gebhart/patrepeval huggingface dataset:
Theonanellasterols and conicasterols from Theonella swinheoi, novel marine natural ligands for human nuclear receptors (2011)

International audience
Viral Protein VP4 Is a Target of Human Antibodies Enhancing Coxsackievirus B4- and B3-Induced Synthesis of Alpha Interferon (2005)

Coxsackievirus B4 (CVB4)-induced production of alpha interferon (IFN-alpha) by peripheral blood mononuclear cells (PBMC) is enhanced in vitro by nonneutralizing anti-CVB4 antibodies from healthy subjects and, to a higher extent, from patients with insulin-dependent diabetes mellitus. In this study, we focused on identification of the viral target of these antibodies in CVB systems. High levels of IFN-alpha were obtained in supernatants of PBMC incubated with CVB4E2 or CVB3 and plasma from healthy subjects and, to a higher extent, from patients. The VP4 capsid proteins dissociated by heating at 56 degrees C from CVB4E2 (VP4(CVB4)) and CVB3 (VP4(CVB3)) but not H antigen preincubated with plasma from healthy subjects or patients inhibited the plasma-dependent enhancement of CVB4E2- and CVB3-induced IFN-alpha synthesis. There was no cross-reaction between VP4(CVB4) and VP4(CVB3) in the inhibiting effect. IFN-alpha levels in culture supernatants showed dose-dependent correlation with anti-VP4 antibodies eluted from plasma specimens using VP4-coated plates. There were higher index values for anti-VP4 antibodies detected by enzyme-linked immunosorbent assay (ELISA) and higher proportions of positive detection in 40 patients than in 40 healthy subjects (80% versus 15% for anti-VP4(CVB4)). There was no relationship between the levels of anti-CVB neutralizing antibodies and the detection of anti-VP4 antibodies by ELISA. The CVB plasma-induced IFN-alpha levels obtained in PBMC cultures in the anti-VP4 antibody-positive groups were significantly higher than those obtained in the anti-VP4 antibody-negative groups regardless of the titers of anti-CVB neutralizing antibodies. These results show that VP4 is the target of antibodies involved in the plasma-dependent enhancement of CVB4E2- and CVB3-induced IFN-alpha synthesis by PBMC.
Predoctoral and Postdoctoral Training Pipeline in Translational Biomaterials Research and Regenerative Medicine (2017)

The translation of biomaterial based and regenerative therapies from the laboratory to patients involves multiple challenges. One of the most pressing challenges is the educational one: to train a cohort of scientists and engineers capable of translating their discoveries from bench to market to clinic. To meet this need, translational training programs are being implemented globally at universities and as partnerships between universities and corporations. In this perspective, we describe two translational NIH T32 graduate and postgraduate training programs that augment the traditional approach to training early stage scientists and engineers. At the graduate level, Boston University developed and implemented the Translational Research in Biomaterials (TRB) predoctoral training program. At the postgraduate level, Rutgers, The State University of New Jersey, developed and implemented the Translational Research in Regenerative Medicine (TRRM) program for postdoctoral training. These programs are motivated by the need for training in translational research in the biomedical field, by young scientists' requests for such training, and by the fundamental challenges facing future discovery and clinical implementation of biomaterial-based technologies. The TRB program immerses trainees in the concept of translating an idea from the research laboratory to the clinic, introduces them to the challenges of such an endeavor, provides discussions with relevant faculty (for example, with businesses, patient care, or clinical trial experience), and educates them in the critical areas required for their future careers. Similarly, the TRRM program emphasizes translational research and the concept of "training without borders," which enables collaborations across several geographically dispersed institutions so as to make regional experts accessible regardless of where they are located physically. Both programs promote interdisciplinary research, expose young scientists and engineers to challenges outside of their specialty, and build interpersonal skills for cross-disciplinary communication. The TRB program focuses on quantitative science and engineering courses, together with translation-based courses in clinical trials and business. The TRRM program focuses on broadening the horizon of its trainees through exposure to a wider network of mentors than traditional postdoctoral programs, and by encouraging trainees to engage in collaborative research across at least two different laboratories. Both programs meet significant public health needs: the skills that trainees acquire are essential in future biomedical careers as they join teams that combine diverse backgrounds to meet a common goal in research, development, and ultimately commercialization.
Decreased physical function and increased pain sensitivity in mice deficient for type IX collagen (2009)

