gebhart/patrepeval huggingface dataset:
Systemic Administration and Targeted Radiosensitization via Chemically Synthetic Aptamer–siRNA Chimeras in Human Tumor Xenografts (2015)

Radiation therapy is a highly effective tool for treating all stages of prostate cancer, from curative approaches in localized disease to palliative care and enhanced survival for patients with distant bone metastases. The therapeutic index of these approaches may be enhanced with targeted radiation-sensitizing agents. Aptamers are promising nucleic acid delivery agents for short interfering RNAs (siRNA) and short hairpin RNAs (shRNA). We have previously developed a radiation-sensitizing RNA aptamer-shRNA chimera that selectively delivers DNA-PK targeting shRNAs to prostate-specific membrane antigen (PSMA) positive cells in the absence of transfection reagents. Although these chimera are effective, their synthesis requires in vitro transcription and their evaluation was limited to intratumoral administration. Here, we have developed a second-generation aptamer-siRNA chimera that can be assembled through the annealing of three separate chemically synthesized components. The resulting chimera knocked down DNA-PK in PSMA-positive prostate cancer cells, without the need of additional transfection reagents, and enhanced the efficacy of radiation-mediated cell death. Following intravenous injection, the chimera effectively knocked down DNA-PK in established subcutaneous PSMA-positive tumors. Systemic treatment with these radiation-sensitizing agents selectively enhanced the potency of external beam radiation therapy for established PSMA-positive tumors.
ChemInform Abstract: Synthesis of Vinylic Lactones via Palladium‐Catalyzed Coupling of Vinylic Halides or Triflates and Unsaturated Carboxylic Acids. (1989)

Abstract Coupling of the 3‐butenoic acids (II) or (VI) with the vinylic halides or triflates (I) or (IV) in the presence of diethylisopropylamine, tetrabutylammonium chloride, and a Pd catalyst yields the vinylic γ‐lactones (III), (V), and (VII).
Analgesic effect in rodents of native and recombinant Phα1β toxin, a high-voltage-activated calcium channel blocker isolated from armed spider venom (2008)

Calcium influx through neuronal voltage-sensitive calcium channels (VSCC S) mediates nociceptive information in the spinal dorsal horn. In fact, spinally administered VSCC S blockers, such as omega-conotoxin MVIIA, have analgesic effect apart of their low therapeutic index and many side effects. Here we study the analgesic potential of Ph alpha 1beta, a calcium channel blocker, in rodent models of acute and persistent pain. Spinally administered Ph alpha 1beta showed higher efficacy and long-lasting analgesia in a thermal model of pain, when compared with omega-conotoxin MVIIA. Moreover, Ph alpha 1beta was more effective and potent than omega-conotoxin MVIIA not only to prevent, but especially to reverse, previously installed persistent chemical and neuropathic pain. Furthermore, the analgesic action of both toxins are related with the inhibition of Ca2+-evoked release of pro-nociceptive neurotransmitter, glutamate, from rat spinal cord synaptosomes and decrease of glutamate overflow in cerebrospinal fluid. When side effects were assessed, we found that Ph alpha 1beta had a therapeutic index wider than omega- conotoxin MVIIA. Finally, recombinant Ph alpha 1beta expressed in Escherichia coli showed marked analgesic activity similar to the native toxin. Taken together, the present study demonstrates that native and recombinant Ph alpha 1beta have analgesic effects in rodent models of pain, suggesting that this toxin may have potential to be used as a drug in the control of persistent pathological pain.
Confidence measures for spontaneous speech recognition (2002)

For many practical applications of speech recognition systems, it is desirable to have an estimate of confidence for each hypothesized word, i.e. to have an estimate of which words of the output of the speech recognizer are likely to be correct and which are not reliable. We describe the development of the measure of the confidence tagger JANKA, which is able to provide confidence information for the words at the output of the speech recognizer JANUS-3-SR. On a spontaneous German human-to-human database, JANKA achieves a tagging accuracy of 90% at a baseline word accuracy of 82%.
The human platelet alloantigens Br(a) and Brb are associated with a single amino acid polymorphism on glycoprotein Ia (integrin subunit alpha 2). (1993)

