bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensemble Dynamics and Bred Vectors
Authors: Balci Nusret , Mazzucato Anna L. , Restrepo Juan M. , Sell George R. 
Published: January 2012

AbstractThe new concept of an ensemble bred vector (EBV) algorithm is introduced to assess the sensitivity of model outputs to changes in initial conditions for weather forecasting. The new algorithm is based on collective dynamics in essential ways. As such, it keeps important geometric features that are lost in the earlier bred vector (BV) algorithm. By construction, the EBV algorithm produces one or more dominant vectors and is less prone to spurious results than the BV algorithm. It retains the attractive features of the BV algorithm with regard to being able to handle legacy codes, with minimal additional coding.The performance of the EBV algorithm is investigated by comparing it to the BV algorithm as well as the finite-time Lyapunov vectors. With the help of a continuous-time adaptation of these algorithms, a theoretical justification is given to the observed fact that the vectors produced by the BV, EBV algorithms, and the finite-time Lyapunov vectors are similar for small amplitudes. The continuum theory establishes the relationship between the two algorithms and general directional derivatives.Numerical comparisons of BV and EBV for the three-equation Lorenz model and for a forced, dissipative partial differential equation of Cahn–Hilliard type that arises in modeling the thermohaline circulation demonstrate that the EBV yields a size-ordered description of the perturbation field and is more robust than the BV in the higher nonlinear regime. The EBV yields insight into the fractal structure of the Lorenz attractor and of the inertial manifold for the Cahn–Hilliard-type partial differential equation.
One Year after Endoscopic Sinus Surgery in Polyposis
Authors: Ehnhage Anders , Olsson Petter , Kölbeck Karl‐Gustav , Skedinger Maria , Stjärne Pär ,   NAFS Study Group
Published: January 2012

ObjectiveNasal polyposis is a disease known to be associated with asthma. The long‐term effects of surgical treatment on lower airways have not been sufficiently studied.Study DesignOne‐year follow‐up of a double‐blind, randomized, placebo‐controlled study.SettingThe study was conducted at the Karolinska University Hospital, Stockholm, Sweden.Subjects and MethodsFifty‐one patients, age 18 years or older, with nasal polyposis and asthma were evaluated 1 year after endoscopic sinus surgery (ESS). Outcomes included dyspnea/cough scores, mean daily peak expiratory flow rate, spirometry, butanol test, olfaction scores, peak nasal inspiratory flow, polyp scores, and health‐related quality of life (SF‐36).ResultsThe short‐term postsurgery improvements in asthma symptom scores, daily peak expiratory flow rate, all nasal parameters including olfaction, and quality‐of‐life scores were generally maintained 1 year after ESS.ConclusionEndoscopic sinus surgery had beneficial long‐term effects on asthma, olfaction, and quality of life in patients with nasal polyposis. This is the first study to show long‐term benefits of ESS on butanol tests in patients with nasal polyposis.
The validity of the DSM-IV PTSD criteria in children and adolescents: A review
Authors: Blom Marloes , Oberink Riëtta 
Published: January 2012

Objective: DSM-V is on its way and doubts have been raised regarding the validity of pediatric PTSD. It is the goal of the current review to critically review the empirical literature on PTSD in youth. Method: A search of PsycINFO, PubMed and reference lists was conducted. Empirical information considered relevant regarding the validity of the criteria was collected. Results/Conclusions: The validity of the symptom criteria and clusters varies, with the Avoidance/Numbing cluster outperforming the Re-experiencing—and Arousal cluster. Factor analytic findings suggest that Arousal criterion D4 should be placed within the Re-experiencing cluster, and that the Avoidance/Numbing cluster should be split up. Some non-DSM-IV PTSD symptoms, among which guilt, have considerable validity in trauma-exposed youth and their inclusion in DSM-V PTSD should be considered. As for preschool children, alternative criteria are recommended that are more developmentally sensitive.
Automatic categorization of diverse experimental information in the bioscience literature
Authors: Fang Ruihua , Schindelman Gary , Auken Kimberly Van , Fernandes Jolene , Chen Wen , Wang Xiaodong , Davis Paul , Tuli Mary Ann , Marygold Steven J , Millburn Gillian , Matthews Beverley , Zhang Haiyan , Brown Nick , Gelbart William M , Sternberg Paul W 
Published: January 2012

AbstractBackgroundCuration of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and theSaccharomycesGenome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such asC. elegansandD. melanogasterto identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance.ResultsWe successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction.ConclusionsOur methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.
The cyclin-like protein Spy1/RINGO promotes mammary transformation and is elevated in human breast cancer
Authors: Al Sorkhy Mohammad , Ferraiuolo Rosa-Maria , Jalili Espanta , Malysa Agnes , Fratiloiu Andreea R , Sloane Bonnie F , Porter Lisa A 
Published: January 2012

Abstract

Background
Spy1 is a novel 'cyclin-like' activator of the G1/S transition capable of enhancing cell proliferation as well as inhibiting apoptosis. Spy1 protein levels are tightly regulated during normal mammary development and forced overexpression in mammary mouse models accelerates mammary tumorigenesis.

