gebhart/patrepeval huggingface dataset:
The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin 4 and 5 genes (1992)

We have developed modifications to direct cDNA selection that allow the rapid and reproducible isolation of low abundance cDNAs encoded by large genomic clones. Biotinylated, cloned genomic DNAs are hybridized in solution with amplifiable cDNAs. The genomic clones and attached cDNAs are captured on streptavidin coated magnetic beads, the cDNAs are eluted and amplified. We have applied this protocol to a 425kb YAC that contains the human IL4 and IL5 genes. After two cycles of enrichment twenty-four cDNAs were evaluated, all of which were homologous to the YAC. DNA sequencing revealed that nine cDNAs were 100% homologous to the interferon regulatory factor 1 (IRF1) gene. Six clones were 70% homologous to the murine P600 gene, which is coexpressed with IL4 and IL5 in mouse Th2 cells. The nine remaining clones were unique within the sequence databases and were non redundant. All of the selected cDNAs were initially present at very low abundance and were enriched by as much as 100,000-fold in two cycles of enrichment. This modified selection technique should be readily applicable to the isolation of many candidate disease loci as well as the derivation of detailed transcription maps across large genomic regions.
Safety and Efficacy of Using LigaSure Vessel Sealing System for Securing the Pedicles in Vaginal Hysterectomy: Randomised Controlled Trial (2005)

This article presents a comparison of the use of LigaSure (Autosuture; Valleylab, Boulder, CO) versus conventional suture ligation for securing the pedicles during vaginal hysterectomy. A total of 116 participants, recruited from the 261 women scheduled to undergo vaginal hysterectomy at the authors' institution between January 2001 and December 2001, were randomized to the LigaSure (group I, n = 57) or conventional (group II, n = 59) arm of the study. The LigaSure device uses low-voltage, high-power current with continuous feedback and computerized algorithms. The current is delivered with 2 disposable electrodes placed on the jaws of a handpiece that is attached to the LigaSure generator. The electrodes are positioned across the hysterectomy pedicles, locking tissue in the jaws, which are then ratcheted to the tightest position. A foot pedal is used to activate the electrical current, which continues until a 2-beep signal indicates complete coagulation has been achieved. The coagulated tissue is then cut and the handpiece removed. Conventional suturing is performed using Vicryl no. 1 suture (Polyglactin; Ethicon, Edinburgh, U.K.) to doubly ligate the pedicles after they are clamped, cut, and transfixed. There were no significant differences in the 2 groups in age, numbers of previous surgeries, indications for surgery, or concomitant procedures performed. Mean operating time was 57 minutes in the LigaSure group and 66 minutes for controls (P < .04). The complication rate was similar for both groups. There were 3 visceral injuries, including 1 bladder injury in each group and a bowel injury in the LigaSure group. All occurred before hemostatic control began and were recognized and treated immediately. Minor complications included 1 patient in each group with postoperative fever, 3 women in the control group who developed a bladder infection, and 1 in the LigaSure group who sustained a labial burn. Overall operative blood loss was similar for both groups. Four women in the conventional ligature group had perioperative bleeding. Two patients were converted to laparotomy to control bleeding from the hysterectomy pedicle, and 1 was returned to the operating room for reclamping and ligation of a bleeding pedicle. Six days after discharge, the fourth woman was readmitted for vaginal bleeding, which necessitated a blood transfusion. She was discovered to have a vault hematoma, which resolved with conservative management.
Cloning and characterization of cDNAs encoding human gastrin-releasing peptide. (1984)

We have prepared and cloned cDNAs derived from poly(A)+ RNA from a human pulmonary carcinoid tumor rich in immunoreactivity to gastrin-releasing peptide, a peptide closely related in structure to amphibian bombesin. Mixtures of synthetic oligodeoxyribonucleotides corresponding to amphibian bombesin were used as hybridization probes to screen a cDNA library prepared from the tumor RNA. Sequencing of the recombinant plasmids shows that human gastrin-releasing peptide (hGRP) mRNA encodes a precursor of 148 amino acids containing a typical signal sequence, hGRP consisting of 27 or 28 amino acids, and a carboxyl-terminal extension peptide. hGRP is flanked at its carboxyl terminus by two basic amino acids, following a glycine used for amidation of the carboxyl-terminal methionine. RNA blot analyses of tumor RNA show a major mRNA of 900 bases and a minor mRNA of 850 bases. Blot hybridization analyses using human genomic DNA are consistent with a single hGRP-encoding gene. The presence of two mRNAs encoding the hGRP precursor protein in the face of a single hGRP gene raises the possibility of alternative processing of the single RNA transcript.
Comparative evaluation of several DNA binding dyes in the detection of apoptosis‐associated chromatin degradation by flow cytometry (1992)

