bluuebunny/crossref_metadata_2025_split huggingface dataset:
The aggregate site frequency spectrum for comparative population genomic inference
Authors: Xue Alexander T. , Hickerson Michael J. 
Published: November 2015

AbstractUnderstanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co‐distributed species for assemblage‐level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large‐scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next‐generation comparative population genomic inference.
Dislocation, Not Dissociation: The Neuroanatomical Argument Against Visual Experience Driving Motor Action
Authors: Kozuch Benjamin 
Published: November 2015

AbstractCommon sense suggests that visual consciousness is essential to skilled motor action, but Andy Clark—inspired by Milner and Goodale's dual visual systems theory—has appealed to a wide range of experimental dissociations to argue that such an assumption is false. Critics of Clark's argument (e.g. Wallhagen, Mole) contend that the content driving motor action is actually within subjects' experience, just not easily discovered. In this article, I argue that even if such content exists, it cannot be guiding motor action, since a review of current visual neuroscience indicates that the visual brain areas producing conscious representations are distinct from those driving motor action.
Influence of carbon dioxide on numbers ofCulicoidesmidges collected with suction light traps in South Africa
Authors: VENTER G. J. , BOIKANYO S. N. B. , MAJATLADI D. M. , MOREY L. 
Published: November 2015

AbstractTo implement risk management against diseases transmitted by species ofCulicoidesLatreille, 1809 (Diptera: Ceratopogonidae), it is essential to identify all potential vectors. Light traps are the most commonly used tool for the collection ofCulicoidesmidges. Given the indiscriminate artificial attraction of light, traps will collect all night‐flying insects rather than only livestock‐associatedCulicoidesmidges. Factors that may increase the efficacy of traps, especially for livestock‐associatedCulicoidesmidges, require investigation. In the present study, results obtained with Centers for Disease Control (CDC) and Onderstepoort light traps baited with carbon dioxide (CO2) were compared with those of unbaited controls. Comparisons were made using two replicates of a 4 × 4 randomized Latin square design. With both trap types, the mean numbers ofCulicoidesmidges collected in 16 baited traps were higher than those caught in 16 unbaited traps. Although exceptionally low numbers were collected with theCDCtraps, the increases in the numbers and frequency of collection ofCulicoides imicolaKieffer, 1913 were more pronounced in theCDCtraps compared with the Onderstepoort traps. These results indicate that the addition ofCO2may increase the efficiency of these traps for the collection ofC. imicolaand other livestock‐associatedCulicoidesspecies.
Utility of IgE (total and Aspergillus fumigatus specific) in monitoring for response and exacerbations in allergic bronchopulmonary aspergillosis
Authors: Agarwal Ritesh , Aggarwal Ashutosh N. , Sehgal Inderpaul S. , Dhooria Sahajal , Behera Digambar , Chakrabarti Arunaloke 
Published: November 2015

SummaryThe role of total and specific IgE in monitoring treatment responses in allergic bronchopulmonary aspergillosis (ABPA) remains poorly studied. Here in, we evaluate the utility of total and Aspergillus fumigatus specific IgE in the follow‐up of ABPA. Eighty‐one consecutive treatment‐naïve patients of ABPA (acute stage) with pulmonary infiltrates and bronchiectasis underwent measurement of total and A. fumigatus specific IgE at baseline, after 8 weeks of glucocorticoid therapy, and during exacerbations. There was clinical and radiological improvement after treatment with median decline of total IgE by 51.9%. The total IgE declined by at least 35%, 25% and 20% in 69 (85.2%), 76 (93.6%) and 78 (96.3%) patients, respectively. On the other hand, the A. fumigatus specific IgE increased in 42 (51.9%) subjects, and the mean increase was 1.4%, after 8 weeks. Among 13 patients with exacerbation, 12 (92.3%) had a rise of total IgE by >50%. The A. fumigatus specific IgE increased in only five (38.5%) subjects during exacerbation. Thus, the total IgE is a useful test in monitoring treatment responses in ABPA while A. fumigatus specific IgE has limited utility.
RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF‐mediated pathway
Authors: Chan Zhulong , Wang Yanping , Cao Minjie , Gong Yuehua , Mu Zixin , Wang Haiqing , Hu Yuanlei , Deng Xin , He Xin‐Jian , Zhu Jian‐Kang 
Published: November 2015

Summary

The C‐REPEAT‐BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood.

In this study, we characterized cold tolerance of null mutant of RNA‐DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA‐directed DNA methylation (RdDM) in Arabidopsis.

The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down‐regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold‐induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3.

We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.
Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments
Authors: Kudoh Hiroshi 
Published: November 2015

SummaryPhenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High‐resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature‐responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC‐mediated long‐term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short‐term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology.

