Decentralized but Globally Coordinated Biodiversity Data.

Centralized biodiversity data aggregation is too often failing societal needs due to pervasive and systemic data quality deficiencies. We argue for a novel approach that embodies the spirit of the Web ("small pieces loosely joined") through the decentralized coordination of data across scientific languages and communities. The upfront cost of decentralization can be offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data. Our decentralized approach encourages the emergence and evolution of multiple self-identifying communities of practice that are regionally, taxonomically, or institutionally localized. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. With no single aggregator to exert centralized control over biodiversity data, decentralization generates loosely connected networks of mid-level aggregators. Global coordination is nevertheless feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities. The decentralized model also poses novel integration challenges, among which the explicit and continuous articulation of conflicting systematic classifications and phylogenies remain the most challenging. We discuss the development of available solutions, challenges, and outline next steps: the global effort of coordination should focus on developing shared languages for data signal translation, as opposed to homogenizing the data signal itself.

To increase trust, change the social design behind aggregated biodiversity data.

Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the sources to the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between individual data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies-frequently called 'backbones'-they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, potentially leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e. unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.

Web based listing of agents associated with new onset work-related asthma.

BACKGROUND: Work-related asthma is common and yet remains a challenge to diagnose. Access to a listing of agents associated with work-related asthma has been suggested as useful in assisting in the diagnosis. METHODS: The Association of Occupational and Environmental Clinics (AOEC) developed criteria that were used to review the peer-reviewed medical literature published in English. Based on this review, substances were designated either as a sensitizing agent or an irritant. The reviews were conducted by a board certified internist/pulmonologist/occupational medicine specialist from 2002 to 2007 and a board certified internist/occupational medicine physician from 2008- date. All reviews were then reviewed by the nine member AOEC board of directors. RESULTS: The original list of agents associated with new onset work-related asthma was derived from the tables of a text book on work-related asthma. After 13 years of review, there are 327 substances designated as asthma agents on the AOEC list; 173 (52.9%) coded as sensitizers, 35 (10.7%) as generally recognized as an asthma causing agent, four (1.2%) as irritants, two (0.6%) as both a sensitizer and an irritant and 113(34.6%) agents that still need to be reviewed. CONCLUSIONS: The AOEC has developed a readily available web based listing of agents associated with new onset work-related asthma in adults. The listing is based on peer-reviewed criteria. The listing is updated twice a year. Regular review of the peer-reviewed medical literature is conducted to determine whether new substances should be added to the list. Clinicians should find the list useful when considering the diagnosis of work-related asthma.

Integrating asthma hazard characterization methods for consumer products.

Despite extensive study, definitive conclusions regarding the relationship between asthma and consumer products remain elusive. Uncertainties reflect the multi-faceted nature of asthma (i.e., contributions of immunologic and non-immunologic mechanisms). Many substances used in consumer products are associated with occupational asthma or asthma-like syndromes. However, risk assessment methods do not adequately predict the potential for consumer product exposures to trigger asthma and related syndromes under lower-level end-user conditions. A decision tree system is required to characterize asthma and respiratory-related hazards associated with consumer products. A system can be built to incorporate the best features of existing guidance, frameworks, and models using a weight-of-evidence (WoE) approach. With this goal in mind, we have evaluated chemical hazard characterization methods for asthma and asthma-like responses. Despite the wealth of information available, current hazard characterization methods do not definitively identify whether a particular ingredient will cause or exacerbate asthma, asthma-like responses, or sensitization of the respiratory tract at lower levels associated with consumer product use. Effective use of hierarchical lines of evidence relies on consideration of the relevance and potency of assays, organization of assays by mode of action, and better assay validation. It is anticipated that the analysis of existing methods will support the development of a refined WoE approach.

Lean mass predicts asthma better than fat mass among females.

The obesity phenotype associated with asthma is not known. Our objective was to define the relative contribution of various distributions of fat and lean mass to asthma prevalence. Data were obtained from 2,525 participants (including 1,422 females) who underwent dual-energy X-ray absorptiometry (DEXA) at the year 20 examination in the Coronary Artery Risk Development in Young Adults (CARDIA) cohort. Total, truncal, arm and leg distributions of fat and lean mass were adjusted to the person's height. Self-reported asthma was the outcome. Asthma among females was associated with greater total fat mass, arm fat mass, total lean mass, truncal lean mass and arm lean mass. Among males, none of these mass measures were significantly associated with asthma. Among females, the association with asthma was stronger for total lean mass than for total fat mass. Further, among various regional distributions of lean and fat mass in females, truncal lean mass was the strongest predictor. Total lean mass is more strongly associated with asthma than total fat mass among females. These findings are contrary to the popular perception that excess physiological fat drives the obesity-asthma association. Rather, we hypothesise that ectopic fat within the "lean" tissues drives this association among females.

Association between asthma and serum adiponectin concentration in women.

