gebhart/patrepeval huggingface dataset:
Implementing statically typed object-oriented programming languages (2011)

Object-oriented programming represents an original implementation issue due to its philosophy of making the program behavior depend on the dynamic type of objects. This is expressed by the late binding mechanism, aka message sending . The underlying principle is that the address of the actually called procedure is not statically determined at compile-time, but depends on the dynamic type of a distinguished parameter known as the receiver . A similar issue arises with attributes, because their position in the object layout may also depend on the object's dynamic type. Furthermore, subtyping introduces another original feature (i.e., runtime subtype checks). All three mechanisms need specific implementations and data structures. In static typing, late binding is generally implemented with so-called virtual function tables . These tables reduce method calls to pointers to functions via a small fixed number of extra indirections. It follows that object-oriented programming yields some overhead, as compared to the usual procedural languages. The different techniques and their resulting overhead depend on several parameters. First, inheritance and subtyping may be single or multiple, and even a mixing is possible, as in Java and ˙NET which present single inheritance for classes and multiple subtyping for interfaces. Multiple inheritance is a well-known complication. Second, the production of executable programs may involve various schemes, from global compilation, which implies the closed-world assumption (CWA), as the whole program is known at compile time, to separate compilation and dynamic loading, where each program unit is compiled and loaded independently of any usage, hence under the open-world assumption (OWA). Global compilation is well-known to facilitate optimization. This article reviews the various implementation techniques available in static typing and in the three cases of single inheritance, multiple inheritance, and multiple subtyping. This language-independent survey focuses on separate compilation and dynamic loading, as they represent the most commonly used and the most demanding framework. However, many works have been undertaken in the global compilation framework, mostly for dynamically typed languages, but also applied to the EIFFEL language. Hence, we also examine global techniques and how they can improve implementation efficiency. Finally, mixed frameworks that combine open and closed world assumptions are considered. For instance, just-in-time (JIT) compilers work under provisional CWA, at the expense of possible recompilations. In contrast, we present an experimental compiler-linker, where separate compilation implies the OWA, whereas the whole program is finally linked under the CWA.
Differences in Fecal Microbiota in Different European Study Populations in Relation to Age, Gender, and Country: a Cross-Sectional Study (2006)

A cross-sectional study on intestinal microbiota composition was performed on 230 healthy subjects at four European locations in France, Germany, Italy, and Sweden. The study participants were assigned to two age groups: 20 to 50 years (mean age, 35 years; n = 85) and >60 years (mean age, 75 years; n = 145). A set of 14 group- and species-specific 16S rRNA-targeted oligonucleotide probes was applied to the analysis of fecal samples by fluorescence in situ hybridization coupled with flow cytometry. Marked country-age interactions were observed for the German and Italian study groups. These interactions were inverse for the predominant bacterial groups Eubacterium rectale-Clostridium coccoides and Bacteroides-Prevotella. Differences between European populations were observed for the Bifidobacterium group only. Proportions of bifidobacteria were two- to threefold higher in the Italian study population than in any other study group, and this effect was independent of age. Higher proportions of enterobacteria were found in all elderly volunteers independent of the location. Gender effects were observed for the Bacteroides-Prevotella group, with higher levels in males than in females. In summary, age-related differences in the microbiota makeup were detected but differed between the study populations from the four countries, each showing a characteristic colonization pattern.
Extreme Fast Charging Technology—Prospects to Enhance Sustainable Electric Transportation (2019)

With the growing fleet of a new generation electric vehicles (EVs), it is essential to develop an adequate high power charging infrastructure that can mimic conventional gasoline fuel stations. Therefore, much research attention must be focused on the development of off-board DC fast chargers which can quickly replenish the charge in an EV battery. However, use of the service transformer in the existing fast charging architecture adds to the system cost, size and complicates the installation process while directly connected to medium-voltage (MV) line. With continual improvements in power electronics and magnetics, solid state transformer (SST) technology can be adopted to enhance power density and efficiency of the system. This paper aims to review the current state of the art architectures and challenges of fast charging infrastructure using SST technology while directly connected to the MV line. Finally, this paper discusses technical considerations, challenges and introduces future research possibilities.
Nanogoldpharmaceutics (2007)

Nanosized gold particles (27 +/− 3 nm) have been proven to be effective in ameliorating the symptoms of mycobacterial-, collagen- and pristane-induced arthritis in rat models. This contrasts with the drug sodium aurothiomalate that was only effective against mycobacterial-induced arthritis but not to the same extent as Au0. Gold in the traditional Indian Ayurvedic medicine,Swarna bhasma (gold ash), has been characterized as globular particles of gold with an average size of 56–57 nm.
Optical Phased Array with Small Spot Size, High Steering Range and Grouped Cascaded Phase Shifters (2016)

