bluuebunny/crossref_metadata_2025_split huggingface dataset:
3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape
Authors: Wang Qi , Tang Biao , Song Lifu , Ren Biao , Liang Qun , Xie Feng , Zhuo Ying , Liu Xueting , Zhang Lixin 
Published: November 2013

Abstract

Background
The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools.

Results
We developed a 3D Cytoscape Client/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies.

Conclusions
Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.
The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity
Authors: Hermann-Bank Marie Louise , Skovgaard Kerstin , Stockmarr Anders , Larsen Niels , Mølbak Lars 
Published: November 2013

Abstract

Background
The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the importance of intestinal bacteria. Several molecular methods can be applied to describe the composition of the microbiota. This study used a new approach, the Gut Microbiotassay: an assembly of 24 primer sets targeting the main phyla and taxonomically related subgroups of the intestinal microbiota, to be used with the high-throughput qPCR chip ‘Access Array 48.48′, AA48.48, (Fluidigm®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets with and without diarrhoea. The PCR amplicons from the 2304 reaction chambers were harvested from the AA48.48, purified, and sequenced using 454-technology.

Results
The Gut Microbiotassay was able to detect significant differences in the quantity and composition of the microbiota according to gut sections and diarrhoeic status. 454-sequencing confirmed the specificity of the primer sets. Diarrhoea was associated with a reduced number of members from the genus Streptococcus, and in particular S. alactolyticus.

Conclusion
The Gut Microbiotassay provides fast and affordable high-throughput quantification of the bacterial composition in many samples and enables further descriptive taxonomic information if combined with 454-sequencing.
The role of arginine and arginine-metabolizing enzymes during Giardia – host cell interactions in vitro
Authors: Stadelmann Britta , Hanevik Kurt , Andersson Mattias K , Bruserud Oystein , Svärd Staffan G 
Published: November 2013

Abstract

Background
Arginine is a conditionally essential amino acid important in growing individuals and under non-homeostatic conditions/disease. Many pathogens interfere with arginine-utilization in host cells, especially nitric oxide (NO) production, by changing the expression of host enzymes involved in arginine metabolism. Here we used human intestinal epithelial cells (IEC) and three different isolates of the protozoan parasite Giardia intestinalis to investigate the role of arginine and arginine-metabolizing enzymes during intestinal protozoan infections.

Results
RNA expression analyses of major arginine-metabolizing enzymes revealed the arginine-utilizing pathways in human IECs (differentiated Caco-2 cells) grown in vitro. Most genes were constant or down-regulated (e.g. arginase 1 and 2) upon interaction with Giardia, whereas inducible NO synthase (iNOS) and ornithine decarboxylase (ODC) were up-regulated within 6 h of infection. Giardia was shown to suppress cytokine-induced iNOS expression, thus the parasite has both iNOS inducing and suppressive activities. Giardial arginine consumption suppresses NO production and the NO-degrading parasite protein flavohemoglobin is up-regulated in response to host NO. In addition, the secreted, arginine-consuming giardial enzyme arginine deiminase (GiADI) actively reduces T-cell proliferation in vitro. Interestingly, the effects on NO production and T cell proliferation could be reversed by addition of external arginine or citrulline.

Conclusions

Giardia affects the host’s arginine metabolism on many different levels. Many of the effects can be reversed by addition of arginine or citrulline, which could be a beneficial supplement in oral rehydration therapy.
Multivariable analysis of the association between fathers’ and youths’ physical activity in the United States
Authors: Isgor Zeynep , Powell Lisa M , Wang Youfa 
Published: November 2013

Abstract

Background
Although the benefits of physical activity have been well-established, a significant number of children and adolescents in the U.S. do not meet the recommended levels of daily physical activity. Parental influences such as parents’ physical activity participation may play an important role in affecting youths’ physical activity.

Methods
This study used the Child Development Supplement of the Panel Study of Income Dynamics to examine the associations between fathers’ vigorous physical activity (VPA) and VPA participation (>0 day(s)/week) and frequency (days/week) of 887 youths aged 10 through 18 based on a nationally representative sample of families in the US. Logistic and negative binomial regression analyses were used to examine the association between past frequency (times/week) and an indicator of recommended (≥3 times/week) frequency of father’s VPA and youth’s VPA participation and youths’ VPA frequency, respectively. We examined the sensitivity to the inclusion of various youth, family, mother’s VPA, and contextual control measures. Analyses also were undertaken by gender.

