gebhart/patrepeval huggingface dataset:
Certain Pairs of Ubiquitin-conjugating Enzymes (E2s) and Ubiquitin-Protein Ligases (E3s) Synthesize Nondegradable Forked Ubiquitin Chains Containing All Possible Isopeptide Linkages (2007)

It is generally assumed that a specific ubiquitin ligase (E3) links protein substrates to polyubiquitin chains containing a single type of isopeptide linkage, and that chains composed of linkages through Lys(48), but not through Lys(63), target proteins for proteasomal degradation. However, when we carried out a systematic analysis of the types of ubiquitin (Ub) chains formed by different purified E3s and Ub-conjugating enzymes (E2s), we found, using Ub mutants and mass spectrometry, that the U-box E3, CHIP, and Ring finger E3s, MuRF1 and Mdm2, with the E2, UbcH5, form a novel type of Ub chain that contains all seven possible linkages, but predominantly Lys(48), Lys(63), and Lys(11) linkages. Also, these heterogeneous chains contain forks (bifurcations), where two Ub molecules are linked to the adjacent lysines at Lys(6) + Lys(11), Lys(27) + Lys(29), or Lys(29) + Lys(33) on the preceding Ub molecule. However, the HECT domain E3s, E6AP and Nedd4, with the same E2, UbcH5, form homogeneous chains exclusively, either Lys(48) chains (E6AP) or Lys(63) chains (Nedd4). Furthermore, with other families of E2s, CHIP and MuRF1 synthesize homogeneous Ub chains on the substrates. Using the dimeric E2, UbcH13/Uev1a, they attach Lys(63) chains, but with UbcH1 (E2-25K), MuRF1 synthesizes Lys(48) chains on the substrate. We then compared the capacity of the forked heterogeneous chains and homogeneous chains to support proteasomal degradation. When troponin I was linked by MuRF1 to a Lys(48)-Ub chain or, surprisingly, to a Lys(63)-Ub chain, troponin I was degraded rapidly by pure 26S proteasomes. However, when linked to the mixed forked chains, troponin I was degraded quite poorly, and its polyUb chain, especially the forked linkages, was disassembled slowly by proteasome-associated isopeptidases. Because these Ring finger and U-box E3s with UbcH5 target proteins for degradation in vivo, but Lys(63) chains do not, cells probably contain additional factors that prevent formation of such nondegradable Ub-conjugates and that protect proteins linked to Lys(63)-Ub chains from proteasomal degradation.
Spectrophotometric Studies on Intact Muscle (1963)

The kinetics of the mitochondrial respiratory chain of intact muscle and the concomitant changes of the intercellular pH were investigated. Addition of lactate and pyruvate under resting conditions produces reductions of DPN and cytochrome b, and, occasionally, of cytochrome c and flavoprotein. Succinate gives similar but smaller changes. In recently excised muscles moderate contractile activity produces a reduction of cytochrome c and oxidations of DPNH, cytochrome b, and sometimes of the flavoproteins. Tetanic contractions and larger numbers of twitches produce reductions of DPN and of cytochromes b and c. In sartorii of the tropical toad, stored for approximately 2 days at 0-3 degrees C, contractile activity always gives rise to long lasting oxidations of DPNH and cytochrome b. Addition of pyruvate or lactate shortens these oxidation cycles with a concomitant reduction of cytochrome c. These responses to contractions agree with those of mitochondria isolated from leg muscles of the toad upon the addition of ADP. Apparently the mitochondria in resting, excised muscles are not supplied with an excess of substrate. Measurements on the intercellular pH showed that even limited activity ( < 5 twitches) initiates glycolysis. The primary control of respiration resides, nevertheless, in the ADP concentration, rather than in the levels of substrate or inorganic phosphate. The results are quantitatively consistent with the view that ATP is the primary energy donor for muscular contraction.
Off-specular x-ray scattering in Langmuir-Blodgett multilayers of a liquid-crystalline polymer (1995)

