bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of the scientific literature into the Semantic Web: Facts from biomedical data resources
Authors: Rebholz Dietrich , Croset Samuel , Grabmueller Christoph 
Published: March 2012

AbstractScientific literature is the primary resource for relevant and innovative information. The integration of the literature with other data resources in the biomedical research community generates overhead that can be avoided through the used of Semantic Web Technology generating openly accessible data. Projects such as SESL and CALBC have producted significant amount of data that that are ready for exploitation.The tutorial will teach different approaches on how to integrate the scientific literature with the content from biomedical databases, and will discuss the inferences that can be achieved. Furthermore, the tutorial will point to the resources that are ready for use and enable integration of the literature at your discretion. A good understanding of Semantic Web technology, ontologies, OWL and the existing biomedical data resources is advantageous to easily follow the tutorial.
Hypogonadism Secondary to Hyperprolactinaemia: Successful Treatment but Adverse Consequences
Authors: Narayanan R. , Bujawansa S. , Qureshi Z. , Rimmer M. , Heald A. 
Published: March 2012

AbstractIt is accepted that care must be taken in initiating testosterone replacement in hypogonadal individuals with historically low androgen levels. However less is reported about the influence of restoration of normal endogenous testosterone production on behaviour.Here we report how the adverse sequelae of successful treatment of hypogonadism secondary to hyperprolactinaemia, manifesting as irritability and low threshold to aggression, were managed through a joint approach between psychiatrist and physician.
Global change and the origins of agriculture.
Authors: Ferrio J. P. , Voltas J. , Araus J. L. 
Published: March 2012

Abstract

This chapter provides an overview of the various approaches to investigating the role of climate in the origins of agriculture, as well as the effects of ancient agriculture on the environment. The role of climate in the development of agriculture in the Near East, and human-induced environmental impact and sustainability of early Mediterranean agriculture are covered.
Global change challenges for horticultural systems.
Authors: Ramos C. , Intrigliolo D. S. , Thompson R. B. 
Published: March 2012

Abstract

This chapter discusses the challenges in the horticulture industry brought about by climate and global change. Research on the effects of the expected changes in temperature, atmospheric carbon dioxide, and water availability on the yield and quality of horticultural crops (vegetables, fruit trees and vines) is summarized. The likely effects of these changes on the N dynamics in the plant-soil system, and the available options to mitigate and adapt to these impacts through water and N fertilizer management are covered.
The impact of high CO2 on plant abiotic stress tolerance.
Authors: Lopes M. S. , Foyer C. H. 
Published: March 2012

Abstract

This chapter reviews the state-of-the-art and current concepts regarding plant responses to elevated CO2, particularly in terms of whole-plant morphology, molecular physiology and development. It is generally accepted that high temperatures have a severe negative effect on grain quality, and this will probably be exacerbated by elevated CO2 levels. The predicted increases in the temperature of the earth, together with the increased likelihood of heat stress, may serve to reverse the positive effects of elevated CO2 on photosynthesis and plant growth, particularly in C3 species. Plant breeding strategies must therefore incorporate marker-assisted selection with genes that confer improved thermo-tolerance in order to address the growing problem of heat stress and its likely negative impacts on food security and grain quality.
STEC O157 in the beef chain - risk assessment and management.
Authors: Nastasijevic I. 
Published: March 2012

