gebhart/patrepeval huggingface dataset:
Ontology-based product line modeling and generation (2011)

Software product line engineering defines a family of related software products. Every software product line engineering method has two essential elements, a set of models representing the product family, and a process for instantiating product members from those models. In this paper, we investigate the use of ontologies to model product lines. We also show how product members can be instantiated from an ontology-based model. We discuss our early experiences using ontologies to specify a family of workflows for a large insurance company.
Growth hormone: current and future therapeutic applications (2000)

The increased availability of growth hormone (GH) in the mid-1980s, as a result of advances in recombinant DNA techniques, has allowed research into the use of this hormone at physiological dosage, as replacement therapy for adults with GH deficiency (GHD) and at pharmacological dosages as a possible therapeutic agent, for a number of disease states. GHD adults have increased body fat and reduced muscle mass and consequently, reduced strength and exercise tolerance. In addition, they are osteopenic, have unfavourable cardiac risk factors and impaired quality of life. In these individuals, replacing GH reverses these anomalies, although it may not alter the reduced insulin-sensitivity. A proportion of adults with GHD perceive a dramatic improvement in their well-being, energy levels and mood following replacement. GH has protein and osteoanabolic, lipolytic and antinatriuretic properties. GH has been considered for the therapeutic treatment of frailty associated with ageing, osteoporosis, morbid obesity, cardiac failure, major thermal injury and various acute and chronic catabolic conditions. Initial small, uncontrolled studies for many of these clinical problems suggested a beneficial effect of GH, although, later placebo-controlled studies have not observed such dramatic effects. Furthermore, with a recent publication demonstrating an approximate 2-fold increase in mortality in critically ill patients receiving large doses of GH, the use of GH should remain in the realms of replacement therapy and research, until there are significant advances in our understanding.
Genetic determinants of bone mass in adults. A twin study. (1987)

The relative importance of genetic factors in determining bone mass in different parts of the skeleton is poorly understood. Lumbar spine and proximal femur bone mineral density and forearm bone mineral content were measured by photon absorptiometry in 38 monozygotic and 27 dizygotic twin pairs. Bone mineral density was significantly more highly correlated in monozygotic than in dizygotic twins for the spine and proximal femur and in the forearm of premenopausal twin pairs, which is consistent with significant genetic contributions to bone mass at all these sites. The lesser genetic contribution to proximal femur and distal forearm bone mass compared with the spine suggests that environmental factors are of greater importance in the aetiology of osteopenia of the hip and wrist. This is the first demonstration of a genetic contribution to bone mass of the spine and proximal femur in adults and confirms similar findings of the forearm. Furthermore, bivariate analysis suggested that a single gene or set of genes determines bone mass at all sites.
Methicillin-Resistant Staphylococcus saprophyticus Isolates Carrying Staphylococcal Cassette Chromosome mec Have Emerged in Urogenital Tract Infections (2008)

Staphylococcus saprophyticus is a uropathogenic bacterium that causes acute uncomplicated urinary tract infections, particularly in female outpatients. We investigated the dissemination and antimicrobial susceptibilities of 101 S. saprophyticus isolates from the genitourinary tracts of patients in Japan. Eight of these isolates were mecA positive and showed beta-lactam resistance. Pulsed-field gel electrophoresis showed that only some isolates were isogenic, indicating that the mecA gene was apparently acquired independently by mecA-positive isolates through staphylococcal cassette chromosome mec (SCCmec). Type determination of SCCmec by multiplex PCR showed a nontypeable element in the eight mecA-positive isolates. Sequence analysis of the entire SCCmec element from a prototype S. saprophyticus strain revealed that it was nontypeable with the current SCCmec classification due to the novel composition of the class A mec gene complex (IS431-mecA-mecR1-mecI genes) and the ccrA1/ccrB3 gene complex. Intriguingly, the attachment sites of SCCmec are similar to those of type I SCCmec in S. aureus NCTC 10442. Furthermore, the genes around the mec gene complex are similar to those of type II/III SCCmec in S. aureus, while those around the ccr gene complex are similar to those of SCC15305RM found in S. saprophyticus ATCC 15305. In comparison with known SCCmec elements, this S. saprophyticus SCCmec is a novel type.
Cloning and developmental expression of Nsk2, a novel receptor tyrosine kinase implicated in skeletal myogenesis. (1995)

