bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative urban classification for malaria epidemiology in sub-Saharan Africa
Authors: Siri Jose G , Lindblade Kim A , Rosen Daniel H , Onyango Bernard , Vulule John , Slutsker Laurence , Wilson Mark L 
Published: February 2008

Abstract

Background
Although sub-Saharan Africa (SSA) is rapidly urbanizing, the terms used to classify urban ecotypes are poorly defined in the context of malaria epidemiology. Lack of clear definitions may cause misclassification error, which likely decreases the accuracy of continent-wide estimates of malaria burden, limits the generalizability of urban malaria studies, and makes identification of high-risk areas for targeted interventions within cities more difficult. Accordingly, clustering techniques were applied to a set of urbanization- and malaria-related variables in Kisumu, Kenya, to produce a quantitative classification of the urban environment for malaria research.

Methods
Seven variables with a known or expected relationship with malaria in the context of urbanization were identified and measured at the census enumeration area (EA) level, using three sources: a) the results of a citywide knowledge, attitudes and practices (KAP) survey; b) a high-resolution multispectral satellite image; and c) national census data. Principal components analysis (PCA) was used to identify three factors explaining higher proportions of the combined variance than the original variables. A k-means clustering algorithm was applied to the EA-level factor scores to assign EAs to one of three categories: "urban," "peri-urban," or "semi-rural." The results were compared with classifications derived from two other approaches: a) administrative designation of urban/rural by the census or b) population density thresholds.

Results
Urban zones resulting from the clustering algorithm were more geographically coherent than those delineated by population density. Clustering distributed population more evenly among zones than either of the other methods and more accurately predicted variation in other variables related to urbanization, but not used for classification.

Conclusion
Effective urban malaria epidemiology and control would benefit from quantitative methods to identify and characterize urban areas. Cluster analysis techniques were used to classify Kisumu, Kenya, into levels of urbanization in a repeatable and unbiased manner, an approach that should permit more relevant comparisons among and within urban areas. To the extent that these divisions predict meaningful intra-urban differences in malaria epidemiology, they should inform targeted urban malaria interventions in cities across SSA.
Sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines
Authors: Fadlelmola Faisal M , Zhou Minglong , de Leeuw Ronald J , Dosanjh Nirpjit S , Harmer Karynn , Huntsman David , Lam Wan L , Banerjee Diponkar 
Published: February 2008

AbstractBackgroundHodgkin lymphoma (HL) and Anaplastic Large Cell Lymphoma (ALCL), are forms of malignant lymphoma defined by unique morphologic, immunophenotypic, genotypic, and clinical characteristics, but both overexpress CD30. We used sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization to screen HL-derived cell lines (KMH2 and L428) and ALCL cell lines (DEL and SR-786) in order to identify disease-associated gene copy number gains and losses.ResultsSignificant copy number gains and losses were observed on several chromosomes in all four cell lines. Assessment of copy number alterations with 26,819 DNA segments identified an average of 20 genetic alterations. Of the recurrent minimally altered regions identified, 11 (55%) were within previously published regions of chromosomal alterations in HL and ALCL cell lines while 9 (45%) were novel alterations not previously reported. HL cell lines L428 and KMH2 shared gains in chromosome cytobands 2q23.1-q24.2, 7q32.2-q36.3, 9p21.3-p13.3, 12q13.13-q14.1, and losses in 13q12.13-q12.3, and 18q21.32-q23. ALCL cell lines SR-786 and DEL, showed gains in cytobands 5p15.32-p14.3, 20p12.3-q13.11, and 20q13.2-q13.32. Both pairs of HL and ALCL cell lines showed losses in 18q21.32-18q23.ConclusionThis study is considered to be the first one describing HL and ALCL cell line genomes at sub-megabase resolution. This high-resolution analysis allowed us to propose novel candidate target genes that could potentially contribute to the pathogenesis of HL and ALCL. FISH was used to confirm the amplification of all three isoforms of the trypsin gene (PRSS1/PRSS2/PRSS3) in KMH2 and L428 (HL) and DEL (ALCL) cell lines. These are novel findings that have not been previously reported in the lymphoma literature, and opens up an entirely new area of research that has not been previously associated with lymphoma biology. The findings raise interesting possibilities about the role of signaling pathways triggered by membrane associated serine proteases in HL and aggressive NHL, similar to those described in epithelial tumors.
NCX-4040, a nitric oxide-releasing aspirin, sensitizes drug-resistant human ovarian xenograft tumors to cisplatin by depletion of cellular thiols
Authors: Bratasz Anna , Selvendiran Karuppaiyah , Wasowicz Tomasz , Bobko Andrey , Khramtsov Valery V , Ignarro Louis J , Kuppusamy Periannan 
Published: February 2008

