bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features
Authors: Tang Buzhou , Cao Hongxin , Wu Yonghui , Jiang Min , Xu Hua 
Published: April 2013

Abstract

Background
Named entity recognition (NER) is an important task in clinical natural language processing (NLP) research. Machine learning (ML) based NER methods have shown good performance in recognizing entities in clinical text. Algorithms and features are two important factors that largely affect the performance of ML-based NER systems. Conditional Random Fields (CRFs), a sequential labelling algorithm, and Support Vector Machines (SVMs), which is based on large margin theory, are two typical machine learning algorithms that have been widely applied to clinical NER tasks. For features, syntactic and semantic information of context words has often been used in clinical NER systems. However, Structural Support Vector Machines (SSVMs), an algorithm that combines the advantages of both CRFs and SVMs, and word representation features, which contain word-level back-off information over large unlabelled corpus by unsupervised algorithms, have not been extensively investigated for clinical text processing. Therefore, the primary goal of this study is to evaluate the use of SSVMs and word representation features in clinical NER tasks.

Methods
In this study, we developed SSVMs-based NER systems to recognize clinical entities in hospital discharge summaries, using the data set from the concept extration task in the 2010 i2b2 NLP challenge. We compared the performance of CRFs and SSVMs-based NER classifiers with the same feature sets. Furthermore, we extracted two different types of word representation features (clustering-based representation features and distributional representation features) and integrated them with the SSVMs-based clinical NER system. We then reported the performance of SSVM-based NER systems with different types of word representation features.

Results and discussion
Using the same training (N = 27,837) and test (N = 45,009) sets in the challenge, our evaluation showed that the SSVMs-based NER systems achieved better performance than the CRFs-based systems for clinical entity recognition, when same features were used. Both types of word representation features (clustering-based and distributional representations) improved the performance of ML-based NER systems. By combining two different types of word representation features together with SSVMs, our system achieved a highest F-measure of 85.82%, which outperformed the best system reported in the challenge by 0.6%. Our results show that SSVMs is a great potential algorithm for clinical NLP research, and both types of unsupervised word representation features are beneficial to clinical NER tasks.
The protective effect and underlying mechanism of metformin on neointima formation in fructose-induced insulin resistant rats
Authors: Lu Jianxin , Ji Jingzhang , Meng Howard , Wang David , Jiang Bo , Liu Lixin , Randell Edward , Adeli Khosrow , Meng Qing H 
Published: April 2013

Abstract

Background
Insulin resistance is strongly associated with the development of type 2 diabetes and cardiovascular disease. However, the underlying mechanisms linking insulin resistance and the development of atherosclerosis have not been fully elucidated. Moreover, the protective effect of antihyperglycemic agent, metformin, is not fully understood. This study investigated the protective effects and underlying mechanisms of metformin in balloon-injury induced stenosis in insulin resistant rats.

Methods
After 4 weeks high fructose diet, rats received balloon catheter injury on carotid arteries and were sacrificed at 1 and 4 weeks post injury. Biochemical, histological, and molecular changes were investigated.

Results
Plasma levels of glucose, insulin, total cholesterol, triglyceride, free fatty acids, and methylglyoxal were highly increased in fructose-induced insulin resistant rats and treatment with metformin significantly improved this metabolic profile. The neointimal formation of the carotid arteries was enhanced, and treatment with metformin markedly attenuated neointimal hyperplasia. A significant reduction in BrdU-positive cells in the neointima was observed in the metformin-treated group (P < 0.01). Insulin signaling pathways were inhibited in insulin resistant rats while treatment with metformin enhanced the expression of insulin signaling pathways. Increased expression of JNK and NFKB was suppressed following metformin treatment. Vasoreactivity was impaired while treatment with metformin attenuated phenylephrine-induced vasoconstriction and enhanced methacholine-induced vasorelaxation of the balloon injured carotid arteries in insulin resistant rats.

