gebhart/patrepeval huggingface dataset:
Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts (2008)

Existing data indicate that sleep-wakefulness is an essential behavior. The biological function(s) of sleep, however, remains unknown, due, in part, to the lack of information available at the intracellular level. Preliminary microarray analyses show that changes in behavioral state influence regional mRNA profiles; however, the impact of sleep on protein signatures is virtually unexplored. In these studies, cortical protein profiles were examined after timed bouts of spontaneous sleep-wakefulness. Within minutes of each behavioral state examined, a small number of spots showing unique expression were detected. Mass spectroscopy analyses of sleep- and wake-related spots identified proteins associated with multiple functional categories. Two sleep-associated proteins were further validated using a sleep deprivation paradigm. We found preliminary evidence for two different post-transcriptional mechanisms-one (GAPDH) in which the amount of protein was increased in the recovery sleep following prolonged waking, while the other (actin) suggested that post-translational modifications may underlie sleep. The similarities between the effects of sleep on both protein and mRNA profiles indicate that dynamic intracellular changes underlie sleep-wake states and are consistent with roles for sleep in multiple biological functions.
Rule-based layout solving and its application to procedural interior generation (2009)

Due to the recent advancement in procedural generation techniques, games are presenting players with ever growing cities and terrains to explore. However most sandbox-style games situated in cities, do not allow players to wander into buildings. In past research, space planning techniques have already been utilized to generate suitable layouts for both building floor plans and room layouts. We introduce a novel rule-based layout solving approach, especially suited for use in conjunction with procedural generation methods. We show how this solving approach can be used for procedural generation by providing the solver with a user-defined plan. In this plan, users can specify objects to be placed as instances of classes, which in turn contain rules about how instances should be placed. This approach gives us the opportunity to use our generic solver in different procedural generation scenarios. In this paper, we will illustrate mainly with interior generation examples
Tailoring of Atlantic Salmon (<i>Salmo salar</i> L.) Flesh Lipid Composition and Sensory Quality by Replacing Fish Oil with a Vegetable Oil Blend (2005)

Atlantic salmon (Salmo salar L.) juveniles were fed either 100% fish oil (FO), 75% vegetable oil (VO), or 100% VO throughout their life cycle to harvest weight followed by a finishing diet period when all groups were fed 100% FO. The two experimental VO diets were tested at two different locations (Scotland and Norway) against the same control diet (100% FO). The VO blend was composed of rapeseed oil, palm oil, and linseed oil using capelin oil as a control for fatty acid class compositions. Flesh fatty acid profiles were measured regularly throughout the experiment, with the times of sampling determined by changes in pellet size/lipid content and fish life stage. Growth and mortality rates were not significantly affected by dietary fatty acid compositions throughout the life cycle, except during the seawater winter period in Norway when both growth and protein utilization were increased in salmon fed 100% VO compared to 100% FO. Flesh fatty acid composition was highly influenced by that of the diet, and after the finishing diet period the weekly intake recommendations of very long chain n-3 polyunsaturated fatty acid (VLCn-3 PUFA) for human health were 80 and 56% satisfied by a 200 g meal of 75% VO and 100% VO flesh, respectively. No effect on flesh astaxanthin levels was observed in relation to changing dietary oil sources. Sensory evaluation showed only minor differences between salmon flesh from the dietary groups, although prior to the finishing diet period, flesh from 100% VO had less rancid and marine characteristics and was preferred over flesh from the other dietary groups by a trained taste panel. After the finishing diet period, the levels of typical vegetable oil fatty acids in flesh were reduced, whereas those of VLCn-3 PUFA increased to levels comparable with a 100% FO fed salmon. No differences in any of the sensory characteristics were observed between dietary groups. By blending VOs to provide balanced levels of dietary fatty acids, up to 100% of the fish oil can be replaced by the VO blend without compromising growth or flesh quality. At the same time, 75% of the dietary fish oil can be replaced without compromising flesh VLCn-3 PUFA content, thereby providing a beneficial nutritional profile for human consumption.
Characterization of skin microbiota in patients with atopic dermatitis and in normal subjects using 16S rRNA gene-based comprehensive analysis (2007)

