bluuebunny/crossref_metadata_2025_split huggingface dataset:
WD Repeat‐containing Protein 73, A Novel Gene Correlated with Gonad Development in Large Yellow Croaker, Larimichthys crocea
Authors: Zhang Dong L. , Yu Da H. , Luo Hui Y. , Wang Zhi Y. 
Published: March 2016

AbstractThe genome of Larimichthys crocea harbors more than 200 putative WD40 proteins. Yet, the function of these WD40 proteins remains unknown. Here a WD40 gene, wd73, was cloned and characterized in L. crocea (named as Lcwdr73). The cDNA is 1706 bp, including a 5′ untranslated region (UTR) of 51 bp, a 3′ UTR of 509 bp, and an open reading frame of 1146 bp encoding 381 amino acid residues. The putative LcWDR73 protein contains three WD40 domain motifs. The tissue expression profiles of both sexes revealed that Lcwdr73 was extremely highly expressed in testis and ovary, moderate in kidney and brain, and low in the other tissues by quantitative polymerase chain reaction analysis. Based on histology, the gonad development of L. crocea was divided into four phases: proliferative stage (Phase I), small developmental stage (Phase II), grand developmental stage (Phase III), and mature stage (Phase IV). With the gonad development, Lcwdr73 mRNA increased and reached a peak in Phase IV, and the expression in testes is significantly higher than that in ovaries, especially from Phase II to Phase IV, indicating that Lcwdr73 may play an important role during gonad development in L. crocea. The resutlts lay a foundation to control precocious puberty of L. crocea.
Hepatic miR‐33a/miR‐144 and their target gene ABCA1 are associated with steatohepatitis in morbidly obese subjects
Authors: Vega‐Badillo Joel , Gutiérrez‐Vidal Roxana , Hernández‐Pérez Hugo A. , Villamil‐Ramírez Hugo , León‐Mimila Paola , Sánchez‐Muñoz Fausto , Morán‐Ramos Sofía , Larrieta‐Carrasco Elena , Fernández‐Silva Itzel , Méndez‐Sánchez Nahúm , Tovar Armando R. , Campos‐Pérez Francisco , Villarreal‐Molina Teresa , Hernández‐Pando Rogelio , Aguilar‐Salinas Carlos A. , Canizales‐Quinteros Samuel 
Published: March 2016

AbstractBackground and AimAbnormal cholesterol metabolism may contribute to the pathogenesis of non‐alcoholic steatohepatitis (NASH) and fibrosis. miR‐33 and miR‐144 regulate adenosine triphosphate binding cassette transporter (ABCA1) and other target genes involved in cholesterol efflux, fatty acid oxidation and inflammation. We explored relationships between non‐alcoholic fatty liver disease (NAFLD) and the hepatic expression of ABCA1/ABCG1, as well as other target genes regulated by miR‐33 (carnitine O‐octanoyltransferase, CROT and hydroxyacyl‐CoA‐dehydrogenase β‐subunit, HADHB) and miR‐144 (toll‐like receptor‐2, TLR2). Moreover, we evaluated whether the expression of these genes is correlated with miR‐33a/b and miR‐144 expression in Mexican individuals with morbid obesity.MethodsEighty‐four morbidly obese subjects undergoing bariatric surgery were included in this study. Liver biopsies were obtained to measure hepatic triglyceride and free cholesterol contents, as well as ABCA1, ABCG1, CROT, HADHB, TLR2, miR‐33a/b and miR‐144 expression.ResultsHepatic free cholesterol content was significantly increased in NASH as compared to non‐NASH subjects, while ABCA1 and ABCG1 protein levels significantly decreased with NASH and fibrosis progression. The relative expression of miR‐33a and miR‐144 correlated inversely with ABCA1 but not with ABCG1 protein levels. Moreover, both miRNAs increased significantly in NASH individuals. miR‐33 target genes CROT and HADHB correlated inversely with miR‐33a. However, the expression of these genes was not associated with NASH.ConclusionsmiR‐33a/144 and their target gene ABCA1 may contribute to the pathogenesis of NASH in morbidly obese subjects.
Genomics of local adaptation with gene flow
Authors: Tigano Anna , Friesen Vicki L. 
Published: March 2016

AbstractGene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress
Authors: Uyhelji Hilary A. , Cheng Changde , Besansky Nora J. 
Published: March 2016

