bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproduction has different costs for immunity and parasitism in a wild mammal
Authors: Albery Gregory F. , Watt Kathryn A. , Keith Rosie , Morris Sean , Morris Alison , Kenyon Fiona , Nussey Daniel H. , Pemberton Josephine M. 
Published: November 2018

Abstract1. Life history theory predicts that reproductive investment draws resources away from immunity, resulting in increased parasitism. However, studies of reproductive tradeoffs rarely examine multiple measures of reproduction, immunity, and parasitism. It is therefore unclear whether the immune costs of reproductive traits correlate with their resource costs, and whether increased parasitism emerges from weaker immunity.2. We examined these relationships in wild female red deer (Cervus elaphus) with variable reproductive investment and longitudinal data on mucosal antibody levels and helminth parasitism. We noninvasively collected faecal samples, counting propagules of strongyle nematodes (order: Strongylida), the common liver flukeFasciola hepaticaand the red deer tissue nematodeElaphostrongylus cervi. We also quantified both total and anti-strongyle mucosal IgA to measure general and specific immune investment.3. Contrary to our predictions, we found that gestation was associated with decreased total IgA but with no increase in parasitism. Meanwhile, the considerable resource demand of lactation had no further immune cost but was associated with higher counts of strongyle nematodes andElaphostrongylus cervi. These contrasting costs arose despite a negative correlation between antibodies and strongyle count, which implied that IgA was indicative of protective immunity.4. Our findings suggest that processes other than classical resource allocation tradeoffs are involved in mediating observed relationships between reproduction, immunity, and parasitism in wild mammals. In particular, reproduction-immunity tradeoffs may result from hormonal regulation or maternal antibody transfer, with parasitism increasing as a result of increased exposure arising from resource acquisition constraints. We advocate careful consideration of resource-independent mechanistic links and measurement of both immunity and parasitism when investigating reproductive costs.
Characterization of functional diversity of the human brain based on intrinsic connectivity networks
Authors: Chu Congying , Fan Lingzhong , Jiang Tianzi 
Published: November 2018

AbstractSpontaneous fluctuations underlying the brain activity can reflect the intrinsic organization of the system, such as the functional brain networks. In large scale, a network perspective has emerged as a new avenue to explore the functional properties of human brain. Here, we studied functional diversity in healthy subjects based on the network perspective. We hypothesized that the patterns of participation of different functional networks were related with the functional diversity of particular brain regions. Independent component analysis (ICA) was adopted to detect the intrinsic connectivity networks (ICNs) based on the data of resting-state functional MRI. An index of functional diversity (FD index) was proposed to quantitatively describe the degree of anisotropic distribution related with participation of various ICNs. We found that FD index continuously varied across the brain, for example, the primary motor cortex with low FD value and the precuneus with significantly high FD value. The FD values indicated the different functional roles of the corresponding brain regions, which were reflected by the various patterns of participation of ICNs. The FD index can be used as a new approach to quantitatively characterize the functional diversity of human brain, even for the changed functional properties caused by the psychiatric disorders.
Reproducing Transformation of Indolent B-cell Lymphoma by T-cell Immunosuppression of L.CD40 Mice
Authors: Vincent-Fabert Christelle , Saintamand Alexis , David Amandine , Alizadeh Mehdi , Boyer François , Arnaud Nicolas , Zimber-Strobl Ursula , Feuillard Jean , Faumont Nathalie 
Published: November 2018

