gebhart/patrepeval huggingface dataset:
Quality Measures of Imaging Mass Spectrometry Aids in Revealing Long-term Striatal Protein Changes Induced by Neonatal Exposure to the Cyanobacterial Toxin β-N-methylamino-L-alanine (BMAA) (2013)

Many pathological processes are not directly correlated to dramatic alterations in protein levels. The changes in local concentrations of important proteins in a subset of cells or at specific loci are likely to play a significant role in disease etiologies, but the precise location might be unknown, or the concentration might be too small to be adequately sampled for traditional proteomic techniques. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a unique analytical method that combines analysis of multiple molecular species and of their distribution in a single platform. As reproducibility is essential for successful biomarker discovery, it is important to systematically assess data quality in biologically relevant MALDI IMS experiments. In the present study, we applied four simple tools to study the reproducibility for individual sections, within-group variation, and between-group variation of data acquired from brain sections of 21 animals divided into three treatment groups. We also characterized protein changes in distinct regions of the striatum from six-month-old rats treated neonatally (postnatal days 9-10) with the cyanobacterial toxin β-N-methylamino-l-alanine (BMAA), which has been implicated in neurodegenerative diseases. The results showed that optimized experimental settings can yield high-quality MALDI IMS data with relatively low variation (14% to 15% coefficient of variance) that allow the characterization of subtle changes in protein expression in various subregions of the brain. This was further exemplified by the dose-dependent reduction of myelin basic protein in the caudate putamen and the nucleus accumbens of adult rats neonatally treated with BMAA (150 and 460 mg/kg). The reduction in myelin basic protein was confirmed through immunohistochemistry and indicates that developmental exposure to BMAA may induce structural effects on axonal growth and/or directly on the proliferation of oligodendrocytes and myelination, which might be important for the previously shown BMAA-induced long-term cognitive impairments.
The role of molecular packing on the UV-visible optical properties of [Re 2 Cl 2 (CO) 6 4,5-(Me 3 Si) 2 pyridazine] (2012)

We report here on two stable polymorphs of the dinuclear complex [Re<sub>2</sub>(&mu;-Cl)<sub>2</sub>(CO)<sub>6</sub>(&mu;-4,5- (Me<sub>3</sub>Si)<sub>2</sub>pyridazine)]. The compound belongs to the recently reported class of dinuclear luminescent Re(I) complexes of general formula [Re<sub>2</sub>(&mu;-Cl)<sub>2</sub>(CO)<sub>6</sub>(&mu;-1,2-diazine)]. In the solid state, the complex exhibits a unique combination of unusual properties: (i) concomitant formation of two highly luminescent polymorphs, and single crystal-to-single-crystal conversion of one form into the other, (ii) remarkable differences in the absorption properties of the two polymorphs due to different redistribution of oscillator strength among the different excitons, and (iii) remarkable differences among the emission properties. In particular, a higher emission quantum yield was found in the solid state than in solution (measured to be 0.52 and 0.56 for the two polymorphs, almost one order of magnitude higher than that of the molecule in solution). Interest in luminescent materials able to efficiently emit in the solid state is continuously growing, because in most applications the dyes are used as solid films. Although rigid environments are expected to freeze rotovibrational relaxation pathways, luminescence efficiency often decreases in the solid state with respect to liquid solution due to concentration quenching, affecting both organic and organometallic emitters. However, an increasing number of molecular-based emitters exhibit enhanced solid state emission. Apart from the importance of bulky substituents in reducing concentration quenching effects, other intra- or inter-molecular phenomena have been invoked as well, such as conformational changes, &pi;-&pi; stacking, hydrogen bonds, or Jaggregates, which cause rearrangements of the energy levels and population. In these two polymorphs the enhancement of the emission with respect to the solution is most likely due to the restricted rotation of the Me3Si groups in the crystals, providing an interesting example of aggregation-induced emission effect (AIE). To provide more insight into the optical properties of the two polymorphs, we present a combined computational and experimental study in the framework of crystal optics in the aim to explore the role of molecular packing on the UV-visible absorption properties of the two known polymorphs of [Re2(&mu;-Cl)<sub>2</sub>(CO)<sub>6</sub> (&mu;-4,5-(Me<sub>3</sub>Si)<sub>2</sub>pyridazine)].
Haben multimodale und perioperative Therapiestrategien das Überleben nach onkologischer Ösophaguschirurgie in den letzten 2 Dekaden verändert? Eine retrospektive Kohortenanalyse über 23 Jahre (2017)

