gebhart/patrepeval huggingface dataset:
Motion Management and Image Guidance for Thoracic Tumor Radiotherapy: Clinical Treatment Programs (2011)

Managing target motion first requires understanding the nature of the motion characteristic of the tumor in the individual patient. It is important to have effective immobilization and patient training strategies to help reduce motion, and then to design appropriate margins and compensation for the residual motion that is quantified. Especially when considering complex, technically demanding treatments that require a degree of patient cooperation, careful patient selection is needed to ensure that the potential benefits of the treatment design are actually realized. Finally, accurate treatment hinges critically on verification - of overall positioning, of target and organ motion at the time of treatment, and of the performance of the selected treatment strategy. Properly selected imaging methods are central to this verification process. This discussion will present practical solutions for motion management and image guidance of radiotherapy for thoracic tumors, and most of these concepts are widely applicable to treatment of other tumor sites as well.
Quick Determination of Copper-Metallization Long-Term Impact on Silicon Solar Cells (2010)

S.H942-H946
Repair of phase defects in extreme-ultraviolet lithography mask blanks (2004)

Phase defects that introduce errors in the printed image are one of the major yield limiters for reticles in extreme-ultraviolet lithography. The basis for a reticle is a mask blank, consisting of an ultra-low-expansion substrate and a reflective multilayer stack that is made up of Mo and Si. A potential methodology for repairing phase defects in these mask blanks is to locally irradiate it with a high-resolution electron beam to induce structural deformations that cancel out the distortion of the multilayer. We present experimental and modeling results that show that the interaction of an electron beam with a mask blank can only be understood when the contraction of the multilayer through silicide formation and substrate compaction, as well as the mechanical response of the mask blank, are considered. One of the consequences is that electron beams with energies around 10 keV that are less than 20 nm in diameter induce depressions in multilayers made up of 50 Mo∕Si bilayers that have a surprisingly large diameter of about a micrometer. Our models suggest that these unacceptably large diameters can only be reduced if the compaction of the substrate is prevented.
Safety Overview of a Recombinant Live-Attenuated Tetravalent Dengue Vaccine: Pooled Analysis of Data from 18 Clinical Trials (2016)

A recombinant live attenuated tetravalent dengue vaccine (CYD-TDV) has been shown to be efficacious in preventing virologically-confirmed dengue disease, severe dengue disease and dengue hospitalization in children aged 2-16 years in Asia and Latin America. We analyzed pooled safety data from 18 phase I, II and III clinical trials in which the dengue vaccine was administered to participants aged 2-60 years, including long-term safety follow-up in three efficacy trials. The participants were analyzed according to their age at enrollment. The percentage of participants aged 2-60 years reporting ≥1 solicited injection-site or systemic reactions was slightly higher in the CYD-TDV group than in the placebo group. The most common solicited injection-site reactions were pain. Headache and malaise were the most common solicited systemic reactions. In both groups 0.3% of participants discontinued for safety reasons. The most common unsolicited adverse events were injection-site reactions, gastrointestinal disorders, and infections. Reactogenicity did not increase with successive doses of CYD-TDV. The frequency and nature of SAEs occurring within 28 days of any dose were similar in the CYD-TDV and placebo groups and were common medical conditions that could be expected as a function of age. Baseline dengue virus serostatus did not appear to influence the safety profile. No vaccine-related anaphylactic reactions, neurotropic events or viscerotropic events were reported. In year 3 after dose 1, an imbalance for dengue hospitalization, including for severe dengue, observed in participants aged <9 years in the CYD-TDV group compared with the placebo group was not observed for participants aged ≥9 years. In Year 4, this imbalance in participants aged <9 years was less marked, giving an overall lower risk of dengue hospitalization or severe dengue from dose 1 to Year 4 in the CYD-TDV group. These results have contributed to the definition of the target population for vaccination (≥9 years old) for which CYD-TDV has a satisfactory safety profile. Long-term safety will continue to be monitored in the ongoing follow-up of efficacy trials. Safety and effectiveness in real-life settings will be assessed through post-licensure studies.
A high-frequency ultrasound imaging system combining limited-angle spatial compounding and model-based synthetic aperture focusing (2011)

