gebhart/patrepeval huggingface dataset:
High-performance, low-complexity decoding of generalized low-density parity-check codes (2002)

A class of pseudo-random compound error-correcting codes, called generalized low-density (GLD) parity-check codes, has been proposed recently. As a generalization of Gallager's low-density parity-check (LDPC) codes, GLD codes are also asymptotically good in the sense of minimum distance criterion and can be effectively decoded based on iterative soft-input soft-output (SISO) decoding of individual constituent codes. The code performance and decoding complexity of GLD codes are heavily dependent on the employed SISO decoding algorithm. In this paper, we show that Max-Log-MAP is an attractive SISO decoding algorithm for GLD coding scheme, considering the trade-off between performance and complexity in the practical implementations. A normalized Max-Log-MAP is presented to improve the GLD code performance significantly compared with using conventional Max-Log-MAP. Moreover, we propose two techniques, decoding task scheduling and reduced search Max-Log-MAP, to effectively reduce the decoding complexity without any performance degradation.
Trauma-specific Grey Matter Alterations in PTSD (2016)

Previous studies have demonstrated that patients with posttraumatic stress disorder (PTSD) caused by different types of trauma may show divergence in epidemiology, clinical manifestation and treatment outcome. However, it is still unclear whether this divergence has neuroanatomic correlates in PTSD brains. To elucidate the general and trauma-specific cortical morphometric alterations, we performed a meta-analysis of grey matter (GM) changes in PTSD (N = 246) with different traumas and trauma-exposed controls (TECs, N = 347) using anisotropic effect-size signed differential mapping and its subgroup analysis. Our results revealed general GM reduction (GMR) foci in the prefrontal-limbic-striatal system of PTSD brains when compared with those of TECs. Notably, the GMR patterns were trauma-specific. For PTSD by single-incident traumas, GMR foci were found in bilateral medial prefrontal cortex (mPFC), anterior cingulate cortex (ACC), insula, striatum, left hippocampus and amygdala; and for PTSD by prolonged traumas in the left insula, striatum, amygdala and middle temporal gyrus. Moreover, Clinician-Administered PTSD Scale scores were found to be negatively associated with the GM changes in bilateral ACC and mPFC. Our study indicates that the GMR patterns of PTSD are associated with specific traumas, suggesting a stratified diagnosis and treatment for PTSD patients.
Cross‐Coupling Reactions on Azoles with Two and More Heteroatoms (2006)

Abstract Recent progress in the field of transition‐metal‐catalyzed cross‐coupling reactions on various azole systems is summarized. Most important C–C‐ and C–X‐bond formation methodologies (Negishi, Suzuki–Miyaura, Stille, Kumada–Corriu–Tamao, Hiyama, Sonogashira, Heck, C–H activation) are reviewed and discussed for the imidazole, oxazole, thiazole, pyrazole, isoxazole, and isothiazole system, as well as for azoles with more than two heteroatoms. This review covers the literature that appeared in the past ten years up to the end of 2005 with corresponding azoles used either as metal organyl or halide (including triflates and some other less frequently applied leaving groups); literature describing azole structures only as ligands was not included.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Toward high-quality modal contact sound (2011)

Contact sound models based on linear modal analysis are commonly used with rigid body dynamics. Unfortunately, treating vibrating objects as "rigid" during collision and contact processing fundamentally limits the range of sounds that can be computed, and contact solvers for rigid body animation can be ill-suited for modal contact sound synthesis, producing various sound artifacts. In this paper, we resolve modal vibrations in both collision and frictional contact processing stages, thereby enabling non-rigid sound phenomena such as micro-collisions, vibrational energy exchange, and chattering. We propose a frictional multibody contact formulation and modified Staggered Projections solver which is well-suited to sound rendering and avoids noise artifacts associated with spatial and temporal contact-force fluctuations which plague prior methods. To enable practical animation and sound synthesis of numerous bodies with many coupled modes, we propose a novel asynchronous integrator with model-level adaptivity built into the frictional contact solver. Vibrational contact damping is modeled to approximate contact-dependent sound dissipation. Results are provided that demonstrate high-quality contact resolution with sound.
Optical crossbar elements used for switching networks (1994)

