gebhart/patrepeval huggingface dataset:
Apoptosis primarily accounts for the growth-inhibitory properties of sulindac metabolites and involves a mechanism that is independent of cyclooxygenase inhibition, cell cycle arrest, and p53 induction. (1997)

Sulindac causes regression of and prevents recurrence of colonic adenomas in patients with familial adenomatous polyposis. Although cell cycle arrest and apoptosis have been proposed, the mechanism of action is poorly understood. In this study, we characterized the growth-inhibitory effects of active metabolites of sulindac in cultured colon adenocarcinoma cells by determining the contribution of apoptosis and cell cycle arrest and the requirement for cyclooxygenase (COX) inhibition and p53 involvement and compared the effects of sulindac metabolites with the chemotherapeutic drug, 5-fluorouracil (5-FU). Time course and dose-response experiments demonstrated that increased apoptosis paralleled the growth-inhibitory effects of the sulfide and sulfone. A relationship among a series of nonsteroidal anti-inflammatory drugs was observed between potency for growth inhibition and ability to induce apoptosis but not potency to inhibit COX. For example, the sulfone was at least 5000-fold less potent than the sulfide for inhibiting COX but only 6.5-fold less potent for inducing apoptosis. Moreover, the prostaglandin analogue, dimethyl-prostaglandin E2, failed to reverse the apoptosis-inducing effects of the sulfide. Sulindac metabolites caused G1 cell cycle arrest in proliferating cells but were comparably effective in nonproliferating cells. In contrast, 5-FU treatment was less effective in nonproliferating cells. Combined treatment with sulindac metabolites and 5-FU did not result in an additive apoptotic response. Treatment of cells with 5-FU increased p53 protein levels, whereas sulindac metabolites did not induce expression. Saos-2 cells, which lack p53, responded to sulindac metabolites but not 5-FU. These results show that apoptosis primarily contributes to growth inhibition by sulindac metabolites. The biochemical pathway does not require COX inhibition or p53 induction and appears to be fundamentally different from the apoptotic response to 5-FU.
Neural Cages for Detail-Preserving 3D Deformations (2019)

We propose a novel learnable representation for detail-preserving shape deformation. The goal of our method is to warp a source shape to match the general structure of a target shape, while preserving the surface details of the source. Our method extends a traditional cage-based deformation technique, where the source shape is enclosed by a coarse control mesh termed \emph{cage}, and translations prescribed on the cage vertices are interpolated to any point on the source mesh via special weight functions. The use of this sparse cage scaffolding enables preserving surface details regardless of the shape's intricacy and topology. Our key contribution is a novel neural network architecture for predicting deformations by controlling the cage. We incorporate a differentiable cage-based deformation module in our architecture, and train our network end-to-end. Our method can be trained with common collections of 3D models in an unsupervised fashion, without any cage-specific annotations. We demonstrate the utility of our method for synthesizing shape variations and deformation transfer.
Pyrosequencing™ technology at elevated temperature (2004)

To date, the Pyrosequencing trade mark technology has been performed at 28 degrees C due to the low thermostability of the firefly luciferase. In this study, firefly luciferase was stabilized in the presence of glycine betaine, allowing DNA sequencing at 37 degrees C. By increasing the temperature to 37 degrees C, false signals due to primer-dimers and loop-structures were decreased significantly. In addition, a combination of (i) replacing the natural dGTP with 7'deaza-dGTP in the polymerase chain reaction (PCR), (ii) 1.6 M glycine betaine, and (iii) an increase of the temperature to 37 degrees C enabled us to sequence a DNA template with the initial sequence 3'-ATGGCCCGGGGGGGAGCTCCA em leader 5'. Furthermore, we describe a method to analyze if a primer forms a primer-dimer with extendable 3'-ends.
Histone H2AX phosphorylation induced by selective photolysis of BrdU‐labeled DNA with UV light: Relation to cell cycle phase (2004)

Photolysis of BrdU-labeled DNA induces DSBs and leads to H2AX phosphorylation. Detection of gammaH2AX IF indicates the presence of the incorporated BrdU, is compatible with concurrent detection of other intracellular antigens, and can be used to demonstrate cell cycle kinetics.
Anti-Candida activity of synthetic hydroxychalcones. (1994)

