gebhart/patrepeval huggingface dataset:
Facioscapulohumeral Muscular Dystrophy (2004)

Facioscapulohumeral muscular dystrophy (FSHD) is the third most common neuromuscular disorder after Duchenne muscular dystrophy and myotonic dystrophy. It is characterized by progressive weakness and atrophy of the facial and shoulder girdle muscles. The other muscles are also involved. Its prevalence is estimated to be 1 in 20,000.KeywordsMuscular DystrophyDuchenne Muscular DystrophyMyotonic DystrophyInclusion Body MyositisFacial WeaknessThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Fusion of Myeloma Cells with Immune Spleen Cells (1988)

Liquid nitrogen storage is the method of choice for long-term safekeeping of hybridoma cell lines. Frozen aliquots of originally isolated hybridomas provide insurance against loss of antibody production and vigor during culture. There are many variations of cell freezing methods in use. However, for freezing and recovering hybridomas and lymphoid cells in general, the protocol described in this unit is simple and has been successful.
Impact of antibody framework residue VH-71 on the stability of a humanised anti-MUC1 scFv and derived immunoenzyme (2004)

Anti-MUC1 single-chain Fv (scFv) fragments generated from the humanised antibody huHMFG1 had adequate antigen-binding properties but very poor stability irrespective of the applied linker or domain orientation. Mutagenesis of heavy-chain framework residue V(H)-71, previously described as a key residue for maintaining the CDR-H2 main-chain conformation and thus important for antigen binding, markedly stabilised the scFv while having only a minor effect on the binding affinity of the molecule. Because of its improved stability, the engineered fragment exhibited immunoreactivity with tumour cells even after 7 days of incubation in human serum at 37 degrees C. It also showed, in contrast to the wild-type scFv, a concentration-dependent binding to the target antigen when displayed on phage. When fusing the scFv to the recombinant ribonuclease rapLRI, only the fusion protein generated with the stable mutant scFv was able to kill MUC1(+) tumour cells with an IC(50) of 80 nM. We expect this novel immunoenzyme to become a promising tool for the treatment of MUC1(+) malignancies.
Tau Monoclonal Antibody Generation Based on Humanized Yeast Models (2014)

A link between Tau phosphorylation and aggregation has been shown in different models for Alzheimer disease, including yeast. We used human Tau purified from yeast models to generate new monoclonal antibodies, of which three were further characterized. The first antibody, ADx201, binds the Tau proline-rich region independently of the phosphorylation status, whereas the second, ADx215, detects an epitope formed by the Tau N terminus when Tau is not phosphorylated at Tyr(18). For the third antibody, ADx210, the binding site could not be determined because its epitope is probably conformational. All three antibodies stained tangle-like structures in different brain sections of THY-Tau22 transgenic mice and Alzheimer patients, and ADx201 and ADx210 also detected neuritic plaques in the cortex of the patient brains. In hippocampal homogenates from THY-Tau22 mice and cortex homogenates obtained from Alzheimer patients, ADx215 consistently stained specific low order Tau oligomers in diseased brain, which in size correspond to Tau dimers. ADx201 and ADx210 additionally reacted to higher order Tau oligomers and presumed prefibrillar structures in the patient samples. Our data further suggest that formation of the low order Tau oligomers marks an early disease stage that is initiated by Tau phosphorylation at N-terminal sites. Formation of higher order oligomers appears to require additional phosphorylation in the C terminus of Tau. When used to assess Tau levels in human cerebrospinal fluid, the antibodies permitted us to discriminate patients with Alzheimer disease or other dementia like vascular dementia, indicative that these antibodies hold promising diagnostic potential.
Asparaginase (native ASNase or pegylated ASNase) in the treatment of acute lymphoblastic leukemia. (2006)

