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Biomedical subjects

David Johnson

Publications and source records attributed to David Johnson.

At least 19 recordsLinked to original sources
PubMed2006

Ultralow thermal conductivity in disordered, layered WSe2 crystals.

The cross-plane thermal conductivity of thin films of WSe2 grown from alternating W and Se layers is as small as 0.05 watts per meter per degree kelvin at room temperature, 30 times smaller than the c-axis thermal conductivity of single-crystal WSe2 and a factor of 6 smaller than the predicted minimum thermal conductivity for this material. We attribute the ultralow thermal conductivity of these disordered, layered crystals to the localization of lattice vibrations induced by the random stacking of two-dimensional crystalline WSe2 sheets. Disordering of the layered structure by ion bombardment increases the thermal conductivity.

Journal Article↗
PubMed2006

Improved fecal DNA test for colorectal cancer screening.

BACKGROUND & AIMS: Fecal DNA testing has shown greater sensitivity than guaiac-based occult blood tests for noninvasive colorectal cancer (CRC) screening. The prototype assay (version 1), which analyzed 22 gene mutations and DNA integrity assay (DIA), showed a sensitivity of 52% for CRC detection and a specificity of 94% in average-risk individuals. The present study was conducted to determine the sensitivity and specificity of a second-generation assay (version 2) that uses improved DNA stabilization/isolation techniques and a new promoter methylation marker. METHODS: Forty patients with CRC and 122 subjects with normal colonoscopy provided stool samples to which DNA preservation buffer was added immediately. DNA was purified using gel-based capture, and analyzed for the original panel of 22 mutations, DIA, and 2 new promoter methylation markers. RESULTS: By using DNA that was optimally preserved and purified from stool, the sensitivity of the prototype version 1 assay increased to 72.5% because of enhanced performance of DIA. Vimentin gene methylation alone provided sensitivity and specificity of 72.5% and 86.9%, respectively. The optimal combination of vimentin methylation plus DIA resulted in 87.5% sensitivity and 82% specificity; cancers were detected regardless of stage or location. False-positive vimentin methylation was associated with older age. CONCLUSIONS: An improved fecal DNA test that incorporates only 2 markers shows much higher sensitivity for CRC. The new assay is easier to perform and should be less costly, thereby facilitating its use for noninvasive CRC screening.

Age Factors↗
PubMed2006

Tolevamer, a novel nonantibiotic polymer, compared with vancomycin in the treatment of mild to moderately severe Clostridium difficile-associated diarrhea.

BACKGROUND: Current antibiotic therapies for Clostridium difficile-associated diarrhea have limitations, including progression to severe disease, recurrent C. difficile-associated diarrhea, and selection for nosocomial pathogens. Tolevamer, a soluble, high-molecular weight, anionic polymer that binds C. difficile toxins A and B is a unique nonantibiotic treatment option. METHODS: In this 3-arm, multicenter, randomized, double-blind, active-controlled, parallel-design phase II study, patients with mild to moderately severe C. difficile-associated diarrhea were randomized to receive 3 g of tolevamer per day (n = 97), 6 g of tolevamer per day (n = 95), or 500 mg of vancomycin per day (n = 97). The primary efficacy parameter was time to resolution of diarrhea, defined as the first day of 2 consecutive days when the patient had hard or formed stools (any number) or < or = 2 stools of loose or watery consistency. RESULTS: In the per-protocol study population, resolution of diarrhea was achieved in 48 (67%) of 72 patients receiving 3 g of tolevamer per day (median time to resolution of diarrhea, 4.0 days; 95% confidence interval, 2.0-6.0 days), in 58 (83%) of 70 patients receiving 6 g of tolevamer per day (median time to resolution of diarrhea, 2.5 days; 95% confidence interval, 2.0-3.0 days), and in 73 (91%) of 80 patients receiving vancomycin (median time to resolution of diarrhea, 2.0 days; 95% confidence interval, 1.0-3.0 days). Tolevamer administered at a dosage of 6 g per day was found to be noninferior to vancomycin administered at a dosage of 500 mg per day with regard to time to resolution of diarrhea (P = .02) and was associated with a trend toward a lower recurrence rate. Tolevamer was well tolerated but was associated with an increased risk of hypokalemia. CONCLUSIONS: Tolevamer, a novel polystyrene binder of C. difficile toxins A and B, effectively treats mild to moderate C. difficile diarrhea and merits further clinical development.

