gebhart/patrepeval huggingface dataset:
The Japanese Experience with Highway Development (2014)

Japan now has one of the world’s most highly developed multimodal transport systems. This was only made possible by successfully building an extensive highway network in a short period of time. The two remarkable aspects of this network have been the scale and layout, which were based not only on traffic volume forecasts but also on the principle of equal access. The Japan Highway Public Corporation (JHPC) was instituted in 1956 to oversee the development and expansion of the highway network. Due to the national government’s limited funding capacity, the JHPC initially relied extensively on debt financing, depending on toll revenues to accelerate the nation’s highway development. Eventually the government, seeking to give as many people as possible access to high-speed transport, introduced a pool system of revenues and costs (plus a uniform toll rate system) for all intercity expressway routes. The costs of each route were to be recovered by tolls paid by its users, cross-subsidisation from other routes and public funds. But over the years, the costs of building such a system soared, thereby increasing debt obligations and leading to the disintegration of the JHPC. Japan is now undergoing rapid transition, deregulation and privatisation of its highways, and is on an ambitious debt repayment programme to recover over ¥40 trillion in less than 40 years. This article is a narrative of the post-war historical experience of the development of highways, especially the expressway category of the road sector in Japan.
Persistent Systemic Inflammation is Associated with Poor Clinical Outcomes in COPD: A Novel Phenotype (2012)

Overall, these results identify a novel systemic inflammatory COPD phenotype that may be the target of specific research and treatment.
Flow synthesis using gaseous ammonia in a Teflon AF-2400 tube-in-tube reactor: Paal–Knorr pyrrole formation and gas concentration measurement by inline flow titration (2012)

Using a simple and accessible Teflon AF-2400 based tube-in-tube reactor, a series of pyrroles were synthesised in flow using the Paal-Knorr reaction of 1,4-diketones with gaseous ammonia. An inline flow titration technique allowed measurement of the ammonia concentration and its relationship to residence time and temperature.
Combined Intralesional Bacille Calmette-Guérin (BCG) and Topical Imiquimod for In-transit Melanoma (2012)

The introduction of numerous immunotherapeutic agents into the clinical arena has allowed the long-time promise of immunotherapy to begin to become reality. Intralesional immunotherapy has demonstrated activity in multiple tumor types, and as the number of locally applicable agents has increased, so has the opportunity for therapeutic combinations. Both intralesional Bacille Calmette-Guérin (ILBCG) and topical 5% imiquimod cream have been used as single agents for the treatment of dermal/subcutaneous lymphatic metastases or in-transit melanoma, but the combination has not previously been reported. We used this combination regimen in 9 patients during the period from 2004 to 2011 and report their outcomes here. All patients were initially treated with ILBCG, followed by topical imiquimod after development of an inflammatory response to BCG. In this retrospective study, we examined their demographics, tumor characteristics, clinical and pathologic response to treatment, associated morbidities, local and distant recurrence, and overall survival. The 9 patients (8 male) had a mean age of 72 years (range, 56-95 y). Mild, primarily local toxicities were noted. Five patients (56%) had complete regression of their in-transit disease and 1 had a partial response. The 3 others had "surgical" complete responses with resection of solitary resistant lesions. The mean interval between the first treatment and complete resolution of in-transit disease was of 6.5 months (range, 2-12 mo). With a mean follow-up of 35 months (range 12-58 mo), 7 patients (78%) had not developed recurrent in-transit disease. Two patients (22%) have died of nonmelanoma causes, and none have died due to melanoma.
Using Confocal Microscopy to Study the Colloidal Glass Transition (2006)

We study concentrated colloidal suspensions, a model system which has a glass transition. We view the motion of colloidal particles using a confocal microscope, and quantify this motion as a function of the concentration.
Automated Semantic Knowledge Acquisition From Sensor Data (2014)

