gebhart/patrepeval huggingface dataset:
Bone Morphogenetic Proteins, Their Antagonists, and the Skeleton (2003)

Skeletal homeostasis is determined by systemic hormones and local factors. Bone morphogenetic proteins (BMP) are unique because they induce the differentiation of mesenchymal cells toward cells of the osteoblastic lineage and also enhance the differentiated function of the osteoblast. However, the activity of BMPs needs to be tempered by intracellular and extracellular antagonists. BMPs bind to specific receptors and signal by phosphorylating the cytoplasmic proteins mothers against decapentaplegic (Smad) 1 and 5, which form heterodimers with Smad 4, and after nuclear translocation regulate transcription. BMP antagonists can be categorized as pseudoreceptors that compete with signaling receptors, inhibitory Smads that block signaling, intracellular binding proteins that bind Smad 1 and 5, and factors that induce ubiquitination and proteolysis of signaling Smads. In addition, a large number of extracellular proteins that bind BMPs and prevent their binding to signaling receptors have emerged. They are the components of the Spemann organizer, noggin, chordin, and follistatin, members of the Dan/Cerberus family, and twisted gastrulation. The antagonists tend to be specific for BMPs and are regulated by BMPs, indicating the existence and need of local feedback mechanisms to temper BMP cellular activities.
The Role of Cytokines and Chemokines in Filovirus Infection (2015)

Ebola- and marburgviruses are highly pathogenic filoviruses and causative agents of viral hemorrhagic fever. Filovirus disease is characterized by a dysregulated immune response, severe organ damage, and coagulation abnormalities. This includes modulation of cytokines, signaling mediators that regulate various components of the immune system as well as other biological processes. Here we examine the role of cytokines in filovirus infection, with an emphasis on understanding how these molecules affect development of the antiviral immune response and influence pathology. These proteins may present targets for immune modulation by therapeutic agents and vaccines in an effort to boost the natural immune response to infection and/or reduce immunopathology.
PRISM: a "reversed" multimedia coding paradigm (2004)

In this work, we present PRISM (power-efficient, robust, high-compression, syndrome-based multimedia coding), a video coding paradigm based on the principles of coding with side information (which, unlike the classical Wyner-Ziv coding scenario Wyner, A et al. (1976), is characterized by an ambiguous state of nature characterizing the side-information Ishwar, P et al. (2003)). PRISM's architectural goals are to inherit the low encoding complexity and robustness of motion-JPEG style intra-frame video codecs while approaching the high compression efficiency of full-motion interframe video codecs. The PRISM paradigm roughly swaps the encoder-decoder complexity with respect to conventional video coding architectures through the novel concept of moving the motion compensation task from the encoder to the decoder. These traits make PRISM well-matched to uplink-rich media applications involving wireless video and security cameras, multimedia-equipped phones and PDA's etc.
Nocturnal gamma-hydroxybutyrate. Effect on periodic leg movements and sleep organization of narcoleptic patients. (1989)

Periodic leg movements during sleep (PMS) is a disorder frequently encountered in narcolepsy. In the present study, 12 narcoleptic patients (six with PMS and six without) were recorded in a sleep laboratory for 2 consecutive nights before and after treatment with gamma-hydroxybutyrate (GHB) taken at bedtime for 1 month. Treatment resulted in decreased rapid eye movement (REM) sleep latency and increased REM efficiency without change in the total duration of REM sleep. GHB was associated with the appearance of pathological levels of PMS in patients who were unaffected before treatment. These results are discussed in relation to the role of dopamine in the physiopathology of narcolepsy and PMS.
Modular Microsystem for the Isolation, Enumeration, and Phenotyping of Circulating Tumor Cells in Patients with Pancreatic Cancer (2013)

In this manuscript, we discuss the development and clinical use of a thermoplastic modular microsystem for the high-throughput analysis of CTCs directly from whole blood. The modular system offers some innovative features that address challenges currently associated with many CTC platforms; it can exhaustively process 7.5 mL of blood in less than 45 min with recoveries >90%. In addition, the system automates the postselection CTC processing steps and thus, significantly reduces assay turnaround time (from selection to enumeration <1.5 h as compared to >8 h for many reported CTC platforms). The system is composed of 3 functional modules including (i) a thermoplastic CTC selection module composed of high aspect ratio (30 μm × 150 μm) channels containing anti-EpCAM antibodies that is scalable in terms of throughput by employing channel numbers ranging from 50 to 320; the channel number is user selected to accommodate the volume of blood that must be processed; (ii) an impedance sensor module for label-less CTC counting; and (iii) a staining and imaging module for the placement of released cells into a 2D array within a common imaging plane for phenotypic identification. To demonstrate the utility of this system, blood samples from patients with local resectable and metastatic pancreatic ductal adenocarcinoma (PDAC) were analyzed. We demonstrate the ability to select EpCAM positive CTCs from PDAC patients in high purity (>86%) and with excellent yields (mean = 53 CTCs per mL for metastatic PDAC patients) using our modular system. In addition, we demonstrate the ability to detect CTCs in PDAC patients with local resectable disease (mean = 11 CTCs per mL).
Integral three-dimensional imaging with digital reconstruction (2001)

