gebhart/patrepeval huggingface dataset:
Bax- and Bak-induced cell death in the fission yeast Schizosaccharomyces pombe. (1997)

The effects of the expression of the human Bcl-2 family proteins Bax, Bak, Bcl-2, and Bcl-XL were examined in the fission yeast Schizosaccharomyces pombe and compared with Bax-induced cell death in mammalian cells. Expression of the proapoptotic proteins Bax and Bak conferred a lethal phenotype in this yeast, which was strongly suppressed by coexpression of the anti-apoptotic protein Bcl-XL. Bcl-2 also partially abrogated Bax-mediated cytotoxicity in S. pombe, whereas a mutant of Bcl-2 (Gly145Ala) that fails to heterodimerize with Bax or block apoptosis in mammalian cells was inactive. However, other features distinguished Bax- and Bak-induced death in S. pombe from animal cell apoptosis. Electron microscopic analysis of S. pombe cells dying in response to Bax or Bak expression demonstrated massive cytosolic vacuolization and multifocal nuclear chromatin condensation, thus distinguishing this form of cell death from the classical morphological features of apoptosis seen in animal cells. Unlike Bax-induced apoptosis in 293 cells that led to the induction of interleukin-1 beta-converting enzyme (ICE)/CED-3-like protease activity, Bax- and Bak-induced cell death in S. pombe was accompanied neither by internucleosomal DNA fragmentation nor by activation of proteases with specificities similar to the ICE/CED-3 family. In addition, the baculovirus protease inhibitor p35, which is a potent inhibitor of ICE/CED-3 family proteases and a blocker of apoptosis in animal cells, failed to prevent cell death induction by Bax or Bak in fission yeast, whereas p35 inhibited Bax-induced cell death in mammalian cells. Taken together, these findings suggest that Bcl-2 family proteins may retain an evolutionarily conserved ability to regulate cell survival and death but also indicate differences in the downstream events that are activated by overexpression of Bax or Bak in divergent cell types.
Antimicrobial peptides: mode of action and perspectives of practical application (2012)

This review is devoted to antimicrobial peptides (AMP's) that demonstrate activity against bacteria, viruses and fungi. It considers structure and mechanism of AMP interaction with lipid membrane and intracellular targets of pathogens. Special attention is paid to modem state and perspectives of AMP practical application and also to approaches that increase efficacy and reduce toxicity of AMP by chemical modification of their structure.
Treatment of melamine formaldehyde fibers for decontaminating biological and chemical warfare agents (2015)

ABSTRACT The demand for protection against biological and chemical warfare agents has increased the need for unique protective materials. N ‐halamines are superior candidates for this task by having rapid inactivation rates against a broad range of microorganisms and the ability to oxidize some pesticides and warfare agents to reduce their toxicity to humans. Thus, the design of N ‐halamine materials having fibrous structure, high halogen loading capacity with enhanced stability, and being relatively inexpensive is very important. This study investigated the effect of acid treatment on the chlorine loading and stability of a commercial flame retardant melamine formaldehyde (MF) fiber to introduce biocidal and detoxifying properties. The fibers formed into a web were treated with diluted sulfuric acid (H 2 SO 4 ) under various conditions. The fiber webs were chlorinated with household bleach, and the stability of bound chlorine was investigated. The treated fabrics have been tested against a Gram‐negative bacterium and a warfare stimulant. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 42799.
Foreword (2018)

for the invention of efficient blue light-emitting diodes which has enabled bright and energy-saving white light sources" illustrates the worldwide societal impact of light-emitting diodes (LEDs). It also emphasizes the importance of lighting throughout the history of human societies, relying on ever-improved lighting technologies and acting as a lead user when new energy sources emerged, leading to fast-increasing light production with improvement of service and cost decrease.
Reactive plasma cleaning and restoration of transition metal dichalcogenide monolayers (2021)

