gebhart/patrepeval huggingface dataset:
Physical Response of Collagen Gels to Tensile Strain (1995)

Extra cellular matrix, which provides physical support to epithelial and endothelial cells and to fibroblasts, also affects a number of important cell biological phenomena, such as cell motility and angiogenesis. Although type I collagen has long been recognized as the primary structural component of the extra cellular matrix, little is known about the physical properties of collagen gels. In this study, we used a servo-controlled linear actuator to impose quick stretches on dilute collagen gels. An axial strain imposed on the gel within few milliseconds resulted in a rapid development of gel tension in the direction of the strain. The gel tension then decayed toward a steady-state value within several seconds. The instantaneous gel stiffness increased and the relaxed gel stiffness decreased with the extent of gel stretching. These rheological parameters were also dependent on the density of the collagen network. Taken together the results indicated that collagen gels possess nonlinear viscoelastic properties.
Changes in Eutopic Endometrial Gene Expression During the Progression of Experimental Endometriosis in the Baboon, Papio Anubis1 (2013)

Endometriosis is associated with aberrant gene expression in the eutopic endometrium of women with disease. To determine if the development of endometriotic lesions directly impacts eutopic endometrial gene expression, we sequentially analyzed the eutopic endometrium across the time course of disease progression in a baboon model of induced disease. Endometriosis was induced in baboons (n = 4) by intraperitoneal inoculation of autologous menstrual endometrium. Eutopic endometria were collected during the midsecretory phase (Days 9-11 postovulation) at 1, 3, 6-7, 10-12, and 15-16 mo after disease induction and compared with tissue from disease-free baboons. RNA was hybridized to Human Genome U133 Plus 2.0 Arrays, and data were extracted using Gene-Chip Operating Software. Subsequently, both Gene Set Enrichment Analysis and Ingenuity Pathways Analysis were used to find biological states that have a statistically significant enrichment concomitant with pairwise comparison of human endometriosis arrays. Within 1 mo of induction of the disease, 4331 genes were differentially expressed (P < 0.05). Hierarchical clustering revealed self-segregation into two groups-a) 1, 3, and 10-12 mo and b) 6-7 and 15-16 mo-together with controls. Clustering analysis at each stage of disease validated dysregulation of several signaling pathways, including Nodal-like receptor, EGF, ERK/MAPK, and PI3/AKT. Sequential analysis of the same animals during disease progression demonstrated an early disease insult and a transitory dominance of an estrogenic phenotype; however, as the disease progressed, a progesterone-resistant phenotype became evident. Furthermore, we demonstrate a 38.6% differential gene expression overlap with endometrial samples in the midsecretory phase from women with endometriosis, concomitant with similar dysregulation in human disease candidate genes Fos, Nodal, Suclg2, and Kras, among others. Molecular changes in the eutopic endometrium, associated with endometriosis, are directly impacted by endometriotic lesions, providing strong evidence that it is the disease rather than inherent defective endometrium that results in aberrant gene expression in the eutopic endometrium. Furthermore, this baboon model provides a powerful means whereby the early events associated with the pathology of disease and the resulting infertility may be elucidated.
A Highly Conductive Solid-State Polymer Electrolyte Based on a Double-Comb Polysiloxane Polymer with Oligo(ethylene oxide) Side Chains (1999)

A double-comb polysiloxane with ethylene oxide side chains, poly[bis(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)propylsiloxane] (1), has been prepared. The conductivity and thermal properties of this polymer are compared to those of a single-comb polysiloxane, −[CH3RSiO]n− (2), which contains an equal number of oxygen donor atoms. Maximum conductivities of 3.9 × 10-4 S cm-1 for 1 and 1.0 × 10-4 S cm-1 for 2 were found at room temperature with oxygen to Li+ ratios of about 40:1.
In Vivo Targeting of Antigens to Maturing Dendritic Cells via the DEC-205 Receptor Improves T Cell Vaccination (2004)

