , Pan Hongda , Hu Maolin , Yan Qiuxia , Song Jinghai , Yang Hua , Zhao Gang , Xiao Gang 
Published: October 2019

Abstract
Background Improved prediction of prognosis for gastrointestinal stromal tumours (GIST) has become increasingly important since the introduction of small molecule tyrosine kinase inhibitors. Here, we aimed to evaluate the prognostic significance of preoperative plasma fibrinogen (Fib) levels in patients with primary GIST and to analyze their correlations with clinicopathological characteristics.Methods A total of 201 previously untreated patients with primary GIST who had underwent radical surgery at our institution between October 2004 and July 2018 were enrolled. Patient demographics, clinicopathological characteristics, preoperative plasma Fib levels and recurrence-free survival (RFS) were analyzed. The optimal cut-off value for Fib levels was calculated using receiver operating characteristic curve analysis. RFS, the primary endpoint, was calculated by the Kaplan–Meier method and compared by the log-rank test. Univariate and multivariate Cox regression models were calculated.Results Patients in high Fib group had a shorter RFS compared with low Fib group (P < 0.001). In multivariate analysis, high preoperative plasma Fib levels were detected as an independent adverse prognostic factor (P = 0.004, hazard ratio 3.443, 95% confidence interval 1.498‒7.916). Furthermore, high preoperative plasma Fib levels also indicated a poor prognosis within the modified National Institutes of Health (mNIH) high-risk subgroup (P = 0.013). In addition, preoperative plasma Fib levels were showed a positive correlation with several prognostic factors, and even linearly with tumour size (Spearman correlation coefficient [ r ] = 0.411, P < 0.001).Conclusions High preoperative plasma Fib levels may indicate a poor prognosis in patients with primary GIST. As a cost-effective biomarker, preoperative assessment of plasma Fib levels may help to further risk stratification for patients with mNIH high-risk GIST and instruct the application of target therapy.
Tririum in urine in residents of Ozyorsk, the Chelyabinsk region in 2016
Authors: Finashov L. V. , Vostrotin V. V. , Yanov A. Yu. 
Published: October 2019

Objectives. To create the model of relation between volume activity of tritium in urine of Ozyorsk residents and physical and biological factors. To define the correspondence of internal exposure doses of Ozyorsk residents obtained from tritium to standards and requirements of present-day radiation security system. In the framework of the objectives the following tasks were solved: measurement of volume activity of tritium in the urine; detection of main factors affecting the volume activity of tritium in the urine; estimation of the distribution of committed effective dose equivalent of internal exposure due to tritium intake in 2016 among Ozyorsk residents under stable radiation environment.Material and methods. 30 samples of urine were taken from resident of Ozyorsk Chelyabinsk region never employed at the Mayak Production Association in 2016. Measurement of tritium volume activity in the urine was performed using up-to-date ultra low level beta spectrometer Quantulus-1220. A questionary was developed that allowed collection of individual data on the water intake regime, on the occupational activity and the living conditions of people under study. Statistical processing was performed using software Excel-2013 and R. In order to develop models of dependency of tritium volume activity in urine of the residents from continuous and/or category variables we used correlation and regression methods of analysis. In order to compare two samples by mean value of tritium volume activity Student t-criterion was used. In order to verify normality of dose distribution Shapiro-Wilk test was used.Results. Volume activity of tritium in urine of adult Ozyorsk residents in 2016 was in average 18.5 ± 1.1 Bq/dm3, volume activity of tritium in urine of children – 12.6 ± 2.3 Bq/dm3 in average. Major statistical characteristics of estimates of committed effective dose equivalent from tritium in Ozyorsk residents due to intake on 2016 under stable radiation environment obtained from a sample of 30 individuals were the following: minimum value made 0.07 µSv, mean value was 0.27 µSv, coefficient of variation made 36%, maximum value made 0.49 µSv. A model of dependence of tritium volume activity in urine of Ozyorsk residents from the water supply source was obtained.Conclusions. Estimates of committed effective dose equivalent of internal exposure from tritium among Ozyorsk residents due to intake in 2016 made: mean value of committed effective dose equivalent was 0.027 and maximum value made 0.05% from the annual effective dose limit for residents under unifactor tritium intake. In 2016, the levels of tritium volume activity in the bodies of adult and children population of Ozyorsk city depended on volume activity of tritium in drinking water supply sourced more than on the age. As of 2016, under stable radiation environment at Mayak Production Association, tritium did not pose any threat for Ozyorsk population.
Effect of Canagliflozin, an SGLT2 Inhibitor, in Comparison with Atorvastatin on Dexamethasone-Induced Hepatic Steatosis in Albino Rats
Authors: Ahmed Eman I. , Shaaban Amany M. , Abdel Latif Abdel Karim M. 
Published: October 2019

