bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust and efficient approach to detect 3D rectal tubes from CT colonography
Authors: Yang Xiaoyun , Slabaugh Greg 
Published: October 2011

Purpose:The rectal tube (RT) is a common source of false positives (FPs) in computer‐aided detection (CAD) systems for CT colonography. A robust and efficient detection of RT can improve CAD performance by eliminating such “obvious” FPs and increase radiologists' confidence in CAD.Methods:In this paper, we present a novel and robust bottom‐up approach to detect the RT. Probabilistic models, trained using kernel density estimation on simple low‐level features, are employed to rank and select the most likely RT tube candidate on each axial slice. Then, a shape model, robustly estimated using random sample consensus (RANSAC), infers the global RT path from the selected local detections. Subimages around the RT path are projected into a subspace formed from training subimages of the RT. A quadratic discriminant analysis (QDA) provides a classification of a subimage as RT or non‐RT based on the projection. Finally, a bottom‐top clustering method is proposed to merge the classification predictions together to locate the tip position of the RT.Results:Our method is validated using a diverse database, including data from five hospitals. On a testing data with 21 patients (42 volumes), 99.5% of annotated RT paths have been successfully detected. Evaluated with CAD, 98.4% of FPs caused by the RT have been detected and removed without any loss of sensitivity.Conclusions:The proposed method demonstrates a high detection rate of the RT path, and when tested in a CAD system, reduces FPs caused by the RT without the loss of sensitivity.
Gaussia princeps Luciferase as a Reporter for Transcriptional Activity, Protein Secretion, and Protein-Protein Interactions in Salmonella enterica Serovar Typhimurium
Authors: Wille Thorsten , Blank Kathrin , Schmidt Christiane , Vogt Vivien , Gerlach Roman G. 
Published: October 2011

ABSTRACT

Gaussia princeps
luciferase (Gluc) is widely used as a reporter in eukaryotes, but data about its applicability in bacteria are very limited. Here we show that a codon-optimized Gluc gene can be efficiently expressed in
Salmonella enterica
serovar Typhimurium. To test different Gluc variants as transcriptional reporters, we used the
siiA
promoter of
Salmonella
pathogenicity island 4 (SPI-4) driving expression of either an episomal or a chromosomally integrated Gluc gene. Most reliable results were obtained from lysates of single-copy Gluc reporter strains. Given the small size, high activity, and cofactor independence of Gluc, it might be especially suited to monitor secretion of bacterial proteins. We demonstrate its usefulness by luminescence detection of fusion proteins of Gluc and C-terminal portions of the SPI-4-encoded, type I-secreted adhesin SiiE in supernatants. The SiiE C-terminal moiety including immunoglobulin (Ig) domain 53 is essential and sufficient for mediating type I-dependent secretion of Gluc. In eukaryotes, protein-protein interaction studies based on split-Gluc protein complementation assays (PCA) could be established. We adapted these methods for use in
Salmonella
, demonstrating the interaction between the SPI-1-encoded effector SipA and its cognate secretion chaperone InvB. In conclusion, the versatile Gluc can be used to address a variety of biological questions, thus representing a valuable addition to the toolbox of modern molecular biology and microbiology.
Subunit Approach to Evaluation of the Immune Protective Potential of Leptospiral Antigens
Authors: Félix Samuel R. , Hartwig Daiane D. , Argondizzo Ana Paula C. , Silva Éverton F. , Seixas Fabiana K. , Neto Amilton C. P. Seixas , Medeiros Marco A. , Lilenbaum Walter , Dellagostin Odir A. 
Published: October 2011

ABSTRACT

Leptospirosis is the most widespread zoonosis in the world. Current vaccines are based on whole-cell preparations that cause severe side effects and do not induce satisfactory immunity. In light of the leptospiral genome sequences recently made available, several studies aimed at identification of protective recombinant immunogens have been performed; however, few such immunogens have been identified. The aim of this study was to evaluate 27 recombinant antigens to determine their potential to induce an immune response protective against leptospirosis in the hamster model. Experiments were conducted with groups of female hamsters immunized with individual antigen preparations. Hamsters were then challenged with a lethal dose of
Leptospira interrogans
. Thirteen antigens induced protective immune responses; however, only recombinant proteins LIC10325 and LIC13059 induced significant protection against mortality. These results have important implications for the development of an efficacious recombinant subunit vaccine against leptospirosis.
Estimation of Dengue Virus IgM Persistence Using Regression Analysis
Authors: Prince Harry E. , Matud Jose L. 
Published: October 2011

