gebhart/patrepeval huggingface dataset:
Equine Infectious Anemia Virus Genomic Evolution in Progressor and Nonprogressor Ponies (2001)

A primary mechanism of lentivirus persistence is the ability of these viruses to evolve in response to biological and immunological selective pressures with a remarkable array of genetic and antigenic variations that constitute a perpetual natural experiment in genetic engineering. A widely accepted paradigm of lentivirus evolution is that the rate of genetic variation is correlated directly with the levels of virus replication: the greater the viral replication, the more opportunities that exist for genetic modifications and selection of viral variants. To test this hypothesis directly, we examined the patterns of equine infectious anemia virus (EIAV) envelope variation during a 2.5-year period in experimentally infected ponies that differed markedly in clinical progression and in steady-state levels of viral replication as indicated by plasma virus genomic RNA assays. The results of these comprehensive studies revealed for the first time similar extents of envelope gp90 variation in persistently infected ponies regardless of the number of disease cycles (one to six) and viremia during chronic disease. The extent of envelope variation was also independent of the apparent steady-state levels of virus replication during long-term asymptomatic infection, varying from undetectable to 10(5) genomic RNA copies per ml of plasma. In addition, the data confirmed the evolution of distinct virus populations (genomic quasispecies) associated with sequential febrile episodes during acute and chronic EIA and demonstrated for the first time ongoing envelope variation during long-term asymptomatic infections. Finally, comparison of the rates of evolution of the previously defined EIAV gp90 variable domains demonstrated distinct differences in the rates of nucleotide and amino acid sequence variation, presumably reflecting differences in the ability of different envelope domains to respond to immune or other biological selection pressures. Thus, these data suggest that EIAV variation can be associated predominantly with ongoing low levels of virus replication and selection in target tissues, even in the absence of substantial levels of plasma viremia, and that envelope variation continues during all stages of persistent infection as the virus successfully avoids clearance by host defense mechanisms.
Control of folding and binding of oligonucleotides by use of a nonnucleotide linker (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTControl of folding and binding of oligonucleotides by use of a nonnucleotide linkerManikrao Salunkhe, Taifeng Wu, and Robert L. LetsingerCite this: J. Am. Chem. Soc. 1992, 114, 23, 8768–8772Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ja00049a003https://doi.org/10.1021/ja00049a003research-articleACS PublicationsRequest reuse permissionsArticle Views544Altmetric-Citations78LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genetic Analysis of Primary and Secondary Immune Responses in the Chicken (1983)

Total agglutinin antibody titers, 2-mercaptoethanol (2-ME) sensitive, and 2-ME resistant antibody titers were determined in 561 White Plymouth Rock chicks. At 38 days of age chicks were intramuscularly injected with .25 ml packed sheep red blood cells (SRBC) and at 66 days of age with .5 ml SRBC. Antibody titers were determined on Days 0, 3, 5, 7, and 10 post-injection. Mean total titer (5.2, log2 value) was highest on Day 7 for the primary response and the secondary response peak titer (7.0) was measured on Day 5. The primary response was characterized by a very low level of 2-ME resistant antibodies. The secondary response consisted of both types of antibody. The heritability estimates indicate that selection for total antibody titer of the primary response can be based on the titer level of Day 5 postinjection (h2s = .39). For the secondary response, Days 3 (h2s = .34) and 5 (h2s = .28) postinjection can be considered. Phenotypic correlations between total antibody titers of first and second injection are not significant on Days 5, 7, and 10 post second injection. The negative relationship between primary and secondary 2-ME sensitive antibody titers in contrast with a positive relationship between primary 2-ME sensitive antibody titers and secondary 2-ME resistant antibody titers explains this result. Additive genetic correlations between total antibody titers of first and second injection tend to be quite negative on Days 5, 7, and 10 post second injection. Selection for an improved prophylactic response, therefore, appears to be not easily achieved either via selection of parameters of the primary immune response or via the secondary response.
Search for Genetic Factors Associated with Susceptibility to Multiple Sclerosis (2006)