Abstract

Since the early 1980s,
Escherichia coli
O157 has emerged as one of the most significant pathogens of public health relevance not because of the incidence of the illness, which is much lower than that of other food-borne pathogens such as
Campylobacter
or
Salmonella
, but because of the severity of the symptoms, the low infectious dose and potential sequelae. Shigatoxin-producing
E. coli
(STEC) is a human pathogen that can cause haemorrhagic colitis (HC; bloody diarrhoea). This can also develop into haemolytic uraemic syndrome (HUS), a life-threatening disease that causes kidney damage. Cattle carry mixtures of O157 and non-O157 STEC in their intestines which are not necessarily pathogenic to humans. The O157 STEC serogroup was until recently responsible for the majority of disease outbreaks reported for STECs in North America. However, now the non-O157 STECs account for almost 50% of the reported human disease outbreaks in North America and Europe. Most available information relates to serotype O157:H7, since it is easily differentiated biochemically from other
E. coli
strains. The O157 STECs are shed at significant levels by healthy/asymptomatic cattle, e.g. cattle with jejunal haemorrhage syndrome (JHS). The shedding leads to contamination of the farm environment. This may lead to direct or indirect contamination of cattle hides, which, in turn, can serve as the main source of carcass contamination during slaughter and dressing of cattle at abattoirs or contamination of fresh beef and beef products. A science-based risk assessment is needed to assess the public health impact, the consumer exposure to the pathogen and to propose possible control strategies. In contrast, risk management should include selection of the most effective control measures, for prevention and reduction of the transmission of beef-borne O157 and non-O157 STECs. Since relatively limited STEC reduction was achieved by applying only one control measure (e.g. decontamination treatments of hides/carcasses and/or adequate cooking), a coordinated, targeted and effective application of control measures at multiple points along the beef chain is necessary. Such an integrated approach has a greater potential to manage the risk of beef-borne STEC infections and it should be based upon: on-farm controls, transport-livestock market-lairage controls, slaughter-dressing controls, chilling-processing-retail controls and controls at the catering-consumer level.
A Rediscovered Friendship in the Republic of Letters: The Unpublished Correspondence of Arcangela Tarabotti and Ismaël Boulliau*
Authors: Westwater Lynn Lara 
Published: March 2012

AbstractThe correspondence between the radical Venetian pro-female polemicist and nun Arcangela Tarabotti (1604–52) and the Copernican French astronomer Ismaël Boulliau (1605–94) — here published for the first time — shows how one of Tarabotti's most controversial works made it to press. She had long and unsuccessfully sought in Italy and in France to print the work, which was, puzzlingly, published two years after her death in Holland. It was subsequently placed on the Index of Forbidden Books. Charting the explosive work's journey to France and its later arrival and reception in Holland, the Tarabotti-Boulliau correspondence provides a case study in the circulation of unorthodox ideas in seventeenth-century Europe. By showing Tarabotti's firm inscription in the well-connected scientist's intellectual circle, the letter exchange furthermore contributes to our expanding notions of women's participation in the Republic of Letters, while also suggesting a confluence of radical scientific and social views.
Fast stochastic algorithm for simulating evolutionary population dynamics
Authors: Mather William H. , Hasty Jeff , Tsimring Lev S. 
Published: March 2012

Abstract
Motivation: Many important aspects of evolutionary dynamics can only be addressed through simulations. However, accurate simulations of realistically large populations over long periods of time needed for evolution to proceed are computationally expensive. Mutants can be present in very small numbers and yet (if they are more fit than others) be the key part of the evolutionary process. This leads to significant stochasticity that needs to be accounted for. Different evolutionary events occur at very different time scales: mutations are typically much rarer than reproduction and deaths.
Results: We introduce a new exact algorithm for fast fully stochastic simulations of evolutionary dynamics that include birth, death and mutation events. It produces a significant speedup compared to direct stochastic simulations in a typical case when the population size is large and the mutation rates are much smaller than birth and death rates. The algorithm performance is illustrated by several examples that include evolution on a smooth and rugged fitness landscape. We also show how this algorithm can be adapted for approximate simulations of more complex evolutionary problems and illustrate it by simulations of a stochastic competitive growth model.
Contact: ltsimring@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of three Xanthomonas axonopodis pv. citri effector proteins in pathogenicity and their interactions with host plant proteins
Authors: DUNGER GERMÁN , GAROFALO CECILIA G. , GOTTIG NATALIA , GARAVAGLIA BETIANA S. , ROSA MARÍA C. PEREDA , FARAH CHUCK S. , ORELLANO ELENA G. , OTTADO JORGELINA 
Published: March 2012

