gebhart/patrepeval huggingface dataset:
Modulation of TCR-induced transcriptional profiles by ligation of CD28, ICOS, and CTLA-4 receptors (2002)

Signals generated by T cell receptor (TCR) and CD28 engagement are required for optimal T cell activation, but how these signals integrate within the cell is still largely unknown. We have used near genome-scale expression profiling to monitor T cell signal transduction pathways triggered via TCR and/or costimulatory receptors. Ligation of CD28 alone induced a set of short-lived early response transcripts in both Jurkat T cells and primary CD4 T cells, thus providing evidence that CD28 engagement can affect gene regulation independently of TCR engagement. Simultaneous signaling through both the TCR and CD28 resulted in altered expression of several thousand genes following several distinct temporal patterns. Most of these gene regulations were induced by TCR signaling alone and were augmented to varying degrees by CD28 costimulation. CD28 and ICOS costimulation had nearly identical effects on gene regulation, but a few transcripts (e.g., IL2, IL9) were significantly more affected by CD28. Therefore, the distinctive functional outcomes of costimulation via CD28 and ICOS are accompanied by relatively few distinct differences in gene expression. Cytotoxic T lymphocyte antigen 4 (CTLA-4) engagement selectively blocked augmentation of gene regulations by CD28-mediated costimulation, but did not ablate gene regulation induced by TCR triggering alone.
Introduction to Digital Audio Coding and Standards (2004)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Function of normal and mutated gamma-globin gene promoters in electroporated K562 erythroleukemia cells (1990)

We examined the importance of cis-acting regulatory elements of the human gamma-globin gene promoter in a cell line (K562) where this gene normally functions. A gamma-Globin promoter fragments were fused to the neomycin phosphotransferase (neoR) gene in a plasmid-based vector and transiently transfected by electroporation into K562 cells. Correctly initiated “A gamma-neo” transcripts were detected with an S1 nuclease protection assay that was internally controlled for transfection efficiency and RNA content. We first optimized the conditions for electroporation, and then determined input DNA concentrations that permitted study of gamma-promoter function in the linear range of the assay. We discovered that a gamma-globin promoter fragment extending from -299 to +36 (with respect to the transcription initiation site) was active in this transient transfection assay, and that the expression of this promoter was increased by the SV40 enhancer. Deletion of the gamma-globin promoter to position -199 did not significantly affect gamma-globin promoter function. However, deletion to -160 reduced gamma promoter strength to 70% that of control, deletion to position -130 to 19% that of control, and deletion to position -61 to 8.7% that of control. Three gamma-globin promoters containing mutations associated with hereditary persistence of fetal hemoglobin (-202 C----G, -196 C----T, and -117 G----A) were not overexpressed in the K562 cell environment, consistent with the hypothesis that these promoters are not overexpressed in fetal erythroblasts, only adult erythroid cells. This system will allow us to further dissect the roles of regulatory globin cis-acting DNA elements in fetal erythroid cells.
Fibroblast growth factor-23 (FGF-23) is independently correlated to aortic calcification in haemodialysis patients (2010)

In haemodialysis patients, FGF-23 and ACI were significantly increased, and FGF-23 was independently associated with aortic calcification.
Diagonal Kernel Point Estimation of"Equation missing" th-Order Discrete Volterra-Wiener Systems (2004)

The estimation of diagonal elements of a Wiener model kernel is a well-known problem. The new operators and notations proposed here aim at the implementation of efficient and accurate nonparametric algorithms for the identification of diagonal points. The formulas presented here allow a direct implementation of Wiener kernel identification up to the th order. Their efficiency is demonstrated by simulations conducted on discrete Volterra systems up to fifth order.
Molecular cloning of a candidate chicken prion protein. (1992)