Multiple sclerosis (MS) is a cell-mediated autoimmune disease characterized by type-1 cytokine production. Environmental and individual genetic background might influence this response particularly in cytokine gene polymorphisms. We evaluated whether polymorphisms of interleukin (IL)-10, IL-12, and tumor necrosis factor (TNF)-alpha genes, which might play a role in MS pathogenesis, are associated with MS susceptibility. Genotype frequencies for all the analyzed polymorphisms were not differently distributed between cases and controls. It is reasonable to suppose that the cytokine single-nucleotide polymorphisms (SNPs) studied must be considered against a larger genetic background involving other functional SNPs of Th1 regulator elements such as IL-21 and IL-23.
Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol. (2007)

Many N-myristoylated proteins play key roles in regulating cellular structure and function. In the previous study, we have applied the machine learning system BONSAI to predict patterns based on which positive and negative examples could be classified. Although BONSAI has helped establish 2 interesting rules regarding the requirements for N-myristoylation, the accuracy rates of these rules are not satisfactory. This paper suggests an enhancement of BONSAI by introducing an "insignificant indexing symbol" and demonstrates the efficiency of this enhancement by showing an improvement in the accuracy rates. We further examine the performance of this enhanced BONSAI by comparing the results of classification obtained the proposed method and an existing public method for the same sets of positive and negative examples.
Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion (2013)

Key Points Marrow CD8+ T-cell infiltrates may be a novel predictor of response to donor lymphocyte infusions in patients with relapsed CML. Reversal of T-cell exhaustion is tightly linked to effective antileukemia responses to donor lymphocyte infusions.
The effect of carbidopa on the pharmacokinetics of intravenously administered levodopa: The mechanism of action in the treatment of parkinsonism (1985)

The pharmacokinetics of short and long intravenous infusions of levodopa with and without concurrent oral administration of carbidopa was studied in 9 parkinsonian patients. Carbidopa reduced by 50% both the infusion rate required to produce a clinical response and the time required for plasma clearance of levodopa. Using this value for clearance, it is estimated that carbidopa doubles the bioavailability of orally administered levodopa. Carbidopa did not alter the therapeutically effective plasma concentration of levodopa, suggesting that carbidopa does not modify the so-called enzymatic blood-brain barrier. The decline of the plasma levodopa concentration was biphasic; carbidopa modestly increased half-lives of both phases. The apparent volume of distribution was not significantly altered. Carbidopa did not change the duration of the clinical response after the discontinuation of short infusions. From these observations we infer that the therapeutic effects of carbidopa can be attributed to doubling the bioavailability of orally administered levodopa and halving its plasma clearance.
A Randomized Trial Comparing Lung-Volume–Reduction Surgery with Medical Therapy for Severe Emphysema (2003)

Overall, lung-volume-reduction surgery increases the chance of improved exercise capacity but does not confer a survival advantage over medical therapy. It does yield a survival advantage for patients with both predominantly upper-lobe emphysema and low base-line exercise capacity. Patients previously reported to be at high risk and those with non-upper-lobe emphysema and high base-line exercise capacity are poor candidates for lung-volume-reduction surgery, because of increased mortality and negligible functional gain.
The peptide recognized by HLA-A68.2-restricted, squamous cell carcinoma of the lung-specific cytotoxic T lymphocytes is derived from a mutated elongation factor 2 gene. (1998)