The protein superfamily of transmembrane receptor tyrosine kinases (RTKs) are essential components of intercellular signalling pathways necessary for normal cellular regulation. We report the cloning and developmental expression pattern of Nsk2, a novel, structurally distinct mammalian RTK characterised by a putative extracellular region bearing four immunoglobulin-like domains. The Nsk2 locus was mapped to the distal region of mouse chromosome 13 and was found to be expressed preferentially in skeletal muscle amongst adult mouse tissues. Moreover, increased steady-state levels of Nsk2 transcripts were apparent on terminal differentiation of committed skeletal myoblast cell lines in vitro and multiple isoforms of the Nsk2 RTK were identified in skeletal myotube cultures. RNA in situ hybridisation studies of mouse embryos confirmed skeletal myogenesis to be a major site of Nsk2 expression during normal embryogenesis, and identified other likely sites of Nsk2 function in ganglia of the developing peripheral nervous system and various embryonic epithelia, including those of kidney, lung and gut, during fetal development. Taken together, our data suggest normal functions for Nsk2 RTKs in distinctive aspects of skeletal muscle development, neurogenesis and mesenchymal-epithelial interactions during organ formation.
Regulatory Proteins of R-Ras, TC21/R-Ras2, and M-Ras/R-Ras3 (2000)

We studied the regulation of three closely related members of Ras family G proteins, R-Ras, TC21 (also known as R-Ras2), and M-Ras (R-Ras3). Guanine nucleotide exchange of R-Ras and TC21 was promoted by RasGRF, C3G, CalDAG-GEFI, CalDAG-GEFII (RasGRP), and CalDAG-GEFIII both in 293T cells and in vitro. By contrast, guanine nucleotide exchange of M-Ras was promoted by the guanine nucleotide exchange factors (GEFs) for the classical Ras (Ha-, K-, and N-), including mSos, RasGRF, CalDAG-GEFII, and CalDAG-GEFIII. GTPase-activating proteins (GAPs) for Ras, Gap1(m), p120 GAP, and NF-1 stimulated all of the R-Ras, TC21, and M-Ras proteins, whereas R-Ras GAP stimulated R-Ras and TC21 but not M-Ras. We did not find any remarkable difference in the subcellular localization of R-Ras, TC21, or M-Ras when these were expressed with a green fluorescent protein tag in 293T cells and MDCK cells. In conclusion, TC21 and R-Ras were regulated by the same GEFs and GAPs, whereas M-Ras was regulated as the classical Ras.
3,3′-Dinitroamino-4,4′-azoxyfurazan and Its Derivatives: An Assembly of Diverse N–O Building Blocks for High-Performance Energetic Materials (2014)

On the basis of a design strategy that results in the assembly of diverse N-O building blocks leading to energetic materials, 3,3'-dinitroamino-4,4'-azoxyfurazan and its nitrogen-rich salts were obtained and fully characterized via spectral and elemental analyses. Oxone (potassium peroxomonosulfate) is an efficient oxidizing agent for introducing the azoxy N-oxide functionality into the furazan backbone, giving a straightforward and low-cost synthetic route. On the basis of heats of formation calculated with Gaussian 03 and combined with experimentally determined densities, energetic properties (detonation velocity, pressure and specific impulse) were obtained using the EXPLO v6.01 program. These new molecules exhibit high density, moderate to good thermal stability, acceptable impact and friction sensitivities, and excellent detonation properties, which suggest potential applications as energetic materials. Interestingly, 3,3'-dinitroamino-4,4'-azoxyfurazan (4) has the highest calculated crystal density of 2.02 g cm(-3) at 173 K (gas pycnometer measured density is 1.96 g cm(-3) at 298 K) for N-oxide energetic compounds yet reported. Another promising compound is the hydroxylammonium salt (6), which has four different kinds of N-O moieties and a detonation performance superior to those of 1,3,5,7-tetranitrotetraazacyclooctane (HMX), and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetracyclododecane (CL-20). Furthermore, computational results, viz., NBO charges and ESP, also support the superior qualities of the newly prepared compounds and the design strategy.
LeukoCatch, a quick and efficient tool for the preparation of leukocyte extracts from blood (2011)