Fractions enriched for acetylcholine receptor-inducing activity from chicken brain were found to contain a protein that was approximately 30% homologous with mammalian prion proteins [Harris, D. A., Falls, D. L., Johnson, F. A. & Fischbach, G. D. (1991) Proc. Natl. Acad. Sci. USA 88, 7664-7668]. To extend these observations, we recovered genomic clones encoding a putative chicken prion protein (PrP). Like mammalian PrP molecules, the candidate chicken PrP is encoded by a single-copy gene and the entire open reading frame is found within a single exon. All of the structural features of mammalian PrP were found in the chicken protein. When the N-terminal repeats of PrP were not considered, the chicken and mammalian proteins were approximately 55% homologous, allowing for conservative substitutions. Screening of a chicken genomic DNA library failed to identify a more closely related chicken PrP homologue. These findings argue that the protein which purifies with acetylcholine receptor-inducing activity is chicken PrP.
Video Stream Quality Impacts Viewer Behavior: Inferring Causality Using Quasi-Experimental Designs (2013)

The distribution of videos over the Internet is drastically transforming how media is consumed and monetized. Content providers, such as media outlets and video subscription services, would like to ensure that their videos do not fail, start up quickly, and play without interruptions. In return for their investment in video stream quality, content providers expect less viewer abandonment, more viewer engagement, and a greater fraction of repeat viewers, resulting in greater revenues. The key question for a content provider or a content delivery network (CDN) is whether and to what extent changes in video quality can cause changes in viewer behavior. Our work is the first to establish a causal relationship between video quality and viewer behavior, taking a step beyond purely correlational studies. To establish causality, we use Quasi-Experimental Designs, a novel technique adapted from the medical and social sciences. We study the impact of video stream quality on viewer behavior in a scientific data-driven manner by using extensive traces from Akamai's streaming network that include 23 million views from 6.7 million unique viewers. We show that viewers start to abandon a video if it takes more than 2 s to start up, with each incremental delay of 1 s resulting in a 5.8% increase in the abandonment rate. Furthermore, we show that a moderate amount of interruptions can decrease the average play time of a viewer by a significant amount. A viewer who experiences a rebuffer delay equal to 1% of the video duration plays 5% less of the video in comparison to a similar viewer who experienced no rebuffering. Finally, we show that a viewer who experienced failure is 2.32% less likely to revisit the same site within a week than a similar viewer who did not experience a failure.
The roles of nucleolar structure and function in the subcellular location of the HIV-1 Rev protein (1995)

The human immunodeficiency virus 1 (HIV-1) Rev transactivator protein plays a critical role in the regulation of expression of structural proteins by controlling the pathway of mRNA transport. The Rev protein is located predominantly in the nucleoli of HIV-1 infected or Rev-expressing cells. Previous studies demonstrated that the Rev protein forms a specific complex in vitro with protein B23 which is suggested to be a nucleolar receptor and/or carrier for the Rev protein. To study the role of the nucleolus and nucleolar proteins in Rev function, transfected COS-7 or transformed CMT3 cells expressing the Rev protein were examined for subcellular locations of Rev and other proteins using indirect immunofluorescence and immunoelectron microscopy. One day after transfection the Rev protein was found in most cells only in the nucleolar dense fibrillar and granular components where it colocalized with protein B23. These were designated class 1 cells. In a second class of cells Rev and B23 accumulated in the nucleoplasm as well as in nucleoli. Treatment of class 1 cells with actinomycin D (AMD) under conditions that blocked only RNA polymerase I transcription caused Rev to completely redistribute from nucleoli to the cytoplasm. Simultaneously, protein B23 was partially released from nucleoli, mostly into the nucleoplasm, with detectable amounts in the cytoplasm. In cells recovering from AMD treatment in the presence of cycloheximide Rev and B23 showed coincident relocation to nucleoli. Class 2 cells were resistant to AMD-induced Rev redistribution. Selective inhibition of RNA polymerase II transcription by alpha-amanitin or by DRB did not cause Rev to be released into the cytoplasm suggesting that active preribosomal RNA transcription is required for the nucleolar location of Rev. However, treatment with either of the latter two drugs at higher doses and for longer times caused partial disruption of nucleoli accompanied by translocation of the Rev protein to the cytoplasm. These results suggest that the nucleolar location of Rev depends on continuous preribosomal RNA transcription and a substantially intact nucleolar structure.
Ultrahigh-resolution optical coherence tomography by broadband continuum generation from a photonic crystal fiber (2003)

