gebhart/patrepeval huggingface dataset:
Synergism and Antagonism in Chemotherapy (1991)

Part 1 Reviews and methods of quantitation: synergism, antagonism and potentiation in chemotherapy - an overview, D.Rideout and T.-C.Chou the median effect principle and the combination index as tools for quantitation of synergism and antagonism, T.-C.Chou clinical studies of combination chemotherapy for cancer, E.Frei combined chemotherapeutic modalities for viral infections - rational and clinical potential, R.F.Schinazi antimalarial synergism and antagonism, J.L.Vennerston, et al quantitation of synergism and antagonism of two or more drugs by computerized analysis, J.Chou. Part 2 Mechanisms of interaction: potentiation through inhibition of metabolic drug inactivation - modulation of drug activity and toxicity by perturbation of glutathione metabolism, H.S.Friedman and O.W.Griffith synergy and antagonism in polymerase-targeted antiviral therapy - effects of deoxynucleoside triphosphate pool modulation on prodrug activation, T.Spector and J.A.Fyfe reversal of multidrug resistance in tumour cells, C.-P.H.Yang, et al biochemical mechanism of the synergistic interaction of antifolates acting on different enzymes of folate metabolic pathways, J.Galivan synergistic and antagonistic drug interactions resulting from multiple inhibition of metabolic pathways, R.C.Jackson enhanced effects of drugs that bind simultaneously to the same macromolecular target, L.Strekowski and W.D.Wilson modulation of 5-fluorouracil by metabolites and antimetabolites, E.Mini and J.R.Bertino synergism and antagonism through direct bond formation between two agents in situ, D.C.Rideout and T.Calogeropoulou chemotherapeutic potentiation through interaction at the level of DNA, B.A.Teicher, et al drug synergism, antagonsim and collateral sensitivity involving genetic changes, S.-H.Huang and J.S.Holcenberg. Part 3 Condition-selective synergism and antagonism: schedule-dependent effects in antineoplastic synergism and antagonsim, B.K.Chang effects of drug distribution and cellular microenvironment on the interaction of cancer chemotherapeutic agents, R.E.Durrand synergistic interactions at the solid tumour level through targeting of therapies against two or more different tumour cell subpopulations, D.W.Siemann and P.C.Keng selective synergism aganist the target versus host bone marrow progenitor cells, E.Berman and T.-T.Chang.
Successful therapy of pemphigus vulgaris with immunoadsorption using the TheraSorb™ adsorber (2008)

Pemphigus vulgaris (PV) is caused by autoantibodies to desmogleins. Standard immunosuppressive therapy may be limited by concomitant diseases or ineffective.In these cases, removal of circulating antibodies by immunoadsorption can induce remission. An 87-year-old woman with PV and considerable co-morbidities suffered from extensive mucous membrane erosions and bouts of skin blistering refractory to treatment with methotrexate,as well as mycopheno-late mofetil and corticosteroids even when combined with plasmapheresis and intravenous immunoglobulin. Adjuvant immunoadsorption therapy with the TheraSorbtrade mark columns-first weekly, than monthly-induced a complete remission, as well as a parallel decrease in PV antibody titers. Continued therapy for 18 months kept the patient in remission but for one infection-related relapse, and remission has been stable over two further years on low-dose methotrex-ate monotherapy. This case confirms the clinical efficacy of immunoad-sorption in PV and adds another type of adsorber column to the armamentarium, which is useful to the dermatologist who has to cooperate with local lipid apheresis or dialysis units.
Reclassification of Ruminococcus obeum as Blautia obeum comb. nov. (2014)

During our previous studies we reclassified Clostridium coccoides and a number of misclassified ruminococci into a novel genus Blautia within the family Lachnospiraceae. However, the Rules of the Bacteriological Code currently require that the types of all species and subspecies with new names (including new combinations) be deposited in two different collections in two different countries. The type strain of Ruminococcus obeum was, at that period in time, only deposited in the American Type Culture Collection (ATCC) and a second independent deposit, as required by the Code, was not available. Consequently, the transfer of this species to the genus Blautia could not be made, because the resulting species name would not conform to the Rules governing the valid publication of species names and deposit of type material (Rules 27 and 30) and consequently would not be considered to be validly published. This resulted in a nomenclatural and taxonomic anomaly with R. obeum being phylogenetically placed among members of the genus Blautia with 16S rRNA gene sequence similarities of between 91.8 and 96.6 %. In order to rectify this unsatisfactory situation, through our discussions with the ATCC, the deposit of strain R. obeum ATCC 29174(T) to the DSMZ as strain number DSM 25238(T) was completed. Hence, the transfer of R. obeum to the genus Blautia as Blautia obeum comb. nov. is now proposed. The type strain is ATCC 29174(T) ( = DSM 25238(T) = KCTC 15206(T)).
Transmission of Ehrlichia canis to Dogs by Ticks (Rhipicephalus sanguineus) (1975)

