gebhart/patrepeval huggingface dataset:
Overexpressed human CD44s promotes lung colonization during micrometastasis of murine fibrosarcoma cells: Facilitated retention in the lung vasculature (1997)

Normally nonmetastatic murine sis-transformed BALB/c 3T3 cells, transfected with human CD44s gene (hCD44s), acquire spontaneous metastatic capacity to the lung. The mechanism(s) of this facilitated micrometastasis was analyzed in an experimental metastasis model. Human CD44s overexpression promoted the earliest stages severalfold (initial implantation and subsequent stabilization of tumor cells) but was irrelevant for later stages (subsequent outgrowth) of lung experimental micrometastasis. By injecting mixed populations of parental (nonmetastatic) and CD44s-transfected cells, it was shown that cell-cell adhesion between tumor and parental cells was not promoted by hCD44s but that promotion of cell-cell adhesion to lung endothelium or specifically between transfected cells (via hyaluronan) are likely mechanisms. Results obtained with hCD44s-negative primary tumor cells and hCD44s-positive or -negative variants of lung micrometastatic cells (after s.c. injection of transfectants) confirmed the importance of CD44s overexpression for early but not late stages of experimental lung metastasis. Therefore, CD44s represents a metastasis-facilitating molecule that is irrelevant for primary tumor outgrowth but that promotes micrometastasis to the lungs at the very earliest stages.
Interpretable Decision Sets (2016)

One of the most important obstacles to deploying predictive models is the fact that humans do not understand and trust them. Knowing which variables are important in a model's prediction and how they are combined can be very powerful in helping people understand and trust automatic decision making systems. Here we propose interpretable decision sets, a framework for building predictive models that are highly accurate, yet also highly interpretable. Decision sets are sets of independent if-then rules. Because each rule can be applied independently, decision sets are simple, concise, and easily interpretable. We formalize decision set learning through an objective function that simultaneously optimizes accuracy and interpretability of the rules. In particular, our approach learns short, accurate, and non-overlapping rules that cover the whole feature space and pay attention to small but important classes. Moreover, we prove that our objective is a non-monotone submodular function, which we efficiently optimize to find a near-optimal set of rules. Experiments show that interpretable decision sets are as accurate at classification as state-of-the-art machine learning techniques. They are also three times smaller on average than rule-based models learned by other methods. Finally, results of a user study show that people are able to answer multiple-choice questions about the decision boundaries of interpretable decision sets and write descriptions of classes based on them faster and more accurately than with other rule-based models that were designed for interpretability. Overall, our framework provides a new approach to interpretable machine learning that balances accuracy, interpretability, and computational efficiency.
Simultaneous Detection of Single Molecules and Singulated Ensembles of Molecules Enables Immunoassays with Broad Dynamic Range (2011)

We report a method for combining the detection of single molecules (digital) and an ensemble of molecules (analog) that is capable of detecting enzyme label from 10(-19) M to 10(-13) M, for use in high sensitivity enzyme-linked immunosorbent assays (ELISA). The approach works by capturing proteins on microscopic beads, labeling the proteins with enzymes using a conventional multistep immunosandwich approach, isolating the beads in an array of 50-femtoliter wells (Single Molecule Array, SiMoA), and detecting bead-associated enzymatic activity using fluorescence imaging. At low concentrations of proteins, when the ratio of enzyme labels to beads is less than ∼1.2, beads carry either zero or low numbers of enzymes, and protein concentration is quantified by counting the presence of "on" or "off" beads (digital regime). (1) At higher protein concentrations, each bead typically carries multiple enzyme labels, and the average number of enzyme labels present on each bead is quantified from a measure of the average fluorescence intensity (analog regime). Both the digital and analog concentration ranges are quantified by a common unit, namely, average number of enzyme labels per bead (AEB). By combining digital and analog detection of singulated beads, a linear dynamic range of over 6 orders of magnitude to enzyme label was achieved. Using this approach, an immunoassay for prostate specific antigen (PSA) was developed. The combined digital and analog PSA assay provided linear response over approximately four logs of concentration ([PSA] from 8 fg/mL to 100 pg/mL or 250 aM to 3.3 pM). This approach extends the dynamic range of ELISA from picomolar levels down to subfemtomolar levels in a single measurement.
A Practitioners Approach to Database Federation. (1999)

