gebhart/patrepeval huggingface dataset:
Experiments with Dataflow on a General-Purpose Parallel Computer. (1991)

The MIT J-Machine, a massively-parallel computer, is an experiment in providing general-purpose mechanisms for communication, synchronization, and naming that will support a wide variety of parallel models of comptuation. We have developed two experimental dataflow programming systems for the J-Machine. For the first system, we adapted Papadopoulos'' explicit token store to implement static and then dynamic dataflow. Our second system made use of Iannucci''s hybrid execution model to combine several dataflow graph nodes into a single sequence, decreasing scheduling overhead. By combining the strengths of the two systems, it is possible to produce a system with competitive performance.
Comprehensive Proteomic Analysis of Influenza Virus Polymerase Complex Reveals a Novel Association with Mitochondrial Proteins and RNA Polymerase Accessory Factors (2011)

ABSTRACT The trimeric RNA polymerase complex (3P, for PA-PB1-PB2) of influenza A virus (IAV) is an important viral determinant of pathogenicity and host range restriction. Specific interactions of the polymerase complex with host proteins may be determining factors in both of these characteristics and play important roles in the viral life cycle. To investigate this question, we performed a comprehensive proteomic analysis of human host proteins associated with the polymerase of the well-characterized H5N1 Vietnam/1203/04 isolate. We identified over 400 proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS), of which over 300 were found to bind to the PA subunit alone. The most intriguing and novel finding was the large number of mitochondrial proteins (∼20%) that associated with the PA subunit. These proteins mediate molecular transport across the mitochondrial membrane or regulate membrane potential and may in concert with the identified mitochondrion-associated apoptosis inducing factor (AIFM1) have roles in the induction of apoptosis upon association with PA. Additionally, we identified host factors that associated with the PA-PB1 (68 proteins) and/or the 3P complex (34 proteins) including proteins that have roles in innate antiviral signaling (e.g., ZAPS or HaxI) or are cellular RNA polymerase accessory factors (e.g., polymerase I transcript release factor [PTRF] or Supt5H). IAV strain-specific host factor binding to the polymerase was not observed in our analysis. Overall, this study has shed light into the complex contributions of the IAV polymerase to host cell pathogenicity and allows for direct investigations into the biological significance of these newly described interactions.
The eye limits the brain's learning potential (2012)

The concept of a critical period for visual development early in life during which sensory experience is essential to normal neural development is now well established. However recent evidence suggests that a limited degree of plasticity remains after this period and well into adulthood. Here, we ask the question, "what limits the degree of plasticity in adulthood?" Although this limit has been assumed to be due to neural factors, we show that the optical quality of the retinal image ultimately limits the brain potential for change. We correct the high-order aberrations (HOAs) normally present in the eye's optics using adaptive optics, and reveal a greater degree of neuronal plasticity than previously appreciated.
The search dashboard (2012)

Most searchers do not know how to use Web search engines as effectively as possible. This is due, in part, to search engines not providing feedback about how search behavior can be improved. Because feedback is an essential part of learning, we created the Search Dashboard, which provides an interface for reflection on personal search behavior. The Dashboard aggregates and presents an individual's search history and provides comparisons with that of archetypal expert profiles. Via a five-week study of 90 Search Dash-board users, we find that users are able to change aspects of their behavior to be more in line with that of the presented expert searchers. We also find that reflection can be beneficial, even without comparison, by changing participants' views about their own search skills, what is possible with search, and what aspects of their behavior may influence search success. Our findings demonstrate a new way for search engines to help users modify their search behavior for positive outcomes.
Attempts to Fill the Gap Between Enzymatic, Homogeneous, and Heterogeneous Catalysis (2004)