Abstract

Background
Ovarian carcinoma is the leading cause of mortality among gynecological cancers in the world. The high mortality rate is associated with lack of early diagnosis and development of drug resistance. The antitumor efficacy and mechanism of NCX-4040, a nitric oxide-releasing aspirin derivative, against ovarian cancer is studied.

Methods
NCX-4040, alone or in combination with cisplatin (cis-diamminedichloroplatinum, cDDP), was studied in cisplatin-sensitive (A2780 WT) and cisplatin-resistant (A2780 cDDP) cell lines as well as xenograft tumors grown in nude mice. Electron paramagnetic resonance (EPR) was used for measurements of nitric oxide and redox state. Immunoblotting analysis of A2780 cDDP tumor xenografts from mice was used for mechanistic studies.

Results
Cells treated with NCX-4040 (25 μM) showed a significant reduction of cell viability (A2780 WT, 34.9 ± 8.7%; A2780 cDDP, 41.7 ± 7.6%; p < 0.05). Further, NCX-4040 significantly enhanced the sensitivity of A2780 cDDP cells (cisplatin alone, 80.6 ± 11.8% versus NCX-4040+cisplatin, 26.4 ± 7.6%; p < 0.01) and xenograft tumors (cisplatin alone, 74.0 ± 4.4% versus NCX-4040+cisplatin, 56.4 ± 7.8%; p < 0.05), to cisplatin treatment. EPR imaging of tissue redox and thiol measurements showed a 5.5-fold reduction (p < 0.01) of glutathione in NCX-4040-treated A2780 cDDP tumors when compared to untreated controls. Immunoblotting analysis of A2780 cDDP tumor xenografts from mice treated with NCX-4040 and cisplatin revealed significant downregulation of pEGFR (Tyr845 and Tyr992) and pSTAT3 (Tyr705 and Ser727) expression.

Conclusion
The results suggested that NCX-4040 could resensitize drug-resistant ovarian cancer cells to cisplatin possibly by depletion of cellular thiols. Thus NCX-4040 appears to be a potential therapeutic agent for the treatment of human ovarian carcinoma and cisplatin-resistant malignancies.
A prospective study of decline in lung function in relation to welding emissions
Authors: Christensen Sigve W , Bonde Jens Peter , Omland Øyvind 
Published: February 2008

AbstractBackgroundNumerous cross-sectional studies have reported reduced lung function among welders but limitations of exposure assessment and design preclude causal inference. The aim of this study was to investigate if long-term exposure to welding fume particulates accelerates the age-related decline in lung function.MethodsLung function was measured by spirometry in 1987 and 2004 among 68 steel welders and 32 non-welding production workers. The decline in forced expiratory volume (FEV1) was analysed in relation to cumulated exposure to fume particulates among welders during the follow-up period.ResultsAmong smokers the decline in FEV1through follow-up period was in average 150 ml larger among welders than non-welders while the difference was negligible among non-smokers. The results did not reach statistical significance and within welders the decline in lung function was not related to the cumulated welding particulate exposure during follow-up periodConclusionLong-term exposure to welding emissions may accelerate the age-related decline of lung function but at exposure levels in the range of 1.5 to 6.5 mg/m3the average annual excess loss of FEV1is unlikely to exceed 25 ml in smokers and 10 ml in non-smokers.
Clinical implications of granulomatous inflammation detected by endobronchial ultrasound transbronchial needle aspiration in patients with suspected cancer recurrence in the mediastinum
Authors: Kennedy Marcus P , Jimenez Carlos A , Mhatre Ashwini D , Morice Rodolfo C , Eapen Georgie A 
Published: February 2008

Abstract

Background
Granulomatous inflammation has been previously reported in association with cancer. Endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) is a new minimally invasive test for investigating mediastinal lymphadenopathy. The identification of granulomatous inflammation by EBUS-TBNA and the clinical implications of such detection in a series of patients with previously treated cancer and new mediastinal lymphadenopathy has not previously been performed.

