gebhart/patrepeval huggingface dataset:
Exploring the Human Leukocyte Phosphoproteome Using a Microfluidic Reversed-Phase−TiO2−Reversed-Phase High-Performance Liquid Chromatography Phosphochip Coupled to a Quadrupole Time-of-Flight Mass Spectrometer (2010)

The study of protein phosphorylation events is one of the most important challenges in proteome analysis. Despite the importance of phosphorylation for many regulatory processes in cells and many years of phosphoprotein and phosphopeptide research, the identification and characterization of phosphorylation by mass spectrometry is still a challenging task. Recently, we introduced an approach that facilitates the analysis of phosphopeptides by performing automated, online, TiO(2) enrichment of phosphopeptides prior to mass spectrometry (MS) analysis. The implementation of that method on a "plug-and-play" microfluidic high-performance liquid chromatography (HPLC) chip design will potentially open up efficient phosphopeptide enrichment methods enabling phosphoproteomics analyses by a broader research community. Following our initial proof of principle, whereby the device was coupled to an ion trap, we now show that this so-called phosphochip is capable of the enrichment of large numbers of phosphopeptides from complex cellular lysates, which can be more readily identified when coupled to a higher resolution quadrupole time-of-flight (Q-TOF) mass spectrometer. We use the phosphochip-Q-TOF setup to explore the phosphoproteome of nonstimulated primary human leukocytes where we identify 1012 unique phosphopeptides corresponding to 960 different phosphorylation sites providing for the first time an overview of the phosphoproteome of these important circulating white blood cells.
The role of electrostatic interaction in the molecular recognition of selective agonists to metabotropic glutamate receptors (2003)

The influence of electrostatic interactions in determining selectivity for individual subtypes of metabotropic glutamate receptors (mGluRs) is evaluated for a small set of agonists by using the program Delphi and the information thus obtained is compared with docking experiments carried out with AutoDock. The evaluation of the electrostatic component of the free energy of binding for L-Glu, L-AP4, or S-PPG to mGluR1, mGluR2, and mGluR4 subtypes allowed for the detection of subtle differences in the electronic properties of the three subtypes, differences that can account for the observed agonist selectivity.
Virtual ghost imaging with Bessel beam illumination (2012)

We present results from experiments performed at the Army Research Laboratory (ARL) demonstrating a single sensor virtual ghost imaging (VGI) configuration using Bessel beams. These experiments were performed in conditions of partially obscuring media or turbulent media to generate images of remote objects. Randomly translated Bessel beams provided improved illumination capabilities for resolving small distant targets in difficult imaging environments. When the object was illuminated through obscuring or turbulent media or a small offset aperture VGI recovered the image of the object when using a relatively coarse Bessel beam. Our experimental results show that VGI using Bessel beams can have advantages over Gaussian beams for imaging remote objects in adverse conditions.
Management of Mechanical Problems of Totally Implantable Venous Catheters (2020)

Objective: Although the most common complications of totally implantable venous catheters(TIVC) are infection and thrombosis, mechanicalcomplications can also affect the treatment and cause catheter removal. This study aimed to investigate mechanical complications of TIVC andprevention methods.Methods: Data of 983 procedures in 961patients who underwent TIVC implantation between 2010 and 2019 in AcibademMaslak, Bakirkoy, andAtakent Hospitals were retrospectively analyzed for mechanical complications.Results: Mechanical complications were encountered in 33(3.3%) cases: 12(1.2%) were detachment of TIVC, 8(0.8%) occlusions, 5(0.5%)pneumothorax, 1(0.1%) hemothorax, 1(0.1%) malposition, 1(0.1%) extravasation, 2(0.2%) TIVC rotation, 3(0.3%) skin necrosis and extrusions.Conclusion: The catheter tip should be placed in distal superior vena cava, reservoir pocket must be sufficient in size, reservoir should be fixedto pectoral muscle or fascia at least two points with nonabsorbable sutures. Subcutaneous fatty tissue resection from reservoir pocket shouldbe performed in obese patients. The nature of the withdrawn blood form Seldinger needle should be checked visually whether venous ornot. Risk of pneumothorax and detachment can be reduced by inserting the catheter from 1/3 outer part of the clavicle during percutaneoustechnique. While complication rate can be reduced by peroperative fluoroscopy use, control X-ray should be taken in symptomatic patients, notroutinely. Malposition can be seen in the peroperative period and can usually be corrected by good manipulation. Percutaneous transcatheterretrieval in addition to surgery is the gold standard treatment for detachment of TIVC. The most important factors in preventing complicationsare surgical experience and good care.
Protease-Mediated Entry via the Endosome of Human Coronavirus 229E (2008)

