bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Bismuth-Tin Alloy for Well Plug and Abandonment
Authors: Zhang Hua , Ramakrishnan T. S. , Elias Quincy K. , Perez Albert 
Published: November 2019

SummaryAs an alternative to cement, bismuth-tin alloy (BiSn) containing 58-wt% bismuth (Bi) and 42-wt% tin (Sn) has been proposed for plug and abandonment of offshore wells. Alloy seals are advantageous over cement because they can be significantly shorter, reducing well-abandonment cost. Besides being able to deliver alloy pellets and melt them in situ, adhesion with common lithologies found in hydrocarbon reservoirs is also necessary. In addition, within the likely extremes of stress variability, the bond should be sufficiently strong to withstand the differential pressure across the plug. In this paper, we present a series of tests conducted in our laboratory for evaluating the alloy/rock bond. To overcome the intrinsic lack of chemical affinity and the resulting nonwetting nature of the alloy, we propose capillary intrusion into the porous-network of the rock. Above the capillary entry pressure, penetration distance by intrusion is controlled by available alloy volume. As a function of intrusion, we measure the quality of the bond through shear and tensile tests. Results for rocks, cement, and cement/limestone cores are also reported for comparison. Isolation quality is evaluated through permeability tests, performed both parallel and perpendicular to the macroscopic bond interface. For shale, we propose a surface treatment before plug placement that also prevents plug displacement under differential pressures. Strength is best achieved by straddling permeable media and shale. For deployments within tubing or casing, similar bond-strength evaluations can be conducted.
Impact of an antimicrobial stewardship program in the antimicrobial-resistant and prevalence of clostridium difficile infection and amount of antimicrobial consumed in cancer patients
Authors: Mardani Masoud , Abolghasemi Sara , Shabani Shiva 
Published: November 2019

Abstract
Objective: The objective of this study was to determine the impact of a hospital antimicrobial stewardship on antimicrobial resistant, clostridium difficile rates and amount of antimicrobial consumed in cancer patients. The intervention effects of ASP plans in 2017–2018 and 2018–2019 were respectively evaluated among hematology/oncology and bone morrow transplant patients in Ayatollah Taleghani University Hospital, Tehran, Iran. In this interventional quasi-experimental study, the ASP repository was utilized to capture four survey questions encompassed in these immunocompromised patients: amount of antibiotics (MPM and VMN) consumption gr-year, number of positive clostridium difficile infection and multidrug resistant positive cases in blood cultures. Results: The number of MDR cases in the time periods of 2017–2018 and 2018–2019 were 145 and 75, respectively (p = 0.011). A significant reduction in positive blood cultures from 2017–2018 to 2018–2019 was found (p = 0.001).The amount of MPM prescriptions in 2018–2019 was significantly decreased from 22464 to 17262 g (p = 0.043). The significant reduction in antibiotic consumption, MDR organisms and CDI can highly promote patients’ health and decreasing medical costs and long-term defects for patients. Finally, future stewardship studies should made efforts for joining clinical and epidemiological studies.
Cell-division pattern and phylogenetic position of a new ciliate genus Parasincirra n. g. (Protista, Ciliophora, Hypotrichia), with report of a new soil species, P. sinica n. sp. found from northwest China
Authors: Ma Jiyang , Zhao Yan , Zhang Tengyue , Shao Chen , Al-Rasheid Khaled A.S. , Song Weibo 
Published: November 2019

