gebhart/patrepeval huggingface dataset:
Serotyping Streptococcus pneumoniae by Multiplex PCR (2003)

The capsule is a major virulence factor of pneumococci, and it was shown that some capsular variants are associated with antimicrobial resistance and certain types of disease. Moreover, pneumococcal capsular typing has received renewed interest since the availability of conjugate vaccines, which include serotypes frequently associated with pediatric disease. Our aim was to develop a simple, reliable, and economical method for detecting epidemiologically important serotypes present in the proposed 11-valent conjugate vaccine. We designed primers based on the sequences available for the capsular types 1, 3, 4, 6B, 14, 18C, 19F, 19A, and 23F and combined them into seven multiplex PCRs. The method involves streamlined DNA template preparation and agarose gel electrophoresis to analyze the amplification products. A total of 446 pneumococci selected from among isolates colonizing the nasopharynx of children attending day care centers in Lisbon, Portugal, were typed both by conventional immunological techniques and by multiplex PCR. Capsular types identified by the PCR method invariably produced results concordant with the conventional serotyping technique. Even when the method presented does not fully type an isolate, the PCR data can guide the experimenter when using immunological serotyping. Multiplex PCR for the analysis of pneumococci provides an accurate, expeditious, and cost-effective way of reducing the number of strains that have to be serotyped by conventional immunological techniques.
CD3+ CD8+ CTL activity within the human female reproductive tract: influence of stage of the menstrual cycle and menopause (1997)

The human female reproductive tract (RT) has been analyzed by others with respect to NK cell cytolytic activity, but not CD3+ T cell (CTL) cytolytic activity. Here, we describe the cytolytic capacity of mucosal CD3+ T cells both longitudinally within the RT (Fallopian tube, uterine endometrium, endocervix, ectocervix, and vaginal mucosa) and temporally throughout the menstrual cycle, using a redirected lysis assay system. Cytolysis by CD3+ CD8+ T cells is found throughout the RT and appears to be hormonally regulated, since in the uterine endometrium, the capacity for CD3+ T cell cytolytic activity is present during the proliferative phase of the menstrual cycle and absent during the subsequent secretory (postovulatory) phase. In contrast, in postmenopausal women the entire RT, including the uterus, retains the capacity for strong CD3+ T cell cytolytic activity. These findings suggest that the high levels of estradiol and progesterone present during days 14 to 28 of the menstrual cycle down-regulate CTL activity in the uterus. As a consequence, the absence of this activity may allow implantation of a semiallogeneic embryo that would otherwise be rejected. Further, these studies indicate that CTL activity is regulated differentially in different regions of the RT, persisting in the cervix and vagina throughout the menstrual cycle.
Antimicrobial, antioxidant, and antimutagenic activities of selected marine natural products and tobacco cembranoids (2011)

Multidrug resistance (MDR) in microorganisms is a cause of major concern for clinicians and pharmaceutical industries. Continuous development of new antimicrobial drugs with multiple targets and potentials is expected to efficiently combat MDR in these microorganisms. In a continued exploration of new antimicrobial drug leads, 11 marine natural products, semisynthetic, or related synthetic analogs (1-11) and two tobacco cembranoids (12 and 13) were screened for their antimicrobial, antioxidant, and antimutagenic activities. Eight compounds showed varying levels of both antibacterial and antifungal activities. Compounds such as 17-O-methyllatrunculin-A, verongiaquinol, (1S,2E,4R,6R,7E,11E)-2,7,11-cembratriene-4,6-diol), and manzamine-A showed a broad spectrum of activity, inhibiting six of seven tested bacteria with zone of inhibition diameter from 9 to 30 mm. Four of these active compounds also showed antifungal activity. The findings of the in vitro time-kill assay of the most active compound, verongiaquinol, against Staphylococcus aureus indicated its subinhibitory effect at the level lower than the minimal inhibitory concentration (MIC) values (i.e., 2 and 4 µg/mL). At the MIC (8 µg/mL), bacterial cells were completely killed within 18 hours of incubation. DPPH free radical scavenging activity was demonstrated by five compounds in the range of 89.65-36.19% decolorization. Further, four compounds evaluated for their antimutagenic activity against the directly acting mutagens, methyl methanesulfonate and sodium azide, in Salmonella typhimurium strains, interestingly, showed no sign of mutagenicity. Verongiaquinol and manzamine A, in fact, reduced the mutagenicity by 50-75% at a dose of 5 µg/plate in different test strains. Our study seems to provide some novel antimicrobial leads with strong antioxidant potential and the associated ability of antimutagenicity.
Tumor-associated angiogenesis: mechanisms, clinical implications, and therapeutic strategies. (1997)

