bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of CD137 to study the full repertoire of CD8+ T cells without the need to know epitope specificities
Authors: Wölfl Matthias , Kuball Jürgen , Eyrich Matthias , Schlegel Paul G. , Greenberg Philip D. 
Published: June 2008

AbstractCD137 (4‐1BB) is a member of the TNFR‐family with costimulatory function, triggering prosurvival signals in activated T‐cells. Upregulation of CD137 upon stimulation allows identifying and isolating live, human antigen‐specific CD8+ T‐cells of all phenotypes, and therefore provides a comprehensive detection method. Furthermore responses against antigen mixtures can be easily detected, enabling antigen discovery in a stepwise deconvoluting approach. In this article, we will discuss various aspects of this methodology, including potential pitfalls as well as a variety of applications, as illustrated by examples from our laboratory. © 2008 International Society for Advancement of Cytometry
Isolation of monoclonal microcarriers colonized by fluorescent E. coli
Authors: Walser Marcel , Leibundgut Reto M. , Pellaux Rene , Panke Sven , Held Martin 
Published: June 2008

AbstractMicroencapsulation gains increasing importance for processing of bacterial libraries and especially in high‐throughput (HT) environments where >106 samples per day are studied. As a rule, a one‐to‐one relationship between an individual cell and analytical results is of key importance. Ideally, each microcarrier would therefore contain exactly one cell or colony. However, synthesis of larger numbers of capsules containing exactly one cell is not feasible as cells are randomly distributed during carrier‐production. The dilemma is that high dilution conditions will yield a satisfactory degree of monoclonality, but also a very large fraction of empty compartments, whereas distribution under low dilution generates unacceptable numbers of polyclonal compartments for whose removal no satisfactory technologies exist. Hydrogel carriers with a volume of 35 nL were used as growth compartments for individual microbial colonies. E. coli cells expressing green fluorescent protein (GFP) were encapsulated at low dilution thereby intentionally producing a considerable amount of polyclonal microcarrieres. Empty and polyclonal microcarriers were then removed from the desired monoclonal fraction by a COPAS Plus particle analyzer. The results were compared with model predictions in order to investigate possible limitations in the analysis and sorting of monoclonal microcarriers by COPAS. Fluorescent E. coli cells (GFP) distributed randomly throughout the microcarrier population. Cells were successfully propagated to colonies in the microcarriers and enriched to 95% monoclonality by a COAPS sorter. Enrichment‐efficiency was found to mainly depend on the colony diameter. With increasing colony size two contrary effects were observed: First, improved sorting efficiency due to increased fluorescence intensity and therefore higher detection efficiency, and second, deterioration of sorting efficiency due to occlusion occurring in polyclonal carriers. The combination of microencapsulation under low dilution conditions followed by HT sorting procedures is an efficient way for isolating larger amount of monoclonal carriers from bacterial libraries while concomitantly keeping the amounts of empty carriers at a moderate level. © 2008 International Society for Advancement of Cytometry
Flowcytometric phenotyping of common variable immunodeficiency
Authors: Warnatz Klaus , Schlesier Michael 
Published: June 2008

AbstractBackgroundCommon variable immunodeficiency (CVID) comprises heterogeneous antibody deficiency disorders. To classify this heterogeneous syndrome, clinical as well as immunologic parameters have been combined. Flowcytometric analysis of circulating T and B lymphocyte subpopulations has become an important tool in this endeavor of disease classification.MethodsMulticolor flowcytometric analysis of circulating lymphocytes.ResultsThe flowcytometric analysis of B and T cell subpopulations in the blood of CVID patients has contributed significantly to the identification of separate groups within the CVID population. In addition, the flowcytometric analysis of the inducible costimulator on activated T cells, CD19 and BAFF‐R on B cells are valid screening methods for three of the four known genetic defects associated with CVID. Only TACI deficiency can not be sufficiently detected by flowcytometric measures.ConclusionsFlowcytometric classification of patients with CVID has become a standard procedure during the diagnostic work up. This should be performed according to common guidelines to guarantee world wide comparability between different immunodeficiency centers. © 2008 Clinical Cytometry Society
A six‐color flow cytometric assay for the analysis of peripheral blood dendritic cells
Authors: Giannelli Stefania , Taddeo Adriano , Presicce Pietro , Villa Maria Luisa , Della Bella Silvia 
Published: June 2008

