bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression
Authors: Funari Vincent A , Day Allen , Krakow Deborah , Cohn Zachary A , Chen Zugen , Nelson Stanley F , Cohn Daniel H 
Published: June 2007

Abstract

Background
Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18–22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed Celsius.

Results
161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as cartilage collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis.

Conclusion
Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.
Large-scale copy number variants (CNVs): Distribution in normal subjects and FISH/real-time qPCR analysis
Authors: Qiao Ying , Liu Xudong , Harvard Chansonette , Nolin Sarah L , Brown W Ted , Koochek Maryam , Holden Jeanette JA , Lewis ME Suzanne , Rajcan-Separovic Evica 
Published: June 2007

Abstract

Background
Genomic copy number variants (CNVs) involving >1 kb of DNA have recently been found to be widely distributed throughout the human genome. They represent a newly recognized form of DNA variation in normal populations, discovered through screening of the human genome using high-throughput and high resolution methods such as array comparative genomic hybridization (array-CGH). In order to understand their potential significance and to facilitate interpretation of array-CGH findings in constitutional disorders and cancers, we studied 27 normal individuals (9 Caucasian; 9 African American; 9 Hispanic) using commercially available 1 Mb resolution BAC array (Spectral Genomics). A selection of CNVs was further analyzed by FISH and real-time quantitative PCR (RT-qPCR).

Results
A total of 42 different CNVs were detected in 27 normal subjects. Sixteen (38%) were not previously reported. Thirteen of the 42 CNVs (31%) contained 28 genes listed in OMIM. FISH analysis of 6 CNVs (4 previously reported and 2 novel CNVs) in normal subjects resulted in the confirmation of copy number changes for 1 of 2 novel CNVs and 2 of 4 known CNVs. Three CNVs tested by FISH were further validated by RT-qPCR and comparable data were obtained. This included the lack of copy number change by both RT-qPCR and FISH for clone RP11-100C24, one of the most common known copy number variants, as well as confirmation of deletions for clones RP11-89M16 and RP5-1011O17.

Conclusion
We have described 16 novel CNVs in 27 individuals. Further study of a small selection of CNVs indicated concordant and discordant array vs. FISH/RT-qPCR results. Although a large number of CNVs has been reported to date, quantification using independent methods and detailed cellular and/or molecular assessment has been performed on a very small number of CNVs. This information is, however, very much needed as it is currently common practice to consider CNVs reported in normal subjects as benign changes when detected in individuals affected with a variety of developmental disorders.
Helicobacter pylori genome variability in a framework of familial transmission
Authors: Kivi Mårten , Rodin Sandra , Kupershmidt Ilya , Lundin Annelie , Tindberg Ylva , Granström Marta , Engstrand Lars 
Published: June 2007

Abstract

Background

Helicobacter pylori infection is exceptionally prevalent and is considered to be acquired primarily early in life through person-to-person transmission within the family. H. pylori is a genetically diverse bacterial species, which may facilitate adaptation to new hosts and persistence for decades. The present study aimed to explore the genetic diversity of clonal isolates from a mother and her three children in order to shed light on H. pylori transmission and host adaptation.

Results
Two different H. pylori strains and strain variants were identified in the family members by PCR-based molecular typing and sequencing of five loci. Genome diversity was further assessed for 15 isolates by comparative microarray hybridizations. The microarray consisted of 1,745 oligonucleotides representing the genes of two previously sequenced H. pylori strains. The microarray analysis detected a limited mean number (± standard error) of divergent genes between clonal isolates from the same and different individuals (1 ± 0.4, 0.1%, and 3 ± 0.3, 0.2%, respectively). There was considerable variability between the two different strains in the family members (147 ± 4, 8%) and for all isolates relative to the two sequenced reference strains (314 ± 16, 18%). The diversity between different strains was associated with gene functional classes related to DNA metabolism and the cell envelope.

Conclusion
The present data from clonal H. pylori isolates of family members do not support that transmission and host adaptation are associated with substantial sequence diversity in the bacterial genome. However, important phenotypic modifications may be determined by additional genetic mechanisms, such as phase-variation. Our findings can aid further exploration of H. pylori genetic diversity and adaptation.
QTL mapping of agronomic traits in tef [Eragrostis tef(Zucc) Trotter]
Authors: Yu Ju-Kyung , Graznak Elizabeth , Breseghello Flavio , Tefera Hailu , Sorrells Mark E 
Published: June 2007

Abstract

Background
Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5).

Results
Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect.

