gebhart/patrepeval huggingface dataset:
Requirement for CD4+ T Cells in the Friend Murine Retrovirus Neutralizing Antibody Response: Evidence for Functional T Cells in Genetic Low-Recovery Mice (1998)

Recovery from infection with the Friend murine leukemia retrovirus complex (FV) requires T-helper cells and cytotoxic T cells as well as neutralizing antibodies. Several host genes, including genes of the major histocompatibility complex (H-2) and an H-2-unlinked gene, Rfv-3, influence these FV-specific immune responses. (B10.A x A/Wy)F1 mice, which have the H-2(a/a) Rfv-3(r/s) genotype, fail to mount a detectable FV-specific T-cell proliferative response but nevertheless produce FV-specific neutralizing immunoglobulin M (IgM) antibodies and can eliminate FV viremia. Thus, this IgM response, primarily influenced by the Rfv-3 gene, may be T-cell independent. To test this idea, mice were depleted of either CD4(+) or CD8(+) T-cell populations in vivo and were monitored for the effect on the neutralizing antibody response following FV infection. Surprisingly, mice in which CD4(+) cells were depleted showed undetectable FV-neutralizing antibody responses and high viremia levels compared to nondepleted or CD8-depleted animals. In addition to knocking out the FV antibody response, CD4(+) T-cell depletion reduced survival time significantly, further indicating the importance of CD4(+) T cells. These studies revealed the first evidence for a functional T-cell response following FV infection in these low-recovery mice and showed that CD4(+) T-helper cells are required for the Rfv-3-controlled FV antibody response.
The catalytic mechanism of the amidotransferase domain of the Syrian hamster multifunctional protein CAD. Evidence for a CAD-glutamyl covalent intermediate in the formation of carbamyl phosphate (1991)

The multifunctional protein CAD catalyzes the first three steps in pyrimidine biosynthesis in mammalian cells, including the synthesis of carbamyl phosphate from bicarbonate, MgATP and glutamine. The Syrian hamster CAD glutaminase (GLNase) domain, a trpG-type amidotransferase, catalyzes glutamine hydrolysis in the absence of MgATP and bicarbonate (Km = 95 microM and kcat = 0.14 s-1). Unlike E. coli carbamyl phosphate synthetase (Wellner, V.P., Anderson, P.M., and Meister, A. (1973) Biochemistry 12, 2061-2066), a stable thioester intermediate did not accumulate when the mammalian enzyme was incubated with glutamine. However, a covalent adduct could be isolated when the protein was denatured in acid. The steady state concentration of the intermediate increased with increasing glutamine concentration to nearly one mole per mole of enzyme with half saturation at 105 microM, close to the Km value for glutamine. The adduct formed at the active site of the glutaminase domain. The rate of breakdown of the intermediate (k4), determined directly, was 0.17 s-1 and the rate of formation (k3) was estimated as 0.52 s-1. In the absence of MgATP and bicarbonate, k4 = kcat indicating that the decomposition of the intermediate is the rate-limiting step. The intermediate was chemically and kinetically competent, and the glutamine dissociation constant (330 microM) and rate constants were consistent with steady state kinetics and accurately predicted the steady state concentration of the intermediate. These studies suggest a mechanism similar to the cysteine proteases such as recently proposed by Mei and Zalkin (Mei, B., and Zalkin, H. (1989) J. Biol. Chem. 264, 16613-16619) who identified a catalytic triad in glutamine phosphoribosyl-5'-pyrophosphate amidotransferase, a purF-type enzyme. MgATP and bicarbonate increased kcat of the glutaminase reaction 14-fold by accelerating both the rate of formation and the rate of breakdown of the intermediate, and prevented the accumulation of the intermediate; however, the Km value for glutamine was not significantly altered. The instability of the thioester intermediate leads to appreciable hydrolysis of glutamine in the absence of the other substrates. However, bicarbonate alone spares glutamine by increasing the Km and Ks of glutamine to 600 and 8960 microM, respectively, thus reducing kcat/Km 3-fold when MgATP is limiting. In the absence of MgATP and bicarbonate, ammonia decreased the rate of hydrolysis and the accumulation of the thioester intermediate indicating that ammonia had direct access to the thioester at the GLNase domain active site.(ABSTRACT TRUNCATED AT 400 WORDS)
Human Primary T Cells: A Practical Guide v4 (2018)

