gebhart/patrepeval huggingface dataset:
Targeting of human p53-overexpressing tumor cells by an HLA A*0201-restricted murine T-cell receptor expressed in Jurkat T cells. (2000)

A potent anti-human (hu) p53 CD8+ CTL response develops in HLA A*0201 transgenic (Tg) mice after immunization with peptides corresponding to HLA A*0201 motifs from hu p53. Mice immunized with the hu P53(149-157) peptide develop a CTL response that is of moderately high affinity and is capable of recognizing hu tumor cells expressing mutated p53. In this report, the mRNAs encoding the predominantly expressed T-cell receptor (TCR) sequences were molecularly cloned from a murine (mu) CTL clone derived from immunized Tg mice, which recognized endogenously processed hu p53 restricted by HLA A*0201. The separate A and B chain TCR cDNAs were transfected in the corresponding TCR A- and B- Jurkat-CD3- mutant T-cell lines, and each rescued CD3 surface expression. Both TCR chains were simultaneously introduced into Jurkat-CD3+ cells, and the transfected Jurkat cells recognized hu T2 cells sensitized with the p53(149-157) CTL epitope but not T2 cells sensitized with a nonspecific CTL epitope. Breast, pancreatic, and sarcoma tumor cell lines, which overexpress endogenous mutated p53, were recognized in the presence of anti-CD28 costimulation, only if they also expressed HLA A*0201. Normal hu fibroblasts established from skin cultures were not recognized. These results represent the first time that a p53-specific TCR capable of recognizing hu cancer cells was heterologously expressed in a naive recipient cell, converting that cell to one recognizing hu tumor cells with mutated p53. This TCR represents a candidate molecule for a genetic strategy in combating hu cancer by an adoptive immunotherapy approach, which uses the strong xenorecognition of hu p53 in mice.
Batch-mode active learning for technology-assisted review (2015)

In recent years, technology-assisted review (TAR) has become an increasingly important component of the document review process in litigation discovery. This is fueled largely by dramatic growth in data volumes that may be associated with many matters and investigations. Potential review populations frequently exceed several hundred thousands documents, and document counts in the millions are not uncommon. Budgetary and/or time constraints often make a once traditional linear review of these populations impractical, if not impossible — which made "predictive coding" the most discussed TAR approach in recent years. A key challenge in any predictive coding approach is striking the appropriate balance in training the system. The goal is to minimize the time that Subject Matter Experts spend in training the system, while making sure that they perform enough training to achieve acceptable classification performance over the entire review population. Recent research demonstrates that Support Vector Machines (SVM) perform very well in finding a compact, yet effective, training dataset in an iterative fashion using batch-mode active learning. However, this research is limited. Additionally, these efforts have not led to a principled approach for determining the stabilization of the active learning process. In this paper, we propose and compare several batch-mode active learning methods which are integrated within SVM learning algorithm. We also propose methods for determining the stabilization of the active learning method. Experimental results on a set of large-scale, real-life legal document collections validate the superiority of our method over the existing methods for this task.
LEWIS: Latent Embeddings for Word Images and their Semantics (2015)

The goal of this work is to bring semantics into the tasks of text recognition and retrieval in natural images. Although text recognition and retrieval have received a lot of attention in recent years, previous works have focused on recognizing or retrieving exactly the same word used as a query, without taking the semantics into consideration. In this paper, we ask the following question: \emph{can we predict semantic concepts directly from a word image, without explicitly trying to transcribe the word image or its characters at any point?} For this goal we propose a convolutional neural network (CNN) with a weighted ranking loss objective that ensures that the concepts relevant to the query image are ranked ahead of those that are not relevant. This can also be interpreted as learning a Euclidean space where word images and concepts are jointly embedded. This model is learned in an end-to-end manner, from image pixels to semantic concepts, using a dataset of synthetically generated word images and concepts mined from a lexical database (WordNet). Our results show that, despite the complexity of the task, word images and concepts can indeed be associated with a high degree of accuracy
DNA Polymerase with Characteristics of Reverse Transcriptase Purified from Human Milk (1979)

