gebhart/patrepeval huggingface dataset:
ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data (2017)

The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/).
Cloning, Functional Characterization, and Mode of Action of a Novel Insecticidal Pore-Forming Toxin, Sphaericolysin, Produced by <i>Bacillus sphaericus</i> (2007)

An insecticidal protein produced by Bacillus sphaericus A3-2 was purified to elucidate its structure and mode of action. The active principle purified from the culture broth of A3-2 was a protein with a molecular mass of 53 kDa that rapidly intoxicated German cockroaches (Blattela germanica) at a dose of about 100 ng when injected. The insecticidal protein sphaericolysin possessed the undecapeptide motif of cholesterol-dependent cytolysins and had a unique N-terminal sequence. The recombinant protein expressed in Escherichia coli was equally as potent as the native protein. Sphaericolysin-induced hemolysis resulted from the protein's pore-forming action. This activity as well as the insecticidal activity was markedly reduced by a Y159A mutation. Also, coapplication of sphaericolysin with cholesterol abolished the insecticidal action, suggesting that cholesterol binding plays an important role in insecticidal activity. Sphaericolysin-lysed neurons dissociated from the thoracic ganglia of the German cockroaches. In addition, sphaericolysin's activity in ganglia was suppressed by the Y159A mutation. The sphaericolysin-induced damage to the cockroach ganglia was greater than the damage to the ganglia of common cutworms (Spodoptera litura), which accounts, at least in part, for the higher sensitivity to sphaericolysin displayed by the cockroaches than that displayed by cutworms.
Test Method to Optimize Acid-Soluble Cement for Unconventional Gas Completions (2008)

Abstract In recent developments of unconventional gas reservoirs, there has been a move towards drilling horizontally to increase formation contact with the objective to increase production. A longer horizontal extension gives greater formation contact. However, these extended laterals must be cemented which has caused constraints on optimal reservoir production. Studies have indicated that conventional cements are one of the primary causes resulting in reduced fracture initiation. Acid-soluble cements have been advocated for use in unconventional gas reservoirs as a means to reduce the rate of inefficient fracture initiations. The logic behind using acid-soluble cement was based on field study examinations completed in 2005. These studies indicated that more than 25% of cemented horizontal laterals experienced fracture initiation problems compared to 4% for uncemented horizontal laterals. In acidizing acid-soluble cement in the area of strategically placed clusters, conditions approaching open hole are obtained similar to that of uncemented horizontal laterals. Cement remaining between clusters provides sufficient zonal isolation for well bore stability. There are no standard tests to define the characteristics of acid-soluble cements such as acid solubility or rate of dissolution that are factors crucial to obtaining good cement removal and minimal near well-bore issues. In this context a prototype test method has been developed to more closely simulate dissolution of acid-soluble cement for unconventional gas reservoir applications. Data obtained indicate the benefits of such a method to define the most appropriate acid-soluble cements, acid treatments and develop improved systems. Published test parameters vary considerably and given the number of variables involved in dissolution techniques there is a question as to what defines a good acid-soluble cement. Development of a test method that simulates down hole conditions provides a tool to design acid-soluble cement systems to optimize open hole around perforations and ultimately minimize fracture initiation problems.
UICE: A High-Performance Cryptographic Module for SoC and RFID Applications. (2007)

In order to overcome proprietary algorithms with respect to the system manufacturers, a free cryptographic module, the Universal Immobilizer Crypto Engine (UICE), will be proposed. This UICE algorithm is tailored to 8-bit microprocessor architectures and is therefore very fast in software and hardware. The dedicated hardware implementation leads to a small gate count, because the registers for input and output are shared. The important non-linear function, here an 8 x 8 SBox, may be built as a gate array or small ROM with the advantage of flexibility. Several tests – statistical and random-number tests - have been performed in order to analyze the strength properties of the algorithm. So far no weakness was found after ten rounds of encryption. Although this cryptographic module was intentionally developed for RadioFrequency Identification (RFID) systems, it is a proper choice for all systems needing embedded cryptography such as SoC with bus encryption or firmware to be secured. RFID-Systems have become commonplace in access control and security applications, the usage and importance of cryptographic co-processors in RFID transponder devices has grown significantly. Improved vehicle security systems, also known as immobilizers, are required due to increased vehicle theft worldwide. Such devices provide high security at low cost and low power.
Liquidity, Asset Prices and Financial Policy (1991)

