gebhart/patrepeval huggingface dataset:
Positive and negative regulatory elements control the steroid-responsive ovalbumin promoter (1988)

Steroid hormones regulate the transcriptional activity of the chicken ovalbumin gene both in vivo and in cell culture. To identify the regulatory elements involved, primary oviduct cell cultures were transfected with constructs containing the promoter and 5'-flanking region of the ovalbumin gene fused to the bacterial chloramphenicol acetyltransferase (CAT) gene. Induction of the OvCAT genes by estrogen, progesterone, or corticosterone mimics that of the endogenous ovalbumin gene, indicating that the transfected DNA is accurately regulated. Deletion analysis revealed that a steroid response element (SRE) resides between nucleotide coordinates -880 and -585 and that a negative regulatory element (NRE) resides between -350 and -248 in the ovalbumin gene. Thus, an NRE represses expression of the ovalbumin gene unless steroid hormones relieve this negative control through interactions involving a more distal SRE. Neither the SRE nor the NRE alone regulates the heterologous thymidine kinase promoter, suggesting either that they function as a single entity or that they are conditional regulatory elements. The NRE is functional in MCF-7 cells, but the SRE cannot be activated by steroids in this heterologous estrogen-responsive cell line. These data indicate that the steroid-receptor complex induces the ovalbumin gene through direct or indirect actions at an SRE to relieve represssion at an NRE.
Early detection of Alzheimer's disease using MRI hippocampal texture (2015)

Cognitive impairment in patients with Alzheimer's disease (AD) is associated with reduction in hippocampal volume in magnetic resonance imaging (MRI). However, it is unknown whether hippocampal texture changes in persons with mild cognitive impairment (MCI) that does not have a change in hippocampal volume. We tested the hypothesis that hippocampal texture has association to early cognitive loss beyond that of volumetric changes. The texture marker was trained and evaluated using T1-weighted MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, and subsequently applied to score independent data sets from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL) and the Metropolit 1953 Danish Male Birth Cohort (Metropolit). Hippocampal texture was superior to volume reduction as predictor of MCI-to-AD conversion in ADNI (area under the receiver operating characteristic curve [AUC] 0.74 vs. 0.67; DeLong test, p = 0.005), and provided even better prognostic results in AIBL (AUC 0.83). Hippocampal texture, but not volume, correlated with Addenbrooke's cognitive examination score (Pearson correlation, r = -0.25, p < 0.001) in the Metropolit cohort. The hippocampal texture marker correlated with hippocampal glucose metabolism as indicated by fluorodeoxyglucose-positron emission tomography (Pearson correlation, r = -0.57, p < 0.001). Texture statistics remained significant after adjustment for volume in all cases, and the combination of texture and volume did not improve diagnostic or prognostic AUCs significantly. Our study highlights the presence of hippocampal texture abnormalities in MCI, and the possibility that texture may serve as a prognostic neuroimaging biomarker of early cognitive impairment.
Universal quantum computation with ideal Clifford gates and noisy ancillas (2005)

We consider a model of quantum computation in which the set of elementary operations is limited to Clifford unitaries, the creation of the state $\ensuremath{\mid}0⟩$, and qubit measurement in the computational basis. In addition, we allow the creation of a one-qubit ancilla in a mixed state $\ensuremath{\rho}$, which should be regarded as a parameter of the model. Our goal is to determine for which $\ensuremath{\rho}$ universal quantum computation (UQC) can be efficiently simulated. To answer this question, we construct purification protocols that consume several copies of $\ensuremath{\rho}$ and produce a single output qubit with higher polarization. The protocols allow one to increase the polarization only along certain ``magic'' directions. If the polarization of $\ensuremath{\rho}$ along a magic direction exceeds a threshold value (about 65%), the purification asymptotically yields a pure state, which we call a magic state. We show that the Clifford group operations combined with magic states preparation are sufficient for UQC. The connection of our results with the Gottesman-Knill theorem is discussed.
2: Identification of Human Minor Histocompatibilty Antigens (mHA) by Combining Bioinformatic Prediction of Peptide Epitopes With Validation of T Cell Reactivity in Patient Blood Samples After Allogeneic Hematopoietic Stem Cell Transplantation (2008)

