gebhart/patrepeval huggingface dataset:
An improved formulation of SYPRO Ruby protein gel stain: Comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation (2002)

SYPRO Ruby protein gel stain is compatible with a variety of imaging platforms since it absorbs maximally in the ultraviolet (280 nm) and visible (470 nm) regions of the spectrum. Dye localization is achieved by noncovalent, electrostatic and hydrophobic binding to proteins, with signal being detected at 610 nm. Since proteins are not covalently modified by the dye, compatibility with downstream proteomics techniques such as matrix-assisted laser desorption/ionisation-time of flight mass spectrometry is assured. The principal limitation of the original formulation of SYPRO Ruby protein gel stain, is that it was only compatible with a limited number of gel fixation procedures. Too aggressive a fixation protocol led to diminished signal intensity and poor detection sensitivity. This is particularly apparent when post-staining gels subjected to labeling with other fluorophores such as Schiff's base staining of glycoproteins with fluorescent hydrazides. Consequently, we have developed an improved formulation of SYPRO Ruby protein gel stain that is fully compatible with commonly implemented protein fixation procedures and is suitable for post-staining gels after detection of glycoproteins using the green fluorescent Pro-Q Emerald 300 glycoprotein stain or detection of beta-glucuronidase using the green fluorescent ELF 97 beta-D-glucuronide. The new stain formulation is brighter, making it easier to manually excise spots for peptide mass profiling. An additional benefit of the improved formulation is that it permits staining of proteins in isoelectric focusing gels, without the requirement for caustic acids.
Paper 163: Proprioception of the Anterior Cruciate Ligament: Human Foetal Receptor Mapping Using Immunohistochimy Analysis (2012)

Mechanoreceptors in the anterior cruciate ligament (ACL) have been thoroughly described. Proprioceptive function has been shown to decrease with ageing. Therefore, an aging effect on numbers and morphology of mechanoreceptors has been recently proved in a rabbit model. However, human ACL mechanoreceptors studies had only investigated nerves fibers receptors in adult ACL. We propose in this anatomical study to investigate the density and the respective representation of the different type of mechanoreceptors in the human foetal ACL and analyse the mapping of these receptors using immunohistochimy analysis.
Enhanced amperometric detection of glucose using Si29 particles (2006)

The 1nm Si29 particle is used as the sensing element for an enzyme-free amperometric electrochemical glucose sensor. The sensor shows selective glucose detection against interfering substances at physiological concentrations with long-term stability, reusability, and the absence of electrode poisoning. The Si29 particle is significantly more efficient in generating signal current compared to both dissolved and immobilized enzyme. This observation suggests that the particle can be used to replace enzyme in making glucose sensors and that the particle is a suitable material for the realization of nanoscale devices that generate signals sufficiently high for use.
Studies of a suitable mask error enhancement factor for 2D patterns (2013)

In advanced 20nm and below technology nodes, the mask enhanced error factor (MEEF) plays an important rule due to the request of stable process control and quality of mask manufacture. It provides us an effective parameter to analyze the process window for lithography. In advanced nodes, MEEF criterion becomes more important than previous nodes because very tight process tolerance is requested, especially in OPC and mask capability control. Therefore, we have to do further studies on this topic. In the simple line/trench design layers (for example: Active and poly), the MEEF is easy to be defined because mask bias is isotropic. However, in the complicated two-dimensional (2D) design layers (for example: Contact and Mvia), they are hard to be defined a suitable definition of MEEF. In the first part, we used the global bias to calculate the MEEF on all patterns. It makes calculation easier to compare with other patterns which are different shapes. However, when we inspected the 2D line-end patterns on the wafer, we found the significant differences between the MEEF of wafer data and aerial simulation. In order to clarify this issue, we perform series simulation studies of the line-end MEEF. Then we knew that it came from the different bias strategies. Furthermore, the simulation studies show that the line-end MEEF of non-preferable orientation is very sensitive to mask X/Y ratio bias due to strong OAI optical behavior by the SMO source. As a result, a new point of view of 2D MEEF is suggested according to physical mask CD error measurement data. In this study, we would find a better description of the MEEF than traditional one for lithographic process development on 2D region.
Femtosecond laser fabrication of photonic devices (2005)

