bluuebunny/crossref_metadata_2025_split huggingface dataset:
NRPSsp: non-ribosomal peptide synthase substrate predictor
Authors: Prieto Carlos , García-Estrada Carlos , Lorenzana Diego , Martín Juan Francisco 
Published: December 2011

Abstract
Summary: Non-ribosomal peptide synthetases (NRPSs) are multi-modular enzymes, which biosynthesize many important peptide compounds produced by bacteria and fungi. Some studies have revealed that an individual domain within the NRPSs shows significant substrate selectivity. The discovery and characterization of non-ribosomal peptides are of great interest for the biotechnological industries. We have applied computational mining methods in order to build a database of NRPSs modules that bind to specific substrates. We have used this database to build a hidden Markov model predictor of substrates that bind to a given NRPS.
Availability: The database and the predictor are freely available on an easy-to-use website at www.nrpssp.com.
Contact: carlos.prieto@unileon.es
Supplementary information: Supplementary data is available at Bioinformatics online.
The TvPirin Gene Is Necessary for Haustorium Development in the Parasitic Plant Triphysaria versicolor
Authors: Bandaranayake Pradeepa C.G. , Tomilov Alexey , Tomilova Natalya B. , Ngo Quy A. , Wickett Norman , dePamphilis Claude W. , Yoder John I. 
Published: December 2011

Abstract
The rhizosphere is teemed with organisms that coordinate their symbioses using chemical signals traversing between the host root and symbionts. Chemical signals also mediate interactions between roots of different plants, perhaps the most obvious being those between parasitic Orobanchaceae and their plant hosts. Parasitic plants use specific molecules provided by host roots to initiate the development of haustoria, invasive structures critical for plant parasitism. We took a transcriptomics approach to identify parasitic plant genes associated with host factor recognition and haustorium signaling and previously identified a gene, TvPirin, which is transcriptionally up-regulated in roots of the parasitic plant Triphysaria versicolor after being exposed to the haustorium-inducing molecule 2,6-dimethoxybenzoquinone (DMBQ). Because TvPirin shares homology with proteins associated with environmental signaling in some plants, we hypothesized that TvPirin may function in host factor recognition in parasitic plants. We tested the function of TvPirin in T. versicolor roots using hairpin-mediated RNA interference. Reducing TvPirin transcripts in T. versicolor roots resulted in significantly less haustoria development in response to DMBQ exposure. We determined the transcript levels of other root expressed transcripts and found that several had reduced basal levels of gene expression but were similarly regulated by quinone exposure. Phylogenic investigations showed that TvPirin homologs are present in most flowering plants, and we found no evidence of parasite-specific gene duplication or expansion. We propose that TvPirin is a generalized transcription factor associated with the expression of a number of genes, some of which are involved in haustorium development.
Overexpression, purification, crystallization and preliminary X-ray analysis of CheY4 from Vibrio cholerae O395
Authors: Biswas Maitree , Khamrui Susmita , Sen Udayaditya , Dasgupta Jhimli 
Published: December 2011

Chemotaxis and motility greatly influence the infectivity of Vibrio cholerae, although the role of chemotaxis genes in V. cholerae pathogenesis is poorly understood. In contrast to the single copy of CheY found in Escherichia coli and Salmonella typhimurium, four CheYs (CheY1–CheY4) are present in V. cholerae. While insertional disruption of the cheY4 gene results in decreased motility, insertional duplication of this gene increases motility and causes enhanced expression of the two major virulence genes. Additionally, cheY3/cheY4 influences the activation of the transcription factor NF-κB, which triggers the generation of acute inflammatory responses. V. cholerae CheY4 was cloned, overexpressed and purified by Ni–NTA affinity chromatography followed by gel filtration. Crystals of CheY4 grown in space group C2 diffracted to 1.67 Å resolution, with unit-cell parameters a = 94.4, b = 31.9, c = 32.6 Å, β = 96.5°, whereas crystals grown in space group P3221 diffracted to 1.9 Å resolution, with unit-cell parameters a = b = 56.104, c = 72.283 Å, γ = 120°.
Effects of measurement methods on the relationship between smoking and delay reward discounting
Authors: Stillwell David J. , Tunney Richard J. 
Published: December 2011