An optical crossbar element that uses birefringent crystal plates and programmable half-wave plates is proposed. It is compact, cascadable, and well suited for realizing an array of switching elements employed in multistage interconnection networks. Arrays of two-input/two-output and four-input/fourputput crossbar switching elements and a Clos (4, 4, 4) network are also presented.
Localization in a vector field map (2012)

Localization using continuous signals such as WiFi or active beacons is a cost-effective approach for enabling systematic navigation of robots. In our previous work we showed how localization maps, represented as regular grids, of such signals can be learned through application of vector field SLAM [1]. In this paper we describe a method that, given such a localization map, finds the pose of a mobile robot from observations of the signals. Our method first generates pose hypotheses by searching the localization map for places that best fit to a measurement taken by the robot. A localization filter using an extended Kalman filter (EKF) then verifies one pose hypothesis by tracking the pose over a short distance. In experiments carried out in a standard test environment equipped with active beacons we obtain an average position accuracy of 10 to 35 cm with a localization success rate of 96 to 99 %. The proposed method enables a robot mapping an environment using vector field SLAM to recover from kidnapping and resume its navigation.
A configuration process for a distributed software development environment (2002)

The authors describe work-in-progress on a configuration facility for a multi-site software development environment. The environment supports collaboration among geographically-dispersed teams of software developers. Addition and deletion of local subenvironment sites to a global environment is performed interactively inside any one of the existing local subenvironments, with the same user interface normally employed for invoking software development tools. This registration process is defined and executed using the same notation and mechanisms, respectively, as for the software development process. Everything described by the authors has been implemented and is working, but since they are in the midst of experimentation, they do not expect that the "final" system will be exactly as described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Long-term effects of tafamidis for the treatment of transthyretin familial amyloid polyneuropathy (2013)

Tafamidis, a transthyretin (TTR) kinetic stabilizer, delayed neuropathic progression in patients with Val30Met TTR familial amyloid polyneuropathy (TTR-FAP) in an 18-month randomized controlled trial (study Fx-005). This 12-month, open-label extension study evaluated the long-term safety, tolerability, and efficacy of tafamidis 20 mg once daily in 86 patients who earlier received blinded treatment with tafamidis or placebo. Efficacy measures included the Neuropathy Impairment Score in the Lower Limbs (NIS-LL), Norfolk Quality of Life-Diabetic Neuropathy total quality of life (TQOL) score, and changes in neurologic function and nutritional status. We quantified the monthly rates of change in efficacy measures, and TTR stabilization, and monitored adverse events (AEs). Patients who continued on tafamidis had stable rates of change in NIS-LL (from 0.08 to 0.11/month; p = 0.60) and TQOL (from -0.03 to 0.25; p = 0.16). In patients switched from placebo, the monthly rate of change in NIS-LL declined (from 0.34 to 0.16/month; p = 0.01), as did TQOL score (from 0.61 to -0.16; p < 0.001). Patients treated with tafamidis for 30 months had 55.9 % greater preservation of neurologic function as measured by the NIS-LL than patients in whom tafamidis was initiated later. Plasma TTR was stabilized in 94.1 % of patients treated with tafamidis for 30 months. AEs were similar between groups; no patients discontinued because of an AE. Long-term tafamidis was well tolerated, with the reduced rate of neurologic deterioration sustained over 30 months. Tafamidis also slowed neurologic impairment in patients previously given placebo, but treatment benefits were greater when tafamidis was begun earlier.
A Comparison of Conventional and Spiral CT (1994)

We conclude that spiral CT can offer improved 3D contrast and spatial resolution. To exploit these advantages, images should be reconstructed in spiral CT at increments of less than half the distance traveled during one 360 degrees tube rotation. With four to five images per such interval, usually equal to the slice width, results very close to the theoretical optimum are achieved. Many of the presented considerations and results apply to other slice imaging modalities like MRI in analogous fashion.
Microfluidic Diffusion-Based Separation and Detection (1999)

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Stress Relief Protein Modulation by Calnexin (1996)

