gebhart/patrepeval huggingface dataset:
Advances in the molecular genetics of metachromatic leukodystrophy (1990)

Metachromatic leukodystrophy is a lysosomal storage disorder caused by the deficiency of arylsulphatase A (EC 3.1.6.1). This results in the intralysosomal storage of cerebroside sulphate, which leads to a progressive demyelination of the nervous system. The patients usually die within a few years from the onset of symptoms. Clinically, there are different forms of the disease and the molecular basis for this heterogeneity is unknown. The gene for arylsulphatase A has recently been cloned and provides a necessary tool for the exact description of the molecular defects occurring in the different forms of metachromatic leukodystrophy. Metachromatic leukodystrophy can also be caused by the deficiency of an arylsulphatase A activator protein (sphingolipid activator protein B). The cDNA for the precursor of this protein has been isolated and a mutant cDNA of one patient has been analysed. A substantial arylsulphatase A deficiency can also occur in healthy individuals, a phenotype termed pseudodeficiency. Two concurrent mutations have been identified in this low arylsulphatase A activity allele. This permitted the development of a rapid assay which allows the detection of the pseudodeficiency allele. Bone marrow transplantation has been tried in several metachromatic leukodystrophy patients and there is evidence that this treatment might slow or even halt the progression of the disease. A final conclusion as to whether bone marrow transplantation is a suitable therapy for metachromatic leukodystrophy cannot be drawn yet.
RNA interference targeting transforming growth factor-beta type II receptor suppresses ocular inflammation and fibrosis. (2004)

TbetaRII specific siRNAs were efficacious both in vitro and in vivo in knocking down the TGF-beta action. A direct application of siRNA into eyes to downregulate TbetaRII expression may provide a novel therapy for preventing ocular inflammation and scarring.
Chemotherapy of Leishmaniasis (2002)

Leishmaniasis, in its variety of visceral (VL), cutaneous (CL) and mucocutaneous (MCL) forms, directly affects about 2 million people per annum, with approximately 350 million individuals at risk worldwide. During the last 10 years there have been extensive epidemics of the visceral form of the disease, which is also emerging as an important opportunistic infection in immunocompromised patients, especially those co-infected with HIV. The control of leishmaniasis remains a problem principally a zoonotic infection, except in epidemics where it is anthroponotic, interruption of transmission is difficult, though not impossible. No vaccines exist for either VL, CL or MCL and chemotherapy is inadequate and expensive. Current regimes use pentavalent antimony as primary therapy, which must be administered parenterally. Should this fail, a number of other drugs may be employed, depending upon the species of Leishmania concerned and the resources available to the health professionals involved. Recommended secondary treatment employs a variety of drugs, again depending on the nature of the infection. The most widely used of these is amphotericin B, which is highly active but has extensive toxicity complications. The newer formulations of this drug are too expensive to use for the majority of endemic countries. Pentamidine and paromomycin are used in some instances, and a new anti-leishmanial, miltefosine, may be used in the future. In short, there remains a pressing need for new anti-leishmanials and this chapter reviews the current status of chemotherapy, the various avenues being investigated by researchers and their potential application in the future.
Combined activin A/LiCl/Noggin treatment improves production of mouse embryonic stem cell‐derived definitive endoderm cells (2010)

Induction of definitive endoderm (DE) cells is a prerequisite for the whole process of embryonic stem (ES) cells differentiating into hepatic or pancreatic progenitor cells. We have established an efficient method to induce mouse ES cell-derived DE cells in suspension embryonic body (EB) culture. Similar to previous studies, mouse ES cell-derived DE cells, which were defined as Cxcr4(+) c-Kit(+) , Cxcr4(+) E-cadherin(+) cells or Cxcr4(+) PDGFRa(-) cells, could be induced in the serum-free EBs at Day 4 of induction. The activations of Wnt, Nodal, and FGF signaling pathways in differentiating EBs promoted DE cell differentiation, while activation of BMP4 signaling inhibited the process. In the present study, we found that chemical activation of canonical Wnt signaling pathway by LiCl could synergize with Activin A-mediated Nodal signaling pathway to promote induction of DE cells, and inhibition of Bmp4 signaling by Noggin along with Activin A/LiCl further improved the efficiency of DE cell differentiation. The derived DE cells were proved for their capacities to become hepatic progenitor cells or pancreatic progenitor cells. In conclusion, we significantly improved the efficiency of generating mouse ES cell-derived DE cells by combined Activin A/LiCl/Noggin treatment. Our work will be greatly helpful to generate ES cell-derived hepatic cells and ES cell-derived pancreatic cells for future regenerative medicine.
Effects of Alkyl Amide Solvents on the Dispersion of Single-Wall Carbon Nanotubes (2004)

