bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression and Interactions of Interleukin‐10, Transforming Growth Factor β, and Vascular Endothelial Growth Factor in Esophageal Squamous Cell Carcinoma
Authors: Gholamin Mehran , Moaven Omeed , Memar Bahram , Farshchian Moein , Naseh Hossein , Malekzadeh Reza , Sotoudeh Masoud , Rajabi‐Mashhadi Mohammad Taghi , Forghani Mohammad Naser , Farrokhi Farid , Abbaszadegan Mohammad Reza 
Published: May 2009

AbstractBackgroundSharing the role of immune suppression, interleukin‐10 (IL‐10), transforming growth factor β (TGF‐β), and vascular endothelial growth factor (VEGF) are critical genes in several aspects of tumorigenesis. To elucidate the role of these cytokines in esophageal squamous cell carcinoma (ESCC), their relative mRNA expression in tumoral tissue compared with corresponding tumor‐free tissue was evaluated.MethodsA total of 49 patients with histologically confirmed ESCC were included in the study prior to any therapeutic interventions. Quantitative analysis of the mRNA expression was performed by real‐time reverse transcription‐polymerase chain reaction and the clinicopathologic associations were assessed.ResultsThe mRNA of IL‐10, VEGF, and TGF‐β was frequently overexpressed in 53.2%, 44.9%, and 37.5% of ESCC patients, respectively. TGF‐β was significantly co‐expressed with IL‐10 and with VEGF. Although VEGF was not independently associated with increased tumor size (p = 0.065), concomitant overexpression of VEGF with TGF‐β was significantly correlated with increased size of the tumor (p < 0.05).ConclusionsOverexpression of IL‐10, TGF‐β, and VEGF plays an important role in ESCC and consequently leads to the frequent event of immune evasion in ESCC. TGF‐β is concomitantly overexpressed with IL‐10 and with VEGF in ESCC. A stimulatory signal from TGF‐β to VEGF is necessary for VEGF to promote tumor progression.
Laparoscopic Cholecystectomy for Gallbladder Disease in Patients with Severe Cardiovascular Disease
Authors: Liu Yu‐Yin , Yeh Chun‐Nan , Lee Hsiang‐Lin , Chu Pao‐Hsien , Jan Yi‐Yin , Chen Miin‐Fu 
Published: May 2009

AbstractBackgroundCardiovascular disease (CVD) and gallstones are reported to be strongly associated because both diseases are frequently part of a metabolic syndrome. Laparoscopic cholecystectomy (LC) has become the standard treatment for gallbladder disease around the world. Cardiovascular disease is considered as an absolute or relative contraindication for LC; however, clinical information regarding the applicability of LC for treating gallbladder disease in CVD patients is lacking. This study aims to assess the suitability of LC for the treatment of gallbladder disease in CVD patients.MethodsThe medical records of 66 patients with severe CVD (including valvular heart disease, ischemic heart disease, and heart failure) and gallbladder disease (CVD‐group) who underwent LC between 1966 and 2005 were retrospectively reviewed. Furthermore, these data were compared with the clinical features and outcomes of 8,834 patients with gallbladder disease who underwent LC but did not have severe CVD (NCVD‐group).ResultsOf the 8,900 patients with gallbladder disease undergoing LC, the 66 (0.74%) who comprised the CVD‐group clearly exhibited advanced age, male predominance, higher blood urea nitrogen (BUN) levels, and a longer duration of hospitalization as compared with the NCVD‐group patients. A longer duration of hospitalization and a higher incidence of acute cholecystitis and chronic cholecystitis were identified as independent factors differentiating the CVD‐group patients, who had previously undergone open‐heart surgery, from the NCVD‐group patients who underwent LC. For the CVD‐group patients, adjustment of anticoagulant therapy contributed to the longer duration of hospitalization, but postoperative complications did not. Advanced age and male predominance were identified as independent factors differentiating the patients who developed ischemic heart disease that required intervention from the NCVD‐group patients undergoing LC. The operative morbidity and mortality rates of LC are likely to be similar when it is used to treat selected patients with severe CVD and gallbladder disease and when it is used to treat patients with gallbladder disease and no CVD.ConclusionsLaparoscopic cholecystectomy is a suitable procedure for treating selected patients with severe CVD and gallbladder disease, and its operative morbidity and mortality rates are similar in these patients and in patients with gallbladder disease alone. Nevertheless, appropriate preoperative preparations and established operative techniques in the hands of an experienced surgeon are mandatory.
The protective capacity of UV-exposedClinostomum complanatummetacercariae against challenge infections inArdeola ibis ibis
Authors: Allam G. , Aboel Hadid S.M. 
Published: May 2009

AbstractExposure of encysted metacercariaeof Clinostomum complanatumto UV light (254 nm) for 60 min reduced their development into adult worms in buff-backed herons (95.7% reduction in worm burden). Metacercariae that succeeded in developing into adult worms, showed low fecundity levels. Furthermore, 30% of eggs laid showed abnormal shape; however, all normal and abnormal eggs failed to hatch into miracidia. The effectiveness of UV-irradiated metacercariae as a vaccine was investigated. Compared to control unvaccinated herons, the vaccinated group showed a significantly high protection rate (73.8%) against challenge.In vitro, worm development after challenge showed decreased fecundity and increased egg abnormalities, where only 1.5% of all eggs produced hatched into miracidia. A passive haemagglutination test revealed increased antibody titres against soluble adult worm antigen in both vaccinated and vaccinated-challenged birds. It was concluded that vaccination of herons using encysted metacercariae UV-irradiated for 60 min can protect them against challenge infection.
Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Authors: Krupke Debra , Begley Dale , Neuhauser Steven , Richardson Joel , Sundberg John , Bult Carol , Eppig Janan 
Published: May 2009

AbstractMany advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.MTB is supported by NCI grant CA089713.
Biocuration Workflow Catalogue
Authors: Burns Gully , Krallinger Martin , Cohen Kevin , Wu Cathy , Hirschman Lynette 
Published: May 2009

AbstractAs the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. We presented this work as a slideshow and publish this account of the catalog as supplementary information.
The ESCRT‐III protein CeVPS‐32 is enriched in domains distinct from CeVPS‐27 and CeVPS‐23 at the endosomal membrane of epithelial cells
Authors: Michelet Xavier , Alberti Adriana , Benkemoun Laura , Roudier Nathalie , Lefebvre Christophe , Legouis Renaud 
Published: May 2009

Background information. Within the endocytic pathway, the ESCRT (endosomal sorting complex required for transport) machinery is essential for the biogenesis of MVBs (multivesicular bodies). In yeast, ESCRTs are recruited at the endosomal membrane and are involved in cargo sorting into intralumenal vesicles of the MVBs.Results. In the present study, we characterize the ESCRT‐III protein CeVPS‐32 (Caenorhabditis elegans vacuolar protein sorting 32) and its interactions with CeVPS‐27, CeVPS‐23 and CeVPS‐4. In contrast with other CevpsE (class E vps) genes, depletion of Cevps‐32 is embryonic lethal with severe defects in the remodelling of epithelial cell shape during organogenesis. Furthermore, Cevps‐32 animals display an accumulation of enlarged early endosomes in epithelial cells and an accumulation of autophagosomes. The CeVPS‐32 protein is enriched in epithelial tissues and in residual bodies during spermatid maturation. We show that CeVPS‐32 and CeVPS‐27/Hrs (hepatocyte‐growth‐factor‐regulated tyrosine kinase substrate) are enriched in distinct subdomains at the endosomal membrane. CeVPS‐27‐positive subdomains are also enriched for the ESCRT‐I protein CeVPS‐23/TSG101 (tumour susceptibility gene 101). The formation of CeVPS‐27 subdomains is not affected by the depletion of CeVPS‐23, CeVPS‐32 or the ATPase CeVPS‐4.Conclusion. Our results suggest that the formation of membrane subdomains is essential for the maturation of endosomes.
PKCϵ has an alcohol-binding site in its second cysteine-rich regulatory domain
Authors: Das Joydip , Pany Satyabrata , Rahman Ghazi M. , Slater Simon J. 
Published: May 2009

