bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Weibull model for survival of patients with gastric cancer
Authors: Zhu Hui P , Xia Xin , Yu Chuan H , Adnan Ahmed , Liu Shun F , Du Yu K 
Published: January 2011

AbstractBackgroundResearchers in the medical sciences prefer employing Cox model for survival analysis. In some cases, however, parametric methods can provide more accurate estimates. In this study, we used Weibull model to analyze the prognostic factors in patients with gastric cancer and compared with Cox.MethodsWe retrospectively studied 1715 patients with gastric cancer. Age at diagnosis, gender, family history, past medical history, tumor location, tumor size, eradicative degree of surgery, depth of tumor invasion, combined evisceration, pathologic stage, histologic grade and lymph node status were chosen as potential prognostic factors. Weibull and Cox model were performed with hazard rate and Akaike Information Criterion (AIC) to compare the efficiency of models.ResultsThe results from both Weibull and Cox indicated that patients with the past history of having gastric cancer had the risk of death increased significantly followed by poorly differentiated or moderately differentiated in histologic grade. Eradicative degree of surgery, pathologic stage, depth of tumor invasion and tumor location were also identified as independent prognostic factors found significant. Age was significant only in Weibull model.ConclusionFrom the results of multivariate analysis, the data strongly supported the Weibull can elicit more precise results as an alternative to Cox based on AIC.
Becoming and staying physically active in adolescents with cerebral palsy: protocol of a qualitative study of facilitators and barriers to physical activity
Authors: Claassen Aniek AOM , Gorter Jan Willem , Stewart Debra , Verschuren Olaf , Galuppi Barbara E , Shimmell Lorie J 
Published: January 2011

Abstract

Background
Adolescents with cerebral palsy (CP) show a reduced physical activity (PA). Currently there are no interventions for adolescents with CP in this critical life phase that optimise and maintain the individuals' physical activity in the long term. To develop such a program it is important to fully understand the factors that influence physical activity behaviours in adolescents with CP. The aim of this study is to explore what makes it easy or hard for adolescents with CP to be and to become physically active.

Methods/Design
A qualitative research method is chosen to allow adolescents to voice their own opinion. Because we will investigate the lived experiences this study has a phenomenological approach. Thirty ambulatory and non-ambulatory adolescents (aged 10-18 years) with CP, classified as level I to IV on the Gross Motor Function Classification System and 30 parents of adolescents with CP will be invited to participate in one of the 6 focus groups or an individual interview. Therapists from all Children's Treatment Centres in Ontario, Canada, will be asked to fill in a survey. Focus groups will be audio- and videotaped and will approximately take 1.5 hours. The focus groups will be conducted by a facilitator and an assistant. In preparation of the focus groups, participants will fill in a demographic form with additional questions on physical activity. The information gathered from these questions and recent research on barriers and facilitators to physical activity will be used as a starting point for the content of the focus groups. Recordings of the focus groups will be transcribed and a content analysis approach will be used to code the transcripts. A preliminary summary of the coded data will be shared with the participants before themes will be refined.

Discussion
This study will help us gain insight and understanding of the participants' experiences and perspectives in PA, which can be of great importance when planning programs aimed at helping them to stay or to become physically active.
Does directly observed therapy (DOT) reduce drug resistant tuberculosis?
Authors: Moonan Patrick K , Quitugua Teresa N , Pogoda Janice M , Woo Gary , Drewyer Gerry , Sahbazian Behzad , Dunbar Denise , Jost Kenneth C , Wallace Charles , Weis Stephen E 
Published: January 2011

Abstract

Background
Directly observed therapy (DOT) is a widely recommended and promoted strategy to manage tuberculosis (TB), however, there is still disagreement about the role of DOT in TB control and the impact it has on reducing the acquisition and transmission of drug resistant TB. This study compares the portion of drug resistant genotype clusters, representing recent transmission, within and between communities implementing programs differing only in their directly observed therapy (DOT) practices.

