gebhart/patrepeval huggingface dataset:
Xenopus SMOC-1 Inhibits Bone Morphogenetic Protein Signaling Downstream of Receptor Binding and Is Essential for Postgastrulation Development in Xenopus (2009)

The bone morphogenetic protein (BMP) family of signaling molecules and their antagonists are involved in patterning of the body axis and numerous aspects of organogenesis. Classical biochemical purification and protein sequencing of highly purified fractions containing potent bone forming activity from bovine cartilage identified several BMPs together with a number of other proteins. One such protein was SMOC-2 (secreted modular calcium-binding protein-2), classified as belonging to the BM-40 family of modular extracellular proteins. Data regarding the biological function of SMOC-2 and closely related SMOC-1 remain limited, and their expression or function during embryological development is unknown. We therefore isolated the Xenopus ortholog of human SMOC-1 (XSMOC-1) and explored its function in Xenopus embryos. In gain-of-function assays, XSMOC-1 acted similarly to a BMP antagonist. However, in contrast to known extracellular ligand-binding BMP antagonists, such as noggin, SMOC antagonizes BMP activity in the presence of a constitutively active BMP receptor, indicating a mechanism of action downstream of the receptor. We provide several lines of evidence to suggest that SMOC acts downstream of the BMP receptor via MAPK-mediated phosphorylation of the Smad linker region. Loss-of-function studies, using antisense morpholino oligonucleotides, revealed XSMOC-1 to be essential for postgastrulation development. The catastrophic developmental failure observed following XSMOC knockdown resembles that observed following simultaneous depletion of three ligand-binding BMP antagonists described in prior studies. These findings provide a direct link between the extracellular matrix-associated protein SMOC and a signaling pathway of general importance in anatomic patterning and cell or tissue fate specification.
Adaptive multi-rate. A speech service adapted to cellular radio network quality (2002)

Adaptive multi-rate (AMR) is an emerging speech service currently being standardized in the ETSI for the GSM system. The new AMR standard will be flexible by adapting the error protection level and the allocated radio resources. A trade-off between speech quality and system capacity can be achieved for a variety of radio channel and operating conditions. The adaptation of the protection level will be fast and speech service specific. Besides the basic source and channel codec for speech signal payload, the AMR system concept further includes channel state tracking and inband transmission of adaptation data. We review the general AMR system concept and discuss the capacity and quality benefits that can be achieved. An example solution for GSM is described including speech coding, channel coding, inband signaling, and the adaptation scheme.
Noise Squeezing Controlled Parametric Bifurcation Tracking of MIP-Coated Microbeam MEMS Sensor for TNT Explosive Gas Sensing (2014)

This paper reports real-time explosive gas sensing (DNT) in atmospheric pressure utilizing the noise squeezing effect that occurs before a bifurcation event. A noise-squeezing controller based on the statistics of phase noise is implemented using high-speed LabVIEW field programmable gated array. A high frequency TNT-molecularly imprinted fixed-fixed microbeam sensor utilizes this nontraditional sensing strategy and performs DNT sensing at various concentrations. Experiments are conducted using both noise-based and sweep-based bifurcation tracking for a direct comparison. Results demonstrate noise-based bifurcation tracking is not only capable of performing reliable frequency tracking, but also show the method is superior to the bifurcation sweep-based tracking. Over three orders of magnitude improvement in acquisition rate is achieved, and as a result, confidence and precision on bifurcation frequency estimation is significantly improved over the bifurcation sweep tracking method, enabling DNT sensing at concentrations much below sub-ppb (parts-per-billion) level.
Fiber Bragg filters For laser- and multicore fibers (2017)

Fiber Bragg gratings (FBGs) have widespread applications in security, information, structural health monitoring, and biophotonics. In telecom applications, FBG inscription has reached a high level of maturity, but remains mainly limited to germanium doped photosensitive single mode fibers. Special applications, like filtering in light harvesting fibers or resonator mirrors for fiber lasers have to deal with special aspects which make the design and realization of FBGs a challenging task. One aspect is the extended wavelength range of these applications. Another aspect is the increasing demand to inscribe fiber Bragg gratings in non-photosensitive germanium-free fibers. Therefore, novel concepts of photosensitivity are proposed. Finally, to increase the amount of captured light the size of the fiber core and the numerical aperture have also to be increased. This goes along with multimode operation and prevents good filtering properties of Bragg gratings.
When Does Stochastic Gradient Algorithm Work Well? (2018)

