gebhart/patrepeval huggingface dataset:
Human Immunodeficiency Virus Type 1envClones from Acute and Early Subtype B Infections for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies (2005)

Induction of broadly cross-reactive neutralizing antibodies is a high priority for AIDS vaccine development but one that has proven difficult to be achieved. While most immunogens generate antibodies that neutralize a subset of T-cell-line-adapted strains of human immunodeficiency virus type 1 (HIV-1), none so far have generated a potent, broadly cross-reactive response against primary isolates of the virus. Even small increments in immunogen improvement leading to increases in neutralizing antibody titers and cross-neutralizing activity would accelerate vaccine development; however, a lack of uniformity in target strains used by different investigators to assess cross-neutralization has made the comparison of vaccine-induced antibody responses difficult. Thus, there is an urgent need to establish standard panels of HIV-1 reference strains for wide distribution. To facilitate this, full-length gp160 genes were cloned from acute and early subtype B infections and characterized for use as reference reagents to assess neutralizing antibodies against clade B HIV-1. Individual gp160 clones were screened for infectivity as Env-pseudotyped viruses in a luciferase reporter gene assay in JC53-BL (TZM-bl) cells. Functional env clones were sequenced and their neutralization phenotypes characterized by using soluble CD4, monoclonal antibodies, and serum samples from infected individuals and noninfected recipients of a recombinant gp120 vaccine. Env clones from 12 R5 primary HIV-1 isolates were selected that were not unusually sensitive or resistant to neutralization and comprised a wide spectrum of genetic, antigenic, and geographic diversity. These reference reagents will facilitate proficiency testing and other validation efforts aimed at improving assay performance across laboratories and can be used for standardized assessments of vaccine-elicited neutralizing antibodies.
Localization of Nitric-oxide Synthase in Plant Peroxisomes (1999)

The presence of nitric-oxide synthase (NOS) in peroxisomes from leaves of pea plants (Pisum sativum L.) was studied. Plant organelles were purified by differential and sucrose density gradient centrifugation. In purified intact peroxisomes a Ca(2+)-dependent NOS activity of 5.61 nmol of L-[(3)H]citrulline mg(-1) protein min(-1) was measured while no activity was detected in mitochondria. The peroxisomal NOS activity was clearly inhibited (60-90%) by different well characterized inhibitors of mammalian NO synthases. The immunoblot analysis of peroxisomes with a polyclonal antibody against the C terminus region of murine iNOS revealed an immunoreactive protein of 130 kDa. Electron microscopy immunogold-labeling confirmed the subcellular localization of NOS in the matrix of peroxisomes as well as in chloroplasts. The presence of NOS in peroxisomes suggests that these oxidative organelles are a cellular source of nitric oxide (NO) and implies new roles for peroxisomes in the cellular signal transduction mechanisms.
Synthesis and enzymatic properties of deoxyribooligonucleotides containing methyl and phenylphosphonate linkages (1979)

Chemical methods for the synthesis of short deoxyribooligonucleotides containing methyl and phenylphosphonodiester linkages have been developed. The interaction of two such nonionic dinucleotide analogs, T(pCH3)T and T(pC6H5)T, with several enzymes has been investigated. Because of the phosphonate linkage each dinucleotide exists as a diastereomeric pair as shown by thin layer chromatography and enzymatic studies. Both isomers of each dinucleotide can be phosphorylated by T4-polynucleotide kinase in the presence of [gamma-32P]ATP. Only one of the diastereoisomers of each dinucleotide is slowly hydrolyzed by snake venom phosphodiesterase and acts as an inhibitor of the enzyme-catalyzed hydrolysis of 5'-labeled oligothymidylic acid. Both isomers of each dinucleotide analog are completely resistant to hydrolysis by spleen phosphodiesterase.
Light-extraction mechanisms in high-efficiency surface-textured light-emitting diodes (2002)