ABSTRACTAims  Delay reward discounting (DRD) measures the degree to which a person prefers smaller rewards soon or larger rewards later. People who smoke have been shown to have higher DRD. There are several ways of measuring DRD, and the method used might influence the association between smoking and DRD. The key differences are the order in which the items are presented, the delays used and the magnitude of the delayed amount.Setting  An international online study running from September 2010 to June 2011.Participants  A total of 9454 individuals; 38% male, mean age = 23.1 years.Design and measurements  Users completed a multi‐item DRD task. They were randomly presented the immediate rewards in an ascending, descending or randomized order. The delays were between 1 week and 5 years. The delayed amounts were $1000 for all delays, and $100 for 1 month. Users also self‐reported their smoking status.Findings  A hyperbolic DRD function fitted better than an exponential function. There were differences in the derived DRD function based on methodology used; items presented in a randomized order, longer delays and smaller rewards showed steeper discounting. However, these did not interact with smoking status, as for all methodologies used daily smokers showed the steepest discounting, followed by non‐daily smokers, then non‐smokers.Conclusions  Smokers discount future consequences more than non‐smokers, irrespective of which measurement is used, but variations in method lead to different estimates that are not comparable between experiments.
Clinical significance of early T‐cell precursor acute lymphoblastic leukaemia: results of the Tokyo Children’s Cancer Study Group Study L99‐15
Authors: Inukai Takeshi , Kiyokawa Nobutaka , Campana Dario , Coustan‐Smith Elaine , Kikuchi Akira , Kobayashi Miyuki , Takahashi Hiroyuki , Koh Katsuyoshi , Manabe Atsushi , Kumagai Masaaki , Ikuta Koichiro , Hayashi Yasuhide , Tsuchida Masahiro , Sugita Kanji , Ohara Akira 
Published: December 2011

SummaryEarly T‐cell precursor acute lymphoblastic leukaemia (ETP‐ALL) is a recently identified subtype of T‐ALL with distinctive gene expression and cell marker profiles, poor response to chemotherapy and a very high risk of relapse. We determined the reliability of restricted panel of cell markers to identify EPT‐ALL using a previously classified cohort. Then, we applied the cell marker profile that best discriminated ETP‐ALL to a cohort of 91 patients with T‐ALL enrolled in the Tokyo Children’s Cancer Study Group L99‐15 study, which included allogeneic stem cell transplantation (allo‐SCT) for patients with poor prednisone response. Five of the 91 patients (5·5%) met the ETP‐ALL criteria. There were no significant differences in presenting clinical features between these and the remaining 86 patients. Response to early remission induction therapy was inferior in ETP‐ALL as compared with T‐ALL. The ETP‐ALL subgroup showed a significantly poorer event‐free survival (4‐year rate; 40%) than the T‐ALL subgroup (70%, P = 0·014). Of note, three of four relapsed ETP‐ALL patients survived after allo‐SCT, indicating that allo‐SCT can be effective for this drug‐resistant subtype of T‐ALL.
Dendritic cell‐targeted protein vaccines: a novel approach to induce T‐cell immunity
Authors: Trumpfheller C. , Longhi M. P. , Caskey M. , Idoyaga J. , Bozzacco L. , Keler T. , Schlesinger S. J. , Steinman R. M. 
Published: December 2011

