gebhart/patrepeval huggingface dataset:
Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations (2016)

We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations, and by taking into account the chromatin's fractal dimension, we derive an analytical expression for the rate of replication initiation. This model predicts with no free parameter the temporal profiles of initiation rate, replication fork density and fraction of replicated DNA, in quantitative agreement with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic nature of replication origins initiation.
Circadian oscillation of nucleotide excision repair in mammalian brain (2020)

The circadian clock regulates the daily rhythms in the physiology and behavior of many organisms, including mice and humans. These cyclical changes at molecular and macroscopic levels affect the organism's response to environmental stimuli such as light and food intake and the toxicity and efficacy of chemo- and radiotherapeutic agents. In this work, we investigated the circadian behavior of the nucleotide excision repair capacity in the mouse cerebrum to gain some insight into the optimal circadian time for favorable therapeutic response with minimal side effects in cancer treatment with chemotherapeutic drugs that produce bulky adducts in DNA. We find that nucleotide excision repair activity in the mouse cortex is highest in the afternoon/evening hours and is at its lowest in the night/early morning hours. The circadian oscillation of the repair capacity is caused at least in part by the circadian oscillation of the xeroderma pigmentosum A DNA damage recognition protein.
Micro-interferometer with high throughput for remote sensing (2009)

We present a novel micro-interferometer implemented using arrays of single-mode planar optical waveguides. The spatial heterodyne waveguide spectrometer offers high resolution and increased optical throughput (etendue) and is compatible with a microsatellite platform. A stationary Fourier technique is employed to reconstruct the input spectrum from the array of outputs. Calibration mitigates waveguide fabrication errors and input illumination non-uniformities and can be readily implemented in the spectral retrieval algorithm. Signal to noise performance is estimated for a remote sensing application using a classical telescope front end with comparison to classical techniques.
The Third Phase of TESS (1991)

The U.S. Navy has developed the Tactical Environmental Support System, third generation, TESS(3), a computer workstation to provide environmental information for the Navy's tactical decision makers. With interfaces to real-time satellite data, to commercial weather teletype, and to naval communication broadcasts, the TESS(3) maintains a dynamic environmental database to support meteorological and oceanographic requirements. This article describes the TESS(3) system.
Viral gene expression, antibody production and immune complex formation in human immunodeficiency virus infection. (1987)

Human immunodeficiency virus (HIV) antigen (HIV-Ag) in polyethylene glycol (PEG) precipitates and supernatants and HIV antibodies (HIV-Ab) to core and envelope antigens were studied in serial serum samples of three HIV-Ab seroconverters and 11 HIV-Ab seropositive men with a mean follow-up time of 16.1 months. In five men not progressing beyond persistent generalized lymphadenopathy (PGL) and two progressing to AIDS, HIV-Ag was detected once in 'free' configuration before HIV-Ab seroconversion and persistently or intermittently 'complexed' thereafter; in six of these men HIV core antibodies were continuously present with a declining level in one. In two men not progressing beyond PGL and five progressing to AIDS HIV-Ag was detected 'complexed' before HIV-Ab seroconversion once and persisted predominantly in 'free' configuration thereafter, while no HIV core antibody was detected in six of these men and a declining level in one. HIV-Ag was detected in 37% (14 out of 38) of HIV core antibody seropositive samples, mostly in 'complexed' form, while HIV-Ag was detected in 86% (43 out of 50) of HIV core antibody seronegative samples, mostly in both 'complexed' and 'free' configuration. Antibodies to HIV envelope antigen were detected in all HIV-Ab seropositive samples. These results indicate that the level of HIV-Ag expression is the primary determinant of detectability of HIV core antigens as well as antibodies. Enhancement of HIV-Ag expression, in a significant number of cases associated with clinical deterioration, appears to lead to clearance of HIV core antibodies in immune complexes, while HIV envelope antibody levels remain relatively unaffected.
Métallurgie pour la microélectronique à support silicium (2020)

La microelectronique repose sur l’assemblage de milliards de transistors sur une meme puce et releve de technologies tres complexes qui se sont developpees depuis les annees 1960. L’augmentation de la vitesse et de la puissance de traitement d’information qui en resulte est a l’origine de la revolution numerique. On oublie souvent que ce developpement repose en grande partie sur la maitrise des materiaux et tout particulierement des metaux et de leurs derives, que ce soit dans l’ingenierie des barrieres de diffusion ou dans celles des interconnexions metalliques. Cet article a pour objectif de rappeler a travers quelques exemples la contribution essentielle de la metallurgie au developpement de ce secteur industriel.
Specific Deposition of Passively Transferred Monoclonal Antibodies against Herpes Simplex Virus Type 1 in Rat Brain Infected with the Virus (1995)

