gebhart/patrepeval huggingface dataset:
An Efficient Approach for Tuberculosis Diagnosis on Chest X-Ray (2022)

Deep learning computer-aided detection (CAD) system for diagnosing abnormal findings related to Tuberculosis (TB) disease on chest X-ray images (CXRs) is growing in research. However, the deep learning model’s reliability depends on model quality, the generalization, and the large dataset. To deal with this problem, we provide a large TB dataset, namely VB-TB Dataset, and propose an efficient approach for TB chest X-ray diagnosis, including TB classification and area segmentation models. In our dataset, we obtained a total of 246,216 clean labeled images, including 228,827 TB negative images and 17,389 TB positive images with 2,982 TB area images annotated in pixel-level for the segmentation task. This study presents an efficient approach that significantly improves TB classification using Knowledge Distillation (KD) from ensemble models of different state-of-the-art (SOTA) convolution neural networks. Our TB classification model achieved outstanding performance compared with previous models on our VB-TB test set and TBX11K dataset. We also firstly applied an efficient semantic segmentation model based on the light-weight U-Net to localize precisely TB areas on CXRs, and the model also obtained impressive results scored by Dice Similarity Coefficient (DSC) on our TB area segmentation testset.
Robot motion planning with task specifications via regular languages (2015)

SUMMARY This paper presents an efficient approach for planning collision-free and dynamically feasible trajectories that enable a mobile robot to carry out tasks specified as regular languages over workspace regions. A sampling-based tree search is conducted over the feasible motions and over an abstraction obtained by combining the automaton representing the regular language with a workspace decomposition. The abstraction is used to partition the motion tree into equivalence classes and estimate the feasibility of reaching accepting automaton states from these equivalence classes. The partition is continually refined to discover new ways to expand the search. Comparisons to related work show significant speedups.
Advances in Human Stem Cell Research (2003)

GERECHT-NIR, SHARON MSc*,†; ELDOR, LIRON MD‡; ITSKOVITZ-ELDOR, JOSEPH MD, DSc†,§ Author Information
Electron Beam Injection Experiments In The University Of New Mexico (UNM) Betatron (1989)

We performed experiments on the injection of a high-power relativistic electron beam (130 A, 300 keV) into the UNM Betatron. The beam entered at an angle of 20° with respect to the main axis of the accelerating ring. An electrostatic inflector provided a transverse electric field which bent the beam onto the main axis of the machine. An electron beam current of 30 A was contained in a well-defined core, as measured at the exit of the first 180° curved section of the ring.
Evaporative Thinning: A Facile Synthesis Method for High Quality Ultrathin Layers of 2D Crystals (2014)

The palette of two-dimensional materials has expanded beyond graphene in recent years to include the chalcogenides among other systems. However, there is a considerable paucity of methods for controlled synthesis of mono- and/or few-layer two-dimensional materials with desirable quality, reproducibility, and generality. Here we show a facile top-down synthesis approach for ultrathin layers of 2D materials down to monolayer. Our method is based on controlled evaporative thinning of initially large sheets, as deposited by vapor mass-transport. Rather than optimizing conditions for monolayer deposition, our approach makes use of selective evaporation of thick sheets to control the eventual thickness, down to a monolayer, a process which appears to be self-stopping. As a result, 2D sheets with high yield, high reproducibility, and excellent quality can be generated with large (>10 μm) and thin (∼ 1-2 nm) dimensions. Evaporative thinning promises to greatly reduce the difficulty involved in isolating large, mono- and few-layers of 2D materials for subsequent studies.
Antibody repertoire analysis of mouse immunization protocols using microfluidics and molecular genomics (2019)