The human GPIa/IIa complex, also known as integrin alpha 2 beta 1, serves as a major receptor for collagen in platelets and other cell types. In addition to its role in platelet adhesion to extracellular matrix, GPIa/IIa is also known to bear the clinically important Br(a) and Brb alloantigenic determinants, which can result in antibody-mediated platelet destruction. Immunochemical studies showed that the Br antigenic epitopes reside solely on the GP Ia subunit and do not depend on sialic acid residues. To define the polymorphism responsible for the Br alloantigen system platelet RNA PCR technique, was used to amplify GPIa mRNA transcripts. Nucleotide sequence analysis of the amplified platelet GPIa cDNA from Br(a/a) and Brb/b individuals revealed a single A<-->G polymorphism at base 1648. MnlI RFLP analysis of cDNA from serologically determined individuals confirmed that this polymorphism segregates with Br phenotype. This single base change results in a substitution of Lys (AAG) in Br(a) to Glu (GAG) in Brb at amino acid residue 505 In spite of the reversal in charge at this position, however, we found no difference in the ability of Bra and Brb homozygous platelets to adhere to collagens types I, III, or V, nor did anti-Bra or anti-Brb alloantibodies interfere with platelet adhesion to any of these fibrillar collagens. The identification of the nucleotide substitution that defines the Bra/Brb alloantigen system will now permit both pre- and postnatal diagnosis for Br phenotype.
Biomedical Applications of Vibration and Acoustics in Imaging and Characterizations (2008)

The primary objective of this book is to compile the latest research topics on biomedical imaging and tissue characterization techniques that utilize vibration and acoustics. This book includes two parts. The first part is dedicated to imaging, which is comprised of eight chapters. The second part is dedicated to the applications of vibration and acoustics in tissue characterization. Readers will find this text a valuable asset in keeping them abreast of the latest techniques in this area. It will appeal not only to fellow researchers, but also to clinicians, practitioners, lecturers and students in this exciting and vital field of study
Large scale analysis of web revisitation patterns (2008)

Our work examines Web revisitation patterns. Everybody revisits Web pages, but their reasons for doing so can differ depending on the particular Web page, their topic of interest, and their intent. To characterize how people revisit Web content, we analyzed five weeks of Web interaction logs of over 612,000 users. We supplemented these findings by a survey intended to identify the intent behind the observed revisitation. Our analysis reveals four primary revisitation patterns, each with unique behavioral, content, and structural characteristics. Through our analysis we illustrate how understanding revisitation patterns can enable Web sites to provide improved navigation, Web browsers to predict users' destinations, and search engines to better support fast, fresh, and effective finding and re-finding.
Coherent Phrase Model for Efficient Image Near-Duplicate Retrieval (2009)

This paper presents an efficient and effective solution for retrieving image near-duplicate (IND) from image database. We introduce the coherent phrase model which incorporates the coherency of local regions to reduce the quantization error of the bag-of-words (BoW) model. In this model, local regions are characterized by <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">visual phrase</b> of multiple descriptors instead of visual word of single descriptor. We propose two types of visual phrase to encode the coherency in feature and spatial domain, respectively. The proposed model reduces the number of false matches by using this coherency and generates sparse representations of images. Compared to other method, the local coherencies among multiple descriptors of every region improve the performance and preserve the efficiency for IND retrieval. The proposed method is evaluated on several benchmark datasets for IND retrieval. Compared to the state-of-the-art methods, our proposed model has been shown to significantly improve the accuracy of IND retrieval while maintaining the efficiency of the standard bag-of-words model. The proposed method can be integrated with other extensions of BoW.
A Goniometric Glove for Clinical Hand Assessment (2000)

