gebhart/patrepeval huggingface dataset:
Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains (2018)

Quantitative PCR is a diagnostic pillar for clinical virology testing, and reference materials are necessary for accurate, comparable quantitation between clinical laboratories. Accurate quantitation of human herpesvirus 6A/B (HHV-6A/B) is important for detection of viral reactivation and inherited chromosomally integrated HHV-6A/B in immunocompromised patients. Reference materials in clinical virology commonly consist of laboratory-adapted viral strains that may be affected by the culture process. We performed next-generation sequencing to make relative copy number measurements at single nucleotide resolution of eight candidate HHV-6A and seven HHV-6B reference strains and DNA materials from the HHV-6 Foundation and Advanced Biotechnologies Inc. Eleven of 17 (65%) HHV-6A/B candidate reference materials showed multiple copies of the origin of replication upstream of the U41 gene by next-generation sequencing. These large tandem repeats arose independently in culture-adapted HHV-6A and HHV-6B strains, measuring 1,254 bp and 983 bp, respectively. The average copy number measured was between 5 and 10 times the number of copies of the rest of the genome. We also report the first interspecies recombinant HHV-6A/B strain with a HHV-6A backbone and a >5.5-kb region from HHV-6B, from U41 to U43, that covered the origin tandem repeat. Specific HHV-6A reference strains demonstrated duplication of regions at U1/U2, U87, and U89, as well as deletion in the U12-to-U24 region and the U94/U95 genes. HHV-6A/B strains derived from cord blood mononuclear cells from different laboratories on different continents with fewer passages revealed no copy number differences throughout the viral genome. These data indicate that large origin tandem duplications are an adaptation of both HHV-6A and HHV-6B in culture and show interspecies recombination is possible within the <i>Betaherpesvirinae.</i><b>IMPORTANCE</b> Anything in science that needs to be quantitated requires a standard unit of measurement. This includes viruses, for which quantitation increasingly determines definitions of pathology and guidelines for treatment. However, the act of making standard or reference material in virology can alter its very accuracy through genomic duplications, insertions, and rearrangements. We used deep sequencing to examine candidate reference strains for HHV-6, a ubiquitous human virus that can reactivate in the immunocompromised population and is integrated into the human genome in every cell of the body for 1% of people worldwide. We found large tandem repeats in the origin of replication for both HHV-6A and HHV-6B that are selected for in culture. We also found the first interspecies recombinant between HHV-6A and HHV-6B, a phenomenon that is well known in alphaherpesviruses but to date has not been seen in betaherpesviruses. These data critically inform HHV-6A/B biology and the standard selection process.
Diversity in medullary thymic epithelial cells controls the activity and availability of iNKT cells (2020)

The thymus supports multiple αβ T cell lineages that are functionally distinct, but mechanisms that control this multifaceted development are poorly understood. Here we examine medullary thymic epithelial cell (mTEC) heterogeneity and its influence on CD1d-restricted iNKT cells. We find three distinct mTEC<sup>low</sup> subsets distinguished by surface, intracellular and secreted molecules, and identify LTβR as a cell-autonomous controller of their development. Importantly, this mTEC heterogeneity enables the thymus to differentially control iNKT sublineages possessing distinct effector properties. mTEC expression of LTβR is essential for the development thymic tuft cells which regulate NKT2 via IL-25, while LTβR controls CD104<sup>+</sup>CCL21<sup>+</sup> mTEC<sup>low</sup> that are capable of IL-15-transpresentation for regulating NKT1 and NKT17. Finally, mTECs regulate both iNKT-mediated activation of thymic dendritic cells, and iNKT availability in extrathymic sites. In conclusion, mTEC specialization controls intrathymic iNKT cell development and function, and determines iNKT pool size in peripheral tissues.
ChemInform Abstract: Effect of Calcium Reagents on Aldol Reactions of Phenolic Enolates with Aldehydes in Alcohol. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
In situ electrical characterization of dielectric thin films directly exposed to plasma vacuum-ultraviolet radiation (2000)

