gebhart/patrepeval huggingface dataset:
Graph-Structured Representations for Visual Question Answering (2017)

This paper proposes to improve visual question answering (VQA) with structured representations of both scene contents and questions. A key challenge in VQA is to require joint reasoning over the visual and text domains. The predominant CNN/LSTM-based approach to VQA is limited by monolithic vector representations that largely ignore structure in the scene and in the question. CNN feature vectors cannot effectively capture situations as simple as multiple object instances, and LSTMs process questions as series of words, which do not reflect the true complexity of language structure. We instead propose to build graphs over the scene objects and over the question words, and we describe a deep neural network that exploits the structure in these representations. We show that this approach achieves significant improvements over the state-of-the-art, increasing accuracy from 71.2% to 74.4% in accuracy on the abstract scenes multiple-choice benchmark, and from 34.7% to 39.1% in accuracy over pairs of balanced scenes, i.e. images with fine-grained differences and opposite yes/no answers to a same question.
Promoter and genotype dependent transient expression of a reporter gene in plant protoplasts. (1991)

For analysis of expression of three different plant promoters such as CaMV 35S, rbc S and mas, compact plasmid vectors were constructed by use of beta-glucuronidase (GUS) gene and nos termination signal. The plasmid molecules were introduced into tobacco and tomato protoplasts by using the Mg2+/PEG transformation protocol described by Negrutiu et al. The transient assays revealed maximum expression two days after DNA uptake. The comparative studies show the following order of promoters mas, CaMV 35S, rbc S as far as the activity is concerned. We also detected genotype-dependent promoter activity in the case of tomato.
Synthesis, Conjugation, and Radiolabeling of a Novel Bifunctional Chelating Agent for 225Ac Radioimmunotherapy Applications (2000)

225Ac (t(1/2) = 10 days) is an alternative alpha-emitter that has been proposed for radioimmunotherapy (RIT) due to its many favorable properties, such as half-life and mode of decay. The factor limiting use of (225)Ac in RIT is the lack of an acceptably stable chelate for in vivo applications. Herein is described the first reported bifunctional chelate for (225)Ac that has been evaluated for stability for in vivo applications. The detailed synthesis of a bifunctional chelating agent 2-(4-isothiocyanatobenzyl)-1,4,7,10,13, 16-hexaazacyclohexadecane- 1,4,7,10,13,16-hexaacetic acid (HEHA-NCS) is reported. This ligand was conjugated to three monoclonal antibodies, CC49, T101, and BL-3 with chelate-to-protein ratios between 1.4 and 2. The three conjugates were radiolabeled with (225)Ac, and serum stability study of the [(225)Ac]BL-3-HEHA conjugate was performed.
Serum YKL-40 Predicts Relapse-Free and Overall Survival in Patients With American Joint Committee on Cancer Stage I and II Melanoma (2006)

Serum YKL-40 may be an early biomarker of relapse and survival in patients with AJCC stage I and II melanoma. Serum YKL-40 may also be useful for patient stratification and follow-up in clinical trials. Our results need confirmation in an independent study.
Analysis of rearranged immunoglobulin heavy chain variable region genes obtained from a bone marrow transplant (BMT) recipient (1997)

Haematopoietic stem cell transplantation has been used for the treatment of many different malignant and non-malignant diseases. The immune system of transplant recipients must be regenerated from the transplant inoculum, and it is not surprising that many transplant recipients are deficient in generating specific antibody responses to exogenous stimuli. This B cell immunodeficiency in these patients is associated with clinically significant infections, although the underlying mechanism remains unknown. We have previously shown that the pattern of usage of V(H) genes was similar between healthy subjects and BMT recipients, indicating that the immunodeficiency was not due to a dramatic imbalance in V(H) utilization. However, motif-specific hybridization analysis indicated that the accumulation of somatic mutations was much greater among rearrangements in controls than in BMT recipients. The failure of BMT recipients to accumulate somatic mutations in rearranged V(H) genes correlates with an absence of IgD- B cells, and is consistent with a defect in antigen-driven B cell responses. In the current study, which extends those findings, we have determined the nucleotide sequences of 68 heavy chain rearrangements from one patient as well as 39 rearrangements from a healthy control. Analysis of these sequences made possible a more precise definition of variable region configuration and of the status of somatic mutation in this BMT recipient. The results validate the hybridization data and support the conclusion that, although somatic hypermutation and, by inference, antigen-driven responses are detected in BMT recipients, they are deficient compared with healthy subjects as late as 1 year after transplant.
Cross-Reactivity among Several Recombinant Calicivirus Virus-Like Particles (VLPs) with Monoclonal Antibodies Obtained from Mice Immunized Orally with One Type of VLP (2002)