The construction of a goniometric glove is described. Each of the sensors in the glove was calibrated over a custom built metal hand using blocks of known angles as angular references. The digital data output from each sensor of the glove were converted into angular displacements at each joint. The glove was validated for consistency of measurement and accuracy over a custom built metal jig and in the human hand. The accuracy of the glove was found to be within the limits of traditional goniometry. It is proposed that goniometric gloves could be useful in the assessment of hand function.
Differentiating untreated and cross-linked porcine corneas of the same measured stiffness with optical coherence elastography (2014)

Structurally degenerative diseases, such as keratoconus, can significantly alter the stiffness of the cornea, directly affecting the quality of vision. Ultraviolet-induced collagen cross-linking (CXL) effectively increases corneal stiffness and is applied clinically to treat keratoconus. However, measured corneal stiffness is also influenced by intraocular pressure (IOP). Therefore, experimentally measured changes in corneal stiffness may be attributable to the effects of CXL, changes in IOP, or both. We present a noninvasive measurement method using phase-stabilized swept-source optical coherence elastography to distinguish between CXL and IOP effects on measured corneal stiffness. This method compared the displacement amplitude attenuation of a focused air-pulse-induced elastic wave. The damping speed of the displacement amplitudes at each measurement position along the wave propagation were compared for different materials. This method was initially tested on gelatin and agar phantoms of the same stiffness for validation. Consequently, untreated and CXL-treated porcine corneas of the same measured stiffness, but at different IOPs, were also evaluated. The results suggest that this noninvasive method may have the potential to detect the early stages of ocular diseases such as keratoconus or may be applied during CLX procedures by factoring in the effects of IOP on the measured corneal stiffness.
Real-time road traffic fusion and prediction with GPS and fixed-sensor data (2012)

GPS devices offer new opportunities for short-term traffic prediction, especially in arterial road networks where traditional fixed-location sensors are sparse or unavailable. However, GPS data is often sparse both temporally and spatially. On its own, it is often insufficient for real-time traffic prediction. Hence, we consider the fusion of two types of data for the purpose of real-time traffic fusion and prediction: GPS data that is provided as point speeds, rather than trajectories, as well as (non real-time) traffic data such as is available from fixed sensors.
Spread Spectrum PWM Signal Generator for Fully Digital Audio Amplifier (2006)

A generation scheme to make a low noise low distortion PWM signal spreading its spectrum for the fully digital audio amplifier is proposed. The carrier frequency of the PWM is fluctuated randomly to spread the spectrum of the carrier component. The noise-shaping filter in the delta-sigma modulator is implemented so that the filter works with a changing sampling period preserving the designed frequency characteristics. Such a filter is designed in continuous-time manner considering the distortion due to the PWM and is realized as a digital filter to compensate the effect of the sampling period fluctuation with feedback manner. A S/(N+D) ratio of over 120 dB is achieved for the generated PWM signal.
Self-Assembly of Gold Nanoparticles at the Surface of Amine- and Thiol-Functionalized Boron Nitride Nanotubes (2007)

Gold nanoparticles have been self-assembled at the surface of both amine- and thiol-functionalized boron nitride nanotubes (BNNTs) in solution. The chemical functionalization of the surface of the BNNTs was achieved following ammonia plasma irradiation in order to generate amine functional groups at the surface of the BNNTs. The amine-functionalized BNNTs (AF-BNNTs) were then covalently modified by the coupling of short-chain thiol-terminated organic molecules to result in thiol-functionalized BNNTs. The functionalization of the BNNTs was characterized using XPS, FT-IR spectroscopy, and EDS, whereas the nanoparticle−nanotube assemblies were characterized using HR-TEM and EELS. This approach constitutes a basis for the preparation of highly functionalized BNNTs and their utilization as nanoscale templates for assembly and integration with other nanoscale materials.
A NEW FEASIBLE NATURAL LANGUAGE DATABASE QUERY METHOD (2006)

