bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity of Plasmodium vivax in Kolkata, India
Authors: Kim Jung-Ryong , Imwong Mallika , Nandy Amitabha , Chotivanich Kesinee , Nontprasert Apichart , Tonomsing Naowarat , Maji Ardhendu , Addy Manjulika , Day Nick PJ , White Nicholas J , Pukrittayakamee Sasithon 
Published: August 2006

Abstract

Background

Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains.

Methods
Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs), the merozoite surface protein 1 (pvmsp 1) and the merozoite surface protein 3-alpha (pvmsp 3-alpha).

Results
Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp 1 and 37 for pvmsp 3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151). The overall rate of mixed genotype infections was 10.6%.

Conclusion
These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria.
Validation of using gene expression in mononuclear cells as a marker for hepatic cholesterol metabolism
Authors: Aggarwal Dimple , Freake Hedley C , Soliman Ghada A , Dutta Amrita , Fernandez Maria-Luz 
Published: August 2006

Abstract
HMG-CoA reductase and the LDL receptor are ubiquitously expressed in major tissues. Since the liver plays a major role in regulating circulating LDL, it is usually of interest to measure the effects of drug or dietary interventions on these proteins in liver. In humans, peripheral blood mononuclear cells have been used as a surrogate for liver to assess regulation of these genes, although there is concern regarding the validity of this approach. The purpose of this study was to evaluate the relationship between liver and mononuclear cell expression of HMG-CoA reductase and the LDL receptor in guinea pigs, a well established model for human cholesterol and lipoprotein metabolism. We extracted RNA from liver and mononuclear cells of guinea pigs from a previous study where the effects of rapamycin, an immunosuppresant drug used for transplant patients, on lipid metabolism were evaluated. Guinea pigs were assigned to three different diets containing the same amount of fat (15 g/100 g) and cholesterol (0.08 g/100 g) for a period of 3 weeks. The only difference among diets was the concentration of rapamycin: 0, 0.0028 or 0.028 g/100 g. There were no differences in plasma LDL cholesterol (LDL-C) among groups. Values were 78.4 ± 14.3, 65.8 ± 17.2 and 68.4 ± 45.4 mg/dL (P > 0.05) for guinea pigs treated with 0, low or high doses of rapamycin, respectively. The mRNA abundance for the LDL receptor and HMG-CoA reductase was measured both in liver (n = 30) and mononuclear cells (n = 22) using reverse transcriptase PCR. In agreement with the finding of no changes in plasma LDL-C, there were also no differences for the expression of HMG-CoA reductase or the LDL receptor among groups. However, a positive correlation was found between liver and mononuclear cells for both HMG-CoA reductase (r = 0.613, P < 0.01) and the LDL receptor (r = 0.622, P < 0.01). These correlations suggest that monocytes can be used in humans as an index for liver to assess diet and drug effects on the expression of HMG-CoA reductase and the LDL receptor.
Health related quality of life trajectories and predictors following coronary artery bypass surgery
Authors: Le Grande Michael R , Elliott Peter C , Murphy Barbara M , Worcester Marian UC , Higgins Rosemary O , Ernest Christine S , Goble Alan J 
Published: August 2006

Abstract

Background
Many studies have demonstrated that health related quality of life (HRQoL) improves, on average, after coronary artery bypass graft surgery (CABGS). However, this average improvement may not be realized for all patients, and it is possible that there are two or more distinctive groups with different, possibly non-linear, trajectories of change over time. Furthermore, little is known about the predictors that are associated with these possible HRQoL trajectories after CABGS.

Methods
182 patients listed for elective CABGS at The Royal Melbourne Hospital completed a postal battery of questionnaires which included the Short-Form-36 (SF-36), Profile of Mood States (POMS) and the Everyday Functioning Questionnaire (EFQ). These data were collected on average a month before surgery, and at two months and six months after surgery. Socio-demographic and medical characteristics prior to surgery, as well as surgical and post-surgical complications and symptoms were also assessed. Growth curve and growth mixture modelling were used to identify trajectories of HRQoL.

Results
For both the physical component summary scale (PCS) and the mental component summary scale (MCS) of the SF-36, two groups of patients with distinct trajectories of HRQoL following surgery could be identified (improvers and non-improvers). A series of logistic regression analyses identified different predictors of group membership for PCS and MCS trajectories. For the PCS the most significant predictors of non-improver membership were lower scores on POMS vigor-activity and higher New York Heart Association dyspnoea class; for the MCS the most significant predictors of non-improver membership were higher scores on POMS depression-dejection and manual occupation.