Immunization of mice followed by hybridoma or B-cell screening is one of the most common antibody discovery methods used to generate therapeutic monoclonal antibody (mAb) candidates. There are a multitude of different immunization protocols that can generate an immune response in animals. However, an extensive analysis of the antibody repertoires that these alternative immunization protocols can generate has not been performed. In this study, we immunized mice that transgenically express human antibodies with either programmed cell death 1 protein or cytotoxic T-lymphocyte associated protein 4 using four different immunization protocols, and then utilized a single cell microfluidic platform to generate tissue-specific, natively paired immunoglobulin (Ig) repertoires from each method and enriched for target-specific binders using yeast single-chain variable fragment (scFv) display. We deep sequenced the scFv repertoires from both the pre-sort and post-sort libraries. All methods and both targets yielded similar oligoclonality, variable (V) and joining (J) gene usage, and divergence from germline of enriched libraries. However, there were differences between targets and/or immunization protocols for overall clonal counts, complementarity-determining region 3 (CDR3) length, and antibody/CDR3 sequence diversity. Our data suggest that, although different immunization protocols may generate a response to an antigen, performing multiple immunization protocols in parallel can yield greater Ig diversity. We conclude that modern microfluidic methods, followed by an extensive molecular genomic analysis of antibody repertoires, can be used to quickly analyze new immunization protocols or mouse platforms.
Introduction to special section: Characterization and monitoring of subsurface contamination (2015)

Subsurface contamination is a significant problem worldwide that directly affects human health, ecosystems, and property. It also can impact valuable resources (e.g., groundwater, surface water, soils). Contaminated sites exist in a variety of sizes and locations, from a leaking underground storage
Learning to solve the elastic wave equation with Fourier neural operators (2023)

ABSTRACT Neural operators are extensions of neural networks, which, through supervised training, learn how to map the complex relationships that exist within the classes of the partial differential equation (PDE). One of these networks, the Fourier neural operator (FNO), has been particularly successful in producing general solutions to PDEs, such as the Navier-Stokes equation. We have formulated an FNO to reproduce solutions of the 2D isotropic elastic wave equation training on synthetic data sets. This requires two significant alterations to the existing FNO structures. By (1) adding the Fourier kernel multiplication with respect to multiple spatial directions and (2) building connections between the Fourier layers, we produce what we refer to as the “one-connection FNO,” which is suitable for use in producing solutions of the elastic wave equation. Post training, the new FNO is examined for accuracy. Compared with the unmodified original FNO, we observe, in particular, an improved prediction of the fields generated with low source frequency, which is suggestive of immediate applicability in inversion. Once trained, the modified FNO operates at approximately 100 times the speed of traditional finite-difference methods on a CPU; this increase in the computational speed, when used within forward modeling, may have important consequences in simulation-intensive inverse problems, such as those based on the Monte Carlo methods.
ChemInform Abstract: Non‐Basic Histamine H1‐Antagonists. Part 1. Synthesis and Biological Evaluation of Some Substituted 2‐(2‐Pyridylaminoalkylamino)pyrimidones and Related Compounds. (1989)

Abstract Besides the most active title compound (IV), 25 further derivatives with a modified pyridylaminoalkylamino moiety as in (V) are prepared by similar procedures.
Effects of Different Coolants on the Cooling Performance of an Impingement Microchannel Cold Plate (2021)

Increasing power densities due to the rise of Artificial Intelligence (AI), high-performance computing (HPC) and machine learning can lead to the increasing cost and complexity of thermal management in electronics devices. With very high specific heat and latent heat compared to air cooling, liquid cooling can be an alternative solution and currently an emerging technology in data center cooling. This paper describes experimental characterization of a liquid cooling cold plate in terms of thermal resistance and pressure drop. The liquid cold plate design incorporates impingement into a microchannel structure. Coolant enters the cold plate at the inlet then impinges down to the base of the cold plate at the trapezoidal groove. A copper block with a top surface area of 1 inch $\times 1$ inch was used to mimic the computer chip surface. Various coolants were used in this study including deionized water (100 % water), a mixture of coolants (10, 20, 30 % ethylene glycol +90,80, 70% water) and dielectric coolant3M Novec 7000 HFE. A comparison in the thermal and hydraulic performance of these coolants was presented. Effects of flow rate and coolant inlet temperature on both thermal resistance and pressure drop were studied in detail.
Simple organic molecules bearing a 3,4-ethylenedioxythiophene linker for efficient dye-sensitized solar cells (2008)

3,4-Ethylenedioxythiophene and bis[2-(2-methoxyethoxy)ethoxy]thiophene bridged donor-acceptor molecules for dye-sensitized solar cells have been synthesized, one of which achieved a solar-to-energy conversion efficiency of 7.3%, compared to 7.7% optimized for N719 dye.
Single and multijunction solar cells with 1.0 eV Si-Ge-Sn junction (2015)

