gebhart/patrepeval huggingface dataset:
Manual and semiautomatic segmentation of bone sarcomas on MRI have high similarity (2020)

The aims of this study were to evaluate the intra- and interobserver reproducibility of manual segmentation of bone sarcomas in magnetic resonance imaging (MRI) studies and to compare manual and semiautomatic segmentation methods. This retrospective study included twelve osteosarcoma and eight Ewing sarcoma MRI studies performed prior to any therapeutic intervention. All cases were histopathologically confirmed. Three radiologists used 3D-Slicer software to perform manual segmentation of bone sarcomas in a blinded and independent manner. One radiologist segmented manually and also performed semiautomatic segmentation with the GrowCut tool. Segmentation exercises were timed for comparison. The dice similarity coefficient (DSC) and Hausdorff distance (HD) were used to evaluate similarity between the segmentation results and further statistical analyses were performed to compare DSC, HD, and volumetric results. Manual segmentation was reproducible with intraobserver DSC varying from 0.83 to 0.97 and HD from 3.37 to 28.73 mm. Interobserver DSC of manual segmentation showed variation from 0.73 to 0.97 and HD from 3.93 to 33.40 mm. Semiautomatic segmentation compared to manual segmentation resulted in DSCs of 0.71-0.96 and HDs of 5.38-31.54 mm. Semiautomatic segmentation required significantly less time compared to manual segmentation (P value ≤0.05). Among all situations compared, tumor volumetry did not show significant statistical differences (P value >0.05). We found excellent intra- and interobserver agreement for manual segmentation of osteosarcoma and Ewing sarcoma. There was high similarity between manual and semiautomatic segmentation, with a significant reduction of segmentation time using the semiautomatic method.
Redox homeostasis protects mitochondria through accelerating ROS conversion to enhance hypoxia resistance in cancer cells (2016)

Mitochondria are the powerhouses of eukaryotic cells and the main source of reactive oxygen species (ROS) in hypoxic cells, participating in regulating redox homeostasis. The mechanism of tumor hypoxia tolerance, especially the role of mitochondria in tumor hypoxia resistance remains largely unknown. This study aimed to explore the role of mitochondria in tumor hypoxia resistance. We observed that glycolysis in hypoxic cancer cells was up-regulated more rapidly, with far lesser attenuation in aerobic oxidation, thus contributing to a more stable ATP/ADP ratio. In hypoxia, cancer cells rapidly convert hypoxia-induced O(2˙)(-) into H2O2. H2O2 is further decomposed by a relatively stronger antioxidant system, causing ROS levels to increase lesser compared to normal cells. The moderate ROS leads to an appropriate degree of autophagy, eliminating the damaged mitochondria and offering nutrients to promote mitochondria fusion, thus protects mitochondria and improves hypoxia tolerance in cancer. The functional mitochondria could enable tumor cells to flexibly switch between glycolysis and oxidative phosphorylation to meet the different physiological requirements during the hypoxia/re-oxygenation cycling of tumor growth.
Automated Temporal Segmentation of Orofacial Assessment Videos (2022)

Computer vision techniques can help automate or partially automate clinical examination of orofacial impairments to provide accurate and objective assessments. Towards the development of such automated systems, we evaluated two approaches to detect and temporally segment (parse) repetitions in orofacial assessment videos. Recorded videos of participants with amyotrophic lateral sclerosis (ALS) and healthy control (HC) individuals were obtained from the Toronto NeuroFace Dataset. Two approaches for repetition detection and parsing were examined: one based on engineered features from tracked facial landmarks and peak detection in the distance between the vermilion-cutaneous junction of the upper and lower lips (baseline analysis), and another using a pre-trained transformer-based deep learning model called RepNet (Dwibedi et al, 2020), which automatically detects periodicity, and parses periodic and semi-periodic repetitions in video data. In experimental evaluation of two orofacial assessments tasks, - repeating maximum mouth opening (OPEN) and repeating the sentence "Buy Bobby a Puppy" (BBP) - RepNet provided better parsing than the landmark-based approach, quantified by higher mean intersection-over-union (IoU) with respect to ground truth manual parsing. Automated parsing using RepNet also clearly separated HC and ALS participants based on the duration of BBP repetitions, whereas the landmark-based method could not.
Mechanical Behavior Modeling of Containers and Octabins Made of Corrugated Cardboard Subjected to Vertical Stacking Loads (2021)