Conclusion
The balloon-injury induced neointimal formation of the carotid arteries is enhanced by insulin resistance. Treatment with metformin significantly attenuates neointimal hyperplasia through inhibition of smooth muscle cell proliferation, migration, and inflammation as well as by improvement of the insulin signaling pathway.
Exome sequencing identifies nonsegregating nonsense ATM and PALB2variants in familial pancreatic cancer
Authors: Grant Robert C , Al-Sukhni Wigdan , Borgida Ayelet E , Holter Spring , Kanji Zaheer S , McPherson Treasa , Whelan Emily , Serra Stefano , Trinh Quang M , Peltekova Vanya , Stein Lincoln D , McPherson John D , Gallinger Steven 
Published: April 2013

Abstract
We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense variant in PALB2 with somatic loss of the variant allele. Both variants were absent in a relative with FPC. These findings question the causal mechanisms of ATM and PALB2 in these families and highlight challenges in identifying the causes of familial cancer syndromes using exome sequencing.
Molecular clonality and antimicrobial resistance in Salmonella entericaserovars Enteritidis and Infantis from broilers in three Northern regions of Iran
Authors: Rahmani Maral , Peighambari Seyed Mostafa , Svendsen Christina Aaby , Cavaco Lina M , Agersø Yvonne , Hendriksen Rene S 
Published: April 2013

AbstractBackgroundMultidrug-resistantSalmonellastrains are frequently encountered problems worldwide with considerable increased occurrences in recent years. The aim of this study was to investigate the occurrence and frequency of antimicrobial resistance and associated resistance genes inSalmonellaisolates from broiler farms in different regions of Iran covering a time period of four years.ResultsFrom 2007 to 2011, 36Salmonellastrains were isolated from broiler farms located in three northern provinces of Iran. The isolates were serotyped, antimicrobial susceptibility tested, and characterized for antimicrobial resistance genes associated to the phenotype. Pulsed-field gel electrophoresis (PFGE) was applied for comparison of genetic relatedness.Two serovars were detected among the isolates;Salmonella entericaserovar Infantis (75%) andS.Enteritidis (25%). Thirty-four (94%) of the isolates exhibited resistance to nalidixic acid and ciprofloxacin caused by a single mutation in the quinolone resistance-determining region (QRDR) ofgyrA. For all strains this mutation occurred in the codon of Asp87leading to a Asp87-Tyr, Asp87-Gly or Asp87-Asn substitutions. AllS.Infantis (n = 27) were resistant to tetracycline, spectinomycin, streptomycin, and sulfamethoxazole and harbored the associated resistance genes;tetA,dfrA14,aadA1, andsulI together with class 1 integrons. The isolates revealed highly similar PFGE patterns indicating clonal relatedness across different geographical locations.ConclusionThe data provided fundamental information applicable when launching future control programs for broilers in Iran with the aim to conserve the effectiveness of important antimicrobials for treatment in humans.
Teaching IELTS Writing Module through English Debate: A Case Study in Thailand
Authors: Sanonguthai Suchada 
Published: April 2013

Abstract
The study explores how effective teaching IELTS writing module through English debate can be for 20 students in their last year in high at a private school in Thailand. The school has acquired Ms Cynthia Luo, a debate coach of the school, to teach Grade 12B academic writing course and this has made it possible for the students to brainstorm, discuss and debate over IELTS oriented issues before they start working on draft 1 and draft 2 of their essays. Three follow-up student interviews and the debate teacher interview were conducted. Active students responded positively to the use of debate in their writing class while expressing their concerns about academic vocabulary and paraphrasing skills. Passive students need more support during debate activities. Additional English activities are introduced for students' accuracy and fluency. The student participants took their IELTS mock test and their scores reflect effectiveness of debate activities in classroom while some of the students need to develop their classroom learning motivation.
The Construct Validity of a Test: A Triangulation of Approaches
Authors: Salehi Mohammad 
Published: April 2013

