gebhart/patrepeval huggingface dataset:
Extended parallel backprojection for standard three‐dimensional and phase‐correlated four‐dimensional axial and spiral cone‐beam CT with arbitrary pitch, arbitrary cone‐angle, and 100% dose usage (2004)

We have developed a new approximate Feldkamp-type algorithm that we call the extended parallel backprojection (EPBP). Its main features are a phase-weighted backprojection and a voxel-by-voxel 180 degrees normalization. The first feature ensures three-dimensional (3-D) and 4-D capabilities with one and the same algorithm; the second ensures 100% detector usage (each ray is accounted for). The algorithm was evaluated using simulated data of a thorax phantom and a cardiac motion phantom for scanners with up to 256 slices. Axial (circle and sequence) and spiral scan trajectories were investigated. The standard reconstructions (EPBPStd) are of high quality, even for as many as 256 slices. The cardiac reconstructions (EPBPCI) are of high quality as well and show no significant deterioration of objects even far off the center of rotation. Since EPBPCI uses the cardio interpolation (CI) phase weighting the temporal resolution is equivalent to that of the well-established single-slice and multislice cardiac approaches 180 degrees CI, 180 degrees MCI, and ASSRCI, respectively, and lies in the order of 50 to 100 ms for rotation times between 0.4 and 0.5 s. EPBP appears to fulfill all required demands. Especially the phase-correlated EPBP reconstruction of cardiac multiple circle scan data is of high interest, e.g., for dynamic perfusion studies of the heart.
GCap: Graph-based Automatic Image Captioning (2005)

Given an image, how do we automatically assign keywords to it? In this paper, we propose a novel, graph-based approach (GCap) which outperforms previously reported methods for automatic image captioning. Moreover, it is fast and scales well, with its training and testing time linear to the data set size. We report auto-captioning experiments on the "standard" Corel image database of 680 MBytes, where GCap outperforms recent, successful auto-captioning methods by up to 10 percentage points in captioning accuracy (50% relative improvement).
Elastase Inhibition by the Inter-α-Trypsin Inhibitor and Derived Inhibitors of Man and Cattle (1983)

The inhibitory properties of HI-14 and BI-14, the active 14-kDa parts released from the corresponding human and bovine inter-alpha-trypsin inhibitors, are compared. The structurally homologous inhibitors composed of two tandem Kunitz-type domains differ in their inhibitory specificity, although the reactive site residue in position P1 is occupied by identical (arginine in the C-terminal domain II) or similar (methionine and leucine in the N-terminal domain I of HI-14 and BI-14, respectively) amino-acid residues. The N-terminal domain I of HI-14 is completely inactive against chymotrypsin and pancreatic elastase, whereas BI-14 is a strong inhibitor of these enzymes. Elastase from polymorphonuclear granulocytes interacts with both inhibitors but with different affinities. Compared with the bovine inhibitor, the human inhibitor shows a much lower affinity from this enzyme. Human ITI and its physiological 30-kDa derivative (HI-30) show the same inhibitory properties as HI-14. The differences between human and bovine inhibitors might be explained by a preceding oxidation of Met in vivo of the reactive site residue in position P1 and/or by the influence of the environmental parts connected with this antielastase reactive site region in human ITI or in the active domains thereof.
Fiber Types in Mammalian Skeletal Muscles (2011)

Mammalian skeletal muscle comprises different fiber types, whose identity is first established during embryonic development by intrinsic myogenic control mechanisms and is later modulated by neural and hormonal factors. The relative proportion of the different fiber types varies strikingly between species, and in humans shows significant variability between individuals. Myosin heavy chain isoforms, whose complete inventory and expression pattern are now available, provide a useful marker for fiber types, both for the four major forms present in trunk and limb muscles and the minor forms present in head and neck muscles. However, muscle fiber diversity involves all functional muscle cell compartments, including membrane excitation, excitation-contraction coupling, contractile machinery, cytoskeleton scaffold, and energy supply systems. Variations within each compartment are limited by the need of matching fiber type properties between different compartments. Nerve activity is a major control mechanism of the fiber type profile, and multiple signaling pathways are implicated in activity-dependent changes of muscle fibers. The characterization of these pathways is raising increasing interest in clinical medicine, given the potentially beneficial effects of muscle fiber type switching in the prevention and treatment of metabolic diseases.
Relation between the RF discharge parameters and plasma etch rates, selectivity, and anisotropy (1984)

