gebhart/patrepeval huggingface dataset:
Requirement for Transcription Factor NFAT in Interleukin-2 Expression (1999)

The nuclear factor of activated T cells (NFAT) transcription factor is implicated in expression of the cytokine interleukin-2 (IL-2). Binding sites for NFAT are located in the IL-2 promoter. Furthermore, pharmacological studies demonstrate that the drug cyclosporin A inhibits both NFAT activation and IL-2 expression. However, targeted disruption of the NFAT1 and NFAT2 genes in mice does not cause decreased IL-2 secretion. The role of NFAT in IL-2 gene expression is therefore unclear. Here we report the construction of a dominant-negative NFAT mutant (dnNFAT) that selectively inhibits NFAT-mediated gene expression. The inhibitory effect of dnNFAT is mediated by suppression of activation-induced nuclear translocation of NFAT. Expression of dnNFAT in cultured T cells caused inhibition of IL-2 promoter activity and decreased expression of IL-2 protein. Similarly, expression of dnNFAT in transgenic mice also caused decreased IL-2 gene expression. These data demonstrate that NFAT is a critical component of the signaling pathway that regulates IL-2 expression.
An antigen shared by a human T cell subset and B cell chronic lymphocytic leukemic cells. Distribution on normal and malignant lymphoid cells. (1980)

We obtained a monoclonal antibody, A50, after immunizing Biozzi's high responder strain of mice with T cell chronic lymphocytic leukemia (T-CLL) cells. A50 recognized an antigen present on the surface of B cell chronic lymphocytic leukemia cells from many patients and from cells of T lineage from any subject we tested. We could not find this antigen either on the surface of normal B cell or on other non-T cell malignancies. On T cells, this antigen was present on a subpopulation of thymus cells, and on most peripheral T cells. The antigen was present on the surface of cells from T-CLL, Sézary's disease, and a subset o T cell lymphoma. The antigen seemed to belong to a complex set of antigenic determinants that we had defined with rabbit antisera.
Bacterial vaginosis: an update on diagnosis and treatment (2009)

Bacterial vaginosis is the most common cause of vaginal complaints. Bacterial vaginosis is further associated with a sizeable burden of infectious complications. Diagnosis relies on standardized clinical criteria or on scoring bacterial cell morphotypes on a Gram-stained vaginal smear. A few point-of-care tests have not gained footage in clinical practice, but molecular diagnosis is now pending. Treatment remains cumbersome and clinicians are currently rather poorly armed to treat bacterial vaginosis in the long run. As an adjuvant to standard treatment with antibiotics, alternative treatments with antiseptics and disinfectants, vaginal-acidifying and -buffering agents, and probiotics hold some promise for long-term prevention.
Nonspecific oral immunity in individuals with HIV infection. (1992)

Lactoferrin, lysozyme, interferon, and neopterin levels were determined in parotid saliva from 44 individuals with different clinical stages of human immunodeficiency virus (HIV) infection and 19 HIV-seronegative controls. The secretory output of individual components was calculated according to the fluid flow rate. No parotid interferon activity was found in any of the HIV-infected subjects or controls, and no significant differences in parotid lysozyme or neopterin outputs were observed. The lactoferrin output was significantly decreased in HIV-seropositive subjects in parallel with their markedly reduced parotid secretory IgA output. This combined deficiency of parotid lactoferrin and secretory IgA may well contribute to the frequent oral infections seen in subjects with HIV infection.
Detection of soft-tissue infections and osteomyelitis using a technetium-99m-labeled anti-granulocyte monoclonal antibody fragment. (1994)

Immunoscintigraphy with 99mTc-NCA-90 Fab' fragments offers rapid localization of foci, rapid and simple use, a negligible HAMA response rate, no effect on granulocyte function and an accuracy comparable to WBC scanning.
Biological effects of dynamic shear stress in cardiovascular pathologies and devices (2008)