We conclude that LeukoCatch is useful not only for diagnosis at the bedside but also for basic research using blood samples or tissue culture cells.
Disclosure social de empresas brasileiras e britânicas à luz da teoria institucional (2012)

O presente estudo objetiva investigar, com base nos indicadores recomendados no Guia de Indicadores de Responsabilidade Corporativa em Relatorios Anuais, da ONU, as principais caracteristicas da divulgacao de informacoes sociais das 30 maiores empresas brasileiras e das 30 maiores empresas britânicas classificadas segundo o ranking The Global 2000, da revista Forbes; e as provaveis explicacoes para os resultados a luz da Teoria Institucional. Trata-se de estudo exploratorio, compreendendo pesquisa documental e analise de relatorios anuais e sociais. A analise dos dados se deu com o emprego de tecnicas como distribuicao de frequencia, media aritmetica e testes de igualdade entre medias amostrais. No exame dos dados obtidos, percebe-se uma maior divulgacao dos indicadores faturamento total bruto e pagamentos ao governo – explicada a partir do pilar regulativo da Teoria Institucional; do indicador contribuicoes voluntarias a sociedade civil – explicada pelo pilar cognitivo da Teoria Institucional; e do indicador novos investimentos – atribuida ao peso do grupo de stakeholders a quem se destina a informacao. Aplicados os testes estatisticos, evidenciou-se uma maior divulgacao social nas empresas brasileiras, em cinco dos quinze indicadores estudados. Este estudo amplia a analise comparativa da divulgacao social de empresas brasileiras e companhias de paises considerados avancados em RSC.
Fabrication of Three-Dimensional Macroporous Membranes with Assemblies of Microspheres as Templates (1998)

Assemblies of polymer beads were used as templates to produce macroporous membranes of polymers and ceramics. These membranes consist of spherical pores whose sizes could be precisely controlled in the range from ∼0.2 to ∼3 μm. The pores are interconnected such that pores (as many as 108/cm2) are completely exposed on both top and bottom surfaces, and a complex, three-dimensional porous structure is formed in the bulk.
Adding Selectivity to Antimicrobial Peptides: Rational Design of a Multidomain Peptide againstPseudomonasspp (2006)

Currently available antimicrobials exhibit broad killing with regard to bacterial genera and species. Indiscriminate killing of microbes by these conventional antibiotics can disrupt the ecological balance of the indigenous microbial flora, often resulting in negative clinical consequences. Species-specific antimicrobials capable of precisely targeting pathogenic bacteria without damaging benign microorganisms provide a means of avoiding this problem. In this communication, we report the successful creation of the first synthetic, target-specific antimicrobial peptide, G10KHc, via addition of a rationally designed Pseudomonas-specific targeting moiety (KH) to a generally killing peptide (novispirin G10). The resulting chimeric peptide showed enhanced bactericidal activity and faster killing kinetics against Pseudomonas spp. than G10 alone. The enhanced killing activities are due to increased binding and penetration of the outer membrane of Pseudomonas sp. cells. These properties were not observed in tests of untargeted bacterial species, and this specificity allowed G10KHc to selectively eliminate Pseudomonas spp. from mixed cultures. This work lays a foundation for generating target-specific "smart" antimicrobials to complement currently available conventional antibiotics.
A Hierarchical ADMM Based Framework for EV Charging Scheduling (2018)

Electric vehicles (EVs) are controllable loads from which distribution grid operator can benefit in order to minimize the load profile variations. In this paper, we proposed a hierarchical distributed optimization framework such that EV management system (EVMS), as a part of distribution grid management system, minimizes the load variance of the grid in communication with the EV aggregators which control EV charging load of the distribution system feeders. The hierarchical distributed framework, based on alternative direction method of multipliers (ADMM), increases the scalability of the EV charging infrastructure while decreases computational burden. In our proposed approach, each EV aggregator schedules the EV charging profiles of its feeder in a distributed fashion which avoids sharing the EV owners' desired charging profile information and enables privacy preserving. To show the performance of our approach, we apply it to a case study with 100% EV penetration, including 4 feeders and 60 EVs, and show how the load variance of the system and charging cost of individual EVs decrease.
Chronic Rhinosinusitis With Nasal Polyps is Associated With Decreased Expression of Mucosal Interleukin 22 Receptor (2007)

