gebhart/patrepeval huggingface dataset:
Run-time self-tuning banked loop buffer architecture for power optimization of dynamic workload applications (2011)

Instruction memory organization is pointed out as one of the major sources of energy consumption in embedded systems. As embedded systems are characterized by restrictive resources and low energy budget, any enhancement in this component allows not only to decrease the total energy consumption, but also to have a better distribution of the energy budget throughout the system. This paper presents a self-tuning banked loop buffer architecture, which is based on a run-time loop buffer controller that optimizes both the dynamic and leakage energy consumption of the instruction memory organization. Results show that using banking in loop buffer architectures leads to higher reduction in the total energy consumption of the instruction memory organization if the tuning approach is applied sparingly. Based on post-layout simulations, our approach improves the total energy consumption by average of 20% in comparison with a loop buffer architecture based on a single monolithic memory, and more than 90% in comparison with instruction memory organizations without loop buffer architectures.
Guest Editorial: Big Media Data: Understanding, Search, and Mining (2015)

The papers in this special section focus on the topic of Big Data. There has been an explosive increase in media data, such as images, videos and social media in the Internet, mobile devices, and desktops. Accordingly, the area of big media data has been attracting a lot of research interest from both academia and industry. Big media data offers a promising possibility for in-depth media understanding, as well as exploring the very big scale media data to bridge the well-known semantic gap between high-level semantics and low-level features. It provides richer information, ranging from social relations to context information associated to rich media data of diverse modalities. It also provides us the opportunity to mine reliable and helpful knowledge from big media data for a wide variety of applications.
A Low-Complexity Sliding-Window Turbo Equalizer for Nonlinearity Compensation (2012)

We propose a low-complexity turbo equalizer consisting of a sliding window MAP estimator, and a low overhead LDPC decoder. By utilizing 2nd order statistics, we obtain 2.5 ∼ 4dB gain with additional improvement with turbo loop.
Optical Breakdown in Particle Suspension (1990)

We have characterized the nonlinearities observed in suspensions of carbon black particles in liquids (CBS). We have developed a preliminary explanation of the optical limiting characteristic of the CBS that qualitatively explains the low limiting thresholds. We have found that the limiting depends primarily on the input optical fluence (J/cm2) rather than irradiance (W/cm2). We have monitored transmission, side scattered light, and the photoacoustic response of the CBS simultaneously. The nonlinear scattered light appears to be the dominant nonlinearity. Additionally, we have observed that the nonlinearities disappear after repeated laser firings. Thus, in essense, we are performing a laser induced damage experiment, and we have prepared a material with a low damage threshold. These data have led us to the following model. The carbon first linearly absorbs the input light efficiently. The carbon is rapidly heated, vaporizes and ionizes to form a rapidly expanding microplasma. This plasma absorbs and scatters subsequent light, thus limiting the transmittance.
Autoencoder-based detection of the residues involved in G protein-coupled receptor signaling (2021)

Regulator binding and mutations alter protein dynamics. The transmission of the signal of these alterations to distant sites through protein motion results in changes in protein expression and cell function. The detection of residues involved in signal transmission contributes to an elucidation of the mechanisms underlying processes as vast as cellular function and disease pathogenesis. We developed an autoencoder (AE) based method that detects residues essential for signaling by comparing the fluctuation data, particularly the time fluctuation of the side-chain distances between residues, during molecular dynamics simulations between the ligand-bound and -unbound forms or wild-type and mutant forms of proteins. Here, the AE-based method was applied to the G protein-coupled receptor (GPCR) system, particularly a class A-type GPCR, CXCR4, to detect the essential residues involved in signaling. Among the residues involved in the signaling of the homolog CXCR2, which were extracted from the literature based on the complex structures of the ligand and G protein, our method could detect more than half of the essential residues involved in G protein signaling, including those spanning the fifth and sixth transmembrane helices in the intracellular region, despite the lack of information regarding the interaction with G protein in our CXCR4 models.
Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non‐invasive prenatal testing (2017)