The antifungal activity of different synthetic hydroxychalcones was determined against Candida species. It was revealed that the presence of hydroxyl groups at C-2, C-4, and C-2' in chalcone was essential to inhibit Candida growth. Among the chalcone derivatives examined, 2,4,2'-trihydroxy-5'-methylchalcone showed the most intensive anti-Candida activity, suggesting that it could be a potential therapeutic agent for candidosis.
Seamless switching of scalable video bitstreams for efficient streaming (2004)

Efficient adaptation to channel bandwidth is broadly required for effective streaming video over the Internet. To address this requirement, a novel seamless switching scheme among scalable video bitstreams is proposed in this paper. It can significantly improve the performance of video streaming over a broad range of bit rates by fully taking advantage of both the high coding efficiency of nonscalable bitstreams and the flexibility of scalable bitstreams, where small channel bandwidth fluctuations are accommodated by the scalability of a single scalable bitstream, whereas large channel bandwidth fluctuations are tolerated by flexible switching between different scalable bitstreams. Two main techniques for switching between video bitstreams are proposed. Firstly, a novel coding scheme is proposed to enable drift-free switching at any frame from the current scalable bitstream to one operated at lower rates without sending any overhead bits. Secondly, a switching-frame coding scheme is proposed to greatly reduce the number of extra bits needed for switching from the current scalable bitstream to one operated at higher rates. Compared with existing approaches, such as switching between nonscalable bitstreams and streaming with a single scalable bitstream, our experimental results clearly show that the proposed scheme brings higher efficiency and more flexibility in video streaming.
Spectral partitioning of random graphs (2001)

Problems such as bisection, graph coloring, and clique are generally believed hard in the worst case. However, they can be solved if the input data is drawn randomly from a distribution over graphs containing acceptable solutions. In this paper we show that a simple spectral algorithm can solve all three problems above in the average case, as well as a more general problem of partitioning graphs based on edge density. In nearly all cases our approach meets or exceeds previous parameters, while introducing substantial generality. We apply spectral techniques, using foremost the observation that in all of these problems, the expected adjacency matrix is a low rank matrix wherein the structure of the solution is evident.
GaAs-based room-temperature continuous-wave 1.59μm GaInNAsSb single-quantum-well laser diode grown by molecular-beam epitaxy (2005)

Starting from the growth of high-quality 1.3μmGaInNAs∕GaAs quantum well (QW), the QW emission wavelength has been extended up to 1.55μm by a combination of lowering growth rate, using GaNAs barriers and incorporating some amount of Sb. The photoluminescence properties of 1.5μm range GaInNAsSb∕GaNAs QWs are quite comparable to the 1.3μm QWs, revealing positive effect of Sb on improving the optical quality of the QWs. A 1.59μm lasing of a GaInNAsSb∕GaNAs single-QW laser diode is obtained under continuous current injection at room temperature. The threshold current density is 2.6kA∕cm2 with as-cleaved facet mirrors.
Outcome of Functional Electrical Stimulation in the Rehabilitation of a Child with C-5 Tetraplegia (1999)

Hand function was provided for a six-year-old child with C-5 American Spinal Injuries Association (ASIA) classification-A tetraplegia through a percutaneous intramuscular (i.m.) functional electrical stimulation (FES) system. In conjunction with implantation of 10 percutaneous i.m. electrodes for provision of grasp and release of her right hand, reconstructive surgery was performed to provide upper extremity positioning to optimize hand use. The subject participated in FES training over a nine-week period for approximately five hours weekly, with an additional five hours each week dedicated to exercise and conditioning of her arm muscles. Physical and functional assessments included range of motion (ROM), manual muscle testing (MMT), activities of daily living (ADL) abilities and the Canadian Occupational Performance Measure (COPM), used to evaluate the effect of stimulated hand function and surgical reconstruction on functional ability. These were conducted prior to FES and surgery and repeated after rehabilitation training. With rehabilitation and training, the child was able to control her FES system. Physical assessments revealed increased strength of both shoulders and more useful range of arm movement. Functional assessments show that the FES system enabled her to perform age-appropriate ADL that previously were achievable only with physical assistance. Her overall level of independence in ADL ability increased, as did self-rated levels of satisfaction and performance on chosen activities. Positive gains demonstrated here suggest the need for further studies of FES systems in young children with SCI.
Pathophysiology and therapy of pruritus in allergic and atopic diseases (2010)

