gebhart/patrepeval huggingface dataset:
The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection (2008)

Fluorescent proteins (FPs) based on green fluorescent protein (GFP) are widely used throughout cell biology to study protein dynamics, and have extensive use as reporters of virus infection and spread. However, FP-tagging of viruses is limited by the constraints of viral genome size resulting in FP loss through recombination events. To overcome this, we have engineered a smaller ( approximately 10 kDa) flavin-based alternative to GFP ( approximately 25 kDa) derived from the light, oxygen or voltage-sensing (LOV) domain of the plant blue light receptor, phototropin. Molecular evolution and Tobacco mosaic virus (TMV)-based expression screening produced LOV variants with improved fluorescence and photostability in planta. One variant in particular, designated iLOV, possessed photophysical properties that made it ideally suited as a reporter of subcellular protein localization in both plant and mammalian cells. Moreover, iLOV fluorescence was found to recover spontaneously after photobleaching and displayed an intrinsic photochemistry conferring advantages over GFP-based FPs. When expressed either as a cytosolic protein or as a viral protein fusion, iLOV functioned as a superior reporter to GFP for monitoring local and systemic infections of plant RNA viruses. iLOV, therefore, offers greater utility in FP-tagging of viral gene products and represents a viable alternative where functional protein expression is limited by steric constraints or genome size.
Control Measures for SARS-CoV-2: A Review on Light-Based Inactivation of Single-Stranded RNA Viruses (2020)

SARS-CoV-2 is a single-stranded RNA virus classified in the family <i>Coronaviridae</i>. In this review, we summarize the literature on light-based (UV, blue, and red lights) sanitization methods for the inactivation of ssRNA viruses in different matrixes (air, liquid, and solid). The rate of inactivation of ssRNA viruses in liquid was higher than in air, whereas inactivation on solid surfaces varied with the type of surface. The efficacy of light-based inactivation was reduced by the presence of absorptive materials. Several technologies can be used to deliver light, including mercury lamp (conventional UV), excimer lamp (UV), pulsed-light, and light-emitting diode (LED). Pulsed-light technologies could inactivate viruses more quickly than conventional UV-C lamps. Large-scale use of germicidal LED is dependent on future improvements in their energy efficiency. Blue light possesses virucidal potential in the presence of exogenous photosensitizers, although femtosecond laser (ultrashort pulses) can be used to circumvent the need for photosensitizers. Red light can be combined with methylene blue for application in medical settings, especially for sanitization of blood products. Future modelling studies are required to establish clearer parameters for assessing susceptibility of viruses to light-based inactivation. There is considerable scope for improvement in the current germicidal light-based technologies and practices.
Synthesis and Anti-HIV Activity of Carbamates of Antiviral Agent Stavudine (2002)

An efficient synthesis of carbamate analogues of the NRTI compound stavudine, has been achieved in five steps starting from commercially available thymidine. The synthesis involves conversion of thymidine into stavudine followed by condensation with carbaimidazole derivative obtained from various aromatic and heterocyclic amines in dimethylformamide solvent. The analogues thus obtained were further purified by crystallization to furnish analytically pure products. Examination of biological activity of these carbamate derivatives of stavudine showed that they inhibited HIV replication only at micro-molar concentrations.
Synthesis and Biological Evaluation of the 1,5-Diarylpyrazole Class of Cyclooxygenase-2 Inhibitors:  Identification of 4-[5-(4-Methylphenyl)-3- (trifluoromethyl)-1<i>H</i>-pyrazol-1-yl]benzenesulfonamide (SC-58635, Celecoxib) (1997)

A series of sulfonamide-containing 1,5-diarylpyrazole derivatives were prepared and evaluated for their ability to block cyclooxygenase-2 (COX-2) in vitro and in vivo. Extensive structure-activity relationship (SAR) work was carried out within this series, and a number of potent and selective inhibitors of COX-2 were identified. Since an early structural lead (1f, SC-236) exhibited an unacceptably long plasma half-life, a number of pyrazole analogs containing potential metabolic sites were evaluated further in vivo in an effort to identify compounds with acceptable pharmacokinetic profiles. This work led to the identification of 1i (4-[5-(4-methylphenyl)-3-(trifluoromethyl)- H-pyrazol-1-yl]benzenesulfonamide, SC-58635, celecoxib), which is currently in phase III clinical trials for the treatment of rheumatoid arthritis and osteoarthritis.
Simulation of SOI devices and circuits using BSIM3SOI (1998)

