bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extent of industrial plantations on Southeast Asian peatlands in 2010 with analysis of historical expansion and future projections
Authors: Miettinen Jukka , Hooijer Aljosja , Shi Chenghua , Tollenaar Daniel , Vernimmen Ronald , Liew Soo Chin , Malins Chris , Page Susan E. 
Published: April 2012

AbstractTropical peatlands cover over 25 Mha in Southeast Asia and are estimated to contain around 70 Gt of carbon. Peat swamp forest ecosystems are an important part of the region's natural resources supporting unique flora and fauna endemic to Southeast Asia. Over recent years, industrial plantation development on peatland, especially for oil palm cultivation, has created intense debate due to its potentially adverse social and environmental effects. The lack of objective up‐to‐date information on the extent of industrial plantations has complicated quantification of their regional and global environmental consequences, both in terms of loss of forest and biodiversity as well as increases in carbon emissions. Based on visual interpretation of high‐resolution (30 m) satellite images, we find that industrial plantations covered over 3.1 Mha (20%) of the peatlands of Peninsular Malaysia, Sumatra and Borneo in 2010, surpassing the area of Belgium and causing an annual carbon emission from peat decomposition of 230–310 Mt CO2e. The majority (62%) of the plantations were located on the island of Sumatra, and over two‐thirds (69%) of all industrial plantations were developed for oil palm cultivation, with the remainder mostly being Acacia plantations for paper pulp production. Historical analysis shows strong acceleration of plantation development in recent years: 70% of all industrial plantations have been established since 2000 and only 4% of the current plantation area existed in 1990. ‘Business‐as‐usual’ projections of future conversion rates, based on historical rates over the past two decades, indicate that 6–9 Mha of peatland in insular Southeast Asia may be converted to plantations by the year 2020, unless land use planning policies or markets for products change. This would increase the annual carbon emission to somewhere between 380 and 920 Mt CO2e by 2020 depending on water management practices and the extent of plantations.
Prevalence of postpartum depression in a hospital setting among Malaysian mothers
Authors: Zainal Nor Zuraida , Kaka Anandjit Singh , Ng Chong Guan , Jawan Rosy , Singh Gill Jesjeet 
Published: April 2012

AbstractIntroductionPostpartum depression (PPD) is a disorder that affects not only mothers, but also can lead to family, social, economic and vocational breakdown. The objective of this study was to determine the prevalence and factors associated with postpartum depression among mothers in an urban hospital setting in Malaysia.MethodsIn this cross‐sectional study, mothers attending routine visits at six to eight weeks postpartum at a postnatal clinic were assessed on socio‐demographic data, obstetric history, social support, breastfeeding status and psychiatric history. Mini International Neuropsychiatric Interview (M.I.N.I.) was administered to establish a diagnosis of postpartum depression.ResultsA total of 411 subjects participated in the study. The prevalence rate of postpartum depression was 6.8%. Univariate analysis found that being a housewife, having a cesarian section, low social support, family history of depression, previous history of depression and non‐exclusive breastfeeding were significantly associated with postpartum depression. Predictors for postpartum depression were non‐exclusive breastfeeding (P < 0.01, OR = 23.7, 95% CI 3.1–179.7) and previous history of depression (P < 0.05, OR = 82.3, 95% CI 1.2–5897.6).DiscussionThe prevalence rate of postpartum depression in urban Malaysian mothers was comparable to the rates in other countries. Mothers who did no exclusively breast feeding their babies appeared to have more risk for postpartum depression. Therefore, screening for depression should become a routine during postpartum period and mothers must be encouraged to exclusively breastfeed their babies.
Adhesion to Er:YAG laser and bur prepared root and crown dentine
Authors: Shirani F , Birang R , Malekipur MR , Zeilabi A , Shahmoradi M , Kazemi S , Khazaei S 
Published: April 2012

AbstractBackground:  The purpose of this study was to evaluate the bond strengths between dentine and resin composite obtained after Er:YAG laser treatment of crown or root dentine used together with self‐etch and total‐etch adhesive systems.Methods:  One etch‐and‐rinse adhesive (Single Bond, 3M, USA) and one self‐etch system (Clearfil SE Bond, Kuraray, Japan) were applied to root and crown dentine prepared with a regular bur in a turbine or with an Er:YAG laser. The shear bond strength was determined after thermocycling and statistically analysed using independent t‐tests.Results:  Crown sites bonded using Clearfil SE Bond and Single Bond adhesives yielded bond strengths similar to that of root dentine sites (p > 0.05). Clearfil SE Bond was stronger in both the lased and non‐lased groups (p < 0.05). The lowest bond strength was obtained when Single Bond without acid etching was used on Er:YAG ablated dentine. When total‐etch adhesive was used, there were significant differences (p < 0.05) between the laser‐ablated and laser‐ablated/acid‐etched and bur‐cut/acid‐etched groups.Conclusions:  Er:YAG laser irradiation of root and crown dentine conducted prior to the adhesive protocol adversely affected adhesion and decreased bond strength compared with traditional preparation.
Freeze-Coring Method for Characterization of Microbial Community Structure and Function in Wetland Soils at High Spatial Resolution
Authors: Franchini Alessandro G. , Zeyer Josef 
Published: April 2012

