gebhart/patrepeval huggingface dataset:
Morphometric and colorimetric analyses of human tumor cell line growth and drug sensitivity in soft agar culture. (1991)

Previous studies have demonstrated the suitability of image analysis of tetrazolium-stained colonies to assess growth and drug sensitivity of human tumor cells cultivated in soft agar culture. In the present study, the potential utility of colorimetric analysis to expedite experimental drug evaluations using human tumor cell lines was investigated. The same culture dishes were assessed by image analysis and by formazan colorimetry for purposes of comparing multiple methods of measuring growth as well as growth inhibition. Replicate cultures treated with 2-(p-iodonitrophenyl)-3-p-nitrophenyl-5-phenyltetrazolium chloride or 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide exhibited nearly identical colony count and volume indices as well as excellent correlation in colorimetric end points. Colony-forming unit volume analysis versus colorimetric assessment of the same cultures following dimethyl sulfoxide extraction of protamine sulfate-rinsed, dried soft agar cultures exhibited excellent linear correlation for both growth (Pearson r ranging from 0.95 to 1.00) and drug sensitivity (Pearson r ranging from 0.90 to 0.99, and Spearman r ranging from 0.82 to 0.97) and similar drug sensitivity profiles. Results of the current investigation indicate that end points of soft agar culture remain stable for a period of at least 2 weeks following assay termination. In addition, a colorimetric detection range of 1.3-2.2 log units permits determinations of survival levels ranging from 100 to 5% of respective control levels. Colorimetric analysis is anticipated to expedite soft agar colony formation assay evaluations (a) by reducing the need to use the more rigorous and time-consuming image analysis procedures to measure activity in preliminary drug sensitivity assays and (b) by permitting the determination of effective concentration ranges of new experimental agents for subsequent, more detailed investigations.
Multilocus Variable-Number Tandem Repeat AnalysisDistinguishes Outbreak and SporadicEscherichia coliO157:H7Isolates (2003)

Escherichia coli O157:H7 is a major cause of food-borne illness in the United States. Outbreak detection involves traditional epidemiological methods and routine molecular subtyping by pulsed-field gel electrophoresis (PFGE). PFGE is labor-intensive, and the results are difficult to analyze and not easily transferable between laboratories. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a fast, portable method that analyzes multiple VNTR loci, which are areas of the bacterial genome that evolve quickly. Eighty isolates, including 21 isolates from five epidemiologically well-characterized outbreaks from Pennsylvania and Minnesota, were analyzed by PFGE and MLVA. Strains in PFGE clusters were defined as strains that differed by less than or equal to one band by using XbaI and the confirmatory enzyme SpeI. MLVA was performed by comparing the number of tandem repeats at seven loci. From 6 to 30 alleles were found at the seven loci, resulting in 64 MLVA types among the 80 isolates. MLVA correctly identified the isolates from all five outbreaks if only a single-locus variant was allowed. MLVA differentiated strains with unique PFGE types. Additionally, MLVA discriminated strains within PFGE-defined clusters that were not known to be part of an outbreak. In addition to being a simple and validated method for E. coli O157:H7 outbreak detection, MLVA appears to have a sensitivity equal to that of PFGE and a specificity superior to that of PFGE.
IL-4-independent induction of airway hyperresponsiveness by Th2, but not Th1, cells. (1998)

We investigated the role of Th1 or Th2 cells in airway hyperresponsiveness (AHR), because both IFN-gamma and IL-4 and IL-5-producing CD4 T cells have been identified in the airways of asthmatics. After transfer of in vitro-generated TCR transgenic Th1 or Th2 cells and exposure to inhaled Ag, Th2 cells induced AHR and airway eosinophilia, whereas Th1 cells induced neutrophilic inflammation without AHR. Next, to determine the precise effector function of IL-4 in Th2 cell-induced AHR, we transferred IL-4(-/-) Th2 cells into wild-type and IL-4(-/-) recipient mice. After exposure to inhaled Ag, both groups of mice exhibited AHR with markedly reduced airway eosinophilia. Thus, IL-4 production by Th2 cells is not essential for the induction of AHR, but is critical for the migration of eosinophils from lung tissue into the airways.
Antigen Processing and Autoimmunity: Evaluation of mRNA Abundance and Function of HLA‐linked Genesa (1998)