A DNA polymerase purified from a particulate fraction of human milk has biochemical and biophysical properties similar to those of viral reverse transcriptases. This enzyme is immunologically distinct from cellular DNA polymerases obtained from a variety of human sources.
High affinity soluble ILT2 receptor: a potent inhibitor of CD8+ T cell activation (2010)

Using directed mutagenesis and phage display on a soluble fragment of the human immunoglobulin super-family receptor ILT2 (synonyms: LIR1, MIR7, CD85j), we have selected a range of mutants with binding affinities enhanced by up to 168,000-fold towards the conserved region of major histocompatibility complex (MHC) class I molecules. Produced in a dimeric form, either by chemical cross-linking with bivalent polyethylene glycol (PEG) derivatives or as a genetic fusion with human IgG Fc-fragment, the mutants exhibited a further increase in ligand-binding strength due to the avidity effect, with resident half-times (t(1/2)) on the surface of MHC I-positive cells of many hours. The novel compounds antagonized the interaction of CD8 co-receptor with MHC I in vitro without affecting the peptide-specific binding of T-cell receptors (TCRs). In both cytokine-release assays and cell-killing experiments the engineered receptors inhibited the activation of CD8(+) cytotoxic T lymphocytes (CTLs) in the presence of their target cells, with subnanomolar potency and in a dose-dependent manner. As a selective inhibitor of CD8(+) CTL responses, the engineered high affinity ILT2 receptor presents a new tool for studying the activation mechanism of different subsets of CTLs and could have potential for the development of novel autoimmunity therapies.
Phase-separation in ion-containing mixtures in electric fields (2007)

When a liquid mixture is subjected to external electric fields, ionic screening leads to field gradients. We point out that, if the mixture is initially in the homogeneous phase, this screening can bring about a robust phase-separation transition with two main features: (i) the phase separation is expected to occur in any electrode geometry, and (ii) the voltage required is typically of the order of 1 V and even less. We discuss several applications of the effect relevant to the field of microfluidics, focusing on the creation of a nanometer-scale lubrication layer in the phase separation process and the modification of the slip length.
Replay compilation (2006)

The performance of Java has been tremendously improved by the advance of Just-in-Time (JIT) compilation technologies. However, debugging such a dynamic compiler is much harder than a static compiler. Recompiling the problematic method to produce a diagnostic output does not necessarily work as expected, because the compilation of a method depends on runtime information at the time of compilation.In this paper, we propose a new approach, called replay JIT compilation, which can reproduce the same compilation remotely by using two compilers, the state-saving compiler and the replaying compiler. The state-saving compiler is used in a normal run, and, while compiling a method, records into a log all of the input for the compiler. The replaying compiler is then used in a debugging run with the system dump, to recompile a method with the options for diagnostic output. We reduced the overhead to save the input by using the system dump and by categorizing the input based on how its value changes. In our experiment, the increase of the compilation time for saving the input was only 1%, and the size of the additional memory needed for saving the input was only 10% of the compiler-generated code.
Neonatal EEG audification for seizure detection (2014)

Technologies for automated detection of neonatal seizures are gradually moving towards cot-side implementation. The aim of this paper is to present an alternative way to visualize the output of a neonatal seizure detection algorithm. For this purpose audified neonatal EEG is considered. The EEG is audified with the aid of the neonatal seizure detection algorithm which selects the representative channels for stereo audio image and controls the signal gain. A survey on the usefulness and accuracy of the presented audification method has been performed. The results of the audification method compare favourably to that of using amplitude integrated EEG for detection of neonatal seizures.
Low-inductance gas switches for linear transformer drivers (2009)

