gebhart/patrepeval huggingface dataset:
Lamprey neurofilaments combine in one subunit the features of each mammalian NF triplet protein but are highly phosphorylated only in large axons (1989)

Compared with heteropolymeric assemblies of neurofilament (NF) triplet proteins in mammalian NFs, lamprey (Petromyzon marinus) NFs are homopolymers of 180 kDa subunits (NF180). We describe unique features of lamprey NF180 that distinguish it as a prototype of vertebrate NF subunits. These features may underlie key functions subserved by the earliest vertebrate NFs. Lamprey NF180 displays properties common to all intermediate filament (IF) proteins, but it also exhibits features that distinguish the mammalian triplet of NF subunits from all other IF proteins. For example, digestion of lamprey NF180 with chymotrypsin produces an insoluble 40 kDa core unit and releases a soluble fragment intermediate in size (140 kDa) to the carboxy-terminal (sidearm) extensions of the 2 high-molecular-weight (Mr) mammalian NF subunits. The core unit contains epitopes similar to those in the core of each mammalian NF triplet protein, while the soluble fragment contains other determinants similar to those in the sidearms of the 2 high-Mr mammalian NF polypeptides. Like these polypeptides, the immunological properties of some NF180 peripheral determinants were strongly affected by their phosphorylation state. Indeed, NF180 shares immunological similarities with the multiphosphorylation repeat domains in the high-Mr mammalian NF subunits. Further similarities with mammalian NF proteins include the preferential expression of poorly phosphorylated NF180 isoforms and of phosphate-dependent NF180 epitopes in axons of all sizes, and the restriction of nonphosphorylated NF180 isoforms to neuronal perikarya. In marked contrast to mammals, however, the most heavily phosphorylated isoforms of NF180 were expressed exclusively in large-diameter axons. We conclude that the single subunit forming lamprey NFs exhibits the essential features of mammalian NFs, i.e., a filament-forming core and a carboxy-terminal extension with a multiphosphorylation site. Further, the sharp restriction of heavily phosphorylated NF180 to large axons suggests that multiphosphorylation domains were acquired during evolution to permit larger axon diameters and faster conduction velocities.
Representing Attribute Based Access Control Policies in OWL (2016)

Attribute Based Access Control (ABAC) models are designed with the intention to overcome the shortcomings of classical access control models (DAC, MAC and RBAC) and unifying their advantages. In ABAC, the access control is provided based on generic attributes of entities. Many organizational security policies condition access decisions on attributes. OWL can be used to formally define and process security policies that can be captured using ABAC models. We have defined models, domains, data and security policies in OWL and used a reasoner to decide what is permitted. In this paper we present a way to represent the ABAC <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">α</sub> model using Web Ontology Language (OWL). The enforcement of policies is done using the EYE reasoner that infers the logical relationship and deduce the access grant for each requested action.
Terahertz Imaging and Sensing Applications With Silicon-Based Technologies (2018)

Traditional terahertz (THz) equipment faces major obstacles in providing the system cost and compactness necessary for widespread deployment of THz applications. Because of this, the field of THz integrated circuit (THz IC) design in CMOS and SiGe HBT technologies has surged in the last decade. An interplay of advances in silicon process technology, design technique, and microelectronic packaging promises to narrow the gap between the requirements and the reality of system cost and performance of THz components. Furthermore, the scalability, reconfigurability, and signal processing features of silicon technology have initiated research in complex THz ICs that expand the functionality of THz systems; this has enabled new applications, methods, and algorithms. This paper reviews the progress in THz IC research and investigates several realizations of THz imaging and sensing applications with silicon-based components regarding their motivation, system performance, and challenges. THz computed tomography, broadband multicolor imaging, high-resolution FMCW radar imaging, subwavelength resolution near-field imaging, and compressed sensing are presented.
A multivariate regression approach to association analysis of a quantitative trait network (2009)

Software for GFlasso is available at http://www.sailing.cs.cmu.edu/gflasso.html.
Effect of post-cure on the glass transition temperature and mechanical properties of epoxy adhesives (2013)

Abstract The effects of post-curing and cure temperature on the glass transition temperature, T g, and the mechanical properties of epoxy adhesives were studied. T g was measured by a dynamic mechanical analysis apparatus developed in-house and the mechanical properties of the adhesives (yield strength, Young's modulus and failure strain) were measured by a tensile machine. The relationships between T g and mechanical performance under various post-cure conditions were investigated. The curing process was the same for all tests, consisting of an initial stage performed at different temperatures followed by cooling at room temperature. Three sets of specimens were considered, sharing the same initial cure process, but with a different post-curing procedure. In the first set, the specimens were only subjected to a curing process; in the second set, the specimens were subjected to a curing process followed by a post-cure performed at a temperature below the T g of the fully cured network, T g∞; and in the third set, the specimens were subjected to a curing process followed by a post-cure performed at a temperature above the T g∞. When post-cured at a temperature above T g∞, the mechanical and physical properties tend to have a constant value for any cure temperature. Keywords: epoxy adhesivesglass transition temperaturecure temperaturepost-curemechanical properties Acknowledgements The authors gratefully acknowledge the funding by the Portuguese Science and Technology Foundation under the project PTDC/EME-PME/098571/2008, Huntsman Iberia for supplying the adhesive Araldite® 2011 and Henkel Iberia for supplying adhesive Loctite Hysol® 3422.
Predictive maintenance based on event-log analysis: A case study (2017)

