gebhart/patrepeval huggingface dataset:
Comparison of Neurite Outgrowth Induced by Intact and Injured Sciatic Nerves: A Confocal and Functional Analysis (1998)

Mechanisms regulating axon growth in the peripheral nervous system have been studied by means of an in vitro bioassay, the tissue section culture, in which regenerating neurons are grown on substrata made up of tissue sections. Sections from intact and degenerated sciatic nerves proved to be different in their ability to support neurite outgrowth of embryonic chick sensory neurons from both qualitative and quantitative points of view. On denervated nerve sections, the total length of neurites elaborated per neuron was almost twice that found on intact nerve sections. In addition, confocal microscopy revealed a striking difference between intact and denervated nerve substrata: on denervated nerve sections, neurites grew inside the internal structures of endoneurial Schwann cell tubes, within the underlying tissue sections, whereas on intact nerve sections neurites extended along endoneurial basal laminae but never entered Schwann cell tubes. Perturbation experiments were used to analyze some of the molecular determinants that control neurite outgrowth in this system. Antibodies directed against the beta1-integrin subunit inhibited neurite extension on both normal and degenerated rat sciatic nerve tissue. Strikingly, however, differential inhibition was observed using antibodies directed against extracellular matrix molecules. Anti-laminin-2 (merosin) antibodies drastically reduced both the percentage of growing neurons and the total length of neurites on denervated nerve sections, but they did not modify these parameters on sections of normal nerve. Taken together, these results suggest that laminin-2/merosin promotes neurite outgrowth in peripheral nerve environments but only after Wallerian degeneration, which is when axons are allowed to extend within endoneurial tubes.
Low-Intensity Electrical Stimulation Affects Network Dynamics by Modulating Population Rate and Spike Timing (2010)

Clinical effects of transcranial electrical stimulation with weak currents are remarkable considering the low amplitude of the electric fields acting on the brain. Elucidating the processes by which small currents affect ongoing brain activity is of paramount importance for the rational design of noninvasive electrotherapeutic strategies and to determine the relevance of endogenous fields. We propose that in active neuronal networks, weak electrical fields induce small but coherent changes in the firing rate and timing of neuronal populations that can be magnified by dynamic network activity. Specifically, we show that carbachol-induced gamma oscillations (25–35 Hz) in rat hippocampal slices have an inherent rate-limiting dynamic and timing precision that govern susceptibility to low-frequency weak electric fields (&lt;50 Hz; &lt;10 V/m). This leads to a range of nonlinear responses, including the following: (1) asymmetric power modulation by DC fields resulting from balanced excitation and inhibition; (2) symmetric power modulation by lower frequency AC fields with a net-zero change in firing rate; and (3) half-harmonic oscillations for higher frequency AC fields resulting from increased spike timing precision. These underlying mechanisms were elucidated by slice experiments and a parsimonious computational network model of single-compartment spiking neurons responding to electric field stimulation with small incremental polarization. Intracellular recordings confirmed model predictions on neuronal timing and rate changes, as well as spike phase-entrainment resonance at 0.2 V/m. Finally, our data and mechanistic framework provide a functional role for endogenous electric fields, specifically illustrating that modulation of gamma oscillations during theta-modulated gamma activity can result from field effects alone.
26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity. (1993)

We have determined the three-dimensional structures of the antigen-binding fragment of the anti-digoxin monoclonal antibody 26-10 in the uncomplexed state at 2.7 A resolution and as a complex with digoxin at 2.5 A resolution. Neither the antibody nor digoxin undergoes any significant conformational changes upon forming the complex. Digoxin interacts primarily with the antibody heavy chain and is oriented such that the carbohydrate groups are exposed to solvent and the lactone ring is buried in a deep pocket at the bottom of the combining site. Despite extensive interactions between antibody and antigen, no hydrogen bonds or salt links are formed between 26-10 and digoxin. Thus the 26-10-digoxin complex is unique among the known three-dimensional structures of antibody-antigen complexes in that specificity and high affinity arise primarily from shape complementarity.
The COOH terminus of the c-Abl tyrosine kinase contains distinct F- and G-actin binding domains with bundling activity [published erratum appears in J Cell Biol 1994 Mar;124(5):865] (1994)

