gebhart/patrepeval huggingface dataset:
Visualization of FISH Probes by Dual-Color Chromogenic In Situ Hybridization (2010)

The overall purpose of the study was to demonstrate applicability of the DAKO dual-color chromogenic in situ hybridization (CISH) assay (DAKO Denmark, Glostrup) with respect to 4 fluorescence in situ hybridization (FISH) probes: MYC (c-MYC), EGFR, ERBB2 (HER2), and TOP2A. The study showed that the dual-color CISH assay can convert Texas red and fluorescein isothiocyanate (FITC) signals into chromogenic signals with an almost complete 1:1 conversion ratio. Agreement studies between the FISH assays for HER2 and TOP2A and the corresponding CISH conversion assays showed 100% concordance (kappa values of 1.0) between the CISH and FISH methods for HER2 and TOP2A status. The correlations of the gene copy number to centromere-17 ratios were similarly high, with a correlation coefficient (r) for HER2 and TOP2A of more than 0.95. Owing to the relatively small number of specimens in this study, it is important that the data are confirmed in a larger study.
Protection and immunity in commercial chicken layers administered Mycoplasma gallisepticum liposomal bacterins. (1988)

Six liposomal Mycoplasma gallisepticum (MG) bacterins, differing in charge and size, and two oil-emulsion vaccines (sonicated and non-sonicated) were given to white leghorns in two doses, at 13 weeks and again 1 month later. At 21 weeks of age, all chickens were challenged with a viable 20-hour culture of MG cells (17,800 colony-forming units) intratracheally and with nonviable MG organisms (0.09 mg protein) injected subcutaneously in the wattle center. The three chicken groups that had the lowest tracheal MG-infection rates postchallenge were those given adjuvants of small multilamellar positively charged liposomes (16.67%), large multilamellar negatively charged liposomes (16.67%), and non-sonicated oil-emulsion bacterin (37.5%). These three groups also had significant levels of antibody in sera 4 weeks after the second dose of vaccine. The group given the small multilamellar positively charged liposome also showed significant delayed-type hypersensitivity (wattle swelling) (P less than or equal to 0.05). The group given the large multilamellar negatively charged liposomes had the highest local antibody response (P less than or equal to 0.01) and was the only group that had no microscopic lesions in the trachea.
Filter-Bank Based Technique for Fast Acquisition of Galileo and GPS Signals (2006)

The computational load and the speed of the code acquisition process of any CDMA system depend on the number of timing hypotheses required to search a given uncertainty window (i.e., the code epoch interval in GPS and Galileo systems). By increasing the spacing between the timing hypotheses (or the time-bin step), this computational load may be reduced and the acquisition speed may be increased. However, the time-bin step is limited by the main lobe width of the correlation function envelope (i.e., the correlation which is performed between the incoming signal and a reference code stored at the receiver). If the width of this main lobe is increased, the time-bin step may be increased as well. Here, a filter-bank based method is proposed, which allows the use of higher time-bin steps than those usually used in GPS/Galileo and, thus, it has the potential of increasing the acquisition speed. Simulation results are shown in comparison with other acquisition methods
Crystal Structures of Two Complexes of the Rare-Earth-DOTA-Binding Antibody 2D12.5:  Ligand Generality from a Chiral System (2003)

We report the crystal structures of antibody 2D12.5 Fab bound to an yttrium-DOTA analogue and separately to a gadolinium-DOTA analogue. The rare earth elements have many useful properties as probes, and 2D12.5 binds the DOTA (1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid) complexes of all of them (Corneillie et al. J. Am. Chem. Soc. 2003, 125, 3436-3437). The structures show that there are no direct protein-metal interactions: a bridging water acts as a link between the protein and metal, with the chelate present as the M isomer in each case. DOTA forms an amphipathic cylinder with the charged carboxylate groups toward the face of the chelate near the metal ion, while nonpolar methylene groups from the macrocycle and the carboxymethyl groups occupy the rear and sides of the molecule. The orientation of the metal-DOTA in the 2D12.5 complex places most of the methylene carbon atoms of DOTA in hydrophobic contact with aromatic protein side chains. Other binding interactions between the metal complex and the antibody include a bidentate salt bridge, four direct H-bonds, and four to five water-mediated H-bonds. We find that 2D12.5 exhibits enantiomeric binding generality, binding yttrium chelates in both Lambda(deltadeltadeltadelta) and Delta(lambdalambdalambdalambda) configurations with modestly different affinities. This develops from the symmetrical nature of the DOTA chelate, which places heteroatoms and hydrophobic atoms in approximately the same relative positions regardless of the helicity of DOTA.
Animal models of inherited neuropathies (2006)