A computed three-dimensional (3-D) display system based on integral imaging is presented. The 3-D image is reconstructed by numerical processing of an optically observed image array formed by a microlens array. The algorithm for reconstructing 3-D images is robust, and it enables us to obtain the images viewed from arbitrary directions. This computer-based image retrieval makes it possible to improve qualities of the image such as contrast, brightness, and resolution by numerical techniques. Also, this method eliminates the need for special purpose optical equipment such as high-quality liquid-crystal display and micro-optics components to display the 3-D images. We present experimental results of 3-D image reconstruction to test and verify the performance of the algorithms and the imaging system.
Immune Phenotyping and Naive T Cells as a Predictor of Response to Therapy In Chronic Lymphocytic Leukemia (CLL) (2010)

Abstract Abstract 1362 The role of anti-tumor immunity is not well understood in CLL but does have the potential to be manipulated to improve treatment responses. We studied the predictive values of 43 immune phenotypes in patients enrolled in a clinical trial of early treatment of high risk CLL. The study enrolled 33 patients with CLL diagnosed using standard NCI-WG96 criteria who had previously untreated early - intermediate stage disease and did not meet NCI-WG96 guidelines for conventional treatment. High risk disease was defined as at least one of the following: 17p13 deletion; 11q22 deletion or unmutated IGHV together with either expression of ZAP-70 (&gt;20%) or CD38 (&gt;30%). Patients were treated with GM-CSF 250 mcg sc 3 × week × 5 weeks, alemtuzumab sc with dose escalation over 3 days then 30 mg/d 3 × week × 4 weeks, and rituximab 375 mg/m2 weekly × 4 weeks for a total duration of therapy of 5 weeks. We measured immune phenotypes (representing Tregs, naïve, effector memory, central memory T cells, B cells, NK cells, monocytes, among others) at the time of enrollment, through treatment and at 1 year after enrollment in 28 patients. We identified pre-treatment immune phenotypes that correlated with disease burden (as measured by the number of circulating B cells). Increased disease burden was correlated with increased absolute numbers of CD3+, CD8+, CD4+ T cells, NK (CD56+CD16+), Dr+CD8+ T cells, and Tregs (CD4+CD25+CD127+); p&lt;0.001. The disease burden was inversely related to the number of circulating monocytes (p&lt;0.01) and unrelated to the circulating number of naïve T cells. We repeated the pre-treatment phenotype correlation studies using the CD19+ cell counts 12 months after treatment for 13 patients who have completed the final analysis. Interestingly, the number of naïve CD4 and CD8 cells (CD4+RA+62L+CD27+ and CD8+RA+62L+CD27+) of the patient prior to treatment correlated with CD19+ cells 12 months after treatment (p=0.024 and p=0.002 respectively; n=13). Finally, we correlated pre-treatment immune phenotypes with time to progression. Again, an elevated T cell phenotype (CD4+RA+62L+CD27- as a percent of CD4+ cells) correlated to increased time to progression (p=0.04; n=28). It is noteworthy that the naïve T cell phenotype did not correlate with tumor burden prior to therapy. Thus, while pre-treatment lymphocyte expansion is commensurate with tumor burden in CLL, the frequency and numbers of naïve T cells prior to treatment has some predictive value to response to treatment. These data suggest that CLL induces the expansion of lymphocytes, suppresses monocytes with an induction in naïve T cells acting as an indicator of higher B cell counts at 12 months in patients with durable remissions. Disclosures: Zent: Genzyme: Research Funding; Genentech: Research Funding; Novartis: Research Funding; G.S.K.: Research Funding.
Comparison of the specificities of p70 S6 kinase and MAPKAP kinase‐1 identifies a relatively specific substrate for p70 S6 kinase: the N‐terminal kinase domain of MAPKAP kinase‐1 is essential for peptide phosphorylation (1995)

