gebhart/patrepeval huggingface dataset:
Idiopathic pulmonary fibrosis is strongly associated with productive infection by herpesvirus saimiri (2013)

Idiopathic pulmonary fibrosis is a fatal disease without effective therapy or diagnostic test. To investigate a potential role for γ-herpesviruses in this disease, 21 paraffin-embedded lung biopsies from patients diagnosed with idiopathic pulmonary fibrosis and 21 lung biopsies from age-matched controls with pulmonary fibrosis of known etiology were examined for a series of γ-herpesviruses' DNA/RNA and related proteins using in situ hybridization and reverse transcriptase-polymerase chain reaction (RT-PCR)-based methods. We detected four proteins known to be in the genome of several γ-herpesviruses (cyclin D, thymidylate synthase, dihydrofolate reductase, and interleukin-17) that were strongly co-expressed in the regenerating epithelial cells of each of the 21 idiopathic pulmonary fibrosis cases and not in the benign epithelia of the controls. Among the γ-herpesviruses, only herpesvirus saimiri expresses all four of these 'pirated' mammalian proteins. We found herpesvirus saimiri DNA in the regenerating epithelial cells of 21/21 idiopathic pulmonary fibrosis cases using four separate probe sets but not in the 21 controls. RT-PCR showed that the source of the cyclin D RNA in active idiopathic pulmonary fibrosis was herpesvirus saimiri and not human. We cloned and sequenced part of genome corresponding to the DNA polymerase herpesvirus saimiri gene from an idiopathic pulmonary fibrosis sample and it matched 100% with the published viral sequence. These data are consistent with idiopathic pulmonary fibrosis representing herpesvirus saimiri-induced pulmonary fibrosis. Thus, treatment directed against viral proliferation and/or viral-associated proteins may halt disease progression. Further, demonstration of the viral nucleic acids or proteins may help diagnose the disease.
Middleboxes no longer considered harmful (2004)

Intermediate network elements, like network address translators (NATs), firewalls, and transparent caches are now commonplace. The usual reaction in the network architecture community to these so-called middleboxes is a combination of scorn (because they violate important architectural principles) and dismay (because these violations make the Internet less flexible). While we appreciate the harm these architectural violations cause, we also recognize that middleboxes have become an Internet fact of life for important reasons. In order to retain their functionality while eliminating their dangerous side-effects, we propose an extension to the Internet architecture, called the Delegation-Oriented Architecture (DOA), that not only allows, but also facilitates, the deployment of middleboxes. DOA involves two relatively modest changes to the current architecture: (a) a set of references that are carried in packets and serve as persistent host identifiers and (b) a way to resolve these references to delegates chosen by the referenced host. We illustrate this architecture with two examples: network-extension boxes and network filters.
Lumbar Discectomy With Bone-Anchored Annular Closure Device in Patients With Large Annular Defects: One-Year Results (2023)

In this post-market study of bone-anchored ACD in patients with large annular defects, rates of symptomatic reherniation, reoperation, and SAEs were all low. Compared to the RCT, the post-market ACD study demonstrated lower rates of reherniation and/or reoperation and measures of back pain one-year post-surgery.
Extracellular Matrix of Current Biological Scaffolds Promotes the Differentiation Potential of Mesenchymal Stem Cells (2016)

This in vitro study shows the differences between commercially available scaffolds for rotator cuff repairs. Therefore, these results support clinical use depending on the surgical intention and the potential of bMSCs to differentiate into bone, tendon, cartilage, and fat tissue.
Synthesis and Coordination Behaviors of New Double-Sided Porphyrinatoiron(II) Complexes: Effect of the Pocket-Size for Imidazole on Dioxygen Binding (1991)

Abstract The synthesis and characteristic ligation behaviors of new “double-sided porphyrinatoiron(II) complexes” having two pockets of different spacing-size on each side of a ring plane and a larger sized one on both sides of a macrocycle, are described. The equilibrium constants for the imidazole derivatives to the four-coordinated porphyrinatoiron(II)s were increased in proportion to the size of the pocket-space, which is reflected by the ΔH term. The five-coordinated complexes of the porphyrinatoirons, obtained by the addition of 1,2-dimethyl-imidazole (1,2-dmin) in a toluene solution, formed stable and reversible dioxygen adducts at 25°C. The oxygen affinities for the iron(II) complexes increased as the steric bulk on the rear side of the porphyrin plane was relieved. These changes in the oxygen affinity are attributed to the strength of the π-electron donation from the imidazole to the central iron ion.
"High gain microstrip patch antenna array using multiple superstrate layers for DSRC applications," Cape Town, South Africa. (2012)

International audience
Bond Activation in Iron(II)‐Coordinated Polypodal Phosphane Ligands (2010)