Animal models have opened up new perspectives on the pathomechanisms and possible treatment strategies of inherited neuropathies.
A Total Variation–Based JPEG Decompression Model (2012)

We propose a variational model for artifact-free JPEG decompression. It is based on the minimization of the total variation over the convex set U of all possible source images associated with given JPEG data. The general case where U represents a pointwise restriction with respect to an $L^2$-orthonormal basis is considered. Analysis of the infinite dimensional model is presented, including the derivation of optimality conditions. A discretized version is solved using a primal-dual algorithm supplemented by a primal-dual gap-based stopping criterion. Experiments illustrate the effect of the model. Good reconstruction quality is obtained even for highly compressed images, while a graphics processing unit (GPU) implementation is shown to significantly reduce computation time, making the model suitable for real-time applications.
BRAF and MEK inhibitors in the era of immunotherapy in melanoma patients (2018)

The treatment landscape in advanced melanoma is changing dramatically with the approval of new drugs. Vemurafenib was the first approved targeted agent for the treatment of <i>BRAF</i>-mutant advanced melanoma. However, treatment with a BRAF inhibitor is linked with acquired resistance occurring in half of the patients after approximately six months. Combination of MEK and BRAF inhibitor therapy results in extension of the time to resistance, translating into longer overall survival of treated patients. Similar clinical benefits are observed with therapy using antibodies against immune-checkpoint inhibitors in the same patient population. Due to the fact that results of randomised studies comparing these two treatment strategies back to back have not been presented yet, the best first and second line treatment option in patients with <i>BRAF</i>-mutant melanoma is unknown. Currently, phase 3 studies are also evaluating the efficacy of targeted therapy combined with immunotherapy in patients with <i>BRAF</i>-mutant and <i>BRAF</i> wild-type advanced melanoma. Identifying a biomarker for the selection of patients benefiting most from the treatment will be crucial for further survival improvement in patients with advanced melanoma.
Efficiencies of translation in three reading frames of unusual non‐ORF sequences isolated from phage display (2000)

An unusual nucleotide sequence, called H10, was previously isolated by biopanning with a random peptide library on filamentous phage. The sequence encoded a peptide that bound to the growth hormone binding protein. Despite the fact that the H10 sequence can be expressed in Escherichia coli as a fusion to the gene III minor coat protein of the M13 phage, the sequence contained two TGA stop codons in the zero frame. Several mutant derivatives of the H10 sequence carried not only a stop codon, but also showed frameshifts, either +1 or -1 in individual isolates, between the H10 start and the gene III sequences. In this work, we have subcloned the H10 sequence and three of its derivatives (one requiring a +1 reading frameshift for expression, one requiring a -1 reading frameshift, and one open reading frame) in gene fusions to a reporter beta-galactosidase gene. These sequences have been cloned in all three reading frames relative to the reporter. The non-open reading frame constructs gave (surprisingly) high expression of the reporter (10-40% of control vector expression levels) in two out of the three frames. A site-directed mutant of the TGA stop codon (to TTA) in the +1 shifter greatly reduced the frameshift and gave expression primarily in the zero frame. By contrast, a site-directed mutant of the TGA in the -1 shifter had little effect on the pattern of expression, and alteration of the first TGA (of two) in H10 itself paradoxically reduced expression by half. We believe these phenomena to reflect a translational recoding mechanism in which ribosomes switch reading frames or read past stop codons upon encountering a signal encoded in the nucleotide sequence of the mRNA, because both the open reading frame derivative (which has six nucleotide changes from parental H10) and the site-directed mutant of the +1 shifter, primarily expressed the reporter only in the zero frame.
Tapping and rubbing (2008)

