gebhart/patrepeval huggingface dataset:
An Evaluation of an Atte m pt at Offloading TCP/IP Protocol Proce ssing onto an i9 60RN-based iNIC (2000)

TCP/IP n e tw ork ing, Inte llige n t Ne tw ork Inte rface Th is re port pre s e nts an e valuation of a TCP/IP offload im ple m e n tation th at utiliz e s a 100Base T inte llige n t Ne tw ork Inte rface Card (iNIC) equipped w ith a 100 M H z i9 60RN processor. Th e e n tire Fre e BSD-de rived n etw ork ing stack from sock e t dow nw ard is im ple m e n ted on th e iNIC w ith th e goal of reducing h ost processor w ork load. For large m e ssages th at result in MTU pack e ts, th e offload im ple m e n tation can sustain w ire -spe e d on re ce ive but only about 80% of w ire -spe e d on transm it. Utiliz ing h ardw are -based profiling of TTCP b ench m ark runs, our e valuation pie ced toge th e r a com pre h ensive picture of transm it b e h avior on th e iNIC. Our first surprise w as th e num b e r of i9 60RN processor cycles consum e d in transm itting large m e ssages --around 17 th ousand processor cycles pe r 1.5k byte (Eth e rn e t M TU) pack e t. Furth e r investigation re ve als th at th is h igh cost is due to a com bination of i9 60RN arch ite ctural sh ortcom ings, poor buffe ring strate gy in th e TCP/IP code running on th e iNIC, and lim itations im posed by th e I20-based h ost-iNIC inte rface . W e also found room for im prove m e n ts in th e im ple m e n tation of th e sock e t buffe r data-structure . Th is re port pre s e nts profiling statistics, as w e ll as code -path analysis th at back up th e s e conclusions. Our results call into question th e h ypoth esis th at a spe cializ e d n etw ork ing softw are e n vironm e nt coupled w ith ch e ap e m bedded processors is a cost e ffe ctive w ay of im proving syste m pe rform ance . At le ast in th e case of th e offload im ple m e n tation on th e i9 60RN-based iNIC, n e ith e r w as th e pe rform ance adequate n or th e syste m ch e ap. Th is conclusion, h ow e ve r, doe s not im ply th at offload is a bad ide a. In fact, m e asure m e n ts w e m ade w ith Alacrite ch 's SLIC NIC, w h ich partially offloads TCP/IP protocol processing to an ASIC, suggests th at offloading can confe r advantages in a cost e ffe ctive w ay. Tak ing th e righ t im ple m e n tation approach is critical.
Enhancement on Primate Corneal Endothelial Cell Survival In Vitro by a ROCK Inhibitor (2009)

The inhibition of Rho/ROCK signaling by specific ROCK inhibitor Y-27632 promoted the adhesion of MCECs, inhibited apoptosis, and increased the number of proliferating cells. These results suggest that the ROCK inhibitor may serve as a new tool for cultivating HCECs for transplantation.
Effect of end group blockage on the properties of a class A amphipathic helical peptide (1993)

In a recent classification of biologically active amphipathic alpha-helixes, the lipid-associating domains in exchangeable plasma apolipoproteins have been classified as class A amphipathic helixes (Segrest, J.P., De Loof, H., Dohlman, J.G., Brouillette, C.G., Anantharamaiah, G.M. Proteins 8:103-117, 1990). A model peptide analog with the sequence, Asp Trp Leu Lys Ala Phe Tyr Asp Lys Val Ala Glu Lys Leu Lys Glu Ala Phe (18A), possesses the characteristics of a class A amphipathic helix. The addition of an acetyl group at the alpha-amino terminus and an amide at the alpha-carboxyl terminus, to obtain Ac-18A-NH2, produces large increases in helicity for the peptide both in solution and when associated with lipid (for 18A vs Ac-18A-NH2, from 6 to 38% helix in buffer and from 49 to 92% helix when bound to dimyristoyl phosphatidylcholine in discoidal complexes). Blocking of the end-groups of 18A stabilizes the alpha-helix in the presence of lipid by approximately 1.3 kcal/mol. There is also an increase in the self-association of the blocked peptide in aqueous solution. The free energy of binding to the PC-water interface is increased only by about 3% (from -8.0 kcal/mol for 18A to -8.3 kcal/mol for Ac-18A-NH2). The Ac-18A-NH2 has a much greater potency in raising the bilayer to hexagonal phase transition temperature of dipalmitoleoyl phosphatidylethanolamine than does 18A. In this regard Ac-18A-NH2 more closely resembles the behavior of the apolipoprotein A-I, which is the major protein component of high-density lipoprotein and a potent inhibitor of lipid hexagonal phase formation. The activation of the plasma enzyme lecithin: cholesterol acyltransferase by the Ac-18A-NH2 peptide is greater than the 18A analog and comparable to that observed with the apo A-I. In the case of Ac-18A-NH2, the higher activating potency may be due, at least in part, to the ability of the peptide to micellize egg PC vesicles.
Contact Electroluminescence (1957)

