gebhart/patrepeval huggingface dataset:
Highly Selective Multiple Gases Detection Using a Thermal-Conductivity-Based MEMS Resonator and Machine Learning (2022)

There is an urgent need to develop innovative and highly selective gas sensors for environmental, residential, and industrial applications. Here, we propose a highly selective multiple gases detection system using an electro-thermally heated silicon micro-resonator and machine- learning algorithms. The device is based on the cooling/heating effect of gases on the thermal stresses of a resonating structure. As a case study, we demonstrate sensitive and selective responses toward He, Ar, and CO2. To generate the unique signature markers for each gas, multiple datasets are collected at three different concentration levels (4%, 10%, and 25%). A principal component analysis (PCA) is conducted using seven customized highly significant and unique signature markers. The markers are obtained through data processing from the response of all gases. Quadratic discriminant and medium Gaussian support vector machines (SVMs) are used for training based on the seven customized features, which yield a high classification accuracy of 100 %. The proposed gas- sensing approach can be promising for the development of intelligent and highly selective compact size sensing platforms without the need for special materials for coating and functionalization.
Studies of Organometallic Self-Assembled Monolayers on Ag and Au Using Surface Plasmon Spectroscopy (1997)

We report the synthesis of a novel rhenium complex, {fac-Re(2,2‘-bipyridine)(CO)3(NC5H4)CH2NHCO(CH2)2S−}2 and its self-assembly behavior on Ag and Au, including characterization of the monolayer using surface plasmon spectroscopy (SPS). Further surface characterization, which proved to be quite complementary to SPS, was accomplished with surface-enhanced Raman spectroscopy (SERS), FTIR, ellipsometry, and contact angle measurements. SERS and FTIR data have also been used to verify the self-assembly of the free ligand and rhenium complexes on Ag to form monolayers (SAMs). Vibrational analysis also provided evidence that the attachment of the free ligand and complexes to the metal substrate occurs by reaction of the disulfide bond and not through the pyridine or bipyridine. The tilt angle of the complex with respect to the surface normal of the metal was also calculated using a projection analysis that incorporated the SPS determined thickness and a molecular mechanics (MM) minimized molecular length. Independently, a MM tilt angle was determined by minimization of a hexagonal grouping of six complexes surrounding one, each bound through a sp hybridized S-metal bond to a hollow surface site. Though this calculation is in need of further refinement, the agreement with our projection analysis is good.
Molecular detection ofCulicoidesspp. andCulicoides imicola, the principal vector of bluetongue (BT) and African horse sickness (AHS) in Africa and Europe (2004)

Bluetongue (BT) and African Horse Sickness (AHS) are infectious arthropod-borne viral diseases affecting ruminants and horses, respectively. Culicoides imicola Kieffer, 1913, a biting midge, is the principal vector of these livestock diseases in Africa and Europe. Recently bluetongue disease has re-emerged in the Mediterranean Basin and has had a devastating effect on the sheep industry in Italy and on the islands of Sicily, Sardinia, Corsica and the Balearics, but fortunately, has not penetrated onto mainland France and Spain. To survey for the presence of C. imicola, an extensive light-trap network for the collection of Culicoides, was implemented in 2002 in southern mainland France. The morphological identification of Culicoides can be both tedious and time-consuming because its size ranges from 1.5 to 3 mm. Therefore, an ITS1 rDNA polymerase chain reaction (PCR)-based diagnostic assay was developed to rapidly and reliably identify Culicoides spp. and C. imicola. The aim of this work was to set up a rapid test for the detection of C. imicola amongst a pool of insects collected in areas at risk for BT. The sequence similarity of the rDNA (nuclear ribosomal DNA), which is greater within species than between species, is the foundation of its utilisation in species-diagnostic assays. The alignment of the 11 ITS1 sequences of Culicoides obtained from Genbank and EMBL databases helped us to identify one region in the 5' end and one in the 3' end that appear highly conserved. PCR primers were designed within these regions to amplify genus-specific fragments. In order to set up a C. imicola-specific PCR, another forward primer was designed and used in combination with the previously designed reverse primer. These primers proved to be highly specific and sensitive and permitted a rapid diagnostic separation of C. imicola from Culicoides spp.
Supplementary Figure 2, Video 3 from Enhancement of Human Cancer Cell Motility and Invasiveness by Anaphylatoxin C5a via Aberrantly Expressed C5a Receptor (CD88) (2023)

