bluuebunny/crossref_metadata_2025 huggingface dataset:
A Paradox of Decreasing Entropy in Multiscale Monte Carlo Grain Growth Simulations
Authors: Nosonovsky Michael , Esche Sven K.
Published: June 2008

Grain growth in metals is driven by random thermal fluctuations and increases the orderliness of the system. This random process is usually simulated by the Monte Carlo (MC) method and Cellular Automata (CA). The increasing orderliness results in an entropy decrease, thus leading to a paradoxical apparent violation of the second law of thermodynamics. In this paper, it is shown that treating the system as a multiscale system resolves this paradox. MC/CA simulations usually take into consideration only the mesoscale entropy. Therefore, the information entropy of the system decreases, leading to an apparent paradox. However, in the physical system, the entropy is produced at the nanoscale while it is consumed at the mesoscale, so that the net entropy is growing.
Bipolar Charge Transport in PCPDTBT‐PCBM Bulk‐Heterojunctions for Photovoltaic Applications
Authors: Morana Mauro , Wegscheider Matthias , Bonanni Alberta , Kopidakis Nikos , Shaheen Sean , Scharber Markus , Zhu Zhengguo , Waller David , Gaudiana Russell , Brabec Christoph
Published: June 2008

An experimental study of the transport properties of a low‐bandgap conjugated polymer giving high photovoltaic quantum efficiencies in the near infrared spectral region (Eg‐opt ∼ 1.35 eV) is presented. Using a organic thin film transistor geometry, we demonstrate a relatively high in‐plane hole mobility, up to 1.5 · × 10−2 cm2 V−1 s−1 and quantify the electron mobility at 3 × · 10−5 cm2 V−1 s−1 on a SiO2 dielectric. In addition, singular contact behavior results in bipolar quasi‐Ohmic injection both from low and high workfunction metals like LiF/Al and Au. X‐ray investigations revealed a degree of interchain π‐stacking that is probably embedded in a disordered matrix. Disorder also manifests itself in a strong positive field dependence of the hole mobility from the electric field. In blends made with the electron acceptor methanofullerene [6,6]‐phenyl C61 butyric acid methyl ester (PCBM), the transistor characteristics suggest a relatively unfavorable intermixing of the two components for the application to photovoltaic devices. We attribute this to a too fine dispersion of [C60]‐PCBM in the polymer matrix, that is also confirmed by the quenching of the photoluminescence signal measured in PCPDTBT [C60]‐PCBM films with various composition. We show that a higher degree of phase separation can be induced during the film formation by using 1,8‐octanedithiol (ODT), which leads to a more efficient electron percolation in the [C60]‐PCBM. In addition, the experimental results, in combination with those of solar cells seem to support the correlation between the blend morphology and charge recombination. We tentatively propose that the drift length, and similarly the electrical fill factor, can be limited by the recombination of holes with electrons trapped on isolated [C60]‐PCBM clusters. Ionized and isolated [C60]‐PCBM molecules can modify the local electric field in the solar cell by build‐up of a space‐charge. The results also suggest that further improvements of the fill factor may also be limited by a strong electrical‐field dependence of the hole transport.
Autosomal STR genetic variability in the Gran Chaco native population: Homogeneity or heterogeneity?
Authors: Crossetti Shaiane Goulart , Demarchi Dario A. , Raimann Paulo Eduardo , Salzano Francisco Mauro , Hutz Mara Helena , Callegari‐Jacques Sidia Maria
Published: June 2008

To investigate the population structure and variation in Gran Chaco's Amerindian population, data from 15 short tandem repeats (STRs) were determined in 128 individuals from three tribes of the Argentinean part of this region. STR genotypic differences, structure analysis, and multidimensional plot for the DA distances indicated that (1) Wichí from the Chaco Province are genetically distinct from the other populations, but still preserve a fair amount of genetic similarity with Wichí from Formosa; (2) the Toba populations studied are genetically indistinguishable; and (3) Toba subjects from Formosa are similar to the Pilagá of the same linguistic group (Guaykurú) and to the Wichí from Formosa who speak a Mataco language. This similarity could be due to their past mobility and the custom of absorbing females taken as prisoners from groups raided by them. Language, geography, and genetics seem to play similar roles in determining the population structure of these groups. Analyses of molecular variance and GST′ values calculated considering three South American regions indicated that the Argentinean Chaco is genetically homogeneous; addition of the Ayoreo Amerindians of the Paraguayan Chaco, however, led to diversity values that are not much different from those of South Amerindians in general. The present data contribute to efforts that try to understand in what way groups with diverse sociocultural settings (tribal, agricultural, and industrial) differ in genetic structure. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.
Occupational exposure to solvents and gasoline and risk of cancers in the urinary tract among Finnish workers
Authors: Lohi Jouni , Kyyrönen Pentti , Kauppinen Timo , Kujala Veikko , Pukkala Eero
Published: June 2008

Background

Bladder cancer (BC) is generally considered as an occupational disease, and some chemical exposures may also be associated with renal cell cancer (RCC). The aim of this study was to estimate the risk of cancers of the urinary tract in relation to occupational exposure to solvents and gasoline.

