gebhart/patrepeval huggingface dataset:
K1 Escherichia coli form foci in the brain at 24h post infection (2022)

K1 capsule type Escherichia coli is the predominant cause of neonatal meningitis. In an intravenous (IV) infection model with a clinical K1 isolate IHE 3034 adult mice die of sepsis within 24 hours. However, by utilising cefazolin, a first-generation cephalosporin known for its inability to pass through the blood brain barrier, it is possible to prevent bacteraemia and study the early phases of E. coli meningitis in the brain. Mice were infected IV with E. coli IHE 3034 and treated with cefazolin at 12 and 24h intraperitoneal to ensure the survival of animals to the determined end points. The results of the experiment show IHE 3034 is present in the brain as early as 12h and it remains in the tissue 72h post infection even if blood is clear. Despite this, at the cellular level, clear foci formation can be observed in the meninges and the choroid plexus around the vascular endothelial cells at 48h, showing IHE 3034’s ability for intracellular replication inside the meningeal region The foci do not appear to be present at 24 or 72h, indicating for a secondary replication site around the major vascular endothelia sites of the brain. This further promotes the bacterial load increase through cell bursting in the tissue with or without a sustained bacterial influx from the blood. These findings show that K1 E. coli can form foci in the brain which may lead to escalated disease progression and severe morbidity following an initially successful clearance of bloodborne bacteria during sepsis.
Activation of Mg-Doped p-Type Al0.17Ga0.83N in Oxygen Ambient (2009)

Annealing in oxygen ambient was found to be effective for realizing a high hole concentration in p-type Al0.17Ga0.83N:Mg. The maximum hole concentration obtained was 1.3×1016 cm-3 at room temperature. Hydrogen dissociation from Mg-doped Al0.17Ga0.83N is found to be enhanced by annealing in a flow of O2 compared with annealing in a flow of N2.
Faculty Opinions recommendation of Direct detection of DNA methylation during single-molecule, real-time sequencing. (2013)

We describe the direct detection of DNA methylation, without bisulfite conversion, through single-molecule, real-time (SMRT) sequencing. In SMRT sequencing, DNA polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands. The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the DNA template, including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine. Measurement of polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect determination of primary DNA sequence. The various modifications affect polymerase kinetics differently, allowing discrimination between them. We used these kinetic signatures to identify adenine methylation in genomic samples and found that, in combination with circular consensus sequencing, they can enable single-molecule identification of epigenetic modifications with base-pair resolution. This method is amenable to long read lengths and will likely enable mapping of methylation patterns in even highly repetitive genomic regions. PMID: 20453866 Funding information This work was supported by: NHGRI NIH HHS, United States Grant ID: 1RC2HG005618-01 NHGRI NIH HHS, United States Grant ID: RC2 HG005618-01 NHGRI NIH HHS, United States Grant ID: RC2 HG005618
Waveguide electro-optic modulators based on intrinsically polar self-assembled superlattices (SASs) (2002)

In this paper we describe methods of fabricating and characterizing organic electro-optic modulators based on intrinsically polar self-assembled superlattices. These structures are intrinsically acentric, and exhibit large second harmonic generation and electro-optic responses without the requirement of poling by an external electric field. A novel wet chemical protection-deprotection approach for the growth of self-assembled superlattices have been developed, and the refractive indices of self-assembled organic electro-optic superlattices may be tuned during the self-assembly process. Prototype electro-optic modulators based on chromophoric self-assembled superlattices have been designed and fabricated. The effective electro-optic coefficient of the self-assembled superlattice film in a phase modulator is estimated as about 20 pm/V at a wavelength of 1064 nm.
Immunotherapy of cancer: experimental approach with activated macrophages proliferating in culture. (1988)

