bluuebunny/crossref_metadata_2025_split huggingface dataset:
INDIVIDUAL‐BASED MODELS AND THE MANAGEMENT OF SHOREBIRD POPULATIONS
Authors: GOSS‐CUSTARD JOHN D. , STILLMAN RICHARD A. 
Published: August 2010

AbstractIndividual‐based models (IBMs) predict how animal populations will be affected by changes in their environment by modeling the responses of fitness‐maximizing individuals to environmental change and by calculating how their aggregate responses change the average fitness of individuals and thus the demographic rates, and therefore size of the population. This paper describes how the need to develop a new approach to make such predictions was identified in the mid‐1970s following work done to predict the effect of building a freshwater reservoir on part of the intertidal feeding areas of the shorebirds Charadrii that overwinter on the Wash, a large embayment on the east coast of England. The paper describes how the approach was developed and tested over 20 years (1976–1995) on a population of European oystercatchersHaematopus ostraleguseating musselsMytilus edulison the Exe estuary in Devon, England.The paper goes on to describe how individual‐based modeling has been applied over the last 10 years to a wide range of environmental issues and to many species of shorebirds and wildfowl in a number of European countries. Although it took 20 years to develop the approach for 1 bird species on 1 estuary, ways have been found by which it can now be applied quite rapidly to a wide range of species, at spatial scales ranging from 1 estuary to the whole continent of Europe. This can now be done within the time period typically allotted to environmental impact assessments involving coastal bird populations in Europe.The models are being used routinely to predict the impact on the fitness of coastal shorebirds and wildfowl of habitat loss from (i) development, such as building a port over intertidal flats; (ii) disturbance from people, raptors, and aircraft; (iii) harvesting shellfish; and (iv) climate change and any associated rise in sea level. The model has also been used to evaluate the probable effectiveness of mitigation measures aimed at ameliorating the impact of such environmental changes on the birds. The first steps are now being taken to extend the approach to diving sea ducks and farmland birds during the nonbreeding season.The models have been successful in predicting the observed behavior and mortality rates in winter of shorebirds on a number of European estuaries, and some of the most important of these tests are described. These successful tests of model predictions raise confidence that the model can be used to advise policy makers concerned with the management of the coast and its important bird populations.
Variation in pH Optima of Hydrolytic Enzyme Activities in Tropical Rain Forest Soils
Authors: Turner Benjamin L. 
Published: August 2010

ABSTRACT

Extracellular enzymes synthesized by soil microbes play a central role in the biogeochemical cycling of nutrients in the environment. The pH optima of eight hydrolytic enzymes involved in the cycles of carbon, nitrogen, phosphorus, and sulfur, were assessed in a series of tropical forest soils of contrasting pH values from the Republic of Panama. Assays were conducted using 4-methylumbelliferone-linked fluorogenic substrates in modified universal buffer. Optimum pH values differed markedly among enzymes and soils. Enzymes were grouped into three classes based on their pH optima: (i) enzymes with acidic pH optima that were consistent among soils (cellobiohydrolase, β-xylanase, and arylsulfatase), (ii) enzymes with acidic pH optima that varied systematically with soil pH, with the most acidic pH optima in the most acidic soils (α-glucosidase, β-glucosidase, and
N
-acetyl-β-glucosaminidase), and (iii) enzymes with an optimum pH in either the acid range or the alkaline range depending on soil pH (phosphomonoesterase and phosphodiesterase). The optimum pH values of phosphomonoesterase were consistent among soils, being 4 to 5 for acid phosphomonoesterase and 10 to 11 for alkaline phosphomonoesterase. In contrast, the optimum pH for phosphodiesterase activity varied systematically with soil pH, with the most acidic pH optima (3.0) in the most acidic soils and the most alkaline pH optima (pH 10) in near-neutral soils. Arylsulfatase activity had a very acidic optimum pH in all soils (pH ≤3.0) irrespective of soil pH. The differences in pH optima may be linked to the origins of the enzymes and/or the degree of stabilization on solid surfaces. The results have important implications for the interpretation of hydrolytic enzyme assays using fluorogenic substrates.
Development and Application of a New Method for Specific and Sensitive Enumeration of Spores of Nonproteolytic
Clostridium botulinum
Types B, E, and F in Foods and Food Materials
Authors: Peck Michael W. , Plowman June , Aldus Clare F. , Wyatt Gary M. , Penaloza Izurieta Walter , Stringer Sandra C. , Barker Gary C. 
Published: August 2010