Two strains of Rhipicephalus sanguineus acquired Ehrlichia canis by feeding as either larvae or nymphs on acutely infected dogs and, in subsequent instars, transmitted the agent to normal dogs. Three strains of R sanguineus transmitted E canis as adults after their larval and nymphal stages fed on infected dogs. More than 400 adult female ticks were fed on infected dogs as larvae or nymphs or both, but none transmitted E canis transovarially.
Modeling and optimization of low-repetition-rate high-energy pulse amplification in cw-pumped erbium-doped fiber amplifiers (1993)

We numerically study amplification of low-repetition-rate high-energy pulses in a cw-pumped erbium-doped fiber amplifier. Maximizing the pulse-energy gain by optimization of the dopant and modal field radii resulted in improvements of as much as 7.3 dB with a 60-mW pump compared with a fiber with small radii suitable for amplification of cw signals. Output pulse energies of 0.15 mJ are possible at the same pump power. The improvements stem from a suppression of the losses from amplified spontaneous emission when the radii are made large.
Synthesis and Biological Activity of New Class of Dioxygenated Anticancer Agents (2005)

This paper describes extensive research on the activity of more of 100 cytotoxic compounds containing an oxygenated ring in their structure and isolated from natural plants or prepared by semisynthesis or synthesis from available intermediates. Anticancer drugs have been classified according to the chemical structure of the natural products that are considered to lead the series. The origin and mechanism of action involved in each case have been considered. This new family of natural, semisynthetic and synthetic products includes compounds with interesting antitumor activity such as podophyllotoxin derivatives, NK-611 (15), TOP-53 (16), NPF (24) and Tafluposide (28); camptothecin analogs such as 45 with a considerable cytotoxicity against beta-cell chronic lymphocytic leukemia (CLL), and 52 (new piperazinyl-CPT analog). New dioxygenated ellipticine analogs showed more activity and stability than the natural pattern when the structure incorporated a lactone function instead of the pyridine ring. In the acridine series the new tetracyclic derivatives 75 and 76 containing ethylenedioxy groups at the 2- and 3-positions of the acridine system exhibited the same activity as m-AMSA in vivo against murine P-388 leukemia. Other isolated compounds containing a dioxygenated ring in their structure such as 100 and 101 showed antitumor activities related to kinase inhibition, and are attractive candidates for development of new synthetic antitumor agents.
Pegylated arginine deiminase (ADI-SS PEG20,000 mw) inhibits human melanomas and hepatocellular carcinomas in vitro and in vivo. (2002)

Some murine melanomas and hepatocellular carcinomas (HCCs) have been shown to be auxotrophic for arginine. Arginine deiminase (ADI; EC 3.5.3.6.), an arginine-degrading enzyme isolated from Mycoplasma, can inhibit growth of these tumors. We found that ADI was specific for arginine and did not degrade other amino acids. Although arginine is not an essential amino acid for most cells, all human melanomas and HCCs tested were found to be inhibited by ADI in vitro. Arginine is synthesized from citrulline in two steps by argininosuccinate synthetase and argininosuccinate lyase. Melanomas and HCCs did not express argininosuccinate synthetase mRNA but did express argininosuccinate lyase mRNA, suggesting that the arginine auxotrophy of these cells was a result of an inability to produce argininosuccinate synthetase. Human melanomas and HCCs were transfected with an expression plasmid containing argininosuccinate synthetase cDNA. The transfected cells were much more resistant to ADI than the parental cells in vitro and in vivo. Initial attempts to use ADI in vivo indicated that this enzyme had little efficacy, consistent with its short circulation half-life. Formulation of ADI with polyethylene glycol to produce ADI-SS PEG(20,000 mw) resulted in an enzyme with a much longer circulation half-life that, and although equally effective in vitro, was more efficacious in the treatment of mice implanted with human melanomas and HCCs. These data indicate that sensitivity of melanoma and HCC is due to the absence of argininosuccinate synthetase in these cells and that an effective formulation of ADI, which causes a sustained decrease in arginine, may be a useful treatment for arginine auxotrophic tumors including melanoma and HCC.
Modulation of angiogenesis by dithiolethione‐modified NSAIDs and valproic acid (2007)

