gebhart/patrepeval huggingface dataset:
Temporal development of the gut microbiome in early childhood from the TEDDY study (2018)

The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases<sup>1-9</sup> such as persistent islet autoimmunity and type 1 diabetes<sup>10-12</sup>. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.
A Multivariate Discretization Method for Learning Bayesian Networks from Mixed Data (2013)

In this paper we address the problem of discretization in the context of learning Bayesian networks (BNs) from data containing both continuous and discrete variables. We describe a new technique for <em>multivariate</em> discretization, whereby each continuous variable is discretized while taking into account its interaction with the other variables. The technique is based on the use of a Bayesian scoring metric that scores the discretization policy for a continuous variable given a BN structure and the observed data. Since the metric is relative to the BN structure currently being evaluated, the discretization of a variable needs to be dynamically adjusted as the BN structure changes.
Face Anti-Spoofing by Fusing High and Low Frequency Features for Advanced Generalization Capability (2020)

In face authentication systems, face anti-spoofing is an indispensable part. Recently, CNN-based approaches have achieved promising results when training and testing in similar scenes. However, performance usually drops drastically when the model is tested on unseen datasets due to the domain generalization problem. In this paper, we propose a new face anti-spoofing model consisting of two streams to fuse high frequency (HF) and low frequency (LF) information of a facial image for high generalization capability. More concretely, three high-pass and low-pass filters are utilized to extract high and low frequency component of a facial image, respectively. The two components are proceeded by two sub-networks with a cross-frequency spatial attention (CFSA) module, which makes two streams communicate and exchange information with each other. Considering the two sub-networks are responsible for different kinds of information, self-channel attention is incorporated after CFSA, then the outputs of the two sub-networks are fused for final classification. Experiments on cross-database results show that the proposed method can largely improve the generalization capacity in face spoofing detection.
Information structures in optimal decentralized control (2012)

This tutorial paper provides a comprehensive characterization of information structures in team decision problems and their impact on the tractability of team optimization. Solution methods for team decision problems are presented in various settings where the discussion is structured in two foci: The first is centered on solution methods for stochastic teams admitting state-space formulations. The second focus is on norm-optimal control for linear plants under information constraints.
Submicron Trenches Reduce the Pseudomonas fluorescens Colonization Rate on Solid Surfaces (2009)

Bacterial adhesion and spreading on biomaterials are considered key features of pathogenicity. Roughness and topography of the substrate have been reported to affect bacterial adhesion, but little is known about their effect on spreading. Submicron row and channel tuning with bacterial diameter (S2) were designed to test bacterial motility on these surfaces. Random nanometer-sized structures (S1) were used as controls. Optical microscopy and AFM were employed to detect biological and surface pattern details in the micro- and nanoscale, respectively. Results showed that motility strategies (flagella orientation, elongation, aggregation in rafts, formation of network structures, and development of a bacterial frontier) were affected by the presence of submicropatterns. Importantly, the rate of bacterial spreading on S2 was significantly reduced and influenced by the orientation of the submicropatterns. Consequently, submicroengineered substrates could be employed as a tool to downgrade bacterial colonization. Such patterns could impact on the design of proper engineered structures to control biofilm spreading on solid surfaces.
InkTag (2013)

InkTag is a virtualization-based architecture that gives strong safety guarantees to high-assurance processes even in the presence of a malicious operating system. InkTag advances the state of the art in untrusted operating systems in both the design of its hypervisor and in the ability to run useful applications without trusting the operating system. We introduce paraverification , a technique that simplifies the InkTag hypervisor by forcing the untrusted operating system to participate in its own verification. Attribute-based access control allows trusted applications to create decentralized access control policies. InkTag is also the first system of its kind to ensure consistency between secure data and metadata, ensuring recoverability in the face of system crashes.
Remaining Useful Lifetime Estimation for Power MOSFETs Under Thermal Stress With RANSAC Outlier Removal (2017)

Reliability of power converters is crucial for mission critical systems. Among the components that are susceptible to failure, power semiconductor devices are one of the major causes of the power converter failures. This paper focuses on the remaining useful lifetime (RUL) estimation of degraded power MOSFETs, which are stressed by thermal cycling. The relative change in on-state resistance is identified as the fault signature. A data-driven RUL estimation algorithm based on a linear approximation model is proposed. The empirical coefficients are estimated by the classical least squares, where the outliers are removed by random sample consensus (RANSAC) algorithm. A sliding window approach is used to track the nonlinearities. The window size, threshold value, and number of samples used by RANSAC are optimized with the genetic algorithm. The accuracy of the proposed RUL estimation tool is verified on a number of thermally aged discrete power MOSFET data.
Effects of traditional oriental medicines as anti-cytotoxic agents in radiotherapy (2017)

