gebhart/patrepeval huggingface dataset:
Retinal vessel architecture and geometry are not impaired in normal-tension glaucoma (2023)

To investigate the associations between retinal vessel parameters and normal-tension glaucoma (NTG). We conducted a case-control study with a prospective cohort, allowing to record 23 cases of NTG. We matched NTG patient with one primary open-angle glaucoma (POAG) and one control per case by age, systemic hypertension, diabetes, and refraction. Central retinal artery equivalent (CRAE), central retinal venule equivalent (CRVE), Arteriole-To-Venule ratio (AVR), Fractal Dimension and tortuosity of the vascular network were measured using VAMPIRE software. Our sample consisted of 23 NTG, 23 POAG, and 23 control individuals, with a median age of 65 years (25-75th percentile, 56-74). No significant differences were observed in median values for CRAE (130.6 µm (25-75th percentile, 122.8; 137.0) for NTG, 128.4 µm (124.0; 132.9) for POAG, and 135.3 µm (123.3; 144.8) for controls, P = .23), CRVE (172.1 µm (160.0; 188.3), 172.8 µm (163.3; 181.6), and 175.9 µm (167.6; 188.4), P = .43), AVR (0.76, 0.75, 0.74, P = .71), tortuosity and fractal parameters across study groups. Vascular morphological parameters were not significantly associated with retinal nerve fiber layer thickness or mean deviation for the NTG and POAG groups. Our results suggest that vascular dysregulation in NTG does not modify the architecture and geometry of the retinal vessel network.
Metrology standards with ellipsometers (1998)

At the October 1997 NIST “Workshop for Thin Dielectric Film Metrology”, uses of ellipsometers, and the role of standard materials for semiconductor metrology were two of several important topics discussed. Much of the workshop discussion centered on metrology for thin gate oxides. This paper is an extension of some of the topics discussed at that workshop.
A Remote Needle Guidance System for Percutaneous Biopsies (2005)

This paper describes a teleoperated needle guidance and insertion tool to assist doctors in performing minimally invasive percutaneous biopsies remotely under computed tomography [CT] guidance. Robopsy is a user-friendly robotic device that grips, positions and inserts a biopsy needle while the patient is imaged to provide the radiologist with simultaneous needle position feedback. Patient care is improved through more precise targeting and shortened procedure times. Robopsy is made primarily of simple, lightweight, snap-together, disposable plastic parts and modular motors; contrasting devices are heavy, complex and expensive. It is designed to be taped onto a patient so as to passively compensate for respiratory chest motion and, additionally, it incorporates a novel feature, which compensates for passive needle oscillation. The design process is outlined and the first prototype presented. Initial results from testing on a cardiac phantom indicate that artifacts from the device in the CT images are negligible and that the device can successfully orientate and insert a needle remotely.
Concerted expansion and contraction of immune receptor gene repertoires in plant genomes (2022)

Abstract Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether or not they co-evolve is unclear. Here we determined the copy numbers of cell-surface and intracellular immune receptors in 208 species. Surprisingly, these receptor gene families contract and/or expand together in plant genomes, suggesting the mutual potentiation of immunity initiated by cell-surface and intracellular receptors is reflected in the concerted co-evolution of the size of their repertoires across plant species.
Toward automated detection and segmentation of aortic calcifications from radiographs (2007)

This paper aims at automatically measuring the extent of calcified plaques in the lumbar aorta from standard radiographs. Calcifications in the abdominal aorta are an important predictor for future cardiovascular morbidity and mortality. Accurate and reproducible measurement of the amount of calcified deposit in the aorta is therefore of great value in disease diagnosis and prognosis, treatment planning, and the study of drug effects. We propose a two-step approach in which first the calcifications are detected by an iterative statistical pixel classification scheme combined with aorta shape model optimization. Subsequently, the detected calcified pixels are used as the initialization for an inpainting based segmentation. We present results on synthetic images from the inpainting based segmentation as well as results on several X-ray images based on the two-steps approach.
A ketogenic diet impacts markers of mitochondrial mass in a tissue specific manner in aged mice (2021)

Declines in mitochondrial mass are thought to be a hallmark of mammalian aging, and a ketogenic diet (KD) may prevent the age-related decreases in mitochondrial content. The objective of this study was to investigate the impact of a KD on markers of mitochondrial mass. Mice were fed an isocaloric control diet (CD) or KD from 12 months of age. Tissues were collected after 1 month and 14 months of intervention, and a panel of commonly used markers of mitochondrial mass (mitochondrial enzyme activities and levels, mitochondrial to nuclear DNA ratio, and cardiolipin content) were measured. Our results showed that a KD stimulated activities of marker mitochondrial enzymes including citrate synthase, Complex I, and Complex IV in hindlimb muscle in aged mice. KD also increased the activity of citrate synthase and prevented an age-related decrease in Complex IV activity in aged brain. No other markers were increased in these tissues. Furthermore, the impacts of a KD on liver and kidney were mixed with no pattern indicative of a change in mitochondrial mass. In conclusion, results of the present study suggest that a KD induces tissue-specific changes in mitochondrial enzyme activities, or structure, rather than global changes in mitochondrial mass across tissues.
Robust feedforward track following control system for an optical disk (2003)