Recent development of Si-Ge-Sn ternary alloys offers an alternative to 1.0 eV bandgap materials for multijunction solar cells. Main advantages of these alloys are tunable gap energy and variable lattice parameter, which can be fitted into the existing designs, thus resulting in a lattice matched solution. Recent growth, optical and structural results from Si-Ge-Sn with ~ 1 eV gaps and lattice matched to Ge substrates are presented. Based on simple device models, prototype single and triple junction cells with SiGeSn junction have been fabricated. Device measurements show that the performance of Si-Ge-Sn material is comparable to other 1.0 eV semiconductors.
Conclusion. Du travail politique aux marchés du travail (2014)

Les contributions réunies dans cet ouvrage saisissent le travail politique sous différents angles : celui de l’expérimentation quotidienne et de la confrontation à un flux débordant de tâches, obligations, responsabilités, sollicitations ; celui de la division des activités et de leur inscription dans des organisations structurant des spécialisations mais aussi des déplacements de territoires ; celui des interprétations des fonctions exercées et de la variété des contextes relationnels et nor...
Regulation of Cell-Specific Inositol Metabolism and Transport in Plant Salinity Tolerance (1998)

myo-Inositol and its derivatives are commonly studied with respect to cell signaling and membrane biogenesis, but they also participate in responses to salinity in animals and plants. In this study, we focused on L-myo-inositol 1-phosphate synthase (INPS), which commits carbon to de novo synthesis, and myo-inositol O-methyltransferase (IMT), which uses myo-inositol for stress-induced accumulation of a methylinositol, D-ononitol. The Imt and Inps promoters are transcriptionally controlled. We determined that the transcription rates, transcript levels, and protein abundance are correlated. During normal growth, INPS is present in all cells, but IMT is repressed. After salinity stress, the amount of INPS was enhanced in leaves but repressed in roots. IMT was induced in all cell types. The absence of myo-inositol synthesis in roots is compensated by inositol/ononitol transport in the phloem. The mobilization of photosynthate through myo-inositol translocation links root metabolism to photosynthesis. Our model integrates the transcriptional control of a specialized metabolic pathway with physiological reactions in different tissues. The tissue-specific differential regulation of INPS, which leads to a gradient of myo-inositol synthesis, supports root growth and sodium uptake. By inducing expression of IMT and increasing myo-inositol synthesis, metabolic end products accumulate, facilitating sodium sequestration and protecting photosynthesis.
Wax-bonded NdFeB micromagnets for microelectromechanical systems applications (2008)

A microfabrication technique is reported for the fabrication of wax-bonded micromagnets in the 100μm–1mm range. This dimensional size is not typically achievable by thin-film deposition techniques or by conventional macroscale magnet processing, and is of interest for magnetic microelectromechanical systems applications. The magnet fabrication approach incorporates a wax powder binder to “lock” the magnetic microparticles together to improve the coercivity. In practice, a NbFeB powder and wax powder are packed into pre-etched trenches in a silicon wafer and subsequently heated, allowing the wax to melt and bond the magnetic powder. Using this method, 500×500×320μm3 magnets have been demonstrated with a coercivity of 737kA∕m and a maximum energy product of 16.6kJ∕m3.
Engineering Cofactor Specificity of a Thermostable Phosphite Dehydrogenase for a Highly Efficient and Robust NADPH Regeneration System (2021)

Nicotinamide adenine dinucleotide phosphate (NADP)-dependent dehydrogenases catalyze a range of chemical reactions useful for practical applications. However, their dependence on the costly cofactor, NAD(P)H remains a challenge which must be addressed. Here, we engineered a thermotolerant phosphite dehydrogenase from <i>Ralstonia</i> sp. 4506 (RsPtxD) by relaxing the cofactor specificity for a highly efficient and robust NADPH regeneration system. The five amino acid residues, Cys174-Pro178, located at the C-terminus of β7-strand region in the Rossmann-fold domain of RsPtxD, were changed by site-directed mutagenesis, resulting in four mutants with a significantly increased preference for NADP. The catalytic efficiency of mutant RsPtxD<sub>HARRA</sub> for NADP (<i>K</i> <sub>cat</sub>/<i>K</i> <sub>M</sub>)<sup>NADP</sup> was 44.1 μM<sup>-1</sup> min<sup>-1</sup>, which was the highest among the previously reported phosphite dehydrogenases. Moreover, the RsPtxD<sub>HARRA</sub> mutant exhibited high thermostability at 45°C for up to 6 h and high tolerance to organic solvents, when bound with NADP. We also demonstrated the applicability of RsPtxD<sub>HARRA</sub> as an NADPH regeneration system in the coupled reaction of chiral conversion of 3-dehydroshikimate to shikimic acid by the thermophilic shikimate dehydrogenase of <i>Thermus thermophilus</i> HB8 at 45°C, which could not be supported by the parent RsPtxD enzyme. Therefore, the RsPtxD<sub>HARRA</sub> mutant might be a promising alternative NADPH regeneration system for practical applications.
Searching for potential multi-hazard events during the last 1.5 million years of the Pleistocene epoch (2022)

