bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant epithelial expression of trefoil family factor 2 and mucin 6 inHelicobacter pyloriinfected gastric antrum, incisura, and body and its association with antralisation
Authors: Xia H H-X , Yang Y , Lam S K , Wong W M , Leung S Y , Yuen S T , Elia G , Wright N A , Wong B C-Y 
Published: July 2004

Aims:To determine gastric expression of trefoil family factor 2 (TFF2) and MUC6 inHelicobacter pyloripositive and negative subjects, and its association with antralisation at the gastric incisura.Methods:Gastric biopsies from the antrum, incisura, and body of 76 dyspeptic patients without ulcers were used for the determination ofH pyloriinfection, histological changes, and epithelial TFF2 and MUC6 expression.Results:In the foveola, the rates of TFF2 and MUC6 immunostaining were greater inH pyloriinfected (n  =  27) than in uninfected patients (n  =  49) at the antrum (59.3%v4.1% for TFF2 and 63.0%v4.1% for MUC6; both p < 0.001) and incisura (44.4%v2.0% for TFF2 and 48.1%v0% for MUC6; both p < 0.001). In the deeper glands, the rates were also greater inH pyloriinfected than in uninfected patients at the incisura (85.2%v22.4% for both TFF2 and MUC6; p < 0.001). Antral-type mucosa was present at the incisura in 28 of the 76 patients. TFF2 and MUC6 expression in the foveola and deeper glands was significantly associated with antral-type mucosa, independent ofH pyloristatus.Conclusions:Helicobacter pyloriinfection increases the expression of TFF2 and MUC6 in the gastric epithelium. Aberrant TFF2 and MUC6 expression is associated with antralisation of gastric incisura.
Increased neutrophil apoptosis in chronic fatigue syndrome: Table 1
Authors: Kennedy G , Spence V , Underwood C , Belch J J F 
Published: July 2004

Background/Aims:Many patients with chronic fatigue syndrome (CFS) have symptoms that are consistent with an underlying viral or toxic illness. Because increased neutrophil apoptosis occurs in patients with infection, this study examined whether this phenomenon also occurs in patients with CFS.Methods:Apoptosis was assessed in patients with CFS in conjunction with concentrations of the anti-inflammatory cytokine, transforming growth factor β1 (TGFβ1).Results:The 47 patients with CFS had higher numbers of apoptotic neutrophils, lower numbers of viable neutrophils, increased annexin V binding, and increased expression of the death receptor, tumour necrosis factor receptor-I, on their neutrophils than did the 34 healthy controls. Patients with CFS also had raised concentrations of active TGFβ1 (p < 0.005).Conclusions:These findings provide new evidence that patients with CFS have an underlying detectable abnormality in their immune cells.
Node retrieval in axillary lymph node dissections: recommendations for minimum numbers to be confident about node negative status
Authors: Somner J E A , Dixon J M J , Thomas J S J 
Published: July 2004

Aims:To determine the minimum number of lymph nodes needed in an axillary lymph node dissection (ALND) specimen to be confident that the axilla is free from metastases.Methods:The Edinburgh Breast Unit selects patients with large and high grade tumours for ALND; 609 consecutive ALNDs performed between October 1999 and December 2002 were reviewed. Full data about the underlying invasive breast cancer were available for 520 patients. Data were collected regarding number of positive nodes and total number of nodes collected, tumour size and grade, and presence of lymphovascular invasion.Results:Axillary node metastases were seen in 64% of patients. The mean number of positive nodes found was 3.56, with a mean of 17.9 nodes collected. The highest proportion of patients with lymph node metastases were in the group with 16–20 nodes recovered/specimen (68%); specimens with >20 nodes recovered did not have a higher rate of nodal involvement. There was a significant difference between the proportion of metastasis positive specimens in those with 1–15 nodes recovered (58.5%) and those with 16 or more recovered (69.1%). A linear association test showed a direct correlation between the number of nodes collected and presence of node metastasis (p = 0.0005).Conclusions:Although there is no minimum number of nodes that should be recovered in an ALND specimen, 16 nodes should be regarded as a target to ensure a high level of confidence that the nodes are negative. Node positivity in an ALND specimen appears to obey the law of diminishing returns.
Sertoli cell nodules in the undescended testis: a histochemical, immunohistochemical, and ultrastructural study of hyaline deposits
Authors: Govender D , Sing Y , Chetty R 
Published: July 2004

