gebhart/patrepeval huggingface dataset:
Androgen receptor localisation and turnover in human prostate epithelium treated with the antiandrogen, casodex (2000)

In vitro models of normal and malignant human prostate are currently limited to a few well established cell lines that, with a single exception (LNCaP), fail to express the androgen receptor (AR) - a common characteristic of prostatic epithelium grown in culture. To investigate the molecular mechanism of action of the non-steroidal antiandrogen Casodex (bicalutamide) against wild-type AR, we have established a transient AR expression model in non-tumorigenic prostate cells of both epithelial and mesenchymal origin. In this model, both dihydrotestosterone and Casodex can effectively transport the AR protein into the nucleus of prostate cells. Whereas the natural ligand, dihydrotestosterone, stabilises the receptor, the AR is rapidly degraded at a nuclear location when the transfected cells are treated with Casodex. In contrast, whereas the mutant AR in the LNCaP line is also degraded on Casodex treatment over the same time period, its intracellular targeting is defective.
T-cell receptor gene transfer for the treatment of leukemia and other tumors (2010)

Almost two decades ago the potency of adoptive T-cell therapy was demonstrated by the success of donor lymphocyte infusions for the treatment of chronic myeloid leukemia after allogeneic stem cell transplantation. Since then several studies have demonstrated the clinical efficacy of adoptively transferred T cells for the treatment of viral infections as well as cancers. The broad application of adoptive immunotherapy using antigen-specific T cells is, however, hampered by the inability to isolate and expand large numbers of T cells with a defined specificity and phenotype. In addition, the T-cell receptor (TCR) repertoire useful for the generation of T cells directed against specific antigens is often lacking. The lack of an effective T-cell repertoire is especially relevant for tumor-associated self-antigens, since high affinity T cells directed against these self-antigens are mostly deleted from the TCR repertoire due to self-tolerance.
Cilostazol Protects Against Brain White Matter Damage and Cognitive Impairment in a Rat Model of Chronic Cerebral Hypoperfusion (2006)

Our results indicate that cilostazol exerts a brain-protective effect through the CREB phosphorylation pathway leading to upregulation of Bcl-2 and COX-2 expressions and suggest that cilostazol is potentially useful for the treatment of cognitive impairment in poststroke patients.
Retargeting of cytosolic proteins to the plasma membrane by the Lck protein tyrosine kinase dual acylation motif (1997)

Several members of the Src family of protein tyrosine kinases have a N-terminal dual acylation motif which specifies their myristoylation and S-acylation. These lipid modifications are necessary for correct intracellular localisation to the plasma membrane and to detergent-resistant glycolipid-enriched membrane domains (GEMs). Using chimaeras of the Lck dual acylation motif with two normally cytosolic proteins (chloramphenicol acetyl transferase and galectin-3), we show here that this motif is sufficient to encode correct lipid modification and to target these chimaeras to the plasma membrane, as demonstrated by subcellular fractionation and confocal immunofluorescence microscopy of transiently transfected COS cells. In addition, the chimaeras are resistant to extraction with cold non-ionic detergent, indicating targeting to GEM subdomains in the plasma membrane. The dual acylation motif has potential for targeting proteins to specific plasma membrane subdomains involved in signalling.
Coupling of electronic charge and spin at a ferromagnetic-paramagnetic metal interface (1988)

Microscopic models are presented to elucidate the concept of interfacial charge-spin coupling. At the interface between a ferromagnet and a paramagnet, the spin subbands are loosely coupled, an interfacial conductance may be defined for each, and a result of their inequivalence is that an electric current flowing from a ferromagnetic metal into a paramagnetic metal will be partially spin polarized, i.e., will have an associated current of magnetization. The inverse is also true; nonequilibrium magnetization present in a paramagnetic metal can be detected as an open circuit voltage across an interface between the paramagnet and a ferromagnet. Using this effect, a new technique to measure conduction electron relaxation times is described.
Mechanisms of Formation Damage and Permeability Impairment Associated With the Drilling, Completion and Production of Low API Gravity Oil Reservoirs (1995)