The gathering of real-world data is facilitated by many pervasive data sources such as sensor devices and smartphones. The abundance of the sensory data raises the need to make the data easily available and understandable for the potential users and applications. Using semantic enhancements is one approach to structure and organize the data and to make it processable and interoperable by machines. In particular, ontologies are used to represent information and their relations in machine interpretable forms. In this context, a significant amount of work has been done to create real-world data description ontologies and data description models; however, little effort has been done in creating and constructing meaningful topical ontologies from a vast amount of sensory data by automated processes. Topical ontologies represent the knowledge from a certain domain providing a basic understanding of the concepts that serve as building blocks for further processing. There is a lack of solution that construct the structure and relations of ontologies based on real-world data. To address this challenge, we introduce a knowledge acquisition method that processes real-world data to automatically create and evolve topical ontologies based on rules that are automatically extracted from external sources. We use an extended k- means clustering method and apply a statistic model to extract and link relevant concepts from the raw sensor data and represent them in the form of a topical ontology. We use a rule-based system to label the concepts and make them understandable for the human user or semantic analysis and reasoning tools and software. The evaluation of our work shows that the construction of a topological ontology from raw sensor data is achievable with only small construction errors.
Efficient planar heterojunction solar cell employing CH<sub>3</sub>NH<sub>3</sub>PbI<sub>2+</sub><i><sub>x</sub></i>Cl<sub>1−</sub><i><sub>x</sub></i>mixed halide perovskite utilizing modified sequential deposition (2015)

In this work, a modified method of sequential deposition of a CH3NH3PbI2+xCl1−x organometal halide perovskite material with a low chlorine fraction and easy morphology control is developed. The as-prepared mixed halide perovskite CH3NH3PbI2+xCl1−x thin film shows an intense adsorption from 400–800 nm. Scanning electron microscopy images show that almost the entire compact TiO2 surface is covered with CH3NH3PbI2+xCl1−x mixed halide perovskite with grain sizes of 250–350 nm. The planar heterojunction solar cell employing CH3NH3PbI2+xCl1−x mixed halide perovskite shows a twofold enhancement of photovoltaic performance, compared with a planar CH3NH3PbI3 heterojunction solar cell, achieving a 9.53% power conversion efficiency (PCE) with a VOC of 0.96 V, a JSC of 18.86 mA/cm2, and a fill factor (FF) of 0.53.
Quantitative proteomic analysis indicates increased synthesis of a quinolone by <i>Pseudomonas aeruginosa</i> isolates from cystic fibrosis airways (2003)

The opportunistic bacterial pathogen Pseudomonas aeruginosa colonizes airways of individuals with cystic fibrosis (CF) with resultant chronic destructive lung disease. P. aeruginosa adaptation to the CF airway includes biofilm formation and antibiotic resistance. Isolates from asymptomatic individuals in the first 3 years of life have unique characteristics, suggesting that adaptation occurs before clinical symptoms. One defined early adaptation is expression of a specific proinflammatory lipopolysaccharide (LPS) that is associated with antimicrobial peptide resistance. This CF-specific LPS is induced when P. aeruginosa is grown in medium that is limited for magnesium. Therefore, qualitative and quantitative proteomic approaches were used to define 1,331 P. aeruginosa proteins, of which 145 were differentially expressed on limitation of magnesium. Among proteins induced by low magnesium were enzymes essential for production of 2-heptyl 3-hydroxy 4-quinolone, the Pseudomonas quinolone signal (PQS), which interacts with the homoserine lactone signaling pathway. Measurement of PQS in P. aeruginosa isolates from asymptomatic children with CF indicated that strains with increased synthesis of PQS are present during early colonization of CF patient airways.
Secondary Bonding Interactions Observed in Two Arsenic Thiolate Complexes (2005)

Treatment of N-(2-mercaptoethyl)-1,8-naphthalimide (HL) with stoichiometric amounts of AsCl(3) and base affords AsL(2)Cl and AsL(3) complexes stabilized in part by secondary As...O bonding interactions.
32nm and below logic patterning using optimized illumination and double patterning (2009)

