bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critical assessment for the value of markers to gate-out undesired events in HLA-peptide multimer staining protocols
Authors: Attig Sebastian , Price Leah , Janetzki Sylvia , Kalos Michael , Pride Michael , McNeil Lisa , Clay Tim , Yuan Jianda , Odunsi Kunle , Hoos Axel , Romero Pedro , Britten Cedrik M ,   the CRI-CIC Assay Working Group
Published: July 2011

Abstract

Background
The introduction of antibody markers to identify undesired cell populations in flow-cytometry based assays, so called DUMP channel markers, has become a practice in an increasing number of labs performing HLA-peptide multimer assays. However, the impact of the introduction of a DUMP channel in multimer assays has so far not been systematically investigated across a broad variety of protocols.

Methods
The Cancer Research Institute's Cancer Immunotherapy Consortium (CRI-CIC) conducted a multimer proficiency panel with a specific focus on the impact of DUMP channel use. The panel design allowed individual laboratories to use their own protocol for thawing, staining, gating, and data analysis. Each experiment was performed twice and in parallel, with and without the application of a dump channel strategy.

Results
The introduction of a DUMP channel is an effective measure to reduce the amount of non-specific MULTIMER binding to T cells. Beneficial effects for the use of a DUMP channel were observed across a wide range of individual laboratories and for all tested donor-antigen combinations. In 48% of experiments we observed a reduction of the background MULTIMER-binding. In this subgroup of experiments the median background reduction observed after introduction of a DUMP channel was 0.053%.

Conclusions
We conclude that appropriate use of a DUMP channel can significantly reduce background staining across a large fraction of protocols and improve the ability to accurately detect and quantify the frequency of antigen-specific T cells by multimer reagents. Thus, use of a DUMP channel may become crucial for detecting low frequency antigen-specific immune responses. Further recommendations on assay performance and data presentation guidelines for publication of MULTIMER experimental data are provided.
Nonlinear thermo-optical properties of two-layered spherical system of gold nanoparticle core and water vapor shell during initial stage of shell expansion
Authors: Pustovalov Victor K , Astafyeva Liudmila G 
Published: July 2011

AbstractNonlinear thermo-optical properties of two-layered spherical system of gold nanoparticle core and water vapor shell, created under laser heating of nanoparticle in water, were theoretically investigated. Vapor shell expansion leads to decreasing up to one to two orders of magnitude in comparison with initial values of scattering and extinction of the radiation with wavelengths 532 and 633 nm by system while shell radius is increased up to value of about two radii of nanoparticle. Subsequent increasing of shell radius more than two radii of nanoparticle leads to rise of scattering and extinction properties of system over initial values. The significant decrease of radiation scattering and extinction by system of nanoparticle-vapor shell can be used for experimental detection of the energy threshold of vapor shell formation and investigation of the first stages of its expansion.PACS: 42.62.BE. 78.67. BF
Strong association between non alcoholic fatty liver disease (NAFLD) and low 25(OH) vitamin D levels in an adult population with normal serum liver enzymes
Authors: Barchetta Ilaria , Angelico Francesco , Ben Maria Del , Baroni Marco Giorgio , Pozzilli Paolo , Morini Sergio , Cavallo Maria Gisella 
Published: July 2011

Abstract

Background
Hypovitaminosis D has been recently recognized as a worldwide epidemic. Since vitamin D exerts significant metabolic activities, comprising free fatty acids (FFA) flux regulation from the periphery to the liver, its deficiency may promote fat deposition into the hepatocytes. Aim of our study was to test the hypothesis of a direct association between hypovitaminosis D and the presence of NAFLD in subjects with various degree of insulin-resistance and related metabolic disorders.

Methods
We studied 262 consecutive subjects referred to the Diabetes and Metabolic Diseases clinics for metabolic evaluation. NAFLD (non-alcoholic fatty liver disease) was diagnosed by upper abdomen ultrasonography, metabolic syndrome was identified according to the Third Report of National Cholesterol Education Program/Adult Treatment Panel (NCEP/ATPIII) modified criteria. Insulin-resistance was evaluated by means of HOMA-IR. Fatty-Liver-Index, a recently identified correlate of NAFLD, was also estimated. Serum 25(OH)vitamin D was measured by colorimetric method.

