gebhart/patrepeval huggingface dataset:
Myxoma virus and oncolytic virotherapy: a new biologic weapon in the war against cancer (2007)

Oncolytic virotherapy is an innovative alternative to more conventional cancer therapies. The ability of some viruses to specifically target and kill malignant cancerous cells while leaving normal tissue unscathed has opened a large repertoire of new and selective cancer killing therapeutic candidates. Poxviruses, such as vaccinia virus, have a long history of use in humans as live vaccines and have more recently been studied as potential platforms for delivery of immunotherapeutics and attenuated variants of vaccinia have been explored as oncolytic candidates. In contrast, the poxvirus myxoma virus is a novel oncolytic candidate that has no history of use in humans directly, as it has a distinct and absolute host species tropism to lagomorphs (rabbits). Myxoma virus has been recently shown to be able to also selectively infect and kill human tumor cells, a unique tropism that is linked to dysregulated intracellular signalling pathways found in the majority of human cancers. This review outlines the existing knowledge on the tropism of myxoma virus for human cancer cells, as well as preclinical data exhibiting its ability to infect and clear tumors in animal models of cancer. This is an exciting new therapeutic option for treating cancer, and myxoma virus joins a growing group of oncolytic virus candidates that are being developed as a new class of cancer therapies in man.
Limitation of the Kirchhoff boundary conditions for aerial image simulation in 157-nm optical lithography (2000)

The aerial images of half-wavelength features with 0/spl deg/ and 180/spl deg/ phases obtained by using the Kirchhoff boundary conditions are compared with those obtained by using rigorous electromagnetic field computation for 248-nm lithography and 157-nm lithography. The discrepancies between the aerial images computed by the two methods are large at both wavelengths, but they are much larger for TM polarization at the wavelength /spl lambda/=157 nm. These discrepancies are due to diffraction effects in the aperture regions, which are more pronounced at /spl lambda/=157 nm because of the larger ratio of the thickness of the chromium absorber to the wavelength required at /spl lambda/=157 nm for a given attenuation factor. This shows that diffraction effects in the aperture regions must be included when simulating aerial images in 157-nm lithography.
The Role of Gremlin, a BMP Antagonist, and Epithelial-to-Mesenchymal Transition in Proliferative Vitreoretinopathy (2007)

EMT occurs in vitro in the ARPE-19 cell line in response to the growth factors TGF-beta1 and EGF. EMT is also induced by Gremlin.
MIMOX: a web tool for phage display based epitope mapping (2006)

A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox.
Classification of cancer types by measuring variants of host response proteins using SELDI serum assays (2005)

Protein expression profiling has been increasingly used to discover and characterize biomarkers that can be used for diagnostic, prognostic or therapeutic purposes. Most proteomic studies published to date have identified relatively abundant host response proteins as candidate biomarkers, which are often dismissed because of an apparent lack of specificity. We demonstrate that 2 host response proteins previously identified as candidate markers for early stage ovarian cancer, transthyretin and inter-alpha trypsin inhibitor heavy chain 4 (ITIH4), are posttranslationally modified. These modifications include proteolytic truncation, cysteinylation and glutathionylation. Assays using Surface Enhanced Laser Desorption/Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS) may provide a means to confer specificity to these proteins because of their ability to detect and quantitate multiple posttranslationally modified forms of these proteins in a single assay. Quantitative measurements of these modifications using chromatographic and antibody-based ProteinChip array assays reveal that these posttranslational modifications occur to different extents in different cancers and that multivariate analysis permits the derivation of algorithms to improve the classification of these cancers. We have termed this process host response protein amplification cascade (HRPAC), since the process of synthesis, posttranslational modification and metabolism of host response proteins amplifies the signal of potentially low-abundant biologically active disease markers such as enzymes.
Influence of carbon and nitrogen sources on Flavobacterium growth and zeaxanthin biosynthesis (1999)

