gebhart/patrepeval huggingface dataset:
Concerted evolution of duplicated protein-coding genes in Drosophila. (1991)

Very rapid rates of gene conversion were observed between duplicated alpha-amylase-coding sequences in Drosophila melanogaster. This gene conversion process was also seen in the related species Drosophila erecta. Specifically, there is virtual sequence identity between the coding regions of the two genes within each species, while the sequence divergence between species is close to that expected based on their phylogenetic relationship. The flanking, noncoding regions are much more highly diverged and do not appear to be subject to gene conversion. Comparison of amylase sequences between the two species provides a clear demonstration that recurrent gene conversion does indeed lead to the concerted evolution of the gene pair.
Bioclipse: an open source workbench for chemo- and bioinformatics (2007)

Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.
Binuclear Initiators for the Telechelic Synthesis of Elastomeric Polyolefins (2010)

Novel binuclear complexes, 4,4'-bis{[N-(2,6-diisopropylphenyl)-2-(2,6-diisopropylphenylimino)propanamidato-κ(2)-N,O-(trimethylphosphine)nickel(II)]methyl}-1,1'-biphenyl (2a) and 4,4'-bis{[N-(2,6-diisopropylphenyl)-2-(2,6-diisopropylphenylimino)-4-methylpentamidato-κ(2)-N,O-(trimethylphosphine)nickel(II)]methyl}-1,1'-biphenyl (2b), were synthesized by linking two nickel centers through a bis(benzyl) fragment. When activated with nickel bis(1,5-cyclooctadiene) (Ni(COD)(2)), 2a and 2b are capable of polymerizing ethylene in a quasi-living fashion, producing polymers with approximately twice the molecular weights relative to those obtained by using a structurally related mononuclear system. In addition, 2b/Ni(COD)(2) was utilized to synthesize a series of pseudo-triblock polyethylene (PE) macroinitiating copolymers, bearing atom-transfer radical polymerization (ATRP) initiators. Pseudo-pentablock copolymers were also prepared by taking advantage of a pressure-pulsing technique, wherein the ethylene pressure was increased from 100 to 500 psi in order to produce semicrystalline ethylene-rich end-blocks. Copolymers with elastomeric properties were synthesized by grafting n-butyl acrylate from the PE macroinitiators via ATRP. Examination using monotonic and step-cyclic stress-strain tests demonstrates that the materials exhibit large strains at break (1600-2000%) and excellent elastic recoveries at large strains (∼80%). That materials with such desirable properties could not be attained using a mononuclear initiator demonstrates the clear advantage of growing the polymer via a telechelic mechanism.
ChemInform Abstract: Asymmetric Selenomethoxylation of Olefins Involving a Chiral C2 Symmetrical Electrophilic Organoselenium Reagent. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
DataMesh, house-building, and distributed systems technology (1993)

article DataMesh, house-building, and distributed systems technology Share on Author: John Wilkes View Profile Authors Info & Claims ACM SIGOPS Operating Systems ReviewVolume 27Issue 2April 1993 pp 104–108https://doi.org/10.1145/155848.155867Online:01 April 1993Publication History 3citation98DownloadsMetricsTotal Citations3Total Downloads98Last 12 Months7Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Effects of concentration and structure on proteoglycan 4 rheology and interaction with hyaluronan (2015)

The finding that rhPRG4 can increase the viscosity of low concentration HA solutions suggests that supplementation with rhPRG4 may help mitigate the loss in synovial fluid viscosity experienced with decreased HA concentration in osteoarthritis.
Conflicts of Interest--Moving Beyond Disclosure (2001)

Management of conflicts of interest at research universities requires balancing the benefits of faculty entrepreneurial activities with the danger that such activities could distract faculty from their primary mission and threaten free inquiry. The Howard Hughes Medical Institute has developed policies to minimize these conflicts; for example, its scientists may consult for a company or engage in uncompensated scientific collaboration with it, but not both. Implementation of such policies is best accomplished by requiring faculty to obtain pre-approval of all commercial agreements, rather than simply disclosing them after the fact.
Multi-Cell Multi-Beam Prediction Using Auto-Encoder LSTM for mmWave Systems (2022)