Murine macrophages isolated from the peritoneal cavity or from the lung were continuously grown and expanded in vitro on a confluent layer of "mesothelial or endothelial" feeding cells. These cell lines could be obtained from C57B16 or BalbC mice and were nontumorogenic in nude mice. The macrophages were characterized by their capacity to phagocytose yeasts and by the presence of nonspecific esterases, of Fc receptors, and of specific antigens (MAC1 ...). In vitro, these macrophages were fully activated and were tumoricidal against different tumor cell lines. In vivo, adoptive transfer of the expanded macrophages to mice bearing EMT6 sarcoma or 3LL metastasizing carcinoma inhibited the growth of the primary tumors and the development of metastases. Local injection in the vicinity of the primary tumor and i.v. transplantation were effective. The adoptive transfer of expanded macrophages could lead to a new kind of immunotherapy of neoplastic diseases combining selective amplification with effective activation of macrophages as key effector cells.
Protein-Coding Variants Implicate Novel Genes Related to Lipid Homeostasis Contributing to Body Fat Distribution (2018)

ABSTRACT Body fat distribution is a heritable risk factor for a range of adverse health consequences, including hyperlipidemia and type 2 diabetes. To identify protein-coding variants associated with body fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, we analyzed 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries for discovery and 132,177 independent European-ancestry individuals for validation. We identified 15 common (minor allele frequency, MAF≥5%) and 9 low frequency or rare (MAF&lt;5%) coding variants that have not been reported previously. Pathway/gene set enrichment analyses of all associated variants highlight lipid particle, adiponectin level, abnormal white adipose tissue physiology, and bone development and morphology as processes affecting fat distribution and body shape. Furthermore, the cross-trait associations and the analyses of variant and gene function highlight a strong connection to lipids, cardiovascular traits, and type 2 diabetes. In functional follow-up analyses, specifically in Drosophila RNAi-knockdown crosses, we observed a significant increase in the total body triglyceride levels for two genes ( DNAH10 and PLXND1 ). By examining variants often poorly tagged or entirely missed by genome-wide association studies, we implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.
Compressive Multiplexing of Ultrasound Signals (2018)

High-quality 3D ultrasound (US) imaging requires dense matrix-array probes with thousands of elements and necessitates an unrealistic number of coaxial cables to connect such probes to back-end systems. To address this issue, many techniques have been developed such as sparse arrays, mechanical scanning, multiplexing and micro-beamforming, which permit to achieve 3D imaging with existing 2D imaging systems but with a degradation in image quality. We propose a novel multiplexing method which relies on compressed-sensing (CS) principles to significantly reduce the number of coaxial cables. We exploit the compressive multiplexer (CMUX) introduced for radio-frequency signals to multiplex US signals in the probe head. The CMUX considers a set of signals as inputs, modulates them with chipping sequences and sums them to form a single output. On the reconstruction side, we propose two methods: one solving a CS-based problem exploiting sparsity of US signals in a pulse-stream model (CS-PS) and another one solving a least-squares problem in the Fourier domain based on bandlimited signal properties of US signals. We demonstrate through simulations and in vivo experiments that the proposed techniques lead to high-quality reconstruction with significantly fewer coaxial cables, up to 12× less with CS-PS.
Carbon ions irradiation on nano- and microcrystalline CaSO4 : Dy (2008)