xxR/KxRxxSxx sequences were phosphorylated with high efficiency by both p70 S6 kinase (p70S6K) and MAPKAP kinase-1. The best substrate for MAPKAP kinase-1 (KKKNRTLSVA) was phosphorylated with a Km of 0.17 microM, and the best substrate for p70S6K (KKRNRTLSVA) with a Km of 1.5 microM. The requirement of both enzymes for Arg/Lys at position n-5 could be partially replaced by inserting basic residues at other positions, especially by an Arg at n-2 or n-4. MAPKAP kinase-1 (but not p70S6K) tolerated lack of any residue at n-5 if Arg was present at n-2 and n-3. p70S6K (but not p90S6K) tolerated Thr at position n and absence of any residue at n + 2. The peptide KKRNRTLTV, which combined these features, was relatively selective for p70S6K having a 50-fold higher Vmax/Km than MAPKAP kinase-1. Inactivation of the N-terminal kinase domain of MAPKAP kinase-1, which is 60% identical to p70S6K, abolished activity towards all peptides tested, but the enzyme retained 30-40% of its activity if the C-terminal kinase domain was inactivated.
BindingDB Entry 5231: Characterization of human A(2B) adenosine receptors: radioligand binding, western blotting, and coupling to G(q) in human embryonic kidney 293 cells and HMC-1 mast cells. (2012)

Recombinant human A(2B) adenosine receptors (A(2B)ARs) and receptors extended on the amino terminus with hexahistidine and the FLAG epitope, DYKDDDDK (H/F-A(2B)) were stably overexpressed (to >20,000 fmol/mg protein) in human embryonic kidney 293 cells (HEK-A(2B)). By Western blotting, the H/F-A(2B) receptor runs as a 34.8-kDa glycoprotein. Pharmacological properties of A(2B)ARs were characterized with (125)I-3-aminobenzyl-8-phenyl-(4-oxyacetic acid)-1-propylxanthine (K(D), 36 nM). In competition binding assays, the affinity of agonists is reduced by substitution on either the N(6)- or the C-2 position of the adenine ring, whereas 5'-substitutions increase affinity, resulting in the potency order: 5'-N-ethylcarboxamidoadenosine (NECA) >> N(6)-aminobenzyl-NECA approximately 2-chloroadenosine > 2-[4-(2-carboxyethyl)phenethylamino]-NECA (CGS21680) > N(6)-aminobenzyladenosine. The A(2B)AR is potently blocked by the A(2A)-selective antagonist 4-(2-[7-amino-2-[2-furyl][1,2, 4]triazolo-[2,3-a][1,3,5] triazin-5-yl-amino]ethyl)phenol (ZM241385; K(I), 32 nM for A(2B), 1.4 nM for A(2A)) and the A(1) selective antagonist 8-cyclopentyl-1,3-dipropylxanthine (K(I), 50.5 nM for A(2B); 2.5 nM for A(1)). The K(I) values for the antiasthmatic xanthines, theophylline (7.8 microM) and enprofylline (6.4 microM), are below their therapeutic plasma concentrations (20 to 50 microM), and agree with K(I) determinations for inhibition of NECA-stimulated cAMP accumulation in HEK-A(2B) cells. NECA or N(6)-(2-iodo)benzyl-5'-N-methylcarboxamidodoadenosine (IB-MECA) stimulate inositol trisphosphates and calcium accumulation in HEK-A(2B) or HEK-A(3) cells, respectively, but only the A(3) response is prevented by pertussis toxin. In human HMC-1 mast cells, A(2B)AR activation stimulates calcium mobilization and cAMP accumulation. We conclude that HEK-A(2B) cells and HMC-1 mast cells possess A(2B)AR glycoproteins that are coupled to both G(q/11) and G(s).
Interface properties of metal-oxide-semiconductor structures on n-type 6H and 4H-SiC (1996)

This work reports on the interface properties of metal-oxide-semiconductor (MOS) structures formed by thermal oxidation of n-type silicon carbide (SiC). The SiC layers, grown homoepitaxially on the silicon-face of 6H-SiC and 4H-SiC substrates, were oxidized at 1100 °C in dry or wet atmosphere. The interface properties of the MOS structures were investigated using both, the Terman and the high-low frequency method. The validity of these methods for wide band-gap semiconductors is clarified in a short theoretical analysis. The experimental results reveal moderate densities of interface states for MOS devices on 6H-SiC as well as on 4H-SiC. Only minor differences were observed between both polytypes. Current-voltage measurements prove earlier results and show good quality independent of the polytype used as substrate material.
Inhibition of Interleukin-6 Signaling with CNTO 328 Enhances the Activity of Bortezomib in Preclinical Models of Multiple Myeloma (2007)