Millimeter wave (mmWave) systems rely on communication in narrow beams for directional and spatial multiplexing gains. A key challenge in realizing these systems is beam tracking, particularly in environments with high mobility and blockage. Additionally, in wide-area mmWave cellular systems, user equipment (UE) devices must often simultaneously track signals from multiple cells, since links to individual cells can be unreliable. Models of the channel dynamics across multiple cells and multiple beams are difficult to derive from first principles. In this work, we propose a fully data-driven approach based on a novel auto-encoder integrated long short term memory (LSTM) network, which predicts multiple beams from multiple cells, one time step in the future. The key innovation is to use an auto-encoder pre-processing step, which reduces the dimensionality of the input– the main challenge in multi-cell, multi-beam tracking. The prediction capability of the proposed network is verified and compared to common baseline predictors as well as popular machine learning (ML) based neural network predictors in realistic system-level simulations using a commercial ray-tracer. We observe that predictions from the proposed network, which utilizes auto-encoders for dimensionality reduction, offers significantly better best beam accuracy and lower beam misalignment loss than common baseline approaches. We also discuss outage prediction and proactive beam switching as applications of the multi-cell multi-beam prediction.
Cover Image (2018)

The cover image is based on the Original Article Staphylococcus aureus-derived extracellular vesicles induce monocyte recruitment by activating human dermal microvascular endothelial cells in vitro by Jihye Kim et al, https://doi.org/10.1111/cea.13289.
On-Wafer Electron Beam Detectors by Floating-Gate FinFET Technologies (2021)

A novel electron beam detector made on Si wafers by the advanced CMOS FinFET processes has been proposed in this study. Through electron beam (e-Beam) charging of on-wafer sensing pads, electron dosage can be registered on the detector for follow-up read-out. Without external power or battery connections, this detector has successfully delivered on-chip dosage, intensity, and energy after e-Beam exposure.
Recombination suppression in the vicinity of the breakpoints of a balanced 1:11 autosomal translocation associated with schizophrenia and other forms of major mental illness (1994)

The frequency and extent of pairing failure around human translocations is unknown. We have examined the pattern of recombination around the breakpoints of a balanced autosomal translocation t(1:11)(q43:q21) associated with major mental illness. We have postulated that the association with mental illness in the family has not arisen by chance, but rather that functional disruption of a gene at or near a breakpoint site is responsible. Efforts to isolate the breakpoints for molecular analysis of the region are now at an advanced stage. On the other hand if pairing failure is occurring in the family in the region of the breakpoints, a susceptibility allele for mental illness, acting independently of the translocation, may be located some distance away. DNA was available from seventeen carriers and ten non-translocation carriers, giving a total of thirty-one informative meioses spanning 4 generations. The derivative one and eleven chromosomes were also isolated in somatic cell hybrids and were used to confirm allele phase. We genotyped the pedigree members using nine markers covering 30 cMs on either side of both the chromosome one and eleven breakpoints. No recombinants were found with markers within 3 cMs of either breakpoint. Four markers at an average of 7 cMs more » respectively on either side of the two breakpoints gave a total of three crossovers from thirty-one meioses versus an expected 9, demonstrating (p<0.05) significant recombination suppression. By contrast, examination of chromosome regions at greater distances from the breakpoints showed recombination rates similar to those expected from CEPH data with no evidence of suppression. We conclude that crossover suppression occurs in this family but is restricted to a region within 7 cMs of the breakpoints. « less
Regulation of Lipoprotein Lipase by the Oxysterol Receptors, LXRα and LXRβ (2001)

Lipoprotein lipase (LPL) is a key enzyme for lipoprotein metabolism and is responsible for hydrolysis of triglycerides in circulating lipoproteins, releasing free fatty acids to peripheral tissues. In liver, LPL is also believed to promote uptake of high density lipoprotein (HDL)-cholesterol and thereby facilitate reverse cholesterol transport. In this study we show that the Lpl gene is a direct target of the oxysterol liver X receptor, LXRalpha. Mice fed diets containing high cholesterol or an LXR-selective agonist exhibited a significant increase in LPL expression in the liver and macrophages, but not in other tissues (e.g. adipose and muscle). Studies in Lxr-deficient mice confirmed that this response was dependent more on the presence of LXRalpha than LXRbeta. Analysis of the Lpl gene revealed the presence of a functional DR4 LXR response element in the intronic region between exons 1 and 2. This response element directly binds rexinoid receptor (RXR)/LXR heterodimers and is sufficient for rexinoid- and LXR agonist-induced transcription of the Lpl gene. Together, these studies further distinguish the roles of LXRalpha and beta and support a growing body of evidence that LXRs function as key regulators of lipid metabolism and are anti-atherogenic.
WHO respiratory disease survey in children: a serological study. (1967)