AbstractTransformation of an indolent B-cell lymphoma is associated with a more aggressive clinical course and poor survival. The role of immune surveillance in the transformation of a B-cell indolent lymphoma towards a more aggressive form is poorly documented. To experimentally address this question, we used the L.CD40 mouse model, which is characterized by B-cell specific continuous CD40 signaling, responsible for spleen indolent clonal or oligoclonal B-cell lymphoma after one year in 60% cases. Immunosuppression was obtained either by T/NK cell depletion or by treatment with the T-cell immunosuppressive drug cyclosporin A. Immunosuppressed L.CD40 mice had larger splenomegaly with increased numbers of B-cells in both spleen and peripheral blood. High-throughput sequencing of immunoglobulin variable segments revealed that clonal expansion was increased in immunosuppressed L.CD40 mice. Tumor B cells of immunosuppressed mice were larger with an immunoblastic aspect, both on blood smears and spleen tissue sections, with increased proliferation rate and increased numbers of activated B-cells. Collectively, these features suggest that immune suppression induced a shift from indolent lymphomas into aggressive ones. Thus, as a preclinical model, immunosuppressed L.CD40 mice reproduce aggressive transformation of an indolent B-cell tumor and highlight the role of the immune surveillance in its clinical course, opening new perspective for immune restoration therapies.Summary statementHighlighting the role of immune surveillance, transformation of indolent B-cell lymphoma into an aggressive malignancy is experimentally reproduced after T-cell immune suppression in the L.CD40 preclinical mouse model.
Lipid Lowering Oxopropanylindole Hydrazone Derivatives with Anti-oxidant and Anti-hyperglycemic Activity
Authors: Varshney Kanika , Gupta Amit K. , Sonkar Ravi , Varshney Salil , Mishra Akanksha , Bhatia Geetika , Gaikwad Anil , Srivastava Arvind Kumar , Saxena Mridula , Jain Sudha , K.Saxena Anil 
Published: November 2018

AbstractA series of substituted oxopropanylindole hydrazone derivatives was synthesized and evaluated for anti-oxidant and anti-dyslipidemic activity. Among these 12 compounds the three compounds6c,7band7dshowed good anti-oxidant activity and the compound6cattenuataed LDL oxidation by 32%. The compounds6cand7dalso showed good anti-dyslipidemic activity by reducing serum levels of total cholesterol (TC), phospholipids (PL) and triglycerides (TG). These two compounds were further evaluated for anti-adipogenic and anti-hyperglycemic activity, where6cwas found most active compound with 44% reduction in lipid accumulation and 20.5% and 24.3% reduction in blood glucose at 5h and 24h respectively, as compared to standard drug metformin.
Extending long-range phasing and haplotype library imputation algorithms to very large and heterogeneous datasets
Authors: Money Daniel , Wilson David , Jenko Janez , Gorjanc Gregor , Hickey John M. 
Published: November 2018

AbstractBackgroundThis paper describes the latest improvements to the long-range phasing and haplotype library imputation algorithms that enable them to successfully phase both datasets with one million individuals and datasets genotyped using different sets of single nucleotide polymorphisms (SNPs). Previous publicly available implementations of long-range phasing could not phase large datasets due to the computational cost of defining surrogate parents by exhaustive all-against-all searches. Further, both long-range phasing and haplotype library imputation were not designed to deal with large amounts of missing data, which is inherent when using multiple SNP arrays.MethodsHere, we developed methods which avoid the need for all-against-all searches by performing long-range phasing on subsets of individuals and then combing results. We also extended long-range phasing and haplotype library imputation algorithms to enable them to use different sets of markers, including missing values, when determining surrogate parents and identifying haplotypes. We implemented and tested these extensions in an updated version of our phasing software AlphaPhase.ResultsA simulated dataset with one million individuals genotyped with the same set of 6,711 SNP for a single chromosome took two days to phase. A larger dataset with one million individuals genotyped with 49,579 SNP for a single chromosome took 14 days to phase. The percentage of correctly phased alleles at heterozygous loci was respectively 90.5% and 90.0% for the two datasets, which is comparable to the accuracy achieved with previous versions of AlphaPhase on smaller datasets.The phasing accuracy for datasets with different sets of markers was generally lower than that for datasets with one set of markers. For a simulated dataset with three sets of markers 2.8% of alleles at heterozygous positions were phased incorrectly whereas the equivalent figure with one set of markers was 0.6%.ConclusionsThe improved long-range phasing and haplotype library imputation algorithms enable AlphaPhase to quickly and accurately phase very large and heterogeneous datasets. This will enable more powerful breeding and genetics research and application.
Entorhinal neurons exhibit cue locking in rodent VR
Authors: Casali Giulio , Shipley Sarah , Dowell Charlie , Hayman Robin , Barry Caswell 
Published: November 2018