These data describe a Col9a1(-/-) behavioral phenotype characterized by altered gait, increased mechanical sensitivity, and impaired function. These gait and functional differences suggest that Col9a1(-/-) mice select locomotive behaviors that limit joint loads. The nature and magnitude of behavioral changes were largest in male mice, which also had the greatest evidence of knee degeneration. These findings suggest that Col9a1(-/-) mice present behavioral changes consistent with anatomic signs of OA and intervertebral disc degeneration.
Prostasin attenuates inducible nitric oxide synthase expression in lipopolysaccharide-induced urinary bladder inflammation (2006)

Prostasin is a glycosylphosphatidylinositol-anchored serine protease, with epithelial sodium channel activation and tumor invasion suppression activities. We identified the bladder as an expression site of prostasin. In the mouse, prostasin mRNA expression was detected by reverse transcription and real-time polymerase chain reaction in the bladder, and the prostasin protein was localized by immunohistochemistry in the urothelial cells. In mice injected intraperitoneally with bacterial lipopolysaccharide (LPS), bladder prostasin mRNA expression was downregulated, whereas the expression of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), interferon-gamma (IFN-gamma), TNF-alpha, IL-1beta, and IL-6 was upregulated. Viral promoter-driven expression of the human prostasin homolog in the bladder of transgenic mice attenuated the LPS induction of iNOS but did not abolish the induction. LPS induction of COX-2, TNF-alpha, IL-1beta, and IL-6 expression, however, was not reduced by prostasin transgene expression. Liposome-mediated delivery of prostasin-expressing plasmid into mouse bladder produced similar attenuation effects on LPS-induced iNOS expression, while not affecting COX-2 or cytokine induction. Mice receiving plasmid expressing a catalytic mutant prostasin did not manifest the iNOS induction attenuation phenotype. We propose a proteolytic mechanism for prostasin to intercept cytokine signaling during LPS-induced bladder inflammation.
Integration of viral DNA sequences in cells transformed by adenovirus 2 or SV40 (1980)

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonculease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.
ChemInform Abstract: SOLID‐STATE CHEMISTRY, KINETICS, AND SPECTROSCOPY OF 1,2‐DIPHENYLPROPYLIDENE (1983)

Abstract Das aus dem Diazo propan (I) in glasartigen Matrizen wie z.B. Ether oder Ethanol entstehende Carben bildet als Triplett durch inter‐ bzw. intramolekulare Prozesse die Produkte (II) bzw. (III)‐(V), wobei die Produktverteilung außer von der Matrix auch von der Temp. abhängt.
Automatic junk e-mail filtering based on latent content (2004)

The explosion in unsolicited mass electronic mail (junk e-mail) over the past decade has sparked interest in automatic filtering solutions. Traditional techniques tend to rely on header analysis, keyword/keyphrase matching and analogous rule-based predicates, and/or some probabilistic model of text generation. This paper aims instead at deciding whether or not the latent subject matter is consistent with the user's interests. The underlying framework is latent semantic analysis: each e-mail is automatically classified against two semantic anchors, one for legitimate and one for junk messages. Experiments show that this approach is competitive with the state-of-the-art in e-mail classification, and potentially advantageous in real-world applications with high junk-to-legitimate ratios. The resulting technology has been successfully released in August 2002 as part of the e-mail client bundled with the MacOS 10.2 operating system.
Efficacy and safety of pegylated interferon-α2b in moderate COVID-19: a phase 3, randomized, comparator-controlled, open-label study (2021)

PEG IFN-α2b induced early viral clearance, improved the clinical status, and decreased the duration of supplemental oxygen. It provides a viable treatment option and can limit the spread of severe acute respiratory syndrome coronavirus-2.
Patterning of circular structure arrays with interference lithography (2003)

We have developed an interference lithography method that enables the production of circular periodic patterns. The range of accessible patterns includes concentric circular rings, spiral- and spoke-like patterns, and dots positioned periodically on concentric circular tracks. The method is based on the use of transmission diffraction gratings to create circular beams with wave fronts that are not accessible with reflective or refractive optics. Diffraction gratings with equally spaced concentric circles are used to obtain diverging or converging conical waves with radial phase variation and spiral-like gratings are used to obtain waves with the phase varying in both radial and azimuthal directions. We have experimentally demonstrated the method with electron-beam written diffraction gratings, which we illuminated with a coherent laser beam to form the interference patterns. Many different designs are possible that bring two, three, or more beams together to form a desired interference pattern. The technique should in general be useful in applications requiring circular periodic patterns, which may include production of patterned magnetic media, spoke patterns for angular encoders, and photonic crystals with circular symmetry.
Statistical performance analysis of the minimum-norm method (2003)

