gebhart/patrepeval huggingface dataset:
The tetraspanin web revisited by super-resolution microscopy (2015)

The spatial organization of membrane proteins in the plasma membrane is critical for signal transduction, cell communication and membrane trafficking. Tetraspanins organize functional higher-order protein complexes called 'tetraspanin-enriched microdomains (TEMs)' via interactions with partner molecules and other tetraspanins. Still, the nanoscale organization of TEMs in native plasma membranes has not been resolved. Here, we elucidated the size, density and distribution of TEMs in the plasma membrane of human B cells and dendritic cells using dual color stimulated emission depletion (STED) microscopy. We demonstrate that tetraspanins form individual nanoclusters smaller than 120 nm and quantified that a single tetraspanin CD53 cluster contains less than ten CD53 molecules. CD53 and CD37 domains were adjacent to and displayed only minor overlap with clusters containing tetraspanins CD81 or CD82. Moreover, CD53 and CD81 were found in closer proximity to their partners MHC class II and CD19 than to other tetraspanins. Although these results indicate that tetraspanin domains are adjacently positioned in the plasma membrane, they challenge the current view of the tetraspanin web of multiple tetraspanin species organized into a single domain. This study increases the molecular understanding of TEMs at the nanoscale level which is essential for comprehending tetraspanin function in cell biology.
High Incidence of Athletic Pubalgia Symptoms in Professional Athletes With Symptomatic Femoroacetabular Impingement (2012)

Level IV, therapeutic, retrospective case series.
Divergent Sequential Reactions of β‐(2‐Aminophenyl)‐α,β‐ynones with Nitrogen Nucleophiles. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Computer‐based determination of size and shape in living cells (1985)

Measurement of cell volume in living epithelial cells has become an important technique in studies of membrane transport processes that function in cell volume regulation. Planimetry of video images of optical sections enables the measurement of the cross sectional area of each section. Cell volume is calculated from the measured area of each section and the known focus displacements. In the past the measurement of cross section area has been done by manual positioning of a cursor superimposed on the video image. Each experiment generates approximately 200 images in which two or more cells may be analysed. We have developed a computer-based method that uses one image as a template, and allows automated area determination of successive images by template matching and digital image processing. This new method is comparable to the older method in speed and accuracy, but requires much less effort from the experimenter.
Scaling CMOS photonics transceivers beyond 100 Gb/s (2012)

We report on the performance of an integrated four-channel parallel optical transceiver built in a CMOS photonics process, operating at 28 Gb/s per channel. The optical engine of the transceiver comprises a single silicon die and a hybrid integrated DFB laser. The silicon die contains the all functionalities needed for an optical transceiver: transmitter and receiver optics, electrical driver, receiver and control circuits. We also describe the CMOS photonics platform used to build such transceiver device, which consists of: an optically enabled CMOS process, a photonic device library, and a design infrastructure that is modeled after standard circuit design tools. We discuss how this platform can scale to higher speeds and channel counts.
E-blackboard Från krittavla till webbgr änssnitt (2014)

This bachelor thesis covers the development of a semi-autonomous system which
helps students by electronically providing information presented on blackboards
during a lecture. The system consists of a camera module connected to a Raspberry
Pi mounted on a rotating frame, which enables the system to cover all of the boards
in the lecture hall. The frame's rotation is controlled by a servo-engine connected
to the Raspberry Pi. Images captured by the system are automatically processed
on the Raspberry Pi through the use of the graphics framework SimpleCV in a
python script. The images are published on an online interface where students can
access them and rehearse the content covered during the lecture.
The project ultimately resulted in a prototype where an image is presented on the
online interface approximately 40 seconds after a blackboard has been completed.
This delay is considered acceptable since a board rarely has to be documented more
frequently. The automatic image processing will correct the perspective as needed
and crop the image to exclude any unnecessary information before publishing the
image on the online interface. The system requires minimal interaction from the
lecturer. This consists of moving the blackboard to the highest position of the
board's frame. The overall result of this project indicates that a system with this
type of functionality can be implemented and is likely to have a positive impact
on students' learning.
Hydrodynamic driven dissolution in porous media with embedded cavities (2020)

