gebhart/patrepeval huggingface dataset:
Protein tandem repeats - the more perfect, the less structured (2010)

We analysed the structural properties of protein regions containing arrays of perfect and nearly perfect tandem repeats. Naturally occurring proteins with perfect repeats are practically absent among the proteins with known 3D structures. The great majority of such regions in the Protein Data Bank are found in the proteins designed de novo. The abundance of natural structured proteins with tandem repeats is inversely correlated with the repeat perfection: the chance of finding natural structured proteins in the Protein Data Bank increases with a decrease in the level of repeat perfection. Prediction of intrinsic disorder within the tandem repeats in the SwissProt proteins supports the conclusion that the level of repeat perfection correlates with their tendency to be unstructured. This correlation is valid across the various species and subcellular localizations, although the level of disordered tandem repeats varies significantly between these datasets. On average, in prokaryotes, tandem repeats of cytoplasmic proteins were predicted to be the most structured, whereas in eukaryotes, the most structured portion of the repeats was found in the membrane proteins. Our study supports the hypothesis that, in general, the repeat perfection is a sign of recent evolutionary events rather than of exceptional structural and (or) functional importance of the repeat residues.
Frameshifting in the P6 cDNA Phage Display System (2010)

Phage display is a powerful technique that enables easy identification of targets for any type of ligand. Targets are displayed at the phage surface as a fusion protein to one of the phage coat proteins. By means of a repeated process of affinity selection on a ligand, specific enrichment of displayed targets will occur. In our studies using C-terminal display of cDNA fragments to phage coat protein p6, we noticed the occasional enrichment of targets that do not contain an open reading frame. This event has previously been described in other phage display studies using N-terminal display of targets to phage coat proteins and was due to uncommon translational events like frameshifting. The aim of this study was to examine if C-terminal display of targets to p6 is also subjected to frameshifting. To this end, an enriched target not containing an open reading frame was selected and an E-tag was coupled at the C-terminus in order to measure target display at the surface of the phage. The tagged construct was subsequently expressed in 3 different reading frames and display of both target and E-tag measured to detect the occurrence of frameshifting. As a result, we were able to demonstrate display of the target both in the 0 and in the +1 reading frame indicating that frameshifting can also take place when C-terminal fusion to minor coat protein p6 is applied.
Low voltage ride-through of single-phase transformerless photovoltaic inverters (2013)

Transformerless photovoltaic (PV) inverters are going to be more widely adopted in order to achieve high efficiency, as the penetration level of PV systems is continuously booming. However, problems may arise in highly PV-integrated distribution systems. For example, a sudden stoppage of all PV systems due to anti-islanding protection may trigger grid disturbances. Thus, standards featuring with ancillary services for the next generation PV systems are under a revision in some countries. The future PV systems have to provide a full range of services as what the conventional power plants do, e.g. Low Voltage Ride-Through (LVRT) under grid faults and grid support service. In order to map future challenges, the LVRT capability of three mainstream single-phase transformerless PV inverters under grid faults are explored in this paper. Control strategies with reactive power injections are also discussed. The selected inverters are the full-bridge inverter with bipolar modulation, full-bridge inverter with DC bypass and the Highly Efficient and Reliable Inverter Concept (HERIC). A 1 kW single-phase grid-connected PV system is analyzed to verify the discussions. The tests confirmed that, although the HERIC inverter is the best candidate in terms of efficiency, it is not very feasible in case of a voltage sag. The other topologies are capable of providing reactive current during LVRT. A benchmarking of those inverters is also provided, which offers the possibility to select appropriate devices and to further optimize the system.
Prediction of visceral response to multi-directional loading as measured by the chestband (2011)