Conclusion
It is incorrect to assume that HRQoL will improve in a linear fashion for all patients following CABGS. Nor was there support for a single response trajectory. It is important to identify characteristics of each patient, and those post-operative symptoms that could be possible targets for intervention to improve HRQoL outcomes.
Evaluating preference weights for the Asthma Symptom Utility Index (ASUI) across countries
Authors: Flood Emuella M , Cock Erwin De , Mörk Ann-Christin , Revicki Dennis A 
Published: August 2006

Abstract

Background
The Asthma Symptom Utility Index (ASUI) is a preference-based outcome measure used in US clinical trials and cost-effectiveness studies for asthma. This study evaluated ASUI preference weights in Europe to determine whether the multi-attribute utility function, based on preferences from a US population, is generalizable across countries.

Methods
Data were collected from ninety asthma patients from Italy, France, and the United Kingdom using the Asthma Control Questionnaire, the Asthma Quality of Life Questionnaire, and the ASUI. Subjects rated their preferences for 10 asthma health states using a visual analogue scale (VAS) and a standard gamble (SG) interview.

Results
All multi-symptom states showed statistically significant differences (p < 0.001) between countries in mean VAS scores. Mean SG utility scores between the US and France and the US and Italy demonstrated statistically significant differences (p < 0.001) for three states: severe wheeze; moderate cough and wheeze; and moderate cough and dyspnea. Because of these differences, the multi-attribute utility functions derived within countries were somewhat different. Despite these differences, country-specific algorithms captured a similar rank ordering of patients by disease severity, were strongly correlated (r = 0.971 to 0.995), and demonstrated similar relationships with symptom and AQLQ scores.

Conclusion
Results of this study suggest that the ASUI may be a complementary patient-reported outcome for clinical studies and may be useful for applications in cost-effectiveness studies comparing different asthma treatments.
Tactile-like corpuscles in gastric mucosa: a case report
Authors: Salim Sadia , Liu Beiqing , Mahmoodi Mandana , Asad Haider , Hou Steve J 
Published: August 2006

Abstract

Background
The presence of tactile corpuscle-like structures in Schwannomas, Neurofibromas and Neuroid Intradermal Melanocytic Nevi is well-documented. We report a case describing the presence of such structures in the lamina propria of grossly normal gastric mucosa.

Case presentation
A 30 year-old male underwent esophagogastrectomy for carcinoma. Examination of hematoxylin and eosin stained sections reveal tactile corpuscle-like structures in the mucosa adjacent to the main tumor mass.

Conclusion
This is a rare phenomenon and a literature search revealed only one paper describing such structures in the benign colonic mucosa of a colectomy done for carcinoma. We did not come across any cases in the literature describing such structures in gastrointestinal specimen resected for reasons other than carcinoma. To our knowledge this would be the first case reporting the existence of tactile corpuscles-like structures in gastric mucosa.
Inhibition of HIV Env binding to cellular receptors by monoclonal antibody 2G12 as probed by Fc-tagged gp120
Authors: Binley James M , Ngo-Abdalla Stacie , Moore Penny , Bobardt Michael , Chatterji Udayan , Gallay Philippe , Burton Dennis R , Wilson Ian A , Elder John H , de Parseval Aymeric 
Published: August 2006

AbstractDuring natural HIV infection, an array of host receptors are thought to influence virus attachment and the kinetics of infection. In this study, to probe the interactions of HIV envelope (Env) with various receptors, we assessed the inhibitory properties of various anti-Env monoclonal antibodies (mAbs) in binding assays. To assist in detecting Env in attachment assays, we generated Fc fusions of full-length wild-type gp120 and several variable loop-deleted gp120s. Through investigation of the inhibition of Env binding to cell lines expressing CD4, CCR5, DC-SIGN, syndecans or combinations thereof, we found that the broadly neutralizing mAb, 2G12, directed to a unique carbohydrate epitope of gp120, inhibited Env-CCR5 binding, partially inhibited Env-DC-SIGN binding, but had no effect on Env-syndecan association. Furthermore, 2G12 inhibited Env attachment to primary monocyte-derived dendritic cells, that expressed CD4 and CCR5 primary HIV receptors, as well as DC-SIGN, and suggested that the dual activities of 2G12 could be valuablein vivofor inhibiting initial virus dissemination and propagation.
Mixing patterns and the spread of close-contact infectious diseases
Authors: Edmunds WJ , Kafatos G , Wallinga J , Mossong JR 
Published: August 2006

AbstractSurprisingly little is known regarding the human mixing patterns relevant to the spread of close-contact infections, such as measles, influenza and meningococcal disease. This study aims to estimate the number of partnerships that individuals make, their stability and the degree to which mixing is assortative with respect to age. We defined four levels of putative at-risk events from casual (physical contact without conversation) to intimate (contact of a sexual nature), and asked university student volunteers to record details on those they contacted at these levels on three separate days. We found that intimate contacts are stable over short time periods whereas there was no evidence of repeat casual contacts with the same individuals. The contacts were increasingly assortative as intimacy increased. Such information will aid the development and parameterisation of models of close contact diseases, and may have direct use in outbreak investigations.
A method for exposing rodents to resuspended particles using whole-body plethysmography
Authors: Wichers Lindsay B , Ledbetter Allen D , McGee John K , Kellogg Robert B , Rowan William H , Nolan Julianne P , Costa Daniel L , Watkinson William P 
Published: August 2006

