bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PhenoGen Informatics website: tools for analyses of complex traits
Authors: Bhave Sanjiv V , Hornbaker Cheryl , Phang Tzu L , Saba Laura , Lapadat Razvan , Kechris Katherina , Gaydos Jeanette , McGoldrick Daniel , Dolbey Andrew , Leach Sonia , Soriano Brian , Ellington Allison , Ellington Eric , Jones Kendra , Mangion Jonathan , Belknap John K , Williams Robert W , Hunter Lawrence E , Hoffman Paula L , Tabakoff Boris 
Published: August 2007

Abstract

Background
With the advent of "omics" (e.g. genomics, transcriptomics, proteomics and phenomics), studies can produce enormous amounts of data. Managing this diverse data and integrating with other biological data are major challenges for the bioinformatics community. Comprehensive new tools are needed to store, integrate and analyze the data efficiently.

Description
The PhenoGen Informatics website http://phenogen.uchsc.edu is a comprehensive toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for "candidate" genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct "in-silico" microarray experiments using their own and/or "shared" data.

Conclusion
The PhenoGen website provides access to tools that can be used for high-throughput data storage, analyses and interpretation of the results. Some of the advantages of the architecture of the website are that, in the future, the present set of tools can be adapted for the analyses of any type of high-throughput "omics" data, and that access to new tools, available in the public domain or developed at PhenoGen, can be easily provided.
Socioeconomic status and hospitalization in the very old: a retrospective study
Authors: Antonelli-Incalzi Raffaele , Ancona Carla , Forastiere Francesco , Belleudi Valeria , Corsonello Andrea , Perucci Carlo A 
Published: August 2007

Abstract

Background
Socioeconomic status could affect the demand for hospital care. The aim of the present study was to assess the role of age, socioeconomic status and comorbidity on acute hospital admissions among elderly.

Methods
We retrospectively examined the discharge abstracts data of acute care hospital admissions of residents in Rome aged 75 or more years in the period 1997–2000. We used the Hospital Information System of Rome, the Tax Register, and the Population Register of Rome for socio-economic data. The rate of hospitalization, modified Charlson's index of comorbidity, and level of income in the census tract of residence were obtained. Rate ratios and 95% confidence limits were computed to assess the relationship between income deciles and rate of hospitalization. Cross-tabulation was used to explore the distribution of the index of comorbidity by deciles of income. Analyses were repeated for patients grouped according to selected diseases.

Results
Age was associated with a marginal increase in the rate of hospitalization. However, the hospitalization rate was inversely related to income in both sexes. Higher income was associated with lower comorbidity. The same associations were observed in patients admitted with a principal diagnosis of chronic condition (diabetes mellitus, heart failure, chron obstructive pulmonary disease) or stroke, but not hip fracture.

Conclusion
Lower social status and associated comorbidity, more than age per se, are associated with a higher rate of hospitalization in very old patients.
Anteroposterior glide versus rotating platform low contact stress (LCS) knee arthroplasty: a randomised controlled trial
Authors: Walley Gayle , Datir Sandeep , Sayana Murali , Rahmatalla Aziz , Dos Remedios Ian , Wynn-Jones Charles , Bridgman Stephen , Maffulli Nicola 
Published: August 2007

AbstractBackgroundFifty thousand knee replacements are performed annually in the UK at an estimated cost of £150 million. Post-operative improvement depends on a number of factors including implant design and patient associated factors. To our knowledge there are no published study's comparing the results of AP glide and rotating platform designs of LCS knee arthroplasty. Therefore we feel that a study is required to investigate and compare the effects of two types of LCS total knee arthroplasty on joint proprioception and range of motion.Methods/DesignPatients will be randomised to receive either a LCS AP glide or Rotating platform prosthesis. Clinical scores (Oxford knee score, American knee society score, EuroQol), range of motion and proprioception will be assessed prior to and at 3,6, 12 and 24 months after the operation. Proprioception will be assessed in terms of absolute error angle (mean difference between the target angle and the response angle). Knee angles will be measured in degrees using an electromagnetic tracking device, Polhemus 3Space Fastrak that detects positions of sensors placed on the test limb. Student's t-test will be used to compare the mean of two groups.DiscussionEvidence is lacking concerning the best prosthesis to use for patients undergoing total knee replacement. This pragmatic randomised trial will test the null hypothesis that anteroposterior glide LCS knee arthroplasty does not result in better post operative knee motion and proprioception as compared to rotating platform LCS knee.Trial RegistrationISRCTN52943804
Physicians' views on resource availability and equity in four European health care systems
Authors: Hurst Samia A , Forde Reidun , Reiter-Theil Stella , Slowther Anne-Marie , Perrier Arnaud , Pegoraro Renzo , Danis Marion 
Published: August 2007