The kinetics of human monoclonal antibody (anti-gB) to herpes simplex virus type 1 (HSV-1) were investigated after intravenous injection of anti-gB into an HSV-1 encephalitis animal model. Immunohistochemical study revealed specific deposition of passively transferred anti-gB in the hippocampus and thalamus of the infected rat brain, and it bound to the same neurons in which HSV-1 antigen was positively stained. To examine the macroscopic distribution of anti-gB in the infected brain, we undertook an 125I-labeled anti-gB injection study, and the same distribution of 125I-labeled anti-gB deposition was observed by brain semimicroautoradiography as in the immunohistochemical study. These results suggest that anti-gB easily permeates the capillary wall and is deposited in the inflammatory site where HSV-1-specific antigen is detectable. The use of radioisotope-labeled anti-gB injection and external brain imaging could lead to a noninvasive diagnostic tool for the early detection of HSV-1 antigen in cases of suspected HSV-1 encephalitis.
PlaTIBART: a Platform for Transactive IoT Blockchain Applications with Repeatable Testing (2017)

With the advent of blockchain-enabled IoT applications, there is an increased need for related software patterns, middleware concepts, and testing practices to ensure adequate quality and productivity. IoT and blockchain each provide different design goals, concepts, and practices that must be integrated, including the distributed actor model and fault tolerance from IoT and transactive information integrity over untrustworthy sources from blockchain. Both IoT and blockchain are emerging technologies and both lack codified patterns and practices for development of applications when combined. This paper describes PlaTIBART, which is a platform for transactive IoT blockchain applications with repeatable testing that combines the Actor pattern (which is a commonly used model of computation in IoT) together with a custom Domain Specific Language (DSL) and test network management tools. We show how PlaTIBART has been applied to develop, test, and analyze fault-tolerant IoT blockchain applications.
5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine as an effective corrosion inhibitor for N80 steel in 3.5% NaCl solution (2014)

The inhibition behavior of 5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine (T4PP) as an environmentbenign corrosion inhibitor for N80 steel was investigated in 3.5 wt.% NaCl solution by means of potentiodynamic polarization, AC impedance, and quantum chemical calculations. The results showed that 5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine can inhibit the corrosion of N80 steel. The adsorption of T4PP on the N80 steel surface obeyed the Langmuir adsorption isotherm. The quantum chemical calculations were applied to elucidate adsorption pattern of inhibitor molecules on steel surface.
Optical tomography with discretized path integral (2015)

We present a framework for optical tomography based on a path integral. Instead of directly solving the radiative transport equations, which have been widely used in optical tomography, we use a path integral that has been developed for rendering participating media based on the volume rendering equation in computer graphics. For a discretized two-dimensional layered grid, we develop an algorithm to estimate the extinction coefficients of each voxel with an interior point method. Numerical simulation results are shown to demonstrate that the proposed method works well.
The syntax and semantics of user-defined modifiers in a transportable natural language processor (1984)

The Layered Domain Class system (LDC) is an experimental natural language processor being developed at Duke University which reached the prototype stage in May of 1983. Its primary goals are (1) to provide English-language retrieval capabilities for structured but unnormalized data files created by the user; (2) to allow very complex semantics, in terms of the information directly available from the physical data file; and (3) to enable users to customize the system to operate with new types of data. In this paper we shall discuss (a) the types of modifiers LDC provides for; (b) how information about the syntax and semantics of modifiers is obtained from users; and (c) how this information is used to process English inputs.
Graph-based code selection techniques for embedded processors (2000)

Code selection is an important task in code generation for programmable processors, where the goal is to find an efficient mapping of machine-independent intermediate code to processor-specific machine instructions. Traditional approaches to code selection are based on tree parsing which enables fast and optimal code selection for intermediate code given as a set of data-flow trees. While this approach is generally useful in compilers for general-purpose processors, it may lead to poor code quality in the case of embedded processors. The reason is that the special architectural features of embedded processors require performing code selection on data-flow graphs, which are a more general representation of intermediate code. In this paper, we present data-flow graph-based code selection techniques for two architectural families of embedded processors: media processors with support for SIMD instructions and fixed-point DSPs with irregular data paths. Both techniques exploit the fact that, in the area of embedded systems, high code quality is a much more important goal than high compilation speed. We demonstrate that certain architectural features can only be utilized by graph-based code selection, while in other cases this approach leads to a significant increase in code quality as compared to tree-based code selection.
The Readmission of Preterm Infants of 30-33 Weeks Gestational Age within 1 Year Following Discharge from Neonatal Intensive Care Unit in Korea (2014)

