gebhart/patrepeval huggingface dataset:
ZRANB3 is a structure-specific ATP-dependent endonuclease involved in replication stress response (2012)

To efficiently duplicate their genomic content, cells must overcome DNA lesions that interfere with processive DNA replication. These lesions may be removed and repaired, rather than just tolerated, to allow continuity of DNA replication on an undamaged DNA template. However, it is unclear how this is achieved at a molecular level. Here we identify a new replication-associated factor, ZRANB3 (zinc finger, RAN-binding domain containing 3), and propose its role in the repair of replication-blocking lesions. ZRANB3 has a unique structure-specific endonuclease activity, which is coupled to ATP hydrolysis. It cleaves branched DNA structures with unusual polarity, generating an accessible 3'-OH group in the template of the leading strand. Furthermore, ZRANB3 localizes to DNA replication sites and interacts with the components of the replication machinery. It is recruited to damaged replication forks via multiple mechanisms, which involve interactions with PCNA, K63-polyubiquitin chains, and branched DNA structures. Collectively, our data support a role for ZRANB3 in the replication stress response and suggest new insights into how DNA repair is coordinated with DNA replication to maintain genome stability.
Toward a Cytological Characterization of the Rice Genome (2001)

Rice (Oryza sativa L.) will be the first major crop, as well as the first monocot plant species, to be completely sequenced. Integration of DNA sequence-based maps with cytological maps will be essential to fully characterize the rice genome. We have isolated a set of 24 chromosomal arm-specific bacterial artificial chromosomes to facilitate rice chromosome identification. A standardized rice karyotype was constructed using meiotic pachytene chromosomes of O. sativa spp. japonica rice var. Nipponbare. This karyotype is anchored by centromere-specific and chromosomal arm-specific cytological landmarks and is fully integrated with the most saturated rice genetic linkage maps in which Nipponbare was used as one of the mapping parents. An ideogram depicting the distribution of heterochromatin in the rice genome was developed based on the patterns of 4',6-diamidino-2-phenylindole staining of the Nipponbare pachytene chromosomes. The majority of the heterochromatin is distributed in the pericentric regions with some rice chromosomes containing a significantly higher proportion of heterochromatin than other chromosomes. We showed that pachytene chromosome-based fluorescence in situ hybridization analysis is the most effective approach to integrate DNA sequences with euchromatic and heterochromatic features.
Impaired tyrosine phosphorylation of membrane type 1-matrix metalloproteinase reduces tumor cell proliferation in three-dimensional matrices and abrogates tumor growth in mice (2008)

Pericellular proteolysis of the extracellular matrix by membrane type 1-matrix metalloproteinase (MT1-MMP) confers tumor cells with the ability to proliferate within three-dimensional (3D) matrices and sustains tumor growth in mice. In this study, we show that in addition to its matrix-degrading activity, phosphorylation of MT1-MMP on its unique tyrosine residue located within its cytoplasmic sequence (Tyr573) may also participate to these processes. Fibrosarcoma cells expressing a proteolytically active but non-phosphorylable mutant of MT1-MMP showed a markedly reduced proliferation rate when embedded within 3D type I collagen matrices, this antiproliferative effect being correlated with arrest in the G(0)/G(1) phase of the cell cycle. Impaired tyrosine phosphorylation of MT1-MMP also inhibits anchorage-independent growth of HT-1080 cells in soft agar as well as their invasion of collagen barriers, two prominent attributes of tumor cells, suggesting a broad inhibitory effect of the MT1-MMP mutant on tumorigenesis. Accordingly, whereas HT-1080 cells formed well-vascularized tumors containing tyrosine-phosphorylated MT1-MMP, tumor growth was completely abolished by expression of the non-phosphorylable MT1-MMP mutant. These findings thus indicate a close co-operation between the matrix-degrading activity of MT1-MMP and tyrosine phosphorylation of its intracellular domain for tumor cell invasion and proliferation and suggest that the targeting of the intracellular signaling pathways leading to tyrosine phosphorylation of MT1-MMP may represent an unexpected alternative strategy for the inhibition of this enzyme.
The Role of Peroxisome Proliferator–Activated Receptor γ in Colon Cancer and Inflammatory Bowel Disease (2003)