Abstract

Background
In response to limited resources, health care systems have adopted diverse cost-containment strategies and give priority to differing types of interventions. The perception of physicians, who witness the effects of these strategies, may provide useful insights regarding the impact of system-wide priority setting on access to care.

Methods
We conducted a cross-sectional survey to ascertain generalist physicians' perspectives on resources allocation and its consequences in Norway, Switzerland, Italy and the UK.

Results
Survey respondents (N = 656, response rate 43%) ranged in age from 28–82, and averaged 25 years in practice. Most respondents (87.7%) perceived some resources as scarce, with the most restrictive being: access to nursing home, mental health services, referral to a specialist, and rehabilitation for stroke. Respondents attributed adverse outcomes to scarcity, and some respondents had encountered severe adverse events such as death or permanent disability. Despite universal coverage, 45.6% of respondents reported instances of underinsurance. Most respondents (78.7%) also reported some patient groups as more likely than others to be denied beneficial care on the basis of cost. Almost all respondents (97.3%) found at least one cost-containment policy acceptable. The types of policies preferred suggest that respondents are willing to participate in cost-containment, and do not want to be guided by administrative rules (11.2%) or restrictions on hospital beds (10.7%).

Conclusion
Physician reports can provide an indication of how organizational factors may affect availability and equity of health care services. Physicians are willing to participate in cost-containment decisions, rather than be guided by administrative rules. Tools should be developed to enable physicians, who are in a unique position to observe unequal access or discrimination in their health care environment, to address these issues in a more targeted way.
Effect of a restrictive transfusion strategy on transfusion-attributable severe acute complications and costs in the US ICUs: a model simulation
Authors: Zilberberg Marya D , Shorr Andrew F 
Published: August 2007

AbstractBackgroundNearly half of all patients in the Intensive Care Unit (ICU) receive red blood cell (pRBC) transfusions (TFs), despite their associated complications. Restrictive transfusion strategy (Hemoglobin [Hb] < 7 g/dL) has been shown to reduce TF exposure. We estimated the potential annual reduction in transfusion-attributable severe acute complications (TSACs) and costs across the US ICUs with the adoption of restrictive strategy.MethodsA model, utilizing inputs from published studies, was constructed. Step 1 calculated potential number of patients appropriate for this strategy. In step 2, total number of pRBC units avoided with the restrictive trigger was extrapolated to the annual TFs in the US ICUs. Step 3 quantified excess acute complications and the number of pRBC units TF/1 TSAC in the TRICC trial. Step 4 transformed restrictive strategy-related avoidance of pRBC units to a reduction in TSACs, and step 5 quantified the associated cost savings.ResultsOf the 4.4 million annual ICU admissions, 1,020,800 comprised the at-risk population. The total of 1,295,126 units of pRBC ($643/unit) could be saved with the restrictive strategy. Based on the data from the TRICC trial, dividing the 49 excess complications in the liberal group into the calculated excess of pRBCs transfused (1,624 units) yielded the rate of 33 pRBC units per one complication. Thus, dividing 1,295,126 units saved by 33 units/1 TSAC, the base-case analysis showed that 39,246 TSACs could potentially be avoided annually in the US ICUs, with the cost savings of $821,109,826.ConclusionThis model demonstrates that a restrictive transfusion strategy in appropriate at risk ICU patients is dominant and could result in improved quality of care and cost savings. Given the potential savings of 40,000 TSACs and nearly $1 billion, it is incumbent upon the intensivist community to promote more ubiquitous adoption of a clinically appropriate restrictive transfusion strategy in the ICU.
Design of an improved set of oligonucleotide primers for genotyping MeCP2tm1.1BirdKO mice by PCR
Authors: Miralvès Julie , Magdeleine Eddy , Joly Etienne 
Published: August 2007

Abstract

Background
The strain of MeCP2tm1.1Bird mice is a broadly used model for Rett syndrome. Because males carrying the invalidated MeCP2 locus are sterile, this strain has to be maintained in a heterozygous state. All animals therefore have to be genotyped at every generation to discriminate those carrying the invalidated allele (+/- females and y/- males) from those that do not. This is conveniently carried out by PCR on tail genomic DNA but because the primer pairs described initially for this purpose yield very similar size DNA bands on the WT and the KO alleles, this requires to carry out two independent PCR reactions on tail DNA preparations from all animals.