Mouse thymocytes readily undergo apoptosis-associated DNA degradation upon exposure to glucocorticoids or ionizing radiation. It has been previously shown that flow cytometric cell cycle analysis of propidium iodide-stained apoptotic thymocytes results in the appearance of a distinct cell cycle region (the A0 region) below the G0/G1 region. Cells in this region were shown to be undergoing apoptosis, and determination of apoptosis by flow cytometric analysis was proposed as a superior method for evaluating thymocyte apoptosis. In this study, a variety of DNA binding dyes with diverse primary binding mechanisms were evaluated for their ability to detect glucocorticoid and ionizing radiation-induced apoptosis in mouse thymocytes. Apoptotic thymocytes stained with DNA binding dyes from the phenanthridinium, acridine, actinomycin, chromomycinone, anthracycline, and bisbenzimidazole groups all demonstrated clearly defined A0 regions with percentages comparable to those obtained for propidium iodide. These results indicate that the appearance of the A0 region is not dependent on a particular dye binding characteristic and may be the consequence of extensive changes in chromatin structure resulting in a significant degree of dye exclusion.
Regulation of whole body energy homeostasis with growth hormone replacement therapy and endurance exercise (2011)

We hypothesized that network analysis is useful to expose coordination between whole body and myocellular levels of energy metabolism and can identify entities that underlie skeletal muscle's contribution to growth hormone-stimulated lipid handling and metabolic fitness. We assessed 112 metabolic parameters characterizing metabolic rate and substrate handling in tibialis anterior muscle and vascular compartment at rest, after a meal and exercise with growth hormone replacement therapy (GH-RT) of hypopituitary patients (n = 11). The topology of linear relationships (| r | ≥ 0.7, P ≤ 0.01) and mutual dependencies exposed the organization of metabolic relationships in three entities reflecting basal and exercise-induced metabolic rate, triglyceride handling, and substrate utilization in the pre- and postprandial state, respectively. GH-RT improved aerobic performance (+5%), lean-to-fat mass (+19%), and muscle area of tibialis anterior (+2%) but did not alter its mitochondrial and capillary content. Concomitantly, connectivity was established between myocellular parameters of mitochondrial lipid metabolism and meal-induced triglyceride handling in serum. This was mediated via the recruitment of transcripts of muscle lipid mobilization (LIPE, FABP3, and FABP4) and fatty acid-sensitive transcription factors (PPARA, PPARG) to the metabolic network. The interdependence of gene regulatory elements of muscle lipid metabolism reflected the norm in healthy subjects (n = 12) and distinguished the regulation of the mitochondrial respiration factor COX1 by GH and endurance exercise. Our observations validate the use of network analysis for systems medicine and highlight the notion that an improved stochiometry between muscle and whole body lipid metabolism, rather than alterations of single bottlenecks, contributes to GH-driven elevations in metabolic fitness.
Genomic islands: tools of bacterial horizontal gene transfer and evolution (2009)

Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.
Optical electronics in modern communications (1997)

1. Electromagnetic Theory 2. The Propagation of Rays and Beams 3. Propagation of Optical Beams in Fibers 4. Optical Resonators 5. Interaction of Radiation and Atomic Systems 6. Theory of Laser Oscillation and its Control in the Continuous and Pulsed Regimes 7. Some Specific Laser Systems 8. Second-Harmonic Generation and Parametric oscillation 9. Electronic Modulation of Laser Beams 10. Noise in Optical Detection and Generation 11. Detection of Optical Radiation 12. Interaction of Light and Sound 13. Propagation of Coupling Modes in Optical Dielectric Waveguides-Periodic Waveguides 14. Holography and Optical Data Storage 15. Semiconductor Lasers-Theory and Applications 16. Advanced Semiconductor Lasers: Quantum Well Lasers, Distributed Feedback Lasers, Vertical Cavity Surface Emitting Lasers 17. Phase Conjugate Optics - Theory and Applications 18. Two-Beam Coupling and Phase Conjugation in Photorefractive Media 19. Optical Solitons 20. A Classical Treatment of Quantum Optics Appendices A. The Kramers-Kroning relations B. The Electrooptic Effect in Cubic 43m Crystals C. Noise in Traveling Wave Lasers Amplifiers D. Transformation of a coherent
Changes in the mechanical properties of dermal sheep collagen during in vitro degradation (1995)