Many powdered crystal phosphors which are normally nonelectroluminescent become electroluminescent if they are simply mechanically mixed with suitable powdered metals, or with some nonmetals of good electrical conductivity. The conclusion is drawn, and supported by many facts, that ordinary electroluminescence in powdered phosphors excited by an alternating electric field (Destriau effect) is also due to substances of relatively high conductivity incorporated as small segregations within the essentially insulating phosphor particles. The electric field near sharp edges of these "contact substance" particles is considerably higher than the average electric field across the phosphor crystals. Preconditions for the electroluminescent excitation process are fulfilled in these localized regions of high field strength.
Application of stains in clinical microbiology (2001)

Stains have been used for diagnosing infectious diseases since the late 1800s. The Gram stain remains the most commonly used stain because it detects and differentiates a wide range of pathogens. The next most commonly used diagnostic technique is acid-fast staining that is used primarily to detect Mycobacterium tuberculosis and other severe infections. Many infectious agents grow slowly on culture media or may not grow at all; stains may be the only method to detect these organisms in clinical specimens. In the hands of experienced clinical microscopists, stains provide rapid and cost-effective information for preliminary diagnosis of infectious diseases. A review of the most common staining methods used in the clinical microbiology laboratory is presented here.
Ehrlichia ewingiiInfection in White-Tailed Deer (Odocoileus virginianus) (2002)

Two closely related zoonotic ehrlichiae, Ehrlichia chaffeensis and E. ewingii, are transmitted by Amblyomma americanum, the lone star tick. Because white-tailed deer (Odocoileus virginianus) are critical hosts for all mobile stages of A. americanum and are important vertebrate reservoirs of E. chaffeensis, we investigated whether deer may be infected with E. ewingii, a cause of granulocytotropic ehrlichiosis in humans and dogs. To test for E. ewingii infection, we used polymerase chain reaction and inoculation of fawns with whole blood from wild deer. Of 110 deer tested from 20 locations in 8 U.S. states, 6 (5.5%) were positive for E. ewingii. In addition, natural E. ewingii infection was confirmed through infection of captive fawns. These findings expand the geographic distribution of E. ewingii, along with risk for human infection, to include areas of Kentucky, Georgia, and South Carolina. These data suggest that white-tailed deer may be an important reservoir for E. ewingii.
Effects of Guanosine Tetraphosphate, Guanosine Pentaphosphate, and β-γ Methylenyl-Guanosine Pentaphosphate on Gene Expression of Escherichia coli In Vitro (1974)

The effects of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), both produced by E. coli, were measured on the activities of several genes in a cell-free system. Gene activity is measured as gene-directed synthesis of biochemically competent protein or transfer RNA. Both ppGpp and pppGpp stimulated the activities of the ara, lac, and trp operons and inhibited the arg operon. Production of transfer-RNA(Tyr) was unaffected by moderate levels of either ppGpp or pppGpp and only slightly inhibited at higher levels of ppGpp. Since the cell-free reaction mixtures hydrolyze pppGpp to ppGpp, we performed similar studies with a hydrolysis-resistant analog of pppGpp, the beta-gamma methylenyl derivative (pcppGpp). In general, pcppGpp shows the same inhibitory potency as pppGpp for the arg operon, but lacks the stimulatory effects on the ara, lac, and trp operons. This result suggests that the stimulation of these gene activities is specific for ppGpp.Under similar conditions, pppGpp and ppGpp show a slight inhibitory effect on the messenger-directed synthesis of beta-galactosidase and no effect on the messenger-directed synthesis of MS2 viral-coat protein. These observations, together with the fact that in the same system these nucleotides affect coupled transcription and translation, lead us to surmise that the activities of pppGpp and ppGpp are exerted at the level of RNA polymerase activity.
Structure modeling and inhibitor prediction of NADP oxidoreductase enzyme from Methanobrevibacter smithii (2011)

