bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response projected clustering for direct association with physiological and clinical response data
Authors: Yi Sung-Gon , Park Taesung , Lee Jae K 
Published: January 2008

AbstractBackgroundMicroarray gene expression data are often analyzed together with corresponding physiological response and clinical metadata of biological subjects, e.g. patients' residual tumor sizes after chemotherapy or glucose levels at various stages of diabetic patients. Current clustering analysis cannot directly incorporate such quantitative metadata into the clustering heatmap of gene expression. It will be quite useful if these clinical response data can be effectively summarized in the high-dimensional clustering display so that important groups of genes can be intuitively discovered with different degrees of relevance to target disease phenotypes.ResultsWe introduced a novel clustering analysis approach,response projected clustering(RPC), which uses a high-dimensional geometrical projection of response data to the gene expression space. The projected response vector, which becomes the origin in the projected space, is then clustered together with the projected gene vectors based on their different degrees of association with the response vector. A bootstrap-counting based RPC analysis is also performed to evaluate statistical tightness of identified gene clusters. Our RPC analysis was applied to thein vitrogrowth-inhibition and microarray profiling data on the NCI-60 cancer cell lines and the microarray gene expression study of macrophage differentiation in atherogenesis. These RPC applications enabled us to identify many known and novel gene factors and their potential pathway associations which are highly relevant to the drug's chemosensitivity activities and atherogenesis.ConclusionWe have shown that RPC can effectively discover gene networks with different degrees of association with clinical metadata. Performed on each gene's response projected vector based on its degree of association with the response data, RPC effectively summarizes individual genes' association with metadata as well as their own expression patterns. Thus, RPC greatly enhances the utility of clustering analysis on investigating high-dimensional microarray gene expression data with quantitative metadata.
Characterization of a newly developed chicken 44K Agilent microarray
Authors: Li Xianyao , Chiang Hsin-I , Zhu James , Dowd Scot E , Zhou Huaijun 
Published: January 2008

Abstract

Background
The development of microarray technology has greatly enhanced our ability to evaluate gene expression. In theory, the expression of all genes in a given organism can be monitored simultaneously. Sequencing of the chicken genome has provided the crucial information for the design of a comprehensive chicken transcriptome microarray. A long oligonucleotide microarray has been manually curated and designed by our group and manufactured using Agilent inkjet technology. This provides a flexible and powerful platform with high sensitivity and specificity for gene expression studies.

Results
A chicken 60-mer oligonucleotide microarray consisting of 42,034 features including the entire Marek's disease virus, two avian influenza virus (H5N2 and H5N3), and 150 chicken microRNAs has been designed and tested. In an important validation study, total RNA isolated from four major chicken tissues: cecal tonsil (C), ileum (I), liver (L), and spleen (S) were used for comparative hybridizations. More than 95% of spots had high signal noise ratio (SNR > 10). There were 2886, 2660, 358, 3208, 3355, and 3710 genes differentially expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum (P < 10-7), respectively. There were a number of tissue-selective genes for cecal tonsil, ileum, liver, and spleen identified (95, 71, 535, and 108, respectively; P < 10-7). Another highlight of these data revealed that the antimicrobial peptides GAL1, GAL2, GAL6 and GAL7 were highly expressed in the spleen compared to other tissues tested.

Conclusion
A chicken 60-mer oligonucleotide 44K microarray was designed and validated in a comprehensive survey of gene expression in diverse tissues. The results of these tissue expression analyses have demonstrated that this microarray has high specificity and sensitivity, and will be a useful tool for chicken functional genomics. Novel data on the expression of putative tissue specific genes and antimicrobial peptides is highlighted as part of this comprehensive microarray validation study. The information for accessing and ordering this 44K chicken array can be found at http://people.tamu.edu/~hjzhou/TAMUAgilent44KArray/
Measuring the financial burden of acute cough in pre-school children: a cost of illness study
Authors: Hollinghurst Sandra , Gorst Catherine , Fahey Tom , Hay Alastair D 
Published: January 2008