The myristoylated form of c-Abl protein, as well as the P210bcr/abl protein, have been shown by indirect immunofluorescence to associate with F-actin stress fibers in fibroblasts. Analysis of deletion mutants of c-Abl stably expressed in fibroblasts maps the domain responsible for this interaction to the extreme COOH-terminus of Abl. This domain mediates the association of a heterologous protein with F-actin filaments after microinjection into NIH 3T3 cells, and directly binds to F-actin in a cosedimentation assay. Microinjection and cosedimentation assays localize the actin-binding domain to a 58 amino acid region, including a charged motif at the extreme COOH-terminus that is important for efficient binding. F-actin binding by Abl is calcium independent, and Abl competes with gelsolin for binding to F-actin. In addition to the F-actin binding domain, the COOH-terminus of Abl contains a proline-rich region that mediates binding and sequestration of G-actin, and the Abl F- and G-actin binding domains cooperate to bundle F-actin filaments in vitro. The COOH terminus of Abl thus confers several novel localizing functions upon the protein, including actin binding, nuclear localization, and DNA binding. Abl may modify and receive signals from the F-actin cytoskeleton in vivo, and is an ideal candidate to mediate signal transduction from the cell surface and cytoskeleton to the nucleus.
Comparative evaluation of the diffusion of tobramycin and cefotaxime out of antibiotic‐impregnated polymethylmethacrylate beads (1988)

Both tobramycin and cefotaxime diffuse from antibiotic-impregnated polymethylmethacrylate (PMMA) beads in quantities sufficient to inhibit the growth of bacteria on agar lawns or in broth cultures over a 28-day period. Extraction of antibiotic from tobramycin or cefotaxime-impregnated PMMA beads revealed that substantial amounts of both antibiotics remained within the beads despite 28 days of diffusion. Diffusion of antibiotic from the PMMA beads during the initial 3-5 days is much greater than occurs for the remainder of the 4-week period. The results of the study suggest that perhaps tobramycin of cefotaxime-impregnated PMMA beads would produce local levels of antibiotic high enough to sterilize a given dead space for a period of 28 days.
8-Hydroxymanzamine A, a β-Carboline Alkaloid from a Sponge, Pachypellina sp. (1994)

The previously described manzamine A [1] and the new 8-hydroxymanzamine A [2] were isolated from an undescribed sponge, Pachypellina sp. Both compounds exhibit moderate antitumor and anti-HSV-II activity.
The teratogenic activity of α thalidomide analogue, EM12, in rabbits, rats, and monkeys (1972)

Abstract ABSTRACT The teratogenic activity of a stable analogue of thalidomide, 2(2,6‐dioxopiperiden‐2‐yl)‐phthalimidine (EM 12 ), has been compared in monkeys, rabbits, and rats. After oral administration of 25‐250 mg/kg, EM 12 was teratogenic in monkeys and rabbits but only slightly so in rats. After iv injection of the compound dissolved in dimethyl sulfoxide and water, teratogenic effects were observed both in offspring of rabbits and rats receiving doses of 10 mg/kg. The malformations observed in monkeys and rabbits were identical with those observed after thalidomide treatment, but those in rats were not the typical thalidomide‐type deformities.
All-trans Retinoic Acid Potentiates the Ability of Interferon Beta-1b to Augment Suppressor Cell Function in Multiple Sclerosis (1998)

Treatment with interferon beta-1b partially restores defective T suppressor cell function in patients with MS. This potentially beneficial action is synergistically potentiated by RA. Interferon beta-1b increases the number of interferon gamma-secreting cells in the circulation when treatment is initiated. A similar increment in interferon gamma-secreting cells is observed when interferon beta-1b is added to cultural peripheral blood mononuclear cells in vitro. This potentially deleterious action of interferon beta-1b is reversed by RA. Interferon beta-1b inhibits lymphocyte proliferation modestly but reproducibly. This action of interferon beta-1b is unaltered by RA. These data provide a rationale for a trial of combination treatment with interferon beta-1b and RA in patients with MS.
British Association of Dermatologists guidelines for use of biological interventions in psoriasis 2005 (2005)

Psoriasis is a common, persistent, relapsing inflammatory&#13;\nskin disease that can be associated with significant morbidity.&#13;\nQuality of life studies in psoriasis reveal a negative&#13;\nimpact on patients comparable with that seen in cancer,&#13;\narthritis and heart disease.1–5 Patients with severe disease&#13;\nconstitute approximately 20–30% of all patients with psoriasis,&#13;\noften require systemic treatment, and represent a major&#13;\neconomic burden to the Health Service.&#13;\nAll standard systemic therapies for severe disease are associated&#13;\nwith the potential for major long-term toxicity, many&#13;\nare expensive, and a proportion of patients has treatmentresistant&#13;\ndisease.6 Biological therapies or ‘biologics’ describe&#13;\nagents designed to block specific molecular steps important&#13;\nin the pathogenesis of psoriasis and have emerged over the&#13;\nlast 3–5 years as potentially valuable alternative therapeutic&#13;\noptions.&#13;\nCurrently, biological therapies for psoriasis comprise two&#13;\nmain groups: (i) agents targeting the cytokine tumour&#13;\nnecrosis factor (TNF)-a (e.g. etanercept, infliximab, adalimumab)&#13;\nand (ii) agents targeting T cells or antigen-presenting&#13;\ncells (e.g. efalizumab, alefacept). Two of these,&#13;\netanercept (Enbrel) and efalizumab (Raptiva) were&#13;\nlicensed in 2004 in the U.K. for patients with moderate to&#13;\nsevere psoriasis.
Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing (2008)