Methods
Using human tissue samples, cell culture models and in vivo analysis we study the implications of Spy1 as a mediator of mammary transformation and breast cancer proliferation.

Results
We demonstrate that this protein can facilitate transformation in a manner dependent upon the activation of the G2/M Cdk, Cdk1, and the subsequent inhibition of the anti-apoptotic regulator FOXO1. Importantly, we show for the first time that enhanced levels of Spy1 protein are found in a large number of human breast cancers and that knockdown of Spy1 impairs breast cancer cell proliferation.

Conclusions
Collectively, this work supports that Spy1 is a unique activator of Cdk1 in breast cancer cells and may represent a valuable drug target and/or a prognostic marker for subsets of breast cancers.
Expression and clinical significance of extracellular matrix protein 1 and vascular endothelial growth factor-C in lymphatic metastasis of human breast cancer
Authors: Wu Qiu-Wan , She Hong-Qiang , Liang Jing , Huang Yu-Fan , Yang Qing-Mo , Yang Qiao-Lu , Zhang Zhi-Ming 
Published: January 2012

Abstract

Background
Extracellular matrix protein 1 (ECM1) and vascular endothelial growth factor-C (VEGF-C) are secretory glycoproteins that are associated with lymphangiogenesis; these proteins could, therefore, play important roles in the lymphatic dissemination of tumors. However, very little is known about their potential roles in lymphangiogenesis. The aim of this study was to investigate whether correlations exist between ECM1 and VEGF-C in human breast cancer, lymphangiogenesis, and the clinicopathological characteristics of the disease.

Methods

ECM1 and VEGF-C mRNA and protein expression levels in 41 patients were investigated using real-time reverse transcriptase polymerase chain reaction (RT-PCR), or immunohistochemical (IHC) staining of breast cancer tissue, matched noncancerous breast epithelial tissues, and suspicious metastatic axillary lymph nodes. D2-40 labelled lymph vessels and lymphatic microvessel density (LMVD) were counted. Correlations between ECM1 or VEGF-C protein expression levels, LMVD, and clinicopathological parameters were statistically tested.

Results
The rate of ECM1 positive staining in breast cancer tissues was higher (31/41, 75.6%) than that in the corresponding epithelial tissues (4/41, 9.8%, P < 0.001) and lymph nodes (13/41, 31.7%, P < 0.001). Similarly, the VEGF-C expression rate in cancer specimens was higher (33/41, 80.5%) than in epithelial tissues (19/41, 46.3%, P < 0.01) or lymph nodes (15/41, 36.6%, P < 0.01). Higher ECM1 and VEGF-C mRNA expression levels were also detected in the tumor tissues, compared to the non-cancerous tissue types or lymph nodes (P < 0.05). ECM1 protein expression was positively correlated with the estrogen receptor status (P < 0.05) and LMVD (P < 0.05). LMVD in the ECM1- and VEGF-C-positive tumor specimens was higher than that in the tissue types with negative staining (P < 0.05).

Conclusions
Both ECM1 and VEGF-C were overexpressed in breast cancer tissue samples. ECM1 expression was positively correlated with estrogen responsiveness and the metastatic properties of breast cancer. We conclude, therefore, that ECM1 and VEGF-C may have a synergistic effect on lymphangiogenesis to facilitate lymphatic metastasis of breast cancer.
Socio-economic variation in CT scanning in Northern England, 1990-2002
Authors: Pearce Mark S , Salotti Jane A , McHugh Kieran , Pyo Kim Kwang , Craft Alan W , Lubin Jay , Ron Elaine , Parker Louise 
Published: January 2012

Abstract
Background
Socio-economic status is known to influence health throughout life. In childhood, studies have shown increased injury rates in more deprived settings. Socio-economic status may therefore be related to rates of certain medical procedures, such as computed tomography (CT) scans. This study aimed to assess socio-economic variation among young people having CT scans in Northern England between 1990 and 2002 inclusive.

Methods
Electronic data were obtained from Radiology Information Systems of all nine National Health Service hospital Trusts in the region. CT scan data, including sex, date of scan, age at scan, number and type of scans were assessed in relation to quintiles of Townsend deprivation scores, obtained from linkage of postcodes with census data, using χ2 tests and Spearman rank correlations.

