gebhart/patrepeval huggingface dataset:
Inter Frame Coding with Template Matching Averaging (2007)

A template matching prediction based on a group of reconstructed pixels surrounding a target block enables prediction of pixels in the target block without motion information. The predictor of a target block is produced by minimizing the matching error of the template. Due to the freedom possessed by the template, the residuals of a target block may become large in flat regions. Our previous paper proposed to predictively encode the decimated version of a target block in flat regions to suppress the prediction errors. In this paper, the performance of template matching prediction is further improved. Multiple candidates are created by template matching at decoder. An average of the multiple candidates then forms the final predictor, which can reduce coding noise residing in the reference frames. Simulation results show that the proposed scheme improves coding efficiency of H.264 up to 7.9%.
Molecular characterization of central neurocytomas: Potential markers for tumor typing and progression (2012)

Central neurocytomas (CNs) are rare intraventricular tumors presenting a favorable prognosis after surgery. Their transcriptomic profile is poorly characterized. We performed a microarray transcriptomic study to search for molecular markers that might improve diagnostic accuracy. Microarray analysis was performed on five CNs (3 primary and 2 recurrent CNs) using CodeLink human whole genome bioarrays, and the gene expression in CNs was compared with that in four pineal parenchymal tumors, consisting of two pineocytomas (PCs) and two pineoblastomas (PBs), other periventricular tumors which may present neuronal differentiation. We identified genes that were highly expressed in CNs compared to normal brain and might be candidates for the molecular typing of CNs. Several genes are part of the Wnt/β-catenin and sonic hedgehog signaling pathways or mainly linked to calcium function or maintenance of neural progenitors. Moreover, several genes are overexpressed in both CNs and PCs and/or PBs such as INSM1 and NEUROD4, involved in neural or neuroendocrine differentiation. The overexpression of eight candidate genes in CNs (CHRDL2, IGF2, KiSS-1, CAL2, NTS, NHLH1, RGS16 and SCGN) was confirmed by real-time RT-PCR. Of the genes overexpressed in the recurrent CNs compared to the primary CNs, AQP5, KiSS-1, FZD7, AURKB, UBE2C and PTTG1 are genes which may be involved in tumor progression. Our study shows the potential involvement of various genes in the pathogenesis of CNs. These genes could be potential candidate markers for improving the characterization of CNs and some could be involved in CN tumorigenesis.
Three‐dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterization of the cel7 gene from the filamentous fungus, Talaromyces emersonii (2004)

The X-ray structure of native cellobiohydrolase IB (CBH IB) from the filamentous fungus Talaromyces emersonii, PDB 1Q9H, was solved to 2.4 A by molecular replacement. 1Q9H is a glycoprotein that consists of a large, single domain with dimensions of approximately 60 A x 40 A x 50 A and an overall beta-sandwich structure, the characteristic fold of Family 7 glycosyl hydrolases (GH7). It is the first structure of a native glycoprotein and cellulase from this thermophilic eukaryote. The long cellulose-binding tunnel seen in GH7 Cel7A from Trichoderma reesei is conserved in 1Q9H, as are the catalytic residues. As a result of deletions and other changes in loop regions, the binding and catalytic properties of T. emersonii 1Q9H are different. The gene (cel7) encoding CBH IB was isolated from T. emersonii and expressed heterologously with an N-terminal polyHis-tag, in Escherichia coli. The deduced amino acid sequence of cel7 is homologous to fungal cellobiohydrolases in GH7. The recombinant cellobiohydrolase was virtually inactive against methylumberiferyl-cellobioside and chloronitrophenyl-lactoside, but partial activity could be restored after refolding of the urea-denatured enzyme. Profiles of cel7 expression in T. emersonii, investigated by Northern blot analysis, revealed that expression is regulated at the transcriptional level. Putative regulatory element consensus sequences for cellulase transcription factors have been identified in the upstream region of the cel7 genomic sequence.
Intranasal immunization with W805EC adjuvanted recombinant RSV rF-ptn enhances clearance of respiratory syncytial virus in a mouse model (2013)