Abstract

Background
Epidemiological studies have reported increased risks of cardiopulmonary-related hospitalization and death in association with exposure to elevated levels of particulate matter (PM) across a wide range of urban areas. In response to these findings, researchers have conducted animal inhalation exposures aimed at reproducing the observed toxicologic effects. However, it is technically difficult to quantitate the actual amount of PM delivered to the lung in such studies, and dose is frequently estimated using default respiration parameters. Consequently, the interpretation of PM-induced effects in rodents exposed via whole-body inhalation is often compromised by the inability to determine deposited dose. To address this problem, we have developed an exposure system that merges the generation of dry, aerosolized particles with whole-body plethysmography (WBP), thus permitting inhalation exposures in the unrestrained rat while simultaneously obtaining data on pulmonary function.

Results
This system was validated using an oil combustion-derived particle (HP12) at three nominal concentrations (3, 12, and 13 mg/m3) for four consecutive exposure days (6 hr/day); a single 6-hour exposure to 13 mg/m3 of HP12 was also conducted. These results demonstrated that the system was both reliable and consistent over these exposure protocols, achieving average concentrations that were within 10% of the targeted concentration. In-line filters located on the exhaust outlets of individual WBP chambers showed relative agreement in HP12 mass for each day and were not statistically different when compared to one another (p = 0.16). Temperatures and relative humidities were also similar between chambers during PM and air exposures. Finally, detailed composition analyses of both HP12 filter and bulk samples showed that grinding and aerosolization did not change particle chemistry.

Conclusion
The results of this study demonstrate that it is possible to expose rodents to resuspended, dry PM via whole-body inhalation while these animals are maintained in WBP chambers. This new methodology should significantly improve the ability to assess dosimetry under minimally stressful exposure conditions.
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
Authors: Mitreva Makedonka , Wendl Michael C , Martin John , Wylie Todd , Yin Yong , Larson Allan , Parkinson John , Waterston Robert H , McCarter James P 
Published: August 2006

Abstract
Background
Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms.

Results
Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts.

Conclusion
Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.
Quantitative magnetic resonance and SPECT imaging for macrophage tissue migration and nanoformulated drug delivery
Authors: Gorantla Santhi , Dou Huanyu , Boska Michael , Destache Chris J , Nelson Jay , Poluektova Larisa , Rabinow Barett E , Gendelman Howard E , Mosley R Lee 
Published: August 2006

Abstract
We posit that the same mononuclear phagocytes (MP) [bone marrow (BM) and blood monocytes, tissue macrophages, microglia, and dendritic cells] which serve as targets, reservoirs, and vehicles for HIV dissemination, can be used as vehicles for antiretroviral therapy (ART). Toward this end, BM macrophages (BMM) were used as carriers for nanoparticle-formulated indinavir (NP-IDV), and the cell distribution was monitored by single photon emission computed tomography (SPECT), transverse relation time (T2)∗ weighted magnetic resonance imaging (MRI), histology, and γ-scintillation spectrometry. BMM labeled with super paramagnetic iron oxide and/or 111 indium oxine were infused i.v. into naïve mice. During the first 7 h, greater than 86% of cell label was recorded within the lungs. On Days 1, 3, 5, and 7, less than 10% of BMM were in lungs, and 74–81% and 13–18% were in liver and spleen, respectively. On a tissue volume basis, as determined by SPECT and MRI, BMM densities in spleen and liver were significantly greater than other tissues. Migration into the lymph nodes on Days 1 and 7 accounted for 1.5–2% of the total BMM. Adoptive transfer of BMM loaded with NP-IDV produced drug levels in lymphoid and nonlymphoid tissues that exceeded reported therapeutic concentrations by 200- to 350-fold on Day 1 and remained in excess of 100- to 300-fold on Day 14. These data show real-time kinetics and destinations of macrophage trafficking and demonstrate the feasibility of monitoring macrophage-based, nanoformulated ART.
HIV accomplices and adversaries in macrophage infection
Authors: Wahl Sharon M , Greenwell-Wild Teresa , Vázquez Nancy 
Published: August 2006