In this article we report a method for in situ electrical characterization of dielectric thin films under direct exposure to plasma in an electron-cyclotron-resonance etcher. This method is based on the development of a special test structure that allows for the measurement of the influence of plasma vacuum-ultraviolet (VUV) radiation on the electrical conductivity of thin dielectric layers. Results show that the measured conductivity of SiO2 layers temporarily increases during exposure to argon and oxygen plasmas, with controlled VUV emission. Based on the measurements made through this method, a model of the VUV-induced conductivity of SiO2 is developed. These measurements are very important for plasma processing of semiconductor devices, because the temporary increase in the conductivity of these layers upon exposure to processing plasmas can decrease the plasma-induced charging of these dielectric layers depending on the intensity of the plasma VUV emission. This can have an impact on the properties and reliability of processed devices.
New Selective Oxidation Reactions by Nitroarenes in Basic Medium Involving Electron-Transfer Processes (2001)

A new synthetic process for oxidation of methyl ketones into their corresponding carboxylic acids using a modified alkaline nitrobenzene method is described. By introduction of a more powerful oxidant, such as 1,3-dinitrobenzene, the oxidation reaction proceeds smoothly in aqueous alkaline solution at 100 °C. The procedure can also be used for oxidation of benzaldehydes and benzyl alcohols into carboxylic acids and to oxidise mandelic acid into its α-keto form, whereas prolonged reaction time results in decarboxylation and gives thus also in this case benzoic acid.
Abstract 5395: Anti-tumor activity of BMS-595, a novel CK2 kinase inhibitor (2015)

Abstract The CK2 protein kinases are a small family of two highly related serine/threonine kinases composed of two catalytic subunits, α and α’, and a single β subunit. Numerous substrates have been reported for CK2 and these proteins are known to participate in diverse cellular processes, including cell signaling, transcription, DNA repair, apoptosis regulation and tumor suppression. Elevated CK2 expression and kinase activity has been observed in many cancer types. Further, mRNA knockdown and enzyme inhibition studies have demonstrated that many cancer cell lines are dependent on CK2 for growth and survival. To further evaluate CK2 kinases as targets for therapeutic intervention in cancer, we identified BMS-595, a potent and selective, ATP-competitive CK2 inhibitor. BMS-595 inhibits the in vitro proliferation of human colorectal and lung cancer cell lines with IC50s ranging from less than 10 nM to greater than 1 μM. In sensitive cell lines, anti-proliferative effects of BMS-595 and structurally related analogs strongly correlated with cellular CK2 kinase inhibition. Oral administration of BMS-595 to mice bearing colorectal cancer and lung cancer xenografts demonstrated pharmacodynamic effects and robust efficacy at tolerated doses. These studies confirm the dependence of a subset of human colon and lung cancer cell lines on CK2 activity for growth and demonstrate that pharmacologic inhibition of CK2 can produce anti-tumor efficacy at tolerated doses. Citation Format: Brent A. Rupnow, Chiang Yu, Jonathan G. Pabalan, Urvashi V. Roongta, Jonathan S. Lippy, Ashok R. Dongre, Mary T. Obermeier, Aberra Fura, Paul A. Elzinga, Benjamin J. Henley, Joseph Fargnoli, Francis Y. Lee, William R. Foster, Christine M. Tarby, Brian E. Fink, John S. Tokarski, Ashvinikumar V. Gavai, Tai W. Wong, John T. Hunt, Gregory D. Vite, Ashok V. Purandare. Anti-tumor activity of BMS-595, a novel CK2 kinase inhibitor. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5395. doi:10.1158/1538-7445.AM2015-5395
Ultra-compact Clamp-on Liquid Level Sensor based on a Low-Voltage CMUT (2020)