Line/space dimensions for 32nm generation logic are expected to be ~45-50nm at ~90-100nm pitch. It is likely that the node will begin at the upper end of the range, and then shrink by ~10% to a "28nm" node. For the lower end of the range, even with immersion scanners, the Rayleigh k<sub>1</sub> factor is below 0.32. The 22nm logic node should begin with minimum pitches of approximately 70nm, requiring some form of double patterning to maintain k<sub>1</sub> above 0.25. Logic patterning has been more difficult than NAND Flash patterning because random logic was designed with complete "freedom" compared to the very regular patterns used in memory. The logic layouts with bends and multiple pitches resulted in larger rules, un-optimized illumination, and a poorly understood process windows with little control of context-dependent "hot spots."[1] The introduction of logic design styles which use strictly one-directional lines for the critical levels now gives the opportunity for illumination optimization. Gridded Design Rules (GDR) have been demonstrated to give areacompetitive layouts at existing 90, 65, and 45nm logic nodes while reducing CD variability.[2] These benefits can be extended to ≤32nm logic using selective double pass patterning.
Ethanol inhibits thrombin-induced secretion by human platelets at a site distinct from phospholipase C or protein kinase C (1990)

Ethanol is known to inhibit the activation of platelets in response to several physiological agonists, but the mechanism of this action is unclear. The addition of physiologically relevant concentrations of ethanol (25-150 mM) to suspensions of washed human platelets resulted in the inhibition of thrombin-induced secretion of 5-hydroxy[14C]tryptamine. Indomethacin was included in the incubation buffer to prevent feedback amplification by arachidonic acid metabolites. Ethanol had no effect on the activation of phospholipase C by thrombin, as determined by the formation of inositol phosphates and the mobilization of intracellular Ca2+. Moreover, ethanol did not interfere with the thrombin-induced formation of diacylglycerol or phosphatidic acid. Stimulation of platelets with phorbol ester (5-50 nM) resulted in 5-hydroxy[14C]tryptamine release comparable with those with threshold doses of thrombin. However, ethanol did not inhibit phorbol-ester-induced secretion. Ethanol also did not interfere with thrombin- or phorbol-ester-induced phosphorylation of myosin light chain (20 kDa) or a 47 kDa protein, a known substrate for protein kinase C. By electron microscopy, ethanol had no effect on thrombin-induced shape change and pseudopod formation, but prevented granule centralization and fusion. The results indicate that ethanol does not inhibit platelet secretion by interfering with the activation of phosphoinositide-specific phospholipase C or protein kinase C by thrombin. Rather, the data demonstrate an inhibition of a Ca2(+)-mediated event such as granule centralization.
Myricetin Suppresses UVB-Induced Skin Cancer by Targeting Fyn (2008)

Skin cancer is currently the most common type of human cancer in Americans. Myricetin, a naturally occurring phytochemical, has potent anticancer-promoting activity and contributes to the chemopreventive potential of several foods, including red wine. Here, we show that myricetin suppresses UVB-induced cyclooxygenase-2 (COX-2) expression in mouse skin epidermal JB6 P+ cells. The activation of activator protein-1 and nuclear factor-kappaB induced by UVB was dose-dependently inhibited by myricetin treatment. Western blot and kinase assay data revealed that myricetin inhibited Fyn kinase activity and subsequently attenuated UVB-induced phosphorylation of mitogen-activated protein kinases. Pull-down assays revealed that myricetin competitively bound with ATP to suppress Fyn kinase activity. Importantly, myricetin exerted similar inhibitory effects compared with 4-amino-5-(4-chloro-phenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine, a well-known pharmacologic inhibitor of Fyn. In vivo mouse skin data also revealed that myricetin inhibited Fyn kinase activity directly and subsequently attenuated UVB-induced COX-2 expression. Mouse skin tumorigenesis data clearly showed that pretreatment with myricetin significantly suppressed UVB-induced skin tumor incidence in a dose-dependent manner. Docking data suggest that myricetin is easily docked to the ATP-binding site of Fyn, which is located between the N and C lobes of the kinase domain. Overall, these results indicated that myricetin exerts potent chemopreventive activity mainly by targeting Fyn in skin carcinogenesis.
Risk of development of tuberculosis in HIV-infected patients. (2000)

The results of this study provide information regarding the high risk of development of active tuberculosis and its associated mortality in HIV-infected persons. The risk of developing TB appears to be equally high in tuberculin positive and negative individuals, suggesting that new infections could play a major role in this susceptible population.
Alterations of CXCR4 function in μ‐opioid receptor‐deficient glia (2010)