Compelling data implicate angiogenesis and tumor-associated neovascularization as a central pathogenic step in the process of tumor growth, invasion, and metastasis. These complex processes involve multiple steps and pathways dependent on the local balance between positive and negative regulatory factors, as well as interactions among the tumor, its vasculature, and the surrounding extracellular tissue matrix. A tumor remains in a dormant state, the cellular proliferation rate balanced by the apoptotic rate, unable to grow in size beyond a few millimeters in the absence of the acquired angiogenic phenotype. The mechanism by which tumors switch to the angiogenic phenotype is unknown. Therapeutic agents and strategies are being devised either to interrupt or inhibit one or more of the pathogenic steps involved in the process of tumor neovascularization or to directly target and destroy the tumor vasculature. Therapies affecting an end target or pathway that cannot be circumvented by alternate mechanisms may significantly enhance efficacy and broaden applicability. These approaches may result in small, avascular tumors maintained in a dormant state or, perhaps in combination with cytotoxic therapies, they may potentiate shrinkage of tumors to, and maintain them, in a dormant state. As more powerful antiangiogenic agents are developed, perhaps even these dormant microscopic foci may be eradicated. Antiangiogenesis agents and strategies differ from the usual cancer therapeutic approaches; therefore, investigators must devise new paradigms for the clinical development of agents that may only have a static effect on tumors and require prolonged, chronic administration. Methods to assess the in vivo biologic activity of these compounds in patients are needed. Ultimately, antiangiogenic therapy may provide an additional novel cancer treatment suitable for combination with standard therapies.
Diagnostic Accuracy of Mini-Mental Status Examination and Revised Hasegawa Dementia Scale for Alzheimer’s Disease (2005)

To compare the diagnostic accuracies of the Revised Hasegawa Dementia Scale (HDS-R) and Mini-Mental Status Examination (MMSE) for Alzheimer's diseases (AD), we administered them simultaneously to 82 AD patients and 82 age- and sex-matched nondemented control subjects. The area under the receiver operator curve (AUC) for AD of the HDS-R (AUC(HDS-R)) and MMSE (AUC(MMSE)) were bigger than 0.90 indicating that both tests are useful for detecting AD. However, AUC(HDS-R) (0.952) was significantly larger than that of the AUC(MMSE )(0.902) regardless of the educational level of the subjects, indicating that the HDS-R is more accurate than MMSE in diagnosing AD. Moreover, the superiority of the HDS-R (AUC(HDS-R) = 0.894) to the MMSE (AUC(MMSE) = 0.704) remained significant in mild AD patients alone, who are the focus of screening. In conclusion, the HDS-R is better than the MMSE as a screening instrument for AD.
Urinary kallikrein in rats bred for their susceptibility and resistance to the hypertensive effect of salt. A new radioimmunoassay for its direct determination. (1978)

Urinary kallikrein was measured in rats bred to be susceptible (S) or resistant (R) to the hypertensive effect of salt. To determine kallikrein, three different methods were used: (1) a new direct radioimmunoassay (RIA) for the enzymic protein: (2) a method based on the capability of kallikrein, when incubated with kininogen, to generate kinins which were then measured by RIA (kininogenase activity); and (3) a method based on the capability of kallikrein to break the ester bond of p-tosyl-L-arginine methyl ester (HCl (TAMe). A significant correlation ( r = 0.90) was found between the direct RIA and the kininogenase method. It was found that urinary kallikrein was significantly decreased in the S as compared to the R rats by the use of these three methods. Urinary kallikrein in the S rats was much lower when measured by the kininogenase method than by direct RIA or esterolytic assay. This difference could be due to excretion of pre-kallikrein and/or kallikrein bound to an inhibitor (inactive kallikrein). It is suggested that the decrease of urinary kallikrein excretion (active and inactive) in the S rats could be a consequence of a genetic defect that may affect the development of hypertension perhaps through the alteration of sodium and water excretion by the kidney.
Forecasting Macroeconomic Variables Using Neural Network Models and Three Automated Model Selection Techniques (2015)