By extending earlier ideas and introducing new ones in this paper, we relate observable rf discharge parameters to the plasma etch characteristics of rate, selectivity, and anisotropy. The ion energy transport ‘‘ellipsoid’’ generated by the electric field across the plasma sheath is shown to induce anisotropic etch reactions and, under certain circumstances, to ‘‘enhance’’ the intrinsic chemical etch selectivity. The plasma sheath electric field is shown to be determined by observable rf discharge parameters. The rf discharge is reduced to an equivalent circuit, which relates the time averaged plasma body and sheath electric fields to the rf discharge parameters of plasma geometry, current or power and discharge excitation frequency. We find two regimes of excitation frequency, for otherwise identical conditions, generating much larger sheath electric fields below than above the ion plasma frequency (∼1 MHz). Fixing the plasma geometry and etch gas chemical composition is identified as central to obtaining simply behaved and reproducible etch characteristics. At comparable etch anisotropy, the only practical distinction between the etch characteristics of ‘‘high’’ pressure ‘‘plasma etching’’ and ‘‘low’’ pressure ‘‘reactive ion etching,’’ is that the former is capable of significantly higher etch rates and selectivities than the latter.
Current status and perspectives of chimeric antigen receptor modified T cells for cancer treatment (2017)

Chimeric antigen receptor (CAR) is a recombinant immunoreceptor combining an antibody-derived targeting fragment with signaling domains capable of activating cells, which endows T cells with the ability to recognize tumor-associated surface antigens independent of the expression of major histocompatibility complex (MHC) molecules. Recent early-phase clinical trials of CAR-modified T (CAR-T) cells for relapsed or refractory B cell malignancies have demonstrated promising results (that is, anti-CD19 CAR-T in B cell acute lymphoblastic leukemia (B-ALL)). Given this success, broadening the clinical experience of CAR-T cell therapy beyond hematological malignancies has been actively investigated. Here we discuss the basic design of CAR and review the clinical results from the studies of CAR-T cells in B cell leukemia and lymphoma, and several solid tumors. We additionally discuss the major challenges in the further development and strategies for increasing anti-tumor activity and safety, as well as for successful commercial translation.
A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding (2003)

BMS-378806 is a recently discovered small molecule HIV-1 inhibitor that blocks viral entrance to cells. The compound exhibits potent inhibitory activity against a panel of R5-(virus using the CCR5 coreceptor), X4-(virus using the CXCR4 coreceptor), and R5/X4 HIV-1 laboratory and clinical isolates of the B subtype (median EC 50 of 0.04 μM) in culture assays. BMS-378806 is selective for HIV-1 and inactive against HIV-2, SIV and a panel of other viruses, and exhibits no significant cytotoxicity in the 14 cell types tested (concentration for 50% reduction of cell growth, &gt;225 μM). Mechanism of action studies demonstrated that BMS-378806 binds to gp120 and inhibits the interactions of the HIV-1 envelope protein to cellular CD4 receptors. Further confirmation that BMS-378806 targets the envelope in infected cells was obtained through the isolation of resistant variants and the mapping of resistance substitutions to the HIV-1 envelope. In particular, two substitutions, M426L and M475I, are situated in the CD4 binding pocket of gp120. Recombinant HIV-1 carrying these two substitutions demonstrated significantly reduced susceptibility to compound inhibition. BMS-378806 displays many favorable pharmacological traits, such as low protein binding, minimal human serum effect on anti-HIV-1 potency, good oral bioavailability in animal species, and a clean safety profile in initial animal toxicology studies. Together, the data show that BMS-378806 is a representative of a new class of HIV inhibitors that has the potential to become a valued addition to our current armamentarium of antiretroviral drugs.
Mammaglobin-A is a target for breast cancer vaccination (2016)

We recently completed a phase 1 clinical trial demonstrating the safety of a mammaglobin-A DNA vaccine in patients with metastatic breast cancer. We are currently enrolling patients with early stage breast cancer in a phase 1b clinical trial. The mammaglobin-A DNA vaccine will be administered concurrently with neoadjuvant endocrine therapy, providing a unique opportunity to examine the impact of vaccination in the tumor microenvironment.
Molecular decoys: ligand-binding recombinant proteins protect mice from curarimimetic neurotoxins. (1988)