SUMMARYXanthomonas axonopodis pv. citri, the bacterium responsible for citrus canker, uses effector proteins secreted by a type III protein secretion system to colonize its hosts. Among the putative effector proteins identified for this bacterium, we focused on the analysis of the roles of AvrXacE1, AvrXacE2 and Xac3090 in pathogenicity and their interactions with host plant proteins. Bacterial deletion mutants in avrXacE1, avrXacE2 and xac3090 were constructed and evaluated in pathogenicity assays. The avrXacE1 and avrXacE2 mutants presented lesions with larger necrotic areas relative to the wild‐type strain when infiltrated in citrus leaves. Yeast two‐hybrid studies were used to identify several plant proteins likely to interact with AvrXacE1, AvrXacE2 and Xac3090. We also assessed the localization of these effector proteins fused to green fluorescent protein in the plant cell, and observed that they co‐localized to the subcellular spaces in which the plant proteins with which they interacted were predicted to be confined. Our results suggest that, although AvrXacE1 localizes to the plant cell nucleus, where it interacts with transcription factors and DNA‐binding proteins, AvrXacE2 appears to be involved in lesion‐stimulating disease 1‐mediated cell death, and Xac3090 is directed to the chloroplast where its function remains to be clarified.
Systematic review: antibodies and anti‐TNF‐α levels in inflammatory bowel disease
Authors: Chaparro M. , Guerra I. , Muñoz‐Linares P. , Gisbert J. P. 
Published: March 2012

SummaryBackgroundThe associations between clinical efficacy and infusion reactions with anti‐TNF‐α drug levels and the presence of antibodies against the drug have been described. However, the clinical utility of these tests in routine clinical practice remains unclear.AimsTo examine the clinical significance of the development of antibodies against anti‐TNF‐α drugs and the relationship between the efficacy of these drugs and their serum levels. We also studied the clinical utility of testing for anti‐TNF‐α antibodies and measuring drug serum levels to optimise treatment of patients with inflammatory bowel disease (IBD) receiving these agents.MethodsA systematic review was undertaken based on electronic searches of the PubMed database from the earliest record to February 2012. The reference lists of all relevant articles and abstracts from meetings were also consulted.ResultsWe observed a close relationship between trough levels of anti‐TNF‐α drug and maintenance of response to these drugs. The role of antibodies in loss of response seems to be limited to their effect favouring the clearance of the drug. The risk of infusion reactions, but not of delayed hypersensitivity reactions, is higher in patients with antibodies against the anti‐TNF‐α drug. Testing anti‐TNF‐α drug and antibody levels, together with clinical and endoscopic or radiological assessment, seems useful when attempting to optimise therapy and prevent inappropriate management of IBD patients.ConclusionMeasurement of serum anti‐TNF‐α trough levels and antibody titres could prove useful in therapeutic drug monitoring in IBD patients treated with anti‐TNF‐α agents.
Inhibition of Methaemoglobin Reduction by Sodium Salicylate
Authors: Worathumrong Nimnuan , Grimes A. J. 
Published: March 2012

Summary. Normal, human red cells containing nitrite‐induced methaemoglobin were incubated in glucose‐supplemented serum in the presence or absence of sodium salicylate. It was shown that sodium salicylate inhibits methaemoglobin reduction.Studies performed on haemolysates demonstrated that this effect on red cells was due to the inhibition by sodium salicylate of diaphorase. This inhibitory action of sodium salicylate was due primarily to salicylate ions and, secondarily, to the accompanying sodium ions.
Epithelial–mesenchymal transition in breast cancer correlates with high histological grade and triple‐negative phenotype
Authors: Jeong Hoiseon , Ryu Young‐joon , An Jungsuk , Lee Youngseok , Kim Aeree 
Published: March 2012

