bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential for the phytoremediation of arsenic-contaminated mine tailings in Fiji
Authors: Ko Byong-Gu , Anderson Christopher W. N. , Bolan Nanthi S. , Huh Keun-Young , Vogeler Iris
Published: October 2008

The objectives of this study were (1) to compare the bioavailability of arsenic (As) to plants in an As-spiked agricultural soil and a naturally contaminated mine tailings, (2) to compare the theoretical ability of various chemical amendments to solubilise As in naturally contaminated mine tailings, and (3) to examine the ability of Brassica juncea (Indian mustard) plants to remove the solubilised As from the soil and tailings. The growth media used for this study included mine tailings from a gold mine in Fiji contaminated with As (683 As mg/kg) due to the presence of arsenopyrite in the mined rock, and a pasture soil from New Zealand (Manawatu sandy loam) amended with lime and/or As. Brassica juncea was grown in these substrates in a glasshouse. In a separate batch experiment, we examined the theoretical ability of several chemical extractants to solubilise As from the mine tailings. Of the tested extractants, only hydrochloric acid (HCl) and a mixture containing ammonium oxalate (NH4)2C2O4, oxalic acid, and ascorbic acid were effective in extracting As from the tailings. In the plant growth experiment, solutions of these 2 chemicals were used as soil amendments at 2 different concentrations to increase As uptake by 6-week-old, actively growing B. juncea plants. Arsenic bioavailability as a function of the growth media influenced the germination rate of B. juncea, the As concentration in the plants, and the water-soluble As concentration in the media. There was approximately a 3-fold reduction in the germination of seeds, and a 64- and 380-fold increase in As concentration in plant and soil solution, respectively, in the spiked Manawatu soil compared with the naturally contaminated Fiji mine tailings. The spiking of soil with As did not mimic naturally contaminated tailings in this experiment. The total amount of As taken up by B. juncea plants increased approximately 9 fold with the addition of the amendments. However, the phytoremediation capacity of B. juncea for As extraction in Fiji mine tailings was too low for efficient remediation even in the presence of solubilising chemicals.
Distribution of heavy metals in a sandy forest soil repeatedly amended with biosolids
Authors: Su Jingjun , Wang Hailong , Kimberley Mark O. , Beecroft Katie , Magesan G. N. , Hu Chengxiao
Published: October 2008

The suitability for land application of biosolids can be limited by the presence of heavy metals. We investigated the distribution of heavy metals in the soil of a research trial within a Pinus radiata (D. Don) plantation following repeated applications of aerobically digested liquid biosolids. The trial is located on a sandy soil at Rabbit Island near Nelson, New Zealand. Biosolids were applied in 1997, 2000, and 2003, at 3 application rates: 0 (control), 300 (standard), and 600 kg N/ha (high). Litter layer and soil samples (down to 1 m) were taken from the trial site and analysed to assess the accumulation of heavy metals (Cu, Zn, Cd, Cr, Pb, and Ni) within the soil profile and the effect of repeated biosolids application on metal availability and mobility. Sequential fractionation methods were used to evaluate the distribution of exchangeable, specifically sorbed, oxide bound, organic bound, and residual fractions of the metals. Concentrations of Cr, Cu, Pb, and Zn in the litter layer were significantly (P < 0.05) higher in the high biosolids-treated plots than the control, indicating that the litter layer had retained considerable amounts of biosolids-derived metals. Significantly elevated concentrations of environmentally available Cu in the topsoil (0–0.1 m) were observed in plots receiving the high biosolids treatment and residual Cu concentration was significantly higher in the biosolids treatments, but apart from an accumulation of oxide-bound Zn in the 0.1–0.25 m layer, no accumulation of other metals in the soil was observed. The residual fraction was the most abundant pool for all metals examined, indicating low bioavailability. Total concentrations of the metals in both biosolids-treated and untreated control soils were very low (e.g. <7 mg Cu/kg, <30 mg Zn/kg). Although there were no significant changes in concentrations below the topsoil, mass balance calculation implied that a proportion of biosolids-derived Zn in the high biosolids treatment may have been leached through the soil profile.
Does atmospheric CO2 concentration influence soil nitrifying bacteria and their activity?
Authors: Bowatte Saman , Carran R. Andrew , Newton Paul C. D. , Theobald Phil
Published: October 2008

Ammonia oxidising bacteria (AOB) are important soil microorganisms that carry out the first step in nitrification, the oxidation of ammonia to nitrite. In this paper we investigated the impact of long-term elevated CO2 on soil nitrification and soil AOB community composition. Soil samples were taken from Hakanoa natural CO2 springs, Kamo, Northland, New Zealand. This site has been exposed to elevated CO2 for several decades. Soils were collected from different points near to CO2-emitting vents where the CO2 concentration at canopy height had been characterised. Nitrification activity was measured using a short-term nitrification assay, and AOB community composition was characterised using polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). A principal component analysis of the DGGE banding pattern was carried out to identify the effect of CO2 on AOB community composition. Soil nitrification activity was markedly decreased with increasing CO2. The variation in DGGE banding patterns revealed differences in the composition of the soil AOB community that were related to CO2 concentration. Principal component analysis showed that the changes in community composition and nitrifying activity were linked and that these changes were related to atmospheric CO2 concentration.
N2O and N2 emissions from pasture and wetland soils with and without amendments of nitrate, lime and zeolite under laboratory condition
Authors: Zaman M. , Nguyen M. L. , Saggar S.
Published: October 2008