Abstract The cleaning of two-dimensional (2D) materials is an essential step in the fabrication of future devices, leveraging their unique physical, optical, and chemical properties. Part of these emerging 2D materials are transition metal dichalcogenides (TMDs). So far there is limited understanding of the cleaning of “monolayer” TMD materials. In this study, we report on the use of downstream H 2 plasma to clean the surface of monolayer WS 2 grown by MOCVD. We demonstrate that high-temperature processing is essential, allowing to maximize the removal rate of polymers and to mitigate damage caused to the WS 2 in the form of sulfur vacancies. We show that low temperature in situ carbonyl sulfide (OCS) soak is an efficient way to resulfurize the material, besides high-temperature H 2 S annealing. The cleaning processes and mechanisms elucidated in this work are tested on back-gated field-effect transistors, confirming that transport properties of WS 2 devices can be maintained by the combination of H 2 plasma cleaning and OCS restoration. The low-damage plasma cleaning based on H 2 and OCS is very reproducible, fast (completed in a few minutes) and uses a 300 mm industrial plasma etch system qualified for standard semiconductor pilot production. This process is, therefore, expected to enable the industrial scale-up of 2D-based devices, co-integrated with silicon technology.
Evaluation of a novel canine activity monitor for at-home physical activity analysis (2015)

Activity data provided by the Whistle activity monitor may be used as an objective outcome measurement in dogs. The total activity time provided by the Whistle application offers an inexpensive method for obtaining at-home, canine, real-time physical activity data. Limitations of the Whistle device include the limited battery life, the need for manual derivation of activity intensity data and data transfer, and the requirement of Wi-Fi and Bluetooth availability for data transmission.
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity (2020)

The human microbiota has a close relationship with human disease and it remodels components of the glycocalyx including heparan sulfate (HS). Studies of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike protein receptor binding domain suggest that infection requires binding to HS and angiotensin converting enzyme 2 (ACE2) in a codependent manner. Here, we show that commensal host bacterial communities can modify HS and thereby modulate SARS-CoV-2 spike protein binding and that these communities change with host age and sex. Common human-associated commensal bacteria whose genomes encode HS-modifying enzymes were identified. The prevalence of these bacteria and the expression of key microbial glycosidases in bronchoalveolar lavage fluid (BALF) was lower in adult COVID-19 patients than in healthy controls. The presence of HS-modifying bacteria decreased with age in two large survey datasets, FINRISK 2002 and American Gut, revealing one possible mechanism for the observed increase in COVID-19 susceptibility with age. <i>In vitro</i> , bacterial glycosidases from unpurified culture media supernatants fully blocked SARS-CoV-2 spike binding to human H1299 protein lung adenocarcinoma cells. HS-modifying bacteria in human microbial communities may regulate viral adhesion, and loss of these commensals could predispose individuals to infection. Understanding the impact of shifts in microbial community composition and bacterial lyases on SARS-CoV-2 infection may lead to new therapeutics and diagnosis of susceptibility.
The effect of music performance on the transcriptome of professional musicians (2015)

Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several neuroscientific studies have demonstrated that the brains of professional musicians and non-musicians differ structurally and functionally and that musical training enhances cognition. However, the molecules and molecular mechanisms involved in music performance remain largely unexplored. Here, we investigated the effect of music performance on the genome-wide peripheral blood transcriptome of professional musicians by analyzing the transcriptional responses after a 2-hr concert performance and after a 'music-free' control session. The up-regulated genes were found to affect dopaminergic neurotransmission, motor behavior, neuronal plasticity, and neurocognitive functions including learning and memory. Particularly, candidate genes such as SNCA, FOS and DUSP1 that are involved in song perception and production in songbirds, were identified, suggesting an evolutionary conservation in biological processes related to sound perception/production. Additionally, modulation of genes related to calcium ion homeostasis, iron ion homeostasis, glutathione metabolism, and several neuropsychiatric and neurodegenerative diseases implied that music performance may affect the biological pathways that are otherwise essential for the proper maintenance of neuronal function and survival. For the first time, this study provides evidence for the candidate genes and molecular mechanisms underlying music performance.
Comparison of subjective methods, with and without explicit reference, for quality assessment of 3D graphics (2019)