Quantitative defects in the density of conformationally correct human lymphocyte antigen (HLA) class I complexes on the surface of lymphocytes are apparent in patients with diverse HLA-linked autoimmune diseases, including Type I diabetes and Sjögren's syndrome. First, HLA class I expression was investigated in individuals with two rare and genetically divergent polyglandular autoimmune diseases. Polyglandular failure patients whose disease showed HLA linkage, but not those whose disease was not HLA linked, exhibited decreased HLA class I expression on the surface of their lymphocytes as well as a reduced abundance of transcripts of the HLA-linked genes Tap1 and Tap2, both of which encode proteins that contribute to HLA class I processing. Second, lymphocytes from patients with insulin-dependent diabetes mellitus (IDDM), Sjögren's syndrome, Graves' disease, and Hashimoto's disease showed varying degrees of decreased abundance of mRNAs that encode Tap1, Tap2, Lmp2, or Lmp7 (the latter two proteins also contribute to HLA class I processing). Third, in twins discordant for IDDM, reduced transcript abundance was preferential to diabetic subjects. Fourth, functional assays of isolated diabetic proteasomes, the peptide cutting complex containing LMP2 and LMP7 proteins, revealed altered peptidase activity. These data suggest that defective transcription of HLA class I-processing genes could contribute to the quantitative defect in cell-surface expression in autoimmune lymphocytes of HLA-controlled disease.
Induction of Oligodendrocytes From Adult Human Olfactory Epithelial‐Derived Progenitors by Transcription Factors (2005)

Neurosphere-forming cell (NSFC) lines have been derived from cultures of adult olfactory neuroepithelium obtained from patients and cadavers. These progenitors remain undifferentiated when maintained in minimal essential medium with 10% fetal bovine serum, but have the potential to differentiate along glial or neuronal lineages. However, few of these cells ever express mature neuronal or glial markers in defined medium. To evaluate the potential of NSFCs to form oligodendrocytes, two transcription factors, Olig2 and Nkx2.2, were introduced into NSFCs to determine whether their expression is sufficient for oligodendrocyte differentiation, as has been shown in the embryonic avian and murine central nervous systems in vivo. NSFCs transfected with Olig2 or Nkx2.2 alone exhibited no phenotypic lineage restriction. In contrast, simultaneous transfection of Olig2 and Nkx2.2 cDNA produced characteristic oligodendrocyte morphology and antigenicity, including myelin basic protein (MBP). Furthermore, a population of Olig2-expressing NSFCs also expressed Sox10. Cotransfection of NSFCs with Nkx2.2 and Sox10, but not Olig2 and Sox10, produced a MBP(+) oligodendrocytic phenotype. Coculture of NSFCs transfected with Olig2 and Nkx2.2 or Nkx2.2 and Sox10 with purified sensory neurons, demonstrated frequent contacts between NSFC processes and axons, including the early stages of ensheathment. These studies demonstrate transcription factors governing early development of chick and mouse oligodendrocyte formation, also apply to human progenitors isolated from adult olfactory neuroepithelium. Our long-term goal is to develop cell populations for future studies used to determine the therapeutic utility of these olfactory-derived NSFCs for autologous transplantation into donors with central nervous system trauma or neurodegenerative diseases.
131I dosimetry and thyroid stunning. (2003)

TO THE EDITOR: 

Dorn et al. have described a dosimetry-guided approach for calculating the largest “safe” dose of 131I for treatment of differentiated thyroid cancer ([1][1]). With this method, a maximal dose was determined assuming an upper limit of <3 Gy for the absorbed dose to the bone
Evolutionarily Related Insertion Pathways of Bacterial, Mitochondrial, and Thylakoid Membrane Proteins (2000)