Abstract The economic production of heavy oil reservoirs requires an indepth understanding of the specific mechanisms of formation damage which are unique to these types of formations. This paper will provide a brief description of some of the dominant mechanisms of permeability impairment which can occur in low API gravity oil-producing zones. These include: Drilling induced damage solids entrainmentfines migrationrock/fluid incompatibilitiesfluid/fluid incompatibilities Reactive clay induced damage Formation of emulsions (water-oil, oil-water) Foamy oil phenomena Sand control and consolidation issues Completion induced damage, acidizing, solvent injection, etc. Thermally induced formation damage mineral transformationsmineral and formation dissolutionwettability alterations Biologically induced formation damage issues Formation damage issues peculiar to the drilling and completion of horizontal wells in heavy oil producing zones. This paper provides a general overview of many of the potential types of formation damage which drilling, production and reservoir engineers as well as geologists and geophysicists should be aware of when planning exploitation programs for heavy oil plays.
Polycomb Protein EZH2 Regulates Tumor Invasion via the Transcriptional Repression of the Metastasis Suppressor RKIP in Breast and Prostate Cancer (2012)

Epigenetic modifications such as histone methylation play an important role in human cancer metastasis. Enhancer of zeste homolog 2 (EZH2), which encodes the histone methyltransferase component of the polycomb repressive complex 2 (PRC2), is overexpressed widely in breast and prostate cancers and epigenetically silences tumor suppressor genes. Expression levels of the novel tumor and metastasis suppressor Raf-1 kinase inhibitor protein (RKIP) have been shown to correlate negatively with those of EZH2 in breast and prostate cell lines as well as in clinical cancer tissues. Here, we show that the RKIP/EZH2 ratio significantly decreases with the severity of disease and is negatively associated with relapse-free survival in breast cancer. Using a combination of loss- and gain-of-function approaches, we found that EZH2 negatively regulated RKIP transcription through repression-associated histone modifications. Direct recruitment of EZH2 and suppressor of zeste 12 (Suz12) to the proximal E-boxes of the RKIP promoter was accompanied by H3-K27-me3 and H3-K9-me3 modifications. The repressing activity of EZH2 on RKIP expression was dependent on histone deacetylase promoter recruitment and was negatively regulated upstream by miR-101. Together, our findings indicate that EZH2 accelerates cancer cell invasion, in part, via RKIP inhibition. These data also implicate EZH2 in the regulation of RKIP transcription, suggesting a potential mechanism by which EZH2 promotes tumor progression and metastasis.
Mitochondria of mammalian<i>Plasmodium</i>spp. (1991)

Highly purified mitochondrial fractions have been isolated from the intraerythrocytic stages of two mammalian Plasmodium spp., Plasmodium yoelii of rodents and Plasmodium falciparum of man. Mitochondria of the former parasite are cristate whereas those of the latter are essentially acristate. Isolated mitochondria from both parasite species were heterogeneous with respect to size, shape, density of matrix staining and extent of internal structure. Respiratory assay, by reduction of exogenous cytochrome c, showed NADH, alpha-glycerophosphate and succinate to be the substrates with the greatest potential for metabolism. Additionally, proline, dihydroorotate and glutamate (P. falciparum only) were oxidized at low rates. A number of NAD(+)-linked substrates were not utilized. The NADH-dependent reduction of cytochrome c was insensitive to rotenone and antimycin A. Fumarate inhibited the NADH-dependent reduction of cytochrome c and stimulated the oxidation of NADH, suggestive of an NADH-fumarate reductase pathway. Oxidation of either alpha-glycerophosphate or succinate was fully inhibited by standard mitochondrial electron transport inhibitors, including a number of Complex III inhibitors, although the concentrations required of such inhibitors (notably myxothiazol) were relatively high compared to mammalian mitochondria. Dithionite-reduced minus oxidized difference spectra indicated the presence of cytochromes aa3, b, c and c1 in mitochondria of both parasite species, but at a higher cytochrome to protein ratio in P. yoelii. Freshly isolated mitochondria from either species exhibited only low respiratory control ratios with alpha-glycerophosphate or succinate as substrates. The apparent absence of a respiratory chain 'Site I' in such mitochondria may mean that NADH-fumarate reductase serves to reoxidize mitochondrial NADH.
Thermal Phase Behaviour of Thallium (I) Branched Alkanoates—Influence of Chain Length and Position of Branching on the Occurrence of the (Anhydrous) Neat Phase (1986)