Nanoparticles of CaSO4 : Dy phosphor with a particle size of around 30 nm have been prepared by the chemical co-precipitation technique. Pellet samples of the nanomaterials were irradiated by a 75 MeV C6+ ion beam at the fluence range 1 × 109–1 × 1013 ions cm−2. Thermoluminescence (TL) glow curves of the irradiated samples were recorded and studied. The microcrystalline form of this sample is also included in the study with the aim of reporting a comparative measurement. The TL analysis shows that the glow curve of the nanomaterial has two peaks at around 166 and 210 °C. These peaks are similar to those induced in the microcrystalline sample with a slight difference in their TL response. The second peak is more prominent in the case of the microcrystalline sample at low fluences, while the first one dominates in the nanostructured sample mainly at higher fluences. The TRIM code based on Monte Carlo simulation was also used for calculating some ion beam parameters. Dosimetric properties of the carbon ion beam irradiated materials show that the nanostructure material has excellent features such as a simple glow curve structure and a linear TL response over a wider range than the corresponding microcrystalline sample. These results show that the nanostructure form of CaSO4 : Dy might be useful for detecting the high doses of carbon ions used in radiotherapy. Thermal analysis of the prepared nano- and microcrystalline materials was also done in the range 50–500 °C using thermogravimetry analysis and differential thermal analysis. No phase transitions within this range of heating for both the materials are observed.
Diagnostic of energy transfers in sputter deposition: a way to investigate the sputtering process and the film growth (2016)

International audience
A low-power high-performance embedded SRAM macrocell (2002)

A new approach to modeling the decoding hierarchy in a hierarchical word line (HWL) SRAM architecture using integer-linear programming (ILP) is introduced. Using this approach, the HWL architecture is shown to be inadequate for very large SRAM sizes. Alternatively, a new low-power high-speed SRAM architecture is described. This architecture is shown to have fairly constant speed and power dissipation for sizes ranging between 32 kb to 4 Mb. Low-power is achieved by a voltage boosting technique not requiring a two-step voltage and by a new method of tristating memory cells during a write operation. The SRAM was implemented in a 0.35 /spl mu/m CMOS technology operated at 150 MHz while dissipating only 10 mW.
Methods for preparing superalloy articles and related articles (2023)

A method for preparing an article including a nickel-based superalloy is presented. The method includes heat-treating a workpiece including a nickel-based superalloy at a temperature above a gamma-prime solvus temperature of the nickel-based superalloy and cooling the heat-treated workpiece with a cooling rate less than 50 degrees Fahrenheit/minute from the temperature above the gamma-prime solvus temperature of the nickel-based superalloy so as to obtain a cooled workpiece. The cooled workpiece includes a gamma-prime precipitate phase having an average particle size less than 250 nanometers at a concentration of at least 10 percent by volume, and is substantially free of a gamma-double-prime phase. An article having a minimum dimension greater than 6 inches is also presented. The article includes a material that has a gamma-prime precipitate phase having an average particle size less than 250 nanometers, and is substantially free of a gamma-double-prime phase.
Traversable path identification in unstructured terrains: A Markov random walk approach (2009)

Many terrains in outdoor robot navigation problems have paths that are distinct and continuous compared to the non-traversable regions. In image space these paths correspond to continuous segments that can be thought of as clusters embedded in image feature space. These segments very often translate directly to traversable ground plane. In this paper we build the intuition for semi-supervised methods in path identification and present a Markov random walk based approach that requires very few labeled points. The method creates a nearest neighbor graph representation of the current image frame using features deemed suitable for the task and propagates labels based on the concept of absorbing Markov chains. We extend this formalism to the task of dynamically identifying traversable and non-traversable regions in the incoming image frames. We present results on actual terrains corresponding to test courses used by the LAGR test team. The results demonstrate that with minimal initial supervision the robot can navigate to the goal. We also conduct comparisons of our path labeling technique against other machine learning techniques including nonlinear support vector machines on hand labeled data. The results demonstrate that our semi-supervised approach is proficient in the domain of path traversal in unstructured domains.
A robust beamformer for OFDM based WLANs against burst interference (2004)

A beamformer for burst interference suppression is proposed for an orthogonal frequency-division multiplexing (OFDM) system with receiver diversity. The proposed beamformer is a generalized sidelobe canceller (GSC) with a modified blocking matrix. The modified GSC blocking matrix using channel estimation results is proposed to combat the fading channel effects. Moreover, the diagonal loading method is used to obtain a beamforming performance robust against system imperfections. The simulation results show that the proposed beamformer greatly improves the system performance when strong interference exists.
Mapping the cellular electrophysiology of rat sympathetic preganglionic neurones to their roles in cardiorespiratory reflex integration: a whole cell recording study in situ (2014)