Alcohols regulate the expression and function of PKC (protein kinase C), and it has been proposed that an alcohol-binding site is present in PKCα in its C1 domain, which consists of two cysteine-rich subdomains, C1A and C1B. A PKCϵ-knockout mouse showed a significant decrease in alcohol consumption compared with the wild-type. The aim of the present study was to investigate whether an alcohol-binding site could be present in PKCϵ. Here we show that ethanol inhibited PKCϵ activity in a concentration-dependent manner with an EC50 (equilibrium ligand concentration at half-maximum effect) of 43 mM. Ethanol, butanol and octanol increased the binding affinity of a fluorescent phorbol ester SAPD (sapintoxin-D) to PKCϵC1B in a concentration-dependent manner with EC50 values of 78 mM, 8 mM and 340 μM respectively, suggesting the presence of an allosteric alcohol-binding site in this subdomain. To identify this site, PKCϵC1B was photolabelled with 3-azibutanol and 3-azioctanol and analysed by MS. Whereas azibutanol preferentially labelled His236, Tyr238 was the preferred site for azioctanol. Inspection of the model structure of PKCϵC1B reveals that these residues are 3.46 Å (1 Å=0.1 nm) apart from each other and form a groove where His236 is surface-exposed and Tyr238 is buried inside. When these residues were replaced by alanine, it significantly decreased alcohol binding in terms of both photolabelling and alcohol-induced SAPD binding in the mutant H236A/Y238A. Whereas Tyr238 was labelled in mutant H236A, His236 was labelled in mutant Y238A. The present results provide direct evidence for the presence of an allosteric alcohol-binding site on protein kinase Cϵ and underscore the role of His236 and Tyr238 residues in alcohol binding.
Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2
Authors: Cozza Giorgio , Mazzorana Marco , Papinutto Elena , Bain Jenny , Elliott Matthew , di Maira Giovanni , Gianoncelli Alessandra , Pagano Mario A. , Sarno Stefania , Ruzzene Maria , Battistutta Roberto , Meggio Flavio , Moro Stefano , Zagotto Giuseppe , Pinna Lorenzo A. 
Published: May 2009

Emodin (1,3,8-trihydroxy-6-methyl-anthraquinone) is a moderately potent and poorly selective inhibitor of protein kinase CK2, one of the most pleiotropic serine/threonine protein kinases, implicated in neoplasia and in other global diseases. By virtual screening of the MMS (Molecular Modeling Section) database, we have now identified quinalizarin (1,2,5,8-tetrahydroxyanthraquinone) as an inhibitor of CK2 that is more potent and selective than emodin. CK2 inhibition by quinalizarin is competitive with respect to ATP, with a Ki value of approx. 50 nM. Tested at 1 μM concentration on a panel of 75 protein kinases, quinalizarin drastically inhibits only CK2, with a promiscuity score (11.1), which is the lowest ever reported so far for a CK2 inhibitor. Especially remarkable is the ability of quinalizarin to discriminate between CK2 and a number of kinases, notably DYRK1a (dual-specificity tyrosine-phosphorylated and -regulated kinase), PIM (provirus integration site for Moloney murine leukaemia virus) 1, 2 and 3, HIPK2 (homeodomain-interacting protein kinase-2), MNK1 [MAPK (mitogen-activated protein kinase)-interacting kinase 1], ERK8 (extracellular-signal-regulated kinase 8) and PKD1 (protein kinase D 1), which conversely tend to be inhibited as drastically as CK2 by commercially available CK2 inhibitors. The determination of the crystal structure of a complex between quinalizarin and CK2α subunit highlights the relevance of polar interactions in stabilizing the binding, an unusual characteristic for a CK2 inhibitor, and disclose other structural features which may account for the narrow selectivity of this compound. Tested on Jurkat cells, quinalizarin proved able to inhibit endogenous CK2 and to induce apoptosis more efficiently than the commonly used CK2 inhibitors TBB (4,5,6,7-tetrabromo-1H-benzotriazole) and DMAT (2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole).
Variably modulated gating of the 26S proteasome by ATP and polyubiquitin
Authors: Li Xiaohua , Demartino George N. 
Published: May 2009