Taken together, our results provide a strong preclinical rationale for the clinical development of the bortezomib/CNTO 328 combination for patients with myeloma.
Erythropoietin production in a primary culture of human renal carcinoma cells maintained in nude mice (1984)

The present studies report erythropoietin (Ep) production in primary cultures of a human renal carcinoma from a patient with erythrocytosis that has been serially transplanted to BALB/c nude mice. The levels of erythropoietin in the culture media were estimated using the exhypoxic polycythemic mouse assay (EHPCMA), fetal mouse liver erythroid colony- forming technique (FMLC), and a radioimmunoassay (RIA). The spent culture media of the exponentially growing cells contained less than 10 mU/ml of Ep measured by RIA. However, after the cells became confluent, Ep levels (RIA) in the spent media showed a marked increase to approximately 300 mU/ml. Ep levels estimated using the FMLC and EHPCMA were approximately 2/3 and 1/10, respectively, of those measured by RIA. Rabbit antiserum to highly purified human urinary Ep (70,400 U/mg protein) was utilized for immunocytochemical (peroxidase-antiperoxidase method) localization of Ep in the cultured cells. Very few of the cells in exponential growth exhibited Ep-like immunoreactivity, whereas intense Ep-like immunoreactivity was observed in the cytoplasm of the cells maintained in culture for a prolonged period after reaching confluency. The most intense staining was observed in some of the cells forming domes. The domes developed after the cells reached confluency, and their numbers increased with increasing time in confluent culture, in parallel with the increase in Ep levels in the spent media. This primary cell culture system of a renal cell carcinoma maintained in nude mice, which produces immunologically and biologically active Ep, may provide a useful model for studies of the mechanism of Ep production.
The value of role play (2005)

Role play takes many different forms: children may play alone, with peers and with adults. It can develop from other forms of play. It involves pretence, imagination, empathy (understanding how someone else thinks and behaves), taking on and acting in a role, and communicating the pretence to others (peers and adults).
Hot Spot for a Large Deletion in the 18- to 19-Centisome Region Confers a Multiple Phenotype in Salmonella enterica Serovar Typhimurium Strain ATCC 14028 (2004)

Loss of the Salmonella MsbB enzyme, which catalyzes the incorporation of myristate destined for lipopolysaccharide in the outer membrane, results in a strong phenotype of sensitivity to salt and chelators such as EGTA and greatly diminished endotoxic activity. MsbB- salmonellae mutate extragenically to EGTA-tolerant derivatives at a frequency of 10(-4) per division. One of these derivatives arose from inactivation of somA, which suppresses sensitivity to salt and EGTA. Here we show that a second mode of MsbB- suppression is a RecA-dependent deletion between two IS200 insertion elements present in Salmonella enterica serovar Typhimurium strain ATCC 14028 but not in two other wild-type strains, LT2 and SL1344, which lack one of the IS200 elements. This deletion occurs spontaneously in wild-type and MsbB- strain 14028 salmonellae and accounts for about one-third of all of the spontaneous suppressors of MsbB- in strain 14028. It spans the region corresponding to 17.7 to 19.9 centisomes, which includes somA, on the sequenced map of Salmonella LT2 (136 ORFs in that strain; ATCC 14028 and other strains showed variability in this region). In addition to conferring EGTA resistance correlated with somA, the deletion confers a MacConkey galactose resistance phenotype on MsbB- Salmonella, indicating that at least one additional gene (distinct from somA) within the deletion is responsible for this phenotype. In the wild type, the deletion mutant grows with normal exponential growth rate in Luria broth but is chlorate resistant and does not grow on citrate agar. The deletion strains have lost hydrogen sulfide production, nitrate reductase activity, and gas production from glucose fermentation.
Shielding Applications from an Untrusted Cloud with Haven (2015)

