bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Authors: Tang Kuo-Hsiang , Barry Kerrie , Chertkov Olga , Dalin Eileen , Han Cliff S , Hauser Loren J , Honchak Barbara M , Karbach Lauren E , Land Miriam L , Lapidus Alla , Larimer Frank W , Mikhailova Natalia , Pitluck Samuel , Pierson Beverly K , Blankenship Robert E 
Published: June 2011

Abstract

Background

Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

Methods
The complete genomic sequence of Cfl. aurantiacus has been determined, analyzed and compared to the genomes of other photosynthetic bacteria.

Results
Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in Cfl. aurantiacus to facilitate life under both anaerobic and aerobic conditions, including duplicate genes and gene clusters for the alternative complex III (ACIII), auracyanin and NADH:quinone oxidoreductase; and several aerobic/anaerobic enzyme pairs in central carbon metabolism and tetrapyrroles and nucleic acids biosynthesis. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of Cfl. aurantiacus. Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO2-anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in Cfl. aurantiacus are discussed. Some features of the Cfl. aurantiacus genome are compared with those of the Roseiflexus castenholzii genome. Roseiflexus castenholzii is a recently characterized FAP bacterium and phylogenetically closely related to Cfl. aurantiacus. According to previous reports and the genomic information, perspectives of Cfl. aurantiacus in the evolution of photosynthesis are also discussed.

Conclusions
The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph Cfl. aurantiacus has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.
Cortical gene transcription response patterns to water maze training in aged mice
Authors: Park Sung-Soo , Stranahan Alexis M , Chadwick Wayne , Zhou Yu , Wang Liyun , Martin Bronwen , Becker Kevin G , Maudsley Stuart 
Published: June 2011

Abstract

Background
The hippocampus mediates the acquisition of spatial memory, but the memory trace is eventually transferred to the cortex. We have investigated transcriptional activation of pathways related to cognitive function in the cortex of the aged mouse by analyzing gene expression following water maze training.

Results
We identified genes that were differentially responsive in aged mice with accurate spatial performance during probe trials or repeated swimming sessions, relative to home cage conditions. Effective learners exhibited significantly greater activation of several pathways, such as the mitogen-activated protein kinase and insulin receptor signaling pathways, relative to swimmers. The genes encoding activity-related cytoskeletal protein (Arc) and brain-derived neurotrophic factor (BDNF) were upregulated in proficient learners, relative to swimmers and home cage controls, while the gene encoding Rho GTPase activating protein 32 (GRIT) was downregulated. We explored the regulation of Arc, BDNF, and GRIT expression in greater morphological detail using in situ hybridization. Recall during probe trials enhanced Arc expression across multiple cortical regions involved in the cognitive component of water maze learning, while BDNF expression was more homogeneously upregulated across cortical regions involved in the associational and sensorimotor aspects of water maze training. In contrast, levels of GRIT expression were uniformly reduced across all cortical regions examined.

Conclusions
These results suggest that cortical gene transcription is responsive to learning in aged mice that exhibit behavioral proficiency, and support a distributed hypothesis of memory storage across multiple cortical compartments.
Serotonin transporter gene polymorphism may be associated with functional dyspepsia in a Japanese population
Authors: Toyoshima Fumihiko , Oshima Tadayuki , Nakajima Shigemi , Sakurai Jun , Tanaka Junji , Tomita Toshihiko , Hori Kazutoshi , Matsumoto Takayuki , Miwa Hiroto 
Published: June 2011

Abstract

Background
Although familial clustering of functional dyspepsia (FD) has been reported, the role of genetics in the susceptibility to FD is still not well understood. In the present study, the association between serotonin transporter (SERT) gene (SLC6A4) polymorphism and FD was explored.

Methods
Subjects were divided into either a postprandial distress syndrome (PDS) group or an epigastric pain syndrome (EPS) group according to the Rome III criteria. The healthy controls were those who had visited a hospital for an annual health check-up. The presence of the SLC6A4 promoter polymorphism, 5-hydroxytryptamin transporter gene linked polymorphic region (5-HTTLPR), was then evaluated, and logistic regression analysis was used to test all variables.