Abstract
Background Ciliated species, unicellular eukaryotes, are extremely diverse and occupy a very broad spectrum of ecological niches. Even though there is a growing recognition that enormous ciliates associates with key ecosystem processes in different niches, their diversity is not well understood. One reason is that ciliates are very tiny and may often be overlooked in routine biodiversity survey. Furthermore, the morphological and genetic diversity of ciliates per se is vast and dwarfs that among other multicellular eukaryotes. A new stichotrichid ciliate, Parasincirra sinica n. g., n. sp. is based on classical living morphology, infraciliature, ontogenesis analyses and a comprehensive phylogenetic studies, and enhance understanding of ciliates diversity in sludge soil.Results This new, monotypic genus is defined by having a bipartite adoral zone of membranelles, three frontal cirri, an amphisiellid median cirral row about as long as, or slightly longer than, the adoral zone, one short frontoventral cirral row, cirrus III/2 and transverse cirri present, buccal cirrus and caudal cirri absent, one right and one left marginal row and three dorsal kineties. The morphogenetic features are: (1) five frontoventral-transverse cirral anlagen (excluding undulating membranes anlage) are formed in primary mode; (2) the amphisiellid median cirral row is formed by anlagen V and VI, while the frontoventral row is generated from anlage IV; (3) cirral streaks IV to VI generate one transverse cirrus each; (4) frontoventral-transverse cirral anlage II generates one or two cirri, while the posterior one will be absorbed in late stages, that is, no buccal cirrus is formed; (5) the posterior part of the parental adoral zone of membranelles is renewed; (6) dorsal morphogenesis follows a typical Gonostomum -pattern; and (7) the macronuclear nodules fuse to form a single mass. Based on the SSU rDNA information, analyses of the phylogenetic relationship inferred from Bayesian inference and maximum likelihood analyses were unable to outline the exact position of this new form among some other species of related genera which are generally assigned in the family Amphisiellida. The morphological/ morphogenetical differences between the new genus/species and other amphisiellids, clearly support the validity of the establishment of this new genus Parasincirra .
Leishmania infection induces a limited differential gene expression in the sand fly midgut
Authors: Coutinho-Abreu Iliano V. , Serafim Tiago D. , Meneses Claudio , Kamhawi Shaden , Oliveira Fabiano , Valenzuela Jesus G. 
Published: November 2019

Abstract
Background: Phlebotomine sand flies are the vectors of Leishmania worldwide. To develop in the sand fly midgut, Leishmania multiplies and undergoes multiple stage differentiations leading to the infective form, the metacyclic promastigotes. To gain a better understanding of the influence of Leishmania infection in midgut gene expression, we performed RNA-Seq comparing uninfected Lutzomyia longipalpis midguts and Leishmania infantum-infected Lutzomyia longipalpis midguts at seven time points which cover the various developmental Leishmania stages including early time points when blood digestion is taking place and late time points when the parasites are undergoing metacyclogenesis. Results: Out of over 13,841 transcripts assembled de novo, only 113 sand fly transcripts, about 1%, were differentially expressed. Further, we observed a low overlap of differentially expressed sand fly transcripts across different time points suggesting a specific influence of each Leishmania stage on midgut gene expression. Two main patterns of sand fly gene expression modulation were noticed. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> -32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 4 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by small fold changes (< 32 fold), and the molecular function of such genes are associated with the metabolism of lipids and detoxification of xenobiotics (P450). Conclusion: Overall, it appears that Leishmania modulates sand fly gene expression early on in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points, when modest midgut gene expression changes correlate with a massive amount of parasites in the anterior midgut.
Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: Potential HIF and NF-κB crosstalk in immune responses in clam
Authors: Nie Hongtao , Wang Huamin , Jiang Kunyin , Yan Xiwu 
Published: November 2019

Abstract
Background: Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophication and resulting hypoxia. As a filter-feeding organism living in the seafloor sediment, Ruditapes philippinarum represents an excellent "sentinel" species to assess the quality of marine environment. In order to gain insight into the molecular response and acclimatization mechanisms to hypoxia stress in marine invertebrates, we examined hypoxia-induced changes in immune-related gene expression and gene pathways involved in hypoxia regulation of R. philippinarum. Results: We investigated the response of the Manila clam R. philippinarum to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and time course qPCR analysis. A total of 75 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, and cell proliferation/apoptosis. Fourteen hypoxia responsive genes were validated significantly up/down regulated at different time 0, 2, 5, and 8 d in gills of R. philippinarum in hypoxia challenged group. Functional enrichment analysis revealed the HIF signaling pathway and NF-κB signaling pathway play pivotal roles in hypoxia tolerance and resistance in R. philippinarum. Conclusion: The HIF signaling pathway and NF-κB signaling pathway play a critical role in hypoxia tolerance and resistance in Manila clam. The immune and defense related genes and pathways obtained here gain a fundamental understanding of the hypoxia stress in marine bivalves and provide important insights into the physiological acclimation, immune response and defense activity under hypoxia challenge. The reduced metabolism is a consequence of counterbalancing investments in immune defense against other physiological processes.
Arg72Pro polymorphism in P53 gene and Breast Cancer Risk Population: a meta-analysis of case-control studies matched
Authors: Diakite Brehima , Kassogue Yaya , Dolo Guimogo , Wang Jun , Neuschler Erin , Kassogue Oumar , Keita Mamadou , Traore Cheick Bougari , Kamate Bakarou , Coulibaly Etienne , Sellama Nadifi , Murphy Robert , Doumbia Seydou , Hou Lifang , Maiga Mamoudou 
Published: November 2019

