gebhart/patrepeval huggingface dataset:
Enhanced intra prediction and transform for video coding (2010)

Intra-coding plays an important role in video coding schemes and it has become a hot research topic of the next generation video coding standard. In this paper, we propose two techniques to improve the efficiency of the prediction and the transform, respectively, for intra-coding. First, we introduce an overlapped block intra-prediction (OBIP) method, which makes use of the intra directional prediction modes of neighboring blocks as well as the mode of the current block. A position dependent weighted sum of several possible predictors will be treated as the final prediction. Second, we propose a multiple-model Karhunen-Loève transform (MMKLT) technique to further improve the mode dependent directional transform (MDDT) method. More than one KLT will be trained offline for each intra-prediction mode based on residual variances. Experimental results indicate that the proposed two methods together can achieve an average bit-rate reduction about 11% compared with H.264 or 5% compared with MDDT in all-intra coding.
A cryptic fimbrial gene in Serratia marcescens (1989)

The gene coding for the mannose-sensitive hemagglutinating fimbriae in Serratia marcescens US5 was cloned into Escherichia coli K4 with a cosmid vector system. One of the transformants, US5-1, expressed two morphologically distinct fimbriae, one that was 5-nm wide and one that was 3-nm wide. The latter fimbria was morphologically and serologically indistinguishable from that of strain US5. Genetic analysis of transformant US5-1 showed that the gene responsible for the 5-nm-wide fimbriae was located more than 10 kilobases away from the gene responsible for the 3-nm-wide fimbriae. The molecular sizes of the subunits of these two fimbriae, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, were 19 kilodaltons for the 3-nm-wide fimbriae and 20 kilodaltons for the 5-nm-wide fimbriae. Serologically, the 5-nm-wide fimbriae did not cross-react with monoclonal or polyclonal antibodies raised against the mannose-sensitive hemagglutinating fimbriae of strain US5. Strain EL101, which expressed only the 5-nm-wide fimbriae, did not agglutinate chicken or human erythrocytes. These experimental results suggest that the gene for the 5-nm-wide fimbriae is cryptic in strain US5 and is expressed in E. coli K4 only after it is moved by transformation.
Phosphorylation of the duck hepatitis B virus capsid protein associated with conformational changes in the C terminus (1994)

The capsid protein of duck hepatitis B virus (DHBV) is phosphorylated at multiple sites during viral infection. A cluster of sites is located near the C terminus of the 262-amino-acid protein. We have used site-directed mutagenesis to show that three serines and one threonine serve as phosphate acceptor amino acids in the C terminus. An additional six potential phosphate acceptor sites in this region were apparently not utilized. Each serine or threonine that served as a phosphate acceptor was adjacent to a downstream proline, while all six serines that were not acceptors for phosphate residues lacked adjacent downstream prolines. Mutation of the downstream proline to glycine at each site had the same effect as mutating the serine itself, suggesting an SP or TP motif as an essential feature for capsid protein phosphorylation. Phosphorylation at these four sites resulted in complex shifts in electrophoretic mobility in sodium dodecyl sulfate gels of the capsid protein or of a C-terminal peptide containing the phosphorylated sites, suggesting that specific conformations of the C terminus are associated with different combinations of phosphorylated serines. We speculate that distinct functions of the C terminus may be associated with different phosphorylated domains on the intact capsid.
T Cell and APC Dynamics In Situ Control the Outcome of Vaccination (2010)

The factors controlling the progression of an immune response to generation of protective memory are poorly understood. We compared the in situ and ex vivo characteristics of CD8 T cells responding to different forms of the same immunogen. Immunization with live Listeria monocytogenes, irradiated L. monocytogenes (IRL), or heat-killed L. monocytogenes (HKL) induced rapid activation of CD8 T cells. However, only IRL and live L. monocytogenes inoculation induced sustained proliferation and supported memory development. Gene and protein expression analysis revealed that the three forms of immunization led to three distinct transcriptional and translational programs. Prior to cell division, CD8 T cell-dendritic cell clusters formed in the spleen after live L. monocytogenes and IRL but not after HKL immunization. Furthermore, HKL immunization induced rapid remodeling of splenic architecture, including loss of marginal zone macrophages, which resulted in impaired bacterial clearance. These results identify initial characteristics of a protective T cell response that have implications for the development of more effective vaccination strategies.
Frontline therapy with rituximab added to the combination of cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) significantly improves the outcome for patients with advanced-stage follicular lymphoma compared with therapy with CHOP alone: results of a prospective randomized study of the German Low-Grade Lymphoma Study Group (2005)