AbstractBackgroundFlow cytometric analysis of peripheral blood dendritic cells (PBDCs) and their myeloid (mDCs) and plasmacytoid (pDCs) subsets is a less invasive procedure that is acquiring growing clinical relevance. Because dendritic cells (DCs) lack unique lineage markers, current methods that are based on 3‐ or 4‐color assays do not allow multiparametric analysis of DC subsets. In this study a dedicated 6‐color assay was developed.MethodsmDCs and pDCs were counted and characterized for the expression of activation/maturation markers by using a single‐platform 6‐color assay. Whole‐blood samples from 20 healthy controls were directly stained with either CD80‐FITC/CD40‐PE/lineage‐PerCP‐Cy5.5/CD123‐PE‐Cy7/CD11c‐APC/HLA‐DR‐APC‐Cy7 or CD86‐FITC/CD83‐PE/lineage‐PerCP‐Cy5.5/CD123‐PE‐Cy7/CD11c‐APC/HLA‐DR‐APC‐Cy7 combination, in the presence of commercial fluorospheres. A dual‐platform 3‐color assay currently in use was run in parallel for comparison.ResultsThe 6‐color assay provided mDCs and pDCs counts similar to counts obtained by the 3‐color assay. Only the 6‐color assay could show differential expression of activation markers by mDCs and pDCs, with pDCs expressing lower levels of costimulatory molecules and HLA‐DR, but higher levels of CD83.ConclusionsThe 6‐color assay described here may be a sensitive tool for assessing possible variations in the number and features of mDCs and pDCs whose reciprocal balance is critical in understanding the more detailed orchestration of immune responses. © 2008 Clinical Cytometry Society
17α‐Ethinylestradiol: An endocrine disrupter of great concern. Analytical methods and removal processes applied to water purification. A review
Authors: Clouzot Ludiwine , Marrot Benoît , Doumenq Pierre , Roche Nicolas 
Published: June 2008

AbstractThe xenobiotic 17α‐ethinylestradiol, an oral contraceptive component, is an endocrine disrupter (EDC) of great concern, with fish feminization induced for concentrations as low as ng L−1. EE2 occurrence in the aquatic environment can be linked to insufficient removal in wastewater treatment plants. The focus of this review is to consider optimum treatment processes for removal of EE2. The main problem of EE2 is concentrations often below authors' limits of detection. Consequently, it is important to fully understand the advantages and disadvantages of different analytical techniques as this will determine confidence in comparison of the efficiency of different treatment processes. Solid‐phase extraction followed by chromatography is widely used but alternative methods, such as solid‐phase microextraction, stir bar sorptive extraction, or passive samplers, appear as promising tools. During the conventional activated sludge (AS) process, the incomplete sludge settlement results in lost of biomass, which means loss of EE2 adsorbed, and in low SRT, unsuited to nitrifying microorganisms that are responsible for EE2 biodegradation. Among bioprocesses, i.e., AS, membrane bioreactors (MBRs), biofilm reactors, and sequencing batch reactors, MBR technology appears as a hopeful solution for the improvement of EDCs removal, and, more precisely, EE2. Alternative treatments such as photodegradation, granulated activated carbon, MnO2, and sand reactor or ozonation were tested in the laboratory and were shown to be inadequate. © 2008 American Institute of Chemical Engineers Environ Prog, 2008
Mobility and exile at 2nd century A.D. khirbet edh‐dharih: Strontium isotope analysis of human migration in western Jordan
Authors: Perry Megan A. , Coleman Drew , Delhopital Nathalie 
Published: June 2008