In conclusion, the robustness of DNS and STR to collect CFCs from peripheral maternal blood for the first time coupled with deep sequencing technique demonstrates the possibility of comprehensive non-invasive prenatal testing of genetic disorders using isolated CFCs.
The Overriding Chemical Principles that Define Asphaltenes (2001)

Asphaltenes are defined in terms of their solubility classification. This operational definition combined with the previous controversy over asphaltene molecular weight have obscured the governing chemical and structural parameters that define the asphaltene fraction. Here, asphaltenes are investigated by several techniques to elucidate relations between structure and properties. In particular, the asphaltene molecular size is compared to the ratio of aromatic to saturated carbon. The conclusion is obtained that asphaltene molecular structure is governed by the balance between the propensity of fused aromatic ring systems to stack via π-bonding, reducing solubility, vs the steric disruption of stacking due alkane groups, increasing solubility.
Multilocus microsatellite typing forCryptococcus neoformansvar.grubii (2008)

Fifteen randomly selected microsatellites (simple sequence repeats; SSRs), from the H99 Cryptococcus neoformans var. grubii (serotype A) genome, were sequenced, characterized and applied to sequence 87 clinical and environmental C. neoformans var. grubii isolates from 12 different countries based on Multilocus Microsatellite Typing (MLMT). Among the 15 SSR loci, three (designated CNG1, CNG2 and CNG3) were polymorphic, while the remaining 12 SSR loci showed no variations. The specific PCR primers of the polymorphic microsatellites, i.e., CNG1, CNG2 and CNG3, amplified those loci only from strains of C. neoformans (C. neoformans var. grubii, C. neoformans var. neoformans and the AD hybrid) but not from Cryptococcus gattii, suggesting a species-specific association. The three polymorphic microsatellites are useful markers for strain genotyping, population genetic analysis, epidemiological studies, and may be helpful for the diagnosis of cryptococcosis due to C. neoformans.
A Decreased Frequency of Regulatory T Cells in Patients with Common Variable Immunodeficiency (2009)

Our results demonstrate that a reduction in Treg cells could have impaired immune function in CVID patients.
The Orphan Nuclear Receptor NGFI-B Regulates Expression of the Gene Encoding Steroid 21-Hydroxylase (1993)

As part of its trophic action to maintain the steroidogenic capacity of adrenocortical cells, corticotropin (ACTH) increases the transcription of the cytochrome P-450 steroid hydroxylase genes, including the gene encoding steroid 21-hydroxylase (21-OHase). We previously identified several promoter elements that regulate 21-OHase gene expression in mouse Y1 adrenocortical tumor cells. One of these elements, located at nucleotide -65, closely resembles the recognition sequence of the orphan nuclear receptor NGFI-B, suggesting that NGFI-B regulates this essential steroidogenic enzyme. To explore this possibility, we first used in situ hybridization to demonstrate high levels of NGFI-B transcripts in the adrenal cortex of the adult rat. In cultured mouse Y1 adrenocortical cells, treatment with ACTH, the major regulator of 21-OHase transcription, rapidly increased NGFI-B expression. Gel mobility shift and DNase I footprinting experiments showed that recombinantly expressed NGFI-B interacts specifically with the 21-OHase -65 element and identified one complex formed by Y1 extracts and the 21-OHase -65 element that contains NGFI-B. Expression of NGFI-B significantly augmented the activity of the intact 21-OHase promoter, while mutations of the -65 element that abolish NGFI-B binding markedly diminished NGFI-B-mediated transcriptional activation. Specific mutations of NGFI-B shown previously to impair either DNA binding or transcriptional activation diminished the effect of NGFI-B coexpression on 21-OHase expression. Finally, an oligonucleotide containing the NGFI-B response element conferred ACTH response to a core promoter from the prolactin gene, showing that this element is sufficient for ACTH induction. Collectively, these results identify a cellular promoter element that is regulated by NGFI-B and implicate NGFI-B in the transcriptional induction of 21-OHase by ACTH.
Structural basis for interaction of DivIVA/GpsB proteins with their ligands (2019)