Results
Patients with NAFLD (n = 162,61.8%) had reduced serum 25(OH) vitamin D levels compared to subjects without NAFLD (14.8 ± 9.2 vs 20.5 ± 9.7 ng/ml, p < 0.001, OR 0.95, IC 95% 0.92-0.98). The relationship between NAFLD and reduced 25(OH)vitamin D levels was independent from age, sex, triglycerides, high density lipoproteins (HDL) and glycaemia (p < 0.005) and Fatty Liver Index inversely correlated with low 25(OH) vitamin D regardless sex, age and HOMA-IR (p < 0.007).

Conclusions
Low 25(OH)vitamin D levels are associated with the presence of NAFLD independently from metabolic syndrome, diabetes and insulin-resistance profile.
Comparison of intravenous immunoglobulin and plasma exchange in treatment of mechanically ventilated children with Guillain Barré syndrome: a randomized study
Authors: El-Bayoumi Mohammed A , El-Refaey Ahmed M , Abdelkader Alaa M , El-Assmy Mohamed MA , Alwakeel Angi A , El-Tahan Hanem M 
Published: July 2011

Abstract
Introduction
Respiratory failure is a life threatening complication of Guillain Barré syndrome (GBS). There is no consensus on the specific treatment for this subset of children with GBS.

Methods
This was a prospective randomized study to compare the outcome of intravenous immunoglobulin (IVIG) and plasma exchange (PE) treatment in children with GBS requiring mechanical ventilation. Forty-one children with GBS requiring endotracheal mechanical ventilation (MV) within 14 days from disease onset were included. The ages of the children ranged from 49 to 143 months.
Randomly, 20 children received a five-day course of IVIG (0.4 g/kg/day) and 21 children received a five-day course of one volume PE daily. Lumbar puncture (LP) was performed in 36 patients (18 in each group).

Results
Both groups had comparable age (p = 0.764), weight (p = 0.764), duration of illness prior to MV (p = 0.854), preceding diarrhea (p = 0.751), cranial nerve involvement (p = 0.756), muscle power using Medical Research Council (MRC) sum score (p = 0.266) and cerebrospinal fluid (CSF) protein (p = 0.606).
Children in the PE group had a shorter period of MV (median 11 days, IQR 11.0 to 13.0) compared to IVIG group (median 13 days, IQR 11.3 to 14.5) with p = 0.037.
Those in the PE group had a tendency for a shorter Pediatric Intensive Care Unit (PICU) stay (p = 0.094).
A total of 20/21 (95.2%) and 18/20 (90%) children in the PE and IVIG groups respectively could walk unaided within four weeks after PICU discharge (p = 0.606).
There was a negative correlation between CSF protein and duration of mechanical ventilation in the PE group (p = 0.037), but not in the IVIG group (p = 0.132).

Conclusions
In children with GBS requiring MV, PE is superior to IVIG regarding the duration of MV but not PICU stay or the short term neurological outcome.
The negative correlation between CSF protein values and duration of MV in PE group requires further evaluation of its clinical usefulness.

Trial Registration
Clinicaltrials.gov Identifier NCT01306578
In-vivovalidation of a new non-invasive continuous ventricular stroke volume monitoring system in an animal model
Authors: Konings Maurits K , Grundeman Paul F , Goovaerts Henk G , Roosendaal Maarten R , Hoefer Imo E , Doevendans Pieter A , Rademakers Frank E , Buhre Wolfgang F 
Published: July 2011

Abstract
Introduction
Recently, a non-invasive, continuous ventricular stroke volume monitoring system using skin electrodes has been developed. In contrast to impedance-based methods, the new technique (ventricular field recognition) enables measurement of changes in ventricular volume. A prototype using this new method was built (the hemologic cardiac profiler, HCP) and validated against a reference method in a pig model during variations in cardiac output.

Methods
In six Dalland pigs, cardiac output was simultaneously measured with the HCP (CO-HCP), and an invasive ultrasonic flow-probe around the ascending aorta (CO-FP). Variations in CO were achieved by change in ventricular loading conditions, cardiac pacing, and dobutamine administration. Data were analysed according to Bland-Altman analysis and Pearson's correlation.

Results
Pearson's correlation between the CO-HCP and the CO-FP was r = 0.978. Bland-Altman analysis showed a bias of - 0.114 L/minute, and a variability of the bias (2 standard deviations, 2SD) of 0.55 L/minute.