The changes in tensile strength, elongation at break, and high strain modulus of dermal sheep collagen (DSC) during in vitro degradation using bacterial collagenase were studied. The changes in mechanical properties were compared with the change in weight of the samples as a function of degradation time. DSC was crosslinked with either glutaraldehyde (GA) or hexamethylene diisocyanate (HMDIC). During degradation, the changes in mechanical properties of the N-DSC, H-DSC or G-DSC samples were more pronounced than the changes in the weight of the samples. Of the mechanical properties studied, the tensile strength was most susceptible to degradation of the DSC samples. After 2.5 h, N-DSC samples had lost only 55% of their initial weight, but the samples had no tensile strength left. Similar results were obtained for H-DSC, which retained no tensile strength after 24 h degradation, whereas only 45% of the initial weight was lost. G-DSC lost 3.5% of its weight after 24 h degradation, but only 25% of the initial tensile strength remained.
Synthesis, Enantiomeric Conformations, and Stereodynamics of Aromatic ortho-Substituted Disulfones (2001)

[structure in text] Aromatic ortho-disulfone derivatives are readily accessible from diiodide precursors by Cu(I)-mediated reactions with sodium sulfinate salts. The sulfone substituents adopt C(2)-symmetric enantiomeric conformations (lambda and delta) as evidenced by X-ray structural analysis and (1)H and (31)P NMR on chiral bis(sulfonyl)veratrol derivatives and hexacoordinated tris(benzenediolato)phosphate anions. Slow dynamic conformational isomerism (DeltaG(++) > or = 19.8 kcal mol(-1)) was detected in solution.
Mode Regularized Generative Adversarial Networks (2016)

Although Generative Adversarial Networks achieve state-of-the-art results on a variety of generative tasks, they are regarded as highly unstable and prone to miss modes. We argue that these bad behaviors of GANs are due to the very particular functional shape of the trained discriminators in high dimensional spaces, which can easily make training stuck or push probability mass in the wrong direction, towards that of higher concentration than that of the data generating distribution. We introduce several ways of regularizing the objective, which can dramatically stabilize the training of GAN models. We also show that our regularizers can help the fair distribution of probability mass across the modes of the data generating distribution, during the early phases of training and thus providing a unified solution to the missing modes problem.
Pattern-driven automatic program transformation and parallelization (2002)

The PARAMAT system is able to automatically parallelize a wide class of sequential numeric codes operating on dense vectors, matrices etc. without any user interaction, for execution on distributed memory message-passing multiprocessors. A powerful pattern recognition tool locally identifies program semantics and concepts in scientific codes. It also works for dusty deck codes that have been 'encrypted' by former machine-specific code transformations. Successful pattern recognition guides sophisticated code transformations including local algorithm replacement. We propose a unified framework for parallel code generation where the user can allow or prevent the system to choose a suitable new parallel algorithm that does not emerge from the sequential program structure by just parallelizing some loops. The partially restored program semantics also supports local array alignment distribution and redistribution, and allows for faster and more exact prediction of the performance of the parallelized target code than usually possible.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acne Vulgaris (1999)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal
Molecular stabilization effects of interactions between anti-metatype antibodies and liganded antibody. (1992)

Anti-metatype antibodies have been described as antibodies which recognize ligand-induced conformational changes in the antibody variable region. Additionally, anti-metatype antibodies, produced by multiple immunizations with liganded high affinity monoclonal anti-fluorescein antibody 4-4-20, enhanced the lifetime of monoclonal antibody 4-4-20-fluorescein complex. To better understand the mechanism of the delayed dissociation rate, deuterium oxide was used to probe the liganded active site. The rate and extent of deuterium oxide-mediated fluorescence enhancement of bound ligand served to monitor the conformational dynamics of the active site in the presence and absence of anti-metatype antibodies. Results showed that anti-metatype antibodies reduced the rate and extent of deuterium oxide-mediated fluorescence enhancement of 4-4-20, a single-chain derivative of 4-4-20 (consisting of the variable domains and a polylinker), and idiotypically related monoclonal anti-fluorescein antibodies suggesting that anti-metatype stabilized the liganded active site. Size exclusion liquid chromatography was utilized to isolate the liganded antibody-anti-metatype complex. Liganded single chain antibody 4-4-20 was mixed with 10-fold molar excess anti-metatype Fab fragments, and a major complex eluted with an apparent M(r) 249,000. The apparent molecular weight of this complex inferred that one liganded single chain antibody was bound by five antimetatype Fab fragments. Spectral analysis confirmed these results and the characteristic delayed rate of ligand dissociation was also observed for the isolated complex. The results suggest that anti-metatype antibodies stabilize the liganded conformation by forming a large, stable, macromolecular complex.
PhoP-PhoQ-Regulated Loci Are Required for Enhanced Bile Resistance in Salmonella spp (1999)

