gebhart/patrepeval huggingface dataset:
Benchtop Evaluation of Miniature Percutaneous Nephrolithotomy Lithotrites (2022)

<b><i>Introduction:</i></b> Percutaneous nephrolithotomy (PCNL) is the preferred treatment for kidney stones >2 cm. While PCNL has traditionally been performed using 24F to 30F access sheaths, there is a trend toward smaller sheaths and scopes to perform mini-PCNL (mPCNL). We performed benchtop assessment of multiple mPCNL lithotrites. <b><i>Methods:</i></b> One 1 cm<sup>3</sup>, hard Begostone phantom was placed in a cylinder with four 5.5 mm cylindrical openings to simulate the size of a 16.5F mPCNL sheath. Lithotripsy was performed with the 1.5 and 1.9 mm Trilogy, 1.83 mm ShockPulse, or a 200 μm Holmium:YAG (Ho:YAG) laser. Suction was used for the mechanical lithotrites. The Trilogy probes were set at 50% impact, 6 Hz, 80% ultrasound and 10% suction. The ShockPulse was used at high-power setting with low suction. The 1.9 mm Trilogy probe was used with a 15F mini-nephroscope. The 1.83 mm ShockPulse, 1.5 mm Trilogy and laser fiber were used with a 12F mini-nephroscope. The 120 W holmium laser was set at 0.5 J/70 Hz Moses-Distance. Ten independent runs were performed with modality. Time to complete stone clearance was recorded and mass stone clearance rates were calculated. <b><i>Results:</i></b> The Trilogy 1.9 mm showed superior stone clearance rate (11.69 ± 3.68 mg/s) <i>vs</i> the ShockPulse (SP) 1.83 mm (6.29 ± 1.37 mg/s, <i>p</i> = 0.003), the laser fiber (4.73 ± 0.61 mg/s, <i>p</i> < 0.0005), and the Trilogy 1.5 mm (6.84 ± 1.21 mg/s). The 200 μm laser fiber was inferior to all mechanical lithotrites. There was no difference between the 1.5 mm Trilogy and the 1.83 mm ShockPulse (<i>p</i> = 0.772). This translates to 3.9, 4.8, and 8.1 minutes less treatment time <i>vs</i> the 1.5 mm Trilogy, SP, and laser, respectively, for a spherical 1.5 cm diameter calcium oxalate monohydrate stone. <b><i>Conclusion:</i></b> Among these four commonly used mPCNL lithotripters, the Trilogy 1.9 mm demonstrated superior stone clearance rates in this benchtop model <i>vs</i> the Ho:YAG laser, 1.83 mm SP, and Trilogy 1.5 mm. Future clinical testing is warranted to evaluate the optimal lithotrite for mPCNL.
Atomic simulation of crystal orientation and workpiece composition effect on nano-scratching of SiGe alloy (2023)

Abstract Silicon–germanium (SiGe) alloy is a new semiconductor material of great interest in thermoelectric devices, optoelectronic devices, infrared detectors, and semiconductor industry. In the present work, molecular dynamics simulation was conducted to investigate the deformation behavior in nano-scratching of SiGe alloy. The effect of scratching direction and Ge composition on material removal mechanism was discussed, aiming to understand the nanoscale deformation mechanism of SiGe alloy. The simulation results indicate that the machining direction and Ge composition have significant influences on the atomic flow and chip formation during nano-scratching. Besides, less subsurface damage and elastic recovery are observed when scratching along the (011)[100] direction with higher Ge composition. The highest crystal purity of the machined surface is achieved when scratching on the Si 60 Ge 40 workpiece. Furthermore, the Ge composition has a significant influence on the workpiece temperature due to the variation of the thermal conductivity of the workpiece. This work could enrich the understanding of the deformation mechanism of SiGe alloy during nanoscale machining and open a potential to improve the machining performance of multicomponent semiconductor materials.
Synthesis of a poly(vinyl ether) containing a benzocyclobutene moiety and its reaction with dienophiles (1999)