Pasture and wetland soils are regarded as the major source of nitrous oxide (N2O) and dinitrogen (N2) emissions as they receive regular inputs of N from various sources. To understand the factors affecting N2O and N2 emissions and their ratio as influenced by soil amendments (zeolite or lime), we conducted laboratory experiments using 10-L plastic containers at 25°C for 28 days. Soil samples (0–0.1 m soil depth) collected from pasture and adjacent wetland sites were treated with nitrate-N (NO3–) at 200 kg N/ha with and without added lime or zeolite. Nitrous oxide and N2 emissions were measured periodically from soil subsamples collected in 1-L gas jars using acetylene (C2H2) inhibition technique, and soil ammonium (NH4+) and NO3– concentrations were determined to assess the changes in N transformation. Soil NO3–-N disappeared relatively faster in wetland soil than that in pasture soil. In the presence of added NO3–, wetland soils emitted significantly more N2O and N2 than pasture soils, while the reverse trend was observed in the absence of NO3–. Total N2O emitted as percentage of the applied N was 25% for wetland and 5.7% for pasture soils. Total N2 emissions expressed as a percentage of the applied N from wetland and pasture soils were 5–9% and 0.29–0.74%, respectively. Higher N2O and N2 emissions and lower N2O : N2 ratios from wetland soils than pasture soils were probably due to the higher water content and greater availability of soluble C in wetland. Zeolite applied to wetland soils reduced N2O emissions but had little effect on N2O emissions from pasture soils. Liming appeared to exacerbate N2O emissions from fertilised lands and treatment wetlands and shift the balance between N2O and N2, and may be considered as one of the potential management tools to reduce the amount of fertiliser N moving from pasture and wetland into waterways.
Physically motivated empirical models for the spread and intensity of grass fires
Authors: Higgins Steven I. , Bond William J. , Trollope Winston S. W. , Williams Richard J.
Published: October 2008

We develop empirical models for the rate of spread and intensity of fires in grass fuels. The models are based on a well-known physical analogy for the rate of spread of a fire through a continuous fuelbed. Unlike other models based on this analogy, we do not attempt to directly estimate the model parameters. Rather, we use data on the rate of spread to indirectly estimate parameters that describe aggregate properties of the fire behaviour. The resulting models require information on the moisture content of the fuel and wind speed to predict the rate of spread of fires. To predict fire intensity, the models additionally use information on the heat yield of the fuel and the amount of fuel consumed. We evaluate the models by using them to predict the intensity of independent fires and by comparing them with linear and additive regression models. The additive model provides the best description of the training data but predicts independent data poorly and with high bias. Overall, the empirical models describe the data better than the linear model, and predict independent data with lower bias. Hence our physically motivated empirical models perform better than statistical models and are easier to parameterise than parameter-rich physical models. We conclude that our physically motivated empirical models provide an alternative to statistical models and parameter-rich physical models of fire behaviour.
Effects of fire frequency and mowing on a temperate, derived grassland soil in south-eastern Australia
Authors: Prober Suzanne M. , Lunt Ian D. , Thiele Kevin R.
Published: October 2008

Frequent disturbances such as fire are widely considered important drivers of plant composition and diversity in productive grassy ecosystems. Effects of fire frequency on grassland soils, however, are less well understood. We established replicated disturbance regimes in a high-quality, representative Themeda australis–Poa sieberiana-derived grassland in south-eastern Australia that had historically been burnt every 4–8 years. Effects on soil chemical, physical and biological properties were measured after 10 years of application of 2-, 4-, and 8-yearly burning, 2-yearly mowing and an undisturbed treatment. Contrary to other grassy ecosystems, there were no detectable effects of disturbance regime on total soil nitrogen and carbon, or a range of other soil chemical properties in the top 10 cm. However, a cumulative effect of burning on the grassland soil was evident from a suite of changes to soil surface properties, available nutrients and biological activity. In particular, on biennially burnt plots, reduced litter and plant protective cover were associated with increased soil surface compaction, decreased infiltration and decreased soil biological activity, which in turn were related to poor sward recovery after fire and drought. These relationships indicate potential for positive feedbacks whereby repeated removal of soil protective cover and changes to soil surface chemistry through very frequent burning ultimately lead to further reduction in soil protective cover through reduced productivity. However, this is only likely in extreme cases: data from unburnt plots indicated that soils that had historically been burnt every 4–8 years had not passed a threshold beyond which such soil changes were irreversible or damaging. Contrary to other predictions, cessation of burning for 13 years did not lead to detectable soil nutrient release through senescence of dominant grasses. Biennial mowing with slash retention was an effective alternative disturbance for maintaining sward vigour while avoiding soil surface damage.
Predicting spatial patterns of fire on a southern California landscape
Authors: Syphard Alexandra D. , Radeloff Volker C. , Keuler Nicholas S. , Taylor Robert S. , Hawbaker Todd J. , Stewart Susan I. , Clayton Murray K.
Published: October 2008