Human caliciviruses (HuCVs) are classified into the Norwalk-like viruses (NLV) and Sapporo-like viruses (SLV) as genera within the family CALICIVIRIDAE: The NLV genus is further classified into genogroups I and II, based on sequence similarities. To study the antigenic determinants on the HuCV capsid protein and develop new diagnostic tools for field samples, we established and characterized monoclonal antibodies (MAbs) against baculovirus-expressed recombinant HuCV virus-like particles (VLPs). Hybrid clones producing MAbs were obtained from cultures of PAI myeloma cells fused with spleen or mesenteric lymph node cells from mice immunized orally with either a single type of recombinant Norwalk virus (rNV), Kashiwa 47 virus (rKAV), Snow Mountain agent (rSMA), or Sapporo virus (rSV) VLP or with mixtures of two types of VLPs from different genogroups. Twenty MAbs, obtained as mouse ascites, were characterized and classified into six groups according to their enzyme-linked immunosorbent assay (ELISA) and Western blotting (WB) cross-reactivity patterns to VLPs. Five groups of MAbs reacted by both WB and ELISA and were classified as follows: common cross-reactive MAbs for four genogroup I and six genogroup II VLPs (group A), genogroup I-specific MAbs (group B), genogroup II-specific MAbs (group C), and strain-specific MAbs (groups D and E). One MAb group (group F) reacted only by ELISA. The group A MAbs, which showed broad cross-reactivity with VLPs of both NLV genogroups, were obtained from mice immunized orally with a single type of VLP (either rNV or rKAV). Two MAbs, which were obtained from mice immunized with rSV, reacted with rSV but not with any NLV VLP. These are the first MAbs to be reported for any SLV. These strain-, genogroup-, and genus-reactive MAbs will be useful tools for further study of the antigenic and structural topography of the HuCV virion and for diagnostic assays for HuCVs.
Phasic pupil dilation response to noxious stimulation in normal volunteers: Relationship to brain evoked potentials and pain report (1999)

Pupillary response to noxious stimulation was investigated in men (n = 11) and women (n = 9). Subjects experienced repeated trials of noxious electrical fingertip stimulation at four intensities, ranging from faint to barely tolerable pain. Measures included pupil dilation response (PDR), pain report (PR), and brain evoked potentials (EPs). The PDR began at 0.33 s and peaked at 1.25 s after the stimulus. Multivariate mixed-effects analyses revealed that (a) the PDR increased significantly in peak amplitude as stimulus intensity increased, (b) EP peaks at 150 and 250 ms differed significantly in both amplitude and latency across stimulus intensity, and (c) PR increased significantly with increasing stimulus intensity. Men demonstrated a significantly greater EP peak amplitude and peak latency at 150 ms than did women. With sex and stimulus intensity effects partialled out, the EP peak latency at 150 ms significantly predicted PR, and EP peak amplitude at 150 ms significantly predicted the PDR peak amplitude.
Phase I Clinical Trial of Repeat Dose Terameprocol Vaginal Ointment in Healthy Female Volunteers (2008)

Terameprocol was well tolerated at a 90 mg dose (2% wt/wt) administered vaginally daily for 7 days. No serious adverse events occurred and any AEs were mild. The excellent safety profile supports future clinical trial to evaluate the application of intravaginal terameprocol in women.
The relationship of running to osteoarthritis of the knee and hip and bone mineral density of the lumbar spine: A 9 year longitudinal study (1998)