The aim of this paper is to characterize the mechanical behavior of corrugated cardboard boxes using simple models that allow an approach to the load capacity and the deformation of the boxes. This is very interesting during a box design stage, in which the box does not exist yet. On the one hand, a mathematical model of strength and deformation of boxes with different geometry is obtained from experiments according to the Box Compression Test and Edge Crush Test standards. On the second hand, a finite element simulation is proposed in which only the material elastic modulus in the compression direction is needed. For that, corrugated cardboard sheets are glued to build billets for testing, and an equivalent elastic modulus is obtained. This idea arises from the fact that the collapse of the box is given by the local bucking of the corrugated cardboard panels, due to the slenderness itself, and the properties in the compression direction are predominant. As a result, the numerical models show satisfactory agreement with experiments, concluding that it is an adequate methodology to simulate in a simple and efficient way this type of boxes built with corrugated cardboard.
Identification of methanogenesis and syntrophy as important microbial metabolic processes for optimal thermophilic anaerobic digestion of energy cane thin stillage (2019)

The aim of this research was to identify key microorganisms for thermophilic (55 °C) anaerobic digestion of thin stillage derived from hydrolysis and ethanol fermentation of energy cane in a conventional stirred tank reactor with a 10-day hydraulic retention time. Efficient thermophilic anaerobic digestion with a specific methane production of 0.43 Lmethane/gtCOD used/d and biogas containing around 56% methane was accomplished. Due to an overnight temperature perturbation the specific methane production decreased to 0.16 Lmethane/gtCOD used/d. Analysis of the microbial community showed the importance of methanogenic Archaea belonging to Methanosarcina and Methanothermobacter as well as syntrophic Bacteria related to Thermacetogenium, Tepidanaerobacter and Anaerobaculum. This indicates that retention of biomass maintaining syntrophy and methanogenesis more efficiently may be useful for thermophilic anaerobic digestion of thin stillage derived from the production of energy cane ethanol.
Accurate catadioptric calibration for real-time pose estimation in room-size environments (2002)

Omnidirectional video cameras are becoming increasingly popular in computer vision. One family of these cameras uses a catadioptric system with a paraboloidal mirror and an orthographic lens to produce an omnidirectional image with a single center-of-projection. In this paper, we develop a novel calibration model that we combine with a beacon-based pose estimation algorithm. Our approach relaxes the assumption of an ideal paraboloidal catadioptric system and achieves an order of magnitude improvement in pose estimation accuracy compared to calibration with an ideal camera model. Our complete standalone system, placed on a radio-controlled motorized cart, moves in a room-size environment, capturing high-resolution frames to disk and recovering camera pose with an average error of 0.56% in a region 15 feet in diameter.
SU‐GG‐T‐429: Implementation of a Geant4 Based GPU Monte Carlo Algorithm and Benchmarking of an IMRT Patient Plan (2010)

Purpose : To calculate the Monte Carlo based dose distribution of an IMRT prostate case on the GPU and thereby significantly increase the computation speed. Method and Materials : A Geant4 based head simulation of an Elekta Synergy accelerator head was utilized to calculate a phase space plane between the head and the patient geometry. An NVIDIA CUDA implementation of the GEANT4 low energy transportation algorithm was programmed validated for regular field shapes and then used to calculate the IMRT dose distribution of one prostate patient. The dose distribution was also calculated using GEANT4 on the same patient geometry. In the GPU implementation as well as in GEANT4 no variance reduction techniques were used. The IMRT patient was optimized with the Corvus treatment planning system (NOMOS). Results : The results showed a good agreement (gamma criteria 4%/3mm &gt; 97 %) between Geant4 CPU based simulations and the GPU based simulations. The computation time was approximately the same (12 minutes) for a 256 node cluster and 2 NVIDIA GTX 295 GPUs installed on one Intel quad core computer. This compares very well to time modern Voxel Monte Carlo based treatment planning systems need for one recalculation. Conclusion : This implementation proves the possibility to calculate complex IMRT plan simulations with a Monte Carlo dose engine on GPUs. This work is the starting point for future investigations leading to new variance reduction techniques suitable for GPUs and improving the speed of Monte Carlo simulations on standard workstations.
Trauma, and Genital and Urethral Reconstruction (2002)

