gebhart/patrepeval huggingface dataset:
Development of a Paper-based Analytical Chip for the Detection of Bacterial 16S rRNA in Wastewater Samples (2020)

Analysis of bacteria in the sewage wastewater treatment process is essential for process stabilization and upgrading. Although bacteria are currently being analyzed by molecular biology techniques targeting the 16S rRNA gene, there is a problem that they are time-consuming and labor-intensive. In this study, we developed a paper-based analytical chip by using two types of DNA molecules that specifically bind to bacterial 16S rRNA. We optimized the fabrication method of the detection probe and the paper-based analytical chip, and then detected synthetic DNA having a nucleotide sequence that hybridizes with the designed DNA molecules and bacterial 16S rRNA extracted from an activated sludge sample. We evaluated the amount of nucleic acids quantitatively by taking images of the detection line on the paper-based analytical chip with a smartphone and analyzing its brightness with an open-source image processing program, ImageJ. Our method was able to detect 85 nM of bacterial 16S rRNA concentration in the extract. Nucleic acids that did not hybridize with either of the designed DNA molecules were not detected, demonstrating high selectivity of our method.
A universal method of accurate S-parameter extraction from FD-TD simulations applicable to oblique ports (2002)

A differential method for accurate extraction of the complete S-parameters from FD-TD simulations is proposed. In reciprocal circuits no a priori knowledge of reference impedances or field distribution in the ports is needed. The method is directly applicable to arbitrarily shaped and inhomogeneous transmission lines, oblique to the FD-TD grid.
Providing deterministic delay guarantees in ATM networks (1998)

B-ISDN is expected to carry various types of traffic for which stringent quality of service (QoS) requirements must be met. In particular, per-packet (per-cell) delay guarantees are an important QoS requirement for real-time applications. Although several methods have been proposed to provide delay guarantees in packet-switching networks, they are either too complex for ATM networks which allow only very simple operations to achieve high bandwidths (hence, high-speed switching and routing), or too inefficient (in using network resources) to be cost effective. In this paper, we propose a cell-multiplexing scheme for the real-time communication service in ATM networks. The proposed scheme achieves an efficiency close to that of packet-by-packet generalized processor sharing, and incurs an implementation cost similar to that of rate controlled static priority queueing. It employs the leaky bucket model as the input traffic description model and regulates the input traffic at the user network interface to follow the input traffic specification. Inside the network, it consists of two components, traffic controller and scheduler. The function of the traffic controller is to shape real-time traffic to have the same input pattern at every switch along the path. The end-to-end delay is bounded by the scheduler which employs a nonpreemptive rate-monotonic priority scheduling policy at each switch on the path. The proposed scheme is compared to three other popular schemes with MPEG-coded movie clips. Finally, we present a hardware implementation of the proposed scheme based on a systolic array priority queue.
Challenge on Ultrasound Beamforming with Deep Learning (CUBDL) (2020)

Recent developments in deep learning have created immense potential for improving ultrasound beamforming. We organized a Challenge on Ultrasound Beamforming with Deep Learning (CUBDL) to benchmark methodologies in this space with two transmission data types: plane wave and focused transmissions. Plane wave ultrasound transmissions have created new opportunities for ultrafast ultrasound imaging, while focused ultrasound transmissions are more traditional and are widely used in most clinical ultrasound systems available today. For both transmission types, we challenged participants to obtain the best image quality under the fastest possible frame rates. CUBDL organizers solicited datasets from several leading ultrasound groups around the world and received a total of 106 data sequences including in vivo, ex vivo, simulated, and experimental phantom datasets. These submissions formed our test datasets, which were not released to participants while the challenge was open. The challenge was composed of three optional tasks (one including two subtasks) that were evaluated using the test datasets. Participants had the option to provide their results for a minimum of one up to a maximum of four tasks or subtasks: (1) beamforming with deep learning after a single plane wave transmission, which had two subtasks to either (a) match or (b) exceed traditional image quality metrics obtained with multiple plane wave transmissions; (2) beamforming with deep learning after a few plane wave transmissions; (3) beamforming with deep learning to achieve dynamic transmit focusing from datasets acquired with a single transmit focus. Evaluation included image quality metrics as well as network complexity metrics. A challenge website was created to provide information and updates: https://cubdl.jhu.edu/.
Hybrid Materials: Highly Luminescent Covalently Linked Silicon Nanocrystal/Polystyrene Hybrid Functional Materials: Synthesis, Properties, and Processability (Adv. Funct. Mater. 10/2014) (2014)