Abstract The thermotropic phase behaviour of anhydrous thallium (I) salts of branched chain aliphatic carboxylic acids was investigated by means of DSC and optical polarisation microscopy. The influence of the alkyl chain length and position of branching on the thermotropic phase behaviour was studied. The salts of α-branched acids did not show a stable neat phase. Salts which are alkyl substituted in the β and higher positions do however show stable neat phases. These results are compared with those found for alkali metal alkanoates. Key Words: neat phasethallium alkanoatesbranched chains
Fixed-pattern noise in photomatrices (1970)

Two MOS photomatrix configurations, voltage sampling and recharge sampling, have been compared with regard to sources of fixed-pattern noise. Voltage sampling provides a high-amplitude low-impedance photosignal, with FPN primarily due to threshold variation in the amplifying MOST at each element. Recharge sampling is used for large high-yield rapidly scanned arrays, with FPN caused mostly by variations in spurious capacitive breakthrough. Production peak-to-peak signal to FPN ratios are 20:1 for voltage sampling and 50:1 for recharge sampling.
Structure of thiolactomycin (1989)

[4R,(2E,5E)]-3-Hydroxy-2,4,6-trimethyl-2,5,7-octatriene-4-thiol ide, C11H14O2S, Mr = 210.30, hexagonal, P6(5), a = b = 9.8514 (6), c = 19.954 (1) A, V = 1677.1 A3, Z = 6, Dx = 1.249 g cm-3, lambda(Cu K alpha) = 1.5418 A, u = 23.07 cm-1, F(000) = 672, T = 298 K, R = 0.028 for 1021 unique reflections [Fo2 greater than 2 sigma(Fo2)]. The absolute configuration was determined by the Bijvoet method. The thiolactone ring is planar with S-C bond distances of 1.774 (3) and 1.856 (3) A, and C-S-C angle of 93.3 (1) degrees. The angle between least-squares planes for the thiolactone and butadienyl groups is 101.7 degrees.
The Reading/Writing Lab: A First-Aid Station for Every School (1985)

In the fall of 1981, Loretta (real student, but fictitious name) cam to the University of Albuquerue as a freshman from nearby Zuni Pueblo. Her placement procedure included the Nelson-Denny Reading Test, Form C, and an essay on the assigned topic, "My Worries About College." Reading scores indicated a vocabulary level of 8.7 and a comprehension level of 9.2.
Reduction in Colon Cancer Risk by Consumption of Kava or Kava Fractions in Carcinogen-Treated Rats (2012)

Epidemiological studies suggest that kava reduces colon cancer risk. However, no experimental studies of the chemopreventive properties of kava toward colon cancer have been reported. Further, there are concerns regarding hepatotoxicity of kava. The goal of this study was to determine whether kava consumption reduces markers of colon cancer in an animal model and to study the safety of kava. An ethanolic extract and polar and nonpolar fractions of the kava extract were fed to rats for 12 days prior to, during, and after administration of dimethylhydrazine, a colon-specific carcinogen. After 14 wk, rats fed the nonpolar extract had a significant reduction in precancerous lesions [aberrant crypt (AC) foci (ACF)] as well as large (≥ 4 AC/ACF) sialomucin-only expressing foci, an indicator of greater tumorigenic potential, compared to the control group. Groups fed the ethanolic extract and polar kava fraction trended toward reductions in ACF and large sialomucin-only expressing foci. The combined kava groups had significantly fewer total AC, ACF, large ACF, and large sialomucin-only expressing foci compared to the control group. Histological examination found no hepatic lesions in animals consuming the kava diets, suggesting that kava is safe to consume. Our results support that kava may reduce colon cancer risk.
CONVERGENCE OF V-CYCLE AND F-CYCLE MULTIGRID METHODS FOR THE BIHARMONIC PROBLEM USING THE MORLEY ELEMENT (2004)

Abstract. Multigrid V-cycle and F-cycle algorithms for the biharmonic problem using the Morley element are studied in this paper. We show that the contraction numbers can be uniformly improved by increasing the number of smoothing steps.
Genome structure and evolution in Drosophila: applications of the framework P1 map. (1994)