Abstract.  Trumpfheller C, Longhi MP, Caskey M, Idoyaga J, Bozzacco L, Keler T, Schlesinger SJ, Steinman RM (The Rockefeller University, New York, NY; and Celldex Therapeutics, Phillipsburg, NJ; USA). Dendritic cell‐targeted protein vaccines: a novel approach to induce T‐cell immunity (Review). J Intern Med 2012; 271: 183–192.Current vaccines primarily work by inducing protective antibodies. However, in many infections like HIV, malaria and tuberculosis as well as cancers, there remains a need for durable and protective T‐cell immunity. Here, we summarize our efforts to develop a safe T‐cell–based protein vaccine that exploits the pivotal role of dendritic cells (DC) in initiating adaptive immunity. Focusing on HIV, gag‐p24 protein antigen is introduced into a monoclonal antibody (mAb) that efficiently and specifically targets the DEC‐205 antigen uptake receptor on DC. When administered together with synthetic double‐stranded RNA, polyriboinosinic:polyribocytidylic acid (poly IC) or its analogue poly IC stabilized with carboxymethylcellulose and poly‐L‐lysine (poly ICLC), as adjuvant, HIV gag‐p24 within anti‐DEC‐205 mAb is highly immunogenic in mice, rhesus macaques, and in ongoing research, healthy human volunteers. Human subjects form both T‐ and B‐cell responses to DC‐targeted protein. Thus, DC‐targeted protein vaccines are a potential new vaccine platform, either alone or in combination with highly attenuated viral vectors, to induce integrated immune responses against microbial or cancer antigens, with improved ease of manufacturing and clinical use.
Is diversification history of maize influencing selection of soil bacteria by roots?
Authors: BOUFFAUD MARIE‐LARA , KYSELKOVÁ MARTINA , GOUESNARD BRIGITTE , GRUNDMANN GENEVIEVE , MULLER DANIEL , MOËNNE‐LOCCOZ YVAN 
Published: December 2011

AbstractA wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant‐microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21‐day‐old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning/sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings.
Caudolateral orbitofrontal regional cerebral blood flow is decreased in abstinent cocaine‐addicted subjects in two separate cohorts
Authors: Adinoff Bryon , Braud Jacquelyn , Devous Michael D. , Harris Thomas S. 
Published: December 2011

ABSTRACTThe orbitofrontal cortex (OFC) is crucial for the inhibition of extraneous stimuli, evaluation of aversive information and emotional regulation—all behaviors impaired in cocaine addiction. Previous studies suggest that cocaine‐addicted subjects have decreased basal activity in the OFC. In this study, we examined regional cerebral blood flow (rCBF) during a saline infusion in two independent populations of abstinent cocaine‐ (and mostly nicotine‐) addicted (n = 33 and 26) and healthy control (n = 35 and 20) men and women. Isolated rCBF decreases (P < 0.001) were observed in the left caudolateral OFC, as well as left superior temporal cortex, in cocaine‐addicted subjects relative to controls in both cohorts and bilaterally in the combined cohort. An anatomically defined region of the caudolateral OFC showed similar findings and were evident in both male and female addicted subjects. The reliability of these findings across two cohorts reveals a functional disruption in the lateral OFC, a brain region implicated in the evaluation of behavior‐terminating stimuli. This may contribute to an addicted individual's persistent drug use despite negative consequences.
Duodenoduodenostomy in pancreas transplantation
Authors: Gunasekaran Ganesh , Wee Alvin , Rabets John , Winans Charles , Krishnamurthi Venkatesh 
Published: December 2011

Gunasekaran G, Wee A, Rabets J, Winans C, Krishnamurthi V. Duodenoduodenostomy in pancreas transplantation.Abstract:  Enteric drainage (ED) using duodenojejunostomy (DJ) is an established technique in pancreatic transplantation. Duodenoduodenostomy (DD), an alternative ED technique, may provide unique advantages over DJ. We compared our experience with these two types of ED through a retrospective review of all pancreas transplants performed at our institution from November 2007 to November 2009. The allograft duodenum was anastomosed to the recipient jejunum or duodenum. Duodenal drainage was performed by a stapled or hand‐sewn technique. Patient demographics, operative times, major post‐operative complications, and graft survival data were analyzed. Of 57 pancreas transplants, DJ was performed in 36 patients, stapled DD in 14 patients, and hand‐sewn DD in seven patients. Two DD grafts (9.5%) thrombosed compared with no DJ grafts (p = NS). Enteric leak and small‐bowel obstruction occurred in 3 of 36 DJ patients and in two DD patients (p = NS). Gastrointestinal bleeding occurred more frequently in stapled DD compared with DJ (4 vs. 0, p < 0.015). In conclusion, DD is technically feasible with no increase in operative time or enteric complications. GI bleeding rates appear to be higher following DD (stapled) technique. Potential complications of DD should be balanced against the benefits conferred by this technique.
Anidulafungin treatment in a kidney transplant recipient with hepatic damage
Authors: De Rosa Francesco G. , Manzione NA. , Ranghino Andrea , Messina Marina , Ottobrelli Antonio , Raviolo Stefania , Di Perri Giovanni , Segoloni Giuseppe Paolo 
Published: December 2011

