gebhart/patrepeval huggingface dataset:
Antigen Mining with Iterative Genome Screens Identifies Novel Diagnostics for the <i>Mycobacterium tuberculosis</i> Complex (2006)

The definition of antigens for the diagnosis of human and bovine tuberculosis is a research priority. If diagnosis is to be used alongside Mycobacterium bovis BCG-based vaccination regimens, it will be necessary to have reagents that allow the discrimination of infected and vaccinated animals. A list of 42 potential M. bovis-specific antigens was prepared by comparative analysis of the genomes of M. bovis, M. avium subsp. avium, M. avium subsp. paratuberculosis, and Streptomyces coelicolor. Potential antigens were tested by applying them in a high-throughput peptide-based screening system to M. bovis-infected and BCG-vaccinated cattle and to cattle without prior exposure to M. bovis. A response hierarchy of antigens was established by comparing responses in infected animals. Three antigens (Mb2555, Mb2890, and Mb3895) were selected for further study, as they were strongly recognized in experimentally infected animals but with low or no frequency in BCG-vaccinated and naïve cows. Interestingly, all three antigens were recognized in animals vaccinated against Johne's disease, suggesting the presences of epitopes cross-reacting with M. avium subsp. paratuberculosis antigens. Eight peptides from the three antigens studied in detail were identified as immunodominant and were characterized in terms of major histocompatibility complex class II restriction element usage and shown to be restricted through both DR and DQ molecules. Reasons for antigenic cross-reactivity with M. avium subsp. paratuberculosis and refinement of the in silico strategy to predict such cross-reactivity from the primary protein sequence will be discussed. Evaluation of the peptides identified from the three dominant antigens by use of larger field studies is now a priority.
DNA and RNA analogues – oligonucleotide phosphoramidates with bridging nitrogen (2002)

Oligonucleotide analogues containing nitrogen replacing either 3′- or 5′-oxygen atoms have been attracting attention of the scientific community for a long time. Originally, it was suggested that these compounds might be used as a functional mimetic of DNA molecules, which could be easier to prepare, due to a higher nucleophilicity of amino vis-a-vie hydroxyl group. Recent advances in development of oligonucleotide-based therapeutic and diagnostic agents significantly increased interest in these compounds as potential antisense and antigene compounds. Among numerous synthesised molecules the N3′→P5′ phosphoramidate oligonucleotides attract particular attention. Uniformly modified oligonucleotide N3′→P5′ phosphoramidates, containing 3′-amino replacing 3′-hydroxyl nucleosides, form very stable duplexes with complementary native phosphodiester DNA, and particularly with RNA strands. The phosphoramidate compounds form extremely stable triple-stranded complexes with single or double-stranded DNA targets and 2′-deoxyoligonucleotide N3′→P5′ phosphoramidates and their duplexes are structurally and functionally similar to those formed by native RNA molecules. This property allowed for application of these compounds as RNA decoys. Further duplex stabilisation was observed for 2′-deoxyoligonucleotide N3′→P5′ oligonucleotides. N3′→P5′ phosphoramidates oligonucleotides are highly resistant to enzymatic digestion by cellular nucleases and their duplexes with complementary RNA strands that are not substrates for RNase H-catalysed hydrolysis in vitro. However, they still exert sequence specific activity in various cellular systems and in vivo in mice, comparable or superior to RNase H-inducing phosphorothioate oligonucleotides. Fluorescently labelled phosphoramidates have also been used as FISH probes for telomeric DNA-directed diagnostic applications.
On the role of evanescent modes and group index tapering in slow light photonic crystal waveguide coupling efficiency (2011)

We investigate effects of different mechanisms on coupling efficiency between strip waveguides and the slow light mode in photonic crystal waveguides (PCWs). Both numerical simulations and experimental results show that group index (ng) tapering improves strip-PCW butt-coupling efficiency when compared to a direct coupling between a strip waveguide and a high-ng PCW. However, coupling efficiency is even higher when an intermediate low-ng PCW is used to couple from a strip waveguide to a high-ng PCW without an ng tapering. Our results suggest that the role of evanescent mode is more dominant in efficient coupling between two PCWs with large ng mismatch.
Antitumor anthracycline antibiotics, aclacinomycin A and analogues. II. Structural determination. (1979)