The emerging important role of PPAR gamma in normal tissue homeostasis and pathologic outcomes suggests this receptor is a good candidate as a drug target. Several potential problems with this approach will require further investigation prior to widespread recommendations for modulation of PPAR as an efficacious therapy for cancer, chemoprevention of colon cancer, or treatment of inflammatory bowel disease. The widespread use of PPAR gamma ligands for management of type 2 diabetes (such as the glitazone class of drugs including rosiglitazone and pioglitazone) may provide a fortuitous assessment of the efficacy of long-term PPAR modulation.
Basic Protein and Peptide Protocols (1994)

The Lowry Method for Protein Quantitation. The Bicinchoninic Acid (BCA) Assay for Protein Quantitation. The Bradford Method for Protein Quantitation. Nondenaturing Polyacrylamide Gel Electrophoresis of Proteins. SDS Polyacrylamide Gel Electrophoresis of Proteins. Gradient SDS Polyacrylamide Gel Electrophoresis. Acetic Acid-Urea Polyacrylamide Gel Electrophoresis of Proteins. Electrophoresis of Peptides. Isoelectric Focusing of Proteins in Ultra-Thin Polyacrylamide Gels. The In Vivo Isotopic Labeling of Proteins for Polyacrylamide Gel Electrophoresis. Two-Dimensional Polyacrylamide Gel Electrophoresis of Proteins. Two-Dimensional Polyacrylamide Gel Electrophoresis Using Immobilized pH Gradients in the First Dimension. Two-Dimensional Polyacrylamide Gel Electrophoresis Using Flat-Bed Isoelectric Focusing in the First Dimension. Quantification of Proteins on Polyacrylamide Gels (Nonradioactive). Detection of Proteins in Polyacrylamide Gels Using an Ultrasensitive Silver Staining Technique. Identification of Glycoproteins on Nitrocellulose Membranes and Gels. The Release of Oligosaccharides from Glycoproteins. Structural Profiling of Oligosaccharides of Glycoproteins. Drying Gels. Fluorography of Polyacrylamide Gels Containing Tritium. The Electrophoretic Elution of Proteins from Polyacrylamide Gels. Preparation of Proteins from Gels for Protein Microsequencing. Comparison of Protein Primary Structures: Peptide Mapping. Protein Blotting. Detection of Polypeptides on Immunoblots Using Secondary Antibodies or Protein A. Detection of Proteins on Blots Using the Avidin-Biotin System. Detection of Proteins on Blots Using Chemiluminescent Systems. The Detection of Proteins on Blots Using Gold or Immunogold. Amino Acid Analysis. Molecular-Weight Estimation for Native Proteins Using Size-Exclusion High-Pressure Liquid Chromatography. Peptide Purification by Reverse-Phase HPLC. Enzymatic Methods for Cleaving Proteins. Chemical Cleavage of Proteins. Chemical Modification of Proteins. The Dansyl Method for Identifying N-Terminal Amino Acids. The Dansyl-Edman Method for Peptide Sequencing. C-Terminal Sequencing of Peptides: The Thiocyanate Degradation Method. Analysis of Cysteine Residues and Disulfide Bonds. Preparation and Characterization of Monoclonal Antibodies to Proteins and Other Cellular Components. The Raising of a Polyclonal Antiserum to a Protein. Production of Antisera to Synthetic Peptides. Production of Antibodies Using Proteins in Gel Bonds. Preparation of Purified Immunoglobulin G (IgG). Enzyme and Biotin Labeling of Antibody. Labeling of Peptides and Proteins by Radioiodination. Radioimmunoassay of Peptides and Proteins. Enzyme-Linked Immunosorbant Assay (ELISA). Free Zone Capillary Electrophoresis. Index.
Energy Transfer in a Nanoscale Multichromophoric System:  Fluorescent Dye-Doped Conjugated Polymer Nanoparticles (2008)