Human primary T cells are invaluable and feasible model systems to study the characteristics of the human immune cells in various contexts, including but not limited to cancer immunotherapy. Following isolation of T cells from fresh human blood samples, it is possible to culture, expand, and manipulate these cells, which allows extensive investigation for research purposes. Techniques for isolation and handling of T cells are well-established but parts of the protocols can highly vary across different labs. These differences in the protocols are, often, there due to historical reasons and are only supported by anecdotal evidence. We systematically modified basic components of the T cell culturing protocols and collected data on how they altered the final yield. Here, based on these data, we provide practical hints and tips on basic cellular and molecular techniques for handling primary human T cells. We hope that this guide will serve as a reference point to allow evaluate, discuss, and improve current practices in T cell culturing and manipulation.
Phase 2 TWR Steam Reforming Test for Sodium-Bearing Waste Treatment (2004)

About one million gallons of acidic, hazardous, and radioactive sodium-bearing waste (SBW) is stored in stainless steel tanks a the Idaho Nuclear Technology and Engineering Center (INTEC), which is a major operating facility of the Idaho National Engineering and Environmental Laboratory (INEEL). Steam reforming is a candidate technology being investigated for converting the SBW into a road ready waste form that can be shipped to the Waste Isolation Pilot Plant in New Mexico for interment. Fluidized bed steam reforming technology, licensed to ThermoChem Waste Remediation, LLC (TWR) by Manufacturing Technology Conversion International, was tested in two phases using an INEEL (Department of Energy) fluidized bed test system located at the Science Applications International Corporation (SAIC) Science and Technology Applications Research Center in Idaho Falls, Idaho. The Phase 1 tests were reported earlier. The Phase 2 tests are reported here. For Phase 2, the process feed rate, reductant stoichiometry, and process temperature were varied to identify and demonstrate how the process might be optimized to improve operation and product characteristics. The first week of testing was devoted primarily to process chemistry and the second week was devoted more toward bed stability and particle size control.
RF Platforms for Cognitive Radio (2016)

In this chapter, we have presented an overview of the functions and specifications for cognitive radio RF platforms. Typically, these combine analog and digital components and signalprocessing systems and offer the user a wide range of options trading off cost, performance, the development effort required, and required computational support. RFICs are attractive for simple applications typically requiring channelized communications with FSK-based waveforms, while SDRs offer power and flexible performance in return for commensurate investment in software development.
FUNCTIONAL OUTCOME AFTER REVISION KNEE ARTHROPLASTY: ANY DIFFERENCE BETWEEN INFECTED AND NON-INFECTED CASES? (2009)

Purpose: Periprosthetic infection (PPI) is a devastating complication. Surgical intervention to treat PPI is often required. The objective of this prospective study is to determine if there is any difference in functional improvement following revision TKA in patients with infected and non-infected failures. Methods: 123 consecutive patients undergoing revision TKA at our institution were prospectively recruited into this study. The indication for revision TKA was PPI in 37 cases and aseptic failure in 86 cases. Detailed patient demographics and functional outcome using SF-36, KSS, Womac, lower extremity functional outcome score were collected at base line and at various time points after revision TKA. The baseline and two year follow up functional scores were calculated and compared. The functional score at the time of diagnosis of PPI (prosthesis in place) were used for baseline comparisons Results: All baseline functional scores, and their individual elements, for the infected cases were worse than the non-infected cases. The functional scores at the two-year follow-up were not different between the infected and non-infected cases. Hence, there was a more impressive improvement (Δ) in functional outcome for the infected cases following revision TKA compared to non-infected cases. However, the general health perception as determined by the patients themselves appeared to deteriorate after revision TKA in both groups. Discussion: It appears that patients with PPI are markedly more disabled at base line than the non-infected cases. These patients, however, benefit the most from surgical intervention compared to the non-infected cases. It appears that the patients’ perception of improvement in functional scores is less optimistic than physician measured parameters.
Automatically recommending multimedia content for use in group reminiscence therap (2013)

This paper presents and evaluates a novel approach for automatically recommending multimedia content for use in group reminiscence therapy for people with Alzheimer's and other dementias. In recent years recommender systems have seen popularity in providing a personalised experience in information discovery tasks. This personalisation approach is naturally suited to tasks in healthcare, such as reminiscence therapy, where there has been a trend towards an increased emphasis on person-centred care. Building on recent work which has shown benefits to reminiscence therapy in a group setting, we develop and evaluate a system, REMPAD, which profiles people with Alzheimer's and other dementias, and provides multimedia content tailored to a given group context. In this paper we present our system and approach, and report on a user trial in residential care settings. In our evaluation we examine the potential to use early-aggregation and late-aggregation of group member preferences using case-based reasoning combined with a content-based method. We evaluate with respect to accuracy, utility and perceived usefulness. The results overall are positive and we find that our best-performing approach uses early aggregation CBR combined with a content-based method. Also, under different evaluation criteria, we note different performances, with certain configurations of our approach providing better accuracy and others providing better utility.
Recent Advances on Thermoelectric Silicon for Low-Temperature Applications (2022)