Determining the liquid level in containers is a challenging task in many industries, as there are different kinds of containers and liquids. The approach for measuring the liquid fill level presented in this paper comprises a low-voltage capacitive micromachined ultrasonic transducer (CMUT). We use a premolded package, providing sufficient acoustic coupling, together with an ultra-compact sensor system. The sensor is simply clamped to the outside of the bottom of the tank, eliminating the requirement to open the container for direct access. Thus, the sensor stays chemically protected. Moreover, the low voltage required allows applications in all kinds of environments, even with no steady power supply. We present finite element simulations for the sensor characteristics, comprising resonance frequency, pull-in voltage and transmit sensitivity. The simulation results are validated with laser Doppler vibrometer measurements. With the CMUT design presented, we achieve operational voltages <; 10 V. Further, our results proof the suitability of flouro-silicone as performant coupling material. With a first test setup, we can demonstrate robust fill level determination up to 1 m in water.
Some Surprises in Estimating the Efficiency of Variable-Speed Pumps with the Pump Affinity Laws (2003)

The pump affinity laws are widely used in adjusting pump performance curves from one pump or speed to another. In most cases, they work fairly well and can be reliably used in modeling studies. This paper describes an experiment undertaken to determine how well these laws apply to a variable speed pump, in which the speed is controlled by a variable-frequency drive, the most common technology used today. The pump speed was varied from full speed to roughly 30 percent of full speed. Over that range, the affinity laws worked quite well for adjusting the pump head characteristic curves. However, the pump efficiency curves fell significantly lower than those predicted by the affinity laws. The explanation for this is most likely the loss of efficiency in the variable-frequency drive itself. Since energy costs are the largest component of pump life-cycle costs, the implications for pump selection are significant. With variable-speed drives costing almost as much as the pumps themselves, it becomes essential for life-cycle cost estimates, whether done manually or with models, to accurately account for the loss of efficiency.
Low profile and directive UWB antenna (2009)

This paper presents the design, the analysis and the characterization of a 2 × 2 UWB patch array on the 3.1 – 5.1 GHz frequency bandwidth, for very high data rate applications using Radio Over Fibre. The topic of the low profile UWB antenna with broadside, directive and frequency independent pattern is adressed. The main contribution of this work consists in using mutual coupling between elements to stabilize the patch radiation pattern over a 50 % relative bandwidth. The prototype with 90 × 90 × 9 mm dimensions shows a realized gain larger than 10 dBi, without no significant beam tilt over the bandwidth.
Cloning and characterization of the gene coding for NADPH-sulfite reductase hemoprotein from Actinobacillus pleuropneumoniae and use of the protein product as a vaccine. (2001)

An expression library was constructed from an Actinobacillus pleuropneumoniae serotype 1 clinical isolate and screened with serum produced in pigs that had been vaccinated with the anionic fraction of a sodium chloride extract. One E. coli transformant was isolated that produced a large amount of a protein with an electrophoretic mobility of about 67,000 molecular mass. The A. pleuropneumoniae-derived DNA encoding the protein was localized and characterized by restriction enzyme digestion and nucleotide sequence analysis which showed strong homology with the cysI gene of E. coli. One open reading frame of 1764 bases in length was detected which encoded a cysI protein from serotype 1, with a calculated molecular mass of 66,678. The DNA encoding the protein was labeled with radio-isotope and the homologous gene was isolated from an A. pleuropneumoniae serotype 5a library. The serotype 5a gene was the same length, but the cysI protein from serotype 5a was slightly larger (66,849) due to 8 substitutions in the amino acid sequence. Expression plasmids containing cysI from either serotype of A. pleuropneumoniae complemented an E. coli cysI mutant. Pigs vaccinated with the recombinant cysI were protected from challenge with A. pleuropneumoniae of the homologous serotype.
A Prospective, Randomized, Double-Blind Study Evaluating the Efficacy of Postoperative Continuous Local Anesthetic Infusion at the Iliac Crest Bone Graft Site After Spinal Arthrodesis (2005)

