gebhart/patrepeval huggingface dataset:
An approach to probabilistic retrieval (1981)

The objective is to relate the effectiveness of retrieval, the fuzzy set concept and the processing of Boolean query. The use of a probabilistic retrieval scheme is motivated. It is found that there is a correspondence between probabilistic retrieval schmes and fuzzy sets. A fuzzy set corresponding to a potentially optimal probabilistic retrieval scheme is obtained. Then the retrieval scheme for the fuzzy set is constructed.
Ketamine rapidly relieves acute suicidal ideation in cancer patients: a randomized controlled clinical trial (2016)

This study was designed to examine the rapid antidepressant effects of single dose ketamine on suicidal ideation and overall depression level in patients with newly-diagnosed cancer. Forty-two patients were enrolled into the controlled trial and randomized into two groups: ketamine group and midazolam group. Patients from the two groups received a sub-anesthetic dose of racemic ketamine hydrochloride or midazolam. Suicidal ideation score, measured with the Beck Scale and suicidal part of the Montgomery-Asberg Depression Rating Scale, significantly decreased on day 1 and day 3 in ketamine-treated patients when compared to those treated with midazolam. Consistently, overall depression levels measured using the Montgomery-Asberg Depression Rating Scale indicated a significant relief of overall depression on day 1 in ketamine-treated patients. Collectively, this study provides novel information about the rapid antidepressant effect of ketamine on acute depression and suicidal ideation in newly-diagnosed cancer patients.
Increased frequency of N-region insertion in a murine pre-B-cell line infected with a terminal deoxynucleotidyl transferase retroviral expression vector. (1987)

The role of terminal deoxynucleotidyl transferase (TdT) in the insertion of N regions into the junctional sites of immunoglobulin genes was investigated. Pre-B-cell lines capable of continuous rearrangement of immunoglobulin light-chain genes and differing only in the presence or apparent absence of TdT were derived by infecting cells with a TdT retroviral expression vector or a control vector. The cell lines were then superinfected with a retrovirus-based artificial immunoglobulin gene rearrangement substrate. The substrate was allowed to rearrange in the cell lines and the rearranged proviruses were rescued from the cell lines. Nucleotide sequence analysis of the V-J junctions of the proviral rearranged genes showed a fivefold greater frequency of N-region insertion in proviruses rescued from the TdT+ cell lines than in those rescued from the TdT- cell lines, so that at least 50% of the rearrangements that occurred in the presence of TdT had N regions. It is thus evident that TdT can stimulate N-region insertion, and the enzyme is presumably directly responsible for adding nucleotides at V-J and other immunoglobulin and T-cell receptor gene junctions.
The Tinkertoy graphical programming environment (1988)

The Tinkertoy graphical interface to Lisp is described, in which programs are 'built' rather than written, out of icons and flexible interconnections. It represents a computer/user interface that can easily exceed the interaction speed of the best text-based language editors and command languages. It also provides a consistent framework for interaction across both editing and command execution. Moreover, because programs are represented graphically, structures that do not naturally conform to the text medium can be clearly described, the new kinds of information can be incorporated into programs and program elements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Linker scanning mutagenesis of the internal ribosome entry site of poliovirus RNA (1992)

The initiation of cap-independent translation of poliovirus mRNA occurs as a result of ribosome entry at an internal site(s) within the 5' noncoding region. A series of linker scanning mutations was constructed to define the genetic determinants of RNA-protein interactions that lead to high-fidelity translation of this unusual viral mRNA. The mutations are located within two distinct stem-loop structures in the 5' noncoding region of poliovirus RNA that constitute a major portion of a putative internal ribosome entry site. On the basis of our data derived from genetic and biochemical assays, the stability of one of the stem-loop structures appears to be essential for translation initiation via internal binding of ribosomes. However, the second stem-loop structure may function in a manner that requires base pairing and proper spacing between specific nucleotide sequences. By employing RNA electrophoretic mobility shift assays, an RNA-protein interaction was detected for this latter stem-loop structure that does not occur in RNAs containing mutations which perturb the predicted hairpin structure. Analysis of in vivo-selected virus revertants, in combination with mobility shift assays, suggests that extensive genetic rearrangement can lead to restoration of 5' noncoding region functions, possibly by the repositioning of specific RNA sequence or structure motifs.
Angiostatin (2004)

