bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of dual‐energy subtraction for converting CT numbers to electron density based on a single linear relationship
Authors: Saito Masatoshi 
Published: March 2012

Purpose:The conversion of the computed tomography (CT) number to electron density is one of the main processes that determine the accuracy of patient dose calculations in radiotherapy treatment planning. However, the CT number and electron density of tissues cannot be generally interrelated via a simple one‐to‐one correspondence because the CT number depends on the effective atomic number as well as the electron density. The purpose of this study is to present a simple conversion from the energy‐subtracted CT number (ΔHU) by means of dual‐energy CT (DECT) to the relative electron density (ρe) via a single linear relationship.Methods:The ΔHU–ρe conversion method was demonstrated by performing analytical DECT image simulations that were intended to imitate a second‐generation dual‐source CT (DSCT) scanner with an additional tin filtration for the high‐kV tube. The ΔHU–ρe calibration line was obtained from the image simulation with a 33 cm‐diameter electron density calibration phantom equipped with 16 inserts including polytetrafluoroethylene, polyvinyl chloride, and aluminum; the elemental compositions of these three inserts were quite different to those of body tissues. The ΔHU–ρe conversion method was also applied to previously published experimental CT data, which were measured using two different CT scanners, to validate the clinical feasibility of the present approach. In addition, the effect of object size on ρe‐calibrated images was investigated by image simulations using a 25 cm‐diameter virtual phantom for two different filtrations: with and without the tin filter for the high‐kV tube.Results:The simulated ΔHU–ρe plot exhibited a predictable linear relationship over a wide range of ρe from 0.00 (air) to 2.35 (aluminum). Resultant values of the coefficient of determination, slope, and intercept of the linear function fitted to the data were close to those of the ideal case. The maximum difference between the ideal and simulated ρe values was −0.7%. The satisfactory linearity of ΔHU–ρe was also confirmed from analyses of the experimental CT data. In the experimental cases, the maximum difference between the nominal and simulated ρe values was found to be 2.5% after two outliers were excluded. When compared with the case without the tin filter, the ΔHU–ρe conversion performed with the tin filter yielded a lower dose and more reliable ρe values that were less affected by the object‐size variation.Conclusions:The ΔHU–ρe calibration line with a simple one‐to‐one correspondence would facilitate the construction of a well‐calibrated ρe image from acquired dual‐kV images, and currently, second generation DSCT may be a feasible modality for the clinical use of the ΔHU–ρe conversion method.
Maternal depression and infant growth and development in British Pakistani women: a cohort study
Authors: Husain Nusrat , Cruickshank John Kennedy , Tomenson Barbara , Khan Sarah , Rahman Atif 
Published: March 2012

ObjectivesPerinatal depression has been found to be a strong and independent risk factor for poor child growth and development in low-income South Asian populations. The authors aimed to study if there was a similar association in first and second-generation British women of Pakistani origin.DesignA prospective cohort study.SettingThe study was conducted in the North-West of England, in areas with high density of Pakistani-origin population. The subjects were recruited from Central Manchester Hospital in the City of Manchester and East Lancashire Hospital in Lancashire.Participants704 physically healthy women were assessed in two phases (screening and detailed assessment of high scorers and a proportion of low scorers) during the third trimester of pregnancy to obtain at birth a cohort of 63 infants of depressed mothers and 173 infants of psychologically well mothers.Primary and secondary outcome measuresAll infants were weighed and measured at birth and 6 months, and their development was assessed using the Bayley Scales of Infant Development–Third Edition.ResultsThere was no difference in the birth weight or weight and height at 6 months of infants of depressed mothers versus infants of psychologically well mothers. The only significant difference between the two groups was in the infants' adaptive behaviour; infants of depressed mothers scored significantly lower than those of psychologically well mothers (mean difference 4.6, t=2.81, df 195, p=0.006). The associations remained significant after adjustment for socio-demographic factors by multivariate analyses.ConclusionsPrenatal depression is not associated with impaired growth in this sample of British Pakistani women. There is, however, an association of prenatal depression with parent-reported problems in the infants' adaptive behaviour. Further research is needed to understand various pathways through which maternal depression affects infant outcomes in low- and high-income settings.
Phenotypic and genetic characterisation of bacterial sexually transmitted infections in Bissau, Guinea-Bissau, West Africa: a prospective cohort study
Authors: Olsen Birgitta , Månsson Fredrik , Camara Cidia , Monteiro Mario , Biai Ansu , Alves Alfredo , Andersson Sören , Norrgren Hans , Unemo Magnus 
Published: March 2012

BackgroundKnowledge regarding characteristics and transmission ofNeisseria gonorrhoeae,Chlamydia trachomatisandMycoplasma genitaliumand antibiotic resistance inN gonorrhoeaein Guinea-Bissau, West Africa, is entirely lacking.ObjectivesTo characteriseN gonorrhoeae,C trachomatisandM genitaliumsamples from Guinea-Bissau and to define bacterial populations, possible transmission chains and forN gonorrhoeaespread of antibiotic-resistant isolates.DesignProspective cohort study.SettingTwo sexual health and family planning clinics, Bissau, Guinea-Bissau.ParticipantsPositive samples from 711 women and 27 men.Material and methodsPositive samples forN gonorrhoeae(n=31),C trachomatis(n=60) andM genitalium(n=30) were examined. The gonococcal isolates were characterised with antibiograms, serovar determination andN gonorrhoeaemultiantigen sequence typing (NG-MAST). TheC trachomatis ompAgene and theM genitalium mgpBgene were sequenced, and phylogenetic analyses were performed.ResultsForN gonorrhoeae, the levels of resistance (intermediate susceptibility) to ciprofloxacin, erythromycin, rifampicin, ampicillin, tetracycline, penicillin G and cefuroxime were 10% (0%), 6% (10%), 13% (10%), 68% (0%), 74% (0%), 68% (16%) and 0% (84%), respectively. All isolates were susceptible to cefixime, ceftriaxone, spectinomycin and azithromycin, and the minimum inhibitory concentrations of kanamycin (range: 8–32 mg/l) and gentamicin (range: 0.75–6 mg/l) were low (no resistance breakpoints exist for these antimicrobials). 19 NG-MAST sequence types (STs) (84% novel STs) were identified. Phylogenetic analysis of theC trachomatis ompAgene revealed genovar G as most prevalent (37%), followed by genovar D (19%). 23mgpBSTs were found among theM genitaliumisolates, and 67% of isolates had unique STs.ConclusionsThe diversity among the sexually transmitted infection (STI) pathogens may be associated with suboptimal diagnostics, contact tracing, case reporting and epidemiological surveillance. In Guinea-Bissau, additional STI studies are vital to estimate the STI burden and form the basis for a national sexual health strategy for prevention, diagnosis and surveillance of STIs.
Decision-making by ambulance clinicians in London when managing patients with epilepsy: a qualitative study
Authors: Burrell Lisa , Noble Adam , Ridsdale Leone 
Published: March 2012

BackgroundIn the UK, epilepsy is the neurological condition with the highest rate of accident and emergency department re-attendance, with most arriving by ambulance. Ambulance clinicians triage patients and assess their need for attendance. This study examined the decision-making process of ambulance clinicians in these situations.MethodsIn-depth interviews with 15 ambulance clinicians working in South London.ResultsInterviewees identified that epileptic seizures that self-resolve present a triage challenge. They reported insufficient training and guidance available for these situations and substantial reliance on experience to direct their practice. Fears of litigation in the event of complications, pressures of public expectation and limited on-scene access to relevant patient information or appropriate alternative care pathways were reported to be significant factors influencing decisions for care for epilepsy seizures.DiscussionAmbulance clinicians reported negotiating a balance between patient safety and patient choice, when deciding whether to transport a patient with epilepsy to hospital or not. Clinician fears and the pressures and limitations of practice may result in hospital conveyance being used as a safety precaution in some instances.ConclusionsDecisions regarding conveyance of patients with epilepsy in this study were substantially guided by ambulance clinician experience rather than by robust training and guidelines. This study supports the need for improved guidance that addresses this common area of practice and the development of alternative care pathways that may be used by ambulance clinicians for patients with epilepsy.
Outcome and relapse risks of thrombotic thrombocytopaenic purpura: an Egyptian experience
Authors: El-Husseiny Noha M , Goubran Hady , Fahmy Hala M , Tawfik Nehad M , Moustafa Heba , Amin Sherif N , El-Ekiaby Magdy 
Published: March 2012

Abstract

Background
Thrombotic thrombocytopaenic purpura (TTP) is a rare life-threatening disease. Plasma exchange has significantly decreased the mortality from this disease, which still tends to recur in a substantial proportion of patients. This study describes the clinical spectrum and response to treatment and explores the risks of relapse in a cohort of patients.

Methods
Patients treated for TTP at the Clinical Haematology Unit, Cairo University, Egypt, between 2000 and 2008 were identified. Complete demographic, clinical history and full clinical examination, laboratory, treatment modalities and duration, and outcome data were collected and analysed. The follow-up duration was 24 months.

Results
30 patients; 13 men (43%) and 17 women (57%) with a median age of 42 years were treated for 46 episodes of TTP. The median duration of disease onset to diagnosis for the first episode was 7 days. Twenty-three patients (76.66%) were diagnosed as idiopathic primary and seven patients (23.33%) were secondary TTP. Four patients died during the first 24 h. Of the 26 patients, 22 (85.6%) achieved remission with an average of 7.55 plasma exchange sessions, Another nine patients had 25 relapses (mean 2.7). Splenectomy was performed in three patients (11.5%). The 24-month overall survival was 80%. The initial low platelet count and high LDH were the only two statistically significant relapse predictors.

Conclusions
The current results conform to the reported literature on the outcome of TTP. The very early mortality due to late referral highlights the need of education about the disease among primary healthcare providers.
ON δ-LOCAL MODULES AND AMPLY δ-SUPPLEMENTED MODULES
Authors: TRIBAK RACHID 
Published: March 2012

The first part of this paper investigates the structure of δ-local modules. We prove that the following statements are equivalent for a module M: (i) M is δ-local; (ii) M is a coatomic module with either (a) M is a semisimple module having a maximal submodule N such that N is projective and M/N is singular, or (b) M has a unique essential maximal submodule K ≤ M such that for every maximal submodule L ≠ K, M/L is projective. The second part establishes some properties of finitely generated amply δ-supplemented modules.
An Apoptosis Methylation Prognostic Signature for Early Lung Cancer in the IFCT-0002 Trial
Authors: de Fraipont Florence , Levallet Guénaëlle , Creveuil Christian , Bergot Emmanuel , Beau-Faller Michèle , Mounawar Mounia , Richard Nicolas , Antoine Martine , Rouquette Isabelle , Favrot Marie-Christine , Debieuvre Didier , Braun Denis , Westeel Virginie , Quoix Elisabeth , Brambilla Elisabeth , Hainaut Pierre , Moro-Sibilot Denis , Morin Franck , Milleron Bernard , Zalcman Gérard 
Published: March 2012

