gebhart/patrepeval huggingface dataset:
EpiCombFlu: exploring known influenza epitopes and their combination to design a universal influenza vaccine (2013)

Abstract Motivation: Influenza is responsible for half a million deaths annually, and vaccination is the best preventive measure against this pervasive health problem. Influenza vaccines developed from surveillance data of each season are strain-specific, and therefore, are unable to provide protection against pandemic strains arising from antigenic shift and drift. Seasonal epidemics and occasional pandemics of influenza have created a need for a universal influenza vaccine (UIV). Researchers have shown that a combination of conserved epitopes has the potential to be used as a UIV. Result: In the present work, available data on strains, proteins, epitopes and their associated information were used to develop a Web resource, ‘EpiCombFlu’, which can explore different influenza epitopes and their combinations for conservation among different strains, population coverage and immune response for vaccine design. Forward selection algorithm was implemented in EpiCombFlu to select optimum combination of epitopes that may be expressed and evaluated as potential UIV. Availability: The Web resource is freely available at http://117.211.115.67/influenza/home.html. Contact: chittaranjan.rout@juit.ac.in Supplementary information: Supplementary data are available at Bioinformatics online.
Phosphorylation of the RSRSP stretch is critical for splicing regulation by RNA-Binding Motif Protein 20 (RBM20) through nuclear localization (2018)

RBM20 is a major regulator of heart-specific alternative pre-mRNA splicing of TTN encoding a giant sarcomeric protein titin. Mutation in RBM20 is linked to autosomal-dominant familial dilated cardiomyopathy (DCM), yet most of the RBM20 missense mutations in familial and sporadic cases were mapped to an RSRSP stretch in an arginine/serine-rich region of which function remains unknown. In the present study, we identified an R634W missense mutation within the stretch and a G1031X nonsense mutation in cohorts of DCM patients. We demonstrate that the two serine residues in the RSRSP stretch are constitutively phosphorylated and mutations in the stretch disturb nuclear localization of RBM20. Rbm20 <sup>S637A</sup> knock-in mouse mimicking an S635A mutation reported in a familial case showed a remarkable effect on titin isoform expression like in a patient carrying the mutation. These results revealed the function of the RSRSP stretch as a critical part of a nuclear localization signal and offer the Rbm20 <sup>S637A</sup> mouse as a good model for in vivo study.
A SURVEY OF COMPOUNDS FOR RADIATION PROTECTION (1962)

Issued by School of Aerospace Medicine, Brooks AFB, Tex. Results are presented for 1200 compounds tested before January 1, 1961, that exhibit prophylactic or therapeutic effectiveness against radiation injury. The toxicity of each compound is also presented. (N.W.R.)
Monoallelic BUB1B mutations and defective mitotic‐spindle checkpoint in seven families with premature chromatid separation (PCS) syndrome (2006)

Cancer-prone syndrome of premature chromatid separation (PCS syndrome) with mosaic variegated aneuploidy (MVA) is a rare autosomal recessive disorder characterized by growth retardation, microcephaly, childhood cancer, premature chromatid separation of all chromosomes, and mosaicism for various trisomies and monosomies. Biallelic BUB1B mutations were recently reported in five of eight families with MVA syndrome (probably identical to the PCS syndrome). We here describe molecular analysis of BUB1B (encoding BubR1) in seven Japanese families with the PCS syndrome. Monoallelic BUB1B mutations were found in all seven families studied: a single-base deletion (1833delT) in four families; and a splice site mutation, a nonsense mutation, and a missense mutation in one family each. Transcripts derived from the patients with the 1833delT mutation and the splice site mutation were significantly reduced, probably due to nonsense-mediated mRNA decay. No mutation was found in the second alleles in the seven families studied, but RT-PCR of BUB1B and Western blot analysis of BubR1 indicated a modest decrease of their transcripts. BubR1 in the cells from two patients showed both reduced protein expression and diminished kinetochore localization. Their expression level of p55cdc, a specific activator of anaphase-promoting complex, was normal but its kinetochore association was abolished. Microcell-mediated transfer of chromosome 15 (containing BUB1B) into the cells restored normal BubR1 levels, kinetochore localization of p55cdc, and the normal responses to colcemid treatment. These findings indicate the involvement of BubR1 in p55cdc-mediated mitotic checkpoint signaling, and suggest that >50% decrease in expression (or activity) of BubR1 is involved in the PCS syndrome.
Two Polymerizable Derivatives of 2,2‘-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (2005)

[structure: see text] A versatile strategy for the synthesis of polymerizable derivatives of the redox-active indicator dye 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) is reported. Two products are shown to illustrate how the final step in the synthetic strategy can be used to alter the physical properties of the product. Both products were characterized spectroscopically and electrochemically. The hydrophilic monomer (sABTS) was polymerized, and the utility of this polymer (polyABTS) is demonstrated in the context of bioelectrocatalysis.
Motion vector refinement for frame rate up conversion on 3D video (2013)