An optical phased array with a record spot size of 0.85°×0.18° and steering range of 46°×36° is demonstrated. Grouped cascaded phase shifters are utilized. Beam powers of 1mW and a free-space data link are achieved.
Chiral Calcium–BINOL Phosphate Catalyzed Diastereo‐ and Enantioselective Synthesis of syn‐1,2‐Disubstituted 1,2‐Diamines: Scope and Mechanistic Studies (2014)

A highly enantioselective, chiral, Lewis acid calcium-bis(phosphate) complex, Ca[3 a]n, which catalyzes the electrophilic amination of enamides with azodicarboxylate derivatives 2 to provide versatile chiral 1,2-hydrazinoimines 4 is disclosed. The reaction gives an easy entry to optically active syn-1,2-disubstituted 1,2-diamines 6 in high yields with excellent enantioselectivities, after a one-pot reduction of the intermediate 1,2-hydrazinoimines 4. The geometry and nature of the N-substituent of the enamide affect dramatically both the reactivity and the enantioselectivity. Although the calcium-bis(phosphate) complex was a uniquely effective catalyst, the exact nature of the active catalytic species remains unclear. NMR spectroscopy and MS analysis of the various calcium complexes Ca[3]n reveals that the catalysts exist in various oligomer forms. The present mechanistic study, which includes nonlinear effects and kinetic measurements, constitutes a first step in understanding these calcium-bis(phosphate) complex catalysts. DFT calculations were carried out to explore the mechanism and the origin of the enantioselectivity with the Ca[3]n catalysts.
Cleaning effectiveness of root canal irrigation with electrochemically activated anolyte and catholyte solutions: a pilot study (2000)

Irrigation with electrochemically activated solutions cleaned root canal walls and may be an alternative to NaOCl in conventional root canal treatment. Further investigation of ECA solutions for root canal irrigation is warranted.
Iterative Image Warping (2012)

Abstract Animated image sequences often exhibit a large amount of inter‐frame coherence which standard rendering algorithms and pipelines are ill‐equipped to exploit, limiting their efficiency. To address this inefficiency we transfer rendering results across frames using a novel image warping algorithm based on fixed point iteration. We analyze the behavior of the iteration and describe two alternative algorithms designed to suit different performance requirements. Further, to demonstrate the versatility of our approach we apply it to a number of spatio‐temporal rendering problems including 30‐to‐60Hz frame upsampling, stereoscopic 3D conversion, defocus and motion blur. Finally we compare our approach against existing image warping methods and demonstrate a significant performance improvement.
Purified yeast translational initiation factor eIF-3 is an RNA-binding protein complex that contains the PRT1 protein. (1994)

Eukaryotic initiation factor-3 (eIF-3) plays a pivotal role in the initiation phase of protein synthesis where it promotes dissociation of 80 S ribosomes into subunits, stabilizes methionyl-tRNAi binding to 40 S ribosomal subunits, and is required for mRNA binding. Mammalian eIF-3 is comprised of eight subunits, but no mammalian cDNA encoding these proteins has been cloned and sequenced, nor has the corresponding factor been characterized in yeast. Since many initiation factors are strongly conserved between mammalian and yeast systems, we employed a mammalian assay for initiation, the synthesis of methionyl-puromycin, to detect eIF-3 activity in yeast subcellular fractions. Yeast eIF-3 was purified from the high salt wash of ribosomes by Superose 6 molecular sieve and MonoS ion exchange chromatography. Yeast eIF-3 contains eight subunits with masses of 16, 21, 29, 33, 39, 62, 90, and 135 kilodaltons all of which coelute with an apparent mass of 550 kilodaltons from the Superose 6 column. Immunoblotting shows that the 90-kDa subunit corresponds to the product of the PRT1 gene whose mutant form, prt1-1, exhibits destabilization of methionyl-tRNAi binding to 40 S ribosomal subunits. eIF-3, and specifically the 62-kDa subunit, bind to RNA. These biochemical approaches to defining yeast eIF-3 complement genetic methods so far used in characterizing the initiation factors and provide another route to defining the yeast translational machinery.
Genetically engineered viral insecticides–A progress report 1986 1989 (1989)