Abstract
Cell surface and intracellular proteins in macrophages influence various steps in the life cycle of lentiviruses. Characterization of these restriction and/or cofactors is essential to understanding how macrophages become unwitting HIV hosts and in fact, can coexist with a heavy viral burden. Although many of the cellular pathways co-opted by HIV in macrophages mimic those seen in CD4+ T cells, emerging evidence reveals cellular constituents of the macrophage, which may be uniquely usurped by HIV. For example, in addition to CD4 and CCR5, membrane annexin II facilitates early steps in infection of macrophages, but not in T cells. Blockade of this pathway effectively diminishes macrophage infection. Viral binding engages a macrophage-centric signaling pathway and a transcriptional profile, including genes such as p21, which benefit the virus. Once inside the cell, multiple host cell molecules are engaged to facilitate virus replication and assembly. Although the macrophage is an enabler, it also possesses innate antiviral mechanisms, including apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3) family DNA-editing enzymes to inhibit replication of HIV. Differential expression of these enzymes, which are largely neutralized by HIV to protect its rebirth, is associated with resistance or susceptibility to the virus. Higher levels of the cytidine deaminases endow potential HIV targets with a viral shield, and IFN-α, a natural inducer of macrophage APOBEC expression, renders macrophages tougher combatants to HIV infection. These and other manipulatable pathways may give the macrophage a fighting chance in its battle against the virus.
Detection of Aberrant Methylation of Four Genes in Plasma DNA for the Detection of Breast Cancer
Authors: Hoque Mohammad O. , Feng Qinghua , Toure Papa , Dem Amadou , Critchlow Cathy W. , Hawes Stephen E. , Wood Troy , Jeronimo Carmen , Rosenbaum Eli , Stern Joshua , Yu Mujun , Trink Barry , Kiviat Nancy B. , Sidransky David 
Published: August 2006

Purpose Novel approaches to breast cancer screening are necessary, especially in the developing world where mammography is not feasible. In this study, we explored the hypothesis that blood-based biomarkers have potential for biomarkers for breast cancer. Patients and Methods We first determined the frequency of aberrant methylation of four candidate genes (APC, GSTP1, Rassf1A, and RARβ2) in primary breast cancer tissues from West African women with predominantly advanced cancers. We used a high-throughput DNA methylation assay (quantitative methylation-specific polymerase chain reaction) to examine plasma from 93 women with breast cancer and 76 controls for the presence of four methylated genes. Samples were randomly divided evenly into training and validation data sets. Cutoff values for gene positivity of the plasma-based assay and the gene panel were determined by receiver operating characteristic curves in the training data set and subsequently evaluated as a screening tool in the validation data set. Results Methylation of at least one gene resulted in a sensitivity of 62% and a specificity of 87%. Moreover, the assay successfully detected 33% (eight of 24) of early-stage tumors. Conclusion These data suggest that epigenetic markers in plasma may be of interest for detection of breast cancer. Identification of additional breast cancer specific methylated genes with higher prevalence in early stage cancers would improve this approach.
Genotype-Phenotype Comparison of German MLH1 and MSH2 Mutation Carriers Clinically Affected With Lynch Syndrome: A Report by the German HNPCC Consortium
Authors: Goecke Timm , Schulmann Karsten , Engel Christoph , Holinski-Feder Elke , Pagenstecher Constanze , Schackert Hans K. , Kloor Matthias , Kunstmann Erdmute , Vogelsang Holger , Keller Gisela , Dietmaier Wolfgang , Mangold Elisabeth , Friedrichs Nicolaus , Propping Peter , Krüger Stefan , Gebert Johannes , Schmiegel Wolff , Rueschoff Josef , Loeffler Markus , Moeslein Gabriela 
Published: August 2006

Purpose Lynch syndrome is linked to germline mutations in mismatch repair genes. We analyzed the genotype-phenotype correlations in the largest cohort so far reported. Patients and Methods Following standard algorithms, we identified 281 of 574 unrelated families with deleterious germline mutations in MLH1 (n = 124) or MSH2 (n = 157). A total of 988 patients with 1,381 cancers were included in this analysis. Results We identified 181 and 259 individuals with proven or obligatory and 254 and 294 with assumed MLH1 and MSH2 mutations, respectively. Age at diagnosis was younger both in regard to first cancer (40 v 43 years; P < .009) and to first colorectal cancer (CRC; 41 v 44 years; P = .004) in MLH1 (n = 435) versus MSH2 (n = 553) mutation carriers. In both groups, rectal cancers were remarkably frequent, and the time span between first and second CRC was smaller if the first primary occurred left sided. Gastric cancer was the third most frequent malignancy occurring without a similarly affected relative in most cases. All prostate cancers occurred in MSH2 mutation carriers. Conclusion The proportion of rectal cancers and shorter time span to metachronous cancers indicates the need for a defined treatment strategy for primary rectal cancers in hereditary nonpolyposis colorectal cancer patients. Male MLH1 mutation carriers require earlier colonoscopy beginning at age 20 years. We propose regular gastric surveillance starting at age 35 years, regardless of the familial occurrence of this cancer. The association of prostate cancer with MSH2 mutations should be taken into consideration both for clinical and genetic counseling practice.