Numerous methodologies for subjective quality assessment exist in the field of image processing. In particular, the Absolute Category Rating with Hidden Reference (ACR-HR) and the Double Stimulus Impairment Scale (DSIS) are considered two of the most prominent methods for assessing the visual quality of 2D images and videos. Are these methods valid/accurate to evaluate the perceived quality of 3D graphics data? Is the presence of an explicit reference necessary, due to the lack of human prior knowledge on 3D graphics data compared to natural images/videos? To answer these questions, we compare these two subjective methods (ACR-HR and DSIS) on a dataset of high-quality colored 3D models, impaired with various distortions. These subjective experiments were conducted in a virtual reality (VR) environment. Our results show differences in the performance of the methods depending on the 3D contents and the types of distortions. We show that DSIS outperforms ACR-HR in term of accuracy and points out a stable performance. Results also yield interesting conclusions on the importance of a reference for judging the quality of 3D graphics. We finally provide recommendations regarding the influence of the number of observers on the accuracy.
Conjugate Heat Transfer in Thermal Inkjet Printheads (2023)

The mass of individual droplets ejected from a thermal inkjet printhead increases with increasing local temperature near the ejector nozzles. The amount of ink deposited on the page and so the printed image density depends on the droplet mass. Thus, printhead temperature nonuniformity results in printed image density variations that can be unacceptable to the end users of the printed output. Such temperature variations arise from a combination of the ink fluid flow and the heat transfer in both the ink and the solid components in the printhead. Conjugate heat transfer (CHT) in thermal inkjet printheads is investigated here using validated numerical simulations. A typical thermal inkjet printhead is considered here for the first time, with cold ink drawn through the solid structural components by the ejector nozzle refill. The effect of the width of the feedhole above the printhead chip on the temperature field within the chip is analyzed. Validation of the simulation model required the derivation of novel analytical solutions for the relatively simple problems of fully developed forced convection in a differentially heated planar channel and conduction against convection in plug flow. The results from numerical simulations of these two problems are found to compare well with the newly derived analytical solutions. CHT in flow over a backward-facing step with a heated downstream wall was also simulated as part of the validation process, and good agreement was observed with earlier numerical studies. For the main part of the study, it was found that increasing the width of the feedhole reduces the gradients in temperature on the surface of the printhead chip, thus reducing temperature-related printing defects.
Dissociation of Immunoregulatory Function of Blood Monocytes from Maturational State and Expression of Interleukin-1 in Humans Chronically Infected with Schistosoma Mansoni (1990)

We investigated the immunoregulatory function and properties of monocytes in 54 S. mansoni infected Egyptians (40-3,840 S. mansoni eggs excreted per gram of stool) 13-35 years of age. Adherent cell-mediated suppression was found in 11 of 36 patients. Cytochemical studies and reactivity with monoclonal antibodies directed at differentiation markers failed to show alterations in the distribution or maturation of monocytes. Peripheral blood mononuclear cells (PBMC) from these individuals produced lower levels of interleukin-1 (IL-1) in response to bacterial lipopolysaccharide and Staphylococcus albus stimulation as compared to the other S. mansoni infected individuals. Overall, IL-1 production by PBMC stimulated with LPS or Staphylococcus albus was higher in infected individuals compared to uninfected controls and correlated with intensity of infection (r = 0.41, P = 0.002 for LPS; r = 0.45, P = 0.006 for S. albus). IL-1 expression by monocytes from individuals with heavy S. mansoni infection exceeded that of subjects with light infection. The intensity-related increase in IL-1 expression did not correlate with the maturational state or the immunoregulatory properties of the monocytes.
The Limitations of Fatigue Testing (2010)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Fatigue testing of components is used to validate new product designs as well as changes made to existing designs. On new designs it is common to initially test parts at the design stage (design verification or DV) and then again at the production stage (production verification or PV) to make sure the performance has not changed. On changes to existing designs typically the life of the new part (B) is compared to that of the old part (A). When comparing the fatigue life Weibull analysis is normally used to evaluate the data. The expectation is that the B10 or B50 life of the new part or PV parts should be equal to or better than that of the old parts or the DV parts. However, fatigue testing has a great deal of inherent variability in the resulting life. In this paper the variability of numerous carburized and induction hardened components is examined. The data indicates that the value of traditional DV to PV or A to B type testing is limited due to the high level of background variation. Instead the value of fatigue testing components is in comparing the data to a well established SN curve or database made from many lots of material tested over a long period of time.&lt;/div&gt;&lt;/div&gt;
Design guidelines of storage class memory/flash hybrid solid-state drive considering system architecture, algorithm and workload characteristic (2016)