AbstractBackgroundContext:Acute cough is a very common symptom presentation among children in primary care and is usually due to respiratory infection, yet its cost is unknown. An estimate of the cost to healthcare providers and parents would aid budgetary decision-making, and provide an insight into the need for interventions to reduce the burden.Purpose:To estimate the cost per child per episode, and the annual population cost in the UK, of acute cough in pre-school children presenting to primary care.MethodsDesign: Incidence and prevalence-based cost-of-illness study from the perspectives of the UK NHS and of parents and caregivers.Setting:11 general practices in Bristol, UK.Subjects:121 children without known asthma aged 3 to 59 months presenting for the first time with an acute (≤ 28 days) cough.ResultsMean cost per episode to the NHS: £27.43 (95% CI: £24.38 – £30.49). Mean cost per episode to parents and carers: £14.77 (£4.90 – £24.65). Annual cost to the NHS in the UK: at least £31.5 m (95% CI: £28.0 m – £35.0 m).ConclusionThe cost burden on the healthcare provider of acute cough in pre-school children is substantial; the majority of this cost arises from consultations with general practitioners. Parents experience some personal cost through travel and expenditure on over-the-counter preparations, and may suffer significantly if loss of earnings is experienced. There is scope for evaluating interventions designed to reduce this burden.
Acquisition of new infection and clearance of type-specific human papillomavirus infections in female students in Busan, South Korea: a follow-up study
Authors: Oh Jin-Kyoung , Ju Young-Hee , Franceschi Silvia , Quint Wim , Shin Hai-Rim 
Published: January 2008

Abstract

Background
Little is known about the natural history of human papillomavirus (HPV) infection in Asian women.

Methods
A follow-up study was conducted, with exfoliated cervicovaginal cells self-collected from, and questionnaires administered to 197 female students, aged 17–26 years, who had been already examined one and half years before. The presence of 25 HPV types was evaluated by a polymerase chain reaction-based assay.

Results
The acquisition of new infection for any HPV type among 171 female students at risk who were negative at baseline, 60% of whom had remained as virgins, was 17.5% (95% confidence interval [CI]: 11.8–23.2). Among individual types, HPV16, 18 and 35 showed the highest rate of new infection. Women who had had first sexual intercourse (OR = 2.9; 95% CI: 1.0–8.8), or had changed sexual partners (OR = 2.9; 95% CI: 0.9–9.3) during the follow-up period showed a higher risk of new HPV infection than women who had remained virgins since baseline. The rate of new infection also tended to be higher in those who started, or continued smoking during the follow-up period, than in nonsmokers. Clearance of HPV infections since baseline examination was 80.6% (95% CI: 67.6–93.5), and did not differ between high-risk and low-risk HPV types or between single- and multiple-type infections.

Conclusion
This study shows that the acquisition of new HPV infection among young women in the Republic of Korea is high and also the clearance is frequent. Self-collection of cervicovaginal cells is applicable to follow-up studies that include virgins.
Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia
Authors: Cao Henian , Alston Lindsay , Ruschman Jennifer , Hegele Robert A. 
Published: January 2008

Abstract

Background
Mice with a deleted Cav1 gene encoding caveolin-1 develop adipocyte abnormalities and insulin resistance. From genomic DNA of patients with atypical lipodystrophy and hypertriglyceridemia who had no mutations in any known lipodystrophy gene, we used DNA sequence analysis to screen the coding regions of human CAV1 (MIM 601047).

Results
We found a heterozygous frameshift mutation in CAV1, designated I134fsdelA-X137, in a female patient who had atypical partial lipodystrophy, with subcutaneous fat loss affecting the upper part of her body and face, but sparing her legs, gluteal region and visceral fat stores. She had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis. In addition, she had some atypical features, including congenital cataracts and neurological findings. Her father was also heterozygous for this mutation, and had a similar pattern of fat redistribution, hypertriglyceridemia and congenital cataracts, with milder neurological involvement. An unrelated patient had a different heterozygous frameshift mutation in the CAV1 gene, designated -88delC. He also had a partial lipodystrophy phenotype, with subcutaneous fat loss affecting the arms, legs and gluteal region, but sparing his face, neck and visceral fat stores. He also had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis; however he had no clinically apparent neurological manifestations. The mutations were absent from the genomes of 1063 healthy individuals.