Predictive maintenance techniques are designed to help anticipate equipment failures to allow for advance scheduling of corrective maintenance, thereby preventing unexpected equipment downtime, improving service quality for customers, and also reducing the additional cost caused by over-maintenance in preventative maintenance policies. Many types of equipment—e.g., automated teller machines (ATMs), information technology equipment, medical devices, etc.—track run-time status by generating system messages, error events, and log files, which can be used to predict impending failures. Aiming at these types of equipment, we present a general classification-based failure prediction method. In our parameterized model, we systematically defined four categories of features to try to cover all possibly useful features, and then used feature selection to identify the most important features for model construction. The general solution is sufficiently flexible and complex to address failure prediction for target equipment types. We chose ATMs as the example equipment and used real ATM run-time event logs and maintenance records as experimental data to evaluate our method on the feasibility and effectiveness. In this paper, we also share insights on how to optimize the model parameters, select the most effective features, and tune classifiers to build a high-performance prediction model.
Molecular Biology and Infection of Hepatitis E Virus (2016)

Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus.
Trithiocarbonates as a Novel Class of HDAC Inhibitors: SAR Studies, Isoenzyme Selectivity, and Pharmacological Profiles (2008)

Inhibitors of histone deacetylases (HDAC) are currently developed for the treatment of cancer. These include compounds with a sulfur containing head group like depsipeptide, alkylthiols, thiocarboxylates, and trithiocarbonates with a carbonyl group in the alpha-position. In the present investigation, we report on the synthesis and comprehensive SAR analysis of HDAC inhibitors bearing a tri- or dithiocarbonate motif. Such trithiocarbonates are readily accessible from either preformed or in situ prepared alpha-halogenated methylaryl ketones. A HDAC isotype selectivity and a substrate competitive mode-of-action is shown for defined analogues. Exploration of the head group showed the necessity of the dithio-alpha-carbonyl motif for potent HDAC inhibition. Highly potent, substrate competitive HDAC6 selective inhibitors were identified (12ac:IC 50 = 65 nM and K i = 110 nM). Trithiocarbonate analogues with an aminoquinoline-substituted pyridinyl-thienoacetyl cap demonstrate a cytotoxicity profile and potency comparable to that of suberoylanilide hydroxamic acid (SAHA) as an approved cancer drug.
Adenovirus type 12-specific RNA sequences during productive infection of KB cells (1976)

The complementary strands of adenovirus type 12 DNA were separated, and virus-specific RNA was analyzed by saturation hybridization in solution. Late during infection whole cell RNA hybridized to 75% of the light (1) strand and 15% of the heavy (H) strand, whereas cytoplasmic RNA hybridized to 65% of the 1 strand and 15% of the h strand. Late nuclear RNA hybridized to about 90% of the 1 strand and at least 36% of the h strand. Double-stranded RNA was isolated from infected cells late after infection, which annealed to greater than 30% of each of the two complementary DNA strands. Early whole cell RNA hybridized to 45 to 50% of the 1 strand and 15% of the h strand, whereas early cytoplasmic RNA hybridized to about 15% of each of the complementary strands. All early cytoplasmic sequences were present in the cytoplasm at late times.
Application of capillary electrophoresis-electrospray ionization mass spectometry in the determination of molecular diversity. (1996)

By means of capillary electrophoresis coupled online to electrospray ionization MS, a library of theoretically 171 disubstituted xanthene derivatives was analyzed. The method allowed the purity and makeup of the library to be determined: 160 of the expected compounds were found to be present, and 12 side-products were also detected in the mixture. Due to the ability of capillary electrophoresis to separate analytes on the basis of charge, most of the xanthene derivatives could be resolved by simple capillary electrophoresis-MS procedures even though 124 of the 171 theoretical compounds were isobaric with at least one other molecule in the mixture. Any remaining unresolved peaks were resolved by MS/MS experiments. The method shows promise for the analysis of small combinatorial libraries with fewer than 1000 components.
Iterative Feedback Tuning (IFT) of Head Positioning Servomechanism in Hard Disk Drive (2008)