BACKGROUND: The association of murine asthma with adiposity may be mediated by adiponectin, an anti-inflammatory adipokine with reduced serum concentrations in obese subjects. A study was undertaken to examine whether the serum adiponectin concentration is associated with human asthma and whether it explains the association between adiposity and asthma, particularly in women and in premenopausal women. METHODS: A cross-sectional analysis was performed of 2890 eligible subjects at year 15 of the Coronary Artery Risk Development in Young Adults (CARDIA) cohort and its YALTA ancillary study who had either current asthma or never asthma at that evaluation. Obesity was defined as body mass index (BMI) >or=30 kg/m(2). Multivariable logistic regression analysis was performed with current asthma status as the dependent variable. RESULTS: Women, but not men, with current asthma had a lower mean unadjusted serum adiponectin concentration than those with never asthma (p<0.001; p for sex interaction <0.001). Similarly, current asthma was related to obesity only in women (OR 3.31, 95% CI 2.00 to 5.46, p for sex interaction = 0.004); this association was little affected by adjusting for serum adiponectin. The prevalence of current asthma in premenopausal women was reduced in the highest compared with the lowest tertile of serum adiponectin concentration (OR 0.46, 95% CI 0.26 to 0.84, p = 0.03), after adjusting for BMI. However, the interaction between serum adiponectin concentration and BMI category on current asthma status was not significant in premenopausal women or women overall. CONCLUSIONS: A high serum adiponectin concentration may protect against current asthma in premenopausal women but does not explain the association between asthma and adiposity.

Discriminative learning for protein conformation sampling.

Protein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Conditional Random Fields (CRFs). Using a discriminative learning method, CRFSampler can automatically learn more than ten thousand parameters quantifying the relationship among primary sequence, secondary structure, and (pseudo) backbone angles. Using only compactness and self-avoiding constraints, CRFSampler can efficiently generate protein-like conformations from primary sequence and predicted secondary structure. CRFSampler is also very flexible in that a variety of model topologies and feature sets can be defined to model the sequence-structure relationship without worrying about parameter estimation. Our experimental results demonstrate that using a simple set of features, CRFSampler can generate decoys with much higher quality than the most recent HMM model.

GTF2IRD1 regulates transcription by binding an evolutionarily conserved DNA motif 'GUCE'.

GTF2IRD1 is a member of a family of transcription factors whose defining characteristic is varying numbers of a helix-loop-helix like motif, the I-repeat. Here, we present functional analysis of human GTF2IRD1 in regulation of three genes (HOXC8, GOOSECOID and TROPONIN I(SLOW)). We define a regulatory motif (GUCE-GTF2IRD1 Upstream Control Element) common to all three genes. GUCE is bound in vitro by domain I-4 of GTF2IRD1 and mediates transcriptional regulation by GTF2IRD1 in vivo. Definition of this site will assist in identification of other downstream targets of GTF2IRD1 and elucidation of its role in the human developmental disorder Williams-Beuren syndrome.

Asthma is associated with weight gain in females but not males, independent of physical activity.

We tested whether asthma diagnosis is associated with weight gain and physical activity in 4,547 18 to 30-yr-old African American and white men and women, followed prospectively for up to 10 yr. Baseline asthma was most frequent in African American men. Incident asthma was more frequent in women. Incident asthma was associated with highest and lowest baseline and change in body mass index (BMI), in a J-shaped curve, after adjustment for other factors. When stratified by sex, this association was seen only in females. Subjects on average decreased physical activity and gained weight over time, but there was no significant difference in asthma prevalence by physical activity at baseline or asthma incidence by change in physical activity. Cigarette smoking in females was significantly associated with asthma incidence, but serum cotinine level at baseline among nonsmokers (reflecting environmental tobacco smoke [ETS] exposure) was not significantly associated with asthma. We conclude that gain in BMI predisposes to new asthma diagnosis in female young adults, but decreased physical activity does not explain the association of weight gain with asthma.

Risk factors for asthma prevalence among urban and nonurban African American children.

Urban residence is a risk factor for asthma. We examined multiple risk factors simultaneously among African American children. We interviewed 2409 African American mothers of newborns who had at least 1 child at home under 18 years of age. Sixteen percent reported at least 1 child with physician-diagnosed asthma. Significantly associated with an asthmatic child were maternal asthma and allergies, maternal cigarette smoking, a humidifying device, and a gas range or oven in the home. Urban residence was related to asthma but became nonsignificant once other factors were controlled for. Asthma associated with urban residence may be explained by identifiable factors.

Hypersensitivity pneumonitis from ordinary residential exposures.

A previously healthy woman developed hypersensitivity pneumonitis of such severity that she required chronic systemic corticosteroid therapy for symptom control. Detailed investigation of her workplace and home environments revealed fungi in her typical suburban home, to which she had specific serum precipitating antibodies. Efforts to remove mold from the home were unsuccessful in relieving symptoms, and moving to another residence was the only intervention that allowed her to be withdrawn from corticosteroid therapy. Hypersensitivity pneumonitis is commonly associated with occupational or avocational exposures, such as moldy hay in farmers or bird antigen in bird breeders. We propose that hypersensitivity pneumonitis may occur in North America, as it does in Japan, from domestic exposures alone.