Conclusion
Thus, very rare CAV1 frameshift mutations appear to be associated with atypical lipodystrophy and hypertriglyceridemia.
Differential regulation of insulin-like growth factor binding protein-1 and -2 by insulin in the baboon (Papio anubis) endometrium
Authors: Fleming Steven D , Fazleabas Asgerally T , Bell Stephen C 
Published: January 2008

Abstract

Background
The purpose of this study was to examine the effect of insulin on expression and synthesis of IGFBP-1 and IGFBP-2 in the baboon endometrium in vitro.

Methods
Baboon endometrial explants collected from cycling, ovariectomized, steroid-treated, simulated-pregnant and pregnant animals were cultured for 48 h in the presence or absence of insulin, with or without estradiol, progesterone and hCG.

Results
Insulin clearly inhibited IGFBP-1 production and mRNA expression in a time- and dose-dependent manner, whereas IGFBP-2 synthesis was not significantly affected. The inhibitory effects of insulin on IGFBP-1 were more evident in explants of non-pregnant tissue or tissue away from the implantation site. In the absence of insulin, synthesis of IGFBP-1 was induced in explants with low levels of de novo synthesis whereas IGFBP-2 synthesis was inhibited. This effect was potentiated by steroids and hCG in the explant cultures.

Conclusion
Insulin differentially regulates endometrial IGFBP-1 and IGFBP-2 secretion in the baboon.
Mortality after infection with methicillin-resistant Staphylococcus aureus(MRSA) diagnosed in the community
Authors: Delaney JA 'Chris' , Schneider-Lindner Verena , Brassard Paul , Suissa Samy 
Published: January 2008

AbstractBackgroundOutbreak reports suggest that community-acquired methicillin-resistantStaphylococcus aureus(MRSA) infections can be life-threatening. We conducted a population based cohort study to assess the magnitude of mortality associated with MRSA infections diagnosed in the community.MethodsWe used the United Kingdom's General Practice Research Database (GPRD) to form a cohort of all patients with MRSA diagnosed in the community from 2001 through 2004 and up to ten patients without an MRSA diagnosis. The latter were frequency-matched with the MRSA patients on age, GPRD practice and diagnosis date. All patients were older than 18 years, had no hospitalization in the 2 years prior to cohort entry and medical history information of at least 2 years prior to cohort entry. The cohort was followed up for 1 year and all deaths and hospitalizations were identified. Hazard ratios of all-cause mortality were estimated using the Cox proportional hazards model adjusted for patient characteristics.ResultsThe cohort included 1439 patients diagnosed with MRSA and 14,090 patients with no MRSA diagnosis. Mean age at cohort entry was 70 years in both groups, while co-morbid conditions were more prevalent in the patients with MRSA. Within 1 year, 21.8% of MRSA patients died as compared with 5.0% of non-MRSA patients. The risk of death was increased in patients diagnosed with MRSA in the community (adjusted hazard ratio 4.1; 95% confidence interval: 3.5–4.7).ConclusionMRSA infections diagnosed in the community are associated with significant mortality in the year after diagnosis.
Differential inhibition of human cytomegalovirus (HCMV) by toll-like receptor ligands mediated by interferon-beta in human foreskin fibroblasts and cervical tissue
Authors: Harwani Sailesh C , Lurain Nell S , Zariffard M Reza , Spear Gregory T 
Published: January 2008

