gebhart/patrepeval huggingface dataset:
Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus (2012)

Bacillus cereus strains elaborate pili on their surface using a mechanism of sortase-mediated cross-linking of major and minor pilus components. Here we used a combination of electron microscopy and atomic force microscopy to visualize these structures. Pili occur as single, double or higher order assemblies of filaments formed from monomers of the major pilin, BcpA, capped by the minor pilin, BcpB. Previous studies demonstrated that within assembled pili, four domains of BcpA - CNA(1), CNA(2), XNA and CNA(3) - each acquire intramolecular lysine-asparagine isopeptide bonds formed via catalytic glutamic acid or aspartic acid residues. Here we showed that mutants unable to form the intramolecular isopeptide bonds in the CNA(2) or CNA(3) domains retain the ability to form pilus bundles. A mutant lacking the CNA(1) isopeptide bond assembled deformed pilin subunits that failed to associate as bundles. X-ray crystallography revealed that the BcpA variant Asp(312) Ala, lacking an aspartyl catalyst, did not generate the isopeptide bond within the jelly-roll structure of XNA. The Asp(312) Ala mutant was also unable to form bundles and promoted the assembly of deformed pili. Thus, structural integrity of the CNA(1) and XNA domains are determinants for the association of pili into higher order bundle structures and determine native pilus structure.
Omics‐based profiling of carcinoma of the breast and matched regional lymph node metastasis (2008)

Axillary lymph node (ALN) status is currently used as an important clinical indicator of breast cancer prognosis. However, the molecular mechanisms underlying lymph node metastasis are poorly understood and the relationship between ALN metastasis and the primary tumor remains unclear. In an effort to reveal structural changes in the genome and related protein responses that may drive regional metastatic progression we have analyzed matched pairs of primary breast tumors and ALN metastases both at the genomic and proteomic levels using comparative genomic hybridization (CGH) array, quantitative high-resolution 2-D PAGE in combination with MS, and immunohistochemistry (IHC). Array CGH revealed a remarkable similarity in genomic aberration profiles between the matched primary tumors and the ALN metastases. Quantitative profiling of 135 known proteins also revealed striking similarities in their overall expression patterns, although we observed distinct changes in the levels of individual proteins in some sample pairs. The remarkable similarities of the overall genomic and proteomic profiles between primary tumors and matched ALN metastases are taken to suggest that, in general, key biological characteristics of the primary breast tumor are maintained in the corresponding lymph node metastases. Given that the omics-based technologies are oblivious to changes that only occur in minor cellular subsets we validated the proteomic data using IHC, which provides protein expression information with a valuable topological component. Besides confirming the omics-derived data, the IHC analysis revealed that in two cases the ALN metastases may have been derived from a distinct minor cell subpopulation present in the primary tumor rather than from the bulk of it.
Supplementary Data from Repurposing the FDA-Approved Antiviral Drug Ribavirin as Targeted Therapy for Nasopharyngeal Carcinoma (2023)

&lt;p&gt;Supplementary Figures 1-6&lt;/p&gt;
Application of Parallel Multiparametric Cell-Based FLIPR Detection Assays for the Identification of Modulators of the Muscarinic Acetylcholine Receptor 4 (M4) (2015)

Muscarinic acetylcholine receptors (mAChRs) have long been viewed as viable targets for novel therapeutic agents for the treatment of Alzheimer's disease and other disorders involving impaired cognitive function. In an attempt to identify orthosteric and allosteric modulators of the muscarinic acetylcholine receptor M(4) (M(4)), we developed a homogenous, multiparametric, 1536-well assay to measure M(4) receptor agonism, positive allosteric modulation (PAM), and antagonism in a single well. This assay yielded a Z' of 0.85 ± 0.05 in the agonist, 0.72 ± 0.07 in PAM, and 0.80 ± 0.06 in the antagonist mode. Parallel screening of the M(1) and M(5) subtypes using the same multiparametric assay format revealed chemotypes that demonstrate selectivity and/or promiscuity between assays and modalities. This identified 503 M(4) selective primary agonists, 1450 PAMs, and 2389 antagonist hits. Concentration-response analysis identified 25 selective agonists, 4 PAMs, and 41 antagonists. This demonstrates the advantages of this approach to rapidly identify selective receptor modulators while efficiently removing assay artifacts and undesirable compounds.
高度な設計と解析手法・高度なデータ構造・グラフアルゴリズム (2012)

