gebhart/patrepeval huggingface dataset:
Myc-mediated apoptosis is blocked by ectopic expression of Bcl-2. (1993)

The product of the c-myc proto-oncogene is an important positive regulator of cell growth and proliferation. Recently, c-Myc has also been demonstrated to be a potent inducer of apoptosis when expressed in the absence of serum or growth factors. To further examine Myc-induced apoptosis, we coexpressed the proto-oncogene bcl2, which has been shown to block apoptosis in other systems, with c-myc in serum-deprived Rat 1a fibroblasts. Here we report that ectopic expression of bcl2 specifically blocks apoptosis induced by constitutive c-myc expression. Constitutive c-myc expression in serum-deprived Rat 1a cells caused a > 15-fold increase in the number of dead cells, accompanied by DNA fragmentation. However, coexpression of bcl2 with c-myc in these cells led to a 10-fold increase in the number of live cells and a significant decrease in DNA fragmentation. Thus, Bcl-2 effectively inhibits Myc-induced apoptosis in serum-deprived Rat 1a fibroblasts without blocking entry into the cell cycle. These results imply that apoptosis serves as a protective mechanism to prevent tumorigenicity elicited by deregulated Myc expression. This protective mechanism is abrogated, however, by Bcl-2 and therefore may explain the synergism between Myc and Bcl-2 observed in certain tumor cells.
High‐level production of amorpha‐4,11‐diene in a two‐phase partitioning bioreactor of metabolically engineered Escherichia coli (2006)

Reconstructing synthetic metabolic pathways in microbes holds great promise for the production of pharmaceuticals in large-scale fermentations. By recreating biosynthetic pathways in bacteria, complex molecules traditionally harvested from scarce natural resources can be produced in microbial cultures. Here we report on a strain of Escherichia coli containing a heterologous, nine-gene biosynthetic pathway for the production of the terpene amorpha-4,11-diene, a precursor to the anti-malarial drug artemisinin. Previous reports have underestimated the productivity of this strain due to the volatility of amorphadiene. Here we show that amorphadiene evaporates from a fermentor with a half-life of about 50 min. Using a condenser, we take advantage of this volatility by trapping the amorphadiene in the off-gas. Amorphadiene was positively identified using nuclear magnetic resonance spectroscopy and determined to be 89% pure as collected. We captured amorphadiene as it was produced in situ by employing a two-phase partitioning bioreactor with a dodecane organic phase. Using a previously characterized caryophyllene standard to calibrate amorphadiene production and capture, the concentration of amorphadiene produced was determined to be 0.5 g/L of culture medium. A standard of amorphadiene collected from the off-gas showed that the caryophyllene standard overestimated amorphadiene production by approximately 30%.
The Crystal Structure of Placental Growth Factor in Complex with Domain 2 of Vascular Endothelial Growth Factor Receptor-1 (2004)

Placental growth factor (PlGF) is a member of the vascular endothelial growth factor (VEGF) family and plays an important role in pathological angiogenic events. PlGF exerts its biological activities through binding to VEGFR1, a receptor tyrosine kinase that consists of seven immunoglobulin-like domains in its extracellular portion. Here we report the crystal structure of PlGF bound to the second immunoglobulin-like domain of VEGFR1 at 2.5 A resolution and compare the complex to the closely related structure of VEGF bound to the same receptor domain. The two growth factors, PlGF and VEGF, share a sequence identity of approximately 50%. Despite this moderate sequence conservation, they bind to the same binding interface of VEGFR1 in a very similar fashion, suggesting that both growth factors could induce very similar if not identical signaling events.
3 Tesla Delayed Contrast Magnetic Resonance Imaging Evaluation of Ménière's Disease (2008)