ABSTRACT
A simple freeze-coring method was developed to obtain structurally intact cores from wetland soils. A copper tube was inserted into the wetland and filled with ethanol and dry ice to freeze the surrounding soil. Biological structure and function could be analyzed, and labile compounds such as mRNA were recovered.
Norwegian Sheep Are an Important Reservoir for Human-Pathogenic Escherichia coli O26:H11
Authors: Brandal Lin T. , Sekse Camilla , Lindstedt Bjørn-Arne , Sunde Marianne , Løbersli Inger , Urdahl Anne Margrete , Kapperud Georg 
Published: April 2012

ABSTRACTA previous national survey ofEscherichia coliin Norwegian sheep detectedeae-positive (eae+)E. coliO26:H11 isolates in 16.3% (80/491) of the flocks. The purpose of the present study was to evaluate the human-pathogenic potential of these ovine isolates by comparing them withE. coliO26 isolates from humans infected in Norway. All humanE. coliO26 isolates studied carried theeaegene and shared flagellar type H11. Two-thirds of the sheep flocks and 95.1% of the patients harbored isolates containingarcAallele type 2 andespKand were classified as enterohemorrhagicE. coli(EHEC) (stxpositive) or EHEC-like (stxnegative). These isolates were further divided into group A (EspK2 positive), associated withstx2-EDL933andstcEO103, and group B (EspK1 positive), associated withstx1a. Although thestxgenes were more frequently present in isolates from patients (46.3%) than in those from sheep flocks (5%), more than half of the ovine isolates in the EHEC/EHEC-like group had multiple-locus variable number of tandem repeat analysis (MLVA) profiles that were identical to those seen instx-positive human O26:H11 isolates. This indicates that EHEC-like ovine isolates may be able to acquirestx-carrying bacteriophages and thereby have the possibility to cause serious illness in humans. The remaining one-third of the sheep flocks and two of the patients had isolates fulfilling the criteria for atypical enteropathogenicE. coli(aEPEC):arcAallele type 1 andespKnegative (group C). The majority of these ovine isolates showed MLVA profiles not previously seen inE. coliO26:H11 isolates from humans. However, according to their virulence gene profile, the aEPEC ovine isolates should be considered potentially pathogenic for humans. In conclusion, sheep are an important reservoir of human-pathogenicE. coliO26:H11 isolates in Norway.
Distribution of Monoclonal Antibody Subgroups and Sequence-Based Types among Legionella pneumophila Serogroup 1 Isolates Derived from Cooling Tower Water, Bathwater, and Soil in Japan
Authors: Amemura-Maekawa Junko , Kikukawa Kiyomi , Helbig Jürgen H. , Kaneko Satoko , Suzuki-Hashimoto Atsuko , Furuhata Katsunori , Chang Bin , Murai Miyo , Ichinose Masayuki , Ohnishi Makoto , Kura Fumiaki ,   and the Working Group for Legionella in Japan
Published: April 2012

ABSTRACT

Legionella pneumophila
serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of
L. pneumophila
SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW;
n
= 50), cooling tower water (CT;
n
= 50), and soil (SO;
n
= 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat.
Catalytic Efficiency Diversification of Duplicate β-1,3-1,4-Glucanases from Neocallimastix patriciarum J11
Authors: Hung Yu-Lung , Chen Hui-Jye , Liu Jeng-Chen , Chen Yo-Chia 
Published: April 2012