DivIVA proteins and their GpsB homologues are late cell division proteins found in Gram-positive bacteria. DivIVA/GpsB proteins associate with the inner leaflet of the cytosolic membrane and act as scaffolds for other proteins required for cell growth and division. DivIVA/GpsB proteins comprise an N-terminal lipid-binding domain for membrane association fused to C-terminal domains supporting oligomerization. Despite sharing the same domain organization, DivIVA and GpsB serve different cellular functions: DivIVA plays diverse roles in division site selection, chromosome segregation and controlling peptidoglycan homeostasis, whereas GpsB contributes to the spatiotemporal control of penicillin-binding protein activity. The crystal structures of the lipid-binding domains of DivIVA from Bacillus subtilis and GpsB from several species share a fold unique to this group of proteins, whereas the C-terminal domains of DivIVA and GpsB are radically different. A number of pivotal features identified from the crystal structures explain the functional differences between the proteins. Herein we discuss these structural and functional relationships and recent advances in our understanding of how DivIVA/GpsB proteins bind and recruit their interaction partners, knowledge that might be useful for future structure-based DivIVA/GpsB inhibitor design.
Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms (2020)

Transcription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.
Pd-Catalyzed Cross-Coupling Reactions of Amides and Aryl Mesylates (2010)

A catalyst, based on a biarylphosphine ligand, for the Pd-catalyzed cross-coupling reactions of amides and aryl mesylates is described. This system allows an array of aryl and heteroaryl mesylates to be transformed into the corresponding N-aryl amides in moderate to excellent yields.
Analysis of Dynamic Changes in Cognitive Workload During Cardiac Surgery Perfusionists′ Interactions With the Cardiopulmonary Bypass Pump (2020)

These preliminary findings suggest the preclamp phase of CPB pump interaction corresponds to higher cognitive workload, which may point to an area warranting further exploration using passive measurement.
Multivalent Tryptophan‐ and Tyrosine‐Containing [60]Fullerene Hexa‐Adducts as Dual HIV and Enterovirus A71 Entry Inhibitors (2021)

Unprecedented 3D hexa-adducts of [60]fullerene peripherally decorated with twelve tryptophan (Trp) or tyrosine (Tyr) residues have been synthesized. Studies on the antiviral activity of these novel compounds against HIV and EV71 reveal that they are much more potent against HIV and equally active against EV71 than the previously described dendrimer prototypes AL-385 and AL-463, which possess the same number of Trp/Tyr residues on the periphery but attached to a smaller and more flexible pentaerythritol core. These results demonstrate the relevance of the globular 3D presentation of the peripheral groups (Trp/Tyr) as well as the length of the spacer connecting them to the central core to interact with the viral envelopes, particularly in the case of HIV, and support the hypothesis that [60]fullerene can be an alternative and attractive biocompatible carbon-based scaffold for this type of highly symmetrical dendrimers. In addition, the functionalized fullerenes here described, which display twelve peripheral negatively charged indole moieties on their globular surface, define a new and versatile class of compounds with a promising potential in biomedical applications.
Remote Lead Through Teaching by Human Demonstration Device (2015)

Industrial robots are playing increasingly important roles in production lines. The traditional pendant programming method, however, is unintuitive and time-consuming. Its complicated operation also sets a high requirement on users. To simplify the robot programming process, many new methods have been proposed, such as lead through teaching, teleoperation, and human direct demonstration. Each of these methods, however, suffers from its own drawbacks. To overcome the drawbacks, a novel robot programming method, remote lead through teaching (RLTT), is introduced in this paper. In RLTT, the operator uses a device to train the robot remotely, allowing the demonstrators to use the mature lead through teaching techniques in a safe environment. In order to implement RLTT, the human demonstration device (HDD) is also designed to transfer the demonstration information from the human to the robot.
Discovery of an Inhibitor of a Transcription Factor Using Small Molecule Microarrays and Diversity-Oriented Synthesis (2003)

