gebhart/patrepeval huggingface dataset:
GP-COM: a distributed, component-based genetic programming system in C++ (1996)

A genetic programming (GP) system is presented that mirrors the conceptual structure of the genetic programming cycle, maximising flexibility and re-use of code. This reduces the effort required to apply GP to a new problem domain.
The role of staging laparotomy in combined modality therapy of Hodgkin's disease: A new treatment plan based on a 6‐year experience (1978)

Abstract From 1969 to 1974, staging laparotomy was performed on 187 consecutive patients with Hodgkin's disease. Laparotomy changed the type of therapy in 59 of 187 patients (32%). Major staging revisions were: IIA to IIIA, 20 patients; IIIA to IA, 6 patients; IIIA to IIA, 12 patients; IIB to IIIB, 14 patients; and IIIB to IIB, 4 patients. Of stage II patients, 32 of 101 (32%) became stage III and of stage III patients, 24 of 61 (39%) became stage I or II. Forty‐four patients with stage IIIA disease received 3,600–4,000 rad total nodal irradiation and their probability of relapse‐free survival at 5 years was 52%. No relapses occurred in 11 stage IIB patients given combination of mantle and periaortic irradiation plus MOPP. Only 3 of 19 stage IIIB patients treated with total nodal irradiation and MOPP relapsed. Stage IIB patients with combined therapy had a diseasefree survival of 100%, while stage IIIB patients had a relapse‐free survival of 77%. These striking results have led to a new treatment plan. Clinical stage IIA, pathological stage IIIA patients, and those with stage IIB disease now receive a combination of mantle and periaortic irradiation plus MOPP. Clinical stage IIIA, pathological stage IIIA patients, as well as those with stage IIIB disease, receive total nodal irradiation and MOPP. Surgical staging in this series has proved essential for effective and precise therapy .
Two-wave emission from an Al<sub>2</sub>O<sub>3</sub>:Ti crystal laser (1989)

The simultaneous emission of stimulated radiation at two wavelengths from a tunable Al2O3:Ti laser pumped optically by second harmonic radiation from a YAG:Nd laser (0.53 μm) is described. The energy, temporal, and frequency characteristics are presented.
Inhibition of human T-cell leukemia virus type I replication in primary human T cells that express antisense RNA (1989)

The human T-cell leukemia virus type I is associated with adult T-cell leukemia-lymphoma in humans, a disease which is induced by a malignant transformation of T lymphocytes. Retrovirus vectors carrying human T-cell leukemia virus type I-derived sequences in reversed transcriptional orientation were used to express antisense RNA transcripts in primary human leukocytes. Human T-cell leukemia virus type I replication and virus-mediated immortalization were inhibited in cells harboring antisense constructs. This study suggests that retrovirus-mediated antisense RNA inhibition can be used to protect primary human T-lymphocytes from human T-cell leukemia virus type I-mediated cell transformation.
Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks (2006)

This paper discusses fast parallel algorithms for evaluating several centrality indices frequently used in complex network analysis. These algorithms have been optimized to exploit properties typically observed in real-world large scale networks, such as the low average distance, high local density, and heavy-tailed power law degree distributions. We test our implementations on real datasets such as the web graph, protein-interaction networks, movie-actor and citation networks, and report impressive parallel performance for evaluation of the computationally intensive centrality metrics (betweenness and closeness centrality) on high-end shared memory symmetric multiprocessor and multithreaded architectures. To our knowledge, these are the first parallel implementations of these widely-used social network analysis metrics. We demonstrate that it is possible to rigorously analyze networks three orders of magnitude larger than instances that can be handled by existing network analysis (SNA) software packages. For instance, we compute the exact betweenness centrality value for each vertex in a large US patent citation network (3 million patents, 16 million citations) in 42 minutes on 16 processors, utilizing 20GB RAM of the IBM p5 570. Current SNA packages on the other hand cannot handle graphs with more than hundred thousand edges.
Nebulisation on a disposable array structured with phononic lattices (2012)