Methods
Genotype clusters were defined as 2 or more patient members with matching IS6110 restriction fragment length polymorphism (RFLP) and spoligotype patterns from all culture-positive tuberculosis cases diagnosed between January 1, 1995 and December 31, 2001. Logistic regression was used to compute maximum-likelihood estimates of odds ratios (ORs) and 95% confidence intervals (CIs) comparing cluster members with and without drug resistant isolates. In the universal DOT county, all patients received doses under direct observation of health department staff; whereas in selective DOT county, the majority of received patients doses under direct observation of health department staff, while some were able to self-administer doses.

Results
Isolates from 1,706 persons collected during 1,721 episodes of tuberculosis were genotyped. Cluster members from the selective DOT county were more than twice as likely than cluster members from the universal DOT county to have at least one isolate resistant to isoniazid, rifampin, and/or ethambutol (OR = 2.3, 95% CI: 1.7, 3.1). Selective DOT county isolates were nearly 5 times more likely than universal DOT county isolates to belong to clusters with at least 2 resistant isolates having identical resistance patterns (OR = 4.7, 95% CI: 2.9, 7.6).

Conclusions
Universal DOT for tuberculosis is associated with a decrease in the acquisition and transmission of resistant tuberculosis.
Characterization of the insulin sensitivity of ghrelin receptor KO mice using glycemic clamps
Authors: Qi Yong , Longo Kenneth A , Giuliana Derek J , Gagne Samantha , McDonagh Tom , Govek Elizabeth , Nolan Anna , Zou Chaoseng , Morgan Kristen , Hixon Jeffrey , Saunders Jeffrey O , DiStefano Peter S , Geddes Brad J 
Published: January 2011

Abstract

Background
We and others have demonstrated previously that ghrelin receptor (GhrR) knock out (KO) mice fed a high fat diet (HFD) have increased insulin sensitivity and metabolic flexibility relative to WT littermates. A striking feature of the HFD-fed GhrR KO mouse is the dramatic decrease in hepatic steatosis. To characterize further the underlying mechanisms of glucose homeostasis in GhrR KO mice, we conducted both hyperglycemic (HG) and hyperinsulinemic-euglycemic (HI-E) clamps. Additionally, we investigated tissue glucose uptake and specifically examined liver insulin sensitivity.

Results
Consistent with glucose tolerance-test data, in HG clamp experiments, GhrR KO mice showed a reduction in glucose-stimulated insulin release relative to WT littermates. Nevertheless, a robust 1st phase insulin secretion was still achieved, indicating that a healthy β-cell response is maintained. Additionally, GhrR KO mice demonstrated both a significantly increased glucose infusion rate and significantly reduced insulin requirement for maintenance of the HG clamp, consistent with their relative insulin sensitivity. In HI-E clamps, both LFD-fed and HFD-fed GhrR KO mice showed higher peripheral insulin sensitivity relative to WT littermates as indicated by a significant increase in insulin-stimulated glucose disposal (Rd), and decreased hepatic glucose production (HGP). HFD-fed GhrR KO mice showed a marked increase in peripheral tissue glucose uptake in a variety of tissues, including skeletal muscle, brown adipose tissue and white adipose tissue. GhrR KO mice fed a HFD also showed a modest, but significant decrease in conversion of pyruvate to glucose, as would be anticipated if these mice displayed increased liver insulin sensitivity. Additionally, the levels of UCP2 and UCP1 were reduced in the liver and BAT, respectively, in GhrR KO mice relative to WT mice.

Conclusions
These results indicate that improved glucose homeostasis of GhrR KO mice is characterized by robust improvements of glucose disposal in both normal and metabolically challenged states, relative to WT controls. GhrR KO mice have an intact 1st phase insulin response but require significantly less insulin for glucose disposal. Our experiments reveal that the insulin sensitivity of GhrR KO mice is due to both BW independent and dependent factors. We also provide several lines of evidence that a key feature of the GhrR KO mouse is maintenance of hepatic insulin sensitivity during metabolic challenge.
Effects of dietary cold-pressed turnip rapeseed oil and butter on serum lipids, oxidized LDL and arterial elasticity in men with metabolic syndrome
Authors: Palomäki Ari , Pohjantähti-Maaroos Hanna , Wallenius Marja , Kankkunen Päivi , Aro Heikki , Husgafvel Sari , Pihlava Juha-Matti , Oksanen Kalevi 
Published: January 2011

Abstract

Background
Rapeseed oil is the principal dietary source of monounsaturated and n-3 polyunsaturated fatty acids in the Northern Europe. However, the effect of rapeseed oil on the markers of subclinical atherosclerosis is not known. The purpose of this study was to compare the effects of dietary intake of cold-pressed turnip rapeseed oil (CPTRO) and butter on serum lipids, oxidized LDL and arterial elasticity in men with metabolic syndrome.