The prevention and treatment of prevalent infectious diseases and tumors should benefit from improvements in the induction of antigen-specific T cell immunity. To assess the potential of antigen targeting to dendritic cells to improve immunity, we incorporated ovalbumin protein into a monoclonal antibody to the DEC-205 receptor, an endocytic receptor that is abundant on these cells in lymphoid tissues. Simultaneously, we injected agonistic alpha-CD40 antibody to mature the dendritic cells. We found that a single low dose of antibody-conjugated ovalbumin initiated immunity from the naive CD4+ and CD8+ T cell repertoire. Unexpectedly, the alphaDEC-205 antigen conjugates, given s.c., targeted to dendritic cells systemically and for long periods, and ovalbumin peptide was presented on MHC class I for 2 weeks. This was associated with stronger CD8+ T cell-mediated immunity relative to other forms of antigen delivery, even when the latter was given at a thousand times higher doses. In parallel, the mice showed enhanced resistance to an established rapidly growing tumor and to viral infection at a mucosal site. By better harnessing the immunizing functions of maturing dendritic cells, antibody-mediated antigen targeting via the DEC-205 receptor increases the efficiency of vaccination for T cell immunity, including systemic and mucosal resistance in disease models.
ERK and p38 MAPK-Activated Protein Kinases: a Family of Protein Kinases with Diverse Biological Functions (2004)

SUMMARY Conserved signaling pathways that activate the mitogen-activated protein kinases (MAPKs) are involved in relaying extracellular stimulations to intracellular responses. The MAPKs coordinately regulate cell proliferation, differentiation, motility, and survival, which are functions also known to be mediated by members of a growing family of MAPK-activated protein kinases (MKs; formerly known as MAPKAP kinases). The MKs are related serine/threonine kinases that respond to mitogenic and stress stimuli through proline-directed phosphorylation and activation of the kinase domain by extracellular signal-regulated kinases 1 and 2 and p38 MAPKs. There are currently 11 vertebrate MKs in five subfamilies based on primary sequence homology: the ribosomal S6 kinases, the mitogen- and stress-activated kinases, the MAPK-interacting kinases, MAPK-activated protein kinases 2 and 3, and MK5. In the last 5 years, several MK substrates have been identified, which has helped tremendously to identify the biological role of the members of this family. Together with data from the study of MK-knockout mice, the identities of the MK substrates indicate that they play important roles in diverse biological processes, including mRNA translation, cell proliferation and survival, and the nuclear genomic response to mitogens and cellular stresses. In this article, we review the existing data on the MKs and discuss their physiological functions based on recent discoveries.
Hypoxia-mediated induction of endothelial cell interleukin-1 alpha. An autocrine mechanism promoting expression of leukocyte adhesion molecules on the vessel surface. (1992)

Tissue injury that accompanies hypoxemia/reoxygenation shares features with the host response in inflammation, suggesting that cytokines, such as IL-1, may act as mediators in this setting. Human endothelial cells (ECs) subjected to hypoxia (PO2 approximately 12-14 Torr) elaborated IL-1 activity into conditioned media in a time-dependent manner; this activity was completely neutralized by an antibody to IL-1 alpha. Production of IL-1 activity by hypoxic ECs was associated with an increase in the level of mRNA for IL-1 alpha, and was followed by induction of endothelial-leukocyte adhesion molecule-1 and enhanced expression of intercellular adhesion molecule-1 (ICAM-1) during reoxygenation. During reoxygenation there was a three- to five-fold increased adherence of leukocytes, partly blocked by antibodies to endothelial-leukocyte adhesion molecule-1 and ICAM-1. Suppressing endothelial-derived IL-1, using either antibodies to IL-1 alpha, specific antisense oligonucleotides or the IL-1 receptor antagonist, decreased leukocyte adherence to reoxygenated ECs, emphasizing the integral role of IL-1 in the adherence phenomenon. Mice subjected to hypoxia (PO2 approximately 30-40 Torr) displayed increased plasma levels of IL-1 alpha, induction of IL-1 alpha mRNA in the lung, and enhanced expression of ICAM-1 in pulmonary tissue compared with normoxic controls. These data suggest that hypoxia is a stimulus which induces EC synthesis and release of IL-1 alpha, resulting in an autocrine enhancement in the expression of adhesion molecules.
Improving quality of colonoscopy by adding simethicone to sodium phosphate bowel preparation (2009)

