gebhart/patrepeval huggingface dataset:
Network Dimensioning and Radio Resource Management for Multi-Tier Machine-Type Communications (2017)

For a radio resource limited multi-tier Machine-type Communication (MTC) network, controlling random access congestion while satisfying the unique requirements of each tier and guaranteeing fairness among nodes is always a challenge. In this paper, we propose three approaches for network dimensioning and radio resource partitioning for the uplink of an MTC network with signal-to-interference ratio (SIR)-based clustering and relaying, where MTC gateways (MTCGs) capture and forward the packets sent from MTC devices (MTCDs) to the base station (BS). Assuming that each tier has a different outage probability constraint, our first resource allocation method achieves maximum sum network capacity, while the other two methods achieve suboptimal sum network capacity with higher degrees of fairness. The proposed methods are also applicable when the objective is the network operator's total revenue instead of sum network capacity.
Optimized Mealtime Insulin Dosing for Fat and Protein in Type 1 Diabetes: Application of a Model-Based Approach to Derive Insulin Doses for Open-Loop Diabetes Management (2016)

This study demonstrates that insulin dose calculations need to consider meal composition in addition to carbohydrate content and provides the foundation for new insulin-dosing algorithms to cover meals of varying macronutrient composition.
Alterations in the Microstructure of the Anterior Mitral Valve Leaflet Under Physiological Stress (2012)

An improved understanding of mitral valve (MV) function remains an important goal for determining mechanisms underlying valve disease and for developing novel therapies. Critical to heart valve tissue homeostasis is the valvular interstitial cells (VICs), which reside in the interstitium and maintain the extracellular matrix (ECM) through both protein synthesis and enzymatic degradation [1]. There is scant quantitative experimental data on the alterations of the MV fiber network reorganization as a function of load, which is critical for implementation of computational strategies that attempt to link this meso-micro scale phenomenon. The observed large scale deformations experienced by VICs could be implicated in mechanotransduction [2], i.e., translation of mechanical stimuli into biochemical signals. Consequently, our goal was to quantitatively characterize the MV microstructure as a function of physiological loads, including localized 3D VIC deformations and relate it to the fiber network.
Experimental transfection of Macaca sylvanus with cloned human hepatitis B virus (2002)

Due to the absence of easily accessible animal models for the study of hepatitis B virus (HBV), the possibility of using Macaca sylvanus, a monkey originating from Morocco, North Africa, was investigated. Three monkeys were intrahepatically inoculated with a replication-competent head-to-tail HBV DNA plasmid dimer construct. The HBV surface antigen and HBV DNA were detected prior to alanine aminotransferase elevation in the serum of two of three HBV-inoculated monkeys at day 2 post-transfection and persisted for several weeks. This indicates that transfected animals developed markers of HBV infection. In addition, electron microscopy of the serum 3 weeks post-transfection showed the presence of virus particles whose shape and size were similar to complete 42 nm HBV Dane particles. Histological examination of liver tissues also revealed pathological changes not observed in uninfected controls, which strongly suggested acute hepatitis. HBV DNA was also detected by PCR in these monkey livers. Taken together, these results indicate that HBV can successfully replicate in this model and that M. sylvanus could be a potentially useful new primate model for the study of HBV replication.
Super-resolution fluorescence microscopy studies of human immunodeficiency virus (2018)

Super-resolution fluorescence microscopy combines the ability to observe biological processes beyond the diffraction limit of conventional light microscopy with all advantages of the fluorescence readout such as labelling specificity and non-invasive live-cell imaging. Due to their subdiffraction size (< 200 nm) viruses are ideal candidates for super-resolution microscopy studies, and Human Immunodeficiency Virus type 1 (HIV-1) is to date the most studied virus by this technique. This review outlines principles of different super-resolution techniques as well as their advantages and disadvantages for virological studies, especially in the context of live-cell imaging applications. We highlight the findings of super-resolution based HIV-1 studies performed so far, their contributions to the understanding of HIV-1 replication cycle and how the current advances in super-resolution microscopy may open new avenues for future virology research.
On secret key generation with massive MIMO antennas using time-frequency-space dimensions (2016)

