gebhart/patrepeval huggingface dataset:
Integrated analysis of the heterogeneous microarray data (2011)

The linear mixed effect model has advantages of allowing for various types of covariance structures over ANOVA model. Further, it can handle easily the correlated microarray data such as paired microarray data and repeated microarray data from the same subject.
Water Nonintrusive Load Monitoring (2014)

Resource conservation decisions require detailed consumption information. This paper presents sensors and signal processing techniques that use pipe vibration signatures to non-intrusively identify water consumption at the appliance level. The method requires as little as one easily installed vibration sensor. This method provides a no-fuss retrofit solution for detecting the operation of a building's water consuming appliances. In addition, flow rate is nonintrusively obtained from a conventional water meter via a new, high sensitivity strap-on magnetic sensor. Together, these two sensors track load operating schedule and water consumption in a building, demonstrated here at three different field test sites.
Somatic Embryogenesis and Plantlet Regeneration on Several Species of Licoric. (1999)

Leaf explants of four species of licorice (Glycyrrhiza glabra L., G. uralensis F., G. echinata L., and G. squamulosa F.) were cultured on Murashige and Skoog (MS) basal medium. G. glabra L. and G. uralensis F. formed adventitious roots from calli on the medium containing NAA (1mgl-1). Both calli induced from G. echinata L. and G. squamulosa F. formed somatic embryos on the medium containing NAA (1mgl-1) and BAP (1mgl-1), or 2, 4-D (0.5mgl-1) alone. Plantlets regenerated from the somatic embryos were transplanted to soil.
Experimental study of sutureless vascular anastomosis with use of glued prosthesis in rabbits (2015)

This technique may provide a feasible and successful alternative in vascular surgery. However, further long-term studies are necessary to elucidate the break pressure and degree of inflammation at the anastomotic site.
Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines (2014)

QSAR modeling using molecular signatures and support vector machines with a radial basis function is increasingly used for virtual screening in the drug discovery field. This method has three free parameters: C, γ, and signature height. C is a penalty parameter that limits overfitting, γ controls the width of the radial basis function kernel, and the signature height determines how much of the molecule is described by each atom signature. Determination of optimal values for these parameters is time-consuming. Good default values could therefore save considerable computational cost. The goal of this project was to investigate whether such default values could be found by using seven public QSAR data sets spanning a wide range of end points and using both a bit version and a count version of the molecular signatures. On the basis of the experiments performed, we recommend a parameter set of heights 0 to 2 for the count version of the signature fingerprints and heights 0 to 3 for the bit version. These are in combination with a support vector machine using C in the range of 1 to 100 and γ in the range of 0.001 to 0.1. When data sets are small or longer run times are not a problem, then there is reason to consider the addition of height 3 to the count fingerprint and a wider grid search. However, marked improvements should not be expected.
Non-orthogonal multiple access (NOMA): Concept, performance evaluation and experimental trials (2015)

Non-orthogonal multiple access (NOMA) has been attracting a lot of attention as a promising downlink multiple access scheme for LTE enhancements and 5G. This paper introduces an overview of the concept, performance evaluation gains and our experimental trials related to NOMA. The goal is to clarify the benefits of NOMA over orthogonal multiple access (OMA) such as OFDMA adopted by Long-Term Evolution (LTE), also its combination with MIMO is discussed. Using computer simulations, NOMA performance gains are assessed from both link-level and system-level perspectives. Also, our NOMA test-bed and the measurement results are explained. Our evaluation results and measurements show that NOMA provides higher gains compared to OFDMA. These gains are more than 30%.
Association of metformin use on metabolic acidosis in diabetic patients with chronic hepatitis B‐related cirrhosis and renal impairment (2021)