Pruritus (itch) is a major characteristic and one of the most debilitating symptoms in allergic and atopic diseases and the diagnostic hallmark of atopic dermatitis. Pruritus is regularly defined as an unpleasant sensation provoking the desire to scratch. Although we achieved rather good knowledge about certain inducers of itch such as neuropeptides, amines, mu-opioids, cytokines and proteases, for example, less is known about the pathophysiological specifities among the different diseases, and the therapeutic consequences which may derive thereoff. This review dissects the role of mediators, receptors and itch inhibitors on peripheral nerve endings, dorsal root ganglia, the spinal cord and the CNS leading to the amplification or - vice versa - suppression of pruritus. As the treatment of pruritus in allergic and atopic skin disease is still not satisfactory, knowing these pathways and mechanisms may lead to novel therapeutic approaches against this frequently encountered skin symptom.
The Role of Antioxidants in Protection from Impulse Noise (1999)

The hearing loss from exposure to noise and ototoxic drugs share a number of audiological and pathological similarities. Recent research has shown that reactive oxygen species (ROS) may be a common factor in both noise- and drug-induced hearing loss. This review describes three experiments that point to ROS as a causative factor in both noise- and drug-induced hearing loss and antioxidants as a protective agent. In the first experiment, the ears of chinchillas were treated with R-N6-phenylisopropyladenoisine (R-PIA) and exposed to 150-dB impulse noise. The treated ears developed substantially less permanent hearing loss (PTS) and hair cell loss than the untreated ears. One interpretation of this experiment is that R-PIA increases the availability of glutathione (GSH). In the second experiment, the role of GSH was specifically examined. The ears of chinchillas were treated with glutathione monoethylester (GEE), a pro-GSH drug that has been shown to readily cross cell membranes and increase GSH levels. The GEE-treated ears had significantly less PTS and hair-cell loss than the nontreated ear. Previous research has shown that moderate levels of noise exposure can increase a subject's resistance to noise, and also increase the availability of antioxidant enzymes in the cochlea. In the third experiment, chinchillas were given a series of "toughening" exposures (i.e., 6 h of a 0.5-kHz OB noise at 95 dB for 10 days). After the series of "toughening" exposures, the subjects were treated with carboplatin, a drug that causes massive inner-hair-cell lesions in the chinchilla. The animals receiving the 10-day toughening exposure developed less PTS and hair-cell loss than the control animals.
Antibody Drug Conjugates as Cancer Therapeutics (2013)

Monoclonal antibody (MAb) based therapies have achieved considerable success in oncology, primarily when used in combination with cytotoxic drugs. Antibody drug conjugates (ADCs) are a class of therapeutics that harness the antigen-selectivity of MAbs to deliver highly potent cytotoxic drugs to antigen-expressing tumor cells. The use of MAb directed delivery can confer a therapeutic index to highly potent cytotoxic drugs, increasing both the efficacy and safety of therapy. Although simple in concept, to achieve the design goal of improved therapeutic efficacy and reduced toxicity, each of the components of an ADC; the MAb, linker and drug need to considered in the context of the targeted antigen, the selectivity of antigen expression and the biology of the tumor type on which the target antigen is expressed. The characteristics of targets, MAbs, linkers and drugs being used in ADC design are discussed.
A photoaffinity derivative of colchicine: 6'-(4'-azido-2'-nitrophenylamino)hexanoyldeacetylcolchicine. Photolabeling and location of the colchicine-binding site on the alpha-subunit of tubulin. (1985)