Growth and production of zeaxanthin by Flavobacterium sp were studied using different carbon and nitrogen sources in a chemically defined medium. The best growth was supported by sucrose, but glucose yielded similar carotenoid concentrations. Both asparagine and glutamine stimulated growth and pigment formation. Carotenoid production and glucose consumption increased as a function of asparagine concentration. In the presence of asparagine, high glucose concentrations decreased pigment production without affecting biomass formation. In the absence of glucose, asparagine could not support growth and zeaxanthin production. When compared to the effect of 55 mM glucose, 10 mM oxaloacetate increased growth and carotenoid production. Pyruvate and other intermediates of the citric acid cycle showed a similar stimulatory effect. The intermediates of glycolysis: glucose 6-phosphate and fructose 1,6-diphosphate did not support growth. These results suggest that Flavobacterium sp utilizes asparagine primarily as a nitrogen source for growth and production of zeaxanthin.
Rapid Induction of Tumor-specific Type 1 T Helper Cells in Metastatic Melanoma Patients by Vaccination with Mature, Cryopreserved, Peptide-loaded Monocyte-derived Dendritic Cells (2002)

There is consensus that an optimized cancer vaccine will have to induce not only CD8+ cytotoxic but also CD4+ T helper (Th) cells, particularly interferon (IFN)-gamma-producing, type 1 Th cells. The induction of strong, ex vivo detectable type 1 Th cell responses has not been reported to date. We demonstrate now that the subcutaneous injection of cryopreserved, mature, antigen-loaded, monocyte-derived dendritic cells (DCs) rapidly induces unequivocal Th1 responses (ex vivo detectable IFN-gamma-producing effectors as well as proliferating precursors) both to the control antigen KLH and to major histocompatibility complex (MHC) class II-restricted tumor peptides (melanoma-antigen [Mage]-3.DP4 and Mage-3.DR13) in the majority of 16 evaluable patients with metastatic melanoma. These Th1 cells recognized not only peptides, but also DCs loaded with Mage-3 protein, and in case of Mage-3DP4-specific Th1 cells IFN-gamma was released even after direct recognition of viable, Mage-3-expressing HLA-DP4+ melanoma cells. The capacity of DCs to rapidly induce Th1 cells should be valuable to evaluate whether Th1 cells are instrumental in targeting human cancer and chronic infections.
Gene genealogies and population variation in plants (2000)

Early in the development of plant evolutionary biology, genetic drift, fluctuations in population size, and isolation were identified as critical processes that affect the course of evolution in plant species. Attempts to assess these processes in natural populations became possible only with the development of neutral genetic markers in the 1960s. More recently, the application of historically ordered neutral molecular variation (within the conceptual framework of coalescent theory) has allowed a reevaluation of these microevolutionary processes. Gene genealogies trace the evolutionary relationships among haplotypes (alleles) with populations. Processes such as selection, fluctuation in population size, and population substructuring affect the geographical and genealogical relationships among these alleles. Therefore, examination of these genealogical data can provide insights into the evolutionary history of a species. For example, studies of Arabidopsis thaliana have suggested that this species underwent rapid expansion, with populations showing little genetic differentiation. The new discipline of phylogeography examines the distribution of allele genealogies in an explicit geographical context. Phylogeographic studies of plants have documented the recolonization of European tree species from refugia subsequent to Pleistocene glaciation, and such studies have been instructive in understanding the origin and domestication of the crop cassava. Currently, several technical limitations hinder the widespread application of a genealogical approach to plant evolutionary studies. However, as these technical issues are solved, a genealogical approach holds great promise for understanding these previously elusive processes in plant evolution.
Zero dispersion slow light with low leakage loss in defect Bragg fiber (2007)