No AccessJournal of UrologyUROLOGICAL SURVEY: Abstracts1 Jun 2002Trauma, and Genital and Urethral Reconstruction Jack W. McAninchM.D. Jack W. McAninchJack W. McAninch More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)65055-0AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Trauma, and Genital and Urethral Reconstruction." The Journal of Urology, 167(6), pp. 2667–2668 © 2002 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 167Issue 6June 2002Page: 2667-2668 Advertisement Copyright & Permissions© 2002 by American Urological Association, Inc.MetricsAuthor Information Jack W. McAninch More articles by this author Expand All Advertisement PDF DownloadLoading ...
Revisiting Liver Imaging with VIBE (2008)

Volume Interpolated Breath-hold Exami-nation (VIBE) [1] offers three-dimensional multiphase image acquisition before and following contrast administration on a breath-hold time scale. The dynamic behavior of liver lesions and structures during the precontrast, arterial, portal venous, early equilibrium and 5-minute-delayed equilibrium phases of enhance-ment allows more accurate characteriza-tion than static pre- and postcontrast analysis. VIBE is specifically designed for this task, and is a central pulse sequence in the MR evaluation of the liver.However, routine clinical constraints present significant challenges in the acquisition of optimal diagnostic images. Delicate diagnostic decisions require fine image detail and appropriate anatomic coverage, but very ill patients preclude extended breath-holding, limiting matrix size and resolution. Short acquisition times are thus critical for both patient comfort and diagnostic success. The VIBE sequence can overcome these challenges and maintain image quality despite clini-cal realities.The VIBE protocol we use at Mallinckrodt Institute of Radiology/ Washington Uni-versity School of Medicine in St. Louis provides the flexibility to ensure robust, high quality images in diverse clinical situations, on both open bore imaging systems such as the Siemens 1.5 Tesla MAGNETOM Espree and standard bore systems such as the 1.5 Tesla MAGNETOM Symphony, A Tim System.
Barriers and solutions to developing and maintaining research networks during a pandemic: An example from the iELEVATE perinatal network (2022)

Adaptability is key to maintaining network sites. Rapidly changing guidelines for beginning and continuing research during the pandemic required frequent intra- and inter-institutional communication to navigate.
Stimulation of Reactive Oxygen Species and Collagen Synthesis by Angiotensin II in Cardiac Fibroblasts (2010)

Superoxide anion generated by NAD(P)H-oxidase has an important role in the pathogenesis of cardiovascular diseases and scavenging superoxide anion can be considered as a reasonable therapeutic strategy. In hypertensive heart diseases there is a mutual reinforcement of reactive oxygen species (ROS) and angiotensin II (ANG II). ANG II increases the NAD(P)H-dependent superoxide anion production and the intracellular generation of ROS in cardiac fibroblasts and apocynin, a membrane NAD(P)H oxidase inhibitor, abrogates this rise. ANG II also stimulates the collagen production, the collagen I and III content and mRNA expression in cardiac fibroblasts and apocynin abolishes this induction. In this review we demonstrate that scavenging superoxide anion by tempol or EUK-8 or administration of PEG-superoxide dismutase (SOD) inhibits collagen production in cardiac fibroblasts. On the contrary increasing superoxide anion formation by inhibition of SOD stimulates collagen production. A vital role of SOD and the generated ROS can be suggested in the regulation and organization of collagen in cardiac fibroblasts. Specific pharmacological intervention with SOD mimetics can probably be an alternative approach for reducing myocardial fibrosis.
Abstract 2288: A novel enzymatic fragmentation library preparation chemistry that greatly reduces sequencing artifacts (2022)