A photoaffinity analog of colchicine, 6-(4'-azido-2'-nitrophenylamino)hexanoyldeacetylcolchicine, was synthesized by reacting deacetylcolchicine or [3H]deacetylcochicine with N-succinimidyl-6-(4'-azido-2'-nitrophenylamino)hexanoate. Homogeneity of the photoaffinity analog was established by thin-layer chromatography and high-pressure liquid chromatography. The structure of the photoaffinity analog was determined by 1H and 13C NMR, infrared and ultraviolet-visible spectroscopies, and elemental analysis. Binding of 6-(4'-azido-2'-nitrophenylamino)hexanoyldeacetylcolchicine to bovine renal tubulin was measured by competition with [3H]colchicine. The value of the apparent Ki for the photoaffinity analog was 0.28 microM in the concentration range of 0.8-1.2 microM of the analog. A value of 0.50 microM for the apparent Kd was measured by the direct binding of the tritiated photoaffinity analog to tubulin. The analog is slightly more potent an inhibitor of microtubule formation than colchicine. The photoaffinity analog reacted with renal tubulin upon irradiation with a mercury lamp equipped with a 420-nm cutoff filter. Spectral and radiochemical analyses of the tubulin after photolysis and dialysis have demonstrated a stoichiometric incorporation of the photoaffinity analog in the alpha-subunit of the tubulin. Covalent labeling of tubulin with the photoaffinity analog decreases the extent of [3H]colchicine binding by more than 90%.
Development of a multiple sclerosis functional composite as a clinical trial outcome measure (1999)

The primary clinical outcome measure for evaluating multiple sclerosis in clinical trials has been Kurtzke's expanded disability status scale (EDSS). New therapies appear to favourably impact the course of multiple sclerosis and render continued use of placebo control groups more difficult. Consequently, future trials are likely to compare active treatment groups which will most probably require increased sample sizes in order to detect therapeutic efficacy. Because more responsive outcome measures will be needed for active arm comparison studies, the National Multiple Sclerosis Society's Advisory Committee on Clinical Trials of New Agents in Multiple Sclerosis appointed a Task Force that was charged with developing improved clinical outcome measures. This Task Force acquired contemporary clinical trial and historical multiple sclerosis data for meta-analyses of primary and secondary outcome assessments to provide a basis for recommending a new outcome measure. A composite measure encompassing the major clinical dimensions of arm, leg and cognitive function was identified and termed the multiple sclerosis functional composite (MSFC). The MSFC consists of three objective quantitative tests of neurological function which are easy to administer. Change in this MSFC over the first year of observation predicted subsequent change in the EDSS, suggesting that the MSFC is more sensitive to change than the EDSS. This paper provides details concerning the development and testing of the MSFC.
The Immunosuppressant SR 31747 Blocks Cell Proliferation by Inhibiting a Steroid Isomerase in Saccharomyces cerevisiae (1996)

SR 31747 is a novel immunosuppressant agent that arrests cell proliferation in the yeast Saccharomyces cerevisiae, SR 31747-treated cells accumulate the same aberrant sterols as those found in a mutant impaired in delta 8- delta 7-sterol isomerase. Sterol isomerase activity is also inhibited by SR 31747 in in vitro assays. Overexpression of the sterol isomerase-encoding gene, ERG2, confers enhanced SR resistance. Cells growing anaerobically on ergosterol-containing medium are not sensitive to SR. Disruption of the sterol isomerase-encoding gene is lethal in cells growing in the absence of exogenous ergosterol, except in SR-resistant mutants lacking either the SUR4 or the FEN1 gene product. The results suggest that sterol isomerase is the target of SR 31747 and that both the SUR4 and FEN1 gene products are required to mediate the proliferation arrest induced by ergosterol depletion.
Electrical functionality of inkjet-printed silver nanoparticle conductive tracks on nanostructured paper compared with those on plastic substrates (2013)

In this study, we use nanostructured paper made from cellulose nanofibres (CNFs) as a flexible printable material for inkjet-printing of silver nanoparticle (AgNP) ink. The nanostructured paper is prepared by sheet casting of 10–40 nm wide mechanically fibrillated aqueous CNFs in suspension. The resulting nanostructured paper, in the form of densely packed laminar layers, has low surface roughness (40 ± 2.3 nm) and a nanoporous network structure. This unique surface feature helps the ink vehicles to permeate through the nanopores and also aids absorption along the fibril direction parallel to the surface while retaining the silver nanoparticles on the surface to compete with the initial spreading and final evaporation processes. As a result, well-defined inkjet-printed AgNP conductive tracks (∼400 μm wide) on nanostructured paper show lower electrical resistance (1.57 ± 0.09 Ω cm−1) than those on commonly used plastics, including polyimide (PI, 2.07 ± 0.17 Ω cm−1) and poly(ethylene naphthalate) (PEN, 2.10 ± 0.16 Ω cm−1), at a moderate curing temperature of 150 °C for 1 h. The inkjet-printed conductive tracks on nanostructured paper also show better electrical performance during and after folding than those printed on plastic substrates, such as PI, and exhibit stable electrical properties throughout a test period of 1000 h in a moisture resistance test (85 °C and 85% relative humidity). The better overall electrical performance compared with that of tracks on plastic substrates highlights the potential of genuinely nanostructured paper as a printing substrate for flexible printed electronics.
Vasodilatory effects of C-type natriuretic peptide on forearm resistance vessels are distinct from those of atrial natriuretic peptide in chronic heart failure. (1994)

