gebhart/patrepeval huggingface dataset:
One dose of SARS-CoV-2 vaccine exponentially increases antibodies in individuals who have recovered from symptomatic COVID-19 (2021)

BACKGROUNDThe COVID-19 vaccines currently in use require 2 doses to achieve optimal protection. Currently, there is no indication as to whether individuals who have been exposed to SARS-CoV-2 should be vaccinated, or whether they should receive 1 or 2 vaccine doses.METHODSWe tested the antibody response developed after administration of the Pfizer/BioNTech vaccine in 124 health care professionals, of whom 57 had a previous history of SARS-CoV-2 exposure with or without symptoms.RESULTSPostvaccine antibodies in SARS-CoV-2-exposed individuals increased exponentially within 5 to 18 days after the first dose compared to naive subjects (P < 0.0001). In a multivariate linear regression (LR) model we showed that the antibody response depended on the IgG prevaccine titer and on the exposure to SARS-CoV-2. In symptomatic SARS-CoV-2-exposed individuals, IgG reached a plateau after the second dose, and those who voluntarily refrained from receiving the second dose (n = 7) retained their antibody response. Gastrointestinal symptoms, muscle pain, and fever markedly positively correlated with increased IgG responses. By contrast, all asymptomatic/paucisymptomatic and unexposed individuals showed an important increase after the second dose.CONCLUSIONOne vaccine dose is sufficient in symptomatic SARS-CoV-2-exposed subjects to reach a high titer of antibodies, suggesting no need for a second dose, particularly in light of current vaccine shortage.TRIAL REGISTRATIONClinicalTrials.gov NCT04387929.FUNDINGDolce & Gabbana and the Italian Ministry of Health (Ricerca corrente).
Numerical and Experimental Time-Reversal of Acoustic Waves in Random Media (2001)

In classical mechanics, a time-reversal experiment with a large number of particles is impossible. Because of the high sensitivity to initial conditions, one would need to resolve the positions and velocities of each particle with infinite accuracy. Thus, it would require an infinite amount of information, which is of course out of reach. In wave physics however, the amount of information required to describe a wave field is limited and depends on the shortest wavelength of the field. Thus we can propose an acoustic equivalent of the experiment we mentioned above. We start with a coherent transient pulse, let it propagate through a disordered highly scattering medium, then record the scattered field and time-reverse it: surprisingly, it travels back to its initial source, which is not predictable by usual theories for random media. Indeed, to study waves propagation in disordered media theoreticians, who find it difficult to deal with one realization of disorder, use concepts defined as an average over the realizations, which naturally leads to the diffusion approximation. But the corresponding equation is not time-reversal invariant and thus fails in describing our experiment. Then, to understand our experimental results and try to predict new ones, we have developed a finite elements simulation based on the real microscopic time-invariant equation of propagation. The experimental and numerical results are found to be in very good agreement.
Description of the Single Note Database SNDB (2018)

Big and well-tagged databases are needed for many tasks in music information retrieval. Therefore, we created the single note database (SNDB) containing over 30000 single notes of 11 orchestra instruments by extracting and combining material of well-established databases. The ground truth was manually checked, corrected and augmented. The result is a large and easy to handle database providing a reliable ground truth with a high variety for each class. Because of well-known original databases, new scientific results can be easily compared to earlier approaches. Here we show the benefit of the SNDB in a simple example. Moreover, we depict how the SNDB was created in the first place and how it can be conveniently reproduced from the original databases.
Monocytes Elicit a Neutrophil-Independent Th1/Th17 Response Upon Immunization With a Mincle-Dependent Glycolipid Adjuvant (2022)