Abstract
Human cytomegalovirus (HCMV) can be acquired sexually and is shed from the genital tract. Cross-sectional studies in women show that changes in genital tract microbial flora affect HCMV infection and/or shedding. Since genital microbial flora may affect HCMV infection or replication by stimulating cells through Toll-like receptors (TLR), we assessed the effects of defined TLR-ligands on HCMV replication in foreskin fibroblasts and ectocervical tissue. Poly I:C (a TLR3-ligand) and lipopolysaccharide (LPS, a TLR4-ligand) inhibited HCMV and induced secretion of IL-8 and Interferon-beta (IFNβ) in both foreskin fibroblasts and ectocervical tissue. The anti-HCMV effect was reversed by antibody to IFNβ. CpG (TLR9 ligand) and lipoteichoic acid (LTA, TLR2 ligand) also inhibited HCMV infection in ectocervical tissue and this anti-HCMV effect was also reversed by anti-IFNβ antibody. In contrast, LTA and CpG did not inhibit HCMV infection in foreskin fibroblasts. This study shows that TLR ligands induce an HCMV-antiviral effect that is mediated by IFNβ suggesting that changes in genital tract flora may affect HCMV infection or shedding by stimulating TLR. This study also contrasts the utility of two models that can be used for assessing the interaction of microbial flora with HCMV in the genital tract. Clear differences in the response to different TLR ligands suggests the explant model more closely reflects in vivo responses to genital infections.
Redundancy and compensation in axon guidance: genetic analysis of the Drosophila Ptp10D/Ptp4E receptor tyrosine phosphatase subfamily
Authors: Jeon Mili , Nguyen Huong , Bahri Sami , Zinn Kai 
Published: January 2008

Abstract
Background
Drosophila has six receptor protein tyrosine phosphatases (RPTPs), five of which are expressed primarily in neurons. Mutations in all five affect axon guidance, either alone or in combination. Highly penetrant central nervous system (CNS) and motor axon guidance alterations are usually observed only when specific combinations of two or more RPTPs are removed. Here, we examine the sixth RPTP, Ptp4E, which is broadly expressed.

Results
Ptp4E and Ptp10D are closely related type III RPTPs. Non-drosophilid insect species have only one type III RPTP, which is closest to Ptp10D. We found that Ptp4E mutants are viable and fertile. We then examined Ptp4E Ptp10D double mutants. These die before the larval stage, and have a mild CNS phenotype in which the outer longitudinal 1D4 bundle is frayed. Ptp10D Ptp69D double mutants have a strong CNS phenotype in which 1D4 axons abnormally cross the midline and the outer and middle longitudinal bundles are fused to the inner bundle. To examine if Ptp4E also exhibits synthetic phenotypes in combination with Ptp69D, we made Ptp4E Ptp69D double mutants and Ptp4E Ptp10D Ptp69D triple mutants. No phenotype was observed in the double mutant. The triple mutant phenotype differs from the Ptp10D Ptp69D phenotype in two ways. First, the longitudinal tracts appear more normal than in the double mutant; two or three bundles are observed, although they are disorganized and fused. Second, axons labelled by the SemaIIB-τMyc marker often cross in the wrong commissure. We also examined motor axon guidance, and found that no phenotypes are observed in any Ptp4E double mutant combination. However, triple mutants in which Ptp4E Ptp10D was combined with Ptp69D or Ptp52F exhibited stronger phenotypes than the corresponding Ptp10D double mutants.

Conclusion
Type III RPTPs are required for viability in Drosophila, since Ptp4E Ptp10D double mutants die before the larval stage. Unlike Ptp10D, Ptp4E appears to be a relatively minor player in the control of axon guidance. Strong phenotypes are only observed in triple mutants in which both type III RPTPs are eliminated together with Ptp69D or Ptp52F. Our results allow us to construct a complete genetic interaction matrix for all six of the RPTPs.
Tuberculous peritonitis in a German patient with primary biliary cirrhosis: a case report
Authors: Vogel Yilin , Bous Jan C , Winnekendonk Guido , Henning Bernhard F 
Published: January 2008

Abstract

Background
The number of cases of tuberculosis as a complication in people with immunodeficiency, people on immunosuppressive therapy and among the immigrant population is increasing in Germany. However, tuberculous peritonitis rarely occurs without these risks, particularly in Germans. The incidence of tuberculous peritonitis in Germany is very low; tuberculosis of the intestinal tract was found in approximately 0.8 % of tuberculosis cases in 2004. The diagnosis of tuberculous peritonitis is often delayed on account of non-specific clinical symptoms. The absence of specific biological markers, long incubation times for cultures and non-specific radiographic or ultrasonographic signs increase the morbidity associated with this treatable condition.

Case presentation
We report a case of tuberculous peritonitis in a 73-year-old female German patient. Her medical history revealed primary biliary cirrhosis (PBC) since 1992. On admission, she complained of abdominal pain, vomiting, ascites and peripheral edema. The patient has been in a seriously reduced general condition and had fever up to 39.6°C. A few weeks earlier, the patient was in another hospital with the same complaint. Inflammatory parameters were elevated, but the procalcitonin level was normal. Blood culture was always negative, as was the tuberculin test. Ultrasonography of the abdomen showed massive ascites with multiple septa. The patient underwent a computed tomography (CT) scan of the abdomen which showed a thickened intestinal wall in the sigmoid colon and a pronounced enhancement of the peritoneum. Computed tomography scans of the lung showed only slight bilateral pleural effusion. Because of the anaesthetic and bleeding risk due to thrombocytopenia, laparoscopy was not immediately undertaken. The culture from ascites was positive for M.tuberculosis after three weeks.

Conclusion
In primary biliary cirrhosis patients with non-specific clinical symptoms, such as vomiting, abdominal pain, ascites, weight loss, and fever, tuberculous peritonitis must be considered in the initial differential diagnosis, although these symptoms may be attributed to cirrhosis of the liver with spontaneous bacterial peritonitis. Ultrasonographic and CT scab findings are not specific for tuberculous peritonitis, but an awareness of the ultrasonographic features and the features of the CT scan may help in the diagnosis of tuberculous peritonitis and avoid clinical mismanagement.
Microarray analysis in B cells among siblings with/without MS - role for transcription factor TCF2
Authors: Avasarala Jagannadha R , Chittur Sridar V , George Ajish D , Tine John A 
Published: January 2008

Abstract

Background
We investigated if global gene expression and transcription networks in B-lymphocytes of siblings with multiple sclerosis (MS) were different from healthy siblings.

Results
Using virus-transformed immortalized B cells and human whole genome bioarrays with validation using RT-qPCR, we found that in siblings with MS, genes for CXCL10, serpin B1 and FUT4 were up regulated whereas CDC5L, TNFRSF19 and HLA-DR were down regulated, among others; transcription analysis showed two intersecting clusters of transcriptional factors - the larger, governed by the upregulated transcription factor 2 (TCF2) and the smaller network regulated by the downregulated CDC5L.

Conclusion
No study has linked TCF2 to MS and to better understand the role of TCF2 in MS, studies in larger cohorts are required.
Robust SNP genotyping by multiplex PCR and arrayed primer extension
Authors: Podder Mohua , Ruan Jian , Tripp Ben W , Chu Zane E , Tebbutt Scott J 
Published: January 2008

Abstract

Background
Arrayed primer extension (APEX) is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs). However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project.

Results
In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs). In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy.

Conclusion
We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.
Mental health policy reforms and case complexity in CMHTs in England: replication study
Authors: Huxley Peter , Evans Sherrill , Munroe Maria , Cestari Leticia 
Published: January 2008

Aims and MethodCommunity mental health team (CMHT) services in many Western countries have been remodelled to focus on people with the most severe illnesses and complex problems. Complexity scores using the Matching Resource to Care (MARC2) measure from CMHT cases in 2004–2005 (n=1481) are compared with scores in 1997–1998 (n=3178) in the same locations, before the introduction of the National Service Framework, and before the impact of the creation of integrated mental health trusts in England.ResultsThe 2004–2005 baseline complexity scores are all worse than those in 1997–1998.Clinical ImplicationsIf increased targeting brought about by the National Service Framework and other reforms has led to a greater proportion of people with complex problems in case-loads, what care services, if any, are now being received by people who were in receipt of CMHT services before the reforms?