Oxygen free radical (OFR)-mediated oxidative stress in myocardial cells following ischemia could damage unit membrane and macromolecules such as nucleic acids (DNA). It is being reported that under this condition these cells produce antioxidants and heat shock proteins (HSP 70). It is implied that this family of proteins could function as a "molecular chaperone" in the cell and hence has to be transported to various target sites. This process is comparable to the induction of oxygen free radicals in melanocytes and its response, melanin production following UV light exposure stress. Lamp-1, trp-1 and tyrosinase are melanosomal-associated stress relief proteins which are involved in the production of melanin in the subcellular organelle, melanosomes. UV exposure studies as well as gene transfection studies and antisense hybridization in human melanoma cells clearly indicated an increase and marked coordinated interaction of all these stress relief proteins in melanogenesis. These proteins are synthesized in the endoplasmic reticulum and have to undergo posttranslation modification, sorting and posting to their respective target sites. We simultaneously identified and characterized an ER resident protein, calnexin. It became the potential candidate for "chaperoning" these proteins following translation. Based on the computer analysis of HSP 70 cDNA, we postulate that similar to stress response proteins in melanogenesis, stress relief proteins in myocardial cells may also be modulated by the same ER resident protein, calnexin.
Pharmacokinetic and pharmacodynamic analysis of a novel leukotriene biosynthesis inhibitor, MK‐0591, in healthy volunteers. (1995)

1. The pharmacokinetic and pharmacodynamic properties of a novel 2-indolealkanoic acid derivative (MK-0591), a potent inhibitor of leukotriene biosynthesis, were investigated in healthy male Japanese volunteers. Single oral doses of 50, 125, 250 and 500 mg and multiple oral doses of 125 mg twice daily for 9.5 days and 250 mg once daily for 10 days were administered. 2. After the single-dose administration following overnight fasting, Cmax and AUC of MK-0591 in plasma increased in a dose-dependent manner, while elimination half-life remained constant (11.2-13.2 h) irrespective of dose. Food intake decreased Cmax and AUC by 71% and 68%, respectively, at a dose of 250 mg. With respect to multiple-dose administration before meals, there were no significant differences in the pharmacokinetic parameters between the first and last days, indicating a lack of significant accumulation of MK-0591 in plasma. Urinary recovery as the unchanged form was negligible throughout the study. 3. Ionophore-stimulated production of leukotriene B4 (LTB4) in blood ex vivo was inhibited significantly from 1 h until 12 to 48 h after single-dose administration as compared with predose value. In parallel, the urinary excretion of endogenous leukotriene E4 (LTE4) was significantly decreased from 4 to 8 h until 48 to 72 h after drug administration. Reduction of ionophore-stimulated LTB4 biosynthesis and urinary excretion of LTE4 following single administration of MK-0591 was statistically significant as compared with placebo group, and the duration of inhibition of LTB4 biosynthesis was dose-related.(ABSTRACT TRUNCATED AT 250 WORDS)
Dealing with asynchronicity in parallel Gaussian Process based global optimization (2011)

During the last decade, Kriging-based sequential algorithms like EGO and its variants have become reference optimization methods in computer experiments. Such algorithms rely on the iterative maximization of a sampling criterion, the expected improvement (EI), which takes advantage of Kriging conditional distributions to make an explicit trade-off between promizing and uncertain search space points. We have recently worked on a multipoints EI criterion meant to simultaneously choose several points, which is useful for instance in synchronous parallel computation. Here we propose extensions of these works to asynchronous parallel optimization and focus on a variant of EI, EEI, for the case where some new evaluation(s) have to be done while the reponses of previously simulations are not all known yet. In particular, different issues regarding EEI's maximization are addressed, and a proxy strategy is proposed.
Marine controlled‐source electromagnetic sounding: 1. Modeling and experimental design (1996)