Recent developments in femtosecond laser fabrication of fiber Bragg grating (FBG) photonics devices and associated ultrafast beam interaction with phase masks are presented. These novel FBG devices are useful for telecommunication and fiber sensor applications.
Data from Unexpected Abundance of HLA Class II Presented Peptides in Primary Renal Cell Carcinomas (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To elicit a long-lasting antitumor immune response, CD8&lt;sup&gt;+&lt;/sup&gt; and CD4&lt;sup&gt;+&lt;/sup&gt; T cells should be activated. We attempted to isolate HLA-DR–presented peptides directly from dissected solid tumors, in particular from renal cell carcinoma, to identify MHC class II ligands from tumor-associated antigens (TAA) for their use in peptide-based immunotherapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Tumor specimens were analyzed by immunohistochemical staining for their HLA class II expression. HLA class II peptides were subsequently isolated and identified by mass spectrometry. Gene expression analysis was done to detect genes overexpressed in tumor tissue. Peptides from identified TAAs were used to induce peptide-specific CD4&lt;sup&gt;+&lt;/sup&gt; T-cell responses in healthy donors and in tumor patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In the absence of inflammation, expression of MHC class II molecules is mainly restricted to cells of the immune system. To our surprise, we were able to isolate and characterize hundreds of class II peptides directly from primary dissected solid tumors, especially from renal cell carcinomas, and from colorectal carcinomas and transitional cell carcinomas. Infiltrating leukocytes expressed MHC class II molecules and tumor cells, very likely under the influence of IFNγ. Our list of identified peptides contains ligands from several TAAs, including insulin-like growth factor binding protein 3 and matrix metalloproteinase 7. The latter bound promiscuously to HLA-DR molecules and were able to elicit CD4&lt;sup&gt;+&lt;/sup&gt; T-cell responses.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Thus, our direct approach will rapidly expand the limited number of T-helper epitopes from TAAs for their use in clinical vaccination protocols.&lt;/p&gt;&lt;/div&gt;
Performance and Impairment Modelling for Hardware Components in Millimetre-wave Transceivers (2018)

This invited paper details some of the hardware modelling and impairment analysis carried out in the EU mmMAGIC project. The modelling work includes handset and Access Point antenna arrays, where specific millimeter-wave challenges are addressed. In power amplifier related analysis, statistical and behavioural modelling approaches are discussed. Phase Noise, regarded as a main impairment in millimeter-wave, is captured under two models and some analysis into to the impact of phase noise is also provided.
Software Prototype for Optimization of Monitoring and Data Logging in Water Distribution Systems (2015)

Collecting field data is a vital task for efficiently managing and operating a water distribution system. A field data collection program can be long-term permanent monitoring and/or short-term data logging for capturing hydraulic (pressures and flows) and water quality characteristics. The challenge for water utilities is to determine how many and where to place the data loggers, which hydrant and how many hydrants to flush for flow test, where and how many water quality sensors needs to be placed in a system. This paper reports the development of a unified method and an integrated software prototype for optimizing pressure logger placement, hydrant selection for flow test and conventional flushing, and water quality sensor placement, and also elaborates on the application of the tool for each type of data collection optimizations. It is illustrated that the tool is easy to use and the methods are effective for practitioners to come up with a technically sound field data collection program that can be long-term permanent monitoring or short-term data logging, hydrant flow testing and conventional flushing.
Disk schedulers for solid state drivers (2009)