Results
Father’s past VPA frequency was positively associated with both youths’ VPA participation and with youths’ VPA frequency for the full and female samples of youths, even after the inclusion of demographic, socio-economic, and local area characteristics. Father’s past recommended VPA frequency was positively associated with youths’ VPA participation in the full sample only and with youths’ VPA frequency in the female sub-sample only. Simulation results showed that an increase in father’s past weekly VPA frequency from zero to the minimum recommended level (three times per week) was associated with an increased predicted probability of youths’ weekly VPA participation from approximately 67% to 74% for the full sample (61% to 73% for females and 74% to 77% for males).

Conclusion
The results from this study suggest that environmental and/or family based interventions that increase fathers’ VPA may help improve youths’ VPA.
Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom Phaeodactylum tricornutum
Authors: Zheng Yuting , Quinn Andrew H , Sriram Ganesh 
Published: November 2013

Abstract

Background
Heterotrophic fermentation using simple sugars such as glucose is an established and cost-effective method for synthesizing bioproducts from bacteria, yeast and algae. Organisms incapable of metabolizing glucose have limited applications as cell factories, often despite many other advantageous characteristics. Therefore, there is a clear need to investigate glucose metabolism in potential cell factories. One such organism, with a unique metabolic network and a propensity to synthesize highly reduced compounds as a large fraction of its biomass, is the marine diatom Phaeodactylum tricornutum (Pt). Although Pt has been engineered to metabolize glucose, conflicting lines of evidence leave it unresolved whether Pt can natively consume glucose.

Results
Isotope labeling experiments in which Pt was mixotrophically grown under light on 100% U-13C glucose and naturally abundant (~99% 12C) dissolved inorganic carbon resulted in proteinogenic amino acids with an average 13C-enrichment of 88%, thus providing convincing evidence of glucose uptake and metabolism. The dissolved inorganic carbon was largely incorporated through anaplerotic rather than photosynthetic fixation. Furthermore, an isotope labeling experiment utilizing 1-13C glucose and subsequent metabolic pathway analysis indicated that (i) the alternative Entner-Doudoroff and Phosphoketolase glycolytic pathways are active during glucose metabolism, and (ii) during mixotrophic growth, serine and glycine are largely synthesized from glyoxylate through photorespiratory reactions rather than from 3-phosphoglycerate. We validated the latter result for mixotrophic growth on glycerol by performing a 2-13C glycerol isotope labeling experiment. Additionally, gene expression assays showed that known, native glucose transporters in Pt are largely insensitive to glucose or light, whereas the gene encoding cytosolic fructose bisphosphate aldolase 3, an important glycolytic enzyme, is overexpressed in light but insensitive to glucose.

Conclusion
We have shown that Pt can use glucose as a primary carbon source when grown in light, but cannot use glucose to sustain growth in the dark. We further analyzed the metabolic mechanisms underlying the mixotrophic metabolism of glucose and found isotopic evidence for unusual pathways active in Pt. These insights expand the envelope of Pt cultivation methods using organic substrates. We anticipate that they will guide further engineering of Pt towards sustainable production of fuels, pharmaceuticals, and platform chemicals.
PftetQ and pfmdt copy numbers as predictive molecular markers of decreased ex vivo doxycycline susceptibility in imported Plasmodium falciparum malaria
Authors: Gaillard Tiphaine , Briolant Sébastien , Houzé Sandrine , Baragatti Meïli , Wurtz Nathalie , Hubert Véronique , Lavina Morgane , Pascual Aurélie , Travaillé Christelle , Le Bras Jacques , Pradines Bruno ,   The French National Reference Centre for Imported Malaria Study Group
Published: November 2013