Hybrid materials consisting of covalently linked non-toxic silicon nanocrystals and polystyrene are synthesized by J. G. C. Veinot and co-workers. These materials exhibit a strong luminescent response throughout the visible and NIR spectral regions and are chemically resistant. Marrying the properties of silicon nanocrystals with polymers like polystyrene significantly increases their solubility and processability, thus providing the opportunity to fabricate robust nano- and microscale architectures that could find application in a variety of optical applications.
CD226 Is Specifically Expressed on the Surface of Th1 Cells and Regulates Their Expansion and Effector Functions (2005)

Surface molecules that are differentially expressed on Th1 and Th2 cells may be useful in regulating specific immune responses in vivo. Using a panel of mAbs, we have identified murine CD226 as specifically expressed on the surface of differentiated Th1 cells but not Th2 or Th0 cells. Although CD226 is constitutively expressed on CD8 cells, it is up-regulated on CD4 cells upon activation. Th1 differentiation results in enhanced CD226 expression, whereas expression is down-regulated upon Th2 polarization. We demonstrate that CD226 is involved in the regulation of T cell activation; in vivo treatment with anti-CD226 results in significant reduction of Th1 cell expansion and in the induction of APCs that inhibit T cell activation. Furthermore, anti-CD226 treatment delays the onset and reduces the severity of a Th1-mediated autoimmune disease, experimental autoimmune encephalomyelitis. Our data suggest that CD226 is a costimulatory molecule that plays an important role in activation and effector functions of Th1 cells.
Performance Characteristics of a PCR Assay for the Detection of KRAS Mutations in Formalin-Fixed Paraffin-Embedded Tissue Samples of Non-Small Cell Lung Cancer (2015)

Introduction: Approximately 25% of non-small cell lung cancer (NSCLC) tumors contain mutations in KRAS. These tumors are insensitive to therapy directed against the epidermal growth factor receptor and appear to be resistant to adjuvant chemotherapy. The current study demonstrates the performance of the cobas KRAS Mutation Test (cobas test), a TaqMelt polymerase chain reaction (PCR) assay designed to detect 19 mutations in codons 12, 13, and 61.
Capillary Forces Assembly of braided DNA - Deposition, stretching and transfer of a DNA network (2010)

International audience
Time dependence of delayed neutron emission for fissionable isotope identification (2005)

The time dependence of delayed neutron emission was examined as a method of fissionable isotope identification. A pulsed bremsstrahlung photon beam was used to induce photofission reactions in U238, Th232, and Pu239 targets. The resulting delayed neutron emission was recorded between irradiating pulses and is a well-known technique for fissionable material detection. Monitoring the decay of delayed neutron emission between irradiating pulses demonstrates the ability to not only detect the presence of fissionable materials, but also to identify which fissionable isotope is present.
Helper-Dependent Adenovirus Transduces the Human and Rat Retina but Elicits an Inflammatory Reaction When Delivered Subretinally in Rats (2019)