\n During the last few years message queuing and workflow systems have\n been established as major elements of the software stack. In\n practice, this middleware is often used to cope with aspects of data\n federation: Message queuing technology is exploited for application\n integration. Workflows extend the notion of stored procedures in a\n federated environment and provide transaction management as well as\n monitoring features for inter-transaction integrity in such an\n environment.\n
Paclitaxel Versus Doxorubicin as First-Line Single-Agent Chemotherapy for Metastatic Breast Cancer: A European Organization for Research and Treatment of Cancer Randomized Study With Cross-Over (2000)

At the dosages and schedules used in the present study, doxorubicin achieves better disease and symptom control than paclitaxel in first-line treatment. Doxorubicin and paclitaxel are not totally cross-resistant, which supports further investigation of these drugs in combination or in sequence, both in advanced disease and in the adjuvant setting.
The Pseudomonas cellulosa glycoside hydrolase family 51 arabinofuranosidase exhibits wide substrate specificity (2001)

To investigate the mechanism by which Pseudomonas cellulosa releases arabinose from polysaccharides and oligosaccharides, a gene library of P. cellulosa genomic DNA was screened for 4-methylumbelliferyl-α-l-arabinofuranosidase (MUAase) activity. A single MUAase gene (abf51A) was isolated, which encoded a non-modular glycoside hydrolase family (GH) 51 arabinofuranosidase (Abf51A) of 57000Da. The substrate specificity of the Abf51A showed that it preferentially removed α1,2- and α1,3-linked arabinofuranose side chains from either arabinan or arabinoxylan, and hydrolysed α1,5-linked arabino-oligosaccharides, although at a much lower rate. The activity of Abf51A against arabinoxylan was similar to a GH62 arabinofuranosidase encoded by a P. cellulosa gene. Glu-194 and Glu-321 of Abf51A are conserved in GH51 enzymes, and it has been suggested that these amino acids comprise the key catalytic acid/base and nucleophile residues, respectively. To evaluate this hypothesis the biochemical properties of E194A and E321A mutants of Abf51A were evaluated. The data were consistent with the view that Glu-194 and Glu-321 comprise the key catalytic residues of Abf51A. These data, in conjunction with the results presented in the accompanying paper [Beylot, Emami, McKie, Gilbert and Pell (2001) Biochem. J. 358, 599–605], indicate that P. cellulosa expresses a membrane-bound GH51 arabinofuranosidase that plays a pivotal role in releasing arabinose from a range of polysaccharides and oligosaccharides.
Discovery and segmentation of activities in video (2000)

Hidden Markov models (HMMs) have become the workhorses of the monitoring and event recognition literature because they bring to time-series analysis the utility of density estimation and the convenience of dynamic time warping. Once trained, the internals of these models are considered opaque; there is no effort to interpret the hidden states. We show that by minimizing the entropy of the joint distribution, an HMM's internal state machine can be made to organize observed activity into meaningful states. This has uses in video monitoring and annotation, low bit-rate coding of scene activity, and detection of anomalous behavior. We demonstrate with models of office activity and outdoor traffic, showing how the framework learns principal modes of activity and patterns of activity change. We then show how this framework can be adapted to infer hidden state from extremely ambiguous images, in particular, inferring 3D body orientation and pose from sequences of low-resolution silhouettes.
Polyhydroxybutyrate, a Biodegradable Thermoplastic, Produced in Transgenic Plants (1992)

Polyhydroxybutyrate (PHB), a high molecular weight polyester, is accumulated as a storage carbon in many species of bacteria and is a biodegradable thermoplastic. To produce PHB by genetic engineering in plants, genes from the bacterium Alcaligenes eutrophus that encoded the two enzymes required to convert acetoacetyl-coenzyme A to PHB were placed under transcriptional control of the cauliflower mosaic virus 35S promoter and introduced into Arabidopsis thaliana. Transgenic plant lines that contained both genes accumulated PHB as electron-lucent granules in the cytoplasm, nucleus, and vacuole; the size and appearance of these granules were similar to the PHB granules that accumulate in bacteria.
Neurogenesis in Adult Mammals: Some Progress and Problems (2002)

