gebhart/patrepeval huggingface dataset:
Abstract 11102: Gb002, A Novel Inhaled Pdgfr Kinase Inhibitor, Demonstrates Efficacy in the Su5416 Hypoxia Rat Model of Pulmonary Arterial Hypertension (pah) (2019)

Introduction: Pulmonary arterial hypertension (PAH) is a progressive disorder characterized by excessive smooth muscle cell proliferation, vascular remodeling, increased pulmonary arterial pressure...
Engineering Substrate Specificity of <i>O</i><sup>6</sup>‐Alkylguanine‐DNA Alkyltransferase for Specific Protein Labeling in Living Cells (2005)

Fusion proteins of human O(6)-alkylguanine-DNA alkyltransferase (AGT) can be specifically labeled with a wide variety of synthetic probes in mammalian cells; this makes them an attractive tool for studying protein function. However, to avoid undesired labeling of endogenous wild-type AGT (wtAGT), the specific labeling of AGT fusion proteins has been restricted to AGT-deficient mammalian cell lines. We present here the synthesis of an inhibitor of wtAGT and the generation of AGT mutants that are resistant to this inhibitor. This enabled the inactivation of wtAGT and specific labeling of fusion proteins of the AGT mutant in vitro and in living cells. The ability to specifically label AGT fusion proteins in the presence of endogenous AGT, after brief incubation of the cells with a small-molecule inhibitor, should significantly broaden the scope of application of AGT fusion proteins for studying protein function in living cells.
Development of a Water Hydraulic Servovale. (1997)

An electrohydraulic servovalve that uses clear water as a pressure medium (water hydraulic servovalve) is developed. A conventional electrohydraulic servovalve cannot work with this hostile fluid. This paper explains the structure and functions of components, and the relationship between them, as well as development procedure of the water hydraulic servovalve. The basic idea for the development is to support the spool of the valve with hydrostatic bearings and to lead the water from the bearings to the flapper-nozzle system, which, in this valve contains a laminar restriction upstream from the nozzle instead of the turbulent restriction in the conventional flapper-nozzle system. This paper also explains the design procedure of the hydrostatic bearing in the valve and the commection of electromagnetic elements and the fluidic elements. The manufactured water hydraulic servovalves show good characteristics in their smooth motion. endurance and controllability, including dynamic characteristics.
A clinical assessment of the Mucus Shaver (2011)

: The Mucus Shaver is a safe, feasible, and efficient device for endotracheal tube cleaning in the clinical setting. The Mucus Shaver is helpful in preventing endotracheal tube colonization by potentially harmful microorganisms.
Acquirement of cold sensitivity by quadruple deletion of the <i>cspA</i> family and its suppression by PNPase S1 domain in <i>Escherichia coli</i> (2001)

Escherichia coli contains a large CspA family, CspA to CspI. Here, we demonstrate that E. coli is highly protected against cold-shock stress, as these CspA homologues existed at approximately a total of two million molecules per cell at low temperature and growth defect was not observed until four csp genes (cspA, cspB, cspE and cspG) were deleted. The quadruple-deletion strain acquired cold sensitivity and formed filamentous cells at 15 degrees C although chromosomes were normally segregated. The cold-sensitivity and filamentation phenotypes were suppressed by all members of the CspA family except for CspD, which causes lethality upon overexpression. Interestingly, the cold sensitivity of the mutant was also suppressed by the S1 domain of polynucleotide phosphorylase (PNPase), which also folds into a beta-barrel structure similar to that of CspA. The present results show that cold-shock proteins and S1 domains share not only the tertiary structural similarity but also common functional properties, suggesting that these seemingly distinct protein categories may have evolved from a common primordial RNA-binding protein.
Ensembles of Radial Basis Function Networks for Spectroscopic Detection of Cervical Pre-Cancer (1999)

The mortality related to cervical cancer can be substantially reduced through early detection and treatment. However, current detection techniques, such as Pap smear and colposcopy, fail to achieve a concurrently high sensitivity and specificity. In vivo fluorescence spectroscopy is a technique which quickly, non-invasively and quantitatively probes the biochemical and morphological changes that occur in pre-cancerous tissue. A multivariate statistical algorithm was used to extract clinically useful information from tissue spectra acquired from 361 cervical sites from 95 patients at 337, 380 and 460 nm excitation wavelengths. The multivariate statistical analysis was also employed to reduce the number of fluorescence excitation-emission wavelength pairs required to discriminate healthy tissue samples from pre-cancerous tissue samples. The use of connectionist methods such as multi layered perceptrons, radial basis function networks, and ensembles of such networks was investigated. RBF ensemble algorithms based on fluorescence spectra potentially provide automated, and near real-time implementation of pre-cancer detection in the hands of non-experts. The results are more reliable, direct and accurate than those achieved by either human experts or multivariate statistical algorithms.
Construction and characterization of a small-bore electrospray ionization source (1993)