Continuous infusion of 0.5% Marcaine at the ICBG harvest site reduced postoperative parenteral narcotic usage by 50% and decreased overall pain scores. No complications were attributed to the infusion-catheter system. The use of continuous local anesthetic infusion at the iliac crest may help in alleviating acute graft-related pain, hastening patient recovery and improving short-term satisfaction.
A New Ionomer Based on Novel PolyPOM Materials (2008)

The heteropoly acids (HPAs) are a class of inorganic oxides that have some of the highest solid state proton conductivities known at room temperature. At elevated temperatures proton diffusion coefficients in these crystalline materials increase, but, not all the protons are mobile resulting in a decrease of the observed proton conductivity. The proton conductivity in these materials is heavily dependant on the hydration state of the HPA. In order to develop new PEMs based on the HPAs for elevated temperature, dry operation, it will be necessary to both immobilize the HPA and ensure that all of the protons are mobile all of the time. If both these objectives can be obtained a new class of PEMs will be developed that could facilitate the use of PEM fuel cells in automotive applications. We have created a new class of PEM by polymerizing HPA monomers with appropriate co-monomers to produce films with unique proton conducting properties.
Additives Lower Pickup Of Moisture By Polyimides (1989)

Series of new polyimide-processing additives decrease free volume and pickup of moisture in new 422 copolyimide. Physical properties of several copolyimides synthesized from linear BDSDA/ODA/MPD homopolymers investigated previously, by positron-annihilation spectroscopy, with results indicating copolyimides have unique transition molecular structure characterized by higher electron densities and stronger bonds. Transition structure permits both physical and chemical entry of water molecules into it.
Can Digital Breast Tomosynthesis Replace Full-Field Digital Mammography? A Multireader, Multicase Study of Wide-Angle Tomosynthesis (2019)

<b>OBJECTIVE.</b> The purpose of this study was to test the hypothesis whether two-view wide-angle digital breast tomosynthesis (DBT) can replace full-field digital mammography (FFDM) for breast cancer detection. <b>SUBJECTS AND METHODS.</b> In a multireader multicase study, bilateral two-view FFDM and bilateral two-view wide-angle DBT images were independently viewed for breast cancer detection in two reading sessions separated by more than 1 month. From a pool of 764 patients undergoing screening and diagnostic mammography, 330 patient-cases were selected. The endpoints were the mean ROC AUC for the reader per breast (breast level), ROC AUC per patient (subject level), noncancer recall rates, sensitivity, and specificity. <b>RESULTS.</b> Twenty-nine of 31 readers performed better with DBT than FFDM regardless of breast density. There was a statistically significant improvement in readers' mean diagnostic accuracy with DBT. The subject-level AUC increased from 0.765 (standard error [SE], 0.027) for FFDM to 0.835 (SE, 0.027) for DBT (<i>p</i> = 0.002). Breast-level AUC increased from 0.818 (SE, 0.019) for FFDM to 0.861 (SE, 0.019) for DBT (<i>p</i> = 0.011). The noncancer recall rate per patient was reduced by 19% with DBT (<i>p</i> < 0.001). Masses and architectural distortions were detected more with DBT (<i>p</i> < 0.001); calcifications trended lower (<i>p</i> = 0.136). Accuracy for detection of invasive cancers was significantly greater with DBT (<i>p</i> < 0.001). <b>CONCLUSION.</b> Reader performance in breast cancer detection is significantly higher with wide-angle two-view DBT independent of FFDM, verifying the robustness of DBT as a sole view. However, results of perception studies in the vision sciences support the inclusion of an overview image.
An improved high yielding immobilization of vanadium Schiff base complexes on mesoporous silica via azide–alkyne cycloaddition for the oxidation of sulfides (2010)

Azide–alkyne [3+2] cycloaddition “click reaction” was found to be a simple yet improved approach for the efficient immobilization of oxo–vanadium(IV) tridentate Schiff base complexes to mesoporous silica via covalent attachment as it occurred under mild reaction conditions and provided high catalyst loading compared to the direct immobilization of oxo–vanadium(IV) tridentate Schiff base complex to 3-chloropropylsilyl functionalized silica support.
Molecular and Cellular Basis of Human Olfaction (2004)

