gebhart/patrepeval huggingface dataset:
Isolation of fetal DNA from nucleated erythrocytes in maternal blood. (1990)

Fetal nucleated cells within maternal blood represent a potential source of fetal genes obtainable by venipuncture. We used monoclonal antibody against the transferrin receptor (TfR) to identify nucleated erythrocytes in the peripheral blood of pregnant women. Candidate fetal cells from 19 pregnancies were isolated by flow sorting at 12 1/2-17 weeks gestation. The DNA in these cells was amplified for a 222-base-pair (bp) sequence present on the short arm of the Y chromosome as proof that the cells were derived from the fetus. The amplified DNA was compared with standardized DNA concentrations; 0.1-1 ng of fetal DNA was obtained in the 20-ml maternal samples. In 7/19 cases, a 222-bp band of amplified DNA was detected, consistent with the presence of male DNA in the isolated cells; 6/7 of these were confirmed as male pregnancies by karyotyping amniocytes. In the case of the female fetus, DNA prepared from samples at 32 weeks of gestation and cord blood at delivery also showed the presence of the Y chromosomal sequence, suggesting Y sequence mosaicism or translocation. In 10/12 cases where the 222-bp band was absent, the fetuses were female. Thus, we were successful in detecting the Y chromosomal sequence in 75% of the male-bearing pregnancies, demonstrating that it is possible to isolate fetal gene sequences from cells in maternal blood. Further refinement in methodology should increase sensitivity and facilitate noninvasive screening for fetal gene mutations.
Anti-V3 Monoclonal Antibodies Display Broad Neutralizing Activities against Multiple HIV-1 Subtypes (2010)

Using standard and new statistical methods of data analysis, 6/7 anti-V3 human mAbs displayed cross-clade neutralizing activity and revealed that a significant proportion of viruses can be neutralized by anti-V3 Abs. The new statistical method for analysis of neutralization data provides many advantages to previously used analyses.
Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation (1984)

The entire subtilisin structural gene from Bacillus subtilis I168 has been cloned, and its nucleotide sequence has been determined. When expressed on a high-copy-number shuttle vector, a fivefold increase in serine protease activity was observed. The DNA sequence of the gene is 80% homologous to the Bacillus amyloliquefaciens subtilisin structural gene, and the translated mature coding sequence is 85% homologous to the published protein sequence of subtilisin BPN'. The chloramphenicol resistance determinant of a plasmid integrated at the subtilisin locus was mapped by PBS1 transduction and was found to be linked to glyB (83%) and argC (60%), but not with metC or purB . The chromosomal locus containing the wild-type subtilisin allele was replaced with an in vitro-derived allele of the gene (delta apr-684) that contained a 684-base-pair deletion. The technique used for introducing the deletion is a variation of the gene replacement methods used in Saccharomyces cerevisiae and Escherichia coli. When used in B. subtilis, deletion mutants could be directly screened among the transformants. Physiological characterization of the delta apr-684 mutation revealed no discernable effect on the formation of heat-resistant endospores, but strains carrying the mutation produced only 10% of wild-type serine protease activity. A model is presented that outlines the pathway for plasmid integration and deletion formation in B. subtilis.
Surface pKa of Saturated Carboxylic Acids at the Air/Water Interface: A Quantum Chemical Approach (2020)

In the present study a theoretical approach is proposed for the pKa estimation of monolayers at the air/water interface on the basis of saturated carboxylic acids. This model involves calculating only the Gibbs energies of formation and dimerization of carboxylic acid associates in the neutral and dissociated forms, as well as the corresponding monomers in the water and gas phases. The model does not require the construction of any thermodynamic cycles. The calculations are performed using semiempirical quantum chemical methods PM3 and PM6 within the framework of the conductor-like screening model for monomers and dimers of carboxylic acids CnH2n+1COOH (n = 6–16). It is shown that the minimum clusterization Gibbs energy corresponds to associates with the degree of dissociation α = 0.5. A relationship is derived between the surface and bulk pKa values. In particular, it follows from this that, unlike the bulk pKa, the surface pKa depends on the alkyl chain length of the surfactant. It is due to the difference between the solvation energies of the alkyl chains of the corresponding neutral and dissociated monomers. Thus, the calculated data show that the lengthening of the carboxylic acid chain by one CH2 fragment leads to an increase in the surface pKa by 0.43 units. The obtained results are in good agreement with the available experimental data.
The MediaXact™ System-A framework for personalized electronic commerce services (2002)