1-Benzocyclobutenyl vinyl ether (1) was easily prepared by the elimination reaction of hydrogen bromide from 1-benzocyclobutenyl 1-bromoethyl ether obtained by 1-bromobenzocyclobutene and ethylene glycol via two steps in a good yield. Cationic polymerizations of 1 was carried out at −78°C for 2 h in toluene in the presence of BF3OEt2 as an initiator to give quantitatively the corresponding polymers (2) as white solids. As a model reaction of the polymer reaction of 2 with dienophiles, the Diels–Alder reactions of 1-methoxybenzocyclobutene with maleic anhydride (MA) in toluene at 100–140°C for 3 h were carried out to obtain the corresponding Diels–Alder adduct quantitatively at 140°C. The polymer reactions of 2 with MA and N-phenylmaleimide (MI) in toluene were carried out to yield the corresponding Diels–Alder adduct polymers in good yields. The degree of introduction of the dienophile could be controlled by temperature, and the unreacted benzocyclobutene moiety could further react with another benzocyclobutene moiety or dienophile. The properties (solubilities, Tg, and temperature of 10% weight loss) of the polymers obtained from the polymer reaction were quite different from those of 2. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 59–67, 1999
Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression (2021)

The ongoing unprecedented severe acute respiratory syndrome caused by the SARS-CoV-2 outbreak worldwide has highlighted the need for understanding viral-host interactions involved in mechanisms of virulence. Here, we show that the virulence factor Nsp1 protein of SARS-CoV-2 interacts with the host messenger RNA (mRNA) export receptor heterodimer NXF1-NXT1, which is responsible for nuclear export of cellular mRNAs. Nsp1 prevents proper binding of NXF1 to mRNA export adaptors and NXF1 docking at the nuclear pore complex. As a result, a significant number of cellular mRNAs are retained in the nucleus during infection. Increased levels of NXF1 rescues the Nsp1-mediated mRNA export block and inhibits SARS-CoV-2 infection. Thus, antagonizing the Nsp1 inhibitory function on mRNA export may represent a strategy to restoring proper antiviral host gene expression in infected cells.
Structural and functional characterization of the Staphylococcus aureus virulence factor and vaccine candidate FhuD2 (2012)

Staphylococcus aureus is a human pathogen causing globally significant morbidity and mortality. The development of antibiotic resistance in S. aureus highlights the need for a preventive vaccine. In the present paper we explore the structure and function of FhuD2 (ferric-hydroxamate uptake D2), a staphylococcal surface lipoprotein mediating iron uptake during invasive infection, recently described as a promising vaccine candidate. Differential scanning fluorimetry and calorimetry studies revealed that FhuD2 is stabilized by hydroxamate siderophores. The FhuD2-ferrichrome interaction was of nanomolar affinity in surface plasmon resonance experiments and fully iron(III)-dependent. We determined the X-ray crystallographic structure of ligand-bound FhuD2 at 1.9 Å (1 Å=0.1 nm) resolution, revealing the bilobate fold of class III SBPs (solute-binding proteins). The ligand, ferrichrome, occupies a cleft between the FhuD2 N- and C-terminal lobes. Many FhuD2-siderophore interactions enable the specific recognition of ferrichrome. Biochemical data suggest that FhuD2 does not undergo significant conformational changes upon siderophore binding, supporting the hypothesis that the ligand-bound complex is essential for receptor engagement and uptake. Finally, immunizations with FhuD2 alone or FhuD2 formulated with hydroxamate siderophores were equally protective in a murine staphylococcal infection model, confirming the suitability and efficacy of apo-FhuD2 as a protective antigen, and suggesting that other class III SBPs might also be exploited as vaccine candidates.
Human keratinocytes are a source for tumor necrosis factor alpha: evidence for synthesis and release upon stimulation with endotoxin or ultraviolet light. (1990)

