gebhart/patrepeval huggingface dataset:
Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum (2004)

Using replicated human serum samples, we applied an error model for proteomic differential expression profiling for a high-resolution liquid chromatography-mass spectrometry (LC-MS) platform. The detailed noise analysis presented here uses an experimental design that separates variance caused by sample preparation from variance due to analytical equipment. An analytic approach based on a two-component error model was applied, and in combination with an existing data driven technique that utilizes local sample averaging, we characterized and quantified the noise variance as a function of mean peak intensity. The results indicate that for processed LC-MS data a constant coefficient of variation is dominant for high intensities, whereas a model for low intensities explains Poisson-like variations. This result leads to a quadratic variance model which is used for the estimation of sample preparation noise present in LC-MS data.
Position-sensitive detector performance and relevance to time-resolved electron energy loss spectroscopy (1986)

The use of position-sensitive detectors (PSDs) has become common in many spectroscopies. The increased signal provided by the parallel detection of many spectral elements affords increases in sensitivity and/or time resolution. Recently, the use of a PSD to increase the temporal resolution of an electron energy loss (EEL) spectrometer has been demonstrated in our laboratory. This article summarizes the present development of EEL spectrometers and then presents a detailed review of four classes of PSDs in the context of their potential application to EEL spectroscopy (EELS). The four classes considered are (a) discrete channel detectors, (b) coincidence array detectors, (c) charge division detectors, and (d) optical detectors imaging phosphor screens. All four designs, as typically implemented, utilize microchannel plates (MCPs) as spatially imaging electron multipliers. The performance of MCPs is reviewed and the constraints that MCP behavior at the high count rates achievable in EELS places on acceptable PSD performance are outlined. The inability of present MCPs to maintain saturation gain at count rates above 1 MHz mm−2 implies that the PSD must tolerate significant gain reduction in the electron multiplier. The possibility of eliminating the MCP and using an electron-bombarded silicon gain mechanism is proposed. Such a device could, in principle, support count rates in excess of 100 MHz/channel, providing an order of magnitude increase in performance over the best existing detectors.
Growth of device quality GaN at 550 °C by atomic layer epitaxy (1995)

GaN single crystal films were grown by atomic layer epitaxy at 550 °C. The room temperature photoluminescence properties of these low-temperature-grown films are dominated by band edge emission with intensity comparable to those grown by metalorganic chemical vapor deposition at 1000 °C. The as-grown films have background-carrier concentrations that can be controlled to levels in the 1016/cm−3 range. Atomic layer epitaxy is therefore a good approach to the low temperature growth of nitride compounds.
Active RC filters employing a single operational amplifier to obtain biquadratic responses (1965)

In this paper, networks are presented in tabular form to simplify the design of RC active filters having magnitude responses characterised by pass-band attenuation ripples and stop-band transmission zeros. The responses of these networks may be described by biquadratic rational functions. In all, the form and element values for 11 different networks are tabulated.The basic network discussed in the paper is an operational amplifier with multiloop feedback in cascade with a passive RC circuit and having a second-order response. Higher-order responses than the second may be obtained by cascading second-order stages of the tabulated networks, with suitable isolating stages when necessary.Two different forms of passive circuit are given, together with their design formulas. Both low-pass and high-pass filters are considered; these can be cascaded to give band-pass or band-stop characteristics.The operational amplifier is assumed to have infinite input and zero output impedance; the effects of departure from these ideal conditions on the filter response is considered.
Substance P receptor expression by inhibitory interneurons of the rat hippocampus: Enhanced detection using improved immunocytochemical methods for the preservation and colocalization of GABA and other neuronal markers (2001)

Two unresolved issues regarding the identification and characterization of hippocampal interneurons were addressed in this study. One issue was the longstanding inability to detect gamma-aminobutyric acid (GABA) in the somata of several hippocampal interneuron subpopulations, which has prevented the unequivocal identification of all hippocampal interneurons as GABA neurons. The second issue was related to the identification of the hippocampal interneurons that constitutively express substance P (neurokinin-1) receptors (SPRs). The recent development of neurotoxins that specifically target SPR-expressing cells suggests that it may be possible to destroy hippocampal inhibitory interneurons selectively for experimental purposes. Although SPRs are apparently expressed in the hippocampus only by interneurons, colocalization studies have found that most interneurons of several subtypes and hippocampal subregions appear SPR-negative. Thus, the identities and locations of the inhibitory interneurons that are potential targets of an SPR-directed neurotoxin remain in doubt. Using newly developed methods designed to copreserve and colocalize GABA and polypeptide immunoreactivities with increased sensitivity, the authors report that virtually all hippocampal interneuron somata that are immunoreactive for parvalbumin (PV), calbindin, calretinin, somatostatin (SS), neuropeptide Y, cholecystokinin, and vasoactive intestinal peptide exhibited clearly detectable, somal, GABA-like immunoreactivity (LI). Hippocampal SPR-LI was detected only on the somata and dendrites of GABA-immunopositive interneurons. All glutamate receptor subunit 2-immunoreactive principal cells, including dentate granule cells, hilar mossy cells, and hippocampal pyramidal cells, were devoid of detectable SPR-LI, even after prolonged electrical stimulation of the perforant pathway that induced the expression of other neuronal proteins in principal cells. Thus, hippocampal interneurons of all subtypes and subregions were found to be SPR-immunoreactive, including the PV-positive interneurons of the dentate hilus and hippocampus, and the SS-positive cells of area CA1, both of which were previously reported to lack SPR-LI. Only minor proportions of hippocampal interneurons appeared clearly devoid of detectable SPR-LI. These results demonstrate for the first time that all identified interneuron subpopulations of the rat hippocampus are GABA-immunoreactive, and that many inhibitory interneurons of all subtypes in all subregions of the rat hippocampus express SPRs constitutively.
Re-Designing CNTK Deep Learning Framework on Modern GPU Enabled Clusters (2016)

Deep learning frameworks have recently gained widespread popularity due to their highly accurate prediction capabilities and availability of low cost processors that can perform training over a large dataset quickly. Given the high core count in modern generation high performance computing systems, training deep networks over large data has now become practical. In this work, while targeting the Computational Network Toolkit (CNTK) framework, we propose new mechanisms and designs to boost the performance of the communications between GPU nodes. We perform thorough analysis of the different phases of the toolkit such as I/O, communications, and computation of CNTK to identify the different bottlenecks that can be potentially alleviated using the high performance capabilities provided by many CUDA aware MPI runtimes. Using a CUDA aware MPI library, we propose CUDA Aware CNTK (CA-CNTK) which does low overhead communications. Different datasets ranging from small to large sizes prove the advantage of our re-design, and how it can show similar results on deep learning frameworks having a similar execution pattern. Our designs show an average improvement of 23%, 21% and 15% per epoch for the popular CIFAR10, MNIST and ImageNet datasets, respectively.
Towards mild metal-catalyzed C–H bond activation (2011)

Functionalizing traditionally inert carbon-hydrogen bonds represents a powerful transformation in organic synthesis, providing new entries to valuable structural motifs and improving the overall synthetic efficiency. C-H bond activation, however, often necessitates harsh reaction conditions that result in functional group incompatibilities and limited substrate scope. An understanding of the reaction mechanism and rational design of experimental conditions have led to significant improvement in both selectivity and applicability. This critical review summarizes and discusses endeavours towards the development of mild C-H activation methods and wishes to trigger more research towards this goal. In addition, we examine select examples in complex natural product synthesis to demonstrate the synthetic utility of mild C-H functionalization (84 references).
Faraday shield effects on a half-turn loop antenna used for ICRF plasma heating (1988)

The characteristics of a half-turn loop antenna having a Faraday shield (used for ion-cyclotron RF plasma heating) have been systematically investigated. The main interest is to clarify the Faraday shield effects on the near-zone electric field distribution. It has been confirmed that, in the presence of the Faraday shield, undesirable field components are sufficiently suppressed, and the heating component E/sub y/, which otherwise is strongly localized as an end effect, has been found to be distributed uniformly along the antenna in the case of a short electric length. It is found that the shielding strips should be uniformly distributed over the entire region around the half-turn loop antenna.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Leptin administration to overweight and obese subjects for 6 months increases free leptin concentrations but does not alter circulating hormones of the thyroid and IGF axes during weight loss induced by a mild hypocaloric diet (2011)

Leptin does not likely mediate changes in neuroendocrine function in response to weight loss induced by a mild hypocaloric diet in overweight and obese subjects.
Psychosocial sequelae of the 1989 Newcastle earthquake: III. Role of vulnerability factors in post-disaster morbidity (1997)

Medium-term post-earthquake morbidity appears to be a function of multiple factors whose contributions vary depending on the type of morbidity experienced and include trait vulnerability, the nature and degree of initial exposure, avoidance coping and the nature and severity of subsequent events.
Dichotomy of decorin activity on the insulin‐like growth factor‐I system (2013)

The stromal-specific proteoglycan decorin has emerged in recent years as a critical regulator of tumor initiation and progression. Decorin regulates the biology of various types of cancer by modulating the activity of several receptor tyrosine kinases coordinating growth, survival, migration, and angiogenesis. Decorin binds to surface receptors for epidermal growth factor and hepatocyte growth factor with high affinity, and negatively regulates their activity and signaling via robust internalization and eventual degradation. The insulin-like growth factor (IGF)-I system plays a critical role in the regulation of cell growth both in vivo and in vitro. The IGF-I receptor (IGF-IR) is also essential for cellular transformation, owing to its ability to enhance cell proliferation and protect cancer cells from apoptosis. Recent data have pointed to a role of decorin in regulating the IGF-I system in both nontransformed and transformed cells. Significantly, there is a surprising dichotomy in the mechanism of decorin action on IGF-IR signaling, which differs considerably between physiological and pathological cellular models. In this review, we summarize the current knowledge on decorin regulation of the IGF-I system in normal and transformed cells, and discuss possible decorin-based therapeutic approaches to target IGF-IR-driven tumors.
Baffle effects on performance of catalytic circulating fluidized bed reactor (1991)

Abstract Baffle effects on the performance of a catalytic circulating fluidized bed reactor were examined experimentally. The circulating fluidized bed reactor or riser was 102 mm in diameter and 6.32 m in height. Reaction was the catalytic decomposition of ozone using FCC particles with a mean diameter of 89 μm, impregnated with ferric oxide as catalysts. Four ring‐type baffles, mounted horizontally around the riser wall, were used in this study. Ozone concentrations were measured in both axial and radial directions under various operating conditions in a riser with and without baffles. Experimental results showed that in a riser with baffles, the ozone concentration in the radial direction was more uniform and the ozone conversion was higher than that in a riser without baffles except at the lowest gas velocity used. A mathematical model developed accounted for the gas‐phase ozone conversion under various operating conditions. The gas‐solid contact efficiency in the riser was discussed in light of the model.
Pareto-Based Multiobjective AI Planning (2013)

Real-world problems generally involve several an-tagonistic objectives, like quality and cost for de-sign problems, or makespan and cost for plan-ning problems. The only approaches to multiob-jective AI Planning rely on metrics, that can incor-porate several objectives in some linear combina-tions, and metric sensitive planners, that are able to give different plans for different metrics, and hence to eventually approximate the Pareto front of the multiobjective problem, i.e. the set of opti-mal trade-offs between the antagonistic objectives. Divide-and-Evolve (DAE) is an evolutionary plan-ner that embeds a classical planner and feeds it with a sequence of subproblems of the problem at hand. Like all Evolutionary Algorithms, DAE can be turned into a Pareto-based multiobjective solver, even though using an embedded planner that is not metric sensitive. The Pareto-based multiobjective planner MO-DAE thus avoids the drawbacks of the aggregation method. Furthermore, using YAHSP as the embedded planner, it outperforms in many cases the metric-based approach using LPG met-ric sensitive planner, as witnessed by experimental results on original multiobjective benchmarks built upon IPC-2011 domains. 1
Operation of high-speed silicon photonic micro-disk modulators at cryogenic temperatures (2017)