The rapid growth of the World Wide Web has created new industries and extended the reach of existing businesses. One of the areas on the verge of expansion is electronic commerce (EC). While still in its infancy, EC is forecasted to increase by over an order of magnitude over the next several years. Notable success stories of selling over the Web — such as those of amazon.com and Dell Computer — are often touted today. A major concern with the creation of EC systems today is the large amount of customization and systems integration work required. We present here the MediaXact† system, a solution to this dilemma that provides a framework separating the service presentation and service logic from the functions that make up the service. This greatly simplifies customization and eases the integration with existing legacy systems and business logic.
Receptor Activator of NF-κB Ligand (RANKL) Activates TAK1 Mitogen-Activated Protein Kinase Kinase Kinase through a Signaling Complex Containing RANK, TAB2, and TRAF6 (2002)

The receptor activator of NF-kappaB (RANK) and its ligand RANKL are key molecules for differentiation and activation of osteoclasts. RANKL stimulates transcription factors AP-1 through mitogen-activated protein kinase (MAPK) activation, and NF-kappaB through IkappaB kinase (IKK) activation. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is essential for activation of these kinases. In the interleukin-1 signaling pathway, TAK1 MAPK kinase kinase (MAPKKK) mediates MAPK and IKK activation via interaction with TRAF6, and TAB2 acts as an adapter linking TAK1 and TRAF6. Here, we demonstrate that TAK1 and TAB2 participate in the RANK signaling pathway. Dominant negative forms of TAK1 and TAB2 inhibit NF-kappaB activation induced by overexpression of RANK. In 293 cells stably transfected with full-length RANK, RANKL stimulation facilitates the formation of a complex containing RANK, TRAF6, TAB2, and TAK1, leading to the activation of TAK1. Furthermore, in murine monocyte RAW 264.7 cells, dominant negative forms of TAK1 and TAB2 inhibit NF-kappaB activation induced by RANKL and endogenous TAK1 is activated in response to RANKL stimulation. These results suggest that the formation of the TRAF6-TAB2-TAK1 complex is involved in the RANK signaling pathway and may regulate the development and function of osteoclasts.
Simultaneous flow cytometric analyses of enhanced green and yellow fluorescent proteins and cell surface antigens in doubly transduced immature hematopoietic cell populations (2000)

Background Cell transduction with multiple genes offers opportunities to investigate specific gene interactions on cell function. Detection of multiple transduced genes in hematopoietic cells requires strategies to combine measurements of gene expression with phenotypic cell discriminants. We describe simultaneous flow cytometric detection of two green fluorescent protein (GFP) variants in immunophenotypically defined human hematopoietic subpopulations using only a minor physical adjustment to a standard FACSCalibur. Methods The accuracy and sensitivity of enhanced GFP (EGFP) and enhanced yellow fluorescent protein (EYFP) detection in mixtures of transduced and nontransduced PG13 packaging cells were evaluated by flow cytometry. Retroviral vectors encoding EGFP or EYFP were used to transduce CD34+ hematopoietic cells derived from umbilical cord blood. The transduction efficiency into subpopulations of hematopoietic cells was measured using multivariate flow cytometry. Results A bicistronic retroviral vector containing the EGFP and puromycin N-acetyltransferase (pac) genes afforded brighter EGFP signals in transduced cells than a retroviral vector encoding a pac-EGFP fusion protein. The sensitivity of detecting EGFP and EYFP-expressing cells among a background of nonexpressing cells was 0.01% and 0.05%, respectively. EGFP or EYFP was expressed in up to 95% of CD34+ DR- or CD34+ 38- subpopulations in cord blood 48 h posttransduction. Simultaneous transduction with EGFP and EYFP viral supernatants (1:1 mixture) led to coexpression of both GFP variants in 15% of CD34+ DR- and 20% of CD34+ 38- cells. Conclusions These results demonstrate simultaneous detection of EGFP and EYFP in immunophenotypically discriminated human hematopoietic cells. This technique will be useful to quantify transduction of multiple retroviral constructs in discriminated subpopulations. Cytometry 40:126–134, 2000. © 2000 Wiley-Liss, Inc.
Differential requirement of DNA replication for the cytotoxicity of DNA topoisomerase I and II inhibitors in Chinese hamster DC3F cells. (1989)