Stable dispersions of both as-produced (raw soot) and purified laser-generated single-wall carbon nanotubes (SWNTs) have been demonstrated with several alkyl amide solvents. Optical absorption analysis over a range of concentrations has been utilized to estimate the dispersion limits for as-produced SWNTs in N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMA), N,N-diethylacetamide (DEA), and N,N-dimethylpropanamide (DMP). In addition, extinction coefficients have been calculated using Beer's law for each solvent at energies of 1.27 and 1.77 eV, corresponding to the electronic transitions of semiconducting and metallic SWNTs, respectively. The results imply that high polarizability and optimal geometries (appropriate bond lengths and bond angles) may account for the favorable interaction between SWNTs and the alkyl amide solvents. The successful dispersion of purified SWNTs in DMA has enabled extinction coefficients of 43.4 and 39.0 mL·mg-1·cm-1 to be calculated at the selected energies, respectively. The magnitude of the dispersion limit and extinction coefficient values has been shown to be strongly dependent on the SWNT sample purity. These findings offer the potential for solution-phase analysis of SWNTs directed at purity assessment and electrophoretic separations in a simple organic solvent.
Molecular cloning and characterization of PKC theta, a novel member of the protein kinase C (PKC) gene family expressed predominantly in hematopoietic cells. (1993)

Members of the protein kinase C (PKC) family of serine/threonine kinases play a key role in regulating the differentiation and growth of diverse cell types and, to date, the cloning of seven mammalian PKC genes encoding eight distinct isoforms has been reported. Here we describe the molecular cloning and deduced primary structure of a cDNA encoding a novel PKC isoform, termed PKC theta, which was isolated in the course of attempts to identify PKC genes that are expressed selectively in hematopoietic cells. Degenerate oligonucleotide primers corresponding to conserved sequence motifs, which distinguish the PKC family from other protein kinases, were employed in polymerase chain reactions (PCR) to amplify partial core sequences of putative PKC genes from a human peripheral blood lymphocyte-derived cDNA library. DNA sequencing of selected clones revealed several PKC-related sequences, including one that, on the basis of sequence comparison with known PKC isoforms, represented a novel PKC isoform. The complete cDNA sequence was determined by anchored PCR cloning and sequencing the entire coding sequence, using cDNA derived from a human leukemic T cell line (Jurkat). Included within this approximately 2.7-kilobase pair cDNA is an open reading frame of 2,118 nucleotides encoding a putative 82-kDa protein. The deduced primary structure contains consensus sequences characteristic of protein kinase catalytic domains and, based on its amino acid sequence and domain structure, is a member of the PKC family. PKC theta displays the highest homology to PKC delta, lacks the Ca(2+)-binding C2 domain and, thus, belongs to the subfamily of Ca(2+)-independent PKC enzymes which also includes the delta, epsilon, zeta, and eta isoforms. RNase protection assays and semiquantitative PCR analysis indicated that, although PKC theta transcripts are expressed ubiquitously, the highest levels are found in hematopoietic tissues and cell lines, including T cells and thymocytes. In contrast, the expression levels in the brain and testes are considerably lower, and no transcripts were detected in several human carcinoma cell lines. A rabbit antiserum raised against a unique (V3 domain) bacterially expressed PKC theta fragment immunoprecipitated specifically an 82-kDa protein from Jurkat cell lysates. Thus, PKC theta represents an additional member of the PKC family, and its predominant expression in hematopoietic cells suggests that it may play a role in signal transduction and growth regulatory pathways unique to these cells.
Use of bone morphogenetic protein—9 gene therapy to induce spinal arthrodesis in the rodent (2000)