Methods
Thirty-seven men with metabolic syndrome completed an open and balanced crossover study. Treatment periods lasted for 6 to 8 weeks and they were separated from each other with an eight-week washout period. Subjects maintained their normal dietary habits and physical activity without major variations. The daily fat adjunct consisted either of 37.5 grams of butter or 35 mL of VirginoR CPTRO. Participants were asked to spread butter on bread on the butter period and to drink CPTRO on the oil period. The fat adjunct was used as such without heating or frying.

Results
Compared to butter, administration of CPTRO was followed by a reduction of total cholesterol by 8% (p < 0.001) and LDL cholesterol by 11% (p < 0.001). The level of oxidized LDL was 16% lower after oil period (p = 0.024). Minimal differences in arterial elasticity were not statistically significant.

Conclusion
Cold-pressed turnip rapeseed oil had favourable effects on circulating LDL cholesterol and oxidized LDL, which may be important in the management of patients at high cardiovascular risk.

Trial registration
ClinicalTrial.gov NCT01119690
A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development
Authors: Katz Ehud , Fon Mario , Eigenheer Richard A , Phinney Brett S , Fass Joseph N , Lin Dawei , Sadka Avi , Blumwald Eduardo 
Published: January 2011

Abstract

Background
Citrus is one of the most important and widely grown commodity fruit crops. In this study a label-free LC-MS/MS based shot-gun proteomics approach was taken to explore three main stages of citrus fruit development. These approaches were used to identify and evaluate changes occurring in juice sac cells in various metabolic pathways affecting citrus fruit development and quality.

Results
Protein changes in citrus juice sac cells were identified and quantified using label-free shotgun methodologies. Two alternative methods, differential mass-spectrometry (dMS) and spectral counting (SC) were used to analyze protein changes occurring during earlier and late stages of fruit development. Both methods were compared in order to develop a proteomics workflow that could be used in a non-model plant lacking a sequenced genome. In order to resolve the bioinformatics limitations of EST databases from species that lack a full sequenced genome, we established iCitrus. iCitrus is a comprehensive sequence database created by merging three major sources of sequences (HarvEST:citrus, NCBI/citrus/unigenes, NCBI/citrus/proteins) and improving the annotation of existing unigenes. iCitrus provided a useful bioinformatics tool for the high-throughput identification of citrus proteins. We have identified approximately 1500 citrus proteins expressed in fruit juice sac cells and quantified the changes of their expression during fruit development. Our results showed that both dMS and SC provided significant information on protein changes, with dMS providing a higher accuracy.

Conclusion
Our data supports the notion of the complementary use of dMS and SC for label-free comparative proteomics, broadening the identification spectrum and strengthening the identification of trends in protein expression changes during the particular processes being compared.
Reconstructive challenge of dermatofibrosarcoma protuberans in the female breast
Authors: Park Tae Hwan , Seo Sang Won , Kim June Kyu , Chang Choong Hyun 
Published: January 2011

Abstract
Dermatofibrosarcoma protuberans is an uncommon locally aggressive malignant neoplasm that most frequently appears in the trunk, followed by the extremities, head, and neck. But occurrence in the breast is extremely rare. We present a case of a 28-year-old woman, who had a history of trauma 5 years previously and excision 1 year before presentation at our clinic. We performed wide excision, together with microscopic and immunohistochemical analysis. No postoperative oncologic treatment was used and she remains disease-free 1 year after the surgery without any tumor recurrence. Here, we report a case of dermatofibrosarcoma protuberans in the female breast and present a detailed discussion of the diagnosis and treatment with reference to available literatures.
Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri
Authors: Carrias Abel , Welch Timothy J , Waldbieser Geoffrey C , Mead David A , Terhune Jeffery S , Liles Mark R 
Published: January 2011