In this paper, we consider a general stochastic optimization problem which is often at the core of supervised learning, such as deep learning and linear classification. We consider a standard stochastic gradient descent (SGD) method with a fixed, large step size and propose a novel assumption on the objective function, under which this method has the improved convergence rates (to a neighborhood of the optimal solutions). We then empirically demonstrate that these assumptions hold for logistic regression and standard deep neural networks on classical data sets. Thus our analysis helps to explain when efficient behavior can be expected from the SGD method in training classification models and deep neural networks.
Research to Develop and Apply Biophotonics to Military Medicine Needs (2012)

Abstract : Photomedicine technologies can provide practical and cost-effective solutions for many military medical problems. This report contains results of twelve projects undertaken by researchers in the Wellman Center for Photomedicine at Massachusetts General Hospital. Seven projects focus on battlefield-related trauma and environmental exposure, and seek methods to preserve life and health by developing diagnostics and therapeutics. Five projects are directed to repair and replacement of tissue with the goal of salvaging tissue and improving rehabilitation.
ChemInform Abstract: Investigations in the Directive Effects of a Single meso‐Substituent via Nitration of 5,12,13,17,18‐Pentasubstituted Porphyrins: Syntheses of Conjugated β‐Nitroporphyrins. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Global Chemical Composition and Antioxidant and Anti-Tuberculosis Activities of Various Extracts of Globularia alypum L. (Globulariaceae) Leaves (2011)

In this work, an evaluation of the biological activities of Globularia alypum L. extracts and their global chemical composition was realized. Extracts from G. alypum were obtained by two extraction methods. The composition of polyphenols (8.5-139.95 g gallic acid equivalent/Kg of dry mass), tannins (1.39-18.65 g catechin equivalent/Kg of dry mass), anthocyanins (8.17-70.69 mg cyanidin equivalent/Kg of dry mass) and flavonoids (0.31-19.28 g quercetin equivalent/Kg of dry mass) was evaluated. The samples were subjected to a screening for their antioxidant activities using the DPPH* and ABTS*+ assays. For the first time, the anti-tuberculosis activity (H(37)Rv) for G. alypum was tested against Mycobacterium tuberculosis. The strongest antioxidant activity was obtained for the methanol extract (IC(50 ) = 15.58 ± 0.168 mg/L) and the best anti-tuberculosis activity was obtained for the petroleum ether extract (IC(50 )= 77 mg/L). We have found a positive correlation between the total phenolics content and the antioxidant activity R2 = 0.88 (DPPH*) and R2 = 0.97 (ABTS*+). We have found also a positive correlation between the flavonoid content and the antioxidant activity R2 = 0.91 (DPPH*) and R2 = 0.91 (ABTS*+).
The role of specific PP2A complexes in the dephosphorylation of γ-H2AX (2014)

The formation of γ-H2AX in response to DNA double-strand breaks (DSBs) marks damaged regions for recognition and repair. Dephosphorylation of γ-H2AX is required for cells to resume cell cycle. However, the mechanisms of γ-H2AX dephosphorylation remain underexplored. Using a loss of function screen, we identified PP2A specific subunits, B56ε and α4, involved in elimination of γ-H2AX during DSBs repair process. In the early stage of DSBs repair the inhibitory subunit α4 binds and renders PP2Ac inactive. As DNA is repaired, α4 releases PP2Ac and triggers the assembly of an active PP2A B56ε holoenzyme. PP2A B56ε, which translocates from cytoplasm into the nucleus upon DNA damage, is responsible for a direct dephosphorylation of γ-H2AX. Suppression of both B56ε and α4 leads to persistence of γ-H2AX and defects in DNA repair. In contrast, the rapid clearance of γ-H2AX in human hepatocarcinoma is correlated with the over-expression of both B56ε and α4. Functional analysis reveals that PP2A B56ε coordinates with α4 in accelerating HR repair upon DNA damage. Together, these observations gain insight of how γ-H2AX dephosphorylation is kinetically regulated during DNA repair response.
Lazy-CFR: fast and near optimal regret minimization for extensive games with imperfect information (2018)