Significant progress has been made in the field of silicon photonics over the past two decades. Silicon photonics provides substantial performance advantages in many data processing and transfer applications. Until now, the benefits of active silicon photonics in cryogenic systems have remained unexplored. Here we demonstrate the operation of a high-speed, CMOS compatible silicon micro-disk modulator transmitting data at rates up to 10 Gb/s and at temperatures down to 4.8 K. This opens the door for the use of silicon photonics as an interface to low temperature, bandwidth intensive systems such as high-performance superconducting-based computing and integrated quantum optics circuits interfacing to superconducting single-photon detectors.
Mouse Model of Enteropathogenic <i>Escherichia coli</i> Infection (2005)

Enteropathogenic Escherichia coli (EPEC) is an important cause of diarrhea in humans. EPEC infection of cultured intestinal epithelial cells induces attaching and effacing (A/E) lesions, alters intestinal ion transport, increases paracellular permeability, and stimulates inflammation. The lack of a small-animal model has restricted in vivo studies examining EPEC-host interactions. The aim of this study was to characterize the C57BL/6J mouse as a model of EPEC infection. We have shown that EPEC can adhere to and colonize the intestinal epithelium of C57BL/6J mice. Animal weight and water intake were not altered during 10 days of EPEC infection. The proximal colon of infected mice contained semisolid stool, with stool pellets forming only in the distal colon. In contrast, the entire colon of control mice contained formed stool. Microvillous effacement and actin rearrangement, characteristic of A/E lesions, were seen in the intestine of infected mice but not control mice. Histological assessment revealed increased numbers of lamina propria neutrophils with occasional crypt abscesses, intraepithelial lymphocytes, and goblet cells in the intestine of EPEC-infected mice. Altogether, these data suggest that the C57BL/6J mouse is susceptible to infection by EPEC and will provide a suitable in vivo model for studying the consequences of EPEC infection.
Comparison of slotline characteristics (1990)

The slot width required for conventional slotlines is very narrow when etched on low dielectric constant substrates. This poses fabrication difficulties and discourages the use of slotlines on these substrates. However, the slotline is finding increased applications in slot antennas. In order to feed the slot antennas, alternate structures must be found that relax the fabricational difficulties. Two such new structures are the bilateral slotline and the asymmetric slotline. In this thesis, design data was developed and comparison was made between the various slotlines with regards to the substrate parameters and the slot width. Use was made of computer codes already developed for these structures.
The Management of Grief: A Study of Black Funeral Practices (1973)

This study is concerned with the nature of the influence of noneconomic values in economic transactions. It deals with the ethnic differences in meeting the bereavement needs of black mourners, as well as the means used by black morticians to impute roles to their clientele; and their means of meeting the bereavement needs of those they serve. Some practices of black morticians are examined in contrast to their white competitors; others are studied in terms of traditional values vs. rational behavior. More than the mere disposal of the dead, the black mortuary emerges as an institution for the sublimation of guilt and the acquisition of social status. This study demonstrates the role of the clergy within the funeral pageantry.
Unilateral remote temperature monitoring to predict future ulceration for the diabetic foot in remission (2019)

Given the high incidence of subsequent diabetic foot complications to the sound foot in patients with a history of proximal LEA and patients being treated for a wound, practice of daily temperature monitoring of a single foot has the potential to significantly improve outcomes and reduce resource utilization in this challenging high-risk population.
Management of Articular Cartilage Defects of the Knee (2010)

