gebhart/patrepeval huggingface dataset:
Performance modeling of virtualized custom logic computations (2014)

Virtualization of custom logic computations (i.e, by sharing a fixed function across distinct data streams) provides a means of computing multiple streams using shared hardware resources. The hardware can be context-switched to support virtualization using C-slow techniques (fine-grained context-switching) or by adding a secondary memory (coarse-grained context-switching). The performance of these computations depends on the circuit, technology, number of pipeline stages, number of streams, cost of a context switch, scheduling period, and arrival rate. In this paper, we analyze a virtualized hardware design and develop a set of analytic modeling equations for predicting the performance of these circuits. We then validate the model equations using a discrete-event simulation.
A component framework for satellite on-board software (2003)

This paper advocates a new approach to satellite software design based on object-oriented framework technology and describes early results from a project for the European Space Agency (ESA) to design a software framework for satellite attitude and orbit control systems (AOCS). Frameworks are collections of components with pre-defined cooperations among them. They make architecture (as opposed to mere code) reuse possible. The framework concept is being tested in a redesign of the AOCS software. This paper illustrates it by describing the implementation of telecommand handling, telemetry handling, and operational mode management.
Function of Cytochrome P450 Enzymes MycCI and MycG in Micromonospora griseorubida, a Producer of the Macrolide Antibiotic Mycinamicin (2012)

The cytochrome P450 enzymes MycCI and MycG are encoded within the mycinamicin biosynthetic gene cluster and are involved in the biosynthesis of mycinamicin II (a 16-membered macrolide antibiotic produced by Micromonospora griseorubida). Based on recent enzymatic studies, MycCI is characterized as the C-21 methyl hydroxylase of mycinamicin VIII, while MycG is designated multifunctional P450, which catalyzes hydroxylation and also epoxidation at C-14 and C-12/13 on the macrolactone ring of mycinamicin. Here, we confirm the functions of MycCI and MycG in M. griseorubida. Protomycinolide IV and mycinamicin VIII accumulated in the culture broth of the mycCI disruption mutant; moreover, the mycCI gene fragment complemented the production of mycinamicin I and mycinamicin II, which are produced as major mycinamicins by the wild strain M. griseorubida A11725. The mycG disruption mutant did not produce mycinamicin I and mycinamicin II; however, mycinamicin IV accumulated in the culture broth. The mycG gene was located immediately downstream of the self-resistance gene myrB. The mycG gene under the control of mycGp complemented the production of mycinamicin I and mycinamicin II. Furthermore, the amount of mycinamicin II produced by the strain complemented with the mycG gene under the control of myrBp was approximately 2-fold higher than that produced by the wild strain. In M. griseorubida, MycG recognized mycinamicin IV, mycinamicin V, and also mycinamicin III as the substrates. Moreover, it catalyzed hydroxylation and also epoxidation at C-14 and C-12/13 on these intermediates. However, C-14 on mycinamicin I was not hydroxylated.
Store‐Operated Calcium Entry Upregulated IL6 Expression in Glomerular Mesangial Cells through NF‐κB Pathway (2020)