Abstract Among the viruses that are pathogenic for insect species, baculoviruses have been shown to be useful as insecticides for pest control. In some cases they have been used as cost‐effective and environmentally acceptable alternatives to chemical insecticides. However, because viruses need to be ingested and replicate extensively in their host before they kill it, baculovirus insecticides are much slower than chemicals or other reagents that kill insects either on contact or shortly after ingestion. The objective of the programme of genetic engineering of baculovirus insecticides is to improve their speed of action while maintaining their host specificity and other attributes that make them desirable alternatives to chemical pesticides. Since 1986 four field releases have been undertaken involving genetically engineered baculovirus insecticides. The first release used a genetically marked Autographa californica nuclear polyhedrosis virus (AcNPV). The study began in 1986 and was terminated in 1987. The results demonstrated that an innocuous piece of DNA, appropriately positioned in the AcNPV genome, was an effective means to tag the virus without affecting its phenotype, allowing it to be identified in bioassays of plant and soil samples. The second release, in 1987, involved a genetically marked virus from which the gene coding for the protective polyhedrin protein of the virus had been removed. The field data obtained with this virus showed that it did not persist in the environment, neither in soil, nor on vegetation, nor in the corpses of caterpillars. The third and fourth releases were undertaken in 1988. For one of these studies the marked, polyhedrin‐negative virus was again used. In the other study a polyhedrin‐negative virus that contained a junk' (/?‐galactosidase) gene was employed.
Mesoporous Silica Nanoparticles Facilitate Delivery of siRNA to Shutdown Signaling Pathways in Mammalian Cells (2010)

A nanocomplex assembly of polyethylenimine and mesoporous silica nanoparticles are used to successfully protect and deliver siRNA into human cells, effectively shutting down both exogenous and endogenous gene signal.
Surface Characterization of Carbohydrate Microarrays (2010)

Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.
High-level potentiation of lysostaphin anti-staphylococcal activity by lysozyme (1982)

The purpose of this study was to determine whether lysostaphin would enhance its anti-staphylococcal efficacy in combination with lysozyme. Minimum inhibitory concentrations (MICs) of lysostaphin and lysozyme were separately determined for 41 strains belonging to 10 different species of human staphylococci. Lysozyme was virtually inactive and showed MICs of 15 mg/ml. On the contrary, all strains were susceptible to lysostaphin and showed MICs ranging from 2.5 to 60 micrograms/ml for the different Staphylococcus species. When the MIC of lysostaphin was determined in media containing submultiples of the MIC of lysozyme, the values obtained were much lower. The reduction of the lysostaphin MIC ranged from 16- to 200-fold in the different species tested. In Staphylococcus aureus, in particular, the combination of lysostaphin with 1.5 mg of lysozyme per ml reduced the MIC of lysostaphin by 25-fold. The activities of two combinations of the two enzymes were evaluated: one combination was expected to be active on S. aureus only, and the other combination was expected to inhibit all Staphylococcus strains. The first combination (0.5 micrograms of lysostaphin plus 0.5 mg of lysozyme per ml) was inhibitory to all of the 84 S. aureus strains tested, whereas 137 of 151 strains of other Staphylococcus species were unaffected. On the contrary, all of the 235 Staphylococcus strains tested were inhibited by the second combination (4 micrograms of lysostaphin plus 5 mg of lysozyme per ml). The possible mechanisms of lysostaphin potentiation by lysozyme are considered, and the potential use of a lysostaphin-lysozyme combination for topical therapy of staphylococcal infections resistant to other antibiotics is discussed.
GROWTH FACTORS AND CANCER (1985)

Recent advances in protein chemistry and genetic engineering have revealed new information about the molecular lesions involved in the induction and maintenance of cancer cells. It is now known that a single base change in the DNA of human cells leads to cancer. The normal pathway of proliferation and differentiation is perturbed by changes to molecules involved in the intracellular biochemical pathways controlled by growth factors. Some cancer cells appear to produce their own growth factor, others have higher concentrations of growth factor receptors on their surface and others have mutated versions of the intracellular proteins linked to the growth factor receptors. This increased understanding of growth control in normal and neoplastic cell populations is gradually providing a foundation for new approaches to cancer therapy.
In Search of a Metric for Managing Architectural Technical Debt (2012)

Practices designed to expedite the delivery of stakeholder value can paradoxically lead to unexpected rework costs that ultimately degrade the flow of value over time. This is especially observable when features are developed based on immediate value, while dependencies that may slow down future development efforts are neglected. The technical debt metaphor conceptualizes this tradeoff between short-term and long-term value: taking shortcuts to optimize the delivery of features in the short term incurs debt, analogous to financial debt, that must be paid off later to optimize long-term success. In this paper, we describe taking an architecture-focused and measurement-based approach to develop a metric that assists in strategically managing technical debt. Such an approach can be used to optimize the cost of development over time while continuing to deliver value to the customer. We demonstrate our approach by describing its application to an ongoing system development effort.
The Innate Immune System and Its Role in Allergic Disorders (2005)

