gebhart/patrepeval huggingface dataset:
The influence of oxygen and high-energy phosphate diffusion on metabolic scaling in three species of tail-flipping crustaceans (2008)

We examined the influence of intracellular diffusion of O(2) and high-energy phosphate (HEP) molecules on the scaling with body mass of the post-exercise whole-animal rate of O(2) consumption (V(O(2))) and muscle arginine phosphate (AP) resynthesis rate, as well as muscle citrate synthase (CS) activity, in three groups of tail-flipping crustaceans. Two size classes in each of three taxa (Palaemonetes pugio, Penaeus spp. and Panulirus argus) were examined that together encompassed a 27,000-fold range in mean body mass. In all species, muscle fiber size increased with body mass and ranged in diameter from 70+/-1.5 to 210+/-8.8 microm. Thus, intracellular diffusive path lengths for O(2) and HEP molecules were greater in larger animals. The body mass scaling exponent, b, for post-tail flipping V(O(2)) (b=-0.21) was not similar to that for the initial rate of AP resynthesis (b=-0.12), which in turn was different from that of CS activity (b=0.09). We developed a mathematical reaction-diffusion model that allowed an examination of the influence of O(2) and HEP diffusion on the observed rate of aerobic flux in muscle. These analyses revealed that diffusion limitation was minimal under most conditions, suggesting that diffusion might act on the evolution of fiber design but usually does not directly limit aerobic flux. However, both within and between species, fibers were more diffusion limited as they grew larger, particularly when hemolymph P(O(2)) was low, which might explain some of the divergence in the scaling exponents of muscle aerobic capacity and muscle aerobic flux.
Arthroscopic evaluation of post-traumatic patellofemoral chondropathy. (1999)

These data suggest that synovitis might have a deleterious effect on the evolution of post-traumatic patellofemoral chondropathy or might be a marker for active cartilage breakdown.
Sensing Cytosolic RpsL by Macrophages Induces Lysosomal Cell Death and Termination of Bacterial Infection (2015)

The intracellular bacterial pathogen Legionella pneumophila provokes strong host responses and has proven to be a valuable model for the discovery of novel immunosurveillance pathways. Our previous work revealed that an environmental isolate of L. pneumophila induces a noncanonical form of cell death, leading to restriction of bacterial replication in primary mouse macrophages. Here we show that such restriction also occurs in infections with wild type clinical isolates. Importantly, we found that a lysine to arginine mutation at residue 88 (K88R) in the ribosome protein RpsL that not only confers bacterial resistance to streptomycin, but more importantly, severely attenuated the induction of host cell death and enabled L. pneumophila to replicate in primary mouse macrophages. Although conferring similar resistance to streptomycin, a K43N mutation in RpsL does not allow productive intracellular bacterial replication. Further analysis indicated that RpsL is capable of effectively inducing macrophage death via a pathway involved in lysosomal membrane permeabilization; the K88R mutant elicits similar responses but is less potent. Moreover, cathepsin B, a lysosomal protease that causes cell death after being released into the cytosol upon the loss of membrane integrity, is required for efficient RpsL-induced macrophage death. Furthermore, despite the critical role of cathepsin B in delaying RpsL-induced cell death, macrophages lacking cathepsin B do not support productive intracellular replication of L. pneumophila harboring wild type RpsL. This suggests the involvement of other yet unidentified components in the restriction of bacterial replication. Our results identified RpsL as a regulator in the interactions between bacteria such as L. pneumophila and primary mouse macrophages by triggering unique cellular pathways that restrict intracellular bacterial replication.
Use of T2MR in Invasive Candidiasis with and Without Candidemia (2018)