Contents

Summary
399

I.
Introduction
400

II.
Definition and methodological advance of molecular phenology
401

III.
In natura systems biology using high‐resolution molecular phenology (HMP) data
402

IV.
Predicting properties of a temperature‐responding machinery (Step 1)
402

V.
FLC as a candidate gene regulatory system for past temperature memory (Step 2)
404

VI.
In natura quantification of past temperature memory by HMP (Step 3)
405

VII.
Development of a molecular phenology‐based mechanistic model (Step 4)
406

VIII.
New insight into and analysis of the mechanism: digital repression of FLC (Step 5)
406

IX.
New insight into and analysis of natural signals: phase lag calendar hypotheses (Step 6)
407

X.
Transcriptomic HMP (revolution in Step 3)
409

XI.
Perspectives: circles of in natura systems biology
409

Acknowledgements
410

References
410
Modification of the PthA4 effector binding elements in Type I CsLOB1 promoter using Cas9/sgRNA to produce transgenic Duncan grapefruit alleviating XccΔpthA4:dCsLOB1.3 infection
Authors: Jia Hongge , Orbovic Vladimir , Jones Jeffrey B. , Wang Nian 
Published: November 2015

SummaryCitrus canker caused by Xanthomonas citri subspecies citri (Xcc) is a severe disease for most commercial citrus cultivars and responsible for significant economic losses worldwide. Generating canker‐resistant citrus varieties will provide an efficient and sustainable solution to control citrus canker. Here, we report our progress in generating canker‐resistant grapefruit by modifying the PthA4 effector binding elements (EBEs) in the CsLOB1 Promoter (EBEPthA4‐CsLOBP) of the CsLOB1 (Citrus sinensis Lateral Organ Boundaries) gene. CsLOB1 is a susceptibility gene for citrus canker and is induced by the pathogenicity factor PthA4, which binds to the EBEPthA4‐CsLOBP to induce CsLOB1 gene expression. There are two alleles, Type I and Type II, of CsLOB1 in Duncan grapefruit. Here, a binary vector was designed to disrupt the PthA4 EBEs in Type I CsLOB1 Promoter (TI CsLOBP) via epicotyl transformation of Duncan grapefruit. Four transgenic Duncan plants with targeted modification of EBEPthA4‐T1 CsLOBP were successfully created. As for Type I CsLOB1 promoter, the mutation rate was 15.63% (#D13), 14.29% (#D17), 54.54% (#D18) and 81.25% (#D22). In the presence of wild‐type Xcc, transgenic Duncan grapefruit developed canker symptoms similarly as wild type. An artificially designed dTALE dCsLOB1.3, which specifically recognizes Type I CsLOBP, but not the mutated Type I CsLOBP or Type II CsLOBP, was developed to infect Duncan transformants. Consequently, #D18 had weakened canker symptoms and #D22 had no visible canker symptoms in the presence of XccΔpthA4:dCsLOB1.3. Our data suggest that activation of a single allele of susceptibility gene CsLOB1 by PthA4 is sufficient to induce citrus canker disease, and mutation in the promoters of both alleles of CsLOB1 is probably required to generate citrus canker‐resistant plants. This work lays the groundwork to generate canker‐resistant citrus varieties via Cas9/sgRNA in the future.
Identification of salt tolerance‐improving quantitative trait loci alleles from a salt‐susceptible rice breeding line by introgression breeding
Authors: Qiu Xianjin , Yuan Zhihua , Liu Huan , Xiang Xiaojiao , Yang Longwei , He Wenjing , Du Bin , Ye Guoyou , Xu Jianlong , Xing Danying 
Published: November 2015

AbstractTo improve salt tolerance of two elite rice varieties, Ce258 and Zhongguangxiang1 (ZGX1), two sets of introgression lines (ILs) each comprising 200 BC1F10lines derived from a common donor, IR75862, and two recipient parents, Ce258 and ZGX1, were used for mapping of QTLs for four salt tolerance‐related traits at the seedling stage. Although the three parents were susceptible to salt, the two IL populations showed transgressive segregations for salt tolerance with 12 and 8 salt tolerance ILs in the Ce258‐ILs and ZGX1‐ILs. Eighteen main‐effect QTLs were identified for the four traits in the two IL populations, and the IR75862 alleles at most loci showed increased and decreased salt tolerance in the ZGX1 and Ce258 backgrounds, suggesting overwhelming genetic background effects on QTL detection for salt tolerance. TheqDSS11simultaneously detected in the two backgrounds was validated in a F2population derived from a salt tolerance line and ZGX1. Our results indicated that salt tolerance‐enhancing allele could be identified in the elite susceptible breeding lines and that introgression of the favourable alleles could facilitate the development of superior lines with greater salt tolerance levels.
Effect of Lipopolysaccharide on the Progression of Non‐Alcoholic Fatty Liver Disease in High Caloric Diet‐Fed Mice
Authors: Matsushita N. , Osaka T. , Haruta I. , Ueshiba H. , Yanagisawa N. , Omori‐Miyake M. , Hashimoto E. , Shibata N. , Tokushige K. , Saito K. , Tsuneda S. , Yagi J. 
Published: November 2015