Methods
All 153 consecutive patients undergoing EBUS-TBNA in an academic cancer institution for suspected cancer in the mediastinum (mediastinal lymphadenopathy by CT imaging) were reviewed. Patients with non-caseating granuloma identified by EBUS-TBNA were included.

Results
EBUS-TBNA identified non-caseating granuloma in 17/153 (11%) patients. A subset of 8/153 (5.2%) had sarcoid like lymphadenopathy mimicking cancer recurrence (5/5 PET positive). Another 8/153 (5.2%) patients with new mediastinal lymphadenopathy and no prior history of cancer had a clinical syndrome consistent with sarcoidosis. One other patient with a history of breast cancer was diagnosed with non-tuberculous mycobacteria infection. No patient required mediastinoscopy and there were no complications.

Conclusion
In an academic cancer institute, at least 5% of patients undergoing EBUS-TBNA have sarcoid-like lymphadenopathy mimicking cancer recurrence. Further studies to define the precise etiology, natural history and prognosis of this phenomenon are warranted.
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
Authors: Goelzer Anne , Bekkal Brikci Fadia , Martin-Verstraete Isabelle , Noirot Philippe , Bessières Philippe , Aymerich Stéphane , Fromion Vincent 
Published: February 2008

Abstract

Background
Few genome-scale models of organisms focus on the regulatory networks and none of them integrates all known levels of regulation. In particular, the regulations involving metabolite pools are often neglected. However, metabolite pools link the metabolic to the genetic network through genetic regulations, including those involving effectors of transcription factors or riboswitches. Consequently, they play pivotal roles in the global organization of the genetic and metabolic regulatory networks.

Results
We report the manually curated reconstruction of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis (transcriptional, translational and post-translational regulations and modulation of enzymatic activities). We provide a systematic graphic representation of regulations of each metabolic pathway based on the central role of metabolites in regulation. We show that the complex regulatory network of B. subtilis can be decomposed as sets of locally regulated modules, which are coordinated by global regulators.

Conclusion
This work reveals the strong involvement of metabolite pools in the general regulation of the metabolic network. Breaking the metabolic network down into modules based on the control of metabolite pools reveals the functional organization of the genetic and metabolic regulatory networks of B. subtilis.
Pulmonary manifestations in a pediatric patient with ulcerative colitis: a case report
Authors: Carvalho Ryan S , Wilson Lindsay , Cuffari Carmen 
Published: February 2008

Abstract

Introduction
Although respiratory involvement has been described in patients with IBD, well-defined interstitial lung disease has not been reported, especially among children with ulcerative colitis.

Case presentation
Herein, we present a case of an adolescent female with ulcerative colitis and extra-intestinal complications involving the lungs that were effectively treated with anti-metabolite therapy.

Conclusion
Children with UC may manifest either interstitial or large airway pulmonary involvement. All children with suspected lung involvement should be screened for tuberculosis prior to starting immunosuppressive therapy.
Determinants of tracheostomy decannulation: an international survey
Authors: Stelfox Henry Thomas , Crimi Claudia , Berra Lorenzo , Noto Alberto , Schmidt Ulrich , Bigatello Luca M , Hess Dean 
Published: February 2008

Abstract
Background
Although tracheostomy is probably the most common surgical procedure performed on critically ill patients, it is unknown when a tracheostomy tube can be safely removed.

Methods
We performed a cross-sectional survey of physicians and respiratory therapists with expertise in the management of tracheostomized patients at 118 medical centers to characterize contemporary opinions about tracheostomy decannulation practice and to define factors that influence these practices.

Results
We surveyed 309 clinicians, of whom 225 responded (73%). Clinicians rated patient level of consciousness, ability to tolerate tracheostomy tube capping, cough effectiveness, and secretions as the most important factors in the decision to decannulate a patient. Decannulation failure was defined as the need to reinsert an artificial airway within 48 hours (45% of respondents) to 96 hours (20% of respondents) of tracheostomy removal, and 2% to 5% was the most frequent recommendation for an acceptable recannulation rate (44% of respondents). In clinical scenarios, clinicians who worked in chronic care facilities (30%) were less likely to recommend decannulation than clinicians who worked in weaning (47%), rehabilitation (53%), or acute care (55%) facilities (p = 0.015). Patients were most likely to be recommended for decannulation if they were alert and interactive (odds ratio [OR] 4.76, 95% confidence interval [CI] 3.27 to 6.90; p < 0.001), had a strong cough (OR 3.84, 95% CI 2.66 to 5.54; p < 0.001), had scant thin secretions (OR 2.23, 95% CI 1.56 to 3.19; p < 0.001), and required minimal supplemental oxygen (OR 2.04, 95% CI 1.45 to 2.86; p < 0.001).

