gebhart/patrepeval huggingface dataset:
Phase 1 First-in-Human Trial of the Vascular Disrupting Agent Plinabulin(NPI-2358) in Patients with Solid Tumors or Lymphomas (2010)

At the RP2D of 30 mg/m², plinabulin showed a favorable safety profile, while eliciting biological effects as evidenced by decreases in tumor blood flow, tumor pain, and other mechanistically relevant adverse events. On the basis of these results additional clinical trials were initiated with plinabulin in combination with standard chemotherapy agents.
Treatment of cutaneous melanoma: current approaches and future prospects (2010)

Melanoma is the most aggressive and deadly type of skin cancer. Surgical resection with or without lymph node sampling is the standard of care for primary cutaneous melanoma. Adjuvant therapy decisions may be informed by careful consideration of prognostic factors. High-dose adjuvant interferon alpha-2b increases disease-free survival and may modestly improve overall survival. Less toxic alternatives for adjuvant therapy are currently under study. External beam radiation therapy is an option for nodal beds where the risk of local recurrence is very high. In-transit melanoma metastases may be treated locally with surgery, immunotherapy, radiation, or heated limb perfusion. For metastatic melanoma, the options include chemotherapy or immunotherapy; targeted anti-BRAF and anti-KIT therapy is under active investigation. Standard chemotherapy yields objective tumor responses in approximately 10%-20% of patients, and sustained remissions are uncommon. Immunotherapy with high-dose interleukin-2 yields objective tumor responses in a minority of patients; however, some of these responses may be durable. Identification of activating mutations of BRAF, NRAS, c-KIT, and GNAQ in distinct clinical subtypes of melanoma suggest that these are molecularly distinct. Emerging data from clinical trials suggest that substantial improvements in the standard of care for melanoma may be possible.
Analysis of energy detection receiver for TOA estimation in IR UWB ranging and a novel TOA estimation approach (2013)

Ultra wideband (UWB) localization has attracted a lot of attention, as it offers the capability of penetration and high precision positioning with low cost. Time-based UWB ranging can take full advantage of the characteristics of impulse radio (IR) signal. The energy detection (ED) receiver instead of the matched filter is used a lot in the area for its low complexity. In the ED receiver, many factors, such as the integration interval, signal waveform, the upper or lower limit of integration, noise floor and pulse width, affect the ranging performance. These factors have not been studied thoroughly on energy collection in ED-based receivers, while energy collection is very important for IR UWB ranging and localization. Many studies focus on how to estimate the time of arrival (TOA) based on the output of the ED receiver. In the study, we will examine the effects of these factors on energy collection and TOA estimation. Some qualitative conclusions are given. We propose an approach to solve some problems caused by these factors and further improve the ranging accuracy. The approach can break through the performance limitation of TOA estimation with the ED receiver to some extent with some low-cost delayers instead of the high sampling rate analog to digital converters. Simulation results prove that the approach works effectively compared with traditional methods under different channels.
UV Laser Machined Polymer Substrates for the Development of Microdiagnostic Systems (1997)

This report describes a UV laser photoablation method for the production of miniaturized liquid-handling systems on polymer substrate chips. The fabrication of fluid channel and reservoir networks is accomplished by firing 200 mJ pulses from an UV excimer laser at substrates moving in predefined computer-controlled patterns. This method was used for producing channels in polystyrene, polycarbonate, cellulose acetate, and poly(ethylene terephthalate). Efficient sealing of the resulting photoablated polymer channels was accomplished using a low-cost film lamination technique. After fabrication, the ablated structures were observed to be well defined, i.e., possessing high aspect ratios, as seen by light, scanning electron, and atomic force microscopy. Relative to the original polymer samples, photoablated surfaces showed an increase in their hydrophilicity and rugosity as a group, yet differences were noted between the polymers studied. These surface characteristics demonstrate the capability of generating electroosmotic flow in the cathodic direction, which is characterized here as a function of applied electric field, pH, and ionic strength of common electrophoretic buffer systems. These results show a correlation between the ablative changes in surface conditions and the resulting electroosmotic flow. The effect of protein coatings on ablated surfaces is also demonstrated to significantly dampen the electroosmotic flow for all polymers. All of these results are discussed in terms of developing liquid-handling capability, which is an essential part of many μ-TAS and chemical diagnostic systems.
A functional MOS transistor featuring gate-level weighted sum and threshold operations (1992)