Kerchoff's principle states that the security of encryption should be based on the key. Thus, increasing the encryption key length has been an essential approach in generating unbreakable ciphers. Recently, physical layer security has gained significant research attention. It allows secure communications between a source and destination without the need to resort to key-based encryption techniques. In this paper, secret key generation using massive multiple input multiple output (MIMO) techniques is investigated. The large number of subcarriers used in orthogonal frequency division multiple access (OFDMA) systems is also used to increase the key length. Several scenarios are investigated and corresponding key lengths are calculated. The combination of massive MIMO and OFDMA also allows to simultaneously implement physical layer security techniques while generating large keys for traditional key-based cryptography.
Identification of Infinite Dimensional Systems via Adaptive Wavelet Neural Networks (1993)

Abstract : We consider identification of distributed systems via adaptive wavelet neural networks (AWNNs). We take advantage of the multiresolution property of wavelet systems and the computational structure of neural networks to approximate the unknown plant successively. A systematic approach is developed in this paper to find the optimal discrete orthonormal wavelet basis with compact support for spanning the subspaces employed for system identification. We then apply backpropagation algorithm to train the network with supervision to emulate the unknown system. This work is applicable to signal representation and compression under the optimal orthonormal wavelet basis in addition to autoregressive system identification and modeling. We anticipate that this work be intuitive for practical applications in the areas of controls and signal processing.
Combining meta- and mega- analytic approaches for multi-site diffusion imaging based genetic studies: From the ENIGMA-DTI working group (2014)

Meta-analyses estimate a statistical effect size for a test or an analysis by combining results from multiple studies without necessarily having access to each individual study's raw data. Multi-site meta-analysis is crucial for imaging genetics, as single sites rarely have a sample size large enough to pick up effects of single genetic variants associated with brain measures. However, if raw data can be shared, combining data in a "mega-analysis" is thought to improve power and precision in estimating global effects. As part of an ENIGMA-DTI investigation, we use fractional anisotropy (FA) maps from 5 studies (total <i>N</i>=2,203 subjects, aged 9-85) to estimate heritability. We combine the studies through meta- and mega-analyses as well as a mixture of the two - combining some cohorts with mega-analysis and meta-analyzing the results with those of the remaining sites. A combination of mega- and meta-approaches may boost power compared to meta-analysis alone.
Spatial Degrees of Freedom of the Multicell MIMO Multiple Access Channel (2011)

We consider a homogeneous multiple cellular scenario with multiple users per cell, i.e., K ≥ 1 where K denotes the number of users in a cell. In this scenario, a degrees of freedom outer bound as well as an achievable scheme that attains the degrees of freedom outer bound of the multicell multiple access channel (MAC) with constant channel coefficients are investigated. The users have M antennas, and the base stations are equipped with N antennas. The found outer bound is general in that it characterizes a degrees of freedom upper bound for K ≥ 1 and L >; 1 where L denotes the number of cells. The achievability of the degrees of freedom outer bound is studied for two cell case (i.e., L = 2). The achievable schemes that attains the degrees of freedom outer bound for L = 2 are based on two approaches. The first scheme is a simple zero forcing with M = Kβ+β and N = Kβ, and the second approach is null space interference alignment with M = Kβ and N = Kβ + β where β >; 0 is a positive integer.
High-resolution ADCs design in sensors (2018)

This paper presents design considerations for high-resolution and high-linearity ADCs for biomedical imaging applications. The work discusses how to improve dynamic specifications such as Spurious Free Dynamic Range (SFDR) and Signal-to-Noise-and-Distortion Ratio (SNDR) in ultra-low power and high-resolution analog-to-digital converters (ADCs) including successive approximation register (SAR) for biomedical imaging application. The results show that with broad range of mismatch error, the SFDR is enhanced by about 10 dB with the proposed performance enhancement technique, which makes it suitable for high resolution image sensors sensing systems.
Progress status on Quanta Image Sensors (2021)