The mortality associated with invasive candidiasis remains unacceptably high. The T2 magnetic resonance (T2MR) assay is a novel US FDA-approved molecular diagnostic assay for the diagnosis of candidemia that can rapidly detect the five most commonly isolated Candida spp. In clinical trials, T2MR has exhibited good clinical sensitivity and specificity. Potential benefits from the adoption of T2MR technology in the diagnostic and therapeutic algorithms for invasive candidiasis can arise from timely diagnosis of disease, increased case detection, tailored therapy and decrease in empiric antifungal treatment. As everyday clinical experience with the assay is evolving, we discuss the utility of T2MR in invasive candidiasis with and without candidemia based on the currently available evidence regarding its performance.
An image processing pipeline using coupled oscillators (2014)

Image Processing Pipelines (IPPs) are systems that iteratively modify an input image into a series of abstractions with the goal of identifying the objects in the image. There have been many proposed IPPs, implemented in both hardware and software, but by and large these designs have been based on Boolean logic based computation and arithmetic. Studies have shown that Boolean computers are hitting a theoretical ceiling on their performance in terms of transistor size, energy consumption/heat dissipation, clock rates, and by extension, computation time. Due to these issues, researchers have proposed using non-Boolean approaches, where possible, for various computations in common algorithms. One of the emerging technologies in the field of non-Boolean computation is the use of coupled oscillators. A proposed use of coupled oscillators is for pattern matching, which can be interpreted as a high-dimensional distance measurement. Using an approach based on using coupled oscillators as a computational primitive, this work utilizes the benefits gained from this new computational paradigm to gain performance in terms of both speed and power with respect to a benchmark IPP, without decreasing its image identification accuracy.
Effects of acetic acid and lactic acid on the growth of Saccharomyces cerevisiae in a minimal medium (2001)

Specific growth rates (mu) of two strains of Saccharomyces cerevisiae decreased exponentially (R2 > 0.9) as the concentrations of acetic acid or lactic acid were increased in minimal media at 30 degrees C. Moreover, the length of the lag phase of each growth curve (h) increased exponentially as increasing concentrations of acetic or lactic acid were added to the media. The minimum inhibitory concentration (MIC) of acetic acid for yeast growth was 0.6% w/v (100 mM) and that of lactic acid was 2.5% w/v (278 mM) for both strains of yeast. However, acetic acid at concentrations as low as 0.05-0.1% w/v and lactic acid at concentrations of 0.2-0.8% w/v begin to stress the yeasts as seen by reduced growth rates and decreased rates of glucose consumption and ethanol production as the concentration of acetic or lactic acid in the media was raised. In the presence of increasing acetic acid, all the glucose in the medium was eventually consumed even though the rates of consumption differed. However, this was not observed in the presence of increasing lactic acid where glucose consumption was extremely protracted even at a concentration of 0.6% w/v (66 mM). A response surface central composite design was used to evaluate the interaction between acetic and lactic acids on the specific growth rate of both yeast strains at 30 degrees C. The data were analysed using the General Linear Models (GLM) procedure. From the analysis, the interaction between acetic acid and lactic acid was statistically significant (P < or = 0.001), i.e., the inhibitory effect of the two acids present together in a medium is highly synergistic.
New Technology in Still Stores — What Are the Implications? (1992)

The practice of storing frozen TV images on computer disks for later recall is now some ten years old. Over that period very significant changes have been made in the technologies applied to still stores, allowing their use to be expanded well beyond the original concepts of a straight store and recall device. Disk capacity, size, and price make on-line stores of 1000 or more images an economic reality, while very large-scale integrated (VLSI) circuitry packs more electronics into smaller frames. To reap the benefits of these advances requires not so much a rebuilding of the hardware with new components as rethinking the part that still stores can play in modern TV production.
Distinguishing Incubation and Acute Disease Stages of Mild-to-Moderate COVID-19 (2022)

While numerous studies have already compared the immune responses against SARS-CoV-2 in severely and mild-to-moderately ill COVID-19 patients, longitudinal trajectories are still scarce. We therefore set out to analyze serial blood samples from mild-to-moderately ill patients in order to define the immune landscapes for differently progressed disease stages. Twenty-two COVID-19 patients were subjected to consecutive venipuncture within seven days after diagnosis or admittance to hospital. Flow cytometry was performed to analyze peripheral blood immune cell compositions and their activation as were plasma levels of cytokines and SARS-CoV-2 specific immunoglobulins. Healthy donors served as controls. Integrating the kinetics of plasmablasts and SARS-CoV-2 specific antibodies allowed for the definition of three disease stages of early COVID-19. The incubation phase was characterized by a sharp increase in pro-inflammatory monocytes and terminally differentiated cytotoxic T cells. The latter correlated significantly with elevated concentrations of IP-10. Early acute infection featured a peak in PD-1<sup>+</sup> cytotoxic T cells, plasmablasts and increasing titers of virus specific antibodies. During late acute infection, immature neutrophils were enriched, whereas all other parameters returned to baseline. Our findings will help to define landmarks that are indispensable for the refinement of new anti-viral and anti-inflammatory therapeutics, and may also inform clinicians to optimize treatment and prevent fatal outcomes.
The Economic Cost of Including the Indirect Land Use Factor in Low Carbon Fuel Policy: Efficiency and Distributional Implications (2016)

Concerns about the indirect land use change (ILUC) caused by biofuels has led to the inclusion of an ILUC factor as a part of the greenhouse gas (GHG) intensity of biofuels in low carbon fuel policies.Here, we develop an integrated modeling framework to simulate the effects of including an ILUC factor in a national Low Carbon Fuel Standard (LCFS) and to assess the variability of these effects depending on the ILUC factor used.We found that additional GHG abatement achieved over the 2017-2027 period ranged from 0.6 to 1.2% while the additional economic costs to the US ranged from $35 to $211 billion depending on the biofuel-specific ILUC factors utilized; more than half of these costs were borne by domestic fuel consumers.The implied per metric ton cost of the additional abatement ranged from $64 to $197 and was substantially larger than the $50 per metric ton social cost of carbon estimated by the US government.
Differential frost heave model for patterned ground formation: Corroboration with observations along a North American arctic transect (2008)

Frost boils in the Arctic are a manifestation of patterned ground in the form of nonsorted circles. Active frost boils involve convection of water through the soil that can bring basic salts from depth to the surface. As such, active frost boils can mitigate acidification and thereby strongly influence the type of vegetation supported by Arctic soils. The presence or absence of active frost boils is thought to play a pivotal role in establishing the sharp demarcation between moist nonacidic tundra (MNT) and moist acidic tundra (MAT) in the Arctic. The focus of this paper is to corroborate the predictions of a mathematical model that relates observable patterned ground features to ecosystem parameters with observations at the field sites along the North American Arctic Transect (NAAT) established by the Biocomplexity of Patterned‐Ground Ecosystems Project. Model predictions indicate that recurrent one‐dimensional frost heave can become unstable and evolve into multidimensional differential frost heave (DFH). A laboratory frost heave simulation produced a 28‐cm pattern in an active layer of 10 cm, which agrees with linear stability theory predictions. A finite element solution predicts three‐dimensional patterns with approximately 3‐m spacing develop in a 1.0‐m active layer with a surface n factor of 0.35, which agrees well with field observations from the NAAT. The lack of significant frost boil activity in the MAT is a result of suppression of DFH owing to denser surface vegetation characterized by low n factors. Prominent active frost boils are observed in the MNT at higher latitudes with more sparse vegetation characterized by higher n factors that promote DFH. However, at the northernmost field sites frost boils cannot be generated even though the n factors are relatively high owing to very rapid freezing conditions that mitigate DFH.
Mid-Term Outcomes of Mitral Valve Annuloplasty in Type I versus Type IIIb Functional Mitral Regurgitation (2019)

Introduction: Functional mitral regurgitation (FMR) represents a heterogeneous clinical entity and the impact of different pathophysiological mechanisms (i.e., type I vs. type IIIb) on long-term outcome has not been analyzed yet. The aim of our study was to evaluate the outcomes of mitral valve annuloplasty in patients with type I versus type IIIb FMR.
Compensation of nonlinearities in high-density magnetic recording channels (1994)