Altered and highly dynamic shear stress conditions have been implicated in endothelial dysfunction leading to cardiovascular disease, and in thromboembolic complications in prosthetic cardiovascular devices. In addition to vascular damage, the pathological flow patterns characterizing cardiovascular pathologies and blood flow in prosthetic devices induce shear activation and damage to blood constituents. Investigation of the specific and accentuated effects of such flow-induced perturbations on individual cell-types in vitro is critical for the optimization of device design, whereby specific design modifications can be made to minimize such perturbations. Such effects are also critical in understanding the development of cardiovascular disease. This review addresses limitations to replicate such dynamic flow conditions in vitro and also introduces the idea of modified in vitro devices, one of which is developed in the authors' laboratory, with dynamic capabilities to investigate the aforementioned effects in greater detail.
Carbon nanotube electronics: recent advances (2014)

Carbon nanotubes (CNTs) are quasi-one-dimensional materials with unique properties and are ideal materials for applications in electronic devices. Significant progress has been made on CNT electronics, and a doping-free approach has emerged from this research. This approach utilizes the contact control on the properties of field-effect transistors (FETs), preserving the perfect lattice of the CNT making it possible for CNT FETs to outperform state-of-the-art Si devices. Both n-type and p-type CNT FETs with near ballistic performance limits have been fabricated, symmetric CMOS devices have been demonstrated, and pass-transistor-logic, a circuit configuration that is more efficient than CMOS is being explored.
Seamless rate adaptation for wireless networking (2011)

This paper aims at designing a Seamless Rate Adaptation for wireless networking which achieves smooth rate adjustment in a broad dynamic range of channel conditions. Conventional rate adaptation can only achieve a stair-case rate adjustment. Even when combining with hybrid ARQ, it suffers from an irreconcilable conflict between throughput and dynamic range. We tackle this problem from a new perspective by relying on modulation, instead of channel coding, for rate adaptation. We propose rate compatible modulation (RCM), in which modulation signals are incrementally generated from information bits through weighted mapping. Rate adaptation is achieved through varying the number of modulated signals. As more signals are transmitted, information bits gradually accumulate energy. The weights in bit-to-symbol mapping are delicately designed to ensure fine-grained energy accumulation so that smoothness and efficiency can both be achieved. We design and implement a rate adaptation system, called SRA and evaluate its performance through a software radio testbed. Results show that, under highly dynamic channel conditions, SRA achieves over 80% throughput gain over 802.11a adaptive modulation and coding, and achieves 28.8% and 43.8% gain over HARQ systems implemented with Turbo code and Raptor code. We believe that the concept of rate compatible modulation opens up a fresh research avenue toward the wireless rate adaptation problem.
Cytokine profiling of prostatic fluid from cancerous prostate glands identifies cytokines associated with extent of tumor and inflammation (2008)

Prostatic fluid cytokines were identified that may be useful for early cancer detection and prognostication efforts and for assessment of prostatic inflammation, particularly if they can be found not only in prostatic fluids obtained ex vivo, but in expressed prostatic secretions or urine samples from men with prostates still in situ.
Beta-glucosidase of Trichoderma: its biosynthesis and role in saccharification of cellulose (1976)

The extracellular beta-glucosidase of Trichoderma viride generally is present in low levels when the organism is cultured on cellulose because it is inactivated under the acid conditions which develop in the medium while the other enzymes of the cellulase complex are more stable. With the appropriate pH control, inactivation of beta-glucosidase is prevented and the activity of this enzyme increases during growth. In the saccharification of crystalline cellulose, or of cellulose at low concentrations, much of the glucose produced is the result of the cleavage of cellobiose by beta-glucosidase. However when high concentrations (10%) of pretreated cellulose are saccharified, significant quantities of glucose are produced by action of enzymes other than beta-glucosidase.
Bursty Tracing: A Framework for Low-Overhead Temporal Profiling (2001)