The inner membranes of eubacteria and mitochondria, as well as the chloroplast thylakoid membrane, contain essential proteins that function in oxidative phosphorylation and electron transport processes or in photosynthesis. Because most of the organellar proteins are nuclear encoded, they are synthesized in the cytoplasm and subsequently imported into the organelle before they are inserted into the membrane. This review focuses on the pathways of protein insertion into the inner membrane of eubacteria and mitochondria and into the chloroplast thylakoid membrane. In many respects, insertion of proteins into the inner membrane of bacteria is a process similar to that used by proteins of the thylakoid membrane. In both of these systems a signal recognition particle (SRP) and a SecYE-translocase are involved, as in translocation into the endoplasmic reticulum. The pathway of proteins into the mitochondrial membranes appears to be different in that it involves no SecYE-like components. A conservative pathway, recently identified in mitochondria, involves the Oxa1 protein for the insertion of proteins from the matrix. The presence of Oxa1 homologues in eubacteria and chloroplasts suggests that this pathway is evolutionarily conserved.
Testing, Testing (2001)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTTesting, TestingJohn W. Moore View Author Information Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706Cite this: J. Chem. Educ. 2001, 78, 7, 855Publication Date (Web):July 1, 2001Publication History Received3 August 2009Published online1 July 2001Published inissue 1 July 2001https://doi.org/10.1021/ed078p855RIGHTS & PERMISSIONSArticle Views392Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (52 KB) Get e-AlertsSUBJECTS:Testing and assessment Get e-Alerts
Polyphosphate Kinase Protects Salmonella enterica from Weak Organic Acid Stress (2005)

Mutants of Salmonella enterica lacking polyphosphate kinase (ppk) grow poorly in the presence of the weak organic acids acetate, propionate, and benzoate. This sensitivity is corrected by methionine and seems to result from destabilization of MetA (homoserine transsuccinylase), the first enzyme in methionine biosynthesis. The MetA protein is known to be sensitive to thermal inactivation, and ppk mutants are more sensitive to heat-induced methionine auxotrophy. Peroxide increases the sensitivity of ppk mutants to both heat and acid and may oxidatively damage (carbonylate) destabilized MetA. While acid appears to impair methionine biosynthesis, it leads to derepression of MetA and may inhibit growth by causing toxic accumulation of denatured protein. This is supported by the observation that the overexpression of MetA in ppk mutants causes acid sensitivity that is not corrected by methionine. We propose that polyphosphate acts as a chemical chaperone that helps refold MetA and/or may stimulate proteolysis of toxic denatured protein. The instability of MetA protein may provide a metabolic fuse that blocks growth under conditions that denature proteins; the sensitivity of this fuse is modulated by polyphosphate.
Capillary Electrophoresis in Clinical Chemistry (2000)

Abstract Capillary electrophoresis (CE) is electrophoresis in capillary format. It is the most efficient and versatile separation technique nowadays for analysis of small and large molecules. Clinical chemistry is a science that applies the knowledge of chemistry to the understanding of the human in health and disease. Implementation of CE technique in clinical laboratories will enhance the capability of the current clinical diagnostic system, and improve the quality of clinical testing. Owing to the nature of clinical diagnostics, the adoption of CE methods in clinical laboratories has been slow. However, CE has begun to replace some older and antiquated methods in some pioneering clinical laboratories. This review includes a brief introduction to the CE technique (i.e. the separation principle, modes of operation, instrumentation, and practical considerations), and a summary of CE's applications in clinical chemistry (i.e. protein analysis, drug monitoring, DNA and RNA analyses, diagnosis of metabolic disorders, and single‐cell analysis), as well as the future prospects for the CE technique.
Prediction of Maximum Acceptable Weight of Lift in the Horizontal and Vertical Planes Using Simulated Job Dynamic Strengths (1986)

An investigation was undertaken to determine the feasibility of predicting maximum weights of lift that are acceptable to individuals by measuring the individuals'simulated job dynamic strengths. Since almost all manual materials handling jobs are dynamic in nature, it was hypothesized that correlations between maximum weights acceptable for lifting and the dynamic strengths measured under similar conditions would be high compared to isometric strengths. If so, then a relatively simple procedure can be developed to estimate what people are willing to lift safely. With the use of a specially designed and constructed three-dimensional dynamic strength simulator, 19 males and 6 females lifted loads in two vertical and two horizontal planes. Their dynamic strengths also were measured under identical conditions. The correlations between simulated job dynamic strengths and acceptable weights of lift were much higher (0.52 to 0.67) compared to correlations between isometric strengths and acceptable weights of lift (0.29 to 0.38). This also confirmed earlier findings that dynamic strengths are more suitable predictors of the maximum weights people are willing to handle. Simple equations are presented between simulated job dynamic strengths and maximum acceptable weights of lift in the horizontal and vertical planes. These equations demonstrate that dynamic strength can be used reliably when matching jobs with individuals.
Tumor suppressor PTEN: modulator of cell signaling, growth, migration and apoptosis (2001)