Humans influence the frequency and spatial pattern of fire and contribute to altered fire regimes, but fuel loading is often the only factor considered when planning management activities to reduce fire hazard. Understanding both the human and biophysical landscape characteristics that explain how fire patterns vary should help to identify where fire is most likely to threaten values at risk. We used human and biophysical explanatory variables to model and map the spatial patterns of both fire ignitions and fire frequency in the Santa Monica Mountains, a human-dominated southern California landscape. Most fires in the study area are caused by humans, and our results showed that fire ignition patterns were strongly influenced by human variables. In particular, ignitions were most likely to occur close to roads, trails, and housing development but were also related to vegetation type. In contrast, biophysical variables related to climate and terrain (January temperature, transformed aspect, elevation, and slope) explained most of the variation in fire frequency. Although most ignitions occur close to human infrastructure, fires were more likely to spread when located farther from urban development. How far fires spread was ultimately related to biophysical variables, and the largest fires in southern California occurred as a function of wind speed, topography, and vegetation type. Overlaying predictive maps of fire ignitions and fire frequency may be useful for identifying high-risk areas that can be targeted for fire management actions.
How DNA coiling enhances target localization by proteins
Authors: van den Broek B. , Lomholt M. A. , Kalisch S.-M. J. , Metzler R. , Wuite G. J. L.
Published: October 2008

Many genetic processes depend on proteins interacting with specific sequences on DNA. Despite the large excess of nonspecific DNA in the cell, proteins can locate their targets rapidly. After initial nonspecific binding, they are believed to find the target site by 1D diffusion (“sliding”) interspersed by 3D dissociation/reassociation, a process usually referred to as facilitated diffusion. The 3D events combine short intrasegmental “hops” along the DNA contour, intersegmental “jumps” between nearby DNA segments, and longer volume “excursions.” The impact of DNA conformation on the search pathway is, however, still unknown. Here, we show direct evidence that DNA coiling influences the specific association rate of EcoRV restriction enzymes. Using optical tweezers together with a fast buffer exchange system, we obtained association times of EcoRV on single DNA molecules as a function of DNA extension, separating intersegmental jumping from other search pathways. Depending on salt concentration, targeting rates almost double when the DNA conformation is changed from fully extended to a coiled configuration. Quantitative analysis by an extended facilitated diffusion model reveals that only a fraction of enzymes are ready to bind to DNA. Generalizing our results to the crowded environment of the cell we predict a major impact of intersegmental jumps on target localization speed on DNA.
Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450BioIACP complex
Authors: Cryle Max J. , Schlichting Ilme
Published: October 2008

Cytochrome P450BioI(CYP107H1) from the biotin operon ofBacillus subtilisforms a seven-carbon diacid through a multistep oxidative cleavage of a fatty acid linked to acyl carrier protein (ACP). Crystal structures of P450BioIin complex with three different length fattyacyl-ACP (Escherichia coli) ligands show that P450BioIbinds the fatty acid such as to force the carbon chain into a U-shape above the active site heme. This positions the C7 and C8 carbons for oxidation, with a large additional cavity extending beyond the heme to accommodate the methyl termini of fatty acids beyond the site of cleavage. The structures explain the experimentally observed lack of stereo- and regiospecificity in the hydroxylation and cleavage of free fatty acids. The P450BioI-ACP complexes represent the only structurally characterized P450-carrier protein complexes to date, which has allowed the generation of a model of the interaction of the vancomycin biosynthetic P450 OxyB with its proposed carrier protein bound substrate.
The keratin-binding protein Albatross regulates polarization of epithelial cells
Authors: Sugimoto Masahiko , Inoko Akihito , Shiromizu Takashi , Nakayama Masanori , Zou Peng , Yonemura Shigenobu , Hayashi Yuko , Izawa Ichiro , Sasoh Mikio , Uji Yukitaka , Kaibuchi Kozo , Kiyono Tohru , Inagaki Masaki
Published: October 2008

The keratin intermediate filament network is abundant in epithelial cells, but its function in the establishment and maintenance of cell polarity is unclear. Here, we show that Albatross complexes with Par3 to regulate formation of the apical junctional complex (AJC) and maintain lateral membrane identity. In nonpolarized epithelial cells, Albatross localizes with keratin filaments, whereas in polarized epithelial cells, Albatross is primarily localized in the vicinity of the AJC. Knockdown of Albatross in polarized cells causes a disappearance of key components of the AJC at cell–cell borders and keratin filament reorganization. Lateral proteins E-cadherin and desmoglein 2 were mislocalized even on the apical side. Although Albatross promotes localization of Par3 to the AJC, Par3 and ezrin are still retained at the apical surface in Albatross knockdown cells, which retain intact microvilli. Analysis of keratin-deficient epithelial cells revealed that keratins are required to stabilize the Albatross protein, thus promoting the formation of AJC. We propose that keratins and the keratin-binding protein Albatross are important for epithelial cell polarization.
Rab-coupling protein coordinates recycling of α5β1 integrin and EGFR1 to promote cell migration in 3D microenvironments
Authors: Caswell Patrick T. , Chan May , Lindsay Andrew J. , McCaffrey Mary W. , Boettiger David , Norman Jim C.
Published: October 2008