Successful subunit vaccination with recombinant proteins requires adjuvants. The glycolipid trehalose-dibehenate (TDB), a synthetic analog of the mycobacterial cord factor, potently induces Th1 and Th17 immune responses and is a candidate adjuvant for human immunization. TDB binds to the C-type lectin receptor Mincle and triggers Syk-Card9-dependent APC activation. In addition, interleukin (IL)-1 receptor/MyD88-dependent signaling is required for TDB adjuvanticity. The role of different innate immune cell types in adjuvant-stimulated Th1/Th17 responses is not well characterized. We investigated cell recruitment to the site of injection (SOI) and to the draining lymph nodes (dLNs) after immunization with the TDB containing adjuvant CAF01 in a protein-based vaccine. Recruitment of monocytes and neutrophils to the SOI and the dramatic increase in lymph node cellularity was partially dependent on both Mincle and MyD88. Despite their large numbers at the SOI, neutrophils were dispensable for the induction of Th1/Th17 responses. In contrast, CCR2-dependent monocyte recruitment was essential for the induction of Th1/Th17 cells. Transport of adjuvant to the dLN did not require Mincle, MyD88, or CCR2. Together, adjuvanticity conferred by monocytes can be separated at the cellular level from potential tissue damage by neutrophils.
Infrared optical fibers for sensors (2013)

At NRL, we are involved in the research and development of specialty infrared optical fibers, glasses, ceramics, and thin films. We have state-of-the-art facilities for making high purity chemicals and unique optical materials of high quality, which are being exploited in optical devices and systems for Navy and DoD applications. One of the core scientific areas that we have pioneered is based primarily on infrared (IR) transmitting glasses and fibers. The IR transmitting glasses are based on chalcogenide materials (S, Se, Te, and their alloys and compounds). One of our major accomplishments has been the purification of these elements and materials to levels well beyond the previous state-of-the-art. This has enabled us to reduce the absorption losses in these materials for both the mid-wave and long wave IR spectral regions. In addition to their use in bulk optics such as windows, we have developed these materials for optical fibers and their applications. The fibers and their applications can be split into two main groups, namely passive and active. In the case of passive fibers, they merely act as a light pipe, transferring infrared energy from one location to another. In the case of active fibers, they actually change the wavelength of light exiting the fiber. Some examples of both are highlighted below.
Inhibitors of the bone morphogenetic protein (BMP) signaling pathway: a patent review (2008-2015) (2016)

The bone morphogenetic protein (BMP) is a critical signaling pathway and plays a diverse role in embryonic pattern formation and is implicated in a variety of disease processes, including anemia, bone formation, atherosclerosis, skin diseases, and cancers, among others. Areas covered: This review covers small molecule inhibitors/antagonists of BMP in patent applications between 2008 - 2015, along with brief synopses of the disclosed inhibitors in the primary literature. Expert opinion: The development of potent and selective BMP inhibitors is ongoing with most of the work centered around improving the selectivity and pharmacokinetic profile. Early work was for the treatment of the rare and neglected disease, fibrodysplasia ossificans progressiva (FOP). Recently, however, there has been increased interest in their use in a number of other diseases such as cancer, atherosclerosis, and anemia of chronic disease, to name a few. Although the primary participants in the early work were from academic laboratories, recently a significant surge from the pharmaceutical industry has elevated the interest in the development of BMP inhibitors for a wide-range of therapeutic indications. Due to this, expect a number of new approaches such as repurposing of other kinase inhibitors to be brought into clinical trials in the near future.
30-km-long optical fiber link at 1397 nm for frequency comparison between distant strontium optical lattice clocks (2014)

We demonstrate a 30-km-long optical fiber link for frequency comparison between two strontium optical lattice clocks being developed at RIKEN and the University of Tokyo. We use a transfer laser at 1397 nm, which is twice the wavelength of the clock transition of strontium clocks. The link stability is estimated to be 1 × 10 −17 for an averaging time of τ = 1 s, which is in good agreement with the theoretical limit calculated from the fiber noise spectrum. We discuss a remote clock comparison with a stability of 1 × 10 −17 (τ/s) −1/2 by synchronously operating two distant clocks.
Targeting TRAF6 E3 ligase activity with a small-molecule inhibitor combats autoimmunity (2018)