A metadata search approach is proposed to provide practical solutions to the natural language database query problem; where the metadata grow in largely linear manner and the search is linguistics-free. A new class of reference dictionary integrates four types of enterprise metadata: enterprise information models, database values, user-words, and query cases. The layered and scalable information models allow user-words to stay in original forms as users articulated them, as opposed to relying on permutations of individual words contained in the original query. A graphical representation method turns the dictionary into searchable graphs representing all possible interpretations of the input. A branch-and-bound algorithm then identifies optimal interpretations, which lead to SQL implementation of the original queries. Query cases enhance both the metadata and the search of metadata, as well as providing case-based reasoning to directly answer the queries. This design assures feasible solutions at the termination of the search, even when the search is incomplete (i.e., the results contain the correct answer to the original query). The necessary condition is that the text input contains at least one entry in the reference dictionary. The sufficient condition is that the text input contains a set of entries corresponding to a complete, correct single SQL query. Laboratory testing shows that the system obtained accurate results for most cases that satisfied only the necessary condition.
A new power combining and outphasing modulation system for high-efficiency power amplification (2010)

This paper describes a new power combining and outphasing system that provides both high efficiency and linear output control. Whereas conventional outphasing systems utilize two power amplifiers, the system introduced here combines power from four or more amplifiers. The proposed technique overcomes the loss and reactive loading problems of previous outphasing systems. It provides ideally lossless power combining, along with nearly resistive loading of the individual power amplifiers over a very wide output power range.
Synthesis and Biological Evaluation of Structurally Highly Modified Analogues of the Antimitotic Natural Product Curacin A (2002)

Structure-activity relationship analysis of synthetic analogues of curacin A revealed the lack of activity of traditional heterocyclic replacements of the thiazoline ring or cyclopropyl analogues of the core diene segment. The significance of the C(3)-C(4)-(Z)-alkene geometry was established, and a novel oxime analogue was designed that displays biological properties that are a close match of the natural product lead. The much less lipophilic, structurally simplified oxime 50 was only slightly weaker at inhibiting the growth of cultured human tumor cells than the natural product and was found to be more potent than curacin A at inhibiting the assembly of purified tubulin. Accordingly, the oxime moiety is likely to serve as a novel bioisostere of the (Z)-alkene group.
A malaria sporozoite surface antigen distinct from the circumsporozoite protein. (1990)

Monoclonal antibody NYS4 recognizes a single 140 kDa antigen on the surface of Plasmodium yoelii sporozoites, an antigen which is distinct from the extensively characterized circumsporozoite (CS) protein. To more thoroughly characterize this additional surface component, a genomic expression library was screened with NYS4 and an immunoreactive clone (M4) was obtained which expressed part of the antigen gene. The deduced amino acid sequence of the M4 peptide included two unique repetitive sequences of amino acids and a conserved sequence motif which is found in several proteins including the CS protein (region II). The cloned DNA hybridized to a PCR (polymerase chain reaction) amplified sporozoite mRNA demonstrating the sporozoite-stage expression of this gene. A synthetic peptide of one of the repeats, (Asn-Pro-Asn-Glu-Pro-Ser), was recognized by NYS4 and mice immunized with (Asn-Pro-Asn-Glu-Pro-Ser)3 conjugated to KLH (keyhole limpet haemocyanin) produced high levels of antibodies that reacted with the surface of sporozoites and specifically to the 140 kDa antigen. Thus, at least two different proteins are on the surface of the P. yoelii sporozoite indicating that the immunoreactive exterior of the infective stage of malaria parasites is more antigenically complex than previously thought.
Milder routes to chelated ruthenium complexes for Z-selective metathesis (2013)

A novel method to effect the salt metathesis and C-H activation of ruthenium-based, Z-selective metathesis catalysts contg. a\nchelated N-heterocyclic carbene (NHC) ligand using sodium carboxylates is reported. This method allows for the successful\nformation of stable chelated species contg. a variety of alterations to the NHC ligand that had decompd. under the previous\napproach. As such, several new, chelated metathesis-active ruthenium complexes are described, including a catalyst system\nexhibiting >95% Z-selectivity and record TONs (up to 8100) in homodimerization reactions of terminal olefins. Moreover, a\ncatalyst has been synthesized that gives highly cis, highly tactic polymers via ring opening metathesis polymn. of strained, cyclic\nolefins, marking the first time tactic polymers have been made using a ruthenium-based metathesis catalysts.
Niemann–Pick Disease: Mutation Update, Genotype/Phenotype Correlations, and Prospects for Genetic Testing (1997)