AbstractBackgroundThe bacterial pathogenEdwardsiella ictaluriis a primary cause of mortality in channel catfish raised commercially in aquaculture farms. Additional treatment and diagnostic regimes are needed for this enteric pathogen, motivating the discovery and characterization of bacteriophages specific toE. ictaluri.ResultsThe genomes of threeEdwardsiella ictaluri-specific bacteriophages isolated from geographically distant aquaculture ponds, at different times, were sequenced and analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp, 42.12 kbp, and 42.69 kbp, respectively, and are greater than 95% identical to each other at the nucleotide level. Nucleotide differences were mostly observed in non-coding regions and in structural proteins, with significant variability in the sequences of putative tail fiber proteins. The genome organization of these phages exhibit a pattern shared by otherSiphoviridae.ConclusionsTheseE. ictaluri-specific phage genomes reveal considerable conservation of genomic architecture and sequence identity, even with considerable temporal and spatial divergence in their isolation. Their genomic homogeneity is similarly observed amongE. ictaluribacterial isolates. The genomic analysis of these phages supports the conclusion that these are virulent phages, lacking the capacity for lysogeny or expression of virulence genes. This study contributes to our knowledge of phage genomic diversity and facilitates studies on the diagnostic and therapeutic applications of these phages.
A Local Anesthetic, Ropivacaine, Suppresses Activated Microglia via a Nerve Growth Factor-Dependent Mechanism and Astrocytes via a Nerve Growth Factor-Independent Mechanism in Neuropathic Pain
Authors: Toda Shigeru , Sakai Atsushi , Ikeda Yumiko , Sakamoto Atsuhiro , Suzuki Hidenori 
Published: January 2011

Background: Local anesthetics alleviate neuropathic pain in some cases in clinical practice, and exhibit longer durations of action than those predicted on the basis of the pharmacokinetics of their blocking effects on voltage-dependent sodium channels. Therefore, local anesthetics may contribute to additional mechanisms for reversal of the sensitization of nociceptive pathways that occurs in the neuropathic pain state. In recent years, spinal glial cells, microglia and astrocytes, have been shown to play critical roles in neuropathic pain, but their participation in the analgesic effects of local anesthetics remains largely unknown. Results: Repetitive epidural administration of ropivacaine reduced the hyperalgesia induced by chronic constrictive injury of the sciatic nerve. Concomitantly with this analgesia, ropivacaine suppressed the increases in the immunoreactivities of CD11b and glial fibrillary acidic protein in the dorsal spinal cord, as markers of activated microglia and astrocytes, respectively. In addition, epidural administration of a TrkA-IgG fusion protein that blocks the action of nerve growth factor (NGF), which was upregulated by ropivacaine in the dorsal root ganglion, prevented the inhibitory effect of ropivacaine on microglia, but not astrocytes. The blockade of NGF action also abolished the analgesic effect of ropivacaine on neuropathic pain. Conclusions: Ropivacaine provides prolonged analgesia possibly by suppressing microglial activation in an NGF-dependent manner and astrocyte activation in an NGF-independent manner in the dorsal spinal cord. Local anesthetics, including ropivacaine, may represent a new approach for glial cell inhibition and, therefore, therapeutic strategies for neuropathic pain.
A forward genetic screen with a thalamocortical axon reporter mouse yields novel neurodevelopment mutants and a distinct emx2 mutant phenotype
Authors: Dwyer Noelle D , Manning Danielle K , Moran Jennifer L , Mudbhary Raksha , Fleming Michael S , Favero Carlita B , Vock Vita M , O'Leary Dennis DM , Walsh Christopher A , Beier David R 
Published: January 2011

Abstract

Background
The dorsal thalamus acts as a gateway and modulator for information going to and from the cerebral cortex. This activity requires the formation of reciprocal topographic axon connections between thalamus and cortex. The axons grow along a complex multistep pathway, making sharp turns, crossing expression boundaries, and encountering intermediate targets. However, the cellular and molecular components mediating these steps remain poorly understood.