SummaryA 50‐year old female was treated with anidulafungin after fluconazole treatment, for a complex clinical picture and immunosuppression. Anidulafungin was chosen when liver function test was abnormal in a setting of multiple causes of liver toxicity.
Obesity‐induced renal impairment is exacerbated in interleukin‐6‐knockout mice
Authors: HARCOURT BROOKE E , FORBES JOSEPHINE M , MATTHEWS VANCE B 
Published: December 2011

ABSTRACT:Aim:  Interleukin‐6 (IL‐6) is secreted from adipose tissue and thought to contribute to obesity‐related disorders. The aim of this study was to assess if IL‐6‐knockout (IL‐6‐/‐) mice would develop obesity‐induced renal impairment.Methods:  Wild‐type (WT) and IL‐6‐/‐ mice were high‐fat fed (HFF) for 16 weeks to induce obesity. At the end of the study, renal function was measured via albumin/creatinine ratio and serum creatinine levels, using enzyme‐linked immunosorbent assay (ELISA) and high‐performance liquid chromatography (HPLC). Glomerulosclerotic index (GSI) was scored in periodic acid Schiff‐stained sections and collagen IV accumulation was assessed by immunohistochemistry. Renal cortical tumour growth factor beta (TGF‐β1) activity and monocyte chemotactic protein‐1 (MCP‐1) levels were measured via ELISA.Results:  Renal IL‐6 concentrations were increased with obesity. Although both WT HFF and IL‐6‐/‐ HFF mice exhibited renal impairment as measured by increased serum creatinine and urinary albumin/creatinine ratios, this was exacerbated in IL‐6‐/‐ mice. Obese mice had renal activation of cortical TGF‐β1, which was also higher in IL‐6‐/‐ mice. Collagen IV staining was not affected by obesity. GSI was increased with obesity in both WT and IL‐6‐/‐ mice.Conclusion:  Obese IL‐6‐/‐ mice demonstrated renal functional and structural abnormalities above that seen in obese WT mice. We suggest that absence or low IL‐6 levels may be an important accelerating factor implicated in the development and progression of obesity‐induced renal disease.
A comparative analysis of chemically induced sex reversal in teleosts: challenging conventional suppositions
Authors: Senior Alistair M , Nakagawa Shinichi 
Published: December 2011

AbstractEnvironmental sex reversal (ESR) occurs when extreme environmental factors overpower predetermined sexual development. Scientific theory is beginning to acknowledge the potential roles of sex‐reversed individuals in influencing population dynamics and driving the evolution of sex‐determination mechanisms. ESR is a phenomenon that has been widely observed in fish and can be induced by exposing individuals to exogenous hormones. However, reports of the susceptibility of fish to hormonally induced ESR vary greatly – a concept we termed ‘inducibility’. It has been suggested that variation in inducibility can be attributed to biological differences among species of different taxonomic groups (i.e. phylogenetic effects are present). Here, we provide the first quantitative test of this theory, which was achieved by combining published data with phylogenetic trees, using phylogenetically controlled comparative analysis. Our results confirm that a great amount of variation exists in the reported inducibility of fish. However, species and taxonomic relationships were responsible for trivial portions of variation. Rather, we found that sampling (measurement) errors in combination with methodological differences across studies accounted for much more variation in inducibility than taxonomy did. Given that our analysis contains representatives from over 25% of all teleost orders, we conclude that inducibility is not a taxonomically constrained trait in teleosts. Therefore, we suggest that the sex‐determination mechanisms of most fish are uniformly plastic. Further, we propose that ESR occurs relatively regularly over evolutionary time in many teleost species, playing a vital role in the maintenance of homomorphic sex chromosomes in this taxonomic group.
Flat whites: who gets progression in the UK café sector?
Authors: Lloyd Caroline , Payne Jonathan 
Published: December 2011

