gebhart/patrepeval huggingface dataset:
Development of Defective and Persistent Sendai Virus Vector (2010)

The ectopic expression of transcription factors can reprogram differentiated tissue cells into induced pluripotent stem cells. However, this is a slow and inefficient process, depending on the simultaneous delivery of multiple genes encoding essential reprogramming factors and on their sustained expression in target cells. Moreover, once cell reprogramming is accomplished, these exogenous reprogramming factors should be replaced with their endogenous counterparts for establishing autoregulated pluripotency. Complete and designed removal of the exogenous genes from the reprogrammed cells would be an ideal option for satisfying this latter requisite as well as for minimizing the risk of malignant cell transformation. However, no single gene delivery/expression system has ever been equipped with these contradictory characteristics. Here we report the development of a novel replication-defective and persistent Sendai virus (SeVdp) vector based on a noncytopathic variant virus, which fulfills all of these requirements for cell reprogramming. The SeVdp vector could accommodate up to four exogenous genes, deliver them efficiently into various mammalian cells (including primary tissue cells and human hematopoietic stem cells) and express them stably in the cytoplasm at a prefixed balance. Furthermore, interfering with viral transcription/replication using siRNA could erase the genomic RNA of SeVdp vector from the target cells quickly and thoroughly. A SeVdp vector installed with Oct4/Sox2/Klf4/c-Myc could reprogram mouse primary fibroblasts quite efficiently; ∼1% of the cells were reprogrammed to Nanog-positive induced pluripotent stem cells without chromosomal gene integration. Thus, this SeVdp vector has potential as a tool for advanced cell reprogramming and for stem cell research.
The asymmetric lossy near-perfect lens (2002)

We extend the ideas of the perfect lens recently proposed [J.B. Pendry, Phys. Rev. Lett. 85, 3966 (2000)] to an alternative structure. We show that a slab of a medium with negative refractive index bounded by media of different positive refractive index also amplifies evanescent waves and can act as a near-perfect lens. We examine the role of the surface states in the amplification of the evanescent waves. The image resolution obtained by this asymmetric lens is more robust against the effects of absorption in the lens. In particular, we study the case of a slab of silver, which has a negative dielectric constant, with air on one side and other media such as glass or GaAs on the other side as an ‘asymmetric’ lossy near-perfect lens for p-polarized waves. It is found that retardation has an adverse effect on the imaging due to the positive magnetic permeability of silver, but we conclude that subwavelength image resolution is possible in spite of it.
A Convenient Method for the Synthesis of ActivatedN-Methylcarbamates (1993)

An investigation of methods to efficiently prepare activated N-methylcarbamates is reported. N-(Methylcarbamoyloxy)succinimide (3a), aryl N-methylcarbamates 3b-d and 2,2,2-trifluoro-1-(trifluoromethyl)ethyl N-methylcarbamate (3e) have been prepared in 70-80% yields from the corresponding chloroformates 5a-e, which were prepared as crystalline solids by the condensation of trichloromethyl chloroformate (1) or bis(trichloromethyl) carbonate (2) with hydroxy compounds 4a-e in high yields.
Detection of the effects of phytoestrogens on sheep and cattle (1995)

Cows and ewes fed estrogenic forage may suffer impaired ovarian function, often accompanied by reduced conception rates and increased embryonic loss. Males are relatively unaffected, but the mammary glands in females and castrate males may undergo hypertrophy of the duct epithelium, accompanied by secretion of clear or milky fluid. In cows, clinical signs resemble those associated with cystic ovaries. The infertility is temporary, normally resolving within 1 mo after removal from the estrogenic feed. However, ewes exposed to estrogen for prolonged periods may suffer a second form of infertility that is permanent, caused by developmental actions of estrogen during adult life. The cervix becomes defeminized and loses its ability to store spermatozoa, so conception rates are reduced, although ovarian function remains normal. Importantly, both temporary and permanent infertility in ewes often occur without observable signs and can be detected only by measurement of phytoestrogens in the diet, or measurement of their effects on the animal. Low background concentrations of dietary phytoestrogens are suggested to play an important role in prevention of disease in humans and laboratory rats, but subclinical effects of phytoestrogens in cattle have not yet been described. Effects of low concentrations of phytoestrogens on reproductive function in ruminants are likely to receive increasing attention.
Restricted expression of galactose/N-acetylgalactosamine-specific macrophage C-type lectin to connective tissue and to metastatic lesions in mouse lung. (1995)