Thoracic and abdominal injury outcomes are correlated to chestband-derived uniaxial metrics in post-mortem human specimen (PMHS) experiments. Yet, uniaxial metrics may neglect deformations remote from the measurement site which still may be relevant to injury risk in motor vehicle crashes. Using 2D chestband contours from PMHS experiments, visceral strain and strain energy density responses were examined using a planar viscoelastic finite element model. The model was exercised by applying to the periphery 21 subject-specific PMHS chestband deformation patterns representing four boundary conditions: (a) lateral impact with close-proximity torso airbag, (b) stationary close-proximity torso airbag loading, (c) flat rigid lateral impact, and (d) antero-lateral oblique rigid impact. ANOVA determined that mean peak responses were dependent on boundary condition (p<0.002). Using matched-pair experiment injury outcomes, 50% risk of visceral trauma corresponded to localized strain and strain energy density of 1.55 and 33.0 kJ/m(3) (p<0.1). Although strains were large, model response demonstrated sensitivity to impact boundary conditions and observed PMHS trauma. This model formulation is useful for comparative examination of injury risk from torso deformations measured experimentally using the chestband device.
Spatially adaptive wavelet-based multiscale image restoration (1996)

In this paper, we present a new spatially adaptive approach to the restoration of noisy blurred images, which is particularly effective at producing sharp deconvolution while suppressing the noise in the flat regions of an image. This is accomplished through a multiscale Kalman smoothing filter applied to a prefiltered observed image in the discrete, separable, 2-D wavelet domain. The prefiltering step involves constrained least-squares filtering based on optimal choices for the regularization parameter. This leads to a reduction in the support of the required state vectors of the multiscale restoration filter in the wavelet domain and improvement in the computational efficiency of the multiscale filter. The proposed method has the benefit that the majority of the regularization, or noise suppression, of the restoration is accomplished by the efficient multiscale filtering of wavelet detail coefficients ordered on quadtrees. Not only does this lead to potential parallel implementation schemes, but it permits adaptivity to the local edge information in the image. In particular, this method changes filter parameters depending on scale, local signal-to-noise ratio (SNR), and orientation. Because the wavelet detail coefficients are a manifestation of the multiscale edge information in an image, this algorithm may be viewed as an "edge-adaptive" multiscale restoration approach.
Experience (2020)

Cellular service carriers often employ reactive strategies to assist customers who experience non-outage related individual service degradation issues (e.g., service performance degradations that do not impact customers at scale and are likely caused by network provisioning issues for individual devices). Customers need to contact customer care to request assistance before these issues are resolved. This paper presents our experience with PACE (<u>P</u>ro<u>A</u>ctive customer <u>C</u>ar<u>E</u>), a novel, proactive system that monitors, troubleshoots and resolves individual service issues, without having to rely on customers to first contact customer care for assistance. PACE seeks to improve customer experience and care operation efficiency by automatically detecting individual (non-outage related) service issues, prioritizing repair actions by predicting customers who are likely to contact care to report their issues, and proactively triggering actions to resolve these issues. We develop three machine learning-based prediction models, and implement a fully automated system that integrates these prediction models and takes resolution actions for individual customers. We conduct a large-scale trace-driven evaluation using real-world data collected from a major cellular carrier in the US, and demonstrate that PACE is able to predict customers who are likely to contact care due to non-outage related individual service issues with high accuracy. We further deploy PACE into this cellular carrier network. Our field trial results show that PACE is effective in proactively resolving non-outage related individual customer service issues, improving customer experience, and reducing the need for customers to report their service issues.
Hemodynamic and Plasma Catecholamine Responses to Epinephrine-Containing Perianal Lidocaine Anesthesia (1985)

Despite the frequent use of large volumes (30-40 ml) of epinephrine-containing local anesthetic solutions for ano-rectal surgery, little is known about the anesthetic-induced hemodynamic consequences. Therefore, we measured the heart rate, blood pressure, and plasma catecholamine (norepinephrine and epinephrine) responses to the perianal injection of 40 ml of 0.5% lidocaine alone (n = 8) or 0.5% lidocaine with 1:200,000 epinephrine (n = 10) in 18 healthy adults undergoing outpatient ano-rectal surgery. The mean +/- SEM plasma epinephrine concentration increased from a baseline of 42 +/- 7 pg/ml to a peak of 622 +/- 94 pg/ml 4 min after injection of epinephrine-containing anesthetic (P less than 0.001), whereas lidocaine alone increased the mean plasma value from 36 +/- 9 pg/ml (baseline) to only 69 +/- 16 pg/ml (not significantly different) at its peak. Despite the increases in plasma epinephrine levels in the group receiving epinephrine-containing anesthesia, no changes in blood pressure, heart rate, or plasma norepinephrine levels were observed. Given the advantages (including prolongation of the duration of anesthesia) of adding epinephrine to perianal local anesthetics, our data support its safe use in healthy adults.
sFRP-1: A functional prognostic marker for gastric cancer? (2011)