We report on the fluorescence properties and the combined effects of energy diffusion and energy transfer in polyfluorene nanoparticles doped with a variety of fluorescent dyes. As the doping host, polyfluorene possesses extraordinary "light harvesting" ability, resulting in higher per-particle brightness as compared to dye-loaded silica nanoparticles of similar dimensions. Both the steady-state fluorescence spectra and time-resolved fluorescence measurements indicate highly efficient energy transfer from the host polymer to the acceptor dye molecules. A model that takes into account the combined effects of energy diffusion, Förster transfer, and particle size was developed. Comparisons of experimental data to the model results elucidate the importance of particle size and energy diffusion within the polymer in determining the optical properties of the doped conjugated polymer nanoparticles. Fluorescence quantum yields of ~40% and peak extinction coefficients of 1.5 × 10(9) M(-1)cm(-1) were determined for aqueous suspensions of ~30 nm diameter polymer nanoparticles doped with perylene or coumarin 6 (2 wt %). Photobleaching experiments indicate that energy transfer phenomena strongly influence the photostability of these dye-doped nanoparticles. Significant features of these nanoparticles include the high brightness, highly red-shifted emission spectrum, and excellent photostability, which are promising for biological labeling and sensing applications. In addition, the nanoparticles are a useful model system for studying energy transfer in dense, nanostructured, multichromophoric systems.
Use of Azo Polymers for Colon-Specific Drug Delivery (1997)

status: Published
Racematspaltung von Aminosäureamiden und ‐hydraziden (1959)

Abstract D, L‐Aminosäureamide und ‐hydrazide bilden mit Weinsäurederivaten wie Dibenzoyl‐D‐weinsäure diastereomere Tartrate, die sich sehr gut zur Trennung in die optischen Antipoden eignen. Die Anwendung dieser Methode wird an mehreren Beispielen erläutert.
Conjugative Transfer by the Virulence System of Legionella pneumophila (1998)

Legionella pneumophila, the causative agent of Legionnaires' pneumonia, replicates within alveolar macrophages by preventing phagosome-lysosome fusion. Here, a large number of mutants called dot (defective for organelle trafficking) that were unable to replicate intracellularly because of an inability of the bacteria to alter the endocytic pathway of macrophages were isolated. The dot virulence genes encoded a large putative membrane complex that functioned as a secretion system that was able to transfer plasmid DNA from one cell to another.
New power supply structure for telecom equipments toward a unique level of conversion (2002)

The authors deal with concepts about supplying power to electronic or optical switching exchanges based on the latest technical developments. They start from current and future energy needs estimations. Reliability data of telecommunications and their impact on the power supply required performance are studied. To support the assumptions, components and architectural progress are examined. The weak points of today's solutions are highlighted and it is shown that evolution is necessary from centralized to decentralized toward unlocalized energy resources. Here, battery packs may back-up groups of telecommunication boards needing low voltages like 3, 5, 12, or -12 V. Due to associated electronic control, they are independent and may be parallelized to increase the autonomy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bupropion and naltrexone: a review of their use individually and in combination for the treatment of obesity (2009)

Both bupropion and naltrexone have been shown individually to induce weight loss. Bupropion has greater efficacy as monotherapy. Naltrexone SR potentiates the effects of bupropion SR; thus, this synergistic combination has the potential for additional weight loss compared to monotherapy. Current Phase III trials will yield further safety and efficacy information regarding these drugs in combination.
17β-O-Aminoalkyloximes of 5β-Androstane-3β,14β-diol with Digitalis-like Activity:  Synthesis, Cardiotonic Activity, Structure−Activity Relationships, and Molecular Modeling of the Na+,K+-ATPase Receptor (2000)