The effect of surface roughness on the static layer undulations of multilayer films of a side-chain liquid-crystalline polymer has been investigated by off-specular x-ray scattering. The roughness correlation length evaluated from the off-specular data is shown to vary inversely with the average roughness of the multilayer film. The features of the off-specular x-ray scattering are similar to those exhibited by inorganic heterostructural films.
A plan for malware containment in the DETER testbed (2007)

This study examined whether HSP70 could bind to and protect against thermal inactivation of SERCA1a, the SERCA isoform expressed in adult fast-twitch skeletal muscle. Sarcoplasmic reticulum vesicles prepared from rat gastrocnemius muscle were incubated with purified HSP70 at both 37 and 41 degrees C for either 30, 60, or 120 min. Maximal SERCA1a activity (micromol/g protein/min) in the absence of HSP70 was reduced progressively with time, with greater reductions occurring at 41 degrees C compared with 37 degrees C. HSP70 protected against thermal inactivation of SERCA1a activity at 37 degrees C but not at 41 degrees C and only at 30 and 60 min but not at 120 min. HSP70 also protected against reductions in binding capacity for fluorescein isothiocyanate, a fluorescent probe that binds to Lys515 in the nucleotide binding domain of SERCA, at 30 and 60 min but not at 120 min, an effect that was independent of temperature. HEK-293 cells were co-transfected with cDNAs encoding rabbit SERCA1a and human HSP-EYFP and subjected to 40 degrees C for 1 h. Immunohistochemistry revealed nearly complete co-localization of SERCA1a with HSP70 under these conditions. Co-immunoprecipitation showed physical interaction between HSP70 and SERCA1a under all thermal conditions both in vitro and in HEK-293 cells. Modeling showed that the fluorescein isothiocyanate-binding site of intact SERCA1a in the E2 form lies in its close proximity to a potential interaction site between SERCA1a and HSP70. These results indicate that HSP70 can bind to SERCA1a and, depending on the severity of heat stress, protect SERCA1a function by stabilizing the nucleotide binding domain.
Abstract #2077: Antagonistic antibodies to c-fms block c-fms-mediated activities, reduce tumor-associated macrophages and decrease tumor growth in preclinical models (2009)

Tumor associated macrophages (TAMs) produce numerous factors that may directly and indirectly support tumor growth and progression. In support of this view, a variety of tumor types with high TAM content, elevated c-fms (CSF-1 receptor) and CSF-1 levels have been associated with poor prognosis in cancer patients. Given that the CSF-1/c-fms signaling pathway drives the proliferation and function of macrophages, we developed antagonistic antibodies to c-fms and assessed the effects of these antibodies on monocytic cells in vitro and TAMs and tumor growth in vivo. In this study, AMG 820, a fully human monoclonal antibody antagonist to c-fms potently inhibited CSF-1 binding to its receptor and CSF-1-driven proliferation of the human myelomonocytic cell line AML-5 as well as primary human bone-marrow derived macrophages (IC-50s range 5-30 pM). Similarly, M279, an antibody to mouse c-fms, inhibited CSF-1-driven mouse myelomonocytic cell line growth. Interestingly, both AMG 820 and M279 significantly inhibited the effects, with similar potencies, of both CSF-1 and IL-34, the recently discovered second ligand for c-fms. M279 and AMG 820 also blocked c-fms activity in vivo in mice and Cynomolgus monkeys, respectively, as shown by significant increases in serum CSF-1 (blockade of c-fms-mediated CSF-1 degradation) as well as decreases in serum Trap 5b through the inhibition of the CSF-1/c-fms axis in osteoclasts. In several preclinical tumor models in mice, these systemic effects were accompanied by consistent reduction of TAMs by 70-80% based upon laser scanning cytofluorometric quantitation of F4/80-positive cells. TAM reduction was associated with a decrease in tumor volume in some models as well as an increase in necrosis and decreased viable tumor by histopathological analysis. Taken together, these data indicate that the treatment with an antagonistic antibody to c-fms reduce TAMs and TAM-mediated support of tumor growth, thus providing a novel approach to cancer therapy. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 2077.
Insecticidal activity of essential oils : octopaminergic sites of action (2001)