We present a detailed quantitative analysis of the light extraction and loss mechanisms in high-efficiency GaAs-AlGaAs surface-textured thin-film light-emitting diodes (LEDs). The analysis is based on a Monte Carlo simulation. Most input parameters, including scattering of photons at the textured surface, sub-bandgap absorption, and absorption at the metal mirror are obtained from experiments or from literature. The simulation also takes into account the effect of photon recycling and the realistic geometry of the diodes. The only remaining fitting parameter is the internal quantum efficiency, which is deduced to be about 80% at room temperature for the experimentally realized 850-nm LEDs with an external quantum efficiency of 44%. The analysis shows further that the most important loss mechanism is reabsorption in the active layer, and in particular in those parts of the active layer that are not electrically pumped. This conclusion is also valid for other types of high-efficiency LEDs. We could furthermore verify the validity of the Monte-Carlo simulation results by conducting experiments at low temperatures, where nonradiative recombination processes are reduced, resulting in the internal quantum efficiency approaching unity. The measured external quantum efficiency at 90 K is 68%, which is close to the theoretically predicted efficiency for a perfect active layer. The results demonstrate that the light extraction from surface-textured LEDs is fully understood and can be quantitatively modeled by a simple raytracing algorithm.
Fungal infections in neutropenia: current problems and chemotherapeutic control (1998)

Invasive fungal infection is a significant problem in neutropenic individuals. The commonest causes of infection are Aspergillus and Candida spp., although a growing number of other organisms (including species of Fusarium and Trichosporon) have been implicated. The clinical manifestations of these infections are described here, and diagnostic problems are discussed. The role of lipid-based formulations of amphotericin B, and of the triazole compounds, itraconazole and fluconazole, in the treatment and prevention of fungal infection is discussed.
A versatile metal–organic framework for carbon dioxide capture and cooperative catalysis (2012)

A multi-functional MOF was constructed from Cu paddlewheel motifs and a judiciously designed novel ligand bearing carboxylate, pyridine, and amide groups. exhibits selective adsorption of CO(2) over CH(4) and excellent catalytic activity in a tandem one-pot deacetalization-Knoevenagel condensation reaction as a cooperative catalyst.
Long-Term Protection of Retinal Structure but Not Function Using RAAV.CNTF in Animal Models of Retinitis Pigmentosa (2001)

The present study aimed to determine whether intravitreal administration of an adeno-associated virus (AAV) carrying ciliary neurotrophic factor (CNTF) can achieve long-term morphological and physiological rescue of photoreceptors in animal models of retinitis pigmentosa, and whether injection of this virus after degeneration begins is effective in protecting the remaining photoreceptors. We injected rAAV.CNTF.GFP intravitreally in early postnatal Prph2(Rd2/Rd2) (formerly rds/rds) mice and in adult P23H and S334ter rhodopsin transgenic rats. Contralateral eyes received an intravitreal injection of rAAV.GFP or a sham injection. We evaluated the eyes at 6 months (rats) and 8.5 to 9 months (mice) postinfection and looked for histological and electoretinographic (ERG) evidence of photoreceptor rescue and CNTF-GFP expression. Intravitreal administration of rAAV resulted in efficient transduction of retinal ganglion cells in the Prph2(Rd2/Rd2) retina, and ganglion, Muller, and horizontal/amacrine cells in the mutant rat retinas. Transgene expression localized to the retinal region closest to the injection site. We observed prominent morphological protection of photoreceptors in the eyes of all animals receiving rAAV.CNTF.GFP. We found the greatest protection in regions most distant from the CNTF-GFP-expressing cells. The Prph2(Rd2/Rd2) ERGs did not exhibit interocular differences. Eyes of the rat models administered rAAV.CNTF.GFP had lower ERG amplitudes than those receiving rAAV.GFP. The discordance of functional and structural results, especially in the rat models, points to the need for a greater understanding of the mechanism of action of CNTF before human application can be considered.
Metabolism of the Hydroxyethylrutosides III. The Fate of Orally Administered Hydroxyethylrutosides in Laboratory Animals; Metabolism by Rat Intestinal Microflorain vitro (1974)