Results
After cloning and sequencing the PCR fragment amplified on the KO allele, we tested several sets of primers that were designed to yield PCR fragments of different sizes on the KO and WT alleles.

Conclusion
We have thus identified a set of three primers that allows for efficient genotyping of the animals by a single PCR reaction. Furthermore, using of this set of primers also resolves a recurrent problem related to the tendency of one of the initial primers to give rise to a non specific band because of its capacity to anneal at both ends of a repeated genomic element which we have identified as MurvyLTR.
Modeling gene expression regulatory networks with the sparse vector autoregressive model
Authors: Fujita André , Sato João R , Garay-Malpartida Humberto M , Yamaguchi Rui , Miyano Satoru , Sogayar Mari C , Ferreira Carlos E 
Published: August 2007

AbstractBackgroundTo understand the molecular mechanisms underlying important biological processes, a detailed description of the gene products networks involved is required. In order to define and understand such molecular networks, some statistical methods are proposed in the literature to estimate gene regulatory networks from time-series microarray data. However, several problems still need to be overcome. Firstly, information flow need to be inferred, in addition to the correlation between genes. Secondly, we usually try to identify large networks from a large number of genes (parameters) originating from a smaller number of microarray experiments (samples). Due to this situation, which is rather frequent in Bioinformatics, it is difficult to perform statistical tests using methods that model large gene-gene networks. In addition, most of the models are based on dimension reduction using clustering techniques, therefore, the resulting network is not a gene-gene network but a module-module network. Here, we present the Sparse Vector Autoregressive model as a solution to these problems.ResultsWe have applied the Sparse Vector Autoregressive model to estimate gene regulatory networks based on gene expression profiles obtained from time-series microarray experiments. Through extensive simulations, by applying the SVAR method to artificial regulatory networks, we show that SVAR can infer true positive edges even under conditions in which the number of samples is smaller than the number of genes. Moreover, it is possible to control for false positives, a significant advantage when compared to other methods described in the literature, which are based on ranks or score functions. By applying SVAR to actual HeLa cell cycle gene expression data, we were able to identify well known transcription factor targets.ConclusionThe proposed SVAR method is able to model gene regulatory networks in frequent situations in which the number of samples is lower than the number of genes, making it possible to naturally infer partial Granger causalities without anya prioriinformation. In addition, we present a statistical test to control the false discovery rate, which was not previously possible using other gene regulatory network models.
Reduced number and impaired function of circulating progenitor cells in patients with systemic lupus erythematosus
Authors: Moonen Jan Renier AJ , de Leeuw Karina , van Seijen Xavier J Gallego Y , Kallenberg Cees GM , van Luyn Marja JA , Bijl Marc , Harmsen Martin C 
Published: August 2007