A previous study using bacterial 16S rRNA gene-based clone libraries revealed that the microbiota in healthy human skin included uncultured micro-organisms, although the micro-organisms in skin exposed to disease conditions remain to be examined. To compare the profiles of skin microbiota in 13 patients with atopic dermatitis (AD) and 10 healthy controls, terminal RFLP analysis of bacterial 16S rRNA genes was applied to 23 swab-scrubbed samples from facial skin. This culture-independent analysis successfully revealed the complex bacterial members of the microbiota as peak patterns following capillary electrophoresis of terminal restriction fragments (T-RFs). Each T-RF peak reflected a micro-organism, and the micro-organism to which each peak was assigned could be identified by computer simulation of T-RF length using the nucleotide sequence data of bacterial species residing in the skin. Among 18 species detected in the study, Stenotrophomonas maltophilia was detected significantly more commonly in AD patients (5/13 for AD patients vs 0/10 for controls), whilst Dietzia maris was detected significantly more commonly in normal controls (8/10 for controls vs 2/13 for AD patients). Moreover, Streptococcus species, which are considered to be uncommon in uninfected skin, were detected in seven patients and eight normal controls. Although further studies should be undertaken to investigate the roles of these micro-organisms in AD, the microbiota were presumed to include hitherto uninvestigated bacterial species in the major population of patients with AD and of healthy controls.
Pannexin 1 and pannexin 3 are glycoproteins that exhibit many distinct characteristics from the connexin family of gap junction proteins (2007)

Pannexins are mammalian orthologs of the invertebrate gap junction proteins innexins and thus have been proposed to play a role in gap junctional intercellular communication. Localization of exogenously expressed pannexin 1 (Panx1) and pannexin 3 (Panx3), together with pharmacological studies, revealed a cell surface distribution profile and life cycle dynamics that were distinct from connexin 43 (Cx43, encoded by Gja1). Furthermore, N-glycosidase treatment showed that both Panx1 (approximately 41-48 kD species) and Panx3 (approximately 43 kD) were glycosylated, whereas N-linked glycosylation-defective mutants exhibited a decreased ability to be transported to the cell surface. Tissue surveys revealed the expression of Panx1 in several murine tissues--including in cartilage, skin, spleen and brain--whereas Panx3 expression was prevalent in skin and cartilage with a second higher-molecular-weight species present in a broad range of tissues. Tissue-specific localization patterns of Panx1 and Panx3 ranging from distinct cell surface clusters to intracellular profiles were revealed by immunostaining of skin and spleen sections. Finally, functional assays in cultured cells transiently expressing Panx1 and Panx3 were incapable of forming intercellular channels, but assembled into functional cell surface channels. Collectively, these studies show that Panx1 and Panx3 have many characteristics that are distinct from Cx43 and that these proteins probably play an important biological role as single membrane channels.
A pattern-matching co-processor for network intrusion detection systems (2004)

This paper explores the design and analysis of an FPGA module that implements pattern-matching functionality for the network intrusion detection problem. The specific features of the pattern-matcher include support for complex regular expressions and approximate matching with bounded substitutions, insertions, and deletions. A module generator is presented that utilizes non-deterministic finite automata to dynamically create efficient circuits for matching patterns specified with a standard rule language. The logic complexity and performance of the generated circuits is measured and analyzed. Results indicate our techniques yield circuits that are more than twice as dense as other reported designs, while maintaining the throughput necessary for processing at gigabit line speeds and beyond. The FPGA pattern-matching processor is integrated with other hardware and software components to form a complete network intrusion detection system.
The Novel Chemical Entity YTR107 Inhibits Recruitment of Nucleophosmin to Sites of DNA Damage, Suppressing Repair of DNA Double-Strand Breaks and Enhancing Radiosensitization (2011)

These data support the hypothesis that inhibition of DNA repair due to inhibition of NPM shuttling increases the efficacy of DNA-damaging therapeutic strategies.
Thermal crosstalk limits for silicon photonic DWDM interconnects (2014)