Phase 2 studies suggest that the monoclonal antibody rituximab may improve the prognosis of patients with follicular lymphoma (FL) when it is added to chemotherapy. In the current study, 428 patients with untreated, advanced-stage FL were randomly assigned for therapy with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) alone (n = 205) or CHOP combined with rituximab (R-CHOP) (n = 223). R-CHOP reduced the relative risk for treatment failure by 60% and significantly prolonged the time to treatment failure (P < .001). In addition, a significantly higher overall response rate (96% vs 90%; P = .011) and a prolonged duration of remission (P = .001) were achieved. In spite of a relatively short observation time, these beneficial effects even translated to superior overall survival (P = .016), with 6 deaths in the R-CHOP group compared with 17 deaths in the CHOP group within the first 3 years. The predominant treatment-related adverse effect was myelosuppression. Severe granulocytopenia was more frequently observed after R-CHOP (63% vs 53%; P = .01). However, severe infections were rare and of similar frequency after R-CHOP and CHOP (5% and 7%). Hence, adding rituximab to CHOP significantly improves the outcome for patients with previously untreated advanced-stage FL and does not induce major adverse effects.
Chemokines and cancer (2006)

The chemokines and their receptors are a superfamily of small secreted molecules that control the migration of many cell types in the body. Several years ago it became clear that some chemokines and receptors regulate the migration of certain cells in the lymphoid system, and this raised the possibility that chemokines could also control the migration of tumor cells in the body. Breast cancer cells were found to express chemokine receptors in a nonrandom manner, and these observations pointed to several chemokine/receptor pairs that control tumor-cell migration. The most important ligand/receptors pairs in these phenomena include CXCL12/CXCR4 and CCL21/CCR7. Since then, there has been intense interest in this area and many studies have been published, especially on CXCR4. These studies point to the following conclusions: (i) Tumors express chemokine receptors in a nonrandom manner. (ii) CXCR4 is the most widely expressed chemokine receptor in many different cancers. (iii) CCR7 is also expressed by many cancers, and is likely to mediate metastasis to the lymph nodes in selected cancers. (iv) The effects of CXCL12 on CXCR4-bearing tumor cells likely include many other functions (growth, differentiation) besides migration. During normal development, the interaction CXCL12/CXCR4 is known to be involved in organogenesis. This process shares many characteristics with metastasis, and represents one of the key areas of future research.
Transport of galactose, glucose and their molecular analogues by Escherichia coli K12 (1977)

1. Strains of Escherichia coli K12 were made that are unable to assimilate glucose by the phosphotransferase system, since they lack the glucose-specific components specified by the genes ptsG and ptsM. 2. Derivative organisms lacking the methyl galactoside or galactose-specific transport system were examined for their ability to transport galactose, d-fucose, methyl beta-D-galactoside, glucose, 2-deoxy-D-glucose and methyl alpha-D-glucoside. 3. Galactose, glucose and to a lesser extent fucose are substrates for both transport systems. 4. 2-Deoxyglucose is transported on the galactose-specific but not the methyl galactoside system. 5. The ability of sugars to elicit anaerobic proton transport is associated with the galactose-specific, but not with the methyl galactoside transport activity. Hence a chemiosmotic mechanism of energization is likely to apply to the former but not to the latter. Alternatively the methyl galactoside system may be switched off under certain conditions, which would indicate a novel regulatory mechanism. 6. Details of the procedure for the derivation of strains may be obtained from the authors, and have been deposited as Supplementary Publication SUP 50074 (8 pages at the) British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1977), 161,1.
Determinants of exercise capacity in patients with coronary artery disease and mild to moderate systolic dysfunction: Role of heart rate and diastolic filling abnormalities (1996)