AbstractPurpose: To evaluate prognostic and predictive molecular biomarkers in early-stage non–small cell lung carcinoma (NSCLC) receiving neoadjuvant chemotherapy.Experimental Design: The IFCT-0002 trial compared two neoadjuvant regimens in 528 stages I to II NSCLC patients. DNA extraction of snap-frozen surgical samples taken from 208 patients receiving gemcitabine-cisplatin or paclitaxel-carboplatin regimens allowed for the identification of 3p allelic imbalance, Ras association domain family 1A (RASSF1A) and death-associated protein kinase 1 (DAPK1) promoter methylation, and epidermal growth factor receptor, K-ras, and TP53 mutations. Multivariate analysis identified prognostic and predictive effects of molecular alterations. A Bootstrapping approach was used to assess stability of the prognostic models generating optimism corrected indexes.Results: RASSF1A methylation correlated significantly with shorter disease-free survival (DFS; adjusted HR = 1.88, 95% CI: 1.25–2.82, P = 0.0048) and shorter median overall survival (OS; adjusted HR = 2.01, 95% CI: 1.26–3.20, P = 0.020). A computed bootstrap resampling strategy led to a prognostic model, including RASSF1A, DAPK1, and tumor stage, dividing patients into three prognostic groups, with median OS ranging from 34 months for high-risk patients (HR for death = 3.85, 95% CI: 1.79–6.40) to more than 84 months for moderate (HR = 1.85, 95% CI: 0.97–3.52) and low-risk patients (reference group; P = 0.00044). In addition, RASSF1A methylation predicted longer DFS in patients treated with paclitaxel-carboplatin compared with gemcitabine-cisplatin (adjusted HR = 0.47, 95% CI: 0.23–0.97, Pinteraction = 0.042).Conclusions: Following neoadjuvant chemotherapy, RASSF1A methylation negatively impacted prognosis of early-stage NSCLC. Along with DAPK1 methylation and tumor stage, RASSF1A methylation allowed definition of three subgroups with strikingly different prognosis. Conversely, significantly longer DFS following paclitaxel-based neoadjuvant chemotherapy for patients whose tumors showed RASSF1A methylation suggested its predictive interest in stages I and II NSCLC. Clin Cancer Res; 18(10); 2976–86. ©2012 AACR.
Prediction of Optimal Deployment Projection for Transcatheter Aortic Valve Replacement
Authors: Binder Ronald K. , Leipsic Jonathon , Wood David , Moore Teri , Toggweiler Stefan , Willson Alex , Gurvitch Ronen , Freeman Melanie , Webb John G. 
Published: March 2012

Background—
Identifying the optimal fluoroscopic projection of the aortic valve is important for successful transcatheter aortic valve replacement (TAVR). Various imaging modalities, including multidetector computed tomography (MDCT), have been proposed for prediction of the optimal deployment projection. We evaluated a method that provides 3-dimensional angiographic reconstructions (3DA) of the aortic root for prediction of the optimal deployment angle and compared it with MDCT.

Methods and Results—

Forty patients undergoing transfemoral TAVR at St Paul's Hospital, Vancouver, Canada, were evaluated. All underwent preimplant 3DA and 68% underwent preimplant MDCT. Three-dimensional angiographic reconstructions were generated from images of a C-arm rotational aortic root angiogram during breath-hold, rapid ventricular pacing, and injection of 32 mL contrast medium at 8 mL/s. Two independent operators prospectively predicted perpendicular valve projections. The implant angle was chosen at the discretion of the physician performing TAVR. The angles from 3DA, from MDCT, the implant angle, and the postdeployment perpendicular prosthesis view were compared. The shortest distance from the postdeployment perpendicular prosthesis projection to the regression line of predicted perpendicular projections was calculated. All but 1 patient had adequate image quality for reproducible angle predictions. There was a significant correlation between 3DA and MDCT for prediction of perpendicular valve projections (
r
=0.682,
P
<0.001). Deviation from the regression line of predicted angles to the postdeployment prosthesis view was 5.1±4.6° for 3DA and 7.9±4.9° for MDCT (
P
=0.01).

Conclusions—
Three-dimensional angiographic reconstructions and MDCT are safe, practical, and accurate imaging modalities for identifying the optimal perpendicular valve deployment projection during TAVR.
The tyrosine phosphatase SHP-1 dampens murine Th17 development
Authors: Mauldin Ileana S. , Tung Kenneth S. , Lorenz Ulrike M. 
Published: March 2012