This paper proposes a new robust feedforward tracking servo system for optical disk recording system based on prediction of tracking error. In optical disk recording systems, its detecting signal is only a tracking error. The tracking servo system, such as CD-R, must have a complete tracking response whose error is less than 0.1 /spl mu/m for amplitude of 100 /spl mu/m of position reference. For this purpose, this paper proposes a new tracking servo system based on the prediction of the tracking error. The proposed robust feedforward tracking control system is constructed by both a "zero phase error tracking" (ZPET) control system and a robust feedback control system. Moreover, this paper considers the saturation of the controller output. The experimental and numerical simulation results point out that the proposed system has a quick and precise tracking response and keeps the residual tracking error below this tolerance smoothly and stably.
28‐1: Invited Paper : Why Focus Cues Matter (2016)

Stereoscopic displays present different images to the two eyes and thereby create a compelling 3D sensation. However, such displays cause a host of perceptual and ergonomic problems. These problems occur because some of the presented depth cues (i.e., perspective and binocular disparity) specify the intended 3D scene while focus cues (blur and accommodation) specify the fixed distance of the display itself. These problems are particularly problematic in VR and AR displays. We have developed a stereoscopic display that circumvents these problems. Using the display, we investigated how incorrect focus cues affect visual perception, visual performance, and, most importantly, visual comfort. With respect to perception, we showed that the ability to perceive correct depth ordering is significantly improved when focus cues are correct. With respect to visual performance, we showed that the ability to binocularly fuse stimuli is substantially improved when the vergence‐accommodation conflict is minimized. Finally, with respect to visual comfort, we showed that comfort is significantly increased when the vergence‐accommodation conflict is zero. I offer suggestions on ways to create nearly correct focus cues in practical stereoscopic displays, particularly VR and AR.
Hydrogen Sulfide Is an Endogenous Regulator of Aging in Caenorhabditis elegans (2013)

Our results show that H2S is an endogenous regulator of oxidative damage, metabolism, and aging in C. elegans and provide new insight into the mechanisms, which control aging in this model organism.
Extensive Mammalian Germline Genome Engineering (2019)

Abstract Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO·3KO·9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO·3KO·9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence Summary Extensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation
Dendrimer-Functionalized Self-Assembled Monolayers as a Surface Plasmon Resonance Sensor Surface (2004)

We report here a multistep route for the immobilization of DNA and proteins on chemically modified gold substrates using fourth-generation NH(2)-terminated poly(amidoamine) dendrimers supported by an underlying amino undecanethiol (AUT) self-assembled monolayer (SAM). Bioactive ultrathin organic films were prepared via layer-by-layer self-assembly methods and characterized by fluorescence microscopy, variable angle spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and attenuated total internal reflection Fourier transform infrared spectroscopy (ATR-FTIR). The thickness of the AUT SAM base layer on the gold substrates was determined to be 1.3 nm from ellipsometry. Fluorescence microscopy and AFM measurements, in combination with analyses of the XPS/ATR-FTIR spectra, confirmed the presence of the dendrimer/biopolymer molecules on the multilayer sensor surfaces. Model proteins, including streptavidin and rabbit immunoglobulin proteins, were covalently attached to the dendrimer layer using linear cross-linking reagents. Through surface plasmon resonance measurements, we found that sensor surfaces containing a dendrimer layer displayed an increased protein immobilization capacity, compared to AUT SAM sensor surfaces without dendrimer molecules. Other SPR studies also revealed that the dendrimer-based surfaces are useful for the sensitive and specific detection of DNA-DNA interactions. Significantly, the multicomponent films displayed a high level of stability during repeated regeneration and hybridization cycles, and the kinetics of the DNA-DNA hybridization process did not appear to be influenced by surface mass transport limiting effects.
Electrochemical Mechanical Planarization (eCMP) of Copper Thin Films (2007)

A novel Electrochemical Mechanical Planarization (eCMP) process was developed and integrated on the copper plating platform to meet the stringent technical requirements including higher planarization efficiency, higher throughput at lower down force and lower defectivity for the manufacture of devices at 65 nm and beyond technology nodes. In the integrated system, following the electroplating process, the wafer is transferred to the planarization module where the bulk of copper is polished and planarized at a high rate, leaving a thin, planar copper film. It was determined that the resulting planar thin film enables conventional chemical mechanical polishing to clear the remaining copper and barrier with low dishing and erosion. The planarization mechanism of the eCMP process was explained on the basis of electrochemical experimental results.
Prospective emission efficiency and in-plane light polarization of nonpolar m-plane InxGa1−xN∕GaN blue light emitting diodes fabricated on freestanding GaN substrates (2006)