Adult↗
PubMed2006

Guidelines for colonoscopy surveillance after polypectomy: a consensus update by the US Multi-Society Task Force on Colorectal Cancer and the American Cancer Society.

Adenomatous polyps are the most common neoplastic findings discovered in people who undergo colorectal screening or who have a diagnostic work-up for symptoms. It was common practice in the 1970s for these patients to have annual follow-up surveillance examinations to detect additional new adenomas and missed synchronous adenomas. As a result of the National Polyp Study report in 1993, which showed clearly in a randomized design that the first postpolypectomy examination could be deferred for 3 years, guidelines published by a gastrointestinal consortium in 1997 recommended that the first follow-up surveillance take place 3 years after polypectomy for most patients. In 2003 these guidelines were updated and colonoscopy was recommended as the only follow-up examination, stratification at baseline into low risk and higher risk for subsequent adenomas was suggested. The 1997 and 2003 guidelines dealt with both screening and surveillance. However, it has become increasingly clear that postpolypectomy surveillance is now a large part of endoscopic practice, draining resources from screening and diagnosis. In addition, surveys have shown that a large proportion of endoscopists are conducting surveillance examinations at shorter intervals than recommended in the guidelines. In the present report, a careful analytic approach was designed to address all evidence available in the literature to delineate predictors of advanced pathology, both cancer and advanced adenomas, so that patients can be stratified more definitely at their baseline colonoscopy into those at lower risk or increased risk for a subsequent advanced neoplasia. People at increased risk have either 3 or more adenomas, high-grade dysplasia, villous features, or an adenoma 1 cm or larger in size. It is recommended that they have a 3-year follow-up colonoscopy. People at lower risk who have 1 or 2 small (<1 cm) tubular adenomas with no high-grade dysplasia can have a follow-up evaluation in 5-10 years, whereas people with hyperplastic polyps only should have a 10-year follow-up evaluation, as for average-risk people. There have been recent studies that have reported a significant number of missed cancers by colonoscopy. However, high-quality baseline colonoscopy with excellent patient preparation and adequate withdrawal time should minimize this and reduce clinicians concerns. These guidelines were developed jointly by the US Multi-Society Task Force on Colorectal Cancer and the American Cancer Society to provide a broader consensus and thereby increase the use of the recommendations by endoscopists. The adoption of these guidelines nationally can have a dramatic impact on shifting available resources from intensive surveillance to screening. It has been shown that the first screening colonoscopy and polypectomy produces the greatest effects on reducing the incidence of colorectal cancer in patients with adenomatous polyps.

Adenomatous Polyposis Coli↗
PubMed2006

Guidelines for colonoscopy surveillance after cancer resection: a consensus update by the American Cancer Society and the US Multi-Society Task Force on Colorectal Cancer.

Patients with resected colorectal cancer are at risk for recurrent cancer and metachronous neoplasms in the colon. This joint update of guidelines by the American Cancer Society and the US Multi-Society Task Force on Colorectal Cancer addresses only the use of endoscopy in the surveillance of these patients. Patients with endoscopically resected Stage I colorectal cancer, surgically resected Stages II and III cancers, and Stage IV cancer resected for cure (isolated hepatic or pulmonary metastasis) are candidates for endoscopic surveillance. The colorectum should be carefully cleared of synchronous neoplasia in the perioperative period. In nonobstructed colons, colonoscopy should be performed preoperatively. In obstructed colons, double-contrast barium enema or computed tomography colonography should be performed preoperatively, and colonoscopy should be performed 3 to 6 months after surgery. These steps complete the process of clearing synchronous disease. After clearing for synchronous disease, another colonoscopy should be performed in 1 year to look for metachronous lesions. This recommendation is based on reports of a high incidence of apparently metachronous second cancers in the first 2 years after resection. If the examination at 1 year is normal, then the interval before the next subsequent examination should be 3 years. If that examination is normal, then the interval before the next subsequent examination should be 5 years. Shorter intervals may be indicated by associated adenoma findings (see "Guidelines for Colonoscopy Surveillance After Polypectomy: A Consensus Update by the US Multi-Society Task Force on Colorectal Cancer and the American Cancer Society"). Shorter intervals also are indicated if the patient's age, family history, or tumor testing indicate definite or probable hereditary nonpolyposis colorectal cancer. Patients undergoing low anterior resection of rectal cancer generally have higher rates of local cancer recurrence compared with those with colon cancer. Although effectiveness is not proven, performance of endoscopic ultrasound or flexible sigmoidoscopy at 3- to 6-month intervals for the first 2 years after resection can be considered for the purpose of detecting a surgically curable recurrence of the original rectal cancer.