The chemokine receptor CXCR4 and the μ-opioid receptor (MOR) are G-protein-coupled receptors that are essential for normal function of the nervous and immune systems. Several studies have suggested that MOR is a key regulator of CXCR4 in the brain; however, the molecular basis of the opioid-chemokine interaction is not fully understood, and it may involve different mechanisms in neuronal and glial cells. Our previous studies demonstrated that MOR stimulation specifically upregulates the protein ferritin heavy chain - an inhibitor of CXCR4 - in neurons, and suggested that additional mechanisms could be operative in glia. In this study, we investigated CXCR4 function in brains and astroglial cultures deprived of MOR. Reduced coupling of CXCR4 to G-proteins was found in brain slices and tissue homogenates of MOR(-/-) mice as compared with wild-type controls. CXCR4-induced signaling was also reduced in glial cultures from MOR(-/-) mice, as shown by analysis of CXCR4 downstream targets (Akt and ERK1/2). Pharmacological studies with δ-opioid receptor (DOR)-specific ligands suggested that DOR-CXCR4 interactions are implicated in the inhibition of CXCR4 in MOR-deficient cells both in vitro and in vivo. Moreover, increased CXCR4/DOR co-immunoprecipitation was found in brain tissue and cultured glia from MOR(-/-) mice. Importantly, CXCR4 function was restored by pretreatment with a DOR antagonist. Overall, these findings indicate that DOR plays a crucial role in the regulation of CXCR4 in glia, probably via silent receptor heterodimers. The data also suggest that the opiate system interferes with normal CXCR4 function in different ways, depending on receptor subtypes.
Characterization of <i>E. coli</i> cell disintegrates from a bead mill and high pressure homogenizers (1990)

The protein releases, the particle size distribution and the viscosity of disrupted E. coli suspensions from Dyno Mill KDL, Manton Gaulin 15 M-8TA and Microfluidizer M-110 were determined. The effects of these parameters on separation of the cell debris from the protein solution by centrifugation and by filtration were also examined. All three disintegration methods investigated give approximately the same protein and enzyme releases but considerably different physical properties of the cell disintegrates which influences centrifugation and filtration. The separation degree of biomass during centrifugation is only slightly affected by increasing degree of disruption (increasing protein releases) in the bead mill, while an increase in the degree of disruption in the two high pressure homogenizers drastically reduces the centrifugal degree of separation. However, increasing degrees of disruption result in shorter filtration times during filtration for all three disintegration methods. The results show further that the cell concentration only has a minor influence on protein releases in the Microfluidizer high-pressure homogenizer, while an increase in the biomass content reduces the separability of the cell disintegrate both in filtration and in centrifugation.
OCTREE-BASED HEXAHEDRAL MESH GENERATION (2000)

An octree-based algorithm for the generation of hexahedral element meshes is presented. The algorithm works in three steps: (i) The geometry to be meshed is approximated by an octree structure. (ii) An unstructured hexahedral element mesh is derived from the octree. (iii) The mesh is adapted to the boundary of the geometry. We focus on step (ii) and describe an algorithm that constructs a hex mesh for a given octree structure.
Top Down Characterization of Larger Proteins (45 kDa) by Electron Capture Dissociation Mass Spectrometry (2002)