The structures of aclacinomycins A and B and 19 analogues were determined by a combination of chemical conversions and degradations and spectral interpretations.
Reversal of multidrug resistance by novel inhibitors of human P‐glycoprotein in cell culture (974.2) (2014)

Multidrug resistance (MDR) and chemotherapy failure are often due to overexpression of members of the ABC‐transporter superfamily of proteins like MDR1 P‐glycoprotein (P‐gp). These membrane transporters protect cells from the accumulation of harmful toxins by using ATP hydrolysis to move a broad range of compounds across the plasma membrane. In MDR, however, the administration of chemotherapeutics selects for cancerous cells which overexpress P‐gp thereby creating a population of cancer cells resistant to many types of chemotherapeutics. Using targeted molecular dynamic simulations and massively parallel drug docking studies, we have identified several novel compounds that inhibit transport by P‐gp by targeting the ATP binding domains. Biochemical and biophysical studies have shown that these inhibitors do indeed bind to the nucleotide binding domains of P‐gp and inhibit ATP hydrolysis. In the studies reported here, we have been able to re‐sensitize MDR prostate and ovarian cancer cell lines in culture to multiple chemotherapeutics when treated with the novel compounds. The compounds reverse the MDR phenotype to sensitivities similar to the original, non‐MDR parental cell lines. Limited toxicity was observed when non‐cancerous cells were treated with the P‐gp inhibitors alone. The results suggest that these novel P‐gp inhibitors may serve as good drug leads for treating MDR and chemotherapy failure. Grant Funding Source : Supported by NIH/NIGMS 1R15GM094771 ‐ 01A1 to PDV and JGW and the Communities Foundation of Texas
Short pulse generation based on ultrafast Transient Bragg Gratings (2015)

We analyze analytically and numerically a configuration where a fs transverse pulse creates a Transient-Bragg-Grating in a fiber/waveguide. We characterize the reflected ultra-short pulses depending on the grating parameters.
Comparison of the Serodia <i>Treponema pallidum</i> Particle Agglutination, Captia Syphilis-G, and SpiroTek Reagin II Tests with Standard Test Techniques for Diagnosis of Syphilis (2000)

We compared the microhemagglutination assay for Treponema pallidum (MHA-TP), a treponemal test, with two other treponemal tests, the Serodia Treponema pallidum particle agglutination (TP-PA) assay and the Captia Syphilis-G enzyme immunoassay, using 390 clinical serum samples. We also compared two nontreponemal tests, the rapid plasma Reagin (RPR) card test and the SpiroTek Reagin II test. Agreements of the MHA-TP with the TP-PA test and the Syphilis-G test were 97.4 and 97.7%, respectively. There was 89.2% agreement between the RPR and Reagin II tests. The Reagin II test was more apt to be reactive if the treponemal test was also reactive. We conclude that either the Serodia TP-PA test or the Captia Syphilis-G test is an appropriate substitute for the MHA-TP and that the Spirotek Reagin II test could substitute for the RPR test as a screening test.
Improvement in operation lives of GaAlAs visible lasers by introducing GaAlAs buffer layers (1981)

It is shown that drastic reduction of the active-layer stress can be obtained by the introduction of a GaAlAs buffer layer in GaAlAs visible lasers. The life tests of the GaAlAs visible lasers with the optimally designed buffer layers were carried out at 50°C in a dry nitrogen ambient. The results indicate that the introduction of the optimal buffer layer leads to a reduction in the stress induced degradation of GaAlAs visible lasers.
Clustering of breakpoints on chromosome 10 in acute T-cell leukemias with the t(10;14) chromosome translocation. (1989)