When forecasting with neural network models one faces several problems, all of which influence the accuracy of the forecasts. First, neural networks are often hard to estimate due to their highly nonlinear structure. To alleviate the problem, White (2006) presented a solution (QuickNet) that converts the specification and nonlinear estimation problem into a linear model selection and estimation problem. We shall compare its performance to that of two other procedures building on the linearization idea: the Marginal Bridge Estimator and Autometrics. Second, one must decide whether forecasting should be carried out recursively or directly. This choice is investigated in this work. The economic time series used in this study are the consumer price indices for the G7 and the Scandinavian countries. In addition, a number of simulations are carried out and results reported in the article.
Delayed Fluroescence and Phosphorescence of Aromatic Ketones in Solution (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDelayed Fluroescence and Phosphorescence of Aromatic Ketones in SolutionJack. Saltiel, Howell C. Curtis, Lewis. Metts, John W. Miley, John. Winterle, and Mark. WrightonCite this: J. Am. Chem. Soc. 1970, 92, 2, 410–411Publication Date (Print):January 1, 1970Publication History Published online10 December 2002Published inissue 1 January 1970https://pubs.acs.org/doi/10.1021/ja00705a617https://doi.org/10.1021/ja00705a617research-articleACS PublicationsRequest reuse permissionsArticle Views702Altmetric-Citations72LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Sequence and expression of a cDNA encoding MyD118: a novel myeloid differentiation primary response gene induced by multiple cytokines. (1991)

We report here the full length cDNA sequence and the deduced amino acid sequence of MyD118, a novel myeloid differentiation primary response gene transiently expressed in M1D+ myeloid precursors following induction of terminal differentiation and growth arrest by IL6. MyD118 expression was observed to be induced also in the absence of protein synthesis, following stimulation of M1D+ cells by IL1, LPS and Leukemia Inhibitory Factor (LIF). Detectable levels of MyD118 RNA were observed in myeloid precursor enriched murine bone marrow, but not in several other nonmyeloid murine tissues.
Gene therapy for prostate cancer. (1999)

Prostate cancer is one of the leading causes of cancer deaths in the western hemisphere. A number of different gene therapy strategies are currently being evaluated. The ex vivo and many of the in vivo therapies involve stimulating a specific antitumor immune response. Autologous vaccines involving interleukin-2 (IL-2)- or granulocyte-macrophage colony-stimulating factor (GM-CSF)-transduced whole tumor cells showed great promise in animal models. Clinical trials of these and other vaccine strategies are underway. In vivo gene therapies involving the replacement of mutant tumor-suppressor genes, antisense strategies, and the insertion of suicide genes are also being evaluated in prostate cancer.
Improved prediction of prostate cancer recurrence through systems pathology (2007)

We have developed an integrated, multidisciplinary methodology, termed systems pathology, to generate highly accurate predictive tools for complex diseases, using prostate cancer for the prototype. To predict the recurrence of prostate cancer following radical prostatectomy, defined by rising serum prostate-specific antigen (PSA), we used machine learning to develop a model based on clinicopathologic variables, histologic tumor characteristics, and cell type-specific quantification of biomarkers. The initial study was based on a cohort of 323 patients and identified that high levels of the androgen receptor, as detected by immunohistochemistry, were associated with a reduced time to PSA recurrence. The model predicted recurrence with high accuracy, as indicated by a concordance index in the validation set of 0.82, sensitivity of 96%, and specificity of 72%. We extended this approach, employing quantitative multiplex immunofluorescence, on an expanded cohort of 682 patients. The model again predicted PSA recurrence with high accuracy, concordance index being 0.77, sensitivity of 77% and specificity of 72%. The androgen receptor was selected, along with 5 clinicopathologic features (seminal vesicle invasion, biopsy Gleason score, extracapsular extension, preoperative PSA, and dominant prostatectomy Gleason grade) as well as 2 histologic features (texture of epithelial nuclei and cytoplasm in tumor only regions). This robust platform has broad applications in patient diagnosis, treatment management, and prognostication.
Determination of the Contribution of Cysteinyl Leukotrienes and Leukotriene B4 in Acute Inflammatory Responses Using 5-Lipoxygenase- and Leukotriene A4 Hydrolase-Deficient Mice (1999)

Arachidonic acid metabolism by 5-lipoxygenase leads to production of the potent inflammatory mediators, leukotriene (LT) B4 and the cysteinyl LT. Relative synthesis of these subclasses of LT, each with different proinflammatory properties, depends on the expression and subsequent activity of LTA4 hydrolase and LTC4 synthase, respectively. LTA4 hydrolase differs from other proteins required for LT synthesis because it is expressed ubiquitously. Also, in vitro studies indicate that it possesses an aminopeptidase activity. Introduction of cysteinyl LT and LTB4 into animals has shown LTB4 is a potent chemoattractant, while the cysteinyl LT alter vascular permeability and smooth muscle tone. It has been impossible to determine the relative contributions of these two classes of LT to inflammatory responses in vivo or to define possible synergy resulting from the synthesis of both classes of mediators. To address this question, we have generated LTA4 hydrolase-deficient mice. These mice develop normally and are healthy. Using these animals, we show that LTA4 hydrolase is required for the production of LTB4 in an in vivo inflammatory response. We show that LTB4 is responsible for the characteristic influx of neutrophils accompanying topical arachidonic acid and that it contributes to the vascular changes seen in this model. In contrast, LTB4 influences only the cellular component of zymosan A-induced peritonitis. Furthermore, LTA4 hydrolase-deficient mice are resistant to platelet-activating factor, identifying LTB4 as one mediator of the physiological changes seen in systemic shock. We do not identify an in vivo role for the aminopeptidase activity of LTA4 hydrolase.
Relationship between echolocation calls and age in the bat species of Rhinolophus pearsoni (2004)