AbstractBackgroundThe objective of this study was to evaluate the distribution of a series of independent doxycycline inhibitory concentration 50% (IC50) values to validate the trimodal distribution previously described and to validate the use of thepftetQandpfmdtgenes as molecular markers of decreasedin vitrodoxycycline susceptibility inPlasmodium falciparummalaria.MethodsDoxycycline IC50values, from 484 isolates obtained at the French National Reference Centre for Imported Malaria (Paris) between January 2006 and December 2010, were analysed for the first time by a Bayesian mixture modelling approach to distinguish the differentin vitrophenotypic groups by their IC50values. Quantitative real-time polymerase chain reaction was used to evaluate thepftetQandpfmdtcopy numbers of 89 AfricanP. falciparumisolates that were randomly chosen from the phenotypic groups.ResultsThe existence of at least three doxycycline phenotypes was demonstrated. The mean doxycycline IC50was significantly higher in the group with apftetQcopy number >1 compared to the group with apftetQcopy number = 1 (33.17 μMversus17.23 μM) and the group with apfmdtcopy number >1 (28.28 μMversus16.11 μM). There was a significant difference between the combined low and medium doxycycline IC50group and the high IC50group in terms of the per cent of isolates with one or more copy numbers of thepftetQgene (0%versus20.69%) orpfmdtgene (8.33%versus37.93%). In the logistic regression model, thepfmdtandpftetQcopy numbers >1 (odds ratio = 4.65 and 11.47) were independently associated with the high IC50group.ConclusionsCopy numbers ofpftetQandpfmdtare potential predictive molecular markers of decreased susceptibility to doxycycline.
Cheek cell fatty acids reflect n-3 PUFA in blood fractions during linseed oil supplementation: a controlled human intervention study
Authors: Grindel Annemarie , Staps Frank , Kuhnt Katrin 
Published: November 2013

Abstract

Background
Adequate biomarkers for the dietary supply of fatty acids (FA) are FA of adipose tissue and blood fractions. In human studies, invasive sample collection is unpleasant for subjects. In contrast, cheek cell sampling can be considered as a non-invasive alternative to investigate FA status.
The aim of this study was to analyze whether cheek cell FA composition reflect the supplementation of alpha-linolenic acid (ALA) using a linseed oil mixture compared to olive oil supplementation. Additionally, it was investigated if cheek cell FA composition correlates with the FA composition of plasma, red blood cells (RBC) and peripheral blood mononuclear cells (PBMC) before and during both interventions.

Methods
During a 10-week randomized, controlled, double-blind human intervention study, 38 subjects provided cheek cell and blood samples. After a two-week run-in period, the test group (n = 23) received 17 g/d of an ALA-rich linseed oil mixture, while the control group (n = 15) received 17 g/d of an omega-3 (n-3) polyunsaturated FA (PUFA)-free olive oil. Cheek cells and blood were collected on days 0, 7 and 56 of the 8-week intervention period.

Results
Compared to olive oil, the linseed oil intervention increased ALA and also the endogenously converted long-chain n-3 metabolites eicosatetraenoic-, eicosapentaenoic- and docosapentaenoic acid in cheek cells (P ≤ 0.05). Docosahexaenoic acid remained unchanged. Reflecting the treatment, the n-6/n- 3 ratio decreased in the test group. In general, cheek cell FA reflected the changes of FA in blood fractions. Independent of treatment, significant correlations (P ≤ 0.05) of n-6 PUFA and n- 3 PUFA between cheek cells and plasma, RBC and PBMC were found, except for linoleic acid and ALA.

Conclusions
The changes in FA composition of cheek cells confirmed that ALA from linseed oil increased endogenously derived n- 3 PUFA in cheek cell lipids. These changes in cheek cells and their correlation to the respective FA in blood fractions indicate the cheek cell FA profile as an adequate non-invasive biomarker for short-term n-3 PUFA intake and metabolism. Therefore, cheek cell FA can be used in human intervention studies or large-scale epidemiological studies, especially for assessment of the n-3 PUFA status.

Trial registration
ClinicalTrials.gov, IDNCT01317290
Effects of selenoprotein S on oxidative injury in human endothelial cells
Authors: Zhao Yin , Li Hua , Men Li-li , Huang Rong-chong , Zhou Hai-cheng , Xing Qian , Yao Jun-jie , Shi Chun-hong , Du Jian-ling 
Published: November 2013

Abstract

Background
Selenoprotein S (SelS) is an important endoplasmic reticulum and plasma membrane-located selenoprotein implicated in inflammatory responses and insulin resistance. However, the effects of SelS on endothelial cells (ECs) have not been reported. In the present study, the role of SelS in oxidative stress and the underlying mechanism were investigated in human ECs.