PTEN (also known as MMAC-1 or TEP-1) is one of the most frequently mutated tumor suppressors in human cancer. It is also essential for embryonic development. PTEN functions primarily as a lipid phosphatase to regulate crucial signal transduction pathways; a key target is phosphatidylinositol 3,4,5-trisphosphate. In addition, it displays weak tyrosine phosphatase activity, which may downmodulate signaling pathways that involve focal adhesion kinase (FAK) or Shc. Levels of PTEN are regulated in embryos and adult organisms, and gene-targeting studies demonstrate that it has a crucial role in normal development. Functions for PTEN have been identified in the regulation of many normal cell processes, including growth, adhesion, migration, invasion and apoptosis. PTEN appears to play particularly important roles in regulating anoikis (apoptosis of cells after loss of contact with extracellular matrix) and cell migration. Gene targeting and transient expression studies have provided insight into the specific signaling pathways that regulate these processes. Characterization of the diverse signaling networks modulated by PTEN, as well as the regulation of PTEN concentration, enzymatic activity, and coordination with other phosphatases, should provide intriguing new insight into the biology of normal and malignant cells.
A Cell Model for Conditional Profiling of Androgen-Receptor-Interacting Proteins (2012)

Partial androgen insensitivity syndrome (PAIS) is associated with impaired male genital development and can be transmitted through mutations in the androgen receptor (AR). The aim of this study is to develop a cell model suitable for studying the impact AR mutations might have on AR interacting proteins. For this purpose, male genital development relevant mouse cell lines were genetically modified to express a tagged version of wild-type AR, allowing copurification of multiprotein complexes under native conditions followed by mass spectrometry. We report 57 known wild-type AR-interacting proteins identified in cells grown under proliferating and 65 under nonproliferating conditions. Of those, 47 were common to both samples suggesting different AR protein complex components in proliferating and proliferation-inhibited cells from the mouse proximal caput epididymus. These preliminary results now allow future studies to focus on replacing wild-type AR with mutant AR to uncover differences in protein interactions caused by AR mutations involved in PAIS.
Mechanisms Involved in Alleviation of Intestinal Inflammation by Bifidobacterium Breve Soluble Factors (2009)

Bb and secreted soluble factors contribute positively to intestinal homeostasis by attenuating chemokine production. The results indicate that Bb down regulate inflammation at the epithelial level by inhibiting phosphorylations involved in inflammatory processes and by protective conditioning of dendritic cells.
Synthesis of deuterated dextromethorphan derivatives (2008)

Dextromethorphan is a widely used NMDA receptor antagonist and sodium channel blocker. Deuterated dextromethorphan and dextrorphan were synthesized via the N-desmethyldextromethorphan intermediate for pharmacokinetic study.
Anomaly detection through registration (2002)

We study an application of image registration in the medical domain. Based on a 3-D hierarchical deformable registration algorithm, we have developed a prototype system which automatically aligns a standard atlas to a subject's data to create a customized atlas. Combined with domain knowledge, the registration algorithm can also detect asymmetries and abnormal variations in the subject's data that indicate the existence and location of pathologies. We have conducted tests on 106 MRI scans of normal brains, 3 MRI and 1 CT scan of brains with pathologies, with results qualitatively comparable to manual segmentation.
A new hydrophobic anchor for the attachment of proteins to liposomal membranes (1986)

The model enzyme alpha-chymotrypsin covalently modified by a phosphatidylethanolamine derivative has been attached to liposomal membranes in high yield. A maximal protein/lipid ratio of 5.4 X 10(-3) mol enzyme/mol lipid was achieved.
Essential, Nonredundant Role for the Phosphoinositide 3-Kinase p110δ in Signaling by the B-Cell Receptor Complex (2002)