In this study, we demonstrate IL-22R1 mRNA and protein expression on nasal epithelial cells. Failure of medical and surgical therapy in CRSwNP is associated with significantly decreased expression of IL-22R1. Further research is needed to determine the potential of IL-22R1 as a therapeutic target in CRSwNP.
Screening catalytic lipase activities with an analytical supercritical fluid extractor (1998)

Abstract Two different screenings of several commercial lipases were performed to find a lipase with superior performance for the conversion of lipid moieties to their fatty acid methyl ester (FAME) derivatives under supercritical conditions. The first screening was done under hydrolytic conditions in a buffer. The second screening was done under supercritical conditions with CO 2 , utilizing some of the same lipases for the methanolysis of different lipids. For the substrates studied, there was a significant difference in lipase activity under the two above conditions. Significant hydrolytic activity was demonstrated for three different lipid types (triglycerides, sterols, and phospholipids) with Lipase PS30, but when the same lipase was immobilized on an Accurel carrier (polypropylene), the activity decreased considerably. The opposite was found for Lipase G, which showed strong activity when immobilized and under supercritical conditions. Furthermore, Chirozyme L‐1 was superior under supercritical conditions. The altered substrate specificity that some of these lipases show in supercritical CO 2 suggests several interesting synthetic options and applications under these conditions.
Monoamine oxidase A and repressor R1 are involved in apoptotic signaling pathway (2006)

Monoamine oxidase A (MAO A) degrades serotonin, norepinephrine, and dopamine and produces reactive oxygen that may cause neuronal cell death. We have previously reported that a novel transcription factor R1 (RAM2/CDCA7L/JPO2) inhibits the MAO A promoter and enzymatic activities. This study reports the roles of MAO A and R1 in apoptosis and proliferation. We have found that in serum starvation-induced apoptosis, p38 kinase, MAO A, and caspase-3 were increased, whereas Bcl-2 and R1 were reduced. Using a p38 kinase inhibitor, R1 overexpression, and MAO A inhibitor, we have shown that MAO A and R1 are downstream of p38 kinase and Bcl-2, but upstream of caspase-3. Inhibition of MAO A prevents cell apoptosis. This notion was further supported by the finding that serum starvation-induced apoptosis is reduced in cortical brain cells from MAO A-deficient mice compared with WT. In addition, we found that MAO A and R1 are involved in the c-Myc-induced proliferative signaling pathway in the presence of serum. Immunoprecipitation and immunohistochemistry experiments indicate that the oncogene c-Myc colocalizes with R1 and induces R1 gene expression. Using R1 overexpression, R1 small interfering RNA, and a MAO A inhibitor, we found that R1 and MAO A act upstream of cyclin D1 and E2F1. In summary, this study demonstrates the functions of MAO A and its repressor R1 in apoptotic signaling pathways.
Rapid ambient mass spectrometric profiling of intact, untreated bacteria using desorption electrospray ionization (2006)

Desorption electrospray ionization (DESI) allows the rapid acquisition of highly reproducible mass spectra from intact microorganisms under ambient conditions; application of principal component analysis to the data allows sub-species differentiation.
Differences in the glucocorticoid to progesterone receptor selectivity of inhaled glucocorticoids (2006)