Conclusion
The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.
Modulation of RANTES expression by HCV core protein in liver derived cell lines
Authors: Ruggieri Anna , Franco Marina , Gatto Ilaria , Kumar Ajit , Rapicetta Maria 
Published: June 2007

Abstract

Background
Hepatitis C virus (HCV) infection is associated with high percentage of chronicity which implies the ability of the virus to evade or modulate host cell immune system. Modulation of chemokines, such as RANTES may be part of the virus induced pathogenicity. We examined the effect of core and structural proteins of HCV on RANTES expression in two liver derived cell lines, HepG2 and Chang Liver (CHL).

Methods
HepG2 and Chang Liver (CHL) cell lines were established and selected for constitutive expression of HCV core and structural genes. Flow cytometry and quantitative RT-PCR analysis were performed to examine the effect of HCV core protein on RANTES expression. Luciferase analysis after RANTES-Luc-promoter transfection of established cell lines was assayed by luminometer measurements (RLU) of RANTES promoter activity. IRF-1 and IRF-7 expression was then examined by immunoblotting analysis.

Results
Results of flow cytometry and RT-PCR analysis indicated that RANTES is differentially regulated by HCV core protein in the two cell lines examined as its expression was inhibited in HepG2 cells, by a reduction of RANTES promoter activity. Conversely, RANTES protein and mRNA were induced by the core protein in CHL cells, through the induction of the promoter.
Since HCV genome modulates IRF-1 and IRF-7 in replicon system and IRF-1, IRF-3 and IRF-7 have been reported to regulate RANTES promoter in various cell systems, analysis of the mechanism underlying RANTES modulation by the core protein revealed that IRF-1 expression was induced in HepG2 cells by the core protein, whereas in CHL cells it was expressed at a very low level that was not influenced by transfection with the core protein construct. This suggested that IRF-1 level may mediate the expression of RANTES in cell lines of liver origin. The effect of the core protein on RANTES promoter was countered by co-transfection with NF90, a double-stranded-RNA binding protein that activates some interferon response genes and acts as a component of cell defense against viral infection.

Conclusion
HCV core protein have opposite effects on the expression of RANTES in different cell types in vitro, possibly reflecting a similar scenario in different microenvironments in vivo.
Innate immunity glycoprotein gp-340 variants may modulate human susceptibility to dental caries
Authors: Jonasson Anette , Eriksson Christer , Jenkinson Howard F , Källestål Carina , Johansson Ingegerd , Strömberg Nicklas 
Published: June 2007

Abstract

Background
Bacterial adhesion is an important determinant of colonization and infection, including dental caries. The salivary scavenger receptor cysteine-rich glycoprotein gp-340, which mediates adhesion of Streptococcus mutans (implicated in caries), harbours three major size variants, designated gp-340 I to III, each specific to an individual saliva. Here we have examined the association of the gp-340 I to III polymorphisms with caries experience and adhesion of S. mutans.

Methods
A case-referent study was performed in 12-year-old Swedish children with high (n = 19) or low (n = 19) caries experiences. We measured the gp-340 I to III saliva phenotypes and correlated those with multiple outcome measures for caries experience and saliva adhesion of S. mutans using the partial least squares (PLS) multivariate projection technique. In addition, we used traditional statistics and 2-year caries increment to verify the established PLS associations, and bacterial adhesion to purified gp-340 I to III proteins to support possible mechanisms.

Results
All except one subject were typed as gp-340 I to III (10, 23 and 4, respectively). The gp-340 I phenotype correlated positively with caries experience (VIP = 1.37) and saliva adhesion of S. mutans Ingbritt (VIP = 1.47). The gp-340 II and III phenotypes tended to behave in the opposite way. Moreover, the gp-340 I phenotype tended to show an increased 2-year caries increment compared to phenotypes II/III. Purified gp-340 I protein mediated markedly higher adhesion of S. mutans strains Ingbritt and NG8 and Lactococcus lactis expressing AgI/II adhesins (SpaP or PAc) compared to gp-340 II and III proteins. In addition, the gp-340 I protein appeared over represented in subjects positive for Db, an allelic acidic PRP variant associated with caries, and subjects positive for both gp-340 I and Db tended to experience more caries than those negative for both proteins.