Abstract
Three approaches of validation enquiry were applied on the data obtained from a proficiency test carried out with 3,398 PhD candidates as a partial requirement for entering PhD program in Iran. The data obtained from the reading section were subjected to an exploratory factor analysis (EFA). The EFA yielded nine factors in the reading section. Furthermore, a design of multitrait-multimethod was also investigated, the traits being grammar and vocabulary and the methods, multiple choice and cloze test. The test demonstrated both convergent and discriminant validity. A third approach was intersubtest correlations as elaborated on by Alderson et al. (1995). For this, different sub-parts of the instrument were correlated with one another and with the total test. The test also showed construct validity as investigated via this approach. It can be concluded that the test had construct validity as revealed by these three approaches.
The Effect of Assessment Type (self vs. peer vs. teacher) on Iranian University EFL Students' Course Achievement
Authors: Khonbi Zainab Abolfazli , Sadeghi Karim 
Published: April 2013

Abstract
This research investigated the effect of self-, peer-, and teacher-assessment on Iranian undergraduate EFL students' course achievement. Four intact classes, including 82 students from Urmia, Tabriz, and Tabriz Islamic Azad universities were randomly assigned into one of the self-, peer-, teacher-assessment, or control groups. The students were pretested on their current Teaching Methods knowledge. After receiving relevant instruction and training, the first experimental group (N = 21) were involved in self-assessment activities, the second one (N = 23) were engaged with peer-assessment tasks, and the third one (N = 21) were subjected to teacher-assessment; however, the control group (N = 19) received no assessment-related treatment. The application of ANCOVA on the results of the achievement posttest indicated differences in the performances of peer-, self-, teacher-assessment, and the control groups F (3, 77) = 23.15, p = .05, in favour of peer-assessment. A medium effect size was found between the independent and dependent variables (partial eta squared= .47); however, the covariate, albeit significant (.03), had a small effect size (partial eta squared= .05). Further findings and implications are discussed in the paper.
Neutrophils promote 6-sulfo LacNAc+ dendritic cell (slanDC) survival
Authors: Micheletti Alessandra , Costantini Claudio , Calzetti Federica , Camuesco Deseada , Costa Sara , Tamassia Nicola , Cassatella Marco A 
Published: April 2013

ABSTRACTThere is increasing evidence supporting the notion that neutrophils and other leukocytes establish cooperative actions in regulating innate and adaptive immune responses. In such a context, we have shown recently that human neutrophils amplify NK cell/slanDC-mediated cytokine production by directly costimulating IFN-γ production by NK cells, as well as by potentiating IL-12p70 release by slanDCs via CD18/ICAM-1 interactions. To gain more insights into the molecular bases of the neutrophil-mediated cytokine potentiation by NK cells and slanDCs under coculture conditions, we now report that neutrophils efficaciously maintain slanDC survival by contact-dependent mechanisms. Such a phenomenon occurs in the absence or presence of NK cells, which, in the presence of LPS and IL-2 or the IL-15/IL-18 combination, accelerates slanDC apoptosis significantly. Noteworthy, αICAM-1- and αCD18-neutralizing antibodies, previously shown to suppress IL-12p70 production by slanDCs and consequently, IFN-γ by NK cells under similar experimental conditions, did not minimally alter the neutrophil-mediated prosurvival effect on slanDCs. Altogether, data not only expand our knowledge on the interactions between human neutrophils and slanDCs but also prove that neutrophil-mediated promotion of slanDC survival and potentiation of slanDC-derived IL-12p70 occur via different mechanisms.
Familial Isolated Pituitary Adenomas (FIPA) and the Pituitary Adenoma Predisposition due to Mutations in the Aryl Hydrocarbon Receptor Interacting Protein (AIP) Gene
Authors: Beckers Albert , Aaltonen Lauri A. , Daly Adrian F. , Karhu Auli 
Published: April 2013

AbstractPituitary adenomas are one of the most frequent intracranial tumors and occur with a prevalence of approximately 1:1000 in the developed world. Pituitary adenomas have a serious disease burden, and their management involves neurosurgery, biological therapies, and radiotherapy. Early diagnosis of pituitary tumors while they are smaller may help increase cure rates. Few genetic predictors of pituitary adenoma development exist. Recent years have seen two separate, complimentary advances in inherited pituitary tumor research. The clinical condition of familial isolated pituitary adenomas (FIPA) has been described, which encompasses the familial occurrence of isolated pituitary adenomas outside of the setting of syndromic conditions like multiple endocrine neoplasia type 1 and Carney complex. FIPA families comprise approximately 2% of pituitary adenomas and represent a clinical entity with homogeneous or heterogeneous pituitary adenoma types occurring within the same kindred. The aryl hydrocarbon receptor interacting protein (AIP) gene has been identified as causing a pituitary adenoma predisposition of variable penetrance that accounts for 20% of FIPA families. Germline AIP mutations have been shown to associate with the occurrence of large pituitary adenomas that occur at a young age, predominantly in children/adolescents and young adults. AIP mutations are usually associated with somatotropinomas, but prolactinomas, nonfunctioning pituitary adenomas, Cushing disease, and other infrequent clinical adenoma types can also occur. Gigantism is a particular feature of AIP mutations and occurs in more than one third of affected somatotropinoma patients. Study of pituitary adenoma patients with AIP mutations has demonstrated that these cases raise clinical challenges to successful treatment. Extensive research on the biology of AIP and new advances in mouse Aip knockout models demonstrate multiple pathways by which AIP may contribute to tumorigenesis. This review assesses the current clinical and therapeutic characteristics of more than 200 FIPA families and addresses research findings among AIP mutation-bearing patients in different populations with pituitary adenomas.
Raf-mediated cardiac hypertrophy in adultDrosophila
Authors: Yu Lin , Daniels Joseph , Glaser Alex E. , Wolf Matthew J. 
Published: April 2013

SummaryIn response to stress and extracellular signals, the heart undergoes a process called cardiac hypertrophy during which cardiomyocytes increase in size. If untreated, cardiac hypertrophy can progress to overt heart failure that causes significant morbidity and mortality. The identification of molecular signals that cause or modify cardiomyopathies is necessary to understand how the normal heart progresses to cardiac hypertrophy and heart failure. Receptor tyrosine kinase (RTK) signaling is essential for normal human cardiac function, and the inhibition of RTKs can cause dilated cardiomyopathies. However, neither investigations of activated RTK signaling pathways nor the characterization of hypertrophic cardiomyopathy in the adult fly heart has been previously described. Therefore, we developed strategies using Drosophila as a model to circumvent some of the complexities associated with mammalian models of cardiovascular disease. Transgenes encoding activated EGFRA887T, Ras85DV12 and Ras85DV12S35, which preferentially signal to Raf, or constitutively active human or fly Raf caused hypertrophic cardiomyopathy as determined by decreased end diastolic lumen dimensions, abnormal cardiomyocyte fiber morphology and increased heart wall thicknesses. There were no changes in cardiomyocyte cell numbers. Additionally, activated Raf also induced an increase in cardiomyocyte ploidy compared with control hearts. However, preventing increases in cardiomyocyte ploidy using fizzy-related (Fzr) RNAi did not rescue Raf-mediated cardiac hypertrophy, suggesting that Raf-mediated polyploidization is not required for cardiac hypertrophy. Similar to mammals, the cardiac-specific expression of RNAi directed against MEK or ERK rescued Raf-mediated cardiac hypertrophy. However, the cardiac-specific expression of activated ERKD334N, which promotes hyperplasia in non-cardiac tissues, did not cause myocyte hypertrophy. These results suggest that ERK is necessary, but not sufficient, for Raf-mediated cardiac hypertrophy.
Type XVIII collagen is essential for survival during acute liver injury in mice
Authors: Duncan Michael B. , Yang Changqing , Tanjore Harikrishna , Boyle Patrick M. , Keskin Doruk , Sugimoto Hikaru , Zeisberg Michael , Olsen Bjorn R. , Kalluri Raghu 
Published: April 2013

Summary
The regenerative response to drug- and toxin-induced liver injury induces changes to the hepatic stroma, including the extracellular matrix. Although the extracellular matrix is known to undergo significant changes during the injury response, its impact on maintaining hepatocyte function and viability in this process remains largely unknown. We demonstrate that recovery from toxin-mediated injury is impaired in mice deficient in a key liver extracellular matrix molecule, type XVIII collagen, and results in rapid death. The type-XVIII-collagen-dependent response to liver injury is mediated by survival signals induced by α1β1 integrin, integrin linked kinase and the Akt pathway, and mice deficient in either α1β1 integrin or hepatocyte integrin linked kinase also succumb to toxic liver injury. These findings demonstrate that type XVIII collagen is an important functional component of the liver matrix microenvironment and is crucial for hepatocyte survival during injury and stress.
CO2 Reforming of Methane to Produce Syngas over γ-Al2O3-Supported Ni–Sr Catalysts
Authors: Al-Fatesh Ahmed Sadeq , Naeem Muhammad Awais , Fakeeha Anis Hamza , Abasaeed Ahmed Elhag 
Published: April 2013

Abstract
Dry reforming reactions have important environmental implications, since they can utilize and/or mitigate greenhouse gases. An experimental study was carried out to prepare suitable catalysts for dry reforming of methane. The Ni/γ-Al2O3 supported catalysts with strontium as a promoter (0.00–2.25 wt %) were prepared by a wet impregnation method. Various experimental techniques such as N2 adsorption–desorption isotherm, H2-TPR, CO2-TPD, XRD, TGA, O2-TPO, and SEM were applied for characterization of fresh and spent catalysts. The results of characterizations and catalyst activity test revealed that addition of Sr in Ni/γ-Al2O3 catalyst has dual effect; it improves the metal support interaction as well as enhances the Lewis basicity of the catalyst. This boost in basicity favors the chemisorption and dissociation of CO2 over the catalyst which in turn decreases the coke deposition. Amongst all tested catalysts, best results in terms of coke suppression were attained when 0.75% Sr loading was used, which showed 3.8% weight loss, less than half of that of the parent Ni–Al catalyst (8.2 wt %).
Electrophysiological properties of mouse and epitope-tagged human cardiac sodium channel Nav1.5 expressed in HEK293 cells
Authors: Reinhard Katja , Rougier Jean-Sébastien , Ogrodnik Jakob , Abriel Hugues 
Published: April 2013

Background: The pore-forming subunit of the cardiac sodium channel, Nav1.5, has been previously found to be mutated in genetically determined arrhythmias. Nav1.5 associates with many proteins that regulate its function and cellular localisation. In order to identify more in situ Nav1.5 interacting proteins, genetically-modified mice with a high-affinity epitope in the sequence of Nav1.5 can be generated.Methods: In this short study, we (1) compared the biophysical properties of the sodium current (INa) generated by the mouse Nav1.5 (mNav1.5) and human Nav1.5 (hNav1.5) constructs that were expressed in HEK293 cells, and (2) investigated the possible alterations of the biophysical properties of the human Nav1.5 construct that was modified with specific epitopes.Results: The biophysical properties of mNav1.5 were similar to the human homolog. Addition of epitopes either up-stream of the N-terminus of hNav1.5 or in the extracellular loop between the S5 and S6 transmembrane segments of domain 1, significantly decreased the amount of INa and slightly altered its biophysical properties. Adding green fluorescent protein (GFP) to the N-terminus did not modify any of the measured biophysical properties of hNav1.5.Conclusions: These findings have to be taken into account when planning to generate genetically-modified mouse models that harbour specific epitopes in the gene encoding mNav1.5.
The Safer Sutton Partnership Service: Blueprint for the Future?
Authors: Lewis Chris 
Published: April 2013

The Safer Sutton Partnership Service (SSPS) is a unique partnership between the London Borough of Sutton and the Metropolitan Police Service. It brings staff together within a single structure and provides services in the field of community safety, and tackling drugs and alcohol abuse. This paper looks at the history of SSPS and its likely future in the light of the continued reduction in resources, the community safety fund no longer being ringfenced and the election of Police and Crime Commissioners (PCCs). It concludes that this could lead to fundamental changes in police structures and behaviour, e.g. the possibility that some PCCs could be tempted to seek political popularity and reelection by giving lower priority to community safety partnerships, on the grounds that solving crime is more popular than preventing crime. Based upon SSPS’ success over many years, the paper aims to show that partnership services such as SSPS give extremely good value for money and their use should be extended rather than curtailed.