In embedded systems and laptops, flash memory storage such as SSDs (Solid State Drive) have been gaining popularity due to its low energy consumption and durability. As SSDs are flash memory based devices, their performance behavior differs from those of magnetic disks. However, little attention has been paid on how to exploit SSDs from the disk scheduling algorithm view point. In this paper, we first describe behaviors of SSDs that inspires us to design a new disk scheduler for the Linux operating system. Specifically, read service time is almost constant in an SSD while write service time is not. Moreover, appropriate grouping of write requests eliminates any ordering-related restrictions and also maximizes write performance. From these observations, we propose two disk schedulers: IRBW-FIFO and IRBW-FIFO-RP. Both schedulers arrange write requests into bundles of an appropriate size while read requests are independently scheduled. Then, the IRBW-FIFO scheduler provides complete FIFO ordering to each bundle of write requests and each individual read requests while the IRBW-FIFO-RP scheduler gives higher priority to read requests than the bundles of write requests. We implement these schedulers in Linux 2.6.23, and results of executing our set of benchmark programs shows that performance improvements of up to 17% compared to existing Linux disk schedulers are achieved.
High-quality factor optical microcavities using oxide apertured micropillars (2005)

An oxide aperture is used to confine optical modes in a micropillar structure. This method overcomes the limitations due to sidewall scattering loss typical in semiconductor etched micropillars. High cavity quality factors (Q) up to 48 000 are determined by external Fabry–Perot cavity scanning measurements, a significantly higher value than prior work in III-V etched micropillars. Measured Q values and estimated mode volumes correspond to a maximum Purcell factor figure of merit value of 72.
Mobile handset antenna solution with optimized matching circuits for carrier aggregation operation (2014)

We proposed a novel antenna solution with optimized matching circuits for carrier aggregation (CA) operation. The proposed design solution provides the best performance for the CA band pair operation because it utilizes optimized matching circuits for each CA band pair combination. The antenna structure is composed of three branched monopole elements, five matching circuits, switches, and a triplexer. The five matching circuits in this proposed solution are optimized for each CA band pair, and the switches select the best matching circuits automatically. The antenna structure is three-dimensional with the size of the antenna being 50 × 5 × 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The proposed design is compact, extending only 5 mm from the ground plane. The CA bands' mismatch loss is less than -6 dB and their isolation is less than -10 dB. The total efficiency of the CA band frequencies varies between -5 and -2 dB.
KEYNOTE ADDRESS The role of vertebral augmentation in multiple myeloma: International Myeloma Working Group Consensus Statement (2008)

Myeloma isthe commonest primary cancer affecting the spine. Painfulvertebral compression fractures (VCFs) affect approximately30% of myeloma patients. As myeloma patients live longer, it isespecially relevant to provide the best available treatment forpain and reduce disabilities that can result from VCFs.
Supplementary Table S1 from Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma (2023)

&lt;p&gt;Table S1&lt;/p&gt;
The Synthesis of Some Derivatives Based on the 4-Benzyl-1H-pyrazole-3,5-diamine Core (2011)

The three-step synthesis of 4-benzyl-1H-pyrazole-3,5-diamines 2 from commercially available aldehydes 3 is given. The Knoevenagel condensation was utilized to assemble the initial carbon framework, resulting in the benzylidenemalononitriles 4 which were directly transformed by the reduction of the electron deficient C=C bond to benzylmalononitriles 5. Subsequent cycloaddition of hydrazine with 5 afforded the desired pyrazoles 2. Due to the high similarity with 4-arylazo-1H-pyrazole-3,5-diamines, the biological activities of the 4-benzyl-1H-pyrazole-3,5-diamines 2 were evaluated while focusing on the inhibition of cyclin-dependent kinases (CDKs), but no significant results were obtained.
927: Alterations in Ex VIVO Biomechanical Properties and Functional Properties of the Proximal Urethra in a Rat Model of Birth Trauma Induced by Vaginal Distension (2005)