The F420-dependent NADP oxidoreductase enzyme from Methanobrevibacter smithii catalyzes the important electron transfer step during methanogenesis. Therefore, it may act as potential target for blocking the process of methane formation. Its protein sequence is available in GenBank (accession number: ABQ86254.1) however no report has been found about its 3D protein structure. In this work, we first time claim 3D model structure of F420-dependent NADP oxidoreductase enzyme from Methanobrevibacter smithii by comparative homology modeling method. Swiss model and ESyPred3d (via Modeller 6v2) software's were generated the 3D model by detecting 1JAX (A) as template along with sequence identities of 34.272% and 35.40%. Furthermore, PROCHECK with Ramachandran plot and ProSA analysis revealed that swiss model produced better model than Modeller6v2 with 98.90% of residues in favored and additional allowed regions (RM plot) as well as with ProSA Z score of -7.26. In addition, we investigated that the substrate F420 bound at the cavity of the model. Subsequently, inhibitor prediction study revealed that Lovastatin (-22.07 Kcal/mol) and Compactin (Mevastatin) (-21.91 Kcal/mol) produced more affinity for model structure of NADP oxidoreducatse as compared to F420 (-14.40 Kcal/mol). It indicates that the Lovastatin and Compactin (Mevastatin) compounds (Negative regulator) may act as potential inhibitor of F420 dependent NADP oxidoreducatse protein.
Ig-Reactive CD4+CD25+ T Cells from Tolerized (New Zealand Black × New Zealand White)F1 Mice Suppress In Vitro Production of Antibodies to DNA (2004)

We have recently shown that tolerogenic administration of an artificial peptide (pConsensus) that is based on sequences within the V(H) regions of several murine anti-dsDNA Ig delays appearance of autoantibodies in female (New Zealand Black (NZB) x New Zealand White (NZW))F(1) (NZB/W F(1)) mice and significantly prolongs their survival. The aim of this study was to characterize the T cell population(s) involved in pConsensus-induced down-regulation of autoimmune responses in tolerized NZB/W F(1) mice. Using MHC class II dimers loaded with tolerogenic peptide, we found that pCons favored expansion of peptide-reactive CD4(+)CD25(+) regulatory T cells (T(R)) that inhibited in vitro production of anti-dsDNA Ab-forming cells. Suppression by T(R) was abrogated by the presence in culture of Ab to glucocorticoid-induced TNFR family member 18 or to TGFbeta latency-associated protein. These findings suggest possible relevance of Ag specificity in the mechanism of T(R)-mediated immune tolerance to Ig-derived peptides in NZB/W F(1) mice.
Molecular analysis of the SNF4 gene of Saccharomyces cerevisiae: evidence for physical association of the SNF4 protein with the SNF1 protein kinase. (1989)

The SNF4 gene is required for expression of glucose-repressible genes in response to glucose deprivation in Saccharomyces cerevisiae. Previous evidence suggested that SNF4 is functionally related to SNF1, another essential gene in this global regulatory system that encodes a protein kinase. Increased SNF1 gene dosage partially compensates for a mutation in SNF4, and the SNF4 function is required for maximal SNF1 protein kinase activity in vitro. We have cloned SNF4 and identified its 1.2-kilobase RNA, which is not regulated by glucose repression. A 36-kilodalton SNF4 protein is predicted from the nucleotide sequence. Disruption of the chromosomal SNF4 locus revealed that the requirement for SNF4 function is less stringent at low temperature (23 degrees C). A bifunctional SNF4-lacZ gene fusion that includes almost the entire SNF4 coding sequence was constructed. The fusion protein was shown by immunofluorescence microscopy to be distributed throughout the cell, with partial localization to the nucleus. The SNF4-beta-galactosidase protein coimmunoprecipitated with the SNF1 protein kinase, thus providing evidence for the physical association of the two proteins.
The gift of Iluvatar: Tolkien's theological vision (2004)

