gebhart/patrepeval huggingface dataset:
Abstract 3528: Novel enzymatic DNA fragmentation integrated into library construction (2019)

Next Generation Sequencing (NGS) is rapidly becoming a powerful tool, by providing a high resolution and global view of the cancer genome mainly through whole genome, whole exome and transcriptome sequencing. This knowledge is important to support drug development targeted towards precision medicine. Obtaining high quality sequencing data begins with optimal sample preparation. DNA fragmentation is one of the critical first steps in the construction of high quality libraries for NGS, but current fragmentation methods create a bottleneck on library preparation throughput. We have developed an efficient, one tube fragmentation system that integrates enzyme-based DNA fragmentation with end-repair and dA-tailing in a single step, followed by adaptor ligation in the same tube. This streamlined method is compatible with a wide range of DNA samples and input amounts, resulting in reproducible and reliable fragment sizes.Genomic DNA (100pg to 500ng) with various GC content, was used in the construction of libraries, that were sequenced on an Illumina platform. For low input samples, PCR amplification was performed prior to sequencing. Libraries constructed using intact genomic DNA and this novel library preparation method produced substantially higher yields than standard methods and mechanically-fragmented DNA. Enzyme-based shearing increases library yield by reducing DNA damage and sample loss. High library yields also enable PCR-free workflows from as little as 50ng starting material. This method can be used for DNA extraction and library preparation from whole blood and dried blood samples.Sequencing quality of libraries generated with inputs ranging from 100pg to 500ng DNA show similar coverage uniformity and fragment size distribution, with minimal GC bias.We have developed an enzymatic DNA fragmentation kit that enables the construction of high quality libraries from a range of sample types and inputs with minimal sequence bias, high yields and low duplication rates. This method eliminates the need for expensive equipment to fragment DNA as well as numerous cleanup and liquid transfer steps thereby reducing the time, cost and errors associated with library construction. These advances in NGS technologies, supported by powerful bioinformatics tools, promises to revolutionize cancer research, diagnosis and therapy.Citation Format: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis. Novel enzymatic DNA fragmentation integrated into library construction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3528.
Study of nanoimprint applications toward 22nm node CMOS devices (2008)

Nanoimprint lithography is one of the candidates for NGL. Recently, the S-FIL TM (Step and Flash Imprint Lithography) has been developed by MII (Molecular Imprints, Inc.). Accordingly, it is necessary to build next-generation devices and study unit processes without delay. Because of good resolution, CD uniformity and LER, nanoimprint lithography is attractive. However, nanoimprint lithography (S-FIL) involves risks. In order to judge whether the S-FIL is applicable to the study of unit processes and test device fabrication, we had studied the feasibility of S-FIL technology. As a result of previous work, we obtained the results of basic evaluation and confirmed the applicability of nanoimprint lithography for unit process study and basic test device fabrication. However, application of nanoimprint lithography to various test devices requires the template resolution of 22nmHP, OL accuracy on multilayer resist, and defect density for various patterns. Therefore, in order to judge whether the S-FIL application is extendable to various test devices, we studied the characteristics of S-FIL. As a result of this work, we confirmed that the nanoimprint application is extendable to fabrication of various test devices. And as a result of basic evaluation, improvement of template resolution is confirmed and the value of 22nmHP is obtained. We confirmed the robustness of the alignment process. The defect density is related in pattern density and spread time. Thus, reduced DD without throughput loss is required.
A peptide-catalyzed asymmetric Stetter reaction (2004)

Thiazolylalanine, in appropriately functionalized form, has been found to function as an enantioselective catalyst for an intramolecular Stetter reaction. Incorporation of the residue in a number of environments has resulted in a family of catalysts that promote the cyclization of a test substrate with up to 81% enantiomeric excess.
Audio-Visual 3D Reconstruction Framework for Dynamic Scenes (2020)