A study was conducted to determine the insecticidal activity and mechanism of action of three essential oils (eugenol, α-terpineol and cinnamic alcohol) and an equal part mixture (3-blend) against American cockroaches (Periplaneta americana). To address species differences in response to treatment with the test oils, Carpenter ants (Camponotus pennsylvanicus De Geer), and German cockroaches (Blattella germanica) were included in this study. Exposed American cockroaches demonstrated hyperactivity followed by hyperextension of the legs and abdomen, then fast knockdown or quick immobilization followed by death. Ants and German cockroaches showed fast immobilization/knockdown followed by mortality. The 1:1:1 mixture (3-blend) was substantially effective against all test insects. One of the most remarkable observations was the increased frequency of heartbeats of American cockroaches in response to topical application of test oils. The changes in the pattern of cAMP level was biphasic. A significant increase in the cAMP level was found in response to 1 nmol/ml of eugenol, or 3-blend or 10 nmol/ml of α-terpineol. At higher concentrations a significant decrease in cAMP level was found. Blockage of octopamine receptors binding sites was also illustrated at lower concentrations of the test chemicals as judged by the decreased binding activity of [3H]octopamine to its receptors. In conclusion: (1) test oils are neuro-insecticides and their insecticidal activity is species-dependent; (2) a synergistic effect of the three oils was found when they were equally mixed (3-blend); and (3) the octpaminergic system mediates the insecticidal activity of eugenol, α-terpienol and the 3-blend.
Antimicrobial Activity of Leaf Extracts of <i>Polyalthia longifolia</i> (1983)

Abstract Leaf extracts of P. longifolia with different solvents of increasing polarity were tested against some pathogenic fungi and bacteria. The nature of the active compound is briefly discussed in view of the observed activity in methanol extracts.
Clenbuterol, a beta 2-agonist, retards atrophy in denervated muscles (1987)

Denervated soleus, anterior tibialis, and gastrocnemius muscles, but not the extensor digitorum longus, contained 95-110% more protein after 2-3 wk of treatment with the adrenergic beta 2-receptor agonist, clenbuterol, than denervated controls. In addition, the twofold difference in the protein content of denervated solei was paralleled by similar changes in contractile strength and muscle fiber cross-sectional area. In contrast, when the innervated contralateral muscles were examined, the extensor digitorum longus and anterior tibialis showed relatively small increases in protein of 32 and 19%, respectively, whereas the soleus and gastrocnemius were unaffected. The magnitude of the effects of clenbuterol in sparing the mass and functional capacity of denervated muscle suggests that this agent may be important in studies of neuromuscular diseases and disuse atrophy.
Quasi-optical antenna array amplifiers (2002)

Several quasi-optical transmission wave amplifiers are presented: (1) a two-level power-combining PHEMT patch-antenna lens amplifier with 8 dB of absolute power gain at 9.7 GHz used for beamforming and beam-switching; (2) a saturated class-A polarization-preserving 24-MESFET patch array which produces 0.7 Watts at 10 GHz with 21% power-added efficiency; and (3) an X-band 2-stage low-noise CPW PHEMT amplifier cell using anti-resonant slot antennas with 21.7 dB active gain, 3.2 dB noise figure and a 6% 3 dB bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Manipulation of colloidal gold nanoparticles in the evanescent field of a channel waveguide (2000)

Colloidal gold spheres of radius 10 nm are reported to move forward in water, under the influence of radiation pressure forces, due to the evanescent field at the surface of an optical channel waveguide. The velocity is linearly dependent upon the optical power in the waveguide, acquiring a maximum velocity of 4 μm/s for modal power of 500 mW in the TM polarization at a wavelength of λ=1.047 μm.
Cancer Chemotherapeutic Agents (1987)

apeutic agents,' data demonstrating the usefulness of cancerchemotherapywere meager. Karnofsky cited three polyfunc tional alkylating agents and two antimetab olites as having some activity in human cancer, activity that was limited totempo
Modified PROPELLER approach for <i>T</i><sub>2</sub>‐mapping of the abdomen (2009)