This paper is a report on the first (serological) phase of a study organized by WHO in collaboration with the WHO International Reference Centre for Respiratory Virus Diseases other than Influenza in Bethesda, Md., USA, to define the viral etiology of severe respiratory infections in children, particularly in tropical areas. Paired sera from 528 children up to 5 years old admitted to hospital with severe respiratory illness of probable viral etiology were collected in 10 countries and sent frozen to the International Reference Centre, where standard complement-fixation tests were made for the following agents: parainfluenza virus types 1, 2 and 3, influenza virus types A and B, adenoviruses, respiratory syncytial virus, Mycoplasma pneumoniae, Coxiella burneti and psittacosis-ornithosis.Some 41% of paired sera showed rising antibody titres for one or more of these agents, multiple infections being observed in 8%. In most of the countries the pattern of infection was similar. RS virus was the most important respiratory tract pathogen of early life, particularly in the first year of life and in cases of bronchiolitis and pneumonia; the parainfluenza viruses were next in importance, particularly in cases of croup, but, in contra-distinction to RS virus infections, they were commoner in older children. Influenza, adenoviruses, and M. pneumoniae were of moderate importance, and C. burneti and the psittacosis-ornithosis agents were relatively rare. This pattern is similar to that which has been observed in temperate climates.
The Characteristics and Risk Factors of Very Asymmetric Keratoconus (2021)

The patient-reported frequency of eye rubbing, allergy, and atopy were similar between KC and very asymmetric KC. Furthermore, we found no association between hand dominance and KC laterality.
Identification of Fractional Differential Models for Lithium-ion Polymer Battery Dynamics (2017)

This paper presents a non-integer order (fractional) derivative model for modeling lithium-ion (Li-ion) battery dynamics in which direct continuous-time (CT) model identification methods are used to estimate the battery model parameters. In particular, the CT least squares-based state-variable filter (lssvf) identification method is extended to be used in fractional differential model identification of a battery system. The model performance and validation accuracy are evaluated on the basis of experimental data of a Li-ion polymer (LiPo) battery. It is shown how the proposed lssvf identification method can accurately capture the fractional order battery dynamics and exhibit better performance than integer order differential models.
Time-resolved particle image velocimetry measurements with wall shear stress and uncertainty quantification for the FDA benchmark nozzle model (2014)

We present validation of benchmark experimental data for computational fluid dynamics (CFD) analyses of medical devices using advanced Particle Image Velocimetry (PIV) processing and post-processing techniques. This work is an extension of a previous FDA-sponsored multi-laboratory study, which used a medical device mimicking geometry referred to as the FDA benchmark nozzle model. Time-resolved PIV analysis was performed in five overlapping regions of the model for Reynolds numbers in the nozzle throat of 500, 2,000, 5,000, and 8,000. Images included a two-fold increase in spatial resolution in comparison to the previous study. Data was processed using ensemble correlation, dynamic range enhancement, and phase correlations to increase signal-to-noise ratios and measurement accuracy, and to resolve flow regions with large velocity ranges and gradients, which is typical of many blood-contacting medical devices. Parameters relevant to device safety, including shear stress at the wall and in bulk flow, were computed using radial basis functions (RBF) to improve accuracy. In-field spatially resolved pressure distributions, Reynolds stresses and energy dissipation rates were computed from PIV measurements. Velocity measurement uncertainty was estimated directly from the PIV correlation plane, and uncertainty analysis for wall shear stress at each measurement location was performed using a Monte Carlo model. (truncated abstract)
Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid–Base Catalysis (2021)

Acid-base catalysis, which involves one or more proton transfer reactions, is a chemical mechanism commonly employed by many enzymes. The molecular basis for catalysis is often derived from structures determined at the optimal pH for enzyme activity. However, direct observation of protons from experimental structures is quite difficult; thus, a complete mechanistic description for most enzymes remains lacking. Dihydrofolate reductase (DHFR) exemplifies general acid-base catalysis, requiring hydride transfer and protonation of its substrate, DHF, to form the product, tetrahydrofolate (THF). Previous X-ray and neutron crystal structures coupled with theoretical calculations have proposed that solvent mediates the protonation step. However, visualization of a proton transfer has been elusive. Based on a 2.1 Å resolution neutron structure of a pseudo-Michaelis complex of <i>E. coli</i> DHFR determined at acidic pH, we report the direct observation of the catalytic proton and its parent solvent molecule. Comparison of X-ray and neutron structures elucidated at acidic and neutral pH reveals dampened dynamics at acidic pH, even for the regulatory Met20 loop. Guided by the structures and calculations, we propose a mechanism where dynamics are crucial for solvent entry and protonation of substrate. This mechanism invokes the release of a sole proton from a hydronium (H<sub>3</sub>O<sup>+</sup>) ion, its pathway through a narrow channel that sterically hinders the passage of water, and the ultimate protonation of DHF at the N5 atom.
Gouverner les conduites (2007)