Conclusion
Patient level of consciousness, cough effectiveness, secretions, and oxygenation are important determinants of clinicians' tracheostomy decannulation opinions. Most surveyed clinicians defined decannulation failure as the need to reinsert an artificial airway within 48 to 96 hours of planned tracheostomy removal.
Copulsing tumor antigen-pulsed dendritic cells with zoledronate efficiently enhance the expansion of tumor antigen-specific CD8+ T cells via Vγ9γδ T cell activation
Authors: Takahara Masashi , Miyai Manami , Tomiyama Mai , Mutou Masato , Nicol Andrew J , Nieda Mie 
Published: February 2008

AbstractWe demonstrate that Vγ9γδ T cells activated by zoledronate can link innate and acquired immunity through crosstalk with dendritic cells (DCs) in a way that can amplify activation and proliferation of tumor antigen-specific CD8+ T cells. DCs pulsed with antigen alone or antigen plus zoledronate were used to stimulate the in vitro expansion of antigen-specific CD8+ T cells. MART-1-modified peptide (A27L peptide) and apoptotic HLA-A∗0201-positive, MART-1-positive JCOCB tumor cell lines were used as tumor antigen sources. The percentage of A27L-specific CD8+ T cells within the responding lymphocytes on Day 7 when immature DCs (imDCs) were cultured in the presence of A27L peptide and 0.01 μM zoledronate was significantly higher (P=0.002, n=11) than that observed when imDCs were cultured with the lymphocytes in the presence of the A27L peptide alone. This enhancing effect of zoledronate was significantly reduced when γδ T cells were depleted from responding lymphocytes (P=0.030, n=5), indicating that the effect is mediated mainly through Vγ9γδ T cells activated by zoledronate-pulsed imDCs. When imDCs copulsed with zoledronate and apoptotic JCOCB tumor cell lines were used, the percentage of A27L-specific CD8+ T cells was higher than that observed using imDCs with the apoptotic JCOCB lines alone, suggesting that zoledronate treatment of imDCs enhances the cross-presentation ability of DCs. These findings suggest a potentially valuable role for Vγ9γδ T cell activation for expanding antigen-specific CD8+T cells using DCs copulsed with tumor antigen and zoledronate in the design of vaccine therapies for malignancy.
Sensing danger—Hsp72 and HMGB1 as candidate signals
Authors: Williams John H H , Ireland H Elyse 
Published: February 2008

AbstractMolecules that behave as danger signals are produced when the body is perceived to be under attack, and they alert the immune system to the problem. The immune system can then mount an appropriate response. Two molecules that have received attention as potential danger signals are heat shock protein 72 (Hsp72) and high mobility group box 1 (HMGB1), which are intracellular proteins but are released when cells are under stress, in particular, when necrosis occurs. This review considers the similarities between these two molecules and then contrasts their mechanism of action and problems that can arise when they are overpresented in the extracellular environment. It is proposed that Hsp72 and HMGB1 are members of a suite of danger molecules that provide a fingerprint of the threat, or stressor, to tissue or organism integrity.
Cigarette smoke stimulates the production of chemokines in mast cells
Authors: Mortaz Esmaeil , Redegeld Frank A , Sarir Hadi , Karimi Khalil , Raats Danielle , Nijkamp Frans P , Folkerts Gert 
Published: February 2008