Small molecule microarrays were screened to identify a small molecule ligand for Hap3p, a subunit of the yeast Hap2/3/4/5p transcription factor complex. The compound, named haptamide A, was determined to have a KD of 5.03 muM for binding to Hap3p using surface plasmon resonance analysis. Haptamide A also inhibited activation of a GDH1-lacZ reporter gene in a dose-dependent fashion. To explore structure-activity relationships, 11 derivatives of haptamide A were prepared using the same synthetic route that was developed for the original library synthesis. Analysis of dissociation constants and IC50 values for the reporter gene assay revealed a more potent inhibitor, haptamide B, with a KD of 330 nM. Whole-genome transcriptional profiling was used to compare effects of haptamide B with a hap3Delta yeast strain. Treatment with haptamide B, like the deletion mutant, reduced lactate-induced transcription of several genes from wild-type levels. Profiling the genetic "knockout" and the chemical genetic "knockdown" led to the identification of several genes that are regulated by Hap3p under nonfermentative conditions. These results demonstrate that a small molecule discovered using the small molecule microarray binding assay can permeate yeast cells and reach its target transcription factor protein in cells.
Oxidation of Cycloalkylamines by Cytochrome P-450 (1989)

Mechanism-based destruction of cytochrome P-450 (P-450) and P-450 heme is observed during the oxidation of N-cyclopropyl and N-cyclobutyl benzylamines. The slower inactivation by the cyclobutylamines relative to cyclopropylamines is consistent with known relative rates of ring opening of cycloalkyl-substituted aminium radicals. Evidence was found that porphyrin meso adducts of the type reported for horseradish peroxidase and cyclopropanone hydrate (Wiseman, J. S., Nichols, J. S., and Kolpak, M. X. (1982) J. Biol. Chem. 257, 6328-6332) were not formed. Radiolabels from cyclopropylamine substrates were covalently attached to protein but essentially only from the cyclopropyl portion and not the benzylic portion. Neither label appeared to be bound to extractable heme; however, during oxidations with cyclopropylamines, labeled P-450 heme became covalently attached to protein. Oxidation of 1-phenylcyclobutylamine by P-450 yielded 2-phenyl-1-pyrroline and 2-phenylpyrrolidine, and the ring expansion is interpreted as evidence for the existence of aminium radicals based on precedents with monoamine oxidase (Silverman, R. B., and Zieske, P. A. (1985) Biochemistry 24, 2128-2138). In addition, purified P-450PB-B oxidized N-(1-phenylcyclobutyl)-benzylamine to N-(1-phenyl)cyclobutyl phenyl nitrone, identified using spectral techniques. This transformation involves two sequential oxidations with either a hydroxylamine or benzylidene intermediate. While P-450 oxidized the amine to both compounds, only the hydroxylamine was rapidly oxidized to give the nitrone. The ring expansion and nitrone products are interpreted in the context of aminium radical intermediates involved in the mechanism of P-450-catalyzed amine oxidation.
Computed tomography porosity and spherical indentation for determining cortical bone millimetre-scale mechanical properties (2019)

The cortex of the femoral neck is a key structural element of the human body, yet there is not a reliable metric for predicting the mechanical properties of the bone in this critical region. This study explored the use of a range of non-destructive metrics to measure femoral neck cortical bone stiffness at the millimetre length scale. A range of testing methods and imaging techniques were assessed for their ability to measure or predict the mechanical properties of cortical bone samples obtained from the femoral neck of hip replacement patients. Techniques that can potentially be applied in vivo to measure bone stiffness, including computed tomography (CT), bulk wave ultrasound (BWUS) and indentation, were compared against in vitro techniques, including compression testing, density measurements and resonant ultrasound spectroscopy. Porosity, as measured by micro-CT, correlated with femoral neck cortical bone's elastic modulus and ultimate compressive strength at the millimetre length scale. Large-tip spherical indentation also correlated with bone mechanical properties at this length scale but to a lesser extent. As the elastic mechanical properties of cortical bone correlated with porosity, we would recommend further development of technologies that can safely measure cortical porosity in vivo.
Multichannel probes for polarization-resolved scanning near-field optical microscopy (2010)

