gebhart/patrepeval huggingface dataset:
Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach (2009)

The analysis of proteome-wide phosphorylation events is still a major analytical challenge because of the enormous complexity of protein phosphorylation networks. In this work, we evaluate the complementarity of Lys-N, Lys-C, and trypsin with regard to their ability to contribute to the global analysis of the phosphoproteome. A refined version of low-pH strong cation exchange was used to efficiently separate N-terminally acetylated, phosphorylated, and nonmodified peptides. A total of 5036 nonredundant phosphopeptides could be identified with a false discovery rate of <1% from 1 mg of protein using a combination of the three enzymes. Our data revealed that the overlap between the phosphopeptide data sets generated with different proteases was marginal, whereas the overlap between two similarly generated tryptic data sets was found to be at least 4 times higher. In this way, the parallel use of Lys-N and trypsin enabled a 72% increase in the number of detected phosphopeptides as compared to trypsin alone, whereas a trypsin replicate experiment only led to a 25% increase. Thus, when focusing solely on the trypsin and Lys-N data, we identified 4671 nonredundant phosphopeptides. Further analysis of the detected sites showed that the Lys-N and trypsin data sets were enriched in significantly different phosphorylation motifs, further evidencing that multiprotease approaches are very valuable in phosphoproteome analyses.
Optical loss and interface morphology in AlGaAs∕GaAs distributed Bragg reflectors (2007)

It is shown that n-type doping of AlGaAs∕GaAs distributed Bragg reflectors (DBRs) grown by metal-organic vapor-phase epitaxy has a profound negative impact on the performance of vertical-cavity surface-emitting lasers (VCSELs) based on such mirrors. Using an intracavity contact scheme, 1.3-μm-range InGaAs VCSELs with and without doping in the bottom DBR are directly compared. Doped mirrors lead to lower slope efficiency, lower output power, and higher threshold current. From x-ray diffraction, high-accuracy reflectance measurements, and atomic force microscopy studies, it is suggested that this performance degradation is due to the doping-enhanced Al–Ga interdiffusion, leading to interface roughening and increased scattering loss.
Age-based garbage collection (1999)

Modern generational garbage collectors look for garbage among the young objects, because they have high mortality; however, these objects include the very youngest objects, which clearly are still live. We introduce new garbage collection algorithms, called age-based, some of which postpone consideration of the youngest objects. Collecting less than the whole heap requires write barrier mechanisms to track pointers into the collected region. We describe here a new, efficient write barrier implementation that works for age-based and traditional generational collectors. To compare several collectors, their configurations, and program behavior, we use an accurate simulator that models all heap objects and the pointers among them, but does not model cache or other memory effects. For object-oriented languages, our results demonstrate that an older-first collector, which collects older objects before the youngest ones, copies on average much less data than generational collectors. Our results also show that an older-first collector does track more pointers, but the combined cost of copying and pointer tracking still favors an older-first over a generational collector in many cases. More importantly, we reopen for consideration the question where in the heap and with which policies copying collectors will achieve their best performance.
Large-scale multimodal gesture recognition using heterogeneous networks (2018)

2017 IEEE. This paper presents the method designed for the 2017 ChaLearn LAP Large-scale Gesture Recognition Challenge. The proposed method converts a video sequence into multiple body level dynamic images and hand level dynamic images as the inputs to Convolutional Neural Networks (ConvNets) respectively through bidirectional rank pooling and adopts Convolutional LSTM Networks (ConvLSTM) to learn long-term spatiotemporal features from short-term spatiotemporal features extracted using a 3D convolutional neural network (3DCNN) at body and hand level. Such a heterogeneous network system learns effectively different levels of spatiotemporal features that are complementary to each other to improve the recognition accuracy largely. The method has been evaluated on the 2017 isolated and continuous ChaLearn LAP Large-scale Gesture Recognition Challenge datasets and the results are ranked among the top performances.
Network Analysis in Public Health: History, Methods, and Applications (2007)