37 Background: Despite being a leading cause of cancer-related death world wide, gastric adenocarcinoma (GA) lacks distinctive biomarkers and targeted therapies. Underexpression of the E-cadherin gene in GA is associated with an aggressive phenotype and a poor prognosis but the mechanisms of this difference are poorly understood. Developing effective therapies for GA requires identification of critical functional markers and deeper understanding of its pathophysiology. Methods: Unsupervised hierarchical clustering analysis of a publicly available 230-sample GA microarray dataset identified a prominent cluster (21.7%) associated with underexpression of E-cadherin and overexpression of a Wnt-family protein: secreted frizzled-related protein 1 (sFRP-1). Archival GA specimens were then assessed for the expression of sFRP-1 by immunohistochemistry. Prognostic significance was assessed using univariate and multivariate analyses. GA cell lines transfected with sFRP-1 were used to determine the role of sFRP-1 in gastric cancer. Results: 85 patients with GA underwent surgery with curative intent; 39 stained positive for sFRP-1 (46%). In this positive group, sFRP-1 staining was focal; was commonly found on the leading edge of the infiltrating tumor mass; and was not restricted to one histopathologic group, grade, or clinical stage. On univariate analysis T stage, nodal involvement, pathologic stage, nuclear grade, E-cadherin status and sFRP-1 status were predictive of overall survival. In a multivariate model, T stage (p &lt; 0.001), nuclear grade (p &lt; 0.001), E-cadherin status (p = 0.031) and sFRP-1 status (p = 0.0097) were predictive of overall survival. Overexpression of sFRP-1 in GA cell lines induced mesenchymal phenotype, enhanced growth and stem cell-like properties. sFRP-1 also attenuated Wnt signaling and E-cadherin expression, but potentiated Notch and Hedgehog signaling known to be involved in GA progression. These findings suggest a Wnt-independent mechanism mediated by sFRP-1. Conclusions: The aggressive biological subtype of gastric cancer may be linked to overexpression of sFRP-1. Our findings identify sFRP-1 as a functional prognostic biomarker for gastric cancer, which may serve as a potential therapeutic target. No significant financial relationships to disclose.
[Effect of quinolones on TNF-alpha production by human monocytes]. (1990)

Previous studies have shown that in lipopolysaccharide (LPS)--stimulated human monocytes, interleukin-1 (IL-1) production is altered by quinoline derivative antibiotics (quinolones), in a way which depends both on the dose and on the agents used. Given that IL-1 and tumor necrosis factor alpha (TNF) are produced in response to LPS and have some overlapping and synergistic activities, we sought to determine if TNF production was altered under the above-mentioned conditions. We investigated the effects of three quinolones: ciprofloxacin (Cip), pefloxacin (Pef) and ofloxacin (Ofl). These quinolones were found to decrease extracellular TNF production in a dose-dependent manner at concentrations higher than 25 micrograms/ml as previously described by our laboratory with regard to IL-1 production. Moreover, the order of the extracellular decrease in TNF and IL-1 induced by each drug was similar. However, in contrast to IL-1 activity, the quinolones studied also reduced cell-associated TNF. The kinetics of TNF production suggested that the quinolones affected TNF production at a very early step, probably during TNF synthesis rather than during its secretion into the extracellular medium. Furthermore, the quinolone-induced accumulation of intracellular cAMP could explain the extracellular decrease in both IL-1 and TNF production.
Abstract 13599: LX2020, an Adeno Associated Viral-Based Plakophilin 2 Gene Therapy Stabilizes Cardiac Disease Phenotype in a Severe Mouse Model of Arrhythmogenic Right Ventricular Cardiomyopathy (2022)