A versatile SOI model derived from the BSIM3v3 bulk MOSFET model is capable of simulating partially and fully depleted devices with options for self-heating and floating body effects. The model can automatically switch between fully and partially depleted regimes. After refining body current models we for the first time present successful dc and transient device and circuit simulation of an SOI MOSFET technology with L/sub eff/ below 0.2 μm.
Abstract 27: Chemotherapy-induced Akt survival signaling is regulated by CD44- Ezrin/Radaxin Moesin (ERM) scaffolding, dependent on EGFR activity (2012)

Abstract Akt survival signaling has emerged as a predictor of poor prognosis in tumors resistant to chemotherapy. Despite the firm correlation between enhanced Akt survival signaling in resistant tumor tissue, there is a poor understanding of the exact mechanisms which elicit this robust pathway activation. In the present study we sought to uncover the full pathway of Akt activation in response to chemotherapy in order to fully elucidate mechanisms and proteins involved in chemotherapy resistance. Using breast and ovarian cancer cells, immunoprecipitations revealed that the CD44 glycoprotein initiates a unique scaffolding effect with the Ezrin/Radixin/Moesin (ERM) proteins and Akt in response to the anti-tubulin chemotherapies, docetaxel and vincrisine. Knockdown of CD44 using siRNA revealed that the activation of Akt(ser473) and ERM(tyr353) by chemotherapy are abolished in a time and dose dependent manner. Flow cytometry, caspase activation and cell viability assays confirmed that loss of Akt signaling sensitizes cancer cells to chemotherapy-induced apoptosis and a similar sensitivity was observed in the absence of CD44 expression. Furthermore, immunoprecipitations revealed that inhibition of EGFR using the small molecule inhibitor, Erlotinib, prevented CD44/ERM/Akt scaffolding in response to chemotherapy. In summary, CD44 and ERM scaffolding is responsible for the activation of Akt survival signaling induced by chemotherapy, in-vitro. Loss of CD44 sensitizes cancer cells to apoptosis. This scaffolding effect is dependent on the activity of EGFR, suggesting that a unique interaction exists between this ErbB1 receptor tyrosine kinase and the CD44 glyco-protein. This is the first evidence for cell surface events which precipitate survival signaling in cancer cells as a consequence of chemotherapy. These findings elucidate novel biomarker interactions for translation in the clinical setting. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 27. doi:1538-7445.AM2012-27
Current concepts in urinary tract infections. (2004)

Urinary tract infections (UTIs) are common infectious diseases that can be associated with substantial morbidity and significant expenditures. This review highlights the current concepts and recent advances in our understanding and management of this condition. Specific topics include pathogenesis, host factors, antimicrobial resistance, recurrent UTIs in women, diagnosis, treatment of uncomplicated and complicated UTIs, prophylaxis, catheter associated bacteriuria, pregnancy, diabetes, UTIs in men, prostatitis, and the chronic pelvic pain syndrome. UTIs can be viewed as an interaction between specific bacterial virulence factors and the patient. A new model explaining the pathogenesis of recurrent UTIs has been presented. There is a need to reconsider traditional treatment recommendations in the face of local resistance patterns, as well as the need to make better use of drugs that are currently available. Prospects for prevention of recurrent UTI include natural compounds, bacterial interference and immunization. With regard to UTI risk in women, patients can be classified based on age, and functional and hormonal status. Appropriate treatment approaches must be based on this classification. In contrast to uncomplicated UTIs, management of most complicated infections depends on clinical experience and resources at individual institutions rather than on evidence based guidelines. Asymptomatic bacteriuria generally should not be treated except in high-risk catheterized patients and in pregnancy. UTIs in men generally require formal urologic evaluation. Our understanding of the etiologies, diagnostic strategies, and treatment options for prostatitis and the chronic pelvic pain syndrome in men continues to evolve.
A simple technique for the stroboscopic observation of magnetic domain response using scanning electron microscopy (1976)