The Quanta Image Sensor (QIS) is a photon-counting image sensor conceptualized in 2004 by Fossum and reduced to practice over the past 8 years at Dartmouth using a CMOS image sensor platform, and now referred to as CIS-QIS. This CIS-QIS device is a photon-number resolving sensor that does not use avalanche multiplication, and has been demonstrated in megapixel format with small pixel pitch. This progress will be reported along with associated progress of the spin-out company Gigajot, and other collaborators. In just the past few years, SPAD devices have also been used to explore the QIS concept. Termed SPAD-QIS, the first megapixel SPAD-QIS was reported just in the past few weeks. A comparison of the advantages of CIS-QIS and SPAD-QIS will be presented. Both represent a paradigm shift in image acquisition and may become important for many quantum photonics applications.
Duodenal Mucosal Resurfacing Elicits Improvement in Glycemic and Hepatic Parameters in Type 2 Diabetes—One-Year Multicenter Study Results (2018)

Aims: Duodenal Mucosal Resurfacing (DMR) is a novel endoscopic procedure which has been shown to improve glycemic control at 6 months in type 2 diabetes (T2D). It is thought to exert insulin-sensitizing effects. DMR entails catheter based circumferential mucosal lifting followed by hydrothermal ablation. This study aimed to extend DMR experience, determining efficacy over 12 months in T2D patients on stable oral glucose lowering treatment. Methods: Single arm, multicenter study. 46 T2D patients on oral glucose lowering medication received a DMR procedure. Impact on glycemic control (HbA1c and fasting plasma glucose), insulin resistance (HOMA-IR) and liver enzymes (AST and ALT) was determined at baseline and 1, 3, 6, 9, 12 mo post DMR. Glucose lowering medication was kept stable 6 mo post DMR and adjusted according to local guidelines thereafter. Results: See figure 1. At 12 mo: δHbA1c -1.0±0.2% (p ≤ 0.001), δFPG -41±8 mg/dL (p ≤ 0.001), δHOMA-IR -3.6±0.9 (p = 0.005), δ weight -2.7±0.6kg (p = 0.003), δALT -10±2 (p = 0.005) and δAST -6±2 (p=0.002). DMR was well tolerated with no related serious adverse events or unexpected adverse device events reported. Conclusions: Single DMR treatment elicited significant and clinically relevant reductions in glycemic and hepatic parameters that were sustained at 12 months, suggesting considerable potential of DMR for the treatment of T2D. Disclosure A.C.G. van Baar: None. M. Nieuwdorp: None. F. Holleman: Other Relationship; Self; Sanofi-Aventis, Bioton, AstraZeneca. J. Deviere: None. L. Crenier: None. R. Haidry: None. R.L. Batterham: Research Support; Self; Fractyl Laboratories, Inc.. Board Member; Self; Novo Nordisk Inc.. Consultant; Self; Novo Nordisk Inc.. Advisory Panel; Self; National Institute for Health and Clinical Excellence, Nestlé. Speaker's Bureau; Self; Orexigen Therapeutics, Inc., Medtronic. D. Hopkins: Advisory Panel; Self; Novo Nordisk A/S, Sanofi-Aventis, Roche Pharma. Speaker's Bureau; Self; Janssen Pharmaceuticals, Inc., AstraZeneca, Eli Lilly and Company, Napp Pharmaceuticals, Ltd., Sunovion Pharmaceuticals Inc.. Other Relationship; Self; Diabetes UK. Speaker's Bureau; Self; Fractyl Laboratories, Inc.. L. Rodriguez Grunert: None. M. Galvao Neto: Consultant; Self; Fractyl Laboratories, Inc., GI Dynamics Inc., GI Windows, Inc., Ethicon US, LLC., Apollo EndoSurgery. P. Vignolo: None. G. Costamagna: None. J.J. Bergman: Research Support; Self; Fractyl Laboratories, Inc..
PcchiB1, encoding a class V chitinase, is affected by PcVelA and PcLaeA, and is responsible for cell wall integrity in Penicillium chrysogenum (2011)