&lt;p&gt;AVI file - 15325K, Time-lapse video analysis-C5aR(+)C5a(-)&lt;/p&gt;
Physical limits to clock synchronization (2001)

Clock synchronization procedures are analyzed in the presence of imperfect communications. In this context we show that there are physical limitations which prevent one from synchronizing distant clocks when the intervening medium is completely dephasing, as in the case of a rapidly varying dispersive medium.
Rates of assembly and degradation of bacterial ice nuclei (1990)

The kinetics of ice-nucleus assembly from newly synthesized nucleation protein were observed following induction of nucleation gene expression in the heterologous host Escherichia coli. Assembly was significantly slower for the small proportion of ice nuclei active above -4.4 degrees C; this was consistent with the belief that these nuclei comprise the largest aggregates of nucleation protein. The kinetics of nucleus degradation were followed after inhibiting protein synthesis. Nucleation activity and protein showed a concerted decay, indicating that most of the functional ice nuclei are in equilibrium with a single cellular pool of nucleation protein. A minority of the ice nuclei decayed much more slowly than the majority; presumably their nucleation protein was distinct either by virtue of different structure or different subcellular compartmentalization, or because of its presence in a metabolically distinct subpopulation of cells.
Liquid Crystal Elastomer-Based Microelectrode Array for In Vitro Neuronal Recordings (2018)

Polymer-based biomedical electronics provide a tunable platform to interact with nervous tissue both in vitro and in vivo. Ultimately, the ability to control functional properties of neural interfaces may provide important advantages to study the nervous system or to restore function in patients with neurodegenerative disorders. Liquid crystal elastomers (LCEs) are a class of smart materials that reversibly change shape when exposed to a variety of stimuli. Our interest in LCEs is based on leveraging this shape change to deploy electrode sites beyond the tissue regions exhibiting inflammation associated with chronic implantation. As a first step, we demonstrate that LCEs are cellular compatible materials that can be used as substrates for fabricating microelectrode arrays (MEAs) capable of recording single unit activity in vitro. Extracts from LCEs are non-cytotoxic (>70% normalized percent viability), as determined in accordance to ISO protocol 10993-5 using fibroblasts and primary murine cortical neurons. LCEs are also not functionally neurotoxic as determined by exposing cortical neurons cultured on conventional microelectrode arrays to LCE extract for 48 h. Microelectrode arrays fabricated on LCEs are stable, as determined by electrochemical impedance spectroscopy. Examination of the impedance and phase at 1 kHz, a frequency associated with single unit recording, showed results well within range of electrophysiological recordings over 30 days of monitoring in phosphate-buffered saline (PBS). Moreover, the LCE arrays are shown to support viable cortical neuronal cultures over 27 days in vitro and to enable recording of prominent extracellular biopotentials comparable to those achieved with conventional commercially-available microelectrode arrays.
Escherichia coli tRNA Tyr Gene Clusters: Organization and Structure (1980)