The T-cell receptor (TCR) alpha/delta chain locus on chromosome 14q11 is nonrandomly involved in translocations and inversions in human T-cell neoplasms. We have analyzed three acute T-lymphoblastic leukemia samples carrying a t(10;14)(q24;q11) chromosome translocation by means of somatic cell hybrids and molecular cloning. In all cases studied the translocation splits the TCR delta chain locus. Somatic cell hybrids containing the human 10q+ chromosome resulting from the translocation retain the human terminal deoxynucleotidyltransferase gene mapped at 10q23-q24 and the diversity and joining, D delta 2-J delta 1, regions of the TCR delta chain, but not the V alpha region (variable region of the TCR alpha chain), demonstrating that the split occurred within the V alpha-D delta 2 region. Molecular cloning of the breakpoint junctions revealed that the TCR delta chain sequences involved are made from the D delta 2 segment. The chromosome breakpoints are clustered within a region of approximately 263 base pairs of chromosome 10. The results suggest that the translocation of the TCR delta chain locus to a locus on 10q, which we have designated TCL3, results in deregulation of this putative oncogene, leading to acute T-cell leukemia.
The feasibility of an inverse geometry CT system with stationary source arrays (2013)

IGCT with stationary source arrays could be an imaging platform potentially capable of imaging a complete 16-cm thick volume within a tenth of a second.
Design, Synthesis, and Biological Evaluation of Tetra‐Substituted Thiophenes as Inhibitors of p38α MAPK (2014)

p38α mitogen-activated protein kinase (MAPK) plays a role in several cellular processes and consequently has been a therapeutic target in inflammatory diseases, cancer, and cardiovascular disease. A number of known p38α MAPK inhibitors contain vicinal 4-fluorophenyl/4-pyridyl rings connected to either a 5- or 6-membered heterocycle. In this study, a small library of substituted thiophene-based compounds bearing the vicinal 4-fluorophenyl/4-pyridyl rings was designed using computational docking as a visualisation tool. Compounds were synthesised and evaluated in a fluorescence polarisation binding assay. The synthesised analogues had a higher binding affinity to the active phosphorylated form of p38α MAPK than the inactive nonphosphorylated form of the protein. 4-(2-(4-fluorophenyl)thiophen-3-yl)pyridine had a K i value of 0.6 μm to active p38α MAPK highlighting that substitution of the core ring to a thiophene retains affinity to the enzyme and can be utilised in p38α MAPK inhibitors. This compound was further elaborated using a substituted phenyl ring in order to probe the second hydrophobic pocket. Many of these analogues exhibited low micromolar affinity to active p38α MAPK. The suppression of neonatal rat fibroblast collagen synthesis was also observed suggesting that further development of these compounds may lead to potential therapeutics having cardioprotective properties.
Acoustical peak identification system (APIS): An acoustical technique for distinguishing between European and Africanized honeybees (1989)

A simple method has been developed to distinguish between European and Africanized honeybees on the basis of differences in the spectral content of sounds made by worker bees in flight. The spectral content of the flight sounds for each subspecies may generally be correlated to characteristic taxonomial features (i.e., wing size, body weight, thorax dimensions, etc.) and physical behavior (i.e., foraging, stinging, etc.). Acoustic signals from over 800 individual flying European and Africanized honeybees were collected. A time-averaged signal was generated for each specimen, and standard Fourier analysis methods were used to generate power spectral density plots. Examination of the PSD's revealed that distinguishing differences exist between the acoustical signatures of flying European honeybees and flying Africanized honeybees. Specifically, the flying European honeybee signature has a fundamental power peak in the 210- to 230-Hz frequency range whereas the flying Africanized honeybee signature has a fundamental power peak in the 260- to 280-Hz frequency range. This substantial difference is easily embodied in a variety of simple identification algorithms. A patent application was submitted for the acoustical peak identification system (APIS), and a simple, inexpensive, field-portable instrument based on acoustical signature techniques has been developed for screening identification of the Africanized subspecies of honeybees. This instrument is called “Buzz Buster” and is being marketed by B-Tec.
Plastic-Based Distributed Feedback Laser Biosensors in Microplate Format (2011)