Abstract
Background The effect of the Arg72Pro variant of the P53 gene on the risk of developing breast cancer remains variable in populations. However, using strategies like grouping age-matched controls with disease cases may provide a strong meta-analysis. Our goal was to perform a meta-analysis in order to study the association of Arg72Pro variant of P53 gene and breast cancer.Methods Databases such as PubMed, Genetics Medical Literature, Harvard University Library, Web of Science and Genesis Library were used to search articles. Age-matched control studies on breast cancer that evaluated the genotype frequencies of the Arg72Pro P53 gene were selected. Fixed and random effects (Mantel-Haenszel) were calculated using pooled odds ratio of 95% CI to determine the disease risk. Hardy-Weinberg equilibrium test was used to measure deviation in the distribution of genotypes in controls. Inconsistency was calculated to determine heterogeneity among the studies. Estimated publication bias was performed through the funnel plot and Egger’s test.Results Nine publications with controls age-matched cases including 4684 disease cases and 4636 controls were evaluated in this meta-analysis, all were in the Caucasian population. Our results suggested that Arg72Pro P53 was associated with a risk for breast cancer in the dominant model (Pro/Pro+Arg/Pro vs. Arg/Arg: OR= 1.16, 95% CI = 1.04-1.31) and the additive model (Pro vs. Arg: OR= 1.13, 95% CI = 1.03-1.24, P= 0.007), but not in the recessive model (Pro/Pro vs. Arg/Arg + Arg/Pro, OR = 1.18, 95% CI = 0.96-1.44; P= 0.12).Conclusions This meta-analysis found significant association between the Arg72Pro polymorphism in the P53 gene and the breast cancer risk. Individuals carrying at least one Pro allele of the P53 gene are more likely to have breast cancer with dominant and additive models than individuals carrying the Arg allele.
Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum
Authors: Sakamoto Takuma , Nishiko Maaya , Bono Hidemasa , Nakazato Takeru , Yoshimura Jin , Tabunoki Hiroko , Iwabuchi Kikuo 
Published: November 2019

Abstract
Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2,000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum . Functional gene annotation is not available for C. floridanum because whole-genome sequencing has not been achieved. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene.
Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation and fatty acid biosynthesis to be upregulated, while cell morphogenesis in the differentiation and integrin signaling pathways were suppressed following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis .
Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum , and identified transcripts with high homology to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.
Cyclic Yield Stability of Ley Farming System in Northern Quebec
Authors: Damar Hada , Ziadi Noura , Lafond Jean , Pageau Denis , Lajeunesse Julie , Parent Léon‐ Etienne 
Published: November 2019

Predicted climate change is a threat to dairy farming operations in northern Quebec. Soil conservation measures and the timeframe of crop management may contribute to reducing yield variability and also support dairy herd populations. Our objective was to compare annual and cyclic barley (Hordeum vulgare L.) and forage yield stability for 3‐yr ley farming system (barley‐mixed, forage‐mixed, forage) over 24 yr of experimentation under contrasting soil conservation practices. Treatments were chisel or moldboard plowing, and mineral fertilization (MIN) or liquid dairy manure (LDM) applied cyclically (across eight 3‐yr cycles) at 85 to 209 kg LDM‐N ha−1 and 90 to 146 kg MIN‐N ha−1 to forage and 87 to 127 kg LDM‐N ha−1 and 70 kg MIN‐N ha−1 to barley. Yield stability assessment was initialized in 1993, 1994, and 1995 and ended in 2014, 2015, and 2016, respectively. While the cyclic assessment showed no significant effect of tillage practice, LDM outperformed MIN, confirming the benefits of manure‐based ley farming systems for dairy farming. Coefficients of variation ranged from 7.8% to 14.4% for barley grain yield, 14.4% to 18.7% for barley straw yield, and 11.8% to 15.3% for forage yield. Coefficients of variation were reduced by factors of 1.86 ± 0.57, 1.87 ± 0.24, and 2.00 ± 0.25 for grain, straw, and forage, respectively, using cyclic assessments. To face the more frequent extreme meteorological events predicted by regional climatic models, feed supply could be stabilized locally and regionally at cyclic rather than yearly timescales to support dairy farming.Core Ideas

Long term 24‐year experiment comparing annual and cyclic grain and forage yield stability.
Cyclic assessment of yield stability provide low coefficient of variation for grain, straw, and forages.
Crop supply and storage could be managed on a cyclic, rather than yearly basis.
Using Living Germplasm Collections to Characterize, Improve, and Conserve Woody Perennials
Authors: Migicovsky Zoë , Warschefsky Emily , Klein Laura L. , Miller Allison J. 
Published: November 2019

ABSTRACTWoody perennial plants make up nearly half of plant diversity and represent one‐third of the world's major crop species, yet effective strategies to maintain and preserve these important species require additional attention. The majority of conservation programs focus on seed storage; however, seeds of many woody perennial plants are difficult to maintain in seed banks because they are recalcitrant. In addition, most woody perennial crops are clonally propagated, and seed‐based conservation efforts miss clonal lineages that form the foundation of woody perennial agriculture. Woody crops are often best maintained as living collections, but these compose only 5.8% of ex situ germplasm collections. Living germplasm collections are critical resources for exploring and conserving genetic and phenotypic diversity and provide novel material for breeding efforts. In this review, we examine how living germplasm collections can be used for for phenotypic description, genetic characterization, and plant breeding. Lastly, we outline the importance of conserving these valuable resources and highlight the need for conservation strategies that are appropriately designed for woody perennial species.
Systematic Review on Rocuronium Continuous Infusion for Deep Neuromuscular Blockade
Authors: Couto Mafalda , Couto Jose G. , Nunes Catarina S. , Vide Sérgio , Amorim Pedro , Mendes Joquim 
Published: November 2019

Background:
Rocuronium is a muscle relaxant with increased use due to its binding
relation with the reversal agent sugammadex. The purpose of this review entails the investigation of
its use for the maintenance of Deep Neuromuscular Block (NMB) via continuous infusion.

Methods:
Based on PRISMA systematic search guidelines, databases included PubMed, ISI Web of
Science, Cochrane Library and Google Scholar. This comprehensive search addresses surgical patients
under deep muscle relaxation via continuous rocuronium infusion. The main indicators were
the rocuronium administration, NMB monitoring approaches and effects in order to maintain the
deep level of relaxation, as well as reversal time after a standard dose of sugammadex.

Results:
Despite the variance in approaches found in the literature, findings show the overall maintenance
of deep NMB requires approximately 0.758 mg.kg-1h-1 of rocuronium (according to the
PTC target of 0-10, 0-5 and 1-2, mean estimates are 0.445, 0.65 and 0.833 mg.kg-1h-1 respectively),
suggesting that a lower range and a smaller maximum of PTC response require higher amount of
rocuronium for its maintenance. The standard dose of sugammadex (4 mg/kg), administered at the
end of the surgery takes longer [2.85 (1.17) min] than when they are administered after moderate
NMB recovery [1.68 (0.47) min].

Conclusion:
Continuous infusion for deep NMB presents inherent advantages in terms of maintenance
and stability of muscle relaxation. Monitoring and rocuronium administration approaches are
fundamental and intrinsically connected to provide a stable and improved maintenance of deep
NMB.
Model with the GBDT for Colorectal Adenoma Risk Diagnosis
Authors: Gao Junbo , Zhang Lifeng , Yu Gaiqing , Qu Guoqiang , Li Yanfeng , Yang Xuebing 
Published: November 2019

Background and Objective:
Colorectal cancer (CRC) is a common malignant tumor of
the digestive system; it is associated with high morbidity and mortality. However, an early
prediction of colorectal adenoma (CRA) that is a precancerous disease of most CRC patients
provides an opportunity to make an appropriate strategy for prevention, early diagnosis and
treatment. It has been aimed to develop a machine learning model to predict CRA that could assist
physicians in classifying high-risk patients, make informed choices and prevent CRC.

Methods:
Patients who had undergone a colonoscopy to fill out a questionnaire at the Sixth People
Hospital of Shanghai in China from July 2018 to November 2018 were instructed. A classification
model with the gradient boosting decision tree (GBDT) was developed to predict CRA. This
model was compared with three other models, namely, random forest (RF), support vector
machine (SVM), and logistic regression (LR). The area under the receiver operating characteristic
curve (AUC) was used to evaluate performance of the models.

Results:
Among the 245 included patients, 65 patients had CRA. The area under the receiver
operating characteristic (AUCs) of GBDT, RF, SVM ,and LR with 10 fold-cross validation was
0.8131, 0.74, 0.769 and 0.763. An online prediction service, CRA Inference System, to
substantialize the proposed solution for patients with CRA was also built.

Conclusion:
Four classification models for CRA prediction were developed and compared, and
the GBDT model showed the highest performance. Implementing a GBDT model for screening
can reduce the cost of time and money and help physicians identify high-risk groups for primary
prevention.