The discovery of the tumor-inhibitory properties of asparaginase (ASNase) began in the early 1950s with the observation that guinea pig serum-treated lymphoma-bearing mice underwent rapid and often complete regression. About 4000 cases of acute lymphoblastic leukemia (ALL) are diagnosed very year in the US and many more through out the world. The majority of these cases are in children and young adults, making ALL the most common form of malignancy in these age groups. The treatment protocols of ALL are complex and use 6-12 drugs. Consequently, the improvement in the protocol design has improved significantly the success rate for long-term event-free survival in the past 20-30 years, which is now approximately 75% for patients afflicted with the higher risk ALL features and just above this percentage for patients with standard or good features. Despite this success, approximately 15% of patients die from ALL, making leukemic relapse the most common cause of treatment failure in pediatric oncology. ASNases have been the cornerstone of ALL therapies since the late 1970s. Native or pegylated L-asparaginase (ASNase or PEG-ASNase) are highly specific for the deamination of L-asparagine (Asn) to aspartic acid and ammonia. Depletion of Asn leads to a nutritional deprivation and inhibition of protein biosynthesis, resulting in apoptosis in T-lymphoblastic leukemias, which require Asn from external sources. The reactions of the host exposed to repeated ASNase treatments as well as the up-regulation of the mammalian enzymes to overcome the ASN-depletion toxic condition are of significant importance and may make us relearn the lessons on this important antileukemic drug.
Zero-crossing rates of mixtures and products of Gaussian processes (1998)

Formulas for the expected zero-crossing rate of non-Gaussian mixtures and products of Gaussian processes are obtained. The approach we take is to first derive the expected zero-crossing rate in discrete time and then obtain the rate in continuous time by an appropriate limiting argument. The processes considered, which are non-Gaussian but derived from Gaussian processes, serve to illustrate the variability of the zero-crossing rate in terms of the normalized autocorrelation function p(t) of the process. For Gaussian processes, Rice's formula gives the expected zero-crossing rate in continuous time as 1//spl pi//spl radic/(-/spl rho/"(0)). We show processes exist with expected zero-crossing rates given by /spl kappa///spl pi//spl radic/(-/spl rho/"(0)) with either /spl kappa//spl Gt/1 or /spl kappa//spl Lt/1. Consequently, such processes can have an arbitrarily large or small zero-crossing rate as compared to a Gaussian process with the same autocorrelation function.
IgE binding studies with large peptides expressed from Der p II cDNA constructs (1991)

The major mite allergen Der p II shows marked resistance to denaturation and is expressed from cDNA in bacteria with almost all of its IgE binding activity. Despite these properties, the IgE binding activity appears to be dependent on maintaining the complete primary structure. Random fragment libraries of cDNA, able to code for up to 93 of the 129 amino acid residue protein, did not express IgE binding peptides. Large overlapping peptides 1-69, 69-129 and 42-117 expressed as the fusions from the glutathione transferase of pGEX vectors only had binding activity with IgE in 15 out of 57 sera, and this was typically weak. Sera from children with atopic dermatitis bound IgE in seven out of eight cases but this was also weak compared with their strong reactivity to intact recombinant Der p II. The inability of such large peptides to form IgE binding structures suggests that the antigenic determinants of Der p II are highly conformational and restricted.
Endurance training and blood pressure in normotensive and hypertensive adults (1989)

Twenty-one male and female adults 43 +/- 4 yr of age completed in 8-wk control period, 16 wk of conditioning, and 12 wk of deconditioning to determine whether exercise alters blood pressure. Subjects were classified as borderline/mild hypertensive (H, diastolic pressure greater than or equal to 85 and less than 104 mm Hg, N = 8) or normotensive (N, diastolic pressure less than 85 mm Hg, N = 13) based on average blood pressure during the control period. Conditioning increased (P less than 0.05) VO2max to a similar extent in both groups (average, 14%) and decreased (P less than 0.05) resting heart rate (H, 78 +/- 5 to 65 +/- 3; N, 75 +/- 3 to 71 +/- 3 beats.min-1). The double product over 24 h of ambulatory monitoring of blood pressure and heart rate decreased (P less than 0.05) in both groups. After deconditioning, VO2max returned to values not different (P greater than 0.05) from those of the control period. Ambulatory 24-h double product and heart rate increased (P less than 0.05). In spite of this strong evidence of a conditioning effect, neither group showed changes (P greater than 0.05) in average 24-h ambulatory or casual blood pressure. The average ambulatory blood pressure for 8-h segments of the day (8 a.m.-4 p.m., 4 p.m.-12 a.m., and 12 a.m.-8 a.m.) was also not altered. Cardiac output and total peripheral resistance at rest did not change (P greater than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)
The Two Open Reading Frames of the 22K mRNA of Human Respiratory Syncytial Virus: Sequence Comparison of Antigenic Subgroups A and B and Expression in Vitro (1990)