AbstractEvolution of osmoregulatory systems is a key factor in the transition of species between fresh‐ and saltwater habitats. Anopheles coluzzii and Anopheles merus are stenohaline and euryhaline malaria vector mosquitoes belonging to a larger group of sibling species, the Anopheles gambiae complex, which radiated in Africa within the last 2 million years. Comparative ecological genomics of these vector species can provide insight into the mechanisms that permitted the rapid radiation of this species complex into habitats of contrasting salinity. Here, we use RNA‐Seq to investigate gene expression differences between An. coluzzii and An. merus after briefly exposing both young and old larval instars of each species to either saltwater (SW) or freshwater (FW). Our study aims to identify candidate genes and pathways responsible for the greater SW tolerance of An. merus. Our results are congruent with the ability of gene induction to mediate salinity tolerance, with both species showing increasing amounts of differential gene expression between SW and FW as salt concentrations increase. Besides ion transporters such as AgAE2 that may serve as effectors for osmoregulation, we also find mitogen‐activated protein kinases that may serve in a phosphorylation signalling pathway responding to salinity, and report potential cross‐talk between the mosquito immune response and osmoregulation. This study provides a key step towards applying the growing molecular knowledge of these malaria vectors to improve understanding of their ecological tolerances and habitat occupancy.
The idea of a Jewish nation in the German discourse about emancipation
Authors: Avraham Doron 
Published: March 2016

AbstractThis article compares the German conservative conceptualization of Judaism and Jewish emancipation with that of liberals, from the Vormärz (1830–1848) to the Neue Ära (1858–1861). It argues that both conservatives and liberals understood Judaism not merely as a religion but also as a nationality. Yet while liberals acknowledged the national dimension of Judaism as a secularized culture, and even supported Jewish emancipation, conservatives developed a different concept. Since the 1830s, conservatives accommodated nationalism while investing the Christian State ideal with national meaning. This national‐religious construction was imposed on Judaism, which was similarly interpreted now as a synthesis between religion and nationality. In accordance with this conceptualization, conservatives rejected Jewish emancipation on national ground while advocating for the establishment of a Jewish nation‐state. This thesis diverges from the existing literature, in which the reluctance of conservatism to embrace nationalism until the 1870s stands as the consensual view.
Pyramids of species richness: the determinants and distribution of species diversity across trophic levels
Authors: Turney Shaun , Buddle Christopher M. 
Published: March 2016

How species richness is distributed across trophic levels determines several dimensions of ecosystem functioning, including herbivory, predation, and decomposition rates. We perform a meta‐analysis of 72 large published food webs to investigate their trophic diversity structure and possible endogenous, exogenous, and methodological causal variables. Consistent with classic theory, we found that published food webs can generally be described as ‘pyramids of species richness’. The food webs were more predator‐poor, prey‐rich and hierarchical than is expected by chance or by the niche or cascade models. The trophic species richness distribution also depended on centrality, latitude, ecosystem‐type and methodological bias. Although trophic diversity structure is generally pyramidal, under many conditions the structure is consistently uniform or inverse‐pyramidal. Our meta‐analysis adds nuance to classic assumptions about food web structure: diversity decreases with trophic level, but not under all conditions, and the decrease may be scale‐dependent.SynthesisThe distribution of species richness across trophic levels has not been evaluated in recent decades, despite improvement in food web resolution and the relevance of biodiversity distribution to ecosystem function. Our meta‐analysis of 72 large, recent food webs, illustrates that published food webs can generally be described as basal‐rich, top‐poor ‘pyramids of species richness’, consistent with classic theory. Although trophic diversity structure is generally pyramidal, under some environmental and ecological conditions the structure is uniform or inverse‐pyramidal. Our meta‐analysis confirms classic theory about food web structure, while adding nuance by describing conditions under which classic pyramid structure is not observed.
Ultrasound‐Guided Superior Hypogastric Plexus Block: A Cadaveric Feasibility Study with Fluoroscopic Confirmation
Authors: Gofeld Michael , Lee Chuan‐Whei 
Published: March 2016

AbstractPlancarte first described a fluoroscopy‐guided superior hypogastric plexus block to manage pelvic pain in 1990. Modifications have since been described using different imaging modalities. Ultrasound‐guided approach has been described in a clinical outcome study. However, the accuracy of an ultrasound‐guided method has never been validated by alternative imaging. We conducted an experiment aiming to develop ultrasound‐guided superior hypogastric plexus block using human cadavers in the supine position. Final needle position and spread of a radiopaque contrast was verified by fluoroscopy, a standard imaging tool. The needle approach to the L5 vertebral body was performed in the short axis as has been recommended. Injection of radiopaque contrast revealed unilateral and cephalad spread to the L5/S1 disk. Additional transabdominal long‐axis scanning of the lumbosacral segment was and the needle trajectory was modified to aim for the apex of the L5/S1 disk. Bilateral spread was achieved by strict midline placement of the needle tip and real‐time observation of injection. The modified ultrasound‐guided technique resulted in a similar spread of injectate as the traditional fluoroscopy‐guided technique that in a clinical scenario would offer complete block of the superior hypogastric plexus.
Early Mississippian sandy siltstones preserve rare vertebrate fossils in seasonal flooding episodes
Authors: Bennett Carys E. , Kearsey Timothy I. , Davies Sarah J. , Millward David , Clack Jennifer A. , Smithson Timothy R. , Marshall John E. A. 
Published: March 2016