Patients undergoing esophageal resection for cancer nowadays are older than in the past decades. Earlier cancer diagnosis, more radical surgical techniques with an extended lymphnode dissection, a decrease in anastomotic leakage and an improved perioperative care seem to compensate for this potential demographic disadvantage. The most important independent predictor of outcome after esophageal resection is the LNR.
Fatty acyl derivatives of glucosamine 1-phosphate in Escherichia coli and their relation to lipid A. Complete structure of A diacyl GlcN-1-P found in a phosphatidylglycerol-deficient mutant. (1983)

We have determined the complete structure of a glycolipid (designated lipid X) previously found to accumulate in certain Escherichia coli mutants defective in phosphatidylglycerol synthesis (Nishijima, M., and Raetz, C.R.H. (1979) J. Biol. Chem. 254, 7837-7844). Based on fast atom bombardment mass spectrometry and proton nuclear magnetic resonance studies, this substance is an acylated metabolite of glucosamine 1-phosphate. Lipid X of E. coli has a Mr = 711.87 as the free acid (C34H66NO12P) and contains two beta-hydroxymyristate moieties, one attached as an amide at the 2 position and the other as an ester at the 3 position of the sugar. It has free hydroxyl groups at the 4 and 6 positions, and the anomeric configuration is alpha. The structure of lipid X from E. coli closely resembles the reducing end subunit of lipid A, and it might represent a very early precursor in the biosynthesis of lipid A. To our knowledge, fatty acyl derivatives of glucosamine 1-phosphate have not been reported previously.
Quantitative phase-contrast imaging: a bridge between qualitative phase-contrast and phase retrieval algorithms (2020)

In the last five decades, iterative phase retrieval methods draw large amount of interest across the research community as a non-interferometric approach to recover quantitative phase distributions from one (or more) intensity measurement. However, in cases where a unique solution does exist, these methods often require oversampling and high computational resources, which limits the use of this approach in important applications. On the other hand, phase contrast methods are based on a single camera exposure but provides only a qualitative description of the phase, thus are not useful for applications in which the quantitative phase description is needed. In this study we adopt a combined approach of the two above-mentioned methods to overcome their respective drawbacks. We show that a modified phase retrieval algorithm easily converges to the correct solution by initializing the algorithm with a phase-induced intensity measurement, namely with a phase contrast image of the examined object. Accurate quantitative phase measurements for both binary and continuously varying phase objects are demonstrated to support the suggested system as a single-shot quantitative phase contrast microscope.
Deconstructing, Replicating, and Engineering Tissue Microenvironment for Stem Cell Differentiation (2020)

