gebhart/patrepeval huggingface dataset:
A suppressive lymphokine derived from Ts clone 13G2 is IL-10. (1992)

CD8+ suppressor T cell (Ts) clone 13G2 produced a soluble suppressive lymphokine, termed the T-cell growth inhibitory factor (TGIF), which suppressed the proliferation of type 1 helper T-cell (Th1) clone 3D20 cells. The specific activity of TGIF was concentrated approximately 66,000-fold (3.7 x 10(6) U/mg of protein) by sequential chromatography from the culture supernatant of 13G2 cells. The suppressive activity of the highly purified TGIF toward the proliferation of Th1 cells was neutralized by the anti-IL-10 monoclonal antibody, and was replaced by IL-10. We detected the IL-10 molecule in the highly purified TGIF by using immunoblotting with the anti-IL-10 antibody. A PCR study showed that mRNA of IL-10 was expressed in the 13G2 cells. From these results, we conclude that TGIF produced from CD8+ T-cell clone 13G2 was IL-10. The suppressive activity of the whole supernatant was also completely blocked by the anti-IL-10 antibody, suggesting that IL-10 could play an important role in immune suppression by Ts cells.
Overexpression of ACE2 Enhances Plaque Stability in a Rabbit Model of Atherosclerosis (2008)

Overexpression of ACE2 results in stabilized atherosclerotic plaques and the mechanism is probably the conversion of vasoconstrictive angiotensin II to vessel protective angiotensin 1-7.
Application of C1-Esterase Inhibitor During Reperfusion of Ischemic Myocardium (2001)

When applied at the correct dose, C1-INH significantly protects ischemic tissue from reperfusion damage. However, overly high doses (>/=100 IU/kg) of C1-INH will provoke detrimental side effects, probably via its procoagulatory action.
Subcellular curvature at the perimeter of micropatterned cells influences lamellipodial distribution and cell polarity (2008)

This paper employs substrates that are patterned with shapes having well-defined geometric cues to characterize the influence of curvature on the polarization of highly metastatic B16F10 rat melanoma cells. Substrates were patterned using microcontact printing to define adhesive islands of defined shape and size on a background that otherwise prevents cell adhesion. Cells adherent to these surfaces responded to local curvature at the perimeter of the adhesive islands; convex features promoted the assembly of lamellipodia and concave features promoted the assembly of stress filaments. Cells adherent to rectangular shapes displayed a polarized cytoskeleton that increased with the aspect ratio of the shapes. Shapes that combined local geometric cues, by way of concave or convex edges, with aspect ratio were used to understand the additive effects of shape on polarization. The dependence of cell polarity on shape was determined in the presence of small molecules that alter actomyosin contractility and revealed a stronger dependence on contractility for shapes having straight edges, in contrast to those having curved edges. This study demonstrates that the cytoskeleton modulates cell polarity in response to multiple geometric cues in the extracellular environment.
The effectiveness of decoupling (1993)

This paper examines the effectiveness of decoupling as an optimization technique for high-performance computer architectures. Decoupled access execute architectures are described, and the concept of control decoupling is introduced and justified. A description of a highly-decoupled architecture is given, and a metric for the effectiveness of decoupling on particular programs, the Loss of Decoupling frequency is introduced. Finally, a number of real benchmark programs are examined and the applicability of decoupling them is analyzed.
Anhydrous Metal Nitrates as Volatile Single Source Precursors for the CVD of Metal Oxide Films (1998)

Anhydrous metal nitrates are useful as single source precursors for CVD of metal oxide films. MOCVD of such films can lead to incorporation of carbon or hydrogen into the films, so single source precursors that cleave directly to metal oxide films with highly volatile byproducts are desirable. In this communication it is shown that, with relatively little optimization, anhydrous metal nitrates exhibit the necessary volatility and reactivity for CVD applications.
Three-axis correction of distortion due to positional drift in scanning probe microscopy (2012)