We demonstrate the use of a phononic crystal to enable the nebulisation of liquid droplets from low-cost disposable arrays, using surface acoustic waves (SAW). The SAWs were generated using interdigitated transducers (IDT) on a piezoelectric surface (LiNbO(3)) and the acoustic waves were coupled into a disposable phononic crystal structure, referred to as a superstrate. Using its excellent reflecting properties, the phononic structures confined the acoustic field within the superstrate, resulting in the concentration of the acoustic energy, in a manner controllable by the excitation frequency. We show that this capability mitigates against coupling losses incurred by the use of a disposable superstrate, greatly reducing the time needed to nebulise a drop of water with respect to an unstructured superstrate for a given power. We also demonstrate that by changing the excitation frequency, it is possible to change the spatial position at which the acoustic energy is concentrated, providing a means to specifically nebulise drops across an array. These results open up a promising future for the use of phonofluidics in high-throughput sample handling applications, such as drug delivery or the "soft" transfer of samples to a mass spectrometer in the field of proteomics.
Molecular Determinants of Treatment Response in Acute Lymphoblastic Leukemia (2008)

Treatment response in patients with acute lymphoblastic leukemia (ALL) is best assessed using assays for minimal residual disease (MRD). The degree of leukemia cytoreduction and MRD clearance is determined by the collective influence of multiple factors. Some of these variables are features of the leukemic cells, such as expression of genes that regulate their susceptibility to cytotoxic drugs and their propensity to undergo apoptosis. Gene profiles depend, in turn, on the cell of origin for leukemic transformation, the type of underlying genetic abnormalities and/or epigenetic regulatory mechanisms. Another set of variables is related to the host, such as age and polymorphisms in genes that metabolize drugs, which together with pharmacologic variables, such as drug pharmacodynamics and drug interactions, influence treatment response. Finally, the bone marrow microenvironment where leukemic cells reside can participate in the generation of drug resistance. Altogether, these variables determine treatment outcome in each patient. Full knowledge of the molecular features associated with treatment response is required for precise leukemia prognostication and monitoring, and can provide clues to useful targets for novel therapies.
dUTPase-minus caprine arthritis-encephalitis virus is attenuated for pathogenesis and accumulates G-to-A substitutions (1997)

The importance of the virally encoded dUTPase for CAEV replication, invasiveness, pathogenesis, and genetic stability was investigated in goats infected by viruses with single point (DU-G) and deletion (DU-1) mutations of the dUTPase gene (DU gene). The DU gene was found to be dispensable for CAEV replication in vivo as judged by times taken to seroconvert, frequencies of viral isolation, and tissue distribution of viral RNAs. DU- reversion at week 34 in one of three goats infected with the single point mutant DU-G, however, suggested that the viral dUTPase confers some advantages for replication in vivo. Moreover, we show that dUTPase is necessary for the timely development of bilateral arthritic lesions of the carpus. Finally, dUTPase was shown to efficiently prevent accumulation of G-to-A transitions in the viral genome.
Anion Conductive Block Poly(arylene ether)s: Synthesis, Properties, and Application in Alkaline Fuel Cells (2011)

Anion conductive aromatic multiblock copolymers, poly(arylene ether)s containing quaternized ammonio-substituted fluorene groups, were synthesized via block copolycondensation of fluorene-containing (later hydrophilic) oligomers and linear hydrophobic oligomers, chloromethylation, quaternization, and ion-exchange reactions. The ammonio groups were selectively introduced onto the fluorene-containing units. The quaternized multiblock copolymers (QPEs) produced ductile, transparent membranes. A well-controlled multiblock structure was responsible for the developed hydrophobic/hydrophilic phase separation and interconnected ion transporting pathway, as confirmed by scanning transmission electron microscopic (STEM) observation. The ionomer membranes showed considerably higher hydroxide ion conductivities, up to 144 mS/cm at 80 °C, than those of existing anion conductive ionomer membranes. The durabilities of the QPE membranes were evaluated under severe, accelerated-aging conditions, and minor degradation was recognized by (1)H NMR spectra. The QPE membrane retained high conductivity in hot water at 80 °C for 5000 h. A noble metal-free direct hydrazine fuel cell was operated with the QPE membrane at 80 °C. The maximum power density, 297 mW/cm(2), was achieved at a current density of 826 mA/cm(2).
The Role of Intercalated Water in Multilayered Graphene Oxide (2010)