Prospective equivalent internal quantum efficiency (ηint) of approximately 34% at 300K was demonstrated for the blue emission peak of nonpolar m-plane (11¯00) InxGa1−xN∕GaN multiple quantum well light emitting diodes (LEDs) fabricated on freestanding m-plane GaN substrates. Although the ηint value is yet lower than that of conventional c-plane blue LEDs (&amp;gt;70%), the results encourage one to realize high performance green, amber, and red LEDs by reducing the concentration of nonradiative defects, according to the absence of the quantum-confined Stark effects due to the polarization fields parallel to the quantum well normal. The electric field component of the blue surface emission was polarized perpendicular to the c axis with the in-plane polarization ratio of 0.58 at 300K.
Improvement in Obstructive Sleep Apnea Diagnosis and Management Wait Times: A Retrospective Analysis of a Home Management Pathway for Obstructive Sleep Apnea (2015)

Obstructive sleep apnea is a common condition within the Canadian population. The current gold standard for diagnosis and management of patients is in-laboratory (in-lab) polysomnography; however, the limited availability of testing options for patients has led to long wait times and increased disease burden within the population. The Sleep Research Laboratory in Saskatoon (Saskatchewan) implemented a home management program to run in parallel with the in-lab system several years ago in an effort to increase their capacity and reduce wait times. The present study was a retrospective analysis of all patients referred to the program between 2009 and 2012. The home management system has improved wait times by diagnosing and managing up to one-half of the referred patient population, reducing the wait for in-lab treatment from a median of 152 days in 2009 to 92 days in 2012 (P&lt;0.0001). Moving forward, home management can provide a viable alternative to in-lab testing for patients who meet strict entry criteria, reducing the in-lab workload and, ultimately, reducing wait times.
Direct Synthesis of 4‐Arylpiperidines via Palladium/Copper(I)‐Cocatalyzed Negishi Coupling of a 4‐Piperidylzinc Iodide with Aromatic Halides and Triflates. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
MicroRNA Markers for the Diagnosis of Pancreatic and Biliary-Tract Cancers (2015)

It is difficult to detect pancreatic cancer or biliary-tract cancer at an early stage using current diagnostic technology. Utilizing microRNA (miRNA) markers that are stably present in peripheral blood, we aimed to identify pancreatic and biliary-tract cancers in patients. With "3D-Gene", a highly sensitive microarray, we examined comprehensive miRNA expression profiles in 571 serum samples obtained from healthy patients, patients with pancreatic, biliary-tract, or other digestive cancers, and patients with non-malignant abnormalities in the pancreas or biliary tract. The samples were randomly divided into training and test cohorts, and candidate miRNA markers were independently evaluated. We found 81 miRNAs for pancreatic cancer and 66 miRNAs for biliary-tract cancer that showed statistically different expression compared with healthy controls. Among those markers, 55 miRNAs were common in both the pancreatic and biliary-tract cancer samples. The previously reported miR-125a-3p was one of the common markers; however, it was also expressed in other types of digestive-tract cancers, suggesting that it is not specific to cancer types. In order to discriminate the pancreato-biliary cancers from all other clinical conditions including the healthy controls, non-malignant abnormalities, and other types of cancers, we developed a diagnostic index using expression profiles of the 10 most significant miRNAs. A combination of eight miRNAs (miR-6075, miR-4294, miR-6880-5p, miR-6799-5p, miR-125a-3p, miR-4530, miR-6836-3p, and miR-4476) achieved a sensitivity, specificity, accuracy and AUC of 80.3%, 97.6%, 91.6% and 0.953, respectively. In contrast, CA19-9 and CEA gave sensitivities of 65.6% and 40.0%, specificities of 92.9% and 88.6%, and accuracies of 82.1% and 71.8%, respectively, in the same test cohort. This diagnostic index identified 18/21 operable pancreatic cancers and 38/48 operable biliary-tract cancers in the entire cohort. Our results suggest that the assessment of these miRNA markers is clinically valuable to identify patients with pancreato-biliary cancers who could benefit from surgical intervention.
SiC trench IGBT with diode-clamped p-shield for oxide protection and enhanced conductivity modulation (2018)