Results
The 5-HTTLPR genotype distribution was 448 SS, 174 SL, and 24 LL in controls and 30 SS, 20 SL, and 3 LL in FD subjects. No significant correlation was found between the 5-HTTLPR genotype and FD. When the genotypes and subtypes of FD were exploratory evaluated, the SL genotype was significantly associated with PDS [odds ratio (OR) = 2.24, 95% confidence interval (CI); 1.16-4.32, P = 0.034 after Bonferroni correction] compared to the SS genotype adjusted for sex and age. Comparison of the SS genotype with the SL/LL genotype also showed a significant association of genotype with PDS (OR = 2.32, 95% CI; 1.23-4.37, P = 0.009).

Conclusion
The present results suggest that 5-HTTLPR L allele may influence the susceptibility to PDS.
The ratio of CRP to prealbumin levels predict mortality in patients with hospital-acquired acute kidney injury
Authors: Xie Qionghong , Zhou Ying , Xu Zhongye , Yang Yanjiao , Kuang Dingwei , You Huaizhou , Ma Shuai , Hao Chuanming , Gu Yong , Lin Shanyan , Ding Feng 
Published: June 2011

Abstract

Background
Animal and human studies suggest that inflammation and malnutrition are common in acute kidney injury (AKI) patients. However, only a few studies reported CRP, a marker of inflammation, albumin, prealbumin and cholesterol, markers of nutritional status were associated with the prognosis of AKI patients. No study examined whether the combination of inflammatory and nutritional markers could predict the mortality of AKI patients.

Methods
155 patients with hospital-acquired AKI were recruited to this prospective cohort study according to RIFLE (Risk, Injury, Failure, Lost or End Stage Kidney) criteria. C-reactive protein (CRP), and the nutritional markers (albumin, prealbumin and cholesterol) measured at nephrology consultation were analyzed in relation to all cause mortality of these patients. In addition, CRP and prealbumin were also measured in healthy controls (n = 45), maintenance hemodialysis (n = 70) and peritoneal dialysis patients (n = 50) and then compared with AKI patients.

Results
Compared with healthy controls and end-stage renal disease patients on maintenance hemodialysis or peritoneal dialysis, patients with AKI had significantly higher levels of CRP/prealbumin (p < 0.001). Higher level of serum CRP and lower levels of albumin, prealbumin and cholesterol were found to be significant in the patients with AKI who died within 28 days than those who survived >28 days. Similarly, the combined factors including the ratio of CRP to albumin (CRP/albumin), CRP/prealbumin and CRP/cholesterol were also significantly higher in the former group (p < 0.001 for all). Multivariate analysis (Cox regression) revealed that CRP/prealbumin was independently associated with mortality after adjustment for age, gender, sepsis and sequential organ failure assessment (SOFA, p = 0.027) while the others (CRP, albumin, prealbumin, cholesterol, CRP/albumin and CRP/cholesterol) became non-significantly associated. The hazard ratio was 1.00 (reference), 1.85, 2.25 and 3.89 for CRP/prealbumin increasing according to quartiles (p = 0.01 for the trend).

Conclusions
Inflammation and malnutrition were common in patients with AKI. Higher level of the ratio of CRP to prealbumin was associated with mortality of AKI patients independent of the severity of illness and it may be a valuable addition to SOFA score to independent of the severity of illness and it may be a valuable addition to SOFA score to predict the prognosis of AKI patients.
Ethnicity and thrombolysis in ischemic stroke: a hospital based study in Amsterdam
Authors: Coutinho Jonathan M , Klaver Eva C , Roos Yvo B , Stam Jan , Nederkoorn Paul J 
Published: June 2011

Abstract

Background
Ethnic differences have been reported with regard to several medical therapies. The aim of this study was to investigate the relation between ethnicity and thrombolysis in stroke patients.

Methods
Retrospective single-centre study. Patients admitted with an ischemic stroke between 2003 and 2008 were included. Ethnicity was determined by self-identification and stratified into white and non-white (all other ethnicities). The main outcome measure was the difference in thrombolysis rate between white and non-white patients. Logistic regression analysis was used to identify potential confounders of the relation between ethnicity and thrombolysis.