４ 高度な設計と解析の手法（動的計画法；貪欲アルゴリズム；ならし解析） ５ 高度なデータ構造（Ｂ木；フィボナッチヒープ；ｖａｎ Ｅｍｄｅ Ｂｏａｓ木 ほか） ６ グラフアルゴリズム（基本的グラフアルゴリズム；最小全域木；単一始点最短路問題 ほか）
P4‐315: Evaluating amyloid‐beta processing using novel gamma‐secretase modulators in preclinical animal models (2015)

A considerable body of genetic evidence supports the pivotal role of γ-secretase in AD. Through the proteolytic cleavage of APP, the γ-secretase enzyme complex is responsible for producing Aβ peptides containing various carboxy-termini. As the final step in the production of Aβ, the γ-secretase complex represents a compelling target for pharmacological intervention aimed at reducing the levels of Aβ42, the most amyloidogenic Aβ isoform, thereby slowing or halting deposition of amyloid plaques and subsequent neuronal damage. Our goal was to use novel γ-secretase modulator (GSM) compounds to assess Aβ modulation, its impact in a plaque-bearing mouse model and multiple preclinical species. The effect of 2 months of GSM treatment on Aβ modulation and brain plaque-progression was assessed in PS1-APP mice by 2-photon imaging, immunohistochemistry and DELFIA. The effect of acute GSM dosing was assessed in brain and CSF by measuring Aβ modulation in multiple preclinical species by IP/MALDI-MS and DELFIA. Chronic administration of a GSM halts amyloid plaque accumulation in a transgenic mouse model of Alzheimer's disease as evaluated by 2-photon imaging and immunohistochemistry. Biochemical analysis of brain homogenates by DELFIA indicates Aβ42 and Aβ40 lowering in parenchyma and vascular brain fractions and no apparent accumulation of shorter Aβ fragments following chronic GSM treatment. In addition, acute administration of a GSM compound in multiple preclinical species revealed a complex shift in the brain and CSF of up to fifteen Aβ peptides as measured by DELFIA and IP/MALDI-MS. The efficacy data from preclinical models provides evidence for a potentially beneficial effect of GSM treatment in AD, by shifting cleavage away from Aβ42 and Aβ40, toward production of carboxy-terminal truncated forms Aβ37 and Aβ38; these fragments are considered less amyloidogenic and neurotoxic forms of Aβ.
CARAT: Context-aware runtime adaptive task migration for multi core architectures (2011)

Multi core architectures that are built to reap performance and energy efficiency benefits from the parallel execution of applications often employ runtime adaptive techniques in order to achieve, among others, load balancing, dynamic thermal management, and to enhance the reliability of a system. Typically, such runtime adaptation in the system level requires the ability to quickly and consistently migrate a task from one core to another. For distributed memory architectures, the policy for transferring the task context between source and destination cores is of vital importance to the performance and to the successful operation of the system. As its performance is negatively correlated with the communication overhead, energy consumption and the dissipated heat, task migration needs to be runtime adaptive to account for the system load, chip temperature, or battery capacity. This work presents a novel context-aware runtime adaptive task migration mechanism (CARAT) that reduces the task migration latency by 93.12%, 97.03% and 100% compared to three state-of-the-art mechanisms and allows to control the maximum migration delay and the performance overhead tradeoff at runtime. This novel mechanism is built on an in-depth analysis of the memory access behavior of several multi-media and robotic embedded-systems applications.
Supplementary Fig 1A from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression (2023)

Supplementary Fig 1A from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression
Performance of white PC LEDs based on violet chips (2006)

The performance of white pc LEDs based on violet chips is analyzed in terms of several metrics (lm/W, mW/lm, and package efficiency). A calculation is developed to evaluate package efficiency using spectroradiometric measurements and accounting for extraneous factors (Stokes' loss, luminous efficacy of the phosphor and bleed). The method is demonstrated on a state of the art "warm white" power LED, and performance entitlement is also discussed.
Use of architectural simulation tools in education (1995)

This paper presents the author's experience in using architectural simulation tools in the instruction of computer architecture courses. In particular, we develop the notion of incrementally building a programmable, trace--driven "timer" tool, for use as a learning vehicle. We show how the cycle--by--cycle simulation output of such timers can be used to illustrate performance bottlenecks, and how this and other output statistics can be interpreted to convey key design tuning issues. As part of the overall simulation toolkit, we also use available cache simulators, trace generators and other utilities in illustrating key performance determinants and architectural trade--off issues.
Ninety day mortality and its predictors after primary shoulder arthroplasty: an analysis of 4,019 patients from 1976-2008 (2011)

90-day mortality following shoulder arthroplasty was low. An underlying diagnosis of tumor, higher comorbidity and higher ASA class were risk factors for higher 90-day mortality, while higher BMI was protective. Pre-operative comorbidity management may impact 90-day mortality following shoulder arthroplasty. A higher unadjusted mortality in patients undergoing TSA versus HHR may indicate the underlying differences in patients undergoing these procedures.
Ferroelectric Random Access Memory Using Pb(Zr,Ti,Nb)O3 Films (2007)

We have succeeded in fabricating Pb(Zr,Ti,Nb)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZTN) thin films with 20-atomic% Nb at B site in ABO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> structure, which was suitable for high density and reliable ferroelectric random access memory (FeRAM). A sol-gel spin-coating method was used to prepare the PZTN thin films. 1 mol% Si co-doping was applied to promote the solid-solution of Nb atom into the original Pb(Zr,Ti)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> films. We suggested that in our PZTN the oxygen vacancies were well suppressed due to Nb substitution comparing with conventional Pb(Zr,Ti)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZT). We also succeeded in obtaining excellent electric properties in 1×1μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> capacitors with PZTN. In addition, we confirmed the no data degradation and the high reliability of our PZTN material has been demonstrated by 64 k-bits FeRAM chip operation.
Novel Heterocycle-Based Two-Photon Absorbing Dyes (2002)

[structure: see text]. The synthesis and nonlinear optical characterization of two novel heteroaromatic-based chromophores is described. The new dyes present an A-pi-D-pi-A general framework, where A is a pi-deficient heteroaromatic ring (pyridine, quinoline, benzothiazole) and D a pi-excessive pyrrolyl moiety. Both systems exhibit large two-photon absorption (TPA) values in the femtoseconds regime (TPA cross section as high as 150 x 10(-50) cm(4) s photon(-1) molecule(-1) with 150 fs laser pulses). Their TPA-based optical limiting activity is also shown.
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies (2022)

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
Diffusion Tensor Imaging of Skeletal Muscle Contraction Using Oscillating Gradient Spin Echo (2021)

Diffusion tensor imaging (DTI) measures water diffusion in skeletal muscle tissue and allows for muscle assessment in a broad range of neuromuscular diseases. However, current DTI measurements, typically performed using pulsed gradient spin echo (PGSE) diffusion encoding, are limited to the assessment of non-contracted musculature, therefore providing limited insight into muscle contraction mechanisms and contraction abnormalities. In this study, we propose the use of an oscillating gradient spin echo (OGSE) diffusion encoding strategy for DTI measurements to mitigate the effect of signal voids in contracted muscle and to obtain reliable diffusivity values. Two OGSE sequences with encoding frequencies of 25 and 50 Hz were tested in the lower leg of five healthy volunteers with relaxed musculature and during active dorsiflexion and plantarflexion, and compared with a conventional PGSE approach. A significant reduction of areas of signal voids using OGSE compared with PGSE was observed in the tibialis anterior for the scans obtained in active dorsiflexion and in the soleus during active plantarflexion. The use of PGSE sequences led to unrealistically elevated axial diffusivity values in the tibialis anterior during dorsiflexion and in the soleus during plantarflexion, while the corresponding values obtained using the OGSE sequences were significantly reduced. Similar findings were seen for radial diffusivity, with significantly higher diffusivity measured in plantarflexion in the soleus muscle using the PGSE sequence. Our preliminary results indicate that DTI with OGSE diffusion encoding is feasible in human musculature and allows to quantitatively assess diffusion properties in actively contracting skeletal muscle. OGSE holds great potential to assess microstructural changes occurring in the skeletal muscle during contraction, and for non-invasive assessment of contraction abnormalities in patients with muscle diseases.
Fast Kalman filtering on quasilinear dendritic trees (2010)

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Adaptive Tracking Control of One-Dimensional Respiration Induced Moving Targets by Real-Time Magnetic Resonance Imaging Feedback (2020)

One of the main challenges in magnetic resonance imaging (MRI) guided interventions is for an instrument to access and track a respiration-induced moving target inside the patient. In this article, we present a mechatronic system that demonstrates such capability for one-dimensional motion in phantom experiments. Our system consists of real-time sensing by MRI acquisition, detection, and localization, MRI-conditional instrument actuation by remotely and hydrostatically actuated fluid actuators, and adaptive control algorithms for tracking real-time measured respiratory motions subject to the sensing and actuation dynamics and uncertainties. Model-based simulations are performed to analyze the tracking performance pertaining to system parameters such as sensing latency and image tracking error. Experimental results obtained from moving phantoms are presented to demonstrate the control system's tracking performance.
Extraction, Quantification, and Antioxidant Activities of Phenolics from Pericarp and Seeds of Bitter Melons (Momordica charantia) Harvested at Three Maturity Stages (Immature, Mature, and Ripe) (2010)

Bitter melon (Momordica charantia) is an exotic vegetable used for consumption and medicinal purposes mainly throughout Asia. Phenolics were extracted from pericarp (fleshy portion) and seeds of bitter melons harvested at three maturation stages (immature, mature, and ripe) using ethanol and water solvent systems. Total phenolic assessment demonstrated 80% of ethanol to be the optimal solvent level to extract phenolics either from pericarp or seed. Main phenolic constituents in the extracts were catechin, gallic acid, gentisic acid, chlorogenic acid, and epicatechin. Free radical scavenging assay using 2,2-diphenyl-1-picrylhydrazyl (DPPH) demonstrated the bitter melon extracts as slow rate free radical scavenging agents. There were low correlations between the total phenolic contents and antiradical power values of the extracts, suggesting a possible interaction among the phenolic constituents occurred. Bitter melon phenolic extracts contain natural antioxidant substances, and could be used as antioxidant agents in suitable food products.
SOLID STATE RESEARCH (1964)

Abstract : Asurvey of solid state research is presented. Major areas covered are solid state devices, lasers, materials, band structure and spectroscopy of solids, and magnetism and resonance. A bibliography of reports by authors engaged in solid state research is also presented.
The design of real-time systems: from specification to implementation and verification (1991)

This paper presents an engineering approach to the design of distributed real-time systems, which guarantee hard deadlines and can tolerate a specified set of faults. The methodology covers the stepwise refinement of the given requirements, expressed in the form of real-time transactions, to task and protocol executions. It also includes a timing analysis and dependability evaluation of the still incomplete design. The testability of the evolving system is considered to be of essential concern. A set of coherent tools for the support of the methodology is described in some detail. The methodology assumes that the runtime architecture is based on static scheduling, and a globally synchronised time-base is available to co-ordinate the system actions in the domain of real time.
Modeling thermophysical properties of glasses (2023)

Metal oxide glasses are important in various industries because their properties can be tailored to meet application-specific requirements. However, there are few rigorous modeling tools for predicting thermomechanical properties of these materials with acceptable accuracy and speed, yet these properties can play a critical role in material design. In this article, a general multi-scale modeling framework based on Monte Carlo simulation and a cubic equation of state for predicting thermomechanical properties is presented. There are two novel and fundamental aspects of this work: (1) characterization of glass transition and softening temperatures as adjacent saddle points on the heat capacity versus temperature curve, and (2) a new moving boundary equation of state that accounts for structure and 'soft' repulsion. In addition, modeling capabilities are demonstrated by comparing thermomechanical properties of a pure B<sub>2</sub>O<sub>3</sub> glass and PbO-B<sub>2</sub>O<sub>3</sub> glass predicted by the equation of state to experimental data. Finally, this work provides a rigorous approach to estimating thermophysical properties for the purpose of guiding experimental work directed at tailoring thermomechanical properties of glasses to fit applications.
Variations in the functional visual field for detection of lung nodules on chest computed tomography: Impact of nodule size, distance, and local lung complexity (2017)

Of the investigated parameters, secondary nodule size, distance from the gaze center and lung complexity (particle number and area) significantly impact nodule detection with peripheral vision.
Secure DoF for the MIMO MAC: The Case of Knowing Eavesdropper's Channel Statistics Only (2019)

Physical layer security has attracted research attention as a means to achieve secure communication without the need for complicated upper layer encryption techniques. The secure degrees of freedom (SDoF) of various networks in the absence of instantaneous eavesdropper channel state information is still unknown. In this work, we study the SDoF of a multiple access network composed of two transmitters and a single receiver in the presence of an eavesdropper. All parties are equipped with multiple antennas and are subject to Gaussian noise in addition to fading channel conditions. A realistic, worst case scenario, where the channel state information (CSI) for the channels between the trusted parties is known to everyone, while the trusted parties can only estimate the channel statistics (environment based) of the eavesdropper is considered. The asymptotic secure network sum capacity (aka sum SDoF) is provided utilizing a novel proposed comprehensive upperbound along with a novel achievable scheme based on exploiting jamming.
CYP2J2 and CYP2C8 polymorphisms and coronary heart disease risk: the Atherosclerosis Risk in Communities (ARIC) study (2020)

The cytochromes P450 epoxygenases CYP2J2 and CYP2C8 synthesize epoxyeicosatrienoic acids, which regulate endothelial function. We sought to determine if genetic variation in CYP2J2 and CYP2C8 was associated with coronary heart disease risk.
ChemInform Abstract: A Novel Approach to Iboga Alkaloids: Total Synthesis of (.+‐.)‐ Ibogamine and (.+‐.)‐epi‐Ibogamine. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.