Network analysis is an approach to research that is uniquely suited to describing, exploring, and understanding structural and relational aspects of health. It is both a methodological tool and a theoretical paradigm that allows us to pose and answer important ecological questions in public health. In this review we trace the history of network analysis, provide a methodological overview of network techniques, and discuss where and how network analysis has been used in public health. We show how network analysis has its roots in mathematics, statistics, sociology, anthropology, psychology, biology, physics, and computer science. In public health, network analysis has been used to study primarily disease transmission, especially for HIV/AIDS and other sexually transmitted diseases; information transmission, particularly for diffusion of innovations; the role of social support and social capital; the influence of personal and social networks on health behavior; and the interorganizational structure of health systems. We conclude with future directions for network analysis in public health.
The case report on pain treatment by extravascular laser system (2006)

Objectives : The purpose of this study was to assess the ability of Extravascular Laser System on pain treatment. Methods : On this study, we carried out with the 9 cases of children who visited in the Department of Pediatrics, OO University Oriental Hospital as pain. 9 children suffering from pain were treated with Extravascular Laser System, and two of these were treated with combined acupuncture. In order to determine the degree of pain relief, a visual analogue scale was used. Results : Extravascular Laser System for pain resulted in a significant decline in the visual analogue scale. For Extravascular Laser System combined with acupuncture, VAS score has fallen by 30% each time compared to 17.5% of Extravascular Laser System only. In 2 cases of chronic pain, VAS score decreased to 0. In 7 cases of acute pain, All of 7 children improved 50% on VAS score, On average VAS score have seen 79.2% reduction. The average treatment times of chronic pain were 5 times, while that of acute pain were 4.1 times. Conclusions : We report the good result of the efficacy of extravascular laser system on children's pain. but, this study's cases were small in number. so more study is need.
Monolithic fabrication of NPN and PNP AlInAs/GaInAs HBTs (2002)

The authors demonstrated the feasibility of a new technique for the monolithic fabrication of complementary heterostructure bipolar transistors (HBTs). The process led to coplanar npn and pnp HBTs, the first in the AlInAs/GaInAs material system, which were comparable with the state of the art in HBTs. These devices exhibited unity current gain cutoff frequencies (f/sub T/) up to 99 GHz and 14 GHz for the npn and pnp transistors, respectively. The fabrication scheme allows each of these device types to have individually designed epitaxial structures that are grown in a single molecular beam epitaxy run. Results show that the devices will be capable of tight packing densities for IC applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Weather Radar Ground Clutter. Part II: Real-Time Identification and Filtering (2009)

Abstract The identification and mitigation of anomalous propagation (AP) and normal propagation (NP) ground clutter is an ongoing problem in radar meteorology. Scatter from ground-clutter targets routinely contaminates radar data and masks weather returns causing poor data quality. The problem is typically mitigated by applying a clutter filter to all radar data, but this also biases weather data at near-zero velocity. Modern radar processors make possible the real-time identification and filtering of AP clutter. A fuzzy logic algorithm is used to distinguish between clutter echoes and precipitation echoes and, subsequently, a clutter filter is applied to those radar resolution volumes where clutter is present. In this way, zero-velocity weather echoes are preserved while clutter echoes are mitigated. Since the radar moments are recalculated from clutter-filtered echoes, the underlying weather echo signatures are revealed, thereby significantly increasing the visibility of weather echo. This paper describes the fuzzy logic algorithm, clutter mitigation decision (CMD), for clutter echo identification. A new feature field, clutter phase alignment (CPA), is introduced and described. A detailed discussion of CPA is given in Part I of this paper. The CMD algorithm is illustrated with experimental data from the Denver Next Generation Weather Radar (NEXRAD) at the Denver, Colorado, Front Range Airport (KFTG); and NCAR’s S-band dual-polarization Doppler radar (S-Pol).
Visual Hull Construction Using Adaptive Sampling (2005)