Respiratory Syncytial Virus (RSV) is a ubiquitous virus that infects almost all people by age two and is a major source of respiratory illness in infants, the elderly and others with compromised immune systems. Currently there is no available vaccine. Prior efforts using formalin-inactivated RSV (FI-RSV) were associated with enhanced respiratory disease upon viral exposure following clinical vaccine trials. Several researchers and pharmaceutical companies have utilized vector-associated live attenuated RSV vaccines in pre-clinical and clinical studies. Another attractive approach, however, is a subunit vaccine which would be easier to produce and quality control. Our group has previously demonstrated in a murine model of infection that intranasal immunization with nanoemulsion-inactivated and adjuvanted RSV induces humoral and cellular immune responses, resulting in protection against RSV infection. The present studies characterize the immune responses elicited by intranasal RSV F protein adjuvanted with nanoemulsion. Intranasal application of nanoemulsion adjuvanted F protein induced a rapid and robust systemic and mucosal antibody response, as well as protection against subsequent RSV challenge. Importantly, RSV challenge in immunized animals did not elicit airway hyper-reactivity, a Th2-skewed immune response or immunopathology associated with hypersensitivity reactions with formalin-inactivated vaccine. These results suggest that RSV F protein adjuvanted with nanoemulsion may be a good mucosal vaccine candidate. Formulating RSV F protein in nanoemulsion creates a well-defined and well-controlled vaccine that can be delivered intranasally to induce T cell mediated immunity without inducing enhanced disease associated with the mouse model of FI-RSV vaccination and infection.
Average optical performance of the human eye as a function of age in a normal population. (1999)

The average optical performance of the human eye progressively declines with age. These MTF results can serve as a reference for determining mean ocular optics according to age.
A Mouse Erythroleukemia Cell Line Possessing Friend Spleen Focus‐forming Virus gp55 Transgene and Temperature‐sensitive Mutant p53 Gene (1995)

Two different erythroleukemia cell lines have been established from the splenic lesions of transgenic mice possessing the Friend spleen focus-forming virus (F-SFFV) gp55 gene. One showed a near-diploid karyotype and a temperature-sensitive (ts) p53 mutation, and the other, a hyper-triploid karyotype with double p53 mutations found by single-strand conformation polymorphism (SSCP) analysis. The cell lines both retained No.11 chromosomes on which p53 genes are localized. Another p53 allele in the cell line with the ts-p53 mutation appeared intact in the SSCP analysis of the genomic exon 5. The cells with the ts-mutant p53 gene showed no apparent change with temperature shift in their growth or dimethylsulfoxide-induced differentiation, although the wild-type p53 gene on the other allele was not expressing. This ts-p53Val-135 gene made p53-deficient fibroblasts anchorage-independent at 37 degrees C but not at 32 degrees C. This non-virus-producing, mouse erythroleukemia cell line will be useful for the study of mutated p53 function during the induction of erythrodifferentiation or apoptotic change.
Severe Factor VII Deficiency Caused by a Novel Mutation His348 to Gln in the Catalytic Domain (2000)

Factor VII is a vitamin K-dependent zymogen that plays a key role in the initiation of the extrinsic pathway. A severe factor VII deficiency was identified in a 45-year old male whose plasma factor VII antigen was less than 60 ng/ml and expressed 5.2% of normal factor VII activity. DNA sequence analysis of the patient's factor VII gene showed a thymidine to guanine transversion at nucleotide 10968 in exon VIII that results in a novel amino acid substitution of His348 to Gln. The patient was homozygous for this mutation, whereas some of his family members were heterozygous. Both wild type and mutant factor VII were transiently expressed in COS-1 cells. The level of secreted mutant factor VII antigen was only 11.0% of the level of wild type factor VII. In CHO cells stably transfected with the mutant factor VII, only 37.3% of the total labeled FVII was secreted into the conditioned media and the remainder was retained inside the cells. These data suggest this mutation leads to factor VII deficiency due to the impaired secretion of the molecule.
Protein‐Loop Mimetics: A Diketopiperazine‐Based Template to Stabilize Loop Conformations in Cyclic Peptides Containing the NPNA and RGD Motifs (1996)

