gebhart/patrepeval huggingface dataset:
ICOS Costimulation Requires IL-2 and Can Be Prevented by CTLA-4 Engagement (2001)

We investigated the relationship between ICOS, CD28, CTLA-4, and IL-2 to gain a better understanding of this family of costimulatory receptors in the immune response. Using magnetic beads coated with anti-CD3 and varying amounts of anti-ICOS and anti-CTLA-4 Abs, we show that CTLA-4 ligation blocks ICOS costimulation. In addition to inhibiting cellular proliferation, CTLA-4 engagement prevented ICOS-costimulated T cells from producing IL-4, IL-10, and IL-13. Both an indirect and direct mechanism of CTLA-4's actions were examined. First, CTLA-4 engagement on resting cells was found to indirectly block ICOS costimulation by interferring with the signals needed to induce ICOS cell surface expression. Second, on preactivated cells that had high levels of ICOS expression, CTLA-4 ligation blocked the ICOS-mediated induction of IL-4, IL-10, and IL-13, suggesting an interference with downstream signaling pathways. The addition of IL-2 not only overcame both mechanisms, but also greatly augmented the level of cellular activation suggesting synergy between ICOS and IL-2 signaling. This cooperation between ICOS and IL-2 signaling was explored further by showing that the minimum level of IL-2 produced by ICOS costimulation was required for T cell proliferation. Finally, exogenous IL-2 was required for sustained growth of ICOS-costimulated T cells. These results indicate that stringent control of ICOS costimulation is maintained initially by CTLA-4 engagement and later by a requirement for exogenous IL-2.
Stage-Specific Excitation of Cannabinoid Receptor Exhibits Differential Effects on Mouse Embryonic Development1 (1999)

Anandamide (N-arachidonoylethanolamine), an arachidonic acid derivative, is an endogenous ligand for both the brain-type (CB1-R) and spleen-type (CB2-R) cannabinoid receptors. We have previously demonstrated that preimplantation mouse embryos express mRNA for these receptors and that the periimplantation uterus contains the highest level of anandamide yet discovered in a mammalian tissue. We further demonstrated that 2-cell mouse embryos exposed to low levels of anandamide (7 nM) or other known cannabinoid agonists in culture exhibit markedly compromised embryonic development to blastocysts and that this effect is mediated by CB1-R. In contrast, the present study demonstrates that blastocysts exposed in culture to the same low levels of cannabinoid agonists exhibited accelerated trophoblast differentiation with respect to fibronectin-binding activity and trophoblast outgrowth. Again, these effects resulted from activation of embryonic CB1-R. There was a differential concentration-dependent effect of cannabinoids on the trophoblast, with an observed inhibition of differentiation at higher doses. These results provide evidence for the first time that cannabinoid effects are differentially executed depending on the embryonic stage and cannabinoid levels in the environment. Since uterine anandamide levels are lowest at the sites of implantation and highest at the interimplantation sites, the new findings imply that site-specific levels of anandamide and/or other endogenous ligands in the uterus may regulate implantation spatially by promoting trophoblast differentiation at the sites of blastocyst implantation.
Video Display Processor (1981)

The Video Display Processor (VDP)*, a single chip video display system, is presented in this paper. The VDP provides high resolution color pattern graphics in combination with object oriented graphics, for display on an ordinary television receiver or simple monitor.
TCCluster: A Cluster Architecture Utilizing the Processor Host Interface as a Network Interconnect (2010)

