gebhart/patrepeval huggingface dataset:
MK800-62F1, a New Inhibitor of Apoptotic Cell Death, from Streptomyces diastatochromogenes MK800-62F1. I. Taxonomy, Fermentation, Isolation, Physico-chemical Properties and Biological Activity. (2000)

A new compound, MK800-62F1, was isolated from a cultured broth of Streptomyces diastatochromogenes MK800-62F1. It inhibited H2O2-induced apoptosis in human small cell lung carcinoma Ms-1 cells as well as in human T-cell leukemia Jurkat cells. In addition, MK800-62F1 also inhibited camptothecin-induced apoptosis in Jurkat cells, which was mediated by intracellular H2O2 generation. MK800-62F1 did not exhibit antioxidative activity in vitro, suggesting that inhibition of apoptosis by MK800-62F1 was not due to the scavenging of H2O2, rather it was due to the modulation of the downstream event of H2O2 generation.
Simplified and optimized multispectral imaging for 5-ALA-based fluorescence diagnosis of malignant lesions (2016)

5-aminolevulinic acid (5-ALA)-based fluorescence diagnosis is now clinically applied for accurate and ultrarapid diagnosis of malignant lesions such as lymph node metastasis during surgery. 5-ALA-based diagnosis evaluates fluorescence intensity of a fluorescent metabolite of 5-ALA, protoporphyrin IX (PPIX); however, the fluorescence of PPIX is often affected by autofluorescence of tissue chromophores, such as collagen and flavins. In this study, we demonstrated PPIX fluorescence estimation with autofluorescence elimination for 5-ALA-based fluorescence diagnosis of malignant lesions by simplified and optimized multispectral imaging. We computationally optimized observation wavelength regions for the estimation of PPIX fluorescence in terms of minimizing prediction error of PPIX fluorescence intensity in the presence of typical chromophores, collagen and flavins. By using the fluorescence intensities of the optimized wavelength regions, we verified quantitative detection of PPIX fluorescence by using chemical mixtures of PPIX, flavins, and collagen. Furthermore, we demonstrated detection capability by using metastatic and non-metastatic lymph nodes of colorectal cancer patients. These results suggest the potential and usefulness of the background-free estimation method of PPIX fluorescence for 5-ALA-based fluorescence diagnosis of malignant lesions, and we expect this method to be beneficial for intraoperative and rapid cancer diagnosis.
P2‐045: Effect of Bace Inhibitor Treatment on Full‐Length and N‐Truncated AB Species in Cellular and Canine Models (2016)

Cleavage of amyloid precursor protein (APP) by β-site APP cleaving enzyme 1 (BACE1) is the rate-limiting step in the generation of Aβ peptides. Multiple lines of evidence support that accumulation of Aβ is an early and necessary step for initiation of the pathological cascade leading to Alzheimer’s disease (AD). Thus reduced Aβ production by inhibition of BACE1 is pursued as a disease-modifying approach for AD. Aβ peptides exist in a variety of forms, including those showing truncations at the N-terminus. Investigation of treatment effect on various Aβ species is needed for more complete characterization of the pharmacology of Aβ-targeting compounds. We developed immunoassays to measure specifically full-length Aβ (Aβ1-40/42, detection with end-specific antibody JRF/AβN/25), full-length and N-truncated Aβ (Aβx-40/42, detection with 4G8) and Aβ11-40/42 (detection with J&JPRD/hAβ11/1). These assays were utilized to investigate the effect of pharmacological intervention with BACE inhibitors on different Aβ species in supernatant of human neuroblastoma cells expressing WT APP695, and in cerebrospinal fluid (CSF) from canines. Our results showed that Aβ11-40, a product of BACE1 cleavage at the β’ site, was reduced to a similar extent as Aβ1-40 after BACE inhibitor treatment in both cell supernatant and dog CSF. When comparing reductions in Aβ1-40/42 and Aβx-40/42 species, differences were noted between cellular and canine models. Comparable reductions of Aβ1-40/42 as well as Aβx-40/42 species were observed in dog CSF after BACE inhibitor treatment. In cell culture supernatant however, BACE inhibitor treatment resulted in a less pronounced effect on Aβx-40/42 species as compared to full-length Aβ1-40/42 species. BACE inhibitor treatment resulted in a similar level of inhibition of β and β’ APP cleavage by BACE1 in the cellular and canine model. Differential effects on reduction of Aβ1-40/42 versus Aβx-40/42 species were shown specifically in the cellular model, underscoring the importance of investigating compound effects across a variety of preclinical in vitro and in vivo models. The reasons for the observed difference between models are currently not clear, but might include APP overexpression in the cellular model and/or different ratios of full-length versus N-truncated Aβ species in cell supernatant compared to dog CSF.
Control of morphology and size of microporous framework MIL-53(Al) crystals by synthesis procedure (2015)

Two methods for the preparation of microporous phenylenecarboxylate framework MIL-53(Al), solvothermal high-pressure procedure and synthesis at atmospheric pressure, were compared in respect of crystal morphology and size. Lower reaction time and temperature featured microwave method providing nanocrystallites of homogeneous distribution in shape and size.
A unifying model for mTORC1-mediated regulation of mRNA translation (2012)

he mTOR complex 1 (mTORC1) kinase nucleates a pathway that promotes cell growth and proliferation and is the target of rapamycin, a drug with many clinical uses. mTORC1 regulates messenger RNA translation, but the overall translational program is poorly defined and no unifying model exists to explain how mTORC1 differentially controls the translation of specific mRNAs. Here we use high-resolution transcriptome-scale ribosome profiling to monitor translation in mouse cells acutely treated with the mTOR inhibitor Torin 1, which, unlike rapamycin, fully inhibits mTORC1. Our data reveal a surprisingly simple model of the mRNA features and mechanisms that confer mTORC1-dependent translation control. The subset of mRNAs that are specifically regulated by mTORC1 consists almost entirely of transcripts with established 5′ terminal oligopyrimidine (TOP) motifs, or, like Hsp90ab1 and Ybx1, with previously unrecognized TOP or related TOP-like motifs that we identified. We find no evidence to support proposals that mTORC1 preferentially regulates mRNAs with increased 5′ untranslated region length or complexity. mTORC1 phosphorylates a myriad of translational regulators, but how it controls TOP mRNA translation is unknown. Remarkably, loss of just the 4E-BP family of translational repressors, arguably the best characterized mTORC1 substrates, is sufficient to render TOP and TOP-like mRNA translation resistant to Torin 1. The 4E-BPs inhibit translation initiation by interfering with the interaction between the cap-binding protein eIF4E and eIF4G1. Loss of this interaction diminishes the capacity of eIF4E to bind TOP and TOP-like mRNAs much more than other mRNAs, explaining why mTOR inhibition selectively suppresses their translation. Our results clarify the translational program controlled by mTORC1 and identify 4E-BPs and eIF4G1 as its master effectors.
Freedom in Tapestrea! Voice-Aware Track Manipulations. (2009)

Sinusoidal tracks in TAPESTREA have too long been oppressed, unable to choose which other tracks they hang out with, and only able to be modified in fixed groups. They had no say in their own lives, no individuality. That ends today. We advocate FREEDOM in TAPESTREA by way of VTAPS, where every track can be interacted with as a distinct, FREE entity. Only thus can it contribute fully to the larger sound scene. Please join our movement by downloading TAPESTREA at
ShrinkWrap: Compiler-Enabled Optimization and Customization of Soft Memory Interconnects (2013)

Today's FPGAs lack dedicated on-chip memory interconnects, requiring users to (1) rely on inefficient, general-purpose solutions, or (2) tediously create an application-specific memory interconnect for each target platform. The CoRAM architecture, which offers a general-purpose abstraction for FPGA memory management, encodes high-level application information that can be exploited to generate customized soft memory interconnects. This paper describes the ShrinkWrap Compiler, which analyzes a CoRAM application for its connectivity and bandwidth requirements, enabling synthesis of highly-tuned area-efficient soft memory interconnects.
Joint Content-Adaptive Dictionary Learning And Sparse Selective Extrapolation For Cross-Spectral Image Reconstruction (2020)

Numerous applications deal with distorted images, e.g., during transmission over lossy channels in image coding, or to reconstruct occlusions in multi-color multi-view imaging scenarios. In many cases, not all spectral channels are distorted, or the losses distribute differently between the channels. Recently, efforts were made to develop reference guided approaches to reconstruct distorted spectral content. However, these methods are only able to exploit information from a single reference, even if there are multiple spectral components available that could be used for reconstruction. To overcome this limitation, a novel method is proposed in this paper, which introduces a content-adaptive dictionary learning approach that is applicable to an arbitrary number of references. With the novel approach, an average PSNR gain of approx. 1.5 dB is achieved in comparison to the best recently published state-of-the-art methods for a single reference component. Moreover, the presence of multiple guidance channels can enhance the reconstruction by another 6 dB on average. At the same time, the complexity of the novel algorithm is significantly lower than for previously published methods.
Decreased Serum Levels of P-Selectin and Eosinophil Cationic Protein in Patients with Mild Asthma after Inhaled Salbutamol (2004)

We conclude that decreases in P-selectin and ECP may have different kinetics, suggesting different pathways of action of salbutamol. We judge that P-selectin may be used as a sensitive marker in mild asthma.
Psychosocial Risk Factors and Retinal Microvascular Signs: The Multi-Ethnic Study of Atherosclerosis (2009)

The association between psychosocial risk factors and retinal microvascular signs was examined in the Multi-Ethnic Study of Atherosclerosis. Subjects were recruited from Baltimore, Maryland; Chicago, Illinois; Forsyth County, North Carolina; Los Angeles County, California; New York, New York; and St. Paul, Minnesota. Levels of depressive symptoms, trait anger, trait anxiety, chronic burdens, emotional support, and cynical distrust were assessed by questionnaire (from July 2000 to July 2002). Digital retinal images (from August 2002 to January 2004) from 6,147 participants were used to evaluate retinopathy and retinal vascular caliber. After controlling for potential confounding factors, the authors found that subjects without access to emotional support (Enriched Social Support Instrument score of <19 vs. > or = 19) had 60% greater odds of retinopathy (odds ratio = 1.6, 95% confidence interval (CI): 1.3, 2.0). Subjects with high Spielberger trait-anxiety scale scores (> or = 22 vs. < or = 14) and subjects with high depressive symptoms (Center for Epidemiology Studies Depression Scale score, > or = 16 vs. <16) were also more likely to have retinopathy (odds ratio = 1.4, 95% CI: 1.1, 1.9 and odds ratio = 1.5, 95% CI: 1.2, 1.9), respectively. In this cross-sectional study, lack of emotional support, increased trait anxiety, and more depressive symptoms were associated with retinopathy signs, independently of other known risk factors.
A strategy for characterization and evaluation of ESD robustness of CMOS semiconductor technologies (2003)

This paper proposes an ESD technology strategy for characterization, evaluation and benchmarking the ESD "robustness" of CMOS semiconductor technologies. The ESD methodology uses a set of CMOS "building block" ESD test structures, matrices of critical ESD layout variables, electrical characterization parameters, and testing and extraction procedures, and ESD metrics. This work is the first step in the development of a common ESD language.
Relationship between electrical bandwidth and FEC overhead in a 100GbE digital coherent transceiver (2010)

The finite electrical bandwidth of a digital coherent transceiver constrains the maximum FEC overhead. We investigate through simulations of a 100GbE system employing PDM-QPSK the impact that electrical bandwidth has on the optimal code rate which minimizes the required OSNR.
Characterization and modeling of mechanical stress in silicon-based devices (2009)

In this paper we show a self-consistent methodology to characterize the stress-induced mobility variation in silicon-based devices. The synergy among different experimental techniques (the application of an external mechanical stress and the measure of the process-induced stress), theoretical calculations (based on the finite elements method and the band structure calculation), and silicon validation (given by particular sets of test structures) is the strength of the characterization tool we propose.
A Multicenter Investigation Examining American Urological Association Recommended Antibiotic Prophylaxis vs Nonstandard Prophylaxis in Preventing Device Infections in Penile Prosthesis Surgery in Diabetic Patients (2020)

Diabetic men with erectile dysfunction who received standard AUA prophylaxis for penile prosthesis surgery had significantly greater odds of experiencing a postoperative device infection and device explantation compared to patients who received nonstandard prophylaxis. Our study provides a strong rationale for a prospective investigation to establish the most appropriate prophylaxis strategy in penile prosthesis surgery.
Measurement of OS services and its application to performance modeling and analysis of integrated embedded software (2003)

Performance analyses for embedded software construction with existing components require knowledge of performance characteristics of both application software and operating system (OS) services, especially those services that are critical for real-time applications. Since end users normally do not control the structure and implementation of OS services, but have to use them to meet the system-level performance constraints, it is essential and critical to characterize the performance of OS services with measurements. As such measurements are taken for performance analysis, not for comparison, the measurement methods should be different from those traditionally, used for comparison. In this paper we present an end-to-end method for measuring the performance of timing and scheduling services in selected real-time OSs for the performance modeling and analysis. The proposed method takes the factors of both OS implementations and application configurations into account to obtain the measured performance close to what applications will experience at runtime. The results have shown that the performance characteristics of OS services can be measured without instrumenting the kernel source code, and hence, can be reused for the analysis of a family of applications.
Overexpression of an Archaeal Geranylgeranyl Diphosphate Synthase inEscherichia coliCells (1998)

An archaeal geranylgeranyl diphosphate synthase was overexpressed in Escherichia coli cells as fusion proteins. These fusion proteins retained their thermostability and had higher specific activity than did a partially purified native enzyme Previously reported. We purified 24.3 mg of MBP (maltose-binding protein)-fusion protein and 5.4 mg of GST (glutathione S-transferase)-fusion protein from a one-liter culture of E. coli. The MBP-fusion proteins existed in dimer, tetramer, octamer, or dodecamer form, and their product specificities were altered according to the oligomerization. The MBP-fusion protein has protease-sensitive sites in the portion corresponding to geranylgeranyl diphosphate synthase.
Morphometric analysis of gap junction density in human myometrium at term (1994)

In the human myometrium, the formation of gap junctions in the various stages of labor and, in correlation with the concentration of progesterone in the maternal blood, has not been described adequately. The accepted hypothesis that raised concentrations of progesterone in maternal blood in animals prevent the formation of gap junctions was scrutinized in human myometrium. Myometrial tissue was examined by electron microscopy for the presence of gap junctions and analyzed morphometrically in 17 women who had an elective or emergency cesarean operation at the 38th or 39th week of pregnancy. The concentrations of progesterone and estradiol in the maternal and cord blood was measured by means of radioimmunoassay. The frequency and area of gap junctions varied in relation to the presence or absence of labor. In the myometrium of women in labor, gap junctions were most frequent (5.2/1000 microns of cell membrane), their area largest (0.32 microns 2/1000 microns of cell membrane) and their fractional area greatest (0.20%). When the women were not in genuine labor or when contractions were weak, the percentage fractional areas of gap junctions were low (0.020-0.090) and the gap junctions very small. In the pre- and active phases of labor, the concentration of progesterone in maternal blood was significantly higher (p < 0.025 and 0.03 respectively) than in women who were not in labor. Hence, despite high concentrations of progesterone in the maternal and cord blood at term, the myometrium presented numerous gap junctions of relatively large area.
The ATHENA x-ray integral field unit (X-IFU) (2018)

The X-ray Integral Field Unit (X-IFU) is the high resolution X-ray spectrometer of the ESA Athena X-ray observatory. Over a field of view of 5’ equivalent diameter, it will deliver X-ray spectra from 0.2 to 12 keV with a spectral resolution of 2.5 eV up to 7 keV on ∼ 5” pixels. The X-IFU is based on a large format array of super-conducting molybdenum-gold Transition Edge Sensors cooled at ∼ 90 mK, each coupled with an absorber made of gold and bismuth with a pitch of 249 &mu;m. A cryogenic anti-coincidence detector located underneath the prime TES array enables the non X-ray background to be reduced. A bath temperature of ∼ 50 mK is obtained by a series of mechanical coolers combining 15K Pulse Tubes, 4K and 2K Joule-Thomson coolers which pre-cool a sub Kelvin cooler made of a 3He sorption cooler coupled with an Adiabatic Demagnetization Refrigerator. Frequency domain multiplexing enables to read out 40 pixels in one single channel. A photon interacting with an absorber leads to a current pulse, amplified by the readout electronics and whose shape is reconstructed on board to recover its energy with high accuracy. The defocusing capability offered by the Athena movable mirror assembly enables the X-IFU to observe the brightest X-ray sources of the sky (up to Crab-like intensities) by spreading the telescope point spread function over hundreds of pixels. Thus the X-IFU delivers low pile-up, high throughput (&lt; 50%), and typically 10 eV spectral resolution at 1 Crab intensities, i.e. a factor of 10 or more better than Silicon based X-ray detectors. In this paper, the current X-IFU baseline is presented, together with an assessment of its anticipated performance in terms of spectral resolution, background, and count rate capability. The X-IFU baseline configuration will be subject to a preliminary requirement review that is scheduled at the end of 2018.
Hybrid coherence for scalable multicore architectures (2011)

This dissertation describes a cache architecture and memory model for 1000-core microprocessors. Our approach exploits workload characteristics and programming model assumptions to build a hybrid memory model that incorporates features from both software-managed coherence schemes and hardware-managed cache coherence. The goal is to achieve the scalability found in compute accelerators, which support relaxed ordering of memory operations and programmermanaged coherence, while providing a programming interface that is akin to the strongly ordered cache coherent memory models found in general-purpose multicore processors today. The research presented in this dissertation supports the following thesis: To be scalable and programmable, future multicore systems require a cached, singleaddress space memory hierarchy. A hybrid software and hardware approach to coherence management is required to support such a memory hierarchy in 1000core processors and is achievable only by leveraging the characteristics of target
Hardware efficient auto-tuned linear-gain based minimum deviation digital controller for indirect energy transfer converters (2017)

This paper introduces a robust, hardware-efficient auto-tuned digital controller applicable to various hard switching dc-dc converters, including indirect energy transfer topologies. Unlike existing fast transient controllers for indirect energy transfer converters, the controller achieves fast transient response and practically minimum deviation of the output voltage without depending on information about converter parameters, i.e. inductor and output capacitor values. This is achieved by utilizing an auto-tuned non-linear controller that, based on the load-step information during a transient, finds the switching sequence for the converter to ramp up/down the inductor current to its new steady state average value in a single on/off switching action. Experimental results obtained from a 1.5 V to 3.3 V, 1A, 500 kHz boost prototype verify response with practically minimum output voltage deviation and demonstrate a more than 50% reduction of both output voltage deviation and recovery time compared to a voltage mode, fast PID-based controller.
Resonant Transmission of Ring Aperture for Switching Terahertz Waves (2011)

We demonstrated extraordinary THz transmission through ring apertures on metal film. Transmission of 60% was obtained with an aperture-to-area ratio of only 1.4%. Silicon-based electro-optic switch for THz waves can be built with this structure.
Applying dynamical systems techniques to real ocean drifters (2022)

Abstract. This paper presents the first comprehensive comparison of several different dynamical-systems-based measures of stirring and Lagrangian coherence, computed from real ocean drifters. Seven commonly used methods (finite-time Lyapunov exponent, trajectory path length, trajectory correlation dimension, trajectory encounter volume, Lagrangian-averaged vorticity deviation, dilation, and spectral clustering) were applied to 135 surface drifters in the Gulf of Mexico in order to map out the dominant Lagrangian coherent structures. Among the detected structures were regions of hyperbolic nature resembling stable manifolds from classical examples, divergent and convergent zones, and groups of drifters that moved more coherently and stayed closer together than the rest of the drifters. Many methods highlighted the same structures, but there were differences too. Overall, 5 out of 7 methods provided useful information about the geometry of transport within the domain spanned by the drifters.