By introducing a defect layer into the periodic cladding of Bragg fiber, the core mode and the defect mode may anticross near their cutoff inside band gap. The defect location suppresses and flattens dramatically the group velocity (vg) of coupled core mode and the defect thickness changes gradually its dispersion. Theoretical investigation reveals zero dispersion and zero dispersion slope at various low vg’s can be achieved simultaneously at arbitrary wavelengths. Specially, the proper defect in the sixth bilayer leads to the lowest vg of 0.074 of light speed in vacuum at 1550nm. The optical energy is confined well in the core and the leakage loss is sufficiently low.
Synthesis and characterization of thiol‐stabilized CdTe nanocrystals (1996)

Abstract In order to expand the range of high‐quality nanosized semiconductor materials that can be obtained as quantum dots through a wet chemical route a series of oxidize‐stable CdTe nanoclusters with narrow size distributions and extremely small particle sizes ranging from 1.3 to 2.4 nm has been prepared in aqueous solution using 2‐mercaptoethanol and 1‐thioglycerol as stabilizers. It has been investigated by means of UV‐vis absorption and photoluminescence spectroscopy, X‐ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM) and energy dispersive x‐ray analysis (EDX).
Calpain 8/nCL-2 and Calpain 9/nCL-4 Constitute an Active Protease Complex, G-Calpain, Involved in Gastric Mucosal Defense (2010)

Calpains constitute a superfamily of Ca2+-dependent cysteine proteases, indispensable for various cellular processes. Among the 15 mammalian calpains, calpain 8/nCL-2 and calpain 9/nCL-4 are predominantly expressed in the gastrointestinal tract and are restricted to the gastric surface mucus (pit) cells in the stomach. Possible functions reported for calpain 8 are in vesicle trafficking between ER and Golgi, and calpain 9 are implicated in suppressing tumorigenesis. These highlight that calpains 8 and 9 are regulated differently from each other and from conventional calpains and, thus, have potentially important, specific functions in the gastrointestinal tract. However, there is no direct evidence implicating calpain 8 or 9 in human disease, and their properties and physiological functions are currently unknown. To address their physiological roles, we analyzed mice with mutations in the genes for these calpains, Capn8 and Capn9. Capn8(-/-) and Capn9(-/-) mice were fertile, and their gastric mucosae appeared normal. However, both mice were susceptible to gastric mucosal injury induced by ethanol administration. Moreover, the Capn8(-/-) stomach showed significant decreases in both calpains 9 and 8, and the same was true for Capn9(-/-). Consistent with this finding, in the wild-type stomach, calpains 8 and 9 formed a complex we termed "G-calpain," in which both were essential for activity. This is the first example of a "hybrid" calpain complex. To address the physiological relevance of the calpain 8 proteolytic activity, we generated calpain 8:C105S "knock-in" (Capn8(CS/CS)) mice, which expressed a proteolytically inactive, but structurally intact, calpain 8. Although, unlike the Capn8(-/-) stomach, that of the Capn8(CS/CS) mice expressed a stable and active calpain 9, the mice were susceptible to ethanol-induced gastric injury. These results provide the first evidence that both of the gastrointestinal-tract-specific calpains are essential for gastric mucosal defense, and they point to G-calpain as a potential target for gastropathies caused by external stresses.
Intravenous Delivery of Cardiosphere‐Derived Cells Improves Striated Muscle Function and Structure in a Murine Model of Duchenne Muscular Dystrophy (2017)