This paper proposes a method for three dimensional (3D) reconstruction using Structure from Motion (SfM) for a scene including moving objects. Because current SfM methods assume a stationary environment with no moving object, moving objects are not reconstructed after performing SfM thereby rendering them invisible in a scene from the reconstructed 3D structure. To solve this problem, this paper proposes an audio-visual SfM approach focusing on sound and vibration associated with moving objects. Sound source localization using microphone array processing is performed at each time frame. The sound information is extracted and the 3D structure of the moving object with its motion information is reconstructed with SfM. In parallel, another SfM is performed for reconstruction of the stationary environment. Finally, two SfM results are integrated to reconstruct a whole scene. The methods was validated by reconstructing a scene including a moving toy train.
EVALUATION OF ALTERNATE CABLE ANCHOR DESIGNS AND THREE-CABLE GUARDRAIL ADJACENT TO STEEP SLOPE (2005)

The three-cable guardrail system is most commonly used to protect motorists from roadside slopes. Due to the fact that the system is limited to sites where relatively large barrier displacement is acceptable, concern arises when the barrier system must be placed close to steep roadside slopes. An additional concern with regard to the use of cable guardrail is that there only exists one approved non-proprietary end terminal which utilizes a large, cast-in-place, reinforced concrete anchor block. The current terminal and anchor design has proven to be quite costly when compared to the entire system. The objectives of the study were: (1) to evaluate three-cable anchor designs in order to develop a more cost-effective anchor alternative and (2) to evaluate South Dakota's three-cable barrier system placed adjacent to 1.5H:1V slopes. Dynamic bogie testing of various anchor alternatives determined the capacity of each anchor. Subsequent, computer simulation modeling with BARRIER VII analyzed and predicted dynamic barrier performance with each anchor alternative. One full-scale crash test, 2,034-kg (4,484-lb) pickup truck impacting at a speed of 98.1 km/h (61.0 mph) and at an angle of 26.2 degrees, was conducted and reported in accordance with the requirements specified in the National Cooperative Highway Research Program (NCHRP) Report No. 350, Recommended Procedures for the Safety Performance Evaluation of Highway Features. The full-scale crash test was conducted to verify that the cable guardrail adjacent to a steep slope performs adequately with the weakest anchor alternative, the driven steel post as shown through computer modeling, but was determined to be unacceptable according to the Test Level 3 (TL-3) evaluation criteria specified in NCHRP Report No. 350 due to vehicle vaulting and rollover. The poor performance observed in the full-scale crash test warranted design modifications. Consequently, additional computer simulation with BARRIER VII predicted that increasing the cable guardrail stiffness with reduced post spacing and increasing the offset from the slope breakpoint significantly improved the barrier's performance. Therefore, it is recommended that a full-scale crash test be conducted on the modified cable barrier to verify its safety performance. Furthermore, the steel post anchor design performed as intended and provided adequate cable tension for the barrier system. However, since the impacting vehicle was not contained nor smoothly redirected, it is recommended that the new anchor alternatives continue to be evaluated in the future.
Effect of the Thermostatic Expansion Valve Characteristics on the Stability of a Refrigeration System (2003)

The combination of increased power dissipation and increased packaging density has led to substantial increases in chip and module heat flux in high-end computers. The challenge has been to limit the rise in chip temperature. In the past virtually all-commercial computers were designed to operate at temperatures above the ambient. However researchers have identified the advantages of operating electronics at low temperatures. The primary purpose of low temperature cooling using vapor compression system are faster switching times of semiconductor devices, increased circuit speed due to lower electrical resistance of interconnecting materials, and a reduction in thermally induced failures of devices and components. Achievable performance improvements range from 1 to 3% for every 10°C lower transistor temperature, depending on the doping characteristics of the chip. The current research focuses on IBM’s mainframe, which uses a conventional refrigeration system to maintain chip temperatures below that of comparable air-cooled systems, but well above cryogenic temperatures. Although performance has been the key driver in the use of this technology, the second major reason for designing a system with low temperature cooling is the improvement achieved in reliability to counteract detrimental effects, which rise as technology is pushed to the extremes. A mathematical model is developed to determine the time constant for expansion valve sensor blub. This time constant varies with variation in thermo-physical properties of sensor element that is bulb size and blub liquid. An experimental bench is built to study the effect of variation of evaporator outlet superheat on system performance. The heat load is varied from no load to full load (1KW) to find out the system response at various loads. Experimental investigation is also done to see how the changes in thermo-physical properties of the liquid in sensor bulb of expansion valve affect the overall system performance. Different types of thermostatic expansion valves are tested to investigate that bulb size; bulb constant and bulb location have significant effect on the behavior of the system. Thermal resistance between the bulb and evaporator return line can considerably affect the system stability and by increasing the thermal resistance, the stability can be further increased.
The effect of sequence and time intervals of combined hyperthermia and radiation treatment of a solid mouse mammary adenocarcinomain vivo (1977)