We have observed a strong correlation between exercise capacity and indices of exercise left ventricular diastolic filling, and have confirmed previous studies showing a poor correlation with resting and exercise indices of systolic function and resting diastolic filling, in patients with coronary artery disease.
Linear-Time Encodable/Decodable Codes With Near-Optimal Rate (2005)

We present an explicit construction of linear-time encodable and decodable codes of rate r which can correct a fraction (1-r-/spl epsiv/)/2 of errors over an alphabet of constant size depending only on /spl epsiv/, for every 0<r<1 and arbitrarily small /spl epsiv/>0. The error-correction performance of these codes is optimal as seen by the Singleton bound (these are "near-MDS" codes). Such near-MDS linear-time codes were known for the decoding from erasures; our construction generalizes this to handle errors as well. Concatenating these codes with good, constant-sized binary codes gives a construction of linear-time binary codes which meet the Zyablov bound, and also the more general Blokh-Zyablov bound (by resorting to multilevel concatenation). Our work also yields linear-time encodable/decodable codes which match Forney's error exponent for concatenated codes for communication over the binary symmetric channel. The encoding/decoding complexity was quadratic in Forney's result, and Forney's bound has remained the best constructive error exponent for almost 40 years now. In summary, our results match the performance of the previously known explicit constructions of codes that had polynomial time encoding and decoding, but in addition have linear-time encoding and decoding algorithms.
Evaluating Oilseed Biofuel Production Feasibility in California’s San Joaquin Valley Using Geophysical and Remote Sensing Techniques (2017)

Though more costly than petroleum-based fuels and a minor component of overall military fuel sources, biofuels are nonetheless strategically valuable to the military because of intentional reliance on multiple, reliable, secure fuel sources. Significant reduction in oilseed biofuel cost occurs when grown on marginally productive saline-sodic soils plentiful in California's San Joaquin Valley (SJV). The objective is to evaluate the feasibility of oilseed production on marginal soils in the SJV to support a 115 ML yr<sup>-1</sup> biofuel conversion facility. The feasibility evaluation involves: (1) development of an Ida Gold mustard oilseed yield model for marginal soils; (2) identification of marginally productive soils; (3) development of a spatial database of edaphic factors influencing oilseed yield and (4) performance of Monte Carlo simulations showing potential biofuel production on marginally productive SJV soils. The model indicates oilseed yield is related to boron, salinity, leaching fraction, and water content at field capacity. Monte Carlo simulations for the entire SJV fit a shifted gamma probability density function: Q = 68.986 + gamma (6.134,5.285), where Q is biofuel production in ML yr<sup>-1</sup>. The shifted gamma cumulative density function indicates a 0.15-0.17 probability of meeting the target biofuel-production level of 115 ML yr<sup>-1</sup>, making adequate biofuel production unlikely.
A Parallel Architecture for In-Line Data De-duplication (2012)

Recently, data de-duplication, the hot emerging technology, has received a broad attention from both academia and industry. Some researches focus on the approach by which more redundant data can be reduced and others investigate how to do data de-duplication at high speed. In this paper, we show the importance of data de-duplication in the current digital world and aim at reducing the time and space requirement for data de-duplication. Then, we present a parallel architecture with one node designated as a server and multiple storage nodes. All the nodes, including the server, can do block level in-line de-duplication in parallel. We have built a prototype of the system and present some performance results. The proposed system uses magnetic disks as a storage technology.
Case study of the trade and transport facilitation in Southeast Europe program (2006)

Trade and Transport Facilitation in Southeast Europe Program (TTFSE's) main objectives are: (a) to reduce non-tariff costs to trade and transport, and (b) to reduce smuggling and corruption at border crossings. As a pilot project, its focus is on 35 border crossing points and 8 inland terminals, or about half out of the total sites in the region. To achieve its objectives, the program supports four sets of activities: Building infrastructure and providing equipment at border crossing facilities; Improving customs information systems; Reforming custom procedures; and Developing other trade facilitation measures such as increasing participants' knowledge in trade, logistics, and international freight transport.
Human neocortical electrical activity recorded on nonpenetrating microwire arrays: applicability for neuroprostheses (2009)