Colectomy↗
PubMed2006

Somali and Oromo refugee women: trauma and associated factors.

AIM: This paper reports a study identifying the demographic characteristics, self-reported trauma and torture prevalence, and association of trauma experience and health and social problems among Somali and Oromo women refugees. BACKGROUND: Nearly all refugees have experienced losses, and many have suffered multiple traumatic experiences, including torture. Their vulnerability to isolation is exacerbated by poverty, grief, and lack of education, literacy, and skills in the language of the receiving country. METHOD: Using data from a cross-sectional population-based survey, conducted from July 1999 to September 2001, with 1134 Somali and Oromo refugees living in the United States of America, a sub-sample of female participants with clearly identified parenting status (n = 458) were analysed. Measures included demographics, history of trauma and torture, scales for physical, psychological, and social problems, and a post-traumatic stress symptom checklist. FINDINGS: Results indicated high overall trauma and torture exposure, and associated physical, social and psychological problems. Women with large families reported statistically significantly higher counts of reported trauma (mean 30, P < 0.001) and torture (mean 3, P < 0.001), and more associated problems (P < 0.001) than the other two groups. Women who reported higher levels of trauma and torture were also older (P < 0.001), had more family responsibilities, had less formal education (P < 0.001) and were less likely to speak English (P < 0.001). CONCLUSION: These findings suggest a need for nurses, and especially public health nurses who work with refugee and immigrant populations in the community, to develop a more comprehensive understanding of the range of refugee women's experiences and the continuum of needs post-migration, particularly among older women with large family responsibilities. Nurses, with their holistic framework, are ideally suited to partner with refugee women to expand their health agenda beyond the biomedical model to promote healing and reconnection with families and communities.

Adaptation, Psychological↗
PubMed2006

Acupuncture prior to and at embryo transfer in an assisted conception unit--a case series.

Over a period of three years, acupuncture was offered to patients entering assisted reproduction therapy. Acupuncture sessions were given at varying, but usually weekly, intervals during the in vitro fertilisation (IVF) cycle, and immediately before and after embryo transfer. Twenty two patients (average age 36.2 years) were treated over a total of 26 IVF cycles and 15 pregnancies were achieved, as determined by presence of foetal heartbeat on ultrasound at four weeks post embryo transfer. This was a success rate of 57.7% compared with 45.3% for patients in the IVF unit not treated with acupuncture (P > 0.05). Relaxing effects were noted following acupuncture and it is speculated that this may have contributed to the increase in pregnancy rate for the acupuncture group.

Acupuncture Therapy↗
PubMed2005

Soil invertebrates disrupt carbon flow through fungal networks.

Annual carbon flux through soil respiration is ten times greater than fossil fuel combustion, but its component parts are poorly understood because they are the product of complex multitrophic interactions between soil organisms. A major component of carbon flux from plants to soil occurs through networks of symbiotic arbuscular mycorrhizal fungi. Here, using 13CO2 pulse labeling, we show that natural densities of the numerically dominant fungal feeding invertebrate Protaphorura armata (order Collembola) reduces 13C enrichment of mycorrhizosphere respiration by 32%. Our findings emphasize the importance of multitrophic interactions in regulating respiration of recent plant photosynthate from soil.

Animals↗
PubMed2005

The genome of the African trypanosome Trypanosoma brucei.

African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.

Amino Acids↗
PubMed2005

Automating genomic data mining via a sequence-based matrix format and associative rule set.