A functional MOS transistor is proposed which works more intelligently than a mere switching device. The functional transistor calculates the weighted sum of all input signals at the gate level, and controls the 'on' and 'off' of the transistor based on the result of such a weighted sum operation. Since the function is quite analogous to that of biological neurons, the device is named a neuron MOSFET, or neuMOS (vMOS). The device is composed of a floating gate and multiples of input gates that capacitively interact with the floating gate. As the gate-level sum operation is performed in a voltage mode utilizing the capacitive coupling effect, essentially no power dissipation occurs in the calculation, making the device ideal for ULSI implementation. The basic characteristics of neuron MOSFETs as well as of simple circuit blocks are analyzed based on a simple transistor model and experiments. Making use of its very powerful function, a number of interesting circuit applications are explored. A soft hardware logic circuit implemented by neuMOS transistors is also proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Pharmacokinetics, Pharmacodynamics, and Safety of Orally Dosed INCB018424 Phosphate in Healthy Volunteers (2011)

INCB018424 phosphate, a potent inhibitor of JAK enzymes with selectivity for JAK1&2, is in development for the treatment of myelofibrosis (MF). The oral dose pharmacokinetics, pharmacodynamics, safety, and tolerability of INCB018424 were evaluated in healthy volunteers in 2 double-blind, randomized, and placebo-controlled studies. The first study evaluated single ascending doses of 5 to 200 mg INCB018424 and the effect of food, whereas the second study evaluated multiple ascending doses, including both once- and twice-daily dosing for 10 days. As a Biopharma-ceutical Classification System class I drug, INCB018424 exhibited good oral bioavailability and dose-proportional systemic exposures. INCB018424 showed low oral dose clearance and a small volume of distribution, with an approximate 3-hour plasma half-life and insignificant accumulation following repeat dosing. A high-fat meal reduced INCB018424 C(max) by 24% but had little effect on INCB018424 AUC. INCB018424 was cleared primarily by metabolism with negligible renal excretion. The pharmacodynamics of INCB018424, evaluated by the inhibition of phosphorylated STAT3 following cytokine stimulation in whole blood, showed good correlation with INCB018424 plasma concentrations. INCB018424 was generally safe and well tolerated, with 25 mg bid and 100 mg qd established as the maximum tolerated doses in healthy volunteers.
LumeNEXT: A Practical Method to Pattern Luminal Structures in ECM Gels (2015)

In vitro biomimetic modeling of physio-logical structures bridges the gap between 2D in vitro culture and animal models. Lumens (tubular structures) are ubiquitous in vivo, being present in blood vessels, mammary ducts, and the lymphatic system. A method 'LumeNEXT' is presented here that allows the fabrication of 3D embedded lumens where size, structure, distance, and configuration can be controlled using standard poly-dimethylsiloxane micromolding methods.
Identification of Bordetella pertussis infection by shared-primer PCR (1994)

A shared-primer PCR method for the detection of infection was developed by using primers derived from DNA sequences upstream of the structural genes for the porin proteins of Bordetella pertussis and Bordetella parapertussis. This method resulted in a 159-bp PCR product specific for B. pertussis and a 121-bp DNA fragment specific for B. parapertussis and allowed for the simultaneous detection of these pathogens. The PCR procedure was shown to be very specific since no PCR product was obtained from 36 non-Bordetella bacterial DNAs. Nasopharyngeal aspirates (NPAs) from children suspected of having pertussis were evaluated by the PCR method, culture, and the Chinese hamster ovary (CHO) cell assay, which detects pertussis toxin. B. pertussis was cultured from 119 of 205 NPAs assayed, and the presence of pertussis toxin was detected in 69 of the NPAs by the CHO cell assay. When ethidium bromide staining was used to detect PCR products, 100 NPAs gave positive results by shared-primer PCR; 94 of these NPAs were also positive by culture. The result indicated a sensitivity of 79% for PCR when culture was used as the standard. The sensitivity of PCR was increased to 95% when a digoxigenin immunoblot system was used. An additional 20 NPAs from patients with suspected pertussis that were culture negative also gave positive results by PCR. The specific and sensitive PCR method described here should be useful for both the clinical diagnosis of pertussis and case identification in vaccine trials.
Transdermal Testosterone Gel prn Application for Hypoactive Sexual Desire Disorder in Premenopausal Women: A Controlled Pilot Study of the Effects on the Arizona Sexual Experiences Scale for Females and Sexual Function Questionnaire (2007)