Hydrodynamics characterization and analysis is an essential part in studying mineral dissolution in porous media with complex heterogeneous pore structures including embedded cavities. Cavities affect the pore-scale pressure and flow distribution in the surrounding porous matrix. Transport of the dissolved solute, concentration gradient, and thermodynamic driving forces in that area will be affected as a result of local flow features. Given the properties of cavities and porous media, vorticities may form, and the cavity may partially or fully contribute to the overall flow. Depending on the shape and alignment of the cavity with respect to the direction of general flow, fluid flow will be focused at certain locations on the cavity boundary. Reaction hotspots can form as a result of the facilitated mineral dissolution at those locations. A rigorous flow modeling approach that preserves the flow features inside the cavity and in the porous matrix is used. Stokes flow and seepage flow are applied as two different physics governing the fluid flow in a fluid-filled cavity and a highly permeable sediment-filled cavity consecutively. The analytical model framework permits capturing the detailed flow structure of a single-phase fluid at the curved interface of a prolate spheroidal cavity. The solutions for flow are used within a fully coupled, fully implicit reactive transport simulator to investigate the mineral dissolution in the porous host matrix. The cavity aspect ratio and slip parameter at the border are investigated as the two parameters that affect the dissolution. The simulation results showed that the reaction hotspots are mainly located on the border of the cavity where the influent enters and leaves the cavity. The midpoint between them is where the minimum mineral dissolution was placed. Approximating the cavity as a highly permeable sediment-filled porous zone showed a higher effective reaction rate compared to the fluid-filled cavity. The cavity aspect ratio showed to have a significant impact on the effective reaction rate of the investigated cases. The cavities with a shape closer to a sphere show a higher effective reaction rate.
Three‐Dimensional Reconstruction of Tissues (2006)

Cellular morphology is inherently three-dimensional. However, most histological techniques for tissue analysis focus on extracting information from two-dimensional slices of fixed samples or dissociated cells. These techniques result in a significant loss of the three-dimensional information of the tissue, including true cell volume, orientation, and whole cell shape. This unit discusses various options for three-dimensional imaging, provides a protocol for performing post-processing reconstruction based on serial slicing, and discusses the current advantages and limitations of the three-dimensional approach to quantitative tissue analysis. The focus of this protocol is on cardiac tissue, but the techniques can be applied to any solid tissue.
Ein neuer Schichtsilicatstrukturtyp: der Zeolithvorläufer RUB‐15: [N(CH3)4]8[Si24O52(OH)4] · 20H2O (1996)

Ein Bindeglied in der Reihe Inselsilicathydrat–Schichtsilicathydrat–Gerüstsilicat ist RUB–15, ein neuartiges Silicathydrat mit einem dreidimensionalen Bindungsnetzwerk aus schichtartig angeordneten Silicat‐Ionen und Wassermolekülen, die durch Wasserstoffbrückenbindungen verknüpft sind. RUB‐15 verdeutlicht die enge kristallchemische Verwandtschaft von SiO 2 und H 2 O. Ein Ausschnitt aus der Struktur ist rechts gezeigt. magnified image
Insights from In Vitro and Clinical Data to Guide Transition from the Novel P2Y12 Antagonist Selatogrel to Clopidogrel, Prasugrel, and Ticagrelor (2021)