A process that combines polymer nanoreplica molding with horizontal dipping was used to fabricate large area ( <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim 3\times 5~{\rm inch}^{2}$</tex> </formula> ) distributed feedback laser biosensors (DFBLB) on flexible plastic substrates, which were subsequently incorporated into standard format 96-well microplates. A room temperature nanoreplica molding process was used to create subwavelength periodic grating structures, while a horizontal dipping process was used to apply a <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\sim {300}~{\rm nm}$</tex></formula> , dye-doped polymer film. In this work, the DFBLB emission wavelength, used to characterize the device uniformity, demonstrated a coefficient of variation (CV) of 0.41% over the fabricated device area, representing a thickness standard deviation of only <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim {35}~{\rm nm}$</tex></formula> for the horizontal dipping process. The fabricated sensors were further characterized for sensitivity uniformity by measuring the bulk refractive index of the media exposed to the sensor surface and by measuring adsorption of biomolecular layers. An assay for detection of the cytokine Tumor Necrosis Factor-alpha (TNF- <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\alpha$</tex> </formula> ) was used to demonstrate the operation of the sensor in the context of label-free detection of a disease biomarker. The demonstrated capability represents an important step towards roll-to-roll manufacturability for this biosensor that simultaneously incorporates high sensitivity with excellent wavelength shift resolution, and adaptability to the microplate format that is ubiquitous in pharmaceutical research.
Holographic optical configurations for eye protection against lasers (1987)

Holographic rejection (notch) filters are used for eye protection against laser radiation because they allow high visual transmission since they reflect only a narrow spectral bandwidth. Their angular dependence, typical of diffractive and interference filters, can be minimized or avoided when the filters also perform as holographic optical elements with particular optical configurations. These configurations are described for two eyewear geometries, and possible options between theoretical design, practical filter construction limitations, and spurious images are investigated.
Characterization of a Lectin in Human Plasma Analogous to Bovine Conglutinin (1987)

The structural characteristics of a human plasma protein analogous to bovine conglutinin were studied. The protein was previously found to bind to complement-reacted IgG in a calcium-dependent and N-acetyl-D-glucosamine-inhibitable manner and it further shows cross-reactivity with anti-bovine conglutinin antibody. By gel permeation chromatography the conglutinin activity in human plasma was localized to fractions containing proteins of Mr at around 700,000. The conglutinin was localized by one ELISA for antigen determinants and by another for biological activity. When analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) under non-reducing conditions these fractions were shown to contain proteins of about 300,000. When human conglutinin-like protein, partially purified by affinity chromatography, was analysed unreduced by SDS-PAGE followed by western blotting, the cross-reacting anti-bovine conglutinin antibody bound to a protein with an Mr of 330,000. When the sample was reduced and alkylated before electrophoresis a band of 66,000 was immunostained. The 330,000 and 66,000 proteins were shown to be collagenase sensitive. 125I-iC3b was seen to bind to the 330,000 band when incubated with western blots of partially purified human conglutinin.
A novel ALS-associated variant in UBQLN4 regulates motor axon morphogenesis (2017)

The etiological underpinnings of amyotrophic lateral sclerosis (ALS) are complex and incompletely understood, although contributions to pathogenesis by regulators of proteolytic pathways have become increasingly apparent. Here, we present a novel variant in <i>UBQLN4</i> that is associated with ALS and show that its expression compromises motor axon morphogenesis in mouse motor neurons and in zebrafish. We further demonstrate that the ALS-associated <i>UBQLN4</i> variant impairs proteasomal function, and identify the Wnt signaling pathway effector beta-catenin as a <i>UBQLN4</i> substrate. Inhibition of beta-catenin function rescues the <i>UBQLN4</i> variant-induced motor axon phenotypes. These findings provide a strong link between the regulation of axonal morphogenesis and a new ALS-associated gene variant mediated by protein degradation pathways.
An Encoder-Embedded Video Denoising Filter Based on the Temporal LMMSE Estimator (2006)

Noise not only degrades the visual quality of video contents, but also significantly affects the coding efficiency. Based on the temporal linear minimum mean square error (LMMSE) estimator, an innovative denoising filter is proposed in this paper. The proposed filter only requires simple operations manipulating on the individual residue coefficients and can be seamlessly integrated into video encoders. Compared to traditional filter-encoder cascaded scheme, embedding the proposed filter into the video encoder can save a large amount of computation. The experimental results show that with the proposed filter embedded, both the noise suppression capability and the coding efficiency of the video encoder can be dramatically improved. Furthermore, as a purely temporal filter, it can well preserve the fine details of video contents and satisfactory visual quality can be achieved
Defined and Scalable Differentiation of Human Oligodendrocyte Precursors from Pluripotent Stem Cells in a 3D Culture System (2017)