High-frequency ultrasound (HFUS) imaging systems are routinely used for medical diagnostics (skin, eyes) and for medical research (small animal imaging). Although systems with array transducers are already commercially available, imaging systems with single-element transducers are still of interest and available as well, because this type of transducer is less complex, less expensive, and technically mature. Nevertheless, drawbacks exist, for example, the need for mechanical scanning units and the limited depth of field. In this paper, we present a high-frequency (20 MHz) ultrasound imaging system equipped with a spherically focused transducer. Limited-angle spatial compounding is utilized to improve the image contrast, to suppress speckle and noise, and to reduce imaging artifacts. To overcome the limitation in depth of field, the system uses a novel synthetic aperture focusing technique based on the correlation of the recorded echo signals with the simulated point spread function of the imaging system. This method results in lower side lobe levels and greater noise reduction compared with delay-and-sum focusing, which is demonstrated by wire phantom measurements. When used in combination with limited-angle spatial compounding, as presented in this paper, the resulting image quality is superior to conventional single-element HFUS imaging systems and to array systems. Examples of measurements on tissue phantoms and small animals (ex vivo) are presented and discussed in detail.
Metal Oxide Varistors (1987)

Gallium is a metal that literally melts in your hand. It has low toxicity, near-zero vapor pressure, and a viscosity similar to water. Despite possessing a surface tension larger than any other liquid (near room temperature), gallium can form nonspherical ...Read More
Emerging new tools to study and treat muscle pathologies: genetics and molecular mechanisms underlying skeletal muscle development, regeneration, and disease (2016)

Skeletal muscle is the most abundant tissue in our body, is responsible for generating the force required for movement, and is also an important thermogenic organ. Skeletal muscle is an enigmatic tissue because while on the one hand, skeletal muscle regeneration after injury is arguably one of the best-studied stem cell-dependent regenerative processes, on the other hand, skeletal muscle is still subject to many degenerative disorders with few therapeutic options in the clinic. It is important to develop new regenerative medicine-based therapies for skeletal muscle. Future therapeutic strategies should take advantage of rapidly developing technologies enabling the differentiation of skeletal muscle from human pluripotent stem cells, along with precise genome editing, which will go hand in hand with a steady and focused approach to understanding underlying mechanisms of skeletal muscle development, regeneration, and disease. In this review, I focus on highlighting the recent advances that particularly have relied on developmental and molecular biology approaches to understanding muscle development and stem cell function. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Synthesis of Tetrazolo[1,5-<i>a</i>]pyridines Utilizing Trimethylsilyl Azide and Tetrabutylammonium Fluoride Hydrate (2008)

A method for the preparation of tetrazolo[1,5-a]pyridines from 2-halopyridines, utilizing trimethylsilyl azide in the presence of tetrabutylammonium fluoride hydrate, is described. In addition, 8-bromotetrazolo[1,5-a]pyridine is further transformed into a variety of novel tetrazolo[1,5-a]pyridine derivatives.
Porous silicon a useful imperfection (2002)

When semiconductor developers noticed in the 1950s that electropolishing of bulk silicon left certain areas rougher than the rest and somewhat porous, they regarded these simply as imperfect areas. It was not until Leigh Canham, a scientist with DERA (the UK’s Defence Evaluation and Research Agency), discovered in 1990 that porous silicon (PSi) emits visible light when activated by external ultraviolet sources1 that this morphological state of the material came to attract significant research interest. Elementary photonic sensors were soon proposed. In 1992 researchers discovered that PSi also emits light when an electric current is applied, a finding that raised prospects for new optronic sensors and other devices coupling light to electronics, including future high-speed computers. Technology extensions have since been found that make the material chemi- and bio-luminescent as well as photo- and electro-luminescent. In sight by the mid- to late-1990s, therefore, was a whole new class of solid-state sensors offering significant advantages over solid-state gas and other sensors. Many of these were based on bulk silicon and semiconducting oxides such as tin or indium oxide and alumina. Compared with them, PSi offers a high surface area-to-volume ratio and hence high reactivity and, as researchers have established, a porous structure whose morphology could be engineered for high selectivity to particular molecules. Along with high sensitivity and selectivity, comes a rapid response time.
Future Frame Prediction for Anomaly Detection -- A New Baseline (2017)