The primary goal of radiotherapy in oncology is to enhance the efficacy of tumor cell death while decreasing damage to surrounding normal cells. Positive therapeutic outcomes may be accomplished by improved targeting, precisely targeting tumor cells or protecting normal cells against radiation-induced damage. The potential for antioxidants to decrease normal tissue damage induced by radiation has been investigated in animal models for a number of decades. In attempts for radioprotection, certain synthetic chemicals are suggested as antioxidants and normal tissue protectors against radiation-induced damage, but they have exhibited limitations in pharmacological application due to undesirable effects and high toxicities at clinical doses. The present review focuses on the radioprotective efficacy of traditional oriental medicines with the advantage of low toxicity at pharmacological doses and how such treatments may influence various harmful effects induced by radiation <i>in vitro</i> and <i>in vivo</i>. In addition, medicinal plants and their active constituents with biological activities that may be associated with alleviation of radiation-induced damage through antioxidant, anti-inflammatory, wound healing and immunostimulatory properties are discussed.
Virtual network resources management: a divide-and-conquer approach for the control of future networks (2002)

We discuss the virtual network concepts and introduce a management architecture for the control of virtual networks. The management architecture is intended to provide a programmable networking environment, where multiple virtual networks can be generated out of a single physical network for various management purposes. We first define a virtual network and related concepts in a generic manner; discuss how physical network resources can be allocated to virtual networks; and present how a hierarchy of virtual networks can be created. We then introduce the virtual network resources management architecture. The architecture allows customization of network control and management functions to corporate customers through dynamic binding techniques.
Paracrine activation of WNT/β-catenin pathway in uterine leiomyoma stem cells promotes tumor growth (2013)

Uterine leiomyomas are extremely common estrogen and progesterone-dependent tumors of the myometrium and cause irregular uterine bleeding, severe anemia, and recurrent pregnancy loss in 15-30% of reproductive-age women. Each leiomyoma is thought to arise from a single mutated myometrial smooth muscle stem cell. Leiomyoma side-population (LMSP) cells comprising 1% of all tumor cells and displaying tumor-initiating stem cell characteristics are essential for estrogen- and progesterone-dependent in vivo growth of tumors, although they have remarkably lower estrogen/progesterone receptor levels than mature myometrial or leiomyoma cells. However, how estrogen/progesterone regulates the growth of LMSP cells via mature neighboring cells is unknown. Here, we demonstrate a critical paracrine role of the wingless-type (WNT)/β-catenin pathway in estrogen/progesterone-dependent tumorigenesis, involving LMSP and differentiated myometrial or leiomyoma cells. Estrogen/progesterone treatment of mature myometrial cells induced expression of WNT11 and WNT16, which remained constitutively elevated in leiomyoma tissues. In LMSP cells cocultured with mature myometrial cells, estrogen-progesterone selectively induced nuclear translocation of β-catenin and induced transcriptional activity of its heterodimeric partner T-cell factor and their target gene AXIN2, leading to the proliferation of LMSP cells. This effect could be blocked by a WNT antagonist. Ectopic expression of inhibitor of β-catenin and T-cell factor 4 in LMSP cells, but not in mature leiomyoma cells, blocked the estrogen/progesterone-dependent growth of human tumors in vivo. We uncovered a paracrine role of the WNT/β-catenin pathway that enables mature myometrial or leiomyoma cells to send mitogenic signals to neighboring tissue stem cells in response to estrogen and progesterone, leading to the growth of uterine leiomyomas.
Effects of estrogen on mineral metabolism in postmenopausal women as evaluated by multiple assays measuring parathyrin bioactivity. (1989)

Data on the effect of estrogen on immunoreactive parathyrin (iPTH) in postmenopausal women are conflicting. We administered estrogen or placebo to 21 postmenopausal women for 12 weeks and measured PTH bioactivity (bioPTH), using the renal cytochemical bioassay. Before treatment, there was a negative correlation between nephrogenous cAMP and the tubular maximum for urinary phosphate excretion and a positive correlation between values measured by a mid-region-specific PTH RIA and those measured in an immunoradiometric assay for intact PTH. Values measured by the midregion-specific RIA were also positively correlated with nephrogenous cAMP. BioPTH values were not correlated with other indices of PTH activity but were increased compared with values for younger subjects. After estrogen treatment there was no change in bioPTH activity despite an early decrease in serum osteocalcin and a later increase in nephrogenous cAMP. PTH concentrations measured by mid-region-specific or intact RIAs were unchanged, but sample size may have been insufficient to exclude the possibility of significant changes in these values. The effects of estrogen on mineral metabolism in postmenopausal women are time-dependent. Early effects are independent of PTH, and later effects are variably associated with increased PTH activity.
A Ferroelectric FET Based In-memory Architecture for Multi-Precision Neural Networks (2020)