The identification of >100 genes causing inherited retinal degeneration and the promising results of recent gene augmentation trials have led to an increase in the number of studies investigating the preclinical efficacy of viral-mediated gene transfer. Despite success using adeno-associated viruses, many disease-causing genes, such as <i>ABCA4</i> or <i>USH2A</i>, are too large to fit into these vectors. One option for large gene delivery is the family of integration-deficient helper-dependent adenoviruses (HDAds), which efficiently transduce postmitotic neurons. However, HDAds have been shown in other organ systems to elicit an immune response, and the immunogenicity of HDAds in the retina has not been characterized. In this study, HDAd serotype 5 (HDAd5) was found to successfully transduce rod and cone photoreceptors in <i>ex vivo</i> human retinal organ cultures. The ocular inflammatory response to subretinal injection of the HDAd5 was evaluated using a rat model. Subretinal injection of HDAd5 carrying cytomegalovirus promoter-driven enhanced green fluorescent protein (HDAd5-CMVp-eGFP) elicited a robust inflammatory response by 3 days postinjection. This reaction included vitreous infiltration of ionized calcium-binding adapter molecule 1 (Iba1)-positive monocytes and increased expression of the proinflammatory protein, intercellular adhesion molecule 1 (ICAM-1). By 7 days postinjection, most Iba1-positive infiltrates migrated into the neural retina and ICAM-1 expression was significantly increased compared with buffer-injected control eyes. At 14 days postinjection, Iba1-positive cells persisted in the retinas of HDAd5-injected eyes, and there was thinning of the outer nuclear layer. Subretinal injection of an empty HDAd5 virus was used to confirm that the inflammatory response was in response to the HDAd5 vector and not due to eGFP-induced overexpression cytotoxicity. Subretinal injection of lower doses of HDAd5 dampened the inflammatory response, but also eGFP expression. Despite their larger carrying capacity, further work is needed to elucidate the inflammatory pathways involved and to identify an immunomodulation paradigm sufficient for safe and effective transfer of large genes to the retina using HDAd5.
Converting natural rubber waste into ring-opening metathesis polymers with oligo-1,4-cis-isoprene sidechains (2018)

Cross-metathesis with acrylates is used as the key-step to recycle natural rubber waste.
Microstructure control of WO3 film by adding nano-particles of SnO2 for NO2 detection in ppb level (2009)

To fabricate more excellent NO2 sensor with high sensor response and good linearity between the sensor response and NO2 concentration, the microstructure of WO3 lamellae was controlled by adding nano-particles of SnO2. It was found that the sintering of WO3 lamellae was inhibited by adding nano-particles of SnO2. The device using WO3 lamellae added a small amount of SnO2 nano-particles had the highest sensor response, exhibiting a high sensor response (S = 60-540) even to dilute NO2 (100–1000 ppb) in air at 200°C.
Oxygen-doped gesbte phase-change memory cells featuring 1.5 V/100-&#x03BC;A standard 0.13&#x03BC;m CMOS operations (2006)

We demonstrated the operation of phase-change memory cells that enabled 1.5-V/100-muA programming through a tungsten-bottom-electrode contact with a diameter of 180 nm. This is the lowest power ever reported. This was achieved with oxygen-doped GeSbTe, and resulted from the high electric resistance of the germanium oxides in this material. Germanium oxides were also estimated to restrain the growth of crystal in GeSbTe, and our cells maintained a 10-year thermal lifetime at 100 degC
Feature-scale simulation of resist-patterned electrodeposition (1993)

A numerical simulation of resist-patterned or “through-mask” electroplating has been performed to investigate shape evolution at the scale of small lithographic features. Shape evolution and step coverage have a significant influence on the shapes of such microelectronic structures as conductor lines, vias, and magnetic pole pieces. The simulation and associated analysis are based on a model for the rate distribution of the electrodeposition reaction that includes the depletion of the depositing metal ions and the inhibiting action of leveling agents. A stagnant boundary layer is assumed to be present, and the diffusion theory of leveling with a one-parameter description of kinetic inhibition is employed. The results show that when the geometry of a feature cavity makes possible the occurrence of concentration-field effects (such as radial diffusion), an uneven metal-ion flux should cause nonuniform growth at high fractions of the limiting current, and leveling agents should exert an opposing effect, even causing a strong reverse nonuniformity in some cases.
Identification and Characterization of a Novel Nuclear Factor of Activated T-cells-1 Isoform Expressed in Mouse Brain (2001)