One of the most crucial components of regenerative medicine is the controlled differentiation of embryonic or adult stem cells into the desired cell lineage. Although most of the reported protocols of stem cell differentiation involve the use of soluble growth factors, it is increasingly evident that stem cells also undergo differentiation when cultured in the appropriate microenvironment. When cultured in decellularized tissues, for instance, stem cells can recapitulate the morphogenesis and functional specialization of differentiated cell types with speed and efficiency that often surpass the traditional growth factor-driven protocols. This suggests that the tissue microenvironment (TME) provides stem cells with a holistic "instructive niche" that harbors signals for cellular reprogramming. The translation of this into medical applications requires the decoding of these signals, but this has been hampered by the complexity of TME. This problem is often addressed by a reductionist approach, in which cells are exposed to substrates decorated with simple, empirically designed geometries, textures, and chemical compositions ("bottom-up" approach). Although these studies are invaluable in revealing the basic principles of mechanotransduction mechanisms, their physiological relevance is often uncertain. This review examines the recent progress of an alternative, "top-down" approach, in which the TME is treated as a holistic biological entity. This approach is made possible by recent advances in systems biology and fabrication technologies that enable the isolation, characterization, and reconstitution of TME. It is hoped that these new techniques will elucidate the nature of niche signals so that they can be extracted, replicated, and controlled. This review summarizes these emerging techniques and how the data they generated are changing our view on TME. Impact statement This review summarizes the current state of art of the understanding of instructive niche in the field of tissue microenvironment. Not only did we survey the use of different biochemical preparations as stimuli of stem cell differentiation and summarize the recent effort in dissecting the biochemical composition of these preparations, through the application of extracellular matrix (ECM) arrays and proteomics, but we also introduce the use of open-source, high-content immunohistochemistry projects in contributing to the understanding of tissue-specific composition of ECM. We believe this review would be highly useful for our peer researching in the same field. "Mr. Tulkinghorn is always the same… so oddly out of place and yet so perfectly at home." -Charles Dickens, <i>Bleak House</i>.
Determining the Number of Bariatric Beds Needed in a U.S. Acute Care Hospital (2021)

The simplified model and cost optimization could be used in many situations to prevent costly errors in equipment planning. However, hospitals should consider customized simulation to estimate demand for high-cost equipment or unique circumstances not fitting the assumptions of these models.
Low-Cost Obfuscated JPEG CODEC IP Core for Secure CE Hardware (2018)

A novel approach for obfuscated JPEG compression/decompression (CODEC) IP core design methodology, suitable for use in re-usable IP core designs, is presented. This incorporates structural obfuscation for architecture or structure hiding from an adversary in order to maximize the complexity against reverse engineering. Additionally, the proposed methodology performs the entire compression and decompression through a single dedicated hardware IP core. To obtain a lightweight (low cost version) of the proposed obfuscated JPEG CODEC IP, particle swarm optimization driven design space exploration is employed. Results of the proposed low cost, obfuscated JPEG CODEC IP core design when compared to un-protected (un-obfuscated) design yielded enhancement in strength of obfuscation of 76%, as well as reduction of 5% compared to un-optimized design.
Polarimetric Properties of Diffuse Scattering From Building Walls: Experimental Parameterization of a Ray-Tracing Model (2012)

Dense multipath components may represent an important part of wireless transmission channels, yet little is known about their physical properties. For this reason, we parameterize an ad hoc diffuse scattering model, which can be easily included in ray-tracing tools. The work, focusing on the polarimetric properties of diffuse contributions scattered off building walls, relies on experimental data. By means of a joint post-processing of the data in conjunction with ray-tracing simulations, characteristic parameters of diffuse scattering are extracted. The analysis reveals that diffuse scattering represents an crucial part of the received power. Regarding depolarization caused by diffuse scattering, our work highlights that depolarization appears to be small for homogeneous brick walls, but is far from negligible for more complex wall structures.
Alternative solid-phase reagents for formation of intramolecular sulfur-sulfur bridges in peptides under mild conditions (2006)

We have recently introduced a family of mild and efficient solid-phase reagents [1], derived from Ellman's reagent, to form disulfide bridges in peptides and protein under a wide range of conditions. Towards the same goal, two additional solid-phase reagents derived from -dithiobisnicotinic acid (1) and -dithiobis(5-nitronicotinic acid) (2) were designed, prepared, and investigated (Fig. 1). Using somatostatin (14 residues, disulfide bridge between residues 3 and 14) and differentially protected derivatives of SI (13 residues, the natural isomer has disulfide bridges between residues 2 and 7; 3 and 13) as substrates, the two reagents were evaluated under various reaction conditions. Their capacity to promote intramolecular disulfide bridge formation was compared to that of the solid-phase Ellman's reagent.
Matrix product operators and central elements: classical description of a quantum state (2012)