This article explores some of the principal theological themes underlying Tolkien's fiction through reference to Tolkien's own comments and observations expressed in his letters, lectures and other creative works. It is my contention in this article that Tolkien's work is explicitly theological and makes an important contribution to contemporary Christian theological discussion, especially with regards to the vocation of Christians and their role in the salvation of the world.
Pathophysiology of the migraine aura (1994)

The characteristic form and development of sensory disturbances during migraine auras suggests that the underlying mechanism is a disturbance of the cerebral cortex, probably the cortical spreading depression (CSD) of Leão. The demonstration of unique changes of brain blood flow during attacks of migraine with aura, which have been replicated in animal experiments during CSD, constitutes another important line of support for the 'spreading depression' theory, which may be a key to an understanding of the migraine attack. Cortical spreading depression is a short-lasting depolarization wave that moves across the cortex at a rate of 3-5 mm/min. A brief phase of excitation heralds the reaction which is immediately followed by prolonged nerve cell depression synchronously with a dramatic failure of brain ion homeostasis, efflux of excitatory amino acids from nerve cells and enhanced energy metabolism. Recent experimental work has shown that CSD in the neocortex of a variety of species including man is dependent on activation of a single receptor, the N-methyl-D-aspartate receptor, one of the three subtypes of glutamate receptors. The combined experimental and clinical studies point to fruitful areas in which to look for migraine treatments of the future and provide a framework within which important aspects of the migraine attack can be modelled.
Does graft-versus-host disease influence the tempo of immunologic recovery after allogeneic human marrow transplantation? An observation on 56 long-term survivors (1978)

This report describes a study of humoral and cellular immune reactivities in 56 patients who have survived for 1 yr to more than 6 yr after marrow transplantation from an HLA-identical sibling for the treatment of aplastic anemia or hematologic malignancy. All were conditioned for the transplant by high doses of cyclophosphamide and/or total body irradiation. Immunologic studies on the marrow donors served to establish the normal range for the tests used. The influence of an episode of graft-versus-host disease (GVHD) on the subsequent immunologic recovery was emphasized. Thirty-two patients had GVHD, which resolved in 19 and evolved into a chronic form in 13. Tests used included serial determinations of serum immunoglobulins, complement (C3 and C4), lymphocyte counts, T and B cells, lymphocyte responses to allogeneic cells and to mitogens, isohemagglutinin titers, clearance of bacteriophage ϕX174 (phage) from the blood, primary and secondary antibody responses to phage and to keyhole limpet hemocyanin (KLH), and tests of skin reactivity to recall and neoantigens, dinitrochlorobenzene, and KLH. Concluded from the study were the following: (1) All patients, regardless of whether they had GVHD or not, had pronounced impairment of all immunologic parameters during the first 4 mo after grafting. (2) The speed of immunologic recovery thereafter was faster in patients without GVHD than in those with GVHD. The deficient immune responsiveness in patients with GVHD lasted approximately 2 yr and thereafter tended to persist only in patients with chronic GVHD. A peculiar and unexplained finding in patients with GVHD was significantly higher than normal IgG levels. As a clinical correlate of the prolonged and intense immune deficiency, patients with GVHD showed a tendency toward more frequent and severe infections than those without GVHD. (3) Given enough time, most patients regained near-normal immune reactivity. This occurred much earlier and more frequently in patients without GVHD than in those with GVHD. Patients who regained near-normal immune reactivity did not have unusually frequent infections.
Molecular Cloning, Expression, Functional Characterization, Chromosomal Localization, and Gene Structure of Junctate, a Novel Integral Calcium Binding Protein of Sarco(endo)plasmic Reticulum Membrane (2000)