We have developed an ultrahigh-resolution optical coherence tomographic system in which broadband continuum generation from a photonic crystal fiber is used to produce high longitudinal resolution. Longitudinal resolution of 1.3-microm has been achieved in a biological tissue by use of continuum light from 800 to 1400 nm. The system employed a dynamic-focusing tracking method to maintain high lateral resolution over a large imaging depth. Subcellular imaging is demonstrated.
Local recurrence in head and neck cancer: relationship to radiation resistance and signal transduction. (2002)

Evaluation of PI3K activation by Akt phosphorylation might be a prognostic marker for response to therapy, and PI3K could be a useful target for therapy. These results also suggest that signaling from EGFR to PI3K can lead to radioresistance.
Alkaline Fuel Cells (2004)

Abstract Alkaline fuel cells may become an important element in pollution free energy conversion. In the literature most papers in the field of low temperature fuel cells are concerned with polymer electrolyte fuel cells. However, there are still a lot of research groups and companies working on alkaline fuel cells. The advantages and disadvantages of AFCs are presented. The main technical problems are solved. It can be concluded, due to work carried out at DLR, that carbon dioxide poisoning of electrodes from rolled DLR electrodes does not take place. These investigations demonstrate that AFCs are highly efficient cells for portable and stationary applications.
Scientific and therapeutic insights into the role of the platelet P2Y12 receptor in thrombosis (2003)

Platelets are important mediators of thrombosis in both healthy and diseased vessels. When platelets become activated by various soluble agonists or by adhesion to subendothelium under high shear, they release adenosine-5'-diphosphate that acts in a positive feedback mechanism on two different G-protein coupled receptors (P2Y(12), P2Y(1)) on platelets. This released adenosine-5'-diphosphate, acting through P2Y(12), is critical for sustained aggregation and stabilization of thrombi. P2Y(12) is the target of antithrombotic drugs (ticlopidine, clopidogrel), whereas the role of P2Y(1) in thrombosis remains to be fully established. Recent studies using either inhibitors of key components of signaling pathways or genetically engineered mice have contributed to our understanding of the signaling mechanisms in platelets mediated by adenosine-5'-diphosphate through the P2Y(12) receptor. Studies of patients with defective adenosine-5'-diphosphate mediated aggregation, as well as P2Y(12)-null mice, have revealed the importance of this receptor in mediating platelet activation and aggregation. Recent clinical trials using approved P2Y(12) blockers have extended the use of these drugs to additional patient populations. Recent data demonstrating the role of P2Y(12) in mediating platelet adhesion to thrombogenic surfaces (collagen, von Willebrand factor) provide further rationale as to the clinical efficacy of P2Y(12) blockers. P2Y(12) antagonists in combination with anticoagulants (thrombin inhibitors, factor Xa inhibitors) act synergistically in inhibiting thrombus formation (similar to aspirin) ex vivo. These findings suggest the potential for combination therapies (P2Y(12) antagonists with inhibitors of GPIIb-IIIa, thrombin or Factor Xa, etc.) to provide additional clinical benefit to patients with various cardiovascular diseases, especially those who may be aspirin-resistant.
Arthroscopic shoulder stabilization. A role for biodegradable materials. (1993)

The use of metallic implants about the shoulder joint can be complicated by loosening, migration, and breakage of the implant. Bioabsorbable implants would be an ideal solution to this problem if their bioabsorption profile could be fine tuned to appropriately share stress with the healing tissues. The development of such an implant must satisfy four basic criteria: (1) The bioabsorbable implant must have adequate initial fixation strength to coapt the soft tissues to bone; (2) The implant's bioabsorption profile must enable it to retain satisfactory strength while the healing tissues are regaining mechanical integrity; (3) The implant must not bioabsorb too slowly or it will behave like its metal counterpart with breakage and migration; and (4) The implant must be made of materials that are completely safe: no toxicity, antigenicity, pyrogenicity, or carcinogenicity.
Na+/H+ Antiporter in Tonoplast Vesicles from Rice Roots (1998)