S-NSAIDs and S-valproate have potent anti-angiogenic activities mediated by their dithiole moieties. The novel properties of S-NSAIDs and S-valproate to inhibit pathological versus developmental angiogenesis suggest that these agents may have a role in cancer treatment.
Structural studies on the linkage unit between poly(galactosylglycerol phosphate) and peptidoglycan in cell walls of Bacillus coagulans (1985)

Structural studies were carried out on the linkage units in the teichoic-acid--glycopeptide complexes isolated from lysozyme digests of the cell walls of Bacillus coagulans AHU 1366. On treatment with 47% hydrogen fluoride, the complexes gave a disaccharide characterized as glucosyl(beta 1----4)N-acetylglucosamine together with major fragments, galactosyl(alpha 1----2)glycerol. By means of Smith degradation and partial acid hydrolysis, the teichoic acid chain was shown to be composed of the repeating units, galactosyl(alpha 1----2)glycerol-3(1)-phosphate, which were joined by phosphodiester bonds at C-6 of the galactose residues. The mild alkaline hydrolysis of teichoic-acid-linked glycan fragments yielded teichoic acid chains and disaccharide-linked glycan fragments, from which the disaccharide, glucosyl(beta 1----4)N-acetylglucosamine, was liberated by mild acid hydrolysis, whereas the same disaccharide linked to the teichoic acid chain was obtained by direct heating of the cell walls at pH 2.5. In addition, the presence of specialized glycerol phosphate units in the linkage region was shown by the isolation of tris(glycerol phosphate)3-glucosyl(beta 1----4)N-acetylglucosamine from the products of the Smith degradation of the teichoic-acid--glycopeptide complexes. Thus, it is concluded that the poly(galactosylglycerol phosphate) chain in the cell walls of B. coagulans AHU 1366 is linked to peptidoglycan through a novel linkage unit, bis(glycerol phosphate)-3-glucosyl(beta 1----4)N-acetylglucosamine.
Comparison of the diagnostic accuracy of CA27.29 and CA15.3 in primary breast cancer. (1999)

CA27.29 discriminates primary breast cancer from healthy subjects better than CA15.3, especially in patients with limited disease. Prospective studies are necessary to confirm this conclusion.
In vitro formation of polyglutamyl derivatives of methotrexate and 7-hydroxymethotrexate in human lymphoblastic leukemia cells. (1983)

The intracellular synthesis of polyglutamyl derivatives of both methotrexate (4-amino-N-10-methylpteroylglutamic acid) and 7-hydroxymethotrexate, the primary plasma metabolite of methotrexate in humans, was evaluated in a methotrexate-sensitive, acute lymphoblastic leukemia cell line, MOLT 4. These studies were performed using a highly specific ion-pairing high-pressure liquid chromatography method which permits the simultaneous determination of methotrexate, 7-hydroxymethotrexate, and their corresponding polyglutamyl derivatives. When MOLT 4 cells were exposed to 1 microM methotrexate, the monoglutamate attained a steady state after 30 min, and polyglutamyl derivatives having from one to 4 additional glutamyl residues were observed over 4 hr. Four additional metabolites were also detected upon incubation with 1 microM 7-hydroxymethotrexate. On the basis of the retention times for these compounds relative to methotrexate polyglutamyl standards and since these metabolites reverted to 7-hydroxymethotrexate upon treatment with a preparation of hog kidney conjugase, they were identified as polyglutamyl derivatives of 7-hydroxymethotrexate. The identification of 7-hydroxymethotrexate polyglutamyl derivatives in vitro raises the possibility of an important new dimension in the pharmacological action of methotrexate. We investigated the effect of extracellular 7-hydroxymethotrexate on net methotrexate uptake and metabolism when cells were exposed simultaneously to 1 microM [3H]-methotrexate and unlabeled 7-hydroxymethotrexate. A decrease in the levels of both intracellular methotrexate and the corresponding polyglutamyl derivatives was noted for cells treated with 1 or 10 microM 7-hydroxymethotrexate. However, no appreciable effect of 7-hydroxymethotrexate on the amount of polyglutamyl derivatives formed relative to the total intracellular antifolate was noted. These studies show that in MOLT 4 cells (a) both methotrexate and 7-hydroxymethotrexate are rapidly converted to polyglutamyl derivatives, and (b) 7-hydroxymethotrexate interferes with net methotrexate accumulation and metabolism when present simultaneously in the extracellular medium. These results, moreover, suggest a potential role for 7-hydroxymethotrexate in modulating the biochemical effects of methotrexate in vivo.
Adhesion of Bioinspired Micropatterned Surfaces:  Effects of Pillar Radius, Aspect Ratio, and Preload (2007)