A detailed in situ infrared spectroscopy analysis of single layer and multilayered graphene oxide (GO) thin films reveals that the normalized infrared absorption in the carbonyl region is substantially higher in multilayered GO upon mild annealing. These results highlight the fact that the reduction chemistry of multilayered GO is dramatically different from the single layer GO due to the presence of water molecules confined in the ∼1 nm spacing between sheets. IR spectroscopy, XPS analysis, and DFT calculations all confirm that the water molecules play a significant role interacting with basal plane etch holes through passivation, via evolution of CO(2) leading to the formation of ketone and ester carbonyl groups. Displacement of water from intersheet spacing with alcohol significantly changes the chemistry of carbonyl formation with temperature.
Patent Thickets and the Market for Innovation:Evidence from Settlement of Patent Disputes (2008)

We study how fragmentation of patent rights ('patent thickets') and the formation of the Court of Appeal for the Federal Circuit (CAFC) affected the duration of patent disputes, and thus the speed of technology diffusion through licensing. We develop a model of patent litigation which predicts faster settlement agreements when patent rights are fragmented and when there is less uncertainty about court outcomes, as was associated with the 'pro-patent shift' of CAFC. The model also predicts that the impact of fragmentation on settlement duration should be smaller under CAFC. We confirm these predictions empirically using a dataset that covers nearly all patent suits in U.S. federal district courts during the period 1975-2000. Finally, we analyze how fragmentation affects total settlement delay, taking into account both reduction in duration per dispute and the increase in the number of required patent negotiations associated with patent thickets.
Giorgio Levi Della Vida: Pitagora, Bardesane e altri studi siriaci. A cura di Riccardo Contini. (Universitá di Roma ‘Studi Orientali’ pubblicati a cura del dipartimento di studi orientali, Vol. vm.) xxi, 194 pp. Rome: Bardi Editore, 1989. (1992)

Giorgio Levi Della Vida: Pitagora, Bardesane e altri studi siriaci. A cura di Riccardo Contini. (Universitá di Roma ‘Studi Orientali’ pubblicati a cura del dipartimento di studi orientali, Vol. vm.) xxi, 194 pp. Rome: Bardi Editore, 1989. - Volume 55 Issue 2
Induction of p53 contributes to apoptosis of HCT-116 human colon cancer cells induced by the dietary compound fisetin (2009)

Fisetin, or 3,3',4',7-tetrahydroxyflavone, is present in fruits and vegetables and has been previously reported to inhibit the proliferation of a variety of cancer cells (Lu X, Jung J, Cho HJ, Lim do Y, Lee HS, Chun HS, Kwon DY, Park JH. J Nutr 135: 2884-2890, 2005). We have demonstrated in a previous work that 20-60 micromol/l fisetin inhibits cyclin-dependent kinase activities resulting in cell cycle arrest in HT-29 colon cancer cells. In the present study, we attempted to characterize the mechanisms by which fisetin induces apoptosis in HCT-116 cells. DNA condensations, cleavage of poly(ADP-ribose) polymerase (PARP), and cleavage of caspases 9, 7, and 3 were induced in HCT-116 cells treated with 5-20 micromol/l of fisetin. Fisetin induced a reduction in the protein levels of antiapoptotic Bcl-xL and Bcl-2 and an increase in the levels of proapoptotic Bak and Bim. Fisetin did not affect the Bax protein levels, but induced the mitochondrial translocation of this protein. Fisetin also enhanced the permeability of the mitochondrial membrane and induced the release of cytochrome c and Smac/Diablo. Additionally, fisetin caused an increase in the protein levels of cleaved caspase-8, Fas ligand, death receptor 5, and TNF-related apoptosis-inducing ligand, and the caspase-8 inhibitor Z-IETD-FMK suppressed fisetin-induced apoptosis and the activation of caspase-3. Furthermore, fisetin increases p53 protein levels, and the inhibition of p53 expression by small interference RNA resulted in a decrease in the fisetin-induced translocation of Bax to the mitochondria, release of mono- and oligonucleosome in the cytoplasm, and PARP cleavage. These results show that fisetin induces apoptosis in HCT-116 cells via the activation of the death receptor- and mitochondrial-dependent pathway and subsequent activation of the caspase cascade. The induction of p53 results in the translocation of Bax to the mitochondria, which contributes to fisetin-induced apoptosis in HCT-116 cells.
Three-phase inverter synchronization control utilizing internal model principle (2015)