In this paper, a diode-clamped p-shield is proposed as a feasible approach for SiC trench IGBT. The introduction of the p-shield effectively suppresses the high electric field in the gate oxide around the trench corner, which is a notorious feature for SiC trench gate devices. Additionally, the p-shield also results in a reduced Crss and thus better switching characteristics. The traditional grounded p-shield (widely adopted in SiC trench MOSFETs), however, significantly reduces the electron/hole density near the emitter side of the SiC trench IGBT. The diode-clamped p-shield structure proposed in this paper successfully solves this issue, since the potential of the p-shield in the on-state is elevated to near the turn-on voltage of the diode, and thus the extraction of holes from the p-shield is suppressed. Therefore, the proposed SiC trench IGBT with a diode-clamped p-shield reduces the high oxide field, improves the switching characteristics and maintains a low Kon simultaneously.
Expression and Function of Suppressor tRNA Genes in Mammalian Cells (1986)

With the availability of cloned normal genes, insertion of genes to correct defects in genetic disorders has become the focus of intense investigations (Cepko et al. 1984; Sorge et al. 1984; Eglitis et al. 1985; Miller et al. 1985). Retrovirus vectors are being used to insert genes into the appropriate cells in enzyme deficiency states such as adenosine deaminase deficiency (Friedman 1985; Williams et al. 1986), Lesch-Nyhan syndrome (Miller et al. 1983, 1984), and Gaucher's disease (Choudary et al. 1986). For the hemoglobinopathies and thalassemia, inserting a normal globin gene is also a theoretical possibility. However, these diseases present special problems because a high level of globin gene expression must be achieved in the erythroid cells in order to produce a beneficial effect; whereas in the enzyme deficiency states, low levels of expression may be sufficient to mitigate the severity of the disease. High levels of expression are not always...
Development of a Flexible End-Shield Using Tungsten Curtains for 3D PET (2006)

In the three-dimensional (3D) acquisition of positron emission tomograph (PET) without septa, random and scatter due to events from outside the field of view (FOV) become a serious problem. They decrease the signal to noise ratio and the quantitation of the image and also limit the count rate capability of the PET system. To reduce these effects, we developed a flexible end-shield using tungsten curtains (curtain-shield) that consists of a mobile stand, a cylindrical support, and flexible tungsten curtains. The tungsten curtains are made of four layers of 30 mm square, 1 mm thick tungsten plates contained in pockets of cloth. Because the tungsten curtains are flexible, they can safely be used even in body studies. Reduction of random and scatter were observed by using the curtain-shield in both phantom and human studies. Results indicate that the curtain-shield has a potential to improve the image quality of PET studies
Diminishing biofilm resistance to antimicrobial nanomaterials through electrolyte screening of electrostatic interactions B Biointerfaces (2019)

The extracellular polymer substances (EPS) generated by biofilms confers resistance to antimicrobial agents through electrostatic and steric interactions that hinder molecular diffusion. This resistance mechanism is particularly evident for antibacterial nanomaterials, which inherently diffuse more slowly compared to small organic antibacterial agents. The aim of this study was to determine if a biofilm’s resistance to antibacterial nanomaterial diffusion could be diminished using electrolytes to screen the EPS’s electrostatic interactions. Anionic (+) alpha-tocopherol phosphate (α-TP) liposomes were used as the antimicrobial nanomaterials in the study. They self-assembled into 700 nm sized structures with a zeta potential of −20 mV that were capable of killing oral bacteria (S. oralis growth inhibition time of 3.34 ± 0.52 h). In a phosphate (-ve) buffer the -ve α-TP liposomes did not penetrate multispecies oral biofilms, but in a Tris (hydroxymethyl)aminomethane (+ve) buffer they did (depth - 12.4 ± 3.6 μm). The Tris did not modify the surface charge of the α-TP nanomaterials, rather it facilitated the α-TP-biofilm interactions through electrolyte screening (Langmuir modelled surface pressure increase of 2.7 ± 1.8 mN/ m). This data indicated that EPS resistance was mediated through charge repulsion and that this effect could be diminished through the co-administration of cationic electrolytes.
Fabrication and characterization of melt-processed YBCO (1997)

Large domain YBCO are fabricated by using a melt processing technique for magnetic levitation applications. A Nd/sub 1+x/Ba/sub 2-x/Cu/sub 3/O/sub y/, seed is used to initiate grain growth and to control the orientation of YBCO grains. Samples as large as 50 mm diameter have been fabricated by utilizing this method. Microstructural studies reveals two distinct regions in these levitators due to different growth mechanisms along the a/b and c axes. Some initial result on the mass production of these; levitators are also reported.
In vivo classification of colorectal neoplasia using high‐resolution microendoscopy: Improvement with experience (2015)

In conclusion, this in vivo study demonstrates that an endoscopist without prior colon HRME experience can achieve greater than 90% accuracy for identifying neoplastic colorectal polyps after 40 polyps imaged. HRME is a promising modality to complement white light endoscopy in differentiating neoplastic from non-neoplastic colorectal polyps.