A series of digitalis-like compounds with a 17-aminoalkoxyiminoalkyl or -alkenyl substituent was synthesized and evaluated for inhibition of Na(+),K(+)-ATPase and for inotropic activity. The highest inhibition was found with compounds having the substituent in configuration 17beta and the amino group at a distance of 6 or 7 bonds from C(17) of the digitoxigenin skeleton. The presence of the oxime function strengthens the interaction with the receptor, more if alpha,beta-unsaturated, thus mimicking the electronic situation of the unsaturated lactone in natural digitalis compounds. The most active compounds showed Na(+),K(+)-ATPase inhibitory potencies (IC(50)) 17-25 times higher than the standards digitoxigenin and digoxin and 3-11 times higher inotropic potencies (EC(50)) in isolated guinea pig left atria. These features are supported by a molecular model suggesting the possible interactions of the groups described above with particular amino acid residues in the H1-H2 domains of Na(+),K(+)-ATPase. Some interactions are the classical ones already described in the literature; a new, very strong interaction of the basic group with the Cys138 was found and adds new possibilities to design compounds interacting with this region of the receptor. The most interesting compounds were also studied in vivo in the anesthetized guinea pig for evaluating their inotropic effect versus the lethal dose. Compounds 9 and 12 showed a slightly higher safety ratio than digoxin and deserve further evaluation.
Identifying And Monitoring Effects Of Lens Aberrations In Projection Printing (1987)

Basic studies of projection printed images are presented to identify the types of patterns which are most susceptible to residual aberrations and to establish test structures which may be used to monitor the presence of critical types of residuals. These effects are explored by including arbitrary lens optical path difference (OPD) aberration functions in a two-dimensional optical image simulation program associated with SAMPLE. The lens aberration function is expressed either in Zernike polynomials or a series expansion. The intensity is calculated from Hopkin's transmission cross-coefficient formula-tion with a self-checking algorithm. A catalog of results is presented here for the dominant primary aberrations of coma and astigmatism for a fixed maximum OPD of 0.4 λ. Contact holes are shown to be much more susceptible to astigmatism than coma and the traditional checkerboard test pattern is verified as a sensitive diagnostic pattern. An alternative structure con-sisting of thin lines with a short break is shown to be even more sensitive to astigmatism and useful for distinguishing it from coma. A further improvement in sensitivity is obtained through the use of small nonprintable defect-like features in proximity to regular features which coherently interact with the blurred image of the feature. A test target of this type is recommended for monitoring coma.
The NF-κB and IκB System in Injured Arteries (1998)

Activation of endothelial cells and dedifferentiation of smooth muscle cells (SMC) are events in the development of vascular disease. The NF-kappaB transcription factor family and its inhibitory proteins (IkappaB) have been implicated in regulating the expression of genes associated with the concomitant inflammatory response. To determine the role of the NF-kappaB/IkappaB system in vivo, the present study used the balloon catheter injury model in the rat carotid artery. Immunoblotting revealed that higher levels of the NF-kappaB family members p50, p52, p65, c-Rel, and RelB were expressed in injured arteries during lesion formation compared to normal vessels. Using electromobility shift assays, low levels of constitutively activated NF-kappaB were seen in normal carotid arteries and an induction occurred during times of rapid SMC proliferation. Furthermore, immediately after injury, the levels of the inhibitor proteins IkappaB alpha, IkappaB beta, and p105 were dramatically reduced. Consistent with the activation of NF-kappaB, vascular cell adhesion molecule-1 (VCAM-1) and monocyte chemotactic protein-1 (MCP-1) were induced in SMC and endothelial cells as early as 4 h after injury and this was accompanied by adhesion of monocytes/macrophages. SMC forming a pseudoendothelium in chronically denuded vessels continued to express high levels of VCAM-1 and MCP-1, thus perpetuating the inflammatory response. These findings link the activation of NF-kappaB to the inflammatory response and to intimal lesion formation following vascular injury.
Metabolic changes within the left dorsolateral prefrontal cortex occurring with electroconvulsive therapy in patients with treatment resistant unipolar depression (2003)