Numerical forward modeling, predicting an observable response given a mathematical representation of the Earth, is an important component of practical exploration work. In addition, derivatives which relate changes in response to changes in the Earth model are useful for experimental design and are a crucial element of linearized inversion techniques. Differentiation of kernels followed by numerical integration using a fast Hankel transform provides an efficient combination of forward and sensitivity modeling for frequency‐domain horizontal electric dipole‐dipole sounding over a layered seafloor. Our code is validated against an independent forward modeling technique using a mode analysis and against central difference derivatives. Efficiency is important in the application of regularized inversion to large data sets; we give an example from the East Pacific Rise, requiring 2000 elements in the Jacobian matrix. We illustrate the use of forward modeling and discrete analogs of the Fréchet kernels to provide aid to physical intuition and experimental design in the context of the electrical conductivity of the oceanic lithosphere. By using the most favorable parts of range‐frequency space, experiments using current technology should be capable of distinguishing a thicker, less resistive, from a thinner, more resistive “lithospheric resistor” layer.
Kinetics and Substrate Specificity of Membrane-Reconstituted Peptide Transporter DtpT of Lactococcus lactis (2000)

The peptide transport protein DtpT of Lactococcus lactis was purified and reconstituted into detergent-destabilized liposomes. The kinetics and substrate specificity of the transporter in the proteoliposomal system were determined, using Pro-[(14)C]Ala as a reporter peptide in the presence of various peptides or peptide mimetics. The DtpT protein appears to be specific for di- and tripeptides, with the highest affinities for peptides with at least one hydrophobic residue. The effect of the hydrophobicity, size, or charge of the amino acid was different for the amino- and carboxyl-terminal positions of dipeptides. Free amino acids, omega-amino fatty acid compounds, or peptides with more than three amino acid residues do not interact with DtpT. For high-affinity interaction with DtpT, the peptides need to have free amino and carboxyl termini, amino acids in the L configuration, and trans-peptide bonds. Comparison of the specificity of DtpT with that of the eukaryotic homologues PepT(1) and PepT(2) shows that the bacterial transporter is more restrictive in its substrate recognition.
Understanding and overcoming shear alignment of fibers during extrusion (2014)

Fiber alignment is the defining architectural characteristic of discontinuous fiber composites and is dictated by shear-dominated processing techniques including flow-injection molding, tape-casting, and mold-casting. However, recent colloidal assembly techniques have started to employ additional forces in fiber suspensions that have the potential to change the energy landscape of the shear-dominated alignment in conditions of flow. In this paper, we develop an energetics model to characterize the shear-alignment of rigid fibers under different flow conditions in the presence of magnetic colloidal alignment forces. We find that these colloidal forces can be sufficient to manipulate the energetic landscape and obtain tunable fiber alignment during flow within even small geometries, such as capillary flow. In most conditions, these colloidal forces work to freeze the fiber orientation during flow and prevent the structure disrupting phenomenon of Jeffrey's orbits that has been accepted to rule fiber suspensions under simple shear flow.
Analysis of the Factor VIIa Binding Site on Human Tissue Factor: Effects of Tissue Factor Mutations on the Kinetics and Thermodynamics of Binding (1995)

Surface plasmon resonance (SPR) measurements on a BIAcore instrument have been used to measure the effects of mutations in human tissue factor (TF), the initiator of blood coagulation, on the kinetics and affinity of binding to human FVIIa. TF mutant proteins were produced in soluble form by expression of the extracellular domain (sTF) in Escherichia coli followed by immunoaffinity purification. Mutants were designed and analyzed on the basis of the structure of sTF recently determined by X-ray crystallography [Muller et al. (1994) Biochemistry 33, 10864-10870]. Wild-type sTF binding to immobilized FVIIa has k(on) = 3.4 +/- 0.8 x 10(5) M-1 s-1 and k(off) = 2.1 +/- 0.1 x 10(-3) s-1 with a calculated KD of 6.3 +/- 1.2 nM and delta G of -11.2 +/- 0.1 kcal mol-1. Calorimetric measurements indicate that binding occurs with a favorable delta H of -32 kcal mol-1, an unfavorable delta S of -70 cal K-1 mol-1, and a delta Cp of -730 cal K mol-1. The value of delta Cp is consistent with burial of a large nonpolar surface area upon binding. Five residues on TF, Lys20, Trp45, Asp58, Tyr94, and Phe140, make a large contribution (delta delta G = 1-2.5 kcal mol-1) to FVIIa binding, a set of 17 mutations result in modest decreases in affinity (delta delta G = 0.3-1 kcal mol-1), and 40 mutations have delta delta G smaller than the experimental uncertainty (+/- 0.3 kcal mol-1). Mutations at four sites result in small (0.3-0.5 kcal mol-1) increases in affinity. Decreases in affinity result primarily from increased rates of dissociation. These data define a putative FVIIa binding site on one face of the TF structure with most of the contacts contributed by the N-terminal fibronectin type III domain. The critical binding residues are found on beta-strands. An additional set of residues located on the surface of the C-terminal fibronectin type III domain opposite the FVIIa binding site have a role in the procoagulant activity of sTF but are not involved in FVIIa binding.
New mustard-linked 2-aryl-bis-benzimidazoles with anti-proliferative activity (2006)