Electronic gating of the video signal, which synchronizes with the sinusoidal drive magnetic field, is used to obtain stroboscopic images. Preliminary observations of the dynamic response of the magnetic domain in Fe-Si samples are also described. This simple technique is easily applicable to the conventional scanning electron microscope without any reconstruction of the electron optical system.
Cardiomyopathy of Duchenne muscular dystrophy: pathogenesis and prospect of membrane sealants as a new therapeutic approach (2006)

Duchenne muscular dystrophy (DMD) is a devastating progressive disease of striated muscle deterioration. This fatal X-linked disorder results from the loss of the protein dystrophin, which in turn causes striated muscle membrane instability. Cardiac dysfunction is a growing problem in patients with DMD, but relatively little is known about the pathophysiology of the dystrophic heart. At present, there is no effective treatment for DMD and the current clinical approaches are primarily supportive in nature. This review will discuss the pathogenesis of DMD in the heart and discuss how these pathogenic processes have led to a new class of agents directed specifically at restoring membrane integrity to dystrophic myocardium. The tri-block poloxamers, specifically poloxamer 188 (P188), are able to stabilize the membranes of dystrophic myocardium in animal models and may offer a new therapeutic approach for cardiac disease in DMD.
Optimization of inoculation for in vivo production of entomopathogenic nematodes. (2002)

Entomopathogenic nematodes are potent biopesticides that can be mass-produced by in vitro or in vivo methods. For in vivo production, consistently high infection rates are critical to efficiency of the process. Our objective was to optimize in vivo inoculation of Steinernema carpocapsae and Heterorhabditis bacteriophora in Galleria mellonella and Tenebrio molitor by determining effects of inoculation method, nematode concentration, and host density. We found immersing hosts in a nematode suspension to be approximately four times more efficient in time than pipeting inoculum onto the hosts. The number of hosts exhibiting signs of nematode infection increased with nematode concentration and decreased with host density per unit area. This is the first report indicating an effect of host density on inoculation efficiency. We did not detect an effect of nematode inoculum concentration on nematode yield per host or per gram of host. Yield was affected by host density in one of the four nematode-host combinations (S. carpocapsae and T. molitor). We conclude that optimization of inoculation parameters is a necessary component of developing an in vivo production system for entomopathogenic nematodes.
Efficient Inter-Layer Motion Compensation for Spatially Scalable Video Coding (2008)

In this paper, an efficient inter-layer motion-compensation technique is proposed for enhancement layer in spatially scalable video coding. The proposed approach exploits the prediction residue correlation between consecutive spatial layers. In enhancement-layer motion compensation, it selects the method with the lowest rate-distortion (RD) cost from three schemes: pyramid motion compensation, subband motion compensation, and encoding the enhancement layer with no base-layer information. To reduce the block artifacts of the enhancement-layer prediction used in the subband method, extended edge prediction is introduced in the proposed approach. Compared with the current scalable H.264/AVC extension (SVC) motion-compensation scheme, our experimental results show that the proposed method exploits the redundancy between the base layer and the enhancement layer more efficiently and hence improves the coding performance. It achieves an improvement up to about 1dB in the enhancement-layer encoding for different coding parameters and video sequences.
Self‐Healing Hydrogels (2016)