Inspired by biological attachment systems, micropatterned elastomeric surfaces with pillars of different heights (between 2.5 and 80 microm) and radii (between 2.5 and 25 microm) were fabricated. Their adhesion properties were systematically tested and compared with flat controls. Micropatterned surfaces with aspect ratios above 0.5 were found to be more compliant than flat surfaces. The adhesion significantly increases with decreasing pillar radius and increasing aspect ratio of the patterned features. A preload dependence of the adhesion force has been identified and demonstrated to be crucial for obtaining adhesives with tunable adherence.
Post-treatment tumor gene expression signatures are more predictive of treatment outcomes than baseline signatures in breast cancer (2009)

Postchemotherapy tumor gene signatures outperformed baseline signatures and clinical predictors in predicting for pathological response and PFS, independent of clinical and pathological response to chemotherapy. Drug-induced tumor gene signatures may be more informative than unchallenged signatures in predicting treatment outcomes. These findings challenge the current practice of relying only on the baseline tumor to predict outcome, which overlooks the contributions of therapeutic interventions.
Variational Autoencoders for Deforming 3D Mesh Models (2018)

3D geometric contents are becoming increasingly popular. In this paper, we study the problem of analyzing deforming 3D meshes using deep neural networks. Deforming 3D meshes are flexible to represent 3D animation sequences as well as collections of objects of the same category, allowing diverse shapes with large-scale non-linear deformations. We propose a novel framework which we call mesh variational autoencoders (mesh VAE), to explore the probabilistic latent space of 3D surfaces. The framework is easy to train, and requires very few training examples. We also propose an extended model which allows flexibly adjusting the significance of different latent variables by altering the prior distribution. Extensive experiments demonstrate that our general framework is able to learn a reasonable representation for a collection of deformable shapes, and produce competitive results for a variety of applications, including shape generation, shape interpolation, shape space embedding and shape exploration, outperforming state-of-the-art methods.
New developments in the management of chronic lymphocytic leukemia: role of ofatumumab (2016)

Ofatumumab is one of the three anti-CD20 monoclonal antibodies currently available for the treatment of chronic lymphocytic leukemia (CLL). The US Food and Drug Administration (FDA) approved the use of ofatumumab in patients with CLL refractory to fludarabine and alemtuzumab in 2009, and the European Medicines Agency (EMA) granted approval for the same indication in 2010. Subsequent positive results of ofatumumab in combination with chlorambucil in treatment-naïve patients led the FDA in April 2014 to approve the use of this combination for first-line treatment of patients with CLL for whom fludarabine-based therapy is considered inappropriate. Later that year, the EMA approved the use of ofatumumab in combination with chlorambucil or bendamustine for the same indication. Ofatumumab has also shown potential as maintenance therapy for patients with relapsed CLL; an application to broaden the label for ofatumumab as maintenance therapy was submitted earlier this year to the EMA and FDA. Finally, ofatumumab has shown promising activity in combination with ibrutinib or idelalisib in relapsed/refractory CLL patients; combinations of ofatumumab with B-cell-receptor pathway inhibitors could represent another potential use of this antibody in the near future.
Increasing Anticarcinoma Activity of an Anti-erbB2 Recombinant Immunotoxin by the Addition of an Anti-EpCAM sFv (2007)

The synthesis of bispecific immunotoxin created a new biological agent with superior in vitro and in vivo activity (over monospecific immunotoxin), more broad reactivity, more efficacy against tumors in vivo, and diminished toxic effects in mice.
Energy management systems: state of the art and emerging trends (2013)

The electric grid is radically evolving and transforming into the smart grid, which is characterized by improved energy efficiency and manageability of available resources. Energy management (EM) systems, often integrated with home automation systems, play an important role in the control of home energy consumption and enable increased consumer participation. These systems provide consumers with information about their energy consumption patterns and help them adopt energy-efficient behavior. The new generation EM systems leverage advanced analytics and communication technologies to offer consumers actionable information and control features, while ensuring ease of use, availability, security, and privacy. In this article, we present a survey of the state of the art in EM systems, applications, and frameworks. We define a set of requirements for EM systems and evaluate several EM systems in this context. We also discuss emerging trends in this area.
Using CSEM to monitor production from a complex 3D gas reservoir—A synthetic case study (2011)