Sympathetic preganglionic neurones (SPNs) convey sympathetic activity flowing from the CNS to the periphery to reach the target organs. Although previous in vivo and in vitro cell recording studies have explored their electrophysiological characteristics, it has not been possible to relate these characteristics to their roles in cardiorespiratory reflex integration. We used the working heart-brainstem preparation to make whole cell patch clamp recordings from T3-4 SPNs (n = 98). These SPNs were classified by their distinct responses to activation of the peripheral chemoreflex, diving response and arterial baroreflex, allowing the discrimination of muscle vasoconstrictor-like (MVC(like), 39%) from cutaneous vasoconstrictor-like (CVC(like), 28%) SPNs. The MVC(like) SPNs have higher baseline firing frequencies (2.52 ± 0.33 Hz vs. CVC(like) 1.34 ± 0.17 Hz, P = 0.007). The CVC(like) have longer after-hyperpolarisations (314 ± 36 ms vs. MVC(like) 191 ± 13 ms, P < 0.001) and lower input resistance (346 ± 49 MΩ vs. MVC(like) 496 ± 41 MΩ, P < 0.05). MVC(like) firing was respiratory-modulated with peak discharge in the late inspiratory/early expiratory phase and this activity was generated by both a tonic and respiratory-modulated barrage of synaptic events that were blocked by intrathecal kynurenate. In contrast, the activity of CVC(like) SPNs was underpinned by rhythmical membrane potential oscillations suggestive of gap junctional coupling. Thus, we have related the intrinsic electrophysiological properties of two classes of SPNs in situ to their roles in cardiorespiratory reflex integration and have shown that they deploy different cellular mechanisms that are likely to influence how they integrate and shape the distinctive sympathetic outputs.
Peptidomimetics and Angiogenesis (2002)

Angiogenesis is the sprouting of new blood capillaries from surrounding preexisting blood vessels. This process is fundamental for embryonic development, wound healing and inflammation. In healthy adults angiogenesis is of minor importance. However, aberrant angiogenesis is essentially involved in disorders as diabetic retinopathy, rheumatoid arthritis and tumor growth, and blocking angiogenesis has emerged as a promising target for antagonizing these diseases. Therefore the development of new anti-angiogenic drugs is of great interest in academic and industrial research. This review focuses on the employment of peptidomimetics in inhibiting pathologic angiogenesis. It will survey the individual aspects of angiogenesis where the usage of peptidomimetics is favored and will consider the current progresses on this field.
Various AGC repeat numbers in the coding region of the human transcription factor gene E2F-4 Communicated by: R.G.H. Cotton Online Citation: Human Mutation, Mutation in Brief #301 (1999) Online http://journals.wiley.com/1059-7794/pdf/mutation/301.pdf (2000)

The E2F family of transcription factors regulates the expression of genes required for DNA synthesis and cell cycle control. The AGC triplet repeat in the coding region of the E2F-4 gene, a member of the family, has been reported to be mutated in colorectal cancers with a microsatellite instability (MSI) phenotype. We found a wider range variation of the repeat number in DNAs from tumors, the corresponding normal mucosa, and healthy individuals. A total of 5 repeat variants, ranging from 8 to 17 AGC repeats, was detected in 6 (9.7%) of the 62 healthy individuals and 8 (8.9%) of the 90 normal DNAs of the patients. The wild-type 13 repeat was present in all of these individuals. The variation of the AGC repeat number may be a polymorphism. Further, loss of heterozygosity (LOH) at the E2F-4 locus in the tumor tissues of 2 (25%) of the 8 informative cases was detected. The variation may be a useful marker for detection of LOH in primary tumors. Hum Mutat 15:296–297, 2000. © 2000 Wiley-Liss, Inc.
Research data supporting "Dynamic flow synthesis of porous organic cages" (2015)