Escherichia coli contains two species of tRNA Tyr that differ from each other by only two bases in the variable loop region (Goodman et al. 1968Goodman et al. 1970). The locus tyrT at 27 minutes (Garen et al. 1965; Signer et al. 1965; Bachman et al. 1976) has been shown to contain duplicate copies of the tRNA 1 Tyr sequence, since the bacteriophage φ80 p su + − 3 stimulates the production of both su + and su − tRNA 1 Tyr (Russell et al. 1970). Derivatives of this bacteriophage, carrying only a single su + tRNA 1 Tyr copy, have been isolated. These are presumed to arise by unequal recombination involving the two tRNA 1 Tyr mature structural sequences (Russell et al. 1970). The tyrU locus, on the opposite side of the E. coli chromosome at 88 minutes (Orias et al. 1972), codes for tRNA 2 Tyr (Eggerston and Adelberg 1965; Orias et al. 1972; Squires et al. 1973) and has been shown to contain a single tRNA 2 Tyr mature structural sequence. We are attempting to determine those aspects of tRNA gene structure and organization that are crucial to the initiation and termination of transcription and the regulation of gene expression. The tRNA Tyr genes of E. coli, which have already figured prominently in this area, afford a model system well suited for studying this group of problems. In the experiments described here, the tRNA 1 Tyr transducing phages φ 80p su +− 3 (doublet) and φ 80p su + 3 (singlet) (Russell et al. 1970), and the tRNA 2 Tyr transducing phages λh80d glyTsu + 36 (Squires et al. 1973) and λ rif d 18 (Kirschbaum and Konrad 1973) have been used to study the structural organizations of regulatory...
Synthesis and Application of Alkenylstannanes Derived from Base-Sensitive Cyclopropenes (2008)

In the presence of stoichiometric potassium fluoride, a range of base-sensitive cyclopropenes undergo direct stannylation using (pentafluoroethyl)tributylstannane. The resulting stannylcyclopropenes serve as precursors to a variety of tetrasubstituted cyclopropenes that might otherwise be difficult to access using alternative methods.
Recovery of the electroretinogram in rabbits after argon laser photocoagulation. (1987)

Argon laser is widely used to coagulate the diabetic retina in order to inhibit the proliferative stage of diabetic retinopathy. Ten pigmented rabbits underwent retinal photocoagulation with argon laser. Retinal function was assessed electroretinographically before treatment and at different time intervals after treatment. The ERG responses measured 4-7 days after treatment were reduced in amplitude by a degree which was proportional to the number of laser applications. In five eyes that were treated with at least 1000 applications the ERG responses were very small when measured 4 days post-treatment. However, a gradual recovery was observed and within 2 months the ERG responses approached the normal pretreatment amplitudes. Histological findings from light and electron-microscopy suggested that the ERG recovery could not be solely explained by healing of the coagulated areas. Structural differences were seen in the pigment epithelial layer between a retina obtained immediately after treatment and one studied after ERG recovery. It is suggested that changes in the electrical resistance of the pigment epithelium may contribute to the ERG reduction seen immediately after laser treatment in the rabbit and to the increase in the ERG amplitude observed during the apparent functional recovery of the retina.
Carbon‐13 and carbon‐14 labeled dabigatran etexilate and tritium labeled dabigatran (2016)

Dabigatran etexilate or pradaxa, a novel oral anticoagulant, is a reversible, competitive, direct thrombin inhibitor. It is used to prevent strokes in patients with atrial fibrillation and the formation of blood clots in the veins (deep venous thrombosis) in adults who have had an operation to replace a hip or a knee. Pradaxa is the only novel oral anticoagulant available with both proven superiority to warfarin and a specific reversal agent for use in rare emergency situations. The detailed description of the synthesis of carbon-13 and carbon-14 labeled dabigatran etexilate, and tritium labeled dabigatran is described. The synthesis of carbon-13 dabigatran etexilate was accomplished in eight steps and in 6% overall yield starting from aniline-<sup>13</sup> C<sub>6</sub> . Ethyl bromoacetate-1-<sup>14</sup> C was the reagent of choice in the synthesis of carbon-14 labeled dabigatran etexilate in six steps and 17% overall yield. Tritium labeled dabigatran was prepared using either direct tritium incorporation under Crabtree's catalytic conditions or tritium-dehalogenation of a diiodo-precursor of dabigatran.
Synergistic induction of endothelial tissue factor by tumor necrosis factor and vascular endothelial growth factor: functional analysis of the tumor necrosis factor receptors (1996)