Increasing attention has been paid to multi-hazards in environmental disaster studies produced during the last decade. Multi-hazard studies focus on the occurrence, interaction and effect of several natural hazards in the same region. Despite the increasing number of multi-hazard studies, few investigations have focused on global-scale multi-hazard events. With the aim of closing this gap, our study focuses on the identification of periods during the last 1.5 million years of the Pleistocene epoch, with the quasi-parallel appearance of natural hazards (e.g., asteroid impacts and large volcanic eruptions with a Volcanic Explosivity Index (VEI) of 8 and 7) amplifying their individual effects and thus causing long-term, global-scale changes. Of the seven identified potential multi-hazard events, three were considered as possible global-scale events with a longer term environmental (paleoclimatic) impact; dated to c.a., 1.4 Ma (marine isotope stage – MIS45), 1.0 Ma (MIS 27), and 100 ka (MIS 5c), respectively. Two additional periods (around 50 and 20 ka) were identified as being associated with more restricted scale multi-hazard events, which might cause a “Little Ice Age-like” climatic episode in the history of the Pleistocene Period. In addition, we present a hypothesis about the complex climatic response to a global-scale multi-hazard event consisting of a series of asteroid impacts and volcanic eruption linked to a geomagnetic polarity change, namely the Matuyama-Brunhes Boundary, which might be accompanied by global cooling and result in the final step of the Early Middle Pleistocene Transition.
Read on Demand Images in Laser‐Written Polymerizable Liquid Crystal Devices (2018)

Abstract Two‐photon laser writing is a powerful technique for creating intricate, high resolution features in polymerizable materials. Here, using a single‐step process to microfabricate polymer inclusions, the ability to generate read‐on‐demand images and identification codes in a liquid crystal (LC) device is demonstrated. These micrometer‐sized polymer features are encoded directly into LC devices using direct laser writing, which locks‐in the local molecular orientation at the moment of fabrication. By reading the devices with the same voltage amplitude that is used to write the polymer structures, features can be made to disappear as the director profile becomes homogeneous with the surrounding regions, effectively cloaking the structure for both polarized and unpolarized light. It is shown how this process can be used to create micrometer‐scale reconfigurable emoticons and quick‐response codes within a fully assembled LC device, with potential use in authenticity and identification applications.
Convolutional Polar Codes on Channels with Memory using Tensor Networks (2018)

Arikan's recursive code construction is designed to polarize a collection of memoryless channels into a set of good and a set of bad channels, and it can be efficiently decoded using successive cancellation. It was recently shown that the same construction also polarizes channels with memory, and a generalization of successive cancellation decoder was proposed with a complexity that scales like the third power of the channel's memory size. In another line of work, the polar code construction was extended by replacing the block polarization kernel by a convoluted kernel. Here, we present an efficient decoding algorithm for finite-state memory channels that can be applied to polar codes and convolutional polar codes. This generalization is most effectively described using the tensor network formalism, and the manuscript presents a self-contained description of the required basic concepts. We use numerical simulations to study the performance of these algorithms for practically relevant code sizes and find that the convolutional structure outperforms the standard polar codes on a variety of channels with memory.
Co-Stimulation of T cells via CD28 inhibits human IgE production; reversal by Pertussis toxin (1995)