AbstractSystemic lupus erythematosus (SLE) is associated with premature and accelerated atherosclerosis. Circulating progenitor cells (CPCs) are circulating bone-marrow derived cells that play an important role in the repair of vascular damage that underlies the development of atherosclerosis. The objective of this study was to determine the number and functionality of CPCs in patients with SLE. The study included 44 female SLE patients in an inactive stage of disease and 35 age-matched female controls. CPC numbers in the circulation were determined by FACS with monoclonals against CD14, CD34 and CD133. Peripheral blood-derived mononuclear cell (PBMNC) fractions were cultured in angiogenic medium. The endothelial-like phenotype was confirmed and the colony forming unit (CFU) capacity, migratory capacity and the potential to form clusters on Matrigel were determined. Expression of apoptosis inhibiting caspase 8L was analyzed in PBMNCs and CPCs by gene transcript and protein expression assays. The number of CD34–CD133 double-positive cells (P < 0.001) as well as the CFU capacity (P = 0.048) was reduced in SLE patients. Migratory activity on tumor necrosis factor-α tended to be reduced in patient CPCs (P = 0.08). Migration on vascular endothelial growth factor showed no significant differences, nor were differences observed in the potential to form clusters on Matrigel. The expression of caspase 8L was reduced at the transcriptional level (P = 0.049) and strongly increased at the protein level after culture (P = 0.003). We conclude that CPC numbers are reduced in SLE patients and functionality is partly impaired. We suggest these findings reflect increased susceptibility to apoptosis of CPCs from SLE patients.
1,1-Bis(3'-indolyl)-1-(p-biphenyl)methane inhibits basal-like breast cancer growth in athymic nude mice
Authors: Su Yunpeng , Vanderlaag Kathryn , Ireland Courtney , Ortiz Janelle , Grage Henry , Safe Stephen , Frankel Arthur E 
Published: August 2007

Abstract
Introduction
1,1-Bis (3'-indolyl)-1-(p-biphenyl) methane (CDIM9) has been identified as a new peroxisome proliferator-activated receptor (PPAR)-γ agonist that exhibits both receptor dependent and independent antitumor activities. CDIM9 has not previously been studied with respect to its effects against basal-like breast cancer. Our goal in the present study was to investigate the anti-basal-like breast tumor activity of CDIM9 in vitro and in vivo.

Methods
The effects of CDIM9 on cell protein and DNA syntheses were determined in basal-like breast cancer MDA-MB231 and BT549 cells in vitro. Maximum tolerated dose and dose-limited toxicity were determined in BalB/c mice, and antitumor growth activities were assessed in MDA-MB231 basal-like breast tumor xenografts in athymic nude mice.

Results
CDIM9 exhibited selective cell cytotoxicity and anti-proliferation effects on basal-like breast cancer lines. In MDA-MB231 cell, CDIM9 induced caveolin-1 and p27 expression, which was significantly downregulated by co-treatment with the PPAR-γ antagonist GW9662. Nonsteroidal anti-inflammatory drug-activated gene-1 and activating transcription factor-3 were upregulated by CDIM9 through a PPAR-γ independent pathway. CDIM9 (40 mg/kg daily, intraperitoneally, for 35 days) inhibited the growth of subcutaneous MDA-MB231 tumor xenografts by 87%, and produced a corresponding decrease in proliferation index. Nearly half of the treated mice (46%) had complete durable remissions, confirmed by histology. The growth of an established tumor was inhibited by CDIM9 treatment (64 mg/kg daily, intraperitoneally, for 10 days), with a mean tumor growth inhibition of 67% as compared with controls. CDIM9 induced increases in tumor caveolin-1 and p27 in vivo, which may contribute to its antitumor activity in basal-like breast cancer.

Conclusion
CDIM9 showed potent antiproliferative effects on basal-like breast cancer cell in tissue culture and dramatic growth inhibition in animal models at safe doses. These findings justify further development of this drug for treatment of basal-like breast cancer.
Placental growth factor down-regulates type 1 T helper immune response by modulating the function of dendritic cells
Authors: Lin Yu-Li , Liang Yu-Chih , Chiang Bor-Luen 
Published: August 2007

AbstractPlacental growth factor (PlGF) belongs to the vascular endothelial growth factor (VEGF) family and represents a key regulator of angiogenic events in development and pathologic conditions. In this study, PlGF-modulated differentiation and maturation of human dendritic cells (DCs) from CD14+ monocytes were investigated. The DC, differentiated from CD14+ monocytes in the presence of PlGF during 5 days, was referred to as “PlGF-DC”, in contrast to the “classical-DC”, obtained in the absence of PlGF. Treatment of PlGF-DC or classical-DC with PlGF resulted in the down-regulation of CD80, CD86, CD83, CD40, and HLA-DR expression, and CD1a was increased, as well as the inhibition of IL-12 p70, p40, IL-8, and TNF-α production in response to LPS stimulation. This PlGF-induced DC dysfunction was recovered by anti-human VEGF receptor 1 mAb. In addition, treatment of PlGF-DC or classical-DC with PlGF resulted in the suppression of naïve CD4+ T cell proliferation in an allogenic MLR but up-regulated the IL-5 and IL-13 secretion of the CD4+ T cell. PlGF was also able to inhibit LPS-induced IκBα phosphorylation and NF-κB activity. Taken together, our data demonstrate that the immunosuppressive properties of PlGF are through the NF-κB signaling pathway. PlGF might play a major role in the pathogenesis of tumors and act as an effector molecule to skew T cell response to the Th2 phenotype, which might be more beneficial for pregnancy.
Inhibitory receptor gp49B regulates eosinophil infiltration during allergic inflammation
Authors: Norris Hillary H , Peterson Mary E , Stebbins Chris C , McConchie Brittany W , Bundoc Virgilio G , Trivedi Shweta , Hodges Marcus G , Anthony Robert M , Urban Joseph F , Long Eric O , Keane-Myers Andrea M 
Published: August 2007