A simple, economical, and efficient electrospray ionization (ESI) source has been constructed in the configuration of a probe that makes use of a standard 13 mm vacuum lock. The principal components have been placed inside a glass tube making use of the electrical insulating properties of the glass while allowing for visual adjustments to be readily made. The ESI source, a variation of an atmospheric pressure ionization interface, is a modified version of designs published by Chait et al. (Rapid Comm. Mass Spectrom. 1990, 4, 81-87) and Knapp et al. (Annl. Chem. 1991, 63, 1658-1660) wherein a heated metal capillary is used for desolvation. The ESI probe has been tested on three different Extrel quadmpole mass spectrometers, with removable ion volumes, using polypeptides and small proteins. No modifications to the standard electron ionization/chemical ionization lens assembly were required to obtain excellent results other than removal of the ion volume. The spectra acquired were in excellent agreement with those previously published.
Watermarking video, hierarchical embedding in motion vectors (2004)

This paper proposes a new video watermarking scheme based on a hierarchical motion analysis, that is robust against classical video processing (filtering, lossy compression...). This model works in the uncompressed domain and disturbs the motion vectors computed by an exhaustive BMA on blocks of size n*n in order to insert an invisible watermark enabling a protection against most attacks. Finally, to increase the robustness, our system inserts the mark by generating a hierarchy of motion vectors of size N*N with N=k*n to spread the mark on the lower level associated to block n*n.
Abstract B52: A novel quantitative proteomics approach to identify proteins that elicit antibody responses in vaccinated pancreatic cancer patients. (2013)

Abstract Pancreatic cancer is the fourth leading cause of cancer deaths in the US. Less than 4% of patients have an overall survival of more than 5 years. Our lab has developed an allogeneic, granulocyte-macrophage colony-stimulating factor (GM-CSF) secreting pancreatic cancer vaccine that has recently completed phase II clinical trials. The application of proteomic approaches has gained ground in the identification of new cancer biomarkers, which are beneficial for both early detection and determination of new targets for development of biologically relevant therapies. We have developed a novel Serum Antibodies based SILAC-Immunoprecipitation (SASI) approach. The SASI approach utilizes immunoprecipitation by serum antibodies, which is coupled to the quantitative stable isotope labeling by amino acids in cell culture (SILAC) to identify proteins that elicit an increased antibody response post-vaccination. Using mass spectrometric analysis, the SASI approach comprehensively identified &gt;40 proteins that elicited at least a 2-fold increase in antibody response post-vaccination, from each of the three patients' sera used. The list of identified proteins includes membrane proteins such as MHC class I complex, transferrin receptor (TFRC) and CD9, secreted proteins such as mesencephalic astrocyte-derived neurotrophic factor (MANF), as well as several cytoplasmic proteins such as regulatory subunit 12A of protein phosphatase 1 (PPP1R12A), galectin 3 and regulatory subunit 8 of the 26S proteasome (PSMC5). Most significantly, the antibody responses detected against these proteins in patients with &gt;3 years disease-free survival suggests an anti-tumor potential of targeting these proteins. We further analyzed PSMC5, TFRC and PPP1R12A for tissue expression in normal, pre-malignant and pancreatic tumor specimens and found these proteins to increase in expression with tumor development. In addition, these proteins were shown to be pancreatic cancer associated antigens that are recognized by post-vaccination antibodies in the sera of patients that received the vaccine and have demonstrated a favorable disease free survival. Overall, our data demonstrates that the novel SASI approach can enable identification of candidate proteins as possible new biomarkers for screening, and as new targets for therapeutic intervention. Citation Format: Darshil T. Jhaveri, Min-Sik Kim, Lanqing Huang, Rajni Sharma, Robert A. Anders, Akhilesh Pandey, Elizabeth M. Jaffee. A novel quantitative proteomics approach to identify proteins that elicit antibody responses in vaccinated pancreatic cancer patients. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology: Multidisciplinary Science Driving Basic and Clinical Advances; Dec 2-5, 2012; Miami, FL. Philadelphia (PA): AACR; Cancer Res 2013;73(1 Suppl):Abstract nr B52.
Genetic analysis of Carney complex: current understanding and future questions (2002)

Carney complex is an inherited tumor syndrome consisting of spotty skin pigmentation, myxomatosis, schwannomas, and endocrine tumors. Linkage analysis has identified 2p16 and 17q22–24 as likely chromosomal loci to harbor genes causing Carney complex. The authors recently identified mutations in the PRKAR1A gene as being responsible for the disease in kindreds mapping to 17q. Inactivating mutations of this gene, which codes for the type 1A regulatory subunit of protein kinase A, lead to dysregulation of protein kinase A function in tumors from patients with Carney complex. Although the causative gene has not yet been located at 2p, this locus also appears to be involved in the molecular pathogenesis of Carney complex, because patient tumors often demonstrate multiple genetic changes in this region. Despite the known genetic heterogeneity in the disease, clinical analysis has not detected any corresponding phenotypic differences between patients with PRKAR1A mutations and those without.
Mechanically Shaped Two-Dimensional Covalent Organic Frameworks Reveal Crystallographic Alignment and Fast Li-Ion Conductivity (2016)