Abstract
Th17 cells represent a subset of CD4+ T helper cells that secrete the proinflammatory cytokine IL-17. Th17 cells have been ascribed both a beneficial role in promoting clearance of pathogenic fungi and bacteria, and a pathogenic role in autoimmune diseases. Here we identify the tyrosine phosphatase SHP-1 as a critical regulator of Th17 development, using 3 complementary approaches. Impaired SHP-1 activity through genetic deletion of SHP-1, transgenic expression of an inducible dominant negative SHP-1, or pharmacologic inhibition of SHP-1 strongly promotes the development of Th17. Ex vivo Th17 skewing assays demonstrate that genetic or pharmacologic disruption of SHP-1 activity in T cells results in a hyper-response to stimulation via IL-6 and IL-21, 2 cytokines that promote Th17 development. Mechanistically, we find that SHP-1 decreases the overall cytokine-induced phosphorylation of STAT3 in primary CD4+ T cells. These data identify SHP-1 as a key modifier of IL-6–and IL-21–driven Th17 development via regulation of STAT3 signaling and suggest SHP-1 as a potential new therapeutic target for manipulating Th17 differentiation in vivo.
Proper desensitization of CXCR4 is required for lymphocyte development and peripheral compartmentalization in mice
Authors: Balabanian Karl , Brotin Emilie , Biajoux Vincent , Bouchet-Delbos Laurence , Lainey Elodie , Fenneteau Odile , Bonnet Dominique , Fiette Laurence , Emilie Dominique , Bachelerie Françoise 
Published: March 2012

Abstract
Desensitization controls G protein–dependent signaling of chemokine receptors. We investigate the physiologic implication of this process for CXCR4 in a mouse model harboring a heterozygous mutation of the Cxcr4 gene, which engenders a desensitization-resistant receptor. Such anomaly is linked to the warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, a human rare combined immunodeficiency. Cxcr4+/mutant(1013) mice display leukocytes with enhanced responses to Cxcl12 and exhibit leukopenia as reported in patients. Treatment with CXCL12/CXCR4 antagonists transiently reverses blood anomalies, further demonstrating the causal role of the mutant receptor in the leukopenia. Strikingly, neutropenia occurs in a context of normal bone marrow architecture and granulocyte lineage maturation, indicating a minor role for Cxcr4-dependent signaling in those processes. In contrast, Cxcr4+/1013 mice show defective thymopoiesis and B-cell development, accounting for circulating lymphopenia. Concomitantly, mature T and B cells are abnormally compartmentalized in the periphery, with a reduction of primary follicles in the spleen and their absence in lymph nodes mirrored by an unfurling of the T-cell zone. These mice provide a model to decipher the role of CXCR4 desensitization in the homeostasis of B and T cells and to investigate which manifestations of patients with WHIM syndrome may be overcome by dampening the gain of CXCR4 function.
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY
Authors: Jang Richard , Gao Xin , Li Ming 
Published: March 2012

Abstract

Background
Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.

Results
We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.

Conclusions
Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures.
Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems
Authors: Parry R Mitchell , Phan John H , Wang May D 
Published: March 2012

Abstract

Background
Selecting an appropriate classifier for a particular biological application poses a difficult problem for researchers and practitioners alike. In particular, choosing a classifier depends heavily on the features selected. For high-throughput biomedical datasets, feature selection is often a preprocessing step that gives an unfair advantage to the classifiers built with the same modeling assumptions. In this paper, we seek classifiers that are suitable to a particular problem independent of feature selection. We propose a novel measure, called "win percentage", for assessing the suitability of machine classifiers to a particular problem. We define win percentage as the probability a classifier will perform better than its peers on a finite random sample of feature sets, giving each classifier equal opportunity to find suitable features.

Results
First, we illustrate the difficulty in evaluating classifiers after feature selection. We show that several classifiers can each perform statistically significantly better than their peers given the right feature set among the top 0.001% of all feature sets. We illustrate the utility of win percentage using synthetic data, and evaluate six classifiers in analyzing eight microarray datasets representing three diseases: breast cancer, multiple myeloma, and neuroblastoma. After initially using all Gaussian gene-pairs, we show that precise estimates of win percentage (within 1%) can be achieved using a smaller random sample of all feature pairs. We show that for these data no single classifier can be considered the best without knowing the feature set. Instead, win percentage captures the non-zero probability that each classifier will outperform its peers based on an empirical estimate of performance.

Conclusions
Fundamentally, we illustrate that the selection of the most suitable classifier (i.e., one that is more likely to perform better than its peers) not only depends on the dataset and application but also on the thoroughness of feature selection. In particular, win percentage provides a single measurement that could assist users in eliminating or selecting classifiers for their particular application.