The quiescent vascular system in the adult body represents the imbalanced net outcome of overproduction of endogenous angiogenesis inhibitors and reduced levels of angiogenic factors. While some endogenous inhibitors are expressed under physiological conditions, they can also be generated in association with tumor growth. Angiostatin is such a specific angiogenesis inhibitor produced by tumors. It inhibits primary and metastatic tumor growth by blocking tumor angiogenesis. Having demonstrated potent antitumor activity in animal studies, angiostatin is now in clinical trials for human cancer therapy. Angiostatin is not a novel protein molecule coded by novel DNA sequences. Instead, it is an internal proteolytic fragment of a known protein, plasminogen. Surprisingly, most kringle domains of plasminogen only inhibit angiogenesis when cleaved as fragments from their parent protein that lacks antiangiogenic activity. These findings suggest that they are cryptic fragments hidden in large protein molecules. Thus, proteolytic processing plays a critical role in down-regulation of angiogenesis. Despite proteolytic processing, the antiangiogenic mechanism of angiostatin remains an enigma. Without knowing the mechanisms, it is difficult to predict the ultimate outcome of ongoing clinical trials. In this article, we discuss what is known about angiostatin and how this molecule specifically inhibits angiogenesis. We hope that the information will be useful for further development of angiostatin and its related inhibitors as therapeutic agents.
Expression of Ia-like antigen molecules on human granulocytes during early phases of differentiation (1977)

Human B lymphocyte antigens analogous to the murine Ia determinants were found on myeloblasts and promyelocytes but not on more mature granulocytes. This was apparent by fluorescent staining with both human alloantisera and rabbit antisera to the isolated Ia-like proteins. The cells of patients with chronic myelocytic leukemia showed this difference especially clearly. Separation of the myeloblasts and promyelocytes by multistep density gradient fractionation produced a marked enrichment of the positive cells. The remaining cells from higher density fractions were more-mature neutrophils that were essentially negative. In acute myeloid leukemia, in which myeloid cells early in differentiation predominate, the vast majority of cells were strongly positive. Similar results were obtained with normal bone marrow cells. Here also, only the early forms of the myeloid series separated by gradient centrifugation had Ia antigens. Evidence was also obtained for the presence of Ia determinants on cells with the appearance of early erythroid precursors. Support for the presence of the Ia determinants on granulocyte-macrophage committed stem cells was provided by the inhibition of granulocyte colony formation in agar cultures following preincubation of normal bone marrow with antiserum and complement. Cross absorptions with purified preparations of immature cells provided evidence for the close similarity of the antigenic determinants on both myeloblasts and B cells. A 28,000-37,000-dalton bimolecular complex obtained from myeloblast membranes contained the Ia determinants and was similar to that obtained from peripheral blood B cell membranes.
Research on Geometrical Definition System of Highway's Horizontal Alignment, Vertical Alignment and Cross Section (2002)

The shortcomings of geometrical definition of horizontal alignment,vertical alignment and cross section in current highway CAD system are analyzed,and it is pointed out that the overall and standardized geometrical definition are important and imperative to the development of integrated highway CAD system.Based on the characteristics of horizontal alignment,vertical alignment and cross section,the concise,flexible,united and universal geometrical definition models of horizontal alignment,vertical alignment and cross section are established to form a geometrical definition system,which can be used as the kernel of integrated highway CAD system.
Structure-Function Comparisons of the Proapoptotic Protein Bax in Yeast and Mammalian Cells (1996)