Abstract After a decade of NGS technology and workflow innovation, personalized medicine is starting to become a reality. DNA fragmentation is still a critical bottleneck during library preparation. Sonication methods have been the gold standard for consistent fragmentation and uniform GC coverage, but are associated with a high upfront investment, expensive consumables, and are prone to oxidative DNA damage. On the other hand, enzymatic fragmentation methods hold the potential to be scalable, automation-friendly workflows that minimize DNA damage. Yet, typical enzymatic fragmentation methods have been shown to introduce systematic hairpin artifacts, exhibit suboptimal uniformity, and have a narrow range of input mass compatibility. We have developed a novel enzymatic fragmentation-based library preparation technology which, together with our high-fidelity library amplification module, effectively overcomes many of the key limitations of related chemistries. Libraries generated using our workflow reduced chimeric reads and terminal hairpin artifacts 10-fold compared to other enzymatic methods, and reached comparable levels of mechanically sheared DNA controls. Furthermore, we observed consistently even coverage uniformity and low sequence-specific bias for human whole genome sequencing. Fragmentation was tested across a broad sample input range from 100 pg to 500 ng. Library insert sizes were highly tunable from 150 bp to 550 bp and consistent across the input titration. High quality libraries with minimal adapter dimer were prepared from as little as 1 picogram of gDNA by adjusting the post amplification clean up conditions. Taken together, this enzymatic fragmentation and library preparation workflow avoids library preparation artifacts that convolute variant calling, is highly scalable, and suitable for ultra-low input samples. Citation Format: Zane Jaafar, Josh Haimes, Thomas Harrison, Lindsay Peterkin, Martin Ranik, Kristin Scott, Brian A. Kudlow. A novel enzymatic fragmentation library preparation chemistry that greatly reduces sequencing artifacts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2288.
Volume-fraction profiles of adsorbed polymers (1990)

The structure of adsorbed polymer layers has been studied extensively, both experimentally and theoretically, in a diverse range of systems. Although the form of the volume-fraction profile of polymer segments, normal to the interface has been predicted in detail from theory, few experimental methods can probe more than the first or second moments of this distribution. In this paper, the role of neutron scattering and magnetic resonance in such studies is surveyed. The results of these studies are compared with various theoretical models. The picture of the adsorbed layer that emerges is one that shows a strong dependence on the structure of the polymer, and the interactions between polymer segments, the interface and solvent(s).
On sound production in brass instruments (1990)

The brass player's lips under playing conditions are displaced both longitudinally along the axis of the air column entryway, and laterally, or perpendicular, to the axis. Existing theories have modeled the valving action of the player's lips as a simple oscillator, or lip reed, but fall into two classes, depending upon whether the lip reed displacement is assumed to be purely longitudinal or lateral. An alternative model of sound production is proposed, retaining the single degree-of-freedom oscillator description, but including both longitudinal and lateral displacements. The lip reed is assumed to execute a circular, outwardly rolling motion. In the limit of small oscillations, this simplifies to linear displacement along an axis inclined relative to the air column entryway axis. The angle of inclination is a model parameter, but should depend upon mouthpiece geometry and player's embouchure. The lip reed is driven longitudinally by the pressure difference between the player's mouth (upstream) and the mouthpiece (downstream). It is driven laterally by the pressure within the lip orifice, which is related to the downstream pressure by momentum flux conservation. The time domain model incorporates reflection functions looking downstream into the air column, and upstream into the player's respiratory tract. The upstream reflection function can similarly be incorporated into player-woodwind models.
Serum albumin and prothrombin time before entecavir treatment in chronic hepatitis B or cirrhosis are related to amelioration of liver function after treatment (2013)

Alb and PT before ETV treatment were related to amelioration of liver function after treatment. With our model, the probability of amelioration of liver function after treatment could be better estimated.
Synthesis of Poly(Methylacrylate-<I>b</I>-&epsilon;-Caprolactone) and Application to Compatibilizer for Poly(L-Lactide)/Poly(&epsilon;-Caprolactone) Blend System (2005)