Abstract A mononuclear iron(II) complex is readily formed when combining equimolar amounts of iron(II) tetrafluoroborate hexahydrate, the pyridine‐derived triphosphane C 5 H 3 N{2‐[CMe(CH 2 PMe 2 ) 2 ]}{6‐[CMe 2 (CH 2 PMe 2 )]} ( 2 ) and diethylphosphane (Et 2 PH) in methanol at room temperature. The chelate ligand is in fact pentadentate, as one of the methyl groups of the neopentyl‐like sidearm engages in a C–H‐bonded contact (agostic interaction) with the metal centre, in addition to the expected NP 3 coordination. The remaining site of what is a distorted coordination octahedron is occupied by monodentate Et 2 PH. The autoclave reaction of this purple complex with CO (10 bar, ethanol solvent, 65 °C) yields a yellow microcrystalline precipitate, whose analysis reveals a mixture of two products, in an approximate ratio of 40:1. One of the products is the cis ‐dicarbonyl complex[Fe( 2 )(CO) 2 ](BF 4 ) 2 ( 4 ), in which the chelate ligand acts as an NP 3 donor, and the other is the monocarbonyl complex of the tetrapodal pentadentate NP 4 ligand 1 . The latter ligand is formed from 2 by incorporation of an additional PMe 2 donor, in what, in effect, is a metal‐mediated phosphenium group transfer. A mechanism is suggested for this reaction. Other species in the reaction mixture have been identified on the basis of mass spectra, and the full NMR spectroscopic assignment of complex 4 ( 1 H, 31 P, 13 C) is reported.
60 GHz OOK Transmitter in 32 nm DG FinFET technology (2012)

There are several 60 GHz transceiver architectures that have been explored and reported in the past employing the On Off Keying (OOK) Modulation. All of these designs are primarily based on the conventional bulk CMOS architecture. In this paper, we propose a power efficient double gate (DG) MOSFET based OOK Transmitter in 32 nm DG FinFET technology. The proposed novel OOK modulator consists of only two DG-MOSFETs, making the circuit extremely power and area efficient. The LC oscillator can be tuned via back gate bias to vary the amplitude as well as frequency. The phase noise of the oscillator has a value of -133 dBc/Hz which is comparable to LC oscillator in conventional CMOS. The wide band power amplifier (PA) in addition to tunable characteristics also excels in other figures of merit such as gain (6-8 dB) and 3-dB bandwidth (>; 40 GHz) when compared to some recent works.
Low-Temperature-Processible, Transparent, and Air-Operable n-Channel Fluorinated Phenylethylated Naphthalenetetracarboxylic Diimide Semiconductors Applied to Flexible Transistors (2008)

New N,N′-disubstituted-1,4,5,8-naphthalene tetracarboxylic acid diimides (NTCDI) with fluorinated phenylethyl groups were synthesized. In particular, N,N′-bis(2-(pentafluorophenyl)ethyl)-1,4,5,8-naphthalene tetracarboxylic acid diimide (5FPE-NTCDI) showed high electron mobility, more than 0.1 cm2/(V s) in air, even though the film was deposited at room temperature. The correlation of the crystallinity, morphology, and mobility with the substrate temperature during deposition (Tsub) was studied using X-ray diffraction (XRD) and atomic force microscopy (AFM). The films of 5FPE-NTCDI exhibited a “thin film phase”, mixed phase, and crystal bulk phase as Tsub was increased. The mixed phase on an octadecyltrimethoxysilane (OTS)-treated substrate also has high electron mobility due to well connected long fiber-shaped grains. The high mobility at low Tsub has enabled fabrication of flexible transistors on the clear plastic substrate poly(ethylene terephthalate) (PET). The highest mobility for a flexible, transparent transistor was 0.23 cm2/(V s), obtained with low hysteresis.
Shark: SQL and Rich Analytics at Scale (2012)

Shark is a new data analysis system that marries query processing with complex analytics on large clusters. It leverages a novel distributed memory abstraction to provide a unified engine that can run SQL queries and sophisticated analytics functions (e.g., iterative machine learning) at scale, and efficiently recovers from failures mid-query. This allows Shark to run SQL queries up to 100x faster than Apache Hive, and machine learning programs up to 100x faster than Hadoop. Unlike previous systems, Shark shows that it is possible to achieve these speedups while retaining a MapReduce-like execution engine, and the fine-grained fault tolerance properties that such engines provide. It extends such an engine in several ways, including column-oriented in-memory storage and dynamic mid-query replanning, to effectively execute SQL. The result is a system that matches the speedups reported for MPP analytic databases over MapReduce, while offering fault tolerance properties and complex analytics capabilities that they lack.
A Discrete-Time Robust Vehicle Traction Controller Design (1989)

A discrete-time robust vehicle traction control algorithm, which includes anti-skid braking and anti-spin acceleration, is proposed. It is a nonlinear feedback scheme and can be designed via classical digital control theory. From a practical viewpoint, it is easy to tune and to modify to incorporate higher order dynamics, which may be unique in particular hardware setup. The robust controller in this paper provides stable and reliable performance under a vast amount of uncertainties involved in the vehicle/brake system, which are either difficult to measure or costly to obtain. The effectiveness of this new scheme is demonstrated by experiments on anti-skid braking.
ChemInform Abstract: Organocatalytic Asymmetric 5‐Hydroxypyrrolidine Synthesis: A Highly Enantioselective Route to 3‐Substituted Proline Derivatives. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Effects of virtual arm representations on interaction in virtual environments (2017)

Many techniques for visualization and interaction that potentially increase user performance have been studied in the growing field of virtual reality. However, the effects of virtual-arm representations on users' performance and perception in selection tasks have not been studied before. This paper presents the results of a user study of three different representations of the virtual arm: "hand only," "hand+forearm," and "whole arm" which includes the upper arm. In addition to the representations' effects on performance and perception in selection tasks, we investigate how the users' performance changes depending on whether collisions with objects are allowed or not. The relationship between the virtual-arm representations and the senses of agency and ownership are also explored. Overall, we found that the "whole arm" condition performed worst.
EXPERIMENTAL AND NUMERICAL STUDY OF PERFORATED OPEN STEEL SECTIONS, SUBJECT TO COMPRESSION (2007)

The results of several perforated steel thin-walled U-shaped sections subject to compression are presented. The ultimate strength obtained from experimental tests is compared to the one obtained from numerical simulation by finite element method. The experimental tests were carried out according to the standard 10.2.02 of the FEM. The meshing, loading, boundary conditions for supports, geometric and material properties are introduced in the model in conformity with the experimental tests. Tests previously carried out on short columns (l = 250÷400 mm) provided local and distortional buckling modes. The aim of this study is to analyze the behaviour of longer columns (l&amp;gt; 1000 mm,) which provide other critical buckling modes.
Survival of non-Western first generations immigrants with stomach cancer in North East Netherlands (2011)

Although the better survival of first generation non-Western immigrants with stomach cancer remains unexplained, it argues against accessibility problems within the Dutch health care system.
Structural Relationship between Calcite–Gelatine Composites and Biogenic (Human) Otoconia (2011)

Abstract Biogenic otoconia (ear dust) are composite materials of calcite with about 2 wt.‐% proteins showing an average longitudinal size of about 10 μm. The tiny biomineral particles are situated in the inner ear (in the maculae) and act as sensors for gravity and linear acceleration. Our comparative study of calcite–gelatine composites (grown by double diffusion) and human otoconia is based on decalcification experiments, scanning electron microscopy, TEM and X‐ray investigations in order to obtain a complete picture of the 3D structure and morphogenesis of the materials. Otoconia as calcite–protein composites display a cylindrical body with terminal rhombohedral faces intersecting at the pointed ends. As evidenced by TEM on focused ion beam cuts, both the artificial composites and human otoconia show a particular distribution of areas with different volume densities leading to a dumbbell‐shape of the more dense parts consisting of rhombohedral branches (with end faces) and a less ordered, less dense area (the belly region). The peculiar inner architecture of otoconia with its dumbbell‐shaped mass/density distribution is assumed to be necessary for optimal sensing of linear accelerations.
Treatment of only the fractional curve for radiculopathy in adult scoliosis: comparison to lower thoracic and upper thoracic fusions (2019)

Treatment of the FC only is associated with a lower complication rate, shorter hospital stay, and less blood loss than complete scoliosis treatment. However, there is a higher associated rate of extension of the construct to the lower or upper thoracic levels, and patients should be counseled when considering their options.
A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations (2022)

Abstract The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines ( Triticum aestivum , CDC Stanley x CDC Landmark), wheat-barley ( T . aestivum x Hordeum vulgare ) and wheat-wheatgrass ( Triticum durum x Thinopyrum intermedium ) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.
Hybrid Silicon-AlGaInAs Lasers and Optical Modulators (2010)

A number of important breakthroughs in the past decade have focused attention on Si as a photonic platform. We review here recent progress on efforts to make lasers on or in silicon and on silicon optical modulators.
Uncertainty Quantification of Michaelis–Menten Kinetic Rates and Its Application to the Analysis of CRISPR‐Based Diagnostics (2022)

