bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguishing benign from malignant mesothelial cells in effusions by Glut‐1, EMA, and Desmin expression: An evidence‐based approach
Authors: Kuperman Michael , Florence Roxanne R. , Pantanowitz Liron , Visintainer Paul F. , Cibas Edmund S. , Otis Christopher N. 
Published: September 2011

AbstractDistinguishing malignant mesothelioma (MM) from reactive mesothelial hyperplasia (RM) may be difficult in effusions. This study tested the hypothesis that immunocytochemistry (IC) in effusion cell blocks (CB) can distinguish MM from RM and that the results may be applied to individual specimens. External validation of a risk score (RS) model associating sensitivity and specificity was applied to an external set of MM and RM specimens from a separate institution.Forty three effusion cytology CBs of 25 confirmed malignant mesotheliomas were compared to CBs of 23 benign mesothelial effusions without inflammation and 13 reactive mesothelial proliferations associated with inflammation. Glut‐1, EMA, and Desmin expression were evaluated by immunocytochemistry on CBs. Each antibody was compared using ROC values, where the area under the curve (AUC) was 0.90, 0.82, and 0.84 for Glut‐1, EMA, and Desmin, respectively. Logistic regression (LR) analysis was applied to a combination of Glut‐1 and EMA. A combined ROC curve was modeled for Glut‐1 and EMA (AUC = 0.93). A RS = 2 × (Glut‐1%) + 1 × (EMA%) was created from this ROC curve. When applied to an external set of MM and RM, the RS resulted in an ROC with AUC = 0.91.In conclusion, a RS derived from a LR of Glut‐1 and EMA IC greatly improves the distinction between MM from RM cells in individual effusions. The study illustrates principles of evidence‐based pathology concerning internal and external test performance in the differential diagnosis of MM versus RM. Diagn. Cytopathol. 2013. © 2011 Wiley Periodicals, Inc
Ancestral network module regulating prdm1 expression in the lamprey neural plate border
Authors: Nikitina Natalya , Tong Leslie , Bronner Marianne E. 
Published: September 2011

Abstractprdm1 is an important transcriptional regulator that plays diverse roles during development of a wide variety of vertebrate and invertebrate species. prdm1 is required for neural crest specification in zebrafish, but not in mouse embryos. The role of this gene in neural crest formation in other species has not been examined, and its regulation during embryonic development is poorly understood. Here, we investigate the expression pattern, function, and the upstream regulatory inputs into prdm1 during lamprey neural crest development. prdm1 is strongly expressed in the lamprey neural plate border, suggesting a conserved ancestral role of this gene in the neural crest formation. We found that lamprey neural plate border expression of prdm1 is activated by Ap‐2 and Msx, but is independent of Pax3/7 and Zic. Developmental Dynamics 240:2265–2271, 2011. © 2011 Wiley‐Liss, Inc.
Use of a Drosophila genome‐wide conserved sequence database to identify functionally related cis‐regulatory enhancers
Authors: Brody Thomas , Yavatkar Amarendra S. , Kuzin Alexander , Kundu Mukta , Tyson Leonard J. , Ross Jermaine , Lin Tzu‐Yang , Lee Chi‐Hon , Awasaki Takeshi , Lee Tzumin , Odenwald Ward F. 
Published: September 2011

AbstractBackground: Phylogenetic footprinting has revealed that cis‐regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full‐advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome‐wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis‐Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis‐regulatory function. To demonstrate the utility of these tools, a temporally‐restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis‐Decoder reveals that co‐regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc.
A Monte Carlo investigation of factors influencing latent class analysis: An application to eating disorder research
Authors: Swanson Sonja A. , Lindenberg Katajun , Bauer Stephanie , Crosby Ross D. 
Published: September 2011