We are investigating several alternate gas-switch designs for use in linear transformer drivers. To meet linear-transformer-driver (LTD) requirements, these air-insulated switches must be DC charged to 200 kV, be triggerable with a jitter of 5 ns or less, have very low prefire and no-fire rates ($\ensuremath{\sim}1$ in ${10}^{4}$ shots), and have a lifetime of at least several thousand shots. Since the switch inductance plays a significant role in limiting the rise time and peak current of the LTD circuit, the inductance needs to be as low as possible. The switches are required to conduct current pulses with $\ensuremath{\sim}100\mathrm{\text{\ensuremath{-}}}\mathrm{ns}$ rise times and 20--80 kA peak currents, depending on the application. Our baseline switch, designed by the High Current Electronics Institute in Tomsk, Russia, is a six-stage switch with an inductance on the order of 115 nH that is insulated with 47--67 psia of air. We are also testing three smaller two-stage switches that have inductances on the order of 66--100 nH. The smaller switches are insulated with 92--252 psia of air.
Isolation of human explant derived cardiac stem cells from cryopreserved heart tissue (2017)

The value of preserving high quality bio specimens for fundamental research is significant as linking cellular and molecular changes to clinical and epidemiological data has fueled many recent advances in medicine. Unfortunately, storage of traditional biospecimens is limited to fixed samples or isolated genetic material. Here, we report the effect of cryopreservation of routine myocardial biopsies on explant derived cardiac stem cell (EDC) culture outcomes. We demonstrate that immediate cryopreservation or delayed cryopreservation after suspension within cardioplegia for 12 hours did not alter EDC yields, proliferative capacity, antigenic phenotype or paracrine signature. Cryopreservation had negligible effects on the ability of EDCs to adopt a cardiac lineage, stimulate new vessel growth, attract circulating angiogenic cells and repair injured myocardium. Finally, cryopreservation did not influence the ability of EDCs to undergo genetic reprogramming into inducible pluripotent stem cells. This study establishes a means of storing cardiac samples as a retrievable live cell source for cardiac repair or disease modeling.
Toward measuring network security using attack graphs (2007)

In measuring the overall security of a network, a crucial issue is to correctly compose the measure of individual components. Incorrect compositions may lead to misleading results. For example, a network with less vulnerabilities or a more diversified configuration is not necessarily more secure. To obtain correct compositions of individual measures, we need to first understand the interplay between network components. For example, how vulnerabilities can be combined by attackers in advancing an intrusion. Such an understanding becomes possible with recent advances in modeling network security using attack graphs. Based on our experiences with attack graph analysis, we propose an integrated framework for measuring various aspects of network security. We first outline our principles andmethodologies. We then describe concrete examples to buildintuitions. Finally, we present our formal framework. It is our belief that metrics developed based on the proposed framework will lead to novel quantitative approaches to vulnerability analysis, network hardening, and attack response.
Adhesion and mechanical properties of amorphic diamond films prepared by a laser plasma discharge source (1992)

Amorphic diamond films can be grown in an ultrahigh vacuum environment free from hydrogen with a laser plasma discharge source. This technique produces films that adhere more readily to materials for which there are important applications as protective coatings. In this work adhesion and mechanical properties of amorphic diamond films have been examined. A beam bending method has been used to measure the internal stress and a relatively low value of compressive stress was found. The dependence of stress on the laser intensities at the graphite ablation target has been studied. Analyses of these films on silicon, SiO2, ZnS, and TiAl6V4 by Rutherford backscattering spectrometry show significant interfacial layers with compositions of SiC, C0.5SiO2, C2.5ZnS, and C0.62Ti0.35Al0.05V0.02, respectively. Adhesion properties on ZnS and other substrates have also been examined for harsh environments. The mechanical properties of hardness, Young’s modulus, and stiffness have been obtained with a nanoindentation technique. These results together with the minimal amount of hydrogen in our process, make amorphic diamond an excellent candidate for direct deposition on several substrates including ZnS.
African Swine Fever Virus Georgia 2007 with a Deletion of Virulence-Associated Gene<i>9GL</i>(B119L), when Administered at Low Doses, Leads to Virus Attenuation in Swine and Induces an Effective Protection against Homologous Challenge (2015)