The nonpenetrating microwire platform showed good potential for allowing differentiated signals to be recorded with high spatial fidelity without cortical penetration.
Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation (2016)

Oncogenic mutations regulate signaling within both tumor cells and adjacent stromal cells. Here, we show that oncogenic KRAS (KRAS(G12D)) also regulates tumor cell signaling via stromal cells. By combining cell-specific proteome labeling with multivariate phosphoproteomics, we analyzed heterocellular KRAS(G12D) signaling in pancreatic ductal adenocarcinoma (PDA) cells. Tumor cell KRAS(G12D) engages heterotypic fibroblasts, which subsequently instigate reciprocal signaling in the tumor cells. Reciprocal signaling employs additional kinases and doubles the number of regulated signaling nodes from cell-autonomous KRAS(G12D). Consequently, reciprocal KRAS(G12D) produces a tumor cell phosphoproteome and total proteome that is distinct from cell-autonomous KRAS(G12D) alone. Reciprocal signaling regulates tumor cell proliferation and apoptosis and increases mitochondrial capacity via an IGF1R/AXL-AKT axis. These results demonstrate that oncogene signaling should be viewed as a heterocellular process and that our existing cell-autonomous perspective underrepresents the extent of oncogene signaling in cancer. VIDEO ABSTRACT.
Innovative Separation Technology for Lithium-6 Enrichment Using Electrodialysis with Lithium Ionic Superconductor (2017)

Tritium needed as a fuel for fusion reactors is produced via neutron capture by lithium-6 ( 6 Li). However, natural Li contains only about 7.8% 6 Li, and enrichment of 6 Li up to 90% is required for adequate tritium breeding in fusion reactors. The mercury amalgam method is superior to some of the lithium isotope enrichment methods. In Japan, lithium isotope enrichment methods have been developed to avoid the environmental hazards of using mercury. However, the isotope separation coefficient and efficiency is too low to meet the practical need of large mass production of 6 Li. Therefore, new Li isotope separation technique using a Li ionic superconductor functioning as a Li isotope separation membrane (LISM) have been developed [1]. Li ions move by electrodialysis through LISM between the cathode and the anode in lithium solutions. Because the mobility of 6 Li ions is higher than that of 7 Li ions, 6 Li can be enriched on the cathode side of a cell. It has been reported that the difference in the mobility between 6 Li and 7 Li become large in ionic superconductor. The isotope effect in ionic superconductor is expected to be applicable to isotope separation membrane. In this research, we numerically investigated the ionic mobility of Li isotopes in ionic superconductor. Combing the first principle and the kinetics Monte Calro simulation, we calculate the diffusion constant of 6 Li and 7 Li. I show the two important effects for the difference in the mobility between isotope of Li. The first is the quantum effect, which decrease the diffusion barrier for Li ion and increase the ratio of the diffusion constant of Li isotopes. The second is the correlation effect between 6 Li, 7 Li and vacancy. Using Li 0.29 La 0.57 TiO 3 (LLTO) as the Li ionic superconductor was prepared, and the relationship between the 6 Li separation coefficient and the electrodialysis time was investigated. After electrodialysis, we obtained a maximum of 1.04 for the 6 Li isotope separation coefficient. This result showed that the 6 Li isotope separation coefficient of this method is the same as that of the amalgamation process using mercury (1.06). Thus, this method has the potential to be a superior 6 Li enrichment method to produce 90% enriched tritium breeder for fusion reactors. Figure 1
Highly manufacturable high density phase change memory of 64Mb and beyond (2005)