Penicillin production in Penicillium chrysogenum is controlled by PcVelA and PcLaeA, two components of the regulatory velvet-like complex. Comparative microarray analysis with mutants lacking PcVelA or PcLaeA revealed a set of 62 common genes affected by the loss of both components. A downregulated gene in both knockout strains is PcchiB1, potentially encoding a class V chitinase. Under nutrient-depleted conditions, transcript levels of PcchiB1 are strongly upregulated, and the gene product contributes to more than 50 % of extracellular chitinase activity. Functional characterization by generating PcchiB1-disruption strains revealed that PcChiB1 is responsible for cell wall integrity and pellet formation in P. chrysogenum. Further, fluorescence microscopy with a DsRed-labelled chitinase suggests a cell wall association of the protein. An unexpected phenotype occurred when knockout strains were grown on media containing N-acetylglucosamine as the sole C and N source, where, in contrast to the recipient, a penicillin producer strain, the mutants and an ancestral strain show distinct mycelial growth. We discuss the relevance of this class V chitinase for morphology in an industrially important fungus.
Determining Concentration of Nanoparticles from Ellipsometry (2008)

A method of using ellipsometry or polarization analysis of light in total internal reflection of a surface to determine the number density of gold nanoparticles on a smooth substrate has been developed. The method can be modified to enable determination of densities of sparse distributions of nanoparticles in general, and is expected to be especially useful for measuring gold-nanoparticle-labeled biomolecules on microarrays. The method is based on theoretical calculations of the of gold nanoparticles. Elements of the calculations include the following: For simplicity, the gold nanoparticles are assumed to be spherical and to have the same radius. The distribution of gold nanoparticles is assumed to be a sub-monolayer (that is, sparser than a monolayer). The optical response of the sub-monolayer is modeled by use of a thin-island-film theory, according to which the polarizabilities parallel and perpendicular to the substrate are functions of the wavelength of light, the dielectric functions (permittivities expressed as complex functions of frequency or wavelength) of the gold and the suspending medium (in this case, the suspending medium is air), the fraction of the substrate area covered by the nanoparticles, and the radius of the nanoparticles. For the purpose of the thin-island-film theory, the dielectric function of the gold nanoparticles is modeled as the known dielectric function of bulk gold plus a correction term that is necessitated by the fact that the mean free path length for electrons in gold decreases with decreasing radius, in such a manner as to cause the imaginary part of the dielectric function to increase with decreasing radius (see figure). The correction term is a function of the nanoparticle radius, the wavelength of light, the mean free path and the Fermi speed of electrons in bulk gold, the plasma frequency of gold, and the speed of light in a vacuum. These models are used to calculate for various concentrations of gold nanoparticles having an assumed radius. The modeled data indicates distinct spectral features for both the real and the imaginary part of the dielectric function. An measurement would determine this distinct feature and thus can be used to measure nanoparticle concentration. By ellipsometric responses is meant the intensities of light measured in various polarization states as functions of the angle of incidence and the polarization states of the incident light. These calculated are used as calibration curves: Data from subsequent measurements on real specimens are compared with the calibration curves. The concentration of the nanoparticles on a specimen is assumed to be that of the calibration curve that most closely matches the data pertaining to that specimen.
Molecular characterization of a Korean porcine epidemic diarrhea virus strain NB1. (2019)

In Korea, for the past 30 years (1987–present), porcine epidemic diarrhea (PED) has been established as an endemic situation in which multiple genogroups of classical G1 and G2b, and the recently introduced pandemic G2a, coexisted. Because of the dynamic nature of the virus, continuous field monitoring for PEDV strains is required. This study is the first to reveal prevalence of PEDV in 9 sampling provinces, with an overall detection rate of 6.70%. Porcine endemic diarrhea virus (PEDV) was present in pigs of all ages, especially in the non-PED vaccinated groups. The highest detection rate was in the finisher group (2.34%), followed by that in the newborn group (1.56%). Secondly, using Sanger sequencing, this study recovered a complete genome (28 005 nucleotides long) of NB1 strain from a farm severely affected by PED. Analyses of nucleotide and deduced amino acid sequences showed that NB1 differed from 18 other Korean PEDV mostly in 4 protein coding genes: ORF1a, ORF1b, S, and N. Two amino acid substitutions (V635E and Y681Q) in the COE and S1D neutralizing epitopes of NB1 resulted in antigenic index alteration of the adjacent sites, one of which contributed to a mutation that escaped neutralizing antibodies.
Nucleotide sequence of the Pseudomonas fluorescens signal peptidase II gene (lsp) and flanking genes (1990)