With the rapid development of digital video technology, frame rate up conversion is widely used. In this paper, a novel motion vector refinement method for frame rate up conversion on depth based 3D video is proposed. Our method involves two major stages in frame rate up conversion which are motion estimation and motion vector filtering. In the motion estimation process, the depth constraint to block matching algorithm is introduced in the bi-directional motion estimation method to obtain the motion vectors. In the motion vector filtering process, a depth-guided filter is designed to enhance the consistence of motions in the same depth plane. The refined motion vectors are used for frame interpolation. Experimental results show that the proposed method achieves 0.45 dB gain in terms of PSNR on average and improves the visual quality of the frame rate up-converted video.
The membrane-associated and secreted forms of the respiratory syncytial virus attachment glycoprotein G are synthesized from alternative initiation codons (1994)

Respiratory syncytial (RS) virus synthesizes two mature forms of its attachment glycoprotein G: an anchored type II integral membrane form and a smaller form that is secreted into the medium. Here we demonstrate that these two forms are synthesized as distinct primary translation products of a single species of G protein mRNA by initiation at either of two different AUGs. Mutant cDNAs which eliminated one of the other of the two AUG codons near the 5' end of the G gene open reading frame were constructed. Analysis of the proteins synthesized from these cDNAs, either by translation of transcripts in a cell-free system or in cells infected with recombinant vaccinia viruses containing either one of the mutant cDNAs, showed that elimination of either the first or the second of these AUG codons abrogated the synthesis of the membrane-anchored or the secreted form of the protein, respectively. Additionally, two unglycosylated forms of G protein which comigrated with the unglycosylated G proteins expressed by these recombinant viruses were detected in RS virus-infected cells. Since the second AUG encodes a methionine residue that lies near the middle of the signal/anchor domain, initiation at this codon resulted in a protein with a hydrophobic amino terminus. This form of the glycoprotein was efficiently secreted from cells infected with the vaccinia virus recombinant, and the amino-terminal sequence of this protein was identical to that of G protein secreted from RS virus-infected cells. Our results demonstrate that the secreted form of RS virus G protein is produced by initiation at the second AUG codon of the G open reading frame, followed by proteolytic removal of the signal/anchor domain.
Biologic therapy for psoriasis: a brief history, I. (2001)

This article, the second in a 2-part series, will review interleukin 10 (IL-10) administration, the T-cell receptor mimic peptide, and CTLA4Ig. We also will review 4 of the most promising therapies currently being investigated for the treatment of psoriasis: infliximab, etanercept, efalizumab, and alefacept.
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling (2005)

The Gibbs sampling method has been widely used for sequence analysis after it was successfully applied to the problem of identifying regulatory motif sequences upstream of genes. Since then, numerous variants of the original idea have emerged: however, in all cases the application has been to finding short motifs in collections of short sequences (typically less than 100 nucleotides long). In this paper, we introduce a Gibbs sampling approach for identifying genes in multiple large genomic sequences up to hundreds of kilobases long. This approach leverages the evolutionary relationships between the sequences to improve the gene predictions, without explicitly aligning the sequences. We have applied our method to the analysis of genomic sequence from 14 genomic regions, totaling roughly 1.8 Mb of sequence in each organism. We show that our approach compares favorably with existing ab initio approaches to gene finding, including pairwise comparison based gene prediction methods which make explicit use of alignments. Furthermore, excellent performance can be obtained with as little as four organisms, and the method overcomes a number of difficulties of previous comparison based gene finding approaches: it is robust with respect to genomic rearrangements, can work with draft sequence, and is fast (linear in the number and length of the sequences). It can also be seamlessly integrated with Gibbs sampling motif detection methods.
Measurement and Determination of Friction Characteristic of Air Flow through Porous Media (2015)

Sintered metal porous media currently plays an important role in air bearing systems. When flowing through porous media, the flow properties are generally represented by incompressible Darcy-Forchheimer regime or Ergun regime. In this study, a modified Ergun equation, which includes air compressibility effects, is developed to describe friction characteristic. Experimental and theoretical investigations on friction characteristic are conducted with a series of metal-sintered porous media. Re = 10 is selected as the boundary for a viscous drag region and a form drag region. Experimental data are first used to determine the coefficient α in the viscous drag region, and then the coefficient β in the form drag region, rather than both simultaneously. Also, the theoretical mass flow rate in terms of the modified Ergun equation provides close approximations to the experimental data. Finally, it is also known that both the air compressibility and inertial effects can obviously enhance the pressure drop.
Sodium fluxes in human fibroblasts: Effect of serum, Ca+2, and amiloride (1981)