In conclusion, patients with Child-Pugh class B cirrhosis or above were at a higher risk of metabolic acidosis. Metformin further increased the risk in patients with Child-Pugh class B cirrhosis or above and stage 3A CKD or above. Dose adjustment in stage 4/5 CKD did not reduce the risk of metabolic acidosis.
Structurally and Functionally Distinct Mouse Hsp70 Family Members Mot-1 and Mot-2 Proteins are Encoded by Two Alleles (2000)

The mouse mortalin proteins Mot-1 and Mot-2 differ by two amino acids in their carboxy-terminus. These proteins are differentially localized in the cell cytoplasm and have contrasting biological activities. The genetic relationship between Mot-1 and Mot-2 was deciphered by mouse family analyses. Mot-1 and Mot-2 segregated in F1 and F2 progeny, providing direct evidence that the two proteins are encoded by two alleles.
A genetic neural network modeling of GaN HEMTs for RF power amplifiers design (2011)

A genetic neural network based large-signal model for GaN HEMT transistor suitable for designing power amplifiers (PAs) is presented along with its parameters extraction procedure. This model is relatively easy to construct and implement in CAD software and requires only DC and S-parameter measurements. The modeling procedure was applied to a 4-W packaged GaN-on-Si HEMT and the developed model is validated by comparing its large-signal simulation to measured data. The model has been employed for simulating a switching-mode inverse class-F power amplifier. Very good agreement between the amplifier simulation and measurement shows the validity of the model.
<title>Irregular periodic sampling of images and their derivatives</title> (1993)

Given a band-limited signal, we consider the sampling of the signal and its first K derivatives in a periodic manner. The mathematical concept of frames is utilized in the analysis of the sequence of sampling functions. It is shown that the frame operator of this sequence can be expressed as matrix-valued function multiplying a vector-valued function. An important property of this matrix is that the maximum and minimum eigenvalues are equal (in some sense) to the upper and lower frame bounds. We present a way for finding the dual frame and, thereby, a way for reconstructing the signal from its samples. Using the matrix approach we also show that if no sampling of the signal itself is involved, the sampling scheme can not be stabilized by oversampling. The formalism can be extended to two dimensions to permit representation of images.
Endoscopic sutured gastroplasty in addition to lifestyle modification: short-term efficacy in a controlled randomised trial (2020)

NCT03255005.
Design and Performance of a New SPECT Detector for Multimodality Small Animal Imaging Platforms (2006)

A new detector for single photon emission computed tomography (SPECT) has been developed for the Siemens microCAT <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">reg</sup> II and Inveon Multimodality preclinical imaging systems. The detector provides an active imaging area of 15 cm times 15 cm. We review the design of this new SPECT detector and present some key performance characteristics. Integral and differential uniformity were 3.7% and 3.0%, respectively. Mean energy resolution for <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc (140 keV) was 12.5%. Sensitivity as high as 1400 cps/MBq was measured for <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc on a dual-detector system, and a spatial resolution of 0.7 mm (FWHM) was obtained using 0.5 mm single pinhole collimators. Additionally, we present data from representative preclinical SPECT studies acquired with single and multi-pinhole collimators and multiple isotopes. Reconstructed images demonstrate that this detector is capable of high-resolution SPECT for multimodality small animal imaging.
The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986T is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity (2023)

The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986<sup>T</sup> (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.
Mouse Mammary Tumor Virus Infects Human Cells (2005)

Mouse mammary tumor virus (MMTV) has long been speculated to be involved in human breast cancer and more recently in human primary biliary cirrhosis. Despite complete proviral sequences markedly homologous to MMTV being identified in human breast cancer tissue, no convincing evidence has been presented to date that MMTV can infect human cells. Using both wild-type and a genetically marked virus (MMTV-EGFP), we show here the successful infection of a number of different human cells by MMTV. Furthermore, infection of human cells is shown to be almost as efficient as the infection of murine mammary epithelial cells. Sequencing of PCR products from integrated proviruses reveals that reverse transcription and integration of the viral genome has occurred as expected. Furthermore, sequencing of two independent MMTV proviral integration sites reveal them to be present only in the human and not in the mouse genome. Infection requires an intact MMTV envelope protein and is blocked either by heat inactivation of the virus or by specific neutralizing anti-MMTV serum, ruling out a nonspecific mechanism of viral transfer. Thus, MMTV can infect human cells and this finding provides a possible explanation for the detection by others of MMTV sequences in human breast cancer patients.
Supplemental figure 3 from Tumor-Infiltrating Lymphocytes Genetically Engineered with an Inducible Gene Encoding Interleukin-12 for the Immunotherapy of Metastatic Melanoma (2023)