The cytotoxicity of topoisomerase inhibitors is thought to result from the induction of enzyme-mediated DNA breaks. The fact that these breaks reverse rapidly in cells programmed to die, led us to investigate further the cytotoxic mechanisms of topoisomerase I (camptothecin) and topoisomerase II inhibitors (VP-16 and amsacrine) in Chinese Hamster lung fibroblasts (DC3F). Exposures (30 min) to camptothecin produced limited cell killing with approximately 20% of the cells naturally resistant. This resistance was overcome by increasing the drug exposure time. Inhibition of DNA synthesis by 5-min pretreatments with aphidicolin or hydroxyurea abolished the cytotoxicity of camptothecin without changing the level of camptothecin-induced DNA breaks. A good correlation was found between the degree of DNA synthesis inhibition by aphidicolin and the reduction of camptothecin cytotoxicity. In similar experiments performed with topoisomerase II inhibitors, aphidicolin prevented only partially against VP-16- and amsacrine-induced cytotoxicities, yet had no effect upon drug-induced DNA breaks. These results indicate that the production of topoisomerase-mediated DNA breaks by antitumor drugs is not sufficient for cell killing. Instead, an interference of moving DNA replication forks with drug-stabilized topoisomerase-DNA complexes is critical for cell death. The cytotoxicity of camptothecin seemed to be completely related to this process, while that of topoisomerase II inhibitors seemed to involve additional mechanisms in DC3F cells.
Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species (2015)

We demonstrate that primary MSCs release small RNAs via exosomes, which are increasingly implicated in intercellular communications. tRNAs species, and in particular tRNA halves, are preferentially released and their specific sorting into exosomes is related to MSC tissue origin and stemness. These findings may help to understand how MSCs impact neighboring or distant cells with possible consequences for their therapeutic usage.
Envelope Conformational Changes Induced by Human Immunodeficiency Virus Type 1 Attachment Inhibitors Prevent CD4 Binding and Downstream Entry Events (2006)

ABSTRACT BMS-488043 is a small-molecule human immunodeficiency virus type 1 (HIV-1) CD4 attachment inhibitor with demonstrated clinical efficacy. The compound inhibits soluble CD4 (sCD4) binding to the 11 distinct HIV envelope gp120 proteins surveyed. Binding of BMS-488043 and that of sCD4 to gp120 are mutually exclusive, since increased concentrations of one can completely block the binding of the other without affecting the maximal gp120 binding capacity. Similarly, BMS-488043 inhibited virion envelope trimers from binding to sCD4-immunoglobulin G (IgG), with decreasing inhibition as the sCD4-IgG concentration increased, and BMS-488043 blocked the sCD4-induced exposure of the gp41 groove in virions. In both virion binding assays, BMS-488043 was active only when added prior to sCD4. Collectively, these results indicate that obstruction of gp120-sCD4 interactions is the primary inhibition mechanism of this compound and that compound interaction with envelope must precede CD4 binding. By three independent approaches, BMS-488043 was further shown to induce conformational changes within gp120 in both the CD4 and CCR5 binding regions. These changes likely prevent gp120-CD4 interactions and downstream entry events. However, BMS-488043 could only partially inhibit CD4 binding to an HIV variant containing a specific envelope truncation and altered gp120 conformation, despite effectively inhibiting the pseudotyped virus infection. Taken together, BMS-488043 inhibits viral entry primarily through altering the envelope conformation and preventing CD4 binding, and other downstream entry events could also be inhibited as a result of these induced conformational changes.
An Azophenol-based Chromogenic Pyrophosphate Sensor in Water (2003)

A new azophenol-based colorimetric sensor shows a selective detection for pyrophosphate in aqueous solution.
Deep Learning over Multi-field Categorical Data: A Case Study on User\n Response Prediction (2016)