The observation that moderate hyperthermia (41–43°C) sensitizes the effect of ionizing radiation has been established quantitatively in vitro (Bronk, 1976; Thrall et al., 1976) and more recently in several studies on normal tissues in vivo (Field et al., 1977; Thrall et al., 1976; Robinson et al., 1974). This sensitizing effect has been shown to be most prominent when the heat is given simultaneously with or immediately before or after radiation (Field et al., 1977; Joshi et al., 1976; Li et al., 1976; Sapareto et al., 1976; Stewart, 1976). As a result, it has been suggested that optimal tumour destruction would be obtained by a similar treatment regimen and recent clinical studies have been based on this assumption.
Intravascular Radiocontrast Iodixanol Increases Permeability of Proximal Tubule Epithelium (2013)

Our in vitro data do not support the hypothesis that direct kidney cell death from Iodixanol is a major mechanism of contrast-induced nephropathy (CIN). However, increased permeability of proximal tubule epithelium caused by Iodixanol may play an important role in CIN.
Synthesis of Dicyclopenta[a,e]pentalenes via a Molybdenum Carbonyl Mediated Tandem Allenic Pauson−Khand Reaction and the X-ray Crystal Structure of a Planar Dicyclopenta[a,e]pentalene (2004)

Two 14 pi cross-linked annulenes which belong to the family of dicyclopenta[a,e]pentalenes have been synthesized, 14 pi bis enol triflate ester 27 and the 3,7-diisopropylsilyl substituted 14 pi dicyclopenta[a,e]pentalene 30. The new allenic tandem Pauson-Khand reaction mediated by Mo(CO)(6) was employed as the key process to construct the core of the tetracycles. The two linear dicyclopenta[a,e]pentalenes 27 and 30 underwent significant electronic delocalization, perhaps even aromaticity, as revealed by the X-ray structure of 27. The tetracyclic rings in 27 assumed a flat geometry (Figure 4); the bond lengths of the tetracycle in 27 also fit well into the criteria for aromatic compounds. A comparison of the NMR and UV spectra of both 27 and 30 demonstrated that they both exhibited similar electronic properties, therefore, the purple colored 14 pi cross linked annulene 30 is planar as well as delocalized.
Large-Signal Performance Optimization of Inverted-F Antenna Tuned by Switchable RF Capacitor (2021)

Harmonics emission by an aperture-tuned IFA (inverted-F antenna) is studied. The analytical analysis is conducted using a transmission-line model of the antenna. Based on the results of analysis, an optimization example for the large-signal performance of a carrier-aggregation front-end tuned by a high-voltage switchable RF capacitor is presented, the findings are supported by the measurements on a hardware demonstrator. According to the experimental results, the power of a second harmonic at 1800 MHz coupled from the main into diversity antenna is reduced by 10 dB by fine-selecting the position of the capacitor-based tuning network along the radiating element of the main antenna.
A Novel Mycothiol-Dependent Detoxification Pathway in Mycobacteria Involving Mycothiol S-Conjugate Amidase (2000)