Constitutive NF-κB signaling represents a hallmark of chronic inflammation and autoimmune diseases. The E3 ligase TNF receptor-associated factor 6 (TRAF6) acts as a key regulator bridging innate immunity, pro-inflammatory cytokines, and antigen receptors to the canonical NF-κB pathway. Structural analysis and point mutations have unraveled the essential role of TRAF6 binding to the E2-conjugating enzyme ubiquitin-conjugating enzyme E2 N (Ubc13 or UBE2N) to generate Lys<sup>63</sup>-linked ubiquitin chains for inflammatory and immune signal propagation. Genetic mutations disrupting TRAF6-Ubc13 binding have been shown to reduce TRAF6 activity and, consequently, NF-κB activation. However, to date, no small-molecule modulator is available to inhibit the TRAF6-Ubc13 interaction and thereby counteract NF-κB signaling and associated diseases. Here, using a high-throughput small-molecule screening approach, we discovered an inhibitor of the TRAF6-Ubc13 interaction that reduces TRAF6-Ubc13 activity both <i>in vitro</i> and in cells. We found that this compound, C25-140, impedes NF-κB activation in various immune and inflammatory signaling pathways also in primary human and murine cells. Importantly, C25-140 ameliorated inflammation and improved disease outcomes of autoimmune psoriasis and rheumatoid arthritis in preclinical <i>in vivo</i> mouse models. Hence, the first-in-class TRAF6-Ubc13 inhibitor C25-140 expands the toolbox for studying the impact of the ubiquitin system on immune signaling and underscores the importance of TRAF6 E3 ligase activity in psoriasis and rheumatoid arthritis. We propose that inhibition of TRAF6 activity by small molecules represents a promising novel strategy for targeting autoimmune and chronic inflammatory diseases.
Bioluminescence Detection Using a Novel MEMS Modulation Technique (2006)

A novel modulation microelectromechanical systems (MEMS) technique is introduced to overcome the low-frequency (flicker) noise of photodiodes. The transmissive shutter is placed as an add-on device between an optical source and a photodiode, and is implemented as a method to enhance the signal-to-noise ratio, adapted for the detection of low-intensity bioluminescence. The detection of the signal below the noise level of photodetector is demonstrated by implementing a lock-in amplifier that registers the modulated signal at four times the frequency of the electrical excitation signal of the modulator. This work represents the first reported attempt to use a MEMS modulation technique for the detection of low-intensity signals.
An Image Is Worth More than a Thousand Favorites: Surfacing the Hidden Beauty of Flickr Pictures (2021)

The dynamics of attention in social media tend to obey power laws. Attention concentrates on a relatively small number of popular items and neglecting the vast majority of content produced by the crowd. Although popularity can be an indication of the perceived value of an item within its community, previous research has hinted to the fact that popularity is distinct from intrinsic quality. As a result, content with low visibility but high quality lurks in the tail of the popularity distribution. This phenomenon can be particularly evident in the case of photo-sharing communities, where valuable photographers who are not highly engaged in online social interactions contribute with high-quality pictures that remain unseen. We propose to use a computer vision method to surface beautiful pictures from the immense pool of near-zero-popularity items, and we test it on a large dataset of creative-commons photos on Flickr. By gathering a large crowdsourced ground truth of aesthetics scores for Flickr images, we show that our method retrieves photos whose median perceived beauty score is equal to the most popular ones, and whose average is lower by only 1.5%.
Versatile and Robust Method for Antibody Conjugation to Nanoparticles with High Targeting Efficiency (2021)