&lt;p&gt;Supplemental figure 3. Association of cytokine production and LFT. Shown on left are serum cytokine levels for IL12 and IFNg over two week period. Shown on right are LFT for aspartate aminotransferase, alkaline phosphatase, and alanine aminotransferase over a two week period. Values shown were obtained from patient 24.&lt;/p&gt;
High efficiency transformation ofSchizosaccharomyces pombeby electroporation (1992)

Journal Article High efficiency transformation of Schizosaccharomyces pombe by electroporation Get access Holly L. Prentice Holly L. Prentice Department of Molecular Biology, Massachusetts General HospitalBoston, MA 02114, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 3, 11 February 1992, Page 621, https://doi.org/10.1093/nar/20.3.621 Published: 11 February 1992 Article history Received: 18 November 1991 Published: 11 February 1992
GRIP Deuterium Excess Reveals Rapid and Orbital-Scale Changes in Greenland Moisture Origin (2005)

The Northern Hemisphere hydrological cycle is a key factor coupling ice sheets, ocean circulation, and polar amplification of climate change. Here we present a Northern Hemisphere deuterium excess profile covering one climatic cycle, constructed with the use of delta18O and deltaD Greenland Ice Core Project (GRIP) records. Past changes in Greenland source and site temperatures are quantified with precipitation seasonality taken into account. The imprint of obliquity is evidenced in the site-to-source temperature gradient at orbital scale. At the millennial time scale, GRIP source temperature changes reflect southward shifts of the geographical locations of moisture sources during cold events, and these rapid shifts are associated with large-scale changes in atmospheric circulation.
Real-time monitoring and gradient feedback enable accurate trimming of ion-implanted silicon photonic devices (2018)

Fabrication errors pose significant challenges on silicon photonics, promoting post-fabrication trimming technologies to ensure device performance. Conventional approaches involve multiple trimming and characterization steps, impacting overall fabrication complexity. Here we demonstrate a highly accurate trimming method combining laser annealing of germanium implanted silicon waveguide and real-time monitoring of device performance. Direct feedback of the trimming process is facilitated by a differential spectroscopic technique based on photomodulation. The resonant wavelength trimming accuracy is better than 0.15 nm for ring resonators with 20-µm radius. We also realize operating point trimming of Mach-Zehnder interferometers with germanium implanted arms. A phase shift of 1.2π is achieved by annealing a 7-μm implanted segment.
Membrane Potential-Dependent Effects of SC-36602, a New Class I Antiarrhythmic Agent on Cardiac Action Potentials (1987)

Summary: The in vitro electrophysiological properties of a new class I antiarrhythmic agent, SC-36602, were evaluated by recording action potentials (APs) from guinea pig papillary muscle. SC-36602 and its (+) and (−) enantiomers (10−6−10−4M) caused a concentration- and only slight frequency-dependent depression of Vmax (maximum rate of rise of the AP). At stimulation rates of 30, 60, 120, and 200 pulses/min, SC-36602 (10−4M) reduced Vmax to 64 ± 2.2, 62 ± 2.8, 60 ± 2.4, and 58 ± 2.7% of control, respectively, and significantly shortened effective refractory period (ERP) (20–40%). The rate constants for onset of block of Vmax during trains of stimuli at 1 or 3.3 Hz were similar (˜0.2 AP−1). Slow recovery from Vmax block following a stimulus train recorded in tissue depolarized by 10 mM [K+]o Tyrode's solution was enhanced following exposure to SC-36602. The normalized relationship between Vmax and membrane potential was shifted 3 and 12 mV in the hyperpolarizing direction at stimulation frequencies of 0.2 and 1 Hz, respectively. These results suggest that SC-36602 would preferentially depress conduction in depolarized tissue in vivo.
A New Antifungal Macrolide Component, Brasilinolide B, Produced by Nocardia brasiliensis. (2000)