Human coronavirus 229E, classified as a group I coronavirus, utilizes human aminopeptidase N (APN) as a receptor; however, its entry mechanism has not yet been fully elucidated. We found that HeLa cells infected with 229E via APN formed syncytia when treated with trypsin or other proteases but not in a low-pH environment, a finding consistent with syncytium formation by severe acute respiratory syndrome coronavirus (SARS-CoV). In addition, trypsin induced cleavage of the 229E S protein. By using infectious viruses and pseudotyped viruses bearing the 229E S protein, we found that its infection was profoundly blocked by lysosomotropic agents as well as by protease inhibitors that also prevented infection with SARS-CoV but not that caused by murine coronavirus mouse hepatitis virus strain JHMV, which enters cells directly from the cell surface. We found that cathepsin L (CPL) inhibitors blocked 229E infection the most remarkably among a variety of protease inhibitors tested. Furthermore, 229E infection was inhibited in CPL knockdown cells by small interfering RNA, compared with what was seen for a normal counterpart producing CPL. However, its inhibition was not so remarkable as that found with SARS-CoV infection, which seems to indicate that while CPL is involved in the fusogenic activation of 229E S protein in endosomal infection, not-yet-identified proteases could also play a part in that activity. We also found 229E virion S protein to be cleaved by CPL. Furthermore, as with SARS-CoV, 229E entered cells directly from the cell surface when cell-attached viruses were treated with trypsin. These findings suggest that 229E takes an endosomal pathway for cell entry and that proteases like CPL are involved in this mode of entry.
Cross-Layer Design and Analysis of Wireless Geophone Networks Utilizing TV White Space (2020)

Traditional seismic data acquisition systems used for surveying during the exploration of oil and gas rely on cables between geophones and the data collection center. Despite the fact that cable-based systems provide reliable seismic data transfer, their deployment and maintenance costs increase substantially as the survey area increases in scale. Therefore, a three layer wireless network architecture is proposed in this work, which consists of wireless geophones (WG) and a data center with an intermediate wireless gateway node (WGN). This paper investigates the aggregate data throughput, transmission time, and energy consumption from WGs to the WGN in a wireless geophone network architecture based on the IEEE 802.11af standard. This standard is considered in order to have the maximum possible range and low power consumption due to operating in TV bands. Analytical expressions of the aforementioned quantities are derived using Markov chain models. Two Markov models are considered for this purpose: one for modeling the access method that allows multiple WGs to connect to a WGN and the other for representing a buffer in a WG. Since seismic data is recorded at regular intervals, arrivals of data packets in the buffer of the WG is deterministic. On the other hand, departure is random due to the multiple access method. Hence, in this work D/M/1/B queue is used for the first time to model the buffer in a wireless geophone. Furthermore, the physical layer constraints are also taken into account together with proper wireless path-loss channel models. The results obtained are useful for designing such wireless seismic networks without extensive simulations. In particular, the proposed joint medium access control, physical layer, and D/M/1/B model enables us to optimize the required number of WGNs. Finally, sectoring is also introduced in order to minimize the total number of WGNs needed to cover the whole surveying area.
Evaluating the Augmented Reality Human-Robot Collaboration System (2008)