ABSTRACT

The highly potent botulinum neurotoxins are responsible for botulism, a severe neuroparalytic disease. Strains of nonproteolytic
Clostridium botulinum
form neurotoxins of types B, E, and F and are the main hazard associated with minimally heated refrigerated foods. Recent developments in quantitative microbiological risk assessment (QMRA) and food safety objectives (FSO) have made food safety more quantitative and include, as inputs, probability distributions for the contamination of food materials and foods. A new method that combines a selective enrichment culture with multiplex PCR has been developed and validated to enumerate specifically the spores of nonproteolytic
C. botulinum
. Key features of this new method include the following: (i) it is specific for nonproteolytic
C. botulinum
(and does not detect proteolytic
C. botulinum
), (ii) the detection limit has been determined for each food tested (using carefully structured control samples), and (iii) a low detection limit has been achieved by the use of selective enrichment and large test samples. The method has been used to enumerate spores of nonproteolytic
C. botulinum
in 637 samples of 19 food materials included in pasta-based minimally heated refrigerated foods and in 7 complete foods. A total of 32 samples (5 egg pastas and 27 scallops) contained spores of nonproteolytic
C. botulinum
type B or F. The majority of samples contained <100 spores/kg, but one sample of scallops contained 444 spores/kg. Nonproteolytic
C. botulinum
type E was not detected. Importantly, for QMRA and FSO, the construction of probability distributions will enable the frequency of packs containing particular levels of contamination to be determined.
Correlation of Particular Bacterial PCR-Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits
Authors: Hernandez-Sanabria Emma , Guan Le Luo , Goonewardene Laksiri A. , Li Meiju , Mujibi Denis F. , Stothard Paul , Moore Stephen S. , Leon-Quintero Monica C. 
Published: August 2010

ABSTRACTThe influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P< 0.05) and tended to have higher concentration in inefficient animals (P= 0.10), while isovalerate was associated with residual feed intake (P< 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.
Site-Directed Mutagenesis of the
Anabaena
sp. Strain PCC 7120 Nitrogenase Active Site To Increase Photobiological Hydrogen Production
Authors: Masukawa Hajime , Inoue Kazuhito , Sakurai Hidehiro , Wolk C. Peter , Hausinger Robert P. 
Published: August 2010

ABSTRACT

Cyanobacteria use sunlight and water to produce hydrogen gas (H
2
), which is potentially useful as a clean and renewable biofuel. Photobiological H
2
arises primarily as an inevitable by-product of N
2
fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In
Anabaena
sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H
2
production by this strain, six nitrogenase amino acid residues predicted to reside within 5 Å of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N
2
. Most of the 49 variants examined were deficient in N
2
-fixing growth and exhibited decreases in their
in vivo
rates of acetylene reduction. Of greater interest, several variants examined under an N
2
atmosphere significantly increased their
in vivo
rates of H
2
production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H
2
compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H
2
in an aerobic, nitrogen-containing environment.
Optimization of Protease Secretion in
Bacillus subtilis
and
Bacillus licheniformis
by Screening of Homologous and Heterologous Signal Peptides
Authors: Degering Christian , Eggert Thorsten , Puls Michael , Bongaerts Johannes , Evers Stefan , Maurer Karl-Heinz , Jaeger Karl-Erich 
Published: August 2010