As enteric pathogens, Salmonella spp. are resistant to the actions of bile. Salmonella typhimurium and Salmonella typhi strains were examined to better define the bile resistance phenotype. The MICs of bile for wild-type S. typhimurium and S. typhi were 18 and 12%, respectively, and pretreatment of log-phase S. typhimurium with 15% bile dramatically increased bile resistance. Mutant strains of S. typhimurium and S. typhi lacking the virulence regulator PhoP-PhoQ were killed at significantly lower bile concentrations than wild-type strains, while strains with constitutively active PhoP were able to survive prolonged incubation with bile at concentrations of >60%. PhoP-PhoQ was shown to mediate resistance specifically to the bile components deoxycholate and conjugated forms of chenodeoxycholate, and the protective effect was not generalized to other membrane-active agents. Growth of both S. typhimurium and S. typhi in bile and in deoxycholate resulted in the induction or repression of a number of proteins, many of which appeared identical to PhoP-PhoQ-activated or -repressed products. The PhoP-PhoQ regulon was not induced by bile, nor did any of the 21 PhoP-activated or -repressed genes tested play a role in bile resistance. However, of the PhoP-activated or -repressed genes tested, two (prgC and prgH) were transcriptionally repressed by bile in the medium independent of PhoP-PhoQ. These data suggest that salmonellae can sense and respond to bile to increase resistance and that this response likely includes proteins that are members of the PhoP regulon. These bile- and PhoP-PhoQ-regulated products may play an important role in the survival of Salmonella spp. in the intestine or gallbladder.
THE UBIQUITIN SYSTEM (1998)

The selective degradation of many short-lived proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Ubiquitin-mediated degradation of regulatory proteins plays important roles in the control of numerous processes, including cell-cycle progression, signal transduction, transcriptional regulation, receptor down-regulation, and endocytosis. The ubiquitin system has been implicated in the immune response, development, and programmed cell death. Abnormalities in ubiquitin-mediated processes have been shown to cause pathological conditions, including malignant transformation. In this review we discuss recent information on functions and mechanisms of the ubiquitin system. Since the selectivity of protein degradation is determined mainly at the stage of ligation to ubiquitin, special attention is focused on what we know, and would like to know, about the mode of action of ubiquitin-protein ligation systems and about signals in proteins recognized by these systems.
Transforming growth factor β: Possible roles in the regulation of normal and leukemic hematopoietic cell growth (1989)

We have recently demonstrated that transforming growth factor (TGF)-beta 1 and TGF-beta 2 are potent inhibitors of the growth and differentiation of murine and human hematopoietic cells. The proliferation of primary unfractionated murine bone marrow by interleukin-3 (IL-3) and human bone marrow by IL-3 or granulocyte/macrophage colony-stimulating factor (GM-CSF) was inhibited by TGF-beta 1 and TGF-beta 2, while the proliferation of murine bone marrow by GM-CSF or murine and human marrow with G-CSF was not inhibited. Mouse and human hematopoietic colony formation was differentially affected by TGF-beta 1. In particular, CFU-GM, CFU-GEMM, BFU-E, and HPP-CFC, the most immature colonies, were inhibited by TGF-beta 1, whereas the more differentiated unipotent CFU-G, CFU-M, and CFU-E were not affected. TGF-beta 1 inhibited IL-3-induced growth of murine leukemic cell lines within 24 h, after which the cells were still viable. Subsequent removal of the TGF-beta 1 results in the resumption of normal growth. TGF-beta 1 inhibited the growth of factor-dependent NFS-60 cells in a dose-dependent manner in response to IL-3, GM-CSF, G-CSF, CSF-1, IL-4, or IL-6. TGF-beta 1 inhibited the growth of a variety of murine and human myeloid leukemias, while erythroid and macrophage leukemias were insensitive. Lymphoid leukemias, whose normal cellular counterparts were markedly inhibited by TGF-beta, were also resistant to TGF-beta 1 inhibition. These leukemic cells have no detectable TGF-beta 1 receptors on their cell surface. Last, TGF-beta 1 directly inhibited the growth of isolated Thy-1-positive progenitor cells. Thus, TGF-beta may be an important modulator of normal and leukemic hematopoietic cell growth.