gebhart/patrepeval huggingface dataset:
Motion compensation based on spatial transformations (1994)

Given the small bit allocation for motion information in very low bit-rate coding, motion compensation using the block matching (BMA) algorithm fails to maintain an acceptable level of prediction errors. The reason is that the motion model, or spatial transformation, assumed in block matching cannot approximate the motion in the real world precisely with a small number of parameters (i.e. motion vectors). To develop an effective motion compensation method for very low bit-rate video coding, The authors address the issues of 1) adopting more sophisticated spatial transformations than block matching, and 2) developing a motion estimation algorithm that is suitable for these spatial transformations. The spatial transformations discussed are affine transformation, bilinear transformation and perspective transformation. Two new motion estimation algorithms, a matching-based algorithm and its fast version, are presented. The performance of the motion compensation methods, which combine the spatial transformations and the proposed motion estimation algorithms, is evaluated theoretically and experimentally using the following criteria: prediction error, amount of motion information, and computational cost. The simulation results show that in the proposed method, the amount of motion information required to achieve a fixed level of prediction error is reduced to one fourth that of block matching. The authors combine the designed motion compensation method with the discrete cosine transform to simulate coding of CIF format images at the transmission rate of 16 kb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
HIV-1 Viremia Prevents the Establishment of Interleukin 2–producing HIV-specific Memory CD4+ T Cells Endowed with Proliferative Capacity (2003)

CD4+ T cell responses are associated with disease control in chronic viral infections. We analyzed human immunodeficiency virus (HIV)-specific responses in ten aviremic and eight viremic patients treated during primary HIV-1 infection and for up to 6 yr thereafter. Using a highly sensitive 5-(and-6)-carboxyfluorescein diacetate-succinimidyl ester–based proliferation assay, we observed that proliferative Gag and Nef peptide-specific CD4+ T cell responses were 30-fold higher in the aviremic patients. Two subsets of HIV-specific memory CD4+ T cells were identified in aviremic patients, CD45RA− CCR7+ central memory cells (Tcm) producing exclusively interleukin (IL)-2, and CD45RA− CCR7− effector memory cells (Tem) that produced both IL-2 and interferon (IFN)-γ. In contrast, in viremic, therapy-failing patients, we found significant frequencies of Tem that unexpectedly produced exclusively IFN-γ. Longitudinal analysis of HIV epitope–specific CD4+ T cells revealed that only cells that had the capacity to produce IL-2 persisted as long-term memory cells. In viremic patients the presence of IFN-γ–producing cells was restricted to periods of elevated viremia. These findings suggest that long-term CD4+ T cell memory depends on IL-2–producing CD4+ T cells and that IFN-γ only–producing cells are short lived. Our data favor a model whereby competent HIV-specific Tcm continuously arise in small numbers but under persistent antigenemia are rapidly induced to differentiate into IFN-γ only–producing cells that lack self-renewal capacity.
A T-type fractal boundary single-feed circularly polarized microstrip antenna (2008)

A single-feed T-type fractal boundary microstrip antenna is presented. It is established that a very good circular polarization is realizable with 3-dB axial ratio bandwidth of 1.27% at the center frequency of 2446 MHz by changing the electrical length in two directions of the square patch by using T-type fractal curve as boundary. Further it is shown that the surface area occupied by the antenna is reduced compared to the Euclidean shaped patch antenna without much degradation in gain of the antenna. Experimental results are compared with simulated results and a very good agreement is obtained. © 2008 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2009.
A Gly145Ser substitution in the transcriptional activator PrfA causes constitutive overexpression of virulence factors in Listeria monocytogenes (1997)