The Na+/H + antiporter in vacuolar membranes transports Na+ from the cytoplasm to vacuoles using a pH gradient generated by proton pumps; it is considered to be related to salinity tolerance. Rice (Oryza sativa L.) is a salt-sensitive crop whose vacuolar antiporter is unknown. The vacuolar pH of rice roots, determined by 31P-nuclear magnetic resonance (NMR), increased from 5.34 to 5.58 in response to 0.1 M NaCl treatment. Transport of protons into the tonoplast vesicles from rice roots was fluorometrically measured. Efflux of protons was accelerated by the addition of Na+. Furthermore, the influx of 22Na+ into the tonoplast vesicles was accelerated by a pH gradient generated by proton-translocating adenosine 5'-triphosphatase (H+-ATPase) and proton-translocating inorganic pyro-phosphatase (H+-PPase). We concluded that this Na+/H+antiporter functioned as a Na+ transporter in the vacuolar membranes. The antiporter had a Km of 10 mM for Na+ and was competitively inhibited by amiloride and its analogues. The Ki values for 5-(N-methyl-N-isobutyl)-amiloride (MIA), 5-(N-ethyl-N-isopropyI)-amiloride (EIPA), and 5-(N, N-hexamethylene)-amiloride (HMA) were 2.2, 5.9, and 2.9 μ M, respectively. Unlike barley, a salt-tolerant crop, NaCl treatment did not activate the antiporter in rice roots. The amount of antiporter in the vacuolar membranes may be one of the most important factors determining salt tolerance.
Suppression of malignant glioma recurrence in a newly developed animal model by endogenous inhibitors. (2002)

Glioma recurrences develop at the borders of the surgical cavity and are the main cause of their poor prognosis. There are no therapeutic advances to reduce the incidence of recurrence or animal models that closely mimic the clinical scenario to evaluate novel therapeutics. This work investigates the efficacy of endogenous inhibitors, in preventing the recurrence of human malignant gliomas, in a newly developed animal model of glioma surgical resection. We developed a nude mice model in which human glioma xenografts were microsurgically removed. After surgery, small islets of tumor cells persisted in the normal brain parenchyma, grew, and formed a recurrence. As inhibitors we used PEX and a fragment of platelet factor 4 (PF-4/CTF), which were administered systemically on a daily basis or in metronomic combination with chemotherapy for 120 days. Treatment was started 1 or 15 days after tumor removal. PEX or PF-4/CTF produced a significant improvement in survival, and delayed the appearance of glioma recurrence. Survival of animals that received daily PEX or PF-4/CTF was similar to that of animals that received metronomic PEX or PF-4/CTF and chemotherapy, respectively. The effect of treatment was dependent on the time at which the treatment was initiated. The highest level of inhibition was observed when the treatment was administered 1 day after surgical resection and when PEX was used as the inhibitor (120 days versus 35 days of the control). Tumors treated with PEX or PF-4/CTF were small and well delineated, with few vessels. Postsurgical administration of PEX or PF-4/CTF significantly reduces the incidence human malignant glioma recurrences for a long period of time.
IL-28A and IL-29 mediate antiproliferative and antiviral signals in intestinal epithelial cells and murine CMV infection increases colonic IL-28A expression (2005)

Human cytomegalovirus virus (CMV) is a major cause of morbidity and mortality in immunocompromised individuals. Recently, a novel group of cytokines [interleukin (IL)-28A/B and IL-29, also termed interferon (IFN)-lambdas] has been described. Here, we demonstrate that intestinal epithelial cell (IEC) lines as well as murine and human colonic tissue express the IFN-lambda receptor subunits IL-28R and IL-10R2. IL-28A and IL-29 binding to their receptor complex activates ERK-1/2 and stress-activated protein kinase/c-Jun NH2-terminal kinase MAPKs and Akt, resulting in increased IL-8 protein expression. IFN-lambdas also induce phosphorylation of signal transducer and activator of transcription 1 and significantly increase mRNA expression of suppressor of cytokine signaling 3 and the antiviral proteins myxovirus resistance A and 2',5'-oligoadenylate synthetase. These signals result in an up to 83% reduction of cells positive for human CMV immediate-early protein after human CMV infection. In mice, IL-28A mRNA expression is upregulated after infection with murine CMV in vivo. Both IL-28A and IL-29 significantly decrease cell proliferation but have no effect on Fas-induced apoptosis. In conclusion, IECs express functional receptors for IFN-lambdas, which mediate antiviral and antiproliferative signals in IECs, suggesting a potential for therapeutic use in certain viral infections and as (antiproliferative) anticancer therapy.
Factor X‐activating procoagulant in normal and malignant breast tissue (1990)