Results
To further elucidate the development of the thalamocortical system, we first created a thalamocortical axon reporter line to use as a genetic tool for sensitive analysis of mutant mouse phenotypes. The TCA-tau-lacZ reporter mouse shows specific, robust, and reproducible labeling of thalamocortical axons (TCAs), but not the overlapping corticothalamic axons, during development. Moreover, it readily reveals TCA pathfinding abnormalities in known cortical mutants such as reeler. Next, we performed an unbiased screen for genes involved in thalamocortical development using random mutagenesis with the TCA reporter. Six independent mutant lines show aberrant TCA phenotypes at different steps of the pathway. These include ventral misrouting, overfasciculation, stalling at the corticostriatal boundary, and invasion of ectopic cortical cell clusters. An outcross breeding strategy coupled with a genomic panel of single nucleotide polymorphisms facilitated genetic mapping with small numbers of mutant mice. We mapped a ventral misrouting mutant to the Emx2 gene, and discovered that some TCAs extend to the olfactory bulbs in this mutant. Mapping data suggest that other lines carry mutations in genes not previously known for roles in thalamocortical development.

Conclusions
These data demonstrate the feasibility of a forward genetic approach to understanding mammalian brain morphogenesis and wiring. A robust axonal reporter enabled sensitive analysis of a specific axon tract inside the mouse brain, identifying mutant phenotypes at multiple steps of the pathway, and revealing a new aspect of the Emx2 mutant. The phenotypes highlight vulnerable choice points and latent tendencies of TCAs, and will lead to a refined understanding of the elements and interactions required to form the thalamocortical system.
See Commentary: http://www.biomedcentral.com/1741-7007/9/1
Hemelipoglycoprotein from the ornate sheep tick, Dermacentor marginatus: structural and functional characterization
Authors: Dupejova Jarmila , Sterba Jan , Vancova Marie , Grubhoffer Libor 
Published: January 2011

Abstract

Background
Tick carrier proteins are able to bind, transport, and store host-blood heme, and thus they function also as antioxidants. Nevertheless, the role of carrier proteins in ticks is not fully understood. Some of them are found also in tick males which do not feed on hosts to such an extent such as females (there are differences in male feeding in different tick species) and thus they are not dealing with such an excess of heme; some of the carrier proteins were found in salivary glands where the processing of blood and thus release of heme does not occur. Besides, the carrier proteins bind relatively low amounts of heme (in one case only two molecules of heme per protein) compared to their sizes (above 200 kDa).
The main aim of this study is the biochemical characterization of a carrier protein from the ornate sheep tick Dermacentor marginatus, hemelipoglycoprotein, with emphasis on its size in native conditions, its glycosylation and identification of its modifying glycans, and examining its carbohydrate-binding specificity.

Results
Hemelipoglycoprotein from D. marginatus plasma was purified in native state by immunoprecipitation and denatured using electroelution from SDS-PAGE separated plasma. The protein (290 kDa) contains two subunits with molecular weights 100 and 95 kDa. It is glycosylated by high-mannose and complex N-glycans HexNAc2Hex9, HexNAc2Hex10, HexNAc4Hex7, and HexNAc4Hex8. The purified protein is able to agglutinate red blood cells and has galactose- and mannose-binding specificity. The protein is recognized by antibodies directed against plasma proteins with hemagglutination activity and against fibrinogen-related lectin Dorin M from the tick Ornithodoros moubata.
It forms high-molecular weight complexes with putative fibrinogen-related proteins and other unknown proteins under native conditions in tick plasma. Feeding does not increase its amounts in male plasma. The hemelipoglycoprotein was detected also in hemocytes, salivary glands, and gut. In salivary glands, the protein was present in both glycosylated and nonglycosylated forms.

Conclusion
A 290 kDa hemelipoglycoprotein from the tick Dermacentor marginatus, was characterized. The protein has two subunits with 95 and 100 kDa, and bears high-mannose and complex N-linked glycans. In hemolymph, it is present in complexes with putative fibrinogen-related proteins. This, together with its carbohydrate-binding activity, suggests its possible involvement in tick innate immunity. In fed female salivary glands, it was found also in a form corresponding to the deglycosylated protein.