Here we show that blocking the adhesive function of αvβ3 integrin with soluble RGD ligands, such as osteopontin or cilengitide, promoted association of Rab-coupling protein (RCP) with α5β1 integrin and drove RCP-dependent recycling of α5β1 to the plasma membrane and its mobilization to dynamic ruffling protrusions at the cell front. These RCP-driven changes in α5β1 trafficking led to acquisition of rapid/random movement on two-dimensional substrates and to a marked increase in fibronectin-dependent migration of tumor cells into three-dimensional matrices. Recycling of α5β1 integrin did not affect its regulation or ability to form adhesive bonds with substrate fibronectin. Instead, α5β1 controlled the association of EGFR1 with RCP to promote the coordinate recycling of these two receptors. This modified signaling downstream of EGFR1 to increase its autophosphorylation and activation of the proinvasive kinase PKB/Akt. We conclude that RCP provides a scaffold that promotes the physical association and coordinate trafficking of α5β1 and EGFR1 and that this drives migration of tumor cells into three-dimensional matrices.
Notch activates cell cycle reentry and progression in quiescent cardiomyocytes
Authors: Campa Víctor M. , Gutiérrez-Lanza Raquel , Cerignoli Fabio , Díaz-Trelles Ramón , Nelson Brandon , Tsuji Toshiya , Barcova Maria , Jiang Wei , Mercola Mark
Published: October 2008

The inability of heart muscle to regenerate by replication of existing cardiomyocytes has engendered considerable interest in identifying developmental or other stimuli capable of sustaining the proliferative capacity of immature cardiomyocytes or stimulating division of postmitotic cardiomyocytes. Here, we demonstrate that reactivation of Notch signaling causes embryonic stem cell–derived and neonatal ventricular cardiomyocytes to enter the cell cycle. The proliferative response of neonatal ventricular cardiomyocytes declines as they mature, such that late activation of Notch triggers the DNA damage checkpoint and G2/M interphase arrest. Notch induces recombination signal-binding protein 1 for Jκ (RBP-Jκ)-dependent expression of cyclin D1 but, unlike other inducers, also shifts its subcellular distribution from the cytosol to the nucleus. Nuclear localization of cyclin D1 is independent of RBP-Jκ. Thus, the influence of Notch on nucleocytoplasmic localization of cyclin D1 is an unanticipated property of the Notch intracellular domain that is likely to regulate the cell cycle in multiple contexts, including tumorigenesis as well as cardiogenesis.
Cdk2 and Pin1 negatively regulate the transcriptional corepressor SMRT
Authors: Stanya Kristopher J. , Liu Yu , Means Anthony R. , Kao Hung-Ying
Published: October 2008

Silencing mediator for retinoic acid and thyroid hormone receptor (SMRT) is a transcriptional corepressor that participates in diverse signaling pathways and human diseases. However, regulation of SMRT stability remains largely unexplored. We show that the peptidyl-prolyl isomerase Pin1 interacts with SMRT both in vitro and in mammalian cells. This interaction requires the WW domain of Pin1 and SMRT phosphorylation. Pin1 regulates SMRT protein stability, thereby affecting SMRT-dependent transcriptional repression. SMRT phosphorylation at multiple sites is required for Pin1 interaction, and these sites can be phosphorylated by Cdk2, which interacts with SMRT. Cdk2-mediated phosphorylation of SMRT is required for Pin1 binding and decreases SMRT stability, whereas mutation of these phosphorylation sites abrogates Pin1 binding and stabilizes SMRT. Finally, decreases in SMRT stability occur in response to the activation of Her2/Neu/ErbB2, and this receptor functions upstream of both Pin1 and Cdk2 in the signaling cascade that regulates SMRT stability and cellular response to tamoxifen.
An Epstein-Barr virus–encoded microRNA targets PUMA to promote host cell survival
Authors: Choy Elizabeth Yee-Wai , Siu Kam-Leung , Kok Kin-Hang , Lung Raymond Wai-Ming , Tsang Chi Man , To Ka-Fai , Kwong Dora Lai-Wan , Tsao Sai Wah , Jin Dong-Yan
Published: October 2008

Epstein-Barr virus (EBV) is a herpesvirus associated with nasopharyngeal carcinoma (NPC), gastric carcinoma (GC), and other malignancies. EBV is the first human virus found to express microRNAs (miRNAs), the functions of which remain largely unknown. We report on the regulation of a cellular protein named p53 up-regulated modulator of apoptosis (PUMA) by an EBV miRNA known as miR-BART5, which is abundantly expressed in NPC and EBV-GC cells. Modulation of PUMA expression by miR-BART5 and anti–miR-BART5 oligonucleotide was demonstrated in EBV-positive cells. In addition, PUMA was found to be significantly underexpressed in ∼60% of human NPC tissues. Although expression of miR-BART5 rendered NPC and EBV-GC cells less sensitive to proapoptotic agents, apoptosis can be triggered by depleting miR-BART5 or inducing the expression of PUMA. Collectively, our findings suggest that EBV encodes an miRNA to facilitate the establishment of latent infection by promoting host cell survival.
Aquaporin-4–binding autoantibodies in patients with neuromyelitis optica impair glutamate transport by down-regulating EAAT2
Authors: Hinson Shannon R. , Roemer Shanu F. , Lucchinetti Claudia F. , Fryer James P. , Kryzer Thomas J. , Chamberlain Jayne L. , Howe Charles L. , Pittock Sean J. , Lennon Vanda A.
Published: October 2008