Reduced pharmacodynamic (PD) effects of irreversible oral P2Y<sub>12</sub> receptor antagonists have been reported when administered during cangrelor infusion. Therefore, the PD interaction liability of the novel P2Y<sub>12</sub> receptor antagonist selatogrel with irreversible (i.e., clopidogrel, prasugrel) and reversible (i.e., ticagrelor) oral P2Y<sub>12</sub> receptor antagonists was investigated in vitro and in healthy subjects. In vitro<i>,</i> selatogrel reduced the effects of clopidogrel and prasugrel in a concentration-dependent manner, while additive effects were observed for the combination of selatogrel and ticagrelor. Accordingly, a single-center, randomized, double-blind, two-way crossover study was conducted consisting of six groups. In each group (<i>N</i> = 12), an open-label loading dose of 300 or 600 mg clopidogrel, 60 mg prasugrel, or 180 mg ticagrelor was administered 30 minutes (i.e., at <i>t</i> <sub>max</sub> of selatogrel) or 12 hours after a single subcutaneous dose of 16 mg selatogrel or placebo. Inhibition of platelet aggregation (IPA) was assessed at various time points up to 48 hours. Reduced IPA was determined when clopidogrel or prasugrel was administered 30 minutes after selatogrel (∼40 and 70% lower IPA, respectively, at 24 hours postdosing). However, when administering prasugrel 12 hours after selatogrel, IPA was not impacted (>90% IPA) and in the case of clopidogrel reduced effects were partially mitigated. Similar IPA was determined for ticagrelor when administered 30 minutes after selatogrel or placebo. In conclusion, reduced IPA was observed for clopidogrel and prasugrel when administered after selatogrel, which can be mitigated by applying an appropriate time interval. No PD interaction with ticagrelor was observed.
Cue scaffolding to train stereo-anomalous observers to rely on disparity cues (2020)

Stereopsis plays an important role in everyday visuomotor tasks. However, abnormal visual experience during development may result in reduced or absent stereopsis. In recent years, laboratory methods have been designed to strengthen stereopsis in adults with abnormal binocular vision. However, these techniques require many trials and are often not engaging. Video games can be used to tackle these challenges. Several studies have reported benefits of using video games to improve both low- and high- level visual functions in the treatment of amblyopia. Furthermore, with recent commercialization of Virtual Reality (VR), depth cue scaffolding has become possible in this approach. Our aim was to test whether depth cue scaffolding in VR can be used to train stereo-anomalous observers to rely on disparity cues. We designed two VR games to train stereovision. Strabismic deviations were corrected using a virtual prism and dichoptic calibration sight, and input to the two eyes was perceptually balanced by reducing the luminance to the dominant eye. Thus, avoiding diplopia and/or suppression. One game required participants to launch a dart when a dartboard, moving in depth, was on the same depth plane as the dart. The other game required participants to destroy the nearest of several targets moving forward. Importantly, initially the games provided multiple cues for judging depth (shadows, perspective, motion parallax, and disparity). As participants progressed through the game, we selectively removed cues (shadows, perspective and motion parallax), finally leaving only disparity cues. Results show that most stereo deficient participants improved in the game, and several showed transfer to both clinical and psychophysical stereoacuity tests (Ding & Levi, 2011). Overall, participants with anisometropia reached a lower stereoacuity threshold at a faster rate compared to participants with strabismus. We conclude that cue scaffolding may be a useful tool for recovering stereopsis in adults with abnormal visual development.
Pre-clinical Evaluation of a Variable Length and Conforming Peritoneal Dialysis Catheter Weighted Anchor: In Vitro Analysis and Cadaver Feasibility Study (2020)

Abstract Purpose Peritoneal dialysis (PD) catheters function best when residing within the retrovesical space of the peritoneal cavity, but they frequently migrate and fail. A novel variable length and conforming PD catheter weighted anchor to prevent migration has been evaluated.Methods Test devices were placed in normal saline for 21 months. The effluent was periodically measured for heavy metals, including tungsten. The water-tight property of the device was also tested separately. Four cadavers were subjected to three-dimensional imaging and maneuvering to evaluate percutaneous insertion, function, stability within the retrovesical space, and percutaneous retrievability in 10 test devices.Results Liquid leakage was low, with a mean absorbance of the test device effluent saline of 0.015. Mean methylene blue absorbance of the test device was significantly lower than the positive control (p-value = 0.01). Leakage of tungsten from devices made with medical grade Silastic tubing was also low, with a mean of 0.362 mg/L in the effluent saline, compared to a background concentration of 0.166 mg/L. Each test device was successfully inserted into the retrovesical space and retrieved percutaneously and remained completely intact following placement and insertion. No test device migrated as shown on axial cone beam CT imaging. Mean flow times and volumes were satisfactory at 3 minutes and 0.92L, respectively, for all test devices. For all catheters, the mean flow rate was 312 cc/min. No significant difference was found between the pre-roll and post-roll mean flow rates of the test devices (p-value = 0.35).Conclusion This PD catheter weighted anchor showed stability, with minimal leakage of tungsten. All test devices were successfully inserted and retrieved percutaneously, with no damage or migration, and mean flow rates were satisfactory. Further investigation is warranted.
16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease (2017)