ABSTRACT
Dengue virus IgM persistence was estimated using follow-up sera from 98 patients (60 with primary infections and 38 with secondary infections) whose first-specimen IgM index was strongly positive, suggesting recent disease onset. Regression analysis of the follow-up IgM index versus days between samples yielded a trend line that reached the cut-point index (1.10) at 179 days for the primary infection group and 139 days for the secondary infection group. This difference reflected significantly higher first-sample IgM indices in primary infections than in secondary infections rather than differences in IgM decay rates.
Physiological and Biochemical Characterization of AnNitA, the Aspergillus nidulans High-Affinity Nitrite Transporter
Authors: Unkles Shiela E. , Symington Vicki F. , Kotur Zorica , Wang Ye , Siddiqi M. Yaeesh , Kinghorn James R. , Glass Anthony D. M. 
Published: October 2011

ABSTRACT

High-affinity nitrite influx into mycelia of
Aspergillus nidulans
has been characterized by use of
13
NO
2
−
, giving average

K
m

and
V
max
values of 48 ± 8 μM and 228 ± 49 nmol mg
−1
dry weight (DW) h
−1
, respectively. Kinetic analysis of a plot that included an additional large number of low-concentration fluxes gave an excellent monophasic fit (
r
2
= 0.96), with no indication of sigmoidal kinetics. Two-dimensional (2D) and three-dimensional (3D) models of AnNitA are presented, and the possible roles of conserved asparagine residues N122 (transmembrane domain 3 ]Tm 3]), N173 (Tm 4), N214 (Tm 5), and N246 (Tm 6) are discussed.
Hepatic haemangiomas: possible association with IL-17
Authors: Wang ZhaoJing , Yuan Yifeng , Zhuang Haiwen , Jiang Runqiu , Hou Jiajie , Chen Qi , Zhang Feng 
Published: October 2011

BackgroundInterleukin-17 (IL-17) has been cast as a major player in angiopoiesis of carcinoma, but its role in hepatic haemangioma is not entirely clear.AimThe aim of this study is to address the expression levels and the molecular mechanism underlying the role of IL-17 on hepatic haemangioma progression.Methods and Results20 hepatic haemangioma patients and 15 healthy subjects were included in this study. IL-17 mRNA levels were examined by PCR-based methods and protein levels by western blot. We observed a significant increase in tissue IL-17 mRNA and protein levels in hepatic haemangioma compared to normal liver tissue. Matrix metalloproteinase protein levels were slightly elevated in haemangiomas compared to normal, and IL-6 and phospho-stat3 levels were markedly elevated. However, no differences in mRNA levels of angiogenesis-associated cytokines such as vascular endothelial growth factor were seen in hepatic haemangiomas compared to normal cases taken from donor livers at the time of organ harvest. IL-17 was localised to CD4-positive cells by flow cytometry and to stromal cells and endothelial cells by immunohistochemistry. Owing to the absence of an animal model of haemangioma, we examined the effects of IL-17 on angiogenesis-related functions of vascular endothelial cells in vitro. Notably, IL-17, when added to cell cultures of human umbilical cord-derived endothelial cells, had an effect on the secretion of IL-6 and p-stat3.ConclusionsBased on these findings, we propose that IL-17 may mediate the angiogenesis in a IL-6-Stat3-dependent manner and play an important role in the pathophysiology of hepatic haemangioma.
Synthesis and X-ray photoelectron spectroscopy (XPS) and thermoelectric studies of ternary Bi2(Te0.5Se0.5)3 mixed-metal chalcogenide thin films by the arrested precipitation technique
Authors: Patil S. M. , Mane S. R. , Mane R. M. , Mali S. S. , Patil P. S. , Bhosale P. N. 
Published: October 2011