AbstractThe 2nd century A.D. Roman annexation of the Nabataean Kingdom may have resulted in significant settlement disruption. Here we investigate the possibility that political refugees occupied Khirbet edh‐Dharih after Roman takeover, using strontium isotope analysis of archaeological human dental enamel. We additionally discuss regional patterning of 87Sr/86Sr in western Jordan based on archaeological faunal dental enamel samples to understand strontium isotope spatial heterogeneity and to facilitate interpretation of the Dharih results. Strontium isotope analysis of small mammal dentition varied as expected based on bedrock geology, but small faunal sample sizes did not accurately reflect the broad range of biologically available strontium at Dharih. Only one person at Khirbet edh‐Dharh appears to be non‐local based on isotopic data. The status of the remaining individuals is unclear, as they could have originated from Dharih or the Nabataean capital city of Petra. Incorporating modern fauna and soil samples to establish the local value may assist in characterizing the local strontium in a geologically complex area such as Dharih. Futhermore, future analysis of elemental strontium to assess dietary composition and diagenetic contamination would facilitate interpretation of the strontium sources in the Dharih individuals. © 2008 Wiley Periodicals, Inc.
A comparison of analytical methods for genetic association studies
Authors: Motsinger‐Reif Alison A. , Reif David M. , Fanelli Theresa J. , Ritchie Marylyn D. 
Published: June 2008

AbstractThe explosion of genetic information over the last decade presents an analytical challenge for genetic association studies. As the number of genetic variables examined per individual increases, both variable selection and statistical modeling tasks must be performed during analysis. While these tasks could be performed separately, coupling them is necessary to select meaningful variables that effectively model the data. This challenge is heightened due to the complex nature of the phenotypes under study and the complex underlying genetic etiologies. To address this problem, a number of novel methods have been developed. In the current study, we compare the performance of six analytical approaches to detect both main effects and gene‐gene interactions in a range of genetic models. Multifactor dimensionality reduction, grammatical evolution neural networks, random forests, focused interaction testing framework, step‐wise logistic regression, and explicit logistic regression were compared. As one might expect, the relative success of each method is context dependent. This study demonstrates the strengths and weaknesses of each method and illustrates the importance of continued methods development. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
The ordered transmission disequilibrium test: detection of modifier genes
Authors: Perdry Hervé , Babron Marie‐Claude , Clerget‐Darpoux Françoise 
Published: June 2008

AbstractWe consider the problem of detection of modifier genes that lead to variations in a disease‐related continuous variable (DRCV), such as the age of onset or a measure of disease severity, in a strategy of candidate genes. We propose a novel method, the ordered transmission disequilibrium test (OTDT), to test for a relation between the clinical heterogeneity expressed by a DRCV and marker genotypes of a candidate gene. The OTDT applies to trio families with one patients and his parents, all three genotyped at a bi‐allelic marker M. The OTDT aims to find a critical value of the DRCV which separates the sample of families in two subsamples in which the transmission rates are significantly different. We investigate the power of the method by simulations under various genetic models and covariate distributions and compare it with a linear regression analysis. Genet. Epidemiol. 2008. ©2008 Wiley‐Liss, Inc.
Association mapping by generalized linear regression with density‐based haplotype clustering
Authors: Igo Robert P. , Li Jing , Goddard Katrina A.B. 
Published: June 2008

AbstractHaplotypes of closely linked single‐nucleotide polymorphisms (SNPs) potentially offer greater power than individual SNPs to detect association between genetic variants and disease. We present a novel approach for association mapping in which density‐based clustering of haplotypes reduces the dimensionality of the general linear model (GLM)‐based score test of association implemented in the HaploStats software (Schaid et al. [2002] Am. J. Hum. Genet. 70:425–434). A flexible haplotype similarity score, a generalization of previously used measures, forms the basis for grouping haplotypes of probable recent common ancestry. All haplotypes within a cluster are assigned the same regression coefficient within the GLM, and evidence for association is assessed with a score statistic. The approach is applicable to both binary and continuous trait data, and does not require prior phase information. Results of simulation studies demonstrated that clustering enhanced the power of the score test to detect association, under a variety of conditions, while preserving valid Type‐I error. Improvement in performance was most dramatic in the presence of extreme haplotype diversity, while a slight improvement was observed even at low diversity. Our method also offers, for binary traits, a slight advantage in power over a similar approach based on an evolutionary model (Tzeng et al. [2006] Am. J. Hum. Genet. 78:231–242).Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
Hydrogeologic controls on streamflow sensitivity to climate variation
Authors: Jefferson Anne , Nolin Anne , Lewis Sarah , Tague Christina 
Published: June 2008