With processor speed increasing much more rapidly than memory access speed, memory system optimizations have the potential to significantly improve program performance. Unfortunately, cache-level optimizations often require detailed temporal information about a program&amp;apos;s references to be effective. Traditional techniques for obtaining this information are too expensive to be practical in an on-line setting. We address this problem by describing and evaluating a framework for low-overhead temporal profiling. Our framework extends the Arnold-Ryder framework that uses instrumentation and counter-based sampling to collect frequency profiles with low overhead. Our framework samples bursts (sub-sequences) of the trace of all runtime events to construct a temporal program profile. Our bursty tracing profiler is built using Vulcan, an executable-editing tool for x86, and we evaluate it on optimized x86 binaries. Like the Arnold-Ryder framework, we have the advantages of not requiring operating system or hardware support and being deterministic. Unlike them, we are not limited to capturing temporal relationships on intraprocedural acyclic paths since our trace bursts can span procedure boundaries. In addition, our framework does not require access to program source or recompilation. A direct implementation of our extensions to the Arnold-Ryder framework results in profiling overhead of 6-35%. We describe techniques that reduce this overhead to 3-18%, making it suitable for use in an on-line setting.
Design of Potent and Selective Inhibitors to Overcome Clinical Anaplastic Lymphoma Kinase Mutations Resistant to Crizotinib (2014)

Crizotinib (1), an anaplastic lymphoma kinase (ALK) receptor tyrosine kinase inhibitor approved by the U.S. Food and Drug Administration in 2011, is efficacious in ALK and ROS positive patients. Under pressure of crizotinib treatment, point mutations arise in the kinase domain of ALK, resulting in resistance and progressive disease. The successful application of both structure-based and lipophilic-efficiency-focused drug design resulted in aminopyridine 8e, which was potent across a broad panel of engineered ALK mutant cell lines and showed suitable preclinical pharmacokinetics and robust tumor growth inhibition in a crizotinib-resistant cell line (H3122-L1196M).
Antigen Processing for Presentation to T Lymphocytes: Function, Mechanisms, and Implications for the T‐Cell Repertoire (1988)

Antigen processing encompasses the metabolic events that a protein antigen must undergo in or on the antigen-presenting cell before it can be recognized by the T lymphocyte. It appears that a primary goal of these events is to unfold the protein to expose residues that are buried in the native conformation, which is designed to be soluble in water. The APC usually accomplishes this task by proteolytic cleavage of the protein, but we have found that artificial unfolding without proteolysis is sufficient. The purpose of unfolding may be to allow different faces of the antigenic site to bind simultaneously to the T-cell receptor and the MHC molecule on the APC, or to interact with other structures on the membrane of the APC. This requirement for unfolding appears to apply to everything from small peptides to large multimeric proteins. We have found that the way the antigen is processed and the structure of the fragments produced can greatly affect the availability of antigenic sites. For instance, some antigenic sites are not recognized when the native protein is used as immunogen, despite the fact that immunization with a small peptide corresponding to that site reveals both the ability of the site to bind to MHC molecules of the animal in question and the presence of a T-cell repertoire specific for that site. The antigenic site is not destroyed by processing, since it can be presented by the same F1 APC to T cells of another MHC type. Similarly, cross-reactivity between homologous epitopes of related proteins may occur at the peptide level even though the native proteins do not crossreact for the same T-cell clone. Since these events occur with monoclonal T cells, they cannot be due to suppressor cells specific for other sites on the native molecule. The best explanation is that the products of natural processing of the protein are larger than the peptides corresponding to the minimal antigenic sites, and contain hindering structures that interfere with binding to some MHC molecules and not others, or to some T-cell receptors and not others. Thus, antigen processing is a third factor that can lead to apparent Ir gene defects - in addition to MHC specificity and holes in the T-cell repertoire - and can significantly influence which antigenic sites are immunodominant.(ABSTRACT TRUNCATED AT 400 WORDS)
Dipeptidyl peptidase IV: development, design, synthesis and biological evaluation of inhibitors. (1994)