Arrested precipitation technique (APT) has been successfully employed for the deposition of Bi2(Te0.5Se0.5)3 thin films. Analytical grade bismuth nitrate complexes with triethanolamine (TEA), sodium tellurosulfite, and sodium selenosulfite were used as precursor materials. The film was obtained at 55 ± 0.5 °C in an aqueous alkaline medium (pH = 10.5 ± 0.2). As-deposited film was characterized by chemical compositional, optical, and electrical analyses. The optical absorption spectrum for the sample was recorded in the wavelength region 400–900 nm. It shows a high coefficient of absorption (α = 105 cm–1) with an allowed direct type of transition. X-ray diffraction (XRD) study of the film shows a nanocrystalline and rhombohedral structure. From scanning electron microscopy (SEM), atomic force microscopy (AFM), and energy dispersive X-ray analysis (EDAX) studies, the deposited film shows uniform morphology and good stoichiometry. X-ray photoelectron spectroscopy (XPS) was used to study the binding energy and surface oxidation of the material. Electrical conduction study shows that material is an n-type semiconductor and shows good thermoelectric figure of merit.
Reaction of iodine with metal oxides
Authors: Gliński Marek , Ulkowska Urszula 
Published: October 2011

The reaction of iodine with various metal oxides has been studied in both vapour phase (373–873 K) and in solution in cyclohexane, under anhydrous conditions. The course of the reaction has been revised in accordance with literature and experimental data. Apart from adsorbed iodine molecules ([I2] < 200 μmol·g–1), the presence of I– ions ([I–] < 50 μmol·g–1) has been noted. IOn– ions have been observed only when both water and strong basic sites, such as those on MgO or La2O3, are present. It has been found that the strength of interaction of iodine with metal oxide increases with basicity of the oxide.
Functional Characterization of an scFv-Fc Antibody that Immunotherapeutically Targets the Common Cancer Cell Surface Proteoglycan CSPG4
Authors: Wang Xinhui , Katayama Akihiro , Wang Yangyang , Yu Ling , Favoino Elvira , Sakakura Koichi , Favole Alessandra , Tsuchikawa Takahiro , Silver Susan , Watkins Simon C. , Kageshita Toshiro , Ferrone Soldano 
Published: October 2011

AbstractCell surface chondroitin sulfate proteoglycan 4 (CSPG4) is an attractive target for antibody-based cancer immunotherapy because of its role in tumor cell biology, its high expression on malignant cells including cancer-initiating cells, and its restricted distribution in normal tissues. The clinical use of CSPG4 has been hampered by the lack of a CSPG4-specific chimeric, humanized, or fully human monoclonal antibody. To overcome this limitation, we generated a CSPG4-specific fully human single-chain antibody termed scFv-FcC21 and characterized its specificity and antitumor activity. Viable CSPG4+ melanoma cells were used in a screen of a human scFv phage display library that included CDR3 engineered to optimize antibody binding sites. The scFv antibody isolated was then recombinantly engineered with a human immunoglobulin G1 Fc region to construct the fully human antibody scFv-FcC21, which recognized tumors of neuroectodermal origin, various types of carcinomas, mesotheliomas, and sarcomas as well as myeloid leukemias. scFv-FcC21 inhibited in vitro growth and migration of tumor cells and in vivo growth of human tumor xenografts. These effects were mediated by inhibition of the activation of extracellular signal–regulated kinase and focal adhesion kinase signaling pathways that are critical for tumor cell growth and migration, respectively. Our findings define the CSPG4-specific fully human scFv-FcC21 antibody as a candidate therapeutic agent to target the many types of tumors that express CSPG4. Cancer Res; 71(24); 7410–22. ©2011 AACR.
Early [18F]Fluorodeoxyglucose Positron Emission Tomography at Two Days of Gefitinib Treatment Predicts Clinical Outcome in Patients with Adenocarcinoma of the Lung
Authors: Takahashi Ryo , Hirata Haruhiko , Tachibana Isao , Shimosegawa Eku , Inoue Atsuo , Nagatomo Izumi , Takeda Yoshito , Kida Hiroshi , Goya Sho , Kijima Takashi , Yoshida Mitsuhiro , Kumagai Toru , Kumanogoh Atsushi , Okumura Meinoshin , Hatazawa Jun , Kawase Ichiro 
Published: October 2011