Counterfactual regret minimization (CFR) is the most popular algorithm on solving two-player zero-sum extensive games with imperfect information and achieves state-of-the-art performance in practice. However, the performance of CFR is not fully understood, since empirical results on the regret are much better than the upper bound proved in \cite{zinkevich2008regret}. Another issue is that CFR has to traverse the whole game tree in each round, which is time-consuming in large scale games. In this paper, we present a novel technique, lazy update, which can avoid traversing the whole game tree in CFR, as well as a novel analysis on the regret of CFR with lazy update. Our analysis can also be applied to the vanilla CFR, resulting in a much tighter regret bound than that in \cite{zinkevich2008regret}. Inspired by lazy update, we further present a novel CFR variant, named Lazy-CFR. Compared to traversing $O(|\mathcal{I}|)$ information sets in vanilla CFR, Lazy-CFR needs only to traverse $O(\sqrt{|\mathcal{I}|})$ information sets per round while keeping the regret bound almost the same, where $\mathcal{I}$ is the class of all information sets. As a result, Lazy-CFR shows better convergence result compared with vanilla CFR. Experimental results consistently show that Lazy-CFR outperforms the vanilla CFR significantly.
Phase II trial of irinotecan/temozolomide/dinutuximab/granulocyte macrophage colony stimulating factor (I/T/DIN/GMCSF) in children with relapsed/refractory neuroblastoma (NBL): A report from the Children's Oncology Group (COG). (2018)

10508 Background: COG ANBL1221 was a randomized Phase II selection design trial for patients (pts) with relapsed/refractory NBL. Randomization was stopped early when I/T/DIN/GMCSF was shown be the optimal combination for further study. In the small cohort assigned to I/T/DIN/GMCSF, the objective response rate was 53%. An expanded cohort was evaluated to more accurately assess response rate and better define the toxicity profile of this combination. Methods: Pts were eligible at first relapse/progression or first designation of refractory disease. Cycles were administered every 21 days. Objective responses were confirmed centrally. Toxicities were graded according to CTCAE v4.0. Results: 53 eligible pts were assigned to I/T/DIN/GMCSF; 17 during the randomized portion, 36 during study expansion. Median age was 5.1 years (range 1.3-15.9), 39 pts (74%) had measurable disease. Fourteen (26%) had MYCN amplified tumors, 20 (38%) had previously undergone high-dose chemotherapy with stem cell rescue, and 14 (26%) had received prior anti-GD2 antibody. 22 (42%) had relapsed disease and 31 (58%) had refractory/progressive disease (PD). Subjects received 378 total cycles (median 6). Of 53 pts assigned to I/T/DIN/GMCSF, 21 experienced objective responses [40%; 95% CI (26, 53)]; 10 PR, 11 CR. Seven had PD, 23 had stable disease. Two did not receive protocol therapy and did not undergo disease evaluations, but were included in the intention-to-treat analysis. Among responders, 4 (19%) had MYCN amplified tumors and 9 (43%) had previously received an anti-GD2 antibody. Of the 51 evaluable for toxicity, 13 (25%) had Grade 3 pain, 8 (16%) had Grade 3 diarrhea, and 4 (8%) had Grade 3 vomiting. Neutropenia (³Grade 3) was observed in 14 (27%), Grade 3 thrombocytopenia in 5 (10%), and Grade 3 fever/infection in 11 (22%). Conclusions: I/T/DIN/GM-CSF showed significant anti-tumor activity in pts with relapsed/refractory NBL. This combination was well-tolerated in a cohort of > 50 pts. Studies of biomarkers that may identify pts most likely to respond to this chemo-immunotherapeutic regimen are in progress. Clinical trial information: NCT01767194.
Multi-Level Coded Residue-Based Content-Addressable-Memory Optical Computing (1985)