Association of reversible alopecia with occupational topical exposure to common borax-containing solutions.

Boron is widely used in industrial materials, most frequently as the salt borax. Systemic exposure (eg, ingestion) to boron in boric acid been associated with reversible toxic alopecia among other manifestations. There is scant clinical literature on alopecia caused by topical exposure to boron. We observed a series of 3 patients in 2 workplaces who suffered reversible alopecia from cutaneous boron exposure. The scalp alopecia was global in 1 patient and patchy in 2 patients. Alopecia was completely reversed by elimination or reduction of exposure to boron-containing materials in all 3 patients. We conclude that occupational topical exposure to boron in solutions may cause reversible alopecia.

Characterization of clinical tolerance to inhaled zinc oxide in naive subjects and sheet metal workers.

Clinical tolerance to the acute effects of zinc oxide inhalation develops in workers during periods of repeated exposure. The aims of this study were to determine whether clinical tolerance is accompanied by a reduction in the acute pulmonary inflammatory and cytokine responses to zinc oxide exposure and whether tolerance can be demonstrated in sheet metal workers who chronically inhale low levels of zinc oxide. Naive (never-exposed) subjects inhaled 5 mg/m3 zinc oxide on 1 or 3 days and underwent bronchoalveolar lavage 20 hours after the final exposure. Sheet metal workers inhaled zinc oxide on 1 day and control furnace gas on another day. Among naive subjects in whom tolerance was induced, bronchoalveolar lavage fluid percent neutrophils and interleukin-6 (IL-6) levels were significantly decreased compared with subjects who underwent only a single exposure. Sheet metal workers were much less symptomatic, but they still experienced a significant increase in plasma IL-6. The results indicate that clinical tolerance to zinc oxide is accompanied by reduced pulmonary inflammation and that chronically exposed sheet metal workers are not clinically affected by exposure to zinc oxide fume at the Occupational Safety and Health Administration Permissible Exposure Limit. The increase in IL-6 levels observed in the clinically responsive, and to a lesser extent, tolerant, states following zinc oxide inhalation is consistent with the dual role of IL-6 as a pyrogen and anti-inflammatory agent.

Hearing conservation for farmers: source apportionment of occupational and environmental factors contributing to hearing loss.

Those who work on farms continue to have a strikingly high prevalence of hearing loss, despite efforts to promote hearing conservation in agriculture. To develop improved hearing conservation programs, we performed a source apportionment analysis for hearing loss in a large, multiphasic health survey, the New York Farm Family Health and Hazard Survey. We used information from audiometric, otoscopic, and tympanometric examinations; detailed general health and farm exposure interviews; and a second interview that focused on additional potential determinants of hearing loss. Hearing loss on audiometry was significantly associated with increased age, male gender, education through high school or less, lifetime years of hunting with guns, lifetime years of use of a grain dryer, and a history of spraying crops during the previous year. Hearing conservation programs for farmers should thus be directed toward reduction in noise exposure, both from occupational and non-occupational sources. Additional study is needed to evaluate the association seen between crop spraying and hearing loss.

Clinical evaluation, management, and prevention of work-related asthma.

Work-related asthma (WRA) is asthma that is attributable to, or is made worse by, environmental exposures in the workplace. WRA has become the most prevalent occupational lung disease in developed countries, is more common than is generally recognized, and can be severe and disabling. Identification of workplace exposures causing and/or aggravating the asthma, and appropriate control or cessation of these exposures can often lead to reduction or even complete elimination of symptoms and disability. This depends on timely recognition and diagnosis of WRA. In this review, the diagnostic evaluation has been organized in a stepwise fashion to make it more practical for primary care physicians as well as physicians specializing in occupational diseases and asthma. WRA merits more widespread attention among clinicians, labor and management health and safety specialists, researchers, health care organizations, public health policy makers, industrial hygienists, and others interested in disease prevention.

Medical evaluation for respirator use.

The purpose of a respirator is to prevent the inhalation of harmful airborne substances or to provide a source of respirable air when breathing in oxygen-deficient atmospheres. For a physician to recommend the use of respirator, general background information on respiratory-protective devices is required. The first part of this clinical practice review describes the general aspects of industrial hygiene, respirators and a respirator-certification program. The second part addresses matters related to medical certification for respirator use. Medical certification for respirators is an important part of the activities of the occupational physician. To determine whether a worker is able to tolerate the added strain of a respiratory protective device is a complex process in which factors such as fitness for work, health of the individual, characteristics of the work itself, and the properties, type, and requirements of the respiratory protective device, have to be considered. Medical certification is of utmost importance for respirator use, and it should be viewed as an element in a comprehensive respiratory protection program. A comprehensive program is the key element in affording the workers' effective respiratory protection once the initial steps of the hierarchy of methods of hazard control have proved insufficient or infeasible. As a result, the need for the industrial hygiene/safety officer, the worker, the employer and the medical professional to work as a team is much more than in any other field of occupational medicine--a necessary requirement for making the right decision.