Covalent organic frameworks (COFs) usually crystallize as insoluble powders, and their processing for suitable devices is thought to be limited. We demonstrate that COFs can be mechanically pressed into shaped objects having anisotropic ordering with preferred orientation between hk0 and 00l crystallographic planes. Five COFs with different functionality and symmetry exhibited similar crystallographic behavior and remarkable stability, indicating the generality of this processing. Pellets prepared from bulk COF powders impregnated with LiClO4 displayed room temperature conductivity up to 0.26 mS cm(-1) and high electrochemical stability. This outcome portends use of COFs as solid-state electrolytes in batteries.
Electric vehicle charging modulation using voltage feedback control (2013)

Electric vehicle integration into the distribution system has been a topic of great interest lately due the potential challenges it poses. Previous works have focused on either centralized charge control or distributed charge control to solve these issues. In this paper a voltage feedback controller for EV charging is proposed that, unlike all other proposed methods, does not require any communication between the EV and the utility. This controller compares the system voltage at the point of charging against a reference. The EV charging is reduced as the system voltage approaches this reference. Simulations show that this method can successfully reduce EV charging to eliminate system voltage violations that would otherwise be caused from EV charging.
Role of Pneumococcal Surface Protein A in the Virulence of Streptococcus pneumoniae (1988)

Pneumococcal surface protein A (PspA) is a cell-surface protein of Streptococcus pneumoniae that is present on a number of clinical isolates as well as on the nonencapsulated laboratory strain Rx1. PspA was originally identified by monoclonal antibodies that can protect mice against intravenous challenge with some pneumococcal strains. A gene, pspA, required for the production of PspA was inactivated with use of insertional inactivation. By immunizing CBA/N (Xid) mice with congenic PspA+ and PspA- pneumococci, it was possible to demonstrate that PspA can elicit protective antipneumococcal antibodies. This result may be significant to future vaccine research, since Xid mice, like children, are not responsive to the present pneumococcal vaccine. When pspA was inactivated in three virulent, encapsulated strains of pneumococci, all three strains showed a reduction in virulence and two became totally avirulent: the 50% lethal dose was less than 10 colony-forming units (cfu) for the parents and greater than 5 x 10(4) cfu for the PspA- mutants.
Predicting Cyber Threats through Hacker Social Networks in Darkweb and Deepweb Forums (2017)

We present an approach that combines social network analysis with machine learning techniques to predict future cyber threats through darkweb/deepweb discussions with hacking-related content. Our approach harnesses features derived from hacker social networks and from online sources of cybersecurity advisories. We address the problem of predicting the exploitability of software vulnerabilities to show that features computed from hacker social networks are important indicators of future cybersecurity incidents. We conduct a suite of experiments on real-world hacker and exploit data and demonstrate that social network data improves recall by about 19%, F1 score by about 6% while maintaining precision. We believe this is because social network structures related to certain exploit authors is indicative of their ability to write exploits that are subsequently employed in an attack.
A Method to Measure Packet Processing Time of Hosts Using High-Speed Transmission Lines (2014)

In this paper, we propose a scheme to measure the packet processing time of a host using Internet Control Message Protocol packets and a packet-capture line card in the same network segment. The proposed scheme is not affected by clock synchronization, the packet generation time, and the transmission speeds of the host under measurement. We show the experimental results of the proposed scheme tested on different hosts and under different transmission speeds, including 1000 Mb/s.
A generalized rule for large piezoelectric response in perovskite oxide ceramics and its application for design of lead-free compositions (2009)

We present a general rule for the perovskite oxide ceramics: “A large piezoelectric constant in ABO3 perovskite ceramics can be obtained by tuning the weight ratio of A and B sites, WA/WB or WB/WA, to 3. Piezoelectric constant decreases significantly when WA/WB or WB/WA is in the range of 0.5–2.0, termed as forbidden zone.” A comparative analysis was conducted for broad range of materials demonstrating the applicability of proposed rule. Further based on this rule optimized compositions in BaTiO3 and alkali niobate based systems were developed. Polycrystalline ceramics in modified BaTiO3 system were found to exhibit longitudinal piezoelectric coefficient (d33) of 330 pC/N, while alkali niobate ceramics showed d33 of 294 pC/N.
What's new in statistical machine translation (2003)