Abstract Objective: To determine whether 3 Tesla (T) magnetic resonance imaging (MRI) with delayed contrast imaging has sufficient anatomic resolution to image the intracochlear fluid spaces (i.e., the scala tympani, scala media, and scala vestibuli) of the inner ear and identify endolymphatic hydrops in vivo. Study Design: Four normal subjects underwent 3T MRI scanning after the administration of gadodiamide intravenous (IV) contrast. MRI region of interest signal intensity was used to determine the diffusion of gadodiamide into the perilymphatic fluid spaces over time. Seven subjects with unilateral Ménière's disease underwent 3T MRI 4 hours after administration of gadodiamide IV contrast agent. Results: All four normal subjects demonstrated perilymphatic enhancement by 4 hours postinjection. Loss of definition of the membranous cochlea was noted in five of the seven subjects with Ménière's disease. Precise definition of the scala media could not be achieved with this imaging protocol. Conclusion: Delayed contrast imaging of the inner ear with 3T MRI revealed in vivo changes of the membranous labyrinth consistent with unilateral Ménière's disease.
Voronoi binding site models: Calculation of binding modes and influence of drug binding data accuracy (1989)

Abstract A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time‐consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three‐region site then as a single region site, but never as a two‐region site.
360 degrees video coding using region adaptive smoothing (2015)

360 degrees video is emerging as a new way of experiencing immersive video due to the ready availability of powerful handheld devices such as smartphones. 360 degrees video enables immersive “real life”, “being there” experience for consumers by capturing the 360 degree view of the world. Users can change their viewpoint and dynamically view any part of the captured scene they desire. 360 degrees video requires higher bitrate than conventional video due to increased video resolution (4K and beyond) needed to support the wider field of view. Efficient compression of 360 degrees video is thus needed to provide high quality immersive video viewing experience to consumers. This paper provides an overview of 360 degrees video and presents a region adaptive video smoothing technique that exploits the unique characteristics of 360 degrees video to provide up to 20% bitrate savings with minimal perceptual quality degradation while requiring no modifications to the video decoder.
Prevention of Activated Neutrophil Adhesion to Endothelium by Soluble Adhesion Protein GMP140 (1990)

Neutrophils and monocytes, but not lymphocytes, adhered strongly to plastic surfaces coated with GMP140, a protein of endothelial cells and platelets. This adhesion of neutrophils was mediated by GMP140 and not by the CD18 integrin complex. By contrast, GMP140 in solution inhibited the CD18-dependent adhesion of tumor necrosis factor-alpha-activated neutrophils to plastic surfaces and resting endothelium, but not of resting neutrophils to tumor necrosis factor-alpha-activated endothelium. Thus, the binding of a soluble form of an adhesion protein selectively inhibited another set of adhesive events. Soluble GMP140 may be important in maintaining the nonadhesiveness of neutrophils in the circulation and may serve to limit inflammatory reactions.
Fourfold to threefold transition in diamondlike amorphous carbon films: A study of optical and electrical properties (1985)

Hard, diamond-like amorphous carbon films (a-C) were prepared as a function of sputtering power density by employing dc planar magnetron sputtering of a graphite target in pure argon. Films deposited at 300 K and at increasing sputtering power density in the range 0.25–25 W cm−2 show a transition of optical and electrical properties, with the room temperature electrical conductivity increasing from 5×10−4 to 5 Ω−1 cm−1 and the optical gap decreasing from 0.74 to 0.40 eV. The imaginary part ε2 of the complex dielectric function is determined in the photon energy range 0.5–7 eV and shows a clear dependence on sputtering power density. The ε2 spectra for a a-C films possess features typical of amorphous semiconductors. neff, the effective number of valence electrons per carbon atom taking part in optical transitions, is determined via a sum rule operation on ε2. Comparisons of neff for each a-C film with that for crystalline graphite allow the average coordination of the carbon atom to be determined. We observe a systematic four-fold to three-fold transition, with the ratio of carbon atoms having four-fold sp3 configuration (diamond-like) to carbon atoms with three-fold sp2 configuration (graphite) varying from 3:1 to 1:1.
Asymmetric Michael Reaction of Acetaldehyde Catalyzed by Diphenylprolinol Silyl Ether (2008)