Neuromyelitis optica (NMO)-immunoglobulin G (IgG) is a clinically validated serum biomarker that distinguishes relapsing central nervous system (CNS) inflammatory demyelinating disorders related to NMO from multiple sclerosis. This autoantibody targets astrocytic aquaporin-4 (AQP4) water channels. Clinical, radiological, and immunopathological data suggest that NMO-IgG might be pathogenic. Characteristic CNS lesions exhibit selective depletion of AQP4, with and without associated myelin loss; focal vasculocentric deposits of IgG, IgM, and complement; prominent edema; and inflammation. The effect of NMO-IgG on astrocytes has not been studied. In this study, we demonstrate that exposure to NMO patient serum and active complement compromises the membrane integrity of CNS-derived astrocytes. Without complement, astrocytic membranes remain intact, but AQP4 is endocytosed with concomitant loss of Na+-dependent glutamate transport and loss of the excitatory amino acid transporter 2 (EAAT2) . Our data suggest that EAAT2 and AQP4 exist in astrocytic membranes as a macromolecular complex. Transport-competent EAAT2 protein is up-regulated in differentiating astrocyte progenitors and in nonneural cells expressing AQP4 transgenically. Marked reduction of EAAT2 in AQP4-deficient regions of NMO patient spinal cord lesions supports our immunocytochemical and immunoprecipitation data. Thus, binding of NMO-IgG to astrocytic AQP4 initiates several potentially neuropathogenic mechanisms: complement activation, AQP4 and EAAT2 down-regulation, and disruption of glutamate homeostasis.
Regulation of class switch recombination and somatic mutation by AID phosphorylation
Authors: McBride Kevin M. , Gazumyan Anna , Woo Eileen M. , Schwickert Tanja A. , Chait Brian T. , Nussenzweig Michel C.
Published: October 2008

Activation-induced cytidine deaminase (AID) is a mutator enzyme that initiates somatic mutation and class switch recombination in B lymphocytes by introducing uracil:guanine mismatches into DNA. Repair pathways process these mismatches to produce point mutations in the Ig variable region or double-stranded DNA breaks in the switch region DNA. However, AID can also produce off-target DNA damage, including mutations in oncogenes. Therefore, stringent regulation of AID is required for maintaining genomic stability during maturation of the antibody response. It has been proposed that AID phosphorylation at serine 38 (S38) regulates its activity, but this has not been tested in vivo. Using a combination of mass spectrometry and immunochemical approaches, we found that in addition to S38, AID is also phosphorylated at position threonine 140 (T140). Mutation of either S38 or T140 to alanine does not impact catalytic activity, but interferes with class switching and somatic hypermutation in vivo. This effect is particularly pronounced in haploinsufficient mice where AID levels are limited. Although S38 is equally important for both processes, T140 phosphorylation preferentially affects somatic mutation, suggesting that posttranslational modification might contribute to the choice between hypermutation and class switching.
Assessing the Integration of Health Center and Community Emergency Preparedness and Response Planning
Authors: Wineman Nicole V. , Braun Barbara I. , Barbera Joseph A. , Loeb Jerod M.
Published: October 2008

Background: To assess the state of health center integration into community preparedness, we undertook a national study of linkages between health centers and the emergency preparedness and response planning initiatives in their communities. The key objectives of this project were to gain a better understanding of existing linkages in a nationally representative sample of health centers, and identify health center demographic and experience factors that were associated with strong linkages.

Methods: The objectives of the study were to gain a baseline understanding of existing health center linkages to community emergency preparedness and response systems and to identify factors that were associated with strong linkages. A 60-item questionnaire was mailed to the population of health centers supported by the Health Resources and Services Administration’s Bureau of Primary Health Care in February 2005. Results were aggregated and a chi square analysis identified factors associated with stronger linkages.

Results: Overall performance on study-defined indicators of strong linkages was low: 34% had completed a hazard vulnerability analysis in collaboration with the community emergency management agency, 30% had their role documented in the community plan, and 24% participated in community-wide exercises. Stronger linkages were associated with experience responding to a disaster and a perception of high risk for experiencing a disaster.

Conclusions: The potential for health centers to participate in an integrated response is not fully realized, and their absence from community-based planning leaves an already vulnerable population at greater risk. Community planners should be encouraged to include health centers in planning and response and centers should receive more targeted resources for community integration. (Disaster Med Public Health Preparedness. 2007;1:96–105)
Allocation of Ventilators in a Public Health Disaster
Authors: Powell Tia , Christ Kelly C. , Birkhead Guthrie S.
Published: October 2008

Background: In a public health emergency, many more patients could require mechanical ventilators than can be accommodated.