Our results indicate that major depressive disorder is accompanied by state-dependent metabolic alterations, especially in glutamate/glutamine metabolism, which can be reversed by successful ECT.
Human cytotoxic T-cell responses against Epstein-Barr virus nuclear antigens demonstrated by using recombinant vaccinia viruses. (1990)

The potentially pathogenic effects of infection with Epstein-Barr virus (EBV), a B-lymphotropic agent with cell growth-transforming potential, are contained in healthy virus carriers by virus-specific cytotoxic T-lymphocyte (CTL) surveillance. The target antigens against which such CTL responses are directed are yet undefined, but the antigens probably derived from one or more of the EBV "latent" proteins constitutively expressed in virus-transformed B cells. We have analyzed target specificity of CTL responses from two EBV-immune donors that are preferentially reactive against autologous cells transformed with type A but not with type B virus isolates. Coding sequences for four EBV latent proteins with allelic polymorphism between A and B virus types--namely, the EBV nuclear antigens (EBNAs) EBNA 2, EBNA 3a, EBNA 3c, and EBNA leader protein--have been introduced into vaccinia virus vectors under control of vaccinia promoter P7.5 and used to express relevant EBNA proteins in appropriate target cells. Thus the CTL response from one donor has been mapped to type A EBNA 2 protein and from a second donor to type A EBNA 3a protein. Thereafter, a series of recombinant vaccinia viruses were constructed that carried specific internal deletions within the EBNA 2 type A coding sequence; by using these vectors, the above EBNA 2 type A-specific CTL response was shown to be directed against an epitope within a 100-amino acid fragment near the N terminus of the protein. This work clearly shows human CTL recognition of virus-coded nuclear antigens in the EBV system; moreover, it establishes an experimental approach that can be extended to all EBV latent proteins and to the more common CTL responses that cross-react against type A and type B virus isolates.
MR Quantification of the Washout Changes in Breast Tumors Under Preoperative Chemotherapy: Feasibility and Preliminary Results (2005)

Quantification of the washout variation in breast tumor based on the use of parametric images is feasible and reproducible. It may add information to the evaluation of tumor response to preoperative therapy.
Endoscopic Surgery of the Lumbar Epidural Space (Epiduroscopy): Results of Therapeutic Intervention in 93 Patients (2003)

Determination and therapy of the underlying pathology in chronic pain syndrome in the lumbar spine is frequently difficult. Minimally invasive and microsurgical techniques may offer advantages. Epiduroscopy is available for visualization of the lumbar epidural space. 93 patients with chronic back-leg pain syndrome were epiduroscopically operated. When findings were appropriate, mechanical instruments and the holmium:YAG laser were applied therapeutically. 45.9 % of these patients presented with positive results in postoperative examination. Pathomorphological processes corresponding to the multifactorial pain processes, which escape detection in modern imaging procedures, can be diagnosed in the epidural space using epiduroscopy Therapeutic intervention is basically possible. However, use is limited due to technical difficulties. Navigation of the endoscope is especially limited in access via the hiatus sacralis.
Phase I Clinical and Pharmacokinetic Study of BMS-247550, a Novel Derivative of Epothilone B, in Solid Tumors (2004)

The recommended dose for Phase II evaluation of BMS-247550 is 40 mg/m(2), although more long-term observations are needed. BMS-247550 has advantages over taxanes in relation to drug resistance and warrants further study.
Cervical dystonia following exposure to high-G forces. (1990)

Injuries to the cervical region have been associated with high-G loads sustained during air combat maneuvering (ACM) in high performance fighter aircraft. The spectrum of injuries ranges from mild neck pain to musculoskeletal strain, injury to the nerve roots or spinal cord, and fracture of the cervical spine. A 36-year-old fighter pilot with 2,800 h in tactical jet aircraft developed progressive cervical dystonia (spasmodic torticollis), following an ACM flight. The patient was successfully treated with local intramuscular injections of botulinum toxin into the affected cervical muscles, resulting in total relief of his spasmodic torticollis. The aeromedical considerations of this rare complication of exposure to G forces in high performance aircraft are discussed.