Conclusions
The results of the present study demonstrate that CO-HCP is comparable to CO-FP in an animal model of cardiac output measurements during a wide variation of CO. Therefore, the HCP has the potential to become a clinical applicable cardiac output monitor.
Microsatellite Instability and Loss of Heterozygosity at Chromosomal Location 18q: Prospective Evaluation of Biomarkers for Stages II and III Colon Cancer—A Study of CALGB 9581 and 89803
Authors: Bertagnolli Monica M. , Redston Mark , Compton Carolyn C. , Niedzwiecki Donna , Mayer Robert J. , Goldberg Richard M. , Colacchio Thomas A. , Saltz Leonard B. , Warren Robert S. 
Published: July 2011

Purpose Colorectal cancer (CRC) develops as a result of a series of accumulated genomic changes that produce oncogene activation and tumor suppressor gene loss. These characteristics may classify CRC into subsets of distinct clinical behaviors. Patients and Methods We studied two of these genomic defects—mismatch repair deficiency (MMR-D) and loss of heterozygosity at chromosomal location 18q (18qLOH)—in patients enrolled onto two phase III cooperative group trials for treatment of potentially curable colon cancer. These trials included prospective secondary analyses to determine the relationship between these markers and treatment outcome. A total of 1,852 patients were tested for MMR status and 955 (excluding patients with MMR-D tumors) for 18qLOH. Results Compared with stage III, more stage II tumors were MMR-D (21.3% v 14.4%; P < .001) and were intact at 18q (24.2% v 15.1%; P = .001). For the combined cohort, patients with MMR-D tumors had better 5-year disease-free survival (DFS; 0.76 v 0.67; P < .001) and overall survival (OS; 0.81 v 0.78; P = .029) than those with MMR intact (MMR-I) tumors. Among patients with MMR-I tumors, the status of 18q did not affect outcome, with 5-year values for patients with 18q intact versus 18qLOH tumors of 0.74 versus 0.65 (P = .18) for DFS and 0.81 versus 0.77 (P = .18) for OS. Conclusion We conclude that MMR-D tumor status, but not the presence of 18qLOH, has prognostic value for stages II and III colon cancer.
Compendium of Unpublished Phase III Trials in Oncology: Characteristics and Impact on Clinical Practice
Authors: Tam Vincent C. , Tannock Ian F. , Massey Christine , Rauw Jennifer , Krzyzanowska Monika K. 
Published: July 2011

Purpose Many phase III trials presented at annual meetings of the American Society of Clinical Oncology (ASCO) remain unpublished. The results of these unpublished trials, if more generally known, might have an impact on clinical practice. Methods Abstracts of large phase III trials evaluating systemic cancer treatment were identified from conference proceedings of the 1989 to 2003 ASCO annual meetings. PubMed, Medline, and Embase were searched for corresponding publications. A compendium of unpublished phase III trials was assembled. Clinical significance of nonpublication was determined by disease site-specific oncology experts from two academic cancer centers in Canada. Results A total of 709 phase III trials were identified of which 66 (9.3%) remain without a subsequent publication at a minimum of 6.5 years of follow-up and 94 (13%) were published after a delay of ≥ 5 years from their initial presentation. Of the unpublished trials, 48% were presented as oral sessions at an ASCO meeting, and 71% of the abstracts reported negative results. The experts judged that 70% of the unpublished trials addressed an important question and 59% might have had clinical impact if their results had been published promptly. Conclusion A substantial number of cancer clinical trials with potential influence on clinical practice remain unpublished and many other trials are published after a substantial delay. Nonpublication of clinical trials breaks an implicit contract with participants, institutional review boards, and sponsors.
Randomized Phase II Study of Pemetrexed, Carboplatin, and Thoracic Radiation With or Without Cetuximab in Patients With Locally Advanced Unresectable Non–Small-Cell Lung Cancer: Cancer and Leukemia Group B Trial 30407
Authors: Govindan Ramaswamy , Bogart Jeffrey , Stinchcombe Thomas , Wang Xiaofei , Hodgson Lydia , Kratzke Robert , Garst Jennifer , Brotherton Timothy , Vokes Everett E. 
Published: July 2011