Methods: To plan for such a crisis, the New York State Department of Health and the New York State Task Force on Life and the Law convened a workgroup to develop ethical and clinical guidelines for ventilator triage.

Results: The workgroup crafted an ethical framework including the following components: duty to care, duty to steward resources, duty to plan, distributive justice, and transparency. Incorporating the ethical framework, the clinical guidelines propose both withholding and withdrawing ventilators from patients with the highest probability of mortality to benefit patients with the highest likelihood of survival. Triage scores derive from the sepsis-related organ failure assessment system, which assigns points based on function in 6 basic medical domains. Triage may not be implemented by a facility without clear permission from public health authorities.

Conclusions: New York State released the draft guidelines for public comment, allowing for revision to reflect both community values and medical innovation. This ventilator triage system represents a radical shift from ordinary standards of care, and may serve as a model for allocating other scarce resources in disasters. (Disaster Med Public Health Preparedness. 2008;2:20–26)
Rethinking Volunteer Management Using a Centralized Volunteer Staging and Training Area
Authors: Aakko Eric , Weed Nathan , Konrad Richard , Wiesman John
Published: October 2008

Public health agencies simply do not have enough trained staff or volunteers to effectively respond to a large-scale disaster. Training volunteers “off the street” will be crucial—but time consuming—in a public health emergency. A centralized volunteer staging and training area can help to efficiently register, credential, and conduct just-in-time training of volunteers, while reducing stress, confusion, traffic congestion, and security issues at various mass dispensing clinics. (Disaster Med Public Health Preparedness. 2008;2:127–129)
A Consensus-based Educational Framework and Competency Set for the Discipline of Disaster Medicine and Public Health Preparedness
Authors: Subbarao Italo , Lyznicki James M. , Hsu Edbert B. , Gebbie Kristine M. , Markenson David , Barzansky Barbara , Armstrong John H. , Cassimatis Emmanuel G. , Coule Philip L. , Dallas Cham E. , King Richard V. , Rubinson Lewis , Sattin Richard , Swienton Raymond E. , Lillibridge Scott , Burkle Frederick M. , Schwartz Richard B. , James James J.
Published: October 2008

Background: Various organizations and universities have developed competencies for health professionals and other emergency responders. Little effort has been devoted to the integration of these competencies across health specialties and professions. The American Medical Association Center for Public Health Preparedness and Disaster Response convened an expert working group (EWG) to review extant competencies and achieve consensus on an educational framework and competency set from which educators could devise learning objectives and curricula tailored to fit the needs of all health professionals in a disaster.

Methods: The EWG conducted a systematic review of peer-reviewed and non–peer reviewed published literature. In addition, after-action reports from Hurricane Katrina and relevant publications recommended by EWG members and other subject matter experts were reviewed for congruencies and gaps. Consensus was ensured through a 3-stage Delphi process.

Results: The EWG process developed a new educational framework for disaster medicine and public health preparedness based on consensus identification of 7 core learning domains, 19 core competencies, and 73 specific competencies targeted at 3 broad health personnel categories.

Conclusions: The competencies can be applied to a wide range of health professionals who are expected to perform at different levels (informed worker/student, practitioner, leader) according to experience, professional role, level of education, or job function. Although these competencies strongly reflect lessons learned following the health system response to Hurricane Katrina, it must be understood that preparedness is a process, and that these competencies must be reviewed continually and refined over time. (Disaster Med Public Health Preparedness. 2008;2:57–68)
Secondary Contamination of Medical Personnel, Equipment, and Facilities Resulting From Hazardous Materials Events, 2003–2006
Authors: Horton D. Kevin , Orr Maureen , Tsongas Theodora , Leiker Richard , Kapil Vikas
Published: October 2008

Background: When not managed properly, a hazardous material event can quickly extend beyond the boundaries of the initial release, creating the potential for secondary contamination of medical personnel, equipment, and facilities. Secondary contamination generally occurs when primary victims are not decontaminated or are inadequately decontaminated before receiving medical attention. This article examines the secondary contamination events reported to the Agency for Toxic Substances and Disease Registry (ATSDR) and offers suggestions for preventing such events.

Methods: Data from the ATSDR Hazardous Substances Emergency Events Surveillance system were used to conduct a retrospective analysis of hazardous material events occurring in 17 states during 2003 through 2006 involving secondary contamination of medical personnel, equipment, and facilities.

Results: Fifteen (0.05%) Hazardous Substances Emergency Events Surveillance events were identified in which secondary contamination occurred. At least 17 medical personnel were injured as a result of secondary contamination while they were treating contaminated victims. Of the medical personnel injured, 12 were emergency medical technicians and 5 were hospital personnel. Respiratory irritation was the most common injury sustained.