This paper discusses an experimental comparison of three user interface techniques for interaction with a mobile robot located remotely from the user. A typical means of operating a robot in such a situation is to teleoperate the robot using visual cues from a camera that displays the robot's view of its work environment. However, the operator often has a difficult time maintaining awareness of the robot in its surroundings due to this single ego-centric view. Hence, a multi-modal system has been developed that allows the remote human operator to view the robot in its work environment through an Augmented Reality (AR) interface. The operator is able to use spoken dialog, reach into the 3D graphic representation of the work environment and discuss the intended actions of the robot to create a true collaboration. This study compares the typical ego-centric driven view to two versions of an AR interaction system for an experiment remotely operating a simulated mobile robot. One interface provides an immediate response from the remotely located robot. In contrast, the Augmented Reality Human-Robot Collaboration (AR-HRC) system interface enables the user to discuss and review a plan with the robot prior to execution. The AR-HRC interface was most effective, increasing accuracy by 30% with tighter variation, while reducing the number of close calls in operating the robot by factors of ~3x. It thus provides the means to maintain spatial awareness and give the users the feeling they were working in a true collaborative environment.
Harmonic Analysis of Air Gap Magnetic Field in Flux-Modulation Double-Stator Electrical-Excitation Synchronous Machine (2019)

This article presents a new field-modulation double-stator electrical-excitation synchronous machine (FM-DSEESM) and analyzes its harmonic components of double-layer air gap magnetic field. The key is that both the types and sources of various harmonic-components of air gap magnetic field are derived by taking into account the permeance components of both inner and outer stator teeth and modulation-ring rotor. The selection criteria of main working harmonic components of excitation field is clarified to achieve the armature-winding configuration. Then, the working harmonic components of air gap magnetic field, which have the same pole pairs, rotating direction, and rotating speed, respectively, can be figured out by comparing the mathematical derivation and finite-element analysis results from the excitation field and armature reaction magnetic field. By analyzing the contributions of the air gap flux density components to the electromagnetic torque, it is found that the electromagnetic torque of the proposed FM-DSEESM mainly consists of two parts, namely the reluctance torque components generated by the stationary working harmonic components and the armature reaction torque components provided by the rotating working harmonic components. A low-speed direct-drive FM-DSEESM prototype is fabricated to verify the validity of the proposed analysis approach.
Improving the FIE Mapping of a 4-Cylinder 4-Stroke Engine for Operation on the European Drive Cycle (2000)

&lt;div class="htmlview paragraph"&gt;Improvements have been made in the electronic fuel injection map of a 1.5 liter of engine spark-ignition engine, using conventional port fuel injection (simultaneous and not synchronized.) The modifications have been made aimed at reducing the specific fuel consumption and the exhaust gas emissions, mainly in the load range of the engine that is most frequent in the stabilized European drive cycle, primarily urban driving.&lt;/div&gt;
Effect of iontophoretic and topical application of antiviral agents in treatment of experimental HSV-1 keratitis in rabbits. (1979)

Cathodal (-) iontophoresis of 9-beta-D-arabinofuranosyl-adenine 5'-monophosphate (vidarabine monophosphate; Ara-AMP) was performed once daily for 3 days for the treatment of experimental herpes simplex virus type 1 (HSV-1) keratitis in rabbit eyes, and the therapeutic efficacy was compared with that of topical treatment of Ara-AMP and idoxuridine (IDU) administered five times daily for 4 days. With the treatment initiated 24 hr after viral inoculation, Ara-AMP cathodal iontophoresis resulted in significant suppression of epithelial and anterior segment disease processes. Topical IDU (0.5%) or Ara-AMP (10%) also significantly improved the disease process when compared to the placebo-treated group; however, iontophoresis of Ara-AMP resulted in a more marked improvement. Slit-lamp examination indicated that iontophoresis did not cause any observable pathologic changes in corneal epithelium, stroma, conjunctiva, or iris of rabbit eyes. This experiment suggests that iontophoresis of Ara-AMP is a safe and effective approach for preventing the development of herpes simplex keratitis in rabbits.
Synthesis, kinetic studies and in-silico investigations of novel quinolinyl-iminothiazolines as alkaline phosphatase inhibitors (2023)