Mimic ligand-binding sites of the nicotinic acetylcholine receptor bind d-tubocurarine and alpha-bungarotoxin in vitro. Injection of such binding sites into mice could act as molecular decoys in vivo, providing protection against toxic ligands. This hypothesis of molecular "decoyance" has been tested in greater than 250 mice. Bacterially produced cholinergic binding sites provided a 2-fold increase in the survival rate of animals challenged with curarimimetic neurotoxins. Possible considerations for decoy designs and their applications are discussed.
P2‐527: Targeting hyperphosphorylated tau protein with a monoclonal antibody at an advanced stage of tau pathology improves cognition in a mouse model (2011)

Immunotherapy targeting pathological tau is emerging as a promising approach to treat tauopathies such as Alzheimer's disease (AD) and frontotemporal dementia. We have previously shown that prophylactic active or passive tau immunotherapy, starting at 2-3 months of age, clears tau pathology and improves function (Asuni A. et al., J. Neurosci. 2007, Boutajangout A. et al., J. Neurosci. 2010, Boutajangout A. et al., ICAD 2010). Here we assessed if a phospho-specific monoclonal, 4E6G7, targeting the same epitope, would be efficacious if treatment commenced at an advanced stage of tau pathology (8-9 months). htau/PS1 mice without mouse tau protein (8-9 months) were injected intraperitoneally (250 μg/125 μl) once per week with a novel phospho-specific tau monoclonal, 4E6G7 (n = 9) or pooled mouse IgG (n = 10) for a total of 13 injections. Their behavior was analyzed at 11-12 months of age and brain tissue subsequently harvested for analyses of treatment efficacy. The immunized mice (n = 7-8) performed substantially better than controls (n = 6) on the Radial Arm Maze (p < 0.0001; post hoc, p < 0.01-0.001 on days 2, 3, 5-9), the Closed Field Symmetrical Maze with 35-69% fewer errors in simple, intermediate and complex tasks (p < 0.05-0.003), and the Object Recognition Task (63% time spent with a novel object vs. 46% for controls, p < 0.05). The groups did not differ in various sensorimotor tasks, indicating that the robust cognitive improvements cannot be explained by sensorimotor effects, which further strengthens our results. Interestingly, more controls died during the study (40%) than immunized mice (22%), providing an additional support for the beneficial effect of the monoclonal tau antibody. Histological and biochemical analyses are underway. These results indicate pronounced efficacy of passive tau immunotherapy at an advanced stage of tauopathy, which suggests that this approach may be beneficial after clinical onset of AD and other tauopathies.
The Relationship between Iranian EFL Learners’ Beliefs about Language Learning and Their Use of Learning Strategies (2013)

The present study investigated the relationship between Iranian EFL learners’ learning strategies use and their language learning beliefs. A sample of 200 Iranian EFL learners who were all English language learners at different language institutes participated in this study. Two instruments, Beliefs about Language Learning Inventory (BALLI) and the Strategy Inventory for Language Learning (SILL), were used to collect data. The data analysis, through Pearson Correlation, revealed a positive significant relationship between overall BALLI and SILL, which indicates that learners with stronger beliefs use more learning strategies. Further, the results of Regression analysis indicated that only the “learning and communication strategies” and “foreign language aptitude” subscales in BALLI are significant predictors of overall strategy use. The findings of the present study suggest that understanding learners’ beliefs about language learning is critical to understand strategies used by learners and accordingly plan proper language instructions.
The Role of Pseudorabies Virus Thymidine Kinase Expression in Trigeminal Ganglion Infection (1983)

The role of pseudorabies virus (PRV) thymidine kinase (TK) expression in the pathogenesis of PRV infection of mice was studied with TK-negative (TK-) mutants. Thymidine phosphorylation and arabinosylthymine inhibition of PRV replication and efficiency of plating were used to characterize TK+ and TK- PRV. In addition, a plaque autoradiography procedure was utilized to determine the TK phenotype of individual plaques. TK+ and TK- PRV replicated well in ocular tissues, while TK+ but not TK- did so in ganglion tissue. Mortality was absent after TK- PRV inoculation and widespread after inoculation of similar amounts of TK+ PRV. Latent infection in mice was not detected with either TK+ or TK- PRV. This study indicated the probable importance of PRV TK expression in acute trigeminal ganglion infection.
Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N‐mediated resistance to tobacco mosaic virus (2002)