Volumetric visual hulls have become very popular in many computer vision applications including human body pose estimation and virtualized reality. In these applications, the visual hull is used to approximate the 3D geometry of an object. Existing volumetric visual hull construction techniques, however, produce a 3-color volume data that merely serves as a bounding volume. In other words it lacks an accurate surface representation. Polygonization can produce satisfactory results only at high resolutions. In this study we extend the binary visual hull to an implicit surface in order to capture the geometry of the visual hull itself. In particular, we introduce an octree-based visual hull specific adaptive sampling algorithm to obtain a volumetric representation that provides accuracy proportional to the level of detail. Moreover, we propose a method to process the resulting octree to extract a crack-free polygonal visual hull surface. Experimental results illustrate the performance of the algorithm.
Diapeutic cancer-targeting alkylphosphocholine analogs may advance management of brain malignancies (2016)

The following is a special report on alkylphosphocholine analogs as targeted imaging and therapy agents for cancer, and their potential role in diagnosis and treatment in glioblastoma and brain metastases. These novel cancer-targeting agents display impressive tumor avidity with low background in the normal brain, and multimodal diagnostic imaging and therapy capabilities. The use of these agents may significantly improve diagnosis, treatment and post-treatment follow-up in patients with brain malignancies.
Radiation dose from a phosphorous-32 impregnated wire mesh vascular stent (1997)

The near field dose distribution of a realistic vascular stent impregnated with radioactive 32P is calculated employing the dose-point-kernel (DPK) method in a homogeneous and uniform medium. The cylindrical wire mesh geometry for the Palmaz-Schatz [Palmaz-Schatz is a tradename of Cordis (a Johnson & Johnson company)] stent is incorporated in the model calculation, and the dose distribution generated by the beta particles emitted from the decayed radioactive 32P is computed at distances ranging from 0.1 to 2 mm exterior to the stent surface. Dose measurements were obtained using radiochromic film dosimetry media on an actual Palmaz-Schatz half-stent impregnated with 32P using ion implantation, and compared to the DPK model predictions. The close agreement between the model calculation and the film dosimetry data confirms the validity of the model which can be adapted to a variety of different stent designs.
Osteoarthritis in patients with familial Mediterranean fever: genetic basis and anti-inflammatory effect of laser acupuncture (2019)

Background Familial Mediterranean fever (FMF) is an autosomal recessive autoimmune disease characterized by recurrent attacks of fever, peritonitis, pleuritis, arthritis, and renal amyloidosis. Arthritis could be the presenting symptom in many cases. Laser acupuncture has analgesic and anti-inflammatory effects on joint arthritis. Aim To highlight the genetic basis of osteoarthritis in patients with FMF and to highlight the anti-inflammatory effect of laser acupuncture on osteoarthritis of knee joint in Egyptian patients with FMF. Patients and methods A randomized controlled study was performed on 40 Egyptian patients with FMF. Molecular analysis of MEFV gene mutations was performed for all selected patients. Twenty patients with FMF were exposed to low-level laser acupuncture sessions (laser acupuncture group) and 20 other patients with FMF did not receive low-level laser acupuncture sessions (control group). Twelve low-level laser acupuncture sessions were implemented for the group treated with laser acupuncture three times per week for a duration of 4 weeks. All patients were checked before and after laser acupuncture sessions for pain intensity, radiography changes, and some inflammatory markers (white blood cell, eosinophils, lymphocytes, erythrocyte sedimentation rate, and C-reactive protein). Results M694V mutation was detected in 40% of patients. Patients with FMF with knee arthritis exposed to low-level laser acupuncture sessions showed significant improvement in pain intensity compared with the control group (P Conclusion M694V variant of MEFV gene is more frequent in the Egyptian patients with FMF with osteoarthritis. Low-level laser acupuncture therapy is effective in ameliorating pain of osteoarthritis in patients with FMF.
Impact of Fluidic Chevrons on Jet Noise (2005)