Two common sources of distortion in scanning probe microscopy are piezo creep and thermal drift, the latter caused by slow thermal expansions of materials in the sample and microscope due to small changes in temperature over the course of a scan. We present a technique for correcting distortion due to thermal drift along all three spatial axes, along with simultaneous correction of z-axis piezo creep. Our method works by comparing each scanned topographical image to a second, partial scan, taken immediately afterwards, on which the fast and slow scan axes have been reversed. We model the positional distortion as a low-order polynomial function in three dimensions, searching for the set of correctional coefficients that minimizes the root-mean-square difference between the two scans. We demonstrate in a variety of real-world and simulated tests that this technique can routinely reduce distortion from these effects by over 90%, often to a precision of better than a single pixel.
Resin activation capture technology: Libraries from stabilized acyl-pyridinium on solid support (2000)

REsin Activation/Capture APproach or REACAP Technology, a novel approach to the synthesis of compound libraries, capitalizes on the formation and retention of a resin-bound reactive intermediate, which can be subsequently transformed into a stable, covalently attached molecule. Any unreacted “reactive intermediate” is quenched and removed from the resin upon work-up, leaving only the desired product on the solid support. In contrast to more traditional solid-supported chemistry that must address issues such as resin-loading, capping of unreactive functionalized moieties, and reaction yields, REACAP offers an attractive alternative with the focus more on the purity of the released products and less on yield. In an endeavor to generate truly non-peptide leads, we describe herein the synthesis of N-acyl-2-substituted-dihydro-4-pyridones, dihydro-4-pyridones, 4-ketopiperidines, tetrahydropyridines, and 2-acyl-3,7,8-substituted-5-oxo-2-azabicyclo[2.2.2]octane and triaza analogs using REACAP Technology. © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng (Comb Chem) 71:78–84, 2000.
Quantitative assessment of intestinal eosinophils and mast cells in inflammatory bowel disease (1996)

Previous studies on the frequency of intestinal mast cells and eosinophils in patients with inflammatory bowel disease yielded conflicting results. In the present morphometric study, we quantified mast cells and eosinophils in the lamina propria by histological and immunohistochemical methods in 64 patients suffering from Crohn's disease (33 cases) or ulcerative colitis (31 cases), and in 29 controls. Histological data from 206 biopsies were related to the presence of mucosal inflammation and clinical parameters. The number of eosinophils was increased in patients with inflammatory bowel conditions (mean +/- SE: 331 +/- 44/mm2) as compared to controls (258 +/- 27/mm2), and was dependent on disease activity and drug treatment. Mean mast cell numbers did not differ between patients and controls. However, a reduced mast cell number was found in toluidine blue-stained sections of actively inflamed tissue areas (143 +/- 16/mm2, versus 206 +/- 18/mm2 in non-inflamed tissue). Immunohistochemical studies using antibodies against the granule proteins tryptase and chymase suggest that this decrease in mast cell numbers is due to mast cell degranulation. The present data show that the number of intestinal mast cells and eosinophils is altered in patients with inflammatory bowel diseases, suggesting that both cell types are involved in the pathogenesis of chronic intestinal inflammation.
Structure of the SecY Complex Unlocked by a Preprotein Mimic (2012)

The Sec complex forms the core of a conserved machinery coordinating the passage of proteins across or into biological membranes. The bacterial complex SecYEG interacts with the ATPase SecA or translating ribosomes to translocate secretory and membrane proteins accordingly. A truncated preprotein competes with the physiological full-length substrate and primes the protein-channel complex for transport. We have employed electron cryomicroscopy of two-dimensional crystals to determine the structure of the complex unlocked by the preprotein. Its visualization in the native environment of the membrane preserves the active arrangement of SecYEG dimers, in which only one of the two channels is occupied by the polypeptide substrate. The signal sequence could be identified along with the corresponding conformational changes in SecY, including relocation of transmembrane segments 2b and 7 as well as the plug, which presumably then promote channel opening. Therefore, we propose that the structure describes the translocon unlocked by preprotein and poised for protein translocation.
HDR video quality evaluation of HEVC and VP9 codecs (2016)