The identification of naturally processed tumor peptides that can stimulate a tumor-specific, CTL response is crucial to the development of a vaccine-based, immunotherapeutic approach to cancer treatment. One type of cancer in which a tumor-specific, CTL response has been observed is squamous cell carcinoma of the lung. In the system investigated here, the tumor-specific CTLs are HLA-A68.2 restricted. Immunoaffinity chromatography was used to isolate the HLA-A68.2 molecules from the tumor cell line, and peptide was eluted with acid from the HLA-A68.2 molecules and subjected to three rounds of separation by reversed phase-high performance liquid chromatography (RP-HPLC). To determine which fractions contained the peptide recognized by the tumor-specific CTLs, an aliquot of each RP-HPLC fraction was added to the autologous, B-lymphoblastoid cell line, and the cells were then tested as targets for tumor-specific CTLs. After the third round of RP-HPLC, mass spectrometry was used to sequence individual peptide candidates, and a peptide with a m/z of 497 was identified as the active peptide. Collision-activated dissociation of m/z 497 allowed identification of the peptide sequence as ETVSEQSNV. With the exception of a single amino acid difference (glutamic acid versus glutamine as the sixth position in the peptide), this peptide is identical to residues 581 to 589 of elongation factor 2. The PCR was used to amplify the elongation factor 2 gene in both the tumor cells and the autologous B cell line, and DNA sequencing of the products revealed the presence of a heterozygous mutation in the tumor cells that accounts for the difference between the two peptide sequences. Although a similar analysis did not reveal the presence of the mutation in three additional lung cell carcinomas, this does not rule out the possibility that a survey of a larger population of tumor cells would reveal the presence of the mutation at a low frequency. These results demonstrate the utility of this approach for identifying tumor-specific antigens that are the targets of a CTL response.
Histology of human alveolar bone regeneration with a porous tricalcium phosphate (2001)

Porous beta-phase tricalcium phosphate particles (pTCP) (Cerasorb) were used in two patients to restore or augment alveolar bone prior to the placement of dental implants. In one patient, pTCP was used to fill a large alveolar defect in the posterior mandible after the removal of a residual cyst, and in another patient to augment the sinus floor. Biopsies were taken at the time of implant placement, 9.5 and 8 months after grafting, respectively, and processed for hard tissue histology. Goldner-stained histological sections showed considerable replacement of the bone substitute by bone and bone marrow. In the 9.5 months biopsy of the mandible, 34% of the biopsy consisted of mineralised bone tissue and 29% of remaining pTCP, while the biopsy at 8 months after sinus floor augmentation consisted of 20% mineralised bone and 44% remaining pTCP. Bone and osteoid were lying in close contact with the remaining pTCP and were also seen within the micropores of the grafted particles. Tartrate resistant-acid phosphatase (TRAP) multinuclear cells, presumably osteoclasts, were found surrounding, within and in close contact with the pTCP particles, suggesting active resorption of the bone substitute. Remodelling of immature woven bone into mature lamellar bone was also found. No histological signs of inflammation were detected. The limited data presented from these two cases suggest that this graft material, possibly by virtue of its porosity and chemical nature, may be a suitable bone substitute that can biodegrade and be replaced by new mineralising bone tissue.
Electrophysiological projections of pulvinar-lateralis posterior complex (P-LP) upon superior colliculus units in the cat. (1986)

The effect of Pulvinar-Lateral Posterior (P-LP) electrical stimulation on superior colliculus unitary responses and eye movements is analyzed in 17 encéphale isolé cats. Twelve of them were curarized. Out of a total of 190 recorded units, 117 were localized in the superior colliculus and 73 units in the Mesencephalic Reticular Formation (MRF) below the superior colliculus. Thirty eight per cent (n = 45) of the collicular units modified their discharge frequency when the ipsilateral P-LP was electrically stimulated. The current intensity thresholds of transynaptic activation had a range between 0.5 and 2.0 mA. Most of the orthodromic responses were produced by ipsilateral P-LP stimulation and were localized in the intermediate and deep layers of the superior colliculus. Three types of responses were obtained: short latency responses between 2 and 10 ms (57%); intermediate latency responses between 15 and 40 ms (29%), and long latency responses between 50 and 200 ms (14%). Thirty one per cent (n = 18) of the units recorded in the MRF responded to P-LP stimulation with 10 ms pulse-trains duration. In the MRF 3 types of responses were observed: 1) a decrease or blockade in the resting discharge during 20 to 100 ms after stimulation (20%); simple responses with a latency between 25 and 150 ms (40%), and complex responses with an early response and a latency between 15-40 ms, and a late response with a latency between 150 and 200 ms (40%).(ABSTRACT TRUNCATED AT 250 WORDS)
The reactivity of thiols and disulfides with different redox states of myoglobin. Redox and addition reactions and formation of thiyl radical intermediates. (1992)