The impact of alternating fluidic core chevrons on the production of jet noise is investigated. Core nozzles for a representative 1/9th scale, bypass ratio 5 model system were manufactured with slots cut near the trailing edges to allow for air injection into the core and fan streams. The injectors followed an alternating pattern around the nozzle perimeter so that the injection alternated between injection into the core stream and injection into the fan stream. For the takeoff condition and a forward flight Mach number of 0.10, the overall sound pressure levels at the peak jet noise angle decrease with increasing injection pressure. Sound pressure levels increase for observation angles less than 110o at higher injection pressures due to increases in high frequency noise. Greater increases in high frequency noise are observed when the number of injectors increases from 8 to 12. When the forward flight Mach number is increased to 0.28, jet noise reduction (relative to the baseline) is observed at aft angles for increasing injection pressure while significant increases in jet noise are observed at forward observation angles due to substantial acoustic radiation at high frequencies. A comparison between inflow and alternating injectors shows that, for equal mass injection rates, the inflow nozzle produces greater low frequency noise reduction (relative to the baseline) than the alternating injectors at 90o and aft observation angles and a forward flight Mach number of 0.28. Preliminary computational fluid dynamic simulations indicate that the spatial decay rate of the hot potential core flow is less for the inflow nozzle than for the alternating nozzles which indicates that gentle mixing may be preferred over sever mixing when fluidic chevrons are used for jet noise reduction.
Generation of polarization-entangled photon pairs and violation of Bell’s inequality using spontaneous four-wave mixing in a fiber loop (2004)

We report the generation of polarization entangled photon pairs in the 1550-nm wavelength band using spontaneous four-wave mixing in a dispersion-shifted fiber loop. The use of the fiber-loop configuration made it possible to generate polarization entangled states very stably. With accidental coincidences subtracted, we obtained coincidence fringes with $>90%$ visibilities, and observed a violation of Bell's inequality by seven standard deviations. We also confirmed the preservation of the quantum correlation between the photons even after they had been separated by 20 km of optical fiber.
Critical dimension small angle X-ray scattering measurements of FinFET and 3D memory structures (2013)

We have demonstrated that transmission critical dimension small angle X-ray scattering (CD-SAXS) provides high accuracy and precision CD measurements on advanced 3D microelectronic architectures. The competitive advantage of CD-SAXS over current 3D metrology methods such as optical scatterometry is that CD-SAXS is able to decouple and fit cross-section parameters without any significant parameter cross-correlations. As the industry aggressively scales beyond the 22 nm node, CD-SAXS can be used to quantitatively measure nanoscale deviations in the average crosssections of FinFETs and high-aspect ratio (HAR) memory devices. Fitting the average cross-section of 18:1 isolated HAR contact holes with an effective trapezoid model yielded an average pitch of 796.9 ± 0.4 nm, top diameter of 70.3 ± 0.9 nm, height of 1088 ± 4 nm, and sidewall angle below 0.1°. Simulations of dense 40:1 HAR contact holes and FinFET fin-gate crossbar structures have been analyzed using CD-SAXS to inquire the theoretical precision of the technique to measure important process parameters such as fin CD, height, and sidewall angle; BOX etch recess, thickness of hafnium oxide and titanium nitride layers; gate CD, height, and sidewall angle; and hafnium oxide and titanium nitride etch recess. The simulations of HAR and FinFET structures mimic the characteristics of experimental data collected at a synchrotron x-ray source. Using the CD-SAXS simulator, we estimate the measurement capabilities for smaller similar structures expected at future nodes to predict the applicability of this technique to fulfill important CD metrology needs.
Summary Abstract: Ion beam control of morphology during the growth of <i>a</i>SiH<i>x</i> thin films (1983)

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Generation of coarse‐scale continuum flow models from detailed fracture characterizations (2006)

A procedure for developing coarse‐scale continuum models from detailed fracture descriptions is developed and applied. The coarse models are in the form of a generalized dual‐porosity representation, in which matrix rock and fractures exchange fluid locally while large‐scale flow occurs through the fracture network. The methodology developed here introduces local subgrids to resolve dynamics within the matrix and provides appropriate coarse‐scale parameters describing fracture‐fracture, matrix‐fracture, and matrix‐matrix flow. The geometry of the local subgrids, as well as the required parameters for the coarse‐scale model, are determined from local flow solutions using the underlying discrete fracture model. The method is applied to two‐ and three‐dimensional single‐phase and two‐phase flow problems, and the accuracy of the coarse models is assessed relative to fully resolved discrete fracture simulations. For the cases considered, it is shown that the technique is capable of generating highly accurate coarse models with many fewer unknowns than the detailed characterizations, and speedups of about a factor of 100 are achieved.
One year in review 2016: systemic sclerosis. (2017)