Many receptor and nonreceptor tyrosine kinases activate phosphoinositide 3-kinases (PI3Ks). To assess the role of the delta isoform of the p110 catalytic subunit of PI3Ks, we derived enzyme-deficient mice. The mice are viable but have decreased numbers of mature B cells, a block in pro-B-cell differentiation, and a B1 B-cell deficiency. Both immunoglobulin M receptor-induced Ca(2+) flux and proliferation in response to B-cell mitogens are attenuated. Immunoglobulin levels are decreased substantially. The ability to respond to T-cell-independent antigens is markedly reduced, and the ability to respond to T-cell-dependent antigens is completely eliminated. Germinal center formation in the spleen in response to antigen stimulation is disrupted. These results define a nonredundant signaling pathway(s) utilizing the delta isoform of p110 PI3K for the development and function of B cells.
Intermolecular Recombination between DNAs Introduced into Mouse L Cells Is Mediated by a Nonconservative Pathway That Leads to Crossover Products (1990)

We describe experiments designed to measure the efficiency of intermolecular recombination between mutant herpesvirus thymidine kinase (tk) genes introduced into mouse L cells. Recombinants were scored as stable transformants containing a functional tk gene. The two recombination substrates used were ptkB8, a pBR322-based plasmid containing a mutant tk gene, with a BamHI linker in an SphI restriction site that is centrally located within the gene, and mp10tk delta 3' delta 5', an mp10 vector with a tk gene deleted at both the 3' and 5' ends. The only homology shared by the two DNAs is 885 base pairs within the tk gene. To determine whether the double-strand break repair model that has been used to explain recombination in yeast cells (J. W. Szostak, T. L. Orr-Weaver, R. J. Rothstein, and F. W. Stahl, Cell 33:25-35, 1983) can account for recombination during the introduction of these DNAs into mammalian cells, we transformed cells with BamHI-linearized ptkB8 and supercoiled mp10tk delta 3' delta 5' replicative-form DNA. These two DNAs should recombine efficiently according to that model and should generate gene conversion products. In this reaction, the supercoiled DNA acts as the donor of information to repair the cleaved tk gene. Our results indicated that the efficiency of this reaction was very low (less than 10 transformants were obtained per 0.1 microgram of each DNA used in the reaction per 10(6) cells). In contrast, if BamHI-cleaved ptkB8 DNA was cotransformed into cells along with a circular DNA molecule containing a tk gene deleted only at its 3' end or only at its 5' end (mp10tk delta 3' or mp10tk delta 5'), then the efficiency of recombination could be more than 4 orders of magnitude higher than it was with circular mp10tk delta 3' delta 5' DNA. Recombination frequencies were highest when the tk delta 3' or tk delta 5' DNA used was cleaved at the tk deletion junction. Southern analyses of DNA from TK+ transformants generated with BamHI-cleaved ptkB8 and BamHI-cleaved mp10tk delta 3' DNAs indicated that recombination was almost always associated with the reassortment of markers flanking the reconstructed tk DNA. Together, these results are more consistent with the nonconservative single-strand annealing model for recombination that we proposed several years ago (F.-L. Lin, K. Sperle, and N. Sternberg, Mol. Cell. Biol. 4:1020-1034, 1984) than they are with the double-strand break repair model.
Hyracks: A flexible and extensible foundation for data-intensive computing (2011)

Hyracks is a new partitioned-parallel software platform designed to run data-intensive computations on large shared-nothing clusters of computers. Hyracks allows users to express a computation as a DAG of data operators and connectors. Operators operate on partitions of input data and produce partitions of output data, while connectors repartition operators' outputs to make the newly produced partitions available at the consuming operators. We describe the Hyracks end user model, for authors of dataflow jobs, and the extension model for users who wish to augment Hyracks' built-in library with new operator and/or connector types. We also describe our initial Hyracks implementation. Since Hyracks is in roughly the same space as the open source Hadoop platform, we compare Hyracks with Hadoop experimentally for several different kinds of use cases. The initial results demonstrate that Hyracks has significant promise as a next-generation platform for data-intensive applications.