gebhart/patrepeval huggingface dataset:
Severe, Early and Selective Loss of a Subpopulation of GABAergic Inhibitory Neurons in Experimental Transmissible Spongiform Encephalopathies (1998)

Little is known about the pathogenetic basis of characteristic symptoms in transmissible spongiform encephalopathies (TSEs) such as myoclonus and characteristic EEG hyperactivity. We investigated the GABAergic system and its subpopulations in mice inoculated with experimental scrapie (ME7, RML, 22A strains) and Creutzfeldt-Jakob disease (CJD; Fujisaki strain), to study damage to inhibitory neurons. Since recent studies have shown electrophysiological changes in prion protein (PrP) knockout mice, we also studied mice lacking or overexpressing the PrP gene. Antibodies against glutamic acid decarboxylase (GAD), parvalbumin (PV), calbindin (CB), and calretinin (CR) were used to stain GABAergic neurons, and isolectin-B4 to stain perineuronal nets around PV+ neurons. In scrapie infected mice, cortical PV+ neurons were severely reduced while CB+ and CR+ neurons were well preserved. In CJD inoculated mice, loss of PV+ neurons was severe and occurred very early after inoculation. PrP-/- and tg20 mice showed normal appearance of PV, CB, CR, GAD+ neurons and their neuropil, and of isolectin-B4+ perineuronal nets. The early, severe and selective loss of cortical PV+ neurons in experimental scrapie and CJD suggest selective loss of PV+ GABAergic neurons as important event during disease development, possibly as one basis of excitatory symptoms in TSEs.
An Integrated Approach for Well Design Optimization with MPD and its Impact on Value (2020)

Abstract In high pressure high temperature (HPHT) reservoirs and exploratory wells, especially in deep water, there is a higher degree of uncertainty, which can increase the operational costs due to non-productive time (NPT) and operational problems due to the unpredictable nature of these wells. For these challenging wells with narrow windows, Managed Pressure Drilling (MPD) techniques offer cost-effective tools to increase the odds for achieving well and cost objectives assurance. There are significant benefits from early implementation of MPD in the project life cycle. These benefits include from improving operational efficiency to risk mitigation and safety enhancement. However, there is an enormous potential that many operators have been missing. This is related to the incorporation of MPD as a driver in optimizing the well design, which could greatly increase the possibilities of reaching target depth, and potentially prepare to eliminate one or more casing strings. Current well design process hinges on the ability to manage uncertainties by company or regulatory requirements, such as kick tolerance and safety factors. This work addresses the value added from implementing MPD in early stages in the project life cycle through the analysis of case studies. The cost savings from the impact on the well design are also discussed. This work also presents a in depth discussion on the benefits, and enablers of this approach. Furthermore, it presents considerations by taking advantage of dynamic processes facilitated with MPD. Finally, new guiding criteria to aim to constitute a systematic and integrated approach to ensure well integrity and optimize well design while also considering the operational implications and integral cost benefits is proposed to the industry. This paper represents the initial phase of a compressive long-term project to integrate two main components of well design. These are MPD adaptive well design, and statistical analysis based on variations of load and/or strength.
Adaptive Hysteresis Current Based ZVS Modulation and Voltage Gain Compensation for High-Frequency Three-Phase Converters (2020)

This article proposed a systematic approach for the control of three-phase bidirectional zero-voltage switching (ZVS) converters. Combining the adaptive hysteresis-band current control and turn-on delay modifications, ZVS conditions are realized in full line-cycle in all loading conditions like active power, reactive power, light load, and heavy load. The soft-switching resonant period is carefully analyzed, and the current band is designed accordingly, which minimized the additional conduction loss. Meanwhile, a zero-sequence voltage injection control is included in the approach, which compensates the voltage gain by 15% and narrows down the switching frequency variation range. The hardware design approach is also provided including the LCL filter design and a low-cost high-bandwidth high-accuracy current sensor design. A highly integrated 5-kW silicon carbide implemented three-phase ZVS converter prototype with printed circuit board integrated inductors and customized current sensors is designed. All the control is implemented in a single microcontroller unit, which achieves a high electromagnetic compatibility. The designed prototype achieves a total power density of 5.5 kW/L and a peak efficiency of 98.5%. All the analysis and the proposed control approach are experimentally verified on the designed prototype.
Detailed comparison of two popular variant calling packages for exome and targeted exon studies (2014)

The Genome Analysis Toolkit (GATK) is often considered to be the “gold standard” for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an adequate comparison against VarScan may have not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (&gt;97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also accessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in accessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.
Influence of combining rules on the cavity occupancy of clathrate hydrates by Monte Carlo simulations (2014)