In order to ensure synchronized operation of inverters used in renewable energy systems, the output voltage magnitude, frequency and phase angle must be consistent with that of the power grid when it is in islanding operation. Based on author's previous work on single-phase inverter synchronization control with internal model principle, this paper extends the application of that principle to achieving synchronized operation of three-phase inverters with balanced load, in islanding operation; without the need for conventional Phase-Locked Loop. Linear Quadratic Regulator was utilized to enhance stability; offset voltage canceller was included in the switching system to compensate for switching components' nonlinearities; and digital redesign was performed to reduce computational burden in real-time by prolonging the calculation period. The simulation results obtained validated the effectiveness of the proposed method.
Proteomics in Vaccinology and Immunobiology:An Informatics Perspective of the Immunone (2003)

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.
Charging and Accounting for Integrated Internet Services - State of the Art, Problems, and Trends (1998)

Today&apos;s information society bears a stringent need for advanced communication services and content. Although solutions for methods of charging and accounting of single service class networks exist and are applied successfully, Integrated Services Networks require a completely different approach. Charging and accounting for the future Internet remain unsolved problems at the time being. This is due to a variety of service characterizations by Quality-of-Service (QoS) and the fact that the shape of the Integrated Services Internet is still not fully defined. In addition, a highly competitive telecommunication service provider market requires dynamic pricing schemes for integrated multiservice networks in order to deal with basic bandwidth allocation and advanced QoS services. Based on basic terminology and general economic models an investigation of best-effort and integrated services Internet characteristics in terms of suitable, applicable, or existent solutions and approaches for char...
Reflection mode photoacoustic measurement of speed of sound (2007)

We present a method to determine the speed of sound in tissue using a double-ring photoacoustic sensor working in reflection mode. This method uses the cross-correlation between the laser-induced ultrasound waves detected by two concentric ring shaped sensors, while a priori information about the depth-position of the photoacoustic source is not required. We demonstrate the concept by estimating the speed of sound in water as a function of temperature. Comparison of the estimated speed with values reported in literature shows an average systematic error of 0.1% and a standard deviation of 0.1%. Furthermore, we demonstrate that the method can be applied to layered media. The method has application in the correction of photoacoustic and ultrasound images afflicted by local speed variations in tissue. Additionally, the concept shows promise in monitoring temperature changes which are reflected in speed of sound changes in tissue.
Identification and Characterization of a <i>Drosophila</i> Proteasome Regulatory Network (2005)

Maintaining adequate proteasomal proteolytic activity is essential for eukaryotic cells. For metazoan cells, little is known about the composition of genes that are regulated in the proteasome network or the mechanisms that modulate the levels of proteasome genes. Previously, two distinct treatments have been observed to induce 26S proteasome levels in Drosophila melanogaster cell lines, RNA interference (RNAi)-mediated inhibition of the 26S proteasome subunit Rpn10/S5a and suppression of proteasome activity through treatment with active-site inhibitors. We have carried out genome array profiles from cells with decreased Rpn10/S5a levels using RNAi or from cells treated with proteasome inhibitor MG132 and have thereby identified candidate genes that are regulated as part of a metazoan proteasome network. The profiles reveal that the majority of genes that were identified to be under the control of the regulatory network consisted of 26S proteasome subunits. The 26S proteasome genes, including three new subunits, Ubp6p, Uch-L3, and Sem1p, were found to be up-regulated. A number of genes known to have proteasome-related functions, including Rad23, isopeptidase T, sequestosome, and the genes for the segregase complex TER94/VCP-Ufd1-Npl4 were also found to be up-regulated. RNAi-mediated inhibition against the segregase complex genes demonstrated pronounced stabilization of proteasome substrates throughout the Drosophila cell. Finally, transcriptional reporter assays and deletion mapping studies in Drosophila demonstrate that proteasome mRNA induction is dependent upon the 5' untranslated regions (UTRs). Transfer of the 5' UTR from the proteasome subunit Rpn1/S2 to a noninducible promoter was sufficient to confer transcriptional upregulation of the reporter mRNA after proteasome inhibition.
Simulation of the color ratio associated with the backscattering of radiation by ice particles at the wavelengths of 0.532 and 1.064 <i>μ</i>m (2009)