The sequence of the 22K mRNA of strain 18537 of antigenic subgroup B of human respiratory syncytial virus (RSV) was determined by sequencing cloned cDNAs of intracellular mRNA. Comparison with the corresponding sequence of the A2 strain of subgroup A showed that there is 78% nucleotide sequence identity overall, that the amino acid sequence of the 22K protein is 92% identical between subgroups and that the 22K mRNA of both subgroups contains a second, internal, overlapping open reading frame (ORF) whose length, nucleotide sequence and potential translational start and stop sites were highly conserved and whose predicted product has 62% amino acid identity between subgroups. Sequence analysis of 36 cDNAs of intracellular 22K mRNA of strain A2 did not detect nucleotide insertions or deletions in the region of overlap between the two ORFs, indicating that the majority of intracellular 22K mRNA is a faithful copy containing the two distinct ORFs. Translation in vitro of mRNAs transcribed from engineered cDNAs showed that an mRNA which contained only the second, internal ORF directed the synthesis of a previously unidentified polypeptide of the predicted size, whereas mRNA representing the complete gene directed the synthesis of both the 22K protein and the product of the internal ORF. This latter species was synthesized in vitro as a discrete, separate protein rather than as a fusion protein. It is not yet known whether this protein is synthesized in RSV-infected cells.
Super-resolution from noisy image sequences exploiting a 2D parametric motion model (2002)

We propose a low cost scheme for reconstructing high resolution images from noisy, and eventually blurred image sequences. The super-resolution is achieved by an iterative back projection method. To account for noise in image sequence, we first apply a spatio-temporal Wiener filter computed via a 3D DFT. In the filtering process, we need to compensate for apparent motion to ensure proper results. Furthermore, the knowledge of subpixel motion is necessary for super-resolution. In both cases, we exploit a parametric motion model to keep a good trade-off between accuracy and computation time.
Affordable CD4 + -T-Cell Counting by Flow Cytometry: CD45 Gating for Volumetric Analysis (2002)

The flow cytometers that are currently supported by industry provide accurate CD4(+)-T-cell counts for monitoring human immunodeficiency virus disease but remain unaffordable for routine service work under resource-poor conditions. We therefore combined volumetric flow cytometry (measuring absolute lymphocyte counts in unit volumes of blood) and simpler protocols with generic monoclonal antibodies (MAbs) to increase cost efficiency. Volumetric absolute counts were generated using CD45/CD4 and CD45/CD8 MAb combinations in two parallel tubes. The percentage values for the various subsets were also determined within the leukocyte and lymphocyte populations utilizing a fully automated protocol. The levels of agreement between the newly developed method and the present industry standards, including both volumetric and bead-based systems using a full MAb panel for subset analysis, were tested by Bland-Altman analyses. The limits of agreement for CD4 counts generated by the volumetric methods using either CD45/CD4 (in a single tube) or the full Trio MAb panel (in three tubes) on the CytoronAbsolute flow cytometer were between -29 and +46 cells/mm(3) with very little bias for CD4 counts (in favor of the Trio method: +8 CD4(+) lymphocytes/mm(3); 0.38% of lymphocytes). The limits of agreement for absolute CD4 counts yielded by the volumetric CD45/CD4 method and the bead-based method were between -118 and +98 cells/mm(3), again with a negligible bias (-10 CD4(+) lymphocytes/mm(3)). In the volumetric method using CD45/CD8, the strongly CD8(+) cells were gated and the levels of agreement with the full Trio showed a minor bias (in favor of the Trio; +40 CD8(+) cells/mm(3); 5.2% of lymphocytes) without a significant influence on CD4/CD8 ratios. One trained flow cytometrist was able to process 300 to 400 stained tubes per day. This workload extrapolates to a throughput of >30,000 samples per year if both CD45/CD4 and CD45/CD8 stainings are performed for each patient or a throughput of >60,000 samples if only CD45/CD4 counts are tested in a single tube. Thus, on the basis of the high efficiency and excellent agreement with the present industry standards, volumetric flow cytometers with automated gating protocols and autobiosamplers, complemented by generic CD45, CD4, and CD8 MAbs used in two-color immunofluorescence, represent the most suitable arrangements for large regional laboratories in resource-poor settings.
Activation and functionalization of benzylic derivatives by palladium catalysts (2007)