Objective. To determine the associations between running and radiographic hip osteoarthritis (OA), the progression of radiographic knee OA, and changes in bone mineral density (BMD) after 9 year followup in 28 members of a running club now aged 60-77 years and 27 nonrunner controls. Methods. Running subjects and non running controls were matched for age (± 2 years), years of education, and occupation. All subjects underwent rheumatologic examination, completed annual questionnaires, and had radiographs taken of the knees in 1984, 1986, 1989, and 1993 and of the hips in 1993. BMD of the first lumbar spine vertebrae was obtained in 36 subjects by quantitative computed tomography (QCT) in 1984, 1986, 1989. and 1993. In 1993, knee radiographs were assessed in pairs (1984 and 1993), and hip radiographs were scored by 2 readers individually without knowledge of running status. Results. Nine year radiographic results for both runners and nonrunners for the knees showed significant within-group progression of both osteophytes and total knee radiographic scores (p = 0.01 for runners and p = 0.05 for nonrunners) and joint space narrowing in nonrunners (p = 0.01). Runners tended to have higher radiographic scores, but no significant differences in between-group differences were seen in 1984 or 1993. Radiographic OA of the hip was not different between the groups. QCT of the first lumbar vertebrae for BMD in 1984, 1986, 1989, and 1993 was greater in runners than nonrunners (p = 0.01 ), but rates of change in QCT values were similar between the 2 groups (p < 0.001). Conclusion. The presence of radiographic hip OA and the progression of radiographic knee OA was similar for older runners and nonrunners. Lumbar spine BMD remained higher in runners, but changes in lumbar BMD were similar for runners and nonrunners over a 9 year period.
Three-Dimensional Cell and Tissue Patterning in a Strained Fibrin Gel System (2007)

Techniques developed for the in vitro reproduction of three-dimensional (3D) biomimetic tissue will be valuable for investigating changes in cell function in tissues and for fabricating cell/matrix composites for applications in tissue engineering techniques. In this study, we show that the simple application of a continuous strain to a fibrin gel facilitates the development of fibril alignment and bundle-like structures in the fibrin gel in the direction of the applied strain. Myoblasts cultured in this gel also exhibited well-aligned cell patterning in a direction parallel to the direction of the strain. Interestingly, the direction of cell proliferation was identical to that of cell alignment. Finally, the oriented cells formed linear groups that were aligned parallel to the direction of the strain and replicated the native skeletal muscle cell patterning. In addition, vein endothelial cells formed a linear, aligned vessel-like structure in this system. Thus, the system enables the in vitro reproduction of 3D aligned cell sets replicating biological tissue patterns.
Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence (2010)

Comparative analysis of genome sequences and gene content confirmed the differentiation of R. solanacearum species complex strains into four phylotypes. Genetic distances between strains, in conjunction with CGH analysis of a larger set of strains, revealed differences great enough to consider reclassification of the R. solanacearum species complex into three species. The data are still too fragmentary to link genomic classification and phenotypes, but these new genome sequences identify a pan-genome more representative of the diversity in the R. solanancearum species complex.
Binding Stoichiometry of the Cytotoxic T Lymphocyte-associated Molecule-4 (CTLA-4) (1995)

CD28 and CTLA-4 are homologous T cell receptors of the immunoglobulin (Ig) superfamily, which bind B7 molecules (CD80 and CD86) on antigen-presenting cells and transmit important costimulatory signals during T cell activation. Here we have investigated the subunit structure of CTLA-4 and the stoichiometry of its binding to B7 molecules. We demonstrate CTLA-4 is a homodimer interconnected by one disulfide bond in the extracellular domain at cysteine residue 120. Each monomeric polypeptide chain of CTLA-4 contains a high affinity binding site for B7 molecules; soluble CTLA-4 and CD86 form complexes containing equimolar amounts of monomeric CTLA-4 and CD86 (i.e. a 2:2 molecular complex). Thus, CTLA-4 and probably CD28 have a receptor structure consisting of preexisting covalent homodimers with two binding sites. Dimerization of CTLA-4 and CD28 is not required for B7 binding, nor is it sufficient to trigger signaling.
Immune Responses in 4-1BB (CD137)-Deficient Mice (2002)