We propose and validate a concept of multichannel near-field fiber probe for the collection and discrimination of optical fields of orthogonal polarizations (linear, elliptic, and circular). The system is achieved by connecting to scanning near-field optical microscope fiber tips an optical stage made up of commercial polarizers, fiber couplers, and polarization controllers. Using radially polarized Bessel beams as test objects, we demonstrate the ability of a three-channel fiber tip to simultaneously and independently probe the transverse vector components of the electric field (parallel to the sample surface) and the overall transverse intensity. The polarization ratio of the near-field collection system exceeds 1:1500. The system can be implemented in collection-mode or reflection-mode near-field microscope configurations, with various kinds of probe and light source (of high or low coherence lengths) for a deeper insight of light polarization effects and vector fields at a subwavelength scale.
Enhanced Electrical Properties of Transparent Carbon Nanotube/Binder Hybrid Thin Films: Effects of the Silane Sol and the Bundle Size of the Carbon Nanotubes (2010)

We report the effects of intermolecular interactions at the few-walled carbon nanotubes (FWNTs)/binder interface and the bundle size of the acid-treated FWNTs on the electrical properties of FWNTs/silane sol hybrid films. The bundle size of the FWNTs was successfully controlled by using acid treatment; assembled bundle structures due to hydrogen bonding were observed only for FWNTs functionalized with hydroxyl groups (FWNTs-OH). It was also confirmed by measuring the UV absorbance that the FWNTs-OH even form bundled structures in the solution state. Tetraethylorthosilicate (TEOS) and methyltriethoxysilane (MTMS) sols were used to manipulate the intermolecular interactions between the nanotubes and binder. We found that the hybridization of relatively large bundled FWNTs with TEOS sol unfavorable to hydrophobic nanotube surfaces enhanced the electrical properties of thin films prepared by spray coating. Moreover, the Raman spectrum of the bundled FWNTs-OH is not affected by the silane sol, whereas the D-to-G ratio and the G band position of the unbundled FWNTs-COOH is noticeably influenced by the silane sol.
The eye's aqueous humor : from secretion to glaucoma (1998)

Overview - transport components of aqueous humor secretion and their regulation, M.M. Civan molecular approaches to the study of the Na+, K+-ATPase and chloride channels in the ocular ciliary epithelium, M. Coca-Prados and J. Sanchez-Torres chloride channels in the ciliary epithelium, T. Jacob the identification of potassium channels in human lens epithelium, J. Rae and A.R. Shepard aquaporin water channels in eye and other channels, M.D. Lee et al gap junctions and interlayer communication in the heterocellular epithelium of the ciliary body, J.M. Wolosin and M. Schutte the travecular meshwork and aqueous humor reabsorption, M. Wiederholt and F. Stumpff circadian rhythms in aqueous humor formation, J. Sears and M.L. Sears clinical measurements of aqueous dynamics - implications for addressing glaucoma, R.F. Brubaker.
Analisi delle problematiche propagative nei sistemi RFID passivi in banda UHF (2006)

The area of applications for radio-frequency identification (RFID) is quickly increasing, especially with the on-going migration of the operating frequencies to the UHF band that is supposed to allow greater interrogation ranges. Nevertheless, the higher the frequency, the stronger the impact of the environment on propagation and on devices radiation properties. Multipath propagation, absorption loss and unwanted interaction between the transponder and the tagged object have been considered and properly analyzed in the present work through electromagnetic and ray-tracing simulation