gebhart/patrepeval huggingface dataset:
Evaluating coagulation tests in patients with atrial fibrillation using direct oral anticoagulants (2015)

Four direct oral anticoagulants (dabigatran, rivaroxaban, apixaban, edoxaban) have been shown to be at least as effective and safe as warfarin for the prevention of stroke in atrial fibrillation and the prevention and treatment of venous thromboembolism. Although they are administered in fixed doses without routine coagulation monitoring, measurement of anticoagulant effect or drug levels may be useful to determine if: anticoagulant effect is present in patients who are bleeding or require an urgent procedure or thrombolysis; levels are within usual on-therapy range in patients with recurrent thromboembolism during treatment; and levels are outside of the usual on-therapy range in patients with overdose or with extreme clinical characteristics. Traditional coagulation assays are widely available but lack sensitivity to detect clinically relevant anticoagulant effects, and lack accuracy in quantitating drug levels. Specific drug assays are less widely available but can accurately measure drug levels and should be preferred.
Prevalence of cataract among Australian commercial airline pilots (2022)

Because little is known about cataract in pilots, we estimated prevalence by anonymously ascertaining all commercial airline pilots diagnosed with cataract 2011-2016 using the electronic Medical Records System of the Australian Civil Aviation Safety Authority. Of 14,163 Australian male commercial pilots licensed in 2011, 1286 aged ≥60 had biennial eye examinations showing a cataract prevalence of 11.6%. Among 12,877 pilots aged <60, based on compulsory eye examinations only when first licensed, prevalence was 0.5%. There was no significant difference by ambient ultraviolet (UV) radiation levels in state of residence though lowest prevalence was seen in the low-UV state of Victoria. Most cataract in pilots ≥60 years was bilateral and of mild severity, while cataract in pilots <60 were more likely to be unilateral and of greater severity.
Developments in megavoltage cone beam CT with an amorphous silicon EPID: Reduction of exposure and synchronization with respiratory gating (2005)

We have studied the feasibility of a low-dose megavoltage cone beam computed tomography (MV CBCT) system for visualizing the gross tumor volume in respiratory gated radiation treatments of nonsmall-cell lung cancer. The system consists of a commercially available linear accelerator (LINAC), an amorphous silicon electronic portal imaging device, and a respiratory gating system. The gantry movement and beam delivery are controlled using dynamic beam delivery toolbox, a commercial software package for executing scripts to control the LINAC. A specially designed interface box synchronizes the LINAC, image acquisition electronics, and the respiratory gating system. Images are preprocessed to remove artifacts due to detector sag and LINAC output fluctuations. We report on the output, flatness, and symmetry of the images acquired using different imaging parameters. We also examine the quality of three-dimensional (3D) tomographic reconstruction with projection images of anthropomorphic thorax, contrast detail, and motion phantoms. The results show that, with the proper choice of imaging parameters, the flatness and symmetry are reasonably good with as low as three beam pulses per projection image. Resolution of 5% electron density differences is possible in a contrast detail phantom using 100 projections and 30 MU. Synchronization of image acquisition with simulated respiration also eliminated motion artifacts in a moving phantom, demonstrating the system's capability for imaging patients undergoing gated radiation therapy. The acquisition time is limited by the patient's respiration (only one image per breathing cycle) and is under 10 min for a scan of 100 projections. In conclusion, we have developed a MV CBCT system using commercially available components to produce 3D reconstructions, with sufficient contrast resolution for localizing a simulated lung tumor, using a dose comparable to portal imaging.
Real-time lane and obstacle detection on the GOLD system (2002)

This paper describes the GOLD (generic obstacle and lane detection) system, a stereo vision-based hardware and software architecture developed to increment road safety of moving vehicles: it allows detection of both generic obstacles (without constraints on symmetry or shape) and the lane position in a structured environment (with painted lane markings). It has been implemented on the PAPRICA system and works at a rate of 10 Hz.
The Endoplasmic Reticulum–associated Degradation of the Epithelial Sodium Channel Requires a Unique Complement of Molecular Chaperones (2010)