You have accessJournal of UrologyPodium, Monday, May 23, 2005, 3:30 - 5:30 pm1 Apr 2005927: Alterations in Ex VIVO Biomechanical Properties and Functional Properties of the Proximal Urethra in a Rat Model of Birth Trauma Induced by Vaginal Distension Rachelle L. Prantil, Ronald J. Jankowski, Yasuhiro Haiho, William C. de Groat, Michael B. Chancellor, Naoki Yoshimura, and David A. Vorp Rachelle L. PrantilRachelle L. Prantil More articles by this author , Ronald J. JankowskiRonald J. Jankowski More articles by this author , Yasuhiro HaihoYasuhiro Haiho More articles by this author , William C. de GroatWilliam C. de Groat More articles by this author , Michael B. ChancellorMichael B. Chancellor More articles by this author , Naoki YoshimuraNaoki Yoshimura More articles by this author , and David A. VorpDavid A. Vorp More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)35083-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "927: Alterations in Ex VIVO Biomechanical Properties and Functional Properties of the Proximal Urethra in a Rat Model of Birth Trauma Induced by Vaginal Distension." The Journal of Urology, 173(4S), pp. 250–251 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 173Issue 4SApril 2005Page: 250-251 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Rachelle L. Prantil More articles by this author Ronald J. Jankowski More articles by this author Yasuhiro Haiho More articles by this author William C. de Groat More articles by this author Michael B. Chancellor More articles by this author Naoki Yoshimura More articles by this author David A. Vorp More articles by this author Expand All Advertisement PDF downloadLoading ...
Tunable resonators with electrostatic self test functionality for frequency selective vibration measurements (2003)

In this paper we present an array of tunable resonators for frequency selective vibration measurements. The resonance frequency tuning is carried out by electrostatic forces directly applied to the seismic mass affecting the total stiffness. Frequency selective sensor systems require the exact knowledge of the resonance frequency. Therefore a method of in-system calibration using electrostatic excitation and capacitive vibration detection was investigated. Coupling problems of the excitation signal into the detection path were solved by using two excitation signals 180/spl deg/ out-of-phase and by contacting the substrate with a backside metallization.
Lyotropic Chromonic Liquid Crystals for Biological Sensing Applications (2005)

ABSTRACT We describe director distortions in the nematic liquid crystal (LC) caused by a spherical particle with tangential surface orientation of the director and show that light transmittance through the distorted region is a steep function of the particle's size. The effect allows us to propose a real-time microbial sensor based on a lyotropic chromonic LC (LCLC) that detects and amplifies the presence of immune complexes. A cassette is filled with LCLC, antibody, and antigen-bearing particles. Small and isolated particles cause no macroscopic distortions of the uniformly aligned LCLC. Upon antibody-antigen binding, the growing immune complexes disrupt the uniformity of the director and cause detectable optical transmittance between crossed polarizers.
Determinants of Bowel Preparation Quality and Its Association With Adenoma Detection (2016)

The predictors of poor bowel preparation in colorectal cancer screening participants have not been adequately studied, and the association between the quality of bowel preparation and adenoma detection has not been firmly established. This study examined the determinants of poor bowel preparation, and evaluated its relationship with adenoma detection.We included subjects aged between 50 and 70 years who received colonoscopy between 2008 and 2014 in a colorectal cancer screening program in Hong Kong. The quality of the bowel preparation was assessed by colonoscopists, and the factors associated with poor bowel cleansing were evaluated by a binary logistic regression analysis. A multivariate regression model was constructed to evaluate if poor bowel preparation was associated with detection of colorectal neoplasia.From 5470 screening participants (average age 57.7 years, SD 4.9), 1891 (34.6%) had poor or fair bowel preparation. The average cecal intubation time was 7.0 minutes (SD 5.4; range 1.22-36.9 minutes) and the average colonoscopy withdrawal time was 10.8 minutes (SD 6.9; range 6.0-107.0 minutes). Among all, 26.5% had colorectal neoplasia and 5.5% had advanced neoplasia. Older age (≥60 years; adjusted odds ratio [AOR] = 1.19-1.38, P = 0.02-0.04), male sex (AOR = 1.38, 95% confidence interval [CI] 1.19-1.60, P < 0.001), and current smoking (AOR = 1.41, 95% CI 1.14-1.75, P = 0.002) were significantly associated with poor/fair bowel preparation. Poorer cleansing resulted in significantly lower detection rate of neoplasia (AOR = 0.35-0.62) and advanced neoplasia (AOR = 0.36-0.50) irrespective of polyp size.Steps to improve proper procedures of bowel preparation are warranted, especially among subjects at risk of poor bowel preparation. Strategies should be implemented to improve bowel cleansing, which is now demonstrated as a definite quality indicator.
Threshold detection of wideband signals: A noise-induced maximum in the mutual information (1996)