The 4-1BB (a TNFR superfamily member) is an inducible costimulatory molecule that can exert regulatory effects on T cells independently of CD28 stimulation. The in vitro expression of 4-1BB (CD137) is induced following activation of T cells with various stimuli, including anti-TCR mAbs, lectins, and a combination of PMA and ionomycin. To delineate further the physiological role of 4-1BB in immunity, mice deficient in this receptor were generated. These mutant mice developed normally, and were viable and fertile. Humoral responses to vesicular stomatitis virus were comparable with those seen in wild-type mice, whereas the IgG2a and IgG3 isotype responses to keyhole limpet hemocyanin were somewhat reduced in the mutant mice. The 4-1BB-deficient mice demonstrated enhanced T cell proliferation in response to mitogens or anti-CD3 even in the environment of reduced ability to secrete growth-supporting cytokines (IL-2 and IL-4). Although T cells from 4-1BB-deficient mice showed enhanced proliferation, the T cell immune responses of these animals, such as cytokine production and CTL activity, were diminished. In addition, 4-1BB deletion appears to play a role in the regulation of myeloid progenitor cell growth, leading to an increase in these precursor cells in peripheral blood, bone marrow, and spleen.
Communication and computation patterns of large scale image convolutions on parallel architectures (2002)

Segmentation and other image processing operations rely on convolution calculations with heavy computational and memory access demands. The article presents an analysis of a texture segmentation application containing a 96/spl times/96 convolution. Sequential execution required several hours an single processor systems with over 99% of the time spent performing the large convolution. 70% to 75% of execution time is attributable to cache misses within the convolution. We implemented the same application on CM-5, iPSC/860 and PVM distributed memory multicomputers, tailoring the parallel algorithms to each machine's architecture. Parallelization significantly reduced execution time, taking 49 seconds on a 512 node CM-5 and 6.5 minutes on a 32 node iPSC/860. The results indicate for large kernel convolutions the size and bandwidth of the fast memory store is more important than processor power or communication overhead.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diphtheria toxin treatment of human advanced cancer. (1982)

Purified diphtheria toxin was administered i.v. to 50 patients with advanced solid tumors. The doses of toxin varied according to the different immunological status of the patients against diphtheria. The prominent toxic effects of the treatment were transient peripheral neuropathy observed in two nonimmune patients and fever (37-41 degrees) which occurred in all immune patients with cell-mediated hypersensitivity to toxin. A partial response to lasting from 2 to 4 weeks was achieved in three of 13 nonimmune patients and in one of three nonimmune patients with cell-mediated hypersensitivity. Of 21 immune patients, nine had partial response lasting from 4 to 12 weeks. Of 13 immune patients with cell-mediated hypersensitivity, six had partial and five complete response lasting from 2 to 12 and from 1 to 25+ months, respectively. The overall response rate was 48%. The results suggest that diphtheria toxin may have a role in cancer immunotherapy.
Mechanisms of DNA sequence selective alkylation of guanine-N7 positions by nitrogen mustards (1987)

Quantitative determinations were carried out of the relative reaction rates of several nitrogen mustards at various guanine-N7 positions in DNA fragments of known sequence. The findings suggest structural hypotheses of the origins of the reaction selectivities. End-labeled DNA fragments were reacted with nitrogen mustards, and the guanine-N7 alkylation sites were analyzed by gel electrophoresis. Relative reaction intensities were determined by computer analysis of digitized densitometer scans. The differences in reaction intensities at different G's were in part attributable to the effects of nearest neighbor base pairs on the molecular electrostatic potential near the reaction site. Uracil and quinacrine mustards have specific sequence preferences for reaction that differ from other mustards. The nature of the specific sequence preferences were determined and hypotheses are proposed to explain their origin.
Quantitation of Indoleacetic Acid Conjugates in Bean Seeds by Direct Tissue Hydrolysis (1989)

Gas chromatography-selected ion monitoring-mass spectral analysis using [(13)C(6)]indole-3-acetic acid (IAA) as an internal standard provides an effective means for quantitation of IAA liberated during direct strong basic hydrolysis of bean (Phaseolus vulgaris L.) seed powder, provided that extra precautions are undertaken to exclude oxygen from the reaction vial. Direct seed powder hydrolysis revealed that the major portion of amide IAA conjugates in bean seeds are not extractable by aqueous acetone, the solvent used commonly for IAA conjugate extraction from seeds and other plant tissues. Strong basic hydrolysis of plant tissue can be used to provide new information on IAA content.
Inhibition of Lipid A Stimulated Activation of Human Dendritic Cells and Macrophages by Amino and Hydroxylamino Monosaccharides (2007)