Supporting information for the synthesis of organic porous cages
Metal nanoparticles as passive and active tools for bioanalytics (2005)

Metal nanoparticles represent an interesting tool for bioanalytics. Due to their small size, attachment to biomolecules does not interfere significantly with specific molecular binding. Therefore particles can be applied as label in affinity assays (e.g., DNA hybridization), using setups with high parallelization. Beside this rather passive use of nanoparticles, these structures can also be utilized as 'nano antenna' for the conversion of laser light pulses into heat. Using DNA-modified particles sequence-specific bound to DNA, a novel restriction technique is in development that applies this conversion for local DNA destruction. Metal nanoparticles combine the ability for highly precise positioning (due to specific molecular binding) with the possibility of optical access in a bright-field mode. They exhibit an interesting potential for spanning the gap between the macroscopic technical environment and the molecular scale, thereby enabling a true integration of nanoscale constructs with today’s technology.
Intradermal immunization with a bovine herpesvirus-1 DNA vaccine induces protective immunity in cattle. (1998)

Although intramuscular (i.m.) injection of DNA encoding glycoprotein D (gD) of bovine herpesvirus-1 (BHV-1) induces immune responses in cattle, this route of delivery is inefficient. Here we assessed three parameters that may enhance the efficacy of a gD DNA vaccine in cattle. First, the immune response generated by i.m. injected plasmid expressing a secreted form of gD (tgD) was determined and found to be very similar in magnitude to the response induced by gD-expressing plasmid. Secondly, gD- and tgD-expressing plasmids were administered by intradermal (i.d.) immunization, which resulted in a superior immune response to the secreted form, but no improvement in the response to the membrane-associated form. However, the form of gD used for immunization did not influence the immunoglobulin subtype, the ratio of antigen- specific IgG1 to IgG2 being approximately 4:1. Finally, the effect of promoter strength was assessed by replacing the Rous sarcoma virus (RSV) promoter, which was used in the original experiments, with the human cytomegalovirus immediate early promoter and first intron A (HCMV/IA). Although upon transfection in vitro the HCMV/IA promoter appeared to be stronger than the RSV promoter, there was only a 2-fold higher antibody response in vivo upon i.d. injection of cattle. Protection against virus challenge was obtained in the calves immunized i.d. with tgD-encoding plasmid, as shown by a significant reduction in weight loss, virus excretion, temperature response and clinical disease. No significant protection was observed in the animals vaccinated i.d. with the gD-expressing plasmid, which correlates with the lower level of immunity pre-challenge.
ChemInform Abstract: Triarylphosphines: Molecular Geometry, Anodic Behavior and ESR Study of the Radical Cations (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Observation of Long Transients in the Electrical Characterization of Thin Film BST Capacitors (2003)

Charge trapping is responsible for long transient leakage currents observed in parallel plate thin film BST capacitors. The presence of such time dependence complicates the measurement of leakage current as a function of an applied voltage, with the voltage sweep introducing hysteresis in the absence of ferroelectricity. The effect of long transients on current-voltage sweeps is discussed, as well as a method of obtaining current-voltage characteristics in the presence of transient leakage currents.
Increased sphingoid base‐1‐phosphates and failure of neural tube closure after exposure to fumonisin or FTY720 (2012)

Elevated sphingoid base-1-P after FB(1) or FTY720 suggest a potential role for these bioactive lipid ligands and activation of S1P receptor signaling pathways in the failure of neural tube closure after FB(1) or FTY720. Sa1P may represent a biomarker for FB(1)-NTD risk assessment.
Acquired haemophilia in recipients of depot thioxanthenes (2000)

We present two cases in which the occurrence of acquired haemophilia is associated with the use of depot preparations of the thioxanthenes zuclopenthixol and flupenthixol. These drugs have not previously been implicated in the aetiology of acquired haemophilia.