Digital operations can be implemented by: 1) converting the operation into a sequence of logic steps that can be realized by gates or 2) reading the output directly from a stored truth table. In spite of the superiority of the latter method in speed, it has not been common in the history of data processing. This is partially due to the large sizes of the tables that need to be stored, and partially due to the numerous efficient algorithms that can be programmed on general von Neumann type computers. However, a variety of recent technological advances and a growing need for parallel processing have generated renewed interest in truth-table look-up processing.
Reflection coefficient measurement using a finite-difference-injection technique (2017)

Experimentally determining the acoustic reflection properties of materials requires accurate knowledge of the incident and reflected wave field at the reflecting interface. Consequently, a number of methods have been proposed for measuring the reflection coefficient, but most are limited to measuring only the normal incidence reflection coefficient or assume plane wave conditions. Here, we derive the reflection coefficient from pressure measurements by using a finite-difference wave field injection technique, which is applicable for a wide range of incidence angles and does not rely on the common plane wave assumption. It requires measurements at three planes parallel to the reflector and addresses two key objectives, namely, (1) the recorded wave field is separated into its incident and reflected components without the need of time-windowing, and (2) the separated components are re-datumed to the reflecting interface. The latter step comprises a forward propagation in time of the incident wave and a time-reversed backward propagation of the reflected wave. We experimentally test the methodology on laboratory data of the reflection from the free surface recorded in water and demonstrate its applicability to accurately measure the reflection coefficient for incidence angles up to 60°.
Localized Ligand Induced Electroless Plating (LIEP) Process for the Fabrication of Copper Patterns Onto Flexible Polymer Substrates (2011)

Abstract The “ligand induced electroless plating (LIEP) process” is a simple process to obtain localized metal plating onto flexible polymers such as poly(ethylene terephtalate) and polyvinylidene fluoride sheets. This generic and cost‐effective process, efficient on any common polymer surface, is based on the covalent grafting by the GraftFast process of a thin chelating polymer film, such as poly(acrylic acid), which can complex copper ions. The entrapped copper ions are then chemically reduced in situ and the resulting Cu 0 species act as a seed layer for the electroless copper growth which, thus, starts inside the host polymer. The present work focuses on the application of the LIEP process to the patterning of localized metallic tracks via two simple lithographic methods. The first is based on a standard photolithography process using a positive photoresist masking to prevent the covalent grafting of PAA in designated areas of the polymer substrate. In the second, the patterning is performed by direct printing of the mask with a commercial laser printer. In both cases, the mask was lifted off before the copper electroless plating step, which provides ecological benefits, since only the amount of copper necessary for the metallic patterning is used.
Increasing the Throughput of Polar Decoders (2013)

The serial nature of successive-cancellation decoding results in low polar decoder throughput. In this letter we present an improved version of the simplified successive-cancellation decoding algorithm that increases decoding throughput without degrading the error-correction performance. We show that the proposed algorithm has up to three times the throughput of the simplified successive-cancellation decoding algorithm and up to twenty-nine times the throughput of a standard successive-cancellation decoder while using the same number of processing elements.
Estimate of the Potential Amount of Low-Level Waste from the Fukushima Prefecture - 12370 (2012)