We investigated expression of macrophage galactose/N-acetylgalactosamine-specific C-type lectin (MMGL) in normal mouse lung tissue and in lungs with metastatic nodules produced by OV2944-HM-1 mouse metastatic ovarian tumour cells. Cells expressing MMGL were detected in tissue sections using a rat monoclonal antibody (mAB) specific for MMGL, mAb LOM-14. The regions containing cells immunostained using mAb LOM-14 were restricted to the connective tissue surrounding blood vessels and respiratory epithelia, whereas alveolar regions of lung parenchyma were essentially devoid of these cells. In contrast, a significant number of cells in the alveolar regions was shown to express Mac-1 antigen (CD11b/CD18) and leucocyte common antigen (CD45). Immunoelectron microscopic study revealed the presence of MMGL in the intracellular vesicles of cells residing in connective tissue. In the tumour-bearing mice, MMGL-positive cells were also present within metastatic nodules. Their localization outside of the nodules was restricted to connective tissue. Cells with Mac-1 antigens were seen both in the nodules and in the alveolar regions. These results indicate that MMGL serves as a unique macrophage marker in mouse lung tissue due to its topographical site-dependent pattern of expression. The present results also suggest a possible involvement of macrophages expressing MMGL in the immune response directed against metastatic tumour cells.
Defined Substrates for Human Embryonic Stem Cell Growth Identified from Surface Arrays (2007)

Methods for the rapid identification of defined cell growth conditions are lacking. This deficiency is a major barrier to the investigation and application of human embryonic stem (ES) cells. To address this problem, we developed a method for generating arrays of self-assembled monolayers (SAMs) in which each element constitutes a defined surface. By screening surface arrays, we identified peptidic surfaces that support ES cell growth and self-renewal. The ability of the active surface array elements to support ES cell growth depends on their composition: both the density of the peptide presented and its sequence are critical. These findings support a role for specific surface-cell interactions. Moreover, the data from the surface arrays are portable. They can be used to design an effective 3D synthetic scaffold that supports the growth of undifferentiated human ES cells. Our results demonstrate that synthetic substrates for promoting and probing human ES cell self-renewal can be discovered through SAM surface arrays.
A pilot study in patients with established advanced liver fibrosis using pirfenidone (2006)

Cirrhosis represents the third cause of mortality among Mexican people of productive age.1 Several drugs have been tested in the clinical scenario2,3 although conclusive evidence concerning drug efficacy has proven elusive.

PFD is an orally bioavailable pyridone derivative (5-methyl-1-phenyl-2-(1H)-pyridone) that affects a variety of profibrogenic cytokines and its mechanism of action mostly resides in its anti-inflammatory and antifibrotic activity.4–6 Here we present data obtained from a pilot clinical trial evaluating the safety and efficacy of PFD in 15 patients with established advanced liver disease caused by hepatitis C virus chronic infection. This is the first report showing improvements in liver histology (that is, necrosis, inflammation, steatosis, fibrosis, and cell regeneration) 12 months after PFD therapy. Colour Doppler ultrasound guided liver biopsies were obtained at baseline and after 12 months of PFD treatment and evaluated for stage of fibrosis and grade of activity according to the modified …
Music Interfaces Based on Automatic Music Signal Analysis: New Ways to Create and Listen to Music (2018)

Music analysis based on signal processing offers new ways of creating and listening to music. This article focuses on applications and interfaces that are enabled by advances in automatic music analysis. By using signal processing, some of these applications provide nonexperts the chance to enjoy music in their daily lives, while other applications apply signal processing to enhance professional music production and create new opportunities for composers and performers. Described in this article are the history and state of the art of music interfaces as well as its future directions that emphasize interactive music applications based on automatic music signal analysis.
Improved Synthesis of Aligned Arrays of Single-Walled Carbon Nanotubes and Their Implementation in Thin Film Type Transistors (2007)