ABSTRACT

Four types of β-1,3-1,4 glucanase (β-glucanase, EC 3.2.1.73) genes, designated
bglA13
,
bglA16
,
bglA51
, and
bglM2
, were found in the cDNA library of
Neocallimastix patriciarum
J11. All were highly homologous with each other and demonstrated a close phylogenetic relationship with and a similar codon bias to
Streptococcus equinus
. The presence of expansion and several predicted secondary structures in the 3′ untranslated regions (3′UTRs) of
bglA16
and
bglM2
suggest that these two genes were duplicated recently, whereas
bglA13
and
bglA16
, which contain very short 3′UTRs, were replicated earlier. These findings indicate that the β-glucanase genes from
N. patriciarum
J11 may have arisen by horizontal transfer from the bacterium and subsequent duplication in the rumen fungus. β-Glucanase genes of
Streptococcus equinus
,
Ruminococcus albus
7, and
N. patriciarum
J11 were cloned and expressed by
Escherichia coli
. The recombinant β-glucanases cloned from
S. equinus
,
R. albus
7, and
N. patriciarum
J11 were endo-acting and had similar substrate specificity, but they demonstrated different properties in other tests. The specific activities and catalytic efficiency of the bacterial β-glucanases were also significantly lower than those of the fungal β-glucanases. Our results also revealed that the activities and some characteristics of enzymes were changed during the horizontal gene transfer event. The specific activities of the fungal β-glucanases ranged from 26,529 to 41,209 U/mg of protein when barley-derived β-glucan was used as the substrate. They also demonstrated similar pH and temperature optima, substrate specificity, substrate affinity, and hydrolysis patterns. Nevertheless, BglA16 and BglM2, two recently duplicated β-glucanases, showed much higher
k
cat
values than others. These results support the notion that duplicated β-glucanase genes, namely,
bglA16
and
bglM2
, increase the reaction efficiency of β-glucanases and suggest that the catalytic efficiency of β-glucanase is likely to be a criterion determining the evolutionary fate of duplicate forms in
N. patriciarum
J11.
Colonization by Pneumocystis jirovecii and Its Role in Disease
Authors: Morris Alison , Norris Karen A. 
Published: April 2012

SUMMARYAlthough the incidence ofPneumocystispneumonia (PCP) has decreased since the introduction of combination antiretroviral therapy, it remains an important cause of disease in both HIV-infected and non-HIV-infected immunosuppressed populations. The epidemiology of PCP has shifted over the course of the HIV epidemic both from changes in HIV and PCP treatment and prevention and from changes in critical care medicine. Although less common in non-HIV-infected immunosuppressed patients, PCP is now more frequently seen due to the increasing numbers of organ transplants and development of novel immunotherapies. New diagnostic and treatment modalities are under investigation. The immune response is critical in preventing this disease but also results in lung damage, and future work may offer potential areas for vaccine development or immunomodulatory therapy. Colonization withPneumocystisis an area of increasing clinical and research interest and may be important in development of lung diseases such as chronic obstructive pulmonary disease. In this review, we discuss current clinical and research topics in the study ofPneumocystisand highlight areas for future research.
Infection Barriers to Successful Xenotransplantation Focusing on Porcine Endogenous Retroviruses
Authors: Denner Joachim , Tönjes Ralf R. 
Published: April 2012

SUMMARY
Xenotransplantation may be a solution to overcome the shortage of organs for the treatment of patients with organ failure, but it may be associated with the transmission of porcine microorganisms and the development of xenozoonoses. Whereas most microorganisms may be eliminated by pathogen-free breeding of the donor animals, porcine endogenous retroviruses (PERVs) cannot be eliminated, since these are integrated into the genomes of all pigs. Human-tropic PERV-A and -B are present in all pigs and are able to infect human cells. Infection of ecotropic PERV-C is limited to pig cells. PERVs may adapt to host cells by varying the number of LTR-binding transcription factor binding sites. Like all retroviruses, they may induce tumors and/or immunodeficiencies. To date, all experimental, preclinical, and clinical xenotransplantations using pig cells, tissues, and organs have not shown transmission of PERV. Highly sensitive and specific methods have been developed to analyze the PERV status of donor pigs and to monitor recipients for PERV infection. Strategies have been developed to prevent PERV transmission, including selection of PERV-C-negative, low-producer pigs, generation of an effective vaccine, selection of effective antiretrovirals, and generation of animals transgenic for a PERV-specific short hairpin RNA inhibiting PERV expression by RNA interference.
Genome Sequence of Amycolatopsis sp. Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete
Authors: Davis Jennifer R. , Goodwin Lynne A. , Woyke Tanja , Teshima Hazuki , Bruce David , Detter Chris , Tapia Roxanne , Han Shunsheng , Han James , Pitluck Sam , Nolan Matt , Mikhailova Natalia , Land Miriam L. , Sello Jason K. 
Published: April 2012

ABSTRACT

We announce the availability of a high-quality draft of the genome sequence of
Amycolatopsis
sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.
Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil
Authors: Lü Zhe , Lu Yahai 
Published: April 2012