An acetaldehyde breakthrough: The catalytic asymmetric Michael addition reaction of acetaldehyde and various nitroalkenes in the presence of a chiral diphenylprolinol silyl ether organocatalyst is described (see scheme; TMS=trimethylsilyl). The desired 1,4-addition products, α-unsubstituted γ-nitro aldehydes, were obtained in good yields with excellent enantioselectivities.
Compact monocrystalline silicon solar modules with high voltage outputs and mechanically flexible designs (2010)

A type of compact (∼cm2) high voltage photovoltaic module that utilizes large collections of ultrathin (∼15 μm), small (∼45 μm wide, ∼1 mm long) silicon solar cells was fabricated and characterized. Integration on thin sheets of plastic yielded flexible modules with per-cell efficiencies of ∼8%, voltage outputs >200 V, and maximum power outputs >1.5 mW.
Gepirone and the Treatment of Panic Disorder (1993)

Gepirone, an azapirone, is a potent 5-hydroxytryptamine 1A (5-HT1A) agonist. We report an uncontrolled 6-week study in 21 patients (4 men, 17 women: mean age, 36.71 years) with a concurrent DSM-III-R diagnosis of generalized anxiety disorder and panic disorder with agoraphobia. After a 2-week medication-free period, patients were started on 2 mg of gepirone per day increasing over 3 weeks to 12 mg/day. Three patients dropped out in the first week, and one patient violated the protocol. They were therefore excluded from analysis. Two patients who dropped out at weeks 4 and 5 because they found the treatment ineffective were included. Twelve of the 17 patients (70.6%) had at least a 50% reduction in their panic attacks by week 6, and 9 of them had at least a 50% reduction by week 3. Ten patients had "0" panic attacks by week 6 (59%). On the Hamilton Anxiety Scale, 65% had a 50% or greater reduction in total score, mostly beginning in week 1. On Global Assessment, by week 6, 11 were much improved or better (65%). Adverse effects were rare and consisted of stomach upset, dizziness, or headaches. This preliminary study suggests the possible efficacy of gepirone in panic disorder.
Recovering guaranteed performance service connections from single and multiple faults (2002)

Fault recovery techniques must be reexamined in the light of the new guaranteed performance services that high-speed packet/cell switched networks will support. We investigate the rerouting of guaranteed performance service connections on the occurrence of link faults, focussing on the aspects of route selection and establishment in the network. In a previous investigation, we explored some components of rerouting in the presence of single link faults in the network. In this paper we study the behavior of our techniques in the presence of multiple link faults in the network. We also examine the technique of retries to improve the success of rerouting. Our schemes are simulated on a cross-section of network workloads, and compared using several performance criteria. We use our results to develop a new delayed retry technique, which performs well for all our performance criteria.
All-fiber electrooptical mode-locking and tuning (2005)

Active mode-locking of a fiber laser with an all-fiber electrooptic modulator is demonstrated. A 1.4-V driving signal was used, creating subnanosecond single pulses at the fundamental frequency of the cavity (12 MHz). The modulator was a packaged Mach-Zehnder interferometer incorporating a poled twin-hole fiber in one of the arms. The switching voltage was 230 V at 1550 nm, with extinction ratio /spl sim/20 dB. The interferometer could be electrooptically tuned by 3.5 nm.
Association of the dopamine transporter gene and ADHD symptoms in a Canadian population‐based sample of same‐age twins (2007)

Attention deficit hyperactivity disorder (ADHD) is the most prevalent psychiatric disorder emerging during childhood. Psychostimulant medications (e.g., methylphenidate) noticeably reduce ADHD symptoms in most children. Since methylphenidate inhibits dopamine transporter activity, the dopamine transporter gene (DAT1) was considered to be the prime candidate risk gene in ADHD. Several studies found evidence for an association between the 10-repeat allele of the variable number of tandem repeat (VNTR) located in the 3' untranslated region and ADHD and/or ADHD symptoms in clinical and population-based samples. However, this finding was not replicated in all samples. In this study, we investigated the association between the DAT1 gene and ADHD symptoms in a population-based twin sample from Québec (Canada). We used two polymorphisms, the VNTR and rs27072, the last providing the most significant results in a clinical sample from Toronto (Ontario, Canada). No association was noted between the VNTR and ADHD symptoms in children at 6 and 7 years of age, as reported by teachers. However, a significant association was found for the rs27072 polymorphism and symptoms of inattention and hyperactivity/impulsivity. These findings indicate that the DAT1 gene contributes to ADHD symptoms in this sample and further suggest that the VNTR may not be the optimal polymorphism for study in all populations.
Correction of Abnormal Cerebroside Sulfate Metabolism in Cultured Metachromatic Leukodystrophy Fibroblasts (1971)