Abstractgp49B, an Ig-like receptor, negatively regulates the activity of mast cells and neutrophils through cytoplasmic immunoreceptor tyrosine-based inhibition motifs. To characterize the role of gp49B further in vivo, gp49B-deficient mice were tested in two allergic models. Responses to ragweed (RW) challenge in the lung and conjunctiva were assessed in models of allergic inflammation and during an infection with parasitic larvae of the nematode Ascaris suum. Infiltration by inflammatory cells into the lung during allergic responses was under negative control of the inhibitory receptor gp49B. Furthermore, an increase in conjunctival inflammation with a predominance of eosinophils, neutrophils, and degranulated mast cells was observed in RW-sensitized, gp49B-deficient mice, which had been challenged in the eye, as compared with C57BL/6 wild-type (WT) controls. Finally, an increase in allergic inflammation in the lungs of A. suum-infected, RW-sensitized mice was observed upon RW challenge, as compared with C57BL/6 WT controls. The observed influx of eosinophils into mucus membranes is characteristic of allergic asthma and allergic conjunctivitis and may contribute to airway hyper-responsiveness, airway remodeling, and mucus production. Expression of gp49B was detected on peripheral eosinophils of control mice and on eosinophils from lungs of mice treated with RW, suggesting a role for gp49B on eosinophils in dampening allergic inflammatory responses.
Insight in psychosis: influence of cognitive ability and self-esteem
Authors: Cooke Michael A. , Peters Emmanuelle R. , Greenwood Kathryn E. , Fisher Peter L. , Kumari Veena , Kuipers Elizabeth 
Published: August 2007

BackgroundInsight in psychosis has previously been associated with both depression and cognitive ability. Some studies have found a curvilinear relationship between insight and cognitive ability but the roles of self-esteem and depression have not been taken into account.AimsTo investigate the relationships between insight and IQ, depression, and self-esteem.MethodCorrelations between self-reported and observer-rated insight, and measures of IQ, depression and self-esteem were examined in 67 people with psychosis.ResultsBetter self-reported insight was associated with higher IQ and poorer self-esteem, but not depression. There was some evidence for a curvilinear relationship between IQ and self-reported insight, specifically the ‘awareness of illness' dimension, which survived correction for symptom variables.ConclusionsThe relationship between insight and IQ might reflect both the basis of insight in intellectual ability and the influence of a psychological mechanism that preserves self-esteem.
Antipsychotic treatment of primary delusional parasitosis
Authors: Lepping Peter , Russell Ian , Freudenmann Roland W 
Published: August 2007

BackgroundLittle is known about the treatment of delusional parasitosis with typical and atypical antipsychotics.AimsTo evaluate the effectiveness of typical and atypical antipsychotics in primary delusional parasitosis (delusional disorder, somatic type).MethodA systematic review was conducted.ResultsNo randomised trials were found and hence we collected the best evidence from 16 other trials and case reports, separating primary from other forms of delusional parasitosis. Studies using typical antipsychotics showed partial or full remission in between 60 and 100% of patients. Analysis of selected patients with primary delusional parasitosis showed that typical and atypical antipsychotics were effective in the majority, but that remission rates did not differ significantly between typical and atypical antipsychotics.ConclusionsIn the absence of controlled trials there is limited evidence that antipsychotics are effective in primary delusional parasitosis. Rigorous studies are needed to evaluate their effectiveness and to compare typical and atypical antipsychotics directly.