Poly(L-lactic acid) (PLLA) was blended with poly(ε-caprolactone) (PCL) using a single-screw extruder in order to modify poor characteristic of these polymers. When the polymer was blended, the block copolymer that is synthesized by methyl acrylate (MA) and ε-caprolactone (ε-CL) via an atom transfer radical polymerization was used as a novel compatibilizer. The structure of the synthesized compatibilizer is determined by 1H or 13C NMR. From this result, it was found that the ring-opening polymerization of the ε-CL was taken place in the hydroxyl end group of MA. Moreover, the morphologies of the PLLA/PCL solvent-cast blend films were observed by the optical microscope and SEM. From the optical microscopic observation, the morphologies of the solvent-cast blend films with the synthesized compatibilizer were more homogeneous than that of the solvent-cast blend films without the compatibilizer. It was confirmed that the phase structure of the solvent-cast blend films with the compatibilizer was more stable than that of solvent-cast blend films without the compatibilizer.
Practical Drug Evaluation Method (1965)

THE USE OF psychopharmacologic agents has assumed a prominent role in the treatment of patients with emotional disturbances. Published reports of well-controlled studies of these drugs are largely limited to psychiatric inpatients, with a noteworthy paucity of satisfactory studies of their use in outpatients. Among other factors, it has been so difficult to accumulate a sufficient population of suitable outpatients who will complete a study of more than one or two week's duration that satisfactory studies, with few exceptions, have been limited to very large clinics in metropolitan centers or to cumbersome difficult collaborative studies.<sup>1-3</sup>Nevertheless, the widespread use of psychoactive drugs in outpatient medical practice demands that continued efforts be made to develop methods for adequately controlled studies in diverse populations since simple clinical impressions have been notoriously unreliable in the past.<sup>4</sup> In an effort to make possible early clinical evaluations
Der Einfluss von NADPH Oxidasen auf die LPS-induzierte Amplifikation der hypoxischen pulmonalen Vasokonstriktion (2008)

Die hypoxische pulmonale Vasokonstriktion (HPV) dient der Anpassung der Lungenperfusion an die lokale Ventilation und somit der Optimierung des Gasaustausches. Im Zuge einer Sepsis kann es zu einer Modulation der Stärke der HPV mit konsekutiver pulmonaler Hypertonie kommen. Ziel war daher, Pathomechanismen der LPS-induzierten HPV-Amplifikation zu untersuchen.
Developing Intercultural Competence and Language Skills Through International Online Collaborative Learning (2017)

Raising the intercultural competence of learners has been one of the most important issues in language education in this global world, but how can we integrate intercultural education into our teaching? This chapter introduces two online exchange projects, one for the beginner level and one for the intermediate level, which were designed for Swedish learners of Japanese as a means to develop their intercultural competence through collaborative language learning. The projects were designed through collaboration between five universities in Europe and Asia. In this chapter, the authors explore how the intercultural competence of learners developed based on learners' reflections after each session and their answers in the questionnaire after the project. The study finds that the different language levels require teachers to take different approaches in designing the intercultural contents of the projects. The chapter ends with further discussions on how to design intercultural education in an online environment.
Coronary Sinus Flow Measurement by Means of Velocity-encoded Cine MR Imaging: Validation by Using Flow Probes in Dogs (2000)

VEC MR imaging has the potential to measure coronary sinus flow during different physiologic conditions and can serve as a noninvasive modality to quantify global LV perfusion in patients.
An Optical Fiber Wavelength Standard for Pinon Flat Observatory (1985)

Abstract : An atomic wavelength standard has been acquired and a single-mode optical fiber network fabricated for the Pinon Flat Geophysical Observatory. These enhancements have greatly increased the precision of this unique facility.
NRL Remote Sensing Experiment (1983)

Seasat synthetic aperture radar (SAR) images of the ocean contain a wealth of ocean features ranging in size from 100 km mesoscale eddies to internal waves and dekameter surface waves [ Beal et al , 1981]. In particular SAR and SLAR (side‐looking airborne, or real‐aperture, radar) images of shallow water (usually less than 40 m deep) near coastal areas (e.g., Nantucket Shoals, English Channel, German Bight, etc.) contain features that relate almost one to one with the bottom topography (see cover figure as an example). Also evident in the cover figure are tide‐induced internal waves (top and middle right in the image), a number of current rips, a current shear front near the bottom edge of the image, and the dark region covering a great part of the middle portion indicating small microwave backscatter power, the result of very stable atmospheric conditions owing to cold upwelling water underneath warm air.