Jeong H, Ryu Y‐j, An J, Lee Y & Kim A(2012) Histopathology 60, E87–E95Epithelial–mesenchymal transition in breast cancer correlates with high histological grade and triple‐negative phenotypeAims:  Epithelial–mesenchymal transition (EMT) is characterized by a loss of epithelial nature and the acquisition of a mesenchymal form. The aim of this study was to assess the role of EMT in human mammary carcinogenesis, by performing immunohistochemical studies of EMT markers with tissue microarrays.Methods and results:  A total of 492 cases were evaluated and classified as hormone receptor (HR)‐positive type, HER2 type and triple‐negative (TN) type by the use of immunohistochemistry and in‐situ hybridization. We compared these groups in terms of epithelial and mesenchymal marker expression patterns. Of the 102 cases of TN‐type breast cancer, 24.5% expressed vimentin, 13.7% expressed N‐cadherin, and 9.8% expressed smooth muscle actin (SMA). Of the 221 cases of HR‐type breast cancer, 4.1% expressed vimentin, 5.9% expressed N‐cadherin, and 0.4% expressed SMA. Regarding epithelial markers, decreased expression was seen in 16.7% of cases for E‐cadherin, in 45.1% for cytokeratin (CK)19 and in 60.8% for CK8 and CK18 (CAM5.2) in TN‐type breast cancer cases. Decreased expression was seen in 11.8% of cases for E‐cadherin, in 6.8% for CK19 and in 3.2% for CAM5.2 in HR‐type cases.Conclusions:  EMT features were particularly seen in TN‐type breast cancer (P < 0.001). EMT was also significantly associated with high histological grade (P < 0.001).
Changes in volatile aroma compounds of pineapple (Ananas comosus) during freezing and thawing
Authors: Kaewtathip Thipthida , Charoenrein Sanguansri 
Published: March 2012

SummaryChanges in the volatile aroma compounds of pineapple (Ananas comosus) during freezing and thawing were compared against fresh samples to determine the effect of freezing on pineapple flavour. An HS‐SPME–GC–MS analysis showed that the Smooth Cayenne pineapple variety had nineteen volatile compounds, in four classes of compounds including fourteen esters, two hydrocarbons, two sulphur‐containing compounds and one lactone. The main characteristic volatile compounds of the fresh pineapple were methyl hexanoate, ethyl hexanoate, ethyl 3‐methylthiopropanoate and 1‐(E,Z)‐3,5‐undecatriene. Freeze–thaw cycles were associated with the loss of some volatile aroma compounds, particularly the esters which were found to be the main characteristic of fresh pineapples. The freezing and thawing process was found to cause damage to the pineapple tissues due to ice recrystallisation and dehydration which lead to the reduction of volatile aroma compounds.
Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes
Authors: LADNER JASON T. , PALUMBI STEPHEN R. 
Published: March 2012

AbstractThe identification of species is one of the most basic, and yet critically important, issues in biology with far‐reaching potential implications for fields such as biodiversity conservation, population ecology and epidemiology. Morphology has long been the primary tool biologists have used to categorize life. However, we now know that a significant portion of natural diversity is morphologically hidden, and therefore, we must integrate nonmorphological tools into the description of biodiversity. Here, we demonstrate the utility of multilocus population genetic data for identifying and characterizing cryptic species complexes, even when species share large amounts of genetic variability. Specifically, we have used DNA sequence data from 12 genomic regions to characterize two widespread species complexes in the coral genus Acropora: A. cytherea and A. hyacinthus. These two morphospecies have each been sampled from 5 to 7 locations throughout their Indo‐Pacific distributions, and with the use of structure and hierarchical clustering, we demonstrate the presence of at least six widespread cryptic species within these two morphospecies complexes. After identifying cryptic lineages, we then utilize the genetic data to examine the history of introgressive hybridization within and between these morphospecies complexes. Our data indicate that these two complexes form a global syngameon with consistent patterns of introgression between species across large geographic distributions.
Dermatoses secondary to Asian cultural practices
Authors: Lilly Evelyn , Kundu Roopal V. 
Published: March 2012