The nuclear factor of activated T-cells (NFAT) family transcription factors play a key role in the control of cytokine gene expression in T-cells. Although initially identified in T-cells, recent data have unveiled unanticipated roles for NFATs in the development, proliferation, and differentiation of other tissues. Here we report the identification, cDNA cloning, and functional characterization of a new isoform of NFAT1 highly expressed in mouse brain. This isoform, which we named NFAT1-D, is identical to NFAT1 throughout the N-terminal regulatory domain and the portion of the Rel domain which includes the minimal region required for specific binding to DNA and interaction with AP-1. The homology stops sharply upstream of the 3'-boundary of the Rel homology domain and is followed by a short unique C-terminal region. NFAT1-D was expressed at high levels in all brain districts and was found as a constitutively active transcription complex. Transfection of a NFAT/luciferase reporter in the neuronal cell line PC12, which also expresses NFAT1-D, showed that these cells expressed a constitutive NFAT activity that was enhanced after nerve growth factor-induced differentiation but was resistant to the immunosuppressant cyclosporin A. NFAT1-D was, however, inducibly activated in a cyclosporin A-sensitive manner when expressed in T-cells, suggesting that the activity of NFAT proteins might be controlled by their specific cellular context.
Scalable Nanostructured Silicon with All‐Dielectric Standard RGB Color (2021)

Structural colors attract widespread attention in the fields of display and imaging devices due to their durable, vivid, and vibrant colors with subdiffraction resolution. Dielectrics with high refractive indices and negligible optical loss can achieve high‐quality structural colors that exceed the standard RGB (sRGB) color gamut. However, the fabrication processes are complicated and costly as well as limited in color‐printing areas. Herein, a facile strategy is developed to achieve scalable nanostructured silicon to enable various structural sRGB colors via a cost‐effective and straightforward wet‐chemical etching method. By adjusting the etching time, the nanostructured silicon can easily tune its color from ultraviolet to red, which occupies 60% of the sRGB color space. An optical simulation method uncovers the structure color generation mechanism, which indicates the structure color correlated with a random nanostructure reflection mode. In addition, different random‐shaped patterned displays are demonstrated on the nanostructured silicon with a centimeter‐sized substrate. This work provides a facile and efficient way to build structural color on all‐dielectric silicon substrates.
Studies on the Crystallization and Melting Behavior of Poly(ethylene 2,6-naphthalate) (2001)

Abstract Crystallization behaviour of low molecular weight (oligomeric) and high molecular weight poly(ethylene 2,6-naphthalate)s (PEN) was studied using wide angle X-ray diffraction (WAXS) and differential scanning calorimetry (DSC). It was found that the crystallization conditions determine the nature of crystalline modification. Crystallization from the glassy state gives a-modification, whereas, crystallizing from the melt above 220°C results in β-modification. In contrast, the oligomers gives both the modifications up on crystallizing from the melt. The equilibrium melting temperatures of PEN were determined from DSC experiments, based on conditions of crystallization of a and β-modifications. Key Words: Poly(ethylene 2,6-naphthalate)CrystallizationCrystalline modifications
Directing the Solid-State Organization of Racemates via Structural Mutation and Solution-State Assembly Processes (2019)

Chirality plays a central role in biomolecular recognition and pharmacological activity of drugs and can even lead to new functions such as spin filters. Although there have been significant advances in understanding and controlling the helical organization of enantiopure synthetic molecular systems, rationally dictating the assembly of mixtures of enantiomer (including racemates) is nontrivial. Here we demonstrate that a subtle change in molecular structure coupled with the understanding of assembly processes of enantiomers and racemates, in both dilute solution and concentrated gels, acts as a stepping stone to rationally control the organization in the solid-state. We have studied trans-1,2-disubstituted cyclohexanes as model systems with carboxamide, thioamide, and their combination as functional groups. On comparing the gelation propensity of individual enantiomers and racemates, we find that racemates of carboxamide, thioamide, and their combination adopt self-sorting, coassembly, and mixed organization, respectively. Remarkably, these modes of assembly of racemates were also retained in solid-state. These results point out that studying the solution-phase assembly is a key link for connecting molecular structure with the assembly in the solid-state, even for racemates.
Intravoxel distribution of DWI decay rates reveals C6 glioma invasion in rat brain (2004)