ABSTRACT

Bacillus subtilis
and
Bacillus licheniformis
are widely used for the large-scale industrial production of proteins. These strains can efficiently secrete proteins into the culture medium using the general secretion (Sec) pathway. A characteristic feature of all secreted proteins is their N-terminal signal peptides, which are recognized by the secretion machinery. Here, we have studied the production of an industrially important secreted protease, namely, subtilisin BPN′ from
Bacillus amyloliquefaciens
. One hundred seventy-three signal peptides originating from
B. subtilis
and 220 signal peptides from the
B. licheniformis
type strain were fused to this secretion target and expressed in
B. subtilis
, and the resulting library was analyzed by high-throughput screening for extracellular proteolytic activity. We have identified a number of signal peptides originating from both organisms which produced significantly increased yield of the secreted protease. Interestingly, we observed that levels of extracellular protease were improved not only in
B. subtilis
, which was used as the screening host, but also in two different
B. licheniformis
strains. To date, it is impossible to predict which signal peptide will result in better secretion and thus an improved yield of a given extracellular target protein. Our data show that screening a library consisting of homologous and heterologous signal peptides fused to a target protein can identify more-effective signal peptides, resulting in improved protein export not only in the original screening host but also in different production strains.
Deletion of Genes Encoding Cytochrome Oxidases and Quinol Monooxygenase Blocks the Aerobic-Anaerobic Shift in
Escherichia coli
K-12 MG1655
Authors: Portnoy Vasiliy A. , Scott David A. , Lewis Nathan E. , Tarasova Yekaterina , Osterman Andrei L. , Palsson Bernhard Ø. 
Published: August 2010

ABSTRACT

The constitutive activation of the anoxic redox control transcriptional regulator (ArcA) in
Escherichia coli
during aerobic growth, with the consequent production of a strain that exhibits anaerobic physiology even in the presence of air, is reported in this work. Removal of three terminal cytochrome oxidase genes (
cydAB
,
cyoABCD
, and
cbdAB
) and a quinol monooxygenase gene (
ygiN
) from the
E. coli
K-12 MG1655 genome resulted in the activation of ArcA aerobically. These mutations resulted in reduction of the oxygen uptake rate by nearly 98% and production of
d
-lactate as a sole by-product under oxic and anoxic conditions. The knockout strain exhibited nearly identical physiological behaviors under both conditions, suggesting that the mutations resulted in significant metabolic and regulatory perturbations. In order to fully understand the physiology of this mutant and to identify underlying metabolic and regulatory reasons that prevent the transition from an aerobic to an anaerobic phenotype, we utilized whole-genome transcriptome analysis,
13
C tracing experiments, and physiological characterization. Our analysis showed that the deletions resulted in the activation of anaerobic respiration under oxic conditions and a consequential shift in the content of the quinone pool from ubiquinones to menaquinones. An increase in menaquinone concentration resulted in the activation of ArcA. The activation of the ArcB/ArcA regulatory system led to a major shift in the metabolic flux distribution through the central metabolism of the mutant strain. Flux analysis indicated that the mutant strain had undetectable fluxes around the tricarboxylic acid (TCA) cycle and elevated flux through glycolysis and anaplerotic input to oxaloacetate. Flux and transcriptomics data were highly correlated and showed similar patterns.
Bar-Coded Pyrosequencing of 16S rRNA Gene Amplicons Reveals Changes in Ileal Porcine Bacterial Communities Due to High Dietary Zinc Intake
Authors: Vahjen W. , Pieper R. , Zentek J. 
Published: August 2010

ABSTRACT

Feeding high levels of zinc oxide to piglets significantly increased the relative abundance of ileal
Weissella
spp.,
Leuconostoc
spp., and
Streptococcus
spp., reduced the occurrence of
Sarcina
spp. and
Neisseria
spp., and led to numerical increases of all Gram-negative facultative anaerobic genera. High dietary zinc oxide intake has a major impact on the porcine ileal bacterial composition.
Patient safety incidents associated with tracheostomies occurring in hospital wards: a review of reports to the UK National Patient Safety Agency
Authors: McGrath B A , Thomas A N 
Published: August 2010

Abstract

Background
Tracheostomies are increasingly common in hospital wards due to the rising use of percutaneous and surgical tracheostomies in critical care and bed pressures in these units. Hospital wards may lack appropriate infrastructure to care for this vulnerable group and significant patient harm may result.