The 26S proteasome is a 2500 kDa protease complex that degrades polyubiquitylated proteins by a mechanism that requires ATP hydrolysis. It also degrades short non-ubiquitylated peptides and certain unstructured proteins by an energy-independent mechanism that requires bound ATP to maintain its component subcomplexes, the 20S proteasome and PA700, in a functionally assembled state. Proteolysis of both types of substrate requires PA700-induced opening of reversible gates at substrate-access pores of the 20S proteasome. In the present study we demonstrate that the rate of peptide substrate hydrolysis, a functional monitor of gate opening, is regulated variably by multiple effectors. ATPγS (adenosine 5′-[γ-thio]triphosphate) and other non-hydrolysable ATP analogues increased peptide substrate hydrolysis by intact 26S proteasomes. Thus nucleotides that maintained 26S proteasome structure, but did not support ATP hydrolysis or the degradation of polyubiquitylated proteins, promoted enhanced rates of peptide hydrolysis. Polyubiquitin and a peptoid that binds selectively to a single ATPase subunit of PA700 also increased rates of peptide hydrolysis but had disparate effects on rates of ATP hydrolysis. The effect of polyubiquitin was specific for ubiquitin–ubiquitin linkages that supported proteolysis of protein substrates. These results indicate that gating of the 26S proteasome is not a simple two-state process but can be variably modulated. Our results suggest that modulated gating of the proteasome may be an important element of the mechanism of proteolysis of polyubiquitylated proteins.
On the Inadequacy of the Ethnic/Civic Antinomy: The Language Politics of Bulgarian Nationalism
Authors: Toshkov Alex 
Published: May 2009

IntroductionThe significance of language and literature as formative to national identity is a major trope within studies of nationalism. The act of imagining and realizing a nation and a nation-state along these lines has been tackled from multiple angles including folklore, linguistics, historical studies of educational institutions and their curricula, with a prominent place reserved for textbook analysis. Even though historical studies for the most part have underscored the rapidity and novelty of these processes, a temporal claim that is part and parcel of the larger and fundamental assertion that nationalism is a modern phenomenon, these processes are negotiated over a period of decades. In Braudelian terms, the standardization of a national language would fall somewhere betweenconjonctureandévénement.
High Frequency of Multidrug-Resistant Gram-Negative Rods in 2 Neonatal Intensive Care Units in the Philippines
Authors: Litzow Jennifer M. , Gill Christopher J. , Mantaring Jose B. V. , Fox Matthew P. , MacLeod William B. , Mendoza Myrna , Mendoza Sookee , Scobie Rebecca , Huskins Charles W. , Goldman Donald A. , Hamer David H. 
Published: May 2009

Background.Although hospital-acquired infections appear to be a growing threat to the survival of newborns in the developing world, the epidemiology of this problem remains poorly characterized.Methods.During a 10-month period, we conducted prospective longitudinal surveillance for colonization and bloodstream infection caused by gram-negative rods among all infants hospitalized in the 2 largest neonatal intensive care units in Manila, the Philippines. We determined antibiotic susceptibilities and calculated adjusted odds ratios for risk factors for bacteremia by means of multivariate logistic regression.Results.Of 1,831 neonates enrolled during a 10-month period, 1,017 (55.5%) became newly colonized and 358 (19.6%) became bacteremic with a drug-resistant gram-negative rod, most commonly Klebsiella species, Enterobacter species, Acinetobacter species, and Pseudomonas aeruginosa. Of the invasive isolates, 20% were resistant to imipenem, 41% to trimethoprim-sulfamethoxazole, 52% to amikacin, 63% to ampicillin-sulbactam, 67% to ceftazidime, and 80% to tobramycin. The factors significantly associated with an increased risk of bacteremia were mechanical ventilation and prematurity. Additionally, colonization with a drug-resistant gram-negative rod was an independent risk factor for bacteremia (odds ratio, 1.4 [95% confidence interval, 1.0-1.9]).Conclusions.Colonization with a drug-resistant gram-negative rod was an independent risk factor for sepsis. If our data are typical, the unusually high intensity of colonization pressure and disease caused by multidrug-resistant gram-negative rods at these 2 neonatal intensive care units indicates an emerging healthcare crisis in the developing world. Improved infection control methods are therefore critically needed in developing countries.
LUMINOUS RED GALAXY POPULATION IN CLUSTERS AT 0.2⩽ z ⩽0.6
Authors: Ho Shirley , Lin Yen-Ting , Spergel David , Hirata Christopher M. 
Published: May 2009