Minor histocompatibility antigens (mHA) are targets of graft versus host disease (GVHD) and graft versus leukemia (GVL) responses. Traditional methods for characterization of mHA are laborious and require the isolation of mHA-specific T cell clones followed by determination of their peptide-MHC specificity. Therefore, the number of mHA discovered thus far is small. We report a novel method for rapid identification of mHA based on in-silico prediction of potential class I restricted mHA peptides and subsequent validation by ELISPOT assay in patient blood samples. The study was performed in HLA-A∗0201 positive patient-donor pairs and focused on the subset of mHA derived from proteins encoded by Y-chromosome genes. Peptide sequences of human protein-coding Y genes were extracted from the NCBI genome database. The entire set of Y-encoded protein sequences was screened for HLA class I binding peptides using IEDB prediction tool (tools.immuneepitope.org/analyze/html/mhc_binding.html). This analysis produced a list of 9- and 10-mer peptides predicted to bind HLA-A∗0201. Peptides derived from proteins classified as hypothetical and those solely expressed in male tissues (e.g. testis, prostate) were excluded. Peptides with high predicted binding affinity (≤100 nM) were further analyzed using sequence similarity search (BLAST) against the UniProt database. Peptides having 100% identity to peptides encoded by paralog genes on any other chromosome (mostly × paralogs) were excluded. Selected candidate peptides were synthesized and peptide/HLA-A2 binding was validated experimentally using two binding assays. T cell reactivity was measured by IFN-γ ELISPOT assay in blood samples from three male patients with GVHD who received grafts from female donors. Forty-three peptides, uniquely encoded by Y-chromosome genes, were identified by in-silico screening. Of these, 41 were synthesized and 39 confirmed as high-affinity binders. The only known Y-encoded HLA-A2 restricted mHA (FIDSYICQV) was predicted by the bioinformatic model and T cell reactivity against this epitope was identified in all 3 patients. At least 2 additional new Y-encoded mHA were identified in these patients. We have combined bioinformatics with standard immunologic assays and demonstrated the utility of this approach to the discovery of novel mHA. This approach can be further generalized by application to other HLA alleles as well as to other genetic polymorphisms predicted to result in immunogenic epitopes.
Effect ofppsdisruption and constitutive expression ofsrfAon surfactin productivity, spreading and antagonistic properties ofBacillus subtilis168 derivatives (2010)

The constitutive overproduction of surfactin enhances the invasive growth and the in vitro antagonistic activity of the mutant strain. Both properties are known to play an important role in the biocontrol of plant diseases. Plipastatin operon disruption increases the surfactin productivity of mutant strains. These mutants are interesting for use in continuous bioprocesses for surfactin production or in bioremediation.
Recombinant vesicular stomatitis viruses from DNA. (1995)

We assembled a DNA clone containing the 11,161-nt sequence of the prototype rhabdovirus, vesicular stomatitis virus (VSV), such that it could be transcribed by the bacteriophage T7 RNA polymerase to yield a full-length positive-strand RNA complementary to the VSV genome. Expression of this RNA in cells also expressing the VSV nucleocapsid protein and the two VSV polymerase subunits resulted in production of VSV with the growth characteristics of wild-type VSV. Recovery of virus from DNA was verified by (i) the presence of two genetic tags generating restriction sites in DNA derived from the genome, (ii) direct sequencing of the genomic RNA of the recovered virus, and (iii) production of a VSV recombinant in which the glycoprotein was derived from a second serotype. The ability to generate VSV from DNA opens numerous possibilities for the genetic analysis of VSV replication. In addition, because VSV can be grown to very high titers and in large quantities with relative ease, it may be possible to genetically engineer recombinant VSVs displaying foreign antigens. Such modified viruses could be useful as vaccines conferring protection against other viruses.
Identical D region sequences expressed by murine monoclonal antibodies specific for a human tumor-associated antigen. (1990)

Sequence analysis has revealed significant structural similarities among murine mAb specific for the human tumor-associated Ag GA733. Antibodies generated in independent immunizations, either with Ag-positive tumor cells or with anti-idiotypic antibodies produced by immunization of goats with a GA733-specific antibody, all use members of the same gene families; remarkably, they also express identical amino acid sequences in their H chain CDR3. Inasmuch as this region normally exhibits considerable sequence variability, the identity displayed by the antibodies indicates a requirement for this particular sequence in the generation of their specificity for the GA733 antigen. Moreover, this homology suggests that the antibodies recognize a common determinant on the Ag, and that the polyclonal anti-idiotypic antibodies can functionally mimic the Ag at the level of the structure of the Ag-specific antibody that is induced.
A nonlinear modeling and online monitoring method for the batch process using multiple local PCA (2004)

Producing good quality products is the common objective in industries. However, Achieving this objective can be very difficult in batch process, especially when quality measurements are not available on-line or they have long time delays. This paper proposes a simple and straight nonlinear dynamic modeling with multi-model structure for batch process online monitoring using minimum window principal component analysis (MWPCA). MWPCA replaces single linear MPCA with multiple local linear sub-models for batch process modeling. It does not estimate any deviations of the ongoing batch from the average trajectories. Since the proposed method eliminates prediction error, the accuracy of process performance monitoring increases. MWPCA modeling procedures, principle and its application are discussed in detail. The presented methodology is successfully applied to PVC batch process.
Structure-Based Design of Spiro-oxindoles as Potent, Specific Small-Molecule Inhibitors of the MDM2−p53 Interaction (2006)

Potent, specific, non-peptide small-molecule inhibitors of the MDM2-p53 interaction were successfully designed. The most potent inhibitor (MI-63) has a K(i) value of 3 nM binding to MDM2 and greater than 10,000-fold selectivity over Bcl-2/Bcl-xL proteins. MI-63 is highly effective in activation of p53 function and in inhibition of cell growth in cancer cells with wild-type p53 status. MI-63 has excellent specificity over cancer cells with deleted p53 and shows a minimal toxicity to normal cells.
Multilingual acoustic models using distributed deep neural networks (2013)

Today's speech recognition technology is mature enough to be useful for many practical applications. In this context, it is of paramount importance to train accurate acoustic models for many languages within given resource constraints such as data, processing power, and time. Multilingual training has the potential to solve the data issue and close the performance gap between resource-rich and resource-scarce languages. Neural networks lend themselves naturally to parameter sharing across languages, and distributed implementations have made it feasible to train large networks. In this paper, we present experimental results for cross- and multi-lingual network training of eleven Romance languages on 10k hours of data in total. The average relative gains over the monolingual baselines are 4%/2% (data-scarce/data-rich languages) for cross- and 7%/2% for multi-lingual training. However, the additional gain from jointly training the languages on all data comes at an increased training time of roughly four weeks, compared to two weeks (monolingual) and one week (crosslingual).
Grating-assisted coupling of light between semiconductor and glass waveguides (1998)

Floquet-Bloch theory is used to calculate the electromagnetic fields in a leaky-mode grating-assisted directional coupler (LM-GADC) fabricated with semiconductor and glass materials. One waveguide is made from semiconductor materials (refractive index /spl ap/3.2) while the second is made from glass (refractive index /spl ap/1.45). The coupling of light between the two waveguides is assisted by a grating fabricated at the interface of the glass and semiconductor materials. Unlike typical GADC structures where power is exchanged between two waveguides using bound modes, this semiconductor/glass combination couples power between two waveguides using a bound mode (confined to the semiconductor) and a leaky mode (associated with the glass). The characteristics of the LM-GADC are discussed. Such LM-GADC couplers are expected to have numerous applications in areas such as laser-fiber coupling, photonic integrated circuits, and on-chip optical clock distribution. Analyses indicate that simple LM-GADC's can couple over 40% of the optical power from one waveguide to another in distances less than 1.25 mm.
Quantitative determination of DRF‐1042 in human plasma by HPLC: validation and application in clinical pharmacokinetics (2003)

A simple and sensitive high-performance liquid chromatography (HPLC) method has been developed and validated for the determination of DRF-1042, a novel orally active camptothecin (CPT) analog, in human plasma. The sample preparation was a simple deproteinization with acidified methanol yielding almost 100% recovery of DRF-1042. An isocratic reverse-phase HPLC separation was developed on a Supelcosil-LC318 column (250 x 4.6 mm, 5 microm) with mobile phase consisting of 1% v/v triethylamine acetate, pH 5.5 and acetonitrile (80:20, v/v) at a fl ow rate of 1.0 mL/min. The eluate was monitored with a fluorescence detector set at excitation and emission wavelengths of 370 and 430 nm, respectively. The standard curves were linear (r(2) > 0.999) in the concentration ranges 5.0-2004 ng/mL. The lower limit of quantification (LLQ) of the assay was 5 ng/mL. The mean measured quality control (QC) concentrations (range 5 ng/mL to 40 microg/mL) deviated from the nominal concentrations in the range of -10.5-0.08 and -14.5-7.97%, inter- and intra-day, respectively. The inter- and intra-day precisions in the measurement of QC samples at four tested concentrations, were in the range 0.64-5.89% relative standard deviation (RSD) and 0.33-14.7% RSD, respectively. The method was found to be suitable for measurement of plasma concentrations above the calibration curve after serial dilutions. Stability of DRF-1042 was confirmed in a battery of studies, viz., on bench-top, in the auto-sampler, in the stock solutions, after four quick freeze-thaw cycles, up to one month at -20 degree C in human plasma and up to 2 months in the ex vivo samples. The method is simple, sensitive and reliable and has been successfully implemented to investigate the clinical pharmacokinetics of DRF-1042 in cancer patients in a phase I clinical trial.
A streamlined implementation of the glutamine synthetase-based protein expression system (2013)

Utilizing just a single fluorescence-activated cell sorting-based selection step, the new streamlined implementation of the glutamine synthetase-based protein expression system offers protein yields sufficient for most research purposes, where <10 mg/L of protein expression is often required but relatively large numbers of constructs frequently need to be trialed.
Toward Automated Discovery of Artistic Influence (2014)

Considering the huge amount of art pieces that exist, there is valuable information to be discovered. Examining a painting, an expert can determine its style, genre, and the time period that the painting belongs. One important task for art historians is to find influences and connections between artists. Is influence a task that a computer can measure? The contribution of this paper is in exploring the problem of computer-automated suggestion of influences between artists, a problem that was not addressed before in a general setting. We first present a comparative study of different classification methodologies for the task of fine-art style classification. A two-level comparative study is performed for this classification problem. The first level reviews the performance of discriminative vs. generative models, while the second level touches the features aspect of the paintings and compares semantic-level features vs. low-level and intermediate-level features present in the painting. Then, we investigate the question "Who influenced this artist?" by looking at his masterpieces and comparing them to others. We pose this interesting question as a knowledge discovery problem. For this purpose, we investigated several painting-similarity and artist-similarity measures. As a result, we provide a visualization of artists (Map of Artists) based on the similarity between their works
Resonant light scattering spectroscopy of gold, silver and gold–silver alloy nanoparticles and optical detection in microfluidic channels (2012)

Dark field resonant light scattering by gold and silver nanoparticles enables the detection and spectroscopy of such particles with high sensitivity, down to the single-particle level, and can be used to implement miniaturised optical detection schemes for chemical and biological analysis. Here, we present a straightforward optical spectroscopic methodology for the quantitative spectrometric study of resonant light scattering (RLS) by nanoparticles. RLS spectroscopy is complementary to UV-visible absorbance measurements, and we apply it to the characterisation and comparison of different types of gold, silver and gold-silver alloy nanoparticles. The potential of gold and silver particles as alternatives for fluorescent probes in certain applications is discussed. RLS spectroscopy is shown to be useful for studying analyte-induced gold nanoparticle assembly and nanoparticle chemistry, which can induce radical changes in the plasmonic resonances responsible for the strong light scattering. Furthermore, the feasibility of dark field RLS detection and quantitation of metal nanoparticles in microfluidic volumes is demonstrated, opening interesting possibilities for the further development of microfluidic detection schemes.
Fault-tolerant control and diagnostics for large-scale systems (1995)