Over the past few years, there has been a great deal of interest in the development of hydrogel materials with tunable structural, mechanical, and rheological properties, which exhibit rapid and autonomous self-healing and self-recovery for utilization in a broad range of applications, from soft robotics to tissue engineering. However, self-healing hydrogels generally either possess mechanically robust or rapid self-healing properties but not both. Hence, the development of a mechanically robust hydrogel material with autonomous self-healing on the time scale of seconds is yet to be fully realized. Here, the current advances in the development of autonomous self-healing hydrogels are reviewed. Specifically, methods to test self-healing efficiencies and recoveries, mechanisms of autonomous self-healing, and mechanically robust hydrogels are presented. The trends indicate that hydrogels that self-heal better also achieve self-healing faster, as compared to gels that only partially self-heal. Recommendations to guide future development of self-healing hydrogels are offered and the potential relevance of self-healing hydrogels to the exciting research areas of 3D/4D printing, soft robotics, and assisted health technologies is highlighted.
Evaluation of a Short, On-Plate Formic Acid Extraction Method for Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Identification of Clinically Relevant Yeast Isolates (2014)

This report describes a short, on-plate formic acid (FA) extraction method for the identification of clinical yeast isolates using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). A total of 41.1% (78/190) and 63.7% (121/190) of yeasts were identified using species log score thresholds of >2.0 and >1.9, respectively. Overall, 97.4% (185/190) of yeasts were identified in combination with conventional FA extraction.
Association of p56lck with the cytoplasmic domain of CD4 modulates HIV-1 expression. (1994)

To investigate the role played by the cytoplasmic domain of the CD4 glycoprotein in the process of HIV infection, we have transfected two CD4-negative human T cell lines with cDNAs encoding the full-length CD4 and a truncated form of the molecule, lacking most of the cytoplasmic domain. Levels of viral replication were significantly higher in cells carrying the truncated version of CD4, in comparison with cells expressing the full-length CD4, as measured by the percentage of cells expressing viral p24 protein and the number of infectious particles released into culture supernatants. The extent of viral entry and reverse transcription was similar in each case, as monitored by an enzymatic test and quantitative PCR. Quantitative differences at RNA and protein levels were responsible for changes in viral production. To further characterize the mechanisms responsible for decreased rates of HIV replication in CD4-expressing cells we have treated the different cell lines, very early after HIV infection, with azidothymidine and soluble CD4, two antiviral agents that inhibit replication of HIV at different stages in the virus replicative cycle. Results from these experiments indicate that a cellular signal is mediated by the CD4 molecule, which negatively regulates the expression of viral DNA already present in such cells. This signal would be initiated following oligomerization of the CD4 molecule by the virus itself. Results from experiments with a CD4 construct containing mutations of the cysteine residues which are responsible for association of CD4 with p56lck demonstrate that p56lck is implicated in the transduction of the signal negatively regulating HIV replication.
Human Immunodeficiency Virus Infection of Newborns (1989)

Although the total number of reported cases of the acquired immunodeficiency syndrome (AIDS) in children in the United States is less than 2 percent of the number in adults, the seriousness of the problem of pediatric AIDS threatens to grow in the coming years, as increasing numbers of women of childbearing age become infected with the human immunodeficiency virus (HIV) through intravenous drug use or heterosexual transmission. The epidemiology of pediatric AIDS is, of course, strikingly different from that of its adult counterpart. At present, approximately 80 percent of the children who have AIDS were infected through perinatal transmission, whereas . . .
MEMEN: Multi-layer Embedding with Memory Networks for Machine Comprehension (2017)

Machine comprehension(MC) style question answering is a representative problem in natural language processing. Previous methods rarely spend time on the improvement of encoding layer, especially the embedding of syntactic information and name entity of the words, which are very crucial to the quality of encoding. Moreover, existing attention methods represent each query word as a vector or use a single vector to represent the whole query sentence, neither of them can handle the proper weight of the key words in query sentence. In this paper, we introduce a novel neural network architecture called Multi-layer Embedding with Memory Network(MEMEN) for machine reading task. In the encoding layer, we employ classic skip-gram model to the syntactic and semantic information of the words to train a new kind of embedding layer. We also propose a memory network of full-orientation matching of the query and passage to catch more pivotal information. Experiments show that our model has competitive results both from the perspectives of precision and efficiency in Stanford Question Answering Dataset(SQuAD) among all published results and achieves the state-of-the-art results on TriviaQA dataset.
Effects of L-156,602, a C5a Receptor Antagonist, on Mouse Experimental Models of Inflammation (1992)