The epithelial sodium channel (ENaC) is composed of a single copy of an alpha-, beta-, and gamma-subunit and plays an essential role in water and salt balance. Because ENaC assembles inefficiently after its insertion into the ER, a substantial percentage of each subunit is targeted for ER-associated degradation (ERAD). To define how the ENaC subunits are selected for degradation, we developed novel yeast expression systems for each ENaC subunit. Data from this analysis suggested that ENaC subunits display folding defects in more than one compartment and that subunit turnover might require a unique group of factors. Consistent with this hypothesis, yeast lacking the lumenal Hsp40s, Jem1 and Scj1, exhibited defects in ENaC degradation, whereas BiP function was dispensable. We also discovered that Jem1 and Scj1 assist in ENaC ubiquitination, and overexpression of ERdj3 and ERdj4, two lumenal mammalian Hsp40s, increased the proteasome-mediated degradation of ENaC in vertebrate cells. Our data indicate that Hsp40s can act independently of Hsp70 to select substrates for ERAD.
Message from the MDDS 2008 Workshop Organizers (2008)

Presents the introductory welcome message from the conference proceedings.
Forhidrol, a bioactive fraction of Phaleria macrocarpa (Scheff.) Boerl., increases reverse cholesterol transport pathway by down-regulation of cholesteryl ester transfer protein activity (2018)

Phaleria macrocarpa (Scheff.) Boerl. is one of the most popular medicinal plants in Indonesia. This plant has traditionally been used to lower cholesterol and control hypertension. This study was performed to examine the effect of Forhidrol, a bioactive fraction of P. macrocarpa (Scheff.) Boerl., to increase reverse cholesterol transport through the down-regulation of cholesteryl ester transfer protein (CETP) activity in hepatocellular carcinoma cell lines. Measurement of target genes including liver X receptor (LXR), sterol regulatory element-binding protein 1 (SREBP1), scavenger receptor class B type 1, low-density lipoprotein (LDL) receptor, apolipoprotein B, CYP11B1, CYP11B2, peroxisome proliferatoractivated receptor α (PPARα), peroxisome proliferator-activated receptor δ (PPARδ) and peroxisome proliferator-activated receptor γ (PPARγ) were done using realtime polymerase chain reaction assay. Secreted CETP and apolipoprotein A-1 were analyzed using western blot. CETP activity in vitro was measured using CETP inhibitor drug screening kit and triglyceride synthesis was measured using enzyme-linked immunosorbent assay. Forhidrol was found to significantly down-regulate CETP mRNA expression, as well as total CETP and cholesteryl esters transfer activity (P&lt;0.05). It specifically reduced transcriptional level of regulatory genes of CETP promoter including SREBP-1 and LXR. Forhidrol also significantly increased PPARδ and PPARα expression (P&lt;0.05) and slightly repressed triglycerides synthesis. In vivo study showed elevated high-density lipoprotein (HDL) levels in rabbits after 4-week treatment of Forhidrol at a dose of 37.5 mg/1.5 kg body weight compared to placebo. Conversely, LDL, triglyceride and CETP activity were decreased. Forhidrol increased HDL levels by reducing CETP-dependent transfer of cholesterol from HDL to LDL particles. Looking at possible side effects, Forhidrol apparently acted as a safe agent without negative effect towards blood pressure. These findings suggested that Forhidrol may be further developed as a potential anti-atherogenic drug.
Exploring <scp>CCRL2</scp> chemerin binding using accelerated molecular dynamics (2022)