The hypothesis was tested that the intravoxel distribution of water diffusion rates, as measured with a stretched-exponential model of diffusion-weighted imaging (DWI), is a marker of brain tumor invasion. Eight rats underwent intracerebral inoculation of C6 glioma cells. In three rats, cells were labeled with a fluorescent dye for microscopy. One rat was inoculated with a saline solution, and five more rats were imaged without inoculation as controls. Five healthy uninoculated rats were also imaged. DWI was performed 14-15 days after inoculation, with diffusion-weighting factor b = 500 to 6500 sec/mm2, and the resulting signal attenuation was fitted with the stretched-exponential model. The heterogeneity index values were significantly lower (P < 0.05) in the peritumor ROI than in normal gray matter and significantly higher than in normal white matter. The distributed diffusion coefficient values were significantly lower than in normal white matter or normal gray matter. Fluorescence microscopy confirmed the presence of tumors in the peritumor region that could be histologically distinguished from the main tumor mass. There was no change in proton density or T2-weighted images in the peritumor region, making vasogenic edema unlikely as a source of contrast. It is therefore thought that the heterogeneity parameter alpha is a marker of brain tumor invasion.
3-Hydroxypropionaldehyde, an inhibitory metabolite of glycerol fermentation to 1,3-propanediol by enterobacterial species (1996)

Glycerol fermentation by Enterobacter agglomerans revealed that both growth and 1,3-propanediol production ceased after consumption of about 430 mM glycerol, irrespective of the initial glycerol content. This phenomenon was assigned to the production of 3-hydroxypropionaldehyde, which was identified by proton nuclear magnetic resonance and which showed a bacteriostatic effect. The accumulation during glycerol fermentation was also observed with two other enterobacterial species, i.e., Klebsiella pneumoniae and Citrobacter freundii.
OdeView: the graphical interface to Ode (1990)

OdeView is the graphical front end for Ode, an object-oriented database system and environment. Ode's data model supports data encapsulation, type inheritance, and complex objects. OdeView provides facilities for examining the database schema (i.e., the object type or class hierarchy), examining class definitions, browsing objects, following chains of references starting from an object, synchronized browsing, displaying selected portions of objects (projection), and retrieving objects with specific characteristics (selection).
Enantioselective Synthesis of the AB-Ring System of the Antitumor Antibiotic Tetrazomine (2001)

The synthesis of the 1,2,3,4-tetrahydroisoquinoline moiety of tetrazomine was accomplished in 18 steps and in 3% overall yield from commercially available o-anisaldehyde. The reaction sequence utilizes a Sharpless asymmetric dihydroxylation to install the stereocenter and an intramolecular Friedel--Crafts hydroxyalkylation with an N-protected 2-oxo-acetamide to close the heterocyclic ring.
Supplementary Figures S1-S2 from Monitoring Caspase-3 Activation with a Multimodality Imaging Sensor in Living Subjects (2023)

Supplementary Figures S1-S2 from Monitoring Caspase-3 Activation with a Multimodality Imaging Sensor in Living Subjects
Integration of silicon photonics in a bulk CMOS memory flow (2013)

Monolithically integrated silicon photonic (SiP) devices have been demonstrated using a modified bulk CMOS flow. Integration was achieved by nominally extending existing process and design collateral without shifting the CMOS parameterization.
Solid state electrochemical composite (2023)

Provided is a composite electrochemical device fabricated from highly electronically conductive materials such as metals, metal alloys, or electronically conductive ceramics. The electronic conductivity of the electrode substrate is maximized. The invention allows for an electrode with high electronic conductivity and sufficient catalytic activity to achieve high power density in ionic (electrochemical) devices such as fuel cells and electrolytic gas separation systems including oxygen generation system.