Today’s cloud computing infrastructure requires substantial trust. Cloud users rely on both the provider’s staff and its globally distributed software/hardware platform not to expose any of their private data. We introduce the notion of shielded execution, which protects the confidentiality and integrity of a program and its data from the platform on which it runs (i.e., the cloud operator’s OS, VM, and firmware). Our prototype, Haven, is the first system to achieve shielded execution of unmodified legacy applications, including SQL Server and Apache, on a commodity OS (Windows) and commodity hardware. Haven leverages the hardware protection of Intel SGX to defend against privileged code and physical attacks such as memory probes, and also addresses the dual challenges of executing unmodified legacy binaries and protecting them from a malicious host. This work motivated recent changes in the SGX specification.
Regulation of RNA Synthesis in Fibroblasts During Transition from Resting to Growing State (1973)

Addition of serum, containing fibroblast growth factors, to a culture of resting 3T6 cells stimulates a transition to the growing state. Studies of ghost monolayers prepared with the aid of detergent at intervals after stimulation showed an increase in the rate of ribosomal RNA synthesis within 10 min. The rate continued to increase for many hours and reached a level 2.5- to 3.5-fold higher by the time DNA synthesis began. The increasing rate of ribosomal RNA synthesis appeared independent of an increase in the number of ribosomal genes, since it was not affected by prevention of DNA synthesis with cytosine arabinoside. In contrast to ribosomal RNA, the overall rate of transscription of heterogeneous nuclear RNA was not directly affected by serum growth factors and does not appear to be regulated during the transition from resting to growing state. It seems, instead, to be fixed in relation to the amount of template, for it increases proportionally to DNA content.
In vivo cancellous bone remodeling on a strontium‐containing hydroxyapatite (sr‐HA) bioactive cement (2003)

The purpose of this study was to investigate the in vivo bone response to the strontium-containing hydroxyapatite (Sr-HA) bioactive bone cement injected into the cancellous bone. Sr-HA cement was injected into the iliac crest of rabbits for 1, 3, and 6 months. Active bone formation and remodeling were observed after 1 month. Newly formed bone was observed to grow onto the bone cement after 3 months. Thick osteoid layer with osteoblasts formed along the bone and guided over the bone cement surface reflected the stimulating effect of Sr-HA. From scanning electron microscopy (SEM) and energy-dispersive X-ray (EDX) analysis, high calcium and phosphorus levels were detected at the interface with a thick layer of 70 microm in width, and fusion of Sr-HA with the bone was observed. Blood vessels were found developing in remodeling sites. The affinity of bone on Sr-HA cement was increased from 73.55 +/- 3.50% after 3 months up to 85.15 +/- 2.74% after 6 months (p < 0.01). In contrast to Sr-HA cement, poly(methyl methacrylate) (PMMA) bone cement was neither osteoconductive nor bioresorbable. Results show that the Sr-HA cement is biocompatible and osteoconductive, which is suitable for use in treating osteoporotic vertebral fractures.
A Chemical Inhibitor of p53 That Protects Mice from the Side Effects of Cancer Therapy (1999)

Chemotherapy and radiation therapy for cancer often have severe side effects that limit their efficacy. Because these effects are in part determined by p53-mediated apoptosis, temporary suppression of p53 has been suggested as a therapeutic strategy to prevent damage of normal tissues during treatment of p53-deficient tumors. To test this possibility, a small molecule was isolated for its ability to reversibly block p53-dependent transcriptional activation and apoptosis. This compound, pifithrin-alpha, protected mice from the lethal genotoxic stress associated with anticancer treatment without promoting the formation of tumors. Thus, inhibitors of p53 may be useful drugs for reducing the side effects of cancer therapy and other types of stress associated with p53 induction.
Maximizing ESD design window by optimizing gate bias for cascoded drivers in 45nm and beyond SOI technologies (2010)

In advanced SOI technologies, the bottom gate voltage plays an important role in achieving the maximum trigger voltage Vt1 of the cascoded drivers. A comparable MOSFET and BJT current handling is needed to ensure maximum Vt1. The minimum and maximum Vt1 window for cascoded driver is shown to range between a single FET Vt1 and twice single FET Vt1.
Alzheimer's Disease (1986)

THE landmark case report of Alzheimer's disease, which was published in 1907,1 described the autopsy findings in a woman who died at 55 with progressive dementia and in whom newly available silver stains demonstrated the presence of abnormal nerve cells containing tangles of fibers (neurofibrillary tangles) and clusters of degenerating nerve endings (neuritic plaques) in the cerebral cortex. The medical world accepted this condition as Alzheimer's disease, a cause of presenile dementia.2 However, during the next several decades, there was conflict among neurologists about whether Alzheimer's disease–like changes that occurred in very elderly persons were identical to those that occurred . . .