Conclusion
Gp-340 I behaves as a caries susceptibility protein.
Fibrinogen gamma-A chain precursor in CSF: a candidate biomarker for Alzheimer's disease
Authors: Lee Joung Wook , Namkoong Hong , Kim Hyun Kee , Kim Sanghee , Hwang Dong Whi , Na Hae Ri , Ha Seon-Ah , Kim Jae-Ryong , Kim Jin Woo 
Published: June 2007

Abstract

Background
Cerebrospinal fluid (CSF) may be valuable for exploring protein markers for the diagnosis of Alzheimer's disease (AD). The prospect of early detection and treatment, to slow progression, holds hope for aging populations with increased average lifespan. The aim of the present study was to investigate candidate CSF biological markers in patients with mild cognitive impairment (MCI) and AD and compare them with age-matched normal control subjects.

Methods
We applied proteomics approaches to analyze CSF samples derived from 27 patients with AD, 3 subjects with MCI and 30 controls. The AD group was subdivided into three groups by clinical severity according to clinical dementia rating (CDR), a well known clinical scale for dementia.

Results
We demonstrated an elevated level of fibrinogen gamma-A chain precursor protein in CSF from patients with mild cognitive impairment and AD compared to the age-matched normal subjects. Moreover, its expression was more prominent in the AD group than in the MCI and correlated with disease severity and progression. In contrast, fibrinogen gamma-A chain precursor protein was detected very low in the age-matched normal group.

Conclusion
These findings suggest that the CSF level of fibrinogen gamma-A chain precursor may be a candidate biomarker for AD.
Variations of care quality for infectious pulmonary tuberculosis in Taiwan: a population based cohort study
Authors: Chung Wei-Sheng , Chang Ray-E , Guo How-Ran 
Published: June 2007

Abstract

Background
Effective and efficient care is required to prevent the spread of infectious pulmonary tuberculosis (PTB). We attempted to compare care quality among different healthcare institutions in Southern Taiwan.

Methods
This study conducted population-based retrospective cohort design. One tuberculosis sanatorium, 2 medical centers, 11 regional hospitals, and 15 district hospitals and primary practitioners in the study area had reported tuberculosis cases, registered from January 1 to June 30 2003. Those cases with sputum positive PTB were followed 15 months after anti-tuberculosis treatment initiation. Meanwhile, Level of conformance with diagnostic guidelines, efficiency of diagnostic and treatment process, and treatment were measured as main outcome. Association was investigated using Chi-square tests, Kruskal Wallis tests, Mann-Whiteney U tests, and multiple logistic regression analysis to evaluate outcome differences among different levels of institutions.

Results
The analyses included 421 patients. In comparison with patients receiving treatment at medical centers, regional hospitals, and district hospitals/primary practitioners, patients at the Chest Specialty Hospital were more likely to provide at least three sputum specimens (74.1% vs. 48.2%, 36.8%, and 50.0%), shorter workdays examining sputum smears (2.4 ± 2.4 days vs. 2.6 ± 2.1, 4.5 ± 3.1, and 3.5 ± 2.6 days), shorter interval between the first consultation and treatment (10.1 ± 18.3 days vs. 31.0 ± 53.6, 31.2 ± 70.4, and 25.4 ± 37.6 days), and a higher successful treatment rate (92.6% vs. 65.2%, 63.9%, and 68.0%). Furthermore, after adjusting age and gender, the patients treated by the pulmonologists and treated at Chest Specialty Hospital had significantly more successful treatment rate, of which odds ratios were 1.74 and 4.58 respectively.

Conclusion
Differences in care quality exist among different types of healthcare institutions and among individual physicians. The implementation of practice guidelines should contribute to an improvement in the care quality of the treatment and diagnosis of PTB.
Bladder sensory desensitization decreases urinary urgency
Authors: Silva Carlos , Silva João , Castro Helder , Reis Frederico , Dinis Paulo , Avelino António , Cruz Francisco 
Published: June 2007

Abstract

Background
Bladder desensitization has been investigated as an alternative treatment for refractory detrusor overactivity. Most open and controlled clinical trials conducted with intravesical RTX showed that desensitization delays the appearance of involuntary detrusor contractions during bladder filling and decreases the number of episodes of urgency incontinence.
Urgency is being recognised as the fundamental symptom of overactive bladder (OAB), a symptomatic complex which recent epidemiological studies have shown to affect more than 10% of the Western population. As anti-muscarinic drugs, the first line treatment for OAB, are far from being able to fully control urgency, the opportunity to test other therapeutic approaches is created. The present work was, therefore, designed as an exploratory investigation to evaluate the effect of bladder desensitization on urinary urgency.