We present theoretical modeling and experimental results of the thermal crosstalk and time constants of micro-disk modulators as a function of the spacing between nearby devices, taking into consideration the effects of dense metallic interconnects.
Analysis of the β-Tubulin Gene from <i>Vittaforma corneae</i> Suggests Benzimidazole Resistance (2007)

We amplified, cloned, and sequenced the beta-tubulin gene of Vittaforma corneae, a microsporidium causing human infections. The beta-tubulin gene sequence has a substitution at Glu(198) (with glutamine), which is one of six amino acids reported to be associated with benzimidazole sensitivity. Benzimidazoles were assayed for antimicrosporidial activity and showed poor parasite inhibition.
Molecular Detection for Unconcentrated Gas With ppm Sensitivity Using 220-to-320-GHz Dual-Frequency-Comb Spectrometer in CMOS (2018)

Millimeter-wave/terahertz rotational spectroscopy of polar gaseous molecules provides a powerful tool for complicated gas mixture analysis. In this paper, a 220-to-320-GHz dual-frequency-comb spectrometer in 65-nm bulk CMOS is presented, along with a systematic analysis on fundamental issues of rotational spectrometer, including the impacts of various noise mechanisms, gas cell, molecular properties, detection sensitivity, etc. Our comb spectrometer, based on a high-parallelism architecture, probes gas sample with 20 comb lines simultaneously. It does not only improve the scanning speed by 20$\times$, but also reduces the overall energy consumption to 90 mJ/point with 1 Hz bandwidth (or 0.5 s integration time). With its channelized 100-GHz scanning range and sub-kHz specificity, wide range of molecules can be detected. In the measurements, state-of-the-art total radiated power of 5.2 mW and single sideband noise figure of 14.6-19.5 dB are achieved, which further boost the scanning speed and sensitivity. Finally, spectroscopic measurements for carbonyl sulfide (OCS) and acetonitrile (CH$_3$CN) are presented. With a path length of 70 cm and 1 Hz bandwidth, the measured minimum detectable absorption coefficient reaches $\alpha _{\text{gas,min}} = \text{7.2}\times \text{10}^{-7}$ cm$^{-1}$ . For OCS that enables a minimum detectable concentration of 11 ppm. The predicted sensitivity for some other molecules reaches ppm level (e.g., 3 ppm for hydrogen cyanide), or 10 ppt level if gas preconcentration with a typical gain of 10$^5$ is used.
In vivo human carboxylesterase cDNA gene transfer to activate the prodrug CPT-11 for local treatment of solid tumors. (1998)

To evaluate the concept that in vivo transfer of the human carboxylesterase gene will confer sensitivity of a solid tumor to the prodrug CPT-11 (irinotecan), we constructed an adenovirus vector (AdCMV.CE) carrying the human carboxylesterase gene driven by the cytomegalovirus (CMV) promoter, infected A549 human lung adenocarcinoma cells in vitro and in vivo, and evaluated cell growth over time. AdCMV.CE produced a functional carboxylesterase protein in A549 cells in vitro and in vivo as evidenced by ability of lysates from the infected cells to convert CPT-11 to its active metabolite SN-38. The AdCMV.CE vector effectively suppressed A549 cell growth in vitro in the presence of CPT-11. Cell mixing studies demonstrated that when as few as 10% of cells expressed the human carboxylesterase gene, there was bystander growth suppression in the presence of CPT-11. Consistent with these in vitro observations, when AdCMV.CE was directly injected into established subcutaneous A549 tumors in nude mice receiving CPT-11, there was 35% reduction in tumor size at day 27 compared to controls, and a 41% reduction at day 34 (P < 0.01, both comparisons to controls). Similar observations were made with the cell line H157 and HeLa. These observations suggest that local gene transfer of the human carboxylesterase gene and concomitant local administration of CPT-11 may have potential as a strategy for control of the growth of solid tumors.
Laziest write posting on bus-based SMPs (2002)