The reactivity of several thiols, including glutathione, dihydrolipoic acid, cysteine, N-acetyl cysteine, and ergothioneine, as well as several disulfides, toward different redox states of myoglobin, mainly met-myoglobin (HX-FeIII) and ferrylmyoglobin (HX-FeIV=O), was evaluated by optical spectral analysis, product formation, and thiyl free radical generation. Only dihydrolipoic acid reduced met-myoglobin to oxy-myoglobin, whereas all the other thiols tested did not interact with met-myoglobin. Although the redox transitions involved in the former reduction were expected to yield the dihydrolipoate thiyl radical, the reaction was EPR silent. Conversely, all thiols interacted to different extent with the high oxidation state of myoglobin, i.e. ferrylmyoglobin, via two processes. First, direct electron transfer to heme iron in ferrylmyoglobin (HX-FeIV=O) with formation of met-myoglobin (HX-FeIII) or oxymyoglobin (HX-FeIIO2); the former transition was effected by all thiols except dihydrolipoate, which facilitated the latter, i.e. the formation of the two-electron reduction product of ferrylmyoglobin. Second, nucleophilic addition onto a pyrrole in ferrylmyoglobin with subsequent formation of sulfmyoglobin. The contribution of either direct electron transfer to the heme iron or nucleophilic addition depended on the physicochemical properties of the thiol involved and on the availability of H2O2 to reoxidize met-myoglobin to ferrylmyoglobin. The thiyl radicals of glutathione, cysteine, and N-acetylcysteine were formed during the interaction of the corresponding thiols with ferrylmyoglobin and detected by EPR in conjunction with the spin trap 5,5'-dimethyl-1-pyroline-N-oxide. The intensity of the EPR signal was insensitive to superoxide dismutase and it was decreased, but not suppressed, by catalase. The disulfides of glutathione and cysteine did not react with ferrylmyoglobin, but the disulfide bridge in lipoic acid interacted efficiently with the ferryl species by either reducing directly the heme iron to form met-myoglobin or adding onto a pyrrole ring to form sulfmyoglobin; either process depended on the presence or absence of catalase (to eliminate the excess of H2O2) in the reaction mixture, respectively. The biological significance of the above results is discussed in terms of the occurrence and distribution of high oxidation states of myoglobin, its specific participation in cellular injury, and its potential interaction with biologically important thiols leading to either recovery of myoglobin or generation of nonfunctional forms of the hemoprotein as sulfmyoglobin.
Dataset for the evaluation of eye detector for gaze estimation (2012)

Being able to perform eye tracking with low cost technology is the key to broaden its applications and one of the major goals for the eye tracking community nowadays. Furthermore, new datasets to evaluate the different methods are needed to reproduce the real conditions in which these algorithms work. In this paper, we present a dataset containing images of subjects with different gaze orientations as a new evaluation tool. First step in eye tracking algorithms is to detect the region of the eyes, and using the Gi4e dataset, we evaluate the best performing public Haar based classifiers under different gaze orientations to detect the eye area, proving this dataset to be a fair evaluation method.
Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation (1997)

Rhodococcus erythropolis TA421, a polychlorinated biphenyl and biphenyl degrader isolated from a termite ecosystem, has seven bphC genes expressing 2,3-dihydroxybiphenyl dioxygenase activity. R. erythropolis TA421 harbored a large and probably linear plasmid on which three (bphC2, bphC3, and bphC4) of the seven bphC genes were located. A non-biphenyl-degrading mutant, designated strain TA422, was obtained spontaneously from R. erythropolis TA421. TA422 lacked the plasmid, suggesting that the three bphC genes were involved in the degradation of biphenyl. Southern blot analyses showed that R. erythropolis TA421 and Rhodococcus globerulus P6 have a similar set of bphC genes and that the genes for biphenyl catabolism are located on plasmids of different sizes. These results indicated that the genes encoding the biphenyl catabolic pathway in Rhodococcus strains are borne on plasmids.
Theory of Semiconductor Superjunction Devices (1997)

