bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Throughput Screening of Gene Function in Stem Cells Using Clonal Microarrays
Authors: Ashton Randolph S. , Peltier Joseph , Fasano Christopher A. , O'Neill Analeah , Leonard Joshua , Temple Sally , Schaffer David V. , Kane Ravi S. 
Published: August 2007

Abstract
We describe a microarray-based approach for the high-throughput screening of gene function in stem cells and demonstrate the potential of this method by growing and isolating clonal populations of both adult and embryonic neural stem cells. Clonal microarrays are constructed by seeding a population of cells at clonal density on micropatterned surfaces generated using soft lithographic microfabrication techniques. Clones of interest can be isolated after assaying in parallel for various cellular processes and functions, including proliferation, signal transduction, and differentiation. We demonstrate the compatibility of the technique with both gain- and loss-of-function studies using cell populations infected with cDNA libraries or DNA constructs that induce RNA interference. The infection of cells with a library prior to seeding and the compact but isolated growth of clonal cell populations will facilitate the screening of large libraries in a wide variety of mammalian cells, including those that are difficult to transfect by conventional methods.
Disclosure of potential conflicts of interest is found at the end of this article.
Adrenocorticotropin concentration following administration of thyrotropin-releasing hormone in healthy horses and those with pituitary pars intermedia dysfunction and pituitary gland hyperplasia
Authors: Beech Jill , Boston Raymond , Lindborg Sue , Russell Gail E. 
Published: August 2007

Abstract
Objective—To compare the effect of thyrotropin-releasing hormone (TRH) administration on endogenous ACTH concentrations in healthy horses and those with pituitary pars inter-media hyperplasia and compare the test with the dexamethasone suppression test (DST).
Design—Prospective case series.
Animals—15 horses with clinical signs of pituitary pars intermedia dysfunction (PPID), 4 horses with equivocal signs of PPID, and 29 horses without signs of PPID.
Procedures—ACTH concentrations prior to and after administration of TRH were measured 61 times in 48 horses. Results of the DST (cortisol response) were compared with those of the TRH test in 29 horses. Thirty-three horses (24 with no clinical signs of PPID, 5 with clinical signs of PPID, and 4 with equivocal clinical signs of PPID) were euthanized and necropsied and their pituitary glands evaluated.
Results—ACTH concentrations increased in all horses, but magnitude and duration of increase were significantly higher in horses with PPID. Endogenous ACTH concentrations were influenced by season. The ACTH baseline concentrations and response to TRH were not correlated with results of the DST. Results of DST were abnormal only in clinically abnormal horses or those with pars intermedia hyperplasia, but were within reference range in 17 of 26 tests in these horses.
Conclusions and Clinical Relevance—The ACTH response to TRH is a useful test for diagnosis of pituitary gland hyperplasia, particularly in horses in which baseline ACTH concentrations are within reference range. The DST was specific but not sensitive and was inconsistent for individuals, and results often did not agree with the TRH test response.
Bubble trapping and coalescence at the baffles in stirred tank reactors
Authors: Sudiyo Rahman , Andersson Bengt 
Published: August 2007

AbstractTurbulent flow and bubble coalescence in water at the leeward side of a baffle in a stirred tank reactor have been studied with PIV and a high‐speed CCD camera. A large stationary vortex was revealed at the leeward side of the baffle. At impeller speeds of 400–600 RPM, the maximum tangential velocity at the vortex was proportional to the impeller tip speed (uθ ≈ 0.27 Utip), giving a pressure difference in the vortex of as much as a few hundred pascal. The main mechanism for coalescence in this area was trapping of bubbles in the vortex, increasing the local hold‐up and coalescence probability by forcing the bubbles together. The force on the bubbles resulting from the local pressure gradient makes the bubbles move fast to the centre, within 10–20 ms. The coalescence efficiency was very high and more than 85% of the coalescence occurred within 2 ms. Bouncing of bubbles was mainly seen for large bubbles moving up in the centre of the vortex. The trapping of the bubbles was modeled successfully by a drag coefficient model corrected for nonspherical bubbles and turbulent continuous phase. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Optimization of desalination location problem using MILP
Authors: Emhamed A. M. , Czuczai B. , Horvath L. , Rev E. , Lelkes Z. 
Published: August 2007