Abstract We explore here an approach to mimic the structures and biological functions of protein loops in small synthetic molecules, by grafting the loop of interest onto an organic template comprising a bicyclic diketopiperazine, prepared by the formal coupling of (2 S ,4 S )‐4‐aminoproline (Pro(NH 2 )) and aspartic acid (Asp). The Fmoc‐protected template 4 is used to prepare cyclo(‐Ala 1 ‐Asn 2 ‐Pro 3 ‐Asn 4 ‐Ala 5 ‐ Ala 6 ‐Temp‐) ( 5 ) and cyclo(‐Ala 1 ‐Arg 2 ‐Gly 3 ‐Asp 4 ‐Temp‐) ( 6 ) (where Temp = template derived from 4 ), containing the Asn‐Pro‐Asn‐Ala (NPNA) and Arg‐Gly‐Asp (RGD) motifs. The conformational properties of these molecules are studied in aqueous solution by NMR and simulated‐annealing methods. The NPNA motif, an immunodominant epitope on the circumsporozoite surface protein of the malaria parasite Plasmodium falciparum , is shown to adopt a stable type‐I β‐turn in 5 . The template in 5 adopts a preferred conformation with Pro(NH 2 )χ 1 ≈︁ −35° and the Asp moiety χ 1 ≈︁ 70°. A different template conformation is inferred for 6 , with Pro(NH 2 )χ 1 ≈︁ 0°, but the ARGD loop appears by NMR to undergo rapid conformational averaging. Solid‐phase binding assays reveal that 6 displays modest antagonist activity towards both the integrin α IIb β 3 and α v β 3 receptors.
Construction of antigen-specific suppressor T cell hybridomas from spleen cells of mice primed for the persistent IgE antibody formation. (1988)

Attempts were made to generate Ag-specific suppressor T cells from Ag-primed spleen cells by using glycosylation inhibiting factor (GIF). BDF1 mice were primed with alum-absorbed OVA and their spleen cells were stimulated with OVA. Ag-activated T cells were then propagated in IL-2-containing conditioned medium. Incubation of the T cells with OVA-pulsed syngeneic macrophages resulted in the formation of IgE-potentiating factor and glycosylation-enhancing factor that has affinity for OVA, i.e., OVA-specific glycosylation-enhancing factor. However, if the same Ag-activated splenic T cells were propagated in the IL-2-containing medium in the presence of GIF T cells obtained in the cultures formed IgE-suppressive factors and OVA-specific GIF on antigenic stimulation. Thus we constructed T cell hybridomas from the Ag-activated T cells propagated by IL-2 in the presence of GIF. A representative hybridoma, 71B4, formed OVA-specific GIF on incubation with OVA-pulsed macrophages of BDF1 mice or C57B1/6 mice. However, if the same hybridoma cells were incubated with OVA alone or with OVA-pulsed macrophages of H-2k or H-2d strains, they produced GIF that had no affinity for OVA. The OVA-specific GIF bound to OVA-Sepharose but did not bind to BSA-Sepharose or KLH Sepharose. Intravenous injections of the OVA-specific GIF from the hybridoma suppressed the IgE and IgG1 anti-DNP antibody response of BDF1 mice to DNP-OVA, but failed to suppress the anti-hapten antibody responses of the strain to DNP-keyhole limpet hemocyanin, indicating that the factors suppressed the antibody response in a carrier-specific manner. However, the same OVA-specific GIF failed to suppress the anti-hapten antibody response of DBA/1 mice to DNP-OVA, suggesting that the immunosuppressive effects of the factors is MHC restricted.
Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. (1979)