(1991). Liquidity, Asset Prices and Financial Policy. Financial Analysts Journal: Vol. 47, No. 6, pp. 56-66.
Intelligent Transport Systems. An Overview on the Intelligent Transport Systems. (1999)

1973,
Acoustic distortion products in humans: Systematic changes in amplitude as a function of <i>f</i>2/<i>f</i>1 ratio (1989)

The effects of primary-tone separation on the amplitude of distortion-product emissions (DPEs) at the 2f1-f2 frequency were systematically examined in ten ears of five subjects. All individuals had normal hearing and middle-ear function based upon standard clinical measures. Acoustic-distortion products were elicited at 1, 2.5, and 4 kHz by equilevel primaries at 65, 75, and 85 dB SPL, while f2/f1 ratios were varied in 0.02 increments from 1.01-1.41 (4 kHz), 1.01-1.59 (2.5 kHz), or 1.01-1.79 (1 kHz). A principal outcome reflected in the detailed structure of both average and individual ratio functions was a nonmonotonic change in DPE amplitude as the ratio of f2/f1 increased. Despite the presence of amplitude nonmonotonicities, there was clearly a region of f1 and f2 separation that generated a maximum DPE. The effects of primary-tone separation on DPE amplitudes were systematically related to DPE frequency and primary-tone level. For all three levels of stimulation, the f2/f1 ratio was inversely related to DPE frequency. Thus larger ratios reflecting a greater separation of f1 and f2 were more effective in generating DPEs at 1 kHz rather than at 4 kHz. The optimal ratio for 2.5 kHz fell at an intermediate value. Conversely, acoustic distortion-product amplitude as a function of primary-tone level was directly related to the frequency separation of the primary tones. Regardless of the frequency region of the primary tones, smaller f2/f1 ratios were superior in generating DPEs in response to 65-dB stimuli, whereas larger ratios elicited bigger DPEs with primaries at 75 and 85 dB SPL. Within any specific stimulus-parameter combination, individual variability in DPE amplitude was noted. When all stimulus conditions describing the variations in frequency and level were considered, an f2/f1 ratio of 1.22 was most effective in maximizing DPE amplitude.
Navigation Function-Based Control of Multiple Wheeled Vehicles (2011)

In this paper, a collision-free navigation method for a group of autonomous wheeled vehicles is investigated. The position and orientation information of individual vehicles is transformed to navigation variables, which are the distance left to the goal position, the angle made by the orientation of the vehicle at the goal position and the vehicle-to-target (v-to-t) vector, and the angle made by the heading direction of the vehicle and the v-to-t vector. As a Lyapunov function for deriving a smooth control law that drives all the vehicles from an initial configuration to a goal configuration, a new navigation function that incorporates the squared norm of the navigation variables, the boundaries of collision-free areas, and the angles made by the vehicle heading direction and the vehicle-to-obstacle (v-to-o) vectors is proposed. The asymptotic stability of the closed-loop system is proved. The effectiveness of the developed algorithm is illustrated through three simulations (three vehicles in a free environment, three vehicles in the presence of a static obstacle, and eight vehicles operating along a corridor) and two experiments (static and moving obstacles avoidance). The proposed algorithm has been implemented on a real forklift and the navigation of the forklift from an arbitrary initial configuration to a goal configuration while avoiding collisions has been demonstrated.
Polishing of Sapphire with Colloidal Silica (1978)