AbstractAssessing the exact amount of gas stored in clathrate-hydrate structures can be addressed by either molecular-level simulations (e.g. Monte Carlo) or continuum-level modelling (e.g. van der Waals–Platteeuw-theory-based models). In either case, the Lorentz–Berthelot (LB) combining rules are by far the most common approach for the evaluation of the parameters between the different types of atoms that form the hydrate structure. The effect of combining rules on the calculations has not been addressed adequately in the hydrate-related literature. Only recently the use of the LB combining rules in hydrate studies has been questioned.In the current study, we report an extensive series of Grand Canonical Monte Carlo simulations along the three-phase (H–Lw–V) equilibrium curve. The exact geometry of hydrate crystals is known from diffraction experiments and, therefore, the formation of hydrates can be simulated as a process of gas adsorption in a solid porous material. We examine the effect of deviations from the LB combining rules on the cavity occupancy of argon hydrates and work towards quantifying it. The specific system is selected as a result of the characteristic behaviour of argon to form hydrates of different structures depending on the prevailing pressure. In particular, an sII hydrate is formed at lower pressures, while an sI hydrate is formed at intermediate pressures, and finally an sH hydrate is formed at higher pressures.Keywords: clathrate hydrateGrand Canonical Monte Carlocavity occupancycombining rulesparametric studyargon hydrate AcknowledgementsThe authors are grateful to the Qatar National Research Fund (a member of The Qatar Foundation), and Texas A&M University at Qatar. The statements made herein are solely the responsibility of the authors.Additional informationFundingFinancial support for this research has been received from Qatar National Research Fund through an NPRP award [grant number NPRP 6-1547-2-632]; Texas A&M University at Qatar to I. N. Tsimpanogiannis through a visiting research position.
Implementing protocols in Java: the price of portability (2002)

As the number and variety of Web- and network-based applications continues to increase, so does the need for flexible communication protocols and services to support them. Traditionally, a major impediment to deployment of new protocols is the need to upgrade millions of end-systems with compatible implementations. At the same time, Java-a language explicitly designed to support development and distribution of new applications via the Web-is emerging as a (potentially) ubiquitous system platform. It is therefore natural to consider whether Java might speed the introduction of protocols to better support new applications. We investigate the tradeoffs involved in using Java for protocol implementation and deployment. Using insights from a Java-based protocol suite and supporting subsystem we have implemented, we describe the benefits of using the Java language and quantify the performance cost of implementing a protocol in Java for various combinations of interpretation and compilation. We find that the present performance cost of using Java-based protocols is roughly equivalent to four years of hardware performance gains, i.e., interpreted, Java-based protocol performance on current hardware is roughly equivalent to the performance of compiled C code on four-year-old hardware.
H1-Antihistamines and the Central Nervous System (2002)

An extensive body of research exists on CNS effects of H1-antagonists. There is great interest in this area due to the well-known adverse CNS effects associated with first-generation H1-antagonists, and the many new second-generation agents claiming to have nonsedative properties. Because the CNS effects of H1-antagonists are complex and cannot be reflected in one measurement, a variety of assessments of CNS function are required. These range from the subjective (e.g., self-rating of drowsiness) to the objective (e.g. 24 h EEG sleep latency, P300), and from the simple (e.g., critical flicker fusion) to the complex (e.g., actual driving). When these tests are applied to the evaluation of the H1-antagonists currently available, it is clear that there is a real distinction between the older first-generation H1-antagonists and the newer second-generation ones. At the recommended dosages, all the second-generation H1-antagonists are clearly less sedating in more patients than their predecessors. These newer medications do not cross the blood-brain barrier readily; are highly specific for H1-receptors; have little to no anticholinergic, antiserotoninergic, or anti-alpha-adrenergic effects; and do not enhance the adverse CNS effects of alcohol or other CNS-active substances such as the benzodiazepines. Since most second-generation H1-antagonists are found to be relatively nonsedating, their benefit/risk ratios will be determined more by their other properties such as non-CNS adverse effects (e.g., potential to cause cardiac arrhythmias), potency, onset of action, duration of action, ease of administration, and cost. The future role and usefulness of the older sedating H1-antagonists, given the availability of the safer second-generation agents, are unclear at the present time. When H1-antagonist treatment is indicated, physicians should recommend an effective H1-antagonist with a favorable clinical pharmacology profile and a wide margin of safety in patients of all ages. The common, often subclinical, adverse CNS effects produced by the old H1-antagonists remain a major concern and, therefore, these compounds are no longer medications of choice in the treatment of allergic rhinitis, allergic conjunctivitis, or urticaria.
Well-Collision-Avoidance Separation Rule (2018)