Results
During the study period, 39,676 scans were recorded on 21,089 patients, with 38,007 scans and 19,485 patients (11344 male and 8132 female) linkable to Townsend scores. The overall distributions of both scans and patients by quintile of Townsend deprivation scores were significantly different to the distributions of Townsend scores from the census wards included in the study (p < 0.0001). There was a significant association between type of scan and deprivation quintile (p < 0.0001), primarily due to the higher proportions of head scans in the three most deprived quintiles, and slightly higher proportions of chest scans and abdomen and pelvis scans in the least deprived groups. There was also a significant association (p < 0.0001) between the patient's age at the time of the CT scan and Townsend deprivation quintiles, with slightly increasing proportions of younger children with increasing deprivation. A similar association with age (p < 0.0001) was seen when restricting the data to include only the first scan of each patient. The number of scans per patient was also associated with Townsend deprivation quintiles (p = 0.014).

Conclusions
Social inequalities exist in the numbers of young people undergoing CT scans with those from deprived areas more likely to do so. This may reflect the rates of injuries in these individuals and implies that certain groups within the population may receive higher radiation doses than others due to medical procedures.
Liver angiosarcoma, a rare liver malignancy, presented with intraabdominal bleeding due to rupture- a case report
Authors: Chien Chin-Ying , Hwang Cheng-cheng , Yeh Chun-nan , Chen Huang-yang , Wu Jui-Teng , Chan Siu-Cheung , Lin Chih-Lang , Yen Cho-li , Wang Wen-yen , Chiang Kun-Chun 
Published: January 2012

AbstractLiver angiosarcoma is a rare disease, however it still ranks as the third of most common primary liver maligancies. The prognosis of liver angiosarcoma is very poor with almost all patients with this kind of disease die within 2 years after diagnosis. No specific symptoms and signs are closely associated with this disease. Here, we report a case presenting shock status at first due to rupture of liver angiosarcoma- induced internal bleeding. After emergent transarterial embolization (TAE), she received partial hepatectomy two weeks later. 4 months after operation, she is still with a good performance status without obvious recurrence or metastasis identified.
The Wiener-Hopf Equation Technique for Solving General Nonlinear Regularized Nonconvex Variational Inequalities
Authors: Balooee Javad , Cho Yeol Je , Kang Mee Kwang 
Published: January 2012

AbstractIn this paper, we introduce and study some new classes of extended general nonlinear regularized non-convex variational inequalities and the extended general nonconvex Wiener-Hopf equations, and by the projection operator technique, we establish the equivalence between the extended general nonlinear regularized nonconvex variational inequalities and the fixed point problems as well as the extended general nonconvex Wiener-Hopf equations. Then by using this equivalent formulation, we discuss the existence and uniqueness of solution of the problem of extended general nonlinear regularized nonconvex variational inequalities. We apply the equivalent alternative formulation and a nearly uniformly Lipschitzian mapping S for constructing some new p-step projection iterative algorithms with mixed errors for finding an element of set of the fixed points of nearly uniformly Lipschitzian mapping S which is unique solution of the problem of extended general nonlinear regularized nonconvex variational inequalities. We also consider the convergence analysis of the suggested iterative schemes under some suitable conditions.Mathematics Subject Classification (2010)Primary 47H05; Secondary 47J20, 49J40
Nonlinear coupled fixed point theorems in ordered generalized metric spaces with integral type
Authors: Cho Yeol Je , Rhoades Billy E , Saadati Reza , Samet Bessem , Shatanawi Wasfi 
Published: January 2012

Abstract
In this article, we study coupled coincidence and coupled common fixed point theorems in ordered generalized metric spaces for nonlinear contraction condition related to a pair of altering distance functions. Our results generalize and modify several comparable results in the literature.

2000 MSC: 54H25; 47H10; 54E50.
The genome and proteome of a Campylobacter coli bacteriophage vB_CcoM-IBB_35 reveal unusual features
Authors: Carvalho Carla M , Kropinski Andrew M , Lingohr Erika J , Santos Sílvio B , King Jonathan , Azeredo Joana 
Published: January 2012

Abstract

Background

Campylobacter is the leading cause of foodborne diseases worldwide. Bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and thus considered an appealing option to control bacterial pathogens. Nevertheless for an effective use of phages as antimicrobial agents, it is important to understand phage biology which renders crucial the analysis of phage genomes and proteomes. The lack of sequence data from Campylobacter phages adds further importance to these studies.

Methods
vB_CcoM-IBB_35 is a broad lytic spectrum Myoviridae Campylobacter phage with high potential for therapeutic use. The genome of this phage was obtained by pyrosequencing and the sequence data was further analyzed. The proteomic analysis was performed by SDS-PAGE and Mass spectrometry.