Private caches are critical components for hiding memory access latency in high performance multiprocessor systems. However, it has been found that, when executing a parallel program, multiple processors may concurrently update a distinct portion of a cache line and cause unnecessary cache invalidation under traditional cache coherence protocols. Such invalidation can be delayed when software enforces a proper order of memory reads and writes using synchronization primitives. Although delaying cache invalidation until the next synchronization instruction avoids unnecessary coherence traffic, it still incurs additional overhead to invalidate and reconcile the inconsistent cache copies. In this paper, a deferred coherence model is presented, which extends the traditional coherence protocol with new partially-modified states to allow multiple writers to simultaneously update different portions of the same cache line. In addition, the proposed model separates the events of write notification and data reconciliation so that the updated data is posted only when another processor asks for the data. Furthermore, an efficient merging mechanism is incorporated to reconcile multiple inconsistent copies of a modified line upon accessing a potentially stale data. Execution-driven simulation of SPLASH-2 applications shows that the deferred coherence model can out-perform the traditional eager coherence model by up to 20%.
Lentiviral Vector Promoter is Decisive for Aberrant Transcript Formation (2017)

Lentiviral vectors hold great promise for the genetic correction of various inherited diseases. However, lentiviral vector biology is still not completely understood and warrants the precise decoding of molecular mechanisms underlying integration and post-translational modification. This study investigated a series of self-inactivating (SIN) and full long terminal repeat (LTR) lentiviral vectors that contained different types of promoters with or without a transgene to gain deeper insights in lentiviral target site selection and potential perturbation of cellular gene expression. Using an optimized nonrestrictive linear amplification-mediated polymerase chain reaction (nrLAM-PCR) protocol, vector structure-dependent integration site profiles were observed upon transduction of mouse lin<sup>-</sup> hematopoietic progenitors in vitro. Initial target site selection mainly depended on the presence of the promoter while being independent of its nature. Despite the increased propensity for read-through transcription of SIN lentiviral vectors, the incidence of viral-cellular fusion transcript formation involving the canonical viral splice donor or cryptic splice sites was reduced in both unselected primary lin<sup>-</sup> cells and transformed 32D cells. Moreover, the strength of the internal promoter in vectors with SIN LTRs is decisive for in vitro selection and for the abundance of chimeric transcripts, which are decreased by moderately active promoters. These results will help to better understand vector biology and to optimize therapeutic vectors for future gene therapy applications.
HYDROGEN-BONDED SUPRAMOLECULAR POLYMERS WITH TUNABLE MATERIAL PROPERTIES (2003)

provide unique opportunities for designing tunable materials. Due to the reversibility of the interactions, the polymer is in continuous equilibrium with its environment and its properties may be adjusted by external stimuli. Furthermore, these systems provide the possibility to mix different monomers to obtain a supramolecular copolymer, or alternatively, create branched or reversibly crosslinked polymers by adding monomers with higher functionalities. Both approaches allow tuning of the material properties of the polymer by simple blending, without the need for additional synthesis, as would be required for covalent copolymers. Previously, we have reported functionalization of low molecular weight bifunctional telechelic polymers with strongly quadruple hydrogen bonding 2-ureido-4[1H]-pyrimidinone (UPy) units. 4 The materials thus obtained combine excellent mechanical properties at room temperature with good processability at elevated temperature, because weakening of the hydrogen bonds at high temperatures results in a low melt viscosity. Well-defined UPyterminated polystyrene (PS), polyisoprene (PI) and PS-b-PI block copolymers were synthesized and characterized by Yamauchi et al. 5 The authors report an increase in glass transition temperature (Tg) and melt viscosity upon functionalization. Furthermore, they propose that the functionalized polymers form aggregates in the melt state. Here we describe reversibly crosslinked supramolecular polymers based on bifunctional and trifunctional telechelic polyesters with UPy end groups. Thermal and mechanical properties of these materials were studied and were found to be tunable by changing the ratio between bifunctional and trifunctional macromonomers.
ULTRASONOGRAPHIC DETECTION OF TOOTH FLAWS (2010)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation C. A. Bertoncini, M. K. Hinders, S. R. Ghorayeb; ULTRASONOGRAPHIC DETECTION OF TOOTH FLAWS. AIP Conf. Proc. 22 February 2010; 1211 (1): 1559–1565. https://doi.org/10.1063/1.3362254 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Rapid thermal processing : science and technology (1993)