L-156,602, a C5a receptor antagonist, was found as an immunosuppressant with preferential effects on delayed-type hypersensitivity (DTH) in our screening program and it was shown that L-156,602 suppressed the efferent phase of DTH. Here, we tested its effects on experimental models of inflammation induced in mice. L-156,602 did not suppress serotonin- and carrageenan- induced inflammation while it completely suppressed concanavalin A-induced inflammation 4 h after elicitation. The inflammation appeared 24 h after the elicitation with concanavalin A and it was significantly suppressed by L-156,602. Muramyl dipeptide (MDP)-induced acute joint inflammation was also significantly suppressed by L-156,602. These results demonstrated the unique immunomodulating properties of L-156,602 in mouse experimental models of inflammation.
TÜRKÇE ÖĞRETMEN ADAYLARININ YARATICI YAZMA ÖRNEKLERİNİN ÇÖZÜMLEYİCİ PUANLAMA YÖNERGESİ BAĞLAMINDA DEĞERLENDİRİLMESİ (2014)

With reference to the opinion that analytic scoring directives are important and effective for the assessment of written scripts, assessment of creative scripts of the teacher candidates who will perform education and training on mother tongue and discussion of results in the context of analytic scoring directive are aimed in this study. In this regard, problem sentence of the research is determined as “what is the success level of the creative scripts of mother tongue teacher candidates in the context of analytic scoring directive?” This research is a descriptive research screening model on a produced structure. Data source of this research based on the screening model is the creative scripts of a hundred 4th year students from Inonu University from the Department of Turkish Language Teaching of the Faculty of Education in 2012-2013 academic years. A clue text was given to the students to enable them to compose a creative script. They were asked to write a creative script considering this clue text. Scripts edited in this context are the data sources of this study. Classification in the analytic scoring directive improved by Arı (2008) is embraced in this study and the creative scripts of the teacher candidates were analyzed in accordance with the classification. Hereunder, the creative scripts of the candidates were examined under 10 sub headings as “form”, “rule”, “word”, “sentence”, “paragraph”, “narration”, title”, “exposition”, “conflict”, “resolution”. Consequently, it is determined that 4th year students of Turkish Language Teaching are not at sufficient level under the determined headings and in accordance with the analytic scoring directive of creative script studies. This can be explained both with the unfamiliarity of Turkish language teacher candidates to the concept of creative script and deficiencies in writing process.
Pulsed I<sub>2</sub>laser pumped by a tunable laser (1985)

An experimental investigation is reported of lasing on the B3Π0+u–X 1Σg+ electronic transitions in molecular iodine, in the wavelength range 550–1340 nm, pumped by coumarin 7 and rhodamine 6G dye lasers. Laser pulse energies of up to 0.3 mJ were attained for a quantum efficiency of the conversion of optical energy of 6%. When intracavity selection was employed for individual doublets of the P and R branch lines, the laser output power approached that obtained in the broad-band regime. When high-energy laser pump sources were used, it proved feasible to obtain lasing on varying the excitation band width over a wide range (0.1–60 cm−1), which made it possible to determine the influence of competition between the pump transitions. An analysis of the results and theoretical estimates indicated that continuous coverage of a large fraction of the lasing range by narrow lines could be achieved.
Single cell analysis of cancer genomes (2014)

Genomic studies have provided key insights into how cancers develop, evolve, metastasize and respond to treatment. Cancers result from an interplay between mutation, selection and clonal expansions. In solid tumours, this Darwinian competition between subclones is also influenced by topological factors. Recent advances have made it possible to study cancers at the single cell level. These methods represent important tools to dissect cancer evolution and provide the potential to considerably change both cancer research and clinical practice. Here we discuss state-of-the-art methods for the isolation of a single cell, whole-genome and whole-transcriptome amplification of the cell's nucleic acids, as well as microarray and massively parallel sequencing analysis of such amplification products. We discuss the strengths and the limitations of the techniques, and explore single-cell methodologies for future cancer research, as well as diagnosis and treatment of the disease.