gebhart/patrepeval huggingface dataset:
Daily running enhances molecular and physiological circadian rhythms in skeletal muscle (2020)

Structured Abstract Objective Exercise is a critical component of a healthy lifestyle and a key strategy for the prevention and management of metabolic disease. Identifying molecular mechanisms underlying adaptation in response to chronic physical activity is of critical interest in metabolic physiology. Circadian rhythms broadly modulate metabolism, including muscle substrate utilization and exercise capacity. Here, we define the molecular and physiological changes induced across the daily cycle by voluntary low intensity daily exercise. Methods Wildtype c57BL6/J male and female mice were housed with or without access to a running wheel for six weeks. Maximum running speed was measured at four different zeitgeber times (ZTs, hours after lights on) using either electrical or manual stimulation to motivate continued running on a motorized treadmill. RNA isolated from plantaris muscles at six ZTs was sequenced to establish the impact of daily activity on genome-wide transcription. Patterns of gene expression were analyzed using Gene Set Enrichment Analysis (GSEA) and Detection of Differential Rhythmicity (DODR). Blood glucose, lactate, and ketones, and muscle and liver glycogen were measured before and after exercise. Results We demonstrate that the use of mild electrical shocks to motivate running negatively impacts maximum running speed and describe a manual method to motivate running in rodent exercise studies. Using this method, we show that time of day influences the increase in exercise capacity afforded by six weeks of voluntary wheel running: when maximum running speed is measured at the beginning of the nighttime active period in mice, there is no measurable benefit from a history of daily voluntary running, while maximum increase in performance occurs at the end of the night. We show that daily voluntary exercise dramatically remodels the muscle circadian transcriptome. Finally, we describe daily rhythms in carbohydrate metabolism associated with the timedependent response to moderate daily exercise. Conclusions Collectively, these data indicate that chronic nighttime physical activity dramatically remodels daily rhythms of muscle gene expression, which in turn support daily fluctuations in exercise performance.
The Olefin-Aldehyde Condensation. The Prins Reaction. (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Olefin-Aldehyde Condensation. The Prins Reaction.E. Arundale and L. A. MikeskaCite this: Chem. Rev. 1952, 51, 3, 505–555Publication Date (Print):December 1, 1952Publication History Published online1 May 2002Published inissue 1 December 1952https://pubs.acs.org/doi/10.1021/cr60160a004https://doi.org/10.1021/cr60160a004research-articleACS PublicationsRequest reuse permissionsArticle Views4223Altmetric-Citations289LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Experimental verification of radio frequency interference mitigation with a focal plane array feed (2007)

We demonstrate the use of spatial filtering algorithms for radio frequency interference (RFI) mitigation in conjunction with a focal plane array of electrically small elements. The array consists of a seven‐element hexagonal arrangement of thickened dipole antennas with 1600 MHz designed center frequency backed by a circular ground plane at the focal plane of a 3 m parabolic reflector. Rooftop‐mounted signal sources were used to simulate a weak signal of interest at boresight and a strong, broadband interferer in the reflector sidelobes. Using an adaptive beamformer, the amplitude of the interfering signal was reduced sufficiently to recover the signal of interest. For an interference to noise ratio of 15 dB as measured at the center array element, the interferer was suppressed to the level of the fluctuations of the 10‐s integrated noise floor (the minimum detectable signal level was interference‐limited and no longer decreased after 10 s integration). Similar cancellation performance was demonstrated for a nonstationary interferer moving at an angular velocity of 0.1° per second. Pattern rumble due to beamformer adaptation was observed and quantified. For a moving RFI source, the degree of pattern rumble was found to be unacceptably large in terms of its effects on the maximum stable integration time and receiver sensitivity. An array feed with more elements together with specialized signal processing algorithms designed to suppress pattern rumble will likely be required in order to use adaptive spatial filtering for astronomical observations.
Can Lucas-Kanade be used to estimate motion parallax in 3D cluttered scenes? (2007)

When an observer moves in a 3D static scene, the motion field depends on the depth of the visible objects and on the observer's instantaneous translation and rotation. By computing the difference between nearby motion field vectors, the observer can estimate the direction of local motion parallax and in turn the direction of heading. It has recently been argued that, in 3D cluttered scenes such as a forest, computing local image motion using classical optical flow methods is problematic since these classical methods have problems at depth discontinuities. Hence, estimating local motion parallax from optical flow should be problematic as well. In this paper we evaluate this claim. We use the classical Lucas-Kanade method to estimate optical flow and the Rieger-Lawton method to estimate the direction of motion parallax from the estimated flow. We compare the motion parallax estimates to those of the frequency based method of Mann-Langer. We find that if the Lucas-Kanade estimates are sufficiently pruned, using both an eigenvalue condition and a mean absolute error condition, then the Lucas- Kanade/Rieger-Lawton method can perform as well as or better than the frequency-based method.
Liquid Keyboard : An Ergonomic, Adaptive QWERTY Keyboard for Touchscreens and Surfaces (2011)