The authors analyze the performance of the minimum-norm method for estimating the direction of arrival (DOA) of plane waves in white noise in the case of a linear equispaced sensor array. They examine the perturbation in the roots of the polynomial formed in the intermediate step of the minimum-norm method. In particular, asymptotic results for the mean-squared error in the estimates of the direction of arrival are derived. Simple closed-form expressions are obtained for the one- and two-source case to get further insight. Computer simulation results that substantiate the analysis are provided and compared to those obtained for Root-MUSIC. It is shown that the relative performance of the two methods is directly dependent on the ratio of their parameter sensitivities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biomechanical Evaluation of Margin Convergence (2010)

Biomechanical rationale exists for the use of margin convergence in large retracted rotator cuff tears.
Fast tuning of observer-based circadian phase estimator using biometric data (2022)

Circadian rhythms play a vital role in maintaining an individual's well-being, and they have been shown to be the product of the master oscillator in the suprachiasmatic nuclei (SCN) located in the brain. The SCN however, is inaccessible for assessment, so existing standards for circadian phase estimation often focus on the use of indirect measurements as proxies for the circadian state. These methods often suffer from severe delays due to invasive methods of sample collection, making online estimation impossible. In this paper, we propose a linear state observer as an elegant solution for continuous phase estimation. This observer-based filter is used in isolating the frequency components of input biometric signals, which are then taken to be the circadian state. We start the design process by fixing the observer's oscillatory frequency at 24 hours, and then we tune its gains using an evolutionary optimization algorithm to extract the target components from individuals' data. The resulting filter was able to provide phase estimates with an average absolute error within 1.5 hours on all test subjects, given their minute-to-minute actigraphy data collected in ambulatory conditions.
Smart City (2018)

Data drives the smart city. From autonomous vehicles to air quality, from rain water and storm sewer systems to smart electric meters on homes and smart parking meters on the street, cities have big data plans. Along with their technology partners, city leaders are in the process of developing systems, ideally systems that their communities actually want. The tech world has often expressed concern over the great volume of data that will be generated in smart cities. The generated volume does justify that concern but data volume is not what citizens worry about. Our work has addressed the citizens of these communities and they have expressed a different concern,. Working at the intersection of anthropology, policy, and technology, we have been asking how citizens think "their" smart city should handle data.
Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers (2018)

Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains. All three biopolymers are synthesized by dehydration reactions that are catalyzed by molecular motors driven by hydrolysis of phosphorylated nucleosides. All three biopolymers can access specific states that protect against hydrolysis. These protected states are folded, using self-complementary interactions among recurrent folding elements within a given biopolymer, or assembled, in associations between the same or different biopolymer types. Self-association in a hydrolytic environment achieves self-preservation. Heterogeneous association achieves partner-preservation. These universal properties support a model in which life's polymers emerged simultaneously and co-evolved in a common hydrolytic milieu where molecular persistence depended on folding and assembly. We believe that an understanding of the structure, function, and origins of any given type of biopolymer requires the context of other biopolymers.
GPU-Accelerated Asynchronous Error Correction for Mixed Precision Iterative Refinement (2011)

In hardware-aware high performance computing, block- asynchronous iteration and mixed precision iterative refinement are two techniques that are applied to leverage the computing power of SIMD accelerators like GPUs. Although they use a very different approach for this purpose, they share the basic idea of compensating the convergence behaviour of an inferior numerical algorithm by a more efficient usage of the provided computing power. In this paper, we want to analyze the potential of combining both techniques. Therefore, we implement a mixed precision iterative refinement algorithm using a block-asynchronous iteration as an error correction solver, and compare its performance with a pure implementation of a block-asynchronous iteration and an iterative refinement method using double precision for the error correction solver. For matrices from theUniversity of FloridaMatrix collection,we report the convergence behaviour and provide the total solver runtime using different GPU architectures.
De Novo Design, Synthesis, and Biological Evaluation of 3,4-Disubstituted Pyrrolidine Sulfonamides as Potent and Selective Glycine Transporter 1 Competitive Inhibitors (2018)