Chemokine (C-C motif) receptor-like 2 (CCRL2), is a seven transmembrane receptor closely related to the chemokine receptors CCR1, CCR2, CCR3, and CCR5. Nevertheless, CCRL2 is unable to activate conventional G-protein dependent signaling and to induce cell directional migration. The only commonly accepted CCRL2 ligand is the nonchemokine chemotactic protein chemerin (RARRES2). The chemerin binding to CCLR2 does induce leukocyte chemotaxis, yet, genetic targeting of CCRL2 was shown to modulate the inflammatory response in different experimental models. This mechanism was shown to be crucial for lung dendritic cell migration, neutrophil recruitment, and Natural Killer cell-dependent immune surveillance in lung cancer. To gain more insight in the interactions involved in the CCRL2-chemerin, the binding complexes were generated by protein-protein docking, then submitted to accelerated molecular dynamics. The obtained trajectories were inspected by principal component analyses followed by kernel density estimation to identify the ligand-receptor regions most frequently involved in the binding. To conclude, the reported analyses led to the identification of the putative hot-spot residues involved in CCRL2-chemerin binding.
New radar waveform based on a chirp sequence (2014)

For all radar applications it is required to measure the target range R and radial velocity v <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> simultaneously and unambiguously with high accuracy and resolution even in multi target situations. In this paper, a new radar waveform is proposed, which is based on a chirp sequence. In the considered case, each chirp signal has a very short duration T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">chirp</sub> . Therefore, the measured beat frequency f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">B</sub> is dominated by the target range R and is less influenced by the radial velocity v <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> . However, the classical chirp sequence waveform suffers from possible ambiguities in the velocity measurement. It is, therefore, the objective of this paper to modify the classical chirp sequence based on an additional frequency modulation from chirp to chirp to get an unambiguous velocity measurement even in multi target situations.
Decoupling network optimization in high speed systems by mixed-integer programming (2014)

Power Integrity is maintained in a high speed system by designing an efficient decoupling network. This paper provides a generic formulation for decoupling capacitor selection and placement problem which is solved by mixed-integer programming. A real-world example is presented for the same. The minimum number of capacitors that could achieve the target impedance over the desired frequency range are found along with their optimal locations. In order to solve an industrial problem, the s-parameters data of power plane geometry and capacitors are used for the accurate analysis including bulk capacitors and VRM.
Age-related reference limits for urine levels of albumin, orosomucoid, immunoglobulin G and protein HC in children (2000)

Urine levels of albumin, orosomucoid (alias alpha1-acid glycoprotein), immunoglobulin G (IgG) and protein HC (alias alpha1-microglobulin) were determined in 247 healthy Swedish infants and children aged 1 day to 15 years. Urine samples were collected and stored in conditions known to guarantee stable protein levels. The protein levels were measured both as mass concentrations (mg l(-1)) and as protein-creatinine ratios (mg mmol(-1)). In an effort to arrive at practically useful upper reference limits, the variability with age for both units was analysed. The variability with age for the levels of three of the four proteins was considerably lower when the levels were expressed as creatinine ratios rather than as mass concentrations. The results allowed suggestion of the following upper reference limits, expressed as mg mmol(-1) creatinine, for use in clinical practise: IgG, 1 month to 15 years: 1.0; protein HC, 1 month to 15 years: 0.8; orosomucoid, 1 month to 15 years: 0.5; albumin, 1 month to 1 year: 3.8; 1-5 years: 3.3; 6-10 years: 2.7; 11-15 years: 2.1. In the immediate neonatal period the urine levels of all proteins were high and very variable.
A new 19F NMR indicator for intracellular sodium (1993)

The effect of increased benzo substitution on the cation-binding strength of diaza-18-crown-6 has been investigated. The planarity constraint imposed by increased substitution reduces the effective cavity size thus giving rise to an increased selectivity for sodium over potassium, magnesium and calcium that is sufficient to provide a class of indicators suitable for measuring intracellular free sodium. The cation binding parameters and the associated spectral changes of a selection of compounds with varied aryl fluorination patterns have shown that there is very little electronic interaction between the aromatic rings and the bound cation through the heteroatoms of the crown ether. Only small adjustments to the cation affinity can therefore be achieved via alteration of the aryl substitution patterns. Aryl substitution adjacent to the hetero atoms gives a reduction in the cation affinity of the tribenzo-crown ether, similar to that found on fluorination of the calcium chelator BAPTA ortho to the oxyethylene bridge. These observations have led to the preparation of a new indicator for intracellular sodium that we have called FCrown-1. The new indicator has a dissociation constant for sodium of 11 mmol dm–3 and a selectivity for sodium over potassium of 173-fold. The sodium concentration is reported by the chemical shift (fast exchange) of one of the two types of fluorine present with a maximum sodium-induced shift of 4.6 ppm downfield. The resonance arising from the other fluorine substituents is insensitive to sodium and acts as an internal chemical shift reference at 8.8 to 13.4 ppm upfield from the reporting signal.
Effects of Foot Orthotics on the Foot Arch Strain related to Plantar Fasciitis During Treadmill Level and Uphill Walking and Running (2005)