Volterra-series models of magnetic-saturation recording channels are used to derive readback structures that compensate for channel nonlinearities. These structures are based on a canceler of linear and nonlinear channel distortions, and can achieve significant improvement in terms of mean-square error and error probability. Proper operation of the canceler requires reliable preliminary decisions to be taken on the information symbols. These decisions are obtained by passing the received signal through a linear equalizer, then processing the equalized signal through a symbol-by-symbol detector or a Viterbi detector. By using the data obtained in [4] for magneto-resistive heads, it was found that symbol-by-symbol preliminary detection performs adequately. A Volterra model was also obtained experimentally for the recording channel generated by magneto-inductive heads that exhibit higher-order nonlinear effects. In order to recover data from this highly distorted channel the preliminary detection scheme needs a 4-state Viterbi detector.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biological denitrification of drinking water using autotrophic organisms with H2 in a fluidized‐bed biofilm reactor (1987)

Abstract Biological denitrification of drinking water was studied in a fluidized sand bed reactor using a mixed culture. Hydrogen gas was used as the reaction partner. The reaction kinetics were calculated with a double Monod saturation function. The K s value for hydrogen was below 0.1% of saturation. No appreciable biofilm diffusion effects were detected. Reactor performance was a function of the culture's past history. Batch experiments always exhibited an accumulation of NO 2 − , but continuous experiments with a sufficiently long residence time always resulted in complete nitrogen removal. Rates of up to 23 mg N/L h, 25 mg N/g DW h, and 7.9 mg H 2 /L h were achieved. Residence times of 4.5 h would be required for complete denitrification of water containing 25 mg NO 3 − –N/L or approximately 1 h for every 5 mg/L.
FPGA Architecture: Principles and Progression (2021)

Since their inception more than thirty years ago, field-programmable gate arrays (FPGAs) have been widely used to implement a myriad of applications from different domains. As a result of their low-level hardware reconfigurability, FPGAs have much faster design cycles and lower development costs compared to custom-designed chips. The design of an FPGA architecture involves many different design choices starting from the high-level architectural parameters down to the transistor-level implementation details, with the goal of making a highly programmable device while minimizing the area and performance cost of reconfigurability. As the needs of applications and the capabilities of process technology are constantly evolving, FPGA architecture must also adapt. In this article, we review the evolution of the different key components of modern commercial FPGA architectures and shed the light on their main design principles and implementation challenges.
Contribution of Partition Walls in Lateral Load–Resisting Systems of Low-Rise Light Wood Frame Buildings (2021)

Prescriptive design is a common practice in North America for low-rise light wood frame buildings. The prescriptive wood-based shear wall details provided in building codes to resist lateral loads were largely derived based on a combination of historical performance and engineering analysis. Inherent within the historical performance assumption is the presence of certain elements such as internal partitions that contribute to direct load resistance and structural redundancy. This inherent assumption is sometimes challenged by design engineers and proponents of alternative lateral load–resisting systems. In an attempt to showcase the contributions of the partition walls, a number of archetypes with various quantities of partitions were analyzed using a finite-element program. In the finite-element models, the wood-based structural shear walls and partition walls with gypsum wallboard were modeled as macroelements, with mechanical properties obtained from previous tests. Assumptions were made for the diaphragm and connection stiffness values. The results show a significant contribution of the partition walls to the lateral load resistance of light wood frame buildings. Partition walls accounted for 55%–71% of the overall lateral resistance of the evaluated buildings. Furthermore, diaphragms and wall-to-diaphragm connections contribute significantly to the overall behavior of the structures.
TiO 2 -based metal-insulator-metal selection device for bipolar resistive random access memory cross-point application (2011)

We report a simple metal-insulator-metal (MIM)-type selection device that can alleviate the sneak current path in cross-point arrays. By connecting a nanometer-scale Pt/TiO2/TiN selection device to a Pt/TiO2−x/TiO2/W resistive random access memory (RRAM), we could significantly reduce read disturbance from unselected memory cells. This selection device could be easily integrated into an RRAM device, in which it suppressed the sneak current and significantly improved the readout margin compared to that obtained for an RRAM not using a selection device. The introduction of this MIM device can fulfill the requirement for an appropriate selection device for bipolar-type RRAM cross-point applications.
Divinylcyclopropane‐CycloheptadieneRearrangement (1992)