So far, large computing clusters consisting of several thousand machines have been constructed by connecting nodes together using interconnect technologies as e.g. Ethernet, Infiniband or Myrinet. We propose an entirely new architecture called Tightly Coupled Cluster (TCCluster) that instead uses the native host interface of the processors as a direct network interconnect. This approach offers higher bandwidth and much lower communication latencies than the traditional approaches by virtually integrating the network interface adapter into the processor. Our technique neither applies any modifications to the processor nor requires any additional hardware. Instead, we use commodity off the shelf AMD processors and exploit the HyperTransport host interface as a cluster interconnect. Our approach is purely software based and does not require any additional hardware nor modifications to the existing processors. In this paper, we explain the addressing of nodes in such a cluster, the routing within such a system and the programming model that can be applied. We present a detailed description of the tasks that need to be addressed and provide a proof of concept implementation. For the evaluation of our technique a two node TCCluster prototype is presented. Therefore, the BIOS firmware, a custom Linux kernel and a small message library has been developed. We present microbenchmarks that show a sustained bandwidth of up to 2500 MB/s for messages as small as 64 Byte and a communication latency of 227 ns between two nodes outperforming other high performance networks by an order of magnitude.
Inhibition of T1/St2 during Respiratory Syncytial Virus Infection Prevents T Helper Cell Type 2 (Th2)- but Not Th1-Driven Immunopathology (2001)

T cells secreting interleukin (IL)-4 and IL-5 (T helper cell type 2 [Th2] cells) play a detrimental role in a variety of diseases, but specific methods of regulating their activity remain elusive. T1/ST2 is a surface ligand of the IL-1 receptor family, expressed on Th2- but not on interferon (IFN)-gamma-producing Th1 cells. Prior exposure of BALB/c mice to the attachment (G) or fusion (F) protein of respiratory syncytial virus (RSV) increases illness severity during intranasal RSV challenge, due to Th2-driven lung eosinophilia and exuberant Th1-driven pulmonary infiltration, respectively. We used these polar models of viral illness to study the recruitment of T1/ST2 cells to the lung and to test the effects of anti-T1/ST2 treatment in vivo. T1/ST2 was present on a subset of CD4(+) cells from mice with eosinophilic lung disease. Monoclonal anti-T1/ST2 treatment reduced lung inflammation and the severity of illness in mice with Th2 (but not Th1) immunopathology. These results show that inhibition of T1/ST2 has a specific effect on virally induced Th2 responses and suggests that therapy targeted at this receptor might be of value in treating Th2-driven illness.
A silicon mems micro power generator for wearable micro devices (2007)

Abstract In this paper, a prototype vibration‐induced micro power generator is fabricated and tested to investigate the feasibility of a wearable silicon micro power source. This prototype device consists of an energy‐collecting electroplated copper coil of 0.1 mm thickness, a nickel‐iron alloy (NiFe) suspension spring and a commercially available neodymium iron boron (NdFeB) magnet of dimension 2 mm ×2 mm ×1 mm. The overall size of the micro power generator is 6 mm ×6 mm ×1mm. The average generated power is 0.32 uW when the device is tapped gently with fingers. This tapping mimics the vibration when the device is worn on a person, and demonstrates power generation feasibility by general human activity. Average power of 1.44uW was measured when the device was placed on a vibration bed excited with a sinusoidal signal of 50 μm amplitude. Key words: micro powermicro generatorvibrationMEMS Notes Corresponding author. (Email: d869001@oz.nthu.edu.tw)
Optimization of photomixers and antennas for continuous-wave terahertz emission (2005)

We have studied terahertz emission from interdigitated finger photomixers coupled to planar antenna structures. Using both pulsed and continuous-wave excitation, polarization measurements reveal that the antenna design dominates the properties of the radiated output at frequencies below 0.6 THz, while the efficiency at higher frequencies is additionally dependent on the design of the photomixer fingers. We have produced terahertz maps of the device, characterizing the photomixer by measuring the generated power as a function of the excitation position. Together, these measurements have allowed us to understand better the distinct roles of the photomixer and antenna in emission at different frequencies and, hence, independently optimize these components.
Isolation of Polymer-Degrading Bacteria and Characterization of the Hindgut Bacterial Community from the Detritus-Feeding Larvae of Tipula abdominalis (Diptera: Tipulidae) (2007)

The Tipula abdominalis larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.
Inactivation of viral agents in bovine serum by gamma irradiation (1990)