Abstract Actuators used in hard disk drives (HDD) are produced en mass and therefore their dynamic properties vary within a given tolerance bound. A nominal model representing the batch of actuators is used to design the head positioning servomechanism. Equal performance can not be expected for all actuators when such controller is used. Disk drive servomechanism is expected to provide performance with increasingly tighter tolerance as the demand for higher storage capacity continues. Moreover, physical properties of any actuator may change over time causing the degradation of performance. All these issues demand for good on-line tuning of controller. This paper explores the usage of Iterative Feedback Tuning (IFT) in HDD servomechanism. Improved performance of the tuned controller is demonstrated using simulation and experimental results.
On foot navigation: continuous step calibration using both complementary recursive prediction and adaptive Kalman filtering (2000)

human positioning. Dead reckoning for on-foot navigation applications cannot be computed by double integration of the antero-posterior acceleration. The main reasons are the alignment problem and the important sensor systematic errors in comparison to human walking speed. However, raw accelerometer signal can furnish helpful information on steps length as a function of the walk dynamics. As stride length naturally varies, a continuous adaptation is necessary. In the absence of satellite observable, a recursive prediction process is used. When GPS signal is available, adaptive Kalman filtering is processed to update both the stride length and the recursive prediction parameters. This paper shows the different necessary stages for individual stride calibration as basis of global on-foot dead reckoning applications. This study lies within the framework of a project that aims at analyzing the daily activity of people. Precise continuous positioning, but not necessarily in real-time conditions, appears of evident interest. The global procedure and several test results are presented. 1.
Filter Bank Based Multi-Mode Multiple Access Scheme For Wireless Uplink (2009)

Publication in the conference proceedings of EUSIPCO, Glasgow, Scotland, 2009
Palladium‐Catalyzed Arylation of Linear and Cyclic Polyamines (2005)

Abstract The palladium‐catalyzed arylation of polyamines is investigated and it is shown that the C−N coupling reaction for a given substrate is strongly dependent on the nature and the concentration of the catalytic system, as well as the nature of the base employed. The arylation of the primary amino group is favored when both primary and secondary amines are present; selective arylation is then possible without using any protecting group. The reaction of dihalobenzenes with polyamines gives the monoamination products in good yields without any significant formation of diamino compounds or reduced derivatives, unlike what is observed when monoamines are used. The extent of polyarylation of polyamines as a function of the excess of aryl halide and the nature and the amount of catalyst is also studied. Finally, N ‐arylation of a macrocyclic tetraamine (cyclam) is performed by using an appropriate catalytic system. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Analytical Variability Among Methods for the Measurement of 25-Hydroxyvitamin D (2013)

Intermethod variability in 25(OH)D assays continues to limit our progress toward the establishment of reference values for 25(OH)D in health and our efforts to gain a better understanding of the role of vitamin D insufficiency as a risk factor for disease.
Antennal sensilla of two female anopheline sibling species with differing host ranges (2006)

The same types of sensilla are found on the antennae of both species. While An. quadriannulatus has greater numbers of each sensilla type, sensilla densities are very similar for each species, suggesting that other factors may be more important to such olfactory-driven behaviours as host preference.
ChemInform Abstract: Applications of Advanced Hybrid Organic—Inorganic Nanomaterials: From Laboratory to Market (2011)

Abstract Review: 526 refs.
Virtex FPGA implementation of a polyphase filter for sample rate conversion (2002)

Many practical applications of DSP require the sampling rate of a signal to be changed. This is usually achieved using linear, time-variant finite impulse response (FIR) filters such as polyphase filters. This paper describes the modelling, design and implementation of a polyphase filter using the Xilinx Virtix FPGA technology. Four solutions were explored. The first (obvious) solution involving reducing the number of multipliers by exploiting the proliferation of zeroes in the filter response. In the second and third approaches, the circuit was transformed to reduce the critical path. The fourth approach involved the development of a multiplier that multiplies a fixed number of coefficients.
CDC reports first case of vancomycin resistant <i>Staphylococcus aureus</i> (2003)

The Centers for Disease Control and Prevention (CDC) has reported that in summer 2002, a 40 year old Michigan woman became the first person worldwide known to have been infected with a strain of Staphylococcus aureus that was resistant to the antibacterial vancomycin.