Aims:To document the morphology, immunohistochemical staining properties, and ultrastructural features of hyaline material in Sertoli cell nodules of undescended testis and contrast them with those of sex cord tumour with annular tubules (SCTAT), which is histologically similar. To highlight the need to distinguish these nodules from other Sertoli cell hyperplasias, such as intratubular Sertoli cell proliferations, which occur in specific clinical contexts.Materials/methods:A retrospective study of 46 orchidectomy specimens from cryptorchid testes, 27 of which contained Sertoli cell nodules. Special histochemical stains, immunohistochemical stains for type IV collagen and fibronectin, and ultrastructural examination of the hyaline material were performed using tissue from paraffin wax embedded tissue blocks.Results:The hyaline deposits in SCTAT and Sertoli cell nodules had similar staining patterns—periodic acid Schiff (PAS) and PAS-diastase positivity with variable staining of Martius scarlet blue and Masson trichrome. Type IV collagen immunoreactivity was seen in hyaline areas, although fibronectin was negative. Electron microscopy of hyaline areas confirmed a compact matrix identical to components of the basement membrane in the adjacent seminiferous tubules.Conclusion:This study describes an unusual form of Sertoli cell proliferation in undescended testes, which must be distinguished from Sertoli cell tumours and other forms of proliferation. In addition, the hyaline material within Sertoli cell nodules in the cryptorchid testis is histochemically, immunohistochemically, and ultrastructurally consistent with both matrix and fibrous components of seminiferous tubule basement membranes. Increased production of basement membrane material, with subsequent invagination into tubules, is the most likely origin of this material.
Secular trends of nocardia infection over 15 years in a tertiary care hospital
Authors: Matulionyte R , Rohner P , Uçkay I , Lew D , Garbino J 
Published: July 2004

Aims:To assess the incidence of nocardia infection over 15 years in a tertiary care hospital.Methods:Over a 15 year period,Nocardiaspp were isolated from 20 patients hospitalised at the Geneva University Hospitals, Switzerland.Results:Sixteen patients had one or more underlying conditions. The median time between symptom onset and diagnosis was 30 days. The most common initial unconfirmed diagnosis was pulmonary tuberculosis (four). The lung was involved in 16 cases, followed by the central nervous system (two) and skin (two); one patient had disseminated infection. The most common species identified wasN asteroides. In vitro susceptibility testing was performed on 14 of 20 strains. All strains were susceptible to imipenem and amikacin. Initial treatment with trimethoprim/sulfamethoxazole (TMP/SMX) was started in 14 patients, although five patients had to be switched to another treatment because of side effects or lack of efficacy. A cure was observed in 15 patients, death in three, and relapse or complications in two.Conclusions:Nocardiosis can become a severe infection and mainly affects profoundly immunocompromised patients. Differential diagnosis often delays the time to diagnosis, which worsens the outcome. New diagnostic tools, such as the polymerase chain reaction, could provide more rapid and reliable results. TMT/SMX was the most commonly prescribed treatment, but needed to be changed for another treatment because of side effects or lack of efficacy in a considerable proportion of patients. Imipenem should be used as an alternative treatment for severely ill patients, and the sulfa combination for less severe infections.
Topographical localisation of cagA positive and cagA negativeHelicobacter pyloristrains in the gastric mucosa; an in situ hybridisation study
Authors: Camorlinga-Ponce M , Romo C , González-Valencia G , Muñoz O , Torres J 
Published: July 2004