Predicting user responses, such as click-through rate and conversion rate,\nare critical in many web applications including web search, personalised\nrecommendation, and online advertising. Different from continuous raw features\nthat we usually found in the image and audio domains, the input features in web\nspace are always of multi-field and are mostly discrete and categorical while\ntheir dependencies are little known. Major user response prediction models have\nto either limit themselves to linear models or require manually building up\nhigh-order combination features. The former loses the ability of exploring\nfeature interactions, while the latter results in a heavy computation in the\nlarge feature space. To tackle the issue, we propose two novel models using\ndeep neural networks (DNNs) to automatically learn effective patterns from\ncategorical feature interactions and make predictions of users' ad clicks. To\nget our DNNs efficiently work, we propose to leverage three feature\ntransformation methods, i.e., factorisation machines (FMs), restricted\nBoltzmann machines (RBMs) and denoising auto-encoders (DAEs). This paper\npresents the structure of our models and their efficient training algorithms.\nThe large-scale experiments with real-world data demonstrate that our methods\nwork better than major state-of-the-art models.\n
Human3.6M: Large Scale Datasets and Predictive Methods for 3D Human Sensing in Natural Environments (2014)

We introduce a new dataset, Human3.6M, of 3.6 Million accurate 3D Human poses, acquired by recording the performance of 5 female and 6 male subjects, under 4 different viewpoints, for training realistic human sensing systems and for evaluating the next generation of human pose estimation models and algorithms. Besides increasing the size of the datasets in the current state-of-the-art by several orders of magnitude, we also aim to complement such datasets with a diverse set of motions and poses encountered as part of typical human activities (taking photos, talking on the phone, posing, greeting, eating, etc.), with additional synchronized image, human motion capture, and time of flight (depth) data, and with accurate 3D body scans of all the subject actors involved. We also provide controlled mixed reality evaluation scenarios where 3D human models are animated using motion capture and inserted using correct 3D geometry, in complex real environments, viewed with moving cameras, and under occlusion. Finally, we provide a set of large-scale statistical models and detailed evaluation baselines for the dataset illustrating its diversity and the scope for improvement by future work in the research community. Our experiments show that our best large-scale model can leverage our full training set to obtain a 20% improvement in performance compared to a training set of the scale of the largest existing public dataset for this problem. Yet the potential for improvement by leveraging higher capacity, more complex models with our large dataset, is substantially vaster and should stimulate future research. The dataset together with code for the associated large-scale learning models, features, visualization tools, as well as the evaluation server, is available online at http://vision.imar.ro/human3.6m.
Inhibition of Binding of Clostridium difficile Toxin by Steroids (1980)

No detectable inhibition of binding of Clostridium difficile toxin to human erythrocyte lysate was found with alpha-D-(+)-fucose, 1-(-)-fucose, ribose, arabinose, mannose, galactose, xylose, galactosamine, glucosamine, mannosamine, N-acetyl glucosamine, N-acetyl galactosamine, N-acetyl mannosamine, N-acetyl neuraminic acid, lactose, sucrose, lactulose, neuraminidase, saponin, or amantadine. Inhibition was found, however, with a number of sterols and bile acids. In general, bile acids were more active than cholesterol and related compounds. When the bile salts were added greater than or equal to 10 min after exposure to toxin, inhibition was no longer observed. These results suggest that the membrane receptor for C. difficile toxin is not likely to be a carbohydrate component. On the other hand, the inhibitory activity by steroids suggests that a lipid component may play an important role in toxin binding.
The pathophysiologic role of alpha 4 integrins in vivo. (1994)

phoid organs, or resident in other tissues ( 1). Also it is found on eosinophils, basophils (9), and various nonhematopoietic tumor cells (e.g., rhabdomyosarcoma, melanoma).
An IkappaB homolog encoded by African swine fever virus provides a novel mechanism for downregulation of proinflammatory cytokine responses in host macrophages (1996)