AbstractThe regular firing pattern exhibited by medial entorhinal (mEC) grid cells of locomoting rodents is hypothesized to provide spatial metric information relevant for navigation. The development of virtual reality (VR) for head-fixed mice confers a number of experimental advantages and has become increasingly popular as a method for investigating spatially-selective cells. Recent experiments using 1D VR linear tracks have shown that some mEC cells have multiple fields in virtual space, analogous to grid cells on real linear tracks. We recorded from the mEC as mice traversed virtual tracks featuring regularly spaced repetitive cues and identified a population of cells with multiple firing fields, resembling the regular firing of grid cells. However, further analyses indicated that many of these were not, in fact, grid cells because: 1) When recorded in the open field they did not display discrete firing fields with six-fold symmetry; 2) In different VR environments their firing fields were found to match the spatial frequency of repetitive environmental cues. In contrast, cells identified as grid cells based on their open field firing patterns did not exhibit cue locking. In light of these results we highlight the importance of controlling the periodicity of the visual cues in VR and the necessity of identifying grid cells from real open field environments in order to correctly characterise spatially modulated neurons in VR experiments.
Assessing the protective potential of H1N1 influenza virus hemagglutinin head and stalk antibodies in humans
Authors: Christensen Shannon R. , Toulmin Sushila A. , Griesman Trevor , Lamerato Lois E. , Petrie Joshua G. , Martin Emily T. , Monto Arnold S. , Hensley Scott E. 
Published: November 2018

AbstractSeasonal influenza viruses are a major cause of human disease worldwide. Most neutralizing antibodies (Abs) elicited by influenza viruses target the head domain of the hemagglutinin (HA) protein. Anti-HA head Abs can be highly potent, but they have limited breadth since the HA head is variable. There is great interest in developing new universal immunization strategies that elicit broadly neutralizing Abs against conserved regions of HA, such as the stalk domain. Although HA stalk Abs can provide protection in animal models, it is unknown if they are present at sufficient levels in humans to provide protection against naturally-acquired influenza virus infections. Here, we quantified H1N1 HA head and stalk-specific Abs in 179 adults hospitalized during the 2015-2016 influenza virus season. We found that HA head Abs, as measured by hemagglutinin-inhibition (HAI) assays, were associated with protection against naturally-acquired H1N1 infection. HA stalk-specific serum total IgG titers were also associated with protection, but this association was slightly attenuated and not statistically significant after adjustment for HA head-specific Ab titers. We found higher titers of HA stalk-specific IgG1 and IgA Abs in sera from uninfected participants than from infected participants; however, we found no difference in sera in vitro antibody dependent cellular cytotoxicity activity. In passive transfer experiments, sera from participants with high HAI activity efficiently protected mice, while sera with low HAI activity protected mice to a lower extent. Our data suggest that human HA head and stalk Abs both contribute to protection against H1N1 infection.ImportanceAbs targeting the HA head of influenza viruses are often associated with protection from influenza virus infections. These Abs typically have limited breadth since mutations frequently arise in HA head epitopes. New vaccines targeting the more conserved HA stalk domain are being developed. Abs that target the HA stalk are protective in animal models, but it is unknown if these Abs exist at protective levels in humans. Here, we found that Abs against both the HA head and HA stalk were associated with protection from naturally-acquired human influenza virus infections during the 2015-2016 influenza season.
Polymorphic 30-nm Chromatin Fiber and Linking Number Paradox. Evidence for the Occurrence of Two Distinct Topoisomers
Authors: Norouzi Davood , Zhurkin Victor B. 
Published: November 2018

AbstractWe discuss various models of spatial organization of the 30-nm fiber that remains enigmatic despite 40 years of intensive studies. Using computer simulations, we found two topologically different families of the fiber conformations distinguished by the linker length, L: the fibers with L = {10n} and {10n+5} bp have DNA linking numbers per nucleosome DLk » –1.5 and –1.0, respectively. The fibers with DLk » –1.5 were observed earlier, while the topoisomer with DLk » –1.0 is novel. These predictions were confirmed for circular nucleosome arrays with precisely positioned nucleosomes. We suggest that topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. In particular, the {10n+5} DNA linkers are likely to produce transcriptionally competent chromatin structures. This hypothesis is consistent with available data for several eukaryotes, from yeast to human. We also analyzed two recent studies of chromatin fibers – on the nucleosome crosslinking in vitro, and on radioprobing DNA folding in human cells. In both cases, we show that the novel topoisomer with DLk » –1.0 has to be taken into account to interpret experimental data. This is yet another evidence for occurrence of two distinct fiber topoisomers. Potentially, our findings may reflect a general tendency of chromosomal domains with different levels of transcription to retain topologically different higher-order structures.
PIN1 isomerisation of BRCA1 promotes replication fork protection
Authors: Daza-Martin Manuel , Jamshad Mohammed , Starowicz Katarzyna , Chauhan Anoop Singh , Beesley James F.J. , Coles Jennifer L. , Stewart Grant S. , Densham Ruth M. , Morris Joanna R. 
Published: November 2018