AbstractA new mixed‐integer linear programming model for location problem is developed in this work in order to find the optimal co‐ordinates of the desalination plants. The model takes into account the given locations and capacities of the water incomes, the demands, and the costs of plants and pipelining. Feasible and infeasible plant regions are distinguished for locating the plants. The model has been developed in two consecutive phases. First, a basic model is developed that provides a solution within short time but does not take into account the possibility of pipeline branching. Application of this model gives rise to redundant pipelines to some connections, involving extra costs. Pipeline branching is dealt with an improved model developed in the second phase. This improved model provides realistic solution but with much longer computation time. The results of applying the different models on motivated examples of different sizes are detailed. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Process trend monitoring using key sensitive index
Authors: Jeng Jyh‐Cheng , Su An‐Jhih , Yu Cheng‐Ching , Huang Hsiao‐Ping 
Published: August 2007

AbstractProcess monitoring is essential to maintain product quality in semiconductor manufacturing. However, unlike chemical processes, semiconductor manufacturing processes exhibit the following characteristics: (1) much shorter (minutes) and often variable (deliberately adjusted) batch time, (2) multiple processing steps (10–20) in each batch, (3) only some particular processing steps constituting the quality‐determining steps, and (4) mixed products for the same batch processing. In this work, instead of incorporating a large number of trajectory data with variable batch time and possibly “missing” data for some process variables using multivariate statistics, a process‐insight‐based approach, key sensitive index (KSI), is taken. From process knowledge, the key sensitive time‐slot in the recipe is identified. Next, possible key sensitive process variables (KSV) are selected and validated according to the process trend correlation. A simple batch reactor example is used to illustrate the KSV selection procedure. Then, an index for these variables is sought. Two integrated circuit processing examples from real fab data are used to illustrate the KSI‐based approach and results clearly indicate that process trend is captured using KSI‐based approach. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Analysis of flux decline behaviors in filtration of very dilute suspensions
Authors: Iritani Eiji , Katagiri Nobuyuki , Sugiyama Yuuki , Yagishita Koichi 
Published: August 2007

AbstractThe gradual decrease in the filtration flux rate with time, which occurred due to the capture of solid particles and/or organic substances onto the surfaces of pores in a thin filter medium, was measured in constant‐pressure filtration of both pool water and pond water. A new theoretical background of the conventional characteristic filtration equation describing the variation of the filtration resistance of the clogged filter medium with time was afforded based on a consideration of the variation of both the porosity and the specific surface area of the filter medium caused by the capture of the solids in the Kozeny‐Carman equation. The flux decline behavior depended solely on the initial filtration rate, influenced by the pore size of the filter medium and the filtration pressure. The variations of the filtration rate and the filtrate volume with the filtration time were very accurately described by the analytical solution based on the characteristic filtration equation. In the case of pond water with a relatively high turbidity compared to pool water, the transition point from depth to cake filtration was determined based on the pressure dependence of the specific filtration resistance of the filter cake, and then the flux attenuation behavior was evaluated by considering the transition from depth to cake filtration. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Autism in African American Families: Clinical‐phenotypic findings
Authors: Cuccaro Michael L. , Brinkley Jason , Abramson Ruth K. , Hall Alicia , Wright Harry H. , Hussman John P. , Gilbert John R. , Pericak‐Vance Margaret A. 
Published: August 2007