Palladium-catalyzed transformations of aryl halides and pseudo-halides involving carbonylation, carbon-carbon and carbon-heteroatom bond-forming reactions, etc. are very well documented, and have already been reviewed several times. The metal-catalyzed activation of benzylic derivatives is much less described. However, during the last decades, a number of papers have shown the interest offered by benzylic derivatives (halides, carbonates, acetates, phosphonates) in selective catalytic reactions for organic synthesis, most of them in the presence of palladium catalysts. The purpose of this tutorial review is to highlight selected examples of palladium-catalyzed transformations involving reactive benzylic derivatives.
Applications of Aptamers in Targeted Imaging: State of the Art (2015)

Aptamers are single-stranded oligonucleotides with high affinity and specificity to the target molecules or cells, thus they can serve as an important category of molecular targeting ligand. Since their discovery, aptamers have been rapidly translated into clinical practice. The strong target affinity/selectivity, cost-effectivity, chemical versatility and safety of aptamers are superior to traditional peptides- or proteins-based ligands which make them unique choices for molecular imaging. Therefore, aptamers are considered to be extremely useful to guide various imaging contrast agents to the target tissues or cells for optical, magnetic resonance, nuclear, computed tomography, ultrasound and multimodality imaging. This review aims to provide an overview of aptamers' advantages as targeting ligands and their application in targeted imaging. Further research in synthesis of new types of aptamers and their conjugation with new categories of contrast agents is required to develop clinically translatable aptamer-based imaging agents which will eventually result in improved patient care.
Model Polyelectrolyte Gels Synthesized by End-Linking of Tetra-Arm Polymers with Click Chemistry: Synthesis and Mechanical Properties (2014)

A series of poly(sodium acrylate) gels was synthesized via end-linking reaction between tetra-arm poly(tert-butyl acrylate)s by copper-catalyzed azide–alkyne cycloaddition followed by deprotection of tert-butyl group and neutralization. Characterization of the gels using gravimetry, IR measurement, and stretching test revealed that they have only small amounts of sol fractions, dangling chains, and trapped entanglements. The relationship between polymer weight fraction (ϕe) and shear modulus (G′) at equilibrium swelling in saline was expressed as G′ ∝ ϕe 2.5. The power index (2.5) was comparable with the theoretical value for nonionic gels swollen in good solvents (2.3). The relationship between G′ and ϕe was superior to that of poly(sodium acrylate) gels synthesized by conventional radical copolymerization. The difference may be partly attributed to the difference in the ratio of chemical cross-links to trapped entanglements.
3-Amino-5-hydroxybenzoic Acid Synthase, the Terminal Enzyme in the Formation of the Precursor of mC7N Units in Rifamycin and Related Antibiotics (1998)

The biosynthesis of ansamycin antibiotics, like rifamycin B, involves formation of 3-amino-5-hydroxybenzoic acid (AHBA) by a novel variant of the shikimate pathway. AHBA then serves as the starter unit for the assembly of a polyketide which eventually links back to the amino group of AHBA to form the macrolactam ring. The terminal enzyme of AHBA formation, which catalyzes the aromatization of 5-deoxy-5-amino-3-dehydroshikimic acid, has been purified to homogeneity from Amycolatopsis mediterranei, the encoding gene has been cloned, sequenced, and overexpressed in Escherichia coli. The recombinant enzyme, a (His)6 fusion protein, as well as the native one, are dimers containing one molecule of pyridoxal phosphate per subunit. Mechanistic studies showed that the enzyme-bound pyridoxal phosphate forms a Schiff's base with the amino group of 5-deoxy-5-amino-3-dehydroshikimic acid and catalyzes both an alpha, beta-dehydration and a stereospecific 1,4-enolization of the substrate. Inactivation of the gene encoding AHBA synthase in the A. mediterranei genome results in loss of rifamycin formation; production of the antibiotic is restored when the mutant is supplemented with AHBA.
A New Sequencer Controller for Multistage Systems of Known Relative Capacities (2002)