Innovative mimics of lipid A were synthesized and shown to efficiently inhibit lipid A induced cytokine production in human dendritic cells and macrophages. These compounds, which consist of a D-glucose unit functionalized with an amine, ammonium, or hydroxylamine group and a five-membered ring at C6 (see structures) are promising leads for antisepsis-drug development owing to their lack of toxicity and their selectivity for the TLR4 receptor. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604932_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Peptide Biosensors for the Electrochemical Measurement of Protein Kinase Activity (2008)

The kinase activities are elucidated using the novel redox-active cosubstrate adenosine 5'-[gamma-ferrocene] triphosphate (Fc-ATP), which enables the kinase-catalyzed transfer of a redox active gamma-phosphate-Fc to a hydroxyamino acid. In this report, a versatile electrochemical biosensor is developed for monitoring the activity and inhibition of a serine/threonine kinase, casein kinase 2 (CK2), and protein tyrosine kinases, Abl1-T315I and HER2, in buffered solutions and in cell lysates. The method is based on the labeling of a specific phosphorylation event with Fc, followed by electrochemical detection. The electrochemical response obtained from the "ferrocenylated" peptides enables monitoring the activity of the kinase and its substrate, as well as the inhibition of small molecule inhibitors on protein phosphorylation. Kinetic information was extracted from the electrochemical measurements for the determination of K(m) and V(m) values, which were in agreement with those previously reported. Kinase reactions were also performed in the presence of well-defined inhibitors of CK2, 4,5,6,7-tetrabromo-2-azabenzimidazole, 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole, and E-3-(2,3,4,5-tetrabromophenyl)acrylic acid as well as the nonspecific kinase inhibitors, staurosporine and N-benzoylstaurosporine. On the basis of the dependency of the Fc signal on inhibitor concentration, K(i) of the inhibitors was estimated, which were also in agreement with the literature values. The performance of the biosensor was optimized including the kinase reaction, incubation with Fc-ATP, and the small molecule inhibitors. Peptide modified electrochemical biosensors are promising candidates for cost-effective in vitro kinase activity and inhibitor screening assays.
Identification of the human eosinophil lineage-committed progenitor: revision of phenotypic definition of the human common myeloid progenitor (2008)

To establish effective therapeutic strategies for eosinophil-related disorders, it is critical to understand the developmental pathway of human eosinophils. In mouse hematopoiesis, eosinophils originate from the eosinophil lineage-committed progenitor (EoP) that has been purified downstream of the granulocyte/macrophage progenitor (GMP). We show that the EoP is also isolatable in human adult bone marrow. The previously defined human common myeloid progenitor (hCMP) population (Manz, M.G., T. Miyamoto, K. Akashi, and I.L. Weissman. 2002. Proc. Natl. Acad. Sci. USA. 99:11872-11877) was composed of the interleukin 5 receptor alpha chain(+) (IL-5Ralpha(+)) and IL-5Ralpha(-) fractions, and the former was the hEoP. The IL-5Ralpha(+)CD34(+)CD38(+)IL-3Ralpha(+)CD45RA(-) hEoPs gave rise exclusively to pure eosinophil colonies but never differentiated into basophils or neutrophils. The IL-5Ralpha(-) hCMP generated the hEoP together with the hGMP or the human megakaryocyte/erythrocyte progenitor (hMEP), whereas hGMPs or hMEPs never differentiated into eosinophils. Importantly, the number of hEoPs increased up to 20% of the conventional hCMP population in the bone marrow of patients with eosinophilia, suggesting that the hEoP stage is involved in eosinophil differentiation and expansion in vivo. Accordingly, the phenotypic definition of hCMP should be revised to exclude the hEoP; an "IL-5Ralpha-negative" criterion should be added to define more homogenous hCMP. The newly identified hEoP is a powerful tool in studying pathogenesis of eosinophilia and could be a therapeutic target for a variety of eosinophil-related disorders.
Organic light-emitting diodes with a bipolar transport layer (1999)

A structure based on a bipolar transport/emitting layer is proposed and implemented for making organic light-emitting diodes. Compared to the conventional heterojunction organic light-emitting diodes, more than a factor of six improvement in device reliability (a projected operating lifetime of 70 000 h) is achieved in the structure. The significant improvement in device lifetime is attributed to the elimination of the heterointerface present in the conventional devices which greatly affects the device reliability.