Physical maps showing the relative locations of cloned DNA fragments in the genome are important resources for research in molecular genetics, genome analysis, and evolutionary biology. In addition to affording a common frame of reference for organizing diverse types of genetic data, physical maps also provide ready access to clones containing DNA sequences from any defined region of the genome. In this paper, we present a physical map of the genome of Drosophila melanogaster based on in situ hybridization with 2461 DNA fragments, averaging approximately 80 kilobase pairs each, cloned in bacteriophage P1. The map is a framework map in the sense that most putative overlaps between clones have not yet been demonstrated at the molecular level. Nevertheless, the framework map includes approximately 85% of all genes in the euchromatic genome. A continuous physical map composed of sets of overlapping P1 clones (contigs), which together span most of the euchromatic genome, is currently being assembled by screening a library of 9216 P1 clones with single-copy genetic markers as well as with the ends of the P1 clones already assigned positions in the framework map. Because most P1 clones from D. melanogaster hybridize in situ with chromosomes from related species, the framework map also makes it possible to determine the genome maps of D. pseudoobscura and other species in the subgenus Sophophora. Likewise, a P1 framework map of D. virilis affords potential access to genome organization and evolution in the subgenus Drosophila.
Clopidogrel‐Associated Bleeding and Related Complications in Patients Undergoing Coronary Artery Bypass Grafting (2008)

Clopidogrel exposure within 7 days before CABG is associated with an increase in major bleeding, hemorrhage-related complications, and transfusion requirements, and leads to potentially greater consumption of health care resources. The overall risks and benefits for each patient should be considered before using the drug.
Fully Solution-Processed Inverted Polymer Solar Cells with Laminated Nanowire Electrodes (2009)

We demonstrate organic photovoltaic cells in which every layer is deposited by solution processing on opaque metal substrates, with efficiencies similar to those obtained in conventional device structures on transparent substrates. The device architecture is enabled by solution-processed, laminated silver nanowire films serving as the top transparent anode. The cells are based on the regioregular poly(3-hexylthiophene) and C(61) butyric acid methyl ester bulk heterojunction and reach an efficiency of 2.5% under 100 mW/cm(2) of AM 1.5G illumination. The metal substrates are adequate barriers to moisture and oxygen, in contrast to transparent plastics that have previously been used, giving rise to the possibility of roll-to-roll solution-processed solar cells that are packaged by lamination to glass substrates, combining the cost advantage of roll-to-roll processing with the barrier properties of glass and metal foil.
Silicon-on-insulator shortwave infrared wavelength meter with integrated photodiodes for on-chip laser monitoring (2014)

This paper demonstrates a very compact wavelength meter for on-chip laser monitoring in the shortwave infrared wavelength range based on an optimized arrayed waveguide grating (AWG) filter with an integrated photodiode array. The AWG response is designed to obtain large nearest neighbor crosstalk (i.e. large overlap) between output channels, which allows accurately measuring the wavelength of a laser under test using the centroid detection technique. The passive AWG is fabricated on a 220 nm silicon-on-insulator (SOI) platform and is combined with GaInAsSb-based photodiodes. The photodiodes are heterogeneously integrated on the output grating couplers of the AWG using DVS-BCB adhesive bonding. The complete device with AWG and detectors has a footprint of only 2 mm(2) while the measured accuracy and resolution of the detected wavelength is better than 20pm.
Concerted Nitric Oxide Formation and Release from the Simultaneous Reactions of Nitrite with Deoxy- and Oxyhemoglobin (2007)

Recent studies reveal a novel role for hemoglobin as an allosterically regulated nitrite reductase that may mediate nitric oxide (NO)-dependent signaling along the physiological oxygen gradient. Nitrite reacts with deoxyhemoglobin in an allosteric reaction that generates NO and oxidizes deoxyhemoglobin to methemoglobin. NO then reacts at a nearly diffusion-limited rate with deoxyhemoglobin to form iron-nitrosyl-hemoglobin, which to date has been considered a highly stable adduct and, thus, not a source of bioavailable NO. However, under physiological conditions of partial oxygen saturation, nitrite will also react with oxyhemoglobin, and although this complex autocatalytic reaction has been studied for a century, the interaction of the oxy- and deoxy-reactions and the effects on NO disposition have never been explored. We have now characterized the kinetics of hemoglobin oxidation and NO generation at a range of oxygen partial pressures and found that the deoxy-reaction runs in parallel with and partially inhibits the oxy-reaction. In fact, intermediates in the oxy-reaction oxidize the heme iron of iron-nitrosyl-hemoglobin, a product of the deoxy-reaction, which releases NO from the iron-nitrosyl. This oxidative denitrosylation is particularly striking during cycles of hemoglobin deoxygenation and oxygenation in the presence of nitrite. These chemistries may contribute to the oxygen-dependent disposition of nitrite in red cells by limiting oxidative inactivation of nitrite by oxyhemoglobin, promoting nitrite reduction to NO by deoxyhemoglobin, and releasing free NO from iron-nitrosyl-hemoglobin.
Superior Therapeutic Index of Calmangafodipir in Comparison to Mangafodipir as a Chemotherapy Adjunct (2012)