Cell culture origin or suckling mouse brain origin viruses of Akabane disease, Aino, bovine ephemeral fever, swine vesicular disease, hog cholera, bluetongue, and minute virus of mice were each suspended in bovine serum. Aliquots (1 mL) were exposed to various doses of gamma radiation from a 60Co source while at -68 degrees C. Aliquots (100-mL) of serum from a steer experimentally infected with foot-and-mouth disease virus were similarly irradiated. The samples were assayed for infectivity in cell culture systems before and after irradiation, and the data points were analyzed by linear regression. The irradiation doses (in megarads) necessary to inactivate one log10 of viral infectivity (D10) was calculated for each virus. D10 is otherwise known as the slope of the regression line. The r2 value, a measure of association with 1.0 = perfect fit, was also calculated for each regression line. The values (D10, r2) for each virus were as follows: Akabane, 0.25, 0.998; Aino, 0.35, 0.997; bovine ephemeral fever, 0.29, 0.961; swine vesicular disease, 0.50, 0.969; foot-and-mouth disease, 0.53, 0.978; hog cholera, 0.55, 0.974; bluetongue, 0.83, 0.958; and minute virus of mice, 1.07, 0.935.
Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors (2017)

Acquired resistance to BRAF<sup>V600E</sup> inhibitors (BRAFi) in melanoma remains a common clinical obstacle, as is the case for any targeted drug therapy that can be developed given the plastic nature of cancers. Although there has been significant focus on the cancer cell-intrinsic properties of BRAFi resistance, the impact of BRAFi resistance on host immunity has not been explored. Here we provide preclinical evidence that resistance to BRAFi in an autochthonous mouse model of melanoma is associated with restoration of myeloid-derived suppressor cells (MDSC) in the tumor microenvironment, initially reduced by BRAFi treatment. In contrast to restoration of MDSCs, levels of T regulatory cells remained reduced in BRAFi-resistant tumors. Accordingly, tumor gene expression signatures specific for myeloid cell chemotaxis and homeostasis reappeared in BRAFi-resistant tumors. Notably, MDSC restoration relied upon MAPK pathway reactivation and downstream production of the myeloid attractant CCL2 in BRAFi-resistant melanoma cells. Strikingly, although combination checkpoint blockade (anti-CTLA-4 + anti-PD-1) was ineffective against BRAFi-resistant melanomas, the addition of MDSC depletion/blockade (anti-Gr-1 + CCR2 antagonist) prevented outgrowth of BRAFi-resistant tumors. Our results illustrate how extrinsic pathways of immunosuppression elaborated by melanoma cells dominate the tumor microenvironment and highlight the need to target extrinsic as well as intrinsic mechanisms of drug resistance. <i>Cancer Res; 77(7); 1599-610. ©2017 AACR</i>.
Use of Electrochemical DNA Biosensors for Rapid Molecular Identification of Uropathogens in Clinical Urine Specimens (2006)

We describe the first species-specific detection of bacterial pathogens in human clinical fluid samples using a microfabricated electrochemical sensor array. Each of the 16 sensors in the array consisted of three single-layer gold electrodes-working, reference, and auxiliary. Each of the working electrodes contained one representative from a library of capture probes, each specific for a clinically relevant bacterial urinary pathogen. The library included probes for Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Enterocococcus spp., and the Klebsiella-Enterobacter group. A bacterial 16S rRNA target derived from single-step bacterial lysis was hybridized both to the biotin-modified capture probe on the sensor surface and to a second, fluorescein-modified detector probe. Detection of the target-probe hybrids was achieved through binding of a horseradish peroxidase (HRP)-conjugated anti-fluorescein antibody to the detector probe. Amperometric measurement of the catalyzed HRP reaction was obtained at a fixed potential of -200 mV between the working and reference electrodes. Species-specific detection of as few as 2,600 uropathogenic bacteria in culture, inoculated urine, and clinical urine samples was achieved within 45 min from the beginning of sample processing. In a feasibility study of this amperometric detection system using blinded clinical urine specimens, the sensor array had 100% sensitivity for direct detection of gram-negative bacteria without nucleic acid purification or amplification. Identification was demonstrated for 98% of gram-negative bacteria for which species-specific probes were available. When combined with a microfluidics-based sample preparation module, the integrated system could serve as a point-of-care device for rapid diagnosis of urinary tract infections.
Application of dual affinity retargeting molecules to achieve optimal redirected T-cell killing of B-cell lymphoma (2011)