There is some evidence that one of major factors to produce plantar fasciitis depends on the magnitude of the foot arch strain. The orthotics that can reduce the foot arch strain during locomotion may be effective to prevent or treat plantar fasciitis. Therefore, the purpose of this study was to investigate the effect of control condition and three types of foot orthotics on 3-dimensional foot arch strain that can produce plantar fasciitis during treadmill level and uphill walking and running. Sixteen male subjects are recruited and the arch length and height strain according to three types of foot orthotics with respect to control condition were measured by using two digital video cameras. The first hypothesis which the comfort of foot orthotics would be increased from arch pad, half length orthotics to full length orthotics was mostly accepted. It suggested that the types of the foot orthotics could be properly prescribed according foot regions that is pain or abnormal. The second hypothesis which the foot arch strain can be reduced by foot orthotics during level heel-toe walking and running and the third hypothesis which the foot arch strain can be reduced by foot orthotics during uphill heel-toe walking and running were rejected. The foot arch length and height strain during walking and running showed small and subject-specific characteristics and could not be optimal biomechanical variable to prove the overall comfort. The forth hypothesis which the foot arch strain cannot be reduced by foot orthotics during uphill toe walking and running was accepted. With the foot arch length and height strain during uphill toe walking and running the windlass mechanism suggested by Hicks can be explained successfully and excessive uphill toe walking and running can be one of cause of plantar fasciitis. The dynamic investigation on the foot arch such as walking and running should be carefully observed with integrated insights considering ligaments and foot bones as well as plantar fascia, extrinsic muscles and tendons, and intrinsic muscles and tendons.
Evaluation of the Background Seismic Noise Level of the Buried Seismometers Installed by Two Caisson Installation Technique (2018)

Two caisson installation technique were conducted in the construction of DONET (Dense Oceanfloor Network System for Earthquakes and Tsunamis); one is using piston core technique [1], and the other is vibration hammer technique [2] that is developed to install the caisson using ROV. This paper describes the background noise level of seismometers installed by two caisson installation technique are discussed.
Maintenance of mitochondrial genomic integrity in the absence of manganese superoxide dismutase in mouse liver hepatocytes (2013)

Manganese superoxide dismutase, encoded by the Sod2 gene, is a ubiquitously expressed mitochondrial antioxidant enzyme that is essential for mammalian life. Mice born with constitutive genetic knockout of Sod2 do not survive the neonatal stage, which renders the longitudinal study of the biochemical and metabolic effects of Sod2 loss difficult. However, multiple studies have demonstrated that tissue-specific knockout of Sod2 in murine liver yields no observable gross pathology or injury to the mouse. We hypothesized that Sod2 loss may have sub-pathologic effects on liver biology, including the acquisition of reactive oxygen species-mediated mitochondrial DNA mutations. To evaluate this, we established and verified a hepatocyte-specific knockout of Sod2 in C57/B6 mice using Cre-LoxP recombination technology. We utilized deep sequencing to identify possible mutations in Sod2 (-/-) mitochondrial DNA as compared to wt, and both RT-PCR and traditional biochemical assays to evaluate baseline differences in redox-sensitive pathways in Sod2 (-/-) hepatocytes. Surprisingly, no mutations in Sod2 (-/-) mitochondrial DNA were detected despite measurable increases in dihydroethidium staining in situ and concomitant decreases in complex II activity indicative of elevated superoxide in the Sod2 (-/-) hepatocytes. In contrast, numerous compensatory alterations in gene expression were identified that suggest hepatocytes have a remarkable capacity to adapt and overcome the loss of Sod2 through transcriptional means. Taken together, these results suggest that murine hepatocytes have a large reserve capacity to cope with the presence of additional mitochondrial reactive oxygen species.
Design and implementation of correlating caches (2004)