AbstractBRCA1, BRCA2 and a subset of Fanconi’s Anaemia proteins act to promote RAD51-mediated protection of newly synthesised DNA at stalled replication forks from degradation by nucleases. How BRCA1 contributes, how it is regulated and whether replication fork protection relates to, or differs from, the roles BRCA1 has in homologous recombination is not clear. Here we show that the canonical BRCA1-PALB2 interaction is not required for fork protection and instead we demonstrate that the ability of BRCA1 to protect nascent DNA is regulated in an unexpected fashion through conformational change mediated by the phosphorylation-directed prolyl isomerase, PIN1. BRCA1 isomerisation enhances BRCA1-BARD1 interaction with RAD51 and consequently RAD51 presence at stalled replication structures. Our data suggest BRCA1-BARD1 promotes fork protection in part by enhancing the RAD51 synapse. Patient missense variants in the regulated BRCA1-BARD1 regions similarly show poor nascent strand protection but proficient homologous recombination, defining novel domains required for fork protection in BRCA1-BARD1 associated with cancer predisposition. Together these findings reveal a previously unrecognised pathway that governs BRCA1-mediated replication fork protection.
Comparisons among Vestibular Examinations and Symptoms of Vertigo in Sudden Sensorineural Hearing Loss Patients
Authors: Lim Kang Hyeon , Jeong Yong Jun , Han Mun Soo , Rah Yoon Chan , Cha Jaehyung , Choi June 
Published: November 2018

AbstractObjectiveVertigo in sudden sensorineural hearing loss (SSNHL) is hypothesized as an extension of the disease caused by the anatomical proximity of the cochlea and vestibule. The present study aimed to demonstrate the association of vestibular function test (VFT) results with SSNHL disease severity and prognosis.Subjects and methodsThis study assessed clinical records of 263 SSNHL patients admitted to our hospital, between January 2010 and October 2017. Steroid treatment comprised high-dose intravenous dexamethasone (16 mg/d) or oral methylprednisolone (64 mg/d) for 4 days and tapered oral methylprednisolone for 8 days after discharge. Caloric tests were performed in all patients, and cervical vestibular-evoked myogenic potential (c-VEMP) and ocular VEMP (o-VEMP) tests were performed in 209 and 144 patients, respectively.ResultsNinety six patients had vertigo, and caloric abnormalities were observed in 119 patients. Initial PTA in patients with vertigo were worse than in those without vertigo (63.0 dB vs 72.7 dB,P=.002). Initial PTA in patients with abnormal o-VEMP was worse than in those with normal o-VEMP (61.4 dB vs 73.0 dB,P=.004). PTA improvement after steroid treatment in patients with vertigo was lower than in those without vertigo (25.0 dB vs 20.9 dB,P=.028). PTA improvement after treatment in patients with abnormal caloric results was lower than in those with normal caloric results (26.0 dB vs 18.4 dB,P=.013).ConclusionsThe functions of vestibular organs, particularly the utricle and lateral semicircular canal, are associated with disease severity and hearing outcome in SSNHL patients.
Curcumin induces mild anemia in a DSS-induced colitis mouse model maintained on an iron-sufficient diet
Authors: Samba-Mondonga Macha , Constante Marco , Fragoso Gabriela , Calvé Annie , Santos Manuela M. 
Published: November 2018