The application of antibodies in nanomedicine is now standard practice in research since it represents an innovative approach to deliver chemotherapy agents selectively to tumors. The variety of targets or markers that are overexpressed in different types of cancers results in a high demand for antibody conjugated-nanoparticles, which are versatile and easily customizable. Considering up-scaling, the synthesis of antibody-conjugated nanoparticles should be simple and highly reproducible. Here, we developed a facile coating strategy to produce antibody-conjugated nanoparticles using 'click chemistry' and further evaluated their selectivity towards cancer cells expressing different markers. Our approach was consistently repeated for the conjugation of antibodies against CD44 and EGFR, which are prominent cancer cell markers. The functionalized particles presented excellent cell specificity towards CD44 and EGFR overexpressing cells, respectively. Our results indicated that the developed coating method is reproducible, versatile, and non-toxic, and can be used for particle functionalization with different antibodies. This grafting strategy can be applied to a wide range of nanoparticles and will contribute to the development of future targeted drug delivery systems.
Utility of meibography in the evaluation of meibomian glands morphology in normal and diseased eyelids (2010)

The newly designed transilluminator permitted the examination of both upper and lower eye lid meibomian glands with minimal discomfort. Evaluating the anatomical changes involving meibomian glands with meibography may help increase our understanding of the meibomian gland-related diseases, monitor the effects of treatment, and provide helpful information for patient education.
Regulation of synoviocyte proliferation, apoptosis, and invasion by the p53 tumor suppressor gene. (1998)

Recent studies show that 1) the p53 tumor suppressor protein is overexpressed by rheumatoid arthritis (RA) synovium and fibroblast-like synoviocytes (FLS) and 2) somatic mutations previously identified in human tumors are present in RA synovium and FLS. We have hypothesized that abnormalities in p53 can contribute to chronic destructive RA synovitis. To understand the functional consequences of p53 abnormalities in FLS, RA and normal FLS expressing wild-type p53 were transduced with a retroviral vector encoding the human papilloma virus 18 E6 gene, which inactivates endogenous p53 protein. Three RA and one normal FLS lines were infected with recombinant retrovirus encoding the neomycin resistance gene (neo) or E6+neo. FLS proliferation, apoptosis, and invasion was studied in E6, neo, and uninfected parental strains (PS). The growth rate for E6 was significantly increased with a sixfold increase in cell number after 7 days compared with a twofold to threefold increase in neo and PS. When FLS were treated with cytokines, proliferative response of E6, neo, and PS to interleukin-1 and transforming growth factor-beta were similar. However, response to platelet-derived growth factor was significantly greater in E6 FLS compared with neo or PS. Apoptosis was studied by incubating FLS with sodium nitroprusside as a source of nitric oxide or hydrogen peroxide for 8 hours and examining DNA fragmentation and E6 cells were significantly less susceptible to cell death. In addition, E6 FLS were more invasive into cartilage extracts than neo or PS using an in vitro cell invasion assay. These data suggest that p53 is a critical regulator of FLS proliferation, apoptosis, and invasiveness. Abnormalities of p53 function might contribute to synovial lining expansion and joint destruction in RA.
How Many Samples are Needed to Learn a Convolutional Neural Network (2018)

It is widely believed that the practical success of Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) owes to the fact that CNNs and RNNs use a more compact parametric representation than their Fully-Connected Neural Network (FNN) counterparts, and consequently require fewer training examples to accurately estimate their parameters. We initiate the study of rigorously characterizing the sample-complexity of estimating CNNs and RNNs. We show that the sample-complexity to learn CNNs and RNNs scales linearly with their intrinsic dimension and this sample-complexity is much smaller than for their FNN counterparts. For both CNNs and RNNs, we also present lower bounds showing our sample complexities are tight up to logarithmic factors. Our main technical tools for deriving these results are a localized empirical process analysis and a new technical lemma characterizing the convolutional and recurrent structure. We believe that these tools may inspire further developments in understanding CNNs and RNNs.
Mathematical Model to Characterize Internal Filtration (2005)