We report optimized chemical vapor deposition growth procedures that can produce arrays of individual single walled carbon nanotubes (SWNTs) in horizontal configurations with perfect linear shapes to within experimental uncertainties and with levels of alignment >99.9%. This process also enables simultaneous growth of random networks of SWNTs integrated with the arrays in complex layouts. The electrical properties of thin film type transistors formed with SWNTs grown in this fashion approach expectations based on the intrinsic properties of the pristine, individual SWNTs. The procedures described here might represent a strategy to large scale integration of SWNTs into devices for applications in electronics and optoelectronics, sensing, nanomechanical systems, and other areas.
Growth Factor/Matrix-Induced Proliferation of Human Adult β-Cells (1995)

Proliferation of human beta-cells in vitro is desirable for both transplantation and biological studies. In this study, human pancreatic islets obtained from cadavers were kept in tissue culture plates that favored cell attachment. When the cells attached to the matrix produced by the rat-bladder carcinoma cell line 804G, 5'-bromo-2'-deoxyuridine (BrdU) labeling increased from 4.7 +/- 2.5 to 13.2 +/- 2.2%, while cells simultaneously labeled for insulin and BrdU increased from 0 to 32%. Addition of the growth factor hepatocyte growth factor/scatter (HGF/SF) increased BrdU labeling to 17.5 +/- 1.8 and the percentage of double positive (BrdU + insulin) cells to 69%. This is the first in vitro demonstration that human beta-cells grown in monolayer culture are able to replicate when exposed to selected matrices and growth factors. These experiments add further evidence that HGF/SF is an important mitogenic agent for human beta-cells.
Mu opioid receptor stimulates a growth promoting and pro-angiogenic tumor microenvironment (2005)

4650 We observed that morphine stimulates MAPK/ERK and PKB/Akt signaling in endothelial cells and promotes proliferation, migration and survival leading to increased angiogenesis and tumor growth in mice (Gupta et al 2002, Cancer Res). Morphine and other opioid analgesics are mu opioid receptor (MOR) agonists, which act centrally as well as peripherally directly and by modulating the secretion of cytokines. Therefore, we examined the role of MOR in endothelium and cancer progression using MOR deleted (MOR-KO) and wild type (wt) mice. We isolated and cultured blood outgrowth endothelial cells (BOEC) and implanted T241 fibrosarcoma tumor cells for in vitro and in vivo studies, respectively. MOR-KO derived BOEC assume round shape after 3 days in culture at P1 and undergo significant apoptosis Vs the wild type BOEC (p
Characterization of a yeast artificial chromosome from human chromosome band 13q12 containing the FLT1 and FLT3 receptor-type tyrosine kinase genes (1994)

A yeast artificial chromosome containing the two receptor-type tyrosine kinase genes FLT1 and FLT3 was isolated, analyzed, and compared to a genomic map in order to establish their organization and linkage. FLT1 and FLT3 are physically linked in a head-to-tail configuration and separated by about 150 kb. The region contains three CpG islands. Two of them are likely to correspond to FLT1 and FLT3, whereas the third one is suggestive of another putative, unidentified RTK gene.
CDB-4124, a Progesterone Receptor Modulator, Inhibits Mammary Carcinogenesis by Suppressing Cell Proliferation and Inducing Apoptosis (2010)

CDB-4124 (Proellex or telapristone acetate) is a modulator of progesterone receptor (PR) signaling, which is currently employed in preclinical studies for prevention and treatment of breast cancer and has been used in clinical studies for treatment of uterine fibroids and endometriosis. Here we provide evidence for its action on steroid hormone-signaling, cell cycle-regulated genes and in vivo on mammary carcinogenesis. When CDB-4124 is given to rats at 200 mg/kg for 24 months, it prevents the development of spontaneous mammary hyperplastic and premalignant lesions. Also, CDB-4124 given as subcutaneous pellets at two different doses suppressed, dose dependently, N-methyl-N-nitrosourea (MNU)-induced mammary carcinogenesis. The high dose (30 mg, over 84 days) increased tumor latency from 66 ± 24 days to 87 ± 20 days (P < 0.02), decreased incidence from 85% to 35% (P < 0.001), and reduced multiplicity from 3.0 to 1.1 tumors/animal (P < 0.001). Tumor burden decreased from 2.6 g/animal to 0.26 g/animal (P < 0.01). CDB-4124 inhibited cell proliferation and induced apoptosis in MNU-induced mammary tumors, which correlated with a decreased proportion of PR(+) tumor cells and with decreased serum progesterone. CDB-4124 did not affect serum estradiol. In a mechanistic study employing T47D cells we found that CDB-4124 suppressed G(1)/G(0)-S transition by inhibiting CDK2 and CDK4 expressions, which correlated with inhibition of estrogen receptor (ER) expression. Taken together, these data indicate that CDB-4124 can suppress the development of precancerous lesions and carcinogen-induced ER(+) mammary tumors in rats, and may have implications for prevention and treatment of human breast cancer.
Nanoparticle polymer composite volume gratings incorporating chain transfer agents for holography and slow-neutron optics (2014)