Abstract
Purpose: Positron emission tomography (PET) with [18F]fluorodeoxyglucose (FDG) is increasingly used in early assessment of tumor response after chemotherapy. We investigated whether a change in [18F]FDG uptake at 2 days of gefitinib treatment predicts outcome in patients with lung adenocarcinoma.
Experimental Design: Twenty patients were enrolled. [18F]FDG-PET/computed tomographic (CT) scan was carried out before and 2 days after gefitinib treatment. Maximum standardized uptake values (SUV) were measured, and post-gefitinib percentage changes in SUV were calculated. Early metabolic response (SUV decline &lt; −25%) was compared with morphologic response evaluated by CT scan and with progression-free survival (PFS).
Results: At 2 days of gefitinib treatment, 10 patients (50%) showed metabolic response, 8 had metabolic stable disease, and 2 had progressive metabolic disease. Percentage changes of SUV at 2 days were correlated with those of tumor size in CT at 1 month (R2 = 0.496; P = 0.0008). EGFR gene was assessable in 15 patients, and of 12 patients with EGFR mutations, 8 showed metabolic response at 2 days and 6 showed morphologic response at 1 month. None of 3 patients with wild-type EGFR showed metabolic or morphologic response. Metabolic response at 2 days was not statistically associated with PFS (P = 0.095), but when a cutoff value of −20% in SUV decline was used, metabolic responders had longer PFS (P &lt; 0.0001).
Conclusion: Early assessment of [18F]FDG tumor uptake with PET at 2 days of gefitinib treatment could be useful to predict clinical outcome earlier than conventional CT evaluation in patients with lung adenocarcinoma. Clin Cancer Res; 18(1); 220–8. ©2011 AACR.
Micromanaging the Classification of Colon Cancer: The Role of the microRNAome
Authors: Vilar Eduardo , Tabernero Josep , Gruber Stephen B. 
Published: October 2011

Abstract
Recent advances in our understanding of the microRNAome (miRNAome) have provided further insights into the molecular pathogenesis of colorectal cancer and shown a potential role for miRNAs in distinguishing molecular subtypes. The mucosa-adenoma-carcinoma model can now integrate miRNAs into the known genetic alterations that drive the progression of colorectal neoplasia. Clin Cancer Res; 17(23); 7207–9. ©2011 AACR.
Hemangioma Is Associated with Atopic Disease
Authors: Grimmer J. Fredrik , Williams Marc S. , Pimentel Richard , Mineau Geraldine , Wood Grant M. , Bayrak‐Toydemir Pinar , Stevenson David A. 
Published: October 2011

ObjectiveTo determine if atopic disease is associated with infantile hemangioma.Study DesignCase control study.SettingState of Utah inpatient and outpatient records obtained from the Department of Health, Intermountain Healthcare medical records, and the University of Utah Health Care medical records using the Utah Population Database.SubjectsPatients given an International Classification of Diseases, Ninth Revision diagnosis of hemangioma prior to age 5 years, from 1991 to 2009.MethodsAllergy, asthma, and eczema rates in the hemangioma cohort compared to randomly matched controls using logistic regression analysis.ResultsThe authors identified 2063 patients in the hemangioma group. The overall odds ratio of atopic disease in patients diagnosed with hemangioma was 1.67 compared to the control group (P <. 0001). In the hemangioma cohort, the authors found a 36% increased risk of allergies (P <. 0001), 67% increased risk of asthma (P < 4e‐12), and 82% increased risk of eczema (P < 2e‐16).ConclusionThis study indicates that allergy, asthma, and eczema are positively associated with hemangioma. Eczema was most strongly associated with hemangioma, with a nearly 2‐fold increased risk. Understanding the relationship between atopic disease and infantile hemangioma may elucidate the pathophysiology of each and ultimately lead to better treatment options.
Relationship Between Proximal Femoral and Acetabular Alignment in Normal Hip Joints Using 3-Dimensional Computed Tomography
Authors: Buller Leonard T. , Rosneck James , Monaco Feno M. , Butler Robert , Smith Travis , Barsoum Wael K. 
Published: October 2011