Tumor necrosis factor alpha (TNF-alpha), in addition to being cytotoxic for certain tumor cells, has turned out as a multifunctional cytokine that is involved in the regulation of immunity and inflammation. Since human keratinocytes have been demonstrated to be a potent source of various cytokines, it was investigated whether epidermal cells synthesize and release TNF-alpha. Supernatants derived from normal human keratinocytes (HNK) and human epidermoid carcinoma cell lines (KB, A431) were tested both in a TNF-alpha-specific ELISA and a bioassay. In supernatants of untreated epidermal cells, no or minimal TNF-alpha activity was found, while after stimulation with lipopolysaccharide (LPS) or ultraviolet (UV) light, significant amounts were detected. Western blot analysis using an antibody directed against human TNF-alpha revealed a molecular mass of 17 kD for keratinocyte-derived TNF-alpha. These biological and biochemical data were also confirmed by Northern blot analysis revealing mRNA specific for TNF-alpha in LPS- or ultraviolet B (UVB)-treated HNK and KB cells. In addition, increased TNF-alpha levels were detected in the serum obtained from human volunteers 12 and 24 h after a single total body UVB exposure, which caused a severe sunburn reaction. These findings indicate that keratinocytes upon stimulation are able to synthesize and release TNF-alpha, which may gain access to the circulation. Thus, TNF-alpha in concert with other epidermal cell-derived cytokines may mediate local and systemic inflammatory reactions during host defense against injurious events caused by microbial agents or UV irradiation.
Learning Print Artifact Detectors (2012)

An important aspect of image and print quality is the existence of artifacts, such as compression or print artifacts. A general perceptual masking model, that describes the perceptual severity of artifacts on general background, could have been used to extract specific artifact detectors. However, currently general models are not mature enough to provide print artifact detectors for commercial print quality control application. Consequently we propose to employ machine learning techniques to learn a specific model for each print artifact based on a relevant set of features. We used the approach to develop two print artifact detectors. While the proposed approach was developed for print quality purpose, the method is general and can be used for learning automatic evaluators for image defects and quality degradation as well.
Silicon carbide MESFET's with 2 W/mm and 50% P.A.E. at 1.8 GHz (1996)

Silicon carbide MESFET's with 0.7 /spl mu/m/spl times/332 /spl mu/m gates under class B bias at 1.8 GHz had P/sub 1dB/=28.3 dBm (2 W/mm CW) and 50.4% PAE. At the same power density, these FET's had 66% PAE at 0.85 GHz. This high power density combined with the extremely high thermal conductivity of SiC makes it a promising technology for high power microwave applications.
Modélisation d'une chaîne de conversion éolienne de petite puissance (2001)

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Randomized, Double-Blind, Placebo-Controlled Study of Intravenous Amisulpride as Treatment of Established Postoperative Nausea and Vomiting in Patients Who Have Had No Prior Prophylaxis (2018)

IV amisulpride at 5 and 10 mg was safe and efficacious in the treatment of established PONV in surgical patients undergoing general anesthesia with no prior PONV prophylaxis.
Altered glutamate signaling in Parkinson’s disease patients with REM sleep behavior disorder (2023)

Abstract Background and Objectives Clinical heterogeneity of patients with Parkinson’s disease is well recognized. Parkinson’s disease with rapid eye movement (REM) sleep behavior disorder (RBD) is a more malignant phenotype with faster motor progression and higher non-motor symptom burden. However, the neural mechanisms underlying this clinical divergence concerning disbalances in neurotransmitter systems remain elusive. Methods Combining magnetic resonance (MR) spectroscopy and 11 C-ABP688 positron emission tomography (PET) on PET/MR hybrid system, we simultaneously investigated two different mechanisms of glutamate signaling in patients with Parkinson’s disease. Thirty-three patients were grouped according to their RBD status in overnight video-polysomnography and compared to 15 age- and sex-matched healthy control (HC) subjects. Total volumes of distribution (V T ) of 11 C-ABP688 were estimated with metabolite-corrected plasma concentrations during steady-state conditions between minutes 45 to 60 of the scan following a bolus-infusion protocol. Glutamate, glutamine, and glutathione levels were investigated with single voxel STEAM MR spectroscopy of the left putamen. Results We measured globally elevated V T of 11 C-ABP688 in patients with Parkinson’s disease and RBD compared to patients without RBD and HC subjects ( F (2,45) = 5.579, p = 0.007). Conversely, glutamatergic metabolites did not differ between groups and did not correlate with the regional V T of 11 C-ABP688. V T of 11 C-ABP688 correlated with the amount of REM sleep without atonia ( F (1,42) = 5.600, p = 0.023), and with dopaminergic treatment response in Parkinson’s disease patients ( F (1,30) = 5.823, p = 0.022). Conclusion Our results suggest that patients with Parkinson’s disease and RBD exhibit altered glutamatergic signaling indicated by higher V T of 11 C-ABP688 despite unaffected glutamate metabolism. The disbalance of glutamate receptors and neurotransmitter might indicate a novel mechanism contributing to the heterogeneity of Parkinson’s disease and warrants further investigation of drugs targeting mGluR5.
Automatic/interactive bead alignment in electron tomographic image processing (1994)