The integration of control design, signal and command validations, and diagnostics is the primary objective of this study. The fault-tolerant control principle consists of parallel control and command validation functions. The parallel control includes a number of control algorithms, each designed to accomplish the same control task using different sets of plant signals. The purpose of command validation is to predict the expected control actions using independent approaches, and to cross-check the control actions. The fault-tolerant control and diagnostics system (FCDS) was demonstrated with application to the regulation of the feedwater system in a four-loop pressurized water reactor (PWR) power plant. Because of a high level of reliability that can be achieved by this tier system for control design approach, this is referred to as a "smart" controller.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Properties of mixtures of silk fibroin/syndiotactic‐rich poly(vinyl alcohol) (1990)

Abstract The gelation of mixed solutions of silk fibroin (SF)/syndiotactic‐rich poly(vinyl alcohol) ( s ‐PVA), the thermal analysis of dry‐gels, and the various properties of blend films were investigated. The rate of gelation of a mixed solution was lower than that of each SF or s ‐PVA solution of the same concentration. In the DSC thermograph of mixed dry‐gel (SF/ s ‐PVA = 2/8–8/2) 2 endothermic peaks corresponding to SF (at 288–299°C: decomposition) and s ‐PVA (at 233–241°C: melting) were found. Namely, microphase segregation took place. This was confirmed by optical and electron microscopes. The mechanical properties of blend films did not have additive properties. The degree of swelling in water of blend films was independent on water temperature or methanol treatment. The mechanochemical behaviors were barely observed by the pH exchange between pH 2 and 12 only under lower loads. The addition of SF into s ‐PVA films promoted the permeation of neutral salts.
Identification of a Putative Binding Site for Negatively Charged Surfaces in the Fibronectin Type II Domain of Human Factor XII (2000)

Monoclonal antibodies directed against functional sites of proteins provide useful tools for structure-function studies. Here we describe a mAb, KOK5, directed against the heavy chain region of human coagulation factor XII (FXII), which inhibits kaolin-induced clotting activity by preventing the binding of FXII to kaolin. Furthermore, mAb KOK5 enhances FXII susceptibility for cleavage by kallikrein and supports FXII autoactivation. Hence, mAb KOK5 likely is directed against the binding site of FXII for negatively charged surfaces. Screening of two phage-displayed random peptide libraries with mAb KOK5 selected phages that could be grouped on the basis of two amino acid consensus sequences: A) FXFQTPXW and B) HQ/LCTHR/KKC. Sequence A contains two motifs: one shares homology with FXII amino acid residues 30-33 (FPFQ), the second one with residues 57-60 (TPNF); both amino acid stretches belonging to the fibronectin type II domain of FXII. Sequence B also reveals homology with part of the fibronectin type II domain, i.e. the stretch 40-47 (HKCTHKGR). A three-dimensional model of FXII residues 28-65, obtained by homology modeling, indicated that the three amino acid stretches 30-33, 40-47 and 57-60 are close to each other and accessible for the solvent, i.e. in a form available for interaction with the monoclonal antibody, suggesting that mAb KOK5 recognizes a discontinuous epitope on the fibronectin type III domain of FXII. Peptides corresponding to FXII sequences 29-37 (FXII29-37) or 39-47 (FXII39-47), were synthesized and tested for the capability to inhibit FXII binding to negatively charged surfaces. Peptide FXII39-47 inhibited the binding of labeled FXII to kaolin and effectively prevented both dextran sulfate- and kaolin-induced activation of the contact system in plasma. Hence, we suggest that the fibronectin type II domain of FXII, in particular residues 39 to 47, contribute to the binding site of FXII for negatively charged surfaces.