Summary The well-collision-avoidance separation rule presented in this paper is a culmination of the work and consensus of industry experts from both operators and service companies in the SPE Wellbore Positioning Technical Section (WPTS). This is the second of two papers and complements the first paper, SPE-184730-PA (Sawaryn et al. 2018), which described the collision-avoidance management practices. These practices are fundamental in establishing the environment in which a minimum allowable separation distance (MASD) (in m) between two adjacent wells can be effectively applied. A standardized collision-avoidance rule is recommended, complete with parameter values appropriate to the management of health, safety, and environment (HSE) risk, and benchmarks for testing it. Together, these should help eliminate the disparate and occasionally contradictory methods currently in use. The consequences of an unplanned intersection with an existing well can range from financial loss to a catastrophic blowout and loss of life. The process of well-collision avoidance involves rules that determine the allowable separation and the management of the associated directional planning and surveying activities. The proposed separation rule is dependent on the pedal-curve method and is expressed as a separation factor, a dimensionless number that is an adjusted center-to-center distance between wells divided by a function of the relative positional uncertainty between the two. The recommended values for the rule's parameters result from a comparison of various industry models and experience. The relationships between key concepts such as the MASD and allowable deviation from the plan (ADP) are discussed, together with their interpretation and application. The dependency on the error distributions of the survey-instrument performance models used to establish the tolerance lines is also discussed. The consequences of implementing a standardized separation rule across the industry are far-reaching. This affects slot separations, trajectories, drilling practices, surveying program, and well shut-in. We show how the MASD can be related to a probability of crossing and being in the unacceptable-risk region of an offset well. We show why this qualification is required for safe drilling practices to be preserved. Examples are presented in Appendices A through D to help the reader validate the calculations and the directional-drilling software necessary to perform them. The geometrical and statistical limitations of the methods are explained and areas are highlighted for further work. The methods outlined here, taken together with SPE-184730-MS, will improve efficiency in planning and executing wells and promote industry focus on the associated collision risks during drilling. The WPTS also supports the current development of API RP 78, Recommended Practices for Wellbore Positioning. Mathematical derivations or references are shown for all the calculations presented in the paper.
In vitro development of CFU‐E and BFU‐E in cultures of embryonic and post‐embryonic chicken hematopoietic cells (1980)

A culture method is proposed for the in vitro development of chicken erythrocytic progenitors. When grown with avian erythropoietin, Colony Forming Unit Erythrocytic (CFU-E) and Burst Forming Unit-Erythrocytic (BFU-E) give rise respectively to erythrocytic colonies and bursts within 3 and 6 days. BFU-E development is greatly enhanced by pokeweed-mitogen-spleen-cell conditioned medium and requires higher erythropoietin concentrations than for CFU-E. An antigen specific to immature red cells can be detected on CFU-E but not on BFU-E, showing that both progenitors represent distinct entities. BFU-E and CFU-E are found in embryonic marrow and yolk sac. In the young blastoderm BFU-E becomes detectable at the primitive streak stage.
[Hepatocellular carcinoma and hyperestrogenia in a male]. (1987)

The case of a 38 year-old man with hepatocellular carcinoma in a non-cirrhotic liver is reported. Hyperestrogenosis with gynecomastia, polycythemia and proteinuria were present. After complete removal of the tumor, estrogen levels, red blood-cell volume and urine analysis did not return to normal and these pathologic findings were probably not paraneoplastic syndromes. Outcome was good, the patient remaining completely well without evidence of recurrence during the ensuing 30 months. The likely explanation for the persistent hyperestrogenosis was an excessive conversion of sexual hormones. The authors suggest that this abnormal hyperestrogenic state could promote hepatic neoplasia as it has been established in animals.
<title>Design of polymer-based mechanical filters for shock-measurement accelerometers</title> (1996)

Shock measurement accelerometers require protection from the high frequency components of input shock spectra which often cause irreversible damage to these transducers. The resonance frequencies of shock accelerometers are usually designed to be much greater than the highest frequency of their operating range. It is not unusual, however, for input shock waveforms to contain spectral components whose frequencies are much greater than the resonance frequencies of shock accelerometers. This is particularly true for shock waveforms of very short duration whose shape approach that of the classical Dirac delta function. Consequently, there is a need for mechanical filters which will isolate the accelerometers from the highest frequency components of shock loadings applied to structures. In this paper, the design of a mechanical filter comprised of metal discs, metal housing and viscoelastic elements is examined using the finite element method. The transformation of the frequency domain complex Young's modulus data to the time domain extensional relaxation function using collocation method is described. The procedures for the derivation of the Prony series coefficients from the time data for input into the finite element analysis code are presented. It is shown that effective mechanical filters can be designed using viscoelastic materials of optimal properties.
Cauda equina syndrome of long-standing ankylosing spondylitis (1990)