Deposition of hydroxyapatite (HA) or alkaline phosphate crystals on soft tissues causes the pathological calcification diseases comprising of end-stage osteoarthritis (OA), ankylosing spondylitis (AS), medial artery calcification and tumour calcification. The pathological calcification is symbolised by increased concentration of tissue non-specific alkaline phosphatase (TNAP). An efficient therapeutic strategy to eradicate these diseases is required, and for this the alkaline phosphatase inhibitors can play a potential role. In this context a series of novel quinolinyl iminothiazolines was synthesised and evaluated for alkaline phosphatase inhibition potential. All the compounds were subjected to DFT studies where <i>N</i>-benzamide quinolinyl iminothiazoline (<b>6g</b>), <i>N</i>-dichlorobenzamide quinolinyl iminothiazoline (<b>6i</b>) and <i>N</i>-nitrobenzamide quinolinyl iminothiazoline (<b>6j</b>) were found as the most reactive compounds. Then during the <i>in-vitro</i> testing, the compound <i>N</i>-benzamide quinolinyl iminothiazoline (<b>6g</b>) exhibited the maximum alkaline phosphatase inhibitory effect (IC<sub>50</sub> = 0.337 ± 0.015 µM) as compared to other analogues and standard KH<sub>2</sub>PO<sub>4</sub> (IC<sub>50</sub> = 5.245 ± 0.477 µM). The results were supported by the molecular docking studies, molecular dynamics simulations and kinetic analysis which also revealed the inhibitory potential of compound <i>N</i>-benzamide quinolinyl iminothiazoline (<b>6g</b>) against alkaline phosphatase. This compound can be act as lead molecule for the synthesis of more effective inhibitors and can be suggested to test at the molecular level.
Immunological Studies on Platinum Complexes and Their Possible Relevance to Autocatalysts (1977)

<div class="htmlview paragraph">Preliminary tests on extracts from exhaust solids support the hypothesis, deduced from tests on refinery workers and estimates of the types of Pt compounds likely to be formed, that no allergenic species are emitted.</div> <div class="htmlview paragraph">A series of Pt complexes has been used for allergy tests on a number of refinery workers who are known to be sensitive to hexachloroplatinate [PtCl<sub>6</sub>]<sup>2-</sup> salts. The results show that the allergy-eliciting compounds appear to be confined to a very small group of ionic complexes containing reactive halogen ligands. Neutral complexes and those containing strongly bound groups are totally inactive. These variations are discussed in terms of established kinetic and thermodynamic parameters and their relevance to autocatalysts.</div>
A novel framework for checking and automating DRC Rules (2022)

Increasing complexity of the integrated circuits in advanced technologies requires carrying out the physical verification process very efficiently to catch up with the semiconductor market demand. With newer technologies coming out and the number and complexity of design rules increasing, finding ways of reducing the development cycle TAT is critical. One of the challenges that PDK team is constantly faced with is to ensure that each design rule description is correctly interpreted into a DRC code that properly captures the intention of the design rule set by the design rule team. This link between the design rule description and DRC code, if not properly handled, can lead to a reduced DRC deck quality (i.e., more errors), and a longer development cycle. So, creating a flow that automatically and efficiently interprets and checks those rules, with minimum human error, can greatly improve the DRC deck quality. We report the standardized, automated flow which interprets each design rule into a pre-determined category, and with the help of a parameterized library, points to the DRC code that accurately captures the intent of the design rule.
Investigation of using bone texture analysis on bone densitometry images (2002)

We previously developed bone texture analysis methods to assess bone strength on digitized radiographs. Here, we compare the analyses performed on digitized screen-film to those obtained on peripheral bone densitometry images. A leg phantom was imaged with both a PIXI (GE Medical Systems; Milwaukee, WI) bone densitometer (0.200-mm pixel size) and a screen-film system, with the films being subsequently digitized by a laser film digitizer (0.100-mm pixel size). The phantom was radiographically scanned multiple times with the densitometer at the default parameters and for increasing exposure times. Fourier-based texture features were calculated from regions of interest from images from both modalities. The bone densitometry images contained more quantum noise than the radiographs resulting in increased values for the first moment of the power spectrum texture feature (1.22 times higher than from the standard radiograph). Presence of such noise may adversely affect the texture feature's ability to distinguish between strong and weak bone. By either increasing the exposure time or averaging multiple scans in the spatial frequency domain, we showed a reduction in the effect of the quantum mottle on the first moment of the power spectrum.
Adsorption of nitrogen on carbon adsorbents at low pressures between 69 and 90 K (1955)

ere foun d to b e ap p rec iab l e at p r essures b el o\\' one m illim eter o f mer cury .
A New Paradigm for Flow Analyses and a Novel Technique to Enhance the Thrust from Scarfed Nozzles (2008)