An improved method of two-dimensional gel electrophoresis has been developed which produces high resolution, reproducible images suitable for computer analysis. In the images that are presented, more than 800 proteins have been resolved without significant overlap, and many more proteins can be detected after longer exposures. To establish the usefulness of such methods for detailed quantitative comparisons of cultured cells, extensive controls have been carried out to test the reproducibility of the electrophoretic procedures, the sample preparation procedures, and the cell culture conditions. A computerized scanning system has been developed which can automatically detect and integrate the densities of the spots on a two-dimensional fluorogram or autoradiogram. The corresponding proteins from two or more samples can then be matched and their intensities compared. Several types of graphic output have been used to display the number and magnitude of the differences between the compared samples. These methods were used to study the patterns of protein synthesis in the nerve cell line B103 and the glial cell line B9. Both exponentially dividing and stationary cultures were analyzed and the relative rates of synthesis of approximately 300 proteins were compared by computer. For each cell line, no major qualitative differences were found between dividing and stationary phase cells although numerous quantitative differences of up to 15-fold were detected. The proteins that were increased or decreased in rate of synthesis as B103 cells became confluent were in general not the same proteins that were increased or decreased in rate of synthesis as B9 cells reached confluence, indicating that most of the changes do not reflect growth control responses common to all cells. When the two cell lines were analyzed in the same state of growth and compared by computer, qualitative differences were found in approximately 5% of the proteins analyzed, and at least 40% of the shared proteins were involved in quantitative differences of 2-fold or more. The rates of synthesis of the shared proteins were more divergent between the two cell lines than between dividing and stationary phase cells of either line. These studies show, therefore, that these cell lines can be distinguished, regardless of growth state, by their cell-specific proteins and by their characteristic rates of synthesis of many of the shared proteins.
Complete genome sequence of Clostridium perfringens , an anaerobic flesh-eater (2002)

Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and animals. The organism is known to produce a variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we report the complete 3,031,430-bp sequence of C. perfringens strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes, showing pronounced low overall G + C content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas production but no enzymes for the tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but many enzymes for amino acid biosynthesis were lacking in the genome. Twenty genes were newly identified as putative virulence factors of C. perfringens, and we found a total of five hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an efficient method for finding four members of the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of C. perfringens. Clearly, C. perfringens obtains various essential materials from the host by producing several degradative enzymes and toxins, resulting in massive destruction of the host tissues.
The genetic basis of systemic lupus erythematosus. (1998)

Although cumulative evidence suggests that a genetic predisposition plays a major role in the development of systemic lupus erythematosus (SLE), the susceptibility genes are mostly unknown. The difficulty in identifying susceptibility genes is due in part to the inherent nature of this polygenic complex disease and the diverse genetic backgrounds of human populations. Murine SLE models that have homogenous genetic backgrounds are less complex for genetic dissection. Genome-wide linkage studies of murine SLE have mapped the position of a number of susceptibility loci. Recently, several of these major murine loci have been shown to link to different clinical and laboratory features of lupus-like phenotypes. In addition, evidence for additional genetic contributions via interaction between murine loci has been reported. In human SLE, many polymorphic genes (which have potential roles in SLE, as suggested by their known functions) have been associated with SLE or SLE subsets by population-based case-control or within-case studies. Because more compelling genetic evidence includes linkage analysis, our group has used the identified murine susceptibility loci as a guide and conducted linkage analysis of genetic markers located within a specific, possibly syntenic human chromosomal region. Evidence for linkage of a chromosome 1q41-42 region was observed in SLE-affected sibling pairs from multiple ethnic groups. This article summarizes recent developments and outlines possible future directions in delineating the genetic basis of SLE.
Epigenetic regulation of Wnt-signaling pathway in acute lymphoblastic leukemia (2006)

Activation of the Wnt/beta-catenin signaling pathway is a hallmark of a number of solid tumors. We analyzed the regulation of the Wnt/beta-catenin pathway in acute lymphoblastic leukemia (ALL) and its role in the pathogenesis of the disease. We found that expression of the Wnt inhibitors sFRP1, sFRP2, sFRP4, sFRP5, WIF1, Dkk3, and Hdpr1 was down-regulated due to abnormal promoter methylation in ALL cell lines and samples from patients with ALL. Methylation of Wnt inhibitors was associated with activation of the Wnt-signaling pathway as demonstrated by the up-regulation of the Wnt target genes WNT16, FZ3, TCF1, LEF1, and cyclin D1 in cell lines and samples and the nuclear localization of beta-catenin in cell lines. Treatment of ALL cells with the Wnt inhibitor quercetin or with the demethylating agent 5-aza-2'-deoxycytidine induced an inactivation of the Wnt pathway and induced apoptosis of ALL cells. Finally, in a group of 261 patients with newly diagnosed ALL, abnormal methylation of Wnt inhibitors was associated with decreased 10-year disease-free survival (25% versus 66% respectively, P < .001) and overall survival (28% versus 61% respectively, P = .001). Our results indicate a role of abnormal Wnt signaling in ALL and establish a group of patients with a significantly worse prognosis (methylated group).
Noisy Spiking Neurons with Temporal Coding have more Computational Power than Sigmoidal Neurons (1996)