The results of this study strongly support the advancement of BMP gene therapy techniques toward clinical use.
An elasticity microscope. Part II: Experimental results (1997)

For pt.I see ibid., vol.44, no.6, pp.1304-19 (1997). Initial experimental results from a 50 MHz elasticity microscope are shown. Using methods discussed previously, we present measured displacement and normal axial strain fields from a tissue mimicking phantom. Results from this homogenous gel are compared to a finite element simulation of the deformation experiment. The spatial resolution is estimated to be approximately 52 /spl mu/m for axial displacements, and 71 /spl mu/m for normal axial strains. These estimates were further tested by imaging a phantom containing a hard cylindrical inclusion with cross-sectional diameter of 265 /spl mu/m. By examining the strain transition between regions in this image, the spatial resolution of the normal axial strain was verified to be at most 88 /spl mu/m. A typical experiment produces peak normal axial strain around 3%. These experiments demonstrate the potential of high frequency ultrasound as a means for elasticity microscopy. Preliminary deformation experiments are presented on porcine epidermis.
Rapamycin (AY-22,989), a new antifungal antibiotic. III. In vitro and in vivo evaluation. (1978)

The activity of rapamycin, a new anti-Candida antibiotic, was not affected by pH values between 6 and 8; at pH 4, however, activity was abolished. The MIC of rapamycin did not vary drastically with the size of inoculum: a ten-fold dilution of the inoculum reduced the MIC only two-fold. Serum binding was extensive. Serum levels obtained in mice were higher on subcutaneous injection than with oral administration. Dogs absorbed rapamycin after oral administration. Rapamycin cured systemic candidosis in mice: PD50 s. c. was 9.5 mg/kg; PD50 p. o. was 11 mg/kg. In the same experimental infections amphotericin B and nystatin exhibited PD50 values of <0.25 mg and >4, 000 units/kg respectively. Rapamycin and amphotericin B, administered at 1, 4 and 24 hours after infection, gave approximately the same percent survival after 30 days of observation. When the above treatment was extended by an additional daily treatment for 6 days, rapamycin by the subcutaneous route yielded a higher percentage of survival than either rapamycin or amphotericin B, administered orally, after a 30-day observation period. Vaginal candidosis in female rats was treated efficiently (91% cure) by rapamycin administered orally. No increase of resistance of C. albicans was observed during treatment.
Neonatal Fc receptor and IgG-based therapeutics (2011)

The majority of potent new biologics today are IgG-based molecules that have demonstrated tissue-targeting specificity with favorable clinical response. Several factors determine the efficacy of these products, including target specificity, serum half-life and effector functions via complement-dependent cytotoxicity, antibody-dependent cell-mediated cytotoxicity or drug conjugates. In this review, we will focus on the interaction between therapeutic antibody and neonatal Fc receptor (FcRn), which is one of the critical factors in determining the circulating antibody half-life. Specifically, we will review the fundamental biology of FcRn, FcRn functions in various organs, Fc mutations designed to modulate binding to FcRn, IgG-based therapeutics that directly exploit FcRn functions and tools and strategies used to study FcRn-IgG interactions. Comprehensive understanding of FcRn-IgG interactions not only allows for development of effective therapeutics, but also avoidance of potential adverse effects.
The Use of Ultrasound for Drug Delivery (2001)

Ultrasound has been in use for the last three decades as a modality for diagnostic imaging in medicine. Recent studies have shown that nonthermal ultrasound energy could be applied for targeting or controlling drug release. This new concept of therapeutic ultrasound combined with drugs has induced interest in various medical fields. Enhanced effects of thrombolytic agents such as urokinase and TPA with acoustic energy have been demonstrated. Ultrasound transducer-tipped catheters are being developed for treatment of cardiovascular diseases. Other devices with ultrasound transducers implanted in transdermal drug patches are also being evaluated for possible delivery of insulin through the skin. Echo contrast microbubbles could also be used to carry and release genes to various tissues and lesions. Chemical activation of drugs by ultrasound energy for treatment of cancers is another new field recently termed "sonodynamic therapy." Various examples of ultrasound application are under investigation that could lead to revolutionary drug delivery systems of the future.
Inhibition of fatty acid synthase (FAS) suppressesHER2/neu(erbB-2) oncogene overexpression in cancer cells (2004)