The amount of waste generated by the cleanup of the Fukushima Prefecture (Fukushima-ken) following the releases from the Fukushima Daiichi nuclear power plant accident (March 2011) is dependent on many factors, including: - Contamination amounts; - Cleanup levels determined for the radioisotopes contaminating the area; - Future land use expectations and human exposure scenarios; - Groundwater contamination considerations; - Costs and availability of storage areas, and eventually disposal areas for the waste; and - Decontamination and volume reduction techniques and technologies used. For the purposes of estimating these waste volumes, Fukushima-ken is segregated into zones of similar contamination level and expected future use. Techniques for selecting the appropriate cleanup methods for each area are shown in a decision tree format. This approach is broadly applied to the 20 km evacuation zone and the total amounts and types of waste are estimated; waste resulting from cleanup efforts outside of the evacuation zone is not considered. Some of the limits of future use and potential zones where residents must be excluded within the prefecture are also described. The size and design of the proposed intermediate storage facility is also discussed and the current situation, cleanup, waste handling, and waste storage issues inmore » Japan are described. The method for estimating waste amounts outlined above illustrates the large amount of waste that could potentially be generated by remediation of the 20 km evacuation zone (619 km{sup 2} total) if the currently proposed cleanup goals are uniformly applied. The Japanese environment ministry estimated in early October that the 1 mSv/year exposure goal would make the government responsible for decontaminating about 8,000 km{sup 2} within Fukushima-ken and roughly 4,900 km{sup 2} in areas outside the prefecture. The described waste volume estimation method also does not give any consideration to areas with localized hot spots. Land use and area dose rate estimates for the 20 km evacuation zone indicate there are large areas where doses to the public can be mitigated through methods other than removal and disposal of soil and other wastes. Several additional options for waste reduction can also be considered, including: - Recycling/reusing or disposing of as municipal waste material that can be unconditionally cleared; - Establishing additional precautionary (e.g., liners) and monitoring requirements for municipal landfills to dispose of some conditionally-cleared material; and - Using slightly-contaminated material in construction of reclamations, banks and roads. Waste estimates for cleanup will continue to evolve as decontamination plans are drafted and finalized. (authors)« less
Silica filler content in NCP and its effects on the reliability of 3D TSV Multi-Stack under thermal shock test (2017)

3D multi-stack integration with through silicon via (TSV) and non-conductive paste (NCP) is one of the candidate packaging technologies that can successfully meet the requirements of high-end electronic products. A clear relationship should be established between the material properties of NCP and reliability of 3D TSV multi-stack chips. This research aims to characterize the mechanical properties of NCP with 0, 20, 30, and 40 wt% silica filler and examine the influence of different silica contents in NCP on the reliability of 3D TSV multi-stack chips under thermal shock test. Results show that adding silica filler does not influence the curing behavior of the NCP material, although it decreases the coefficient of thermal expansion and increases Young's modulus and viscosity. The thermal shock test reveals that the specimens bonded with NCP without silica filler fail before those bonded with NCP of 40 wt%. The failure mechanism for all specimens is recognized as a crack in the TSV/redistribution layer interface. These results suggest that the NCP is beneficial to the reliability of 3D TSV multi-stack chips.
Covalent Functionalization of Carbon Nanohorns with Porphyrins: Nanohybrid Formation and Photoinduced Electron and Energy Transfer (2007)

Abstract The covalent attachment of carbon nanohorns (CNHs) to α‐5‐(2‐aminophenyl)‐α‐15‐(2‐nitrophenyl)‐10,20‐bis(2,4,6‐trimethyl‐phenyl)‐porphyrin (H 2 P) via an amide bond is accomplished. The resulting CNH–H 2 P nanohybrids form a stable inklike solution. High‐resolution transmission electron microscopy (HRTEM) images demonstrate that the original dahlia‐flowerlike superstructure of the CNHs is preserved in the CNH–H 2 P nanohybrids. Steady‐state and time‐resolved fluorescence studies show efficient quenching of the excited singlet state of H 2 P, suggesting that both electron and energy transfer occur from the singlet excited state of H 2 P to CNHs, depending on the polarity of the solvent. In the case of electron transfer, photoexcitation of H 2 P results in the reduction of the nanohorns and the simultaneous oxidation of the porphyrin unit. The formation of a charge‐separated state, CNH • – –H 2 P • + , has been corroborated with the help of an electron mediator, hexyl‐viologen dication (HV 2+ ), in polar solvents. Moreover, the charge‐separated CNH • – –H 2 P • + states have been identified by transient absorption spectroscopy.
Multi-Unit Auction Revenue with Possibilistic Beliefs (2017)

The revenue of traditional auction mechanisms is benchmarked solely against the players' own valuations, despite the fact that they may also have valuable beliefs about each other's valuations. Not much is known about generating revenue in auctions of multiple identical copies of a same good. (In particular the celebrated Vickrey mechanism has no revenue guarantees.) For such auctions, we (1) put forward an attractive revenue benchmark, based on the players' possibilistic about each other, and (2) construct a mechanism that achieves such benchmark, assuming that the players are two-level rational (where the rationality is in the sense of Aumann).