Virtual touchscreen keyboards provide poor text input performance in comparison to physical keyboards, a fact, which can partly be attributed to the weaker tactile feedback, they offer. Users are unable to feel the keys on which their fingers are resting, and usually hover their hands over the keyboard, hitting each key individually. Consequently, users cannot use all ten fingers for typing, which decreases their input speed and causes hand fatigue. We present a keyboard prototype called LiquidKeyboard, which adapts to the userâs natural finger positions on a touchscreen and discuss options to allow for the fingers to rest on the screen while typing. When invoked, the keyboard appears directly under the userâs fingertips and is able to follow finger movements. As the positions of the surrounding keys are fixed in relation to each finger, users can find and touch the keys without tactile feedback. Additionally the user controlled positioning of the keys allows the keyboard to adapt to the physical specification of the userâs hand, such as the size of each finger.
Fabrication of hierarchical biomimetic polymeric nanostructured surfaces (2017)

Modification of the NSL process enables the replication and modification of the complex and often hierarchical surface topographies displayed by insect cuticles.
Metal Tetrazole Complexes: Bis-(5-aminotetrazolato)-copper(II) (1960)

Two crystalline forms of bis-(5-aminotetrazolato)-copper (II) have been prepared and characterized. Visible and ultraviolet spectra of aqueous copper (II)-5-aminotetrazole solution have been examined. Continuous variation experiments reveal 1:2 interactions and a formation constant for the complex in solution has been determined and is about 1012. Infrared studies suggest coördination involves the ring and not the 5-amino group. Acids decompose the complexes and bring about rupture of the tetrazole ring, while decomposition by ammonia does not affect the ring.
Modeling the novel SERD elacestrant in cultured fulvestrant-refractory HR-positive breast circulating tumor cells (2023)

Serial endocrine therapy is the mainstay of management for metastatic HR+breast cancer, but acquisition of drug resistance highlights the need for better therapies. Elacestrant is a recently FDA-approved novel oral selective estrogen receptor degrader (SERD), with demonstrated efficacy in the EMERALD phase 3 clinical trial of refractory HR+breast cancer. Subgroup analysis of the EMERALD clinical trial identifies clinical benefit with elacestrant in patients who had received prior fulvestrant independent of the mutational status of the ESR1 gene, supporting its potential utility in treating refractory HR+breast cancer. Here, we use pre-clinical models, including ex vivo cultures of circulating tumor cells and patient-derived xenografts, to demonstrate the efficacy of elacestrant in breast cancer cells with acquired resistance to fulvestrant.
Painless Venipuncture. A Clinical Trial of Iontophoresis of Lidocaine for Venipuncture in Blood Donors (1984)

Discomfort or frank pain at venipuncture may be a reason for abstaining from giving blood. In an attempt to offer a painless alternative, a method for iontophoretic application of local anaesthetics was developed. Its effectiveness in producing anaesthesia for venipuncture was tested in a double-blind trial in 47 blood donors. A positive result was obtained in 89%, as against 28% in the placebo group.
Phasin Proteins Activate Aeromonas caviae Polyhydroxyalkanoate (PHA) Synthase but Not Ralstonia eutropha PHA Synthase (2014)

In this study, we performed in vitro and in vivo activity assays of polyhydroxyalkanoate (PHA) synthases (PhaCs) in the presence of phasin proteins (PhaPs), which revealed that PhaPs are activators of PhaC derived from Aeromonas caviae (PhaCAc). In in vitro assays, among the three PhaCs tested, PhaCAc was significantly activated when PhaPs were added at the beginning of polymerization (prepolymerization PhaCAc), whereas the prepolymerization PhaCRe (derived from Ralstonia eutropha) and PhaCDa (Delftia acidovorans) showed reduced activity with PhaPs. The PhaP-activated PhaCAc showed a slight shift of substrate preference toward 3-hydroxyhexanoyl-CoA (C6). PhaPAc also activated PhaCAc when it was added during polymerization (polymer-elongating PhaCAc), while this effect was not observed for PhaCRe. In an in vivo assay using Escherichia coli TOP10 as the host strain, the effect of PhaPAc expression on PHA synthesis by PhaCAc or PhaCRe was examined. As PhaPAc expression increased, PHA production was increased by up to 2.3-fold in the PhaCAc-expressing strain, whereas it was slightly increased in the PhaCRe-expressing strain. Taken together, this study provides evidence that PhaPs function as activators for PhaCAc both in vitro and in vivo but do not activate PhaCRe. This activating effect may be attributed to the new role of PhaPs in the polymerization reaction by PhaCAc.
Continuous speech recognition (1995)