Abstract Bio‐inspired and single site metal complex catalysts have been discussed to direct towards a rational design of solid heterogeneous catalysts. When concepts derived from catalytic antibodies, molecular imprinting and molecular recognition, and site isolation and modification by appropriate ligands are combined, with new techniques to prepare, tailor made solid materials, catalysts can be prepared that improve reaction rate and selectivity by increasing the concentration and activation of reactants in the vicinity of the active sites, and by stabilizing transition states or intermediate products. It is also shown that enzymatic, homogeneous and hetergeneous catalysts can be combined to perform "one‐pot" cascade reactions. Keywords: Catalytic antibodiesMolecular imprinting for catalysisSingle site catalysisHeterogeneization of homogeneous catalystsMultifunctional catalysts Acknowledgments The authors thanks Comisión Interministerial de Ciencia y Tecnología (CICYT) (Project MAT 2003‐07945‐C02‐01) for financial support.
A comparison between micro- and nanocellulose-filled composite adhesives for oil paintings restoration (2015)

Cellulose nanocrystals (CNC) and microcrystals (CMC) were selected as reinforcing fillers for poly(2-ethyl-2-oxazoline), a water-soluble thermoplastic adhesive widely used in the restoration of oil paintings. Thin composite films containing 5, 10, and 30 wt% of CNC or CMC were produced by solution mixing and casting. UV-vis spectroscopy showed how CNC preserved the adhesive transparency even at the highest CNC content, while for CMC, a progressive loss of transparency was observed. Thermal analysis evidenced a progressive increase of the glass transition temperature of the polymer matrix induced by CNC, while no effects were observed for CMC. Both micro- and nanocellulose were able to improve the elastic modulus and reduce the thermal expansion coefficient and creep compliance of the adhesive, with effects more pronounced for CNC nanoparticles. Finally, single-lap shear test on bonded ancient oil painting substrates confirmed the improved dimensional stability of the joint imparted by CNC in the adhesive under both quasi-static and creep conditions.
Consistent and High Rates of Gene Transfer Can Be Obtained Using Flow-Through Transduction over a Wide Range of Retroviral Titers (1996)

Flow-through transduction methods have been developed to overcome physical limitations imposed by Brownian motion on retroviral delivery. This method uses net fluid flow of retroviral supernatants through a porous membrane on which the target cells are placed. It is shown that in comparison to static transduction methods, flow-through transductions have the following advantages: (i) flow-through transductions lead to transduction rates that exceed those obtained by static transduction; (ii) flow-through transductions lead to high transduction rates even at low viral concentrations, eliminating many of the concerns associated with the production of high-titer virus supernatants; (iii) flow-through transductions are insensitive to viral titers, eliminating the need to produce consistently retroviral supernatants at given virus concentrations; (iv) flow-through transductions can be carried out without the use of polycations, such as polybrene; and (v) the volume of viral supernatants needed for gene transfer can be sharply reduced. Taken together, these advantages of flow-through transductions are likely to lead to their widespread use for gene transfer work, both in research and clinical settings.
Design of Capacitor Array in 16-Bit Ultra High Precision SAR ADC for the Wearable Electronics Application (2020)

This paper proposes a 16-bit 6-channel high-voltage successive approximation register (SAR) ADC with an optimized 5 + 5 + 6 segmented capacitor array. The lower 10 bits of the capacitor array are all composed of unit capacitors without any calibration unit. Without calibration, the lower 10 bits of the capacitor array can ensure 10-bit conversion accuracy. Every of the upper 6 bits of the capacitor array contains a linearity calibration unit. The linearity error of the upper 6 bits is calibrated by the linearity calibration unit. The 16-bit is manufactured by a 0.6μm standard COMS process, and the total chip area of 6-channel ADC including pads is 6.6mm × 6.6mm. As for single channel SAR ADC, the area is 0.9mm × 2.0mm. The measurement results show that the effective conversion accuracy of the SAR ADC reaches 13 bits by using novel differential nonlinearity (DNL) and integral nonlinearity (INL) calibration methods. The power is 80mW, corresponding to a Figure of Merit (FOM) of 48 pJ/conv.-step.
Persistent excitation in bilinear systems (1991)

Discrete-time systems described by difference equations which are polynomial in the input and linear in the output are discussed. Bilinear systems are special members of this class. Two issues are examined. First, a multidimensional polynomial-based algebraic condition which is necessary and sufficient for such systems to be identifiable is given. Second, subject to an identifiability assumption, a condition on the input sequence which guarantees persistent excitation is given. The principle analytic tool used in this study involves multidimensional polynomials.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Turn-on Detection of Targeted Biochemical Reactions by Triple Resonance NMR Analysis Using Isotope-labeled Probe (2010)