Tissue factor expression on the surface of endothelial cells can be induced by tumor necrosis factor (TNF) and vascular endothelial growth factor (VEGF) in a synergistic manner. We have investigated the role of the two different TNF receptors for this synergy. Firstly, stimulation of the 60 kDa TNF receptor (TNFR60) by a mutant of TNF specific for TNFR60 induced responses comparable to wild-type TNF. In contrast, stimulation of TNFR80 by a TNFR80-specific TNF mutein did not result in enhancement of tissue factor expression even in the presence of a suboptimal TNFR60 triggering. Secondly, we tested neutralizing TNF receptor antibodies for inhibition of tissue factor synthesis induced by VEGF and TNF. A TNFR60-specific antibody inhibited tissue factor production over a broad range of TNF concentrations, indicating an essential role of TNFR60 in the TNF/VEGF synergy. In contrast, blocking of TNF binding to TNFR80 strongly inhibited TNF-induced tissue factor expression at low, but less pronounced at high, TNF concentrations. In conclusion, these data are in agreement with a model in which TNFR80 participates in the synergy between VEGF and low concentrations of soluble TNF by passing the ligand to the signalling TNFR60.
Regulation of immune receptor kinases plasma membrane nanoscale landscape by a plant peptide hormone and its receptors (2020)

ABSTRACT Spatial partitioning is a propensity of biological systems orchestrating cell activities in space and time. The dynamic regulation of plasma membrane nano-environments has recently emerged as a key fundamental aspect of plant signaling, but the molecular components governing it are still mostly unclear. The receptor kinase FERONIA (FER) controls complex formation of the immune receptor kinase FLAGELLIN SENSING 2 (FLS2) with its co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and this function is inhibited by the FER ligand RAPID ALKALANIZATION FACTOR 23 (RALF23). Here, we show that FER regulates the plasma membrane nanoscale organization of FLS2 and BAK1. Our study demonstrates that akin to FER, leucine-rich repeat (LRR) extensin (LRXs) proteins contribute to RALF23 responsiveness, regulate BAK1 nanoscale organization and immune signaling. Furthermore, RALF23 perception leads to rapid modulation of FLS2 and BAK1 nanoscale organization and its inhibitory activity on immune signaling relies on FER kinase activity. Our results suggest that perception of RALF peptides by FER and LRXs actively modulates the plasma membrane nanoscale landscape to regulate cell surface signaling by other receptor kinases.
An interactive statistical imaging system and pilot application to characterize axillary lymph nodes in breast cancer (2008)

11059 Background: Clinical decisions in oncology are increasingly individualized and dependent upon accurate assessment of tumor biology, such as hormone receptor status. Imaging techniques are limited by subjective interpretation of staining patterns and limited tissue sampling leading to variability in patient care. We developed a novel imaging algorithm capable of quantifying multidimensional relationships between cell populations of interest on large tissue sections in a high-throughput fashion. Methods: An image analysis program was constructed in Java uniquely designed with supervised learning technology. Through an interactive visualization system, our technology allows a user to train the algorithm to detect cell types of interest. By incorporating statistical learning algorithms, cell classification can be improved rapidly with highly accurate results. The image analysis algorithm was applied to a series of IHC-stained sections of breast cancer-involved axillary lymph nodes. Four panels of three chromagens characterized the immune profile and breast tumor cells in 29,054 images. Cell type, location, and relative position to tumor were assessed by spatial analysis using R. Results: Following image training, cell classification remained highly accurate (>90%) among all images analyzed. Analysis quantified architectural patterns over an entire tissue section. Percent functional CD8 T cells with cytotoxic activity determined by granzyme B expression, percent CD4 T cells with T regulatory phenotype by CD25 and FoxP3 expression, and percent of dendritic cells actively presenting antigen were significantly dependent upon distance from lymph node-infiltrating tumor. Quantified cell populations of CD4 regulatory T cells and relative maturation status of antigen- presenting dendritic cells were statistically significant predictors of 5-year disease-free survival. Conclusions: We present imaging technology which is provided open-source for public use, that provides accurate quantification of cell populations in a high-throughput manner. We present novel, prognostically significant, architectural patterns of immune dysregulation dependent upon location of infiltrating breast cancer that warrant further study. No significant financial relationships to disclose.
Nocardia anaemiae sp. nov. Isolated from an Immunocompromised Patient and the First Isolation Report of Nocardia vinacea from Humans (2005)