In patients with CHF the peripheral vasodilatory effect of ANP is attenuated, but CNP-induced peripheral vasorelaxation is preserved, with CNP being less potent for equimolar doses.
Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon (2002)

The effects of endoribonuclease sites, secondary structures in mRNA, and gene placement on protein production and mRNA stability and steady-state levels were tested in a dual-gene operon containing the genes encoding beta-galactosidase (lacZ) from Escherichia coli and green fluorescent protein (gfp) from Aequorea victoria. Two previously identified RNase E sites were placed separately between the coding regions to direct cleavage in this area and produce two secondary transcripts, each containing a single-gene coding region. Novel secondary structures were engineered into the 3' and 5' ends of each of the coding regions to protect the transcript from inactivation by endoribonucleases (5' hairpins) and degradation by exoribonucleases (3' hairpins). In addition, the effects of relative gene placement were examined by switching the locations of the two coding regions. Depending on the particular secondary structures and RNase E sites placed between the genes the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 2.5-fold and 4-fold, respectively. By changing gene location and incorporating secondary structures and RNase E sites the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 100-fold and 750-fold, respectively.
Cytostatic Gene Therapy for Vascular Proliferative Disorders with a Constitutively Active form of the Retinoblastoma Gene Product (1995)

Vascular smooth muscle cell (SMC) proliferation in response to injury is an important etiologic factor in vascular proliferative disorders such as atherosclerosis and restenosis after balloon angioplasty. The retinoblastoma gene product (Rb) is present in the unphosphorylated and active form in quiescent primary arterial SMCs, but is rapidly inactivated by phosphorylation in response to growth factor stimulation in vitro. A replication-defective adenovirus encoding a nonphosphorylatable, constitutively active form of Rb was constructed. Infection of cultured primary rat aortic SMCs with this virus inhibited growth factor-stimulated cell proliferation in vitro. Localized arterial infection with the virus at the time of balloon angioplasty significantly reduced SMC proliferation and neointima formation in both the rat carotid and porcine femoral artery models of restenosis. These results demonstrate the role of Rb in regulating vascular SMC proliferation and suggest a gene therapy approach for vascular proliferative disorders associated with arterial injury.
Antitumor effects of α‐bisabolol against pancreatic cancer (2011)

In the present study, we investigated whether α-bisabolol, a sesquiterpene alcohol present in essential oils derived from a variety of plants, has antitumor effects against pancreatic cancer. α-Bisabolol induced a decrease in cell proliferation and viability in pancreatic cancer cell lines (KLM1, KP4, Panc1, MIA Paca2), but not in pancreatic epithelial cells (ACBRI515). α-Bisabolol treatment induced apoptosis and suppressed Akt activation in pancreatic cancer cell lines. Furthermore, α-bisabolol treatment induced the overexpression of early growth response-1 (EGR1), whereas EGR1 siRNA decreased the α-bisabolol-induced cell death of KLM1 cells. Tumor growth in both subcutaneous and peritoneal xenograft nude mouse models was significantly inhibited by intragastric administration of 1000 mg/kg of α-bisabolol, once a week for three weeks. The results indicate that α-bisabolol could be a novel therapeutic option for the treatment of pancreatic cancer.
Matrices that preserve vectors of fixed sign variation (2007)

For each k≥ 0, those nonsingular matrices that transform the set of totally nonzero vectors with k sign variations into (respectively, onto) itself are studied. Necessary and sufficient conditions are provided. The cases k=0,1,2,n-3,n-2,n-1 are completely characterized.