Abstract We report on a strategy for the “turn-on” detection of target biochemical (metabolic) reactions using a triple resonance NMR technique with an isotope-labeled probe. Our NMR study clearly reveals that otherwise NMR-nonactive-13C/2H-labeled glucose actually turns “on” its 1H NMR signal by conversion to an important biomarker lactate as the end product of anaerobic glycolysis in cells and in injected mice with high selectivity.
Highly thermally conductive substrates with adjustable CTE for diode laser bar packaging (2003)

The design of a novel mounting substrate for high power diode laser bars is presented. This substrate is combining the high thermal conductivity of diamond with the property of being able to adjust its coefficient of thermal expansion (CTE) to that of the laser material GaAs. Such a unique feature has become possible by attributing to the hard material diamond an artificial ductility by laser cutting of stress relieving openings in the diamond substrates. Combining two of these substrates in a sandwich with a middle layer of copper, one is able to realize a desired CTE just by choosing the right copper layer thickness. Based on the results of 3D-FEM calculations, some of these diamond-copper-diamond substrates have been produced with different copper thicknesses. The technique of electronic speckle pattern interferometry (ESPI) has been employed to measure the average CTE of these substrates. For diamond thicknesses of 0,3 mm, a copper foil thickness of 0,05 mm enabled a CTE-match with GaAs. A nearly stress free state in the laser bars mounted on these substrates has been demonstrated by photocurrent spectroscopy.
On the Energy Efficiency of Limited-Backhaul Cell-Free Massive MIMO (2019)

We investigate the energy efficiency performance of cell-free Massive multiple-input multiple-output (MIMO), where the access points (APs) are connected to a central processing unit (CPU) via limited-capacity links. Thanks to the distributed maximum ratio combining (MRC) weighting at the APs, we propose that only the quantized version of the weighted signals are sent back to the CPU. Considering the effects of channel estimation errors and using the Bussgang theorem to model the quantization errors, an energy efficiency maximization problem is formulated with per-user power and backhaul capacity constraints as well as with throughput requirement constraints. To handle this non-convex optimization problem, we decompose the original problem into two sub-problems and exploit a successive convex approximation (SCA) to solve original energy efficiency maximization problem. Numerical results confirm the superiority of the proposed optimization scheme.
Complexity and quality evaluation of structure extrapolation methods within a fully automatic inpainting framework (2010)

A novel, automatic restoration framework of large picture areas is proposed in this paper. While the damaged picture areas may have been caused by accident or transmission loss, the challenge consists in repairing the occluded or missing image regions in an undetectable way. In this work, the new inpainting method is used as framework for systematic evaluation of relevant structure extrapolation strategies. The important issue of quality-complexity optimization is thoroughly discussed and efficient inpainting tools are established. Recovery of missing dominant structures is done via tensor voting, regression analysis or a combination of both. Combined structure extrapolation considerably reduces the complexity of structure restoration, compared to genuine tensor voting, with overall graceful to imperceptible degradation of the inpainting result. Furthermore, limitations of the tensor voting approach can be avoided by means of polynomial interpolation with additional savings in terms of complexity.
High Thermoelectric Performance SnTe–In2Te3 Solid Solutions Enabled by Resonant Levels and Strong Vacancy Phonon Scattering (2015)

Herein, we report a significantly improved thermoelectric figure of merit ZT of ∼1.1 at ∼923 K in p-type SnTe through In2Te3 alloying and iodine doping. We propose that the introduction of indium at Sn sites in SnTe creates resonant levels inside the valence bands, thereby considerably increasing the Seebeck coefficients and power factors in the low-to-middle temperature range. Unlike SnTe–InTe, the SnTe–In2Te3 system displays much lower lattice thermal conductivity. Utilizing a model for point defect scattering, we analyze the origin of the low thermal conductivity in SnTe–In2Te3 and attribute it mainly to the strong vacancy originated phonon scattering between Sn atoms and the vacancies introduced by In2Te3 alloying and partly to the interfacial scattering by In-rich nanoprecipitates present in SnTe matrix. By alloying only In2Te3 with SnTe, a ZT value of ∼0.9 at 923 K was achieved. ZT can be further increased to ∼1.1 at 923 K through adjusting the charge carriers by iodine doping at Te sites.
Inhibitors of vacuolar ATPase proton pumps inhibit human prostate cancer cell invasion and prostate‐specific antigen expression and secretion (2012)