The lsp gene encoding prolipoprotein signal peptidase (signal peptidase II) is organized into an operon consisting of ileS and three open reading frames, designated genes x, orf149, and orf316 in both Escherichia coli and Enterobacter aerogenes. A plasmid, pBROC128, containing a 5.8-kb fragment of Pseudomonas fluorescens DNA was found to confer pseudomonic acid resistance on E. coli host cells and to contain the structural gene of ileS from P. fluorescens. In addition, E. coli strains carrying pBROC128 exhibited increased globomycin resistance. This indicated that the P. fluorescens lsp gene was present on the plasmid. The nucleotide sequences of the P. fluorescens lsp gene and of its flanking regions were determined. Comparison of the nucleotide sequences of the lsp genes in E. coli and P. fluorescens revealed two highly conserved domains in this enzyme. Furthermore, the five genes which constitute an operon in E. coli and Enterobacter aerogenes were found in P. fluorescens in the same order as in the first two species.
α-Synuclein Regulates Peripheral Insulin Secretion and Glucose Transport (2021)

Cumulatively, this data suggests that α-syn modulates both pancreatic beta cell function and glucose transport in peripheral tissues, thereby playing a pivitol role in the maintenance of normal glucose homeostasis.
The Trisubstituted Isoxazole MMV688766 Exerts Broad-Spectrum Activity against Drug-Resistant Fungal Pathogens through Inhibition of Lipid Homeostasis (2022)

<i>Candida</i> species are among the most prevalent causes of systemic fungal infection, posing a growing threat to public health. While Candida albicans is the most common etiological agent of systemic candidiasis, the frequency of infections caused by non<i>-albicans Candida</i> species is rising. Among these is Candida auris, which has emerged as a particular concern. Since its initial discovery in 2009, it has been identified worldwide and exhibits resistance to all three principal antifungal classes. Here, we endeavored to identify compounds with novel bioactivity against C. auris from the Medicines for Malaria Venture's Pathogen Box library. Of the five hits identified, the trisubstituted isoxazole MMV688766 emerged as the only compound displaying potent fungicidal activity against C. auris, as well as other evolutionarily divergent fungal pathogens. Chemogenomic profiling, as well as subsequent metabolomic and phenotypic analyses, revealed that MMV688766 disrupts cellular lipid homeostasis, driving a decrease in levels of early sphingolipid intermediates and fatty acids and a concomitant increase in lysophospholipids. Experimental evolution to further probe MMV688766's mode of action in the model fungus Saccharomyces cerevisiae revealed that loss of function of the transcriptional regulator <i>HAL9</i> confers resistance to MMV688766, in part through the upregulation of the lipid-binding chaperone <i>HSP12</i>, a response that appears to assist in tolerating MMV688766-induced stress. The novel mode of action we have uncovered for MMV688766 against drug-resistant fungal pathogens highlights the broad utility of targeting lipid homeostasis to disrupt fungal growth and how screening structurally-diverse chemical libraries can provide new insights into resistance-conferring stress responses of fungi. <b>IMPORTANCE</b> As widespread antimicrobial resistance threatens to propel the world into a postantibiotic era, there is a pressing need to identify mechanistically distinct antimicrobial agents. This is of particular concern when considering the limited arsenal of drugs available to treat fungal infections, coupled with the emergence of highly drug-resistant fungal pathogens, including Candida auris. In this work, we demonstrate that existing libraries of drug-like chemical matter can be rich resources for antifungal molecular scaffolds. We discovered that the small molecule MMV688766, from the Pathogen Box library, displays previously undescribed broad-spectrum fungicidal activity through perturbation of lipid homeostasis. Characterization of the mode of action of MMV688766 provided new insight into the protective mechanisms fungi use to cope with the disruption of lipid homeostasis. Our findings highlight that elucidating the genetic circuitry required to survive in the presence of cellular stress offers powerful insights into the biological pathways that govern this important phenotype.