Factor X-activating activity (FXAA) was determined by a chromogenic assay in normal and malignant breast tissue. FXAA was found in all tissue (n = 38) irrespective of pathology, and the activity of normal tissue was similar to that of tumours. FXAA correlated with tissue hemoglobin in normal breast (p less than 0.02) but not in tumours. FXAA was markedly reduced by aluminium hydroxide, barium citrate, anti-human factor VII, DFP, PMSF and phospholipase C, but was unaffected by iodoacetamide and mercuric chloride. It is concluded that FXAA is a serine protease with the properties of a tissue factor-factor VII complex. FXAA occurs in normal and malignant breast tissue, although the 'normal' activity may be an artefact of the homogenization process.
Projection photolithography-liftoff techniques for production of 0.2-&#181;m metal patterns (1981)

A technique which allows the use of projection photolithography with the photoresist liftoff process, for fabrication of Submicrometer metal patterns, is described. Through-the-substrate (back-projection) exposure of the photoresist produces the undercut profiles necessary for liftoff processing. Metal lines and superconducting microbridges of 0.2-µm width have been fabricated with this technique. Experimental details and process limits are discussed.
Pathology of Pulmonary Arterial Hypertension (2012)

Vascular lesions found in lungs of patients with pulmonary hypertension are probably responsible for the increase of pulmonary arterial pressures and share some peculiarities that appear characteristic. The fibrotic and proliferative lesions mainly concern small lung vessels; precapillary lesions are typically located in muscular arteries <500 µm diameter and arterioles in patients with pulmonary arterial hypertension (PAH), while septal veins and preseptal venules are involved in patients with postcapillary pulmonary veno-occlusive disease (PVOD)/pulmonary capillary hemangiomatosis (PCH). During the World Symposium at Dana Point, California, in 2008, PVOD/PCH was assigned to a novel, distinctive category of pulmonary venous hypertension (Group 1’) due to important differences in clinical management. However, many similarities between those two conditions can be observed, and conditions with mixed (arterial and venous) involvement may be encountered, a fact that is taken into consideration by this ‘soft’ prime separation.
Lethal Antibody Enhancement of Dengue Disease in Mice Is Prevented by Fc Modification (2010)

Immunity to one of the four dengue virus (DV) serotypes can increase disease severity in humans upon subsequent infection with another DV serotype. Serotype cross-reactive antibodies facilitate DV infection of myeloid cells in vitro by promoting virus entry via Fcgamma receptors (FcgammaR), a process known as antibody-dependent enhancement (ADE). However, despite decades of investigation, no in vivo model for antibody enhancement of dengue disease severity has been described. Analogous to human infants who receive anti-DV antibodies by transplacental transfer and develop severe dengue disease during primary infection, we show here that passive administration of anti-DV antibodies is sufficient to enhance DV infection and disease in mice using both mouse-adapted and clinical DV isolates. Antibody-enhanced lethal disease featured many of the hallmarks of severe dengue disease in humans, including thrombocytopenia, vascular leakage, elevated serum cytokine levels, and increased systemic viral burden in serum and tissue phagocytes. Passive transfer of a high dose of serotype-specific antibodies eliminated viremia, but lower doses of these antibodies or cross-reactive polyclonal or monoclonal antibodies all enhanced disease in vivo even when antibody levels were neutralizing in vitro. In contrast, a genetically engineered antibody variant (E60-N297Q) that cannot bind FcgammaR exhibited prophylactic and therapeutic efficacy against ADE-induced lethal challenge. These observations provide insight into the pathogenesis of antibody-enhanced dengue disease and identify a novel strategy for the design of therapeutic antibodies against dengue.