We study planar two-dimensional quantum systems on a lattice whose Hamiltonian is a sum of local commuting projectors of bounded range. We consider whether or not such a system has a zero energy ground state. To do this, we consider the problem as a one-dimensional problem, grouping all sites along a column into “supersites”; using C ‐algebraic methods (Bravyi and Vyalyi [9]), we can solve this problem if we can characterize the central elements of the interaction algebra on these supersite. Unfortunately, these central elements may be very complex, making brute force impractical. Instead, we show a characterization of these elements in terms of matrix product operators with bounded bond dimension. This bound can be interpreted as a bound on the number of particle types in lattice theories with bounded Hilbert space dimension on each site. Topological order in this approach is related to the existence of certain central elements which cannot be “broken” into smaller pieces without creating an end excitation. Using this bound on bond dimension, we prove that several special cases of this problem are in NP, and we give part of a proof that the general case is in NP. Further, we characterize central elements that appear in certain specific models, including toric code and Levin‐Wen models, as either product operators in the Abelian case or matrix product operators with low bond dimension in the non-Abelian case; this matrix product operator representation may have practical application in engineering the complicated multi-spin interactions in the Levin‐Wen models. 81P16 The subject of Hamiltonian complexity theory is devoted to the study of the computational complexity of various problems in quantum many-body physics. A general framework for this problem is as follows. We consider a quantum system whose Hilbert space is the tensor product of N different Hilbert spaces. Each of these N Hilbert spaces is referred to as the Hilbert space of a “site”. We are interested in the case that each site has Hilbert space dimension that is poly.N/ (indeed, in many practical settings it is O.1/). The Hamiltonian will be a sum of at most poly.N/ terms, where each term in the Hamiltonian acting on at most O.1/ sites. Often, a locality condition is imposed on these terms in the Hamiltonian: there is some given graph and each term in the Hamiltonian only acts on a set of sites which has small diameter with respect to
Comparative Evaluation of Polyphase Bearingless Slice Motors for Fluid-Handling Applications (2009)

For the bearingless slice motor (BSM) concept, which has been successfully introduced in semiconductor fluid-handling and medical applications over the last years, different motor configurations in terms of stator construction, number of phases, and winding arrangement exist. This paper comparatively evaluates these topologies for their suitability in possible future industry applications, such as the food, biotechnology, and pharmaceutical industries. The comparison is carried out for two-, three-, and four-phase BSM concepts based on performance indexes such as motor losses, losses in the power electronics, and voltampere requirements depending on the required magnetic bearing force and the motor torque. Finally, the performance data are discussed, and also, practical aspects such as realization effort, copper and iron mass, control effort, and scalability of the concepts are taken into account.
A fully integrated CMOS hall sensor with a 3.65μT 3σ offset for compass applications (2005)

A fully-integrated CMOS Hall sensor suitable for use in compass applications has a 3/spl sigma/ offset spread less than 4.5 /spl mu/T. After artificial aging it drifts less than 250 nT. Using two such sensors, a fully integrated electronically calibrated compass with a stability of 0.5/spl deg/ is realized. The sensor has an analog PWM and a digital RS232/SPI//spl mu/wire interface.
An associative memory architecture for concurrent production systems (2002)

This paper presents a novel parallel architecture for production systems. It relies on modern associative memory techniques to construct an environment in which productions can be fired in parallel even before the actions of previously fired productions are fully processed. This approach is made possible by the use of the serializability criterion for correctness. An approximate solution for the rule partitioning problem is presented. Measurements of speedup obtained from a detailed event-driven simulator indicate the potential of this new architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis, structure and magnetism of a unique dodecanuclearcopper(ii) ‘picture frame’ held in a 4 × 4 grid-like assemblyElectronic supplementary information (ESI) available: plot of magnetic susceptibility of 1 versus temperature. See http://www.rsc.org/suppdata/cc/b2/b210891g/ (2003)