Expression of the proapoptotic protein Bax under the control of a GAL10 promoter in Saccharomyces cerevisiae resulted in galactose-inducible cell death. Immunofluorescence studies suggested that Bax is principally associated with mitochondria in yeast cells. Removal of the carboxyl-terminal transmembrane (TM) domain from Bax [creating Bax (deltaTM)] prevented targeting to mitochondrial and completely abolished cytotoxic function in yeast cells, suggesting that membrane targeting is crucial for Bax-mediated lethality. Fusing a TM domain from Mas70p, a yeast mitochondrial outer membrane protein, to Bax (deltaTM) restored targeting to mitochondria and cytotoxic function in yeast cells. Deletion of four well-conserved amino acids (IGDE) from the BH3 domain of Bax ablated its ability to homodimerize and completely abrogated lethality in yeast cells. In contrast, several Bax mutants which retained ability to homodimerize (deltaBH1, deltaBH2, and delta1-58) also retained at least partial lethal function in yeast cells. In coimmunoprecipitation experiments, expression of the wild-type Bax protein in Rat-1 fibroblasts and 293 epithelial cells induced apoptosis, whereas the Bax (deltaIGDE) mutant failed to induce apoptosis and did not associate with endogenous wild-type Bax protein. In contrast to yeast cells, Bax (deltaTM) protein retained cytotoxic function in Rat-1 and 293 cells, was targeted largely to mitochondria, and dimerized with endogenous Bax in mammalian cells. Thus, the dimerization-mediating BH3 domain and targeting to mitochondrial membranes appear to be essential for the cytotoxic function of Bax in both yeast and mammalian cells.
Carbonyl and oxidative stress in patients with breast cancer--is there a relation to the stage of the disease? (2007)

breast cancer patients had an early increase of AGEs (marker of the carbonyl stress) followed by further increase of AGEs and elevation of AOPP (marker of oxidative stress) in patients with progressive disease. As the clinical significance of these observations is currently uncertain further studies are clearly warranted, especially with respect to their potential therapeutic implications.
Fundamentals of DNA Hybridization Arrays for Gene Expression Analysis (2000)

For hybridization arrays, the general approach is to immobilize gene-specific sequences (probes) on a solid state matrix (nylon membranes, glass microscope slides, silicon/ceramic chips). These sequences are then queried with labeled copies of nucleic acids from biological samples (targets). The underlying theory is that the greater the expression of a gene, the greater the amount of labeled target, and hence, the greater output signal. In spite of the simplicity of the experimental design, there are at least four different platforms and several different approaches to processing and labeling the biological samples. Moreover, investigators must also determine whether they will utilize commercially available arrays or generate their own. This review will cover the status of the hybridization array field with an eye toward underlying principles and available technologies. Future developments and technological trends will also be evaluated.
Cooperative Learning and Conflict Resolution: Perspectives of Urban Middle School Adolescents (1995)

This two-year study of 499 urban middle school adolescents in grades 6, 7, and 8 presents students' perspectives on cooperative learning and conflicts that inevitably arise when they work in groups. Dimensions of cooperative learning that students found favorable or unfavorable are delineated and examined, with both qualitative and quantitative results indicating some differences by demographic variables such as gender, ethnicity, grade, special programs, and reading achievement scores. A majority of urban adolescents like cooperative learning and prefer this instructional strategy to working alone. Nonetheless, the most appealing aspects of cooperative learning--peer interaction and opportunities for different points of view--are also the most problematic for them in that these are fertile grounds for conflicts that arise around academic tasks and interpersonal skills. While cooperative learning is a viable instructional strategy for middle school students, conflict resolution needs to be its vital component.
Consolidative Dendritic Cell-based Immunotherapy Elicits Cytotoxicity against Malignant Mesothelioma (2010)

This study demonstrated that autologous tumor lysate-pulsed dendritic cell-based therapy is feasible, well-tolerated, and capable of inducing immunological response to tumor cells in mesothelioma patients. Clinical trial registered with www.clinicaltrials.gov (NCT00280982).
Covalently Bonded Organic Monolayers on a Carbon Substrate:  A New Paradigm for Molecular Electronics (2001)

