gebhart/patrepeval huggingface dataset:
Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic (2020)

Understanding how genes and experience work in concert to generate phenotypic variability will provide a better understanding of individuality. Here, we considered this in the main olfactory epithelium, a chemosensory structure with over a thousand distinct cell types in mice. We identified a subpopulation of olfactory sensory neurons, defined by receptor expression, whose abundances were sexually dimorphic. This subpopulation of olfactory sensory neurons was over-represented in sex-separated mice and robustly responsive to sex-specific semiochemicals. Sex-combined housing led to an attenuation of the dimorphic representations. Single-cell sequencing analysis revealed an axis of activity-dependent gene expression amongst a subset of the dimorphic OSN populations. Finally, the pro-apoptotic gene <i>Bax</i>was necessary to generate the dimorphic representations. Altogether, our results suggest a role of experience and activity in influencing homeostatic mechanisms to generate a robust sexually dimorphic phenotype in the main olfactory epithelium.
HIV-1 Vpr regulates expression of β chemokines in human primary lymphocytes and macrophages (2000)

Abstract The HIV-1 vpr gene encodes a 14-kDa virion-packaged protein that has been implicated in viral pathogenesis. Vpr exhibits profound effects on human primary cells influencing proliferation, differentiation, apoptosis, and cytokine production, in part through NF-κB-mediated transcription. NF-κB, a potent transcription factor, activates many proinflammatory cytokines/chemokines upon infection. Here, we analyzed the effect of extracellular Vpr as well as the virion-associated Vpr on β chemokines (MIP-1α, MIP-1β, and RANTES) production in human macrophages and primary lymphocytes (PBLs). Macrophages and PBLs exposed to HIV-1 vpr+ viruses or to recombinant Vpr protein produced significantly less β chemokines compared with cells infected with HIV-1 vpr− viruses or irrelevant control protein (Gag)-exposed cells. These results suggest that a Vpr-mediated increase in virus replication could be in part through down-regulation of chemokine production.
Discovery and Preclinical Evaluation of BMS-955829, a Potent Positive Allosteric Modulator of mGluR5 (2016)

Positive allosteric modulators (PAMs) of the metabotropic glutamate receptor subtype 5 (mGluR5) are of interest due to their potential therapeutic utility in schizophrenia and other cognitive disorders. Herein we describe the discovery and optimization of a novel oxazolidinone-based chemotype to identify BMS-955829 (4), a compound with high functional PAM potency, excellent mGluR5 binding affinity, low glutamate fold shift, and high selectivity for the mGluR5 subtype. The low fold shift and absence of agonist activity proved critical in the identification of a molecule with an acceptable preclinical safety profile. Despite its low fold shift, 4 retained efficacy in set shifting and novel object recognition models in rodents.
Advanced metrology for the 14 nm node double patterning lithography (2014)

In microelectronics the two crucial parameters for the lithography step are the critical dimension, which is the width of the smallest printable pattern, and the misalignment error of the reticle, called overlay. For the 14 nm node, the limit of scanner resolution can be overcome by the double patterning technique, which requires a maximum overlay error between the two reticles of 3 nm <sup>[1]</sup>. The current approach in the measurements of critical dimension and overlay is to treat them separately, but it has become much more complex in the double patterning context, since they are no longer independent. In this paper, a strategy of a common measurement is developed. The aim of the strategy is to measure simultaneously overlay and critical dimension in the metal level double patterning grating before the second etch process. The scatterometry technique is well known for critical dimension measurement. This study demonstrates that the overlay between the two gratings can also be deduced. Thanks to this original scatterometry-based method, it becomes possible to provide information on the lithography step quality before the second etch process; therefore the lithography can be reworked if it is necessary.
SpArch: Efficient Architecture for Sparse Matrix Multiplication (2020)

Generalized Sparse Matrix-Matrix Multiplication (SpGEMM) is a ubiquitous task in various engineering and scientific applications. However, inner product based SpGEMM introduces redundant input fetches for mismatched nonzero operands, while outer product based approach suffers from poor output locality due to numerous partial product matrices. Inefficiency in the reuse of either inputs or outputs data leads to extensive and expensive DRAM access. To address this problem, this paper proposes an efficient sparse matrix multiplication accelerator architecture, SpArch, which jointly optimizes the data locality for both input and output matrices. We first design a highly parallelized streaming-based merger to pipeline the multiply and merge stage of partial matrices so that partial matrices are merged on chip immediately after produced. We then propose a condensed matrix representation that reduces the number of partial matrices by three orders of magnitude and thus reduces DRAM access by 5.4x. We further develop a Huffman tree scheduler to improve the scalability of the merger for larger sparse matrices, which reduces the DRAM access by another 1.8x. We also resolve the increased input matrix read induced by the new representation using a row prefetcher with near-optimal buffer replacement policy, further reducing the DRAM access by 1.5x. Evaluated on 20 benchmarks, SpArch reduces the total DRAM access by 2.8x over previous state-of-the-art. On average, SpArch achieves 4x, 19x, 18x, 17x, 1285x speedup and 6x, 164x, 435x, 307x, 62x energy savings over OuterSpace, MKL, cuSPARSE, CUSP, and ARM Armadillo, respectively.
Clinical Scenarios in Acute Kidney Injury: Post-Renal Acute Kidney Injury (2016)

The incidence of acute kidney injury related to urinary tract obstruction is low (1-10%). It occurs in bilateral renal or lower urinary tract obstruction or in ureter obstruction in patients with a single functioning kidney or with pre-existing chronic kidney disease. The etiology and the incidence of obstruction vary on the basis of age and gender. Conventional ultrasound has a high sensitivity (>95%), but low specificity (<70%) in the diagnosis of urinary tract obstruction. Nevertheless, color Doppler is used through the evaluation of renal resistive indexes, ureteral jet and twinkling artifact.
Phase Locking an Array of Fiber Amplifiers onto a Remote Object (2010)

Experiments demonstrating a novel technique that coherently combines an array of beams and automatically corrects for turbulence in the beam path are presented. This technique is insensitive to near field backscattering from aerosols and particulates.
Minimum Word-Length Requirements for MIMO-OFDM (2004)

The first step in the design and implementation of a MIMO-OFDM system is to analyze the characteristics of the baseband modulated signal. This is crucial in order to minimize the complexity of the digital signal processing. This paper demonstrates the generalized derivation of the minimum word-length requirements for the main data-path in OFDM systems based on the analytical evaluation of the normalized power distribution, clipping noise effect, and essential dynamic range. We have formulated the minimum word-length requirements for the main data path in both transmitter and the receiver. The theoretical analyses are also supported by system level simulations.
Designer DNA NanoGripper (2023)

DNA has shown great biocompatibility, programmable mechanical properties, and structural addressability at the nanometer scale, making it a versatile material for building high precision nanorobotics for biomedical applications. Herein, we present design principle, synthesis, and characterization of a DNA nanorobotic hand, called the "NanoGripper", that contains a palm and four bendable fingers as inspired by human hands, bird claws, and bacteriophages evolved in nature. Each NanoGripper finger has three phalanges connected by two flexible and rotatable joints that are bendable in response to binding to other entities. Functions of the NanoGripper have been enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We showcase that the NanoGripper can be engineered to interact with and capture various objects with different dimensions, including gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. When carrying multiple DNA aptamer nanoswitches programmed to generate fluorescent signal enhanced on a photonic crystal platform, the NanoGripper functions as a sensitive viral biosensor that detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~ 100 copies/mL, providing RT-PCR equivalent sensitivity. Additionally, we use confocal microscopy to visualize how the NanoGripper-aptamer complex can effectively block viral entry into the host cells, indicating the viral inhibition. In summary, we report the design, synthesis, and characterization of a complex nanomachine that can be readily tailored for specific applications. The study highlights a path toward novel, feasible, and efficient solutions for the diagnosis and therapy of other diseases such as HIV and influenza.
Preparing and Filtering Compound Databases for Virtual and Experimental Screening (2011)

This chapter contains sections titled: Introduction Ligand Databases Considering Physicochemical Properties Undesirables Property-Based Filtering for Selected Targets Summary References
A Pre-Correlation RFI Mitigation Algorithm for L-Band Interferometric Radiometers (2021)

Radio Frequency Interference (RFI) is a major concern for both real and synthetic aperture radiometers. After the lessons learnt from SMOS, ESA is preparing the next generation of L-band interferometric radiometers with RFI mitigation integrated into the cross-correlators. This work presents a preliminary design and results of a pre-correlation RFI mitigation algorithm tailored for interferometric radiometers. The results show that the correlation error introduced by the RFI is reduced on average to the half, with peaks of 20 dB of mitigation.
Metamaterial for Simulation of Imaging Through Nanodroplets in Wet Steam (2022)

We describe a metamaterial that simulates scattering by steam nanodroplets. Fabricated samples made with alumina nanoparticles compare favorably to previous powerplant measurements. Imaging at 850 nm demonstrates potential for in situ inspections through steam.
Automotive headlamp optics for a pixelated µLED source (2021)

Advances in LED technology facilitate a variety of new application scenarios in automotive exterior lighting. Attractive features in this field are related to dynamic lighting scenarios. To replace mechanical adjustments of the past, the newest μLED technology provides a high-resolution source array based on a monolithic block of IC-chip, opto chip, and converter layer. Nevertheless, design and implementation of a corresponding optical system are required to project the μLED array onto the road.
Electron-Transfer and Acid−Base Properties of a Two-Electron Oxidized Form of Quaterpyrrole that Acts as Both an Electron Donor and an Acceptor (2008)