The human microbiome is of considerable interest to pediatric inflammatory bowel disease (PIBD) researchers with 1 potential mechanism for disease development being aberrant immune handling of the intestinal bacteria. This study analyses the fecal microbiome through treatment in newly diagnosed PIBD patients and compares to cohabiting siblings where possible. Patients were recruited on clinical suspicion of PIBD before diagnosis. Treatment-naïve fecal samples were collected, with further samples at 2 and 6 weeks into treatment. Samples underwent 16S ribosomal ribonucleic acid (RNA) gene sequencing and short-chain fatty acids (SCFAs) analysis, results were analyzed using quantitative-insights-into-microbial-ecology. Six PIBD patients were included in the cohort: 4 Crohn disease (CD), 1 ulcerative colitis (UC), 1 inflammatory bowel disease (IBD) unclassified, and median age 12.6 (range 10-15.1 years); 3 patients had an unaffected healthy sibling recruited. Microbial diversity (observed species/Chao1/Shannon diversity) was reduced in treatment-naïve patients compared to siblings and patients in remission. Principal coordinate analysis using Bray-Curtis dissimilarity and UniFrac revealed microbial shifts in CD over the treatment course. In treatment-naïve PIBD, there was reduction in functional ability for amino acid metabolism and carbohydrate handling compared to controls (P = .038) and patients in remission (P = .027). Metabolic function returned to normal after remission was achieved. SCFA revealed consistent detection of lactate in treatment-naïve samples. This study adds in-depth 16S rRNA sequencing analysis on a small longitudinal cohort to the literature and includes sibling controls and patients with UC/IBD unclassified. It highlights the initial dysbiosis, reduced diversity, altered functional potential, and subsequent shifts in bacteria from diagnosis over time to remission.
Modulation of Susceptibility to HIV-1 Infection by the Cytotoxic T Lymphocyte Antigen 4 Costimulatory Molecule (1999)

CD4 T cells activated in vitro by anti-CD3/28-coated beads are resistant to infection by CC chemokine receptor 5 (CCR5)-dependent HIV-1 isolates. In vivo, antigen-presenting cells (APCs) activate CD4 T cells in part by signaling through the T cell receptor and CD28, yet cells stimulated in this manner are susceptible to HIV-1 infection. We show that cytotoxic T lymphocyte antigen 4 (CTLA-4) engagement counteracts the CD28 antiviral effects, and that the ratio of CTLA-4 to CD28 engagement determines the susceptibility of HIV-1 infection. Furthermore, unopposed CTLA-4 signaling provided by CD28 blockade promotes vigorous HIV-1 replication, despite minimal T cell proliferation. Finally, CTLA-4 antibodies decrease the susceptibility of antigen-activated CD4 T cells to HIV, suggesting a potential approach to prevent or limit viral spread in HIV-1-infected individuals.
Lysine Methyltransferase SETD7 (SET7/9) Regulates ROS Signaling through mitochondria and NFE2L2/ARE pathway (2015)

Reactive oxygen species (ROS) homeostasis requires stringent regulation. ROS imbalance, especially ROS accumulation, has profound implications in various disease pathogenesis. Lysine methylation of histone and non-histone proteins has been implicated in various cellular responses. The main objective of this study is to investigate the role of SET domain containing lysine methyltransferase SETD7 (SET7/9) in the regulation of ROS-mediated signaling. Here we report that inhibition of SETD7 with siRNA or a SETD7 small molecule inhibitor in both macrophages and a human bronchial epithelial cell line (Beas-2B) were able to counter NF-ĸB-induced oxidative stress and pro-inflammatory cytokine production. Meanwhile, inhibition of SETD7 elevates mitochondria antioxidant functions via negative regulation of PPARGC1A and NFE2L2. Using a co-expression system and purified proteins, we detected direct interaction between SETD7 and NFE2L2. These results indicate that lysine methylation by SETD7 is important for the fine-tuning of ROS signaling through its regulation on pro-inflammatory responses, mitochondrial function and the NFE2L2/ARE pathway. Up-regulation of multiple antioxidant genes and improved ROS clearance by inhibition of SETD7 suggests the potential benefit of targeting SETD7 in treating ROS-associated diseases.
Melody Extraction from Polyphonic Music Signals: Approaches, applications, and challenges (2014)