Current increasing effort in the television industry towards High Dynamic Range (HDR) imaging has raised the issue of the compression of HDR content. Offering a higher peak luminance and wider color gamut, HDR video introduces new challenges to the state-of-the-art video codecs such as High Efficiency Video Coding (HEVC) or VP9, which have been designed and optimized for the compression of Standard Dynamic Range (SDR) content. This study presents a performance comparison between HEVC and VP9 in the HDR context through both objective and subjective evaluations. The experimental objective results have shown that HEVC offers from 0.6% to 38.2% bit rate savings over VP9 depending on the objective metric which is used. The subjective study demonstrated that, on average, bit rate savings greater than 47.7% can be achieved by HEVC for the same perceived quality as VP9.
Correction: Functional Characterization of Circulating Tumor Cells with a Prostate-Cancer-Specific Microfluidic Device (2012)

Cancer metastasis accounts for the majority of cancer-related deaths owing to poor response to anticancer therapies. Molecular understanding of metastasis-associated drug resistance remains elusive due to the scarcity of available tumor tissue. Isolation of circulating tumor cells (CTCs) from the peripheral blood of patients has emerged as a valid alternative source of tumor tissue that can be subjected to molecular characterization. However, issues with low purity and sensitivity have impeded adoption to clinical practice. Here we report a novel method to capture and molecularly characterize CTCs isolated from castrate-resistant prostate cancer patients (CRPC) receiving taxane chemotherapy. We have developed a geometrically enhanced differential immunocapture (GEDI) microfluidic device that combines an anti-prostate specific membrane antigen (PSMA) antibody with a 3D geometry that captures CTCs while minimizing nonspecific leukocyte adhesion. Enumeration of GEDI-captured CTCs (defined as intact, nucleated PSMA+/CD452 cells) revealed a median of 54 cells per ml identified in CRPC patients versus 3 in healthy donors. Direct comparison with the commercially available CellSearchH revealed a 2-400 fold higher sensitivity achieved with the GEDI device. Confocal microscopy of patient-derived GEDI-captured CTCs identified the TMPRSS2:ERG fusion protein, while sequencing identified specific androgen receptor point mutation (T868A) in blood samples spiked with only 50 PC C4-2 cells. On-chip treatment of patient-derived CTCs with docetaxel and paclitaxel allowed monitoring of drug-target engagement by means of microtubule bundling. CTCs isolated from docetaxel-resistant CRPC patients did not show any evidence of drug activity. These measurements constitute the first functional assays of drug-target engagement in living circulating tumor cells and therefore have the potential to enable longitudinal monitoring of target response and inform the development of new anticancer agents.
Potent antitumor activity of MS-247, a novel DNA minor groove binder, evaluated by an in vitro and in vivo human cancer cell line panel. (1999)

We synthesized a novel anticancer agent MS-247 (2-[[N-[1-methyl-2-[5-[N-[4-[N,N-bis(2-chloroethyl) amino] phenyl]] carbamoyl]-1H-benzimidazol-2-yl] pyrrol-4-yl] carbamoyl] ethyldimethylsulfonium di-p-toluenesulfonate) that has a netropsin-like moiety and an alkylating residue in the structure. We evaluated antitumor activity of MS-247 using a human cancer cell line panel coupled with a drug sensitivity database and subsequently using human cancer xenografts. The average MS-247 concentration required for 50% growth inhibition against a panel of 39 cell lines was 0.71 microM. The COMPARE analysis revealed that the differential growth inhibition pattern of MS-247 significantly correlated with those of camptothecin analogues and anthracyclins, indicating that MS-247 and the two drug groups might have similar modes of action. MS-247 exhibited remarkable antitumor activity against various xenografts. A single i.v. injection of MS-247 significantly inhibited the growth of all 17 xenografts tested, which included lung, colon, stomach, breast, and ovarian cancers. In many cases, MS-247 was more efficacious than cisplatin, Adriamycin, 5-fluorouracil, cyclophosphamide, VP-16, and vincristine and was almost comparable with paclitaxel and CPT-11; these are the most clinically promising drugs at present. MS-247 was noticeably more effective than paclitaxel (in HCT-15) and CPT-11 (in A549, HBC-4, and SK-OV-3). The toxicity of MS-247, indicated by body weight loss, was reversible within 10 days after administration. The MS-247 mode of action showed DNA binding activity at the site where Hoechst 33342 bound, inhibited topoisomerases I and II (as expected by the COMPARE analysis) blocked the cell cycle at the G2-M phase, and induced apoptosis. These results indicate that MS-247 is a promising new anticancer drug candidate to be developed further toward clinical trials.
α,β-D-CNA induced rigidity within oligonucleotides (2008)