Solid-state drives (SSDs), composed of NAND flash memories, are replacing hard disk drives (HDDs) rapidly. In addition, storage class memories (SCMs) bridge the bandwidth gap between DRAM and NAND flash, thus introducing SCM to SSD further improves the solid storage performance. Different from schemes that use SCM to store file system metadata or logical to physical mapping tables, two architectures 1) use SCM as a write-back non-volatile memory (NVM) based cache, 2) use SCM as a storage device are presented in this paper. Since SCM chip latency varies due to memory device and circuit design, three SSD data management algorithms are evaluated under five SCM chip design scenarios to provide useful design guidelines of SCM/NAND flash hybrid SSD. SCM interface and capacity requirement are also analyzed. From the experimental results, less than 10% of the SCM/NAND flash capacity ratio is enough for SCM chips with 500 ns read and 5 μs write latency to boost NAND flash-only SSD speed by over 10 times when workloads own high IO skew <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Mental Models of Mere Mortals with Explanations of Reinforcement Learning (2020)

How should reinforcement learning (RL) agents explain themselves to humans not trained in AI? To gain insights into this question, we conducted a 124-participant, four-treatment experiment to compare participants’ mental models of an RL agent in the context of a simple Real-Time Strategy (RTS) game. The four treatments isolated two types of explanations vs. neither vs. both together. The two types of explanations were as follows: (1) saliency maps (an “Input Intelligibility Type” that explains the AI’s focus of attention) and (2) reward-decomposition bars (an “Output Intelligibility Type” that explains the AI’s predictions of future types of rewards). Our results show that a combined explanation that included saliency and reward bars was needed to achieve a statistically significant difference in participants’ mental model scores over the no-explanation treatment. However, this combined explanation was far from a panacea: It exacted disproportionately high cognitive loads from the participants who received the combined explanation. Further, in some situations, participants who saw both explanations predicted the agent’s next action worse than all other treatments’ participants.
Efficacy and safety of adalimumab in patients with non-radiographic axial spondyloarthritis: results of a randomised placebo-controlled trial (ABILITY-1) (2012)

In patients with nr-axSpA, adalimumab treatment resulted in effective control of disease activity, decreased inflammation and improved quality of life compared with placebo. Results from ABILITY-1 suggest that adalimumab has a positive benefit-risk profile in active nr-axSpA patients with inadequate response to NSAIDs.
DRAMA+: Disaster Management With Mitigation Awareness for Translucent Elastic Optical Networks (2022)

Elastic optical networks (EONs) have emerged as attractive candidates to satisfy the dramatic growth of demand in 5G and cloud applications. EONs promise to provide high spectrum utilization due to flexibility in resource assignment. In translucent EONs, the spectrum efficiency can be further improved by deploying regenerators. Because of their extremely high flexibility, developing efficient mechanisms and strategies to ensure the survivability of translucent EONs is a challenging problem. In this paper, we consider disaster mitigation in translucent EONs. We propose a new approach to disaster management by introducing the concept of mitigation zone, which identifies a region surrounding the disaster zone wherein lightpaths may be reconfigured with degraded service (with a penalty) in order to improve overall performance. We formulate an integer linear program (ILP) to minimize the penalty due to service degradation after a disaster, and present a heuristic algorithm named Disaster Management Algorithm with Mitigation Awareness and 3R regenerators (DRAMA+). Simulation results demonstrate that the proposed algorithms have a better performance in terms of total penalty and blocking ratio than conventional disaster recovery algorithms.
Supplementary Table S1 from A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors (2023)