Abstract This paper presents a method for controlling multistage systems where the relative capacities of each stage are known. The method, based on the split-range control concept, allows multiple stages to be controlled by a single feedback controller, such as a proportional integral (PI) controller. The method incorporates a procedure that determines combinations of stage states that provide contiguous control across the range of the multistage system. During operation, the control method selects an appropriate combination according to demand and calculates a split-range control signal that is used to regulate the output of one individual stage, either by means of a switching control law such as pulse-width modulation (PWM) or by direct modulation. In this way, the method is applicable to digital or analog multistage systems. Hysteretic dead zones are incorporated to improve robustness around points where stage combinations are changed. The paper shows how the assumption of a tuned PI feedback controller allows the size of the dead zones to be related to control performance requirements that are scalable across classes of similar systems. A simulated HVAC&R system is used to evaluate the method and compare it with alternative approaches. A test result is also presented from experiments carried out on a real two-stage DX rooftop air-conditioner.
Immunologic and structural characterization of the dominant 66- to 73-kDa antigens of Borrelia burgdorferi (1991)

The 66- to 73-kDa proteins of Borrelia burgdorferi are dominant immunogens and expressed in all strains of B. burgdorferi. The humoral response to these Ag occurs relatively early during the course of infection. Two-dimensional Western blot analysis of this group of Ag revealed them to consist of a tetrad of proteins with apparent molecular mass of 66, 68, 71, and 73 kDa. Furthermore, in this study we demonstrate the 66-kDa protein to be a potent inducer of lymphoproliferation in the patient immune to B. burgdorferi. Monospecific polyclonal antibodies and mAb demonstrate that each of these proteins was immunologically distinct. However, direct amino acid sequence of the 66- and 68-kDa Ag was almost identical and had a high level of sequence similarity to the GroEL heat-shock protein (Hsp60) of Escherichia coli and the 60-kDa immunodominant protein of Treponema pallidum. The amino terminal sequence of the 71- and 73-kDa proteins of B. burgdorferi was almost identical and these proteins had remarkable sequence similarity to the DnaK heat-shock protein of E. coli (Hsp70). It appears likely, therefore, that proteins related to the heat-shock family are potent immunogens of B. burgdorferi.
RAFT Polymerization of Vinyl Sulfonate Esters for the Controlled Synthesis of Poly(lithium vinyl sulfonate) and Sulfonated Block Copolymers (2010)

Four vinyl sulfonate ester derivatives, neopentyl ethenesulfonate (NES), 1-butyl ethenesulfonate (BES), isopropyl ethenesulfonate (IPES), and phenyl ethenesulfonate (PES), were polymerized by conventional radical polymerization and reversible addition−fragmentation chain transfer (RAFT) polymerization. Three xanthate-type chain transfer agents (CTAs), a dithiocarbamate-type CTA, and a dithioester-type CTA were compared for these RAFT polymerizations. Among various CTAs, O-ethyl-S-(1-methoxycarbonyl) ethyldithiocarbonate was the most efficient to obtain poly(NES) and poly(BES) having low polydispersities. The effects of several parameters, such as temperature and CTA to initiator molar ratio, were examined in order to determine the conditions, leading to optimal control of the polymerization. With the xanthate-type CTA under suitable conditions, reasonable control of the polymerization of NES was confirmed by the formation of the relatively low polydispersity products, linear increase in the molecular weight with the conversion, and feasibility in the control of the molecular weight based on the ratio of monomer consumed to the amount of CTA used. The polymerization behavior of BES was comparable to that of NES. Deprotection of the neopentyl group of the poly(NES) proceeded smoothly to give water-soluble poly(lithium vinyl sulfonate). Synthesis of the well-defined block copolymer involving the poly(lithium vinyl sulfonate) segment was conducted by RAFT polymerization of NES using poly(N-vinylcarbazole) macro-CTA, followed by deprotection.