The main problem for controlling ASF is the lack of vaccines. Studies on ASFV virulence lead to the production of genetically modified attenuated viruses that induce protection in pigs but only against homologous virus challenges. Here we produced a recombinant ASFV lacking virulence-associated gene 9GL in an attempt to produce a vaccine against virulent ASFV-G, a highly virulent virus isolate detected in the Caucasus region in 2007 and now spreading though the Caucasus region and Eastern Europe. Deletion of 9GL, unlike with other ASFV isolates, did not attenuate completely ASFV-G. However, when delivered once at low dosages, recombinant ASFV-G-Δ9GL induces protection in swine against parental ASFV-G. The protection against ASFV-G is highly effective after 28 days postvaccination, whereas at 21 days postvaccination, animals survived the lethal challenge but showed signs of ASF. Here we report the design and development of an experimental vaccine that induces protection against virulent ASFV-G.
Self-similar pulse evolution in an all-normal-dispersion laser (2010)

Parabolic amplifier similaritons are observed inside a normal-dispersion laser. The self-similar pulse is a local nonlinear attractor in the gain segment of the oscillator. The evolution in the laser exhibits large (20 times) spectral breathing, and the pulse chirp is less than the group-velocity dispersion of the cavity. All of these features are consistent with numerical simulations. The amplifier similariton evolution also yields practical features such as parabolic output pulses with high energies, and the shortest pulses to date from a normal-dispersion laser.
Developmental and environmental regulation of antifreeze proteins in the mealworm beetle <i>Tenebrio molitor</i> (2000)

The yellow mealworm beetle, Tenebrio molitor, contains a family of small Cys-rich and Thr-rich thermal hysteresis proteins that depress the hemolymph freezing point below the melting point by as much as 5. 5 degrees C (DeltaT = thermal hysteresis). Thermal hysteresis protein expression was evaluated throughout development and after exposure to altered environmental conditions. Under favorable growth conditions, small larvae (11-13 mg) had only low levels of thermal hysteresis proteins or thermal hysteresis protein message, but these levels increased 10-fold and 18-fold, respectively, by the final larval instar (> 190 mg), resulting in thermal hysteresis > 3 degrees C. Exposure of small larvae (11-13 mg) to 4 weeks of cold (4 degrees C) caused an approximately 20-fold increase in thermal hysteresis protein concentration, well in excess of the less than threefold developmental increase seen after 4 weeks at 22 degrees C. Exposure of large larvae (100-120 mg) to cold caused 12-fold and sixfold increases in thermal hysteresis protein message and protein levels, respectively, approximately double the maximum levels they would have attained in the final larval instar at 22 degrees C. Thus, thermal hysteresis increased to similar levels (> 4 degrees C) in the cold, irrespective of the size of the larvae (the overwintering stage). At pupation, thermal hysteresis protein message levels decreased > 20-fold and remained low thereafter, but thermal hysteresis activity decreased much more slowly. Exposure to cold did not reverse this decline. Desiccation or starvation of larvae had comparable effects to cold exposure, but surprisingly, short daylength photoperiod or total darkness had no effect on either thermal hysteresis or message levels. As all environmental conditions that caused increased thermal hysteresis also inhibited growth, we postulate that developmental arrest is a primary factor in the regulation of T. molitor thermal hysteresis proteins.
Method and apparatus for energizing an array of acoustic transducers to eliminate grating lobes (1980)

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Phylogenetic Analysis of Enteroaggregative and Diffusely Adherent <i>Escherichia coli</i> (1999)

The phylogenetics of the various pathotypes of diarrheagenic Escherichia coli are not completely understood. In this study, we identified several plasmid and chromosomal genes in the pathogenic enteroaggregative E. coli (EAEC) prototype strain 042 and determined the prevalence of these loci among EAEC and diffusely adherent E. coli strains. The distribution of these genes is analyzed within an evolutionary framework provided by the characterization of allelic variation in housekeeping genes via multilocus enzyme electrophoresis. Our data reveal that EAEC strains are heterogeneous with respect to chromosomal and plasmid-borne genes but that the majority harbor a member of a conserved family of virulence plasmids. Comparison of plasmid and chromosomal relatedness of strains suggests clonality of chromosomal markers and a limited transfer model of plasmid distribution.
A Coated Tube Assay for the Detection of Blocking Thyrotropin Receptor Autoantibodies (2004)