We introduce a new cache architecture that can be used to increase performance and reduce energy consumption in Network Processors. This new architecture is based on the observation that there is a strong correlation between different memory accesses. In other words, if load X and load Y are two consecutively executed load instructions, the offset between the source addresses of these instructions remain usually constant between different iterations. We utilize this information by building a correlating cache architecture. This architecture consists of a Dynamic Correlation Extractor, a Correlation History Table, and a Correlation Buffer. We first show simulation results investigating the frequency of correlating loads. Then, we evaluate our architecture using SimpleScalar/ARM. For a set of representative applications, the correlating cache architecture is able to reduce the average data access time by as much as 52.7% and 36.1% on average, while reducing the energy consumption of the caches by as much as 49.2% and 25.7% on average.
High-dimensional phenotyping to define the genetic basis of cellular morphology (2023)

Abstract The morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combined genomic and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identified novel associations between rare protein altering variants in WASF2, TSPAN15 , and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirmed their role in cell morphology. Analysis of common variants yielded one significant association and nominated over 300 variants with suggestive evidence (P&lt;10 -6 ) of association with one or more morphology traits. Our results showed that, similar to other molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.
Targeting the Epidermal Growth Factor Receptor in EGFR-Mutated Lung Cancer: Current and Emerging Therapies (2021)

Epidermal growth factor receptor-targeting tyrosine kinase inhibitors (EGFR TKIs) are the standard of care for patients with EGFR-mutated metastatic lung cancer. While EGFR TKIs have initially high response rates, inherent and acquired resistance constitute a major challenge to the longitudinal treatment. Ongoing work is aimed at understanding the molecular basis of these resistance mechanisms, with exciting new studies evaluating novel agents and combination therapies to improve control of tumors with all forms of EGFR mutation. In this review, we first provide a discussion of EGFR-mutated lung cancer and the efficacy of available EGFR TKIs in the clinical setting against both common and rare EGFR mutations. Second, we discuss common resistance mechanisms that lead to therapy failure during treatment with EGFR TKIs. Third, we review novel approaches aimed at improving outcomes and overcoming resistance to EGFR TKIs. Finally, we highlight recent breakthroughs in the use of EGFR TKIs in non-metastatic EGFR-mutated lung cancer.
ML Detection with Blind Linear Prediction for Differential Space-Time Block Code Systems (2006)

This paper proposes a maximum likelihood detection (MLD) method for the differential space-time block code (DSTBC) in cooperation with blind linear prediction (BLP) of fast frequency-flat fading channels. The method, which linearly predicts the fading complex envelope, determines the linear prediction coefficients by the method of Lagrange multipliers, and does not use decision-feedback nor require information on channel parameters such as the maximum Doppler frequency in contrast to conventional ones. Computer simulations under a fast fading condition demonstrate that the proposed method with a proper degree of polynomial approximation can be superior in BER performance to a conventional method that estimates the coefficients by the RLS algorithm using a training sequence.
A Haptic Interface for Interventional Radiology (2006)

Low trauma, reduced costs, fast recovery are few factors why minimally invasive surgery (MIS) is taking over classical surgical methods. Interventional Radiology (IR) is a MIS technique where thin tubular instruments are steered through the patient’s vascular system under the X-ray imaging. These procedures demand highly trained and experienced specialists. A computer-based haptic interface is proposed as a quality training environment. The system is composed of a virtual reality (VR) environment and force feedback units for the surgical instruments. This paper describes the 4 degrees of freedom (DOFs) haptic interface that has been developed for this purpose.