Background: The bony architecture of the hip depends upon functional adaptation to mechanical usage via the dynamic interaction between the acetabulum and femoral head. Acetabular retroversion is thought to be a contributing factor of pincer-type femoroacetabular impingement. Studies of pathological hip joints suggest proximal femoral anatomy compensates for acetabular retroversion. Hypothesis/Purpose: The purpose of this study was to determine if a predictable relationship exists between proximal femoral and acetabular angles, age, and gender in normal hip joints. We hypothesized that, through functional adaptation to mechanical loading, a complementary developmental relationship exists between the acetabulum and proximal femur. Study Design: Descriptive laboratory study. Methods: The femoral neck version, femoral neck shaft angle, acetabular version, acetabular inclination, and center edge angle were measured in 230 normal hip joints in 115 adults using 3-dimensional reconstruction software. Correlations between the angles, age, and gender were examined using the methods of stepwise regression and backward elimination. Results: Regarding side-to-side comparison and variability, there was no statistically significant difference between the left and right sides in the average value of each angle measurement. The correlations specifically between angles, age, and gender were similar on the left and right sides for all pairs except femoral version and acetabular inclination. Regarding significant findings of the study, a positive correlation ( P < .05) was found between femoral version and acetabular version (0.38° to 1°). A positive correlation was found between femoral neck shaft angle and acetabular version (0.21° to 1°). A negative correlation was found between femoral neck shaft angle and age (–0.17° to 1°). A positive correlation was found between acetabular version and female gender (2.6° to 1°). A positive correlation was found between center edge angle and female gender (2.8° to 1°). A negative correlation was found between femoral version and acetabular inclination (–0.49° to 1°), although this latter relationship was only observed unilaterally (ie, left hip). Conclusion: This study demonstrates that a correlation exists between multiple proximal femoral and acetabular angles in normal hip joints. These findings support the hypothesis that a complementary developmental relationship occurs between the femoral head and acetabulum. Clinical Relevance: The results of this study suggest that, in some patients, what is thought to be pathological acetabular retroversion may actually be normal anatomy with a compensated femoral version. Investigating the relationship between these angles in patients with the signs and symptoms of pincer-type femoroacetabular impingement may alter a surgeon’s approach to this patient population.
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast
Authors: Deniz Özgen , Flores Oscar , Battistini Federica , Pérez Alberto , Soler-López Montserrat , Orozco Modesto 
Published: October 2011

Abstract

Background
In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive.

Results
Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions.

Conclusions
Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.
The changing seroepidemiology of enterovirus 71 infection among children and adolescents in Singapore
Authors: Ang Li-Wei , Phoon Meng-Chee , Wu Yan , Cutter Jeffery , James Lyn , Chow Vincent T 
Published: October 2011

AbstractBackgroundEnterovirus 71 (EV71) has caused recurrent epidemics of hand, foot and mouth disease among children in Singapore. Between August 2008 and July 2010, we conducted a survey to estimate the seroprevalence of EV71 infection among children and adolescents aged 1-17 years. We compared our EV71 seroepidemiologic findings with a previous study conducted in 1996-1997.MethodsThe survey involved the prospective collection of 1,200 residual sera from Singapore residents aged 1-17 years in two hospitals. Neutralizing antibodies to EV71 were detected by the microneutralization test. The geometric mean titer (GMT) of EV71 antibodies and 95% confidence intervals (CI) were calculated and compared by age groups. Statistical significance was taken asP< 0.05.ResultsThe overall EV71 antibody prevalence was 26.9% (95% CI: 24.5-29.5%). It increased significantly from 14.3% in children aged 1-6 years to 27.8% in those aged 7-12 years, and reached 38.8% in adolescents aged 13-17 years. The seroconversion rate differed by about 12% between the consecutive age groups. The GMT of EV71 antibodies was higher among primary school children aged 7-12 years in our study than that among the 6-12 year age group in the 1996-1997 study.ConclusionsHigher antibody titers were observed in children aged 1-6 years than those in the other two age groups, indicating that most of the infections had been acquired during early childhood. EV71 infection is common among children and adolescents in Singapore, with 39% infected by the time they are in secondary school (13-17 years of age).