Articular cartilage has a poor intrinsic capacity for healing. The goal of surgical techniques to repair articular cartilage injuries is to achieve the regeneration of organized hyaline cartilage. Microfracture and other bone marrow stimulation techniques involve penetration of the subchondral plate in order to recruit mesenchymal stem cells into the chondral defect. The formation of a stable clot that fills the lesion is of paramount importance to achieve a successful outcome. Mosaicplasty is a viable option with which to address osteochondral lesions of the knee and offers the advantage of transplanting hyaline cartilage. However, limited graft availability and donor site morbidity are concerns. Transplantation of an osteochondral allograft consisting of intact, viable articular cartilage and its underlying subchondral bone offers the ability to address large osteochondral defects of the knee, including those involving an entire compartment. The primary theoretical advantage of autologous chondrocyte implantation is the development of hyaline-like cartilage rather than fibrocartilage in the defect, which presumably leads to better long-term outcomes and longevity of the healing tissue. Use of synthetic scaffolds is a potentially attractive alternative to traditional cartilage procedures as they are readily available and, unlike allogeneic tissue transplants, are associated with no risk of disease transmission. Their efficacy, however, has not been proven clinically.
Analysis of partial volume effects in diffusion‐tensor MRI (2001)

The diffusion tensor is currently the accepted model of diffusion in biological tissues. The measured diffusion behavior may be more complex when two or more distinct tissues with different diffusion tensors occupy the same voxel. In this study, a partial volume model of MRI signal behavior for two diffusion-tensor compartments is presented. Simulations using this model demonstrate that the conventional single diffusion tensor model could lead to highly variable and inaccurate measurements of diffusion behavior. The differences between the single and two-tensor models depend on the orientations, fractions, and exchange between the two diffusion tensor compartments, as well as the diffusion-tensor encoding technique and diffusion-weighting that is used in the measurements. The current single compartment model's inaccuracies could cause diffusion-based characterization of cerebral ischemia and white matter connectivity to be incorrect. A diffusion-tensor MRI imaging experiment on a normal human brain revealed significant partial volume effects between oblique white matter regions when using very large voxels and large diffusion-weighting (b approximately 2.69 x 10(3) sec/mm(2)). However, the apparent partial volume effects in white matter decreased significantly when smaller voxel dimensions were used. For diffusion tensor studies obtained using typical diffusion-weighting values (b approximately 1 x 10(3) sec/mm(2)) partial volume effects are much more difficult to detect and resolve. More accurate measurements of multiple diffusion compartments may lead to improved confidence in diffusion measurements for clinical applications.
Poliovirus mutant that contains a cold-sensitive defect in viral RNA synthesis (1988)

By manipulating an infectious cDNA clone of poliovirus, we have introduced a single-codon insertion into the 3A region of the viral genome which has been proposed to encode a functional precursor of the virion-linked protein VPg. The resulting mutant was cold sensitive in monkey kidney cells. Viral RNA synthesis was poor at 32.5 degrees C, although no other function of the virus was obviously affected. The synthesis of both positive and negative strands was severely depressed. Temperature shift experiments suggest that a normal level of production of the affected function was required only during the early (exponential) phase of RNA synthesis. Analysis of viral polyprotein processing at the nonpermissive temperature revealed that some of the normal cleavages were not made, most likely as a consequence of the defect in RNA synthesis or as a result of the concomitant reduction in the level of virally encoded proteases.
Hierarchical Triple-Modular Redundancy (H-TMR) Network For Digital Systems (2009)

Hierarchical application of Triple-Modular Redundancy (TMR) increases fault tolerance of digital Integrated Circuit (IC). In this paper, a simple probabilistic model was proposed for analysis of fault masking performance of hierarchical TMR networks. Performance improvements obtained by second order TMR network were theoretically compared with first order TMR network.