Methods
A SelS over-expression plasmid (pc-SelS) and a SelS-siRNA plasmid were transfected into human umbilical vein endothelial cells (American Type Culture Collection, USA). The cells were divided into four groups: control, SelS over-expression (transfected with pc-SelS), vector control, and SelS knockdown (transfected with siRNA-SelS). After treating the cells with H2O2, the effects of oxidative stress and the expression of caveolin-1 (Cav-1) and protein kinase Cα (PKCα) were investigated.

Results
Following treatment with H2O2, over-expression of SelS significantly increased cell viability and superoxide dismutase (SOD) activity, and decreased malondialdehyde (MDA) production and Cav-1 gene and protein expression. However, no effects on PKCα were observed. In contrast, knockdown of SelS significantly decreased cell viability, SOD activity, and PKCα gene and protein expression, and increased MDA production and Cav-1 gene and protein expression.

Conclusions
SelS protects ECs from oxidative stress by inhibiting the expression of Cav-1 and PKCα.
Discovery of a diaminoquinoxaline benzenesulfonamide antagonist of HIV-1 Nef function using a yeast-based phenotypic screen
Authors: Trible Ronald P , Narute Purushottam , Emert-Sedlak Lori A , Alvarado John Jeff , Atkins Katelyn , Thomas Laurel , Kodama Toshiaki , Yanamala Naveena , Korotchenko Vasiliy , Day Billy W , Thomas Gary , Smithgall Thomas E 
Published: November 2013

AbstractBackgroundHIV-1 Nef is a viral accessory protein critical for AIDS progression. Nef lacks intrinsic catalytic activity and binds multiple host cell signaling proteins, including Hck and other Src-family tyrosine kinases. Nef binding induces constitutive Hck activation that may contribute to HIV pathogenesis by promoting viral infectivity, replication and downregulation of cell-surface MHC-I molecules. In this study, we developed a yeast-based phenotypic screen to identify small molecules that inhibit the Nef-Hck complex.ResultsNef-Hck interaction was faithfully reconstituted in yeast cells, resulting in kinase activation and growth arrest. Yeast cells expressing the Nef-Hck complex were used to screen a library of small heterocyclic compounds for their ability to rescue growth inhibition. The screen identified a dihydrobenzo-1,4-dioxin-substituted analog of 2-quinoxalinyl-3-aminobenzene-sulfonamide (DQBS) as a potent inhibitor of Nef-dependent HIV-1 replication and MHC-I downregulation in T-cells. Docking studies predicted direct binding of DQBS to Nef which was confirmed in differential scanning fluorimetry assays with recombinant purified Nef protein. DQBS also potently inhibited the replication of HIV-1 NL4-3 chimeras expressing Nef alleles representative of all M-group HIV-1 clades.ConclusionsOur findings demonstrate the utility of a yeast-based growth reversion assay for the identification of small molecule Nef antagonists. Inhibitors of Nef function discovered with this assay, such as DQBS, may complement the activity of current antiretroviral therapies by enabling immune recognition of HIV-infected cells through the rescue of cell surface MHC-I.
In vitro inhibition of mumps virus by retinoids
Authors: Soye Kaitlin J , Trottier Claire , Di Lenardo Thomas Z , Restori Katherine H , Reichman Lee , Miller Wilson H , Ward Brian J 
Published: November 2013

AbstractBackgroundMumps virus (MuV) is a highly infectious paramyxovirus closely related to measles virus (MeV). Despite the availability of a mumps vaccine, outbreaks continue to occur and no treatment options are available. Vitamin A and other naturally occurring retinoids inhibit the replication of MeVin vitro.MethodsAnti-viral effects of retinoids were observed in cell culture using the myelomonocytic U937, NB4/R4, and Huh7/7.5 cells. Observations of anti-viral effect were quantified using TCID50 analysis. Molecular properties of the antiviral effect were analysed using quantitative RT-PCR and western blot.ResultsThe current work demonstrates that retinoids inhibit MuVin vitrodue to up-regulation of type I interferon (IFN) and IFN stimulated genes. This effect is mediated by nuclear retinoid receptor signalling and RIG-I is required. The antiviral retinoid-induced state makes cells less permissive to viral replication from subsequent challenge with either MuV or MeV for less than 12 hours.ConclusionsThese results demonstrate that retinoids inhibit MuV replication in uninfected bystander cells through a retinoid inducible gene I (RIG-I), retinoic acid receptor (RAR) and IFN dependent manner making them refractory to subsequent rounds of viral replication. These observations raise the possibility that pharmacological doses of retinoids might have clinical benefit in MuV infection.
Interventions for increasing ankle joint dorsiflexion: a systematic review and meta‐analysis
Authors: Young Rebekah , Nix Sheree , Wholohan Aaron , Bradhurst Rachael , Reed Lloyd 
Published: November 2013