Computing-in-memory (CIM) is a promising approach to improve the throughput and the energy efficiency of deep neural network (DNN) processors. So far, resistive nonvolatile memories have been adapted to build crossbar-based accelerators for DNN inference. However, such structures suffer from several drawbacks such as sneak paths, large ADCs/DACs, high write energy, etc. In this paper we present a mixed signal in-memory hardware accelerator for CNNs. We propose an in-memory inference system that uses FeFETs as the main nonvolatile memory cell. We show how the proposed crossbar unit cell can overcome the aforementioned issues while reducing unit cell size and power consumption. The proposed system decomposes multi-bit operands down to single bit operations. We then re-combine them without any loss of precision using accumulators and shifters within the crossbar and across different crossbars. Simulations demonstrate that we can outperform state-of-the-art efficiencies with 3.28 TOPS/W and can pack 1.64 TOPS in an area of 1.52mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> using 22 nm FDSOI technology,
Atrial Electrogram Analysis: Antegrade Versus Retrograde (1988)

Automatic discrimination between antegrade and retrograde atrial electrograms would prevent endless loop tachycardia and contribute to tachycardia detection algorithms. We tested its feasibility by comparing antegrade and retrograde atrial electrograms in 129 patients at the time of atrial lead implantation. Only unipolar, passive-fixation, endocardial, right atrial appendage leads were included. The mean antegrade amplitude was 4.2 +/- 2.2 mV, and retrograde 2.4 +/- 1.5 mV (P less than 0.001); the mean antegrade slew rate was 2.6 +/- 2.1 mV/ms, and retrograde 1.3 +/- 1.1 mV/ms (P less than 0.001). Morphology was similar in 84 patients (65%). The antegrade amplitude exceeded the retrograde by 1.0 mV in 67%, and by 0.5 mV in 81% of patients. Morphology and slew rate contributed little to the discriminating power of amplitude alone. Thus, amplitude criteria reliably distinguish antegrade from retrograde atrial activity.
Lower bounds on the existence of binary error-correcting variable-length codes (2004)

The paper deals with codes that combine source and channel encoding operations. After discussing the potential usefulness of these variable-length error correcting (VLEC) codes, necessary conditions on their length distribution are established. It is shown that, depending on the targetted application, several families of VLEC codes can be defined, whose conditions of existence differ.
Uncertainty and Risk in Petroleum Exploration and Development: The Expectation Curve Method (1989)

ABSTRACT Hydrocarbons are being recovered from ever greater depth and offshore in deeper waters. More marginal (offshore) projects are often only viable due to the use of new and innovative engineering solutions. Furthermore, these technically more advanced projects are being planned in today's volatile, economic climate where oil prices are relatively low and uncertain. It is therefore not surprising that project feasibility and economic analysis methods are becoming more elaborate, methods that take proper account of uncertainties and risks in all aspects of a project. Statistical distribution methods have been in use since the early 1900's, but Monte Carlo methods were generally not applied until the 1940's, methods that were based on game theory of von Neumann and Ulam. While those early applications were mainly in science and some selective engineering areas as for example defence, wider technological use1 and business applications2 were not prevalent until the fifty's and early sixty's. Simple statistical methods used in petroleum engineering, in common use since the early sixty's, were generally replaced by full Monte Carlo methods in the seventy's, with recent, more elaborate calculation methods requiring considerable computer power, as for example in reserves calculations of the North West Shelf Gas Development3. The expectation curve, also known as cumulative frequency distribution, S-curve or exceedance chart, may be the result of simple statistical frequency analysis or more comprehensive probabilistic (Monte Carlo) modelling. As will be described, the use of the expectation curve is a universal and powerful technique which allows for a quantitative appreciation of data in all areas of exploration and production, situations where variation and uncertainties in variables are of importance. Risk can be considered to fall into two categories: situations which give rise to equipment failure or human error leading to a major accident, as for example the recent Piper Alpha platform disaster, and those situations which are related to uncertainty, the subject of this paper. A number of Australian examples are presented.
Influence of secretagogues on volume and protein pattern in rabbit lacrimal fluid (1985)