The synthesis, structure and preliminary magnetic studies of a novel dodecanuclearcopper(II) grid-like assembly are reported.
Analytical and numerical computation of the no-load magnetic field in induction motors (1998)

In the paper a comparison between the analytical and numerical method of no-load computation will be made taking into account the initial hypothesis and computational effort face to the concrete obtainable results. It is concluded that the reduced fixed-mesh FEM analysis of the induction motors is very suitable for no-load computation because it relates directly to the well known equivalent circuit parameters. The symmetry of the machine allows for the computation only on a small part of the magnetic circuit so that the time of computation can be reduced even when a relatively fine mesh is used. However, for the optimal design of the motor it appears that analytical methods are very suitable owing to the simplicity and accuracy of the design.
Beyond block I/O (2013)

The basic block I/O interface used for interacting with storage devices hasn't changed much in 30 years. With the advent of very fast I/O devices based on solid-state memory, it becomes increasingly attractive to make many devices directly and concurrently available to many clients. However, when multiple clients share media at fine grain, retaining data consistency is problematic: SCSI, IDE, and their descendants don't offer much help. We propose an interface to networked storage that reduces an existing software implementation of a distributed shared log to hardware. Our system achieves both scalable throughput and strong consistency, while obtaining significant benefits in cost and power over the software implementation.
Frame structure design for wake-up system using DTV excess bandwidth for emergency alerting (2014)

In this paper, we design a frame structure of the wake-up system using DTV excess bandwidth for emergency alerting based on the Advanced Television Systems Committee (ATSC) terrestrial DTV system. The proposed frame structure of that system is based on the FSK modulation for indoor reception in receiver. Laboratory test and simulation results show that the proposed frame structure can provide an emergency alerting service without additional frequency assignment.
Reexamination of magnetic effects in the Bose gas (1989)

The breakdown of the Meissner-Ochsenfeld effect in the three-dimensional Bose gas as the applied field passes through its critical value is an entropy-driven weakly first-order transition, rather than the second-order transition usually ascribed to the system. The transition is second order at the usual Bose condensation temperature ${T}_{c}$ as well as at T=0, with a line of first-order transitions connecting these critical points. The first-order transitions make the Bose gas resemble familiar superconductors, and a Landau-Ginzburg analysis indicates that the Bose gas is always a type-I superconductor.
Energy optimization for a FC/SC power supply system for the traction of electric vehicles (2016)

Campus France PHC Stefanik 2016, Slovak University of Technology, Bratislava.
Formalization of a test experiment-II (2013)

The paper develops the approach to testing considered in [1]. A formal model of test interaction of the most general type and reduction-type conformance are proposed for which there is hardly any dependence between errors. It is shown that many known types of conformance in various interaction semantics are particular cases of this general model. The paper is devoted to the problem of dependence between errors defined by specification and to the related problem of optimization of tests. There is dependence between errors if there exists a strict subset of errors such that any nonconformal implementation (i.e., implementation that contains some error) contains an error from this subset. Accordingly, it is sufficient that the tests detect errors only from this subset. In the general model proposed, the dependence between errors may arise when one chooses, as a class of implementations under test, some strict subset of the class of all implementations. Partial interaction semantics and/or various implementation hypotheses (in particular, a safety hypothesis) precisely suggest that an implementation under test is not arbitrary but belongs to some subclass of (safe) implementations.
Multispectral infrared vibrational nano-imaging (2013)

We demonstrate multispectral infrared vibrational scattering-scanning near-field optical microscopy. Spatio-spectral images with 10 nm spatial and 1 cm−1 spectral resolution reveal nano-phase behavior in molecular nanostructured model systems with unprecedented sensitivity and structural detail.