AbstractChronic obstructive pulmonary disease is a major health problem and will become the third largest cause of death in the world by 2020. It is currently believed that an exaggerated inflammatory response to inhaled irritants, in particular, cigarette smoke (CS), causes the progressive airflow limitation, in which macrophages and neutrophils are attracted by chemokines, leading to oxidative stress, emphysema, small airways fibrosis, and mucus hypersecretion. Smoking is also associated with an increase in mast cell numbers in bronchial mucosa. This study was conducted to determine the direct effects of CS on mast cell function, using murine bone marrow-derived mast cells (BMMC) as an in vitro model. BMMC were cultured from BALB/cBy mice for 3 weeks. Cells were treated with CS medium (CSM) for 30 min or 16 h. The effects of CSM on mast cell degranulation and chemokine production were measured. Moreover, we investigated the effect of CSM on IκB-α degradation and p38, Erk1/2, p65, and CREB expression by Western blotting. We found that CSM stimulated the release of chemokines in a noncytotoxic manner but did not induce mast cell degranulation. CSM induced phosphorylation of Erk1/2, p38, and CREB and increased translocation of p65 without degradation of IκB-α NF-κB in mast cells. The induction of chemokine production by CSM in mast cells could promote and prolong the inflammatory process. Our observations suggest that mast cells may contribute to the pathogenesis of emphysema through a direct effect of CS on the production of proinflammatory chemokines.
Measures of Childhood Fitness and Body Mass Index are Associated With Bone Mass in Adulthood: A 20-Year Prospective Study
Authors: Foley Stella , Quinn Stephen , Dwyer Terry , Venn Alison , Jones Graeme 
Published: February 2008

Abstract
The long-term effects of childhood exercise and body mass index (BMI) on bone mass remain uncertain. We measured 1434 children, 7–15 yr of age, as part of the Australian Schools Health and Fitness Survey in 1985 and ∼20 yr later (mean age, 31 yr). Fitness measures included a 1.6-km run and a 50-m sprint (childhood only), leg strength, standing long jump, and physical work capacity at 170 beats/min (PWC170; childhood and adulthood). BMI was assessed at both time points. A single Sahara bone ultrasound densitometer was used to determine heel bone mass. We found, in females, there were modest but significant beneficial relationships between the childhood 1.6-km run, 50-m sprint, standing long jump, and adult bone mass. In both sexes, PWC170 at 9 yr of age had a greater influence on adult bone mass (r2 = 5–8%, all p &lt; 0.05) than it did for 15 yr olds (r2 = &lt;1%, all p &gt; 0.05), independent of adult performance. In the 12 yr olds, childhood PWC170 was also associated with female adult bone mass (broadband ultrasound attenuation: r2 = 6%, p = 0.045). In males, childhood BMI (but no performance measures) was positively associated with adult bone mass after adjustment for adult BMI. In conclusion, childhood fitness levels, particularly in females and in the early pubertal years, are predictive of adult skeletal status as measured by quantitative ultrasound, whereas BMI is predictive in males only. These results suggest that increased skeletal loading in childhood leads to an increase in peak bone mass independent of current loading.
Vitamin D Receptor Polymorphisms and Falls Among Older Adults Living in the Community: Results From the ilSIRENTE Study
Authors: Onder Graziano , Capoluongo Ettore , Danese Paola , Settanni Silvana , Russo Andrea , Concolino Paola , Bernabei Roberto , Landi Francesco 
Published: February 2008

Abstract
Vitamin D receptor (VDR) genotypes were associated with cognitive status, depressive symptoms, strength, and sarcopenia, but, thus far, no study has assessed their relationship with falls. The objective of this study is to evaluate whether, in a population of older adults living in the community, VDR FokI and BsmI genotypes are associated with falls. To this aim, we used data from the baseline evaluation of the ilSIRENTE study, which enrolled older adults ≥80 yr of age living in the community in Italy. Falls occurring within 90 days of assessment were assessed by study personnel. The mean age of 259 study participants was 85.0 ± 4.5 (SD) yr; 172 (66.4%) were women. Overall, 33 (12.7%) participants reported one or more falls. The rate of falls was 19.5% in participants with the BB genotype, 11.1% in those with Bb genotype, and 5.9% in those with bb genotype (p for linear trend = 0.02). After adjusting for potential confounders, compared with participants with the BB genotype, those with the bb genotype had a significantly lower OR for falls 0.14 (95% CI, 0.03–0.66). Rate of falls did not differ significantly across FokI genotypes (FF: 14.4%, Ff: 11.9%, ff: 9.1%; p = 0.43). In conclusion, the VDR bb genotype of the BsmI gene is associated with a reduced rate of falls compared with the BB genotype, whereas no effect on falls was shown for FokI polymorphism. Further studies conducted in larger population are needed to confirm the association of BsmI genotype and falls and to understand reasons for these findings.