The marine controlled-source electromagnetic (CSEM) method is most commonly used in targeted exploration or appraisal studies as a tool for detecting and delineating hydrocarbon reservoirs (see, for example, Constable and Srnka 2007). Whereas seismic surveys can detect the structures that may contain hydrocarbons with great accuracy, distinguishing hydrocarbon fluids from water within these structures is more problematic. Originally developed in the late 1970s (Young and Cox, 1981), the CSEM method uses a high-powered horizontal electric dipole (HED) to transmit a low-frequency electromagnetic signal through the sea floor to an array of multicomponent electromagnetic receivers. Bulk electrical resistivity of the sea floor can be determined at scales of a few tens of meters to depths of several kilometers. In many cases this resistivity is driven by the fluid content and saturation of subsurface formations.
Terphenyl-Based Bak BH3 α-Helical Proteomimetics as Low-Molecular-Weight Antagonists of Bcl-x L (2005)

We describe a general method for the mimicry of one face of an alpha-helix based on a terphenyl scaffold that spatially projects functionality in a manner similar to that of two turns of an alpha-helix. The synthetic scaffold reduces the flexibility and molecular weight of the mimicked protein secondary structure. We have applied this design to the development of antagonists of the alpha-helix binding protein Bcl-x(L). Using a sequential synthetic strategy, we have prepared a library of terphenyl derivatives to mimic the helical region of the Bak BH3 domain that binds Bcl-x(L). Fluorescence polarization assays were carried out to evaluate the ability of terphenyl derivatives to displace the Bcl-x(L)-bound Bak peptide. Terphenyl 14 exhibited good in vitro affinity with a K(i) value of 0.114 muM. These terphenyl derivatives were more selective at disrupting the Bcl-x(L)/Bak over the HDM2/p53 interaction, which involves binding of the N-terminal alpha-helix of p53 to HDM2. Structural studies using NMR spectroscopy and computer-aided docking simulations suggested that the helix binding area on the surface of Bcl-x(L) is the target for the synthetic ligands. Treatment of human embryonic kidney 293 (HEK293) cells with terphenyl derivatives resulted in the disruption of the binding of Bcl-x(L) to Bax in intact cells.
Carbohydrases, protease, and phytase have an additive beneficial effect in nutritionally marginal diets for broiler chicks (2005)

To investigate the additive effects of xylanase, amylase, protease, and phytase in the diets of broiler chickens, a study was conducted using 1,152 growing broiler chicks (8 treatments with 12 replicate pens of 12 chicks). The birds were fed a corn/soybean-based negative control (NC) diet that was formulated to be nutritionally marginal in terms of metabolizable energy, Ca, and P. A nutritionally adequate positive control (PC) diet was fed for comparison. The NC diet was supplemented with phytase; a cocktail of xylanase, amylase, and protease (XAP); or a combination of phytase and XAP at 100 or 200 mg of each enzyme/kg (200 mg of XAP/kg provided a guaranteed minimum of 300 U of xylanase, 400 U of amylase, and 4,000 U of protease/kg; 200 mg of phytase/kg provided a guaranteed minimum of 1,000 U of phytase/kg). Growth performance, ileal digestible energy (IDE), and the digestibility coefficients of N, Ca, P, and DM were calculated. Individually and in combination, both phytase and XAP improved (P < 0.05) gain-to-feed ratio compared with the NC diet, particularly at the highest inclusion concentration. Body weight gain followed a similar trend, showing an improvement of approximately 6 to 7% with either enzyme individually and a 14% improvement with a combination of phytase and XAP. The effect of enzymes on IDE and nutrient digestibility coefficients was not as marked, but a 165 kcal/kg reduction in IDE was noted between the NC and PC diets, and a combination of phytase and XAP improved IDE by >100 kcal/kg. It can be concluded that the use of phytase and XAP individually in a corn/soybean meal-based diet is effective in improving nutrient digestibility and performance of broilers fed nutritionally marginal diets. Furthermore, there may be an additive effect of phytase and XAP on broiler performance, giving a cost-effective nutritional strategy for the profitable production of poultry products.