The authors focus on a tutorial description of the hybrid HMM/ANN method. The approach has been applied to large vocabulary continuous speech recognition, and variants are in use by many researchers, The method provides a mechanism for incorporating a range of sources of evidence without strong assumptions about their joint statistics, and may have applicability to much more complex systems that can incorporate deep acoustic and linguistic context. The method is inherently discriminant and conservative of parameters. Despite these potential advantages, the hybrid method has focused on implementing fairly simple systems, which do surprisingly well on large continuous speech recognition tasks, Researchers are only beginning to explore the use of more complex structures with this paradigm. In particular, they are just beginning to look at the connectionist inference of language models (including phonology) from data, which may be required in order to take advantage of locally discriminant probabilities rather than simply translating to likelihoods. Finally, the authors' current intuition is that more advanced versions of the hybrid method can greatly benefit from a perceptual perspective.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clustering par apprentissage de distance guidé par des préférences sur les attributs (2016)

National audience
Simulação computacional do Sistema Imunológico através de sistemas multiagentes: um estudo da resposta imune e da terapêutica antimicrobiana na glomerulonefrite pós-infecciosa (GNPE) por Streptococcus pyogenes (2013)

The Sophisticated homeostasis mechanisms of the immune system are designed to protect us against the millions of microorganisms with which Homo sapiens sapiens lives daily. The Immune System is considered an area of great complexity, deserving therefore a diverstiy of research approaches, among which the computer simulation. This approach is interesting both for medicine, which would have the possibility of meeting new possibilities for treatment of diseases, and for computer science, which, once gaining a better undestanding of Immune System processes, would have inspiration for the construction of algorithms to solve complex problems. The purpose of this work is to create a model of computational experiments to demonstrate the role of the immune response and antimicrobial therapy in post-infectious glomerulonephritis (APSGN) by Streptococcus pyogenes. For this, we attempt to identify the requirements for the extension of AutoSimmune model to simulate the phenomena involved in the installation of APSGN. We added functionality in AutoSimmune tool for simulation of the immune system, implementing the proposed model. We included among others, two environments - the kidneys and upper airways - besides neutrophils. We used the approach of multi- agent systems (MAS) based on autonomous agents, and the model was implemented using Repast Simphony framework, as well as the original tool. In our experiments, we could also simulate the administration of antimicrobials, showing the consequent reduction of the risk to APSGN occurrence. This also opened the possibility of future investigation for the role of antimicrobials in infectious processes.
From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors (2022)

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.
Pharmacokinetics and tolerance of acyclovir, a new anti-herpesvirus agent, in humans (1982)

The pharmacokinetics and tolerance of acyclovir administered intravenously in single doses of 2.5, 5.0, 10.0, and 15.0 mg/kg were studied in 13 volunteers. The mean concentrations (+/- standard deviations) at the end of infusion as measured by radioimmunoassay were 4.52 +/0 0.31, 8.28 +/- 2.61, 14.6 +/- 2.30, and 22.7 +/- 10.4 microgram/ml, respectively. Drug elimination during and after the infusion of acyclovir was well described by a two-compartment open model. The mean terminal plasma half-life for each of the groups was 2.85, 2.80, 3.30, and 2.38 h, respectively. Within 72 h after the start of the infusion, 70% of the administered drug was recovered in the urine as unchanged acyclovir. The renal clearance of acyclovir accounted for about 77% of the total clearance and was about threefold greater than the creatinine clearance. This confirms that acyclovir is eliminated predominantly by the kidneys in patients with normal renal function and suggests that renal secretion and glomerular filtration may both be involved. The only adverse effect found by clinical and laboratory monitoring was irritation at he intravenous site after extravasation (in two cases), which resolved without significant sequelae.
Structural, bonding, and elastic properties of Si:X (X = B, Al, and Ga): a theoretical study (2020)