Objectives
To identify and analyse tracheostomy related incident reports from hospital wards between 1 October 2005 and 30 September 2007, and to make recommendations to improve patient safety based on the recurrent themes identified. The study was performed between August 2008 and August 2009.

Methods
968 tracheostomy related critical incidents reported to the National Patient Safety Agency over the 2 year period, identified by key letter searches, were analysed. Incidents were categorised to identify common themes, and root cause analysis attempted where possible.

Results
In the 453 incidents where patients were directly affected, 338 (75%) were associated with some identifiable patient harm, of which 83 (18%) were associated with more than temporary harm. In 29 incidents (6%) some intervention was required to maintain life, and in 15 cases the incident may have contributed to the patient’s death. Equipment was involved in 176 incidents and 276 incidents involved tracheostomies becoming blocked or displaced.

Conclusions
By identifying and analysing themes in incident reports associated with tracheostomies, recommendations can be made to improve safety for this group of patients. These recommendations include improvements in infrastructure, competency and training, equipment provision, and in communication.
Tobacco smoking in seven Latin American cities: the CARMELA study
Authors: Champagne B M , Sebrié E M , Schargrodsky H , Pramparo P , Boissonnet C , Wilson E 
Published: August 2010

ObjectiveThis study aimed to explore tobacco smoking in seven major cities of Latin America.MethodsThe Cardiovascular Risk Factor Multiple Evaluation in Latin America (CARMELA) study is a cross-sectional epidemiological study of 11 550 adults between 25 and 64 years old in Barquisimeto, Venezuela; Bogota, Colombia; Buenos Aires, Argentina; Lima, Peru; Mexico City, Mexico; Quito, Ecuador; and Santiago, Chile. Tobacco smoking, including cigarettes, cigars and pipes, was surveyed among other cardiovascular risk factors.ResultsSantiago and Buenos Aires had the highest smoking prevalence (45.4% and 38.6%, respectively); male and female rates were similar. In other cities, men smoked more than women, most markedly in Quito (49.4% of men vs 10.5% of women). Peak male smoking prevalence occurred among the youngest two age groups (25–34 and 35–44 years old). Men and women of Buenos Aires smoked the highest number of cigarettes per day on average (15.7 and 12.4, respectively). Men initiated regular smoking earlier than women in each city (ranges 13.7–20.0 years vs 14.2–21.1 years, respectively). Exposure to secondhand tobacco smoke at workplace for more than 5 h per day was higher in Barquisimeto (28.7%), Buenos Aires (26.8%) and Santiago (21.5%). The highest prevalence of former smokers was found among men in Buenos Aires, Santiago and Lima (30.0%, 26.8% and 26.0% respectively).ConclusionsSmoking prevalence was high in the seven CARMELA cities, although patterns of smoking varied among cities. A major health and economic burden is inevitable in urban Latin America unless effective comprehensive tobacco control measures recommended by the World Health Organisation Framework Convention on Tobacco Control are implemented.
CAV1 Inhibits Metastatic Potential in Melanomas through Suppression of the Integrin/Src/FAK Signaling Pathway
Authors: Trimmer Casey , Whitaker-Menezes Diana , Bonuccelli Gloria , Milliman Janet N. , Daumer Kristin M. , Aplin Andrew E. , Pestell Richard G. , Sotgia Federica , Lisanti Michael P. , Capozza Franco 
Published: August 2010