ABSTRACT

Members of the order
Methanocellales
play a key role in methane emissions in paddy fields. Because of their slow growth and fastidious culture conditions, pure cultures are difficult to isolate and have been unavailable until recently. Here we report the complete genome sequence of a novel isolate in this group,
Methanocella conradii
strain HZ254.
Draft Genome Sequences of Helicobacter pylori Strains 17874 and P79
Authors: Clancy Ceara D. , Forde Brian M. , Moore Stanley A. , O'Toole Paul W. 
Published: April 2012

ABSTRACT

Helicobacter pylori
is a human pathogen that colonizes the human gastric mucosa, causing gastritis, duodenal and gastric ulcers, and gastric carcinoma. Here we announce the draft genomes of
H. pylori
strain 17874, commonly used for studying motility, and P79, a strain for which plasmid vectors have been developed.
Katabatic Flows and Their Relation to the Formation of Convective Clouds—Idealized Case Studies
Authors: Trachte Katja , Bendix Joerg 
Published: April 2012

AbstractThe formation of a convective cloud system as a result of a katabatic-induced surface cold front at the eastern Andes Mountains of South America was investigated in a numerical model study. The occurrence of this cloud system is hypothesized to be a consequence of converging cold-air drainage from slopes and valleys resulting from the concave shape of the terrain. Simplified terrain configurations were applied to three different atmospheric experiments to determine the influence of the terrain and the ambient stratification on the underlying processes. The simulation demonstrated the occurrence of a convective cloud, but not in every simulation. The initial stable stratification experiment did not initiate convective activity. Further analysis of the development of the convective cells confirmed the terrain’s impact, but it also showed a dependence on atmospheric conditions. The katabatic flows and the surface fluxes from which they are induced are sensitive to the ambient stratification, which was seen when only a weak cold front developed in response to a decrease in the surface inversion and the downslope velocity. On the basis of specific characteristics of katabatic flows and the heat-exchange budget, the presence of these flows and their significance as the driving force behind the cloud-formation process were confirmed.
Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations
Authors: Muller Caroline J. , Held Isaac M. 
Published: April 2012

Abstract
In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.
The authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.
The sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback.
An Improved Dynamical Downscaling Method with GCM Bias Corrections and Its Validation with 30 Years of Climate Simulations
Authors: Xu Zhongfeng , Yang Zong-Liang 
Published: April 2012

Abstract
An improved dynamical downscaling method (IDD) with general circulation model (GCM) bias corrections is developed and assessed over North America. A set of regional climate simulations is performed with the Weather Research and Forecasting Model (WRF) version 3.3 embedded in the National Center for Atmospheric Research's (NCAR's) Community Atmosphere Model (CAM). The GCM climatological means and the amplitudes of interannual variations are adjusted based on the National Centers for Environmental Prediction (NCEP)–NCAR global reanalysis products (NNRP) before using them to drive WRF. In this study, the WRF downscaling experiments are identical except the initial and lateral boundary conditions derived from the NNRP, original GCM output, and bias-corrected GCM output, respectively. The analysis finds that the IDD greatly improves the downscaled climate in both climatological means and extreme events relative to the traditional dynamical downscaling approach (TDD). The errors of downscaled climatological mean air temperature, geopotential height, wind vector, moisture, and precipitation are greatly reduced when the GCM bias corrections are applied. In the meantime, IDD also improves the downscaled extreme events characterized by the reduced errors in 2-yr return levels of surface air temperature and precipitation. In comparison with TDD, IDD is also able to produce a more realistic probability distribution in summer daily maximum temperature over the central U.S.–Canada region as well as in summer and winter daily precipitation over the middle and eastern United States.
An Inversion of Acoustical Attenuation Measurements to Deduce Bubble Populations
Authors: Czerski H. 
Published: April 2012

Abstract
Measurement of natural bubble populations is required for many areas of ocean science. Acoustical methods have considerable potential for achieving this goal because bubbles scatter sound strongly close to their natural frequency, which depends largely on the bubble radius. The principle of using bulk acoustical attenuation caused by a bubble population to infer the number and size of bubbles present is well established, and appropriate methods for measuring broadband acoustical attenuation are also well developed. However, the numerical methods currently used to invert the acoustical attenuation to get the bubble size distribution are complex and time consuming. In this paper, a method for the inversion is presented that uses the physics of bubble resonance to restructure the problem so that it can be accurately carried out using a simple matrix inversion. This inversion method produces results that are correct to within a few percent over two orders of magnitude of bubble size. The most significant remaining issue for acoustical bubble measurement is the potential presence of bubbles that are resonant outside the measurement frequency range. The mathematical structure outlined here considerably simplifies the investigation of this problem, and calculations are presented that show this effect to be minor in many cases.