&lt;p&gt;- PDF file 94K, Top 100 FDA-approved drugs identified by a bioinformatics drug- repositioning approach&lt;/p&gt;
A 10-W S-band class-B GaN amplifier with a dynamic gate bias circuit for linearity enhancement (2013)

In the present paper, we present a dynamic gate biasing technique applied to a 10 W, S-band GaN amplifier. The proposed methodology addresses class-B operation of power amplifiers that offers the potential for high efficiency but requires a careful attention to maintain good linearity performances at large output power back-off. This work proposes a solution to improve the linearity of class-B amplifiers driven by radio frequency-modulated signals having large peak to average power ratios. An important aspect of this work concerns the characterization of the dynamic behavior of GaN devices for gate bias trajectory optimization. For that purpose, the experimental study reported here is based on the use of a time-domain envelope setup. A specific gate bias circuit has been designed and connected to a 10 W – 2.5 GHz GaN amplifier demo board from CREE. Compared to conventional class-B operation with a fixed gate bias, a 10-dB improvement in terms of third-order intermodulation is reached. When applied to the amplification of 16-QAM signals the proposed technique demonstrates significant ACPR reduction of order of 6 dB along with error vector magnitude (EVM) improvements of five points over 8 dB output power back-off with a minor impact on power-added efficiency performances.
Influence of the amorphous-crystalline interface morphology on dislocation nucleation in pre-amorphized silicon (1984)

Cross-sectional high-resolution transmission electron microscopy and secondary-ion mass spectrometry are applied to the characterization of defects formed during rapid thermal annealing of pre-amorphized and subsequently BF/sub 2//sup +/-implanted (100) silicon substrates. The occurrence of hairpin dislocations is shown to be directly related to the degree of total disorder (i.e. amorphization) in the transition region between amorphous and crystalline material before annealing. A model for the nucleation and propagation of these dislocations is developed on the basis of the microscopy results. Finally, pre-amorphization conditions which minimize the density of hairpin dislocations are discussed.
Analysis of the Cellular Localization of Bdr Paralogs in Borrelia burgdorferi , a Causative Agent of Lyme Disease: Evidence for Functional Diversity (2000)

The bdr (Borrelia direct repeat) gene family of the genus Borrelia encodes a polymorphic group of proteins that carry a central repeat motif region containing putative phosphorylation sites and a hydrophobic carboxyl-terminal domain. It has been postulated that the Bdr proteins may anchor to the inner membrane via the C-terminal domain. In this study, we used cellular fractionation methodologies, salt and detergent treatments, and immunoblot analyses to assess the association of the Bdr proteins with the cellular infrastructure in both Borrelia burgdorferi (a Lyme disease spirochete) and B. turicatae (a relapsing fever spirochete). Triton X-114 extraction and partitioning experiments demonstrated that most Bdr paralogs are associated with the inner membrane-peptidoglycan complex. Analyses of cells treated with the highly chaotropic bile salt detergent deoxycholic acid demonstrated that some Bdr paralogs may also interact with the peptidoglycan, as evidenced by their tight association with the insoluble cellular matrix. In addition, immunoprecipitation (IP) experiments revealed an enhanced IP of all Bdr paralogs when the cell lysates were boiled prior to addition of the precipitating antibody. Furthermore, some Bdr paralogs were accessible to antibody in the IP experiments only in the boiled cell lysates. These observations suggest that different Bdr paralogs may carry out different structural-functional roles. Demonstration of the inner membrane localization of the Bdr proteins and of the differences in nature of the interaction of individual Bdr paralogs with the cell infrastructure is an important step toward defining the functional role of this unique protein family in the genus Borrelia.