Dipeptidyl peptidase IV (DPP IV, EC 3.4.14.5) is a highly specific serine protease which cleaves off N-terminal dipeptides from peptides with a penultimate proline or alanine. The enzyme is widely distributed in mammalian cells and tissues, but specific activities differ greatly. In the hematopoietic system it is found almost exclusively on T cells, where it is identified as CD26, a T cell activation molecule. DPP IV may be involved in the metabolism of peptides, intestinal assimilation and cell adhesion and it plays an integral role in T cell activation. DPP IV inhibitors may provide help during the further elucidation of the biological function(s) of this enzyme. Moreover, because of the integral role the enzyme plays in T cell activation, specific inhibition of DPP IV may constitute a new way of immune modulation. N-Peptidyl-O-acylhydroxylamines and boronic acid analogues of proline and alanine are two known DPP IV inhibitors. The major drawbacks for their therapeutic use are for the hydroxylamines, the toxicity and for the boronic acid derivatives, the chemical liability. A low toxicity, acceptable stability and a high specificity are essential criteria for the design of inhibitors that are suitable, not only for experimental, but also for therapeutic use. Therefore we proposed 5 types of potential DPP IV inhibitors: azapeptides, azetidines, Michael substrates, reduced peptides and phosphonic acids. All the synthesized compounds possess a substrate-like structure, which is a pre-requisite for recognition by the enzyme. We choose for a modified proline or alanine at the penultimate position, substituted with glycine, alanine, valine, isoleucine or phenylalanine at the N-terminus. The prepared compounds were screened biologically at a 5 mM concentration with a fluorometric method using Gly-Pro-4-Me-2NA as substrate.
A monoclonal antibody to the human leukocyte adhesion molecule intercellular adhesion molecule-2. Cellular distribution and molecular characterization of the antigen (1991)

The DNA of the human leukocyte adhesion molecule intercellular adhesion molecule-2 (ICAM-2) was synthesized by the polymerase chain reaction, and a protein A-ICAM-2 fusion protein was expressed in Escherichia coli. The fusion protein was used as immunogen to obtain mAb to ICAM-2. The 6D5 antibody was selected by its reactivity in immunofluorescence with the endothelial cell line Eahy926. The antibody precipitated a 55,000 m.w. glycoprotein from radioactivity surface labeled cells and also reacted in Western blotting. As measured by immunofluorescence flow cytometry, the antibody reacted with lymphoblastoid B cells of normal origin, some Burkitt lymphoma cell lines, vascular endothelial cells, the endothelial cell line Eahy926, 4 and a subpopulation of Con A-stimulated blood mononuclear cells. The two Ig-like domains of ICAM-2 were separately expressed in E. coli, and the antibody was shown to react with the NH2-terminal domain. The antibody inhibited the CD11/CD18-dependent binding of HL-60 promyelocytic leukemia cells to transfected COS-1 cells.
Immunohistochemistry Can Be Used to Subtype Acute Myeloid Leukemia in Routinely Processed Bone Marrow Biopsy Specimens (2000)

Flow cytometry (FC) is the preferred method of immunophenotyping acute myeloid leukemia (AML). However, there are situations in which FC is unavailable and in which immunohistologic staining of bone marrow biopsy specimens can be used to provide immunophenotypic information. To evaluate immunohistologic staining and to confirm its value, we selected 80 newly diagnosed cases of AML that were classified according to French-American-British (FAB) criteria and confirmed by flow cytometric analysis for this study. Paraffin-embedded bone marrow specimens were stained using a panel of antibodies that included CD34 (QBEND10), antimyeloperoxidase (anti-MPO), antihemoglobin, factor VIII-related antigen, and 3 epitopes of CD68 (HAM56, KP1, and PG-M1). Our findings suggest that with the use of the paraffin-reactive antibodies CD34 (QBEND10), MPO, CD68 (PG-M1), antihemoglobin, and factor VIII-related antigen, immunohistochemistry can be used to subclassify AML. Comparison of immunohistochemical results with FC immunophenotyping suggests that there is significant concordance in the results for markers that can be used with both techniques, indicating that the sensitivity and specificity of both methods is comparable (P > .53 in all cases).
Error removal in microchip-synthesized DNA using immobilized MutS (2014)