Purpose: This study was conducted to evaluate the readmission rate of preterm infants of 30-33 weeks gestational age (GA) within 1 year following discharge from the neonatal intensive care unit (NICU).\nMethods: This research was a part of the Retrospective Study to Evaluate Rehospitalization &amp; Health Care Utilization after NICU Discharge in Preterm Infants (≤33 weeks) II (RHANPI II) project conducted by the Committee on Data Collection and Statistical Analysis of the Korean Society of Neonatology. Enrolled infants (n=1,257) of 46 hospitals from April to September 2012, were retrospectively studied.\nResults: The average GA and birth weight of the study population was 32+2±1+1 weeks and 1,785±386 g, respectively. The cumulative readmission rate during the 360 days following discharge from the NICU was 27.3%. The cumulative readmission rate according to GA was 36.4%, 30.1%, 25.9% and 22.7% for infants born at 30, 31, 32 and 33 weeks GA, respectively. The corresponding respiratory readmission rate was 16.3%; this was 59.8% of total readmissions. There was no significant difference in the respiratory readmission rate according to GA group (log-rank test for trend, P-value=0.0558). Of the infants who were readmitted with respiratory problems, 57.0% (n=53/93) tested positive for respiratory syncytial virus (RSV).\nConclusion: The cumulative readmission rate during the 360 days following discharge from the NICU was 27.3%. Respiratory problems were the most common cause of readmission, and RSV was the most common virus associated with respiratory readmission. Additionally, there was no difference in the rate of respiratory readmission according to GA group.
A Re-ranking Model for Dependency Parser with Recursive Convolutional Neural Network (2015)

In this work, we address the problem to model all the nodes (words or phrases) in a dependency tree with the dense representations. We propose a recursive convolutional neural network (RCNN) architecture to capture syntactic and compositional-semantic representations of phrases and words in a dependency tree. Different with the original recursive neural network, we introduce the convolution and pooling layers, which can model a variety of compositions by the feature maps and choose the most informative compositions by the pooling layers. Based on RCNN, we use a discriminative model to re-rank a $k$-best list of candidate dependency parsing trees. The experiments show that RCNN is very effective to improve the state-of-the-art dependency parsing on both English and Chinese datasets.
A 0.13- $\mu \text{m}$ CMOS Dynamically Reconfigurable Charge Pump for Electrostatic MEMS Actuation (2016)

An eight-stage reconfigurable charge pump for microelectromechanical system (MEMS) electrostatic actuation was designed and fabricated in a standard 0.13-μm CMOS technology. The purpose of the circuit is to generate sufficient on-chip voltages that are continually reconfigurable for MEMS actuation. Small 1-pF pumping capacitors are used to reduce the circuit area. Digitally programmable voltage levels can be out putted by varying the number of stages and the clock drive levels dynamically. Reduced power consumption is achieved using a variable frequency clock. The circuit attains a measured maximum output voltage of 10.1 V from a 1.2 V supply. Its nominal clock is set to 50 MHz. The circuit has a compact area of 215 μm × 300 μm and consumes 864 μW at a 50-MHz clock and 252 μW at an 8-MHz clock.
Post-translational regulation of RORγt—A therapeutic target for the modulation of interleukin-17-mediated responses in autoimmune diseases (2016)

Retinoic acid-related orphan receptor gamma t (RORγt) is a nuclear receptor, which is selectively expressed by various lymphocytes. RORγt is critical for the development of secondary and tertiary lymphoid organs, and for the thymic development of the T cell lineage. RORγt has been extensively studied as the master transcription factor of IL-17 expression and Th17 cells, which are strongly associated with various inflammatory and autoimmune conditions. Given its essential role in promoting pro-inflammatory responses, it is not surprising that the expression of RORγt is tightly controlled. By its nature as a nuclear receptor, RORγt activity is also regulated in a ligand-dependent manner, which makes it an attractive drug target. In addition, multiple post-translational mechanisms, including post-translational modifications, such as acetylation and ubiquitinylation, as well as interactions with various co-factors, modulate RORγt function. Here we attempt a comprehensive review of the post-translational regulation of RORγt, an area that holds the potential to transform the way we target the RORγt/IL-17 pathway, by enabling the development of safe and highly selective modulators of RORγt activity.
Reply to Paul and Leibovici (2022)

To theEditor—Mical Paul and Leonard Leibovici raised concern that our recently published study [1] may be harmful to antibiotic stewardship attempts. As they have noted, current guidelines recommend adding macrolide or fluoroquinolone, therapy for atypical pathogens, to beta-lactam in all patients with severe community-acquired pneumonia (CAP) [2]. Their assumption is that all patients who did not receive macrolides were likely to be elderly or critically ill patients from nursing homes, and thus at higher risk for mortality. Notably, in our study, more than 30% of the patients who did not receive macrolides received quinolones (Supplementary Table 1). Although quinolones are given for the same indication to patients with similar characteristics, we did not detect an association of quinolones with survival as observed with the macrolides [1], thereby highlighting the macrolide-specific effect in this patient population. They have also questioned the validity of the study results due to lack of a dose effect of macrolide use. However, the macrolide effect in our cohort was most likely immunomodulatory and such effect may not be related to conventional expected dose effects—that is, longer treatment duration may not be necessarily better.
Multi-channel Optical Switch in Photonic Crystal (2008)