We report herein the fabrication of a molecular junction in which a thin (8−15 Å) layer of oriented organic molecules is positioned between two electronic conductors. The molecular layer becomes a component in an electronic circuit and exhibits properties that depend strongly on molecular structure. Bonding between the carbon substrate and the molecular layer is covalent and conjugated, and thus differs fundamentally from that of the widely studied self-assembled monolayers of alkane thiols on metal surfaces. The chemisorbed molecular layer is densely packed and stable and does not contain the tunneling barrier imposed by a sulfur atom. The current/voltage behavior of methyl-phenyl, n-butyl phenyl, tert-butyl phenyl, and stilbene monolayers between pyrolytic carbon and mercury indicates a negligible pinhole density and shows weak dependence on temperature. The action of a nitroazobenzene molecular junction as a bistable switch is demonstrated, and switching behavior persisted for many on−off cycles and over a period of at least 14 h. Carbon-based molecular junctions represent a new paradigm for molecular electronics, which shows promising electronic behavior and is amenable to low cost, benchtop processing.
Pathogenesis and Host Response in Syrian Hamsters following Intranasal Infection with Andes Virus (2011)

Hantavirus pulmonary syndrome (HPS), also referred to as hantavirus cardiopulmonary syndrome (HCPS), is a rare but frequently fatal disease caused by New World hantaviruses. In humans HPS is associated with severe pulmonary edema and cardiogenic shock; however, the pathogenesis of this disease remains unclear largely due to a lack of suitable animal models for the study of disease progression. In this study we monitored clinical, virological, pathophysiological parameters and host immunological responses to decipher pathological factors and events in the lethal Syrian hamster model of HPS following intranasal inoculation of Andes virus. Transcriptional profiling of the host gene responses demonstrated a suppression of innate immune responses in most organs analyzed during the early stage of infection, except for in the lung which had low level activation of several pro-inflammatory genes. During this phase Andes virus established a systemic infection in hamsters, with viral antigen readily detectable in the endothelium of the majority of tissues analyzed by 7-8 days post-inoculation. Despite wide-spread infection, histological analysis confirmed pathological abnormalities were almost exclusively found in the lungs. Immediately preceding clinical signs of disease, intense activation of pro-inflammatory and Th1/Th2 responses were observed in the lungs as well as the heart, but not in peripheral organs, suggesting that localized immune-modulations by infection is paramount to pathogenesis. Throughout the course of infection a strong suppression of regulatory T-cell responses was noted and is hypothesized to be the basis of the aberrant immune activations. The unique and comprehensive monitoring of host immune responses to hantavirus infection increases our understanding of the immuno-pathogenesis of HPS and will facilitate the development of treatment strategies targeting deleterious host immunological responses.
Multi-core Architectures with Dynamically Reconfigurable Array Processors for the WiMAX Physical Layer (2008)

Wireless internet access technologies have significant market potential, especially the WiMAX protocol which can offer data rate of tens of Mbps. A significant demand for embedded high performance WiMAX solutions is forcing designers to seek single-chip multiprocessor or multi-core systems that offer competitive advantages in terms of all performance metrics, such as speed, power and area. Through the provision of a degree of flexibility similar to that of a DSP and performance and power consumption advantages approaching that of an ASIC, emerging dynamically reconfigurable processors are proving to be strong candidates for future high performance multi-core processor systems. This paper presents several new single-chip multi-core architectures, based on newly emerging dynamically reconfigurable processor cores, for the WiMAX physical layer. A simulation platform is proposed in order to explore and implement various multi-core solutions combining different memory architectures and task partitioning schemes. The paper describes the architectures, the simulation environment, and demonstrates that up to 4.2x speedup can be achieved by employing four dynamically reconfigurable processor cores with individual local memory units.
Magnetic Field-Induced T Cell Receptor Clustering by Nanoparticles Enhances T Cell Activation and Stimulates Antitumor Activity (2014)