AbstractAnemia is frequently encountered in patients with inflammatory bowel disease (IBD), decreasing the quality of life and significantly worsening the prognosis of the disease. The pathogenesis of anemia in IBD is multifactorial and results mainly from intestinal blood loss in inflamed mucosa and impaired dietary iron absorption. Multiple studies have proposed the use of the polyphenolic compound curcumin to counteract IBD pathogenesis since it has significant preventive and therapeutic properties as an anti-inflammatory agent and very low toxicity, even at high dosages. However, curcumin has been shown to possess properties consistent with those of an iron-chelator, such as the ability to modulate proteins of iron metabolism and decrease spleen and liver iron content. Thus, this property may further contribute to the development and severity of anemia of inflammation and iron deficiency in IBD. Herein, we evaluate the effects of curcumin on systemic iron balance in the dextran sodium sulfate (DSS) model of colitis in C57Bl/6 and BALB/c mouse strains that were fed an iron-sufficient diet. In these conditions, curcumin supplementation caused mild anemia, lowered iron stores, worsened colitis and significantly decreased overall survival, independent of the mouse strain. These findings suggest that curcumin usage as an anti-inflammatory supplement should be accompanied by monitoring of erythroid parameters to avoid exacerbation of iron deficiency anemia in IBD.Core tipOur study shows that curcumin supplementation of an iron-sufficient diet causes mild anemia, depletes iron stores, worsens colitis and decreases survival, independent of the mouse strain. These findings demonstrate that curcumin may have a potential adverse activity in chronic inflammatory diseases, such as IBD, since the iron chelating properties of curcumin may play a role in iron deficiency and the severity of colitis.
Black pod disease profile: Monitoring its outbreak in Southwest, Nigeria
Authors: Etaware Peter M. , Adedeji Adegboyega R. 
Published: November 2018

AbstractBlack pod disease (BPD) has been and still remains a major threat to cocoa farmers worldwide due to its annual recurrence, fast spread and highly destructive nature. The disease has caused great anxiety in many cocoa producing communities due to the inability of indigenous cocoa farmers to determine when and where BPD outbreak will take place. Twelve (12) stations were structured from four important cocoa-producing States in the Southwestern region of Nigeria. An investigation of BPD outbreak was conducted in 2015/2016 within these regions. Infected cocoa pods and topsoil samples were collected for laboratory analysis. Pests attack, cherelle wilt and BPD outbreak were seasonal with 50% chances of occurrence in all the stations. Black pod diseases outbreak was recorded in all the States (100%) during the rainy season. The disease was at its peak in August 2015 in almost all the stations (station 1 (30.0%), station 3 (23.0%), station 11 (16.0%), station 4 (9.0%), station 5 (7.0%), and station 8 (3.0%). The height of disease severity was in September 2015 (station 1 (100.0%), station 3 (96.7%), station 5 (85.7%), station 11 (84.3%), and station 4 (70.0%), with station 8 reaching the 100% mark in October 2015. Most cocoa farmlands are now being abandoned, unless concerted efforts are made to effectively manage the disease, BPD will greatly reduce cocoa production in Nigeria and around the world.
Assessing the functional efficiency of agricultural futures markets in China
Authors: Ronghua Ju , Zhiling Yang 
Published: November 2018

Purpose
The purpose of this paper is to quantitatively analyse the changes in the functional efficiency of the six Chinese agricultural futures markets and compare the relative behaviour of different futures markets. In addition, this paper analyses the causes of differences in the functional efficiency of agricultural futures markets and advances policy suggestions.

Design/methodology/approach
The method used in this paper is the social loss index proposed by Stein (1981, 1986). This method can quantitatively measure the functional efficiency of agricultural futures markets from the perspective of social welfare. The indicator is calculated for the 2009–2017 period and for several sub-periods. The data are from the CSMAR research data services in China.

Findings
Preliminary results suggest that the longer it takes for an agricultural futures contract to reach maturity, the lower the functional efficiency of its market. Second, the functional efficiency of the agricultural futures markets in China is improved except for that of the wheat futures market. Finally, the corn futures market is most efficient probably due to the progress of marketization, while the strong wheat futures market is most inefficient probably due to the decrease in futures market liquidity.

Originality/value
This paper uses a more reasonable method to study the functional efficiency of Chinese agricultural futures markets and then analyses the causes of differences in the functional efficiency of agricultural futures markets.