AbstractBackgroundAnkle joint equinus, or restricted dorsiflexion range of motion (ROM), has been linked to a range of pathologies of relevance to clinical practitioners. This systematic review and meta‐analysis investigated the effects of conservative interventions on ankle joint ROM in healthy individuals and athletic populations.MethodsKeyword searches of Embase, Medline, Cochrane and CINAHL databases were performed with the final search being run in August 2013. Studies were eligible for inclusion if they assessed the effect of a non‐surgical intervention on ankle joint dorsiflexion in healthy populations. Studies were quality rated using a standard quality assessment scale. Standardised mean differences (SMDs) and 95% confidence intervals (CIs) were calculated and results were pooled where study methods were homogenous.ResultsTwenty‐three studies met eligibility criteria, with a total of 734 study participants. Results suggest that there is some evidence to support the efficacy of static stretching alone (SMDs: range 0.70 to 1.69) and static stretching in combination with ultrasound (SMDs: range 0.91 to 0.95), diathermy (SMD 1.12), diathermy and ice (SMD 1.16), heel raise exercises (SMDs: range 0.70 to 0.77), superficial moist heat (SMDs: range 0.65 to 0.84) and warm up (SMD 0.87) in improving ankle joint dorsiflexion ROM.ConclusionsSome evidence exists to support the efficacy of stretching alone and stretching in combination with other therapies in increasing ankle joint ROM in healthy individuals. There is a paucity of quality evidence to support the efficacy of other non‐surgical interventions, thus further research in this area is warranted.
Amino acid digestibility of heat damaged distillers dried grains with solubles fed to pigs
Authors: Almeida Ferdinando Nielsen , Htoo John Kyaw , Thomson John , Stein Hans Henrik 
Published: November 2013

AbstractThe primary objective of this experiment was to determine the effects of heat treatment on the standardized ileal digestibility (SID) of amino acids (AA) in corn distillers dried grains with solubles (DDGS) fed to growing pigs. The second objective was to develop regression equations that may be used to predict the concentration of SID AA in corn DDGS. A source of corn DDGS was divided into 4 batches that were either not autoclaved or autoclaved at 130°C for 10, 20, or 30 min. Four diets containing DDGS from each of the 4 batches were formulated with DDGS being the only source of AA and CP in the diets. A N-free diet also was formulated and used to determine the basal endogenous losses of CP and AA. Ten growing pigs (initial BW: 53.5 ± 3.9 kg) were surgically equipped with a T-cannula in the distal ileum and allotted to a replicated 5 × 4 Youden square design with 5 diets and 4 periods in each square. The SID of CP decreased linearly (P < 0.05) from 77.9% in non-autoclaved DDGS to 72.1, 66.1, and 68.5% in the DDGS samples that were autoclaved for 10, 20, or 30 min, respectively. The SID of lysine was quadratically reduced (P < 0.05) from 66.8% in the non-autoclaved DDGS to 54.9, 55.3, and 51.9% in the DDGS autoclaved for 10, 20, or 30 min, respectively. The concentrations of SID Arginine, Histidine, Leucine, Lysine, Methionine, Phenylalanine, or Threonine may be best predicted by equations that include the concentration of acid detergent insoluble N in the model (r2 = 0.76, 0.68, 0.67, 0.84, 0.76, 0.73, or 0.54, respectively). The concentrations of SID Isoleucine and Valine were predicted (r2 = 0.58 and 0.54, respectively) by the Lysine:CP ratio, whereas the concentration of SID Tryptophan was predicted (r2 = 0.70) by the analyzed concentration of Tryptophan in DDGS. In conclusion, the SID of AA is decreased as a result of heat damage and the concentration of SID AA in heat-damaged DDGS may be predicted by regression equations developed in this experiment.