Quantitative abdominal T(2) measurements may be useful for lesion differentiation and functional tissue characterization. However, T(2) mapping of the abdomen with conventional spin-echo (SE) and turbo-spin-echo (TSE) approaches can be challenging due to physiologic motion artifacts. Multishot TSE-based PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) can provide superior image quality due to reduced sensitivity to motion artifacts. With echo-reordering to accurately estimate effective echo times and an extended slice thickness ratio to reduce stimulated echo effects, a modified PROPELLER approach may permit accurate, robust abdominal T(2) measurements. We validated the accuracy of our modified PROPELLER T(2)-mapping approach by comparison to conventional SE measurements in a phantom model and demonstrated the feasibility of acquiring accurate, high-quality abdominal T(2) maps in normal volunteers.
Comparison of recovery rates of various organisms from clinical hypertonic blood cultures by using various concentrations of sodium polyanethol sulfonate (1975)

By using parallel culture techniques, the recovery rates of a wide spectrum of organisms encountered in hypertonic clinical blood cultures was determined from four different blood culture bottles. Each bottle was identical except for the amount of sodium polyanethol sulfonate (SPS) present. Flasks A, B, C, and D contained SPS in final concentrations of 0.025, 0.05, 0.075, and 0%, respectively. Of 144 patients found to have clinically relevant organisms in their blood cultures, 127 had positive A flasks, 144 had positive B flasks, 140 had positive C flasks, and 110 had positive D flasks. There was no significant difference in the time required to obtain organism recovery from the A, B, or C flasks; however, the time required to obtain organism recovery from the D flask was considerably longer, ranging up to 5 days in many cases. Of the various organisms recovered, 3 of 7 strains of anaerobic streptococci and 1 of 28 strains of Streptococcus pneumoniae appeared to be inhibited by SPS when the concentration was 0.075%. In no case was an organism recovered from either the A or D flask but not from the B flask, indicating that a concentration of 0.05% SPS in hypertonic media does not inhibit the growth of a wide spectrum of organisms in clinical blood cultures.
The Obstructing Prostate: Its Treatment, Surgical and Otherwise (1939)

No AccessJournal of Urology1 Aug 1939The Obstructing Prostate: Its Treatment, Surgical and Otherwise1 George Gilbert Smith George Gilbert SmithGeorge Gilbert Smith More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)71501-7AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1939 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited ByOrmond J (2018) Radical Perineal Prostatectomy for CarcinomaJournal of Urology, VOL. 58, NO. 1, (61-67), Online publication date: 1-Jul-1947. Volume 42Issue 2August 1939Page: 145-157 Advertisement Copyright & Permissions© 1939 by The American Urological Association Education and Research, Inc.MetricsAuthor Information George Gilbert Smith More articles by this author Expand All Advertisement Loading ...
Analysis of multiply antimicrobial-resistant isolates of Streptococcus pneumoniae from the United States (1992)

Streptococcus pneumoniae isolates resistant to penicillin, chloramphenicol, tetracycline and sulfamethoxazole-trimethroprim are being recovered with increasing frequency in the United States. We analyzed the penicillin-binding proteins (PBPs), multilocus enzyme electrophoresis (MLEE) genotypes, and ribotypes of 22 multiresistant serotype 23F isolates of S. pneumoniae from the United States and 1 isolate each from Spain and South Africa. Also included were seven multiresistant isolates of other serotypes, three penicillin-resistant but chloramphenicol-susceptible serotype 23F isolates, and two penicillin-susceptible isolates (one penicillin-susceptible isolate was serotype 23F). Fifteen of the 22 multiresistant isolates from the United States and the isolates from Spain and South Africa had identical PBP patterns, MLEE profiles, and ribotypes. Six of the remaining seven multiresistant isolates were related by PBP pattern, but demonstrated slightly different MLEE and/or ribotype profiles, possibly because of acquisition of additional resistance markers (four of the six isolates were also resistant to erythromycin). The remaining multiresistant serotype 23F isolate had a unique PBP pattern and ribotype and was only distantly related to the other pneumococcal isolates by MLEE analysis. The PBP patterns, MLEE profiles, and ribotypes of the multiresistant serotype 23F isolates were easily distinguished from those of six multiresistant isolates of other serotypes; three other penicillin-resistant, chloramphenicol-susceptible, serotype 23F isolates; and two penicillin-susceptible isolates. One exception was a multiresistant serotype 19A isolate that was highly related to the clonal group by PBP pattern and MLEE analysis and that had a ribotype similar to those of the other erythromycin-resistant serotype 23F isolates. MLEE analysis and ribotyping were more discriminating than were the PBP patterns in discerning strain differences. These data strongly suggest that a multiresistant clone of S. pneumoniae serotype 23F that is related to multiresistant isolates from Spain and South Africa has become disseminated in the United States. Clinicians should be alerted to the spread of these multiresistant strains in the United States.
Point of View (2006)