Tactile feedback allows devices to communicate with users when visual and auditory feedback are inappropriate. Unfortunately, current vibrotactile feedback is abstract and not related to the content of the message. This often clash-es with the nature of the message, for example, when sending a comforting message.
A new fiducial marker for Image-guided radiotherapy of prostate cancer: Clinical experience (2008)

The preliminary result of an on going clinical study of a Ni Ti prostate stent, potentially a new fiducial marker for image guided radiotherapy, looks promising. The risk of migration appears to be much lower compared to previous designs.
Reconstructing the 3D Shape and Bone Mineral Density Distribution of the Proximal Femur From Dual-Energy X-Ray Absorptiometry (2011)

The accurate diagnosis of osteoporosis has gained increasing importance due to the aging of our society. Areal bone mineral density (BMD) measured by dual-energy X-ray absorptiometry (DXA) is an established criterion in the diagnosis of osteoporosis. This measure, however, is limited by its two-dimensionality. This work presents a method to reconstruct both the 3D bone shape and 3D BMD distribution of the proximal femur from a single DXA image used in clinical routine. A statistical model of the combined shape and BMD distribution is presented, together with a method for its construction from a set of quantitative computed tomography (QCT) scans. A reconstruction is acquired in an intensity based 3D-2D registration process whereby an instance of the model is found that maximizes the similarity between its projection and the DXA image. Reconstruction experiments were performed on the DXA images of 30 subjects, with a model constructed from a database of QCT scans of 85 subjects. The accuracy was evaluated by comparing the reconstructions with the same subject QCT scans. The method presented here can potentially improve the diagnosis of osteoporosis and fracture risk assessment from the low radiation dose and low cost DXA devices currently used in clinical routine.
Comparison of genotypic and phenotypic techniques for assessing the variability of the fungus<i>Epicoccum nigrum</i> (2002)

This work evaluates the predictive value of several phenotypic techniques on a collection of fungal isolates, and compares the results obtained with genotypic techniques performed on the same strains.
Effect of isosorbide mononitrate on the human optic nerve and choroidal circulations (1999)

These results suggest that, in normal subjects, ISMO increases significantly ON flow but not Ch flow. The inverse correlation observed between PP and ON flow suggests that the same mechanism(s) responsible for systemic vasodilatation and blood pressure decrease may also cause the ON flow increase.
BDD minimization using symmetries (1999)

In this paper we study the effect of using information about (partial) symmetries for the minimization of reduced ordered binary decision diagrams (ROBDD's). The influence of symmetries for the integration in dynamic variable ordering is studied for both completely and incompletely specified Boolean functions. The problems above are studied from a theoretical and practical point of view. Statistical results and benchmark results are reported to underline the efficiency of the approach. They prove that our techniques lead to improvements of the ROBDD sizes by up to 70%.
Charge transport in an AC plasma panel (1981)

A transverse voltage applied between a display cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> and a transfer cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> on a standard 60 lines/inch ac plasma panel can simultaneously cause a previously ON cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> to fire and transport a large amount of electrons from cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> toward cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> . The same transverse voltage combines with the voltage due to transported electrons to produce subsequent discharges which, initiated near cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> , grow rapidly as they propagate along the row toward cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> . A voltage pulse (≃sustain pulse), applied to cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> , will combine with the local row wall voltage to produce another sequence of discharges along the row. These discharges, initiated near cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> , gain intensity as they spread toward cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> . This dynamic process results in a large and controllable charge transfer between the display cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> and the transfer cell <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> , a key mechanism for shift address display. By reversing the polarity of the transverse voltage, ions also can be transported, but ion transport produces smaller charge transfer.
Phase I/II Trial of Multiple Dose<sup>131</sup>Iodine-MAb LL2 (CD22) in Patients with Recurrent Non-Hodgkin's Lymphoma (2000)