Abstract The first documented report of a possible Cope rearrangement was probably that of Baeyer, who prepared eucarvone by hydrobromination of carvone in 1894. Although the transformation was briefly studied at that time, it was not until the 1950s that this and other Cope‐type rearrangements received detailed attention. The thermal isomerization of cis ‐divinylcyclopropane to cycloheptan‐1,4‐diene was reported by Vogel in 1960 during his studies of the Cope rearrangement of 1,5‐hexadienes annulated by a homologous series of carbocyclic rings. Scores of mechanistic studies followed this discovery upon the realization that the rearrangement could be related to the conceptually similar vinylcyclopropane–cyclopentene isomerization discovered a year earlier. It was also recognized that this rearrangement might be operating in the formation of cycloheptatriene from norcaradiene during photolysis of diazomethane in benzene. The topic received considerable attention in the 1960s, an era of mechanistic investigations of various concerted transformations. During the 1970s it enjoyed exploitation in many synthetic strategies, and the following decade the elements of this rearrangement were incorporated into tandem or multistep procedures in a preconceived manner. Many aspects of the various permutations of the Cope rearrangement have been previously reviewed. The purpose of this review is to summarize the mechanistic, stereochemical, and practical results in this area in the context of the evolution of synthetic achievements during the last 40 years. Also described in this chapter are the transformations of several of the simple heteroatom permutations of this rearrangement in order to render appropriate comparisons of various systems. A discussion addresses those rearrangements of cyclopropanes, oxiranes, thiiranes, and aziridine rings substituted with vicinal vinyl groups. Excluded from this review are rearrangements of those divinylsubstituted three‐membered rings that contain more than a single heteroatom within the reacting manifold. Brief mention of these systems along with a guide to the literature is found in the last section of this chapter. The literature is covered through December 1990. Many of the principal researchers in this field have been contacted and many unpublished transformations have been included in the tables.
The case for Hinkley – or not (2016)

(2016). The case for Hinkley – or not. Construction Research and Innovation: Vol. 7, No. 3, pp. 20-23.
Advanced Femto-Caching File Placement Technique for Overlapped Helper Coverage (2014)

Due to the tremendous growth of mobile data traffic, some technologies from small cell deployment are still ongoing as nominated solutions. Without enlarged wired backhaul capacity, however, the performance of small cell techniques are inevitably degraded. The approach employing the storage capacity in order to off-load the backhaul capacity, as known as femto-caching, has been proposed to minimize the delay within downloading data [1]. In this paper, we consider more practical scenario such as distribution of users' position in whole networks and extend the previous researches in the manner of file placement strategies. Simulation results verify that our proposed scheme has better performance gains with respect to increased opportunity to obtain more various downloading data if helpers' coverages are overlapped.
Small-computer program for optical design and analysis written in "C" (1991)

The use of electronic computers in optical design and analysis is well established. In fact, optical calculations were among the first applications of the first computers that were built in the 40's, and Donald Feder, starting in 1951 [1], proved that the use of these machines went far beyond removing the tediousness of laborious calculations and offered new dimensions in understanding the actual design process [2]. By today's standards, of course, the equipment which had such a remarkable impact at its time, was primitive and slow. A modern inexpensive programmable calculator easily outperforms the any computers in both speed and memory capacity, not to mention accuracy and reliability. This also implies, that today, even computers at the low end of the cost and performance scale can be turned into remarkably powerful tools for optical design and analysis. This has been demonstrated for the class of programmable calculators [3] but applies, of course, even more convincingly to the present generation of low-cost personal computers, which are typically based on 16- or 32-bit processors, and where prices start well below $ 1000.-. Any degree of higher performance is available at steadily increased prices, so that there appears to be a fit for each requirement.