We describe the application of a novel, bispecific antibody platform termed dual affinity retargeting (DART) to eradicate B-cell lymphoma through coengagement of the B cell-specific antigen CD19 and the TCR/CD3 complex on effector T cells. Comparison with a single-chain, bispecific antibody bearing identical CD19 and CD3 antibody Fv sequences revealed DART molecules to be more potent in directing B-cell lysis. The enhanced activity with the CD19xCD3 DART molecules was observed on all CD19-expressing target B cells evaluated using resting and prestimulated human PBMCs or purified effector T-cell populations. Characterization of a CD19xTCR bispecific DART molecule revealed equivalent potency with the CD19xCD3 DART molecule, demonstrating flexibility of the DART structure to support T-cell/B-cell associations for redirected T cell-killing applications. The enhanced level of killing mediated by DART molecules was not accompanied by any increase in nonspecific T-cell activation or lysis of CD19(-) cells. Cell-association studies indicated that the DART architecture is well suited for maintaining cell-to-cell contact, apparently contributing to the high level of target cell killing. Finally, the ability of the CD19xTCR DART to inhibit B-cell lymphoma in NOD/SCID mice when coadministered with human PBMCs supports further evaluation of DART molecules for the treatment of B-cell malignancies.
Analysis of signal transducer and activator of transcription 3 (STAT3) in gastrointestinal stromal tumors. (2003)

Several signaling pathways have been recognized in normal c-kit-mediated signal transduction following stem cell factor (SCF) stimulation including Janus kinase (JAK)/signal transducer and activator of transcription (STAT), mitogen-activated protein kinase (MAPK) and phosphoinositol 3-kinase (PI-3 K) pathways. In gastrointestinal stromal tumor (GIST), c-kit activation is considered to play a central role in its tumorigenesis. However, the signal transduction cascades specific for the SCF-independent c-kit activation in GIST remains to be elucidated. In this study, we examined for the expression of the activated form of STAT3 [phospho-STAT3 (tyr 705)] in eleven cases of GIST by immunohistochemistry. All GISTs had strong nuclear and variable cytoplasmic expression of phospho-STAT3 (tyr 705). Survival and proliferation of two established primary GIST cell lines with c-kit exon-11 mutations were then assessed for their response to inhibitors of c-kit (STI-571), JAK 2 (Tyrphostin AG490), MAPK kinase (PD98059) and PI-3 K(LY294002). GIST cells showed significant inhibition of proliferation and apoptosis when treated with STI571 or AG490 but not in cells treated with PD98059 or LY294002. Bcl-2 was expressed in all of the GIST cases (11 out of 11) and was down-regulated in the primary GIST cells following treatment with AG490. This study demonstrates that STAT3 is constitutively activated in GIST and JAK2 blockade leads to tumor growth inhibition and apoptosis indicating the involvement of the JAK/STAT signaling pathway in GIST cellular survival.
Abstract 3422: Asymmetric Division of Human Cardiac Progenitor Cells Involves Immortal DNA Strand Cosegregation (2008)