The purpose of this to evaluate in a phase I/II study the efficacy and toxicity of a multi-dose administration of 131I labeled CD22 monoclonal antibody (131I-MAb-LL2) in escalating dose cohorts administered to relapsed non-Hodgkin's lymphoma (NHL) patients. Twenty-one patients with relapsed NHL received one of four dose levels of 131-MAb-LL2 administered in a twice weekly pattern. Starting with dose level 2, the patients also received 20 mg of unlabeled LL2 prior to each radiolabeled dose administered. Previously stored autologous peripheral blood progenitors were reinfused in case of prolonged cytopenias. Patients could repeat the same treatment if they had stable disease or a response to the first therapy at 8 weeks, and had not received their peripheral blood progenitors with the first cycle. Combining all of the dose cohorts, there were 5 complete responses or complete responses (undetermined) and 2 partial responses for a total response rate of 7/21 (33%). There was no dose response effect with responses documented at all dose levels. Expected toxicities were hematopoietic, requiring stem cell re-infusion in 5 patients. Other toxicities included hypothyroidism in 3 patients, and human anti-mouse antibody formation (HAMA) in 4 patients. In conclusion, 131I-MAb-LL2, when administered in a multi-dose fashion with 20 mg unlabeled antibody pre-dosing, resulted in a response rate of 33% in heavily pre-treated NHL patients. Non-hematologic toxicities were mild and few in number. Further evaluation of this treatment is warranted and further dose escalation will be possible.
<sup>31</sup>P NMR spectroscopy in the quality control and authentication of extra‐virgin olive oil: A review of recent progress (2007)

This review is a brief account on the application of a novel methodology to the quality control and authentication of extra-virgin olive oil. This methodology is based on the derivatization of the labile hydrogens of functional groups, such as hydroxyl and carboxyl groups, of olive oil constituents with the phosphorus reagent 2-chloro-4,4,5,5-tetramethyldioxaphospholane, and the use of the (31)P chemical shifts to identify the phosphitylated compounds. Various experimental aspects such as pertinent instrumentation, sample preparation, acquisition parameters and properties of the phosphorus reagent are reviewed. The strategy to assign the (31)P signals of the phosphitylated model compounds and olive oil constituents by employing 1D and 2D NMR experiments is presented. Finally, the capability of this technique to assess the quality and the genuineness of extra-virgin olive oil and to detect fraud is discussed.
Cancer-associated fibroblasts induce antigen-specific deletion of CD8 + T Cells to protect tumour cells (2018)

Tumours have developed strategies to interfere with most steps required for anti-tumour immune responses. Although many populations contribute to anti-tumour responses, tumour-infiltrating cytotoxic T cells dominate, hence, many suppressive strategies act to inhibit these. Tumour-associated T cells are frequently restricted to stromal zones rather than tumour islands, raising the possibility that the tumour microenvironment, where crosstalk between malignant and "normal" stromal cells exists, may be critical for T cell suppression. We provide evidence of direct interactions between stroma and T cells driving suppression, showing that cancer-associated fibroblasts (CAFs) sample, process and cross-present antigen, killing CD8<sup>+</sup> T cells in an antigen-specific, antigen-dependent manner via PD-L2 and FASL. Inhibitory ligand expression is observed in CAFs from human tumours, and neutralisation of PD-L2 or FASL reactivates T cell cytotoxic capacity in vitro and in vivo. Thus, CAFs support T cell suppression within the tumour microenvironment by a mechanism dependent on immune checkpoint activation.
The mouse and human genes encoding the recognition component of the N-end rule pathway (1998)