The development of glycine transporter 1 (GlyT1) inhibitors may offer putative treatments for schizophrenia and other disorders associated with hypofunction of the glutaminergic N-methyl-d-aspartate (NMDA) receptor. Herein, we describe the synthesis and biological evaluation of a series of 3,4-disubstituted pyrrolidine sulfonamides as competitive GlyT1 inhibitors that arose from de novo scaffold design. Relationship of chemical structure to drug-drug interaction (DDI) and bioactivation was mechanistically investigated. Murine studies were strategically incorporated into the screening funnel to provide early assessments of in vivo target occupancy (TO) by ex vivo binding studies. Advanced compounds derived from iterative structure-activity relationship (SAR) studies possessed high potency in ex vivo binding studies and good brain penetration, promising preliminary in vivo efficacy, acceptable preclinical pharmacokinetics, and manageable DDI and bioactivation liabilities.
Optimizing Data Augmentation for Semantic Segmentation on Small-Scale Dataset (2019)

Augment the training data has a significant effect for deep learning on small-scale dataset. For practical semantic segmentation applications, it is a hard work to collect and annotate enough training data for training the deep neural network. In this paper, we focus on which data augmentation (DA) method is better, and what combination of different DA methods can improve the network performance more. Our target application is highland AI-Ranch which is hard to collect many training data. We firstly collect and produce a small-scale open source of sheep segmentation dataset including hundreds images, referred to as SSG dataset. Seven frequently used data augmentation methods are evaluated, including global augmentation (augment for the whole image) such as flipping, and local augmentation (augment only for the region of interest) such as cropping, etc. Especially, a novel image compression global DA method is proposed which can achieve the best augmentation performance in global methods. Furthermore, we explore the performance of the cross-combination data augmentation technique when applying to a small-scale semantic segmentation dataset. As different DA method will cover the different sample distribution, more augmentation fed more good training data and meanwhile more bad training data to the network. Therefore, too much augmentation may pull down the performance sometimes. Experiment results show that the combination of compression, cropping and local shift can achieve the best augmentation performance for our AI-Ranch application, the average coverage mean-IoU improve from 73.3% to 91.3%, even better than the combination of whole augmentation methods.
TESTING OF STATE ROADSIDE SAFETY SYSTEMS. VOLUME I: TECHNICAL REPORT (1996)

The purpose of this study is to crash test and evaluate new or modified roadside safety hardware and, where necessary, redesign the devices to improve their impact performance. The three major areas addressed in this study are the impact performance of bridge railings, transitions from guardrails to bridge railings, and end treatments for guardrails and median barriers. This report presents a summary of the results of various laboratory, pendulum, and crash tests conducted under this study. A total of 36 full-scale crash tests were conducted, covering 12 different types of roadside safety appurtenances. The crash tests were conducted in accordance with guidelines set forth in National Cooperative Highway Research Program (NCHRP) Report 230, NCHRP Report 350, and/or the 1989 American Association of State Highway Transportation Officials (AASHTO) Guide Specifications for Bridge Railings, depending on the specific appurtenance being tested. In addition, laboratory and pendulum tests were conducted on a modified breakaway modified eccentric loader terminal (MELT) post design.\n
Reversible Optical Change of Amorphous Red Phosphorus in Reduced Phosphate Glasses (1985)

Amorphous red phosphorus formed in reduced phosphate glasses was found to show a photodarkening effect by illuminating the glasses with light approximately equivalent to its absorption edge; the optical transmission edge shifts toward longer wavelengths on illumination, and then a distinct deepening of the reddish color is observable visually. The photo‐darkened specimen recovers its original transmission when it is heated at 300° to 350°C. This darkening‐restoring process is confirmed to be reversible by repeated illumination and heating. Transmission measurements over a range of elevated temperatures suggest that this optical characteristic of red phosphorus is unique to its amorphous state.
Using Metabolomics to Identify the Exposure and Functional Biomarkers of Ginger (2022)

Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics has become an important tool to increase our understanding of how diet affects human health. However, public and commercial mass spectral libraries of dietary metabolites are limited, resulting in the greatest challenge in converting mass spectrometry data into biological insights. In this study, we constructed an LC-MS/MS ginger library as an example to demonstrate the importance of dietary libraries for discovering food biomarkers. The functional and exposure biomarkers of ginger were investigated using plasma samples from mice treated with control and ginger extract diets. Our results showed clear discrimination between the metabolome of mice on normal and ginger extract diets. Using the in-house ginger library, we identified 20 ginger metabolites that can be used as exposure biomarkers of ginger. However, without the LC-MS/MS ginger library, none of the ginger metabolites could be accurately identified based on online mass databases. In addition, ginger treatment significantly impacts the endogenous metabolome, especially the purine metabolism and phenylalanine, tyrosine, and tryptophan biosynthesis. Overall, we demonstrated that the construction of LC-MS/MS spectra dietary libraries would enhance the ability to identify potential dietary biomarkers and correlate potential health benefits associated with food consumption.