The tobacco N gene confers resistance to tobacco mosaic virus (TMV) and encodes a Toll-interleukin-1 receptor/nucleotide binding site/leucine-rich repeat (TIR-NBS-LRR) class protein. We have developed and used a tobacco rattle virus (TRV) based virus induced gene silencing (VIGS) system to investigate the role of tobacco candidate genes in the N-mediated signalling pathway. To accomplish this we generated transgenic Nicotiana benthamiana containing the tobacco N gene. The transgenic lines exhibit hypersensitive response (HR) to TMV and restrict virus spread to the inoculated site. This demonstrates that the tobacco N gene can confer resistance to TMV in heterologous N. benthamiana. We have used this line to study the role of tobacco Rar1-, EDS1-, and NPR1/NIM1- like genes in N-mediated resistance to TMV using a TRV based VIGS approach. Our VIGS analysis suggests that these genes are required for N function. EDS1-like gene requirement for the N function suggests that EDS1 could be a common component of bacterial, fungal and viral resistance signalling mediated by the TIR-NBS-LRR class of resistance proteins. Requirement of Rar1- like gene for N-mediated resistance to TMV and some powdery mildew resistance genes in barley provide the first example of converging points in the disease resistance signalling pathways mediated by TIR-NBS-LRR and CC-NBS-LRR proteins. The TRV based VIGS approach as described here to study N-mediated resistance signalling will be useful for the analysis of not only disease resistance signalling pathways but also of other signalling pathways in genetically intractable plant systems.
Positronium formation in porous materials for antihydrogen production (2010)

Positronium (Ps) formation measurements in several porous materials as: Vycor, germanate Xerogel, Metal-Organic Frameworks MOF-177 and Aerogel with two densities (20 and 150 mg/cm3), were performed by means of a variable energy positron beam provided with a Ge detector and a positron lifetime spectrometer. An efficient formation of cooled Ps atoms is a requisite for the production of antihydrogen, with the aim of a direct measurement of the Earth gravitational acceleration g of antimatter, which is a primary scientific goal of AEGIS (Antimatter Experiment: Gravity, Interferometry, Spectroscopy). Porous materials are necessary to form a high yield of Ps atoms as well as to cool Ps through collisions with the inner walls of the pores. The different materials were characterized and produce Ps into the pores. Lifetime measurements give an estimation of the typical pores dimension of the substances. A comparative study of the positron lifetime and the Ps fraction values in the above mentioned materials indicates that silica Aerogel, with the appropriate density, is an excellent candidate for an efficient formation of cold Ps atoms for the AEGIS project. © 2010 IOP Publishing Ltd.
Differential toxicity of carbovir and AZT to human bone marrow hematopoietic progenitor cells in vitro. (1990)

We have studied the in vitro effects of carbovir as compared to 3'-azido-3'-deoxythymidine (AZT) on the growth of clonal bone marrow-derived hematopoietic progenitor cells. (-)Carbovir, the enantiomer with anti-human immunodeficiency virus (HIV) activity, exhibited significantly less toxicity to hematopoietic cells than AZT. These in vitro studies suggest that (-)carbovir will exhibit less hematologic toxicity in the therapy of patients infected with HIV either as a single agent or in combination with other agents that inhibit HIV proliferation.
IMPROVEMENT OF POWER SYSTEM DYNAMIC STABILITY INCLUDING WIND FARM INTERCONNECTED MULTIMACHINE SYSTEM (2015)

Wind farms influences dynamic performance in power system and so wind energy penetration in power grid has increased tremendously over the time. The wind farm performance now became a concern such as to make appropriate stability analysis and their system models. This study aids to develop stability for the power system model in which aggregated wind machines like induction machine and conventional machines like synchronous machine operate together. The developed model is to be tested using stability analysis techniques such as state space matrix system, eigen solution method and time domain response. In the system the induction generator operating with a synchronous generator is proposed and compared with a synchronous-synchronous generator model. The results of time domain response for both generator models show the effective operation of proposed model. Recently, particle swarm optimization (PSO) technique appeared as a promising algorithm for handling the optimization problems. PSO based power system stabilizers (PSS) controllers on synchronous generators linked with wind power generation is also considered to improve the performance of the system by damping the power system oscillations.
Sequence and expression of the gene encoding the corrinoid/iron-sulfur protein from Clostridium thermoaceticum and reconstitution of the recombinant protein to full activity. (1993)