Background:The cagA gene is a marker for the presence of the cag pathogenicity island, and the presence of cagA positive strains ofHelicobacter pylorican identify individuals with a higher risk of developing gastrointestinal diseases.Aims:To study the interaction betweenH pyloricagA(+) and cagA(−) strains and the gastric mucosa.Methods:Patients withH pyloriassociated gastritis and peptic ulcers were studied. Biopsies were obtained from the antrum, corpus, fundus, and incisura forH pyloriculture, and for in situ hybridisation studies. From each biopsy, multiple singleH pyloricolonies were isolated and propagated for DNA isolation, and cagA was detected by the polymerase chain reaction (PCR). For in situ detection ofH pylorian oligonucleotide specific for anH pyloricommon antigen and an oligonucleotide specific for cagA were used as probes. Biotinylated probes were incubated with biopsy sections, developed with streptavidin–horseradish peroxidase, and amplified with the tyramide system.Results:PCR results for cagA in isolated colonies confirmed the in situ hydridisation studies. In situ hybridisation identified cagA(+) bacteria in patients with cagA(+) isolates; cagA(−) bacteria in patients with cagA(−) isolates, and cagA(+) and cagA (−) bacteria in patients with both cagA(+) and cagA(−) isolates. CagA(−) bacteria usually colonised the mucous gel or the apical epithelial surface, whereas cagA(+) bacteria colonised the immediate vicinity of epithelial cells or the intercellular spaces.Conclusions:These results document a different in vivo interaction betweenH pyloricagA(+) orcagA(−) strains and the gastric mucosa.
Lepirudin for prophylaxis of thrombosis in patients with acute isolated heparin-induced thrombocytopenia: an analysis of 3 prospective studies
Authors: Lubenow Norbert , Eichler Petra , Lietz Theresia , Farner Beate , Greinacher Andreas 
Published: July 2004

Abstract
This analysis of 3 prospective multicenter trials in patients with laboratory-confirmed acute heparin-induced thrombocytopenia (HIT) without clinically evident thromboembolic complications (TECs), isolated HIT, assessed the combined individual end points of death, new TECs, and limb amputation. Patients with the same inclusion criteria who did not receive lepirudin or danaparoid served as a contemporaneous control group. Ninety-one patients were treated with lepirudin (intravenous infusion 0.10 mg/kg/h, no bolus, activated partial thromboplastin time [aPTT]–adjusted to 1.5-2.5 times baseline) for a median of 11.0 days (range, 1-68 days). During the observation period (median 24 days), 13 (14.3%) deaths, 4 (4.4%) new TECs, 3 (3.3%) limb amputations (combined 18 [19.8%]), and 13 (14.3%) major bleeding events occurred. In comparison to the control group (N = 47), the combined end point (P = .0281) and new TECs (P = .02) were reduced, and major bleeding was not significantly different between groups (P = .5419). In renal impairment, lepirudin did not reach its steady state within 4 hours, and additional monitoring every 4 hours after start of lepirudin until steady state is reached is recommended. Lepirudin seems to be effective in patients with isolated HIT. Dose reductions in renal impairment are important. Keeping the aPTT in the range corresponding to 600 to 700 μg/L lepirudin during treatment may minimize bleeding complications.
Peripheral blood stem cell transplantation in 16 patients with POEMS syndrome, and a review of the literature
Authors: Dispenzieri Angela , Moreno-Aspitia Alvaro , Suarez Guillermo A. , Lacy Martha Q. , Colon-Otero Gerardo , Tefferi Ayalew , Litzow Mark R. , Roy Vivek , Hogan William J. , Kyle Robert A. , Gertz Morie A. 
Published: July 2004

Abstract
POEMS syndrome is characterized by peripheral neuropathy (PN), a clonal plasma cell disorder (PCD), organomegaly, endocrinopathy, skin changes, edema, sclerotic bone lesions, and thrombocytosis. Based on the improved response rates observed with peripheral blood stem cell transplantation (PBSCT) in patients with other PCDs, autologous PBSCT may be an attractive treatment option for this syndrome. Sixteen patients with POEMS syndrome have undergone PBSCT at Mayo. Of these patients, 15 had a severe rapidly progressive sensorimotor PN (9 were wheelchair dependent) and 14 were male. Median age was 51 years (range, 19-62 years). The median number of prior therapies was 3 (range, 0-7). From first symptoms and from diagnosis of POEMS the times to transplantation were 42 months and 5 months (ranges, 8-185 months and 2-149 months), respectively. There were 15 patients who had significantly abnormal pretransplant pulmonary function tests. There was one transplant-related death. During the peritransplant period, 5 patients required intubation for respiratory compromise, including one who required intubation during his stem cell mobilization period. Another patient required noninvasive biphasic positive airway pressure throughout his course. Of the 14 evaluable patients, all have had neurologic improvement or stabilization. Other features have improved substantially. PBSCT for POEMS syndrome is effective therapy but may also be associated with significant morbidity. (Blood. 2004;104:3400-3407)
In vivo clearance of surfactant lipids during acute pulmonary inflammation.
Authors: Malloy Jaret L , Wright Jo Rae 
Published: July 2004

Abstract
Background
A decrease in pulmonary surfactant has been suggested to contribute to the lung dysfunction associated with pulmonary inflammation. A number of studies have implicated surfactant clearance as a possible mechanism for altered pool sizes. The objective of the current study was to specifically investigate the mechanisms of surfactant clearance in a rodent model of acute pulmonary inflammation.