We demonstrate twofold enhancement of the saturated refractive index modulation (Δn(sat)) recorded in a photopolymerizable nanoparticle-acrylate polymer composite film by incorporating thiols acting as chain transfer agents. The chain transfer reaction of thiols with (meth)acrylate monomer reduces the polymer crosslinking density and facilitates the mutual diffusion of nanoparticles and monomer during holographic exposure. These modifications provide increased density modulations of nanoparticles and the formed polymer, resulting in the enhancement of Δn(sat) as high as 1.6×10(-2) at a wavelength of 532 nm. The incorporation of thiols also leads to shrinkage suppression and to improvement of the grating's spatial frequency response. Such simultaneous improvement is very useful for holographic applications in light and neutron optics.
Interactive Augmented Reality (1998)

Thesis (Ph. D.)--University of Rochester. Dept. of Computer Science, 1998. Simultaneously published in the Technical Report series.
Identification and Characterization of ERK MAP Kinase Phosphorylation Sites in Smad3 (2005)

Smad3 is phosphorylated by ERK MAP kinase upon EGF treatment. We have mapped the ERK phosphorylation sites to Ser 207, Ser 203, and Thr 178 in Smad3. We show that, upon EGF treatment, Smad3 is rapidly phosphorylated in these sites, peaking at approximately 15-30 min and that MEK1 inhibitors PD98059 and U0216 inhibit Smad3 phosphorylation induced by EGF. Ser 207 is the best ERK site in Smad3. Its phosphorylation shows the highest EGF induction in Smad3. It is also a very sensitive site to EGF treatment, significantly responding to low concentrations of EGF. These three sites are also phosphorylated by recombinant ERK2 in vitro. We have compared the kinetic parameters of Smad3 with those of ELK1 and MBP for ERK2. We further show that mutation of the ERK phosphorylation sites increases the ability of Smad3 to stimulate a Smad target gene, suggesting that ERK phosphorylation inhibits Smad3 activity.
The knowledge value chain: a pragmatic knowledge implementation network (2005)

In this article, we address the issue of knowledge management (KM) implementation by developing a pragmatic yet theoretically rigorous knowledge implementation framework, referred to hereinafter as the knowledge value chain. The model consists of KM processes (identification, acquisition, codification, storage, dissemination, refinement, application and creation), KM enablers (knowledge system, knowledge culture, organizational memory, knowledge sharing and knowledge benchmarking). Such processes and enabling factors lead to enhanced organizational capabilities – strategic flexibility, new product development, organizational learning, and responsiveness to customers – which are antecedents to performance. The knowledge value chain provides a tool to systematically examine resources and infrastructures. We further highlight the elements in the knowledge value chain that create synergies and enable effective implementation of three generic KM strategies.
Flavivirus Immunization with Capsid-Deletion Mutants: Basics, Benefits, and Barriers (2004)