Virulence genes in Listeria monocytogenes are coordinately expressed under the control of the transcriptional activator PrfA, encoded by prfA, a member of the cyclic AMP (cAMP) receptor protein (CRP)/FNR family of bacterial regulators. Strain P14-A is a spontaneous mutant of L. monocytogenes serovar 4b which produces elevated levels of virulence factors (M. T. Ripio, G. Domínguez-Bernal, M. Suárez, K. Brehm, P. Berche, and J. A. Vázquez-Boland, Res. Microbiol. 147:371-384, 1996). Here we report that P14-A and other variant strains with the same phenotype carry a point mutation in codon 145 of prfA, leading to a Gly-->Ser substitution. trans-complementation experiments with PrfA-deficient mutants demonstrated that the Gly145Ser prfA allele causes overexpression of virulence factors in L. monocytogenes, to the levels found in the virulence factor-overexpressing variants. In strain P14-A with a chromosomal Glyl45Ser prfA background, transcription of prfA and of PrfA-dependent virulence genes remained constitutively high under culture conditions in which virulence factor expression is downregulated in wild-type L. monocytogenes. The Glyl45Ser substitution is located in a PrfA stretch (residues 141 to 151) showing high sequence similarity to the D alpha-helix of CRP. Interestingly, well-characterized crp* mutations, which make CRP functionally active in the absence of cAMP, map in this region (i.e., Gly141Ser and Ala144Thr substitutions). By analogy with the CRP model, the phenotype conferred to L. monocytogenes by the Gly145Ser substitution in PrfA could be due to the mutant regulatory protein being locked in a transcriptionally active, cofactor-independent conformational state. Our observations allow the construction of a model for PrfA-dependent virulence gene regulation in which the levels of virulence factor expression depend primarily on the conformational state of the PrfA protein, which alternates between active and inactive forms according to its interaction with an environmentally regulated signal molecule or cofactor.
Conformational changes inE.coliRNA polymerase during promoter recognition (1993)

We analysed complexes formed during recognition of the lacUV5 promoter by E. coli RNA polymerase using formaldehyde as a DNA-protein and protein-protein cross-linking reagent. Most of the cross-linked complexes specific for the open complex (RPO) contain the beta' subunit of RNA polymerase cross-linked with promoter DNA in the regions: -50 to -49; -5 to -10; + 5 to +8 and +18 to +21. The protein-protein cross-linking pattern of contacting subunits is the same for the RNA polymerase in solution and in RPO: there are strong sigma-beta' and beta-beta' interactions. In contrast, only beta-beta' cross-links were detected in the closed (RPC) and intermediate (RPI) complexes. In presence of lac repressor before or after formation of the RPO cross-linking pattern is similar with that of RPI (RPC) complex.
CD23 interacts with a new functional extracytoplasmic domain involving N-linked oligosaccharides on CD21. (1994)

Human CD21 has been described as a receptor for the C3d,g and iC3b proteins of complement, for the Epstein-Barr virus, and also for IFN-alpha. We reported recently that CD23, a low affinity receptor for IgE (Fc epsilon R2), is a new functional ligand for CD21. To determine the site of interaction of CD23 on CD21, we analyzed the ability of purified recombinant CD23 incorporated into fluorescent liposomes to bind CD21 mutants bearing various deletions of extracytoplasmic short consensus repeats (SCRs). We found that the site of interaction of CD23 on CD21 is on SCRs 5 to 8, with contribution of SCRs 1 and 2. Tunicamycin treatment of CD21-transfected K562 cells strongly inhibited the binding of CD23-liposomes, suggesting that an N-linked sugar, present on SCRs 5 to 8, is involved in the CD23/CD21 interaction. By mutating together or individually, the three asparagines present on SCRs 5 to 8, asparagines (Asn) 370 and 295, but not Asn 492, were shown to be involved critically in the binding of CD23. Furthermore, we mapped the binding sites of a panel of anti-CD21 mAbs and found that at least six epitopes can be detected on CD21. The mAbs that inhibit the most CD23 binding to CD21 map in SCRs 5 to 8. This study indicates that SCRs 5 to 8 represent a novel functional domain on the CD21 molecule, and is the first demonstration of an activity of an extracytoplasmic region of the CD21 outside of SCRs 1 to 4.
Novel Integrase-Defective Lentiviral Episomal Vectors for Gene Transfer (2004)