The addition of simethicone is of benefit for colonoscopic bowel preparation by diminishing air bubbles, which results in enhanced visibility. Endoscopist and patient satisfaction is also increased.
Herpes Simplex 1716—an ICP 34.5 Mutant—Is Severely Replication Restricted in Human Skin Xenograftsin Vivo (1996)

HSV-1716 is a replication-restricted, neuroattenuated ICP 34.5 gene mutant of herpes simplex virus type 1 (HSV-1). Because of the attenuated phenotype of ICP 34.5 mutants in rodent models of HSV disease, they have been promoted as potential vaccine strains and gene therapy vectors and have been used by us and others as therapeutic agents for the treatment of experimental malignant tumors. However, all data on the phenotype of HSV-1716 and other ICP 34.5 mutants are from animal model systems, while humans are the natural hosts of HSV-1. To achieve an initial characterization of the phenotype of 1716 in human tissue, we have studied its replication in mature human skin xenografts on SCID mice. We find that replication of 1716 is severely restricted in such human skin grafts relative to both parental wild-type HSV-1 strain 17+ and the HSV-1716 revertant virus 1716R, in which the 759-bp ICP 34.5 gene deletions have been repaired. Moreover, the replication of both 1716 and 17+ is significantly better in the human skin grafts than it is in mouse skin. The implications of these findings are discussed.
Software pipelining: an effective scheduling technique for VLIW machines (1988)

This paper shows that software pipelining is an effective and viable scheduling technique for VLIW processors. In software pipelining, iterations of a loop in the source program are continuously initiated at constant intervals, before the preceding iterations complete. The advantage of software pipelining is that optimal performance can be achieved with compact object code. This paper extends previous results of software pipelining in two ways: First, this paper shows that by using an improved algorithm, near-optimal performance can be obtained without specialized hardware. Second, we propose a hierarchical reduction scheme whereby entire control constructs are reduced to an object similar to an operation in a basic block. With this scheme, all innermost loops, including those containing conditional statements, can be software pipelined. It also diminishes the start-up cost of loops with small number of iterations. Hierarchical reduction complements the software pipelining technique, permitting a consistent performance improvement be obtained. The techniques proposed have been validated by an implementation of a compiler for Warp, a systolic array consisting of 10 VLIW processors. This compiler has been used for developing a large number of applications in the areas of image, signal and scientific processing.
Diprotin A Infusion into Nonobese Diabetic/Severe Combined Immunodeficiency Mice Markedly Enhances Engraftment of Human Mobilized CD34 + Peripheral Blood Cells (2007)

Hematopoietic stem cell (HSC) graft cell dose impacts significantly on allogeneic transplant. Similarly, HSC gene therapy outcome is affected by loss of repopulating cells during culture required for ex vivo retrovirus transduction. Stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4 play a central role in marrow trafficking of HSCs, and maneuvers that enhance CXCR4 activation might positively impact outcome in settings of limiting graft dose. CD26/dipeptidyl peptidase IV (DPP-IV) is an ectoenzyme protease that cleaves SDF-1, thus reducing CXCR4 activation. We show that injection of irradiated nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice with >or=2 micromol Diprotin A (a tripeptide specific inhibitor of CD26 protease activity) at the time of transplant of human granulocyte colony-stimulating factor (G-CSF) mobilized CD34(+) peripheral blood cells (CD34(+) PBCs) results in a >3.4-fold enhancement of engraftment of human cells. We also show that CD26 on residual stromal cells in the irradiated recipient marrow milieu, and not any CD26 activity in the human CD34(+) PBC graft itself, plays the critical role in regulating receptivity of this environment for the incoming graft. Human marrow stromal cells also express CD26, raising the possibility that Diprotin A treatment could significantly enhance engraftment of HSCs in humans in settings of limiting graft dose just as we observed in the NOD/SCID mouse human xenograft model.
Über Verbindungen mit Urotropin‐Struktur, XII. Monofunktionelle Adamantan‐Derivate (1959)

Abstract Die experimentellen Befunde weisen bei dem durch direkte Bromierung von Adamantan leicht erhältlichen Monobromadamantan auf die 1‐Stellung des Halogens hin. Ausgehend von dieser Verbindung wurden durch nucleophile Substitutionsreaktionen eine große Anzahl von monofunktionellen Adamantan‐Derivaten erhalten. Auf Grund der Reaktionen muß eine besondere Bevorzugung des Adamantyl‐Carboniumions gefordert werden.
Molecular cloning of a mercurial-insensitive water channel expressed in selected water-transporting tissues. (1994)

Two mercurial-inhibitable water-transporting proteins have been identified: CHIP28, an erythrocyte water channel also expressed in kidney tubules and selected extrarenal epithelia, and WCH-CD, a kidney collecting duct water channel. In searching for a protein responsible for the high transcellular water permeability in lung alveolus, we cloned a 32-kDa water channel (mercurial-insensitive water channel (MIWC)) from a rat lung cDNA library with several novel features. Water permeability was strongly increased in Xenopus oocytes expressing MIWC in a mercurial-insensitive manner, in contrast to known water channels. By in situ hybridization, MIWC showed an unique distribution in cells that do not express CHIP28, including kidney papillary vasa recta, cells lining the subarachnoid space and ventricles in brain, the inner nuclear layer in retina, and the conjunctival epithelium. An alternatively spliced form of MIWC with a 165-base pair deletion in the coding sequence was also identified; relative expression of the spliced mRNA was tissue-specific. The MIWC water channel may participate in the urinary concentrating mechanism, the absorption of cerebrospinal fluid, and other physiological processes.
Hemolymph‐dependent and ‐independent responses in Drosophila immune tissue (2004)

Insects possess an antimicrobial defense response that is similar to the mammalian innate immune response. The innate immune system is designed to recognize conserved components of microorganisms called pathogen-associated molecular patterns (PAMPs). How host receptors detect PAMPs and transmit the signals to mount the immune response is being elucidated. Using GFP-Dorsal, -Dif, and -Relish reporter proteins in ex vivo assays, we demonstrate that Drosophila fat bodies, a major immune tissue, have both hemolymph-dependent and -independent responses. Microbial preparations such as lipoteichoic acid (LTA) and peptidoglycan (PGN) can stimulate some responses from dissected and rinsed larval fat bodies. Therefore, at least some aspects of recognition can occur on fat body cell surfaces, bypassing the requirement of hemolymph. Our results also show that supernatants from bacterial cultures can stimulate the nuclear translocation of Dorsal in dissected fat bodies, but this stimulation is strictly hemolymph-dependent. Various biochemical assays suggest that the factors from bacterial supernatants that stimulate the hemolymph-dependent nuclear translocation are likely made up of proteins. We further show that Dorsal mutant larvae have much lower phenoloxidase activity, consistent with a more important role of Dorsal in innate immunity than previously shown.
Sarcomere dynamics and contraction‐induced injury to maximally activated single muscle fibres from soleus muscles of rats. (1997)

1. The focal nature of contraction-induced injury to skeletal muscle fibres may arise from heterogeneities in sarcomere length that develop during contractions. We tested the hypothesis that when a maximally activated single permeabilized fibre segment is stretched and a deficit in maximum isometric force (force deficit) is produced, the regions of sarcomeres with the longest lengths of prior to the stretch contain the majority of the damaged sarcomeres when the fibre is returned to optimum length (Lo) after the stretch. 2. Single fibre segments (n = 16) were obtained from soleus muscles of rats. Average sarcomere length at five discrete positions along the length of each fibre was determined by lateral deflection of a diode laser spot. Diffraction patterns were obtained while fibres were relaxed and immediately before, during and after a single stretch of 40% strain relative to Lo. Following the stretch, the regions of each fibre that potentially contained damaged sarcomeres were identified by an increased scatter of the first-order diffraction patterns. The damage was confirmed by light and electron microscopy. 3. While single fibre segments were in relaxing solution, the mean value for all of the average sarcomere lengths sampled (n = 80) was 2.53 +/- 0.01 microns (range, 2.40-2.68 microns). During the maximum isometric contraction before each stretch, the mean sarcomere length decreased to 2.42 +/- 0.02 microns and the range increased to 2.12-3.01 microns. 4. During the stretch of 40% strain, all regions of sarcomeres were stretched onto the descending limb of the length-force curve, but sarcomere lengthening was non-uniform. After the stretch, when the maximally activated fibres were returned to Lo, the force deficit was 10 +/- 1%. Microscopic evaluation confirmed that the regions with the longest sarcomere lengths before the stretch contained the majority of the damaged sarcomeres after the stretch. We conclude that when heterogeneities in sarcomere length develop in single permeabilized fibre segments during a maximum isometric contraction, the sarcomeres in the regions with the longest lengths are the most susceptible to contraction-induced injury.
PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data (2013)