AbstractFlood‐generated sandy siltstones are under‐recognised deposits that preserve key vertebrate (actinopterygians, rhizodonts, and rarer lungfish, chondrichthyans and tetrapods), invertebrate and plant fossils. Recorded for the first time from the lower Mississippian Ballagan Formation of Scotland, more than 140 beds occur throughout a 490 m thick core succession characterised by fluvial sandstones, palaeosols, siltstones, dolostone ‘cementstones’ and gypsum from a coastal–alluvial plain setting. Sandy siltstones are described as a unique taphofacies of the Ballagan Formation (Scotland, UK); they are matrix‐supported siltstones with millimetre‐sized siltstone and very fine sandstone lithic clasts. Common bioclasts include plants and megaspores, fish, ostracods, eurypterids and bivalves. Fossils have a high degree of articulation compared with those found in other fossil‐bearing deposits, such as conglomerate lags at the base of fluvial channel sandstones. Bed thickness and distribution varies throughout the formation, with no stratigraphic trend. The matrix sediment and clasts are sourced from the reworking of floodplain sediments including desiccated surfaces and palaeosols. Secondary pedogenic modification affects 30% of the sandy siltstone beds and most (71%) overlie palaeosols or desiccation cracks. Sandy siltstones are interpreted as cohesive debris flow deposits that originated by the overbank flooding of rivers and due to localised floodplain sediment transport at times of high rainfall; their association with palaeosols and desiccation cracks indicates seasonally wet to dry cycles throughout the Tournaisian. Tetrapod and fish fossils derived from floodplain lakes and land surfaces are concentrated by local erosion and reworking, and are preserved by deposition into temporary lakes on the floodplain; their distribution indicates a local origin, with sediment transported across the floodplain in seasonal rainfall episodes. These deposits are significant new sites that can be explored for the preservation of rare non‐marine fossil material and provide unique insights into the evolution of early terrestrial ecosystems.
Health‐adjusted neuropsychological test norms based on 463 older Swedish car drivers
Authors: Bergman Ingvar , Johansson Kurt , Almkvist Ove , Lundberg Catarina 
Published: March 2016

There is a need for improved normative information in particular for older persons. The present study provides neuropsychological test norms on seven cognitive tests used in a sample representing the general older driving population, when uncontrolled and controlled for physical health. A group of 463 healthy Swedish car drivers, aged 65 to 84 years, participated in a medical and neuropsychological examination. The latter included tests of visual scanning, mental shifting, visual spatial function, memory, reaction time, selective attention, and simultaneous capacity. Hierarchical regression analyses demonstrated that, when uncontrolled for health, old age was associated with significant impairment on all seven tests. Education was associated with a significant advantage for all tests except most reaction time subtests. Women outperformed men on selective attention. Controlling for health did not consistently change the associations with education, but generally weakened those with age, indicating rises in normative scores of up to 0.36 SD (residual). In terms of variance explained, impaired health predicted on average 2.5%, age 2.9%, education 2.1% and gender 0.1%. It was concluded (1) that individual regression‐based predictions of expected values have the advantage of allowing control for the impact of health on normative scores in addition to the adjustment for various demographic and performance‐related variables and (2) that health‐adjusted norms have the potential to classify functional status more accurately, to the extent that these norms diverge from norms uncontrolled for physical health.
Subgroup Analysis with Time‐to‐Event Data Under a Logistic‐Cox Mixture Model
Authors: Wu Ruo‐fan , Zheng Ming , Yu Wen 
Published: March 2016

AbstractSubgroup detection has received increasing attention recently in different fields such as clinical trials, public management and market segmentation analysis. In these fields, people often face time‐to‐event data, which are commonly subject to right censoring. This paper proposes a semiparametric Logistic‐Cox mixture model for subgroup analysis when the interested outcome is event time with right censoring. The proposed method mainly consists of a likelihood ratio‐based testing procedure for testing the existence of subgroups. The expectation–maximization iteration is applied to improve the testing power, and a model‐based bootstrap approach is developed to implement the testing procedure. When there exist subgroups, one can also use the proposed model to estimate the subgroup effect and construct predictive scores for the subgroup membership. The large sample properties of the proposed method are studied. The finite sample performance of the proposed method is assessed by simulation studies. A real data example is also provided for illustration.
Evaluation of two rapid screening assays for detecting hepatitis C antibodies in resource‐constrained settings
Authors: Kosack Cara S. , Nick Sigrid 
Published: March 2016