Introduction: Arrhythmogenic right ventricular cardiomyopathy (ARVC) increases risk of sudden cardiac death (SCD) and can progress to heart failure. Clinical studies have established 40-50% prevalence of mutations to desmosomal genes, with plakophilin-2 (PKP2) being the most frequent. To date, no effective treatment exists for ARVC. LX2020 is a novel AAV gene therapy that restores cardiac expression of human PKP2. A proof-of-concept study with LX2020 was conducted in a severe novel PKP2 mutant mouse model that exhibits all classic phenotypes of ARVC. Hypothesis: LX2020 mediated PKP2 expression is sufficient to scaffold the desmosomal cell-cell complex to promote survival as well as preserving cardiac electrical and mechanical function. Methods: A total of N=16 PKP2 Hom mice were randomized for vehicle/formula control (VC), low dose (LD) and high dose (HD). LX2020 was administered at postnatal day 2 and mice were analyzed 4-weeks post administration. Endpoints included survival, EKG, cardiac MRI and desmosomal levels of PKP2, desmoplakin (DSP), desmoglein-2 (DSG2), plakoglobin (JUP), along with fascia-adherens (N-Cad), and gap junction (CX43), using western blot analyses. Results: LX2020 showed dose dependent improvements in ARVC related deficits in PKP2 mice, including survival. HD resulted in 100% survival of PKP2 mutant mice, while LD resulted in 60% survival, when compared to 50% survival with VC. ECG data revealed suppression of ectopic beats in 100% of PKP2 mutant mice at HD and 75% suppression at LD when compared to 60% with VC. MRI HD improved left and right ejection fraction, as well as reduced right and left end-diastolic and systolic volumes, when compared to VC. LD showed a mild impact on left ventricular end-diastolic and end-systolic volumes like HD. Mechanistically, while LD showed limited increase in cardiac PKP2 expression, HD showed substantial cardiac PKP2 expression. Significantly increased levels of other desmosomal proteins, especially DSP and DSG2, were seen suggesting scaffolding functions to PKP2. Conclusions: These data indicate that the restoration of cardiac PKP2 expression can halt or slow ARVC disease progression, making LX2020 a promising gene therapy candidate for treating PKP2 mutation patients.
Predictors of Hospital Readmission in Patients Undergoing Creation of an Intestinal Ostomy (2023)

These factors provide a basis for identifying patients at higher risk for hospital readmission following ileostomy or colostomy surgery. For patients at higher risk for readmission following ostomy surgery, heightened surveillance and management in the immediate postoperative period may be necessary to avert potential complications.
Endoscopic Gastroenteric Anastomosis Using Magnets (2005)

Our results demonstrate the feasibility, safety. and efficacy of this technique for creating a gastroenteric anastomosis. The success rate was 86.6 %, there were no immediate complications, and there was no mortality related to the procedure.
Corrosion Evaluation of Iron-Chromium-Aluminum Alloys in Used Fuel Cooling Pools (2019)

Abstract One accident tolerant fuel solution to replace the zirconium cladding of the nuclear fuel is using iron-chromium-aluminum -FeCrAl- alloys, which offer extraordinary resistance to high temperature reaction with air or steam due to the formation of a protective alumina layer on the external surface. It is important to characterize the behavior of FeCrAl not only under accident conditions but also in the entire fuel cycle, which may include the cooling for 5-20 years in water pools before going to dry cask storage. FeCrAl alloys may have never been used industrially before under wet condition applications. Current results show that FeCrAl would be resistant to corrosion in the cooling pools. Electrochemical tests were performed in seawater type environments and it was found that the localized corrosion resistance of ferritic FeCrAl follow the behavior given by the pitting resistance equivalent (PRE), generally used for austenitic stainless steels. APMT was more resistant to localized corrosion than type 304H SS.
Feasibility Study for Computer-Aided Diagnosis System with Navigation Function of Clear Region for Real-Time Endoscopic Video Image on Customizable Embedded DSP Cores (2021)