Cultured fibroblasts derived from patients with late infantile metachromatic leukodystrophy incorporated arylsulfatase A from the growth medium. Upon exposure to cerebroside sulfate, they exhibited patterns of uptake and hydrolysis indistinguishable from cells derived from control subjects. Furthermore, inclusion granules formed in the metachromatic leukodystrophy fibroblasts upon exposure to sulfatides were cleared by subsequent supplementation of the growth medium with arylsulfatase A.
Regulation of Bone Formation (1983)

DURING the past two decades our ideas about the regulation of bone formation have been expanded by new findings at the molecular, cellular, and tissue level. At the molecular level we have learned how collagen, the major component of bone matrix, is synthesized, and we have identified several noncollagen proteins in bone. At the cellular level we have learned more about the hormonal control of the osteoblasts that synthesize bone matrix. At the tissue level the concept of coupling between osteoclastic bone resorption and osteoblastic bone formation in bone remodeling has provided a new way to describe the relation between . . .
ChemInform Abstract: An Effective and Convenient Esterification of Cephalosporin Derivatives by Using Quaternary Ammonium Salts as Catalysts. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Reflectance spectroscopy with polarized light: is it sensitive to cellular and nuclear morphology (1999)

We present a method for selective detection of size-dependent scattering characteristics of epithelial cells in vivo based on polarized illumination and polarization sensitive detection of scattered light. We illustrate the method using phantoms designed to simulate squamous epithelial tissue and progressing to epithelial tissue in vitro and in vivo. Elastic light scattering spectroscopy with polarized illumination/detection dramatically reduces background signals due to both diffuse stromal scattering and hemoglobin absorption. Resulting spectra can be described as a linear combination of forward and backscattering components determined from Mie theory. Nuclear sizes and refractive indices extracted by fitting experimental spectra to this model agree well with previous measurements. Reflectance spectroscopy with polarized light can provide quantitative morphological information which could potentially be used for non-invasive detection of neoplastic changes.
Fluorescence Studies of Exchangeable Apolipoprotein-Lipid Interactions (1998)

Apolipophorin III (apoLp-III) from the Sphinx moth, Manduca sexta, is an 18-kDa exchangeable apolipoprotein that reversibly associates with lipoprotein particles. In the absence of lipid, apoLp-III exists as an elongated bundle of five amphipathic alpha-helices. Upon lipid association, the protein is postulated to undergo a major conformational change, wherein the bundle opens around hinge loop regions, resulting in exposure of its hydrophobic interior. Fluorescence quenching techniques have been employed to study apoLp-III helix topography and spatial arrangement in phospholipid disc complexes and intact lipoprotein particles. Intrinsic fluorescence of the single tyrosine in apoLp-III was exploited to monitor the location of helix 5 in model disc complexes. To investigate other regions of the protein, site-directed mutagenesis was performed to introduce cysteine residues, replacing Asn-40 (helix 2, N40C) or Leu-90 (helix 3, L90C), thereby providing two mutant apoLp-IIIs, each with a single site for covalent attachment of the extrinsic fluorescent probe, N-(1-pyrene) maleimide. In the lipid-free state, pyrene-N40C- and pyrene-L90C-apoLp-III were highly accessible to the negatively charged aqueous quencher KI, yielding Ksv values of 27.1 and 19.8 M-1, respectively. Upon binding to the surface of a spherical lipoprotein particle, Ksv values for KI decreased by about 90% for both pyrene-labeled apoLp-IIIs, indicating a significant change in the local microenvironment of the fluorophores. A lesser decrease in Ksv was observed when the pyrene-labeled apoLp-IIIs were bound to phospholipid disc complexes. When spin-labeled fatty acids 5-doxylstearic acid and 12-doxylstearic acid were used as lipophilic quenchers, tyrosine and pyrene fluorescence were more effectively quenched by 5-doxylstearic acid in both phospholipid bilayer disc complexes and spherical lipoprotein particles. These data provide insight into the spatial topography of apoLp-III alpha-helices in phospholipid disc complexes and support the concept that interaction with spherical lipoprotein particles results in superficial contact of apoL-III helical segments with the monolayer surface, providing a basis for its reversible binding ability.
The Isopeptidase USP2a Protects Human Prostate Cancer from Apoptosis (2006)