The polishing of sapphire with colloidal silica has been studied. Stock removal rates have been found to vary with the solids content in the polishing fluid and the temperature on the polishing pad. The pH of the polishing fluid has also been found to be a factor influencing removal rate. Because concentrated silica solutions are unstable at high temperatures, a compromise between temperature and concentration must be made. Still, practical removal rates over 25 μ/hr have been achieved. Work damage, an important factor in polishing operations, has been found to extend about 1.0–1.5 mils into the surface of commercially available sawn or ground sapphire blanks. When all embedded diamond from the slicing and grinding operations is removed prior to polishing, a scratch‐free, featureless surface is produced on which high quality, epitaxial silicon films can be deposited. C‐MOS devices built into the films without the use of any specific processing technique to minimize the effect of the interface showed n‐channel leakage of with negligible wafer‐to‐wafer variations (1). The polishing of sapphire by colloidal silica is believed to follow a chemical reaction leading to aluminum silicate dihydrate as described in previous literature. For the reaction
Quantification and Three-Dimensional Imaging of the Insulitis-Induced Destruction of β-Cells in Murine Type 1 Diabetes (2010)

Our data provide a powerful tool for phenotypic analysis of genetic and environmental effects on type 1 diabetes etiology as well as for evaluating the potential effect of therapeutic regimes.
Report of a subcommittee of the Joint Council of the American Association for Vascular Surgery and Society for Vascular Surgery (2003)

Decision-making in regard to elective repair of abdominal aortic aneurysms (AAA) requires careful assessment of factors that influence rupture risk, operative mortality, and life expectancy. Individualized consideration of these factors in each patient is essential, and the role of patient preference is of increasing importance. It is not possible or appropriate to recommend a single threshold diameter for intervention which can be generalized to all patients. Based upon the best available current evidence, 5.5 cm is the best threshold for repair in an average patient. However, subsets of younger, good-risk patients or aneurysms at higher rupture risk may be identified in whom repair at smaller sizes is justified. Conversely, delay in repair until larger diameter may be best for older, higher-risk patients, especially if endovascular repair is not possible. Intervention at diameter <5.5 cm appears indicated in women with AAA. If a patient has suitable anatomy, endovascular repair may be considered, and it is most advantageous for older, higher-risk patients or patients with a hostile abdomen or other technical factors that may complicate standard open repair. With endovascular repair, perioperative morbidity and recovery time are clearly reduced; however, there is a higher reintervention rate, increased surveillance burden, and a small but ongoing risk of AAA rupture. There is no justification at present for different indications for endovascular repair, such as earlier treatment of smaller AAA. Until long-term outcome of endoluminal repair is better defined and results of randomized trials available, the choice between endovascular and open repair will continue to rely heavily on patient preference. (J Vasc Surg 2003;37:1106-17.)
Identification of the Decay-Accelerating Factor CD55 as a Peanut Agglutinin–Binding Protein and Its Alteration in Non–Small Cell Lung Cancers (2006)

DAF was identified as a new PNA-binding protein in the human lung. The down-regulation and heavy sialylation of DAF was associated with pathology in NSCLC, and these alterations make this protein a potential marker for NSCLC.
Cai cach thue o Viet Nam : huong toi mot he thong hieu qua va cong bang hon (2011)