Source code freely available at the following URL: https://code.google.com/p/pyrohmmvar/, implemented in C++ and supported on Linux. .
Synchronous Neural Afterdischarges in Rat Hippocampal Slices Without Active Chemical Synapses (1982)

Extracellular field potential and intracellular recordings from neurons in rat hippocampus show that, even with synaptic transmission blocked, antidromic electrical stimuli can trigger afterdischarges of up to 9 seconds duration; during these discharges action potentials of a single neuron were synchronized with extracellularly recorded population spikes. Apparently mechanisms other than recurrent chemical synapses can synchronize and recruit epileptiform events. Measurements of transmembrane potential indicate that transient extracellular electrical fields (ephaptic interactions) contribute to the observed synchrony; electrotonic coupling and changes in the concentration of extracellular ions may also contribute.
Homologous recombination in hybridoma cells: heavy chain chimeric antibody produced by gene targeting. (1989)

We demonstrate that murine myeloma cells can efficiently mediate homologous recombination. The murine myeloma cell line J558L was shown to appropriately recombine two transfected DNA molecules in approximately 30% of cells that received and integrated intact copies of both molecules. This activity was then exploited to direct major reconstructions of an endogenous locus within a hybridoma cell line. Production of antigen-specific chimeric heavy chain was achieved by targeting the human IgG1 heavy chain constant region (C gamma 1) exons to the genomic heavy chain locus of a hybridoma cell line secreting antibody specific for a human tumor-associated antigen. The frequency of productive genomic recombinations was approximately 1 in 200 transfectants, with accumulation of the chimeric protein reaching greater than 20 micrograms/ml in culture supernatants.
Improved brain delivery of AZT using a glycosyl phosphotriester prodrug (1992)

The concentration of AZT in mice plasma and brain was measured using HPLC after an ingestion of 20 mg/kg of AZT or the molar equivalent of hexadecyl 2-(alpha-D-mannopyranosidyl)ethyl 3'-azido-3'-deoxy-5'-thymidinyl phosphate 3. The results demonstrated the promising qualities of the prodrug 3 which gave AZT-5'-phosphate as the main metabolite: the total concentration of AZT derivatives detected in brain presented a peak of 156 nmol/g (5 nmol/g for AZT) at 1 h; the half-life was about 24 h (1 h for AZT) with an AUC of 4366 nmol h/g as compared to 4 nmol h/g for AZT. The lipophilic properties of 3 were confirmed by its in vitro transport of inside synaptosomes. The derivative 2-(alpha-D-mannopyranosidyl)ethyl 3'-azido-3'-deoxy-5'-thymidinyl phosphate (2) provided also a good delivery of AZT to the central nervous system, with values intermediate between those of AZT and 3.
Antibacterial Natural Products in Medicinal Chemistry—Exodus or Revival? (2006)

To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.
Growth and maturation factors (1983)

Fibroblast Growth Factor Ocular Growth and Differentiation Factors Regulation of Neuronal Survival and Neuritic Growth in the Avian Ciliary Ganglion by Trophic Factors Glia Maturation Factor and Other Factors Acting on Glia Target Analysis of Growth Factor Receptors Growth Factors in Fetal Development The Mitogenic Effects of Proteases Growth Factor Action and Ionic Signal Transduction: Characterization and Relation to Receptor Expression Retinoids and Their Modulation of Cell Growth B-Cell Growth Factors Index.