Methods
Twenty-three OAB patients with refractory urgency entered, after given informed consent, a 30 days run-in period in which medications influencing the bladder function were interrupted. At the end of this period patients filled a seven-day voiding chart where they scored, using a 0–4 scale, the bladder sensations felt before each voiding. Then, patients were instilled with 100 ml of 10% ethanol in saline (vehicle solution) and 30 days later a second seven-day voiding chart was collected. Finally, patients were instilled with 100 ml of 50 nM RTX in 10% ethanol in saline. At 1 and 3 months additional voiding charts were collected.
At the end of the vehicle and 3 months period patients were asked to give their subjective impression about the outcome of the treatment and about the willingness to repeat the previous instillation.

Results
At the end of the run-in period the mean number of episodes of urgency per week was 71 ± 12 (mean ± SEM). After vehicle instillation, the mean number of episodes of urgency was 56 ± 11, but only 4 patients (17%) considered that their urinary condition had improved enough to repeat the treatment. At 1 and 3 months after RTX the number of episodes of urgency decreased to 39 ± 9 (p = 0.002) and 37 ± 6 (p = 0.02), respectively (p indicates statistical differences against vehicle). The percentage of patients with subjective improvement after RTX and willing to repeat the instillation at a later occasion was 69%.

Conclusion
In OAB patients with refractory urgency bladder desensitization should be further investigated as an alternative to the standard management. Additionally, the specific effect of RTX on TRPV1 receptors suggests that urothelium and sub-urothelial C-fibers play an important role to the generation of urgency sensation.
Medicine in words and numbers: a cross-sectional survey comparing probability assessment scales
Authors: Witteman Cilia LM , Renooij Silja , Koele Pieter 
Published: June 2007

Abstract

Background
In the complex domain of medical decision making, reasoning under uncertainty can benefit from supporting tools. Automated decision support tools often build upon mathematical models, such as Bayesian networks. These networks require probabilities which often have to be assessed by experts in the domain of application. Probability response scales can be used to support the assessment process. We compare assessments obtained with different types of response scale.

Methods
General practitioners (GPs) gave assessments on and preferences for three different probability response scales: a numerical scale, a scale with only verbal labels, and a combined verbal-numerical scale we had designed ourselves. Standard analyses of variance were performed.

Results
No differences in assessments over the three response scales were found. Preferences for type of scale differed: the less experienced GPs preferred the verbal scale, the most experienced preferred the numerical scale, with the groups in between having a preference for the combined verbal-numerical scale.

Conclusion
We conclude that all three response scales are equally suitable for supporting probability assessment. The combined verbal-numerical scale is a good choice for aiding the process, since it offers numerical labels to those who prefer numbers and verbal labels to those who prefer words, and accommodates both more and less experienced professionals.
Patients' understanding of genetic susceptibility testing in mainstream medicine: qualitative study on thrombophilia
Authors: Saukko Paula M , Ellard Sian , Richards Suzanne H , Shepherd Maggie H , Campbell John L 
Published: June 2007

Abstract
Background
UK and US policy initiatives have suggested that, in the future, patients and clinicians in mainstream medicine could use genetic information to prevent common illnesses. There are no studies on patients' experience and understanding of the process of testing for common genetic susceptibilities in mainstream medicine.

Methods
Qualitative interviews with 42 individuals who had undergone testing for a genetic susceptibility for deep vein thrombosis in primary and secondary care in the UK.

Results
Some participants, often from higher social classes, had a good understanding of the test and its implications. They had often sought additional information on thrombophilia from relatives and from the Internet. Others, often from less privileged backgrounds, had a poorer understanding of the test – seven individuals were unaware of having had the genetic test. Features of genetic information led to misunderstandings: (i) at referral, (ii) when communicating results, and (iii) when making sense of the implications of testing. Participants' accounts indicated that non-specialist doctors may feel obliged to refer a patient for a genetic test they know little about, because a patient requests it after a relative had tested positive. Sometimes a referral for a genetic test was lost under information overload when multiple tests and issues were considered. The inconsistent and informal ways of communicating test results – for example by phone – in mainstream medicine also led to confusion. Participants did not generally overestimate their risk, but some were uncertain about whether they were taking the right preventive actions and/or whether their children were at risk. Information about genetic susceptibilities was difficult to make sense of, as it related to ambiguous risks for participants and family members, complicated and unfamiliar terminology and multiple genes and preventive strategies.

Conclusion
Policy visions of clinicians and patients in mainstream medicine seeking and using genetic information at their own initiative may not be realistic. Patients need more direct support in making sense of genetic information, if this information is to bring the anticipated health benefits, and not fuel health inequalities or create ethical problems. Clinicians in secondary and primary care need guidance to help them introduce genetic tests, communicate their results and explain their implications.