This paper presents examination result of possibility for automatic unclear region detection in the CAD system for colorectal tumor with real time endoscopic video image. We confirmed that it is possible to realize the CAD system with navigation function of clear region which consists of unclear region detection by YOLO2 and classification by AlexNet and SVMs on customizable embedded DSP cores. Moreover, we confirmed the real time CAD system can be constructed by a low power ASIC using customizable embedded DSP cores.
Dipyridamole enhances ischaemia‐induced reactive hyperaemia by increased adenosine receptor stimulation (2008)

Caffeine prevented the augmenting effect of dipyridamole on PORH. This indicates that dipyridamole-induced augmentation of PORH is mediated via increased adenosine receptor stimulation as a result of elevated extracellular formation of adenosine during ischaemia.
Processor capacity reserves: operating system support for multimedia applications (1994)

Multimedia applications have timing requirements that cannot generally be satisfied using the time-sharing scheduling algorithms of general purpose operating systems. The authors provide the predictability of real-time systems while retaining the flexibility of a time-sharing system. They designed a processor capacity reservation mechanism that isolates programs from the timing and execution characteristics of other programs in the same way that a memory protection system isolates them from outside memory accesses. In the paper, they describe a scheduling framework that supports reservation and admission control, and introduce a novel reserve abstraction, specifically designed for the microkernel architecture, for measuring and controlling processor usage. The authors have implemented processor capacity reserves in Real-Time Mach, and they describe the performance of their system on several types of applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Imaging multiple cortical areas with high spatio-temporal resolution using innovative wide-field imaging system (2020)

Recording brain activity at the mesoscopic scale has a strong potential to unveil many new fundamental neuronal operations. Optical imaging offers a unique opportunity to measure brain activity over a large area with high spatio-temporal resolutions (20 &mu;m x 1 ms). However, two major limitations of this imaging technique partially explain the lack of development in this field. The cortex being non-planar, the field's depth limits the region in focus to a small region close to the center of the field of view. This is particularly significant for the highly curved lissencephalic small cortex of non-human primates that are becoming popular in neuroscience experiments. The ideal technique would be a method that compensates for such curvature; it would enable imaging the whole visual system at once, from the primary to the fifth visual cortices, in small non-human primates. Additionally, the signal-to-noise ratio is strongly degraded by the dynamic evolution of the brain curvature due to physiological rhythms (heartbeat, breathing, etc.). This strongly limits the ability to work at a single-trial level and to unravel the real dynamics of neuronal processing, such as spatio-temporal waves. Here in this project, we present an interdisciplinary approach for imaging of the non-human primate cortex, using technologies from astronomical instrumentation to overcome current technological limits. This will be of interest to a wide neuroscientific audience but also will impact the clinical community interested in mapping the nervous activity at the mesoscopic scale. Our current preliminary development involves redesigning the illumination source and the optical design.
Effect of the temperature on the off-diagonal Giant Magneto-Impedance (GMI) sensors (2018)

The influence of the temperature on the off-diagonal GMI sensors was studied. The sample was a Co-rich amorphous wire of 100 μm diameter and 5 cm long. The range of investigated temperature was [20 °C; 120 °C]. It included the industrial range. Particular attention was paid to the temperature dependence of the intrinsic sensitivity and offset of the off-diagonal component of the impedance tensor which are the most relevant parameters for the sensor implementation The results showed that the intrinsic odd symmetry of this off-diagonal component with respect to the zero field-point was not modified with temperature. The quasi-zero offset was also very little changed. The sensitivity near the zero-field was increased with temperature by about 36%. Furthermore, a general comparison, based on previous reported results, with the diagonal component of the impedance tensor showed that sensitivity was increased in an almost similar way for both components, but the off-diagonal component clearly exhibited best offset stability.