We describe new methodology for the synthesis of symmetric bis-benzimidazoles carrying 2-aryl moieties, including 2-[4-(3'-aminopropoxy)phenyl] and 2-[4-(3'-aminopropanamido)phenyl] substituents, together with the synthesis of novel hybrid molecules comprising bis-benzimidazoles in ester and amide combination with the N-mustard chlorambucil. The in vitro activities of these compounds against five cancer cell lines are also provided.
In vivo1H chemical shift imaging of silicone implants (1993)

In order to study the aging process (i.e., silicone migration, fat infiltration) of silicone (polydimethylsiloxane, PDMS) based biomaterials in living subjects by NMR imaging, a hybrid 1H selective excitation and saturation chemical shift imaging technique (IR/CHESS-CSSE) has been developed. This sequence allows selective mapping of the distribution of silicone protons in vivo, while suppressing the contributions of fat and water. Our results indicate that a combined inversion recovery and CHESS pulse, followed by a spoiler gradient, must be applied to suppress all contributions of fat protons to the NMR signal. The sensitivity of our experiments allows the detection of a chemically unchanged silicone concentration of 5% in a voxel of 0.9 mm3 at a signal/noise ratio of 2.
Temporal and chromatic properties of motion mechanisms (1995)

We measured threshold contours in color space for detecting drifting sinusoidal gratings over a range of temporal frequencies, and for identifying their direction of motion. Observers were able to correctly identify the direction of motion in all directions of color space, given a sufficiently high contrast. At low temporal frequencies we found differences between luminance and isoluminance conditions; for isoluminance there was a marked threshold elevation for identification when compared to detection. The threshold elevation for identification is dependent on eccentricity as well as on temporal frequency. At high temporal frequencies there were no differences between detection and identification thresholds, or between thresholds for luminance and isoluminance. A quantitative analysis of the threshold contours allowed us to identify two mechanisms contributing to motion: a color-opponent mechanism with a high sensitivity at low temporal frequencies and a luminance mechanism whose relative sensitivity increases with temporal frequency. An analysis of the cone contributions to motion detection and identification showed that L-cones dominated threshold behavior for both detection and identification at high temporal frequencies. There was a weak S-cone input to motion detection and identification at high temporal frequencies.
Psychedelics as Medicines: An Emerging New Paradigm (2016)

Scientific interest in serotonergic psychedelics (e.g., psilocybin and LSD; 5-HT<sub>2A</sub> receptor agonists) has dramatically increased within the last decade. Clinical studies administering psychedelics with psychotherapy have shown preliminary evidence of robust efficacy in treating anxiety and depression, as well as addiction to tobacco and alcohol. Moreover, recent research has suggested that these compounds have potential efficacy against inflammatory diseases through novel mechanisms, with potential advantages over existing antiinflammatory agents. We propose that psychedelics exert therapeutic effects for psychiatric disorders by acutely destabilizing local brain network hubs and global network connectivity via amplification of neuronal avalanches, providing the occasion for brain network "resetting" after the acute effects have resolved. Antiinflammatory effects may hold promise for efficacy in treatment of inflammation-related nonpsychiatric as well as potentially for psychiatric disorders. Serotonergic psychedelics operate through unique mechanisms that show promising effects for a variety of intractable, debilitating, and lethal disorders, and should be rigorously researched.