Our continuing studies on biologically active compounds from pathogenic microorganism1 2) showed that Nocardia brasiliensis IFM 0466 produces a new antifungal brasilinolide group antibiotic3~5), brasilinolide B (1), distinguishable from brasilinolide A3~5) by its chromatographic properties. This paper describes the fermentation, isolation and structural elucidation of this macrolide (1).
Genome-wide discovery of loci influencing chemotherapy cytotoxicity (2004)

Little is known about the heritability of chemotherapy activity or the identity of genes that may enable the individualization of cancer chemotherapy. Although numerous genes are likely to influence chemotherapy response, current candidate gene-based pharmacogenetics approaches require a priori knowledge and the selection of a small number of candidate genes for hypothesis testing. In this study, an ex vivo familial genetics strategy using lymphoblastoid cells derived from Centre d'Etude du Polymorphisme Humain reference pedigrees was used to discover genetic determinants of chemotherapy cytotoxicity. Cytotoxicity to the mechanistically distinct chemotherapy agents 5-fluorouracil and docetaxel were shown to be heritable traits, with heritability values ranging from 0.26 to 0.65 for 5-fluorouracil and 0.21 to 0.70 for docetaxel, varying with dose. Genome-wide linkage analysis was also used to map a quantitative trait locus influencing the cellular effects of 5-fluorouracil to chromosome 9q13-q22 [logarithm of odds (LOD) = 3.44], and two quantitative trait loci influencing the cellular effects of docetaxel to chromosomes 5q11-21 (LOD = 2.21) and 9q13-q22 (LOD = 2.73). Finally, 5-fluorouracil and docetaxel were shown to cause apoptotic cell death involving caspase-3 cleavage in Centre d'Etude du Polymorphisme Humain lymphoblastoid cells. This study identifies genomic regions likely to harbor genes important for chemotherapy cytotoxicity using genome-wide linkage analysis in human pedigrees and provides a widely applicable strategy for pharmacogenomic discovery without the requirement for a priori candidate gene selection.
ECoNet: Estimating Everyday Conversational Network From Free-Living Audio for Mental Health Applications (2022)

Sociability impairment, such as decreased social network size and socialization, is implicated in mental health disorders. To complement the existing self-reports-based assessment of sociability measures, which could be error-prone and burdensome, we propose to estimate an individual’s everyday conversational network from free-living speech recordings obtained with a wearable. Our first contribution is ECoNet, an automatic method to estimate the everyday conversational network using a modular audio processing architecture. Our second contribution is using ECoNet to analyze multiday egocentric audio recordings from 32 individuals representing diverse mental health conditions (healthy controls, depressive disorders, and psychotic disorders). Specifically, we discover that the conversational network size as a sociability measure has a significant correlation with mental health scores. For example, the correlation coefficient between network size and depression severity score was $-0.56$-0.56 ($p<0.01$p<0.01). Audio-based estimation of conversational network size using ECoNet, therefore, could provide a pervasive computing solution to complement existing mental health assessment methods.
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics (2020)