AbstractAlthough Asian cultural practices, such as acupuncture and threading, are widely used, there is limited medical literature describing their cutaneous effects and complications. This review briefly describes therapeutic cultural practices (traditional Chinese medicine, acupuncture, cupping, moxibustion, coining, Ayurveda, and aromatherapy) and cosmetic cultural practices (hair oils, henna, bindis, saris, and threading), with particular attention to dermatoses secondary to these practices. Traditional Chinese medicine and Ayurveda may cause heavy metal toxicity, severe cutaneous adverse reactions, and contact dermatitis. Cupping, moxibustion, and coining lead to dermatoses that may be mistaken for abuse by people unfamiliar with the practices. Hair oils may cause contact dermatitis and folliculitis. Paraphenylenediamine in black henna and bindi dyes and adhesives can cause severe allergic contact dermatitis. The drawstring in saris causes frictional irritation, which can lead to tinea corporis, koebnerization, and even squamous cell carcinoma. Threading may cause folliculitis, impetigo, and verrucae. The increasing prevalence of Asian cultural practices, which are performed inside and outside of Asia in this era of globalization, demands that dermatologists be familiar with the secondary dermatoses that may develop.
Myeloid leukemia cutis in the setting of myelodysplastic syndrome: a crucial dermatological diagnosis
Authors: Patel Laju M. , Maghari Amin , Schwartz Robert A. , Kapila Rajendra , Morgan Aaron J. , Lambert W. Clark 
Published: March 2012

AbstractCutaneous involvement by myeloid leukemic cells is an unusual phenomenon. Clinical manifestations vary from erythematous papules to plum‐colored plaques and nodules that may become purpuric and ulcerate. The definitive diagnosis of myeloid leukemia cutis requires the analysis of biopsy specimens using immunohistochemical staining to determine the expression of selective cell surface markers. We will review myeloid leukemia when first evident in the skin, particularly in the setting of myelodysplastic syndrome. The diagnosis of leukemia cutis in patients with myelodysplastic syndrome is indicative of concomitant or impending acute leukemic transformation. The early recognition and accurate identification of leukemic skin infiltrates in myelodysplastic patients is crucial, as this finding can have significant therapeutic and prognostic implications.
Natural‐source d‐α‐tocopheryl acetate inhibits oxidant stress and modulates atopic asthma in humans in vivo
Authors: Hoskins Aimee , Roberts Jackson L. , Milne Ginger , Choi Leena , Dworski Ryszard 
Published: March 2012

AbstractBackgroundAsthma is associated with oxidant stress and diminished antioxidant defenses. Yet, the mechanistic role of oxidant stress and antioxidant supplementation in human asthmatics remains uncertain. We determined the effect of high doses of the antioxidant natural‐source d‐α‐tocopheryl acetate for 16 weeks on allergen‐induced airway oxidant stress, inflammation, and bronchial responsiveness to methacholine and allergen in atopic asthmatics in vivo.MethodsThirty‐three mild atopic asthmatics underwent bronchoscopy with baseline bronchoalveolar lavage and segmental allergen challenge. The allergen‐challenged airway was lavaged 24 h later. At least 3 weeks later, patients underwent inhaled challenges with methacholine and specific allergen. Volunteers took 1500 IU of natural‐source d‐α‐tocopheryl acetate daily for at least 16 weeks. At the end of the treatment, the two bronchoscopies and inhaled methacholine and allergen challenges were repeated. F2‐isoprostanes, specific markers of oxidant stress, and selected Th1 and Th2 cytokines were analyzed in the lavage fluid.ResultsFollowing supplementation of natural‐source d‐α‐tocopheryl acetate, plasma concentrations of α‐tocopherol increased and γ‐tocopherol decreased. Both baseline and allergen‐induced F2‐isoprostanes significantly decreased, providing biochemical evidence for an antioxidant effect. Natural‐source d‐α‐tocopheryl acetate reduced allergen‐provoked concentrations of interleukin 3 and interleukin 4 and augmented levels of interleukin 12 in bronchoalveolar lavage fluid. Natural‐source d‐α‐tocopheryl acetate improved airway responsiveness to methacholine but did not alter airway reactivity to specific allergen.ConclusionsInhibition of oxidant stress by natural‐source d‐α‐tocopheryl acetate modulates allergic inflammation and airway hyperresponsiveness in human atopic asthmatics in vivo. These results need to be confirmed by a randomized placebo‐controlled trial.