Duchenne muscular dystrophy (DMD), the most common inherited muscular disease, affects approximately 1 in 3,500 live‐born males worldwide. Loss of dystrophin results in a myriad of dysfunctional cellular processes that ultimately manifest as severe and progressive muscle‐wasting in both cardiac and skeletal muscle. DMD patients are clinically characterized by an early loss of ambulation followed by dilated cardiomyopathy in the second decade of life. There is no cure for DMD and current treatments marginally slow the progression of the disease course. Cardiosphere‐derived cells (CDCs) are cardiac progenitor/stromal cells with regenerative, angiogenic, anti‐inflammatory, and anti‐fibrotic properties. Previous research has demonstrated that CDCs are efficacious in treating both ischemic and non‐ischemic heart disease, including Duchenne cardiomyopathy in mdx mice – a mouse model of DMD. The latter work motivated the ongoing HOPE‐Duchenne clinical trial to treat DMD‐associated cardiomyopathy. Here, we sought to explore the potential of CDCs to treat both cardiac and skeletal myopathies when delivered systemically. A single bolus of syngeneic CDCs or vehicle were administered via the femoral vein of 10‐month‐old mdx mice. Baseline and three week follow up measurements of ambulatory capacity, in vivo cardiac function, and isolated skeletal muscle function were recorded. Systemic delivery of CDCs partially reversed the dystrophic phenotype in the heart and skeletal muscle of mdx mice. Specifically, CDC treated mice ran 34.6% (p = 0.01) farther than vehicle‐treated mice. Moreover, CDC treatment improved cardiac ejection fraction by 18.7% (p = 0.008) and isometric force developed by the soleus muscle by 47.8% (p &lt; 0.001), to levels comparable to those in age‐matched wild type controls. Histological examination of the hearts and solei revealed fewer necrotic lesions in CDC treated mice. Interestingly, solei from CDC treated mice contained more centrally nucleated myofibers (208.7 ± 20.7 vs 106.8 ± 9.0, p = 0.004), consistent with enhanced active regeneration. Further, immunohistological staining of the soleus demonstrated that CDC treatment promoted nascent myotube formation, indicating replenishment of a pool of fusion‐competent myoblasts. These data demonstrate that a single intravenous infusion of syngeneic CDCs is sufficient to impact favorably on the phenotype of the mdx mouse. Given that CDCs are already in advanced clinical testing, the present work motivates clinical testing of CDCs delivered systemically to DMD patients, looking for improvements in cardiac and skeletal muscle function and biomarkers. Support or Funding Information NIH T32 HL116273
Fractal-based image sequence compression scheme (1993)

The dominant image transformation used in the existing fractal coding schemes is the affine function. Although an affine transformation is easy to compute and understand, its linear approximation ability limits the employment of larger range blocks, that is, it limits further improvement in compression efficiency. We generalize the image transformation from the usual affine form to the more general form, e.g., quadratic form, and provide theoretical requirements for the generalized transformation to be contractive. Based on the <i>self-transformation system</i> (STS) model, an image sequence coding scheme-fractal-based image sequence coding-is proposed. In this coding scheme, our generalized transformation is used to model the self-transformation from the domain block to its range blocks. Experimental results on a real image sequence show that for the same size of blocks, the SNR can be improved by 10 dB, or, for the same SNR of the decoded image sequence, the compression ratio is raised twofold when the new generalized transformation is used to replace the usual affine transformation. In addition, due to the utilization of the STS model, the computational complexity is only linearly related to the size of the 3-D blocks. This provides for fast encoding and decoding.
Gold nanostructures: a class of multifunctional materials for biomedical applications (2010)

Gold nanostructures have proven to be a versatile platform for a broad range of biomedical applications, with potential use in numerous areas including: diagnostics and sensing, in vitro and in vivo imaging, and therapeutic techniques. These applications are possible because of the highly favorable properties of gold nanostructures, many of which can be tailored for specific applications. In the first part of this tutorial review, we will discuss the most critical properties of gold nanostructures for biomedical applications: surface chemistry, localized surface plasmon resonance (LSPR), and morphology. In the second part of the review, we will discuss how these properties can be harnessed for a selection of biomedical applications, aiming to give the reader an overview of general strategies as well as highlight some recent advances in this field.
Photochemistry of acid hydrazides. Determination of modes of reaction and identification of photoproducts (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of acid hydrazides. Determination of modes of reaction and identification of photoproductsArthur C. Watterson Jr. and Sami A. ShamaCite this: J. Org. Chem. 1975, 40, 1, 19–24Publication Date (Print):January 1, 1975Publication History Published online1 May 2002Published inissue 1 January 1975https://pubs.acs.org/doi/10.1021/jo00889a004https://doi.org/10.1021/jo00889a004research-articleACS PublicationsRequest reuse permissionsArticle Views161Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Transition from Dexmedetomidine to Enteral Clonidine for ICU Sedation: An Observational Pilot Study (2015)