AbstractObjective:Latent class analysis (LCA) has frequently been used to identify qualitatively distinct phenotypes of disordered eating. However, little consideration has been given to methodological factors that may influence the accuracy of these results.Method:Monte Carlo simulations were used to evaluate methodological factors that may influence the accuracy of LCA under scenarios similar to those seen in previous eating disorder research.Results:Under these scenarios, the aBIC provided the best overall performance as an information criterion, requiring sample sizes of 300 in both balanced and unbalanced structures to achieve accuracy proportions of at least 80%. The BIC and cAIC required larger samples to achieve comparable performance, while the AIC performed poorly universally in comparison. Accuracy generally was lower with unbalanced classes, fewer indicators, greater or nonrandom missing data, conditional independence assumption violations, and lower base rates of indicator endorsement.Discussion:These results provide critical information for interpreting previous LCA research and designing future classification studies. © 2011 by Wiley Periodicals, Inc. (Int J Eat Disord 2011)
Real‐time cell electrophysiology using a multi‐channel dielectrophoretic‐dot microelectrode array
Authors: Fatoyinbo Henry O. , Kadri Nahrizul A. , Gould David H. , Hoettges Kai F. , Labeed Fatima H. 
Published: September 2011

AbstractDielectrophoresis (DEP) has been used for many years for the analysis of the electrophysiological properties of cells. However, such analyses have in the past been time‐consuming, such that it can take 30 min or more to collect sufficient data to make valid interpretations from a single DEP spectrum. This has limited the application of the technology to a rapid tool for non‐invasive, label‐free research in areas from drug discovery to diagnostics. In this paper we present the development of a programmable, multi‐channel DEP system for rapid biophysical assessment of populations of biological cells. A new assay format has been developed for continuous near‐real‐time monitoring, using simultaneous application of up to eight alternating current electrical signals to independently addressable dot microelectrodes in an array format, allowing a DEP spectrum to be measured in 20 s, with a total cycle time between measurements of 90 s. To demonstrate the system, human leukaemic K562 cells were monitored after exposure to staurosporine and valinomycin. The DEP response curves showed the timing and manner in which the membrane properties changed for the actions of these two drugs at the early phase of induction. This technology shows the great potential for increasing our understanding of the role of electrophysiology in drug action, by observing the changes in electrical characteristics as they occur.
Subtyping Children and Adolescents Who Are Overweight Based on Eating Pathology and Psychopathology
Authors: Braet Caroline , Beyers Wim , Goossens Lien , Verbeken Sandra , Moens Ellen 
Published: September 2011

AbstractChildren and adolescents who are overweight can differ on dimensions measuring dietary restraint and psychopathology. Classifying clinical obese children and adolescents based on these psychological characteristics is shown to be useful in making differential prognoses. The present study aimed to research the validity of subtyping children and adolescents with overweight (N = 138) in a non‐clinical sample. Using cluster analysis, results revealed three subtypes: a dietary restraint/internalizing group (DR + IN; n = 41), a pure internalizing group (IN; n = 20) and a non‐symptomatic group (NS; n = 77). The DR + IN group outscored both other groups on measures of eating pathology, whereas the IN group outscored both other groups on measures of negative offect. Interestingly, the three groups did not differ on degree of overweight. The results seem to suggest that different psychological mechanisms can be observed in subgroups of young overweight adolescents. Further research should explore how individual psychological characteristics can be helpful when stipulating weight loss treatment programmes. Copyright © 2011 John Wiley & Sons, Ltd and Eating Disorders Association.
Photodegradation of lambda-cyhalothrin and cypermethrin in aqueous solution as affected by humic acid and/or copper: Intermediates and degradation pathways
Authors: Xie Jimin , Wang Pingli , Liu Jun , Lv Xiaomeng , Jiang Deli , Sun Cheng 
Published: September 2011

Abstract
The influence of coexisting humic acids (HA) or Cu2+ on the photodegradation of pesticides lambda-cyhalothrin (λ-CHT) and cypermethrin (CPM) in aqueous solution was studied under xenon lamp irradiation. The removal efficiency of pesticides λ-CHT and CPM were enhanced in the presence of either Cu2+ or HA but restrained in the presence of both Cu2+ and HA. The photodegradation of λ-CHT and CPM followed first-order reaction kinetics. The photodegradation intermediates of λ-CHT and CPM were determined using gas chromatography/mass spectrometry. Possible photodegradation pathways included decarboxylation, ester bond cleavage, dechlorination, and phenyl group removal. Environ. Toxicol. Chem. 2011;30:2440–2448. © 2011 SETAC
T‐cell lymphoblastic lymphoma shows differences and similarities with T‐cell acute lymphoblastic leukemia by genomic and gene expression analyses
Authors: Basso Katia , Mussolin Lara , Lettieri Antonella , Brahmachary Manisha , Lim Wei Keat , Califano Andrea , Basso Giuseppe , Biondi Andrea , Cazzaniga Giovanni , Rosolen Angelo 
Published: September 2011