High levels of circular viral extrachromosomal DNA (E-DNA) are normally produced after infection with integration-competent and -incompetent lentiviruses. Although E-DNA has been shown to be transcriptionally active, it lasts for only a short time in replicating cells. Here, we report an integrase (IN)-defective lentiviral episomal vector in which insertion of the simian virus 40 (SV40) promoter, containing the origin of replication (ori), is associated with long-term expression and persistence of E-DNA in the presence of SV40 large T antigen (TAg) from 293T cells. 293 and 293T cell lines transduced with IN-competent lentiviral vectors expressing green fluorescent protein (GFP) or luciferase from the cytomegalovirus (CMV) or SV40 promoter gave similar levels of transduction and expression. In contrast, only transient reporter expression occurred when using the CMV IN-defective control vector in both 293 and 293T cells. However, reporter gene expression was maintained for more than 8 weeks in 293T, but not 293, cells transduced with the IN-defective lentiviral vector containing the SV40-ori promoter. Polymerase chain reaction for two-long terminal repeat (2LTR) extrachromosomal circular forms, a marker of lentiviral E-DNA, and fluorescence in situ hybridization analysis confirmed the persistence and episomal nature of circular E-DNA up to 60 days after transduction. Taken together, these results indicate that insertion of the SV40-ori promoter in a lentiviral vector contributes to long-term expression by promoting episomal replication when TAg is provided in trans. Lentiviral episomal vectors may serve as specific tools for therapeutic approaches to diseases, particularly those associated with episomal replication of DNA viruses including papillomaviruses, polyomaviruses, and herpesviruses.
Requirement for CDK6 in MLL-rearranged acute myeloid leukemia (2014)

Chromosomal rearrangements involving the H3K4 methyltransferase mixed-lineage leukemia (MLL) trigger aberrant gene expression in hematopoietic progenitors and give rise to an aggressive subtype of acute myeloid leukemia (AML). Insights into MLL fusion-mediated leukemogenesis have not yet translated into better therapies because MLL is difficult to target directly, and the identity of the genes downstream of MLL whose altered transcription mediates leukemic transformation are poorly annotated. We used a functional genetic approach to uncover that AML cells driven by MLL-AF9 are exceptionally reliant on the cell-cycle regulator CDK6, but not its functional homolog CDK4, and that the preferential growth inhibition induced by CDK6 depletion is mediated through enhanced myeloid differentiation. CDK6 essentiality is also evident in AML cells harboring alternate MLL fusions and a mouse model of MLL-AF9-driven leukemia and can be ascribed to transcriptional activation of CDK6 by mutant MLL. Importantly, the context-dependent effects of lowering CDK6 expression are closely phenocopied by a small-molecule CDK6 inhibitor currently in clinical development. These data identify CDK6 as critical effector of MLL fusions in leukemogenesis that might be targeted to overcome the differentiation block associated with MLL-rearranged AML, and underscore that cell-cycle regulators may have distinct, noncanonical, and nonredundant functions in different contexts.
Blind separation and capture of communication signals using a multitarget constant modulus beamformer (2003)

A multitarget least-squares CMA (constant modulus algorithm) that blindly adapts a narrowband beamformer to separate and capture multiple communication signals by exploiting only the low modulus variation of the communication waveforms is presented. It is shown that the algorithm can detect and classify transient and nontransient communication signals on the basis of modulus variation and extract those signals with maximum attainable output SINR (signal-to-interference and -noise ratio) in environments containing strong transient or nontransient cochannel interference. This is demonstrated via computer simulation for a narrowband (25 kHz bandwidth) four-element antenna array in environments containing FSK (frequency shift keying) bursts received at low ( approximately 4 dB signal-to-white-noise ratio) power levels in the presence of severe ( approximately -50-dB signal-to-interference ratio) interference. It is shown that the algorithm can capture the FSK bursts in less than 2 ms, and maintain capture on the signals as other signals appear and disappear over the signal ON times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
β‐Cyclodextrin‐Appended Giant Amphiphile: Aggregation to Vesicle Polymersomes and Immobilisation of Enzymes (2008)