Systemic sclerosis is a rare acquired systemic disease characterised by a complex pathogenesis and multi organ involvement. Every year, novel insights into the pathogenesis, diagnosis and treatment of this severe disease are published. Herewith, we provide an overview of the most significant literature contributions published over the last year.
Emergent verbal behaviour in human-robot interaction (2011)

The paper describes emergent verbal behaviour that arises when speech components are added to a robotics simulator. In the existing simulator the robot performs its activities silently. When speech synthesis is added, the first level of emergent verbal behaviour is that the robot produces spoken monologues giving a stream of simple explanations of its movements. When speech recognition is added, human-robot interaction can be initiated by the human, using voice commands to direct the robot's movements. In addition, cooperative verbal behaviour emerges when the robot modifies its own verbal behaviour in response to being asked by the human to talk less or more. The robotics framework supports different behavioural paradigms, including finite state machines, reinforcement learning and fuzzy decisions. By combining finite state machines with the speech interface, spoken dialogue systems based on state transitions can be implemented. These dialogue systems exemplify emergent verbal behaviour that is robot-initiated: the robot asks appropriate questions in order to achieve the dialogue goal. The paper mentions current work on using Wikipedia as a knowledge base for open-domain dialogues, and suggests promising ideas for topic-tracking and robot-initiated conversational topics.
Quiet gradient coils: active acoustically and magnetically screened distributed transverse gradient designs (1995)

The principle of active acoustic screening, recently introduced by Mansfield, Glover and Bowtell into the design of gradient coils for MRI, utilizes Lorentz force balancing to reduce acoustic noise. In this paper, the active acoustic screening principle is used to design cylindrical transverse gradients with distributed conductor or fingerprint designs for the primary. A second distributed conductor on a second surface is used to balance all Lorentz forces on the coil system. A third conductor wound on a third surface is employed to provide active magnetic screening of the whole system. Alternative distributed conductor arrangements are analysed in terms of their practical performance.
Family 39 α-<scp>l</scp>-Iduronidases and β-<scp>d</scp>-Xylosidases React through Similar Glycosyl−Enzyme Intermediates:  Identification of the Human Iduronidase Nucleophile (2003)

The inclusion of both beta-D-xylosidases and alpha-L-iduronidases within the same sequence-related family (family 39), despite the considerable difference in substrate structures and poor sequence conservation around the putative nucleophile, raises concerns about whether a common mechanism is followed by the two enzymes. A novel anchimeric assistance mechanism for iduronidases involving a lactone intermediate is one possibility. NMR analysis of the methanolysis reaction catalyzed by human alpha-L-iduronidase reveals that, as with the beta-D-xylosidases, alpha-L-iduronidase is a retaining glycosidase. Using two different mechanism-based inactivators, 5-fluoro-alpha-L-iduronyl fluoride and 2-deoxy-2-fluoro-alpha-L-iduronyl fluoride, the active site nucleophile in the human alpha-L-iduronidase was identified as Glu299 within the (295)IYNDEAD(301) sequence. The equivalent, though loosely predicted, glutamic acid was identified as the nucleophile in the family 39 beta-D-xylosidase from Bacillus sp. [Vocadlo, D., et al. (1998) Biochem. J. 335, 449-455]; thus, a common mechanism involving a covalent glycosyl-enzyme intermediate that adopts the rather uncommon (2,5)B conformation is predicted.
The combined treatment of 1,25-dihydroxyvitamin D3 and a non-steroid anti-inflammatory drug is highly effective in suppressing prostate cancer cell line (LNCaP) growth. (2005)

Although both 1,25(OH)2D3 and ibuprofen demonstrate in vitro anti-carcinogenic activities as a single drug treatment, the present results showed that the combined use of 1,25(OH)2D3 with ibuprofen is superior to treatment with a single drug.