Mycothiol, 1-D-myo-inosityl-2-(N-acetylcysteinyl)amido-2-deoxy-alpha-D-glucopyranoside (MSH), is composed of N-acetylcysteine (AcCys) amide linked to 1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside (GlcN-Ins) and is the major thiol produced by most actinomycetes. When Mycobacterium smegmatis was treated with the alkylating agent monobromobimane (mBBr), the cellular mycothiol was converted to its bimane derivative (MSmB). The latter was rapidly cleaved to produce GlcN-Ins and the bimane derivative of N-acetylcysteine (AcCySmB), a mercapturic acid that was rapidly exported from the cells into the medium. The other product of cleavage, GlcN-Ins, was retained in the cell and utilized in the resynthesis of mycothiol. The mycothiol S-conjugate amidase (amidase) responsible for cleaving MSmB was purified to homogeneity from M. smegmatis. A value of K(m) = 95 +/- 8 microM and a value of k(cat) = 8 s(-)(1) was determined for the amidase with MSmB as substrate. Activity with 100 microM mycothiol or with the monobromobimane derivative of 1-D-myo-inosityl-2-(L-cysteinyl)amido-2-deoxy-alpha-D-glucopyra nos ide (CySmB-GlcN-Ins) or of 2-(N-acetyl-L-cysteinyl)amido-2-deoxy-(alpha, beta)-D-glucopyranoside (AcCySmB-GlcN) was at least 10(3) lower than with 100 microM MSmB, demonstrating that the amidase is highly specific for S-conjugates of mycothiol. Conjugates of mycothiol with the antibiotic cerulenin, N-ethylmaleimide, 3-(N-maleimidopropionyl)-biocytin, and 7-diethylamino-3-(4'-maleimidylphenyl)-4-methylcoumarin also exhibited significant activity. The sequence of the amino-terminal 20 residues was determined, and an open reading frame (Rv1082) coding for 288 residues having an identical predicted amino-terminal amino acid sequence was identified in the Mycobacterium tuberculosis genome. The Rv1082 gene (mca) from M. tuberculosis was cloned and expressed in Escherichia coli, and the expressed protein was shown to have substrate specificity similar to the amidase from M. smegmatis. These results indicate that mycothiol and mycothiol S-conjugate amidase play an important role in the detoxification of alkylating agents and antibiotics.
Inositol triphosphate produces different patterns of cytoplasmic Ca2+ spiking depending on its concentration (1991)

In single mouse pancreatic acinar cells the effects of intracellular infusion of inositol 1,4,5‐trisphosphate (InsP 3 ) or the non‐metabolizable InsP 3 analogue inositol 1,4,5‐triphosphorothioate (InsPS 3 ) have been investigated using a wide range of concentrations. Different types of cytosolic Ca 2+ fluctuation patterns (monitored as Ca 2+ ‐dependent Cl − current in patch‐clamp whole‐cell recording experiments) could be generated by InsP 3 or InsPS 3 , dependent on concentration, resembling those previously shown to be evoked by varying degrees or receptor activation in these cells. Low InsPS 3 concentrations evoked repetitive local Ca 2+ spikes whereas at relatively high concentrations repetitive Ca 2+ waves were produced. In the presence of intracellular citrate a much lower messenger level was sufficient to generate waves. The InsP 3 concentration determines whether the cytosolic Ca 2+ signals are local or global.
Why technology matters as much as science in improving healthcare (2012)

More than half a million new items of biomedical research are generated every year and added to Medline. How successful are we at applying this steady accumulation of scientific knowledge and so improving the practice of medicine in the USA? The conventional wisdom is that the US healthcare system is plagued by serious cost, access, safety and quality weaknesses. A comprehensive solution must involve the better translation of an abundance of clinical research into improved clinical practice. Yet the application of knowledge (i.e. technology) remains far less well funded and less visible than the generation, synthesis and accumulation of knowledge (i.e. science), and the two are only weakly integrated. Worse, technology is often seen merely as an adjunct to practice, e.g. electronic health records. Several key changes are in order. A helpful first step lies in better understanding the distinction between science and technology, and their complementary strengths and limitations. The absolute level of funding for technology development must be increased as well as being more integrated with traditional science-based clinical research. In such a mission-oriented federal funding strategy, the ties between basic science research and applied research would be better emphasized and strengthened. It bears repeating that only by applying the wealth of existing and future scientific knowledge can healthcare delivery and patient care ever show significant improvement.
Nucleotide sequence characterization of a Drosophila retrotransposon, 412 (1986)