Fatty acid synthase (FAS) activity is a potential therapeutic target to treat cancer and obesity. Here, we have identified a molecular link between FAS and HER2 (erbB-2) oncogene, a marker for poor prognosis that is overexpressed in 30% of breast and ovarian cancers. Pharmacological FAS inhibitors cerulenin and C75 were found to suppress p185(HER2) oncoprotein expression and tyrosine-kinase activity in breast and ovarian HER2 overexpressors. Similarly, p185(HER2) expression was dramatically down-regulated when FAS gene expression was silenced by using the highly sequence-specific mechanism of RNA interference (RNAi). Pharmacological and RNAi-mediated silencing of FAS specifically down-regulated HER2 mRNA and, concomitantly, caused a prominent up-regulation of PEA3, a transcriptional repressor of HER2. A cytoplasmic redistribution of p185(HER2) was associated with marked morphological changes of FAS RNAi-transfected cells, whereas chemical inhibitors of FAS promoted a striking nuclear accumulation of p185(HER2). The simultaneous targeting of FAS and HER2 by chemical FAS inhibitors and the humanized antibody directed against p185(HER2) trastuzumab, respectively, was synergistically cytotoxic toward HER2 overexpressors. Similarly, concurrent RNAi-mediated silencing of FAS and HER2 genes synergistically stimulated apoptotic cell death in HER2 overexpressors. p185(HER2) was synergistically down-regulated after simultaneous inhibition of FAS and HER2 by either pharmacological inhibitors or small interfering RNA. These findings provide evidence of an active role of FAS in cancer evolution by specifically regulating oncogenic proteins closely related to malignant transformation, strongly suggesting that HER2 oncogene may act as the key molecular sensor of energy imbalance after the perturbation of tumor-associated FAS hyperactivity in cancer cells.
A little stress is good: IFN-γ, demyelination, and multiple sclerosis (2007)

The exact role(s) of the cytokine IFN-gamma in the demyelinating disease multiple sclerosis remain controversial, with evidence suggesting both detrimental and protective effects of the cytokine in MS and MS models such as EAE. The study by Lin and coworkers in this issue of the JCI produces evidence that protective effects of IFN-gamma on mature oligodendrocytes during EAE induction are mediated via activation of the pancreatic ER kinase (PERK), resulting in induction of the endoplasmic reticular stress response pathway (see the related article beginning on page 448). Modulation of this stress pathway has what we believe to be novel therapeutic potential for MS.
Noninvasive Multimodality Imaging of the Tumor Microenvironment: Registered Dynamic Magnetic Resonance Imaging and Positron Emission Tomography Studies of a Preclinical Tumor Model of Tumor Hypoxia (2009)

In vivo knowledge of the spatial distribution of viable, necrotic, and hypoxic areas can provide prognostic information about the risk of developing metastases and regional radiation sensitivity and may be used potentially for localized dose escalation in radiation treatment. In this study, multimodality in vivo magnetic resonance imaging (MRI) and positron emission tomography (PET) imaging using stereotactic fiduciary markers in the Dunning R3327-AT prostate tumor were performed, focusing on the relationship between dynamic contrast-enhanced (DCE) MRI using Magnevist (Gd-DTPA) and dynamic (18)F-fluoromisonidazole ((18)F-Fmiso) PET. The noninvasive measurements were verified using tumor tissue sections stained for hematoxylin/eosin and pimonidazole. To further validate the relationship between (18)F-Fmiso and pimonidazole uptake, (18)F digital autoradiography was performed on a selected tumor and compared with the corresponding pimonidazole-stained slices. The comparison of Akep values (kep = rate constant of movement of Gd-DTPA between the interstitial space and plasma and A = amplitude in the two-compartment model (Hoffmann U, Brix G, Knopp MV, Hess T and Lorenz WJ (1995). Magn Reson Med 33, 506-514) derived from DCE-MRI studies and from early (18)F-Fmiso uptake PET studies showed that tumor vasculature is a major determinant of early (18)F-Fmiso uptake. A negative correlation between the spatial map of Akep and the slope map of late (last 1 hour of the dynamic PET scan) (18)F-Fmiso uptake was observed. The relationships between DCE-MRI and hematoxylin/eosin slices and between (18)F-Fmiso PET and pimonidazole slices confirm the validity of MRI/PET measurements to image the tumor microenvironment and to identify regions of tumor necrosis, hypoxia, and well-perfused tissue.
Electroporation: theory and methods, perspectives for drug delivery, gene therapy and research (2003)