Vacuolar ATPases (V-ATPases) comprise specialized and ubiquitously distributed pumps that acidify intracellular compartments and energize membranes. To gain new insights into the roles of V-ATPases in prostate cancer (PCa), we studied the effects of inhibiting V-ATPase pumps in androgen-dependent (LNCaP) and androgen-independent (C4-2B) cells of a human PCa progression model. Treatment with nanomolar concentrations of the V-ATPase inhibitors bafilomycin A or concanamycin A reduced the in vitro invasion in both cell types by 80%, regardless that V-ATPase was prominent at the plasma membrane of C4-2B cells and only traces were detected in the low-metastatic LNCaP parental cells. In both cell types, intracellular V-ATPase was excessive and co-localized with prostate-specific antigen (PSA) in the Golgi compartment. V-ATPase inhibitors reversibly excluded PSA from the Golgi and led to the accumulation of largely dispersed PSA-loaded vesicles of lysosomal composition. Inhibition of acridine orange staining and transferrin receptor recycling suggested defective endosomal and lysosomal acidification. The inhibitors, additionally, interfered with the AR-PSA axis under conditions that reduced invasion. Bafilomycin A significantly reduced steady-state and R1881-induced PSA mRNA expression and secretion in the LNCaP cells which are androgen-dependent, but not in the C4-2B cells which are androgen ablation-resistant. In the C4-2B cells, an increased susceptibility to V-ATPase inhibitors was detected after longer treatments, as proliferation was reduced and reversibility of bafilomycin-induced responses impaired. These findings make V-ATPases attractive targets against early and advanced PCa tumors.
A Gene Therapy Approach to Improve Copper Metabolism and Prevent Liver Damage in a Mouse Model of Wilson Disease (2019)

Wilson disease (WD), an autosomal recessive disease caused by mutations in a copper-transporting P-type ATPase (Atp7b), causes severe liver damage. This disease is currently treated with the lifelong use of copper chelation therapy, which has side effects and does not fix copper metabolism. Here, we thoroughly characterized a mouse model of WD, the toxic milk mouse, and used the model to test a gene therapy approach for treating WD. WD mice accumulated copper in the liver from birth; severe copper accumulation and concurrent liver disease were evident by 2 months of age. Intravenously administering an adeno-associated viral (AAV) 8 vector expressing a codon-optimized version of the human ATP7B transgene into 2-month-old WD mice significantly decreased liver copper levels compared with age-matched, uninjected, WD mice. We also observed a significant dose-dependent decrease in liver disease. Male mice injected with 10<sup>11</sup> genome copies of AAV8 vector showed only mild histopathological findings with a complete lack of liver fibrosis. Therefore, we conclude that administering gene therapy at the early stages of disease onset is a promising approach for reducing liver damage and correcting copper metabolism in WD.
Downhole Wettability: The Potential of NMR (2018)

Abstract A review of several nuclear magnetic resonance (NMR) based techniques published in the literature to extract wettability information that have the potential to be applicable in downhole formation. The techniques include T2 shift, T2 vs saturation, NMR T1 dispersion, T1/T2 ratio, and restricted diffusion. The theoretical basis and the advantages and disadvantages of each have implications for downhole applications. Due to the flexibility of NMR, adjusting the experiment for the specific application is very common, and this shows the strength and flexibility of NMR. Numerous references provide detailed readings for each discussed technique.
Palladium Mediated Synthesis of Protein–Polyarene Conjugates (2022)