Electron-transfer interconversion between the four-electron oxidized form of a quaterpyrrole (abbreviated as P4 for four pyrroles) and the two-electron oxidized form (P4H2) as well as between P4H2 and its fully reduced form (P4H4) bearing analogous substituents in the alpha- and beta-pyrrolic positions was studied by means of cyclic voltammetry and UV-visible spectroelectrochemistry combined with ESR and laser flash photolysis measurements. The two-electron oxidized form, P4H2, acts as both an electron donor and an electron acceptor. The radical cation (P4H2*+) and radical anion (P4H2*-) are both produced by photoinduced electron transfer from dimeric 1-benzyl-1,4-dihydronicotinamide to P4H2, whereas the cation radical form of the compound is also produced by electron-transfer oxidation of P4H2 with [Ru(bpy)3]3+. The ESR spectra of P4H2*+ and P4H2*- were recorded at low temperature and exhibit spin delocalization over all four pyrrole units. Thus, the two-electron oxidized form of the quaterpyrrole (P4H2) displays redox and electronic features analogous to those seen in the case of porphyrins and may be considered as a simple, open-chain model of this well-studied tetrapyrrolic macrocycle. The dynamics of deprotonation from P4H2*+ and disproportionation of P4H2 were examined by laser flash photolysis measurements of photoinduced electron-transfer oxidation and reduction of P4H2, respectively.
Acoustic cloaking and transformation acoustics (2010)

In this review, we give a brief introduction to the application of the new technique of transformation acoustics, which draws on a correspondence between coordinate transformation and material properties. The technique is formulated for both acoustic waves and linear liquid surface waves. Some interesting conceptual devices can be designed for manipulating acoustic waves. For example, we can design acoustic cloaks that make an object invisible to acoustic waves, and the cloak can either encompass or lie outside the object to be concealed. Transformation acoustics, as an analog of transformation optics, can go beyond invisibility cloaking. As an illustration for manipulating linear liquid surface waves, we show that a liquid wave rotator can be designed and fabricated to rotate the wave front. The acoustic transformation media require acoustic materials which are anisotropic and inhomogeneous. Such materials are difficult to find in nature. However, composite materials with embedded sub-wavelength resonators can in principle be made and such `acoustic metamaterials' can exhibit nearly arbitrary values of effective density and modulus tensors to satisfy the demanding material requirements in transformation acoustics. We introduce resonant sonic materials and Helmholtz resonators as examples of acoustic metamaterials that exhibit resonant behaviour in effective density and effective modulus.
Sparse R-CNN: An End-to-End Framework for Object Detection (2023)

Object detection serves as one of most fundamental computer vision tasks. Existing works on object detection heavily rely on dense object candidates, such as k anchor boxes pre-defined on all grids of an image feature map of size H×W. In this paper, we present Sparse R-CNN, a very simple and sparse method for object detection in images. In our method, a fixed sparse set of learned object proposals ( N in total) are provided to the object recognition head to perform classification and localization. By replacing HWk (up to hundreds of thousands) hand-designed object candidates with N (e.g., 100) learnable proposals, Sparse R-CNN makes all efforts related to object candidates design and one-to-many label assignment completely obsolete. More importantly, Sparse R-CNN directly outputs predictions without the non-maximum suppression (NMS) post-processing procedure. Thus, it establishes an end-to-end object detection framework. Sparse R-CNN demonstrates highly competitive accuracy, run-time and training convergence performance with the well-established detector baselines on the challenging COCO dataset and CrowdHuman dataset. We hope that our work can inspire re-thinking the convention of dense prior in object detectors and designing new high-performance detectors.
Interferon-gamma is produced by activated immature mouse thymocytes and inhibits the interleukin 4-induced proliferation of immature thymocytes. (1987)