There is an enormous amount of information encoded in each genome--enough to create living, responsive and adaptive organisms. Raw sequence data alone is not enough to understand function, mechanisms or interactions. Changes in a single base pair can lead to disease, such as sickle-cell anemia, while some large megabase deletions have no apparent phenotypic effect. Genomic features are varied in their data types and annotation of these features is spread across multiple databases. Herein, we develop a method to automate exploration of genomes by iteratively exploring sequence data for correlations and building upon them. First, to integrate and compare different annotation sources, a sequence matrix (SM) is developed to contain position-dependant information. Second, a classification tree is developed for matrix row types, specifying how each data type is to be treated with respect to other data types for analysis purposes. Third, correlative analyses are developed to analyze features of each matrix row in terms of the other rows, guided by the classification tree as to which analyses are appropriate. A prototype was developed and successful in detecting coinciding genomic features among genes, exons, repetitive elements and CpG islands.

Base Sequence↗
PubMed2005

Vinorelbine plus cisplatin vs. observation in resected non-small-cell lung cancer.

BACKGROUND: We undertook to determine whether adjuvant vinorelbine plus cisplatin prolongs overall survival among patients with completely resected early-stage non-small-cell lung cancer. METHODS: We randomly assigned patients with completely resected stage IB or stage II non-small-cell lung cancer to vinorelbine plus cisplatin or to observation. The primary end point was overall survival; principal secondary end points were recurrence-free survival and the toxicity and safety of the regimen. RESULTS: A total of 482 patients underwent randomization to vinorelbine plus cisplatin (242 patients) or observation (240); 45 percent of the patients had pathological stage IB disease and 55 percent had stage II, and all had an Eastern Cooperative Oncology Group performance status score of 0 or 1. In both groups, the median age was 61 years, 65 percent were men, and 53 percent had adenocarcinomas. Chemotherapy caused neutropenia in 88 percent of patients (including grade 3 febrile neutropenia in 7 percent) and death from toxic effects in two patients (0.8 percent). Nonhematologic toxic effects of chemotherapy were fatigue (81 percent of patients), nausea (80 percent), anorexia (55 percent), vomiting (48 percent), neuropathy (48 percent), and constipation (47 percent), but severe (grade 3 or greater) toxic effects were uncommon (<10 percent). Overall survival was significantly prolonged in the chemotherapy group as compared with the observation group (94 vs. 73 months; hazard ratio for death, 0.69; P=0.04), as was relapse-free survival (not reached vs. 46.7 months; hazard ratio for recurrence, 0.60; P<0.001). Five-year survival rates were 69 percent and 54 percent, respectively (P=0.03). CONCLUSIONS: Adjuvant vinorelbine plus cisplatin has an acceptable level of toxicity and prolongs disease-free and overall survival among patients with completely resected early-stage non-small-cell lung cancer.

Adult↗
PubMed2005

How do plants regulate the function, community structure, and diversity of mycorrhizal fungi?

In many semi-natural and natural ecosystems, mycorrhizal fungi are the most abundant and functionally important group of soil micro-organisms. They are almost wholly dependent on their host plants to supply them with photosynthate in return for which they enable the plant to access greater quantities of nutrients. Thus, there is considerable potential for plant communities to regulate the structure and function of mycorrhizal communities. This paper reviews some of the key recent developments that have enabled the influence of plant species richness, composition, and age on mycorrhizal communities in boreal forests and temperate grassland to be determined. It discusses the emerging evidence that, in some situations, plant species richness is related to mycorrhizal species richness, in contrast to previous thinking. The paper also includes some preliminary data on the effect of host stand age on root-associated basidiomycete communities. It concludes by highlighting some of the new methodological advances that promise to unravel the linkages between mycorrhizal diversity and their function in situ.

Biodiversity↗
PubMed2005

Inhaled corticosteroids for abnormal pulmonary function in children with a history of chronic lung disease of infancy: study protocol [ISRCTN55153521].