Introduction of alpha,beta-D-CNA featuring canonical values of the torsional angles alpha and beta within oligonucleotides leads to an overall stabilization and improved rigidity of the duplex DNA as demonstrated by UV experiments, circular dichroism and corroborated by molecular dynamics simulations.
Molecular Control of Gene Co-suppression in Transgenic Soybean via Particle Bombardment (2006)

Molecular co-suppression phenomena are important to consider in transgene experiments. Embryogenic cells were obtained from immature cotyledons and engineered with two different gene constructs (pHV and pHVS) through particle bombardment. Both constructs contain a gene conferring resistance to hygromycin (hpt) as a selective marker and a modified glycinin (11S globulin) gene (V3-1) as a target. sGFP(S65T) as a reporter gene was, however, inserted into the flanking region of the V3-1 gene (pHVS). Fluorescence microscopic screening after the selection of hygromycin, identified clearly the expression of sGFP(S65T) in the transformed soybean embryos bombarded with the pHVS construct. Stable integration of the transgenes was confirmed by polymerase chain reaction (PCR) and Southern blot analysis. Seeds of transgenic plants obtained from the pHV construct frequently lacked an accumulation of endogenous glycinin, which is encoded by homologous genes to the target gene V3-1. Most of the transgenic plants expressing sGFP(S65T) showed highly accumulation of glycinin. The expression of sGFP(S65T) and V3-1 inherits into the next generations. sGFP(S65T) as a reporter gene may be useful to increase the transformation efficiency of transgenic soybean with avoiding gene co-suppression.
Delivery of Herpes Simplex Virus-Based Vectors to the Nervous System (2004)

Gene transfer to the nervous system is an attractive option to treat a wide variety of neurological insults. The expression of trophic factor and/or antiapoptotic genes may be beneficial in halting the slow neurodegeneration in such conditions as Parkinson's disease (4,5), the rapid neuronal cell death following trauma to the brain or spinal cord (6,7), or in treating peripheral neuropathies associated with diabetes or use of chemotherapeutic agents (8,9). Introduction of dominant-negative mutant genes or antisense RNA to treat diseases such as Huntington's disease, or transfer of genes to replace lost or mutated endogenous proteins to treat disorders such as lysosomal storage diseases, may prove useful. In addition, gene transfer to overexpress endogenous antinociceptive proteins has great potential in pain management. The problem faced by all of these applications is finding a suitable methodology that will facilitate the transfer of exogenous genes to the appropriate nerve cells; virusbased vectors have proven quite efficient in transferring genes to many different cell types.
The acoustic cough monitoring and manometric profile of cough and throat clearing (2013)

Cough and throat clearing might be difficult to differentiate when trying to detect them acoustically or manometrically. The aim of this study was to assess the accuracy of acoustic monitoring for detecting cough and throat clearing, and to also determine whether these two symptoms present with different manometric profiles on esophageal pressure topography. Ten asymptomatic volunteers (seven females, mean age 31.1) were trained to simulate cough and throat clearing in a randomized order every 6 minutes during simultaneous acoustic monitoring and high-resolution manometry. The accuracy of automated acoustic analysis and two blinded reviewers were compared. The pattern of the events and the duration of the pressure changes were assessed using the 30 mmHg isobaric contour. There were 50 cough and 50 throat-clearing events according to the protocol. The sensitivity and specificity of automated acoustic analysis was 84% and 50% for cough, while the blinded analysis using sound revealed a sensitivity and specificity of 94% and 92%. The manometric profile of both cough and throat clearing was similar in terms of qualitative findings; however, cough was associated with a greater number of repetitive pressurizations and a more vigorous upper esophageal sphincter contraction compared with throat clearing. The acoustic analysis software has a moderate sensitivity and poor specificity to detect cough. The profile of cough and throat clearing in pressure topography revealed a similar qualitative pattern of pressurization with more vigorous pressure changes and a greater rate of repetitive pressurizations in cough.
Eosinophil Apoptosis and the Resolution of Airway Inflammation in Asthma (1996)