In 2010, after two decades of rapid economic growth, Vietnam passed the threshold to become a lower-middle-income economy. Sustained market-oriented reforms combined with intensive efforts to integrate into the world economy are among the key drivers of this achievement. The reform of tax policy and administration has been a vital part of this transition. This is leading to a fundamental change in the composition of taxpayers, from large state-owned enterprises (SOEs) and foreign-invested companies to a myriad of small and medium private enterprises. Economic transition is also leading to an equally important change in the sources of government revenue, away from cross-border trade-related taxes and revenue collection from crude oil toward a greater share of domestic tax revenue, in particular taxation of business profits, labor income, and capital gains on land. However, completing the transition to a market economy will require changes going beyond tax collection and administration procedures, and will involve changes to the tax instruments themselves. At the end of this process, Vietnam should have a set of taxes that is simple and transparent, secures a stable flow of revenues for the government, encourages an efficient allocation of resources, and does not risk constituting a source of inequality or unfairness. The purpose of the series of studies in this volume is to shed light on the issues Vietnam will be facing in the process of reforming its tax policy and administration. The studies are also expected to lead to concrete policy recommendations contributing to the preparation of key policies and legislative documents to ensure the achievement of the state budget revenue target and other tax administration reform targets in the SEDP 2011-2015. It is expected that the individual studies in this series will become useful inputs into the debate surrounding the issuance of new laws and regulations. It is also hoped that the volume will support the reform momentum in the tax policy area, leading to increased efficiency, transparency, and equity.
Democratizing authority in the built environment (2017)

Operating systems and applications in the built environment have relied upon central authorization and management mechanisms which restrict their scalability, especially with respect to administrative overhead. We propose a new set of primitives encompassing syndication, security, and service execution that unifies the management of applications and services across the built environment, while enabling participants to individually delegate privilege across multiple administrative domains with no loss of security or manageability. We show how to leverage a decentralized authorization syndication platform to extend the design of building operating systems beyond the single administrative domain of a building. The authorization system leveraged is based on blockchain smart contracts to permit decentralized and democratized delegation of authorization without central trust. Upon this, a publish/subscribe syndication tier and a containerized service execution environment are constructed. Combined, these mechanisms solve problems of delegation, federation, device protection and service execution that arise throughout the built environment. We leverage a high-fidelity city-scale emulation to verify the scalability of the authorization tier, and briefly describe a prototypical democratized operating system for the built environment using this foundation.
Microstructure and Magnetic Properties of Lead Ferrite (1969)

Unoriented lead ferrite specimens were prepared by calcining and sintering techniques. Specimens having an initial composition of Pb0.5Fe 2 O 3 had the best permanent magnet properties (for nondoped material). The effects of small amounts of added oxides on the microstructure and magnetic properties were also determined. Silica and boria were most effective in raising the (B a H a ) max to over 1.4 × 10 6 G.Oe as compared to 0.9 to 1.1 × 10 5 G.Oe for commercial un oriented barium ferrite magnets. Optical and electron microscopy revealed that silica and boria form low melting phases as the specimens are sintered, which, acting as fluxes (probably by a solution‐precipitation mechanism), enhance the densification of the magnets, thereby raising the B r , and (B a H a ) max , values. On cooling, these nonmagnetic low‐melting phases are retained at the ferrite grain boundaries where they inhibit domain wall motion which would otherwise lead to a reduction in coercive force. Although these magnets are termed “un oriented” to distinguish them from “oriented” ferrites which are purposely aligned before sintering, a slight orientation is imparted to the polycrystalline compact during the pressing operation before sintering. The silica and boria additions increase the degree of orientation by accelerating the rate of densification. The increase in orientation accounts for part of the increase in B r , and (B a , H a ) max .
A Numerical Method of Resolving Peak Areas in Gas Chromatography (1971)

Journal Article A Numerical Method of Resolving Peak Areas in Gas Chromatography Get access Bernard Goldberg Bernard Goldberg Shell Development Company, Exploration and Research Center, Houston, Texas 70001 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 9, Issue 5, May 1971, Pages 287–292, https://doi.org/10.1093/chromsci/9.5.287 Published: 01 May 1971 Article history Received: 04 March 1970 Published: 01 May 1971
Reduction of cogging torque in permanent magnet motors (1988)