We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH(2))(2))-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.
Domain structure of 3-hydroxy-3-methylglutaryl coenzyme A reductase, a glycoprotein of the endoplasmic reticulum. (1985)

We present and evaluate a model for the secondary structure and membrane orientation of 3-hydroxy-3-methylglutaryl coenzyme A reductase, the glycoprotein of the endoplasmic reticulum that controls the rate of cholesterol biosynthesis. This model is derived from proteolysis experiments that separate the 97-kilodalton enzyme into two domains, an NH2-terminal membrane-bound domain of 339 residues and a COOH-terminal water-soluble domain of 548 residues that projects into the cytoplasm and contains the catalytic site. These domains were identified by reaction with antibodies against synthetic peptides corresponding to specific regions in the molecule. Computer modeling of the reductase structure, based on the amino acid sequence as determined by molecular cloning, predicts that the NH2-terminal domain contains 7 membrane-spanning regions. Analysis of the gene structure reveals that each proposed membrane-spanning region is encoded in a separate exon and is separated from the adjacent membrane-spanning region by an intron. The COOH-terminal domain of the reductase is predicted to contain two beta-structures flanked by a series of amphipathic helices, which together may constitute the active site. The NH2-terminal membrane-bound domain of the reductase bears some resemblance to rhodopsin, the photoreceptor protein of retinal rod disks and the only other intracellular glycoprotein whose amino acid sequence is known.
Application of monoclonal antibody libraries for the measurement of glycation adducts (2003)

Immunological approaches have been used to demonstrate the presence of advanced glycation end-products (AGEs) in several human and experimental animal tissues. We previously prepared polyclonal and monoclonal anti-AGE antibodies by immunizing AGE-modified proteins such as BSA and RNase. Although these antibodies contributed to demonstrate the presence of AGE-modified protein in vivo, the epitope structure of these antibodies had not been identified. We subsequently prepared several antibodies against AGE structures such as pentosidine, pyrraline, 3-deoxyglucosone imidazolone and N epsilon-(carboxyethyl)lysine by immunizing single AGE structures. These structure-specific antibodies have greatly helped broaden our understanding of AGE structures in aging and age-enhanced disease process. Monoclonal anti-AGE antibody is also used for the identification of major AGE structures in some pathological tissues, such as human atherosclerosis lesions. Based on the strategy, we successfully identified a novel AGE structure named glycolaldehyde-pyridine, which is the major antigenic AGE derived from glycolaldehyde. Therefore a monoclonal antibody library for AGE structures has served an important role in the elucidation of the biological significance of AGE.
Laser Capture Microdissection: Molecular Analysis of Tissue (1997)

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A s the list of expressed human genes expands, a major scientific and medical challenge is to understand the molecular events that drive normal tissue morphogenesis and the progression of
The effect of fetal hemoglobin on the survival characteristics of sickle cells (2006)

The determinants of sickle red blood cell (RBC) life span have not been well-defined but may include both intrinsic factors (eg, the tendency to sickle) and extrinsic factors (eg, the capacity of the reticuloendothelial system to remove defective RBCs). Fetal hemoglobin (HbF) is heterogeneously distributed among sickle RBCs; F cells contain 20% to 25% HbF, whereas the remainder have no detectable HbF (non-F cells). Autologous sickle RBCs were labeled with biotin and reinfused to determine overall survival, non-F- and F-cell survival, and time-dependent changes in HbF content (%HbF) for the surviving F cells. A total of 10 patients were enrolled, including 2 who were studied before and after the percentage of F cells was increased by treatment with hydroxyurea. As expected, F cells survived longer in all subjects. Non-F-cell survival correlated inversely with the percentage of F cells, with the time for 30% cell survival ranging from 6 days in patients with more than 88% F cells to 16 days in patients with less than 16% F cells. As the biotin-labeled RBCs aged in the circulation, the HbF content of the surviving F-cell population increased by 0.28%/d +/- 0.21%/d, indicating that within the F-cell population those with higher HbF content survived longer.
Analysis of Amino Acid Variation in the P2 Domain of the GII-4 Norovirus VP1 Protein Reveals Putative Variant-Specific Epitopes (2008)

Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.
Characterization and correction of optical proximity effects in deep-ultraviolet lithography using behavior modeling (1996)