AbstractThe incidence of non‐alcoholic steatohepatitis (NASH) is increasing. Because gut microbiota have been highlighted as one of the key factors in the pathogenesis of metabolic syndrome, we investigated the involvement of the bacterial component in the progression of non‐alcoholic fatty liver (NAFL) to NASH. C57BL/6 mice were fed with maintenance food (MF, groups A and B) or a high caloric diet (HCD, groups C and D) for 1 month. Mice were then divided into four groups: Groups A and C were inoculated with PBS, while groups B and D were inoculated with lipopolysaccharide (LPS) plus complete Freund's adjuvant (CFA). The inoculations were performed a total of 3 times over 3 months. At 6 months, while hepatic steatosis was observed in groups C and D, cellular infiltration and fibrosis were less evident in group C than in group D. Inflammatory cytokines were upregulated in groups B and D. 16S rRNA pyrosequencing of whole colon homogenates containing faeces showed that certain bacterial groups, such as Bacteroidaceae, Peptostreptococcaceae and Erysipelotrichaceae, were increased in groups C and D. Although loading of bacterial components (LPS) resulted in hepatic inflammation in both MF‐ and HCD‐fed mice, HCD feeding was more crucial in the progression of NAFL during the triggering phase.
Epidemiology of hepatitis E virus infection during pregnancy in Benin
Authors: De Paschale Massimo , Ceriani Cristina , Romanò Luisa , Cerulli Teresa , Cagnin Debora , Cavallari Serena , Ndayake Joseph , Zaongo Dieudonné , Diombo Kouma , Priuli Gianbattista , Viganò Paolo , Clerici Pierangelo 
Published: November 2015

AbstractObjectivesHepatitis E virus (HEV) is the cause of enterically transmitted non‐A, non‐C hepatitis (an infection that is particularly severe during pregnancy) in tropical and subtropical countries. As there are no published data concerning the prevalence of HEV antibodies in Benin, their presence was investigated in pregnant women undergoing routine HIV screening in a rural area in northern Benin and in pregnant women with acute non‐A, non‐C hepatitis.MethodsA total of 278 serum samples were collected from asymptomatic pregnant women in 2011 were tested for HEV and hepatitis A virus (HAV) antibodies, and the HEV IgM‐positive samples were further tested for HEV‐RNA. A further seven samples of pregnant women with acute non‐A, non‐C hepatitis collected during episodes of acute hepatitis in 2005 were also analysed.ResultsOf the 278 samples collected in 2011, 16.19% were positive for HEV IgG and 1.44% for HEV IgM (none positive for HEV‐RNA), and 99.64% were positive for total HAV antibodies (none positive for HAV IgM). Six of the seven samples collected in 2005 were positive for HEV IgG and IgM, and two were also positive for HEV‐RNA.ConclusionsThe circulation of HEV infection is significant among pregnant women in Benin, in whom the consequences may be fatal.
Bacterial isolates, antimicrobial susceptibility, and clinical characteristics of bacterial keratitis in dogs presenting to referral practice in Australia
Authors: Hindley Kate E. , Groth Allyson D. , King Martyn , Graham Kathleen , Billson F. Mark 
Published: November 2015

AbstractObjectiveTo identify clinical characteristics, bacterial isolates, and their antimicrobial susceptibility patterns in a prospective study of dogs presenting with suspected bacterial keratitis to aid selection of appropriate therapy.AnimalsSeventy‐one client‐owned dogs presenting to two referral hospitals in Australia.ProcedureCorneal swabs and clinical information were collected from dogs presenting with suspect bacterial keratitis from April 2012 to December 2014. Cytology and bacteriologic culture were performed on samples with in vitro antimicrobial susceptibility performed on bacterial isolates.ResultsPositive cultures were obtained from 42 of the 71 ulcers sampled (59%), with 45 bacteria isolated. The most commonly isolated bacteria were β‐hemolytic Streptococcus (14/45, 31%), Pseudomonas (14/45, 31%), and Staphylococcus species (8/45, 18%). β‐Hemolytic Streptococcus spp. were resistant to neomycin, polymyxin B, gentamicin, framycetin and fusidic acid and >80% were resistant to ciprofloxacin but remained susceptible to chloramphenicol and cephalexin. Pseudomonas aeruginosa isolates were resistant to chloramphenicol, cephalexin, and fusidic acid; however, >90% were susceptible to ciprofloxacin, polymyxin B, and gentamicin. Brachycephalic breed (34/42, 81%), previous ocular surgery (15/42, 36%), prior use of a topical corticosteroid (13/42, 31%), and concurrent ocular surface disease (10/42, 24%) were common in dogs with bacterial keratitis.ConclusionOur study identified β‐hemolytic Streptococcus and Pseudomonas spp. as the most common bacterial pathogens in canine bacterial keratitis presenting for referral. Many cases exhibited clinical factors known to influence corneal integrity that may predispose them to ulceration and infection. Based on in vitro antimicrobial susceptibility patterns and clinical outcomes, monotherapy with a fluoroquinolone may be ineffective in ulcers caused by β‐hemolytic Streptococcus spp.
Retrobulbar pigmented peripheral nerve sheath tumor in a dog
Authors: Curto Elizabeth , Clode Alison B , Durrant Jessica , Montgomery Keith W , Gilger Brian C 
Published: November 2015