Background:
Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease that is considered the most common liver disease all over the world. It causes metabolic and hepatic damage that can progress to cirrhosis and hepatocellular carcinoma.

Objective:
Our research pointed to study the preventive effects of canagliflozin (CANA) or atorvastatin (ATO) on dexamethasone-induced hepatic steatosis and dyslipidemia.

Methods:
Animals were grouped as; control group; DEX group; ATO/DEX-treated group; CANA/DE-treated group and ATO+CANA/DEX-treated group. Results: Significant elevations in GSH, SOD and CAT activities, while high significant decreases in serum GOT, GPT, ALP, urea, blood glucose, CK-MB, LDH, T.G, T.C, MDA and P.C levels were demonstrated in treated groups as compared to DEX group in the experimental periods. Also, significant reductions in SGPT, SGPT, ALP, CK-MB, LDH, T.C and T.G levels were detected in CANA/DEX group as compared to ATO/DEX group. All these results were confirmed with histopathological findings where the severe damages and fatty degeneration in both kidney and liver tissues developed by dexamethasone administration resolved by administration of atorvastatin alone or better with Canagliflozin.

Conclusion:
These results indicate that canagliflozin was as effective as atorvastatin or combination of both in reducing dyslipidemia and hepatic steatosis. The antioxidant and hypolipidemic effects of canagliflozin may be responsible for the beneficial effects.
Molecular Characterization of Fasciola and Dicrocoelium Species Isolated from Ruminant Livestock in Qazvin, Iran
Authors: Shahnazi Mojtaba , Ebadi Maryam , Abbaspoor Zahra , Hajialilo Elham , Javadi Amir , Heydarian Peyman , Saraei Mehrzad , Alizadeh Safar Ali 
Published: October 2019

Introduction:
Fascioliasis and dicrocoeliasis are the most frequent zoonotic diseases
with increasing human health problems in different parts of Iran. Two species, Fasciola hepatica
(F. hepatica) and Fasciola gigantica (F. gigantica), are spread in the country. Molecular approaches
have a decisive role in identifying both the species. The aim of this study was to detect
Fasciola spp. and Dicrocoelium spp. by amplifying the ITS-2 and 28S rDNA gene sequence.

Methods:
Overall, 30 infected liver samples were collected from the livestock of Qazvin, Iran.
The adult flukes were collected from different livestock. DNA extraction and PCR amplification
of ribosomal RNA gene region (ITS2) and 28S rDNA gene fragment were conducted and a
phylogenetic tree was constructed.

Results:
All the isolates obtained from the cattle (No: 7) and 82.6% (No: 19) of sheep isolates were
infected with F. hepatica species, whereas 17.4% (No: 4) of sheep isolates were infected with F.
gigantica. It was also shown that F. hepatica was the predominant species of Fasciola present in
the region. All the specimens were infected with Dicrocoelium dendriticum (D. dendriticum).

Conclusion:
Both the species of Fasciola were found in Qazvin. D. dendriticum was the sole infecting
species of the Dicrocoelium genus in the livestock of the city of Qazvin. Further research
studies are needed to determine the intermediate host of the parasites in the region.
The Knowledge and Attitude of Integrated Pest Management Farmers Field Schools Alumni toward the Use of Pesticides in Klaten, Central Java, Indonesia
Authors: Kusumawardani Andriarti , Martono Edhi , Trisyono Y. Andi , Putra Nugroho Susetya 
Published: October 2019