These preliminary results suggest that testosterone gel given prn before intercourse has effects on sexual arousal, and further research is needed to define dosage and time schedule to optimize this effect and determine its clinical relevance.
Epitopes Involved in Antibody-Mediated Protection from Ebola Virus (2000)

To determine the ability of antibodies to provide protection from Ebola viruses, monoclonal antibodies (mAbs) to the Ebola glycoprotein were generated and evaluated for efficacy. We identified several protective mAbs directed toward five unique epitopes on Ebola glycoprotein. One of the epitopes is conserved among all Ebola viruses that are known to be pathogenic for humans. Some protective mAbs were also effective therapeutically when administered to mice 2 days after exposure to lethal Ebola virus. The identification of protective mAbs has important implications for developing vaccines and therapies for Ebola virus.
Assays for reverse transcriptase activity and p53 protein : applications for characterisation of HIV RT mutants and inhibitors, and for p53 expression in breast cancer (1996)

Assays for reverse transcriptase activity and p53 protein : applications for characterisation of HIV RT mutants and inhibitors and for p53 expression in breast cancer
Efficiency enhancement of InGaN/GaN solar cells with nanostructures (2014)

We demonstrate InGaN/GaN multi-quantum-well solar cells with nanostructures operating at a wavelength of 520 nm. Nanostructures with a periodic nanorod or nanohole array are fabricated by means of modified nanosphere lithography. Under 1 sun air-mass 1.5 global spectrum illumination, a fill factor of 50 and an open circuit voltage of 1.9 V are achieved in spite of very high indium content in InGaN alloys usually causing degradation of crystal quality. Both the nanorod array and the nanohole array significantly improve the performance of solar cells, while a larger enhancement is observed for the nanohole array, where the conversion efficiency is enhanced by 51%.
Mechanisms for modulating TNF alpha in immune and inflammatory disease. (2001)

The development of tumor necrosis factor-alpha (TNF alpha) inhibitors has been one of the most active areas of drug development over the last ten years for the treatment of inflammatory diseases. Following the definition of TNF alpha as a key mediator of inflammatory disease and the success demonstrated by various anti-TNF alpha strategies in the treatment of rheumatoid arthritis and inflammatory bowel disease, many investigators have sought to refine mechanisms by which to modulate TNF alpha in vivo. Many advances are presently being made in the understanding of how TNF alpha production is regulated, and with this knowledge comes the identification of new targets and pathways for therapeutic intervention. Here, we review the development of the currently available therapeutics and the progressive steps that are being made to improve clinical efficacy of anti-TNF alpha strategies.
Methylthiol:coenzyme M methyltransferase from Methanosarcina barkeri, an enzyme of methanogenesis from dimethylsulfide and methylmercaptopropionate (1997)

During growth on acetate, Methanosarcina barkeri expresses catabolic enzymes for other methanogenic substrates such as monomethylamine. The range of substrates used by cells grown on acetate was further explored, and it was found that cells grown on acetate also converted dimethylsulfide (DMS) and methylmercaptopropionate (MMPA) to methane. Cells or extracts of cells grown on trimethylamine or methanol did not utilize either DMS or MMPA. During growth on acetate, cultures demethylated MMPA, producing methane and mercaptopropionate. Extracts of acetate-grown cells possessed DMS- and MMPA-dependent coenzyme M (CoM) methylation activities. The activity peaks of CoM methylation with either DMS or MMPA coeluted upon gel permeation chromatography of extracts of acetate-grown cells consistent with an apparent molecular mass of 470 kDa. A 480-kDa corrinoid protein, previously demonstrated to be a CoM methylase but otherwise of unknown physiological function, was found to methylate CoM with either DMS or MMPA. MMPA was demethylated by the purified 480-kDa CoM methylase, consuming 1 mol of CoM and producing 1 mol of mercaptopropionate. DMS was demethylated by the purified protein, consuming 1 mol of CoM and producing 1 mol of methanethiol. The methylthiol:CoM methyltransferase reaction could be initiated only with the enzyme-bound corrinoid in the methylated state. CoM could demethylate, and DMS and MMPA could remethylate, the corrinoid cofactor. The monomethylamine corrinoid protein and the A isozyme of methylcobamide:CoM methyltransferase (proteins homologous to the two subunits comprising the 480-kDa CoM methylase) did not catalyze CoM methylation with methylated thiols. These results indicate that the 480-kDa corrinoid protein functions as a CoM methylase during methanogenesis from DMS or MMPA.
Characterization of the ‘unusual’ mobility of large circular DNAs in pulsed field-gradient electroplioresis (1988)