This study explores a simulation of ice cloud optical properties similar to those observed using the Cloud‐Aerosol Lidar with Orthogonal Polarization (CALIOP), a dual‐wavelength (0.532 and 1.064 μ m) lidar. The goal is to better understand the sensitivity of the color ratio (the ratio of the backscatter coefficients at the wavelengths of 1.064 and 0.532 μ m) to ice particle habit. The single‐scattering properties of randomly oriented hexagonal ice particles are simulated from the finite difference time domain (FDTD) method for particles with size parameters less than 50, and from an improved geometric optics method (IGOM) for particles with larger size parameters (a quantity proportional to the ratio of the particle characteristic dimension to the incident wavelength). Based on the assumption that ice particles are hexagonal particles, the color ratio values are found to be less than unity with a peak value near 0.7 for columns and 0.8 for plates. If spherical ice particles are assumed, the color ratio values can be larger than unity and may even approach 2 for many size distributions. The deviation in the value of the color ratio from unity is due to different distributions of size parameters for the two wavelengths, and to smaller single‐scattering albedo values for large particles at 1.064 μ m than at 0.532 μ m. The present simulations of the color ratio for hexagonal columns are qualitatively consistent with measurements from a ground‐based lidar, located at Hampton University in Hampton, Virginia, which peak near 0.88, but the two results differ quantitatively by 10–20 percent.
Extenders and zinc rich paints (1972)

Whilst accepting the economic necessity for adding extenders to zinc rich paints, there are several problems which need careful consideration.
Recuperation of Regenerative Braking Energy in Electric Rail Transit Systems (2019)

Electric rail transit systems are the large consumers of energy. In trains with regenerative braking capability, a fraction of the energy used to power a train is regenerated during braking. This regenerated energy, if not properly captured, is typically dumped in the form of heat to avoid overvoltage. Finding a way to recuperate regenerative braking energy can result in economic as well as technical merits. In this comprehensive paper, the various methods and technologies that were proposed for regenerative energy recuperation have been analyzed, investigated, and compared. These technologies include: train timetable optimization, energy storage systems (onboard and wayside), and reversible substations.
Monitoring Phosphatidic Acid Formation in Intact Phosphatidylcholine Bilayers upon Phospholipase D Catalysis (2014)

We have monitored the production of the negatively charged lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid acid (POPA), in supported lipid bilayers via the enzymatic hydrolysis of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC), a zwitterionic lipid. Experiments were performed with phospholipase D (PLD) in a Ca(2+) dependent fashion. The strategy for doing this involved using membrane-bound streptavidin as a biomarker for the charge on the membrane. The focusing position of streptavidin in electrophoretic-electroosmotic focusing (EEF) experiments was monitored via a fluorescent tag on this protein. The negative charge increased during these experiments due to the formation of POPA lipids. This caused the focusing position of streptavidin to migrate toward the negatively charged electrode. With the use of a calibration curve, the amount of POPA generated during this assay could be read out from the intact membrane, an objective that has been otherwise difficult to achieve because of the lack of unique chromophores on PA lipids. On the basis of these results, other enzymatic reactions involving the change in membrane charge could also be monitored in a similar way. This would include phosphorylation, dephosphorylation, lipid biosynthesis, and additional phospholipase reactions.