Human fibroblasts that have been serum deprived for 4 hours have a digitoxin-insensitive Na influx of 9.5 +/- 1.0 (n = 4) mumol/g prot/min which is not significantly different from the influx of 9.4 +/- 0.6 (n = 3) mumol/g prot/min measured in cells arrested in the G1/G0 state by serum-deprivation for a period of four days. The Na influx in serum-deprived cells is rapidly stimulated (within one minute) simply by assaying the cells in medium containing 10% fetal bovine serum (FBS). The digitoxin-insensitive NA influx for cells in the presence of 10% FBS is 22.9 +/- 1.1 (n = 6) mumol/g prot/min. The stimulation of Na influx in serum-deprived cells can also be achieved by the addition of the purified mitogen, epidermal growth factor (EGF). Addition of EGF to serum-deprived cells gives a maximal stimulation of Na influx of approximately 1.6-fold, with the concentration for half-maximal stimulation being 7.5 ng/ml. The stimulation of Na influx results from the activation of an amiloride-sensitive pathway, which appears to be minimally active in serum-deprived cells. Kinetic analysis of Na influx experiments in the presence of 10% FBS and varying concentrations of amiloride indicate that at infinite concentrations of amiloride the Na flux would be reduced to 8.9 mumol/g prot/min, which is comparable to the level of Na flux measured in serum-deprived cells in the presence of 5 mM amiloride. Thus, amiloride can totally inhibit the serum-stimulated component of Na influx while inhibiting less than 10% of the Na influx in serum-deprived cells. The Na influx in serum-deprived cells can also be stimulated 2.5-fold by preincubating cells in the presence of the Ca+ ionophore A23187 to elevate the intracellular Ca content. This stimulation of Na influx by intracellular Ca+2 can be virtually eliminated by adding 1 mM amiloride.
Pharmacodynamics and pharmacokinetics of intramuscular dexmedetomidine (1992)

The pharmacodynamics and pharmacokinetics of intramuscular dexmedetomidine--a novel alpha 2-adrenergic receptor agonist under development for preanesthetic use--were studied in healthy male volunteers. Single intramuscular doses of dexmedetomidine (0.5, 1.0, and 1.5 microgram/kg) and placebo were administered to six subjects in a single-blind, multiple crossover study. Dexmedetomidine induced dose-related impairment of vigilance assessed both objectively and subjectively. The drug also caused moderate decreases in blood pressure and heart rate. Plasma norepinephrine was dose-dependently (maximum 89%) decreased. The intramuscular doses resulted in linearly dose-related plasma concentrations of dexmedetomidine. Pharmacokinetic calculations revealed a time to maximum concentration from 1.6 to 1.7 hours, an elimination half-life of 1.6 to 2.4 hours, an apparent total plasma clearance of 0.7 to 0.9 L/hr/kg, and apparent volume of distribution of 2.1 to 2.6 L/kg. The sedative effect of dexmedetomidine dissipated during the 6-hour observation time, but all other effects were still evident 6 hours after administration of the higher doses, paralleling the plasma concentration curves. The relationship of plasma concentrations of dexmedetomidine to pharmacodynamic variables was consistent with a linear pharmacodynamic model. The pharmacodynamic-pharmacokinetic profile of intramuscular dexmedetomidine may be suited to the proposed preanesthetic clinical use of this alpha 2-agonist.
Characterization of Monoclonal Antibodies Directed to the Amino-Terminus of the WT1, Wilms' Tumor Suppressor Protein (1998)

We have produced and characterized three monoclonal antibodies (MAbs) directed to the amino terminus of the WT1 Wilms' tumor suppressor transcription factor and compared their properties to rabbit polyclonal sera raised to the same immunogen. A recombinant protein consisting of amino acids 1-181 of human WT1 was overexpressed in E. coli, purified, and used as the immunogen. Three MAbs designated 6F-H2, 6F-H7, and 6F-HC-17--all of the IgG1 subclass--were selected and further characterized. Each recognized all isoforms of the full-length WT1 protein in Western blot assays and immunoprecipitated WT1 in both physiologic buffers and under high detergent/high salt (RIPA) conditions. Preliminary epitope mapping suggests that all three MAbs recognize a region in the amino terminal 84 amino acids of WT1 and that the MAbs do not recognize the polyglycine or polyproline regions of the protein. The WT1 antibodies do not recognize the structurally and functionally related early growth response (EGR)1, EGR2, EGR3, or EGR4 proteins. All WT1 MAbs recognize the murine WT1 protein and immunohistochemical staining of murine embryonic and newborn kidney sections show strong staining of condensing metanephric mesenchyme and primitive podocytes in developing glomeruli. These WT1-specific MAbs should be useful in characterizing the biochemical and developmental roles of WT1 and in defining the emerging role of WT1 as a diagnostic and/or prognostic marker in mesothelioma, leukemias, and breast cancer.
The effects of probiotic supplementation on the content of intestinal microflora and chemical composition of worker honey bees (Apis mellifera) (2005)