Melody extraction algorithms aim to produce a sequence of frequency values corresponding to the pitch of the dominant melody from a musical recording. Over the past decade, melody extraction has emerged as an active research topic, comprising a large variety of proposed algorithms spanning a wide range of techniques. This article provides an overview of these techniques, the applications for which melody extraction is useful, and the challenges that remain. We start with a discussion of ?melody? from both musical and signal processing perspectives and provide a case study that interprets the output of a melody extraction algorithm for specific excerpts. We then provide a comprehensive comparative analysis of melody extraction algorithms based on the results of an international evaluation campaign. We discuss issues of algorithm design, evaluation, and applications that build upon melody extraction. Finally, we discuss some of the remaining challenges in melody extraction research in terms of algorithmic performance, development, and evaluation methodology.
Interdigitated 3-D Silicon Ring Microelectrodes for DEP-Based Particle Manipulation (2012)

This paper describes the design, the fabrication, and the characterization of an interdigitated 3-D silicon (Si) ring microelectrodes for dielectrophoretic (DEP) manipulation of particles. The 3-D microelectrodes are derived from a high-aspect-ratio comb structure etched in a doped single crystal Si on an insulating dielectric (silicon-on-insulator). Fingers of the comb are evolved into ring microelectrodes once perforated with a linear array of well-defined round lateral constrictions. This is achieved by the segmented finger layout and the Si dry release strategy borrowed from inertial microelectromechanical systems. The fingers and their interspaces are sealed with a cover layer forming a microfluidic flow chamber surrounded by 3-D microelectrodes and accessible via single inlet/outlet. The functionality of the device has been verified on 2- and 10-μm polystyrene microspheres in pressure-driven flow through the ring microelectrodes at 3.3 μL/min effectively focusing them into streams or trapping them around the fingers at moderate voltage levels (20-40 Vpp).
In situ evolution of stress gradients in Cu films induced by capping layers (2010)

Depth-dependent stress distributions within copper films possessing capping layers were measured during in situ thermal anneals. Glancing-incidence x-ray diffraction measurements of SiCxNyHz capped Cu films revealed that a strain gradient near the cap/Cu interface, created by constraint imposed by the cap during its deposition process, decreased as the sample temperature increased to 350 °C. Although the increase in sample temperature allowed Cu to approach its equilibrium lattice spacing at the cap deposition temperature and minimize the corresponding stress gradient, both the gradient and concomitant increase in residual bulk stress of the Cu film reappeared after cooling to room temperature.
Tailored resonance dependence on input optical power in silicon microring resonators (2012)

We demonstrate the ability to tailor the resonance dependence on input power in silicon microring resonators using a passive technique by utilizing two counteracting processes, free carrier dispersion blueshift and thermo-optic redshift. In our fabricated silicon microring resonators, we achieve an effective blueshift, as well as effective redshift. We also design and fabricate a power insenstive silicon microring that has a five-fold improvement in cavity energy handling capability compared to a regular microring.
Nanomanipulation and Characterization of Individual Carbon Nanotubes (2006)

We describe the implementation of new tools for the measurement of the mechanics of nanostructures. These tools have been used to measured the stiffness, fracture strength, and various tribological properties, of carbon nanotubes.
Treatment of recurrent giant iris cyst with intracyst administration of mitomycin C (2000)

Endophthalmitis following globe perforation with a hypodermic needle EDITOR,-Exogenous endophthalmitis is a common complication of intraocular foreign bodies (IOFBs). 1 It commonly occurs in association with a non-metallic foreign body and often results in profound visual loss. 2 Early diagnosis and treatment with intravitreal antibiotics are essential in its treatment. 3 We describe an unusual case of exogenous endophthalmitis caused by a heroin filled needle, the patient rapidly losing vision despite active intervention.