Anomaly detection in videos refers to the identification of events that do not conform to expected behavior. However, almost all existing methods tackle the problem by minimizing the reconstruction errors of training data, which cannot guarantee a larger reconstruction error for an abnormal event. In this paper, we propose to tackle the anomaly detection problem within a video prediction framework. To the best of our knowledge, this is the first work that leverages the difference between a predicted future frame and its ground truth to detect an abnormal event. To predict a future frame with higher quality for normal events, other than the commonly used appearance (spatial) constraints on intensity and gradient, we also introduce a motion (temporal) constraint in video prediction by enforcing the optical flow between predicted frames and ground truth frames to be consistent, and this is the first work that introduces a temporal constraint into the video prediction task. Such spatial and motion constraints facilitate the future frame prediction for normal events, and consequently facilitate to identify those abnormal events that do not conform the expectation. Extensive experiments on both a toy dataset and some publicly available datasets validate the effectiveness of our method in terms of robustness to the uncertainty in normal events and the sensitivity to abnormal events.
Manipulating sex ratios for conservation: short-term risks and long-term benefits (2002)

Manipulating family sex ratio is often possible, either through non-invasive methods like changing sex-determining ecological or social factors, or through more invasive methods such as hormone treatment of embryos or sperm sexing prior to using assisted reproductive technologies. If the number of available eggs limits population growth, the production of relatively more daughters than sons may eventually lead to increased population growth in terms of absolute numbers. However, any deviation of the effective sex ratio from equality increases the rate of inbreeding and the loss of genetic variance in the next generation. I show here that there is a range of female biased sex ratios where increased population growth outweighs the effect of an enhanced inbreeding rate during the first generation or the first few generations after the start of a sex ratio manipulation programme. This is especially so in small and declining populations, where some sex ratio manipulations not only increase the effective population number Ne, but also shift the population quickly into population numbers that are safe against the Allee effect. Consequently, an optimal sex ratio manipulation with respect to the genetic quality of a population means sending an endangered population first through a genetic bottleneck to achieve increased Ne, and hence decreased rates of inbreeding, in the long run.
Highly Efficient Thermally Activated Delayed Fluorescence from an Excited-State Intramolecular Proton Transfer System (2017)

Thermally activated delayed fluorescence (TADF) materials have shown great potential for highly efficient organic light-emitting diodes (OLEDs). While the current molecular design of TADF materials primarily focuses on combining donor and acceptor units, we present a novel system based on the use of excited-state intramolecular proton transfer (ESIPT) to achieve efficient TADF without relying on the well-established donor-acceptor scheme. In an appropriately designed acridone-based compound with intramolecular hydrogen bonding, ESIPT leads to separation of the highest occupied and lowest unoccupied molecular orbitals, resulting in TADF emission with a photoluminescence quantum yield of nearly 60%. High external electroluminescence quantum efficiencies of up to 14% in OLEDs using this emitter prove that efficient triplet harvesting is possible with ESIPT-based TADF materials. This work will expand and accelerate the development of a wide variety of TADF materials for high performance OLEDs.
Structure-Guided Design of <i>N</i>-Phenyl Tertiary Amines as Transrepression-Selective Liver X Receptor Modulators with Anti-Inflammatory Activity (2008)