Highly manufacturable 64Mbit PRAM has been successfully fabricated using N-doped Ge/sub 2/Sb/sub 2/Te/sub 5/ (GST) and optimal GST etching process. Using those technologies, it was possible to achieve the low writing current of 0.6 mA and clear separation between SET and RESET resistance distributions. The 64Mb PRAM was designed to support commercial NOR flash memory compatible interfaces. Therefore, the fabricated chip was tested under the mobile application platform and its functionality and reliability has been evaluated by operation temperature dependency, disturbance, endurance, and retention. Finally, it was clearly demonstrated that high density PRAM can be fabricated in the product level with strong reliability to produce new nonvolatile memory markets.
Heparan Sulfate Proteoglycans as Adhesive and Anti-invasive Molecules (1998)

ARH-77 cells do not adhere to type I collagen and readily invade into collagen gels, but following expression of the transmembrane heparan sulfate proteoglycan syndecan-1, they bind collagen and fail to invade. We now show that cells transfected with syndecan-2 or syndecan-4 also bind collagen and are non-invasive. In contrast, cells transfected with the glycosylphosphatidylinositol-anchored proteoglycan glypican-1 do not bind to collagen and remain invasive, even though glypican- and syndecan-expressing cells have similar surface levels of heparan sulfate, and their proteoglycans have similar affinities for collagen. Analysis of cells expressing syndecan-1-glypican-1 chimeric proteoglycans reveals that inhibition of invasion requires the extracellular domain of syndecan but not its transmembrane or cytoplasmic domain. Surprisingly, cells bearing a chimera composed of the glypican extracellular domain fused to the syndecan transmembrane and cytoplasmic domains bind to collagen but remain invasive, implying that adhesion to collagen is not by itself sufficient to inhibit invasion. Apparently, the extracellular domain of syndecan-1, presumably by interacting with cell-surface signal transducing molecules, directly regulates complex cell behaviors such as motility and invasiveness. These results also show for the first time that syndecans and glypicans can have distinct functions, even when expressed by the same cell type.
Asymmetric Synthesis and Antimicrobial Activity of Some New Mono and Bicyclic β-Lactams (2004)

Reaction of the amino acid D-phenylalanine ethyl ester (4) with cinnamaldehyde gave chiral Schiff base 5, which underwent an asymmetric Staudinger [2+2] cycloaddition reaction with phthalimidoacetyl chloride to give the monocyclic beta-lactam 6 as a single stereoisomer. Ozonolysis of 6 followed by reduction with lithium aluminum tri(tert-butoxy) hydride afforded the hydroxymethyl beta-lactam 8. Treatment of 8 with methansulfonyl chloride gave the mesylated monocyclic beta-lactam 9, which was converted to the bicyclic beta-lactam 10 upon treatment with 1,8-diazabicyclo[5,4.0] undec-7-ene (DBU). Deprotection of the phthalimido group in beta-lactams 6 and 10 by methylhydrazine and subsequent acylation of the free amino beta-lactams with different acyl chlorides in the presence of pyridine afforded mono and bicyclic beta-lactams 14a-d and 15a-d respectively. The compounds prepared were tested against Escherichia coli, Staphilococcus citrus, Klebsiella pneumanie and Bacillus subtillis. Some of these compounds showed potential antimicrobial activities.
Applications of Mathematical Flood Plain Modelling (1984)

Recent developments in mathematical modelling of complex flood plains are discussed and illustrated with specific examples of different projects. In each case the advantages of such modelling are described and future developments in the modelling field are anticipated.
Molecular genetic analysis of FNR‐dependent promoters (1989)

In enteric bacteria, the expression of many genes encoding various anaerobic electron transfer functions is controlled by FNR, the product of the autoregulated fnr gene. FNR is structurally and functionally homologous to CAP, the catabolite gene activator protein, and increased FNR production strongly stimulates transcription of its target genes. By analysis of RNA produced in vivo the promoters of four FNR-dependent genes were localized and shown to display a common arrangement. A 22bp dyad symmetry was found about 30 nucleotides upstream of the transcriptional startpoints and a similar sequence was shown to overlap the site of transcription initiation in the negatively controlled fnr gene. The consensus sequence for the half site recognized by FNR (AAA-TTGAT) is only slightly different from that of CAP (AA-TGTGA). Studies with two mutant frd promoters from Escherichia coli, displaying altered regulation and FNR response, provided additional evidence for recognition of this sequence by FNR.