AbstractClimate models project warmer temperatures for the north‐west USA, which will result in reduced snowpacks and decreased summer streamflow. This paper examines how groundwater, snowmelt, and regional climate patterns control discharge at multiple time scales, using historical records from two watersheds with contrasting geological properties and drainage efficiencies. In the groundwater‐dominated watershed, aquifer storage and the associated slow summer recession are responsible for sustaining discharge even when the seasonal or annual water balance is negative, while in the runoff‐dominated watershed subsurface storage is exhausted every summer. There is a significant 1 year cross‐correlation between precipitation and discharge in the groundwater‐dominated watershed (r = 0·52), but climatic factors override geology in controlling the inter‐annual variability of streamflow. Warmer winters and earlier snowmelt over the past 60 years have shifted the hydrograph, resulting in summer recessions lasting 17 days longer, August discharges declining 15%, and autumn minimum discharges declining 11%. The slow recession of groundwater‐dominated streams makes them more sensitive than runoff‐dominated streams to changes in snowmelt amount and timing. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of hydrodynamic models of different complexities to model floods with emergency storage areas
Authors: Chatterjee Chandranath , Förster Saskia , Bronstert Axel 
Published: June 2008

AbstractA flood emergency storage area (polder) is used to reduce the flood peak in the main river and hence, protect downstream areas from being inundated. In this study, the effectiveness of a proposed flood emergency storage area at the middle Elbe River, Germany in reducing the flood peaks is investigated using hydrodynamic modelling. The flow to the polders is controlled by adjustable gates. The extreme flood event of August 2002 is used for the study. A fully hydrodynamic 1D model and a coupled 1D–2D model are applied to simulate the flooding and emptying processes in the polders and flow in the Elbe River. The results obtained from the 1D and 1D–2D models are compared with respect to the peak water level reductions in the Elbe River and flow processes in the polders during their filling and emptying. The computational time, storage space requirements and modelling effort for the two models are also compared. It is concluded that a 1D model may be used to study the water level and discharge reductions in the main river while a 1D‐2D model may be used when the study of flow dynamics in the polder is of particular interest. Further, a detailed sensitivity analysis of the 1D and 1D–2D models is carried out with respect to Manning's n values, DEMs of different resolutions, number of cross‐sections used and the gate opening time as well as gate opening/closing duration. Copyright © 2008 John Wiley & Sons, Ltd.
Integrative outpatient treatment for returning service members
Authors: Batten Sonja V. , Pollack Stacey J. 
Published: June 2008

AbstractVeterans returning from Operations Enduring and Iraqi Freedom (OEF/OIF) frequently present with multiple psychological and physical symptoms. The authors propose an innovative approach in which primary care providers, polytrauma specialists, vocational rehabilitation specialists, and mental health clinicians work together to provide care that is not simply concurrent, but truly integrated. All members of this interdisciplinary team must provide a consistent message that supports treatment engagement and progress. The authors illustrate this approach with a case report of a soldier deployed to both OEF and OIF, requiring subsequent treatment for joint pain, headaches, mild traumatic brain injury, posttraumatic stress disorder, depression, and substance abuse. Despite the emphasis on early intervention, treatment engagement and retention remain challenges in this population. © 2008 Wiley Periodicals, Inc. J Clin Psychol: In Session 64:1–12;, 2008.
Effects of nerve injury and segmental regeneration on the cellular correlates of neural morphallaxis
Authors: Martinez Veronica G. , Manson Josiah M.B. , Zoran Mark J. 
Published: June 2008

AbstractFunctional recovery of neural networks after injury requires a series of signaling events similar to the embryonic processes that governed initial network construction. Neural morphallaxis, a form of nervous system regeneration, involves reorganization of adult neural connectivity patterns. Neural morphallaxis in the worm, Lumbriculus variegatus, occurs during asexual reproduction and segmental regeneration, as body fragments acquire new positional identities along the anterior–posterior axis. Ectopic head (EH) formation, induced by ventral nerve cord lesion, generated morphallactic plasticity including the reorganization of interneuronal sensory fields and the induction of a molecular marker of neural morphallaxis. Morphallactic changes occurred only in segments posterior to an EH. Neither EH formation, nor neural morphallaxis was observed after dorsal body lesions, indicating a role for nerve cord injury in morphallaxis induction. Furthermore, a hierarchical system of neurobehavioral control was observed, where anterior heads were dominant and an EH controlled body movements only in the absence of the anterior head. Both suppression of segmental regeneration and blockade of asexual fission, after treatment with boric acid, disrupted the maintenance of neural morphallaxis, but did not block its induction. Therefore, segmental regeneration (i.e., epimorphosis) may not be required for the induction of morphallactic remodeling of neural networks. However, on‐going epimorphosis appears necessary for the long‐term consolidation of cellular and molecular mechanisms underlying the morphallaxis of neural circuitry. J. Exp. Zool. (Mol. Dev. Evol.) 310B:520–533, 2008. © 2008 Wiley‐Liss, Inc.
Voice, swallowing and quality of life in patients after transoral laser surgery for supraglottic carcinoma
Authors: Roh Jong‐Lyel , Kim Dong‐Hyun , Park Chan Il 
Published: June 2008

AbstractBackgroundTransoral laser surgery is a conservative surgical method used to treat supraglottic carcinomas, but little is known about functional and quality of life (QOL) outcomes relative to extent of resection.MethodsWe prospectively examined functional and oncological outcomes of 21 patients with T1–T3 supraglottic carcinomas underwent partial (group A, n = 8) or radical (group B, n = 13) laser supraglottic resection and bilateral neck dissection. Subjective and objective evaluation of voice, swallowing and QOL before and after endoscopic supraglottic resection were compared between the two groups.ResultsNo major complications were encountered, but local recurrence developed in two patients (9%). Vocal function was not generally affected by surgery. Postsurgical swallowing and social eating scores were higher in group B than in group A (P < 0.05). Aspiration occurred in most patients soon after surgery, but recovered within 3–6 months, with recovery being faster in group A. Three‐year locoregional control, disease‐free survival and overall survival rates were 81%, 71% and 79%, respectively.ConclusionSwallowing was affected by the extent of laser resection for supraglottic carcinomas, but eventually recovered in most patients, indicating favourable functional and oncological outcomes. J. Surg. Oncol. 2008;98:184–189. © 2008 Wiley‐Liss, Inc.
Hidden potential: Embracing conflict can pay off for teams
Authors: Flanagan Tim A. , Runde Craig E. 
Published: June 2008

AbstractAs more and more organizations rely on teams and teamwork, leaders need to be aware of and ready to deal with the inevitability that conflicts will arise among members of teams, especially dispersed teams. If teams can not only learn to effectively resolve conflict but also find ways to turn conflict to their advantage, the diversity of perspectives and ideas among teammates can lead to discovery rather than discord.
Polymer “Clicking” by CuAAC Reactions
Authors: Meldal Morten 
Published: June 2008

AbstractThe CuAAC “click” reaction has developed as one of the most useful and widely employed reactions in ligation within polymer chemistry. This is due to the unique properties of the Cu(I) catalysis which renders the reaction quantitative even at low concentrations, orthogonal with other chemistries and extremely robust. The formed triazole on the other hand is of intermediate polarity and chemically and biochemically “invisible”, and the CuAAC provides the ideal “click” reaction for stitching together polymer architectures of unprecedended complexity as was it molecular LEGO. The CuAAC “clicking” in polymer chemistry is increasing exponentially and lead to highly defined polymer materials with novel properties.magnified image