Transitioning from dexmedetomidine to clonidine may be an efficacious, safe, and less costly method of maintaining α2A -receptor agonist therapy in critically ill adults; these results warrant confirmation in expanded studies.
Towardsin-vivoK-edge imaging using a new semi-analytical calibration method (2014)

Flat field calibration methods are commonly used in computed tomography (CT) to correct for system imperfections. Unfortunately, they cannot be applied in energy-resolving CT when using bow-tie filters owing to spectral distortions imprinted by the filter. This work presents a novel semi-analytical calibration method for photon-counting spectral CT systems, which is applicable with a bow-tie filter in place and efficiently compensates pile-up effects at fourfold increased photon flux compared to a previously published method without degradation of image quality. The achieved reduction of the scan time enabled the first K-edge imaging in-vivo. The method employs a calibration measurement with a set of flat sheets of only a single absorber material and utilizes an analytical model to predict the expected photon counts, taking into account factors such as x-ray spectrum and detector response. From the ratios of the measured x-ray intensities and the corresponding simulated photon counts, a look-up table is generated. By use of this look-up table, measured photon-counts can be corrected yielding data in line with the analytical model. The corrected data show low pixel-to-pixel variations and pile-up effects are mitigated. Consequently, operations like material decomposition based on the same analytical model yield accurate results. The method was validated on a experimental spectral CT system equipped with a bow-tie filter in a phantom experiment and an in-vivo animal study. The level of artifacts in the resulting images is considerably lower than in images generated with a previously published method. First in-vivo K-edge images of a rabbit selectively depict vessel occlusion by an ytterbium-based thermoresponsive polymer.
A Comparison of Particle Swarm Optimization and the Genetic Algorithm (2005)

Particle Swarm Optimization (PSO) is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. PSO is similar to the Genetic Algorithm (GA) in the sense that these two evolutionary heuristics are population-based search methods. In other words, PSO and the GA move from a set of points (population) to another set of points in a single iteration with likely improvement using a combination of deterministic and probabilistic rules. The GA and its many versions have been popular in academia and the industry mainly because of its intuitiveness, ease of implementation, and the ability to effectively solve highly nonlinear, mixed integer optimization problems that are typical of complex engineering systems. The drawback of the GA is its expensive computational cost. This paper attempts to examine the claim that PSO has the same effectiveness (finding the true global optimal solution) as the GA but with significantly better computational efficiency (less function evaluations) by implementing statistical analysis and formal hypothesis testing. The performance comparison of the GA and PSO is implemented using a set of benchmark test problems as well as two space systems design optimization problems, namely, telescope array configuration and spacecraft reliability-based design.
Importance of extra- and intracellular domains of TLR1 and TLR2 in NFκB signaling (2003)

Recognition of ligands by toll-like receptor (TLR) 2 requires interactions with other TLRs. TLRs form a combinatorial repertoire to discriminate between the diverse microbial ligands. Diversity results from extracellular and intracellular interactions of different TLRs. This paper demonstrates that TLR1 and TLR2 are required for ara-lipoarabinomannan- and tripalmitoyl cysteinyl lipopeptide-stimulated cytokine secretion from mononuclear cells. Confocal microscopy revealed that TLR1 and TLR2 cotranslationally form heterodimeric complexes on the cell surface and in the cytosol. Simultaneous cross-linking of both receptors resulted in ligand-independent signal transduction. Using chimeric TLRs, we found that expression of the extracellular domains along with simultaneous expression of the intracellular domains of both TLRs was necessary to achieve functional signaling. The domains from each receptor did not need to be contained within a single contiguous protein. Chimeric TLR analysis further defined the toll/IL-1R domains as the area of crucial intracellular TLR1-TLR2 interaction.