The nucleotide sequence of the internal region of a Drosophila retrotransposon. 412, was determined. The genome of 412 was found to consist of two long open-reading frames (ORFs 1 and 2), an unusually long putative leader region and long terminal repeats (LTRs). As with 17.6, 297 and gypsy, ORFs 1 and 2 slightly overlap each other and are out of phase by +2. ORF2 includes the nucleotide sequences coding for the putative protease, reverse transcriptase and integrase, and is similar in entire organization to the pol gene of Moloney murine leukaemia virus. In spite of the difference in insertion specificity, integrase, an enzyme presumably responsible for insertion, was found to be similar in amino acid sequence to the counterparts of 17.6, 297 and gypsy. There is no ORF in 412 which corresponds to retroviral env or ORF3s of 17.6 and 297. Analysis of 412 transcripts suggested that 412 LTR is composed of U3, R and U5. The gene for a potential primer tRNA for putative reverse transcription of 412 was also surveyed and the 3'-terminal 15 nucleotides of a putative arginine tRNA were found to be exactly complementary to the putative primer-binding site of 412.
OUTCOMES OF A NOVEL TECHNIQUE COMBINING DIAPHYSEAL IMPACTION GRAFTING AND METAPHYSEAL CONES FOR SEVERE BONE LOSS IN REVISION TOTAL KNEE ARTHROPLASTIES (2019)

Introduction Metaphyseal cones with cemented stems are frequently used in revision total knee arthroplasties (TKAs). However, if the diaphysis has been previously violated (as in revision of a fail...
Assessment of potential impact of the Clinch River Breeder Reactor Plant thermal effluent on the Watts Bar Reservoir striped bass population (1983)

This report is an assessment of potential adverse impact to striped bass (Morone saxatilis) in Watts Bar Reservoir caused by thermal effluent from operation of the Clinch River Breeder Reactor Plant (CRBRP). The Clinch River arm of Watts Bar Reservoir is occupied by adult striped bass during the warmest months of the year. Concern was raised that operation of the CRBRP, specifically thermal discharges, could conflict with management of striped bass. In all cases examined the thermal plume becomes nearly imperceptible within a short distance from the discharge pipe (about 30 ft (10 m)) compared to river width (about 630 ft (190 m)). Under worst case conditions any presence of the plume in the main channel (opposite side of the river from the discharge) will be confined to the surface layer of the water. An ample portion of river cross sections containing ambient temperature water for passage or residence of adult striped bass will always be available in the vicinity of this thermal effluent. Although a small portion of river cross section would exceed the thermal tolerance of striped bass, the fish would naturally avoid this area and seek out adjacent cooler water. Therefore, it is concluded the CRBRP thermal effluent will not significantly affect the integrity of the striped bass thermal refuge in the Clinch River arm of Watts Bar Reservoir. At this time there is no need to consider alternative diffuser designs and thermal modeling. 8 references, 3 figures, 2 tables.
Kinetics and mechanism of the substitution reactions of (.eta.5-pentamethylcyclopentadienyl)dicarbonylrhodium(I) and (.eta.5-pentamethylcyclopentadienyl)dicarbonylcobalt(I) (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics and mechanism of the substitution reactions of (.eta.5-pentamethylcyclopentadienyl)dicarbonylrhodium(I) and (.eta.5-pentamethylcyclopentadienyl)dicarbonylcobalt(I)Mark E. Rerek and Fred BasoloCite this: Organometallics 1983, 2, 3, 372–376Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://pubs.acs.org/doi/10.1021/om00075a003https://doi.org/10.1021/om00075a003research-articleACS PublicationsRequest reuse permissionsArticle Views274Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts