gebhart/patrepeval huggingface dataset:
Influenza – A Model of an Emerging Virus Disease (1993)

Influenza A viruses continue to emerge from the aquatic avian reservoir and cause pandemics. Phylogenetic analysis of the nucleotide sequence of all eight influenza A virus RNA segments indicate that all of the influenza viruses in mammalian hosts originate from the avian gene pool. In contrast to the rapid progressive changes in both the nucleotide and amino acid sequences of mammalian virus gene lineages, avian virus genes show far less variation and, in most cases, appear to be in evolutionary stasis. There are periodic exchanges of influenza virus genes or whole viruses between species giving rise to pandemics of diseases in humans, lower animals and birds. The periodic emergence of influenza viruses in mammalian species has been illustrated by the appearance of a new influenza virus in horses in northern China in 1989. Phylogenetic analysis of classical H1N1, avian-like H1N1 and human H3N2 viruses circulating in Italian pigs reveals that genetic reassortment is taking place between avian- and human-like viruses in the European pig population. These studies provide evidence supporting the possibility that pigs serve as a mixing vessel for reassortment between influenza viruses in mammalian and avian hosts and raise the question of whether the next pandemic of influenza will emerge in Europe!
Dynamics of continuous time Markov chains with applications to stochastic reaction networks (2019)

This paper contributes to an in-depth study of properties of CTMCs on
non-negative integer lattices, with particular interest in one-dimensional
CTMCs with polynomial transitions rates. We study the classification of states
for general CTMCs on the non-negative integer lattices, by characterizing the
set of states (absorbing, trapping, escaping, positive irreducible components
and quasi-irreducible components). For CTMCs on non-negative integers with
polynomial transition rates, we provide threshold checkable criteria (in terms
of parameters) for various dynamical properties-explosivity, recurrence versus
transience, positive recurrence versus null recurrence, implosivity, as well as
existence and non-existence of passage times; in particular, checkable
sufficient conditions for exponential ergodicity of stationary and
quasi-stationary distributions are obtained. Moreover, an identity for
stationary measures is established and asymptotics of tails of stationary
distributions are estimated. Similar identity as well as asymptotics are
derived for quasi-stationary distributions. As a prominent application, we
apply our results to stochastic (biochemical) reaction networks (SRNs). In
particular, we show all weakly reversible mass-action reaction networks with
one-dimensional stoichiometric subspaces not only are positive recurrent but
have a unique exponentially ergodic stationary distribution with
Conley-Maxwell-Poisson tail on every positive irreducible component, which
confirms in one-dimensional case the recently proposed positive recurrence
conjecture [D.F. Anderson and J. Kim, Some network conditions for positive
recurrence of stochastically modeled reaction networks, SIAM J. Appl. Math., 78
(2018), 2692--2713.].
Experimental investigation on the effect of accelerating motion of contact line on the dynamic contact angle (2014)

The dynamic contact angle, the angle between the surfaces of the liquid and the solid at a moving contact line, is one of the primary conditions for the dynamics of the liquid surface confined by solid wall. It has been commonly modeled as a function of the velocity of the contact line relative to the solid surface under steady state condition. Some situations, such as the impact of a drop on a solid surface or sudden release of a contact line stuck on an edge of solid, however, involve a transient motion of the contact line, which would lead to a deviation of the dynamic contact angle from the steady one. In this study, dynamic contact angle for an accelerating or decelerating contact line advancing on glass surface is measured in two experimental systems different with other, i.e. one with a rapid meniscus formation after contact of a descending rod with the liquid surface, and the other with accelerating advance of liquid column in a circular tube. The experimental results revealed that the contact angle is increased with the (positive) acceleration of the contact line relative to the solid and vice versa. The critical condition for the appearance of the deviation of the contact angle brought with the acceleration is also discussed.
The dimensionality of scene appearance (2009)

Low-rank approximation of image collections (e.g., via PCA) is a popular tool in many areas of computer vision. Yet, surprisingly little is known justifying the observation that images of an object or scene tend to be low dimensional, beyond the special case of Lambertian scenes. This paper considers the question of how many basis images are needed to span the space of images of a scene under real-world lighting and viewing conditions, allowing for general BRDFs. We establish new theoretical upper bounds on the number of basis images necessary to represent a wide variety of scenes under very general conditions, and perform empirical studies to justify the assumptions. We then demonstrate a number of novel applications of linear models for scene appearance for Internet photo collections. These applications include, image reconstruction, occluder-removal, and expanding field of view.
Point-, Line-, and Edge-Spread Function Measurement of MTF (2021)

There are several ways we can measure MTF using targets that have an impulsive nature, each with positive aspects as well as drawbacks. In this chapter, we first develop the mathematical relationships between the data and the MTF for the point-spread function (PSF), line-spread function (LSF), and edge-spread function (ESF). One item of notation in this section is that we use * to denote a one-dimensional convolution, and ** to denote a twodimensional convolution. We then compare the measurement techniques and consider options for increasing the signal-to-noise ratio and extending the spatial-frequency range of the measurements.
A comparison of UV cross-linking and vacuum baking for nucleic acid immobilization and retention. (1990)

The effectiveness of UV cross-linking and in vacuo baking for the immobilization and retention of DNA to various solid supports was investigated. Optimal immobilization treatments for supported and unsupported nitrocellulose and nylon membranes were: UV cross-linking at 254 nm with an exposure of 120 milliJoules/cm2, or baking in vacuo for two hours at 80 degrees C. UV-immobilized nitrocellulose-based membranes showed no increase in sensitivity when compared to baked membranes. An increase in sensitivity was observed for UV-immobilized nylon membranes as compared with baked nylon membranes in some instances, although this varied within lots of the membranes tested. Repeated strippings and heterologous reprobings resulted in loss of target DNA from UV-immobilized nylon membranes as compared to baked nylon membranes. Loss of target DNA from UV-immobilized nitrocellulose-based membranes due to repeated strippings and reprobings was even more pronounced. In vacuo baking of supported and unsupported nitrocellulose and nylon membranes was more effective for immobilization, and more importantly, for retention of target DNA through many reprobings of the same blot.
Dominant role of many-body effects on the carrier distribution function of quantum dot lasers (2016)

Abstract The effects of free-carrier-induced shift and broadening on the carrier distribution function are studied considering different extreme cases for carrier statistics (Fermi–Dirac and random carrier distributions) as well as quantum dot (QD) ensemble inhomogeneity and state separation using a Monte Carlo model. Using this model, we show that the dominant factor determining the carrier distribution function is the free carrier effects and not the choice of carrier statistics. By using empirical values of the free-carrier-induced shift and broadening, good agreement is obtained with experimental data of QD materials obtained under electrical injection for both extreme cases of carrier statistics.
A Pilot Study of In Vivo Liver-Directed Gene Transfer with an Adenoviral Vector in Partial Ornithine Transcarbamylase Deficiency (2002)

Ornithine transcarbamylase deficiency (OTCD) is an inborn error of urea synthesis that has been considered as a model for liver-directed gene therapy. Current treatment has failed to avert a high mortality or morbidity from hyperammonemic coma. Restoration of enzyme activity in the liver should suffice to normalize metabolism. An E1- and E4-deleted vector based on adenovirus type 5 and containing human OTC cDNA was infused into the right hepatic artery in adults with partial OTCD. Six cohorts of three or four subjects received 1/2 log-increasing doses of vector from 2 x 10(9) to 6 x 10(11) particles/kg. This paper describes the experience in all but the last subject, who experienced lethal complications. Adverse effects included a flu-like episode and a transient rise in temperature, hepatic transaminases, thrombocytopenia, and hypophosphatemia. Humoral responses to the vector were seen in all research subjects and a proliferative cellular response to the vector developed in apparently naive subjects. In situ hybridization studies showed transgene expression in hepatocytes of 7 of 17 subjects. Three of 11 subjects with symptoms related to OTCD showed modest increases in urea cycle metabolic activity that were not statistically significant. The low levels of gene transfer detected in this trial suggest that at the doses tested, significant metabolic correction did not occur.
Treatment of Simple Renal Cysts by Percutaneous Aspiration and OK-432 Sclerotherapy (2008)

PURPOSE: Percutaneous aspiration with sclerotherapy has been widely used for the treatment of symptomatic or large simple renal cysts. Ethanol has been most commonly used as a sclerosing agent; however, a temporary percutaneous nephrostomy for multiple ethanol injections is necessary to achieve a low recurrence rate. Thus, we used OK-432 as a new sclerosing agent without a temporary percutaneous nephrostomy for multiple injections, and also compared our results with the results of previous studies. MATERIALS AND METHDOS: Between October 2005 and April 2006, 50 patients (63 simple renal cysts) who underwent percutaneous OK-432 sclerotherapy for simple renal cysts were evaluated. The simple renal cysts were aspirated under ultrasonography and fluoroscopy, after which OK-432 was injected into the cyst. Follow-up was performed with ultrasonography or CT scan after 3 months. Regression of the renal cyst or a &gt;70% reduction in size with no symptoms was considered a treatment success. RESULTS: Among 63 renal cysts in 50 patients, complete regression occurred in 17(27.0%). Greater than a 90% reduction in size occurred in 8(12.7%), a 80-90% reduction in size occurred in 21(33.3%), and a 70-80% reduction in size occurred in 15(23.8%); a &lt;70% reduction in size occurred in 2 (3%). The overall efficacies of success were 96.8%. After the procedure, there were only some minor complications, such as mild fever, local pain, and liver function test elevation that subsided with symptomatic treatment. CONCLUSIONS: Percutaneous OK-432 sclerotherapy is simple, safe, and effective and can be an alternative first-line therapy of simple renal cysts.
Reply to Million et al.: Lactobacilli and listeriosis (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Analysis of a Low-Cost Air-Gap Winding for Permanent Magnet Synchronous Motors (2009)

This paper presents an analysis of a concentrated air-gap winding concept intended for low-cost, high-speed applications where the reduced winding construction cost can motivate its use. Expressions for magnet flux linkage, torque, winding inductance, and unbalanced magnetic pull are derived and compared, with good agreement, to measurements and results obtained from finite-element simulations.
VIABILIDADE DA ENERGIA SOLAR NA UNICAMP. (2006)

Com o intuito de propiciar uma economia para a UNICAMP, alem de incentivar o uso de energia alternativa, realizou-se um estudo sobre a viabilidade do uso da energia solar no campus. A analise foi feita com base nos precos dos componentes obtidos para a implantacao dessa fonte alternativa e com base no custo da energia para a universidade. Primeiramente avaliou-se para casos ilustrativos, iluminacao publica e computadores. Por fim, generaliza-se e simula-se para precos de kWh e placas solares, diferentes dos atuais.
DeTrust-FL: Privacy-Preserving Federated Learning in Decentralized Trust Setting (2022)

Federated learning has emerged as a privacy-preserving machine learning approach where multiple parties can train a single model without sharing their raw training data. Federated learning typically requires the utilization of multi-party computation techniques to provide strong privacy guarantees by ensuring that an untrusted or curious aggregator cannot obtain isolated replies from parties involved in the training process, thereby preventing potential inference attacks. Until recently, it was thought that some of these secure aggregation techniques were sufficient to fully protect against inference attacks coming from a curious aggregator. However, recent research has demonstrated that a curious aggregator can successfully launch a disaggregation attack to learn information about model updates of a target party. This paper presents DeTrust-FL, an efficient privacy-preserving federated learning framework for addressing the lack of transparency that enables isolation attacks, such as disaggregation attacks, during secure aggregation by assuring that parties’ model updates are included in the aggregated model in a private and secure manner. DeTrust-FL proposes a decentralized trust consensus mechanism and incorporates a recently proposed decentralized functional encryption scheme in which all parties agree on a participation matrix before collaboratively generating decryption key fragments, thereby gaining control and trust over the secure aggregation process in a decentralized setting. Our experimental evaluation demonstrates that DeTrust-FL outperforms state-of-the-art FE-based secure multi-party aggregation solutions in terms of training time and reduces the volume of data transferred. In contrast to existing approaches, this is achieved without creating any trust dependency on external trusted entities.
Fast and efficient free induction decay MR spectroscopic imaging of the human brain at 9.4 Tesla (2016)