Results and conclusions
The DNA sequence data of vB_CcoM-IBB_35 consists of five contigs for a total of 172,065 bp with an average GC content of 27%. Attempts to close the gaps between contigs were unsuccessful since the DNA preparations appear to contain substances that inhibited Taq and ϕ29 polymerases. From the 210 identified ORFs, around 60% represent proteins that were not functionally assigned. Homology exists with members of the Teequatrovirinae namely for T4 proteins involved in morphogenesis, nucleotide metabolism, transcription, DNA replication and recombination. Tandem mass spectrometric analysis revealed 38 structural proteins as part of the mature phage particle.

Conclusions
Genes encoding proteins involved in the carbohydrate metabolism along with several incidences of gene duplications, split genes with inteins and introns have been rarely found in other phage genomes yet are found in this phage. We identified the genes encoding for tail fibres and for the lytic cassette, this later, expressing enzymes for bacterial capsular polysaccharides (CPS) degradation, which has not been reported before for Campylobacter phages.
Carcinoma involving the gallbladder: a retrospective review of 23 cases - pitfalls in diagnosis of gallbladder carcinoma
Authors: Giang Tran H , Ngoc Tran TB , Hassell Lewis A 
Published: January 2012

Abstract

Background
Carcinoma of the gallbladder (GBC) clinically mimics benign gallbladder diseases and often escapes detection until advanced stage. Despite the frequency of cholecystectomy, diagnosis of GBC remains problematic in many situations. We sought to identify pathologic features that contribute to the difficulty in recognition of GBC.

Methods
We identified 23 patients (ranged from 45 to 86 years, male to female ratio 1:4.5) with carcinoma involving the gallbladder referred to an academic medical center over a period of 10 years for study. This includes 10 cases of primary GBC, 6 cases of metastatic tumor to gallbladder, 6 cases of directly invasive adenocarcinoma arising elsewhere in the biliary tree, and one case of unidentified origin adenocarcinoma. Primary tumors include adenocarcinoma not otherwise specified (NOS) in 6 cases, papillary adenocarcinoma in 2 cases, and single cases of undifferentiated carcinoma and combined adenocarcinoma and neuroendocrine carcinoma (NEC). Metastatic tumors to gallbladder were from a wide range of primary sites, predominantly the gastrointestinal tract.

Results
These cases illustrate seven potential pitfalls which can be encountered. These include: 1) mistakenly making a diagnosis of adenocarcinoma of gallbladder when only benign lesions such as deeply penetrating Rokitansky-Aschoff sinuses are present (overdiagnosis), 2) misdiagnosing well-differentiated invasive carcinoma with minimal disease as benign disease (underdiagnosis), 3) differentiating between primary NEC of gallbladder and metastasis, 4) confusing primary mucinous adenocarcinoma of gallbladder with pseudomyxoma peritonei from a low grade appendiceal neoplasm disseminated to gallbladder, 5) confusing gangrenous necrosis related to cholecystitis with geographic tumoral necrosis, 6) undersampling early, grossly occult disease, and 7) misinterpreting extracellular mucin pools.

Conclusions
Clinical history and a high index of suspicion are prerequisite to detecting GBC. Detection of GBC at an early stage is difficult because the symptoms mimic benign gallbladder diseases. Misinterpretation of subtle microscopic abnormalities contributes diagnostic failures in early cases. Careful attention to any evidence of mural thickening, thorough sampling, particularly in older patients, and close examination of any deeply situated glandular structures are critical. Correlations with radiographic and clinical findings are important helps to avoid misdiagnosis in this commonly resected organ.

Virtual Slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1443233938651038.
Safety and efficacy of rituximab treatment for vasculitis in hepatitis B virus-associated type II cryoglobulinemia: a case report
Authors: Pasquet Florian , Combarnous François , MacGregor Brigitte , Coppere Brigitte , Mausservey Christelle , Ninet Jacques , Hot Arnaud 
Published: January 2012

Abstract

Introduction
Systemic B-cell depletion and clinical remission of the systemic effects of cryoglobulins have already been achieved using rituximab in hepatitis C virus-positive immunocompetent patients. Conversely, to the best of our knowledge there are no reports in the literature regarding the use of rituximab in hepatitis B virus-associated cryoglobulinemia.

Case presentation
We report here the case of a 60-year-old Caucasian man who presented with hepatitis B virus-associated type II cryoglobulinemia with severe multisystem disease, including membranoproliferative glomerulonephritis with acute renal failure. The vasculitis was refractory to conventional and antiviral therapy but rituximab use led to a fall in cryoglobulin levels and disease control. The B-cell depletion was safe and efficient to induce a complete remission of the disease.

Conclusion
Our case highlights the benefit and the efficacy of rituximab in association with antiviral therapy in small vessel vasculitis related to hepatitis B virus-associated mixed cryoglobulinemia.