Methods

A cross‐sectional cohort of all economically active Finns from the 1970 population census was followed up for BC (10,277 cases) and RCC (9,954 cases). Census occupations were assigned estimates of exposure to hydrocarbon (HC) solvents and gasoline with a job exposure matrix. Relative risk (RR) estimates were defined using Poisson regression models, adjusted for smoking and obesity.

Results

Exposure to solvents was positively associated with the incidence of BC in women but not in men. The RR estimates were above 1.2 in nearly all exposure categories of all exposures studied but a statistically significant excess was only seen for middle levels of chlorinated HC solvents (1.7; 95% CI = 1.2–2.5) and a low level of aromatic HC solvents (1.6; 95% CI = 1.3–2.1). The RR estimates for RCC were close to unity in all categories of exposure.

Conclusions

Our findings suggest that occupational exposure to certain solvents may have an impact on BC risk. The risk of RCC does not appear to be altered by exposure to HC solvents or gasoline. Am. J. Ind. Med. 51:668–672, 2008. Published 2008 Wiley‐Liss, Inc.
Ornamental lakes — an overlooked conservation resource?
Authors: Sayer C. D. , Davidson T. A. , Kelly A.
Published: June 2008

Shallow lakes excavated for ornamental purposes during the 18th and 19th centuries are abundant in lowland Europe. However, relative to older man‐made and/or natural lakes, these lakes may have been undervalued from the perspective of nature conservation.

To evaluate this idea a comparison was made between the aquatic macrophyte communities (submerged and floating‐leaved vegetation) of 66 shallow, English lakes including 34 ornamental lakes and 32 flooded medieval peat workings (the Norfolk and Suffolk Broads system), the latter being widely protected by conservation legislation.

Some 47%, 38% and 15% of the lakes studied were phytoplankton‐dominated, macrophyte‐dominated or deemed too shallow (<50 cm water depth), respectively, to support a macrophyte vegetation. A higher proportion of the ornamental lakes were macrophyte‐dominated (51%) by comparison with the broads (34%). In addition, many of the ornamental lakes contained diverse plant communities including abundant populations of Characeae, a common feature of lakes in the region before the major onset of eutrophication.

From the perspectives of macrophyte species richness, charophyte communities and indeed ‘reference condition macrophyte assemblages’, many of the studied ornamental lakes can be considered to be of high conservation value. Yet, in contrast to the broads, the vast majority of ornamental lakes have little conservation protection and are rarely subject to biological monitoring and/or surveying, thus leaving them vulnerable to eutrophication and inappropriate management. This study suggests that ornamental lakes are worthy of much greater attention from conservation organizations.

Copyright © 2008 John Wiley & Sons, Ltd.
Lymphangiogenesis and Its Relationship With Lymphatic Metastasis and Prognosis in Malignant Melanoma
Authors: Liu Baoquan , Ma Jing , Wang Xiaolei , Su Fei , Li Xuemei , Yang Shucai , Ma Wenping , Zhang Yafang
Published: June 2008