Approximately 40 years after its first report, the addition of neurons to the brains of adult mammals has now been generally accepted. We now know that several endocrine and experiential variables modulate adult neurogenesis. However, several methodological problems in its quantitative study remain. One is the use of low doses of the exogenous marker of cell proliferation, bromodeoxyuridine (BrdU). A second is the transient lifetime of most of the adult-generated cells. A third is that the survival of new neurons may depend on stimuli that are lacking in standard laboratory conditions. This review considers these issues as well as the possible functions of new neurons.
Epothilone C Macrolactonization and Hydrolysis Are Catalyzed by the Isolated Thioesterase Domain of Epothilone Polyketide Synthase (2003)

Epothilone C is produced by the combined action of one nonribosomal peptide synthetase (NRPS) and nine polyketide synthase (PKS) modules in a multienzyme system. The final step in the biosynthesis is the thioesterase (TE)-catalyzed cyclorelease of epothilone from the EpoF protein. It has been unclear whether isolated PKS TE domains could exhibit macrolactonization activity. Here we demonstrate that the excised epothilone TE domain can catalyze the efficient cyclization of the N-acetylcysteamine thioester of seco-epothilone C to generate epothilone C (kcat/KM = 0.41 +/- 0.03 min-1 mM-1). The TE domain also catalyzes the hydrolysis of both the N-acetylcysteamine thioester of seco-epothilone C (kcat = 0.087 +/- 0.005 min-1, KM = 291 +/- 53 muM) and that of the epothilone C (kcat = 0.67 +/- 0.01 min-1, KM = 117 +/- 5 muM) to form seco-epothilone C.
Neutralizing (54K) and Non-neutralizing (54K and 48K) Monoclonal Antibodies against Structural and Non-structural Yellow Fever Virus Proteins Confer Immunity in Mice (1986)

The capacity of monoclonal antibodies to protect mice passively against yellow fever (YF) virus infection was investigated. Both neutralizing (54K-specific) and non-neutralizing (54K- and 48K-specific) antibodies protected mice against challenge with the RMP substrain of YF virus. Average survival times of mice inoculated intracerebrally with a standard lethal dose of YF virus differed according to the strain used: thus mice inoculated with the most neurovirulent viruses, FNV and Asibi, survived for 6 X 50 and 7 X 65 days respectively, and those with RMP virus survived for 15 X 75 days. The capacity of antibodies to protect mice passively against virus challenge was directly related to virus neurovirulence. Possible mechanisms and the significance of protection by antibodies against non-structural proteins that do not mediate neutralization, are discussed.
Influence of Solvents and Detergents on Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Measurements of Proteins and Oligonucleotides (1997)

The effect of solvents was found to be critical for sample preparation in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For proteins and oligonucleotides the use of 2-propanol/water as a solvent for different matrices can significantly improve the quality of spectra. This effect is demonstrated with proteins ranging in molecular weight from 12 to 150 kDa and with a special 19-mer oligonucleotide. A comparison of MALDI-MS using of 2-propanol as matrix solvent and high-performance capillary electrophoresis resulted in identical relative peak intensities for a p(dT)12-18 oligonucleotide mixture. Additionally, the effect of detergents for characterization of high molecular weight proteins in very dilute solutions was studied with this solvent. It was found that Triton X-100, up to a concentration of 1%, was highly compatible with MALDI measurements and even could improve the quality of spectra. Use of detergents for cell profiling has extended the detectable mass range to about m/z 75,000.
科比·布莱恩特：华丽的转身 (2007)

科比·布莱恩特，28岁，今年是他在NBA的第十一个年头。在本赛季开始之前，他已经在球场上战斗了三万多分钟——25239分钟是他的常规赛出场时间，还有4870分钟是在季后赛；三次总冠军得主；作为NBA历史上最伟大的高中生运动员已毫无争议。
Conversation and behavior games in the pragmatics of dialogue (1993)