ABSTRACT
We investigate statistical properties of luminous red galaxies (LRGs) in a sample of X-ray-selected galaxy clusters at intermediate redshift (0.2 ⩽ z ⩽ 0.6) of mass range from ∼1 × 1014
M
☉ to ∼8 × 1014
M
☉. The LRGs are selected based on carefully designed color criteria, and the cluster membership is assessed via photometric redshifts. As clusters and LRGs are both viewed as promising tracer of the underlying dark matter distribution, understanding the distribution of LRGs within clusters is an important issue. Our main findings include (1) the halo occupation distribution (HOD) of LRGs inside our cluster sample is 〈N(M)〉 = k(M/1014
h
−1
M
☉)
a
, where a = 0.495 ± 0.105 and k = 1.455 ± 0.285 assuming a Poisson distribution for N(M). If we assume the form of 〈N(M)〉 = 1 + k(M/1014
h
−1
M
☉)
a
, where a = 0.580 ± 0.130 and k = 0.975 ± 0.240 assuming a Poisson distribution for N(M). (2) The HOD of LRGs [N(M)] and the satellite distribution of LRGs [N(M) − 1] are both consistent with being Poisson. To be more quantitative, we find Var(N)/〈N〉 = 1.43 ± 0.35 and Var(N − 1)/〈N − 1〉 = 1.82 ± 0.50. (3) The radial profile of LRGs within clusters when fitted with a Navarro–Frenk–White profile gives a concentration of 17.5+7.1
−4.3 (6.0+3.2
−1.9) including (excluding) brightest LRGs (BLRGs). In essence, the BLRGs are more concentrated toward the center of the clusters than the other LRGs in clusters. We also discuss the implications of these observations on the evolution of massive galaxies in clusters.
DIANA-mirPath: Integrating human and mouse microRNAs in pathways
Authors: Papadopoulos G. L. , Alexiou P. , Maragkakis M. , Reczko M. , Hatzigeorgiou A. G. 
Published: May 2009

Abstract
Summary: DIANA-mirPath is a web-based computational tool developed to identify molecular pathways potentially altered by the expression of single or multiple microRNAs. The software performs an enrichment analysis of multiple microRNA target genes comparing each set of microRNA targets to all known KEGG pathways. The combinatorial effect of co-expressed microRNAs in the modulation of a given pathway is taken into account by the simultaneous analysis of multiple microRNAs. The graphical output of the program provides an overview of the parts of the pathway modulated by microRNAs, facilitating the interpretation and presentation of the analysis results.
Availability: The software is available at http://microrna.gr/mirpath and is free for all users with no login or download requirement.
Contact: papadopoulos@fleming.gr or hatzigeorgiou@fleming.gr
Media Reporting of the Emergence of the 1968 Influenza Pandemic in Hong Kong: Implications for Modern-day Situational Awareness
Authors: Wilson James M. , Iannarone Marissa , Wang Chunhui 
Published: May 2009

ABSTRACTObjective:We investigated local media reporting during the emergence of influenza A/Hong Kong/68 in Hong Kong to understand how indolent social awareness contributed to delays in warning of the pandemic.Methods:Daily output from 1 English-language and 4 local Chinese-language newspapers published in Hong Kong between July 1 and August 31, 1968 were manually reviewed for all references to the presence of respiratory disease or influenza in southern China and Hong Kong. Public announcements from the World Health OrganizationWeekly Epidemiological Recordwere used to approximate international awareness.Results:Influenza A/Hong Kong/68 appeared abruptly in Hong Kong and within 1 week began to affect the functioning of the health care sector as well as civil infrastructure due to worker infection and absenteeism. Substantial delays in communication between Guangzhou, China, and Hong Kong officials contributed to delays in warning globally.Conclusions:The 1968 experience emphasizes the need to use the news media in the operational setting as a critical component in warning of a pandemic. (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S148–S153)