Catalyst transfer polymerization (CTP) is widely applied to the synthesis of well-defined π-conjugated polymers. Unlike other polymerization reactions that can be performed in water (e.g., controlled radical polymerizations and ring-opening polymerizations), CTP has yet to be adapted for the modification of biopolymers. Here, we report the use of protein-palladium oxidative addition complexes (OACs) that enable catalyst transfer polymerization to furnish protein-polyarene conjugates. These polymerizations occur with electron-deficient monomers in aqueous buffers open to air at mild (≤37 °C) temperatures with full conversion of the protein OAC and an average polymer length of nine repeating units. Proteins with polyarene chains terminated with palladium OACs can be readily isolated. Direct evidence of protein-polyarene OAC formation was obtained using mass spectrometry, and all protein-polyarene chain ends were uniformly functionalized via C-S arylation to terminate the polymerization with a small molecule thiol or a cysteine-containing protein.
Bioactive Adrenomedullin, Organ Support Therapies, and Survival in the Critically Ill: Results from the French and European Outcome Registry in ICU Study (2019)

Early measurement of bioactive adrenomedullin is a strong predictor of the need of organ support and of short-term mortality in critically ill patients.
Minimax Bounds for Blind Network Inference (2021)

We take the first step towards understanding the fundamental limits of blind wireless network inference performed by a distributed network of single-antenna adversary nodes. The distributed adversary nodes are assumed to be blind to the protocol parameters as well as the modulation, coding and encryption schemes used by the network being monitored. Focusing on the special case of inferring the channel access probabilities of the monitored nodes, we derive minimax bounds for blind inference. We show that blind inference is possible with similar sample complexity (asymptotically) as non-blind inference given certain network connectivity conditions are satisfied.
Laser heating of scanning probe tips for thermal near-field spectroscopy and imaging (2016)

Spectroscopy and microscopy of the thermal near-field yield valuable insight into the mechanisms of resonant near-field heat transfer and Casimir and Casimir-Polder forces, as well as providing nanoscale spatial resolution for infrared vibrational spectroscopy. A heated scanning probe tip brought close to a sample surface can excite and probe the thermal near-field. Typically, tip temperature control is provided by resistive heating of the tip cantilever. However, this requires specialized tips with limited temperature range and temporal response. By focusing laser radiation onto AFM cantilevers, we achieve heating up to ∼1800 K, with millisecond thermal response time. We demonstrate application to thermal infrared near-field spectroscopy (TINS) by acquiring near-field spectra of the vibrational resonances of silicon carbide, hexagonal boron nitride, and polytetrafluoroethylene. We discuss the thermal response as a function of the incident excitation laser power and model the dominant cooling contributions. Our results provide a basis for laser heating as a viable approach for TINS, nanoscale thermal transport measurements, and thermal desorption nano-spectroscopy.
Novel tools to streamline the conference review process (2010)

The SIGKDD'09 Research Track received 537 paper submissions, which were reviewed by a Program Committee of 199 members, and a Senior Program Committee of 22 members. We used techniques from artificial intelligence and data mining to streamline and support this complicated process at three crucial stages: bidding by PC members on papers, assigning papers to reviewers, and calibrating scores obtained from the reviews. In this paper we report on the approaches taken, evaluate how well they worked, and describe some further work done after the conference.
Ocean salinity observations with SMOS mission (2002)

The purpose of this paper is to present the capabilities of SMOS (Soil Moisture and Ocean Salinity mission) for the global mapping of ocean salinity from space. SMOS has been selected by the European Space Agency as the second Earth Explorer Opportunity with a launch date in June 2005. The sensor embarked on SMOS is MIRAS, a Microwave Imaging Radiometer with Aperture Synthesis. MIRAS works at L-band, in the two-polarisations, and has full polarimetric capability. The measurement of sea surface salinity (SSS) is one of the challenges of SMOS. This paper presents first the scientific requirements for a number of oceanographic applications. The scientific requirements are then translated into instrument accuracy, sensitivity, stability and spatial resolution. Major sources of error in the retrieval of ocean salinity will be addressed through an experimental campaign which is described.
Organometallic compounds in organic synthesis: nucleophilic substitution reactions of N-methylindoletricarbonyl chromium(0) (1978)

A. P. Kozikowski and K. Isobe, J. Chem. Soc., Chem. Commun., 1978, 1076 DOI: 10.1039/C39780001076