&lt;i&gt;Background:&lt;/i&gt; There has been an increasing prevalence of allergic diseases in the Western world over the last decades. The hygiene hypothesis has been proposed as a possible explanation for this epidemical trend in allergy. A key role in this theory is assigned to the reduced microbial stimulation of the Toll-like receptors (TLRs) in early life, which could lead to a weaker Th1 response and a stronger Th2 response to allergens. The individual immunological response is determined by the interplay between the dose and timing of exposure to endotoxins, other environmental factors and genetic predisposition. In the development and progression of allergic disorders, the innate immune system plays an important role. &lt;i&gt;Objective:&lt;/i&gt; In this review, we discuss the paradoxical effects that may appear when the innate immune components are triggered. We review the influence of changes in the gene sequence and TLR expression in relation to the overall pattern of commensals and pathogens. We explored the possibility of alternative stimulations of the immune system by CpG oligodeoxynucleotides and probiotics as therapeutic devices against this endemic disease in Western society. &lt;i&gt;Methods:&lt;/i&gt; Selection of papers was based on the importance of their contribution to the understanding of innate immunity and its implications. &lt;i&gt;Results and Conclusion:&lt;/i&gt; The innate immune system plays an important role in both the protection against and the enhancement of allergic disorders, but the mechanisms are still unclear. Nevertheless, gene polymorphisms and triggers of the innate immune system provide therapeutic targets for protection against and treatment of allergic disorders.
Rat middle cerebral artery occlusion: evaluation of the model and development of a neurologic examination. (1986)

We have examined the incidence and size of infarction after occlusion of different portions of the rat middle cerebral artery (MCA) in order to define the reliability and predictability of this model of brain ischemia. We developed a neurologic examination and have correlated changes in neurologic status with the size and location of areas of infarction. The MCA was surgically occluded at different sites in six groups of normal rats. After 24 hr, rats were evaluated for the extent of neurologic deficits and graded as having severe, moderate, or no deficit using a new examination developed for this model. After rats were sacrificed the incidence of infarction was determined at histologic examination. In a subset of rats, the size of the area of infarction was measured as a percent of the area of a standard coronal section. Focal (1-2 mm) occlusion of the MCA at its origin, at the olfactory tract, or lateral to the inferior cerebral vein produced infarction in 13%, 67%, and 0% of rats, respectively (N = 38) and produced variable neurologic deficits. However, more extensive (3 or 6 mm) occlusion of the MCA beginning proximal to the olfactory tract--thus isolating lenticulostriate end-arteries from the proximal and distal supply--produced infarctions of uniform size, location, and with severe neurologic deficit (Grade 2) in 100% of rats (N = 17). Neurologic deficit correlated significantly with the size of the infarcted area (Grade 2, N = 17, 28 +/- 5% infarction; Grade 1, N = 5, 19 +/- 5%; Grade 0, N = 3, 10 +/- 2%; p less than 0.05). We have characterized precise anatomical sites of the MCA that when surgically occluded reliably produce uniform cerebral infarction in rats, and have developed a neurologic grading system that can be used to evaluate the effects of cerebral ischemia rapidly and accurately. The model will be useful for experimental assessment of new therapies for irreversible cerebral ischemia.
Fragment-Based Discovery of 7-Azabenzimidazoles as Potent, Highly Selective, and Orally Active CDK4/6 Inhibitors (2012)

Herein, we describe the discovery of potent and highly selective inhibitors of both CDK4 and CDK6 via structure-guided optimization of a fragment-based screening hit. CDK6 X-ray crystallography and pharmacokinetic data steered efforts in identifying compound 6, which showed >1000-fold selectivity for CDK4 over CDKs 1 and 2 in an enzymatic assay. Furthermore, 6 demonstrated in vivo inhibition of pRb-phosphorylation and oral efficacy in a Jeko-1 mouse xenograft model.
In Vivo Imaging Reveals Dissociation between Caspase Activation and Acute Neuronal Death in Tangle-Bearing Neurons (2008)

Accumulation of neurofibrillary tangles (NFTs) in Alzheimer's disease correlates with neuronal loss and cognitive decline, but the precise relationship between NFTs and neuronal death and downstream mechanisms of cell death remain unclear. Caspase cleaved products accumulate in tangles, implying that tangles may contribute to apoptotic neuronal death. To test this hypothesis, we developed methods using multiphoton imaging to detect both neurofibrillary pathology and caspase activation in the living mouse brain. We examined rTg4510 mice, a reversible mouse model of tauopathy that develops tangles and neuronal loss. Only a small percentage of imaged neurons were caspase activity positive, but the vast majority of the cells with active caspases contained NFTs. We next tested the hypothesis that caspase activation led to acute, apoptotic neuronal death. Caspase positive cell bodies did not degenerate over hours of imaging, despite the presence of activated executioner caspases. Suppression of the transgene, which stops ongoing death, did not suppress caspase activity. Finally, histochemical assessments revealed evidence of caspase-cleaved tau, but no TUNEL (terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling) positive or apoptotic nuclei. With the novel technique of observing NFTs and caspase activation in the living brain, we demonstrate that aggregated tau in neurons can be associated with caspase activation, but that caspase activation is not sufficient to cause acute neuronal death in this model.