Conclusions: Adequate preplanning and drills, proper decontamination procedures, good field-to-hospital communication, appropriate use of personal protective equipment, and effective training can help prevent injuries of medical personnel and contamination of transport vehicles and medical facilities. (Disaster Med Public Health Preparedness. 2008;2:104–113)
Ethics of Triage in the Event of an Influenza Pandemic
Authors: Tabery James , Mackett Charles W. ,   University of Pittsburgh Medical Center Pandemic Influenza Task Force's Triage Review Board
Published: October 2008

The prospect of a severe influenza pandemic poses a daunting public health threat to hospitals and the public they serve. The event of a severe influenza pandemic will put hospitals under extreme stress; only so many beds, ventilators, nurses, and physicians will be available, and it is likely that more patients will require medical attention than can be completely treated. Triage is the process of sorting patients in a time of crisis to determine who receives what level of medical attention. How will hospitals sort patients to determine priority for treatment? What criteria will be used? Who will develop these criteria? This article formulates an answer to these questions by constructing a conceptual framework for anticipating and responding to the ethical issues raised by triage in the event of a severe influenza pandemic. (Disaster Med Public Health Preparedness. 2008;2:114–118)
Hospital Response to a Major Freeway Bridge Collapse
Authors: Hick John L. , Chipman Jeffery , Loppnow Gregory , Conterato Marc , Roberts David , Heegaard William G. , Beilman Greg , Clark Michael , Pohland Jonathan , Ho Jeffrey D. , Brunette Douglas D. , Clinton Joseph E.
Published: October 2008

Background: We describe the hospital system response to the Interstate 35W bridge collapse in Minneapolis into the Mississippi River on August 1, 2007, which resulted in 13 deaths and 127 injuries. Comparative analysis of response activities at the 3 hospitals that received critical or serious casualties is provided.

Methods: First-hand experiences of hospital physicians, issues identified in after-action reports, injury severity scores, and other relevant patient data were collected from the 3 hospitals that received seriously injured patients, including the closest hospitals to the collapse on each side of the river.

Results/Discussion: Injuries were consistent with major acceleration/deceleration force injuries. The most critical patients arrived first at each hospital, suggesting appropriate prehospital triage. Capacity of the health care system was not overwhelmed and the involved hospitals generally reported an overresponse by staff. Communication and patient tracking problems occurred at all of the hospitals. Situational awareness was limited due to the scope of structural collapse and incomplete information from the scene.

Conclusions: Hospitals were generally satisfied with their surge capacity and incident management plan activation. Issues such as communications, patient tracking, and staff overreporting that have been identified in past incidents also were problematic in this event. Hospitals will need to address deficiencies and build on successful actions to cope with future, potentially larger incidents. (Disaster Med Public Health Preparedness. 2008;2(Suppl 1):S11–S16)
Evolving Need for Alternative Triage Management in Public Health Emergencies: A Hurricane Katrina Case Study
Authors: Klein Kelly R. , Pepe Paul E. , Burkle Frederick M. , Nagel Nanci E. , Swienton Raymond E.
Published: October 2008

In many countries, traditional medical planning for disasters developed largely in response to battlefield and multiple casualty incidents, generally involving corporal injuries. The mass evacuation of a metropolitan population in the aftermath of Hurricane Katrina evolved into life-and-death triage scenarios involving thousands of patients with nontraumatic illnesses and special medical needs. Although unprecedented in the United States, triage management needs for this disaster were similar to other large-scale public health emergencies, both natural and human-generated, that occurred globally in the past half-century. The need for alternative triage-management processes similar to the methodologies of other global mass public health emergencies is illustrated through the experience of disaster medical assistance teams in the first 3 days following Katrina's landfall. The immediate establishment of disaster-specific, consensus-based, public health emergency–related triage protocols—developed with ethical and legal expertise and a renewed focus on multidimensional, multifactorial matrix decision-making processes—is strongly recommended. (Disaster Med Public Health Preparedness. 2008;2(Suppl 1):S40–S44)
Public Health Practice vs Research: Implications for Preparedness and Disaster Research Review by State Health Department IRBs
Authors: Perlman David
Published: October 2008

Under the current US Department of Health and Human Services regulatory and ethical system for research involving human subjects, research is defined in terms of several key concepts: intent, systematic investigation, and generalizability. If an investigator engages in a systematic investigation designed or intended to contribute to generalizable knowledge, then he or she is engaged in research. If that research involves living individuals and the investigator will either interact or intervene with people or obtain their identifiable personal information, then the research must be prospectively reviewed by an institutional review board (IRB), a federally mandated committee that ensures the ethical and regulatory appropriateness of proposed research. In public health institutions, and especially at state departments of health, this definition of research may prove vexing for determining when particular public health activities must be reviewed by IRBs. This article outlines several reasons for such vexation and 2 key responses from major public health stakeholders. In the current climate of public health preparedness initiatives at state health departments for disasters and bioterrorism, how research is defined vis-à-vis public health interventions may add even more confusion to preparedness initiatives and pose difficulties in determining when IRB review and the added protections it affords are appropriate. This article suggests several practical ways to avoid confusion and attempts to strike a balance between the need for expeditious approvals of research-based responses to public health disasters and to ensure proper protections for human subjects at state health departments. It is hoped that these suggestions can assist not only state health departments but also academically based researchers who either collaborate with those departments or whose research will need to be reviewed by their IRBs. (Disaster Med Public Health Preparedness. 2008;2:185–191)
Non-laminar cerebral cortex in teleost fishes?
Authors: Ito Hironobu , Yamamoto Naoyuki
Published: October 2008