Electroporation designates the use of short high-voltage pulses to overcome the barrier of the cell membrane. By applying an external electric field, which just surpasses the capacitance of the cell membrane, transient and reversible breakdown of the membrane can be induced. This transient, permeabilized state can be used to load cells with a variety of different molecules, either through simple diffusion in the case of small molecules, or through electrophoretically driven processes allowing passage through the destabilized membrane--as is the case for DNA transfer. Initially developed for gene transfer, electroporation is now in use for delivery of a large variety of molecules: From ions to drugs, dyes, tracers, antibodies, and oligonucleotides to RNA and DNA. Electroporation has proven useful both in vitro, in vivo and in patients, where drug delivery to malignant tumours has been performed. Whereas initial electroporation procedures caused considerable cell damage, developments over the past decades have led to sophistication of equipment and optimization of protocols. The electroporation procedures used in many laboratories could be optimized with limited effort. This review (i) outlines the theory of electroporation, (ii) discusses factors of importance for optimization of electroporation protocols for mammalian cells, (iii) addresses particular concerns when using electroporation in vivo, e.g. effects on blood flow and considerations regarding choice of electrodes, (iv) describes DNA electrotransfer with emphasis on use in the in vivo setting, and (v) sums up data on safety and efficacy of electroporation used to enhance delivery of chemotherapy to tumours in cancer patients.
The Arabidopsis NIM1 Protein Shows Homology to the Mammalian Transcription Factor Inhibitor IkB (1997)

John Ryals, Kris Weymann, Kay Lawton, Leslie Friedrich, Daniel Ellis, Henry-York Steiner, Jay Johnson, Terrence P. Delaney, Taco Jesse, Pieter Vos, Scott Uknes, The Arabidopsis NIM1 Protein Shows Homology to the Mammalian Transcription Factor Inhibitor IκB, The Plant Cell, Vol. 9, No. 3 (Mar., 1997), pp. 425-439
Spatio-temporal analysis for smart grids with wind generation integration (2013)

In this paper, we propose a spatio-temporal analysis approach for short-term forecasting of wind farm generation. Specifically, using extensive measurement data from an actual wind farm, the probability distribution and the level crossing rate (LCR) of wind farm generation are characterized by using tools from graphical learning and time-series analysis. Based on these spatial and temporal characterizations, finite state Markov chain models for wind farm generation are developed. Point-forecast of wind farm generation is derived using the Markov chains and integrated into power system economic dispatch. Numerical study on economic dispatch using the IEEE 30-bus test system demonstrates the significant improvement compared with conventional wind-speed-based forecasting methods.
Vaccinia virus immune evasion (1997)

Vaccinia virus and other poxviruses express a wide variety of proteins which are non-essential for virus replication in culture but help the virus to evade the host response to infection. Examples include proteins which oppose apoptosis, synthesise steroids, capture chemokines, counteract complement, interfere with interferon and intercept interleukins. This review provides an overview of such proteins, with an emphasis on work from our laboratory, and illustrates how the study of these proteins can increase our understanding of virus pathogenesis, the function of the immune system and how to make safer and more immunogenic poxvirus-based vaccines.
Database resources of the National Center for Biotechnology Information (2000)

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov