bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice
Authors: Martinů Jana , Hypša Václav , Štefka Jan 
Published: October 2018

AbstractA degree of host specificity, manifested by the processes of host–parasite cospeciations and host switches, is assumed to be a major determinant of parasites’ evolution. To understand these patterns and formulate appropriate ecological hypotheses, we need better insight into the coevolutionary processes at the intraspecific level, including the maintenance of genetic diversity and population structure of parasites and their hosts. Here, we address these questions by analyzing large‐scale molecular data on the louse Polyplax serrata and its hosts, mice of the genus Apodemus, across a broad range of European localities. Using mitochondrial DNA sequences and microsatellite data, we demonstrate the general genetic correspondence of the Apodemus/Polyplax system to the scenario of the postglacial recolonization of Europe, but we also show several striking discrepancies. Among the most interesting are the evolution of different degrees of host specificity in closely related louse lineages in sympatry, or decoupled population structures of the host and parasites in central Europe. We also find strong support for the prediction that parasites with narrower host specificity possess a lower level of genetic diversity and a deeper pattern of interpopulation structure as a result of limited dispersal and smaller effective population size.
Implications of survey effort on estimating demographic parameters of a long‐lived marine top predator
Authors: Symons John , Sprogis Kate R. , Bejder Lars 
Published: October 2018

AbstractEffective management of wildlife populations rely on knowledge of their abundance, survival, and reproductive rates. Maintaining long‐term studies capable of estimating demographic parameters for long‐lived, slow‐reproducing species is challenging. Insights into the effects of research intensity on the statistical power to estimate demographic parameters are limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes, and reproductive output of Indo‐Pacific bottlenose dolphins (Tursiops aduncus), using a 3‐year subsample of a long‐term, capture–recapture study off Bunbury, Western Australia. Photo‐identification on individual dolphins was collected following Pollock's Robust Design, where seasons were defined as “primary periods”, each consisting of multiple “secondary periods.” The full dataset consisted of 12 primary periods and 72 secondary periods, resulting in the study area being surveyed 24 times/year. We simulated reduced survey effort by randomly removing one, two, or three secondary periods per primary period. Capture–recapture models were used to assess the effect of survey intensity on the power to detect trends in population abundance, while individual dolphin sighting histories were used to assess the ability to conduct home range analyses. We used sighting records of adult females and their calving histories to assess survey effort on quantifying reproductive output. A 50% reduction in survey effort resulted in (a) up to a 36% decline in population abundance at the time of detection; (b) a reduced ability to estimate home range sizes, by increasing the time for individuals to be sighted on ≥30 occasions (an often‐used metric for home range analyses) from 7.74 to 14.32 years; and (c) 33%, 24%, and 33% of annual calving events across three years going undocumented, respectively. Results clearly illustrate the importance of survey effort on the ability to assess demographic parameters with clear implications for population viability analyses, population forecasting, and conservation efforts to manage human–wildlife interactions.
DNA barcoding the flowering plants from the tropical coral islands of Xisha (China)
Authors: Li Shengchun , Qian Xin , Zheng Zexin , Shi Miaomiao , Chang Xiaoyu , Li Xiaojuan , Liu Junfang , Tu Tieyao , Zhang Dianxiang 
Published: October 2018

AbstractAimDNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future.LocationXisha Islands, China.MethodsThis study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic‐based method to assess the barcoding resolution.ResultsAll the three DNA barcodes showed high levels of PCR success (96%–99%) and sequencing success (98%–100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%–90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes.Main conclusionsThis study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
Can AI predict animal movements? Filling gaps in animal trajectories using inverse reinforcement learning
Authors: Hirakawa Tsubasa , Yamashita Takayoshi , Tamaki Toru , Fujiyoshi Hironobu , Umezu Yuta , Takeuchi Ichiro , Matsumoto Sakiko , Yoda Ken 
Published: October 2018

AbstractFocal animal sampling and continuous recording of behavior in situ are essential in the study of ecology. However, observation gaps and missing records are unavoidable because the focal individual can move out of sight and recording devices do not always work properly. Using an inverse reinforcement learning (IRL) framework, we have developed a novel gap‐filling method to predict the most likely route that an animal would have traveled; within this framework, an algorithm learns a reward function from animal trajectories to find the environmental features preferred by the animal. We applied this approach to GPS trajectories obtained from streaked shearwaters (Calonectris leucomelas) and provide evidence of the advantages of the IRL approach over previously used interpolation methods. These advantages are as follows: (1) No assumptions about the parametric distribution governing movements are needed, (2) no assumptions regarding landscape preferences and restrictions are needed, and (3) large spatiotemporal gaps can be filled. This work demonstrates how IRL can enhance the ability to fill gaps in animal trajectories and construct reward‐space maps in heterogeneous environments. The proposed methodology can assist movement research, which seeks to understand phenomena that are ecologically and evolutionarily significant, such as habitat selection and migration.
Development of discrete CoFFWA for distribution network reconfigurations
Authors: Ikegami Hiromitsu , Mori Hiroyuki 
Published: October 2018

AbstractIn this article, an efficient Discrete CoFFWA method is proposed to deal with distribution network reconfigurations. It is useful for minimizing the active power network losses by switching on/off sectionalizing switches and shunt capacitors. The mathematical formulation may be expressed as one of combinatorial optimization problems. This article presents a discrete version of cooperative framework for fireworks algorithm (CoFFWA) of advanced metaheuristics to solve distribution network reconfigurations efficiently. It is one of the efficient Fireworks Algorithms that imitate the behavior of firework explosion. To improve the solution accuracy, CoFFWA makes use of new strategies such as the independent selection method and the crowdness‐avoiding cooperative strategy. The proposed method transforms CoFFWA into discrete one with multipoint mutation. The proposed method is successfully applied to the IEEE 69‐node and 119‐node distribution networks.
Postprocessing‐based interpolation schemes for nested Cartesian finite difference grids of different size
Authors: Figueroa Alejandro , Löhner Rainald 
Published: October 2018

SummaryNested Cartesian grid systems by design require interpolation of solution fields from coarser to finer grid systems. While several choices are available, preserving accuracy, stability, and efficiency at the same time require careful design of the interpolation schemes. Given this context, a series of interpolation algorithms based on postprocessing halo information on nested Cartesian finite difference grids of different size were developed and tested. The results obtained indicate that most of these do not yield the expected improvement, and some even tend to make the solver unstable. However, some third‐ and fourth‐order interpolation functions do yield considerable accuracy improvement, are stable, and are worth implementing.
Calcium‐regulated mitochondrial ATP‐Mg/Pi carriers evolved from a fusion of an EF‐hand regulatory domain with a mitochondrial ADP/ATP carrier‐like domain
Authors: Harborne Steven P. D. , Kunji Edmund R. S. 
Published: October 2018

AbstractThe mitochondrial ATP‐Mg/Pi carrier is responsible for the calcium‐dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N‐terminal regulatory domain with four calcium‐binding EF‐hands similar to calmodulin, (ii) a loop domain containing an amphipathic α‐helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF‐hands. We discuss how their combined function has led to a mechanism for calcium‐regulated transport of adenosine nucleotides. Finally, we compare the ATP‐Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1222–1232, 2018
Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?
Authors: van Esveld S. L. , Huynen M. A. 
Published: October 2018

AbstractMost eukaryotic cells contain mitochondria with a genome that evolved from their α‐proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA‐interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 70(12):1240–1250, 2018
NT5E inhibition suppresses the growth of sunitinib‐resistant cells and EMT course and AKT/GSK‐3β signaling pathway in renal cell cancer
Authors: Peng Dan , Hu Zhiquan , Wei Xian , Ke Xinwen , Shen Yuanqing , Zeng Xing 
Published: October 2018

AbstractWe aimed to explore the mechanisms of sunitinib‐resistance in renal cell cancer (RCC) and provide new therapeutic evidence and biomarkers for RCC treatment using human clear‐cell renal cell carcinoma (ccRCC) cell line, 786‐O. Microarray analysis, quantitative real time PCR (qRT‐PCR), Western blot, and immunohistochemistry were used to detect Ecto‐5′‐nucleotidase (NT5E) expressions in sunitinib‐resistant tissues in RCC. 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2‐H‐tetrazolium bromide, Thiazolyl Blue Tetrazolium Bromide (MTT), cell‐count kit 8 (CCK‐8), wound healing, and Transwell assays were used to investigate the influences of sunitinib and NT5E on 786‐O cell line and sunitinib‐resistant 786‐O cell line (S786‐O). Protein expressions related to epithelial–mesenchymal transition (EMT) and AKT/GSK‐3β signaling pathway in 786‐O cells and S786‐O cells were determined by Western blot. In vivo experiment was performed using NCr‐nu/nu mice to explore the effects of NT5E on cell growth and EMT signal in sunitinib environment. NT5E expression was upregulated in sunitinib‐resistant RCC tissues and cells. NT5E downregulation repressed RCC cell proliferation, migration as well as invasion. EMT course and AKT/GSK‐3β signal pathway both in vitro and in vivo in sunitinib environment was suppressed to varying degrees via NT5E inhibition. NT5E inhibition could suppress the growth of sunitinib‐resistant RCC cells and restrain EMT course and AKT/GSK‐3β signal pathway in sunitinib environment in RCC. © 2018 IUBMB Life, 71(1):113–124, 2019
Poly r(C) Binding Protein 1 Regulates Posttranscriptional Expression of the Ubiquitin Ligase TRIM56 in Ovarian Cancer
Authors: Zhao Lei , Wang Zhi‐gang , Zhang Ping , Yu Xiu‐feng , Su Xiao‐jie 
Published: October 2018

AbstractOur earlier work has shown that the E3 ligase TRIM56 messenger RNA (mRNA) level and vimentin protein expression followed an inverse correlation in ovarian carcinoma patients; however, the regulatory mechanisms underlying TRIM56 expression is unclear. Steady state expression of TRIM56 mRNA expression in the normal ovarian cell line Moody and ovarian cancer cell lines SKOV‐3, A2780, and Caov‐3 were not significantly different; however, TRIM56 protein expression was significantly lower in the ovarian cancer cell lines compared to the Moody cell line. Polysome profiling showed significant increase in translation of TRIM56 messenger RNA in the Moody cells compared to the SKOV‐3 cells. We performed RNA‐affinity pulldown using biotinylated TRIM56 5 ‘and 3’‐UTR and postnuclear extracts from Moody and SKOV‐3 cells. Whereas no notable difference was observed in affinity pull‐down obtained with the 5’‐UTR, there was obvious difference in protein binding patterns with the 3’‐UTR. Mass spectrometry was used to determine the most differentially binding protein as poly r (c) binding protein 1 (PCBP1). PCBP1 expression and binding to the 3’‐UTR was both higher in SKOV‐3 cells compared to the Moody cells. Silencing of TRIM56 in Moody cells cause an increase in in vitro migration and invasion, and a similar effect was mimicked by overexpression of PCBP1. Conversely, silencing of PCBP1 or overexpression of TRIM56 in SKOV‐3 cells significantly decreased in vitro migration and invasion. In xenograft assays, SKOV‐3 cells stably overexpressing shRNA targeting PCBP1 decreased metastasis, whereas shRNA‐targeting TRIM56 potentiated detection of metastatic lesions, compared to the parental SKOV‐3 cells themselves. Taken together our results reveal a yet undefined posttranscriptional regulatory mechanism underlying low expression of TRIM56 in ovarian cancer. © 2018 IUBMB Life, 71(1):177–182, 2019
Impact of Body Weight Dynamics Following Intentional Weight Loss on Fracture Risk: Results from The Action for Health in Diabetes Study
Authors: Beavers Kristen M , Neiberg Rebecca H , Johnson Karen C , Davis C Hunter , Casanova Ramon , Schwartz Ann V , Crandall Carolyn J , Lewis Cora E , Pi‐Sunyer Xavier , Kritchevsky Stephen B ,   the Look AHEAD Research Group
Published: October 2018

AbstractThe purpose of this study is to explore the impact of body weight change following intentional weight loss on incident fracture and bone mineral density (BMD) in overweight and obese adults with diabetes. A total of 1885 individuals with type 2 diabetes (baseline age: 58.5 ± 6.7 years, 58% women, body mass index: 35.7 ± 6.0 kg/m2) who participated in the Look AHEAD study and lost any weight 1 year after being randomized to an intensive lifestyle intervention were assessed. Body weight was measured annually and participants were categorized as weight regainers, weight cyclers, or continued losers/maintainers based on a ±3% annual change in weight from year 1 to year 4. Adjudicated overall fracture incidence was captured from years 4 through 13 (median follow‐up duration 11.5 years). Hip and spine BMD was assessed in a subset of participants at baseline, year 4 (n = 468), and year 8 (n = 354), using dual‐energy X‐ray absorptiometry. Cox proportional hazards and linear regression models, adjusted for relevant covariates, were performed for fracture and BMD outcomes, respectively. Fifty‐eight percent, 22%, and 20% of participants were classified as weight regainers, weight cyclers, and continued losers/maintainers, respectively; and 217 fractures (men n = 63; women n = 154) were recorded during the follow‐up period. There were no statistically significant differences in total incident fracture rates for weight regainers (HR [95% CI]: 1.01 [95% CI, 0.71 to 1.44]) or weight cyclers (HR [95% CI]: 1.02 [95% CI, 0.68 to 1.53]) when compared to continued losers/maintainers (p = 0.99). Similarly, follow‐up BMD estimates did not significantly vary by weight pattern group, although consistent trends for lowered BMD in the hip region were noted for continued losers/maintainers and weight cyclers compared with weight regainers. Patterns of weight change in the 3 years following 1 year of intentional weight loss were not associated with subsequent fracture or significantly reduced BMD in this cohort of overweight and obese adults with type 2 diabetes. © 2018 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
A Comprehensive Overview of the Clinical Pharmacokinetics of Clobazam
Authors: Tolbert Dwain , Larsen Frank 
Published: October 2018

AbstractClobazam (CLB) is a 1,5‐benzodiazepine that has been widely used as an anxiolytic and antiseizure drug (ASD) since it was first synthesized over 50 years ago. CLB was approved in the United States in 2011 as adjunctive therapy for seizures in patients ≥2 years old with Lennox‐Gastaut syndrome. CLB pharmacokinetics (PK) have been studied in single‐ and multiple‐dose administrations in healthy subjects. Salient features include high bioavailability, linear PK, and negligible effects from coadministration of other ASDs. CLB is highly and extensively absorbed, with little effect from food; time to maximum plasma concentration is 0.5 to 4 hours following the dose. After CLB doses of 20 to 40 mg/day, the volume of distribution is 99 to 120 L, with oral clearance ranging from 1.9 to 2.3 L/h. CLB is lipophilic and distributes throughout the body after oral administration. It is metabolized in the liver by cytochrome P450 (CYP) isoenzymes CYP3A, CYP2C19, and CYP2B6, and its main active metabolite isN‐desmethylclobazam. The half‐life of CLB after a single oral dose ranges from 36 to 42 hours; the half‐life ofN‐desmethylclobazam ranges from 59 to 74 hours. The metabolites of CLB are primarily excreted renally. Population PK modeling using data from healthy subjects and patients with Lennox‐Gastaut syndrome indicates that race, sex, age, weight, and renal function do not influence CLB PK. As CLB has been extensively studied since the 1970s, this review is meant to provide a consolidated and comprehensive resource on CLB PK for both prescribers and scientists alike.
Peritumoural adipose tissue pro‐inflammatory cytokines are associated with tumoural growth factors in cancer cachexia patients
Authors: Neto Nelson Inácio Pinto , Murari Ariene Soares de Pinho , Oyama Lila Missae , Otoch José Pinhata , Alcântara Paulo Sérgio Martins , Tokeshi Flavio , Figuerêdo Raquel Galvão , Alves Michele Joana , Lima Joanna Darck Carola Correia , Matos‐Neto Emídio Marques de , Seelaender Marilia , Oller do Nascimento Claudia Maria 
Published: October 2018

AbstractBackgroundCancer cachexia (CC) is a multifactorial syndrome, often irreversible, that affects patients with cancer influenced, in part, by the inflammatory condition. Peritumoural adipose tissue produces adipokines and angiogenic, apoptotic, and growth factors; given the possible crosstalk between the peritumoural adipose tissue and tumour, these may play an important role in cancer biology and carcinogenesis.MethodsThe aim of this study was to evaluate the factors produced by peritumoural adipose tissue in a cohort of 16 colorectal cancer patients with either weight‐stable cancer (WSC; n = 7) or CC (n = 9). The study was approved by the Ethics Research Committee (972.914). Samples of peritumoural adipose tissue were analysed for concentrations of TNF‐α, IL‐1β, STAT‐1, STAT‐3, RANTES, IL‐1Ra, IP‐10, IL‐15, MCP‐1, IFN‐α, GCSF, FADD, and TGF‐β. The cytokines and proteins were measured using Multiplex. Correlations between the proteins and cytokines were evaluated.ResultsTNF‐α, STAT‐1, and FADD, a factor involved in apoptosis, were significantly higher in CC group than in the WSC group. In the peritumoural adipose tissue of the CC group, RANTES showed a significant positive correlation with IL‐1Ra and IP‐10 and a negative correlation with IFN‐α; and GCSF showed significant negative correlations with IL‐1Ra, IP‐10, IL‐15, and MCP‐1 and a positive correlation with IFN‐α. In the peritumoural adipose tissue of the WSC group, no significant correlations were detected between RANTES, GCSF, IL‐3, FADD, and STAT‐1 and the cytokines/chemokines analysed.ConclusionsThese results indicated that inflammatory and tumorigenic pathways were altered in peritumoural adipose tissue in CC. Furthermore, inflammatory cytokines were correlated with growth factors in the peritumoural adipose tissue of cachectic patients, suggesting that inflammatory cytokines modulated the proliferative environment closely linked to the tumour.