A giant amphiphile consisting of polystyrene end-capped with permethylated beta-cyclodextrin was synthesised and found to form vesicular structures when injected as a solution in THF into water. The ability of the cyclodextrins on the surface of the polymersomes to form inclusion complexes with hydrophobic compounds was tested by carrying out a competition experiment with a fluorescent probe sensitive to the polarity of the surrounding medium. It was found that 1-adamantol can displace the fluorescent probe from the cavities of the cyclodextrin moieties of the polymersomes. The recognition of molecules by cell membranes in nature is often based on interactions with specific membrane receptors. To mimic this behaviour, the enzyme horseradish peroxidase was modified with adamantane groups through a poly(ethylene glycol) spacer and its interaction with the polymersomes was investigated. It was established that the presence of adamantane moieties on each enzyme allowed a host-guest interaction with the multifunctional surface of the polymersomes.
West African timbers. Part XII. The inter-relation of gedunin and khivorin (1966)

Gedunin and khivorin have both been converted into deacetoxy-7-oxoisogedunin. As the structure of gedunin has been confirmed by X-ray analysis this conversion supplies proof that the structure of khivorin previously proposed is correct. Several other transformation products of gedunin and khivorin are described.
Lung cancer (1995)

In recent years, adenocarcinoma has replaced squamous cell carcinoma as the most frequent histologic subtype for all sexes and races combined. These shifts in histologic types by sex and race may be related to differences in exposure to tobacco products, dietary factors, environmental or occupational carcinogens, and host characteristics. Increased use of transbronchial and needle biopsy may have also influenced these trends to some extent. Over the study period, 5-year relative survival rate did not change appreciably for lung cancer, suggesting that therapeutic advances have had little effect.
Test of Time (2009)

Watson and Rayner's (1920) ;Little Albert' experiment has become one of the most famous studies in psychology. It is a staple of many general psychology textbooks and is part of the very fabric of the discipline's folklore. Despite this fame, the study has been widely criticized in the nearly 90 years since it was published for its lack of methodological rigour. This article attempts to evaluate the contribution of the ;little Albert' study to modern clinical psychology by speculating on what theories and treatments of child anxiety would look like in a parallel universe in which the study never took place because ;little Albert' escaped from the hospital in which Watson tested him.
Early events in erythroid differentiation: accumulation of the acidic peroxidoxin (PRP/TSA/NKEF-B) (1995)

The acidic peroxidoxin [also named thiol-specific antioxidant protein (TSA) or protector protein (PRP)], which plays a role in the response against oxidative stress, is one of the major proteins of red blood cells. In this work, we show that this protein is induced at early stages of erythroid differentiation prior to haemoglobin accumulation, which suggests that it may play a role at the erythroblast stage, where haemoglobinized, nucleated and genetically active cells are submitted to a maximally dangerous oxidative stress. The early accumulation of this protein has been demonstrated both on transformed cell systems and on normal differentiating human erythroid cells. This suggests that this protein may play an important role in the differentiation of the erythroid cells.
Reversed‐phase high‐performance liquid chromatography prefractionation prior to two‐dimensional difference gel electrophoresis and mass spectrometry identifies new differentially expressed proteins between striate cortex of kitten and adult cat (2003)

Two-dimensional difference gel electrophoresis (2-D DIGE), in combination with mass spectrometry, is a highly effective method for the rapid and reproducible detection of differentially expressed proteins. This approach, however, has the unfortunate drawback that it preferentially displays rather abundantly expressed proteins. Nevertheless, comparison of the protein expression levels of the striate cortex of adult cats and 30-day-old kittens, resulted in the identification of several proteins related to postnatal brain development and possibly age-dependent plasticity as well (Van den Bergh et al., J. Neurochem. 2003, in press). The goal of the present study was the selective enrichment and identification of less abundant proteins within the same paradigm. Hereto, we performed a reversed-phase chromatography prefractionation of our tissue lysate to separate the proteins in four fractions based on their hydrophobicity prior to 2-D DIGE analysis. This approach not only confirmed the differential expression levels of a number of proteins from the previous study, but also identified three additional proteins preferentially expressed in kitten visual cortex and five additional proteins with higher expression levels in adult cat visual cortex. These spots were not visible on the total tissue lysate protein maps, indicating that the high-performance liquid chromatography (HPLC) prefractionation enabled us to visualize additional, less abundant proteins.
Partial down-regulation of protein kinase C in C3H 10T 1/2 mouse fibroblasts transfected with the human Ha-ras oncogene. (1988)