The human olfactory systems recognize and discriminate a large number of different odorant molecules. The detection of chemically distinct odorants begins with the binding of an odorant ligand to a specific receptor protein in the ciliary membrane of olfactory neurons. To address the problem of olfactory perception at a molecular level, we have cloned, functionally expressed, and characterized some of the human olfactory receptors from chromosome 17. Our results show that a receptor protein is capable of recognizing the particular chemical substructure of an odor molecule and, therefore, is able to respond only to odorants that have a defined molecular structure. These findings represent the beginning of the molecular understanding of odorant recognition in humans. In the future, this knowledge could be used for the design of synthetic ideal receptors for specific odors (biosensors), or the perfect odor molecule for a given receptor.
ChemInform Abstract: Mechanism of the Cyclooctatetraene Synthesis from Ethyne Employing Nickel Catalysts. (1987)

Abstract The mechanism of the Reppe cyclization to cyclooctatetraene was investigated by employing ethyne‐l‐13C as a substrate in the nickel‐catalyzed reaction.
Strong stabilizability of systems with multiaffine uncertainties and numerator denominator coupling (2005)

This paper considers a set of proper transfer functions whose numerator and denominator polynomial coefficients display dependent multiaffine parametric uncertainties. It is shown that provided no member transfer function has positive real pole zero cancellations, all members satisfy the parity interlacing property iff all corner members do the same. Notice, while this implies that each member is strongly stabilizable, it does not imply the existence of a single stable controller that stabilizes the whole set. The paper also shows that whenever the numerator and denominator polynomials lie in dependent polytopes, the task of verifying the absence of positive real pole zero cancellations can be accomplished by checking the edges.
Novel synthetic RORγ agonist compounds as a potential anti-tumor therapeutic approach (2014)

Meeting abstracts Selective enhancement (or activation) of the immune system by novel small molecules may be a potential therapeutic approach for the treatment of cancer. RORγt ( R etinoic Acid Receptor-related o rphan r eceptor) is the key transcription factor for the development of CD4+ Th17
Oligomerization of 1-butene with a homogeneous catalyst system based on allylic nickel complexes (2015)

The oligomerization of 1-butene with a nickel-based catalyst system constitutes an elegant synthesis method for obtaining linear octenes from readily available chemicals.
Concept-based classification for multi-document summarization (2011)

Documents often contain inherently many concepts reflecting specific and generic aspects. To automatically generate a short summary text of documents on similar topics, it is imperative that we discover general aspects in documents be cause summaries usually contain general rather than specific concepts. This paper presents a semi-supervised extractive summarization model based upon latent concept classification that can differentiate between the two types of aspects as hidden concepts being mentioned in documents. A classifier is trained on hidden concepts discovered from documents and their corresponding human-generated summaries using a probabilistic Bayesian model: the summary-focused topic model. Experimental results based on ROUGE evaluations indicate that ranking sentences to be included in summary text based on the latent summary concept classification has improvements on the quality of the generated summaries.
Improved Thermoelectric Power Factor in Completely Organic Nanocomposite Enabled by l-Ascorbic Acid (2019)

High power factor organic thermoelectric nanocomposites are assembled by alternately depositing polyaniline (PANi) and double walled-carbon nanotubes (DWNT), stabilized by graphene oxide (GO) in water, using the layer-by-layer assembly technique. A 40 bilayer (BL) thin film, comprised of a PANi/DWNT–GO repeating sequence, exhibits an electrical conductivity of 197 S/cm and Seebeck coefficient of 83 μV/K. The reduction of this system with l-ascorbic acid simultaneously increases the electrical conductivity (to 950 S/cm) and Seebeck coefficient (to 115 μV/K), yielding a power factor of 1260 μW/m·K2. This relatively simple treatment creates more opportunity for practical use of organic thermoelectrics.