We present the characterization of optical proximity effects and their correction in deep-UV lithography using an empirically derived model for calculating feature sizes in resist. The model is based on convolution of the mask pattern with a set of kernels determined from measuring the printed test structures in resist. The fit of the model to the measurement data is reviewed. The model is then used for proximity correction using commercially available proximity correction software. Corrections based on this model is effective in restoring resist linearity and in reducing line-end shortening. It is also more effective in reducing optical proximity effects than corrections based only on aerial image calculations.
Characterization of Marek's disease virus insertion and deletion mutants that lack US1 (ICP22 homolog), US10, and/or US2 and neighboring short-component open reading frames (1994)

We report the characterization of Marek's disease virus (MDV) strains having mutations in various genes that map to the unique short (US) region of the viral genome. A deletion mutant (GA delta 4.8lac) lacks 4.8 kbp of US region DNA, the deleted segment having been replaced by the lacZ gene of Escherichia coli. This deletion results in the loss of the MDV-encoded US1, US10, and US2 homologs of herpes simplex virus type 1, as well as three putative MDV-specific genes, Sorf1, Sorf2, and Sorf3. Two mutants containing lacZ insertions in the US1 and US10 genes have been constructed, and we have previously reported a US2lac insertion mutant (J. L. Cantello, A. S. Anderson, A. Francesconi, and R. W. Morgan, J. Virol. 65:1584-1588, 1991). The isolation of these mutants indicates that the relevant genes are not required for growth of MDV in chicken embryo fibroblasts. The mutants had early growth kinetics indistinguishable from those of their parent viruses; however, 5 to 7 days after being plated, the US1 insertion mutant (US1lac) and the GA delta 4.8lac deletion mutant showed a 5- to 10-fold decrease in virus growth. This decrease in virus accumulation correlated with a 30 to 50% decrease in plaquing efficiency when these viruses were plated onto established versus fresh chicken embryo fibroblast monolayers compared with a 10 to 15% decrease seen for the parent viruses and for the US10lac or US2lac insertion mutants. Finally, GA delta 4.8lac could be reisolated from chickens, indicating that the deleted genes are not required for the infection of chickens following intra-abdominal inoculation of an attenuated serotype 1 MDV.
Single‐Domain Antibody‐Conjugated Nanoaggregate‐Embedded Beads for Targeted Detection of Pathogenic Bacteria (2009)

Cells aglow: Nanoaggregate-embedded beads (NAEBs) linked to a pathogen-specific single-domain antibody (sdAb) are used as an ultra-bright surface-enhanced Raman scattering (SERS) tag for detection of Staphylococcus aureus bacteria by SERS microscopy. The image shows a single S. aureus cell labeled with NAEBs and its corresponding NAEB–SERS spectrum.
Algae Burgers for a Hungry World? The Rise and Fall of Chlorella Cuisine (1997)

Les scientifiques ont demontre que l'algue Chlorella etait riche en proteines et pouvait etre utilisee comme element de base pour la preparation d'aliments synthetiques
Thin-film peeling-the elastic term (1975)

An energy balance shows that the force required to peel an elastic film from a rigid substrate depends not only on the adhesive surface energy but also on an elastic deformation term. This elastic term, tending to reduce the adhesion force, can only be significant in two instances: for materials which can support stresses approaching the elastic modulus without fracturing, and for very small peel angles. Experiments using rubber peeling from glass over a range of peel angles support the theory.
A novel driving scheme for high-resolution large-area a-Si:H AMOLED displays (2005)

Organic (polymeric) light-emitting diode (OLED) displays have demonstrated promising features such as high-resolution, potentially low-cost, and wide-viewing angle. More importantly, the OLED requires a small current to emit light along with a very low operating voltage (3-10 V), leading to a very power efficient devices. The programming time of high-resolution active matrix organic light emitting diode (AMOLED) displays is 20 /spl mu/s. However, the settling time of the conventional AMOLED driving schemes is of the order of ms. This paper presents a novel high-speed driving scheme for different pixel circuits based on hydrogenated amorphous silicon (a-Si:H) technology. The programming time of the new driving scheme is under 20 /spl mu/s, which is adequate for high-resolution, large-area AMOLED displays such as XVGA (1024/spl times/768).
Cytotoxic Spliceostatins from Burkholderia sp. and Their Semisynthetic Analogues (2014)

The spliceostatin class of natural products was reported to be potent cytotoxic agents via inhibition of the spliceosome, a key protein complex in the biosynthesis of mature mRNA. As part of an effort to discover novel leads for cancer chemotherapy, we re-examined this class of compounds from several angles, including fermentation of the producing strains, isolation and structure determination of new analogues, and semisynthetic modification. Accordingly, a group of spliceostatins were isolated from a culture broth of Burkholderia sp. FERM BP-3421, and their structures identified by analysis of spectroscopic data. Semisynthesis was performed on the major components 4 and 5 to generate ester and amide derivatives with improved in vitro potency. With their potent activity against tumor cells and unique mode of action, spliceostatins can be considered potential leads for development of cancer drugs.