Regional lymph node metastasis is one of the important indicators of cutaneous malignant melanoma. Newly formed lymphatic vessels are considered to provide a route whereby tumor cells can migrate to the lymph nodes. Both vascular endothelial growth factors (VEGF) ‐C and ‐D have been confirmed to participate in tumor lymphangiogenesis, but the prognostic significance of VEGF‐C, VEGF‐D, and lymphangiogenesis in cutaneous malignant melanoma remains controversial. To clarify the effects of these factors and to evaluate the relationships between lymphangiogenesis, lymph node metastasis, and prognosis in patients with malignant melanoma, the expressions of VEGF‐C, VEGF‐D, and their receptor (VEGFR) ‐3 were detected by immunohistochemistry and reverse transcriptase‐polymerase chain reaction. The expressions of both VEGF‐C and VEGF‐D proteins were concomitantly detected in the cytoplasm of the malignant cells. VEGF‐C and VEGF‐D expressions were associated with VEGFR‐3 expression and were significantly correlated with both peritumoral lymphangiogenesis and lymph node metastasis. The incidence of peritumoral lymphatic vessels was significantly higher in lymph node metastatic melanomas than that in nonmetastatic melanomas. Univariate and multivariate analyses indicated that VEGF‐C and VEGF‐D were independent prognostic factors for overall survival and disease‐free survival in patients with malignant melanoma. This study suggests that both VEGF‐C and VEGF‐D are involved in peritumoral lymphangiogenesis and lymphatic metastasis. VEGF‐C and VEGF‐D expression may be clinically useful indicators for prognostic evaluation in patients with cutaneous malignant melanoma. Anat Rec, 2008. © 2008 Wiley‐Liss, Inc.
Vertically combined shaved cell method in a z‐coordinate nonhydrostatic atmospheric model
Authors: Yamazaki Hiroe , Satomura Takehiko
Published: June 2008

The vertically combined shaved cell method is implemented into a z‐coordinate nonhydrostatic two‐dimensional atmospheric model based on the finite‐volume method. Quasi‐flux form fully compressible equations are employed as governing equations. The results of flow over a bell‐shaped mountain and a semicircular mountain are compared to those from a model using terrain‐following coordinates. These results indicate that the proposed method does not suffer from vertical velocity errors at the edge of the cells, and reproduces smooth and accurate mountain waves over not only gentle but also steep slopes where significant errors are observed in the terrain‐following model. Copyright © 2008 Royal Meteorological Society
Summer air temperature distribution and thermal environment in urban areas of Japan
Authors: Aikawa Masahide , Hiraki Takatoshi , Eiho Jiro
Published: June 2008

The air temperature distribution was measured, and the thermal environment was studied in August (summer season) in an urban area of approximately 10 km × 15 km in Hyogo Prefecture, Japan. We introduced a new index to evaluate the thermal condition. Combining the newly introduced index with other indices enabled us to show the thermal conditions in more detail. The inland thermal conditions were milder than those in the coastal areas when the air temperature was lower than 30 °C. In contrast, the inland thermal conditions were more severe than those in the coastal areas when the air temperature was higher than 30 °C. Copyright © 2008 Royal Meteorological Society
Infrared microscopy for the study of biological cell monolayers. I. Spectral effects of acetone and formalin fixation
Authors: Hastings Gary , Wang Ruili , Krug Peter , Katz David , Hilliard Julia
Published: June 2008

Infrared spectroscopy of biological cell monolayers grown on surfaces is a poorly developed field. This is unfortunate because these monolayers have potential as biological sensors. Here we have used infrared microscopy, in both transmission and transflection geometries, to study air‐dried Vero cell monolayers. Using both methods allows one to distinguish sampling artefactual features from real sample spectral features. In transflection experiments, amide I/II absorption bands down‐shift 9/4 cm−1, respectively, relative to the corresponding bands in transmission experiments. In all other spectral regions no pronounced frequency differences in spectral bands in transmission and transflection experiments were observed. Transmission and transflection infrared microscopy were used to obtain infrared spectra for unfixed and acetone‐ or formalin‐fixed Vero cell monolayers. Formalin‐fixed monolayers display spectra that are very similar to that obtained using unfixed cells. However, acetone fixation leads to considerable spectral modifications. For unfixed and formalin‐fixed monolayers, a distinct band is observed at 1740 cm−1. This band is absent in spectra obtained using acetone‐fixed monolayers. The 1740 cm−1 band is associated with cellular ester lipids. In support of this hypothesis, two bands at 2925 and 2854 cm−1 are also found to disappear upon acetone fixation. These bands are associated with CH modes of the cellular lipids. Acetone fixation also leads to modification of protein amide I and II absorption bands. This may be expected as acetone causes coagulation of soluble cellular proteins. Other spectral changes associated with acetone or formalin fixation in the 1400–800 cm−1 region are discussed. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 921–930, 2008.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
The molecular structure and physical properties of elastin fibers as revealed by Raman microspectroscopy
Authors: Green Ellen , Ellis Richard , Winlove Peter
Published: June 2008

Raman microspectroscopy has been used to investigate the structure of α‐elastin and fibrous elastin from ligament and aorta, and to explore changes associated with mechanical strain and temperature. Although no vibrational modes associated with cross‐linking of the fibers could be identified, the secondary structure of dehydrated fibrous elastin was significantly different from α‐elastin. The former differed from previous experimental measurements, but was close to the theoretical predictions with 36% β‐structures, 46% unordered, and 18% α‐helix. α‐Elastin contained 29% β‐structures, 53% unordered, and 18% α‐helix. In nuchal fibers the amide I mode was polarized, consistent with the peptide bond. Strains of up to 60% in ligament fiber bundles resulted in no significant shifts in peak position or in secondary structure. Polarization measurements revealed that the peptide bonds and several side chains re‐orientated closer to the fiber axis. Heating nuchal fibers to 60°C to increase the energetic component of the elasticity was associated with a 30% increase in the proportion of β‐structures in the amide I band, a 50% increase in the amide III band, and a 50% reduction in the signal from bound water. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 931–940, 2008.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Enantioselective cyanosilylation of ketones catalyzed by recyclable polymeric and dimeric MN(III) salen complexes at room temperature
Authors: Khan Noor‐Ul H. , Agrawal Santosh , Kureshy Rukhsana I. , Abdi Sayed H.R. , Prathap K. Jeya , Jasra Raksh V.
Published: June 2008

Recyclable polymeric 1 and dimeric 2 chiral Mn(III) salen complexes catalyzed enantioselective cyanosilylation of various ketones in the presence of triphenylphosphine oxide as an additive proceeded smoothly at room temperature, providing excellent yields (up to 98%) and enantiomeric excess (up to 86%) of respective cyanohydrin trimethylsilyl ether. For most of the substrates, the Catalyst 1 showed slightly better reactivity and enantioselecitivity than the Catalyst 2 nevertheless both the catalysts were easily recovered and reused four times with the retention of their efficiency. Chirality, 2009. © 2008 Wiley‐Liss, Inc.
Sarcomere alignment is regulated by myocyte shape
Authors: Bray Mark‐Anthony , Sheehy Sean P. , Parker Kevin Kit
Published: June 2008

Cardiac organogenesis and pathogenesis are both characterized by changes in myocyte shape, cytoskeletal architecture, and the extracellular matrix (ECM). However, the mechanisms by which the ECM influences myocyte shape and myofibrillar patterning are unknown. We hypothesized that geometric cues in the ECM align sarcomeres by directing the actin network orientation. To test our hypothesis, we cultured neonatal rat ventricular myocytes on islands of micro‐patterned ECM to measure how they remodeled their cytoskeleton in response to extracellular cues. Myocytes spread and assumed the shape of circular and rectangular islands and reorganized their cytoskeletons and myofibrillar arrays with respect to the ECM boundary conditions. Circular myocytes did not assemble predictable actin networks nor organized sarcomere arrays. In contrast, myocytes cultured on rectangular ECM patterns with aspect ratios ranging from 1:1 to 7:1 aligned their sarcomeres in predictable and repeatable patterns based on highly localized focal adhesion complexes. Examination of averaged α‐actinin images revealed invariant sarcomeric registration irrespective of myocyte aspect ratio. Since the sarcomere sub‐units possess a fixed length, this observation indicates that cytoskeleton configuration is length‐limited by the extracellular boundary conditions. These results indicate that modification of the extracellular microenvironment induces dynamic reconfiguring of the myocyte shape and intracellular architecture. Furthermore, geometric boundaries such as corners induce localized myofibrillar anisotropy that becomes global as the myocyte aspect ratio increases. Cell Motil. Cytoskeleton 2008. © 2008 Wiley‐Liss, Inc.
Heterogeneous modes of uptake for latex beads revealed through live cell imaging of phagocytes expressing a probe for phosphatidylinositol‐(3,4,5)‐trisphosphate and phosphatidylinositol‐(3,4)‐bisphosphate
Authors: Giorgione Jennifer , Clarke Margaret
Published: June 2008

Latex beads are the preferred phagocytic substrate in biochemical studies of phagosome composition and maturation. Using living Dictyostelium cells and fluorescent probes, we compared the properties of phagosomes formed to ingest latex beads or digestible prey. Significant differences were found during the initial steps of phagocytosis. During uptake of bacteria or yeast, PHcrac‐GFP, a probe that binds to membranes enriched in PI(3,4,5)P3 and PI(3,4)P2, always labeled the nascent phagosome and faded shortly after it sealed. However, labeling of bead‐containing phagosomes was highly variable. Beads were engulfed by phagosomes either lacking or displaying the PHcrac‐GFP label, and that label, if present, often persisted for many minutes, revealing that early trafficking steps for bead‐containing phagosomes are quite heterogeneous. Later stages of the endocytic pathway appeared more similar for phagosomes containing prey and latex beads. Both types of phagosomes fused with acidic endosomes while undergoing transport along microtubules, both acquired the V‐ATPase and lost it prior to exocytosis, and both bound the late endosome marker vacuolin B, which was transferred to the plasma membrane upon exocytosis. We conclude that caution is needed in extrapolating results from latex bead phagosomes to phagosomes containing physiological substances, especially in early stages of the endocytic pathway. Cell Motil. Cytoskeleton 2008. © 2008 Wiley‐Liss, Inc.
Quadratic form: A robust metric for quantitative comparison of flow cytometric histograms
Authors: Bernas Tytus , Asem Elikplimi K. , Robinson J. Paul , Rajwa Bartek
Published: June 2008

Comparison of fluorescence distributions is a fundamental part of the analysis of flow cytometric data. This approach is applied to detect differences between control and test sample and thus analyze a biological response. Comparison of standard test samples over time provides an estimate of instrument stability for quality control. However, application of statistical methods of distribution comparison in flow cytometry is difficult owing to instrument noise and the complex shape of intensity distributions. We applied quadratic form (QF) as a mathematical metric for comparison of flow cytometry histograms. QF operates on histograms as vectors and calculates the total distance in an interbin manner using a matrix of distances between single histogram bins. Euclidean interbin distance and histograms normalized to unity were used. Critical values corresponding to 95% significance level were calculated using Monte‐Carlo simulation and single‐maximum Gaussian distributions populated with several numbers of events. The QF statistic was then validated for non‐Gaussian single‐maximum distributions and multiple‐maxima distributions. We determined that the critical values for Gaussian distributions depended on standard deviations and number of events in the compared histograms. A simple empirical function was constructed to characterize this dependence. Furthermore, it was verified that critical values (corresponding to 95% significance) for non‐Gaussian histograms were similar to values for the Gaussian histograms characterized by the same standard deviation. We applied the QF statistic to estimate the differences between histograms of DNA content (ploidy) in cells of old and young leaf tissue of Brassica campestris. Furthermore, we quantified differences in fluorescence intensity in immunostaining of human lymphocytes. Quadratic form (QF) provides a true (mathematical) metric for estimation of distance between flow cytometry histograms of arbitrary shape. QF can be applied as a statistical test for estimation of significance of the distance measure. The respective critical values depend only on the number of events and standard deviations of compared histograms and are not affected by distribution shape. Therefore, applications of QF do not require assumptions concerning distribution shape and can be easily implemented in practice. This notion was confirmed using empirical distributions of DNA content in plant tissue and distributions of immunofluorescence in human cells. © 2008 International Society for Advancement of Cytometry
Chromatic aberration correction and deconvolution for UV sensitive imaging of fluorescent sterols in cytoplasmic lipid droplets
Authors: Wüstner Daniel , Færgeman Nils J.
Published: June 2008

Intrinsically fluorescent sterols, like dehydroergosterol (DHE), mimic cholesterol closely and are therefore suitable to determine cholesterol transport by fluorescence microscopy. Disadvantages of DHE are its low quantum yield, rapid bleaching, and the fact that its excitation and emission is in the UV region of the spectrum. Thus, one has to deal with chromatic aberration and low signal‐to‐noise ratio. We developed a method to correct for chromatic aberration between the UV channel and the red/green channel in multicolor imaging of DHE compared with the lipid droplet marker Nile Red in living macrophage foam cells and in adipocytes. We used deconvolution microscopy and developed image segmentation techniques to assess the DHE content of lipid droplets in both cell types in an automated manner. Pulse‐chase studies and colocalization analysis were performed to monitor the redistribution of DHE upon adipocyte differentiation. DHE is targeted to transferrin‐positive recycling endosomes in preadipocytes but associates with droplets in mature adipocytes. Only in adipocytes but not in foam cells fluorescent sterol was confined to the droplet‐limiting membrane. We developed an approach to visualize and quantify sterol content of lipid droplets in living cells with potential for automated high content screening of cellular sterol transport. © 2008 International Society for Advancement of Cytometry
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

CD137 (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

Microencapsulation 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

Background

Common 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.

Methods

Multicolor flowcytometric analysis of circulating lymphocytes.

Results

The 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.

Conclusions

Flowcytometric 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

Background

Flow 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.

Methods

mDCs 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.

Results

The 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.

Conclusions

The 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

The 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

The 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

The 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

We 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

Haplotypes 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

Climate 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

A 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

Veterans 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

Functional 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

Background

Transoral 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.

Methods

We 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.

Results

No 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.

Conclusion

Swallowing 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

As 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

The 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.

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