A cocrystal structure of T1317 (3) bound to hLXRbeta was utilized in the design of a series of substituted N-phenyl tertiary amines. Profiling in binding and functional assays led to the identification of LXR modulator GSK9772 ( 20) as a high-affinity LXRbeta ligand (IC 50 = 30 nM) that shows separation of anti-inflammatory and lipogenic activities in human macrophage and liver cell lines, respectively. A cocrystal structure of the structurally related analog 19 bound to LXRbeta reveals regions within the receptor that can affect receptor modulation through ligand modification. Mechanistic studies demonstrate that 20 is greater than 10-fold selective for LXR-mediated transrepression of proinflammatory gene expression versus transactivation of lipogenic signaling pathways, thus providing an opportunity for the identification of LXR modulators with improved therapeutic indexes.
Apical secretion of a cytosolic protein by Madin-Darby canine kidney cells. Evidence for polarized release of an endogenous lectin by a nonclassical secretory pathway (1993)

In the classical secretory pathway proteins containing a signal peptide are translocated from the cytoplasm of the cell into the lumen of the endoplasmic reticulum (ER). From the ER they are transported to the Golgi apparatus and finally to the plasma membrane (PM) where they are released into the extracellular compartment. However, some proteins are synthesized without a signal peptide and maintain a predominantly cytosolic distribution until they are released from the cell. As a marker for this nonclassical secretory pathway we have chosen L-29, a soluble lectin of M(r) about 29,000, that has affinity for lactose and other beta-galactoside containing glycoconjugates. We were interested in determining if cultured epithelial cells secrete L-29 and if they do so in a polarized fashion. Madin-Darby canine kidney (MDCK)-II cells were found to express large quantities of L-29 (about 1% of the detergent soluble protein). The lectin was diffusely distributed in the cytosol, with little or none in vesicular compartments. The polarity of L-29 secretion, when analyzed in pulse-chase experiments, was selectively into the apical compartment of filter-grown MDCK cells. This secretion was not inhibited by brefeldin A or monensin, drugs that are known to inhibit protein transport through the ER-Golgi-PM pathway. Secretion of L-29 was augmented 3-5-fold by the calcium ionophore A23187 and by increasing the temperature to 42 degrees C, whereas lowering the temperature to 20 degrees C or addition of nocodazole prevented secretion. These results demonstrate the polarized secretion of a cytosolic protein by a nonclassical secretory pathway.
Role for Serine Protease HtrA (DegP) of<i>Streptococcus pyogenes</i>in the Biogenesis of Virulence Factors SpeB and the Hemolysin Streptolysin S (2004)

The serine protease HtrA is involved in the folding and maturation of secreted proteins, as well as in the degradation of proteins that misfold during secretion. Depletion of HtrA has been shown to affect the sensitivity of many organisms to thermal and environmental stresses, as well as being essential for virulence in many pathogens. In the present study, we compared the behaviors of several different HtrA mutants of the gram-positive pathogen Streptococcus pyogenes (group A streptococcus). Consistent with prior reports, insertional inactivation of htrA, the gene that encodes HtrA, resulted in a mutant that grew poorly at 37 degrees C. However, an identical phenotype was observed when a similar polar insertion was placed immediately downstream of htrA in the streptococcal chromosome, suggesting that the growth defect of the insertion mutant was not a direct result of insertional inactivation of htrA. This conclusion was supported by the observation that a nonpolar deletion mutation of htrA did not produce the growth defect. However, this mutation did affect the production of several secreted virulence factors whose biogenesis requires extensive processing. For the SpeB cysteine protease, the loss of HtrA was associated with a failure to proteolytically process the zymogen to an active protease. For the streptolysin S hemolysin, a dramatic increase in hemolytic activity resulted from the depletion of HtrA. Interestingly, HtrA-deficient mutants were not attenuated in a murine model of subcutaneous infection. These data add to the growing body of information that implies an important role for HtrA in the biogenesis of secreted proteins in gram-positive bacteria.
Studies on Soybean Trypsin Inhibitors (1974)