Automatic translation from one human language to another using computers, better known as machine translation (MT), is a long-standing goal of computer science. Accurate translation requires a great deal of knowledge about the usage and meaning of words, the structure of phrases, the meaning of sentences, and which real-life situations are plausible. For general-purpose translation, the amount of required knowledge is staggering, and it is not clear how to prioritize knowledge acquisition efforts.Recently, there has been a fair amount of research into extracting translation-relevant knowledge automatically from bilingual texts. In the early 1990s, IBM pioneered automatic bilingual-text analysis. A 1999 workshop at Johns Hopkins University saw a re-implementation of many of the core components of this work, aimed at attracting more researchers into the field. Over the past years, several statistical MT projects have appeared in North America, Europe, and Asia, and the literature is growing substantially. We will provide a technical overview of the state-of-the-art.
Effect of low hole mobility on the efficiency droop of AlGaN nanowire deep ultraviolet light emitting diodes (2019)

Compared to the extensive studies on the efficiency droop of InGaN visible light emitting diodes (LEDs), the efficiency droop of AlGaN deep ultraviolet (UV) LEDs is much less studied. In this context, we discuss the efficiency droop of AlGaN ternary nanowire deep UV LEDs. The device active region consisted of AlGaN double heterojunctions, which were grown by molecular beam epitaxy on silicon substrates. Through detailed analysis of the device optical characteristics under both continuous-wave and pulsed operations, as well as of the electrical characteristics from 293 K to 77 K, it is suggested that the efficiency droop is largely rooted in the low hole mobility, due to the dominant Mg impurity band conduction at room temperature in highly p-doped AlGaN alloys.
Galectins in cancer: carcinogenesis, diagnosis and therapy. (2014)

A major breakthrough in the field of medical oncology has been the discovery of galectins and their role in cancer development, progression and metastasis. In this review article we have condensed the results of a number of studies published over the past decade in an effort to shed some light on the unique role played by the galectin family of proteins in neoplasia, and how this knowledge may alter the approach to cancer diagnosis as well as therapy in the future. In this review we have also emphasized the potential use of galectin inhibitors or modulators in the treatment of cancer and how this novel treatment modality may affect patient outcomes in the future. Based on current pre-clinical models we believe the use of galectin inhibitors/modulators will play a significant role in cancer treatment in the future. Early clinical studies are underway to evaluate the utility of these promising agents in cancer patients.
Fabrication and characterization of graphene based film (2017)

Large area, freestanding graphene papers fabricated from 2D graphene nanosheets with optimized microstructure, graphene sheet alignment and superior properties have a wide range of functional applications. In this paper, we propose a novel approach to fabricate graphene film by Electro-spray deposition (ESD), which is considered as the preparation for a roll-to-roll industrial production of the further. Expanded graphite, as the raw materials, was dispersed into N-Methyl-2-pyrrolidone (NMP) which is used as the feeding solution for ESD. It is also shown that high-shear mixing and high ultra-sonication of graphite powder in NMP solvent result in large-scale exfoliation, giving good dispersions of graphene nanosheets. The fabrication of the film with different thicknesses is based on ESD onto the surface of a heated aluminum foil at around 140°C. Brunauer-Emmett-Teller method is used to test the surface area of raw material, which has been reported to reach 1200 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /g. Raman spectroscopy and scanning electron microscope (SEM) are used to characterize the microstructure and morphology of the film, contributing to the optimization of electrospray's parameters. Joule heating was utilized to quantify thermal conductivity of the film.
Assessing the effect of laser beam width on quantitative evaluation of optical properties of intraocular lens implants (2014)

The design and manufacture of intraocular lenses (IOLs) depend upon the identification and quantitative preclinical evaluation of key optical properties and environmental parameters. The confocal laser method (CLM) is a new technique for measuring IOL optical properties, such as dioptric power, optical quality, refractive index, and geometrical parameters. In comparison to competing systems, the CLM utilizes a fiber-optic confocal laser design that significantly improves the resolution, accuracy, and repeatability of optical measurements. Here, we investigate the impact of changing the beam diameter on the CLM platform for the evaluation of IOL dioptric powers. Due to the Gaussian intensity profile of the CLM laser beam, the changes in focal length and dioptric power associated with changes in beam diameter are well within the tolerances specified in the ISO IOL standard. These results demonstrate some of the advanced potentials of the CLM toward more effectively and quantitatively evaluating IOL optical properties.
Synthesis, Crystal Structure, and Luminescence Properties of a Novel Green-Yellow Emitting Phosphor LiZn<sub>1−<i>x</i></sub>PO<sub>4</sub>:Mn<sub><i>x</i></sub> for Light Emitting Diodes (2008)

A novel green-yellow emitting Mn2+-doped LiZnPO4 phosphor can be excited under ultraviolet and blue light. The phosphor will be an attractive candidate as an ascendant phosphor for potential applications in light emitting diodes.