Methods
Inflammation was induced by intrapulmonary instillation of lipopolysaccharide (LPS: 100 μg/kg). Lipid clearance was assessed at 18 and 72 hours post-LPS instillation by intratracheal administration of radiolabel surfactant-like liposomes 2 hours prior to isolation and analysis of inflammatory cells and type II cells.

Results
At both 18 and 72 hours after LPS instillation there was significantly less radioactivity recovered in the lavage fluid compared to respective control groups (p < 0.05). At both time points, the number of cells recovered by lavage and their associated radioactivity was greater compared to control groups (p < 0.01). There was no difference in recovery of radioactivity by isolated type II cells or other cells obtained from enzymatic digestion of lung tissue.

Conclusion
These results show that increased clearance of surfactant lipids in our model of acute pulmonary inflammation is primarily due to the inflammatory cells recruited to the airspace and not increased uptake by alveolar type II cells.
Graph-based iterative Group Analysis enhances microarray interpretation
Authors: Breitling Rainer , Amtmann Anna , Herzyk Pawel 
Published: July 2004

Abstract
Background
One of the most time-consuming tasks after performing a gene expression experiment is the biological interpretation of the results by identifying physiologically important associations between the differentially expressed genes. A large part of the relevant functional evidence can be represented in the form of graphs, e.g. metabolic and signaling pathways, protein interaction maps, shared GeneOntology annotations, or literature co-citation relations. Such graphs are easily constructed from available genome annotation data. The problem of biological interpretation can then be described as identifying the subgraphs showing the most significant patterns of gene expression. We applied a graph-based extension of our iterative Group Analysis (iGA) approach to obtain a statistically rigorous identification of the subgraphs of interest in any evidence graph.

Results
We validated the Graph-based iterative Group Analysis (GiGA) by applying it to the classic yeast diauxic shift experiment of DeRisi et al., using GeneOntology and metabolic network information. GiGA reliably identified and summarized all the biological processes discussed in the original publication. Visualization of the detected subgraphs allowed the convenient exploration of the results. The method also identified several processes that were not presented in the original paper but are of obvious relevance to the yeast starvation response.

Conclusions
GiGA provides a fast and flexible delimitation of the most interesting areas in a microarray experiment, and leads to a considerable speed-up and improvement of the interpretation process.
Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells
Authors: Yao Bin , Rakhade Sanjay N , Li Qunfang , Ahmed Sharlin , Krauss Raul , Draghici Sorin , Loeb Jeffrey A 
Published: July 2004

Abstract
Background
cDNA microarrays are a powerful means to screen for biologically relevant gene expression changes, but are often limited by their ability to detect small changes accurately due to "noise" from random and systematic errors. While experimental designs and statistical analysis methods have been proposed to reduce these errors, few studies have tested their accuracy and ability to identify small, but biologically important, changes. Here, we have compared two cDNA microarray experimental design methods with northern blot confirmation to reveal changes in gene expression that could contribute to the early antiproliferative effects of neuregulin on MCF10AT human breast epithelial cells.

Results
We performed parallel experiments on identical samples using a dye-swap design with ANOVA and an experimental design that excludes systematic biases by "correcting" experimental/control hybridization ratios with control/control hybridizations on a spot-by-spot basis. We refer to this approach as the "control correction method" (CCM). Using replicate arrays, we identified a decrease in proliferation genes and an increase in differentiation genes. Using an arbitrary cut-off of 1.7-fold and p values <0.05, we identified a total of 32 differentially expressed genes, 9 with the dye-swap method, 18 with the CCM, and 5 genes with both methods. 23 of these 32 genes were subsequently verified by northern blotting. Most of these were <2-fold changes. While the dye-swap method (using either ANOVA or Bayesian analysis) detected a smaller number of genes (14–16) compared to the CCM (46), it was more accurate (89–92% vs. 75%). Compared to the northern blot results, for most genes, the microarray results underestimated the fold change, implicating the importance of detecting these small changes.