We developed a coated tube assay to discriminate TSH-receptor-stimulating autoantibodies [thyroid-stimulating antibodies (TSAb)] from those autoantibodies blocking TSH binding without intrinsic activation [thyroid-blocking antibodies (TBAb)]. The wild-type TSH receptor in the TSH binding-inhibitory assay was exchanged for a chimeric receptor where a TSAb epitope (amino acids 8-165) was replaced by comparable LH-R residues. Binding of (125)I-labeled TSH to this chimera could be inhibited by sera containing TBAb up to 95%. Sera from 316 patients with Graves' disease and 17 with autoimmune thyroid disease were grouped according to their bioassay activity. At the decision threshold, the chimera A assay had a sensitivity of 78.0% for TBAb with a specificity of 90.2%. In detail, 19 of 22 (86.4%) TBAb sera and 15 of 23 (65.2%) TSAb/TBAb sera were positive but only 32 of 216 (14.0%) TSAb sera and 5 of 72 (6.9%) bioassay negative sera. There was a weak but significant positive correlation (r = 0.46) between the chimera assay and the bioassay for TBAb. This is the first report of a coated tube assay for the determination of TBAb employing an adaptation of the TSH binding-inhibitory format, which could be a useful alternative to the bioassay.
Development of a rapid method for the determination of frying oil quality based on capillary penetration (2015)

Summary A novel rapid method and apparatus for the determination of frying oil quality based on capillary penetration is presented. The method measures the rate (or time vs. distance) of penetration of the oil in a substrate. Several porous media made of different materials (glass, cellulose, polyethylene) having different pore sizes were examined as potential substrates. A polyethylene substrate was selected as the most appropriate. This substrate was used for measurements with olive and sunflower oil at different levels of degradation (at 170 °C for up to 32 h). The fresh and degraded oil polymer and polar compounds were measured using HPSEC . The results of the method were linearly related to the oil degradation time ( R 2 = 0.95) and the concentration of polymer ( R 2 = 0.95) and polar ( R 2 = 0.91) compounds. The results of this work suggest that the capillary penetration method is a promising novel method that merits further investigation and development.
Evaluation of Mass Spectrometry-Based Detection of Panfungal Serum Disaccharide for Diagnosis of Invasive Fungal Infections: Results from a Collaborative Study Involving Six European Clinical Centers (2019)

A mass spectrometry (MS) method that detects a serum disaccharide (DS) (MS-DS) was recently described for the diagnosis of invasive fungal infections (IFI). We carried out a European collaborative study to evaluate this assay. Patients with the following IFI were selected according to the availability of sera obtained at about the time that IFI was documented: invasive candidiasis (IC; <i>n</i> = 26 patients), invasive aspergillosis (IA; <i>n</i> = 19), and mucormycosis (MM; <i>n</i> = 23). Control sera originated from 20 neutropenic patients and 20 patients with bacteremia. MS-DS was carried out in blind manner for the diagnosis of IFI. A diagnosis of IC or IA was confirmed by detection of mannan (Man) or galactomannan (GM), respectively, associated with detection of (1,3)-β-d-glucan (BDG) in both infections. MM was detected by quantitative real-time PCR (qPCR). All tests discriminated sera from patients with IC from sera from control subjects with bacteremia (<i>P</i> ≤ 0.0009). For IC, the MS-DS sensitivity and specificity were 51% and 87%, respectively. MS-DS complemented the high specificity of Man monitoring. All tests discriminated sera from IA patients from sera from neutropenic controls (<i>P</i> ≤ 0.0009). For IA, MS-DS sensitivity and specificity were 64% and 95%, respectively. Only 13/36 serum samples from patients with MM were concordant by MS-DS and qPCR (6 were positive, and 7 were negative); 14 were positive by MS-DS alone. qPCR and MS-DS made a similar contribution to the diagnosis of MM. In patients undergoing long-term monitoring, the persistent circulation of serum disaccharide was observed, whereas DNA was detected only for a short period after initiation of treatment. MS-DS has an important role to play in the early diagnosis of IFI. Its panfungal nature and complementarity with other tests may justify its use in the management of IFI.