Screening a cDNA library from human skeletal muscle and cardiac muscle with a cDNA probe derived from junctin led to the isolation of two groups of cDNA clones. The first group displayed a deduced amino acid sequence that is 84% identical to that of dog heart junctin, whereas the second group had a single open reading frame that encoded a polypeptide with a predicted mass of 33 kDa, whose first 78 NH(2)-terminal residues are identical to junctin whereas its COOH terminus domain is identical to aspartyl beta-hydroxylase, a member of the alpha-ketoglutarate-dependent dioxygenase family. We named the latter amino acid sequence junctate. Northern blot analysis indicates that junctate is expressed in a variety of human tissues including heart, pancreas, brain, lung, liver, kidney, and skeletal muscle. Fluorescence in situ hybridization analysis revealed that the genetic loci of junctin and junctate map to the same cytogenetic band on human chromosome 8. Analysis of intron/exon boundaries of the genomic BAC clones demonstrate that junctin, junctate, and aspartyl beta-hydroxylase result from alternative splicing of the same gene. The predicted lumenal portion of junctate is enriched in negatively charged residues and is able to bind calcium. Scatchard analysis of equilibrium (45)Ca(2+) binding in the presence of a physiological concentration of KCl demonstrate that junctate binds 21.0 mol of Ca(2+)/mol protein with a k(D) of 217 +/- 20 microm (n = 5). Tagging recombinant junctate with green fluorescent protein and expressing the chimeric polypeptide in COS-7-transfected cells indicates that junctate is located in endoplasmic reticulum membranes and that its presence increases the peak amplitude and transient calcium released by activation of surface membrane receptors coupled to InsP(3) receptor activation. Our study shows that alternative splicing of the same gene generates the following functionally distinct proteins: an enzyme (aspartyl beta-hydroxylase), a structural protein of SR (junctin), and a membrane-bound calcium binding protein (junctate).
On-line schema update for a telecom database (2002)

Telecom databases need very high availability for both read and write transactions. Thus it is desired that not even schema changes are allowed to block any type of transactions. We show in this paper a method to handle schema changes which is based on a transaction oriented change with the aid of triggers. The old and the new schema can be used concurrently so it is never necessary to block any transactions. A nice feature of the method presented in this paper is that it is easy to integrate into an already existing DBMS. This functionality is rarely, if ever, found in neither products nor research articles.
Finding lost wrenches: Using continuum robots for contact detection and estimation of contact location (2010)

This paper presents a novel modeling framework for contact detection and estimation of contact location on multi-backbone continuum robots. The paper presents modified kinematics for constrained continuum robots and introduces the concept of Fixed Centrode Deviation (FCD) for continuum robots. It is shown that the change in fixed centrode locus may be used for detection of contact and for contact location estimation. An alternative method for contact detection using Joint Force Deviation (JFD) is investigated and a lower bound for contact detectability is derived while considering uncertainties in joint forces. An estimation framework for the location of contact is presented based on FCD and the constrained kinematics Jacobian of the continuum robot. These methods are validated by simulation and experiments. This framework may be used for enhancing the safety of robotic surgical slaves and for exploration of unknown environments such as in scenarios of search and rescue.
“Intelligent infill” for cost effective 3D seismic marine acquisitions (2008)

Total Nigeria has implemented a new approach to infill management by leveraging the power of interpolation available during processing and availability of steerable streamers to obtain more cost effective 3D seismic marine acquisitions. The paper covers an optimization to 3D seismic infill strategy, leveraging the power of trace interpolation at processing, loss of high frequencies with increasing offset. After having shown the methodology/strategy implemented, the relevance of the power of interpolation at processing, the optimization of infill rate and the cost saving will be illustrated through an example such as EGINA 3D HD survey located in the Deep Offshore Nigerian waters.
A sham-controlled, phase II trial of transcranial direct current stimulation for the treatment of central pain in traumatic spinal cord injury (2006)

Past evidence has shown that motor cortical stimulation with invasive and non-invasive brain stimulation is effective to relieve central pain. Here we aimed to study the effects of another, very safe technique of non-invasive brain stimulation--transcranial direct current stimulation (tDCS)--on pain control in patients with central pain due to traumatic spinal cord injury. Patients were randomized to receive sham or active motor tDCS (2mA, 20 min for 5 consecutive days). A blinded evaluator rated the pain using the visual analogue scale for pain, Clinician Global Impression and Patient Global Assessment. Safety was assessed with a neuropsychological battery and confounders with the evaluation of depression and anxiety changes. There was a significant pain improvement after active anodal stimulation of the motor cortex, but not after sham stimulation. These results were not confounded by depression or anxiety changes. Furthermore, cognitive performance was not significantly changed throughout the trial in both treatment groups. The results of our study suggest that this new approach of cortical stimulation can be effective to control pain in patients with spinal cord lesion. We discuss potential mechanisms for pain amelioration after tDCS, such as a secondary modulation of thalamic nuclei activity.