The field schools in Indonesia employ an extension alternative model that is considered appropriate to change the habits and behavior of farmers to make them IPM experts in their field. This study was conducted to understand the behavior (knowledge and attitude) of farmers who have joined field schools, i.e. Integrated Pest Management Farmers Field School (IPM-FFS) and Landscape Integrated Pest Management (Landscape IPM), toward the use of pesticides in Klaten, Central Java, Indonesia. The research used a survey method with purposively selected respondents comprising 55 farmers of the IPM alumni and 25 farmers of the Landscape IPM alumni. A descriptive analysis was conducted to analyze the farmers’ knowledge and attitude toward the use of pesticides. Mann-Whitney U-test analysis was performed using Statistical Product and Service Solution (SPSS) version 23, to compare the knowledge and attitude of farmers regarding the use of pesticides. The results showed that the knowledge of farmers of the Landscape IPM alumni regarding the use of pesticides was higher than that of farmers of the IPM-FFS alumni. There was no difference in the behavior of farmers between the IPM-FFS alumni and the Landscape IPM alumni regarding their attitude toward the use of pesticides.
Improving the Beam-Balanced Pumping Unit
Authors: Volokhin E. A. , Terent’ev A. N. , Volokhin A. V. 
Published: October 2019

Описана усовершенствованная телескопическая конструкция головки с балансиром, электродвигателем c дистанционным управлением, возможностью менять длину плеча балансира для подготовки привода штанговой скважинной насосной установки (ШСНУ) к проведению оперативного ремонта скважин с минимальным участием человека. Усовершенствование узла станка-качалки направлено на повышение автоматизации работы, уменьшение затрат времени и трудоемкости, повышение безопасности при подготовке привода станка-качалки к подземному ремонту скважины.Представлена методика расчета на прочность подвижной и неподвижной частей телескопической конструкции головки с балансиром: определено максимальное напряжение от изгиба, коэффициент запаса при хрупком разрушении и пластической деформации, коэффициент запаса прочности на циклические нагрузки. Полученные результаты расчета соответствуют минимально допустимым коэффициентам для надежного использования станка-качалки.Приведена методика подбора электродвигателя для передвижения продольно-подвижной части плеча балансира, в которой определены необходимые параметры: частота вращения вала колеса, статическая мощность, мощность двигателя с учетом динамики разгона. Показано техническое решение лестницы с предохранительно-автоматическим отключением электродвигателя станка-качалки при несанкционированном поднятии по ней постороннего человека.
Study of the Effectiveness of Signal-Code Options Designs for Tuning a Cognitive Radio System
Authors: Sharipov T. A. , Shishakov K. V. 
Published: October 2019

Рассматриваются результаты моделирования эффективности сигнально-кодовых конструкций (СКК) для настройки когнитивной радиосистемы. При этом СКК формируются разными комбинациями цифровых модуляторов и помехоустойчивых кодеров. Среди модуляторов для исследования выбраны PAM, ASK, PSK, QAM, FSK, MSK с разной степенью многопозиционности. Среди помехоустойчивых кодов выбраны коды БЧХ, Рида – Соломона, Голея, сверточные, Хэмминга. Исследование СКК проведено на стенде National Instruments на основе технологии SDR с использованием готовых подпрограмм для модуляторов и помехоустойчивых кодеров, реализованных в среде LabView. Приведены результаты моделирования влияния шума в канале связи на эффективность работы разных цифровых модемов, характеризуемых различными скоростями передачи информации. Исследована задача, как с помощью введения помехоустойчивых кодеров повысить стойкость СКК к шуму с одновременным сохранением повышенных скоростей передачи информации. Показано, как результаты проведенных исследований могут быть использованы для создания когнитивной радиосистемы. Описан алгоритм адаптивной настройки СКК когнитивной радиосистемы на изменяющийся уровень шума в канале радиосвязи. Процесс его работы продемонстрирован на примере группы СКК, состоящей из разных комбинаций модуляторов QAM с повышающейся многопозиционностью и помехоустойчивых кодеров Рида – Соломона разной силы. Показано, что выполненное моделирование эффективности СКК для настройки когнитивной радиосистемы является первым шагом практического создания конкретной когнитивной радиосистемы, выполненной на основе технологии SDR.