Purpose Cancer and Leukemia Group B conducted a randomized phase II trial to investigate two novel chemotherapy regimens in combination with concurrent thoracic radiation therapy (TRT). Patients and Methods Patients with unresectable stage III non–small-cell lung cancer (NSCLC) were randomly assigned to carboplatin (area under the curve, 5) and pemetrexed (500 mg/m2) every 21 days for four cycles and TRT (70 Gy; arm A) or the same treatment with cetuximab administered concurrent only with TRT (arm B). Patients in both arms received up to four cycles of pemetrexed as consolidation therapy. The primary end point was the 18-month overall survival (OS) rate; if the 18-month OS rate was ≥ 55%, the regimen(s) would be considered for further study. Results Of the 101 eligible patients enrolled (48 in arm A and 53 in arm B), 60% were male; the median age was 66 years (range, 32 to 81 years); 44% and 35% had adenocarcinoma and squamous carcinoma, respectively; and more patients enrolled onto arm A compared with arm B had a performance status of 0 (58% v 34%, respectively; P = .04). The 18-month OS rate was 58% (95% CI, 46% to 74%) in arm A and 54% (95% CI, 42% to 70%) in arm B. No significant difference in OS between patients with squamous and nonsquamous NSCLC was observed (P = .667). The toxicities observed were consistent with toxicities associated with concurrent chemoradiotherapy. Conclusion The combination of pemetrexed, carboplatin, and TRT met the prespecified criteria for further evaluation. This regimen should be studied further in patients with locally advanced unresectable nonsquamous NSCLC.
Positron Emission Tomography–Computed Tomography (PET-CT) After Induction Therapy Is Highly Predictive of Patient Outcome in Follicular Lymphoma: Analysis of PET-CT in a Subset of PRIMA Trial Participants
Authors: Trotman Judith , Fournier Marion , Lamy Thierry , Seymour John Francis , Sonet Anne , Janikova Andrea , Shpilberg Ofer , Gyan Emmanuel , Tilly Hervé , Estell Jane , Forsyth Cecily , Decaudin Didier , Fabiani Bettina , Gabarre Jean , Salles Bruno , Van Den Neste Eric , Canioni Danielle , Garin Etienne , Fulham Michael , Vander Borght Thierry , Salles Gilles 
Published: July 2011

Purpose The utility of [18F]fluorodeoxyglucose (FDG) positron emission tomography–computed tomography (PET-CT) in assessing response at the end of induction therapy is well documented in Hodgkin's and diffuse large B-cell lymphomas, but its role in follicular lymphoma (FL) remains undetermined. We investigated the prognostic significance of PET-CT performed after first-line therapy in patients with FL treated in the prospective Primary Rituximab and Maintenance (PRIMA) study. Patients and Methods Results of PET-CT scans performed after induction immunochemotherapy were recorded retrospectively. Patients went on to either observation or rituximab maintenance per protocol independent of the PET-CT result. Patient characteristics and outcomes were then evaluated. Results Of 122 PET-CT scans performed at the end of the induction immunochemotherapy, 32 (26%) were reported as positive by the local investigator. Initial demographic or disease characteristics did not differ between PET-CT–positive (PET-positive) and PET-CT–negative (PET-negative) patients. PET status correlated with conventional response criteria (P < .001). Patients remaining PET positive had a significantly (P < .001) inferior progression-free survival at 42 months of 32.9% (95% CI, 17.2% to 49.5%) compared with 70.7% (95% CI, 59.3% to 79.4%) in those who became PET negative. PET status, but not conventional response (complete response or complete response unconfirmed v partial response) according to IWC 1999, was an independent predictive factor for lymphoma progression. The risk of death was also increased in PET-positive patients (hazard ratio 7.0; P = .0011). Conclusion [18F]FDG PET-CT status at the end of immunochemotherapy induction in patients with FL is strongly predictive of outcome and should be considered a meaningful clinical end point in future studies.
A Unified Framework for Dynamic Prediction Market Design
Authors: Agrawal Shipra , Delage Erick , Peters Mark , Wang Zizhuo , Ye Yinyu 
Published: July 2011