AbstractObjectiveTo evaluate the diagnostic accuracy of the OraQuick HCV rapid antibody test from OraSure and the Multisure HCV antibody assay from MP Biomedicals.MethodsFive seropanels from patients, intravenous drug users and blood donors with and without HCV infection were used on the two rapid immunochromatographic tests. Sensitivity, specificity and predictive values were calculated. In addition, seropanels from 10 seroconverters were used to assess early identification of HCV infection. The study was undertaken in a laboratory at Paul Ehrlich Institute in Germany.ResultsPanel 1 contained of 55 positive and 25 negative samples. The OraQuick HCV test had a sensitivity of 100% (95% CI: 93.5–100) and a specificity of 100% (95% CI: 86.3–100). The Multisure HCV test had a sensitivity of 100% (95% CI: 93.5–100) and a specificity of 96% (95% CI: 79.6–99.9). Panel 2 consisted of 193 pre‐characterised anti‐HCV‐positive patient samples. The OraQuick HCV test identified 191 samples correctly and the Multisure HCV 192. The sensitivity was 99.0% (95% CI: 96.3–99.9) for the OraQuick HCV test and 99.5% (95% CI: 97.1–100) for the Multisure HCV test. Panel 3 was composed of seroconversion samples of 10 patients. The OraQuick HCV test detected all of these 10 infections while the Multisure HCV test detected six and was indeterminate on 2. Panel 4 included 53 anti‐HCV negative blood samples from blood donors. Both tests correctly identified all 53. Panel 5 consisted of 26 samples of HCV/HIV co‐infected patients. The sensitivity of the OraQuick HCV test was 65.2% (95% CI: 42.8–82.8) after 20 min and 73.9% (95% CI: 51.3–88.9) after 40 min of incubation. The Multisure HCV test had a sensitivity of 96.2% (95% CI: 80.4–99.9).ConclusionThis evaluation revealed good sensitivity for both rapid screening assays. The detection of seroconverters, however, was lower in the MutiSure HCV test. Therefore the MultiSure test should be used with hesitation in high incidence settings. The OraQuick gave HCV false‐negative results in almost 25% of the HIV‐positive sera. Therefore may the OraQuick be less suited in HIV prevalent areas.
Salivary proteins of spider mites suppress defenses in Nicotiana benthamiana and promote mite reproduction
Authors: Villarroel Carlos A. , Jonckheere Wim , Alba Juan M. , Glas Joris J. , Dermauw Wannes , Haring Michel A. , Van Leeuwen Thomas , Schuurink Robert C. , Kant Merijn R. 
Published: March 2016

SummarySpider mites (Tetranychidae sp.) are widely occurring arthropod pests on cultivated plants. Feeding by the two‐spotted spider mite T. urticae, a generalist herbivore, induces a defense response in plants that mainly depends on the phytohormones jasmonic acid and salicylic acid (SA). On tomato (Solanum lycopersicum), however, certain genotypes of T. urticae and the specialist species T. evansi were found to suppress these defenses. This phenomenon occurs downstream of phytohormone accumulation via an unknown mechanism. We investigated if spider mites possess effector‐like proteins in their saliva that can account for this defense suppression. First we performed an in silico prediction of the T. urticae and the T. evansi secretomes, and subsequently generated a short list of candidate effectors based on additional selection criteria such as life stage‐specific expression and salivary gland expression via whole mount in situ hybridization. We picked the top five most promising protein families and then expressed representatives in Nicotiana benthamiana using Agrobacterium tumefaciens transient expression assays to assess their effect on plant defenses. Four proteins from two families suppressed defenses downstream of the phytohormone SA. Furthermore, T. urticae performance on N. benthamiana improved in response to transient expression of three of these proteins and this improvement was similar to that of mites feeding on the tomato SA accumulation mutant nahG. Our results suggest that both generalist and specialist plant‐eating mite species are sensitive to SA defenses but secrete proteins via their saliva to reduce the negative effects of these defenses.
A whole‐genome, radiation hybrid mapping resource of hexaploid wheat
Authors: Tiwari Vijay K. , Heesacker Adam , Riera‐Lizarazu Oscar , Gunn Hilary , Wang Shichen , Wang Yi , Gu Young Q. , Paux Etienne , Koo Dal‐Hoe , Kumar Ajay , Luo Ming‐Cheng , Lazo Gerard , Zemetra Robert , Akhunov Eduard , Friebe Bernd , Poland Jesse , Gill Bikram S. , Kianian Shahryar , Leonard Jeffrey M. 
Published: March 2016

SummaryGenerating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole‐genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics‐based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole‐genome using these approaches is nearly impossible. We developed a whole‐genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high‐density single nucleotide polymorphism (SNP) array. At the whole‐genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500. The 7296 unique mapping bins provided a five‐ to eight‐fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low‐cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS‐WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high‐quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.