The corrinoid/iron-sulfur protein (C/Fe-SP) from Clostridium thermoaceticum acts as a methyl group carrier in the anaerobic acetyl-CoA pathway of CO and CO2 fixation. Consisting of a small (approximately 33 kDa) and a large (approximately 55 kDa) subunit, the C/Fe-SP contains 1 mol of cobalt in a corrinoid cofactor and 1 mol of [4Fe-4S]2+/1+ cluster/mol of alpha beta dimer. Cobalt is the site of methylation, and the [4Fe-4S] center appears to serve an electron transfer function. The genes encoding both subunits have been cloned previously and are located within a gene cluster that includes other genes required for CO2 fixation by anaerobic bacteria. When the genes encoding the C/Fe-SP were expressed in Escherichia coli, the protein was found to be inactive. We report the amino acid sequences of the large and small subunits of the C/Fe-SP based on the DNA sequences of the cloned genes. The [4Fe-4S] cluster was found to be located in the large subunit. Although the primary structural lattice for cobamide binding resides in the small subunit, both subunits are required for formation of a stable cobamide-binding protein. Based on sequence comparisons with other [4Fe-4S]-containing proteins, 3 of the 4 cysteine residues that serve as ligands to the iron sites in the cluster have been located. The two subunits were independently overexpressed in E. coli to a level of 30-50% of cell protein; however, the resulting protein was inactive, lacked stoichiometric amounts of Fe-S cluster, and lacked cobamide. By combining the recombinant subunits, unfolding them with urea, and refolding in the presence of cobamide, iron, and inorganic sulfide, the resulting C/Fe-SP was found to contain stoichiometric amounts of cobamide and [4Fe-4S] cluster and had spectroscopic and enzymatic properties similar to those of the native protein. We expect that the methods developed here may be used for heterologous overexpression and reconstitution of other complex metalloenzymes. The C/Fe-SP was found to utilize with equal efficiency either vitamin B12 or the natural cofactor 5-methoxybenzimidazolylcobamide as a methyl carrier.
A genetically engineered, protein-based optical biosensor of myosin II regulatory light chain phosphorylation. (1994)

Myosin II is an important motor in the contraction of smooth and striated muscle as well as in a variety of non-muscle cell motile events including cytokinesis, cortical contractions during migration of fibroblasts, and capping of receptors. Phosphorylation of the 20-kDa light chain by myosin light chain kinase is part of the regulation of smooth muscle and mammalian nonmuscle myosin II. We designed, characterized, and tested the use of a protein-based optical biosensor to monitor this phosphorylation "switch." A regulatory light chain was genetically engineered to contain a single cysteine at amino acid position 18. The mutant light chain (Cys18.LC20), reacted with the fluorophore acrylodan, responded to phosphorylation of serine 19 with a fluorescence emission quenching of 60% and a 28-nm red-shift. When the acrylodan-labeled mutant light chain (AC-Cys18.LC20) was exchanged into turkey gizzard myosin II, it exhibited a 25% fluorescence emission quenching and a 10-nm red-shift upon phosphorylation of serine 19. The myosin II optical biosensor exhibited nearly control levels of the rate of phosphorylation, K+ATPase activity, and in vitro motility. The acrylodan-labeled light chain was exchanged into the A-bands of chicken pectoralis myofibrils in situ to demonstrate the localization and activity of the biosensor in a highly ordered contractile system. Fluorometry and quantitative fluorescence microscopic imaging experiments demonstrated that AC-Cys18.LC20 exchanged myofibrils expressed a phosphorylation-dependent fluorescence change. Labeled light chains were also incorporated into stress fibers of living fibroblasts and smooth muscle cells. This general approach of combining molecular biology and fluorescence spectroscopy to create novel protein-based optical biosensors should provide valuable tools for investigations with model systems and solution studies and ultimately yield important information about temporal-spatial chemical and molecular changes in live cells.