Results
510 patients were included, 392 (77%) white and 118 (23%) non-white. Non-white patients were younger (median 69 vs. 60 years, p < 0.001), had a higher blood pressure at admission (median systolic 150 vs. 160 mmHg, p = 0.02) and a lower stroke severity (median NIHSS 5 vs. 4, p = 0.04). Non-white patients were significantly less often treated with thrombolysis compared to white patients (odds ratio 0.34, 95% CI 0.17-0.71), which was partly explained by a later arrival at the hospital. After adjustment for potential confounders (late arrival, age, blood pressure above upper limit for thrombolysis, and oral anticoagulation use), a trend towards a lower thrombolysis rate in non-whites remained (adjusted odds ratio 0.38, 95% CI 0.13 to 1.16).

Conclusions
Non-white stroke patients less often received thrombolysis than white patients, partly as a result of a delay in presentation. In this single centre study, potential bias due to hospital differences or insurance status could be ruled out as a cause. The magnitude of the difference is worrisome and requires further investigation. Modifiable causes, such as patient delay, awareness of stroke symptoms, language barriers and treatment of cardiovascular risk factors, should be addressed specifically in these ethnic groups in future stroke campaigns.
Measuring and modelling occupancy time in NHS continuing healthcare
Authors: Chahed Salma , Demir Eren , Chaussalet Thierry J , Millard Peter H , Toffa Samuel 
Published: June 2011

Abstract

Background
Due to increasing demand and financial constraints, NHS continuing healthcare systems seek to find better ways of forecasting demand and budgeting for care. This paper investigates two areas of concern, namely, how long existing patients stay in service and the number of patients that are likely to be still in care after a period of time.

Methods
An anonymised dataset containing information for all funded admissions to placement and home care in the NHS continuing healthcare system was provided by 26 (out of 31) London primary care trusts. The data related to 11289 patients staying in placement and home care between 1 April 2005 and 31 May 2008 were first analysed. Using a methodology based on length of stay (LoS) modelling, we captured the distribution of LoS of patients to estimate the probability of a patient staying in care over a period of time. Using the estimated probabilities we forecasted the number of patients that are likely to be still in care after a period of time (e.g. monthly).

Results
We noticed that within the NHS continuing healthcare system there are three main categories of patients. Some patients are discharged after a short stay (few days), some others staying for few months and the third category of patients staying for a long period of time (years). Some variations in proportions of discharge and transition between types of care as well as between care groups (e.g. palliative, functional mental health) were observed. A close agreement of the observed and the expected numbers of patients suggests a good prediction model.

Conclusions
The model was tested for care groups within the NHS continuing healthcare system in London to support Primary Care Trusts in budget planning and improve their responsiveness to meet the increasing demand under limited availability of resources. Its applicability can be extended to other types of care, such as hospital care and re-ablement. Further work will be geared towards updating the dataset and refining the results.
Different metastasis promotive potency of small G-proteins RalA and RalB in in vivo hamster tumor model
Authors: Rybko Vera A , Knizhnik Anna V , Komelkov Andrei V , Aushev Vasily N , Trukhanova Lyubov S , Tchevkina Elena M 
Published: June 2011

Abstract

Background
Previously we have shown that oncogenic Ha-Ras stimulated in vivo metastasis through RalGEF-Ral signaling. RalA and RalB are highly homologous small G proteins belonging to Ras superfamily. They can be activated by Ras-RalGEF signaling pathway and influence cellular growth and survival, motility, vesicular transport and tumor progression in humans and in animal models. Here we first time compared the influence of RalA and RalB on tumorigenic, invasive and metastatic properties of RSV transformed hamster fibroblasts.

Methods
Retroviral vectors encoding activated forms or effector mutants of RalA or RalB proteins were introduced into the low metastatic HET-SR cell line. Tumor growth and spontaneous metastatic activity (SMA) were evaluated on immunocompetent hamsters after subcutaneous injection of cells. The biological properties of cells, including proliferation, clonogenicity, migration and invasion were determined using MTT, wound healing, colony formation and Boyden chamber assays respectively. Protein expression and phosphorylation was detected by Westen blot analysis. Extracellular proteinases activity was assessed by substrate-specific zymography.