A large skull is disadvantageous to animals that move quickly in three-dimensional space, such as fishes and birds in water or air. A cerebral neocortex with a six-layered sheet has not evolved, most likely due to the limited cranial space. Instead of the laminar cortex, telencephalic nuclear masses seem to have evolved as the pallium in teleost fishes. We consider that the nuclear masses contain rather simple neural circuits sharing a skeleton of simple circuits in the mammalian cortex, which have been elaborated by additional circuits in mammals. Such basic similarities at the connectional level shared by nuclear and cortical pallium might underlie similar or equivalent functions.
genBlastA: Enabling BLAST to identify homologous gene sequences
Authors: She Rong , Chu Jeffrey S.-C. , Wang Ke , Pei Jian , Chen Nansheng
Published: October 2008

BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs (“signals”), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs (“noises”). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.
Holcoglossum nujiangense (Orchidaceae: Aeridinae) – a new species and its pollination system
Authors: Jin Xiao‐Hua , Chen Sing‐Chi , Li De‐Zhu
Published: October 2008

Based on herbarium and field observations, a new species, Holcoglossum nujiangense, is described and illustrated. It is morphologically similar to Holcoglossum sinicum and H. weixiense. Holcoglossum nujiangense differs from H. weixiense by smaller flowers with broadly rhombic midlobe and from H. sinicum by its broadly rhombic midlobe, papillose spur and notable callus on the disc. The chromosome number of this species was found to be 2n=38. The pollinator for this new species was Micraphis andreniformis Smith that carried the pollinia of Holcoglossum nujiangense on its head. The visiting behavior of the pollinator is food‐search kind, although there is no obvious nectar in the spur.
Impatiens angulata (Balsaminaceae), a new species from Guangxi, China
Authors: Yu Sheng‐Xiang , Chen Yi‐Lin , Qin Hai‐Ning
Published: October 2008

Impatiens angulata S. X. Yu, Y. L. Chen et H. N. Qin sp. nova (Balsaminaceae), a new species from Guangxi, China, is described and illustrated. This species is close to I. hainanensis in morphological characters. Both have succulent stems, 4 lateral sepal connected upper lobes of lateral united petals, but are distinguished by the base of stems with 6–9 ridges, leaves oblong or oblanceolate, the outer lateral sepals with 9 veins, inner lateral sepals ovate and dorsal sepal with deep bilobate spur.
New records of cup‐fungi from Iceland with comments on some previously reported species
Authors: Pfister Donald H. , Gyða Eyjólfsdóttir Guðríður
Published: October 2008

Twelve species of cup‐fungi in the orders Pezizales and Helotiales are reported for the first time from Iceland and comments are made on eight species previously reported. Distributions and habitats are noted. Newly reported records of species occurrences are as follows: Ascocoryne cylichnium, Gloeotinia granigena, Melastiza flavorubens, Octospora melina, O. leucoloma, Ombrophila violacea, Peziza apiculata sensu lato, P. phyllogena, P. succosa, Pseudombrophila theioleuca, Ramsbottomia macracantha and Tarzetta cupularis. Recent work allows the re‐identification of Peziza granulosa as P. fimeti.
Cephalaria duzceënsis (Dipsacaceae), a new species from the western Black Sea region, Turkey
Authors: Aksoy Necmi , Süleyman Göktürk R. , Açık Leyla , Çelebi Ayten
Published: October 2008

A new species, Cephalaria duzceënsis N. Aksoy & R. S. Göktürk (Dipsacacae) from western Black Sea region of Turkey is described. It is illustrated in line drawings and the morphology of the new species is compared with Cephalaria speciosa. Molecular and morphological methods were used to separate the two species. Both species were first identified morphologically and then studied by randomly amplified polymorphic DNA (RAPD) markers. Genetic similarities were calculated based on the RAPD data and used to construct a UPGMA dendrogram. According to the result, two main clusters were observed using the character differences. It is concluded that C. duzceënsis sp. nov. is different from C. speciosa.
Leguminosae of Philippines in the Vidal herbarium at Real Jardín Botánico, Madrid
Authors: De La Estrella Manuel , Calabrese Graciela M. , Cámara Beatriz , Velayos Mauricio
Published: October 2008

This study provides a checklist of the specimens kept in the Real Jardín Botánico herbarium (MA) belonging to the family Leguminosae and collected by Sebastián Vidal in Philippines, during the period 1876 to 1887. More than 750 specimens were studied. In the subfamily Caesalpinioideae we found 39 species (14 genera); Mimosoideae 24 species (10 genera) and Papilionoideae 85 species (40 genera). Twenty six species collected by Vidal should be considered introduced in the country. Although this collection is dated from the 19th century, five species are reported for the first time from the country: Albizia splendens, Bauhinia ferruginea, Caesalpinia andamanica, Sindora coriacea and Sindora wallichii. The whole Vidal collections (series 1, 2 and M) were studied and a map of localities with coordinates is provided. A statistical summary is presented at the end of the checklist.