SUMMARYTwo probiotics, Biogen-N and Trilac, were used as supplements to pollen substitute in feeding honey bees, Apis mellifera. The probiotics were given either throughout the entire 14-day experiment or only for 2 days, just after bee emergence. The midgut of worker bees was colonized by bacteria present in probiotics, including Lactobacillus spp., Pediococcus acidilactici, Bifidobacterium bifidum and Enterococcus faecium. Advantages of probiotic supplementation include better bee survival and higher dry mass and crude fat level in comparison with bees fed with pollen substitute only. We did not observe significant differences in total protein in the dry mass of bees. There was no correlation between the duration of feeding with probiotics and the chemical composition of the bees. This suggests that to achieve an increase in dry mass and crude fat level, it is sufficient to supply probiotics only in the beginning of the feeding period, directly after bee emergence.Keywords: Apis melliferafeedingpollen substituteprobiotics
Isolation and structure determination of two new analogs of teicoplanin, a glycopeptide antibiotic. (1989)

Teicoplanin is an antibiotic produced by fermentation of Actinoplanes teichomyceticus as a complex formed by five closely related glycopeptides characterized by different fatty acid chains of ten and eleven carbon atoms. In addition, minor quantities of related substances are present. Two of them, named RS-1 and RS-2, were shown to be teicoplanins having as fatty acid chains 10-methylundecanoic acid and n-dodecanoic acid, respectively. Other two related substances, named RS-3 and RS-4, have now been isolated and purified starting from fermentation broths of a mutant of the same microorganism producing them in substantial amounts. This was achieved by semipreparative reversed-phase liquid chromatography carried out on high-pressure scale. The structures were assigned on the basis of 1H NMR spectra and homonuclear COSY 2D experiments and fast atom bombardment MS spectrometry, in comparison with the large mass of data till now accumulated on teicoplanin. RS-3 and RS-4 are teicoplanins having as fatty acid chains 6-methyloctanoic acid and n-nonanoic acid, respectively.
Translation lookaside buffer consistency: a software approach (1989)

We discuss the translation lookaside buffer (TLB) consistency problem for multiprocessors, and introduce the Mach shootdown algorithm for maintaining TLB consistency in software. This algorithm has been implemented on several multiprocessors, and is in regular production use. Performance evaluations establish the basic costs of the algorithm and show that it has minimal impact on application performance. As a result, TLB consistency does not pose an insurmountable obstacle to multiprocessors with several hundred processors. We also discuss hardware support options for TLB consistency ranging from a minor interrupt structure modification to complete hardware implementations. Features are identified in current hardware that compound the TLB consistency problem; removal or correction of these features can simplify and/or reduce the overhead of maintaining TLB consistency in software.
The E1 protein of bovine papilloma virus 1 is an ATP-dependent DNA helicase. (1993)

For efficient DNA replication of papillomaviruses, only two viral-encoded proteins, E1 and E2, are required. Other proteins and factors are provided by the host cell. E2 is an enhancer of both transcription and replication and is known to help E1 bind cooperatively to the origin of DNA replication. E1 is sufficient for replication in extracts prepared from permissive cells, but the activity is enhanced by E2. Here we show that purified E1 can act as an ATP-dependent DNA helicase. To measure this activity, we have used strand displacement, unwinding of topologically constrained DNA, denaturation of duplex fragments, and electron microscopy. The ability of E1 to unwind circular DNA is found to be independent of origin-specific viral DNA sequences under a variety of experimental conditions. In unfractionated cellular extracts, E1-dependent viral DNA replication is origin-dependent, but at elevated E1 concentrations, replication can occur on non-origin-containing DNA templates. This conversion from an origin-dependent replication system to a nonspecific initiator system is discussed in the context of the current understanding of the initiation of chromosomal DNA replication.
Neurospora crassa clock-controlled genes are regulated at the level of transcription. (1991)

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.
Sensitivity of CaM Kinase II to the Frequency of Ca 2+ Oscillations (1998)

The transduction of many cellular stimuli results in oscillations in the intracellular concentration of calcium ions (Ca2+). Although information is thought to be encoded in the frequency of such oscillations, no frequency decoder has been identified. Rapid superfusion of immobilized Ca2+- and calmodulin-dependent protein kinase II (CaM kinase II) in vitro showed that the enzyme can decode the frequency of Ca2+ spikes into distinct amounts of kinase activity. The frequency response of CaM kinase II was modulated by several factors, including the amplitude and duration of individual spikes as well as the subunit composition and previous state of activation of the kinase. These features should provide specificity in the activation of this multifunctional enzyme by distinct cellular stimuli and may underlie its pivotal role in activity-dependent forms of synaptic plasticity.