Biochemical and immunological comparison of mouse C3H 10T 1/2 fibroblasts and C3H 10T 1/2 fibroblasts transfected with human activated Ha-ras oncogene indicated significantly lower levels of protein kinase C (PKC) activity and protein in the ras-transfected cells. This effect was observed in three clonal cell lines transfected with an activated ras oncogene. Cytosolic extracts of the ras-transfected cells contained calcium-activated, phospholipid-dependent protein kinase (PKC) activity at 61% of the level of activity present in C3H 10T 1/2 cells. A similarly decreased level of phorbol ester-binding activity was observed in these cells. Analysis of the subcellular distribution of PKC activity in cells failed to indicate significant differences between these cell lines. Immunoblots showed a lower abundance of the Mr 80,000 PKC in ras-transfected cell homogenates and extracts compared to C3H 10T 1/2 cells. Both C3H 10T 1/2 cells and cells transfected with ras expressed only one of the PKC isozymes as resolved by hydroxylapatite chromatography demonstrating that ras transfection of cells did not induce expression of alternative PKC isozymes. These observations indicate that PKC was partially down-regulated in ras-transfected cells, perhaps resulting from constitutively elevated levels of products of phosphatidylinositol-4,5-bisphosphate hydrolysis. Although C3H 10T 1/2 cells were previously shown to be distinct from NIH 3T3 cells in their sensitivity to transformation by the T24-ras oncogene, ras transformation appears to partially down-regulate PKC in C3H 10T 1/2 cells in a manner identical to that for ras-transformed NIH 3T3 cells. This indicates that down-regulation of PKC directly results from the expression of an activated ras oncogene independently of cellular sensitivity to transformation by expression of ras. The common action of ras transformation and phorbol esters to down-regulate PKC provides a possible mechanism for synergism during multistage carcinogenesis.
Mechanically stable solvent-free lipid bilayers in nano- and micro-tapered apertures for reconstitution of cell-free synthesized hERG channels (2017)

The self-assembled bilayer lipid membrane (BLM) is the basic component of the cell membrane. The reconstitution of ion channel proteins in artificially formed BLMs represents a well-defined system for the functional analysis of ion channels and screening the effects of drugs that act on them. However, because BLMs are unstable, this limits the experimental throughput of BLM reconstitution systems. Here we report on the formation of mechanically stable solvent-free BLMs in microfabricated apertures with defined nano- and micro-tapered edge structures. The role of such nano- and micro-tapered structures on the stability of the BLMs was also investigated. Finally, this BLM system was combined with a cell-free synthesized human ether-a-go-go-related gene channel, a cardiac potassium channel whose relation to arrhythmic side effects following drug treatment is well recognized. Such stable BLMs as these, when combined with a cell-free system, represent a potential platform for screening the effects of drugs that act on various ion-channel genotypes.
Fine-Grained Failover Using Connection Migration (2018)

This paper presents a set of techniques for providing fine-grained failover of long-running connections across a distributed collection of replica servers, and is especially useful for fault-tolerant and load-balanced delivery of streaming media and telephony sessions. Our system achieves connection-level failover across both local- and wide-area server replication, without requiring a front-end transport- or application-layer switch. Our approach uses recently proposed end-to-end ``connection migration'' mechanisms for transport protocols such as TCP, combined with a soft-state session synchronization protocol between replica servers. The end result is a robust, fast, and fine-grained connection failover mechanism that is transparent to client applications, and largely transparent to the server applications. We describe the details of our design and Linux implementation, as well as experimental data that suggests this approach is an attractive way to engineer robust systems for distributing long-running streams; connections suffer relatively small performance degradation even when migration occurs every few seconds, and the associated server overhead is small.