In this article we present the bases for a computational theory of the cognitive processes underlying human communication. The core of the article is devoted to the analysis of the phases in which the process of comprehension of a communicative act can be logically divided: (1) literal meaning, where the reconstruction of the mental states literally expressed by the actor takes place: (2) speaker's meaning, where the partner reconstructs the communicative intentions of the actor; (3) communicative effect, where the partner possibly modifies his own beliefs and intentions; (4) reaction, where the intentions for the generation of the response are produced; and (5) response, where an overt response is constructed. The model appears to be compatible with relevant facts about human behavior. Our hypothesis is that, through communication, an actor tries to exploit the motivational structures of a partner so that the desired goal is generated. A second point is that social behavior requires that cooperation be maintained at some level. In the case of communication, cooperation is, in general, pursued even when the partner does not adhere to the actor's goals, and therefore no cooperation occurs at the behavioral level. This important distinction is reflected in the two kinds of game we introduce to account for communication. The main concept implied in communication is that two agents overtly reach a situation of shared mental states. Our model deals with sharedness through two primitives: shared beliefs and communicative intentions.
Expression and copy number analysis of TRPS1, EIF3S3 and MYC genes in breast and prostate cancer (2004)

The long arm of chromosome 8 is one of the most common regions of amplification in cancers of several organs, especially carcinomas of the breast and prostate. TRPS1, MYC and EIF3S3 genes are located in one of the minimal regions of amplification, 8q23-q24, and have been suggested to be the target genes of the amplification. Here, our goal was to study copy number and expression of the three genes in order to investigate the significance of the genes in breast and prostate cancer. By using fluorescence in situ hybridisation (FISH), we first found that TRPS1 and EIF3S3 were amplified together in about one-third of hormone-refractory prostate carcinomas. Next, we analysed the mRNA expression of the three genes by real-time quantitative RT-PCR and the gene copy number by FISH in six breast and five prostate cancer cell lines. Breast cancer cell line, SK-Br-3, which contained the highest copy number of all three genes, showed overexpression of only EIF3S3. Finally, the expression levels of TRPS1, EIF3S3 and MYC were measured in freshly frozen clinical samples of benign prostate hyperplasia (BPH), as well as untreated and hormone-refractory prostate carcinoma. The TRPS1 and MYC expression levels were similar in all prostate tumour groups, whereas EIF3S3 expression was higher (P=0.029) in prostate carcinomas compared to BPH. The data suggest that the expression of EIF3S3 is increased in prostate cancer, and that one of the mechanisms underlying the overexpression is the amplification of the gene.
Transphosphorylation as the mechanism by which the high-affinity receptor for IgE is phosphorylated upon aggregation. (1994)

When aggregated, the high-affinity receptors for IgE on mast cells (Fc epsilon RI) launch a series of phosphorylations, particularly of protein tyrosines. We have analyzed how aggregation initiates this cascade. We examined Fc epsilon RI from unstimulated cells and from cells exposed to a polyvalent hapten conjugate that aggregates the Fc epsilon RI via the receptor-bound anti-hapten IgE. We also examined the latter receptors after they had been disaggregated in vitro with monovalent hapten. By an in vitro kinase assay: (i) Unaggregated and disaggregated receptors are associated with a kinase that phosphorylates an exogenous (peptide) substrate but minimally, or not at all, the subunits of Fc epsilon RI or associated proteins (endogenous substrates). After aggregation, phosphorylation of the exogenous substrate is linear with time, but the modification of the endogenous substrates reaches a plateau, presumably because only those endogenous substrates that are adjacent to the kinase are phosphorylated. (ii) Aggregated receptors and disaggregated receptors have enhanced kinase activity toward exogenous substrate. The state of phosphorylation of the receptor correlates strongly with the yield of enhanced kinase activity. We propose that upon aggregation of Fc epsilon RI, a constitutively associated kinase phosphorylates endogenous substrates by transphosphorylation. As a result, additional kinase activity becomes manifest and this promotes further transphosphorylation. In view of the homology between Fc epsilon RI and other receptors central to the immune response, the latter receptors likely utilize a similar transphosphorylation mechanism.
An improved pragmatic turbo encoding scheme for high spectral efficiency using constellation shaping (2004)