This is the first definitive book on rapid thermal processing (RTP), an essential namufacturing technology for single-wafer processing in highly controlled environments. Written and edited by nine experts in the field, this book covers a range of topics for academics and engineers alike, moving from basic theory to advanced technology for wafer manufacturing. The book also provides new information on the suitability or RTP for thin film deposition, junction formation, silicides, epitaxy, and in situ processing. Complete discussions on equipment designs and comparisons between RTP and other
FimH‐mediated autoaggregation of <i>Escherichia coli</i> (2001)

Autoaggregation is a phenomenon thought to contribute to colonization of mammalian hosts by pathogenic bacteria. Type 1 fimbriae are surface organelles of Escherichia coli that mediate d-mannose-sensitive binding to various host surfaces. This binding is conferred by the minor fimbrial component FimH. In this study, we have used random mutagenesis to identify variants of the FimH adhesin that confer the ability of E. coli to autoaggregate and settle from liquid cultures. Three separate autoaggregating clones were identified, all of which contained multiple amino acid changes located within the N-terminal receptor-binding domain of FimH. Autoaggregation could not be inhibited by mannose, but was inhibited by growth at temperatures at or below 30 degrees C. Using green fluorescent protein (GFP) as a reporter, we show that the autoaggregating clones do not mix with wild-type fimbriated cells. Electron microscopy shows that autoaggregating cells produce fimbriae with a twisted and entangled appearance. We present evidence that autoaggregating versions of FimH also occur in nature. Our results stress the highly adaptive nature of the ubiquitous FimH adhesin.
Practical Method to Limit Tip–Sample Contact Stress and Prevent Wear in Amplitude Modulation Atomic Force Microscopy (2013)

Amplitude modulation atomic force microscopy (AM-AFM) is one of the most popular AFM modes because of the reduced tip-sample interaction, compared to contact mode AFM, and the ability to acquire high-resolution images while interrogating the sample's material composition through phase imaging. Despite the reduced tip-sample interaction, tip and sample wear can occur through gradual atomic scale processes that can significantly accumulate due to the high frequency of the tip-sample interaction and through high intermittent contact stresses. Starting from existing analytical formulations, we introduce a method for selecting an appropriate probe and free oscillation amplitude that avoids exceeding a critical contact stress to minimize tip/sample damage. The approach is presented for the case of both a Hertzian- and a Derjaguin-Müller-Toporov-like tip-sample contact. Stress maps and related simplified formulas are provided that enable one to determine allowable free oscillation amplitudes to stay below a target contact stress for given cantilever and sample parameters (combined into a single "cantilever-sample constant" that we introduce). Experimental results show how sharp silicon tips, either uncoated or coated with diamond-like carbon and silicon nitride, interacting with a hard and wear-resistant sample (ultrananocrystalline diamond) can be preserved while attaining high-quality AM-AFM images by using our proposed scheme. We also show that using our analysis to select parameters that exceed the target contact stress indeed leads to significant tip wear. This method provides AM-AFM users with a better understanding of contact stresses and enables selection of AM-AFM cantilevers and experimental parameters that preserve the tip for long periods of use and prevents the sample from damage.
PROPERTIES OF MARAGING STEEL 300 PRODUCED BY POWDER METALLURGY (1974)

Powders of 300-grade maraging steel have been produced by two different atomizing processes and consolidated by hot isostatic pressing, extrusion, hot rolling, or a combination of these methods. The tensile properties of the PM alloys were equivalent or superior to those of the conventionally cast and forged alloys, but no improvement in fatigue and fracture-toughness properties was gained. Fine grain sizes (1–5 μm) were obtained by hot rolling either conventionally processed or PM bars of grade-300 maraging steel at 760, 820, and 870°C, followed by air-cooling. In all cases, the tensile properties and fracture toughness were improved by grain-size refinement.