Conclusions
We validated two experimental design paradigms for cDNA microarray experiments capable of detecting small (<2-fold) changes in gene expression with excellent fidelity that revealed potentially important genes associated with the anti-proliferative effects of neuregulin on MCF10AT breast epithelial cells.
The six-minute walk test in community dwelling elderly: influence of health status.
Authors: Bautmans Ivan , Lambert Margareta , Mets Tony 
Published: July 2004

Abstract
Background
The 6 minutes walk test (6MWT) is a useful assessment instrument for the exercise capacity of elderly persons. The impact of the health status on the 6MWT-distance in elderly, however, remains unclear, reducing its value in clinical settings. The objective of this study was to investigate to what extent the 6MWT-distance in community dwelling elderly is determined by health conditions.

Methods
One hundred and fifty-six community dwelling elderly people (53 male, 103 female) were assessed for health status and performed the 6MWT. After clinical evaluation, electrocardiography and laboratory examination participants were categorized into a stratified six-level classification system according to their health status, going from A (completely healthy) to D (signs of active disease at the moment of examination).

Results
The mean 6MWT-distance was 603 m (SD = 178). The 6MWT-distance decreased significantly with increasing age (ANOVA p = 0.0001) and with worsening health status (ANCOVA, corrected for age p < 0.001).
A multiple linear regression model with health status, age and gender as independent variables explained 31% of the 6MWT-distance variability. Anthropometrical measures (stature, weight and BMI) did not significantly improve the prediction model. A significant relationship between 6MWT-distance and stature was only present in category A (completely healthy).

Conclusions
Significant differences in 6MWT-distance are observed according to health status in community-dwelling elderly persons. The proposed health categorizing system for elderly people is able to distinguish persons with lower physical exercise capacity and can be useful when advising physical trainers for seniors.
Caveolin-2 associates with intracellular chlamydial inclusions independently of caveolin-1
Authors: Webley Wilmore C , Norkin Leonard C , Stuart Elizabeth S 
Published: July 2004

Abstract
Background
Lipid raft domains form in plasma membranes of eukaryotic cells by the tight packing of glycosphingolipids and cholesterol. Caveolae are invaginated structures that form in lipid raft domains when the protein caveolin-1 is expressed. The Chlamydiaceae are obligate intracellular bacterial pathogens that replicate entirely within inclusions that develop from the phagocytic vacuoles in which they enter. We recently found that host cell caveolin-1 is associated with the intracellular vacuoles and inclusions of some chlamydial strains and species, and that entry of those strains depends on intact lipid raft domains. Caveolin-2 is another member of the caveolin family of proteins that is present in caveolae, but of unknown function.

Methods
We utilized a caveolin-1 negative/caveolin-2 positive FRT cell line and laser confocal immunofluorescence techniques to visualize the colocalization of caveolin-2 with the chlamydial inclusions.

Results
We show here that in infected HeLa cells, caveolin-2, as well as caveolin-1, colocalizes with inclusions of C. pneumoniae (Cp), C. caviae (GPIC), and C. trachomatis serovars E, F and K. In addition, caveolin-2 also associates with C. trachomatis serovars A, B and C, although caveolin-1 did not colocalize with these organisms. Moreover, caveolin-2 appears to be specifically, or indirectly, associated with the pathogens at the inclusion membranes. Using caveolin-1 deficient FRT cells, we show that although caveolin-2 normally is not transported out of the Golgi in the absence of caveolin-1, it nevertheless colocalizes with chlamydial inclusions in these cells. However, our results also show that caveolin-2 did not colocalize with UV-irradiated Chlamydia in FRT cells, suggesting that in these caveolin-1 negative cells, pathogen viability and very likely pathogen gene expression are necessary for the acquisition of caveolin-2 from the Golgi.

Conclusion
Caveolin-2 associates with the chlamydial inclusion independently of caveolin-1. The function of caveolin-2, either in the uninfected cell or in the chlamydial developmental cycle, remains to be elucidated. Nevertheless, this second caveolin protein can now be added to the small number of host proteins that are associated with the inclusions of this obligate intracellular pathogen.