The objective of this study was to determine whether asymmetric division of human cardiac progenitor cells (hCPCs) occurs by: random DNA template segregation; selective retention of the old template DNA strand; or a combination of both processes. Myocardial samples were enzymatically dissociated and hCPCs were sorted for the stem cell antigen c-kit. During in vitro expansion, hCPCs were exposed to BrdU for 36 hours to reach a 90% degree of labeling. BrdU-tagged hCPCs were plated at limiting dilution to obtain single cell-derived clones. Sixty clones comprising 10 –125 c-kit-positive hCPCs developed in 7–10 days. In four cases, one single BrdU-bright hCPC was identified while the remaining clonogenic cells were negative for the halogenated nucleotide. In these clones, the number of BrdU-negative hCPCs was 25, 85, 95, and 111. Conversely, in 56 clones hCPCs were uniformly labeled and showed very low levels of BrdU. In a second group of experiments, hCPCs in late-anaphase initial-telophase were identified and the distribution of BrdU in the two clusters of chromosomes was analyzed. In 5% of mitotic cells, three-dimensional reconstruction by confocal microscopy documented that BrdU-labeling was restricted at one pole only of the dividing hCPCs. PCNA which is highly expressed in newly synthesized DNA was restricted to the BrdU-negative chromosomes. In a third set of studies, hCPCs were loaded with quantum dots, cultured for 36 hours in the presence of BrdU and examined 96 hours later. Quantum dots are progressively diluted by cell division independently from the modality of DNA template segregation. Thus, hCPCs with minimal levels of quantum dots and bright BrdU localization were interpreted as replicating cells which retained the old DNA strand. By this approach, 5% hCPCs displayed these two critical properties. The uneven distribution of the cell fate determinants Numb and α-adaptin confirmed that hCPCs underwent asymmetric division. In conclusion, these data support the hypothesis that immortal DNA strand cosegregation participates in asymmetric kinetics of hCPCs although random-segregation of DNA template is the prevailing mechanism of hCPC growth.
Cytotoxic Agents in the Era of Molecular Targets and Genomics (2002)

Cancer treatment is evolving due to the development of molecularly targeted agents and the utilization of pharmacogenomics and pharmacogenetics to identify patients who are at an increased risk for toxicity or may be uniquely responsive to cytotoxic therapies. By identifying polymorphisms in the human genome that confer changes in the ability to metabolize or activate cancer agents, a more patient-specific treatment approach can be initiated. Molecularly targeted therapies such as PS-341, flavopiridol, Iressa, and anti-vascular endothelial growth factor antibodies may help to overcome resistance to cytotoxic therapies by lowering the apoptotic threshold and increasing cytotoxicity. Using molecularly targeted agents in combination with traditional cytotoxic agents may increase the percentage of patients who achieve disease stabilization and prolonged survival. With the development of genetic tools and genotyping of tumor and patient prior to initiating treatment, antitumor efficacy may be increased with a substantial reduction in toxicity.
Incidence and Predictors of Left Atrial Thrombus Prior to Catheter Ablation of Atrial Fibrillation (2008)

Despite oral anticoagulation treatment, there is a small but significant incidence of LA thrombus by TEE prior to AF ablation. A CHADS(2) score >or= 2 and larger LA diameter are independent predictors of LA thrombus in this patient population, while type of AF or rhythm at the time of TEE is not. The risk of LA thrombus is low in patients with a CHADS(2) score of 0 and in patients with an LA diameter < 4.5 cm.
Abrogation of Transforming Growth Factor-β Signaling by SMAD7 Inhibits Collagen Gel Contraction of Human Dermal Fibroblasts (2005)

Human fibroproliferative disorders like hypertrophic scarring of the skin are characterized by increased contractility and excess extracellular matrix synthesis. A beneficial role of transforming growth factor (TGF)-beta in wound healing was proposed; however, chronic stimulation by this cytokine leads to fibrosis. In the present report, the intracellular TGF-beta signaling in fibroblasts derived from hypertrophic scars and normal skin was examined. In an attempt to intervene in profibrogenic TGF-beta functions, ectopic expression of Smad7 or dominant negative Smads3/4 completely inhibited contractility of scar-derived and normal fibroblasts after suspension in collagen gels. Both cell types displayed constitutive Smad2/3 phosphorylation and (CAGA)9-MLP-Luc activity with expression and phosphorylation of Smad3 being predominant in hypertrophic scar-derived fibroblasts. Down-regulation of intrinsic signaling with various TGF-beta antagonists, e.g. soluble TGF-beta receptor, latency-associated peptide, and anti-TGF-beta1 antibodies, confirms autocrine TGF-beta stimulation of both cell populations. Further, Smad7 expression inhibited alpha1 (I) collagen and alpha-smooth muscle actin expression. In summary, our data indicate that autocrine TGF-beta/Smad signaling is involved in contractility and matrix gene expression of fibroblasts from normal and hypertrophic scars. Smad7 inhibits these processes and may exert beneficial effects on excessive scar formation.