Cytokines stimulate inflammatory defenses against viral infections. In order to evade host defenses, viruses have developed strategies to counteract antiviral cytokines. African swine fever virus (ASFV) is a large, double-stranded DNA virus that infects macrophages. This study demonstrates that ASFV effectively inhibited phorbol myristic acid-induced synthesis of antiviral, proinflammatory cytokines alpha interferon, tumor necrosis factor alpha, and interleukin-8 in infected macrophages as assessed by enzyme-linked immunosorbent assay and reverse transcriptase PCR. In contrast, levels of mRNA and protein for transforming growth factor beta, an anti-inflammatory cytokine, were increased by ASFV infection, suggesting that ASFV-induced inhibition of cytokine synthesis may be limited to cytokines activated by NFkappaB. An interleukin-8 promoter, containing an NFkappaB enhancer site, driving expression of a luciferase reporter gene was used to show that NFkappaB-dependent transcription was inhibited by the virus and by a cloned ASFV gene, A238L. This gene encodes a protein with homology to IkappaB, the inhibitor of NFkappaB. Electrophoretic mobility shift assay showed that cells expressing the A238L gene inhibited NFkappaB binding to DNA. These results suggest that the A238L gene product interacts with NFkappaB to prevent transcription and downregulate proinflammatory cytokine production. This novel viral evasion strategy encoded in a single IkappaB-like protein may be capable of inhibiting most macrophage NFkappaB-dependent antiviral mechanisms and may provide insights into how ASFV causes a fatal hemorrhagic disease of domestic pigs and a persistent infection in the African warthog, which is its natural permissive host.
Raman imaging on high‐quality graphene grown by hot‐filament chemical vapor deposition (2012)

We report the synthesis of high‐quality graphene on Cu foils using hot‐filament chemical vapor deposition technique and demonstrate that by suitably varying the CH 4 and H 2 flow rates, one can also obtain hydrogenated graphene. Micro‐Raman spectroscopy studies confirm the growth of monolayer graphene as inferred from the intensity ratio of 2D to G peak which is nearly four in unhydrogenated samples. Detailed Raman area mapping confirms the uniform coverage of monolayer graphene. The grown layer is also transferred onto a Si substrate over ~10 × 10 mm sq. area. The present results provide a leap in synthesis technology of high‐quality graphene and pave way for scaling up the process. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Immunotherapy for colorectal cancer (2013)

The incidence of colorectal cancer (CRC) is on the rise, and the prognosis for patients with recurrent or metastatic disease is extremely poor. Although chemotherapy and radiation therapy can improve survival rates, it is imperative to integrate alternative strategies such as immunotherapy to improve outcomes for patients with advanced CRC. In this review, we will discuss the effect of immunotherapy for inducing cytotoxic T lymphocytes and the major immunotherapeutic approaches for CRC that are currently in clinical trials, including peptide vaccines, dendritic cell-based cancer vaccines, whole tumor cell vaccines, viral vector-based cancer vaccines, adoptive cell transfer therapy, antibody-based cancer immunotherapy, and cytokine therapy. The possibility of combination therapies will also be discussed along with the challenges presented by tumor escape mechanisms.
Factors associated with unknown aetiology in patients with community-acquired pneumonia (2002)

Despite comprehensive diagnostic work-up, the aetiology of community-acquired pneumonia (CAP) remains undetermined in 30-60% of cases. The authors studied factors associated with undiagnosed pneumonia. Patients hospitalised with CAP and being evaluated by two blood cultures, at least one valid lower respiratory tract sample, and serology on admission were prospectively recorded. Patients who had received antimicrobial pretreatment were excluded. Patients with definite or probable aetiology were compared to those with undetermined aetiology by uni- and multivariable analysis. A total 204 patients were eligible for the study. The aetiology remained undetermined in 82 (40%) patients, whereas a definite aetiology could be established in 89 (44%) and a probable one in 33 (16%). In multivariable analysis, factors associated with undetermined aetiology included age >70 yrs, renal and cardiac comorbidity, and nonalveolar infiltrates on the chest radiograph. There was no association of undiagnosed pneumonia with mortality. Age and host factors were associated with unknown aetiology of community-acquired pneumonia. Some of these cases may also represent fluid volume overload mimicking pneumonia.
Allergenic Oxidation Products (1999)

animal assay for use in the investigation of surfactants (paper TT) . . . . . . . . .