AbstractUnlike other complex diseases, the study of autism has been almost exclusively limited to Caucasian families. This study represents a first effort to examine clinical and phenotypic findings in individuals with autism from African American families. Drawing from an ongoing genetic study of autism we compared African American (N = 46, mean age = 118 months) and Caucasian (N = 298, mean age = 105 months) groups on autism symptoms and developmental language symptoms. The African American group showed greater delays in language but did not differ from the Caucasian group on core autism symptoms. These findings, while suggestive of a more severe phenotype, may reflect an ascertainment bias. Nonetheless, we believe that more studies of racial‐ethnic groups should be conducted with several goals in mind including strengthening recruiting strategies to include more ethnic‐racial groups and more thoughtful evaluation of phenotypic traits. Such considerations will aid greatly in the search for genetic variants in autism. © 2007 Wiley‐Liss, Inc.
Polymorphisms TaqI A of the DRD2, BalI of the DRD3, exon III repeat of the DRD4, and 3′ UTR VNTR of the DAT: Association with childhood ADHD in male African‐Caribbean cocaine dependents?
Authors: Ballon Nicolas , Leroy Sophie , Roy Christianne , Bourdel Marie‐Chantal , Olie Jean‐Pierre , Charles‐Nicolas Aimé , Krebs Marie‐Odile , Poirier Marie‐France 
Published: August 2007

AbstractThe conflicting results reported by genetic studies with the variants of the genes coding for the dopaminergic system in cocaine addicts could be partially explained by the difficulties to constitute homogenous sample of patients. Childhood attention‐deficit/hyperactivity disorder (ADHD), and/or impulsivity are frequently associated with cocaine addiction and could participate in the heterogeneity of the samples in cocaine addicts. Accordingly, it is hypothesized that cocaine addiction would be associated with the variants of the genes coding for the dopamine system in an homogenized sample of cocaine addicts, especially in individuals with childhood ADHD comorbidity, or with a high impulsivity score. The potential association of the variants TaqI A of the DRD2, BalI of the DRD3, exon III repeat of the DRD4, and 3′ UTR VNTR of the DAT was examined in African‐Caribbean males, smoked‐cocaine dependents. All the subjects were assessed with the Diagnostic Interview of Genetic Studies, the Barratt's impulsivity scale, and the Wender Utah rating scale for childhood ADHD. A positive association was found with the DRD2 and DRD4 polymorphisms in the subgroups of patients with childhood ADHD, or with a high impulsivity score, which represented, respectively, 53.3 and 73.0% of the patients. Conversely, no positive association was found for any of the polymorphisms studied when the group of patients was examined as a whole. Therefore, our results suggest that the clinical dimensions of childhood ADHD and of impulsivity could be taken into account to homogenize the samples of patients in cocaine association studies. © 2007 Wiley‐Liss, Inc.
Gene‐based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: Association with HMG2L1 and TOM1
Authors: Potash James B. , Buervenich Silvia , Cox Nancy J. , Zandi Peter P. , Akula Nirmala , Steele Jo , Rathe Jennifer A. , Avramopoulos Dimitrios , Detera‐Wadleigh Sevilla D. , Gershon Elliot S. , DePaulo J. Raymond , Feinberg Andrew P. , McMahon Francis J. 
Published: August 2007

AbstractGenetic linkage studies in both bipolar affective disorder (BPAD) and schizophrenia have implicated overlapping regions of chromosome 22q. We previously reported that BPAD pedigrees containing multiple members with psychotic symptoms showed suggestive linkage to chromosome 22q12.3. Now we have tested 189 single nucleotide polymorphisms (SNPs) spanning a 3 Mb region around the linkage peak for association with BPAD in 305 families, unrelated cases, and controls. SNPs were selected in or near genes, resulting in coverage at a density of 1 SNP per 6.7 kb across the 22 annotated genes in the region. The strongest signal emerged from family‐based association analysis of an 11‐SNP, 54 kb haplotype straddling the gene HMG2L1 and part of TOM1. A 3‐marker haplotype of SNPs within TOM1 was associated with BPAD (allele‐wise P = 0.0011) and with psychotic BPAD (allele‐wise P = 0.00049). As hypothesized, the mean odds ratio for the risk alleles across the region was 1.39 in the psychotic but only 0.96 in the non‐psychotic subset. Genotype‐wise analyses yielded similar results, but the psychotic/non‐psychotic distinction was more pronounced with mean odds ratios of 1.91 versus 0.8. Permutation of genotype‐wise results for rs2413338 in HMG2L1 showed an empirical P = 0.037 for the difference between subsets. HMG2L1 is a negative regulator of Wnt signaling, a pathway of interest in psychotic BPAD as it is activated by both mood stabilizer and anti‐psychotic medications. Further work is needed to confirm these results and uncover the functional variation underlying the association signal. © 2007 Wiley‐Liss, Inc.
Crystalline structure of poly(ethylene terephthalate) filaments
Authors: Youssefi M. , Morshed M. , Kish M. H. 
Published: August 2007