Background IL6 is a pleotropic cytokine and functions as a pro‐ as well as anti‐inflammatory mechanism depending on the cell type or the specific pathological environment. It is unclear if a particular signaling pathway confers IL6 with this property. Immunological and inflammatory mechanisms play a significant role in the development of diabetic nephropathy (DN). Locally produced cytokines/chemokines contributes to the early changes and histological impairment in DN. Glomerular mesangial cell (MC) is a major cell type in glomerulus to produce cytokines/chemokines in response to diabetes and a major contributor to mesangial expansion in DN. We have previously demonstrated that the Orai‐1 mediated store‐operated calcium entry (SOCE) suppressed ECM protein production by MCs. The aim of this study was to determine whether and how SOCE in MCs regulated IL6 production by MCs. Methods Orai1, the channel protein mediating SOCE in MCs was knocked down using the targeted nanoparticle‐siRNA delivery system in wild type C57BLKS/J mice at the age of 16 weeks. Immunohistochemistry was performed on the paraffin embedded kidney sections to examine glomerular IL6 expression. In cultured human MCs, the expression of IL6 was examined in culture media and whole cell lysates using ELISA and Western blot analysis, respectively in the presence of normal glucose (5 mM D‐glucose + 20 mM L‐glucose) with/without an activator (thapsigargin at 1 μM) or inhibitor (GSK‐7975A 10 μM) of SOCE for 15 hrs. To determine the role of NF‐κB in SOCE effects on IL6 production, human MCs were treated with an inhibitor of NF‐κB, helenaline or siRNA against p65 subunit of NF‐κB. Furthermore, the effect of SOCE on the nuclear translocation of p65 was examined by assessing abundance of nuclear p65 protein in response to activation and inhibition of SOCE. Results The IL6 expression level was reduced in the glomeruli of the mice treated with nanoparticle/Orai1 siRNA for 2 weeks compared to that in the control mice. In cultured human MCs, thapsigargin significantly increased IL‐6 level in supernatant media and in whole cell lysates of MCs, and this effect was attenuated by GSK 7975‐A, a selective inhibitor of SOCE. However, tunicamycin, an ER stress inducer did not alter the amount of IL6 as thapsigargin did. Treatment with helenaline, an inhibitor of NF‐κB pathway, or knockdown of p65, a subunit of NF‐κB significantly blunted the thapsigargin‐induced increase in IL6 protein abundance. Moreover, thapsigargin stimulated the nuclear translocation of p65 in human MCs. Conclusion Orai1‐mediated SOCE positively regulates IL6 production by MCs through activation of NF‐κB pathway. Support or Funding Information Research Support: NIH/NIDDK (1RO1 DK115424); AHA Southwest Affiliate.
Reliable Synthesis of Various Nucleoside Diphosphate Glycopyranoses (2009)

A reliable and high yielding synthetic pathway for the synthesis of the biologically highly important class of nucleoside diphosphate sugars (NDP-sugars) was developed by using various cycloSal-nucleotides 1 and 9 as active ester building blocks. The reaction with anomerically pure pyranosyl-1-phosphates 2 led to the target NDP-sugars 20-45 in a nucleophilic displacement reaction, which cleaves the cycloSal moiety in anomerically pure forms. As nucleosides cytidine, uridine, thymidine, adenosine, 2'-deoxy-guanosine and 2',3'-dideoxy-2',3'-didehydrothymidine were used while the phosphates of D-glucose, D-galactose, D-mannose, D-NAc-glucosamine, D-NAc-galactosamine, D-fucose, L-fucose as well as 6-deoxy-D-gulose were introduced.
Dissociation of iridium(III) phosphorescent emitters upon adsorption on Cu(110) revealed by scanning tunneling microscopy (2006)

The phosphorescent emitters used in organic light emitting diodes (OLEDs) play a crucial role for tuning the color and the luminescence intensity. The authors have investigated by scanning tunneling microscopy the adsorption of iridium(III) phosphorescent emitter molecules used in OLEDs on a partly oxidized Cu(110) surface. Surprisingly they find that 50% of the emitters have dissociated upon adsorption at the substrate. The findings suggest that the decrease in the lifetime of OLEDs, which are manufactured by vacuum vaporization technique, is due to the dissociation of emitter molecules present in the device.
Electrochemical Deposition and Spectroelectrochemical Response of Bromophenol Blue Films on Gold (2015)

Abstract Bromophenol blue (BPB) was electropolymerized onto a Au substrate. The effects of voltammetric cycle number, BPB concentration, and pH on film thickness, density, optical absorption, and electrochemical susceptibility were evaluated, and favorable deposition conditions were identified. Quantitative measurement of the film mass via quartz crystal microbalance enabled determination of the molar volume and revealed a strong dependence of film density with deposition pH. Finally, electrochemical control of the optical properties of BPB films was demonstrated via in situ spectroelectrochemistry. We believe this is the first demonstration of electropolymerization of pure BPB on Au, and thus the first demonstration of poly(BPB) as an electrochemically switchable optical coating.
A Review of Selected Types of Indoor Air Purifiers in Terms of Microbial Air Contamination Reduction (2022)

Aims: With the ongoing pandemic and increased interest in measures to improve indoor air quality, various indoor air purifiers have become very popular and are widely used. This review presents the advantages and disadvantages of various types of technologies used in air purifiers in terms of reducing microbial contamination. Methods: A literature search was performed using Web of Science, Scopus, and PubMed, as well as technical organizations dealing with indoor air-quality to identify research articles and documents within our defined scope of interest. Relevant sections: The available literature data focus mainly on the efficiency of devices based on tests conducted in laboratory conditions with test chambers, which does not reflect the real dimensions and conditions observed in residential areas. According to a wide range of articles on the topic, the actual effectiveness of air purifiers is significantly lower in real conditions than the values declared by the manufacturers in their marketing materials as well as technical specifications. Conclusions: According to current findings, using indoor air purifiers should not be the only measure to improve indoor air-quality; however, these can play a supporting role if their application is preceded by an appropriate technical and environmental analysis considering the real conditions of its use.
Tm:YVO_4 microchip laser (1995)

When pumped with a 1-W laser diode, a Tm:YVO(4) microchip laser produced 150 mW of 1.92-µm output in a near-diffraction-limited beam at room temperature. Using a Ti:Al(2)O(3) laser to pump the same device, we showed that reducing the temperature of the Tm:YVO(4) from 20 to -30 °C resulted in no measurable change in threshold and increased the slope efficiency by only 20%.
Fucose-Containing Sulfated Polysaccharides from Brown Seaweeds Inhibit Proliferation of Melanoma Cells and Induce Apoptosis by Activation of Caspase-3 in Vitro (2011)

Fucose-containing sulfated polysaccharides (FCSPs) extracted from seaweeds, especially brown macro-algae, are known to possess essential bioactive properties, notably growth inhibitory effects on tumor cells. In this work, we conducted a series of in vitro studies to examine the influence of FCSPs products from Sargassumhenslowianum C. Agardh (FSAR) and Fucus vesiculosus (FVES), respectively, on proliferation of melanoma B16 cells and to investigate the underlying apoptosis promoting mechanisms. Cell viability analysis showed that both FCSPs products, i.e., FSAR and FVES, decreased the proliferation of the melanoma cells in a dose-response fashion, with FSAR being more potent at lower dosages, and FVES being relatively more anti-proliferative than FSAR at higher dosages. Flow cytometric analysis by Annexin V staining of the melanoma cells exposed to the FCSPs products confirmed that both FSAR and FVES induced apoptosis. The FCSPs-induced apoptosis was evidenced by loss of plasma membrane asymmetry and translocation of the cell membrane phospholipids and was accompanied by the activation of caspase-3. The FCSPs bioactivity is proposed to be attributable to distinct structural features of the FCSPs, particularly the presence of sulfated galactofucans (notably in S.henslowianum) and sulfated fucans (notably in F. vesiculosus). This study thus indicates that unfractionated FCSPs may exert bioactive effects on skin cancer cells via induction of apoptosis through cascades of reactions that involve activation of caspase-3.
CANOES: detecting rare copy number variants from whole exome sequencing data (2014)

We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and specificity is comparable to that of XHMM. Moreover, the method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data.
Licensed recombinant hepatitis B vaccines protect chimpanzees against infection with the prototype surface gene mutant of hepatitis B virus (1999)

The emergence in vaccinated individuals of hepatitis B virus (HBV) mutants with amino acid substitutions within the a determinant of the surface protein has raised the possibility that such variants represent neutralization escape mutants. We previously demonstrated that one such mutant HBV, strain AS, with an arginine substituted for glycine at surface gene codon 145, was infectious and pathogenic in seronegative chimpanzees. In the present study, the protective efficacy of licensed hepatitis B vaccines was evaluated against challenge with this mutant virus. Four chimpanzees were immunized with 1 of 2 licensed recombinant hepatitis B vaccines. Shortly after the chimpanzees developed antibodies to hepatitis B surface antigen (anti-HBs), they were challenged intravenously with mutant HBV strain AS. Two unvaccinated chimpanzees served as positive controls. The 4 vaccinated chimpanzees did not develop evidence of HBV infection or hepatitis during 2 years following virus challenge. In contrast, the 2 unvaccinated chimpanzees developed HBV infection and hepatitis. Serum anti-HBs in the vaccinated chimpanzees reacted not only with wild-type surface antigen, but also with mutant surface antigen by competition enzyme-linked immunosorbent assay (ELISA). Thus, immunization of chimpanzees with licensed recombinant hepatitis B vaccines stimulates anti-HBs that is broadly reactive and affords protection against infection with a surface gene mutant of HBV, suggesting that properly immunized individuals are not at significant risk of infection with this prototype variant strain of HBV.
Local Administration of Soluble CD40:Fc to the Salivary Glands of Non-Obese Diabetic Mice Does Not Ameliorate Autoimmune Inflammation (2012)

Although endogenous CD40 is expressed in SG inflammatory foci in the SG of NOD mice, the expression of soluble CD40:Fc did not lead to reduced overall inflammation and/or improved salivary gland function. These data indicate possible redundancy of the CD40 pathway in the SG and suggests that targeting CD40 alone may not be sufficient to alter the disease phenotype.
Direct measurement of 248- and 193-nm excimer-induced densification in silica–germania waveguide blanks: reply to comment (2002)

The criticisms raised by Poumellec and Niay in their Comment on our paper are primarily based on their misreading the original paper. We respond to their concerns and reiterate that Bragg gratings are not formed primarily by compaction from 248-nm exposure. New calculations are presented that corroborate our previous analysis.
Optical Interconnects for Board-Level Signal Distribution at 10 Gb/s Using Hybrid Integration (2006)

A board-level optical-to-electrical prototype for 10 Gb/s signal distribution over each of four channels is demonstrated. An improved multimode interference (MMI) splitter and the simultaneous alignment between waveguides and photodetectors make the prototype fully functional
MANF Is Essential for Neurite Extension and Neuronal Migration in the Developing Cortex (2017)

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER) resident protein with neuroprotective effects. Previous studies have shown that MANF expression is altered in the developing rodent cortex in a spatiotemporal manner. However, the role of MANF in mammalian neurogenesis is not known. The aim of this study was to determine the role of MANF in neural stem cell (NSC) proliferation, differentiation, and cerebral cortex development. We found that MANF is highly expressed in neural lineage cells, including NSCs in the developing brain. We discovered that MANF-deficient NSCs in culture are viable and show no defect in proliferation. However, MANF-deficient cells have deficits in neurite extension upon neuronal differentiation. <i>In vivo</i>, MANF removal leads to slower neuronal migration and impaired neurite outgrowth. <i>In vitro</i>, mechanistic studies indicate that impaired neurite growth is preceded by reduced <i>de novo</i> protein synthesis and constitutively activated unfolded protein response (UPR) pathways. This study is the first to demonstrate that MANF is a novel and critical regulator of neurite growth and neuronal migration in mammalian cortical development.
A Randomized Controlled Trial to Evaluate the Safety and Efficacy of a Novel Inhaled Biologic Therapeutic in Adults with Respiratory Distress Secondary to COVID-19 Infection (2021)

Clinicaltrials.gov identifier: NCT04606784.
SINIR GÜVENLİĞİ İÇİN BÜYÜK VERİ TEKNOLOJİLERİ İLE BORU HATTI TASARIMI (2016)

Developing technology, communication and transportation facilities have led borders to the gradual disappearance. The incidents taking place in different countries go beyond the limits and being felt by large audiences. Solutions to rapidly increasing terrorist attacks and internal turmoil caused security problems in recent years which have become very complicated. Protecting and controlling the borders, finding rapid and comprehensive solutions to illegal border passing problems have become a major problem in many countries. When considering the scope of the border security, it would be understood to examine the data which comes at different times from different sources and types in real time. This can be achieved by a collaboration of different principles. In addition, when large-scale unstructured data analysis also considered for a comprehensive solution, it would be a rational method to develop a pipeline using the Big Data technologies. In this study, we aim to achieve cost-effective, robust, scalable and flexible system to solve the border security problems. The use of Lambda Architecture which provides real time data processing and batch processing capabilities was investigated in border security applications. System development was explained and all information on its principles was provided.
Alpha 1‐adrenergic effects on intracellular pH and calcium and on myofilaments in single rat cardiac cells. (1992)

1. The cellular effects of alpha 1-adrenoceptor stimulation by phenylephrine were studied in the presence of propranolol in single cells isolated from the ventricles of rat hearts. 2. Phenylephrine (10-100 microM) induced a biphasic pattern of inotropism in these cells: a transient negative followed by a sustained positive inotropic effect as usually observed in cardiac tissues. 3. In Snarf-1-loaded cells, phenylephrine induced an alkalinization. This effect was reversible on wash-out and inhibited by prazosin, an alpha 1-adrenoceptor antagonist. 4. The alpha 1-adrenoceptor-mediated increase in intracellular pH (pHi) was 0.1 pH unit in HEPES buffer containing 4.4 mM-NaHCO3 and in Krebs buffer containing 25 mM-NaHCO3. 5. The alkalinization was blocked by the Na(+)-H+ antiport blocker, ethylisopropylamiloride (EIPA). 6. The recovery from an acidosis induced by a NH4Cl pre-pulse was accelerated by phenylephrine. The phenylephrine-induced alkalinization was attributed to activation of the Na(+)-H+ antiport. 7. Despite its ability to increase pHi, phenylephrine did not alter Ca2+ current amplitude and kinetics. 8. Ca2+ transients recorded in Indo-1-loaded cells were not augmented by phenylephrine. Diastolic calcium level was decreased. 9. In single skinned cells, the Ca2+ sensitivity of the contractile proteins was increased by a pre-treatment with phenylephrine even when the alpha 1-adrenoceptor-mediated alkalinizing effect had been prevented by EIPA. 10. These results lead us to propose that the alpha 1-adrenergic-induced positive inotropic response of heart muscle could result from an increased sensitivity of the myofilaments to Ca2+ ions. This alpha 1-adrenoceptor-mediated Ca2+ sensitization could result both from an intracellular alkalinization and from a direct effect on contractile proteins.
Scaling of 32nm low power SRAM with high-K metal gate (2008)

This paper describes SRAM scaling for 32 nm low power bulk technology, enabled by high-K metal gate process, down to 0.149 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 0.124 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . SRAM access stability and write margin are significantly improved through a 50% Vt mismatch reduction, thanks to HK-MG T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">inv</sub> scaling. Cell read current is increased by 70% over Poly-SiON process. Ultra dense cell process window is expanded with optimized contact process. A dual-ground write assist option can additionally enable ultra dense 0.124 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> cell to meet low power application requirements.
Spatially Adaptive De-Normalization Based Shadow Removal from a Single Image (2022)

단일 영상 내 그림자 제거는 영상 처리 및 많은 컴퓨터 시각 분야에서 중요한 문제이다. 이 논문에서는 이러한 그림자를 제거하기 위하여, 추가적인 그림자 감지를 필요로 하지 않는 조건부 적대적 생성 신경망 기반의 새로운 신경망 구조를 제안한다. 제안하는 구조에서는, 신경망 내 다양하게 존재하는 정규화층으로 인해 발생되는, 입력 영상 데이터의 정보 손실 문제를 방지하기 위해 공간 적응적 비정규화 방식을 활용하였고, 그림자 제거와 관련된 공인 데이터 세트를 활용한 다양한 실험들로부터, 제안된 기법이 기존의 신경망 기반의 최신 방법론들과 비교하여 적어도 5㏈ 높은 PSNR 성능을 가지는 것을 확인할 수 있다.
P-Frame Coding with Generalized Difference: A Novel Conditional Coding Approach (2022)

Motion compensated inter frame prediction is a common component of all video coders and greatly reduces temporal redundancy. With the rise of deep learning-based image and video compression, this concept has been successfully taken over from traditional coding approaches. These approaches offer a larger flexibility than traditional transform coding and therefore enable efficient conditional coding. In this work, we develop a novel conditional coding approach based on the generalized difference and generalized sum operators. This approach is a special case of a general conditional coder and has a very small complexity overhead. We also propose an extension which enables dynamic content-adaptive switching between conditional and residual coding. We show that the extended generalized difference coding outperforms both residual and conditional coding, saving 27.8% Bjøntegaard delta rate compared to the former.
Venom Peptides as a Rich Source of Cav2.2 Channel Blockers (2013)

Ca(v)2.2 is a calcium channel subtype localized at nerve terminals, including nociceptive fibers, where it initiates neurotransmitter release. Ca(v)2.2 is an important contributor to synaptic transmission in ascending pain pathways, and is up-regulated in the spinal cord in chronic pain states along with the auxiliary α2δ1 subunit. It is therefore not surprising that toxins that inhibit Ca(v)2.2 are analgesic. Venomous animals, such as cone snails, spiders, snakes, assassin bugs, centipedes and scorpions are rich sources of remarkably potent and selective Ca(v)2.2 inhibitors. However, side effects in humans currently limit their clinical use. Here we review Ca(v)2.2 inhibitors from venoms and their potential as drug leads.