Mangafodipir is a magnetic resonance imaging contrast agent with manganese superoxide dismutase (MnSOD) mimetic activity. The MnSOD mimetic activity protects healthy cells against oxidative stress-induced detrimental effects, e.g., myelosuppressive effects of chemotherapy drugs. The contrast property depends on in vivo dissociation of Mn(2+) from mangafodipir-about 80% dissociates after injection. The SOD mimetic activity, however, depends on the intact Mn complex. Complexed Mn(2+) is readily excreted in the urine, whereas dissociated Mn(2+) is excreted slowly via the biliary route. Mn is an essential but also a potentially neurotoxic metal. For more frequent therapeutic use, neurotoxicity due to Mn accumulation in the brain may represent a serious problem. Replacement of 4/5 of Mn(2+) in mangafodipir with Ca(2+) (resulting in calmangafodipir) stabilizes it from releasing Mn(2+) after administration, which roughly doubles renal excretion of Mn. A considerable part of Mn(2+) release from mangafodipir is governed by the presence of a limited amount of plasma zinc (Zn(2+)). Zn(2+) has roughly 10(3) and 10(9) times higher affinity than Mn(2+) and Ca(2+), respectively, for fodipir. Replacement of 80% of Mn(2+) with Ca(2+) is enough for binding a considerable amount of the readily available plasma Zn(2+), resulting in considerably less Mn(2+) release and retention in the brain and other organs. At equivalent Mn(2+) doses, calmangafodipir was significantly more efficacious than mangafodipir to protect BALB/c mice against myelosuppressive effects of the chemotherapy drug oxaliplatin. Calmangafodipir did not interfere negatively with the antitumor activity of oxaliplatin in CT26 tumor-bearing syngenic BALB/c mice, contrary calmangafodipir increased the antitumor activity.
Biological activity of benzylating N-nitroso compounds. Models of activated N-nitrosomethylbenzylamine (1983)

Unsymmetrically substituted N-nitrosomethylbenzylamine is an oesophageal carcinogen with potential methylating and benzylating properties. Whereas the methylating activity of the compound has been investigated, little is known of its potential benzylating properties. In order to elucidate the biological consequences of benzylation, related model compounds which are presumed benzylating agents were synthesized and tested for mutagenicity. N-nitrosobenzylurea and its structural analogue N-nitroso-p-methylbenzylurea were direct acting mutagens in Salmonella typhimurium TA 98. Activity was also present in TA 1535, but it was less pronounced. N-nitroso-alpha-acetoxybenzyl-benzylamine was equally mutagenic in S. typhimurium TA and TA 1535. N-nitroso-acetoxymethyl-benzylamine and N-nitrosoacetoxy-methyl-p-methylbenzylamine are two model compounds which may decompose by hydrolysis or through esterases to yield intermediates also though to arise after alpha-C hydroxylation of the methyl group of the parent nitrosamines. These compounds needed additional activation by enzymes present in the post-mitochondrial supernatant of rat liver. They were distinctly mutagenic in TA 98. Furthermore, all compounds also caused the induction of phage lambda in a qualitative assay with Escherichia coli Br 513. Thus, benzylation of DNA clearly results in a biological consequence. These findings are supportive of the theory that if enzymic attack occurs on the methyl group of N-nitrosomethylbenzylamine, benzylation may also contribute to the overall biological activity of the compound.
Efficient Deep Learning for Stereo Matching (2016)

In the past year, convolutional neural networks have been shown to perform extremely well for stereo estimation. However, current architectures rely on siamese networks which exploit concatenation followed by further processing layers, requiring a minute of GPU computation per image pair. In contrast, in this paper we propose a matching network which is able to produce very accurate results in less than a second of GPU computation. Towards this goal, we exploit a product layer which simply computes the inner product between the two representations of a siamese architecture. We train our network by treating the problem as multi-class classification, where the classes are all possible disparities. This allows us to get calibrated scores, which result in much better matching performance when compared to existing approaches.