In the electron tomographic (EM) reconstruction process the mutual alignment between projections of different view angles is a crucial step. The routinely used alignment method is based on fiducial markers': a single-axis tilt projection series is collected with gold particles distributed on the specimen, the positions of high density gold beads on the projections are found, and the relationship between the specimen and the digital projection coordinate systems is determined from least-square fitting these found bead positions. There are four alignment parameters for each projection: two in shifts, one in in-plane rotation, and one in magnification. In the threedimensional studies of subcellular biological structures, we routinely collect data sets of more than 100 projections in the tilt range of ±75 ° with our automated EM set-up. Normally around 10 bead positions are used on each projection to achieve the alignment. Bead alignment used to be a laborious task since approximately 1000 bead positions need to be hand-picked for each data set.
New Mechanism of Noise Reduction in Electron Beams (1959)

Experiments have demonstrated that the basic noise quantities of an electron beam can be transformed and optimized by varying the field configuration and flow characteristics in the multivelocity region near the cathode. Tube noise figures as low as 2.9 db and numerical values of beam noisiness 2π/kTc(S−Π) &amp;lt;0.27 have been attained at microwave frequencies (S band). A detailed investigation of the conditions for minimum beam noisiness is presented. The beam is injected from the edge of the cathode into a highly divergent electric field and results in a distorted potential profile which greatly extends the low-velocity region below ½ v. It is shown that these features satisfy the physical conditions necessary for realizing a quasi-one-dimensional model in which the transforming properties of a ``multivelocity noise transducer'' can be adjusted by varying the rate of acceleration through this region. The experiments also suggest other models and possible approaches for further theoretical and experimental investigation.
Packaging of high-density fiber/laser modules using passive alignment techniques (2003)

A novel method for packaging a laser-fiber module is explored in which the critical laser-fiber alignment is carried out not with the usual active means, i.e., with the laser activated, but by a passive method based on the registration principles of photolithography. The novel method relies on an index scheme in which fiducial marks are lithographically placed on the laser chip and on a fiber carrier. At 850 nm, using the index technique with cleaved multimode fibers, it has been possible to achieve the same laser-fiber coupling efficiency as attained by active alignment; with cleaved single-mode fibers about 80% of the active-alignment coupling efficiency was achieved. Details of the novel index-alignment method are discussed, and a brief description of an improved computer-controlled version of the apparatus is given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Advanced Methods for Quasiprobabilistic Quantum Error Mitigation (2020)

Current quantum computers are plagued by prohibitive amounts of noise, which complicates the experimental realization of useful quantum algorithms that outperform classical computers.Quantum error mitigation techniques could constitute a potential avenue to demonstrate this feat without the need for fault-tolerant quantum error correction.One method in this family of mitigation techniques is the quasiprobability method introduced by Temme et al. [1].It simulates a noise-free quantum computer with a noisy one, with the caveat of only producing the correct expected values of measurement observables.The cost of a quasiprobability simulation manifests as a sampling overhead which scales exponentially in the number of error-mitigated gates in the circuit.In this thesis we aim to reduce the exponential basis of that overhead, which in turn allows the application of the quasiprobability method to deeper quantum circuits.A central result is the introduction of a novel scheme, which we call Stinespring algorithm, that aims to choose the quasiprobability decomposition in a noise-aware manner.Along the way, we introduce a generalization of the quasiprobability method, which we denote approximate quasiprobability method, that allows for a tradeoff between an approximation error and the sampling overhead.This method is already interesting on its own and we present a few potential applications.Finally, we present some ideas how quantum error correction can benefit from the quasiprobability method.This final part is separate to the other topics of the master thesis and gives a rough overview of a new research project that started towards the end of the thesis and that we will continue to pursue in the future.i Overview of ContributionsWe summarize the novel contributions from this thesis: Many details in the presentation of Chapter 2 have not been stated in such precision in previous literature.However, we estimate that many of these contributions are evident for someone knowledgeable in the domain. The channel difference decomposition (Section 2.6). The approximate QPD and its applications (Chapter 3). The Stinespring algorithm (Chapter 4).
Basic Research in Kidney Cancer (2020)