Cauda equina syndrome as a neurological complication of long-standing ankylosing spondylitis was first reported in 1961. The syndrome is relatively uncommon and its pathophysiology is still poorly understood. Based on their experience with such a case, the authors review the clinical, electrographic, histological, and radiographic features of the syndrome, including the findings of magnetic resonance (MR) imaging. The addition of MR imaging to the evaluation of patients with ankylosing spondylitis and the cauda equina syndrome not only aids in the diagnosis of the syndrome but may also provide valuable insight into the pathophysiology of this condition.
Muscle‐derived interleukin‐6: possible biological effects (2001)

Interleukin-6 (IL-6) is produced locally in working skeletal muscle and can account for the increase in plasma IL-6 during exercise. The production of IL-6 during exercise is related to the intensity and duration of the exercise, and low muscle glycogen content stimulates the production. Muscle-derived IL-6 is released into the circulation during exercise in high amounts and is likely to work in a hormone-like fashion, exerting an effect on the liver and adipose tissue, thereby contributing to the maintenance of glucose homeostasis during exercise and mediating exercise-induced lipolysis. Muscle-derived IL-6 may also work to inhibit the effects of pro-inflammatory cytokines such as tumour necrosis factor alpha. The latter cytokine is produced by adipose tissue and inflammatory cells and appears to play a pathogenetic role in insulin resistance and atherogenesis.
INSCRIPTIONS OF ASSURBANIPAL, B.C. 668 TO 626 (2014)

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Prestin, the Motor Protein of Outer Hair Cells (2002)

Prestin is a gene recently cloned from mammalian cochlear outer hair cells (OHC) using a single cell type, outer minus inner hair cell, specific suppressive subtractive hybridization procedure. The localization and gene expression profile of the prestin protein fits the pattern of OHC's development of electromotility. When prestin is abundantly expressed in normally nonmotile kidney cells, nonlinear capacitance and motility that are normally only seen in OHCs can be recorded. Furthermore, both nonlinear capacitance and motility can be reduced by salicylate, a well-known inhibitor of electromotility. These data suggest that prestin is the motor protein of OHCs. Amino acid sequence and gene structure analysis indicate that prestin is the fifth member of a newly discovered anion transport family (SLC26) that includes PDS, DRA and DTDST, which are chloride-iodide transporters, Cl-/HCO3- exchangers or sulfate transporters. Prestin shares overall structure similarity with this anion transporter family. Recently, intracellular anions (chloride or bicarbonate) were found to be essential for OHC electromotility and prestin's function.
Ministarters and mini blue jets in air and nitrogen at a pulse-periodic discharge in a laboratory experiment (2017)

Miniature analogs of starters and blue jets that are observed in the upper atmosphere of the Earth and have dimensions of tens of kilometers are formed and studied in air and nitrogen at pressures of tens and hundreds of Torr. Ministarters and mini blue jets have been obtained in laboratory experiments owing to the application of a pulse-periodic discharge with a plasma jet referred to as apokamp. The velocities of propagation of apokamps have been measured at various pressures. It has been found that the average values of these velocities are about the velocities of propagation of starters and blue jets in the atmosphere of the Earth. It has been shown that jets (apokamps) with the maximum length are observed in the pressure range corresponding to the altitudes of appearance and propagation of starters and blue jets.
Accurate formulas for interaction force and energy in frequency modulation force spectroscopy (2004)

Frequency modulation atomic force microscopy utilizes the change in resonant frequency of a cantilever to detect variations in the interaction force between cantilever tip and sample. While a simple relation exists enabling the frequency shift to be determined for a given force law, the required complementary inverse relation does not exist for arbitrary oscillation amplitudes of the cantilever. In this letter we address this problem and present simple yet accurate formulas that enable the interaction force and energy to be determined directly from the measured frequency shift. These formulas are valid for any oscillation amplitude and interaction force, and are therefore of widespread applicability in frequency modulation dynamic force spectroscopy.
Limits of the output power in Er 3+ :ZBLANsinglemode fibrelasers (1995)

The saturation of the 2.71 µm laser output has been measured in erbium-doped ZBLAN singlemode fibres with Er3+ concentrations of 1000, 5000 and 10000 ppm mol. Limits of the single-mode-laser output are discussed.