The development of economical de novo gene synthesis methods using microchip-synthesized oligonucleotides has been limited by their high error rates. In this study, a low-cost, effective and improved-throughput (up to 32 oligos per run) error-removal method using an immobilized cellulose column containing the mismatch binding protein MutS was produced to generate high-quality DNA from oligos, particularly microchip-synthesized oligonucleotides. Error-containing DNA in the initial material was specifically retained on the MutS-immobilized cellulose column (MICC), and error-depleted DNA in the eluate was collected for downstream gene assembly. Significantly, this method improved a population of synthetic enhanced green fluorescent protein (720 bp) clones from 0.93% to 83.22%, corresponding to a decrease in the error frequency of synthetic gene from 11.44/kb to 0.46/kb. In addition, a parallel multiplex MICC error-removal strategy was also evaluated in assembling 11 genes encoding ∼21 kb of DNA from 893 oligos. The error frequency was reduced by 21.59-fold (from 14.25/kb to 0.66/kb), resulting in a 24.48-fold increase in the percentage of error-free assembled fragments (from 3.23% to 79.07%). Furthermore, the standard MICC error-removal process could be completed within 1.5 h at a cost as low as $0.374 per MICC.
Evidence that a human soluble beta-galactoside-binding lectin is encoded by a family of genes. (1986)

Two cDNA clones were isolated by immunoscreening a human hepatoma cDNA library with an antiserum that bound specifically to a human soluble beta-galactoside-binding lectin with Mr of approximately 14,000. The deduced amino acid sequences of the inserts of these two clones show considerable homology with each other, the sequence of chicken skin beta-galactoside-binding lectin, and eight peptides derived from purified human lung lectin of Mr approximately 14,000. However, the sequence differences between the two hepatoma clones as well as among each clone and the lung peptides suggest that at least three variants of the gene encoding this lectin are expressed in human tissue.
A Novel Approach to Statistical Energy Analysis Model Validation (1995)

&lt;div class="htmlview paragraph"&gt;Statistical Energy Analysis (SEA) is a tool for estimating the response of complex dynamic systems at high modal density. This tool is seeing ever wider application in a range of industries, including aerospace industry, marine industry, and building trades. The automotive industry is beginning to explore the application of SEA to high frequency vehicle acoustic design. The SEA model of vibrational power transmission has a direct analogy to thermal power transmission (diffusion). As thermal power flow is proportional to temperature difference, vibrational power flow is proportional to modal energy difference. In this paper the thermal analogy is exploited to visualize the SEA results. This is accomplished by color coding a finite element representation of the structure.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In this paper, the thermal analogy is used to correlate test data with SEA model results. This is accomplished by constructing a test based modal power thermogram. The test based modal powers are calculated from a space averaged velocity and a space averaged drive point impedance. The drive point impedance is a representation of a mass normalized modal density. Dividing the mean square velocity by the averaged impedance results in an estimate of the energy divided by the modal density (modal power). This test derived quantity is then used to construct a thermogram in the same sense as the analytical results. The correlation of the test and analytical thermograms then insures that the desired response is correctly predicted and that the energy transfer path is also correct. This insures that the proper response is calculated and that the model is robust.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This procedure is applied to a D-class trimmed body for structureborne input. The structureborne response is calculated and test and analytical thermograms are shown.&lt;/div&gt;
Induction and decay of human fibroblast interferon mRNA. (1977)

Polyadenylylated interferon mRNA, obtained from induced human fibroblasts, was quantitatively assayed by synthesis of biologically active human interferon in Xenopus laevis oocytes. The assay for interferon mRNA was used to distinguish between various hypotheses relating to interferon induction and biosynthesis. The data demonstrate that on induction with poly(I-poly(C) human fibroblasts accumulate interferon mRNA for 1-1.5 hr, after which time the mRNA is rapidly degraded with a half-life (t 1/2) of 18 min. Treatment of cells with cycloheximide prolongs the period of accumulation to 3 hr and decreases the rate of mRNA inactivation (t 1/2 = 49 min). Treatment with actinomycin D decreases the rate of inactivation still further (t 1/2 = 68 min). A comparison of cellular interferon synthesis with the relative amounts of interferon m RNA after simple induction or inductionin the presence of the inhibitors (superinduction) indicated a general correlation. Thus, on induction, the genes for interferon are activated to produce a transcript for a short time. The superinducing treatments prolong the period of accumulation and decrease the rate of degradation of this transcript.