From the Department of Orthopaedic Surgery, University of Kentucky, Lexington, KY. The manuscript submitted does not contain information about medical device(s)/drug(s). No funds were received in support of this work. No benefits in any form have been or will be received from a commercial party related directly or indirectly to the subject of this manuscript. Address correspondence and reprint requests to William O. Shaffer, MD, Department of Orthopaedic Surgery, University of Kentucky, 740 South Limestone, Kentucky Clinic K-416, Lexington, KY 40536; E-mail: [email protected]
Recent advances of Cowpea mosaic virus-based particle technology (2011)

Particles of cowpea mosaic virus (CPMV) have enjoyed considerable success as a means of presenting peptides for vaccine purposes. However, the existing technology has limitations in regard to the size and nature of the peptides which can be presented and has problems regarding bio-containment. Recent developments suggest ways by which these problems can be overcome, increasing the range of potential applications of CPMV-based particle technology.
Controlling Race Conditions in OpenFlow to Accelerate Application Verification and Packet Forwarding (2015)

OpenFlow is a Software Defined Networking (SDN) protocol that is being deployed in many network systems. SDN application verification takes an important role in guaranteeing the correctness of the application. Through our investigation, we discover that application verification can be very inefficient under the OpenFlow protocol since there are many race conditions between the data packets and control plane messages. Furthermore, these race conditions also increase the control plane workload and packet forwarding delay. We propose Attendre, an OpenFlow extension, to mitigate the ill effects of the race conditions in OpenFlow networks. We have implemented Attendre in NICE (a model checking verifier), Open vSwitch (a software virtual switch), and NOX (an OpenFlow controller). Experiments show that Attendre can reduce verification time by several orders of magnitude, and significantly reduce TCP connection setup time.
Subquery Allocations in Distributed Databases Using Genetic Algorithms (2010)

Minimization of query execution time is an important performance objective in distributed databases design. While total time is to be minimized for On Line Transaction Processing (OLTP) type queries, response time has to be minimized in Decision Support type queries. Thus different allocations of subqueries to sites and their execution plans are optimal based on the query type. We formulate the subquery allocation problem and provide analytical cost models for these two objective functions. Since the problem is NP-hard, we solve the problem using genetic algorithm (GA). Our results indicate query execution plans with total minimization objective are inefficient for response time objective and vice versa. The GA procedure is tested with simulation experiments using complex queries of up to 20 joins. Comparison of results with exhaustive enumeration indicates that GA produced optimal solutions in all cases in much less time.
Face recognition using fractal codes (2002)

In this paper we propose a new method for face recognition using fractal codes. Fractal codes represent local contractive, affine transformations which when iteratively applied to range-domain pairs in an arbitrary initial image result in a fixed point close to a given image. The transformation parameters such as brightness offset, contrast factor, orientation and the address of the corresponding domain for each range are used directly as features in our method. Features of an unknown face image are compared with those pre-computed for images in a database. There is no need to iterate, use fractal neighbor distances or fractal dimensions for comparison in the proposed method. This method is robust to scale change, frame size change and rotations as well as to some noise, facial expressions and blur distortion in the image.