AbstractA 1‐year‐old male castrated Pug was referred for unilateral exophthalmos unresponsive to oral antibiotic and anti‐inflammatory therapy. Clinical findings included exophthalmos of the left eye with lateral strabismus, resistance to retropulsion, and an elevated nictitans. Hematologic and biochemical analyses were within normal limits. Findings following computed tomography (CT) of the head included an expansile retrobulbar soft tissue mass with bony lysis extending into the left nasal cavity and nasopharynx. Ultrasound‐guided fine‐needle aspirates and biopsy samples obtained via rhinoscopy were nondiagnostic. Palliative exenteration was elected; the patient was euthanized 13 weeks following exenteration due to development of neurologic signs and perceived poor quality of life. The histopathologic diagnosis was a malignant pigmented peripheral nerve sheath tumor.
Coalescing-Branching Random Walks on Graphs
Authors: Dutta Chinmoy , Pandurangan Gopal , Rajaraman Rajmohan , Roche Scott 
Published: November 2015

We study a distributed randomized information propagation mechanism in networks we call the
coalescing-branching
random walk (cobra walk, for short). A cobra walk is a generalization of the well-studied “standard” random walk, and is useful in modeling and understanding the Susceptible-Infected- Susceptible (SIS)-type of epidemic processes in networks. It can also be helpful in performing light-weight information dissemination in resource-constrained networks. A cobra walk is parameterized by a
branching factor
k
. The process starts from an arbitrary vertex, which is labeled
active
for step 1. In each step of a cobra walk, each active vertex chooses
k
random neighbors to become active for the next step (“branching”). A vertex is active for step
t
+ 1 only if it is chosen by an active vertex in step
t
(“coalescing”). This results in a stochastic process in the underlying network with properties that are quite different from both the standard random walk (which is equivalent to the cobra walk with branching factor 1) as well as other gossip-based rumor spreading mechanisms.

We focus on the
cover time
of the cobra walk, which is the number of steps for the walk to reach all the vertices, and derive almost-tight bounds for various graph classes. We show an
O
(log
2
n
) high probability bound for the cover time of cobra walks on expanders, if either the expansion factor or the branching factor is sufficiently large; we also obtain an
O
(log
n
) high probability bound for the
partial cover time
, which is the number of steps needed for the walk to reach at least a constant fraction of the vertices. We also show that the cover time of the cobra walk is, with high probability,
O
(
n
log
n
) on any
n
-vertex tree for
k
≥ 2,
Õ
(

n
1/d

) on a
d
-dimensional grid for
k
≥ 2, and
O
(log
n
) on the complete graph.
Urokinase Exerts Antimetastatic Effects by Dissociating Clusters of Circulating Tumor Cells
Authors: Choi Jin Woo , Kim Jun Ki , Yang Yun Jung , Kim Pilhan , Yoon Kwon-Ha , Yun Seok Hyun 
Published: November 2015

Abstract
Clusters of circulating tumor cells (CTC) exhibit more robust metastatic properties than single CTC. Thus, understanding the distinct behaviors of CTC clusters and how CTC clustering is regulated may offer new insights into how to limit metastasis. In this study, we utilized an in vivo confocal system to observe the clustering behavior of CTC in real time, finding that the number of clusters increased proportionally with the growth of the primary tumor. Our experiments also indicated that the flow rate of the CTC clusters in blood vessels was relatively slower than single CTC due to increased vessel wall adhesion. Depending on disease stage, 5% to 10% of total CTC in circulation were in clusters, with this proportion increasing to &gt;24% within lung metastases examined. Notably, in the 4T1 mouse model of breast cancer metastasis, we found that injecting host animals with urokinase-type plasminogen activator, a clinical thrombolytic agent, was effective at preventing the assembly of CTC clusters and prolonging overall host survival by approximately 20% relative to control animals. Our results suggest a tractable approach to limit metastasis by suppressing the formation or stability of CTC clusters circulating in the blood of cancer patients. Cancer Res; 75(21); 4474–82. ©2015 AACR.