Abstract Extremely high doping has recently been used in electrical and optical applications of semiconductor devices, but advances in doping have been hindered by poor understanding of their fundamental properties. Here, we present a theoretical study to resolve the structural, bonding, and elastic properties of Si:X alloys (X = B, Al, and Ga). Density functional theory calculations revealed the structural distortion caused by the substitutional incorporation of group IIIA elements into the Si host lattices, thus allowing an accurate comparison of both their bonding length and lattice parameters with previous experimental values. The change of atomic structure and bonding characteristics when incorporating group IIIA elements was investigated using Bader volume and charge density analyses. Furthermore, elastic properties were studied to understand the elastic behavior and the pseudomorphic growth of Si 1− x B y , Si 1− x Al y , and Si 1− x Ga y on Si, yielding a perpendicular lattice parameter in the growth direction. Finally, from a detailed analysis of the lattice parameters of Si 1− x − y Ge x B y , we found that the tensile strain caused by 8.4 atom% Ge can be compensated by adding 1 atom% B in pseudomorphic Si 1− x − y Ge x B y films. Our findings highlight the effect of doping on material properties and may open up opportunities for the design of doped semiconductor devices based on doping and epitaxial growth results.
Functional analysis of MLH1 mutations linked to hereditary nonpolyposis colon cancer (2002)

Hereditary nonpolyposis colon cancer (HNPCC) is associated with malfunction of postreplicative mismatch repair (MMR). While a majority of HNPCC-associated mutations in the MMR genes MLH1, MSH2, or MSH6 genes cause truncations—and thus loss of function—of the respective polypeptides, little is currently known about the biochemical defects associated with nontruncating mutations. We studied the interactions of six MLH1 variants, carrying either missense mutations or in-frame deletions, with normal PMS2 and tested the functionality of these heterodimers of MLH1 and PMS2 (MutLα) in an in vitro MMR assay. Three MLH1 carboxy-terminal mutations, consisting of internal deletions of exon 16 (amino acids 578–632) or exon 17 (amino acids 633–663), or a missense R659P mutation in exon 17, affected the formation of a functional MutLα. Interestingly, mutations C77R and I107R in the amino-terminal part of MLH1 did not affect its heterodimerization with PMS2. The complexes MLH1(C77R)/PMS2 and MLH1(I107R)/PMS2, however, failed to complement a MMR-deficient extract lacking a functional MutLα. As all these five mutations were identified in typical HNPCC families and produce nonfunctional proteins, they can be considered disease-causing. In contrast, the third amino-terminal mutation S93G did not affect the heterodimerization, and the MLH1(S93G)/PMS2 variant was functional in the in vitro MMR assay, given thus the nature of the HNPCC family in question. Although the missense mutation segregates with the disease, the mean age of onset in the family is unusually high (∼65 years). © 2002 Wiley-Liss, Inc.
Synthesis and an Antiviral Activity Evaluation of Nucleoside 5′-O-(N-acyl) Phosphoramidates (2011)

loss of compound antiviral potency in the CEM/TK(-) cells suggested an eventual conversion of the test compounds to the free nucleosides prior to further phosphorylation to the active 5´-triphosphate metabolite.
SlimFL: Federated Learning With Superposition Coding Over Slimmable Neural Networks (2023)

Federated learning (FL) is a key enabler for efficient communication and computing, leveraging devices’ distributed computing capabilities. However, applying FL in practice is challenging due to the local devices’ heterogeneous energy, wireless channel conditions, and non-independently and identically distributed (non-IID) data distributions. To cope with these issues, this paper proposes a novel learning framework by integrating FL and width-adjustable slimmable neural networks (SNN). Integrating FL with SNNs is challenging due to time-varying channel conditions and data distributions. In addition, existing multi-width SNN training algorithms are sensitive to the data distributions across devices, which makes SNN ill-suited for FL. Motivated by this, we propose a communication and energy-efficient SNN-based FL (named <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SlimFL</i> ) that jointly utilizes <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">superposition coding (SC)</i> for global model aggregation and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">superposition training (ST)</i> for updating local models. By applying SC, SlimFL exchanges the superposition of multiple-width configurations decoded as many times as possible for a given communication throughput. Leveraging ST, SlimFL aligns the forward propagation of different width configurations while avoiding inter-width interference during backpropagation. We formally prove the convergence of SlimFL. The result reveals that SlimFL is not only communication-efficient but also deals with non-IID data distributions and poor channel conditions, which is also corroborated by data-intensive simulations.