A new flow analysis paradigm and a novel technique to enhance scarfed nozzle thrust are presented. The new paradigm, the space-time Conservation Element and Solution Element (CESE) method, a truly unsteady and genuinely multi-dimensional flow solver that provides accurate solutions for Euler and Navier-Stokes flows, is well suited for next generation flow analyses.In this study, the space-time CESE method was applied to solve scarfed nozzles flow-fields. Nozzle scarfing is frequently used for vectoring control of a space propulsion sub-system; it reduces nozzle weight and length and lowers nozzle thrust. A novel technique to enhance scarfed nozzles' thrust is discussed and investigated. Results of 2D and 3D flow analyses are presented.
Suppressor cell-inducing factor: a new lymphokine secreted by a natural suppressor cell line with natural cytotoxic activity. I. Purification to apparent homogeneity and initial characterization of suppressor cell-inducing factor. (1988)

The lymphokine suppressor cell-inducing factor (SIF), obtained from 15 liters of serum-free culture supernatants of the natural suppressor cell line, M1-A5, has been purified to apparent homogeneity by a combination of gel filtration, ion exchange chromatography, and reverse-phase-HPLC. Purity of SIF was assessed by the migration of the factor as a single band on SDS-PAGE, and the elution from reverse-phase-HPLC column as a single and sharp peak. SIF activity was retained after both procedures. Two protein factors with SIF activity were isolated from M1-A5 culture supernatants. The first protein factor (SIF alpha) had a Mr of 43 kDa, and the second protein factor (SIF beta) had a Mr of 6 kDa. Final purification of SIF alpha yielded 5 micrograms protein with specific activity of 4 x 10(6) U/mg protein. Final purification of SIF beta yielded 40 micrograms protein with specific activity of 7.5 x 10(7) U/mg protein. The relationship between SIF alpha and SIF beta, as well as the relationship with other suppressor factors, will be addressed.
Allele-specific Differences in Activity of a Novel Cannabinoid Receptor 1 (CNR1) Gene Intronic Enhancer in Hypothalamus, Dorsal Root Ganglia, and Hippocampus (2012)

Polymorphisms within intron 2 of the CNR1 gene, which encodes cannabinoid receptor 1 (CB(1)), have been associated with addiction, obesity, and brain volume deficits. We used comparative genomics to identify a polymorphic (rs9444584-C/T) sequence (ECR1) in intron 2 of the CNR1 gene that had been conserved for 310 million years. The C-allele of ECR1 (ECR1(C)) acted as an enhancer in hypothalamic and dorsal root ganglia cells and responded to MAPK activation through the MEKK pathway but not in hippocampal cells. However, ECR1(T) was significantly more active in hypothalamic and dorsal root ganglia cells but, significantly, and in contrast to ECR1(C), was highly active in hippocampal cells where it also responded strongly to activation of MAPK. Intriguingly, rs9444584 is in strong linkage disequilibrium with two other SNPs (rs9450898 (r(2) = 0.841) and rs2023239 (r(2) = 0.920)) that have been associated with addiction, obesity (rs2023239), and reduced fronto-temporal white matter volumes in schizophrenia patients as a result of cannabis misuse (rs9450898). Considering their high linkage disequilibrium and the increased response of ECR1(T) to MAPK signaling when compared with ECR1(C), it is possible that the functional effects of the different alleles of rs9444584 may play a role in the conditions associated with rs9450898 and rs2023239. Further analysis of the different alleles of ECR1 may lead to a greater understanding of the role of CNR1 gene misregulation in these conditions as well as chronic inflammatory pain.