Cyanogen bromide treatment of soybean trypsin inhibitor (Kunitz) gives two peptide fragments; fragments ABC and D. The isolated fragment ABC or D alone shows no trypsin inhibitory activity. The activity, however, is largely regenerated on mixing the two components at neutral or weakly basic pH. The reconstituted inhibitor, STI-C, had nearly the full native inhibitory activity. The CD spectrum showed that the reconstitution of the inhibitor was almost complete 40min after mixing, that the half time for the reconstitution was about 3min, and that the basic conformation of native STI was essentially recovered. STI-C dissociated at acidic pH, or even at neutral or weakly basic pH in the presence of 4 m urea. Lyophilization of the fragments appears to produce species incapable of reconstituting the active inhibitor due to aggregation of the fragments. STI-C which had been concentrated by lyophilization showed “temporary inhibition.” One tryptophan residue in STI-C was oxidized by hydrogen peroxide in 10% dioxane with an oxidation curve similar to that of native STI. At 0.8 mole of tryptophan oxidized, STI-C retained about 80% of the native inhibitory activity. After separation of the oxidized STI-C into two fragments by gel filtration in the presence of 4M urea, the modified tryptophan residue was identified as tryptophan-117 in fragment D. Isolated intact fragments ABC and D were individually oxidized with hydrogen peroxide and mixed at weakly basic pH with an equimolar amount of intact D or ABC, respectively. In both cases, complexes between ABC and D were formed. The CD spectra showed that the complex with tryptophan-117 oxidized had recovered almost the same conformation as H,2O2-oxidized STI-C, while the complex with tryptophan-93 oxidized had a rather different conformation. Trypsin inhibitory activity was found for the complex with tryptophan-117 oxidized, but not for the complex with tryptophan-93 oxidized, indicating that tryptophan-93 plays an important role either in the maintenance of the native structure or in the inhibitory activity of STI, while tryptophan-117 plays a minor role both in the tertiary structure and in the inhibitory activity of STI. This paper is concerned with the relationship between the inhibitory activity and the conformation of various derivatives of STI-C on the basis of their CD spectra.
Editorial: Europeanization of Europe (2013)

Today Europeanization is a notion that is frequently used; however, there is a clear shortage of, or even fragmentariness of scientific knowledge, within this scope. The research into the Europeanization processes were initiated by political scientists in the 1970s, although the notion itself only gained popularity in the 1990s alongside the realization of the commom European market. From that moment, Europeanization is a research problem that has attracted interest in numerous fields and scientific disciplines. David Floyd [2001, p. 109] emphasizes the fact that the majority of market changes which have occurred since the beginning of the twenty-first century took place as a result of Europeanization processes which are explicite, defined as the phenomenon of the regionalization processes. As Neil Fligstein [2009, p. 107] highlights, the “majority of the research concerning the European integration focuses only on political and legal processes (…) which is the reason for which researchers overlook the fact how deep the European economy has been reorganized”. There are few works of the kind cited above, nor have there been many recent papers seeking to undertake broad and deep research into the Europeanization processes in both economic (including macro- and microeconomic fields) and noneconomic dimensions.
Design space exploration of multiple loops on FPGAs using high level synthesis (2014)

Real-world applications such as image processing, signal processing, and others often contain a sequence of computation intensive kernels, each represented in the form of a nested loop. High-level synthesis (HLS) enables efficient hardware implementation of these loops using high-level programming languages. HLS tools also allow the designers to evaluate design choices with different trade-offs through pragmas/directives. Prior design space exploration techniques for HLS primarily focus on either single nested loop or multiple loops without consideration to the data dependencies among them. In this paper, we propose efficient design space exploration techniques for applications that consist of multiple nested loops with or without data dependencies. In particular, we develop an algorithm to derive the Pareto-optimal curve (performance versus area) of the application when mapped onto FPGAs using HLS. Our algorithm is efficient as it effectively prunes the dominated points in the design space. We also develop accurate performance and area models to assist the design space exploration process. Experiments on various scientific kernels and real-world applications demonstrate that our design space exploration technique is accurate and efficient.
The Application of Isothermal Titration Calorimetry to Drug Discovery (2004)

This chapter contains sections titled: Introduction Overview of the drug discovery process Experimental measurement of thermodynamic binding parameters ITC in drug discovery Summary References