Niemann-Pick Disease (NPD) is an autosomal recessive lysosomal storage disorder caused by a deficiency of acid sphingomyelinase (ASM). NPD occurs in two forms, neuronopathic Type A and nonneuronopathic Type B. The incidence of Type A NPD is highest among Ashkenazi Jews. Type B NPD is more common in non-Jews but has been reported in Ashkenazi Jews. Different mutations in ASM are presumed to be responsible for the different NPD phenotypes. Three mutations are predicted to account for > 95% of all Type A NPD chromosomes among Ashkenazi Jews (L302P, R496L, fsP330). Based on limited screens for these mutations among Ashkenazi Jews, a carrier frequency for Type A NPD of 1:90 is reported for this population. Less is known about mutations responsible for Type B NPD, although one mutation (delta R608) has been identified in both Ashkenazi Jews and non-Jews. Screening of the Ashkenazi Jewish population to detect > 95% of NPD carriers can be accomplished with a four-mutation panel that includes L302P, R496L, fsP330, and delta R608, the three predominant Type A mutations and one recurrent Type B mutation.
Narrow plasmon resonances enabled by quasi-freestanding bilayer epitaxial graphene (2017)

Exploiting the underdeveloped terahertz range (~1012–1013 Hz) of the electromagnetic spectrum could advance many scientific fields (e.g. medical imaging for the identification of tumors and other biological tissues, non-destructive evaluation of hidden objects or ultra-broadband communication). Despite the benefits of operating in this regime, generation, detection and manipulation have proven difficult, as few materials have functional interactions with THz radiation. In contrast, graphene supports resonances in the THz regime through structural confinement of surface plasmons, which can lead to enhanced absorption. In prior work, the achievable plasmon resonances in such structures have been limited by multiple electron scattering mechanisms (i.e. large carrier scattering rates) which greatly broaden the resonance (>100 cm−1; 3 THz). We report the narrowest room temperature Drude response to-date, 30 cm−1 (0.87 THz), obtained using quasi-free standing bilayer epitaxial graphene (QFS BLG) synthesized on (0 0 0 1)6H–SiC. This narrow response is due to a 4-fold increase in carrier mobility and improved thickness and electronic uniformity of QFS BLG. Moreover, QFS BLG samples patterned into microribbons targeting 1.8–5.7 THz plasmon resonances also exhibit low scattering rates (37–53 cm−1). Due to the improved THz properties of QFS BLG, the effects of e-beam processing on carrier scattering rates was determined and we found that fabrication conditions can be tuned to minimize the impact on optoelectronic properties. In addition, electrostatic gating of patterned QFS BLG shows narrow band THz amplitude modulation. Taken together, these properties of QFS BLG should facilitate future development of THz optoelectronic devices for monochromatic applications.
A surface receptor specific for human IgA on group B streptococci possessing the Ibc protein antigen. (1984)

A number of group B streptococcal strains of various serotypes, Ia, Ib, Ic, II, and III were examined for their ability to bind human IgG and IgA. No strains of group B streptococci were found to bind IgG, but many strains possessing the Ibc protein antigen(s) were found to bind a significant amount of IgA. The extent of IgA binding correlated with the amount of a 130,000 mol wt, detergent-extractable protein, and reactivity with the Ic typing sera. Using nitrocellulose blots, it was found that the 130,000 mol wt protein bound human IgA. A method was developed to purify the protein while retaining its ability to bind human IgA. Using solid phase radioimmunoassays, it was determined that the protein bound to the Fc region of monomeric or polymeric IgA and that it failed to bind IgM or any IgG isotype.