A new theory of semiconductor devices, called “semiconductor superjunction (SJ) theory”, is presented. To overcome the trade-off relationship between breakdown voltage and on-resistance of conventional semiconductor devices, SJ devices utilize a number of alternately stacked, p- and n-type, heavily doped, thin semiconductor layers. By controlling the degree of doping and the thickness of these layers, according to the SJ theory, this structure operates as a pn junction with low on-resistance and high breakdown voltage. Analytical formulas for the ideal specific on-resistance and the ideal breakdown voltage of SJ devices are theoretically derived. Analysis based on the formulas and device simulations reveals that the on-resistance of SJ devices can be reduced to less than 10 -2 that of conventional devices.
The effect of overlying tissue on the spatial sensitivity profile of near-infrared spectroscopy (1995)

The exact volume of brain tissue interrogated in near-infrared spectroscopy (NIRS) studies of cerebral oxygenation in unknown, the inhomogeneity of the head and resulting variation in optical paths making determination of the interrogated volume difficult. In this study, the spatial sensitivity profiles in simple two-component inhomogeneous cylindrical models are predicted by Monte Carlo simulation in order to reveal the effects of the overlying tissue on the volume of tissue interrogated by NIRS. The predictions are validated by experimental measurements on solid "tissue equivalent' cylindrical phantoms. The phantom diameter is 30 mm and the thickness of the outer layer is 2 mm. The optical properties of the inner cylinder match those of adult brain white matter (mu' s1 = 6.4 mm-1 and mu' a1 = 0.02 mm-1), but those of the outer layer are changed (mu' s0 from 1.7 to 8.3 mm-1 and mu' a0 from 0.002 to 0.1 mm-1). Results show that the spatial sensitivity profile is largely confined to the outer layer at small optode spacing (< 15 degrees) and to the inner layer at large spacing (> 120 degrees). At intermediate angles, the sensitivity profiles are sensitive to the optical properties of the outer layer. A low mu' s0 or mu' a0 moves the profile toward the surface, at high mu' a0 it moves in towards the inner layer and at high mu' a0 it is similar to the homogeneous case.
Expression and activation of B-Raf kinase isoforms in human and murine leukemia cell lines. (1995)

The B-raf/c-Rmil proto-oncogene belongs to the raf/mil family of serine/threonine protein kinases. It encodes multiple protein isoforms previously shown to be expressed predominantly in neural tissues. We report here that B-Raf proteins of 95 and 72 kDa are also expressed in various human and murine hematopoietic cell lines. Their relative level of expression is variable depending on the cell line examined. The highest level of expression of p95B-raf was found in UT-7 cells, a human pluripotent cell line established from a patient with a megakaryoblastic leukemia. These cells are able to differentiate toward erythroid or myeloid lineage phenotypes in presence of erythropoietin (EPO) or granulocyte-macrophage colony-stimulating factor (GM-CSF) respectively. We show that treatment of UT-7 cells with EPO, GM-CSF or stem cell factor (SCF) rapidly induces phosphorylation of p95B-raf as indicated by a shift of electrophoretic mobility. This increase in phosphorylation is correlated with a three-fold increase of B-Raf kinase activity. B-Raf activation also increases in a dose-dependent manner in response to EPO and GM-CSF. We also show that both p95B-raf and p72B-raf can be activated by IL-3 in murine BAF-3 pro-B cells and by anti-CD3 in human Jurkat cells, respectively. These observations provide the first evidence that the B-Raf kinase is involved in signal transduction pathways regulating proliferation and differentiation of hematopoietic cells of both myeloid and lymphoid lineages.