After certain tear proteins had been found to be markers of duct cell activity in the rabbit lacrimal gland, different secretagogues were tested to increase volume and protein secretion. Carbamyl-choline and the peptides eledoisin and vasoactive intestinal peptide (VIP) stimulated volume flux as well as secretion of the marker proteins indicating duct cell activation. Beta-adrenergic stimulation also increased secretion of a further tear protein. This might indicate that water is secreted by the duct cells. These are stimulated by the secretagogues mentioned above. Beta-adrenergic stimulation might in addition activate the acinar cell system.
P3‐026: Trial of S‐Equol in Alzheimer’s Disease (SEAD) (2016)

Mitochondrial dysfunction has been observed in Alzheimer’s disease (AD) patients. Specifically, cytochrome oxidase (COX, a mitochondrial electron transport chain enzyme) activity is reduced in both brain and platelet mitochondria from AD patients. S-equol is an estrogen receptor beta (ER-beta) agonist. ERbeta are localized within mitochondria, and activation stimulates mitochondrial function and mitochondrial biogenesis. Based on these observations we hypothesized S-equol may benefit AD subjects. 15 female AD participants (CDR 0.5 or 1) were enrolled into this 6-week, single-blind trial. The trial was designed to assess the primary outcome of platelet COX activity at baseline, in response to S-equol, and after a washout period. Participants were treated with twice a day placebo for two weeks, followed by 10mg twice a day S-equol for two weeks followed by a 2 week washout period. Phlebotomy, vitals, safety assessments, and a brief cognitive assessment (Montreal Cognitive Assessment exam (MoCA)) were completed at baseline, 2 weeks, 4 weeks, and 6 weeks. 15 participants were enrolled and 14 have completed the study. One subject dropped out prior to initiating the study due to non-study related reasons. In order to be considered a “responder” (i.e. increasing COX activity in response to treatment) the individual change (slope) between visits 2 and 3 had to be greater than the change (slope) between visits 3 and 4. When normalized to citrate synthase (CS) activity and protein concentration, 10 of the participants were considered responders, while 4 were considered non-responders. Of the 4 non-responders, one subject did show an increase in COX activity (normalized to protein and CS), but the visit 3 to 4 slope was greater than the visit 2 to 3 slope. S-equol was well-tolerated by and appeared safe in these AD participants. The study currently plans to enroll at least one additional subject, and upon completion of the study all endpoints will be analyzed. Our data suggest S-equol may increase platelet COX activity, warranting further testing in AD participants.
Aloin isoforms (A and B) selectively inhibits proteolytic and deubiquitinating activity of papain like protease (PLpro) of SARS-CoV-2 in vitro (2022)

Abstract The most common host entry point of human adapted coronaviruses (CoV) including SARS-CoV-2 is through the initial colonization in the nostril and mouth region which is responsible for spread of the infection. Most recent studies suggest that the commercially available oral and nasal rinse products are effective in inhibiting the viral replication. However, the anti-viral mechanism of the active ingredients present in the oral rinses have not been studied. In the present study, we have assessed in vitro enzymatic inhibitory activity of active ingredients in the oral mouth rinse products: aloin A and B, chlorhexidine, eucalyptol, hexetidine, menthol, triclosan, methyl salicylate, sodium fluoride and povidone, against two important proteases of SARS-CoV-2 PLpro and 3CLpro. Our results indicate only aloin A and B effectively inhibited proteolytic activity of PLpro with an IC 50 of 13.16 and 16.08 μM. Interestingly, neither of the aloin isoforms inhibited 3CLpro enzymatic activity. Computational structural modelling of aloin A and B interaction with PLpro revealed that, both aloin isoforms form hydrogen bond with Tyr 268 of PLpro, which is critical for their proteolytic activity. Furthermore, 100 ns molecular dynamics (MD) simulation studies predicted that both aloin isoforms have strong interaction with Glu 167 , which is required for PLpro deubiquitination activity. Our results from the in vitro deubiquitinase inhibition assay show that aloin A and B isomers exhibit deubiquitination inhibitory activity with an IC 50 value of 15.68 and 17.51 µM, respectively. In conclusion, the isoforms of aloin inhibit both proteolytic and the deubiquitinating activity of SARS-CoV-2 PLpro, suggesting potential in inhibiting the replication of SARS-CoV-2 virus.