Convective-diffusive dialysis techniques have recently gained considerable favor. Indeed, convective fluxes through dialyzer membranes have been demonstrated to play a role in enhancing the clearance of middle-molecular-weight solutes. An interesting opportunity is given by exploiting the internal filtration (IF)/back filtration mechanism that occurs spontaneously in high-flux dialyzers, but is difficult to quantify. In view of overcoming this drawback, a semi-empirical, lumped-parameter mathematical model for characterization of IF phenomena was developed. The model considers a dialyzer as composed by N adjacent axial blocks. For each block, hydrodynamics in the blood and dialysate compartments are determined considering hydraulic resistance and calculating local filtration. Blood viscosity and oncotic pressure are calculated locally based on hematocrit and protein concentration. Resistance parameters were determined experimentally for the BS-UL (Toray Industries Inc., Tokyo, Japan) dialyzers. The set of equations describing the model, implemented into a software program, is solved using a numerical method. Simulations allow highlighting the role of device-, treatment- and patient-dependent parameters in affecting IF. Provided an extensive validation is carried out, the use of a mathematical model could be the key to make IF more understandable and its use reliable in clinical practice.
In the Days of Beginning Global Warming: Cool Is Beautiful (2007)

When blood is withdrawn from a human being, this is the beginning of hypothermia – provided this is not done at ambient temperatures at or above 37 °C (i.e. 98.6 °F, 370 K). The same holds for any tissue or organ removed at room temperature. This removal is already the start of a sometimes not very well controlled cooling process; it is the first step towards hypothermia, which is characterized by a lowering of biochemical and biophysical reaction rates. For biochemical reactions, this relationship is well described by the Arrhenius law, which can be written in various forms, one of which is
Microglial Modulation as a Target for Chronic Pain: From the Bench to the Bedside and Back (2019)

With a widespread opioid epidemic and profound biopsychosocial implications, chronic pain is a multifaceted public health issue requiring urgent attention. The treatment of chronic pain is particularly important to anesthesiologists given our unique role as perioperative physicians and pain medicine specialists. The present review details the recent shift from a neuronal theory of chronic pain to one that includes complex neuron-glia interactions. In particular, we highlight microglia, the myeloid-lineage cells of the central nervous system, as initiators of a postinjury neuroimmune response that contributes to the acute to chronic pain transition. We discuss ever-advancing preclinical studies, wherein significant success has been made through pharmacologic and genetic modulation of microglia, and we emphasize where these approaches have made the transition to the clinical realm. Furthermore, we highlight the most current, novel efforts to visualize glial activation in vivo using positron emission tomography and improve the diagnosis of chronic pain through radiotracer binding of specific targets, like the 18 kDa translocator protein in microglia and myeloid-lineage cells. Our rapidly advancing knowledge about microglia and their involvement in pain suggests that the era of glial-targeted therapeutics is just beginning so long as we refocus our attention on optimizing preclinical studies using a clinically informed approach, before translation.
Outphasing Energy Recovery Amplifier With Resistance Compression for Improved Efficiency (2009)

We describe a new outphasing energy recovery amplifier (OPERA) which replaces the isolation resistor in the conventional matched combiner with a resistance-compressed rectifier for improved efficiency. The rectifier recovers the power normally wasted in the isolation resistor back to the power supply, while a resistance compression network (RCN) reduces the impedance variation of the rectifier as the output power varies. Because the combiner requires a fixed resistance at the isolation port to ensure matching and isolation between the two outphased power amplifiers (PAs), the RCN serves to maintain high linearity as well as high efficiency in the switching-mode PAs. For demonstration, a prototype OPERA system is designed and implemented with discrete components at an operating frequency of 48 MHz, delivering 20.8 W peak power with 82.9% PAE. The measurement results show an efficiency improvement from 17.9% to 42.0% for a 50-kHz 16-QAM signal with a peak-to-average power ratio of 6.5 dB.
Reliability Challenges Related to TSV Integration and 3-D Stacking (2015)

This article identifies four major reliability challenges related to TSV-based 3-D integrated circuits and their solutions that are being developed at imec.