Considering the typically long duration of high-resolution MRSI, the proposed technique may be of interest for clinical applications and/or studies that focus on following the biochemistry of dynamic processes. Magn Reson Med 78:1281-1295, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Uniaxial Alignment of Polycyclic Aromatic Hydrocarbons by Solution Processing (2005)

The self-organization of two polycyclic aromatic hydrocarbons with different aromatic core sizes, dodecylphenyl-substituted hexa-peri-hexabenzocoronene and an extended disk consisting of 96 carbon atoms 6-fold-alkyl-substituted, on the surface from solution has been investigated. Highly ordered surface layers of both materials could be obtained by the zone-casting technique, despite an apparently low self-organization in drop-cast films. The zone-cast films revealed high macroscopic uniaxial orientation of the columns with a molecular edge-on arrangement on the glass support as confirmed by polarized optical microscopy, UV−vis measurements in polarized light, high-resolution transmission electron microscopy, and X-ray diffraction. Electron diffraction indicated a high intracolumnar periodicity of the molecules, but a low intercolumnar correlation of the disks due to the increased molecular dynamics in the liquid crystalline phase.
Flux-Balancing Scheme for PD-Modulated Parallel-Interleaved Inverters (2016)

A simple scheme to realize phase-disposition carrier pulse width modulation (PD PWM) for parallel two-level voltage-source converters (2L-VSCs) is presented in this paper. The proposed implementation only uses a single carrier signal and can easily be implemented using a digital signal processor. The operation of the parallel VSCs with the coupled inductor (CI) under the PD PWM is briefly discussed, and the associated dc flux injection problem is investigated. A CI saturation issue during the band transition under the PD PWM scheme is also explored, and the strategy to avoid this problem is presented. In addition, the proposed strategy also maintains a volt-second balance to synthesize desired reference space voltage vector during the band transition. As a result, a smooth transition from one modulation band to the other is ensured without causing disturbances in the line-to-line voltage. The switching losses and the harmonic performance of the proposed implementation are also compared with the commonly used phase-shifted carrier pulse width modulation. The implementation issues are discussed and the experimental results are also presented.
Parallel photomask pattern data conversion and verification system (1996)

This system is designed to convert and to verify different types of LSI layout design data and EB writer data, such as GDS-II, MEBES, and JEOL, with the help of its original internal format. The internal format data can be processed not only by a single workstation sequentially but also by network-linked workstations or a single workstation having two or more processing units concurrently. This parallel processing mechanism enables the system to reduce total processing time when handling large volume of data. The resultant internal format data produced by the conversion processes including logical operations, magnifications, and re-sizing operations can be immediately verified by built-in DRC program that is driven by a series of user commands, which consequently yields highly reliable output EB writer data. The built-in pattern viewer can graphically visualize any combination of the layout design data, the EB writer data, and the results of each conversion and verification in the same display window to provide users with an intuitive and easy method for verification. The features of the system and the parallel processing performance are described in this paper.
Characteristics of SME Biodiesel-Fueled Diesel Particle Emissions and the Kinetics of Oxidation (2006)

Biodiesel is one of the most promising alternative diesel fuels. As diesel emission regulations have become more stringent, the diesel particulate filter (DPF) has become an essential part of the aftertreatment system. Knowledge of kinetics of exhaust particle oxidation for alternative diesel fuels is useful in estimating the change in regeneration behavior of a DPF with such fuels. This study examines the characteristics of diesel particulate emissions as well as kinetics of particle oxidation using a 1996 John Deere T04045TF250 off-highway engine and 100% soy methyl ester (SME) biodiesel (B100) as fuel. Compared to standard D2 fuel, this B100 reduced particle size, number, and volume in the accumulation mode where most of the particle mass is found. At 75% load, number decreased by 38%, DGN decreased from 80 to 62 nm, and volume decreased by 82%. Part of this decrease is likely associated with the fact that the particles were more easily oxidized. Arrhenius parameters for the biodiesel fuel showed a 2-3times greater frequency factor and approximately 6 times higher oxidation rate compared to regular diesel fuel in the range of 700-825 degrees C. The faster oxidation kinetics should facilitate regeneration when used with a DPF.
Segmentation of textured images using a multiple resolution approach (2003)