Two actinomycete strains that were isolated from patients in Japan were assigned provisionally to the genus Nocardia based on their morphological characteristics. The two isolates were further studied to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rDNA sequence data for the strains showed that they are most similar to Nocardia vinacea. DNA-DNA hybridization experiments indicated that strain IFM 0344 should be identified as N. vinacea, and that strain IFM 0323T is classifiable as a new species. This report describes the first isolation of N. vinacea from clinical samples. A new species of the genus Nocardia is proposed based on their phenotypic and phylogenetic characteristics: Nocardia anaemiae for IFM 0323T (=NBRC 100462T=JCM 12396T=DSM 44821T).
Prospective Randomized Comparison of 8‐mm Gold‐Tip, Externally Irrigated‐Tip and 8‐mm Platinum‐Iridium Tip Catheters for Cavotricuspid Isthmus Ablation (2007)

This study demonstrates equivalent efficacies of gold, platinum-iridium and externally Irr. tip catheters for successful de novo ablation of the CTI.
Investigations of low amplitude radio frequency pulses at and away fro m rotary resonance conditions for I = 5/2 nuclei (2002)

Additional experimental evidence of rotary resonance effects for multiple-quantum coherence conversion in a spin-5/2 system is presented. Two dimensional plots of the relative efficiency of MQ excitation and conversion are given as a function of radio frequency (rf) amplitude and pulse width. Data are presented for the excitation of five-quantum coherence (5QC), as well as for 5QC to three-quantum coherence (3QC) conversion, 5QC to 1QC (the central transition coherence) conversion, and 3QC to 1QC conversion. A two-fold increase in the signal-to-noise ratio is achieved by substituting low amplitude rf pulses in place of hard rf pulses for 5QC excitation and 5QC to 3QC conversion in a mixed multiple-quantum MAS (MMQMAS) experiment. The anisotropic line shape for the low amplitude rf pulse version of the MMQMAS experiment was observed to be distorted from the MAS line shape. The cause and implications of the distortion are discussed.
Reconstruction of “unreconstructable” critical limb ischemia with hybrid techniques (2016)

This case describes the surgical repair of critical limb ischemia in a patient with diffuse multilevel peripheral arterial disease. It demonstrates the value of patient-specific approaches that employ hybrid endovascular and open surgical techniques to reconstruct blood flow in patients who are not ideal candidates for traditional revascularization. We detail a technique that combines endarterectomy, femoropopliteal bypass, angioplasty, and stenting. This case suggests that innovative hybrid approaches can be used to achieve limb salvage in some patients with multilevel peripheral vascular disease who would otherwise undergo primary amputation.
Rethinking Softmax Cross-Entropy Loss for Adversarial Robustness (2020)

Previous work shows that adversarially robust generalization requires larger sample complexity, and the same dataset, e.g., CIFAR-10, which enables good standard accuracy may not suffice to train robust models. Since collecting new training data could be costly, we focus on better utilizing the given data by inducing the regions with high sample density in the feature space, which could lead to locally sufficient samples for robust learning. We first formally show that the softmax cross-entropy (SCE) loss and its variants convey inappropriate supervisory signals, which encourage the learned feature points to spread over the space sparsely in training. This inspires us to propose the Max-Mahalanobis center (MMC) loss to explicitly induce dense feature regions in order to benefit robustness. Namely, the MMC loss encourages the model to concentrate on learning ordered and compact representations, which gather around the preset optimal centers for different classes. We empirically demonstrate that applying the MMC loss can significantly improve robustness even under strong adaptive attacks, while keeping state-of-the-art accuracy on clean inputs with little extra computation compared to the SCE loss.