Silicon is the most widely used functional material, as it is geo-abundant and atoxic. Unfortunately, its efficiency as a thermoelectric material is very poor. In this paper, we present and discuss advances of research on silicon and related materials for thermoelectric applications, mostly focusing on the comparison between the two strategies deployed to increase its performance, namely either reducing its thermal conductivity or, in polycrystalline materials, increasing its power factor. Special attention will be paid to recent results concerning silicon thin films. The enhancement of Si performances has motivated efforts to develop integrated heat microharvesters operating around room temperature, which will be reviewed also in view of their applications to power wireless sensors for the Internet of Things.
Exceptional Points of Degeneracy in lossless Periodic Coupled Waveguides (2018)

We present general aspects of exceptional points of degeneracy (EPD) of order 2,3, and 4, that appear also in lossless periodic waveguides. We report unconventional scaling of the quality factor in coupled resonators optical waveguides.
Practical Synthesis of the High-Quality Antitumor Agent KW-2189 from Duocarmycin B2 Using a Facile One-Pot Synthesis of an Intermediate (1998)

A facile and large-scale preparation process of a potent antitumor agent KW-2189 (2), derived from the antitumor antibiotic duocarmycin B2 (1), has been developed. This new synthetic route required three steps: (i) one-pot carbamoylation and subsequent reduction, (ii) Wagner−Meerwein rearrangement of the methoxycarbonyl group for the production of the pyrrole compound 6, and (iii) formation of the hydrobromide salt 2. The key strategic improvement was to obtain good quality hydroxy compound 4 in a reasonable yield without isolation of the unstable keto intermediate 3a. During commercial-scale production at a scale of about 50 g, this strategy provided high-quality KW-2189 (2) in a 55% overall yield from 1. Potential degradation compounds 7−9 were also synthesized and shown to be absent in the KW-2189 (2) prepared.
Gradients of Counterfactuals (2016)

Gradients have been used to quantify feature importance in machine learning models. Unfortunately, in nonlinear deep networks, not only individual neurons but also the whole network can saturate, and as a result an important input feature can have a tiny gradient. We study various networks, and observe that this phenomena is indeed widespread, across many inputs. We propose to examine interior gradients, which are gradients of counterfactual inputs constructed by scaling down the original input. We apply our method to the GoogleNet architecture for object recognition in images, as well as a ligand-based virtual screening network with categorical features and an LSTM based language model for the Penn Treebank dataset. We visualize how interior gradients better capture feature importance. Furthermore, interior gradients are applicable to a wide variety of deep networks, and have the attribution property that the feature importance scores sum to the the prediction score. Best of all, interior gradients can be computed just as easily as gradients. In contrast, previous methods are complex to implement, which hinders practical adoption.
Dual comb generation in a monochromatically driven crystalline microresonator (2019)

Recent works on Kerr frequency combs demonstrated the possibility to simultaneously generate multiple soliton states with different group velocities in a single microresonator, which could be beneficial for many applications utilizing dual-comb systems. In this work we demonstrate a dual-comb configuration in a single crystalline microresonator by monochromatically pumping counter-propagating solitons in the same spatial mode with equal powers. Moreover, we demonstrate experimentally and through simulations the key role of Cherenkov radiation interferences on the repetition rate of a multi-soliton state. This result not only shines new light on the impact of dispersive waves on dissipative Kerr solitons but also introduces a novel approach to develop coherent dual-comb spectrometer based on microcombs.
Terrain Stability Mapping with SINMAP, technical description and users guide for version 1.00 (1998)

Disclaimers Although care has been taken in developing and testing SINMAP, errors and inadequacies may still occur, particularly in new applications. A user must therefore make the final evaluation as to the usefulness of SINMAP for his/her application. SINMAP is a tool to be used by investigators who have some knowledge and experience concerning landslide behaviour. It requires engineering judgement and common sense in developing input parameters and interpretation of the results. In making these judgements the user should understand the concepts and limitations of the SINMAP theory presented in this document. This understanding should include a comprehension of the geomorphic processes which the program is attempting to model and the model's limitations. Finally, the user should be aware of the accuracy limitations of the DEM, soil, and hydrologic data used as input for these analyses. The authors of SINMAP assume no liability or responsibility for the use of SINMAP, the interpretation of SINMAP results, or the consequences of management decisions that are based upon SINMAP. In no event shall the authors be liable for any damages whatsoever arising out of the use, or attempts to use SINMAP. The terms ESRI, Arc/Info, ArcView, and Avenue are registered trademarks of Environmental Systems Research Institute.
Cortical bone responses to 2G hypergravity in growing rats. (1998)