Deubiquitinating enzymes can prevent the destruction of protein substrates prior to proteasomal degradation. The ubiquitin-specific protease 2a (USP2a) deubiquitinates the antiapoptotic proteins Fatty Acid Synthase and Mdm2. Here, we show that when USP2a is overexpressed in nontransformed cells, it exhibits oncogenic behavior both in vitro and in vivo and prevents apoptosis induced by chemotherapeutic agents. Notably, USP2a silencing in several human cancer cell lines results in apoptosis. Gene set enrichment analysis, which focuses on groups of genes sharing biological function or regulatory pathways, was done on microarray expression data from human prostate cancers. The cell death-related gene set, as well as a selected cluster of validated p53 target genes, were significantly enriched in the low USP2a expression group of tumors. Conversely, genes implicated in fatty acid metabolism were significantly associated with tumors expressing high USP2a (44%). The expression profile analysis is consistent with the effects of USP2a on its known targets, i.e., Fatty Acid Synthase and Mdm2, defining a subset of prostate tumors resistant to apoptosis. USP2a thus represents a therapeutic target in prostate cancer.
A 12.5Gb/s SerDes in 65nm CMOS Using a Baud-Rate ADC with Digital Receiver Equalization and Clock Recovery (2007)

A DSP-based low-power 12.5Gb/s SerDes using a baud-rate ADC and a digital data-path is developed for backplane data communication. A digital 2-tap FFE and a 5-tap DFE in the RX provide channel compensation. A BER of <10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-15</sup> is measured over legacy backplanes with 24dB loss at Nyquist. The power consumption and die area are 330mW and 0.45mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> per TX/RX pair
Protecting Effect of Chitin and Chitosan on Experimentally Induced Murine Candidiasis (1984)

Chitin and chitosan were found to exhibit a protective effect on mice administered these polysaccharides intraperitoneally against infection of the viable cells of Candida albicans NIH A-207 strain. A significant difference was observed between the protective effects of chitin and chitosan, i.e., chitin was much more effective than chitosan when the C. albicans cells were challenged via the intravenous route. In intraperitoneal inoculations of C. albicans cells, however, chitosan provided stronger resistance for mice than chitin. It has also been revealed that the number of polymorphonuclear leukocytes from circulating blood of chitin-administered mice increased remarkably compared with that of untreated and chitosan-treated mice, and that the increase of active oxygen-generating phagocytic cells was significant. On the other hand, the number of peritoneal exudate cells (PEC) and the amounts of active oxygen generated from these cells in chitosan-treated mice were larger than those of chitin-treated mice. However, candidacidal activities of PEC per fixed cell number in mice treated with chitin or with chitosan were almost the same and greater than those of untreated mice.
Quantitative Structure-Activity Relationship (QSAR) and Rational Drug Design for Some Antineoplastic Thalidomide and Glutarimide Derivatives. (1976)

Department of Pharmacy, Jadavpur University, Calcutta-700 032, India. <em>Manuscript received 27 October 1975 ; revised 12 May 1976 ; accepted 7 June 1976</em> Quantitative structure-activity relationship (QSAR) of 38 thalidomide and glutari­mide derivatives, earlier synthesized and evaluated as possible antineoplastic agents against Ehrlich ascites carcinoma, has been determined with the help of Free-Wilson's Mathematical Model which results in the prediction and rational designing of the most potent member in this class of compounds.