In lymphocyte cultures, IgE production was achieved by stimulating T cells with anti-CD2 and IL-2. Here we show that anti-CD28, in the presence or absence of IL-2, reduces this IgE production approximately 10-fold. This inhibition of IgE production was almost completely reversed by Pertussis toxin (PT). PT had no effect on IgE production when the cells were stimulated in the absence of anti-CD28. No major effects of PT were found on IgM production. PT had no effect on purified B cells, stimulated with IL-4 and anti-CD40. In the presence of saturating amounts of rIL-4 similar results were obtained, albeit the absolute amounts of IgE produced were higher in all situations. Furthermore, PT-induced IgE production was still dependent on IL-4, as was evident from experiments in which anti-IL-4 was added to the culture. The IgE enhancing effect was dependent on the adenosine diphosphate (ADP)-ribosyltransferase activity of PT, because a mutant molecule lacking this activity was not able to restore anti-CD28-induced inhibition of IgE synthesis. Thus, we show that co-stimulation with anti-CD28 causes an inhibition of T cell-dependent IgE production by B cells, which inhibition can be specifically overcome by PT. An analysis of the molecular pathways underlying this phenomenon may contribute to our understanding of the regulation of IgE synthesis in (patho)physiological conditions.
Molecular biology and the control of viral vaccines (1990)

The live attenuated vaccines against poliomyelitis developed by Sabin are among the safest and most effective antiviral vaccines in current use and have eliminated poliomyelitis as a public health problem in many countries. They form the main basis of the WHO intention to eliminate poliomyelitis from the world by the year 2000, and the molecular basis of their attenuated phenotype and some of its virological consequences are increasingly clear. Nonetheless, the data reviewed here show how poorly understood their mechanism of action is in use. Our studies raise the possibility of in vitro neurovirulence tests and may help to identify features of particular importance in the attenuation of the virus for human rather than simian recipients. On the other hand it is clear that when a live virus is used as a vaccine it is not possible to control it in the same way that genetically engineered products may be controlled in so far as replication in the recipient makes it possible for the live vaccine strain to alter in ways which may or may not be undesirable.
Femtosecond study of exciton dynamics in9,9−di−n−hexylfluorene/anthracenerandom copolymers (2000)

Exciton dynamics of $9,9\ensuremath{-}\mathrm{di}\ensuremath{-}n\ensuremath{-}\mathrm{h}\mathrm{e}\mathrm{x}\mathrm{y}\mathrm{l}\mathrm{f}\mathrm{l}\mathrm{u}\mathrm{o}\mathrm{r}\mathrm{e}\mathrm{n}\mathrm{e}/\mathrm{a}\mathrm{n}\mathrm{t}\mathrm{h}\mathrm{r}\mathrm{a}\mathrm{c}\mathrm{e}\mathrm{n}\mathrm{e}$ (DHF/ANT) statistical copolymers have been measured using femtosecond transient absorption spectroscopy. An investigation of the excitation intensity dependence over the range of $0.1--1.0$ mJ/(pulse ${\mathrm{cm}}^{2}$) for solutions and $1.0--17$ \ensuremath{\mu}J/(pulse ${\mathrm{cm}}^{2}$) for thin films has been conducted to explore exciton relaxation mechanisms below excitation densities where exciton-exciton interaction is important. Intrachain relaxation of photoexcited singlet excitons is observed in dilute solutions. In contrast, interchain relaxation mechanisms become predominant in thin films. Decay dynamics are independent of excitation intensity for dilute solutions and thin films of DHF/ANT when probed at 790 and 750 nm. In addition, time-resolved measurements for a DHF homopolymer and two copolymer thin films have been carried out as a function of probe wavelength. A stimulated emission (SE) feature and a photoinduced absorption (PA) feature are observed in the visible region. The SE and PA dynamics are similar for the copolymers, suggesting that the same excited state species, the singlet exciton, is responsible for both the SE and PA. There is a significant difference between the SE and PA dynamics for DHF thin films on the 0--3-ps timescale. The SE dynamics show a pulse-width limited rise and a subsequent decay. In contrast, both the 600 and 750 nm PA dynamics show a ``double'' rise that represents contributions from two separate photophysical processes. These results, in combination with the steady-state photoluminescence spectrum, which indicates excimer emission, lead to the conclusion that interchain species, such as excimers, are formed in 〈1 ps in DHF homopolymer films following photoexcitation. That the copolymer dynamics show no evidence of excited state species other than the singlet, emissive exciton, is consistent with the interpretation that anthracene substituents in the polymer backbone prevent interchain interactions in films.