We propose a new turbo encoding scheme for high spectral efficiency with performance close to the Gaussian channel capacity. The scheme combines nonuniform signaling on a Gaussian channel, and pragmatic turbo coded modulation for simple and flexible implementation. A table is used to map equiprobable input symbols into nonequiprobable points in the QAM constellation. It is shown that the new scheme provides shaping gains of 0.6 dB and 0.93 dB, at rates 2 and 3 bits/dim respectively compared to the equiprobable pragmatic turbo coded modulation, and reach about 1 dB from the Gaussian channel capacity.
MMP11: A Novel Target Antigen for Cancer Immunotherapy (2009)

Our study describes the identification of MMP11 as a novel broadly expressed tumor associated antigen as target candidate for cancer immunotherapy.
Pattern recognition of emotion with neural network (2002)

Proposes an emotion model for communication which also transfers personality and character information. The emotion model customizes to individual human communication partners by learning. Learning is achieved by neural networks converting input voice signals to an emotion state. The emotion state decides the response of the partner. The emotion state is divided into four categories: sadness; cheerfulness; happiness; and anger. For example, a loud voice causes the emotion of anger. This paper also discusses the emotion model as network agent between two human communication partners.
Close phenotypic and functional similarities between human and murine αβ T cells expressing invariant TCR α-chains (1997)

Several studies have demonstrated the existence of a murine NK1.1+ alphabeta T cell subset expressing V alpha14+ TCR alpha-chains with highly conserved invariant junctional sequences and able to secrete Th2 cytokines when exposed to CD1+ stimulator cells. In humans, alphabeta T cells carrying invariant V alpha24+ TCR alpha-chains highly homologous to those expressed by murine NK1.1 cells have been recently described. Here we show that these cells (referred to as V alpha24inv T cells) and murine NK1.1+ alphabeta T cells resemble each other in several ways. First, like their murine counterparts, T cells expressing high levels of V alpha24inv TCRs can be either CD4- CD8- double negative (DN) or CD4+, but they never express heterodimeric CD8 molecules. Second, most V alpha24inv T cells are brightly stained by NKRP1-specific mAb but not by mAb directed against other type II transmembrane proteins of the NK complex. Third, DN and particularly CD4+ V alpha24inv T cells are greatly enriched for IL-4 producers. The concomitant expression of highly conserved TCRs of a particular set of NK markers and of Th2 cytokines in human and murine alphabeta T cells suggests a coordinate acquisition of these phenotypic and functional properties. Furthermore, the relatively high frequency of human V alpha24inv T cells, which are presently shown to represent on average 1/500 PBL, and the high interindividual variations of the size of this cell subset under physiologic conditions go for a major role played by alphabeta T cells carrying invariant TCR in a large array of immune responses.
EFFECTS OF ANTI-INFLAMMATORY DRUGS ON TRIPLE VACCINE-INDUCED PLEURISY IN RATS (1982)

Effects of various anti-inflammatory drugs on triple vaccine-induced pleurisy, a model of delayed hypersensitivity, were examined and compared with those on carrageenin-induced pleurisy in rats. Steroidal drugs depressed markedly the volume of exudate and the number of leucocytes in both types of pleurisy. Gold compounds also depressed both types of pleurisy. Non-steroidal anti-inflammatory drugs were apt to show depressive effects on carrageenin-induced pleurisy, especially on increased exudate volume. BW755C produced a depressive effect on carrageenin-induced pleurisy, but on triple vaccine-induced pleurisy, BW755C produced only a slight depressive effect. Cyproheptadine produced a slight depressive effect on carrageenin-induced pleurisy, but not on triple vaccine-induced pleurisy. Promethazine had a slight depressive effect on both types of pleurisy. D-penicillamine and levamisole did not show any depressive effects on triple vaccine-induced pleurisy. The results show that reported mediators in carrageenin-induced pleurisy (prostaglandin, serotonin, leukotriene B, etc.) are not relevant to triple vaccine-induced pleurisy. Specific lymphognes and/or degradated products of complement may participate in the latter. This triple vaccine-induced pleurisy seems to be a good model for screening non-steroidal antiinflammatory drugs which have steroidal-like activity.