Our findings suggest that short term exposure to 2G does not enhance bone formation or induce changes in cortical bone composition, or alter specific gravity. These data also suggest that bone maturation as reflected by collagen cross-linking is upregulated. However, it is undetermined at this time whether the enhanced content of mature bone collagen in the centrifuged rats is a result of either an increased rate of cross-linking or reduction in the degradation of "older collagen."
A Computer Aided Cam Synthesis Tool for Arbitrary Follower Motion Functions (2000)

Abstract This paper describes a cam mechanism synthesis and analysis software CamSyn based on Matlab platform. The key feature of this software is its ability to synthesize a cam system with arbitrary follower motion functions. In particular, CamSyn can synthesize a cam profile for multi-rise and multi-return follower displacement functions and is therefore not restricted to typical single dwell-rise-return motion functions. Design examples are given to demonstrate the effectiveness of the software. The underlying design methods and strategies implemented in this software are well known in the published literature.
TrilobiTe biosTraTigraphy of The Králův Dvůr formaTion (upper KaTian, prague basin, CzeCh republiC): global faunal Changes or faCies-relaTeD DisTribuTion? (2011)

Eight trilobite associations and sub-associations have been distinguished in the late Katian Kralův Dvůr Formation. Spatial distribution of these associations reflects lithology but their succession was dictated also by global climatic changes and palaeogeographical positioning. Locally developed “Podoli Ore Horizon” trilobite association contains low-diversity but specific forms showing survivals from the underlying Bohdalec Formation combined with the late Katian taxa ( Chlustinia , Duftonia , Onnia , etc.). The Amphitryon – Kloucekia Association is newly established for the lower two thirds of the formation. It is characterized by abundant benthic scavenger-predators accompanied by filter feeders and common pelagic/nektic predators. Within Amphitryon –Kloucekia Association can be distinguished four sub-Association 1) the newly established Onnia ultima sub-Association is characterized by a dominance of Onnia and Flexicalymene; it is developed at the lowermost levels of the formation, 2) the deeper-water Nankinolithus granulatus sub-Association (originally established as horizon), 3) rather shallow-water, brachiopod-dominated Dedzetina -Tretaspis sub-Association with rare trilobites and 4) the trilobite-dominated Tretaspis anderssonni sub-Association (originally horizon). Last three sub-associations are considered as rather facies-related, with limited stratigraphical applicability only. Impure bioclastic limestone below top of the formation contains a rich shallow- and temperate-water Marekolithus kosoviensis Association, which better corresponds with the original horizon concept. This association is dominated by small benthic scavenger-predator trilobites, which are associated by the filter feeder Marekolithus . The Mucronaspis Association of medium-sized scavenger-predators is characteristic for the uppermost portion of formation and persisted till the early onset of the glaciation at the base of Hirnantian. Minute detritus feeders are rare but present in all the above-discussed associations excluding the last one.
Ultrafast Contrast Enhanced Magnetic Resonance Imaging of Congenital Hydronephrosis in a Rat Model (1994)

Since new ultrafast magnetic resonance imaging (MRI) might offer unique advantages for evaluating renal blood flow, anatomy and urinary excretion, we used this technique to characterize a rat model with congenital partial ureteropelvic junction obstruction. MRI of 9 rats from an inbred colony with unilateral congenital (nonsurgical) hydronephrosis was compared with the contralateral nonhydronephrotic kidney serving as control. Our new imaging technique consisted of a 1-minute ultrafast gradient recalled imaging sequence during the first minute (64 images per imaging time 960 milliseconds) after contrast bolus injection with gadolinium-diethylenetriaminepentaacetic acid for assessment of renal blood flow followed by a 30-minute period with image acquisition every 30 seconds to study contrast distribution and excretion. Signal intensities were analyzed continuously over selected, different regions of interest. Anatomic analysis of MRI noncontrast studies showed precise delineation of the hydronephrotic pelvis and corticomedullary junction. After contrast gadolinium-diethylenetriaminepentaacetic acid injection signal intensity from the region of interest from hydronephrotic kidneys differed from nonhydronephrotic kidneys by showing less cortical decrease, suggesting decreased blood flow, less medullary decrease and delayed contrast excretion. Clear contrast distribution among the cortex, medulla and collecting system allowed selective estimation of different regions of interest and excellent anatomic evaluation. Renal anatomy and renal pelvic pressures were confirmed after scans were completed. Ultrafast contrast enhanced MRI allows simultaneous assessment of renal morphology, blood flow and function. In hydronephrotic partially obstructed kidneys distinct flow and excretion patterns measured with contrast enhanced MRI allow differentiation between the obstructed and nonobstructed kidney on physiological rather than purely anatomic means. This imaging technique may provide a useful method of evaluating congenital hydronephrosis obviating the need for multiple different diagnostic procedures.