In some nonlinear dynamic systems, the addition of noise to a weak periodic signal can increase the detectability of the signal, a phenomenon belonging to a class of noise-induced cooperative behavior known as stochastic resonance (SR). There has been much recent speculation on the possible role of SR in signal processing by sensory neurons. However, most results have focused exclusively on increasing the output signal-to-noise ratio (SNR) of time-periodic signals, even though many real-world signals (e.g., those encountered in some neurophysiological and communications applications) are not of this form. Here we consider a generalization of SR, based on the Shannon mutual information between the transmitted and received signal. This generalization can be applied to cases (e.g., the information transmitted by the output spike train of an integrate-fire model neuron which we consider here), involving aperiodic input signals for which the output SNR might be ill-defined, uninformative, or irrelevant. Since the SR-like effect in the transmitted information disappears with the optimal choice of model parameters, we suggest that such an effect is likely to be particularly relevant to systems, e.g., neuronal populations, in which natural circuit constraints may render parameter optimization impractical.
Multi-Objective Parameterization of Graphite Heat Spreader for Portable Systems Applications (2007)

The advancement made in portable electronic systems has primarily been due to miniaturization of electronic systems. This in turn leads to an increase in power density which leads to higher temperatures and formation of hot spots. There is a temperature specification of system surfaces for human comfort (such as the surface close to a keyboard on laptops). Challenge in cooling portable devices is that there is not enough room to accommodate heat sinks. It is therefore important to have heat spreaders that can transfer the heat from critical devices to regions where cooling is available. Traditionally, copper has been the best heat spreader due to its high thermal conductivity. However, copper has a relatively high density and correspondingly high weight. Graphite is a suitable alternative. Recent advances in graphite technology have resulted in fairly high conductivity in the planar directions. In spite of these advances, the cost of graphite is an issue. In this paper, a multi-objective parameterization is utilized that considers weight and temperature distribution of the graphite heat spreader as objective parameters. The data is then compared to published data that utilizes graphite in a laptop.
A Zeolite Structure (ITQ‐13) with Three Sets of Medium‐Pore Crossing Channels Formed by 9‐ and 10‐Rings (2003)

In der Zuschrift „A Zeolite Structure (ITQ-13) with Three Sets of Medium-Pore Crossing Channels Formed by 9- and 10-Rings“ von A. Corma et al. in1, hätte schon am Anfang des Manuskripts deutlich gemacht werden sollen, dass die Synthese des ITQ-13-Materials erstmals in einem 2002 veröffentlichten Patent beschrieben wurde (T. Boix, M. Puche, M. A. Camblor, A. Corma, US Patent 6 471 941 B1, 2002; Lit. [12] im Manuskript). Weiterhin wurde wegen eines redaktionellen Versehens der Literaturverweis zu diesem Patent in der Experimental Section falsch eingetragen: Statt Lit. [13] sollte es dort richtigerweise Lit. [12] lauten und umgekehrt. Wir bitten unsere Leser und die Autoren des genannten Patents um Entschuldigung. Avelino Corma (Korrespondenzautor) Peter Gölitz (Chefredakteur)