The Michigan woman developed foot ulcers and other skin infections after becoming infected with the bacterium following an amputation. She …
A double precision floating point multiply (2003)

A 2.2GHz 53/spl times/54 bit pipelined multiplier is fabricated in 130nm CMOS technology with an area of 0.15mm/sup 2/. The circuit implementation results in a 50% size reduction over the previously reported values. The circuit operates at 2.2GHz and uses 522mW at 80% switching factor, 1.2V supply and 25/spl deg/C.
Nucleotide excision repair 3' endonuclease XPG stimulates the activity of base excision repairenzyme thymine glycol DNA glycosylase (2020)

An ionizing radiation-induced DNA lesion, thymine glycol, is removed from DNA by a thymine glycol DNA glycosylase with an apurinic/apyrimidinic (AP) lyase activity encoded by the Escherichia coli endonuclease III ( nth ) gene and its homolog in humans. Cells from Cockayne syndrome patients with mutations in the XPG gene show approximately 2-fold reduced global repair of thymine glycol. Hence, I decided to investigate the molecular mechanism of the effect of XPG protein observed in vivo on thymine glycol removal by studying the interactions of XPG protein and human endonuclease III (HsNTH) protein in vitro and the effect of XPG protein on the activity of HsNTH protein on a substrate containing thymine glycol. The XPG protein stimulates the binding of HsNTH protein to its substrate and increases its glycosylase/AP lyase activity by a factor of approximately 2 through direct interaction between the two proteins. These results provide in vitro evidence for a second function of XPG protein in DNA repair and a mechanistic basis for its stimulatory activity on HsNTH protein.
Sp1 and Sp3 Are Oxidative Stress-Inducible, Antideath Transcription Factors in Cortical Neurons (2003)

Neuronal cell death in response to oxidative stress may reflect the failure of endogenous adaptive mechanisms. However, the transcriptional activators induced by oxidative stress in neurons that trigger adaptive genetic responses have yet to be fully elucidated. We report that basal DNA binding of the zinc finger transcription factors Sp1 and Sp3 is unexpectedly low in cortical neurons in vitro and is significantly induced by glutathione depletion-induced or hydrogen peroxide-induced oxidative stress in these cells. The increases in Sp1/Sp3 DNA binding reflect, in part, increased levels of Sp1 and Sp3 protein in the nuclei of cortical neurons. Similar induction of Sp1 and Sp3 protein is also observed in neurons in vivo in a chemical or a genetic model of Huntington's disease, two rodent models in which neuronal loss has been attributed to oxidative stress. Sustained high-level expression of full-length Sp1 or full-length Sp3, but not the Sp1 zinc finger DNA-binding domain alone, prevents death in response to oxidative stress, DNA damage, or both. Taken together, these results establish Sp1 and Sp3 as oxidative stress-induced transcription factors in cortical neurons that positively regulate neuronal survival.
Neutrophil CD64 as a sepsis biomarker (2011)

Neutrophilic granulocytes express their Fcgamma receptor, also known as the CD64 antigen, predominantly when they are activated. This makes neutrophil CD64 a potential biomarker for infection and sepsis. Indeed there is ample literature on the diagnostic utility of neutrophil CD64 in a variety of diseases. This review summarizes the literature on its application as a sepsis biomarker, in adults as well as in neonates and infants. The available data indicate that neutrophil CD64 seems to have high sensitivity (86%) and specificity (87%), but the methodological quality of most studies is questionable. Nevertheless, neutrophil CD64 appears to be a better diagnostic test than traditional hematological assays, C-reactive protein and probably even procalcitonin. Application of neutrophil CD64 in other conditions than sepsis is briefly presented. Finally, future clinical studies are discussed which are needed in order to confirm the diagnostic performance of this promising biomarker.
Solution Blowing of Soy Protein Fibers (2011)

Solution blowing of soy protein (sp)/polymer blends was used to form monolithic nanofibers. The monolithic fibers were blown from blends of soy protein and nylon-6 in formic acid. The sp/nylon-6 ratio achieved in dry monolithic nanofibers formed using solution blowing of the blend was equal to 40/60. In addition, solution blowing of core-shell nanofibers was realized with soy protein being in the core and the supporting polymer in the shell. The shells were formed from nylon-6. The sp/nylon-6 ratio achieved in dry core-shell fibers was 32/68. The nanofibers developed in the present work contain significant amounts of soy protein and hold great potential in various applications of nonwovens.
Fitting model fields to observations by using singular value decomposition: An ensemble‐based 4DVar approach (2007)

An ensemble‐based four‐dimensional variational data assimilation (4DVar) method is proposed to fit the model field to 4‐D observations in an increment form in the analysis step of data assimilation. The fitting is similar to that in the 4DVar but the analysis increment is expressed by a linear combination of the leading singular vectors extracted from an ensemble of 4‐D perturbation solutions, so the fitting is computationally very efficient and does not require any adjoint integration. In the cost function used for the fitting, the background error covariance matrix is constructed implicitly by the perturbation solutions (through their representative singular vectors) similarly to that in the ensemble Kalman filter, but the perturbation solutions are not updated by the analysis into the next assimilation cycle, so the analysis is simpler and more efficient than that in the ensemble Kalman filter. The potential merits of the method are demonstrated by three sets of observing system simulation experiments performed with a shallow‐water equation model. The method is shown to be robust even when the model is imperfect and the observations are incomplete.