The flaviviruses comprise a number of arthropod-transmitted human disease agents that cause significant and increasing health threats in major parts of the world. The development of new vaccines is of vital importance, but the stringent need for safety, efficacy and cost-effectiveness together with the problems associated with the specific immune pathogenesis of some flavivirus infections impose significant challenges to innovative vaccine research. Using tick-borne encephalitis virus (TBEV) as a model, the viral capsid protein gene was recently identified as a novel target for generating flavivirus vaccines. This approach can be applied to produce either attenuated strains that can serve as live vaccines or to make a new type of a genetic vaccine consisting of non-infectious RNA replicons from which subviral particles are synthesized in vivo. Flaviviruses are small, enveloped viruses with an unsegmented positive-stranded RNA genome encoding a single polyprotein that is cleaved into the individual viral proteins. The specific introduction of various deletions and other mutations into the genomic segment coding for the capsid protein C and the biochemical and immunological characterization of the resulting mutants in cell culture and an animal model have revealed remarkable properties of this building block of the nucleocapsid and yielded information that opened the way for new vaccine approaches. In this review the in vitro and in vivo findings with various capsid deletion mutants of TBEV are summarized and discussed in the context of recent structural and biochemical data obtained for protein C of various flaviviruses. Potential benefits of this new strategy for generating flavivirus vaccines as well as hurdles that still have to be overcome are discussed in comparison to conventional or other experimental approaches. Capsid-deletion mutants can be used to rationally design safe and effective vaccine strains or to create new vaccines that combine advantages of genetic vaccination, conventional inactivated, and live vaccines.
Structural properties of the perovskite manganites (2001)

The structural distortions arising from the condensations of two essential kinds of phonon modes: the triply degenerated rotational modes (φx,φy,φz) of MnO6 and the doubly degenerated Jahn–Teller (JT) active modes (Q1,Q2), have been systematically investigated in the perovskite manganites. The microstructure features of several typical structural phases have been characterized by transmission-electron microscopy investigations. Due to the strong coupling among crystal lattice, carriers, and spins, the condensations of the rotational modes evidently impact the fundamental behaviors of the low-temperature JT polarization and magnetic orders. In the A-type antiferromagnetic Pr(Sr)MnO3 and Nd(Sr)MnO3 materials, the properties of charge-ordering transitions and structural distortions have been extensively investigated. Several typical kinds of defect structures, including the antiphase boundaries and the 90°-twin domains in the charge-order states, have been analyzed.
ChemInform Abstract: Synthesis and Biological Evaluation of 5,6‐Diarylimidazo(2.1‐b) thiazole as Selective COX‐2 Inhibitors. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Matrix‐assisted laser desorption ionization of oligonucleotides with various matrices (1993)

Ferulic acid, 3-hydroxypicolinic acid (3-HPA), and 2,5-dihydroxybenzoic acid (2,5-DHB) were used as matrices in MALDI of various oligonucleotides. It was found that 2,5-DHB is an excellent matrix for polydeoxyribothymidylic acid. A poly-T oligonucleotide with a size of 130 bases was successfully detected. 3-HPA was found to be a good matrix for MALDI of homo-oligomeric deoxynucleotides as well as those containing four different bases. Parent ions of pd(A)60, d(T)100, d(G)40, and d(C)40 were observed, and a mixed-base oligonucleotide of 150-mer was also detected. Polymer ions of poly-A as large as 420-mer were measured; however, the efficiency for detecting poly-T with 3-HPA as a matrix was slightly worse than when 2,5-DHB was used. Comparisons of three matrices for various oligonucleotides is also presented.
The effect of vanilla flavoured calf starter on performance of Holstein calves (2009)

Twenty one male Holstein calves were used to evaluate the effects of vanilla flavour added to starter on preweaning and postweaning calf performance. Following 3 d of colostrum and transition milk feeding, calves were assigned in a completely randomized design to two treatments including: 1. unflavoured starter and 2. flavoured starter. Calves were fed whole milk at 10% of the initial body weight daily and had free access to starter and water. The weaning criterion was defined as the calf age at a daily intake of 0.80 kg of starter for 2 days, consecutively. Calves fed flavoured starter weighed more at weaning and at the end of experiment and the preweaning average daily gains increased significantly compared with calves fed unflavoured starter. The starter consumption during the preweaning but not postweaning period was significantly higher in calves fed flavoured starter. The calves fed flavoured starter met weaning criteria at a younger age, so that they had 2 to 3 days shorter preweaning period (P<0.03). These findings demonstrate that supplementing starter with vanilla as a flavour agent is advantageous to calf performance.