Due to the high affinity of new inhaled corticosteroids (ICS) towards the glucocorticoid receptor (GR), and because of the similarities between the binding domains of the GR and the progesterone receptor (PR), the present study focused on assessing the relative binding affinities (RBA) of glucocorticoids (systemic and ICS) to PR (RBAPR). By comparison with the affinities towards the GR (RBAGR) the binding selectivities were also assessed. In general, the selectivity of the investigated glucocorticoids showed a decreasing trend with increasing lipophilicity. When orally administered, less lipophilic glucocorticoids showed the highest selectivity, with RBAGR/RBAPR ratios of 1,375, 760 and 476 for betamethasone, beclomethasone and dexamethasone, respectively. For ICS, mometasone furoate, the most lipophilic steroid, was the least selective (1.1), followed by beclomethasone monopropionate (9), fluticasone propionate (12), triamcinolone acetonide (18), mometasone (25) and budesonide (44), which shows the highest selectivity among inhaled glucocorticoids. In conclusion, the present study revealed that there are differences in selectivity among commercially available glucocorticoids. Future clinical studies are needed to investigate whether the high affinity of some of the investigated glucocorticoids to the progesterone receptor is of clinical relevance.
Paraphrase Generation with Deep Reinforcement Learning (2018)

Automatic generation of paraphrases from a given sentence is an important yet challenging task in natural language processing (NLP). In this paper, we present a deep reinforcement learning approach to paraphrase generation. Specifically, we propose a new framework for the task, which consists of a generator and an evaluator, both of which are learned from data. The generator, built as a sequenceto-sequence learning model, can produce paraphrases given a sentence. The evaluator, constructed as a deep matching model, can judge whether two sentences are paraphrases of each other. The generator is first trained by deep learning and then further fine-tuned by reinforcement learning in which the reward is given by the evaluator. For the learning of the evaluator, we propose two methods based on supervised learning and inverse reinforcement learning respectively, depending on the type of available training data. Experimental results on two datasets demonstrate the proposed models (the generators) can produce more accurate paraphrases and outperform the stateof-the-art methods in paraphrase generation in both automatic evaluation and human evaluation.
Fighting Cancer with Viruses: Oncolytic Virus Therapy in China (2017)

As part of oncolytic virotherapy to treat cancer, oncolytic viruses (OVs) can selectively infect tumor cells to promote oncolysis of cancer cells, local immunological reactions, and systemic antitumor immunity with minimal toxicity to normal tissues. The immunostimulatory properties of OVs provide enormous benefits for the treatment of cancer. A variety of OVs, including genetically engineered and natural viruses, have shown promise in preclinical models and clinical studies. In 2005, the China Food and Drug Administration approved its first OV drug, Oncorine (H101), for treatment of advanced head and neck cancer. To explore new treatment strategies, >200 recombinant or natural OVs are undergoing in-depth investigation in China, and >250 oncolytic virotherapy-related reports from the OV community in China have been published in the past 5 years. These studies investigated a variety of exogenous genes and combination therapeutic strategies to enhance the treatment effects of OVs. To date, five clinical trials covering four OV agents (Oncorine, OrienX010, KH901, and H103) are ongoing, and additional OV agents are awaiting approval for clinical trials in China. Overall, this research emphasizes that combination therapy, especially tumor immunotherapy coupled with effective system administration strategies, can promote the development of oncolytic virotherapies. This article focuses on studies that were carried out in China in order to give an overview of the past, present, and future of oncolytic virotherapy in China.
Mode-hopping noise in index-guided semiconductor lasers and its reduction by saturable absorbers (1985)

Mode-hopping noise in index-guided semiconductor lasers is investigated. It is found that random switching between lasing modes and output power differences in those modes cause mode-hopping noise. An effective method to suppress such mode-hopping noise is proposed. High Te doping to an n-type GaAlAs cladding layer completely suppresses the noise. Te in GaAlAs forms a DX center that acts as a saturable absorber. This property stabilizes the laser mode and prevents mode competition. The minimum loss difference between lasing and nonlasing modes to suppress mode-hopping noise is also discussed.
Nucleophilic Catalysis of Hydrazone Formation and Transimination:  Implications for Dynamic Covalent Chemistry (2006)

Aniline accelerates hydrazone formation and transimination through nucleophilic catalysis. To demonstrate the method, unprotected peptides are reacted and then scrambled using a hydrazone reaction under conditions relevant for biological applications. The strong enhancement in the rate of hydrazone equilibration broadens the scope of this stable imine in the field of dynamic covalent chemistry.