Oligodendrocyte precursor cells (OPCs) offer considerable potential for the treatment of demyelinating diseases and injuries of the CNS. However, generating large quantities of high-quality OPCs remains a substantial challenge that impedes their therapeutic application. Here, we show that OPCs can be generated from human pluripotent stem cells (hPSCs) in a three-dimensional (3D), scalable, and fully defined thermoresponsive biomaterial system. We used CRISPR/Cas9 to create a NKX2.2-EGFP human embryonic stem cell reporter line that enabled fine-tuning of early OPC specification and identification of conditions that markedly increased the number of OLIG2<sup>+</sup> and NKX2.2<sup>+</sup> cells generated from hPSCs. Transplantation of 50-day-old OPCs into the brains of NOD/SCID mice revealed that progenitors generated in 3D without cell selection or purification subsequently engrafted, migrated, and matured into myelinating oligodendrocytes in vivo. These results demonstrate the potential of harnessing lineage reporter lines to develop 3D platforms for rapid and large-scale production of OPCs.
Structure-property relationships of carbon aerogels (1993)

Of the organic reactions in sol-gel polymerizations, the most studied reaction is the aqueous polycondensation of resorcinol with formaldehyde; the resulting crosslinked gels are supercritically dried from CO{sub 2} to give resorcinol-formaldehyde (RF) aerogels. These aerogels can be pyrolyzed to form vitreous carbon monoliths with black color, high porosity, ultrafine cell/pore size, high surface area, and interconnected particles of the organic precursor. The structure and properties of the carbon aerogels depend on R/C (resorcinol/catalyst) ratio of starting solution, pyrolysis temperature, and chemical activation. Each variable is discussed. Carbon aerogels provide an almost ideal electrode material (in double-layer capacitors) owing to low electrical resistivity (<40 mohm-cm), controllable pore size distribution (5--500 {angstrom}), and high volumetric surface areas ({approximately}500 m{sup 2}/cm{sup 3}).
Prostaglandin EP<sub>4</sub>Antagonists (2013)

Prostaglandin antagonists, with their pharmacological effects, are well-known drugs capable of treating widely diffused illnesses, including pain and inflammation disorders. In recent years, a major research focus has been devoted to the identification of agents able to selectively antagonize each receptor with which prostaglandins interact. This review attempts to give a broad overview of molecules capable of selectively blocking the prostaglandin PGE2 EP4 receptor. Further therapeutic applications and uses have also been disccussed, including the first drug candidate to have reached clinical trials within the last few years.
CEST, ASL, and magnetization transfer contrast: How similar pulse sequences detect different phenomena (2018)

Chemical exchange saturation transfer (CEST), arterial spin labeling (ASL), and magnetization transfer contrast (MTC) methods generate different contrasts for MRI. However, they share many similarities in terms of pulse sequences and mechanistic principles. They all use RF pulse preparation schemes to label the longitudinal magnetization of certain proton pools and follow the delivery and transfer of this magnetic label to a water proton pool in a tissue region of interest, where it accumulates and can be detected using any imaging sequence. Due to the versatility of MRI, differences in spectral, spatial or motional selectivity of these schemes can be exploited to achieve pool specificity, such as for arterial water protons in ASL, protons on solute molecules in CEST, and protons on semi-solid cell structures in MTC. Timing of these sequences can be used to optimize for the rate of a particular delivery and/or exchange transfer process, for instance, between different tissue compartments (ASL) or between tissue molecules (CEST/MTC). In this review, magnetic labeling strategies for ASL and the corresponding CEST and MTC pulse sequences are compared, including continuous labeling, single-pulse labeling, and multi-pulse labeling. Insight into the similarities and differences among these techniques is important not only to comprehend the mechanisms and confounds of the contrasts they generate, but also to stimulate the development of new MRI techniques to improve these contrasts or to reduce their interference. This, in turn, should benefit many possible applications in the fields of physiological and molecular imaging and spectroscopy.