ABSTRACTThe article examines the opportunities for, and barriers to, career progression in the UK café sector. The research finds that some workers are able to move up within organisations to reach managerial levels, regardless of their qualifications. However, the limited positions available, the nature of the work and low rewards mean that most workers either do not want progression or feel that they are unlikely to succeed.
Cost‐efficacy of adalimumab, etanercept, infliximab and ustekinumab for moderate‐to‐severe plaque psoriasis
Authors: Ferrándiz C. , García A. , Blasco A.J. , Lázaro P. 
Published: December 2011

AbstractBackground  Different biological agents are used for the treatment of psoriasis. Previous data have shown adalimumab to be the most efficient drug in terms of cost‐efficacy. However, newer data are required to include recent drugs.Objective  To estimate the cost‐efficacy ratios of biological agents licensed in Spain (adalimumab, etanercept, infliximab and ustekinumab) for the treatment of patients with moderate‐to‐severe psoriasis.Methods  An economic evaluation model was developed by building a decision tree for each drug regimen for which scientific evidence was available. The payer perspective (Spanish National Health System) was considered, taking into account only the drug costs. Data on efficacy [proportion of patients with a 75% reduction in the Psoriasis Area and Severity Index score (PASI 75)] reported in the randomized controlled trials were used. When more than one trial for each treatment had been published, a meta‐analysis was performed. In case of weight‐dependent doses (infliximab), weight of the study subjects was standardized by age and gender of the Spanish population, corrected for the increase in weight in subjects with psoriasis. Uncertainty was assessed by sensitivity analysis.Results  Incremental efficacy ranged from 31.19% (etanercept at a dosage of 25 mg twice a week for 12 weeks) to 78.35% (infliximab at 5 mg/kg for 24 weeks). Efficiency, in terms of incremental cost‐efficacy, ranged from 8013€ (adalimumab) to 17 981€ (ustekinumab at a dose of 90 mg) per PASI 75 responder gained.Conclusion  In terms of cost‐efficacy, the most efficient biological drug was adalimumab. The robustness of this finding was confirmed by sensitivity analysis.
The effect of topical negative pressure on wound biofilms using an in vitro wound model
Authors: Ngo Quan D. , Vickery Karen , Deva Anand K. 
Published: December 2011

AbstractChronic non‐healing wounds affect a significant number of patients worldwide. Although the etiologies of these wounds are varied, bacterial infection has been suggested as a major factor responsible for the perpetual inflammation and tissue destruction observed in such wounds. Recent evidence has emerged suggesting that bacterial biofilms in particular may have a significant role in this process. At the same time, topical negative pressure dressing is gaining acceptance as a therapy which promotes healing in recalcitrant wounds. In this study an in vitro Pseudomonas aeruginosa biofilm model was developed to mimic potential surface wound biofilms. Topical negative pressure dressing was applied to the model and the effects of topical negative pressure dressing on the in vitro wound biofilms were examined using both quantitative microbiological counting technique and imaging studies. The results demonstrated a small but statistically significant reduction in biofilm bacteria at 2 weeks when exposed to topical negative pressure. When this was combined with silver impregnated foam, the reduction was far more significant and was observable within 24 hours. Microscopically, it was also noted that topical negative pressure compressed the biofilm architecture with a reduction in thickness and diffusion distance.