We have recently shown that interleukin 4 (IL-4) (formerly called BSF-1) is a potent stimulator of fetal and adult immature thymocyte proliferation and that adult L3T4-/Lyt-2-thymocytes can be stimulated by calcium ionophore (A23187) and phorbol ester to secrete IL-4 (Zlotnik, A., J. Ransom, G. Frank, M. Fischer, and M. Howard. 1987. Proc. Natl. Acad. Sci. (USA) 84:3856). This report shows that fetal thymocytes (day 15 of gestation) can also be activated to produce IL-4 suggesting that IL-4 may be a mediator of fetal as well as adult immature thymocyte proliferation. Furthermore, we demonstrate that interferon-gamma (IFN-gamma) inhibits the IL-4-mediated proliferation of both fetal and adult L3T4-/Lyt-2-thymocytes. The inhibition of proliferation is blocked by anti-IFN-gamma antibody and is unaffected by indomethacin suggesting that IFN-gamma directly inhibits immature thymocyte proliferation. IFN-gamma does not block the IL-4/phorbol myristate acetate-mediated proliferation of an adult thymocyte population, which is enriched for L3T4-/Lyt-2+ and L3T4+/Lyt-2- cells, suggesting that the inhibitory effect of IFN-gamma is limited to the immature thymocyte population. Both fetal (day 15) and adult L3T4-/Lyt-2--thymocytes can be activated to secrete an IFN-gamma like activity. This activity is neutralized by a monoclonal anti-IFN-gamma antibody indicating that the activity is due to IFN-gamma. mRNA analysis of adult L3T4-/Lyt-2- thymocytes stimulated with A23187 and phorbol myristate acetate confirms that mRNA for both IL-4 and IFN-gamma is induced in adult L3T4-/Lyt-2- thymocytes. These results indicate that IL-4 and IFN-gamma can regulate immature thymocyte proliferation.
A high-efficiency low-cost wire-bond loop antenna for CMOS wafers (2009)

The performance of a vertical-type loop antenna made by two asymmetrical wire bonds on a low-resistivity silicon substrate was investigated. The large-loop height was increased from 0 to 0.3 lambda <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> , and the peak gain and radiation efficiency were observed after numerically removing the feed-line loss of 4 dB/mm at 50 GHz. When the loop height was increased from 0 to 0.2 lambda <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> , the radiation efficiency showed a big improvement from 5.3 % to 40.2 % on a silicon substrate of ~8 Omega.cm resistivity. Wire bonding is not only a cost-effective but also repeatable process, and this antenna can be easily connected to the front-end circuit with a differential-feed network. Therefore, the proposed vertical-type wire-bond antenna is a promising technique for high-efficiency on-chip radio antennas.
Possibilities of Laser Processing of Paper Materials (2015)

Nowadays, lasers are applied in many industrial processes: the most developed technologies include such processes as laser welding, hybrid welding, laser cutting of steel, etc. In addition to laser processing of metallic materials, there are also many industrial applications of laser processing of non-metallic materials, like laser welding of polymers, laser marking of glass and laser cutting of wood-based materials. It is commonly known that laser beam is suitable for cutting of paper materials as well as all natural wood-fiber based materials. This study reveals the potential and gives overview of laser application in processing of paper materials. In 1990's laser technology increased its volume in papermaking industry; lasers at paper industry gained acceptance for different perforating and scoring applications. Nowadays, with reduction in the cost of equipment and development of laser technology (especially development of CO2 technology), laser processing of paper material has started to become more widely used and more efficient. However, there exists quite little published research results and reviews about laser processing of paper materials. In addition, forest industry products with pulp and paper products in particular are among major contributors for the Finnish economy with 20% share of total exports in the year 2013. This has been the standpoint of view and motivation for writing this literature review article: when there exists more published research work, knowledge of laser technology can be increased to apply it for processing of paper materials.
Information processing and signal integration in bacterial quorum sensing (2009)

Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum-sensing network of the marine bacterium Vibrio harveyi uses three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the information contained within these three autoinducer signals remains a mystery. Here, we develop a new framework for analyzing signal integration on the basis of information theory and use it to analyze quorum sensing in V. harveyi. We quantify how much the cells can learn about individual autoinducers and explain the experimentally observed input-output relation of the V. harveyi quorum-sensing circuit. Our results suggest that the need to limit interference between input signals places strong constraints on the architecture of bacterial signal-integration networks, and that bacteria probably have evolved active strategies for minimizing this interference. Here, we analyze two such strategies: manipulation of autoinducer production and feedback on receptor number ratios.
Enhanced Complex Space Vector Modeling and Control System Design of Multiphase Magnetically Levitated Rotary–Linear Machines (2019)

Rotary-linear electric machines can perform coupled rotary and linear motion. In addition, they can have magnetic bearings (MBs) integrated and magnetically coupled with the rotary, linear, or rotary-linear machine operation. Since rotary-linear machines with MBs have not been thoroughly analyzed in the literature, the models that provide understanding of their operation and give basis for the control system implementation are not entirely covered. Hence, in this article, an enhanced complex space vector-based model of the rotary-linear machine with MBs is derived and expressions for the torque, thrust force, and MB force are given. The rotary-linear machine complex space vector of the voltage, current, or flux linkage is defined using the proposed transformation with two complex frames: one related to the rotation and MBs and another to the linear motion. This results in complex space vectors with two complex units; however, the techniques used for a conventional complex space vector calculation can also be applied to the proposed complex space vector description. This is also experimentally validated on a hardware prototype of a magnetically levitated linear tubular actuator (MALTA), whose position control system is designed and implemented based on the enhanced space vector modeling approach, with the dynamic operation of the MALTA, including linear motor operation with an axial stroke of 10mm and a mechanical frequency of 17Hz.