gebhart/patrepeval huggingface dataset:
Atomic Structures of Minor Proteins VI and VII in Human Adenovirus (2017)

ABSTRACT Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon—the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2—and, by extension, that of genome-condensing pVII—to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses. IMPORTANCE Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses.
Non‐A, non‐b hepatitis virus: identification of a core antigen‐antibody system that cross reacts with hepatitis b core antigen and antibody (1981)

Using immunodiffusion, a major cross-reactivity had been previously demonstrated between hepatitis B(HBe/3 Ag) and the antigen reported in the serum on non A, non-B hepatitis patients, therefore redesignated NANBe Ag. By direct immunofluorescence a new antigen associated with, but distinct from, NANBe Ag has now been identified in the liver of 14/26 patients with NANB chronic active hepatitis. The homologous antibody was detected in the serum of these 14 patients. Behaving like HBc Ag and cross reacting with it by immunofluorescence, the new antigen was termed NANBc Ag. Anti NANBc also became detectable in serial acute phase and convalescence sera from 5/5 NANB Ag-positive posttransfusion hepatitis cases. Further characterization of NANBe and NANBc antigens achieved by fractionation of a NANB virus-infected liver showed NANBc Ag to be expressed on 22-25 nm HB core-like particles containing DNA polymerase activity. Cross-reactivity between NANBc and HBc antigens was confirmed by immunodiffusion. Liver-derived NANBe Ag identical to serum NANBe Ag exhibited the same physical properties as HBe/3 Ag and could be similarly released by disruption of the non-A, non-B, virus cores. These results indicate that hepatitis B and NANB virions not only share the same structure and DNA polymerase activity but are also antigenically related and belong to the same new class of DNA viruses.
Coronavirus infections and immune responses (2020)

Coronaviruses (CoVs) are by far the largest group of known positive-sense RNA viruses having an extensive range of natural hosts. In the past few decades, newly evolved Coronaviruses have posed a global threat to public health. The immune response is essential to control and eliminate CoV infections, however, maladjusted immune responses may result in immunopathology and impaired pulmonary gas exchange. Gaining a deeper understanding of the interaction between Coronaviruses and the innate immune systems of the hosts may shed light on the development and persistence of inflammation in the lungs and hopefully can reduce the risk of lung inflammation caused by CoVs. In this review, we provide an update on CoV infections and relevant diseases, particularly the host defense against CoV-induced inflammation of lung tissue, as well as the role of the innate immune system in the pathogenesis and clinical treatment.
[An anesthetic study of 120 cases of orolingual tumor operations] (1995)

The anesthetic techniques of 120 cases of orolingual tumor operations was studied.The ages of 66 male and 54 female patients ranged from 7 months-77 years,averaging 48.5 years.All the cases included 34 benign tumors and 86 malignant tumors.This article analyses and discussed the choice of anesthetic methods,methods of induction and intubation and the features of control during operation and postoperative recovery.
Rinite, sinusite e asma: indissociáveis? (2006)

The objective of this study was to review the literature and to discuss epidemiological and physiopathological aspects and therapeutical implications of an unified approach to allergic rhinosinusitis and asthma. The bibliographic survey was based on the information provided by the following databases: Medline, MD Consult, Highwire, Medscape, LILACS and through direct search over thirty years, using the terms allergic rhinitis and asthma. Fifty-five original articles were selected in the no systematically review addressing the issue of clinical association between allergic rhinusinusitis and asthma. It is noteworthy that in the late years, with the use of specific topical medications for the lower airways or else, to the upper airways, the therapeutical approach has been distinct. However, numerous epidemiological surveys, immunopatological and clinical studies demonstrate the inter-relationship between asthma and allergic rhinossinusitis, characterized by: i) allergic rhinitis is associated to asthma and constitute an independent risk factor for its occurrence; ii) the immunopathological characteristics of allergic rhinitis and asthma are similar; iii) allergic rhinitis and asthma are manifestations of a systemic disease; iv) control of rhinitis favors asthma control. taking into consideration the close inter-relationship between allergic rhinitis and asthma, the approach to diagnosis, treatment and prophylaxis of these illnesses should be integrated. Therapeutical options that allow for the simultaneous control of asthma and allergic rhinitis offer advantages related both to costs and tolerability.
Synthesis of the Ti−Silicate Form of BEC Polymorph of β-Zeolite Assisted by Molecular Modeling (2008)

The K+ free pure silica form of polymorph C (BEC) of β-zeolite has been synthesized with a cationic organic structure directing agent (SDA) that was predicted best, out of a series of nine potentials, by means of modeling techniques. On the bases of this synthesis method, the Ti−BEC zeolite has been obtained which owing to the pore topology and dimensions shows a higher epoxidation activity than the Ti−β-polymorph either with H2O2 or organic peroxides as oxidants.
A MATLAB differentiation matrix suite (2000)

A software suite consisting of 17 MATLAB functions for solving differential equations by the spectral collocation (i.e., pseudospectral) method is presented. It includes functions for computing derivatives of arbitrary order corresponding to Chebyshev, Hermite, Laguerre, Fourier, and sinc interpolants. Auxiliary functions are included for incorporating boundary conditions, performing interpolation using barycentric formulas, and computing roots of orthogonal polynomials. It is demonstrated how to use the package for solving eigenvalue, boundary value, and initial value problems arising in the fields of special functions, quantum mechanics, nonlinear waves, and hydrodynamic stability.
Effective Delay-Controlled Load Distribution over Multipath Networks (2011)

Owing to the heterogeneity and high degree of connectivity of various networks, there likely exist multiple available paths between a source and a destination. An effective model of delay-controlled load distribution becomes essential to efficiently utilize such parallel paths for multimedia data transmission and real-time applications, which are commonly known to be sensitive to packet delay, packet delay variation, and packet reordering. Recent research on load distribution has focused on load balancing efficiency, bandwidth utilization, and packet order preservation; however, a majority of the solutions do not address delay-related issues. This paper proposes a new load distribution model aiming to minimize the difference among end-to-end delays, thereby reducing packet delay variation and risk of packet reordering without additional network overhead. In general, the lower the risk of packet reordering, the smaller the delay induced by the packet reordering recovery process, i.e., extra delay induced by the packet reordering recovery process is expected to decrease. Therefore, our model can reduce not only the end-to-end delay but also the packet reordering recovery time. Finally, our proposed model is shown to outperform other existing models, via analysis and simulations.
A novel digital signal processing bit synchronizer for a prml recording channel (1993)

Abstract The partial‐response maximum likelihood (PRML) system currently is investigated for practical applications as a modulation/demodulation scheme for digital magnetic recording equipment. This paper proposes a construction of the bit synchronizer by complete digital signal processing. The operational principle is verified by experiment. The proposed bit synchronizer is composed of the decision‐feedback digital PLL and the interpolator. The decision‐feedback digital PLL receives the data‐asynchronous sampled signal sequence as the input, which is the result of sampling by the fixed clock of two samples/bit, and regenerates the clock. The interpolator calculates the signal value at the data point indicated by the phase of the decision‐feedback digital PLL output. The result is given to the Viterbi decoder. By applying the proposed scheme, the PRML demodulator from the equalizer to the Viterbi decoder can be realized as a digital signal processing circuit, which operates synchronously with the single fixed master clock. A PRML demodulator is constructed based on the proposed bit synchronizer, and the operational principle is verified by an experiment using a magnetic disk device. The bit‐error rate less than 10 −6 is obtained for the channel bit rate of 10 Mbps.
Feasibility of Shockwave Coronary Intravascular Lithotripsy for the Treatment of Calcified Coronary Stenoses (2019)

We sought to determine the feasibility of coronary intravascular lithotripsy (IVL) as a novel modality for modification of heavily calcified atherosclerotic plaques before stenting
Self-organizing publish/subscribe (2005)

The increasing availability of broadband Internet access coming along with cheap flatrate tariffs changed the way the Internet is used over the last years. As a result, we observe more users that become producers and collaborate instead of solely consuming information as they did before. Besides that, the Internet has become a tool for daily use and information dissemination. As push-based information services are heavily needed for collaboration and information dissemination, it seems like the breakthrough of distributed push publish/subscribe on the open Internet is just imminent today, although research has been around already for many years now. One reason why most publish/subscribe applications are still based on a rather basic centralized mechanism and not on a distributed scalable notification service, as it is commonly proposed in state-of-the-art publish/subscribe systems in research, is the unsolved management issue.This extended research abstracts is intended to give an overview of my Ph.D. project on self-organizing publish/subscribe, where I want to tackle management issues for better applicability. After giving an introduction to the pub/sub communication paradigm and motivating the necessity to make such systems self-organizing, I will point out the contributions of my work. They are centered around making publish/subscribe systems self-stabilizing and adaptive by means of self-organizing mechanisms. While my work on self-stabilization is nearly finished, introducing adaptivity by self-organization is still in an early stage.
Broad spectrum infrared thermal desorption of wipe-based explosive and narcotic samples for trace mass spectrometric detection (2017)

Wipe collected analytes were thermally desorbed using broad spectrum near infrared heating for mass spectrometric detection. Employing a twin tube filament-based infrared emitter, rapid and efficiently powered thermal desorption and detection of nanogram levels of explosives and narcotics was demonstrated. The infrared thermal desorption (IRTD) platform developed here used multi-mode heating (direct radiation and secondary conduction from substrate and subsequent convection from air) and a temperature ramp to efficiently desorb analytes with vapor pressures across eight orders of magnitude. The wipe substrate experienced heating rates up to (85 ± 2) °C s<sup>-1</sup> with a time constant of (3.9 ± 0.2) s for 100% power emission. The detection of trace analytes was also demonstrated from complex mixtures, including plastic-bonded explosives and exogenous narcotics, explosives, and metabolites from collected artificial latent fingerprints. Manipulation of the emission power and duration directly controlled the heating rate and maximum temperature, enabling differential thermal desorption and a level of upstream separation for enhanced specificity. Transitioning from 100% power and 5 s emission duration to 25% power and 30 s emission enabled an order of magnitude increase in the temporal separation (single seconds to tens of seconds) of the desorption of volatile and semi-volatile species within a collected fingerprint. This mode of operation reduced local gas-phase concentrations, reducing matrix effects experienced with high concentration mixtures. IRTD provides a unique platform for the desorption of trace analytes from wipe collections, an area of importance to the security sector, transportation agencies, and customs and border protection.
SPF: Selective Pipeline Flush (2018)

Branch mispredictions are inevitable in modern processors, but their high penalty in power and performance can be alleviated by selectively flushing the pipeline. In this paper, we present a practical technique to opportunistically determine the presence of correct path instructions in the processor pipeline and preserve those instructions instead of throwing them away. In our experiments, selective pipeline flush reduced the fetched instruction count by 7% (up to 26%), while increasing the performance by 2% (up to 15%).
A method for accurate detection of time of arrival: Analysis and design of an ultrasonic ranging system (1992)

Many industrial applications demand accurate ranging operations, for example, robotic end-effector positioning and measurement of vibrations in machine monitoring tasks. For instance, measurement of the position of a robotic end effector in high-accuracy applications demands the following stringent specifications from a ranging system: (1) absolute ranging accuracy of ±0.025 mm (±0.001 in.), (2) working range of approximately 2 m (6.56 ft), (3) update rate &gt;100 Hz, and (4) high reliability. It is shown that an ultrasonic ranging system that meets the above specifications may be feasible. The system model is based on measuring the distance between a transmitter and a receiver. A novel method to detect the instant when the signal arrives at the receiver is described. The method combines envelope peak detection and phase measurement to determine the time of arrival, and it gets close to meeting the accuracy criteria. To verify the analytical predictions, distances of up to 0.9 m were measured using a prototype system. The absolute accuracy of such measurements was ±0.150 mm (±0.006 in.). The tests performed indicate that the errors are caused primarily by air turbulence and may be decreased by averaging more samples. In this paper ultrasonic ranging from a transmitter to a receiver in a three-dimensional space setting is addressed.
1.5- mu m InGaAs/InAlGaAs quantum-well microdisk lasers (1993)

Microdisk lasers with three InGaAs/InAlGaAs quantum wells were demonstrated for the first time. The selective etching method used to fabricate the laser structure is discussed. Lasers 20 mu m in diameter lased with single mode at 1.5- mu m wavelength when optically pumped by a pulsed argon-ion laser at 80 K.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The <i>Arabidopsis MALE STERILITY1</i> (<i>MS1</i>) gene is a transcriptional regulator of male gametogenesis, with homology to the PHD‐finger family of transcription factors (2001)

We report here the molecular characterisation of the Arabidopsis MALE STERILITY1 gene, which is a critical sporophytic controlling factor for anther and pollen development. Homozygous ms1 mutants do not produce viable pollen, but are otherwise phenotypically normal. Degeneration of pollen occurs soon after microspore release from the tetrads, at which time the tapetum also appears abnormally vacuolated. The MS1 gene is expressed at low levels in anthers from closed buds, with expression in the tapetum at the stage of microspore release. No expression is seen in open flowers. The deduced MS1 protein sequence shows strong homology to the PHD-finger motif found in known transcription factors from humans, yeast and higher plants. Six alleles of ms1 have been identified; all result in premature termination of the MS1 protein and loss of the PHD-finger motif. MS1 is likely to play a key role in regulating transcription during specific stages of male gametogenesis and anther development. As such, MS1 provides a valuable tool for the manipulation of male sterility in higher plants.
A portable physiological data recording/decoding system (1980)

Counting the number of heart beats and footsteps during successive minute periods permits assessment of the physical condition of a subject undertaking planned exercise. We describe the design, and assess the use, of a small, 4 channel, solid state recorder for storing these physiological signals and the rapid retrieval of this data using a portable decoder. The actual number of heart beats and footsteps are counted and stored after each successive minute period. One channel is used to code sequentially the subjects under test, and a further channel is used for event marking. Data are retrieved by linking the recorder to the decoder; entering the required subject's code onto a numeric key board initiates the presentation of data. A LED display and paper print-out provide visual and permanent records.
General Resistance in Maize to Southern Rust (<i>Puccinia polysora</i> Underw.) (2011)

ABSTRACT Southern corn rust (Puccinia polysora Underw.) is a major tropical disease that can lead to severe yield losses in the tropics. Occasionally it becomes of concern in temperate regions, as in 2010. We summarize 45 yr of research on the occurrence, genetic basis, and breeding of general resistance. Trials were conducted in Colombia, Hawaii, Nigeria, the Philippines, Texas, and Thailand. Temperate maize proved uniformly susceptible. No racially specific monogenes were effective. Resistance varied continuously among tropical inbreds and many of these showed stable intermediate tolerance. Two diallel populations revealed high correlations of inbred values with hybrid array means and slight heterosis for resistance. Narrow‐sense heritabilities were 51% and 66%, and mean square ratios for general to specific combining ability (GCA:SCA) were 7.8 and 10.7 to 1. Generation mean analyses were performed on six sets of families. Mean and additive effects were significant across families, while significant nonadditive effects were rare. Heritability values ranged from 19% to 49%. A set of recombinant lines segregated a primary susceptibility locus on chromosome 6. Studies of 137 near‐isogenic inbred lines (NILs) of resistant tropical inbred Hi27 revealed a dominant susceptibility quantitative trait locus (QTL) in the NIL for dwarf‐1 locus, but linkage could not be confirmed. Premature senescence was associated with rust infections in many NILs, emphasizing the ubiquity of modifying genes. No correlation existed between resistance to southern and common rusts. Resistant tropical inbreds and populations were bred to serve as sources for future improvement.
Design of a single-turn microstrip write head for ultra-high data rate recording (1999)

This paper describes the design of a single-turn write head, where the standard coil is replaced with a microstrip transmission line. The frequency and transient response of this head are expected to be superior to current high-speed write heads, and the head power dissipation is also expected to be much lower at high frequencies due to greatly reduced inductance.
A Case for Resource Efficient Prefetching in Multicores (2014)

Modern processors typically employ sophisticated prefetching techniques for hiding memory latency. Hardware prefetching has proven very effective and can speed up some SPEC CPU 2006 benchmarks by more than 40% when running in isolation. However, this speedup often comes at the cost of prefetching a significant volume of useless data (sometimes more than twice the data required) which wastes shared last level cache space and off-chip bandwidth. This paper explores how an accurate resource-efficient prefetching scheme can benefit performance by conserving shared resources in multicores. We present a framework that uses low-overhead runtime sampling and fast cache modeling to accurately identify memory instructions that frequently miss in the cache. We then use this information to automatically insert software prefetches in the application. Our prefetching scheme has good accuracy and employs cache bypassing whenever possible. These properties help reduce off-chip bandwidth consumption and last-level cache pollution. While single-thread performance remains comparable to hardware prefetching, the full advantage of the scheme is realized when several cores are used and demand for shared resources grows. We evaluate our method on two modern commodity multicores. Across 180 mixed workloads that fully utilize a multicore, the proposed software prefetching mechanism achieves up to 24% better throughput than hardware prefetching, and performs 10% better on average.