Neurotoxicity caused by nonfibrillar amyloid β (Aβ) oligomers in the brain is suggested to be associated with the onset of Alzheimer’s disease (AD). Elucidating the structural features of Aβ oligomers is critical for promoting drug discovery research for AD. One of the Aβ oligomers, known as Aβ*56, is a dodecamer that impairs memory when injected into healthy rats, suggesting that Aβ*56 may contribute to cognitive deficits in AD patients. Another dodecamer structure, formed by 20-residue peptide segments derived from the Aβ peptide (Aβ17–36), has been revealed by X-ray crystallography. The structure of the Aβ17–36 dodecamer is composed of trimer units and shows the oligomer antibody A11 reactivity, which are characteristic of Aβ*56, indicating that Aβ*56 and the Aβ17–36 dodecamer share a similar structure. However, the structure of the C-terminal regions (Aβ37–42) remains unclear. The C-terminal region, which is abundant in hydrophobic residues, is thought to play a key role in stabilizing the oligomer structure by forming a hydrophobic core. In this study, we employed dissipative particle dynamics, a coarse-grained simulation method with soft core potentials, utilizing the crystal structure information to unravel Aβ dodecamer structures with C-terminal regions. The simulation results were validated by the reported experimental data. Hence, an analysis of the simulation results can provide structural insights into Aβ oligomers. Our simulations revealed the stabilization mechanism of the dodecamer structure at the molecular level. We showed that C-terminal regions spontaneously form a hydrophobic core in the central cavity, contributing to stabilizing the dodecamer structure. Furthermore, four consecutive hydrophobic residues in the C-terminal region (i.e., Val39–Ala42) are important for core formation.
Raman Scattering in GaN/AlN Multiple Quantum Disk Nanocolumns (2007)

We have studied phonon modes in GaN/AlN multiple quantum disk nanocolumns, which are self‐organized on Al2O3 and Si substrates by RF‐MBE, by means of Raman scattering. The Raman spectrum drastically changes with increasing thickness of the GaN quantum disk. We find the confined, quasi‐confined and interface phonon modes, which are not observed in the usual GaN/AlN superlattice thin film. They are activated by confinement in the columnar nanostructures and a multiple‐scattering process.
Fe–N–C Electrocatalysts’ Durability: Effects of Single Atoms’ Mobility and Clustering (2020)

Atomically dispersed (or single atom) iron–nitrogen–carbon (Fe–N–C) catalysts are promising alternatives to platinum group metal nanoparticles supported on dispersed carbon as a cathode material in proton-exchange membrane fuel cells. Here, the degradation mechanism of Fe–N–C catalysts, synthesized by the sacrificial support method (SSM), was investigated by conducting accelerated stress tests under the “load cycling” protocol (i.e. from 0.6 to 1.0 V vs the reversible hydrogen electrode). Electrocatalyst activity toward the oxygen reduction reaction (ORR) was studied for a SSM-derived material, obtained by a single pyrolysis under a 7% H2 atmosphere (Fe-HT1) and juxtaposed to that of a catalyst derived from the same sample, but subjugated to a second pyrolysis under 10% NH3 (noted as Fe-HT2). Several findings can be highlighted: (i) the second pyrolysis results in the skewing of the mesopore size toward higher diameter, along with an increase in iron content and N-pyridinic moieties, leading to a combined benefit in terms of ORR activity and selectivity, (ii) the morphological changes of these catalysts during ageing are drastically different depending on whether they were exposed to a second pyrolysis as, for example, (iii) for Fe-HT2, the formation of Fe-clusters was observed after the load cycling ageing protocol performed at T = 80 °C, along with the partial corrosion of the amorphous domains. No clustering was observed at T = 60 °C concomitantly with a higher ORR mass activity retention providing some guidelines to improve the stability of Fe–N–C materials.
Room Temperature Sonoelectrochemical Synthesis of Molybdenum Sulfide Fullerene-Like Nanoparticles (1999)

Electrochemistry and sonochemistry have been combined to prepare fullerene-like structures of MoS2 at room temperature and in high yield. Either electrodeposition or ultrasonic irradiation alone results in amorphous products, whereas the application of an electric current pulse followed by a burst of ultrasonic energy gives rise to well-crystallized MoS2 structures such as the polyhedron shown in the Figure.