Five adult and two young female bats of Rhinolophus pearsoni were captured in Mingu town,Zhenfeng County of Guizhou Province.Their echolocation calls were received with ultrasound detector(D980,ULTRASOUND DETECTOR),read out at one-tenth of the original speed,and then recorded to computer.Batsound 3.10 software was used to analyze the recorded echolocation calls.The result showed that the adult bat emitted FM-CF-FM calls often with 2-3 harmonics,the calls dominant frequency,pulse duration and interpulse interval were 56.80±0.62 kHz,34.62±5.29 ms and 86.50±19.72 ms at fly,and 58.05±0.24 kHz,41.08±5.87 ms and 117.29±66.44 ms at hang,respectively,and duty cycle was (44.06±12.58)% at fly and (46.00±24.25)% at hang.The young bat emitted CF-FM calls with 5-8 harmonics.The calls dominant frequency of the young was lower,FM bandwidth was narrower,pulse duration and interpulse interval were shorter,and duty cycle was lower than those of the adult.It is suggested that the echolocation call was correlated with the age in bats R.pearsoni.The adult call responded for detecting the information of food and surroundings,and the young one was for communicating with its mother.
A new 3-D surface measurement system using a structured light (2003)

The authors present a 3-D measurement method using a projected grid that permits an optimal geometrical exploitation of the calculated 3-D data. They propose a reliable method for solving the correspondence that establishes the link between the imaged grid and the original grid curve per curve without any ambiguity. The imaged grid is extracted by an efficient method that describes the distorted grid as a network of curves rather than a graph, and hence provides regular and precise 2-D information. The 3-D projected grid is calculated per curve by using the triangulation principle. Thus, two independent families of 3-D curves that parameterize the object surfaces can be used for a surface geometrical study.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sorghum Genome Sequencing by Methylation Filtration (2004)

Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis.
Malignant epithelial cells in primary human lung carcinomas coexpress in vivo platelet-derived growth factor (PDGF) and PDGF receptor mRNAs and their protein products. (1992)

Lung cancer represents one of the major human carcinomas with the highest degree of mortality. Epidemiologic studies have linked this disease to "chronic injury," largely induced by cigarette smoking. In the present studies, we demonstrate the in vivo expression of platelet-derived growth factor (PDGF) and PDGF receptor (PDGF-R) beta mRNAs and their respective protein products in malignant epithelial cells of primary human lung carcinomas. In contrast, nonmalignant epithelial cells in control, normal lung tissue specimen did not express PDGF and PDGF-R mRNAs and did not produce their respective protein products. Epithelial cells in lung specimen from patients with idiopathic pulmonary fibrosis expressed only PDGF mRNA but not PDGF-R beta mRNA. These findings of the inappropriate coexpression of a potent mitogen, PDGF, and its receptor in lung cancer epithelial cells suggest the presence of a powerful in vivo mechanism contributing to the self-stimulation and unregulated growth of lung cancer tumor cells.
Linear feature space projections for speaker adaptation (2002)

We extend the well-known technique of constrained maximum likelihood linear regression (MLLR) to compute a projection (instead of a full rank transformation) on the feature vectors of the adaptation data. We model the projected features with phone-dependent Gaussian distributions and also model the complement of the projected space with a single class-independent, speaker-specific Gaussian distribution. Subsequently, we compute the projection and its complement using maximum likelihood techniques. The resulting ML transformation is shown to be equivalent to performing a speaker-dependent heteroscedastic discriminant (or HDA) projection. Our method is in contrast to traditional approaches which use a single speaker-independent projection, and execute speaker adaptation in the resulting subspace. Experimental results on Switchboard show a 3% relative improvement in the word error rate over constrained MLLR in the projected subspace only.
Platelet microRNA-mRNA coexpression profiles correlate with platelet reactivity (2011)

MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'-untranslated regions of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5, and miR-107:CLOCK) were selected from this list, and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.