Abstract Michaelis–Menten kinetics is an essential model to rationalize enzyme reactions. The quantification of Michaelis–Menten parameters can be very challenging as it is sensitive to even small experimental errors. We here present a quantification of the uncertainty inherent to the experimental determination of kinetic rate parameters for enzymatic reactions. We study the influence of several sources of uncertainty and bias, including the inner filter effect, pipetting errors, number of points in the Michaelis–Menten curve, and flat‐field correction. Using Monte Carlo simulations and analyses of experimental data, we compute typical uncertainties of , , and catalytic efficiency . As a salient example, we analyze the extraction of such parameters for CRISPR‐Cas systems. CRISPR diagnostics have recently attracted much interest and yet reports of these enzymatic kinetic rates have been highly unreliable and inconsistent.
FRET Measurements Using Multispectral Imaging (2005)

This chapter discusses the use of multispectral imaging in Forster resonance energy transfer (FRET) measurements. Multispectral imaging, also known as hyperspectral imaging, is an important tool for confocal microscopy as it uses the entire spectral response from cells. By acquiring data from multiple wavelengths, the relative contribution of individual molecular components is determined through mathematical analysis. The variations in spectral information are determined by measuring intensity differences at different wavelengths from the same field of view, much like using a spectrometer to measure fluorescence from a cuvette at different wavelengths. Image data sets are analyzed for individual spectral frequencies and pixels with matching spectral information, often showing similar structures, are classified to produce an image. Spectral variations can be used to resolve details in the field of view that cannot be seen in single images taken when all the light from the visible spectrum is used or with single filters.
Porous Polymer and Cell Composites That Self‐Assemble In Situ (2003)

A cell‐laden 3D network is formed upon the addition of avidin to biotinylated polymer particles in the presence of a suspension of cells (see Figure). Applications in tissue engineering and drug delivery are demonstrated; a shape‐retaining biomaterial is formed within minutes of injecting the components into a cavity. The molecular interaction mechanism of self‐assembly differentiates this polymer/cell composite from other injectable systems.
Neurotransmitter-Induced Novel Modulation of a Nonselective Cation Channel by a cAMP-Dependent Mechanism in Rat Pineal Cells (1998)

In the rat, circadian rhythm in melatonin is regulated by noradrenergic and neuropeptide inputs to the pineal via adenosine 3',5'-cyclic monophosphate (cAMP)- and Ca2+-dependent mechanisms. We have identified a large conductance (170 pS), voltage-dependent, nonselective cation channel on rat pineal cells in culture that shows a novel mode of modulation by cAMP. Pituitary adenylate cyclase activating peptide (PACAP), norepinephrine, or 8-Br-cAMP increase channel open probability (Po) with a hyperpolarizing shift in voltage dependence such that the channel becomes active at resting membrane potentials. The increase in Po was accompanied by a change in current rectification properties such that the channel was transformed from being inactive at rest to an inwardly rectifying cation conductance in the presence of agonist, which depolarizes the cell. This channel is calcium insensitive, is blocked by Cs+, and shows a permeability sequence: K+ > Na+ >/= NH+4 > Li+. The data suggest that PACAP and norepinephrine acting through a cAMP-dependent mechanism modulate this nonselective cation channel, resulting in a slow onset depolarization that may be important in regulation of pineal cell excitability.
Multi-mJ ultrafast laser machining with flexible multi-spot patterns (2022)

We demonstrate how high-energy ultrafast laser sources can be used to efficiently drive well-known low-energy micro-machining applications such as surface structuring of opaque and transparent materials. The presented optical concept employs micro-lens arrays, thus standard components, as central beam splitting elements to generate multiple focal spots for parallel processing. Here, a simple and robust opto-mechanical concept enables to control the number of foci ranging from a few ten up to a few hundred spots. Throughput scaling and complete use of the industry-grade ultrafast laser platform is discussed by means of selected micro-machining examples.
Noise spectroscopy of local surface levels in semiconductors (2000)

A method is proposed for extracting parameters of local surface levels in semiconductors from noise spectroscopic data. Analytical expressions have been derived to calculate the energy position of the surface level in the forbidden gap, Ets , capture cross section n , and surface concentration Nts . The results are applied to noise data for a 4H-SiC field-effect transistor with buried p+ -n gate. The parameters of the surface level responsible for the low frequency noise at elevated temperatures are found: Ec- Ets 1.3 eV, n~ 10-14cm2 , Nts 1.5 × 1012cm-2 .
Photoacoustic Tomography Detects Early Vessel Regression and Normalization During Ovarian Tumor Response to the Antiangiogenic Therapy Trebananib (2015)

Photoacoustic tomography is able to evaluate both vessel regression and normalization in response to trebananib. Noninvasive imaging data were supported by modulation of serum markers in vitro and ex vivo histopathology.