A method is presented for segmenting images into a discrete set of classes by first segmenting at low resolution and then progressing to finer resolutions until individual pixels are classified. This multiple resolution method results in accurate segmentations and requires significantly less computation than some previously known methods. The segmentation algorithm used at each resolution is based on maximum a posteriori estimation of the field of pixel classifications, which is modeled as a Markov random field. The maximization is performed by a deterministic greedy algorithm which iteratively chooses the classification of individual pixels or blocks of pixels. A texture model is also developed which allows the extraction of a texture statistic for each pixel and is well suited for use with the proposed algorithm. Measurements of algorithm performance under varying conditions of region size and signal-to-noise ratio are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data from Milatuzumab-Conjugated Liposomes as Targeted Dexamethasone Carriers for Therapeutic Delivery in CD74<sup>+</sup> B-cell Malignancies (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Corticosteroids are widely used for the treatment of B-cell malignancies, including non–Hodgkin lymphoma, chronic lymphocytic leukemia (CLL), and acute lymphoblastic leukemia; however, this class of drug is associated with undesirable off-target effects. Herein, we developed novel milatuzumab-conjugated liposomes as a targeted dexamethasone carrier for therapeutic delivery in CD74&lt;sup&gt;+&lt;/sup&gt; B-cell malignancies and explored its effect against the disease.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The targeting efficiency of milatuzumab-targeted liposomes to CD74&lt;sup&gt;+&lt;/sup&gt; cells was evaluated &lt;i&gt;in vitro&lt;/i&gt;. The effect of CD74-targeted liposomal dexamethasone was compared with free dexamethasone in primary CLL cells and cell lines &lt;i&gt;in vitro&lt;/i&gt;. The therapeutic efficacy of CD74-targeted liposomal dexamethasone was evaluated in a Raji-severe combined immunodeficient (SCID) xenograft model &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Milatuzumab-targeted liposomes promoted selective incorporation of carrier molecules into transformed CD74-positive B cells as compared with CD74-negative T-cells. The CD74-dexamethasone–targeted liposomes (CD74-IL-DEX) promoted and increased killing in CD74-positive tumor cells and primary CLL cells. Furthermore, the targeted drug liposomes showed enhanced therapeutic efficacy against a CD74-positive B-cell model as compared with free, or non-targeted, liposomal dexamethasone in SCID mice engrafted with Raji cells &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These studies provide evidence and support for a potential use of CD74-targeted liposomal dexamethasone as a new therapy for B-cell malignancies. &lt;i&gt;Clin Cancer Res; 19(2); 347–56. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Microtubule destabilization and nuclear entry are sequential steps leading to toxicity in Huntington's disease (2003)

There has been a longstanding debate regarding the role of proteolysis in Huntington's disease. The toxic peptide theory posits that N-terminal cleavage fragments of mutant Huntington's disease protein [mutant huntingtin (mhtt)] enter the nucleus to cause transcriptional dysfunction. However, recent data suggest a second model in which proteolysis of full-length mhtt is inhibited. Importantly, the two competing theories differ with respect to subcellular distribution of mhtt at initiation of toxicity: nuclear if cleaved and cytoplasmic in the absence of cleavage. Using quantitative single-cell analysis and time-lapse imaging, we show here that transcriptional dysfunction is "downstream" of cytoplasmic dysfunction. Primary and reversible toxic events involve destabilization of microtubules mediated by full-length mhtt before cleavage. Restoration of microtubule structure by taxol inhibits nuclear entry and increases cell survival.