AbstractT‐cell acute lymphoblastic leukemia (T‐ALL) and lymphoma (T‐LBL) share common morphological and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations, suggesting that they may represent two different biological entities. To investigate the genetic characteristics of T‐LBL and T‐ALL, we used genomic and transcriptional profiling approaches. Genome‐wide gene expression profiling, performed on 20 T‐LBL and 10 T‐ALL diagnostic specimens, revealed that the two malignancies shared a large fraction of their transcriptional profile while a subset of genes appeared to be differentially expressed in T‐LBL versus T‐ALL. This signature included genes involved in chemotactic responses and angiogenesis, which may play a role in tumor cell localization. Genome‐wide copy number alteration analysis was performed on a subset of the samples analyzed by gene expression profiling and detected 41 recurrently altered genetic loci. Although most aberrations were found in both entities, several were selectively identified in T‐LBL or T‐ALL. In addition, NOTCH1 mutational status was found to correlate with a subset of genetic aberrations. Taken together, these results suggest that T‐LBL and T‐ALL are indeed two distinct diseases with unique transcriptional and genetic characteristics. © 2011 Wiley Periodicals, Inc.
Reduction in expression of the astrocyte glutamate transporter, GLT1, worsens functional and histological outcomes following traumatic spinal cord injury
Authors: Lepore Angelo C. , O'donnell John , Kim Andrew S. , Yang Eun Ju , Tuteja Alisha , Haidet‐Phillips Amanda , O'Banion Colin P. , Maragakis Nicholas J. 
Published: September 2011

AbstractThe astrocyte glutamate transporter, GLT1, is responsible for the vast majority of glutamate uptake in the adult central nervous system (CNS), thereby regulating extracellular glutamate homeostasis and preventing excitotoxicity. Glutamate dysregulation plays a central role in outcome following traumatic spinal cord injury (SCI). To determine the role of GLT1 in secondary cell loss following SCI, mice heterozygous for the GLT1 astrocyte glutamate transporter (GLT1+/−) and wild‐type mice received thoracic crush SCI. Compared with wild‐type controls, GLT1+/− mice had an attenuated recovery in hindlimb motor function, increased lesion size, and decreased tissue sparing. GLT1+/− mice showed a decrease in intraspinal GLT1 protein and functional glutamate uptake compared with wild‐type mice, accompanied by increased apoptosis and neuronal loss following crush injury. These results suggest that astrocyte GLT1 plays a role in limiting secondary cell death following SCI, and also show that compromise of key astrocyte functions has significant effects on outcome following traumatic CNS injury. These findings also suggest that increasing intraspinal GLT1 expression may represent a therapeutically relevant target for SCI treatment. © 2011 Wiley‐Liss, Inc.
Evaluating and reducing the impact of white matter lesions on brain volume measurements
Authors: Battaglini Marco , Jenkinson Mark , De Stefano Nicola 
Published: September 2011

AbstractMR‐based measurements of brain volumes may be affected by the presence of white matter (WM) lesions. Here, we assessed how and to what extent this may happen for WM lesions of various sizes and intensities. After inserting WM lesions of different sizes and intensities into T1‐W brain images of healthy subjects, we assessed the effect on two widely used automatic methods for brain volume measurement such as SIENAX (segmentation‐based) and SIENA (registration‐based). To explore the relevance of partial volume (PV) estimation, we performed the experiments with two different PV models, implemented by the same segmentation algorithm (FAST) of SIENAX and SIENA. Finally, we tested potential solutions to this issue. The presence of WM lesions did not bias measurements for registration‐based method such as SIENA. By contrast, the presence of WM lesions affected segmentation‐based brain volume measurements such as SIENAx. The misclassification of both gray matter (GM) and WM volumes varied considerably with lesion size and intensity, especially when the lesion intensity was similar to that of the GM/WM interface. The extent to which the presence of WM lesions could affect tissue‐class measures was clearly driven by the PV modeling used, with the mixel‐type PV model giving a lower error in the presence of WM lesions. The tissue misclassification due to WM lesions was still present when they were masked out. By contrast, refilling the lesions with intensities matching the surrounding normal‐appearing WM ensured accurate tissue‐class measurements and thus represents a promising approach for accurate tissue classification and brain volume measurements. Hum Brain Mapp 33:2062–2071, 2012. © 2011 Wiley Periodicals, Inc.
MEASURING THE EFFECT OF POLICY INTERVENTIONS AT THE POPULATION LEVEL: SOME METHODOLOGICAL CONCERNS
Authors: D. Huesch Marco , Østbye Truls , K. Ong Michael 
Published: September 2011

SUMMARYHealth policy evaluations estimate the response of population aggregate outcomes to interventions. However, clarity on the form of the expected causal relationship, the parameter identification strategy, and the mode of hypothesis testing is required to overcome a number of conceptual and methodological problems. We use the New Jersey statewide smoking ban as an example. We examine statewide admission rates for acute myocardial infarctions, strokes and lower limb fractures, and emergency room encounter rates for asthma exacerbations before and after the smoking ban. We discuss the identification options and show the sensitivity of estimates of the response function to different specifications of the stochastic and intervention components and to different modes of inference. Model misspecification is demonstrated by rolling Chow tests for structural breaks in repeated observations. Copyright © 2011 John Wiley & Sons, Ltd.
Vanderbilt head and neck symptom survey version 2.0: Report of the development and initial testing of a subscale for assessment of oral health
Authors: Cooperstein Emily , Gilbert Jill , Epstein Joel B. , Dietrich Mary S. , Bond Stewart M. , Ridner Sheila H. , Wells Nancy , Cmelak Anthony , Murphy Barbara A. 
Published: September 2011

AbstractBackgroundThe prevalence, severity, and functional implications of adverse oral health outcomes attributed to head and neck cancer therapy are largely undefined. We report development of an oral health outcome subscale for the Vanderbilt Head and Neck Symptom Survey (VHNSS).MethodsOral health outcome questions were formulated through literature review and consultation with an expert panel. Questions were incorporated into the VHNSS resulting in a 50‐item survey, scored 0 (none) to 10 (severe). The tool was administered to 70 subjects who completed radiation to assess for feasibility.ResultsPatient acceptance was high with a completion time <10 minutes. A full range of scores was noted for 46 of 50 questions. Oral health symptom burden was high early and late posttreatment.ConclusionsThe VHNSS version 2.0 was feasible and could be completed in a timely manner. Validation studies are ongoing. The high prevalence of adverse oral health outcomes warrants further study. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Two‐dimensional flow patterns near contour grass hedges
Authors: Vieira Dalmo A. N. , Dabney Seth M. 
Published: September 2011

AbstractGrass hedges are narrow strips of stiff‐stemmed vegetation used to control erosion and sediment delivery. When planted on the contour, the hydraulic resistance of the vegetation slows runoff, creates ponding, and promotes sediment deposition. When tillage is performed between grass hedges, soil may be thrown against the vegetation, where it settles to form a berm within the hedge. Tillage‐induced berms divert part of runoff, causing it to flow alongside the hedge without crossing it. Such flow partitioning created by grass hedges was measured on experimental plots located on silt loam loess soil near Holly Springs, Mississippi, USA, where hedges planted at the bottom of 5%, 22.1‐m‐long slopes evolved berms averaging 0.13 m in height. They diverted about 80% of the runoff for events smaller than 5 mm and about 50% for large events. A two‐dimensional model was developed to determine overland flow patterns over complex terrains, accounting for oriented roughness created by tillage corrugations, crop rows, and larger features such as berms and vegetative barriers. The model was used to reproduce the flow partition observed in the field experiments and to determine how berm height and slope steepness and length affected runoff redistribution. Numerical simulations indicated that for most runoff events, ponded runoff depths were not high enough to overtop the berm but rather crossed the berms through cracks and gaps, represented in the model as small triangular weirs. The model also was applied to a 6.0‐ha watershed in Western Iowa, USA, where nine grass hedges were planted across 12–16% slopes. Computed dynamic flow properties showed that berms increased the amount of runoff flowing laterally upslope of the hedges and that a large portion of the runoff crossed the vegetative strips at a few locations and with high flow depths, increasing the risk of development of ephemeral gullies. Copyright © 2011 John Wiley & Sons, Ltd.
Abrupt changes in the discharge and sediment load of the Pearl River, China
Authors: Zhang Qiang , Xu Chong‐Yu , Chen Xiaohong , Lu Xixi 
Published: September 2011

AbstractThe abrupt changes in the streamflow and sediment load at nine hydrological stations of the Pearl River basin were systematically analysed by using the simple two‐phase linear regression scheme and the coherency analysis technique. Possible underlying causes were also discussed. Our study results indicated that abrupt changes in the streamflow occurred mainly in the early 1990s. The change points were followed by significant decreasing streamflow. Multiscale abrupt behaviour of the sediment load classified the hydrological stations into two groups: (1) Xiaolongtan, Nanning and Liuzhou; and (2) Qianjiang, Dahuangjiangkou, Wuzhou, Gaoyao, Shijiao and Boluo. The grouped categories implied obvious influences of water reservoirs on the hydrological processes of the Pearl River. On the basis of analysis of the locations and the construction time of the water reservoirs, and also the time when the change points occurred, we figured out different ways the water reservoirs impacted the hydrological processes within the Pearl River basin. As for the hydrological variation along the mainstream of the Pearl River, the water reservoirs have considerable influences on both the streamflow and sediment load variations; however, more influences seemed to be exerted on the sediment load transport. In the North River, the hydrological processes seemed to be influenced mainly by climate changes. In the East River, the hydrological variations tended to be impacted by the water reservoirs. The study results also indicated no fixed modes when we address the influences of water reservoirs on hydrological processes. Drainage area and regulation behaviour of the water reservoirs should be taken into account. The results of this study will be of considerable importance for the effective water resources management of the Pearl River basin under the changing environment. Copyright © 2011 John Wiley & Sons, Ltd.
Attribution of human papillomavirus types to cervical intraepithelial neoplasia and invasive cancers in Southern China
Authors: Chan Paul K.S. , Cheung Tak‐Hong , Li Wai‐Hon , Yu Mei Y. , Chan May Y.M. , Yim So‐Fan , Ho Wendy C.S. , Yeung Apple C.M. , Ho King‐Man , Ng H.K. 
Published: September 2011

AbstractThe attribution of individual human papillomavirus (HPV) types to cervical neoplasia, especially intraepithelial lesions, varies ethnogeographically. Population‐specific data are required for vaccine cost‐effectiveness assessment and type replacement monitoring. HPV was detected from 2,790 Chinese women (444 invasive cervical cancers [ICC], 772 cervical intraepithelial neoplasia [CIN] grade 3, 805 CIN2 and 769 CIN1. The attribution of each HPV type found in multiple‐type infections was approximated by the fractional contribution approach. Multiple‐type infection was common and correlated inversely with lesion severity (54.7% for CIN1, 48.7% for CIN2, 46.2% for CIN3, 27.5% for ICC). Vaccine‐covered high‐risk types (HPV16/18) attributed to 59.5% of squamous cell carcinoma, 78.6% of adenocarcinoma, 35.9% of CIN3, 18.4% of CIN2 and 7.4% of CIN1. Distinct features compared to worldwide were a higher attribution of HPV52 and HPV58, and a much lower attribution of HPV45. Inclusion of HPV52 and HPV58 in future vaccines would provide the highest marginal increase in coverage with 11.7% for squamous cell carcinoma, 14.4% for CIN3, 22.6% for CIN2 and 17.7% for CIN1. The attribution of HPV types in southern China is different from elsewhere, which should be considered in prioritizing HPV types for vaccine and screening assay development.