Using coupled cavities it is possible to create a multi-channel slow-light waveguide. We show that this platform can also be the basis for an ultra-compact, multi-channel optical modulator that is ideal for on-chip applications.
Hydrogen generation from formic acid and alcohols using homogeneous catalysts (2009)

This tutorial review describes recent progress in the development of homogeneous catalytic methodology for the direct generation of hydrogen gas from formic acid and alcohols.
Prediction of Protein Helices with a Derivative of the Strip-of-Helix Hydrophobicity Algorithm (1989)

The strip-of-helix hydrophobicity algorithm was devised to identify protein sequences which, when coiled as alpha or 3(10) helices, had one axial, hydrophobic strip and otherwise variably hydrophilic residues. The strip-of-helix hydrophobicity algorithm also ranked such sequences according to an index, the mean hydrophobicity of amino acids in the axial strip. This algorithm well predicted T cell-presented fragments of antigenic proteins. A derivative of this algorithm (the structural helices algorithm (SHA] was tested for the prediction of helices in crystallographically defined proteins. For the SHA, eight amino acid sequences, 2 cycles plus one amino acid in an alpha helix, with strip-of-helix hydrophobicity indices greater than 2.5, were selected with overlapping segments joined. These selections were terminated according to simple "capping rules," which took into account the roles of N-terminal Asn or Pro and C-terminal Gly in the stability of helices. In analyses of 35 crystallographically defined proteins with known alpha and 3(10) helices, the predictions with the SHA overlapped (had overlap indices x greater than or equal to 0.5) with 34% of known helices, touched (had overlap indices 0.5 greater than x greater than 0) or overlapped with 66% of known helices, or were neighboring (came within 6 residues) or touched or overlapped with 82% of known helices. At each level of judging the quality of prediction, the SHA was usually less sensitive (correct predictions/total number of known helices) and more efficient (correct predictions/total number of predictions) than the Chou-Fasman and Garnier-Robson methods. It was simpler in design and calculation. The chemical mechanisms underlying these algorithms appear to apply both to protein folding and to selection of T cell-presented antigenic sequences.
A Phosphorylation Site Regulates Sorting of the Vesicular Acetylcholine Transporter to Dense Core Vesicles (2000)

Vesicular transport proteins package classical neurotransmitters for regulated exocytotic release, and localize to at least two distinct types of secretory vesicles. In PC12 cells, the vesicular acetylcholine transporter (VAChT) localizes preferentially to synaptic-like microvesicles (SLMVs), whereas the closely related vesicular monoamine transporters (VMATs) localize preferentially to large dense core vesicles (LDCVs). VAChT and the VMATs contain COOH-terminal, cytoplasmic dileucine motifs required for internalization from the plasma membrane. We now show that VAChT undergoes regulated phosphorylation by protein kinase C on a serine (Ser-480) five residues upstream of the dileucine motif. Replacement of Ser-480 by glutamate, to mimic the phosphorylation event, increases the localization of VAChT to LDCVs. Conversely, the VMATs contain two glutamates upstream of their dileucine-like motif, and replacement of these residues by alanine conversely reduces sorting to LDCVs. The results provide some of the first information about sequences involved in sorting to LDCVs. Since the location of the transporters determines which vesicles store classical neurotransmitters, a change in VAChT trafficking due to phosphorylation may also influence the mode of transmitter release.
CHRONIC ULTRAVIOLET RADIATION‐INDUCED INCREASE IN SKIN IRON and THE PHOTOPROTECTIVE EFFECT OF TOPICALLY APPLIED IRON CHELATORS 1,* (1991)

In the skin of albino hairless mice (Skh:HR-1) there is a basal level of non-heme iron. Chronic exposure of mice to sub-erythemal doses of ultraviolet (UV) B radiation results in an increased skin level of non-heme iron. The iron increase may be the result of a UVB radiation-induced increase in vascular permeability, which we measured in vivo with the dye marker Evans Blue. We also observed greater non-heme iron in sun-exposed vs non-exposed body sites of human skin, suggesting that similar events occur in man. Iron may have a role in skin photodamage by participating in formation of reactive oxygen species. These species have been implicated in skin photodamage. It is known that iron can contribute to oxygen radical production by acting catalytically in the formation of species such as hydroxyl radical. While the basal level of skin iron may be available for catalysis, the elevated iron content of UV-exposed skin increases the potential for iron-catalyzed radical production. Topical application of certain iron chelators to Skh albino hairless mice dramatically delayed the onset of UVB radiation-induced skin photodamage. Non-chelating analogs provided no significant protection.