Large circular amplified DNAs (30 and 85 kb) present in methotrexate-resistant Leishmania major appear to migrate anomalously in pulsed field-gradient electrophoresis (PFGE), exhibiting pulse time-dependent mobility and migrating along a different apparent path relative to the large linear chromosomal DNAs. Quantitative studies indicate that the relative pulse-time dependence is actually conferred by the mobility properties of the large linear DNAs. One contributing factor to the difference in migration path is variability in the intrinsic voltage-dependence of mobility of supercoiled and linear DNAs, in combination with the asymmetrical/inhomogeneous voltage gradients. Certain linear chromosomes exhibit a previously undescribed pulse-time dependence in the voltage-dependence of mobility. When enzymatically relaxed or physically nicked the large circular DNAs fail to leave the well using any pulse time, a property also observed in conventional electrophoresis. These findings are relevant to PFGE theory, and its application to the study of circular DNA amplification in Leishmania and other species.
Polymorphism: The Phenomenon Affecting the Performance of Drugs (2014)

Polymorphism is the ability of solid materials to exist in two or more crystalline forms with different arrangements or conformations of the constituents in the crystal lattice.These polymorphic forms of a drug differ in the physicochemical properties like dissolution and solubility, chemical and physical stability, flowability and hygroscopicity.These forms also differ in various important drug outcomes like drug efficacy, bioavailability, and even toxicity.Polymorphic studies are important as a particular polymorph can be responsible for a particular property which might not be exhibited by any other form.This review will discuss the applied nature of polymorphism starting from their preparation, characterization and pharmaceutical importance with a special emphasis on drugs.
Proteolytic Footprinting of Vaccinia Topoisomerase Bound to DNA (1995)

Vaccinia DNA topoisomerase, a member of the eukaryotic type I enzyme family, binds duplex DNA and forms a covalent protein.DNA complex at sites containing a conserved sequence element 5'-CCCTT decreases. The structure of the enzyme in the free and DNA-bound states was probed by limited proteolysis. The free topoisomerase (a 314-amino acid polypeptide) consists of protease-resistant amino- and carboxyl-terminal structural domains flanking a protease-sensitive "hinge." The hinge region, located between residues 135 and 142, is defined by accessibility to three different proteases. The amino-terminal region is punctuated by a trypsin-sensitive "bridge" at Arg-80, suggesting at least a tripartite domain structure overall. A specific subset of residues accessible to proteases in the free enzyme becomes resistant to proteolysis in the DNA-bound state. The trypsin-sensitive site at Arg-80 is protected almost completely in the covalent complex. Within the hinge region, Lys-135, Tyr-136, and Glu-139 are protected from trypsin, chymotrypsin, and V8, respectively. Acquisition of altered protease sensitivity upon DNA binding occurs prior to covalent adduct formation. The 20-kDa carboxyl domain by itself binds noncovalently to duplex DNA, albeit without the sequence specificity characteristic of the full-sized topoisomerase.
Starcode: sequence clustering based on all-pairs search (2015)

The C source code is available at http://github.com/gui11aume/starcode.
Enhancement of the photocatalytic activity of TiO2through spatial structuring and particle size control: from subnanometric to submillimetric length scale (2007)