The structural characterization of proteins expressed from the genome is a major problem in proteomics. The solution to this problem requires the separation of the protein of interest from a complex mixture, the identification of its DNA-predicted sequence, and the characterization of sequencing errors and posttranslational modifications. For this, the "top down" mass spectrometry (MS) approach, extended by the greatly increased protein fragmentation from electron capture dissociation (ECD), has been applied to characterize proteins involved in the biosynthesis of thiamin, Coenzyme A, and the hydroxylation of proline residues in proteins. With Fourier transform (FT) MS, electrospray ionization (ESI) of a complex mixture from an E. coli cell extract gave 102 accurate molecular weight values (2-30 kDa), but none corresponding to the predicted masses of the four desired enzymes for thiamin biosynthesis (GoxB, ThiS, ThiG, and ThiF). MS/MS of one ion species (representing approximately 1% of the mixture) identified it with the DNA-predicted sequence of ThiS, although the predicted and measured molecular weights were different. Further purification yielded a 2-component mixture whose ECD spectrum characterized both proteins simultaneously as ThiS and ThiG, showing an additional N-terminal Met on the 8 kDa ThiS and removal of an N-terminal Met and Ser from the 27 kDa ThiG. For a second system, the molecular weight of the 45 kDa phosphopantothenoylcysteine synthetase/decarboxylase (CoaBC), an enzyme involved in Coenzyme A biosynthesis, was 131 Da lower than that of the DNA prediction; the ECD spectrum showed that this is due to the removal of the N-terminal Met. For a third system, viral prolyl 4-hydroxylase (26 kDa), ECD showed that multiple molecular ions (+98, +178, etc.) are due to phosphate noncovalent adducts, and MS/MS pinpointed the overall mass discrepancy of 135 Da to removal of the initiation Met (131 Da) and to formation of disulfide bonds (2 x 2 Da) at C32-C49 and C143-C147, although 10 S-S positions were possible. In contrast, "bottom up" proteolysis characterization of the CoaBC and the P4H proteins was relatively unsuccessful. The addition of ECD substantially increases the capabilities of top down FTMS for the detailed structural characterization of large proteins.
Fragment-Hopping-Based Discovery of a Novel Chemical Series of Proto-Oncogene PIM-1 Kinase Inhibitors (2012)

A new chemical series, triazolo[4,5-b]pyridines, has been identified as an inhibitor of PIM-1 by a chemotype hopping strategy based on a chemically feasible fragment database. In this case, structure-based virtual screening and in silico chemogenomics provide added value to the previously reported strategy of prioritizing among proposed novel scaffolds. Pairwise comparison between compound 3, recently discontinued from Phase I clinical trials, and molecule 8, bearing the selected novel scaffold, shows that the primary activities are similar (IC(50) in the 20 to 150 nM range). At the same time, some ADME properties (for example, an increase of more than 45% in metabolic stability in human liver microsomes) and the off-target selectivity (for example, an increase of more than 2 log units in IC(50)vs. FLT3) are improved, and the intellectual property (IP) position is enhanced. The discovery of a reliable starting point that fulfills critical criteria for a plausible medicinal chemistry project is demonstrated in this prospective study.
Design approaches with a lenslet array and a single, high-numerical-aperture annular-field objective lens for optical data storage systems that incorporate large numbers of parallel read–write–erase channels (1999)

To achieve very high data rates (>10(9) bits/s) in optical data storage systems it is necessary to employ a large number of laser beams for parallel read-write-erase operations. Bringing all these beams to diffraction-limited focus with a high-numerical-aperture objective lens (while maintaining focus and tracking) requires techniques that are fundamentally different from those that are currently practiced in the field of optical data storage. We present two possible solutions to the problem of designing an objective lens for such systems, one involving an array of high-quality lenslets and the other based on a single, high-numerical-aperture annular-field-of-view conventional lens. Both approaches have advantages and disadvantages, on which we elaborate in the course of our discussions.
Let the power fall [portable device power management] (2006)

Power management has become a major headache for designers. To try to stop the battery draining in a matter of minutes, large sections of a portable device need to be turned off or at least slowed down when they are not heavily used. Doing this effectively needs cooperation between the system functions and the power-management circuitry. But, right now, as there are few standards in place, this level of power management needs cooperation between the suppliers of system devices and those making the power components. Changes in battery chemistry will force alterations to the power circuits in portable systems.
Fingerprint segmentation based on PCNN and morphology (2009)

As an important step in an automatic fingerprint recognition system, fingerprint segmentation aims to extract the foreground of a fingerprint image in an efficient way. In this paper, an initiative algorithm for fingerprint segmentation is presented. First, the model of Pulse Coupled Neural Networks (PCNN) is utilized to binarize the fingerprint image. Then, morphological methods are adopted to obtain compact clusters of the binary fingerprint image. Since there might be other interfering regions after morphological operation, we also use the labeling method to find the largest compact cluster as the foreground region of the fingerprint image. Experimental results show that this method is robust to the complicated backgrounds of fingerprint images while keeping a smooth contour of the foreground region.