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. The N-end rule pathway is one proteolytic pathway of the ubiquitin system. The recognition component of this pathway, called N-recognin or E3, binds to a destabilizing N-terminal residue of a substrate protein and participates in the formation of a substrate-linked multiubiquitin chain. We report the cloning of the mouse and human Ubr1 cDNAs and genes that encode a mammalian N-recognin called E3alpha. Mouse UBR1p (E3alpha) is a 1,757-residue (200-kDa) protein that contains regions of sequence similarity to the 225-kDa Ubr1p of the yeast Saccharomyces cerevisiae. Mouse and human UBR1p have apparent homologs in other eukaryotes as well, thus defining a distinct family of proteins, the UBR family. The residues essential for substrate recognition by the yeast Ubr1p are conserved in the mouse UBR1p. The regions of similarity among the UBR family members include a putative zinc finger and RING-H2 finger, another zinc-binding domain. Ubr1 is located in the middle of mouse chromosome 2 and in the syntenic 15q15-q21.1 region of human chromosome 15. Mouse Ubr1 spans approximately 120 kilobases of genomic DNA and contains approximately 50 exons. Ubr1 is ubiquitously expressed in adults, with skeletal muscle and heart being the sites of highest expression. In mouse embryos, the Ubr1 expression is highest in the branchial arches and in the tail and limb buds. The cloning of Ubr1 makes possible the construction of Ubr1-lacking mouse strains, a prerequisite for the functional understanding of the mammalian N-end rule pathway.
A bio-robotics approach to real-time skeletal joint fluoroscopy during natural movements (2011)

A new class of fluoroscopy, using a robotic mobile platform, is being developed. The Tracking Fluoroscope System (TFS) is intended to be an orthopedic diagnostic tool that provides more accurate and detailed in vivo pre-operative and post-operative information for surgeons. This is accomplished through the ability to fluoroscope natural and uninterrupted human joint motion during level walking, step climbing, and ramp walking. This overall functionality requires independent tracking of the position and orientation of the body with respect to the robotic platform, as well as the position of the joints with respect to the body. The overall robotic system, embodied in the TFS, necessary to accurately perform real-time imaging of joints in motion is discussed. Recent subject and joint tracking experimental results are presented.
Using machine vision to control pointing device (2012)

Paper deals with using machine vision to control pointing device. It focuses on creating control software for movement and positioning with pointing device based on machine vision. Using the account information on the identification and location of the object positioning obtained using machine vision techniques.
Herbicide-resistant alfalfa cells: an example of gene amplification in plants. (1984)

We have selected alfalfa suspension cell lines that are 20- to 100-fold more resistant than wild-type cells to the nonselective herbicide L-phosphinothricin, a mixed competitive inhibitor of glutamine synthetase (GS). GS enzyme levels are three- to sevenfold elevated in the variant cell line. Partial amino acid sequences of two cyanogen bromide cleavage peptides have been determined on GS purified from the variant cell line and used to confirm the identity of a 276-base pair GS cDNA clone. Southern blot analysis of wild-type and variant cell DNAs using this cDNA as a probe indicate that resistance to L-phosphinothricin is a consequence of a four- to 11-fold amplification of one GS gene resulting in about an eightfold increase in mRNA levels, and an increased enzyme synthesis sufficient to overcome the toxic effects of the inhibitor.
Cross-Protection in Animals Infected with Group A Arboviruses (1963)

Summary Experiments were carried out to investigate the phenomenon of cross-protection among Venezuelan equine encephalomyelitis (VEE), eastern equine encephalomyelitis (EEE) and Semliki Forest (SF) viruses in a variety of laboratory animals after immunization by the intraperitoneal, subcutaneous or respiratory routes; the last was effected by exposing the animals to aerosols of virus. One injection of an attenuated strain of VEE virus (9t) protected guinea pigs against a lethal challenge dose of EEE or SF virus in guinea pigs and mice, respectively. Two injections of live SF virus protected guinea pigs against small doses of VEE or EEE virus. Mice vaccinated with strain 9t responded by demonstrating resistance mechanisms that appeared to operate in series. This consisted of, first, an early nonspecific interference phase, followed by a second, specific phase. The second phase also included a partially specific mechanism of resistance of unknown origin and of relatively long duration manifested as cross-protection in the group A viruses.