Abstract
Caveolin-1 (CAV1) is the main structural component of caveolae, which are plasma membrane invaginations that participate in vesicular trafficking and signal transduction events. Although evidence describing the function of CAV1 in several cancer types has recently accumulated, its role in melanoma tumor formation and progression remains poorly explored. Here, by using B16F10 melanoma cells as an experimental system, we directly explore the function of CAV1 in melanoma tumor growth and metastasis. We first show that CAV1 expression promotes proliferation, whereas it suppresses migration and invasion of B16F10 cells in vitro. When orthotopically implanted in the skin of mice, B16F10 cells expressing CAV1 form tumors that are similar in size to their control counterparts. An experimental metastasis assay shows that CAV1 expression suppresses the ability of B16F10 cells to form lung metastases in C57Bl/6 syngeneic mice. Additionally, CAV1 protein and mRNA levels are found to be significantly reduced in human metastatic melanoma cell lines and human tissue from metastatic lesions. Finally, we show that following integrin activation, B16F10 cells expressing CAV1 display reduced expression levels and activity of FAK and Src proteins. Furthermore, CAV1 expression markedly reduces the expression of integrin β3 in B16F10 melanoma cells. In summary, our findings provide experimental evidence that CAV1 may function as an antimetastatic gene in malignant melanoma. Cancer Res; 70(19); 7489–99. ©2010 AACR.
GP369, an FGFR2-IIIb–Specific Antibody, Exhibits Potent Antitumor Activity against Human Cancers Driven by Activated FGFR2 Signaling
Authors: Bai Ailin , Meetze Kristan , Vo Nhi Y. , Kollipara Sriram , Mazsa Elizabeth K. , Winston William M. , Weiler Solly , Poling Laura L. , Chen Ting , Ismail Nesreen S. , Jiang Jinwei , Lerner Lorena , Gyuris Jeno , Weng Zhigang 
Published: August 2010

Abstract
Dysregulated fibroblast growth factor (FGF) signaling has been implicated in the pathogenesis of human cancers. Aberrant activation of FGF receptor 2 (FGFR2) signaling, through overexpression of FGFR2 and/or its ligands, mutations, and receptor amplification, has been found in a variety of human tumors. We generated monoclonal antibodies against the extracellular ligand-binding domain of FGFR2 to address the role of FGFR2 in tumorigenesis and to explore the potential of FGFR2 as a novel therapeutic target. We surveyed a broad panel of human cancer cell lines for the dysregulation of FGFR2 signaling and discovered that breast and gastric cancer cell lines harboring FGFR2 amplification predominantly express the IIIb isoform of the receptor. Therefore, we used an FGFR2-IIIb–specific antibody, GP369, to investigate the importance of FGFR2 signaling in vitro and in vivo. GP369 specifically and potently suppressed ligand-induced phosphorylation of FGFR2-IIIb and downstream signaling, as well as FGFR2-driven proliferation in vitro. The administration of GP369 in mice significantly inhibited the growth of human cancer xenografts harboring activated FGFR2 signaling. Our findings support the hypothesis that dysregulated FGFR2 signaling is one of the critical oncogenic pathways involved in the initiation and/or maintenance of tumors. Cancer patients with aberrantly activated/amplified FGFR2 signaling could potentially benefit from therapeutic intervention with FGFR2-targeting antibodies. Cancer Res; 70(19); 7630–9. ©2010 AACR.
Reading the Panarion as Collective Biography: The Heresiarch as Unholy Man
Authors: Kim Young Richard 
Published: August 2010

AbstractThis article proposes a reading of the Panarion, a fourth-century heresiology, as a collective biography, a genre that compiled shortened biographical snapshots of prominent individuals who together embodied an idealized way of life. Epiphanius, the defender and model of orthodoxy, augmented his power and authority through his writing and heresy-hunting activities. The Panarion included miniature biographies of heresiarchs in many of the entries, and together these biographies constructed the composite image and character of the heresiarch and collectively portrayed the unholy life.
Faces of China: New Chinese Migrants in South Africa, 1980s to Present
Authors: Huynh Tu T. , Jung Park Yoon , Ying Chen Anna 
Published: August 2010

Abstract
Contrary to media arguments that Chinese migration to Africa is part of a Chinese state project, the vast majority of new Chinese migrants in South Africa arrived (or made decisions to stay) independently, motivated by their desires to improve their lives. Newer Chinese migrants tend to follow paths cut by those who came earlier; some of these earlier migrants from the PRC came with Taiwanese businesses or state-owned enterprises. Today’s Chinese migrants are quite diverse: they come from various parts of China, with different levels of education and experience, and from different class backgrounds. Migration processes and migration successes are linked to sending country, receiving country and global conditions; however, Chinese migrants themselves play an integral role in shaping perceptions, constructing new identities and changing spaces, giving substance to the idea of a “global south”.