Asthma is accompanied by the accumulation of potentially damaging eosinophils within inflamed airways. How eosinophils may be removed from the airways is not clear. The phagocytic removal of eosinophils in vitro requires that they undergo apoptosis, a form of cell death. We postulated that eosinophil apoptosis may occur in vivo, promoting the removal of airway eosinophils and the resolution of inflammation in asthma. We examined eosinophil apoptosis in sputum samples obtained from 11 subjects during an asthma exacerbation and 2 wk after corticosteroid treatment of the exacerbation. Airway function improved following corticosteroid treatment, and eosinophilic inflammation subsided, with significant decreases occurring in the number of airway eosinophils and the percentage of activated eosinophils. The proportion of apoptotic airway eosinophils increased significantly following corticosteroid treatment, and eosinophil products were apparent within macrophages. Our findings indicate that eosinophil apoptosis is clinically relevant in asthma. Apoptosis may represent a mechanism that promotes the resolution of eosinophilic inflammation in asthma.
22.1: Invited Paper : Technological Challenges for Large‐Size AMOLED Display (2008)

Abstract In this work, we review the current technological challenges for large‐Size AMOLED displays with an emphasis on the backplane technology. Then, it will be discussed how the new technology of oxide TFTs combines the advantages of LTPS and a‐Si TFTs to make an optimal solution for large‐Size backplanes. In particular, we reveal the technological challenges in oxide TFTs by comparing the device characteristics of conventional excimer laser annealing (ELA) LTPS and amorphous indium‐gallium‐zinc‐oxide (a‐IGZO) TFTs. Finally, we demonstrate a 12.1″ WXGA AMOLED prototype display fabricated by an a‐IGZO TFT backplane.
New Potential Anticancer Agents Based on the Anthranilic Acid Scaffold. Synthesis and Evaluation of Biological Activity (2005)

The synthesis and anticancer activity of new compounds designed on the anthranilic acid scaffold are reported. The antiproliferative activity was assayed by the National Cancer Institute in established in vitro and in vivo anticancer experimental models. Structural variations based on the flufenamic acid motif afforded a series of (hetero)aryl esters of N-(2-(trifluoromethyl)pyridin-4-yl)anthranilic acid, which showed in vitro growth inhibitory properties against human tumor cell lines in nanomolar to low micromolar concentrations. The pyridinyl ester 25 exhibited very potent in vitro antiproliferative efficacy, with a chemosensitive profile showing a number of GI(50) values at concentrations lower than 10(-7) M in the full panel of human tumor cell lines. Compound 25 was also tested in vivo as a potential anticancer agent in the hollow fiber assay and in human tumor xenografts, showing moderate inhibitory properties. Analysis of biological activities and the COMPARE procedure was utilized to support putative biochemical mechanisms implicated with the antiproliferative activity.
Oligonucleotides Containing Phosphotriester Internucleotidic Groups as Novel Substrates for Polynucleotide Enzymes (1975)

Synthetic oligonucleotides containing internal 3′,5′-phosphotriester groups have been found to act as substrates for the enzymes polynucleotide kinase induced by bacteriophage T4 and terminal deoxynucleotidyi transferase.
In vitro biosynthesis of diphthamide, studied with mutant Chinese hamster ovary cells resistant to diphtheria toxin. (1984)

Diphthamide, a unique amino acid, is a post-translational derivative of histidine that exists in protein synthesis elongation factor 2 at the site of diphtheria toxin-catalyzed ADP-ribosylation of elongation factor 2. We investigated steps in the biosynthesis of diphthamide with mutants of Chinese hamster ovary cells that were altered in different steps of this complex post-translational modification. Biochemical evidence indicates that this modification requires a minimum of three steps, two of which we accomplished in vitro. We identified a methyltransferase activity that transfers methyl groups from S-adenosyl methionine to an unmethylated form of diphthine (the deamidated form of diphthamide), and we tentatively identified an ATP-dependent synthetase activity involved in the biosynthesis of diphthamide from diphthine. Our results are in accord with the proposed structure of diphthamide (B. G. VanNess, et al., J. Biol. Chem. 255:10710-10716, 1980).