AbstractContextAdvances in basic research will enhance prognosis, diagnosis, and treatment of renal cancer patients.ObjectiveTo discuss advances in our understanding of the molecular basis of renal cancer, targeted therapies, renal cancer and immunity, and genetic factors and renal cell carcinoma (RCC).Evidence acquisitionData on recently published (2005–2011) basic science papers were reviewed.Evidence synthesisAdvances in basic research have shown that renal cancers can be subdivided based on specific genetic profiles. Now that this molecular basis has been established, it is becoming clear that additional events play a major role in the development of renal cancer. For example, aberrant chromatin remodelling appears to be a main driving force behind tumour progression in clear cell RCC. A large number of potential biomarkers have emerged using various high-throughput platforms, but adequate biomarkers for RCC are still lacking. To bring the potential biomarkers and biomarker profiles to the clinical arena is a major challenge for the field.The introduction of tyrosine kinase inhibitors (TKIs) for therapy has shifted the interest away from immunologic approaches. Nevertheless, a wealth of evidence supports immunotherapy for RCC. Interestingly, studies are now appearing that suggest a combination of TKI and immunotherapy may be beneficial.Thus far, little attention has been paid to patient-specific differences. With high-throughput methods becoming cheaper and with the advances in sequencing possibilities, this situation is expected to change rapidly.ConclusionsGreat strides have been made in the understanding of molecular mechanisms of RCC. This has led this field to the enviable position of having a range of molecularly targeted therapies. Large sequencing efforts are now revealing more and more genes responsible for tumour development and progression, offering new targets for therapy. It is foreseen that through integration of high-throughput platforms, personalised cancer treatment for RCC patients will become possible.
Integrating message-passing and shared-memory (1993)

This paper discusses some of the issues involved in implementing a shared-address space programming model on large-scale, distributed-memory multiprocessors. While such a programming model can be implemented on both shared-memory and message-passing architectures, we argue that the transparent, coherent caching of global data provided by many shared-memory architectures is of crucial importance. Because message-passing mechanisms ar much more efficient than shared-memory loads and stores for certain types of interprocessor communication and synchronization operations, hwoever, we argue for building multiprocessors that efficiently support both shared-memory and message-passing mechnisms. We describe an architecture, Alewife, that integrates support for shared-memory and message-passing through a simple interface; we expect the compiler and runtime system to cooperate in using appropriate hardware mechanisms that are most efficient for specific operations. We report on both integrated and exclusively shared-memory implementations of our runtime system and two applications. The integrated runtime system drastically cuts down the cost of communication incurred by the scheduling, load balancing, and certain synchronization operations. We also present preliminary performance results comparing the two systems.
Evolving Concepts in Phases I and II Drug Development for Crohn’s Disease (2016)

The highest attrition rates during drug development programmes occur at the proof of concept stage. Given the large number of molecules under development for Crohn's disease, a need exists to improve the efficiency of early drug development by fast-tracking promising agents and terminating ineffective ones. Multiple opportunities are available to achieve these goals, including the use of more responsive outcome measures, and the incorporation of sophisticated pharmacokinetic modelling and/or highly specific pharmacodynamic markers into exposure-based dosing regimens and novel trial designs. In this article we review these strategies and propose an integrated paradigm of early drug development in Crohn's disease.