Results
We have showed that although both Ral proteins stimulated SMA, RalB was more effective in metastasis stimulation in vivo as well as in potentiating of directed movement and invasion in vitro. Simultaneous expression of active RalA and RalB didn't give synergetic effect on metastasis formation. RalB activity decreased expression of Caveolin-1, while active RalA stimulated MMP-1 and uPA proteolytic activity, as well as CD24 expression. Both Ral proteins were capable of Cyclin D1 upregulation, JNK1 kinase activation, and stimulation of colony growth and motility. Among three main RalB effectors (RalBP1, exocyst complex and PLD1), PLD1 was essential for RalB-dependent metastasis stimulation.

Conclusions
Presented results are the first data on direct comparison of RalA and RalB impact as well as of RalA/RalB simultaneous expression influence on in vivo cell metastatic activity. We showed that RalB activation significantly more than RalA stimulates SMA. This property correlates with the ability of RalB to stimulate in vitro invasion and serum directed cell movement. We also found that RalB-PLD1 interaction is necessary for the acquisition of RalB-dependent high metastatic cell phenotype. These findings contribute to the identification of molecular mechanisms of metastasis and tumor progression.
Effect of fruit and vegetable concentrates on endothelial function in metabolic syndrome: A randomized controlled trial
Authors: Ali Ather , Yazaki Yuka , Njike Valentine Y , Ma Yingying , Katz David L 
Published: June 2011

Abstract

Background and Objective
Dehydrated fruit and vegetable concentrates provide an accessible form of phytonutrient supplementation that may offer cardioprotective effects. This study assessed the effects of two blends of encapsulated juice powder concentrates (with and without added berry powders) on endothelial function in persons with metabolic syndrome, a risk factor for type 2 diabetes and cardiovascular disease.

Methods
Randomized, double blind, placebo controlled crossover clinical trial with three treatment arms. 64 adults with metabolic syndrome were enrolled and received 8-week sequences of each blend of the concentrates and placebo. The primary outcome measure was change in endothelial function (assessed as flow-mediated dilatation of the brachial artery) 2 hr after consuming a 75 g glucose load, after 8-weeks of daily consumption (sustained) or 2 hr after consumption of a single dose (acute). Secondary outcome measures included plasma glucose, serum insulin, serum lipids, and body weight.

Results
No significant between-group differences in endothelial function with daily treatment for 8 weeks were seen. No other significant treatment effects were discerned in glucose, insulin, lipids, and weight.

Conclusion
Encapsulated fruit and vegetable juice powder concentrates did not alter insulin or glucose measures in this sample of adults with metabolic syndrome.

Trial Registration
clinicaltrials.gov NCT01224743
Real-world comparison of two molecular methods for detection of respiratory viruses
Authors: Ali S Asad , Gern James E , Hartert Tina V , Edwards Kathryn M , Griffin Marie R , Miller E Kathryn , Gebretsadik Tebeb , Pappas Tressa , Lee Wai ming , Williams John V 
Published: June 2011

Abstract

Background
Molecular polymerase chain reaction (PCR) based assays are increasingly used to diagnose viral respiratory infections and conduct epidemiology studies. Molecular assays have generally been evaluated by comparing them to conventional direct fluorescent antibody (DFA) or viral culture techniques, with few published direct comparisons between molecular methods or between institutions. We sought to perform a real-world comparison of two molecular respiratory viral diagnostic methods between two experienced respiratory virus research laboratories.

Methods
We tested nasal and throat swab specimens obtained from 225 infants with respiratory illness for 11 common respiratory viruses using both a multiplex assay (Respiratory MultiCode-PLx Assay [RMA]) and individual real-time RT-PCR (RT-rtPCR).

Results
Both assays detected viruses in more than 70% of specimens, but there was discordance. The RMA assay detected significantly more human metapneumovirus (HMPV) and respiratory syncytial virus (RSV), while RT-rtPCR detected significantly more influenza A. We speculated that primer differences accounted for these discrepancies and redesigned the primers and probes for influenza A in the RMA assay, and for HMPV and RSV in the RT-rtPCR assay. The tests were then repeated and again compared. The new primers led to improved detection of HMPV and RSV by RT-rtPCR assay, but the RMA assay remained similar in terms of influenza detection.