AbstractFully oriented, partially oriented, drawn, and quenched samples of poly (ethylene terephthalate) (PET) filaments were examined. Crystalline fraction and the average size of crystallites were measured by a wide angle X‐ray scattering diffractometer. Sample geometry in X‐ray diffraction was found to affect the intensity of the diffraction patterns. The crystalline fraction of the samples can be measured by X‐ray diffraction in a symmetrical reflection geometry accompanied with curve fitting computer software. Annealing improves the average size of crystallites in a direction perpendicular to (010) plane more than the two other directions, namely perpendicular to (100) and (−105) planes. Fourier transform infrared spectroscopy was used to determine the percentage of trans configuration, and the volume crystalline fraction was determined from density measurements. A good correlation was obtained between the percentage of trans configuration and weight percentage of crystalline fraction determined by density measurements. The molecular orientation of the samples was measured by a polarizing microscope and its results conform to the other findings. The presence of extended chains in the noncrystalline regions supports the idea of the presence of oriented amorphous (amorphous with correlation) and nonoriented amorphous domains in PET drawn filaments. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Panitumumab monotherapy in patients with previously treated metastatic colorectal cancer
Authors: Hecht J. Randolph , Patnaik Amita , Berlin Jordan , Venook Alan , Malik Imtiaz , Tchekmedyian Simon , Navale Lynn , Amado Rafael G. , Meropol Neal J. 
Published: August 2007

AbstractBACKGROUND.The safety and efficacy of the fully human antibody panitumumab was evaluated in patients with metastatic colorectal cancer refractory to available therapies.METHODS.This phase 2 open‐label, multicenter study of panitumumab enrolled patients with metastatic colorectal cancer who had progressed on chemotherapy that included a fluoropyrimidine and irinotecan or oxaliplatin, or both. All patients had tumors with ≥10% 1+ epidermal growth factor receptor (EGFr) staining by immunohistochemistry. Patients were stratified into 2 strata (high or low staining intensity) and received intravenous panitumumab 2.5 mg/kg weekly 8 of every 9 weeks until disease progression or unacceptable toxicity.RESULTS.In all, 148 patients received panitumumab, 105 in the high EGFr stratum, 43 in the low EGFr stratum. Overall response by central review was 9% (95% confidence interval [CI], 5%–15%) and was similar between strata. An additional 29% of patients had stable disease. Median progression‐free survival was 14 weeks (95% CI, 8–16) and median overall survival was 9 months (95% CI, 6–10). Toxicities were manageable, with skin toxicity reported in 95% of patients (5% grade 3 or 4). Four patients discontinued therapy because of toxicity. No antipanitumumab antibodies were detected. One patient had an infusion reaction but was able to continue therapy.CONCLUSIONS.Panitumumab given weekly was well tolerated and had single‐agent activity in previously treated patients with colorectal cancer. Dermatologic toxicity was common but rarely severe. Ongoing studies will determine panitumumab activity earlier in the course of treatment for colorectal cancer and in combination with other antineoplastic agents. Cancer 2007. © 2007 American Cancer Society.
Collocated discrete least‐squares (CDLS) meshless method: Error estimate and adaptive refinement
Authors: Afshar M. H. , Lashckarbolok M. 
Published: August 2007

AbstractMeshless methods are new approaches for solving partial differential equations. The main characteristic of all these methods is that they do not require the traditional mesh to construct a numerical formulation. They require node generation instead of mesh generation. In other words, there is no pre‐specified connectivity or relationships among the nodes. This characteristic make these methods powerful. For example, an adaptive process which requires high computational effort in mesh‐dependent methods can be very economically solved with meshless methods. In this paper, a posteriori error estimate and adaptive refinement strategy is developed in conjunction with the collocated discrete least‐squares (CDLS) meshless method. For this, an error estimate is first developed for a CDLS meshless method. The proposed error estimator is shown to be naturally related to the least‐squares functional, providing a suitable posterior measure of the error in the solution. A mesh moving strategy is then used to displace the nodal points such that the errors are evenly distributed in the solution domain. Efficiency and effectiveness of the proposed error estimator and adaptive refinement process are tested against two hyperbolic benchmark problems, one with shocked and the other with low gradient smooth solutions. These experiments show that the proposed adaptive process is capable of producing stable and accurate results for the difficult problems considered. Copyright © 2007 John Wiley & Sons, Ltd.
Novel aphidicolin‐inducible common fragile site FRA9G maps to 9p22.2, within the C9orf39 gene
Authors: Sawińska Małgorzata , Schmitt Jens Guido , Sagulenko Evgeny , Westermann Frank , Schwab Manfred , Savelyeva Larissa 
Published: August 2007

AbstractCommon fragile sites represent a component of normal chromosome structure that form gaps and breaks on metaphase chromosomes after partial inhibition of DNA synthesis. In humans, cytogenetic locations of 89 common fragile sites are listed in the Genome Database; however, the exact number of fragile sites remains unknown. The application of high resolution mapping approaches continues to reveal new common fragile sites in the human genome. Here, we identified a novel aphidicolin‐inducible common fragile site FRA9G, which maps to chromosomal band 9p22.2. We have characterized the structure of the fragile DNA sequence that extends over a genomic region of ∼300 kb within the C9orf39 (chromosome 9 open reading frame 39) gene. Analysis of incidence in healthy individuals showed that FRA9G is commonly expressed in the population. Heterozygous BRCA2 mutation carriers exhibit an almost sevenfold increase of FRA9G expression compared to an unrelated control population group. Identification of a novel aphidicolin‐inducible common fragile site at 9p22 may have implications for understanding the mechanism of genetic instability in tumorigenesis and other genetic disorders. © 2007 Wiley‐Liss, Inc.
Lack of response to exogenous interferon-α in the liver of chimpanzees chronically infected with hepatitis C virus
Authors: Lanford Robert E. , Guerra Bernadette , Bigger Catherine B. , Lee Helen , Chavez Deborah , Brasky Kathleen M. 
Published: August 2007

Abstract

The mechanism of the interferon-alpha (IFNα)–induced antiviral response is not completely understood. We recently examined the transcriptional response to IFNα in uninfected chimpanzees. The transcriptional response to IFNα in the liver and peripheral blood mononuclear cells (PBMCs) was rapidly induced but was also rapidly down-regulated, with most interferon-alpha–stimulated genes (ISGs) returning to the baseline within 24 hours. We have extended these observations to include chimpanzees chronically infected with hepatitis C virus (HCV). Remarkably, using total genome microarray analysis, we observed almost no induction of ISG transcripts in the livers of chronically infected animals following IFNα dosing, whereas the response in PBMCs was similar to that in uninfected animals. In agreement with this finding, no decrease in the viral load occurred with up to 12 weeks of pegylated IFNα therapy. The block in the response to exogenous IFNα appeared to be HCV-specific because the response in a hepatitis B virus–infected animal was similar to that of uninfected animals. The lack of a response to exogenous IFNα may be due to an already maximally induced ISG response because chronically HCV-infected chimpanzees already have a highly up-regulated hepatic ISG response. Alternatively, negative regulation may block the response to exogenous IFNα, yet it does not prevent the continued response to endogenous ISG stimuli. The IFNα response in chronically HCV-infected chimpanzees may be mechanistically similar to the null response in the human population.

Conclusion:

In chimpanzees infected with HCV, the highly elevated hepatic ISG expression may prevent the further induction of ISGs and antiviral efficacy following an IFNα treatment. (HEPATOLOGY 2007.)