BACKGROUND: There is considerable evidence from the literature that children with chronic lung disease of infancy (CLD) have abnormal pulmonary function in childhood and this could have an impact on their life quality and overall health. There are similarities between CLD and asthma, and corticosteroids are the mainstay treatment for asthma. Many physicians use inhaled corticosteroids in children with CLD with no evidence. Therefore we wish to conduct a randomized double-blinded placebo controlled trial to test for the role of inhaled corticosteroids in children aged from 3 to 9 years with a history of CLD. Our primary hypothesis will be that inhaled corticosteroids are beneficial in children with CLD. METHODS: Our primary hypothesis is that using inhaled steroids; Beclomethasone Dipropionate (QVAR) 100 mcg 2 puffs 2 times a day for 6 weeks will improve the respiratory system resistance and the quality of life in children with CLD. DISCUSSION: We propose that Beclomethasone Dipropionate (QVAR) will affect the pulmonary function after 6 weeks of treatment. In summary we think that our study will highlight knowledge on whether the use of inhaled steroids is clinically effective for CLD.

Anti-Asthmatic Agents↗
PubMed2005

Nicotinic acid limitation regulates silencing of Candida adhesins during UTI.

The adherence of Candida glabrata to host cells is mediated, at least in part, by the EPA genes, a family of adhesins encoded at subtelomeric loci, where they are subject to transcriptional silencing. We show that normally silent EPA genes are expressed during murine urinary tract infection (UTI) and that the inducing signal is the limitation of nicotinic acid (NA), a precursor of nicotinamide adenine dinucleotide (NAD+). C. glabrata is an NA auxotroph, and NA-induced EPA expression is likely the result of a reduction in NAD+ availability for the NAD+-dependent histone deacetylase Sir2p. The adaptation of C. glabrata to the host, therefore, involves a loss of metabolic capacity and exploitation of the resulting auxotrophy to signal a particular host environment.

Animals↗
PubMed2005

Steel dust in the New York City subway system as a source of manganese, chromium, and iron exposures for transit workers.

The United States Clean Air Act Amendments of 1990 reflected increasing concern about potential effects of low-level airborne metal exposure on a wide array of illnesses. Here we summarize results demonstrating that the New York City (NYC) subway system provides an important microenvironment for metal exposures for NYC commuters and subway workers and also describe an ongoing pilot study of NYC transit workers' exposure to steel dust. Results from the TEACH (Toxic Exposure Assessment, a Columbia and Harvard) study in 1999 of 41 high-school students strongly suggest that elevated levels of iron, manganese, and chromium in personal air samples were due to exposure to steel dust in the NYC subway. Airborne concentrations of these three metals associated with fine particulate matter were observed to be more than 100 times greater in the subway environment than in home indoor or outdoor settings in NYC. While there are currently no known health effects at the airborne levels observed in the subway system, the primary aim of the ongoing pilot study is to ascertain whether the levels of these metals in the subway air affect concentrations of these metals or related metabolites in the blood or urine of exposed transit workers, who due to their job activities could plausibly have appreciably higher exposures than typical commuters. The study design involves recruitment of 40 transit workers representing a large range in expected exposures to steel dust, the collection of personal air samples of fine particulate matter, and the collection of blood and urine samples from each monitored transit worker.

Air Pollutants↗
PubMed2005

Genetic linkage of prostate cancer risk to the chromosome 3 region bearing FHIT.

We conducted linkage analysis of 80 candidate genes in 201 brother pairs affected with prostatic adenocarcinoma. Markers representing two adjacent candidate genes on chromosome 3p, CDC25A and FHIT, showed suggestive evidence for linkage with single-point identity-by-descent allele-sharing statistics. Fine-structure multipoint linkage analysis yielded a maximum LOD score of 3.17 (P = 0.00007) at D3S1234 within FHIT intron 5. For a subgroup of 38 families in which three or more affected brothers were reported, the LOD score was 3.83 (P = 0.00001). Further analysis reported herein suggested a recessive mode of inheritance. Association testing of 16 single nucleotide polymorphisms (SNP) spanning a 381-kb interval surrounding D3S1234 in 202 cases of European descent with 143 matched, unrelated controls revealed significant evidence for association between case status and the A allele of single nucleotide polymorphism rs760317, located within intron 5 of FHIT (Pearson's chi(2) = 8.54, df = 1, P = 0.0035). Our results strongly suggest involvement of germline variations of FHIT in prostate cancer risk.

Acid Anhydride Hydrolases↗