Recently, coinciding with and perhaps driving the increased popularity of prediction markets, several novel pari-mutuel mechanisms have been developed such as the logarithmic market-scoring rule (LMSR), the cost-function formulation of market makers, utility-based markets, and the sequential convex pari-mutuel mechanism (SCPM). In this work, we present a convex optimization framework that unifies these seemingly unrelated models for centrally organizing contingent claims markets. The existing mechanisms can be expressed in our unified framework by varying the choice of a concave value function. We show that this framework is equivalent to a convex risk minimization model for the market maker. This facilitates a better understanding of the risk attitudes adopted by various mechanisms. The unified framework also leads to easy implementation because we can now find the cost function of a market maker in polynomial time by solving a simple convex optimization problem. In addition to unifying and explaining the existing mechanisms, we use the generalized framework to derive necessary and sufficient conditions for many desirable properties of a prediction market mechanism such as proper scoring, truthful bidding (in a myopic sense), efficient computation, controllable risk measure, and guarantees on the worst-case loss. As a result, we develop the first proper, truthful, risk-controlled, loss-bounded (independent of the number of states) mechanism; none of the previously proposed mechanisms possessed all these properties simultaneously. Thus, our work provides an effective tool for designing new prediction market mechanisms. We also discuss possible applications of our framework to dynamic resource pricing and allocation in general trading markets.
Perinatal and Neonatal Risk Factors for Autism: A Comprehensive Meta-analysis
Authors: Gardener Hannah , Spiegelman Donna , Buka Stephen L. 
Published: July 2011

BACKGROUND:The etiology of autism is unknown, although perinatal and neonatal exposures have been the focus of epidemiologic research for over 40 years.OBJECTIVE:To provide the first review and meta-analysis of the association between perinatal and neonatal factors and autism risk.METHODS:PubMed, Embase, and PsycInfo databases were searched for studies that examined the association between perinatal and neonatal factors and autism through March 2007. Forty studies were eligible for the meta-analysis. For each exposure, a summary effect estimate was calculated using a random-effects model. Heterogeneity in effect estimates across studies was examined, and, if found, a meta-regression was conducted to identify measured methodological factors that could explain between-study variability.RESULTS:Over 60 perinatal and neonatal factors were examined. Factors associated with autism risk in the meta-analysis were abnormal presentation, umbilical-cord complications, fetal distress, birth injury or trauma, multiple birth, maternal hemorrhage, summer birth, low birth weight, small for gestational age, congenital malformation, low 5-minute Apgar score, feeding difficulties, meconium aspiration, neonatal anemia, ABO or Rh incompatibility, and hyperbilirubinemia. Factors not associated with autism risk included anesthesia, assisted vaginal delivery, postterm birth, high birth weight, and head circumference.CONCLUSIONS:There is insufficient evidence to implicate any 1 perinatal or neonatal factor in autism etiology, although there is some evidence to suggest that exposure to a broad class of conditions reflecting general compromises to perinatal and neonatal health may increase the risk. Methodological variations were likely sources of heterogeneity of risk factor effects across studies.
Simulation in Pediatrics: The Reliability and Validity of a Multiscenario Assessment
Authors: McBride Mary E. , Waldrop William B. , Fehr James J. , Boulet John R. , Murray David J. 
Published: July 2011

OBJECTIVE:
The goal of this study was to develop an inventory of simulated scenarios that mimic pediatric crises and determine if the resident scores could be used to establish the reliability and validity of a multiple-scenario assessment. The long-term objective is to provide pediatric residents with experiences in the recognition, diagnosis, and management of a range of simulated acute conditions.

METHODS:
Twenty scenarios were constructed. Each resident participated in 10 scenarios that were scored by 2 independent raters using an action-item checklist and a global score. Debriefing occurred after each scenario. Several analyses were performed to investigate the psychometric adequacy of the scores.

RESULTS:
Twenty-nine residents participated. The residents' scores in both sets of 10 scenarios were reliable when using either the checklist or global scoring method (&gt;0.79). Generalizability analyses indicated that the major source of variance in scores was attributable to the scenario and scenario-resident interaction. The variance attributable to the rater was low, yielding high interrater reliability values. The more-experienced residents who participated in the study outperformed the less-experienced interns.

CONCLUSIONS:
An inventory of critical events was designed to assess pediatric residents' diagnostic and management skills. A reliable measure of ability could be obtained, provided the residents managed multiple scenarios. The residents outscored the interns, providing evidence to support the construct validity of the scores. Additional validity evidence is needed, including studies to determine if this type of training improves physicians' management of real-life critical events.