This review summarizes the physical approaches towards enhancement of the photocatalytic activity of titanium dioxide by controlling this semiconductor in a certain length scale from subnanometric to submillimetric distances and provides examples in which the photocatalytic activity of TiO2 is not promoted by doping or changes in the chemical composition, but rather by application of physical concepts and spatial structuring of the semiconductor. Thus, encapsulation inside the micropores and cavities of zeolites (about 1 nm) renders small titanium oxide clusters with harnessed photocatalytic activity. On the other hand, nanometric titanium particles can be ordered forming structured periodic mesoporous materials with high specific surface area and well defined porosity. Titiania nanotubes of micrometric length, either independent or forming a membrane, also exhibit unique photocatalytic activity as consequence of the long diffusion length of charge carriers along the nanotube axis. Finally, photonic crystals with an inverse opal structure and the even more powerful concept of photonic sponges can serve to slow down visible light photons inside the material, increasing the effective optical path in such a way that light absorption near the absorption onset of the material is enhanced considerably. All these physical-based approaches have shown their potential in enhancing the photocatalytic activity of titania, paving the way for a new generation of novel structured photocatalysts in which physical and chemical concepts are combined.
Identification of novel thiocarboxanilide derivatives that suppress a variety of drug-resistant mutant human immunodeficiency virus type 1 strains at a potency similar to that for wild-type virus (1996)

A large variety of carboxanilide and thiocarboxanilide derivatives in which the original oxathiin or aliphatic moieties present in the prototype compounds UC84 and UC38 were replaced by an (un) substituted furanyl, thienyl, phenyl, or pyrrole entity have been evaluated for activity against wild-type human immunodeficiency virus type 1 strain IIIB [HIV-1 (IIIB)] and a series of mutant virus strains derived thereof. The mutant viruses contained either the Leu-100-->Ile, Lys-103-->Asn, Val-106-->Ala, Glu-138-->Lys, Tyr-181-->Cys, or Tyr-188-->Leu mutation in their reverse transcriptase. Several 3-(2-methylfuranyl)- and 3-(2-methylthienyl)-thiocarboxanilide ester, (thio)ether, and oxime ether derivatives showed exquisitely potent antiviral activity against wild-type HIV-1 (50% effective concentration, 0.009 to 0.021 microM). The pentenylethers of the 2-methylfuranyl and 2-methylthienyl derivatives (i.e., 313, N-[4-chloro-3-(3-methyl-2-butenyloxy)phenyl]- 2-methyl-3-furancarbothioamide or UC-781, and 314, N-[4-chloro-3-(3-methyl-2-butenyloxy)phenyl] -2-methyl-3-thiophenecarbothioamide or UC-82) proved virtually equally inhibitory for wild-type and the Ile-100, Ala-106, and Lys-138 mutant virus strains (50% effective concentration, 0.015 to 0.021 microM). Their inhibitory effect against the Asn-103 and Cys-181 reverse transcriptase mutant virus strains was decreased only four- to sevenfold compared with wildtype virus. UC-781 and UC-82 should be considered potential candidate drugs for the treatment of HIV-1-infected individuals.
Rapid tyrosine phosphorylation and activation of Bruton's tyrosine/Tec kinases in platelets induced by collagen binding or CD32 cross-linking. (2000)

Stimulation of the platelet nonintegrin collagen receptor, glycoprotein VI, evokes a signaling response similar to that induced by antigen receptor activation in B and T lymphocytes. A key transducer of the lymphocyte signaling pathways is the Bruton's tyrosine kinase (Btk)/Tec kinase family, which connects receptors to the elevation of intracellular-free calcium levels. An important signaling function for Btk in collagen-induced platelet activation in vitro was recently demonstrated by other researchers using Btk-deficient platelets from patients with X-linked agammaglobulinemia (XLA). Since Btk-deficiency does not induce an overt platelet-based bleeding disorder in vivo, collagen receptor responses may include other Btk/Tec kinase family members in normal platelets. Both Btk and Tec had increased tyrosine following stimulation of collagen receptors or CD32 cross-linking. Data from kinetic analyses and inhibitor studies and the use of phosphopeptide-specific antibodies recognizing 2 Btk regulatory phosphorylated tyrosine residues suggest a mechanism for coordinate recruitment of Btk and Tec through the immunoreceptor tyrosine-based activation motif, Src family kinases, and phosphatidylinositol 3-kinase. In XLA platelets, collagen treatment increased tyrosine phosphorylation of Tec and several other signaling proteins, including Lyn, Fyb, Slp-76, and the Wiskott-Aldrich syndrome protein. This indicates that important elements of the collagen signaling pathway proximal and distal to Btk and Tec are preserved despite the lack of functional Btk. The results are consistent with the conclusion that activation of Tec may sustain XLA platelet function in vivo, while some in vitro assays of nonintegrin collagen receptor signaling through the Btk/Tec kinase family reflect the additive dosage of the transducers. (Blood. 2000;95:1663-1670)