Iron-dextran nanoparticles functionalized with T cell activating proteins have been used to study T cell receptor (TCR) signaling. However, nanoparticle triggering of membrane receptors is poorly understood and may be sensitive to physiologically regulated changes in TCR clustering that occur after T cell activation. Nano-aAPC bound 2-fold more TCR on activated T cells, which have clustered TCR, than on naive T cells, resulting in a lower threshold for activation. To enhance T cell activation, a magnetic field was used to drive aggregation of paramagnetic nano-aAPC, resulting in a doubling of TCR cluster size and increased T cell expansion in vitro and after adoptive transfer in vivo. T cells activated by nano-aAPC in a magnetic field inhibited growth of B16 melanoma, showing that this novel approach, using magnetic field-enhanced nano-aAPC stimulation, can generate large numbers of activated antigen-specific T cells and has clinically relevant applications for adoptive immunotherapy.
Composição específica e abundância de peixes de zonas rasas dos cinco estuários do Rio Grande do Sul, Brasil (2015)

Foram comparadas, quanto a composição específica e abundância, as comunidades de peixes de zonas rasas dos cinco estuários do Rio Grande do Sul. Realizaram-se amostragens de inverno e verão, utilizando rede de arrasto de praia (picaré) de 9 m de comprimento por 1,2 m de altura e malhas de 5 mm no pano central e 13 mm nas asas. Para a análise da abundância considerou-se a CPUE. O caráter transicional entre a tropicalidade e a subtropicalidade pode ser evidenciado na composição da assembléia de peixes de zonas rasas que ocorrem nestes ambientes. As zonas rasas dos estuários do Rio Mampituba, Rio Tramandaí e Arroio Chuí, quanto à abundância de peixes, foram dominadas pela família Mugilidae, enquanto que os estuários da Lagoa do Peixe e Laguna dos Patos, dominados pela família Atherinidae. A abundância parece estar relacionada ao gradiente latitudinal de temperatura e à área do estuário.
Question Answering through Transfer Learning from Large Fine-grained Supervision Data (2017)

We show that the task of question answering (QA) can significantly benefit from the transfer learning of models trained on a different large, fine-grained QA dataset. We achieve the state of the art in two well-studied QA datasets, WikiQA and SemEval-2016 (Task 3A), through a basic transfer learning technique from SQuAD. For WikiQA, our model outperforms the previous best model by more than 8%. We demonstrate that finer supervision provides better guidance for learning lexical and syntactic information than coarser supervision, through quantitative results and visual analysis. We also show that a similar transfer learning procedure achieves the state of the art on an entailment task.
Molecular basis for the substrate specificity of protein kinase B; comparison with MAPKAP kinase‐1 and p70 S6 kinase (1996)

The substrate specificity of protein kinase‐Bα (PKBα, also known as RAC kinase or Akt) was investigated using synthetic peptide substrates related to the sequence surrounding the phosphorylation site on glycogen synthase kinase‐3 (GSK3). The minimum sequence motif required for efficient phosphorylation was Arg‐Xaa‐Arg‐Yaa‐Zaa‐Ser/Thr‐Hyd, where Xaa is any amino acid, Yaa and Zaa are small residues other than glycine and Hyd is a bulky hydrophobic residue (Phe, Leu). The most effective substrate, Arg‐Pro‐Arg‐Thr‐Ser‐Ser‐Phe, was phosphorylated with a K m of 5 μM and V max of 260 U/mg. PKBα phosphorylated histone H2B ( K m 5 μM, V max 68 Ulmg) specifically at Ser‐36 which also lies in an Arg‐Xaa‐Arg‐Xaa‐Xaa‐Ser‐Hyd motif. The peptide Arg‐Pro‐Arg‐Ala‐Ala‐Thr‐Phe may be a relatively specific substrate for PKBα because, unlike other substrates, it is not phosphorylated by p70 S6 kinase or MAP kinase activated protein (MAPKAP) kinase‐1.