Cogging torque in a permanent magnet motor, which arises from the interaction of the rotor magnets with the steel teeth on the stator, can be reduced by skewing the stator teeth, but only at the expense of added complexity in stator construction and some loss of output torque. It is shown that by appropriate choice of the angular width of the magnet relative to the tooth-plus-slot dimension, the cogging torque can be reduced to about 1% of rated torque. A further reduction to about 0.3% resulted from a rotational shift of one pair of poles with respect to the other pair in a four-pole motor. The analysis of cogging torques with both surface mounted and inset magnet rotors as well as experimental confirmation are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pharmacological and biochemical analysis of FPL 67156, a novel, selective inhibitor of ecto‐ATPase (1995)

FPL 67156 (6‐N,N‐diethyl‐β,γ‐dibromomethylene‐ d ‐ATP), is a newly synthesized analogue of ATP. In a rabbit isolated tracheal epithelium preparation, measuring P 2U ‐purinoceptor‐dependent chloride secretion, FPL 67156 was discovered to potentiate the responses to UTP but not those to ATP‐γ‐S. UTP agonist‐concentration effect (E/[A]) curves were shifted to the left by 5‐fold in the presence of 100 μ m FPL 67156. The differential effect of FPL 67156 on UTP and ATP‐γ‐S was hypothesized to be due to the greater susceptibility of UTP to enzymatic dephosphorylation and the ability of FPL 67156 to inhibit this process. FPL 67156 was tested as an ecto‐ATPase inhibitor in a human blood cell assay, measuring [γ 32 P]‐ATP dephosphorylation. The compound inhibited [γ 32 P]‐ATP degradation with a pIC 50 of 4.6. FPL 67156 was then tested for its effects on ATP and α,β‐methylene‐ATP responses at P 2X ‐purinoceptors in the rabbit isolated ear artery. In the concentration range 30 μ m ‐1 m m , the compound potentiated the contractile effects of ATP but not those of α,β‐methylene‐ATP. At 1 m m , FPL 67156 produced a 34‐fold leftward shift of ATP E/[A] curves. The effects of FPL 67156 on ATP E/[A] curves in the rabbit ear artery were analysed using a theoretical model (Furchgott, 1972) describing the action of an enzyme inhibitor on the effects of a metabolically unstable agonist. This analysis provided an estimate of the p K 1 for FPL 67156 as an ecto‐ATPase inhibitor of 5.2. Using appropriate assays, FPL 67156 was shown to have weak antagonist effects at P 2X ‐ and P 2T ‐purinoceptors (p A 2 ≅ 3.3 and 3.5 respectively), and weak agonist effects at P 2U ‐purinoceptors (p[ A 50 ] ≅ 3.5). The degree of potentiation of ATP and UTP effects elicited by FPL 67156 confirms previous results concerning the influence that ecto‐ATPase has on the position of E/[A] curves for metabolically unstable agonists. The magnitude of this influence is predicted to have a major effect on the agonist potency orders currently used to designate purinoceptors. This study indicates FPL 67156 to be a potentially valuable probe in studies on the action of nucleotides and in the classification of purinoceptors.
Soft Contact Lens-Related Dryness with and without Clinical Signs (2012)

Symptoms of dryness in SCL wearers stem from a variety of underlying causes. However, nearly one-quarter of these symptomatic SCL wearers appear to be free of signs of dryness. The effective management of CL-related dryness requires a comprehensive range of clinical assessments and the use of a diverse range of management strategies.
Screening for Prostate Cancer — The Controversy That Refuses to Die (2009)

In the United States, most men over the age of 50 years have had a prostate-specific–antigen (PSA) test,1 despite the absence of evidence from large, randomized trials of a net benefit. Moreover, about 95% of male urologists and 78% of primary care physicians who are 50 years of age or older report that they have had a PSA test themselves,2 a finding that suggests they are practicing what they preach. And indeed, U.S. death rates from prostate cancer have fallen about 4% per year since 1992, five years after the introduction of PSA testing.3 Perhaps the answer to the PSA . . .