1. The absorption, metabolism and excretion of hydroxyethylrutosides in rat and other mammals have been studied. Following oral administration to rats of 3′,4′,7-tri-O-(β-hydroxyethyl)rutoside, 4′,7-di-O-(β-hydroxyethyl)ruto-side and 7-O-(β-hydroxyethyl)rutoside, significant levels of the administered compounds and their conjugates in bile were observed, but 3′,4′,5,7-tetra-O-(β-hydroxyethyl)rutoside was poorly absorbed. The major portion of the dose of each rutoside was excreted as the aglycone in faeces. Urinary excretion of all rutosides was low.2. Levels of excretion of 14C in the urine of rabbits and rhesus monkeys given 3′,4′,7-tri-O-(β-hydroxy[14C2]ethyl)rutoside and 3′,4′,5,7-tetra-O-(β-hydroxy[14C2]ethyl)rutoside were similar (<2.5% of dose) to those observed in the rat.3. The hydroxyethylrutosides and rutin are degraded to their aglycones by the rat intestinal microflora both in vivo and in vitro. The B rings of rutin and 7-O-(β-hydroxyethyl)rutoside give rise to the same phenolic acid metabolites. Mono-O-(β-hydroxyethyl)phloroglucinol is formed from the A ring of 7-O-(β-hydroxyethyl)rutoside. Excretion of these metabolites in urine is suppressed by concurrent administration of neomycin.4. 3′,4′,7-Tri-O-(β-hydrcxyethyl)rutoside did not undergo cleavage to metabolites other than the aglycone after continuous administration to rats for periods of up to 5 months.
Interactions of human mannose-binding protein with lipoteichoic acids (1996)

We explored the interaction of human recombinant mannose-binding protein and lipoteichoic acids (LTAs) by enzyme-linked immunosorbent assay. The best ligand was Micrococcus luteus lipomannan, followed by Enterococcus spp. LTA containing mono-, di-, and oligoglucosyl substituents. LTAs lacking terminal sugars (those of Streptococcus pyogenes and Staphylococcus aureus) or containing galactosyl substituents (those of Listeria spp. and Lactococcus spp.) were poor ligands. These results are consistent with known structural requirements for binding through the mannose-binding protein carbohydrate recognition domain.
An Unstable Triplet Repeat in a Gene Related to Myotonic Muscular Dystrophy (1992)

Synthetic oligonucleotides containing GC-rich triplet sequences were used in a scanning strategy to identify unstable genetic sequences at the myotonic dystrophy (DM) locus. A highly polymorphic GCT repeat was identified and found to be unstable, with an increased number of repeats occurring in DM patients. In the case of severe congenital DM, the paternal triplet allele was inherited unaltered while the maternal, DM-associated allele was unstable. These studies suggest that the mutational mechanism leading to DM is triplet amplification, similar to that occurring in the fragile X syndrome. The triplet repeat sequence is within a gene (to be referred to as myotonin-protein kinase), which has a sequence similar to protein kinases.
Synthetic Salmonella-type lipid A antigen with high serological specificity (1986)

A synthetic compound (compound 516), beta(1-6)-linked D-glucosamine disaccharide 1,4'-bisphosphate, which is acylated by (R)-3-hexadecanoyloxytetradecanoyl, (R)-3-hydroxytetradecanoyl, (R)-3-dodecanoyloxytetradecanoyl, and (R)-3-tetradecanoyloxytetradecanoyl groups at positions 2,3,2', and 3', respectively, exhibited in vitro antigenic reactivity of high specificity comparable to that of free lipid A from Salmonella minnesota R595. This was confirmed by an enzyme-linked immunosorbent assay and an enzyme-linked immunosorbent assay inhibition test with monoclonal and conventional antibodies. The results of comparative analysis performed with several synthetic lipid A analogs as well as three monosaccharide derivatives suggested that the complete structure involving both phosphate groups at the C-1 and C-4' positions and the 3-acyloxyacyl groups at the C-2, C-2', and C-3' positions of the glucosamine disaccharide are required for the expression of the serological specificity of Salmonella-type lipid A. This was deduced from the observations that compound 506, a synthetic Escherichia coli-type lipid A which has the same structure as that of compound 516, except that 3-hydroxytetradecanoyl group is substituted for an acyloxyacyl residue at the C-2 position, exhibited significantly reduced antigenic reactivity as compared with compound 516 and that the replacement by the hydrogen atom of the phosphoryl group at the C-1 position or by 3-hydroxytetradecanoyl or tetradecanoyl groups of acyl residues at the 2, 3, 2', and 3' positions of compound 516 results in a marked reduction of reactivity with monoclonal antibodies 5G and 36G. Similar results were obtained by assays with conventional rabbit antibodies, but the structural difference between compounds 516 and 506 could not be distinguished by these polyclonal antibodies. The results of cross-reactions among synthetic analogs with monoclonal antibodies 161M and 1-9M, which have been confirmed to exhibit different serological specificities from the 5G or 36G antibody, also suggested that the nature and linkage of fatty acyl residues as well as the backbone structure of lipid A play an important role in determining serological specificity of the lipid A molecule.
Characterization of a new member of the human /-adaptin gene family from chromosome 22q12, a candidate meningioma gene (1994)

A 140 kb homozygous deletion from 22q12 in one meningioma directed us towards the cloning and characterization of a new member of the human beta-adaptin gene family (named BAM22). Adaptins are essential for the formation of clathrin coated vesicles in the course of intracellular transport of receptor-ligand complexes. The BAM22 gene is totally inactivated in the tumor with homozygous deletion. Northern blot analysis of 70 sporadic meningiomas showed specific loss of expression in 8 tumors, suggesting inactivation of BAM22. Based on this, we propose BAM22 as a second chromosome 22 locus important in meningioma development, after the neurofibromatosis type 2 gene.
Strong and Regulated Expression of Escherichia coli β-Galactosidase in Insect Cells with a Baculovirus Vector (1984)

The N-terminal region of the gene encoding polyhedrin, the major occlusion protein of the insect baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV), has been fused to DNA encoding Escherichia coli beta-galactosidase. The fused gene was inserted into the AcNPV DNA genome by cotransfection of insect cells with recombinant plasmid DNA and wild-type AcNPV genomic DNA. Recombinant viruses were selected as blue plaques in the presence of a beta-galactosidase indicator, 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside. Studies of one such virus, L1GP-gal3, indicated that the synthesis of beta-galactosidase is temporally controlled beginning late (20 h) in infection after the release of infectious virus particles from the cell. By 48 h postinfection, a remarkably high level of expression is achieved. On the basis of these results, AcNPV should be a useful vector for the stable propagation and expression of passenger genes in a lepidopteran cell background. A generalized transplacement vector that facilitates the construction and selection of recombinant viruses carrying passenger genes under their own promoter control has also been developed.
Optimization of the simultaneous localization and map-building algorithm for real-time implementation (2001)

Addresses real-time implementation of the simultaneous localization and map-building (SLAM) algorithm. It presents optimal algorithms that consider the special form of the matrices and a new compressed filler that can significantly reduce the computation requirements when working in local areas or with high frequency external sensors. It is shown that by extending the standard Kalman filter models the information gained in a local area can be maintained with a cost /spl sim/O(N/sub a//sup 2/), where N/sub a/ is the number of landmarks in the local area, and then transferred to the overall map in only one iteration at full SLAM computational cost. Additional simplifications are also presented that are very close to optimal when an appropriate map representation is used. Finally the algorithms are validated with experimental results obtained with a standard vehicle running in a completely unstructured outdoor environment.
Design of pH Sensitive Binding Proteins from the Hyperthermophilic Sso7d Scaffold (2012)

We have engineered pH sensitive binding proteins for the Fc portion of human immunoglobulin G (hIgG) (hFc) using two different strategies - histidine scanning and random mutagenesis. We obtained an hFc-binding protein, Sso7d-hFc, through mutagenesis of the Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus; Sso7d-hFc was isolated from a combinatorial library of Sso7d mutants using yeast surface display. Subsequently, we identified a pH sensitive mutant, Sso7d-his-hFc, through systematic evaluation of Sso7d-hFc mutants containing single histidine substitutions. In parallel, we also developed a yeast display screening strategy to isolate a different pH sensitive hFc binder, Sso7d-ev-hFc, from a library of mutants obtained by random mutagenesis of a pool of hFc binders. In contrast to Sso7d-hFc, both Sso7d-his-hFc and Sso7d-ev-hFc have a higher binding affinity for hFc at pH 7.4 than at pH 4.5. The Sso7d-mutant hFc binders can be recombinantly expressed at high yield in E. coli and are monomeric in solution. They bind an epitope in the CH3 domain of hFc that has high sequence homology in all four hIgG isotypes (hIgG(1-4)), and recognize hIgG(1-4) as well as deglycosylated hIgG in western blotting assays. pH sensitive hFc binders are attractive candidates for use in chromatography, to achieve elution of IgG under milder pH conditions. However, the surface density of immobilized hFc binders, as well as the avidity effect arising from the multivalent interaction of dimeric hFc with the capture surface, influences the pH dependence of dissociation from the capture surface. Therefore, further studies are needed to evaluate if the Sso7d mutants identified in this study are indeed useful as affinity ligands in chromatography.
The dual-tree complex wavelet transform (2005)

The paper discusses the theory behind the dual-tree transform, shows how complex wavelets with good properties can be designed, and illustrates a range of applications in signal and image processing. The authors use the complex number symbol C in CWT to avoid confusion with the often-used acronym CWT for the (different) continuous wavelet transform. The four fundamentals, intertwined shortcomings of wavelet transform and some solutions are also discussed. Several methods for filter design are described for dual-tree CWT that demonstrates with relatively short filters, an effective invertible approximately analytic wavelet transform can indeed be implemented using the dual-tree approach.
Emotional Voice Conversion using Multitask Learning with Text-to-speech (2019)

Voice conversion (VC) is a task to transform a person's voice to different style while conserving linguistic contents. Previous state-of-the-art on VC is based on sequence-to-sequence (seq2seq) model, which could mislead linguistic information. There was an attempt to overcome it by using textual supervision, it requires explicit alignment which loses the benefit of using seq2seq model. In this paper, a voice converter using multitask learning with text-to-speech (TTS) is presented. The embedding space of seq2seq-based TTS has abundant information on the text. The role of the decoder of TTS is to convert embedding space to speech, which is same to VC. In the proposed model, the whole network is trained to minimize loss of VC and TTS. VC is expected to capture more linguistic information and to preserve training stability by multitask learning. Experiments of VC were performed on a male Korean emotional text-speech dataset, and it is shown that multitask learning is helpful to keep linguistic contents in VC.
Feasibility study of the Fab fragment of a monoclonal antibody against tissue factor as a diagnostic tool (2015)

Tissue factor (TF) is expressed strongly in various types of cancer, especially cancers that are often refractory to treatment, such as pancreatic cancer. In this study, we compared the differences in the biophysical and pharmacological properties of whole IgG and the Fab fragment of anti-human TF monoclonal antibody (1849 antibodies), in order to determine their suitability for application in the diagnosis and treatment of cancers. In the biophysical examination, we investigated the characteristics of 1849-whole IgG and 1849-Fab by SPR sensing and confocal fluorescence microscopy analysis using recombinant human TF antigen and TF-overexpressing human pancreatic cancer cell line, BxPC3, respectively. After conjugation with Alexa-Flour-647, in vivo imaging was conducted in mice bearing BxPC3 xenograft tumors. Furthermore, the distribution of the conjugates in tumors and major organs was evaluated by ex vivo study. The in vitro experiments showed that 1849 antibodies had high affinity against TF antigen. In addition, 1849-Fab showed a faster dissociation rate from the antigen than 1849-whole IgG. In mice, 1849-Fab-Alexa-Flour-647 showed rapid renal clearance and faster tumor accumulation, achieving a high contrast signal over nearby normal tissues in the early phase and enhanced tumor penetration after administration. On the other hand, 1849-whole IgG-Alexa-Flour-647 showed slow clearance from the blood and sustained high tumor accumulation. These results suggest that 1849-Fab may be a useful tool for pancreatic cancer diagnosis.
An economic way to see in the broadband dawn (passive optical network) (2003)

The author describes a passive optical network (PON) approach using TDMA (time-division multiple access) at one wavelength for telephony and TDM/WDM (time-division multiplexing/wavelength division multiplexing) at other wavelengths for broadband services such as CATV (cable TV), HDTV (high definition TV), B-ISDN (broadband integrated services digital network), and ATD. He suggests that the approach offers an attractive entry strategy for the telephone company as well as significant practical advantages for telephony. He examines passive network advantage for telephony, the low initial investment, filed practices, security, methods of upgrade to broadband, and the advantages of PONs for broadband. He presents some counter arguments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>