L’experience blairiste du pouvoir : entretien avec Florence Faucher-King et Patrick Le Gales.
Retinal Nerve Fiber Layer Thinning in Alzheimer’s Disease (2016)

Retinal nerve fiber layer (RNFL) thickness, ganglion cell layer (GCL) thickness, and macular volume (MV) utilizing spectral domain optical coherence tomography (SD-OCT) were compared among patients with Alzheimer's disease (AD) dementia, non-Alzheimer's disease (non-AD) dementia, amnestic mild cognitive impairment (aMCI), Parkinson's disease (PD), and age- and sex-matched controls in a cross-sectional cohort study. A total of 116 participants were diagnosed and evaluated (21 AD, 20 aMCI, 20 non-AD, 20 PD, and 34 controls) after comprehensive neurological, neuropsychology, and magnetic resonance imaging (MRI) volumetric evaluations. Retinal nerve fiber layer thickness, GCL thickness, and MV were measured. Analysis of variance models were used to compare groups on MRI volumetric measures, cognitive test results, and SD-OCT measures. Associations between SD-OCT measures and other measures were performed using mixed-effect models. Spectral domain optical coherence tomography analysis of retinal markers, including RNFL thickness, GCL thickness, and MV, did not differ between amnestic MCI, AD dementia, PD, non-AD, dementia, and age- and sex-matched controls in a well-characterized patient cohort.
Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir (2020)

The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that, contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. By selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies on HIV persistence.
Functional Fault Modeling of a Cryogenic System for Real-Time Fault Detection and Isolation (2010)

The purpose of this paper is to present the model development process used to create a Functional Fault Model (FFM) of a liquid hydrogen (L H2) system that will be used for realtime fault isolation in a Fault Detection, Isolation and Recover (FDIR) system. The paper explains th e steps in the model development process and the data products required at each step, including examples of how the steps were performed fo r the LH2 system. It also shows the relationship between the FDIR req uirements and steps in the model development process. The paper concl udes with a description of a demonstration of the LH2 model developed using the process and future steps for integrating the model in a live operational environment.
Criteria for dynamics of one-dimensional continuous time Markov chains with applications (2020)

This paper studies the dynamics of continuous time Markov chains with possibly unbounded jump sizes on the non-negative integers with polynomial transition rate functions. Such stochastic processes are abundant in applications, in particular in biology. We provide threshold criteria in terms of easily computable parameters for various dynamical properties such as explosivity, recurrence, transience, certain absorption, positive/null recurrence, implosivity, and existence and non-existence of moments of hitting times. In particular, simple sufficient conditions for exponential ergodicity of stationary distributions and quasi-stationary distributions are obtained, and the few gap cases are identified and well-illustrated by examples. Subtle differences in conditions for different dynamical properties are revealed in terms of examples. Finally, we apply our results to stochastic reaction networks, an extended class of branching processes, a general bursty single-cell stochastic gene expression model, and population processes, none of which are birth-death processes.
Pharmacokinetics of (-)-β-D-2,6-Diaminopurine Dioxolane and its Metabolite, Dioxolane Guanosine, in Woodchucks (Marmota Monax) (1996)

The woodchuck ( Marmota monax) is a useful animal model for evaluating the in-vivo efficacy of antiviral agents against hepatitis B viral infection (HBV). The pharmacokinetics of a newly synthesized antiviral agent (-)-β-D-2,6-diaminopurine dioxolane (DAPD) in woodchucks is reported. DAPD is a nucleoside analogue, having potent and selective activity against human immunodeficiency virus and HBV in vitro. DAPD is susceptible to deamination in vivo by the ubiquitously present enzyme adenosine deaminase yielding the active metabolite dioxolane guanosine (DXG). The pharmacokinetics of DAPD and DXG were characterized following intravenous (i.v.) and oral (p.o.) administration of 20 mg kg −1 of DAPD to woodchucks. Plasma and urine samples were collected, and nucleoside concentrations were determined by HPLC. Following intravenous administration, the half-life of DAPD averaged 6.7 ± 4.3 h, and that of DXG averaged 17.6 ± 14.5 h. The mean total clearance and steady state volume of distribution of DAPD were 0.33 ± 0.14 L h kg −1 and 1.76 ± 0.65 L kg −1 , respectively. The oral bioavailability of DAPD ranged from 3.7-8.2%; however, the apparent availability of DXG following oral administration of DAPD was 10.5-53%.