Conclusions
Given the absence of a gold standard, clinical and research laboratories should regularly correlate the results of molecular assays with other PCR based assays, other laboratories, and with standard virologic methods to ensure consistency and accuracy.
An unusual case of autoimmune pancreatitis presenting as pancreatic mass and obstructive jaundice: a case report and review of the literature
Authors: Efeovbokhan Nephertiti , Makol Ashima , Cuison Reuben V , Minter Rebecca M , Kotaru Veera-Pavan , Conley Barbara A , Chandana Sreenivasa R 
Published: June 2011

Abstract

Background
Autoimmune pancreatitis is a rare chronic inflammatory pancreatic disease that is increasingly being diagnosed worldwide. As a result of overlap in clinical and radiological features, it is often misdiagnosed as pancreatic cancer. We report the case of a patient with autoimmune pancreatitis that was initially misdiagnosed as pancreatic cancer.

Case presentation
A 31-year-old Caucasian man presented to our hospital with epigastric pain, jaundice and weight loss. His CA 19-9 level was elevated, and computed tomography and endoscopic ultrasound revealed a pancreatic head mass abutting the portal vein. Endoscopic retrograde cholangiopancreaticography showed narrowing of the biliary duct and poor visualization of the pancreatic duct. Fine-needle aspiration biopsy revealed atypical ductal epithelial cells, which raised clinical suspicion of adenocarcinoma. Because of the patient's unusual age for the onset of pancreatic cancer and the acuity of his symptoms, he was referred to a tertiary care center for further evaluation. His immunoglobulin G4 antibody level was 365 mg/dL, and repeat computed tomography showed features typical of autoimmune pancreatitis. The patient's symptoms resolved with corticosteroid therapy.

Conclusion
Autoimmune pancreatitis is a rare disease with an excellent response to corticosteroid therapy. Its unique histological appearance and response to corticosteroid therapy can reduce unnecessary surgical procedures. A thorough evaluation by a multidisciplinary team is important in rendering the diagnosis of autoimmune pancreatitis.
Promoter polymorphisms in the chitinase 3-like 1 gene influence the serum concentration of YKL-40 in Danish patients with rheumatoid arthritis and in healthy subjects
Authors: Nielsen Kaspar R , Steffensen Rudi , Boegsted Martin , Baech John , Lundbye-Christensen Soeren , Hetland Merete L , Krintel Sophine B , Johnsen Hans E , Nyegaard Mette , Johansen Julia S 
Published: June 2011

Abstract
Introduction
The present study investigates the association between single nucleotide polymorphisms (SNPs) in the chitinase 3-like 1 (CHI3L1) gene and serum concentrations of YKL-40 in Danish patients with rheumatoid arthritis (RA) and healthy controls as well as the association with RA in the Danish population. The CHI3L1 gene is located on chromosome 1q32.1 and encodes the YKL-40 glycoprotein. YKL-40 concentrations are elevated in the serum of patients with RA compared to healthy subjects, and YKL-40 has been suggested to be an auto-antigen and may play a role in development of RA and in inflammation.

Methods
Eight SNPs in the CHI3L1 gene and promotor were genotyped in 308 patients with RA and 605 controls (healthy blood donors) using TaqMan allele discrimination assays. Serum concentrations of YKL-40 were determined by an enzyme-linked immunosorbent assay (ELISA).

Results
We found significant association between the serum concentrations of YKL-40 and polymorphism in the CHI3L1 gene among both patients with RA and controls. The g.-131(C > G) polymorphism (rs4950928) was most strongly associated with age adjusted serum concentrations of YKL-40 in patients with RA (P < 2.4e-8) and controls (P < 2.2e-16). No significant allelic- or genotypic association with RA was found in this Danish cohort.

Conclusions
We suggest that the g.-131(C > G) promoter polymorphism has a substantial impact on serum concentrations of YKL-40 in patients with RA and healthy subjects. However, the polymorphism does not seem to confer risk to RA itself. The effect of CHI3L1 polymorphism on clinical outcome or the response to treatment in patients with RA remains to be investigated.