We exhibit a novel way of simulating sigmoidal neural nets by networks of noisy spiking neurons in temporal coding. Furthermore it is shown that networks of noisy spiking neurons with temporal coding have a strictly larger computational power than sigmoidal neural nets with the same number of units.
Albumin Conjugates of the Anticancer Drug Chlorambucil: Synthesis, Characterization, and In Vitro Efficacy (1998)

In our efforts to improve the selectivity and toxicity profile of antitumor agents, four maleimide derivatives of chlorambucil (1–4) were bound to thiolated human serum albumin which differ in the stability of the chemical link between drug and spacer. 1 is an aliphatic maleimide ester derivative of chlorambucil, whereas 2–4 are acetaldehyde, acetophenone, and benzaldehyde caboxylic hydrazone derivatives. HPLC stability studies at pH 5.0 with the related model compounds 5, 7, 8, und 9, in which chlorambucil was substituted by 4-phenylbutyric acid, demonstrated that the carboxylic hydrazone derivatives have acid-sensitive properties; the acid lability of 7 was particular prominent with a half-life of only a few hours. The alkylating activity of albumin-bound chlorambucil was determined with the aid of 4-(4-nitrobenzyl)-pyridine (NBP), demonstrating that on average three equivalents were protein-bound. Evaluation of the cytotoxicity of free chlorambucil and the respective albumin conjugates in the MCF7 mamma carcinoma and MOLT4 leukemia cell line employing a propidium iodide fluorescence assay demonstrated that the conjugate in which chlorambucil was bound to albumin through an ester bond was not as active as chlorambucil. In contrast, the conjugates in which chlorambucil was bound to albumin through carboxylic hydrazone bonds were as or more active than chlorambucil in both cell lines. In particular, the conjugate in which chlorambucil was bound to albumin through an acetaldehyde carboxylic hydrazone bond exhibited IC50 values which were approximately 4-fold (MDF7) to 13-fold (MOLT4) lower than those of chlorambucil. Preliminary toxicity studies in mice showed that this conjugate can be administered at higher doses in comparison to unbound chlorambucil.
Enzyme screening with synthetic multifunctional pores: Focus on biopolymers (2003)

This report demonstrates that a single set of identical synthetic multifunctional pores can detect the activity of many different enzymes. Enzymes catalyzing either synthesis or degradation of DNA (exonuclease III or polymerase I), RNA (RNase A), polysaccharides (heparinase I, hyaluronidase, and galactosyltransferase), and proteins (papain, ficin, elastase, subtilisin, and pronase) are selected to exemplify this key characteristic of synthetic multifunctional pore sensors. Because anionic, cationic, and neutral substrates can gain access to the interior of complementarily functionalized pores, such pores can be the basis for very user-friendly screening of a broad range of enzymes.
The Ray and Wave Theory of Lenses (1995)

Calculations on lens systems are often marred by the unjustifiable use of the small-angle approximation. This book describes in detail how the ray and wave pictures of lens behaviour can be combined and developed into a theory capable of dealing with the large angles encountered in real optical systems. A distinct advantage of this approach is that Fourier optics appears naturally, in a form valid for arbitrarily large angles. The book begins with extensive reviews of geometrical optiks, eikonal functions and the theory of wave propagation. The propagation of waves through lenses is then treated by exploiting the close connection between eikonal function theory and the stationary phase approximation. Aberrations are then discussed, and the book concludes with various applications in lens design and analysis, including chapters on laser beam propagation and diffractive optical elements. Throughout, special emphasis is placed on the intrinsic limitations of lens performance. The many practical insights it contains, as well as the exercises with their solutions, will be of interest to graduate students as well as to anyone working in optical design and engineering.