gebhart/patrepeval huggingface dataset:
A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis (2017)

The <i>Salmonella</i> Syst-OMICS consortium is sequencing 4,500 <i>Salmonella</i> genomes and building an analysis pipeline for the study of <i>Salmonella</i> genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the <i>Salmonella</i> Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how <i>Salmonella</i> evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
S-Band: A New Age in Mobile Satellite Services (2008)

The launch in early 2009 of the first satellite with an S-band payload serving Europe will open the way to a new set of mobile services. This paper contains updated information on this new exciting project, and in particular on the future mobile applications that will benefit from this innovative satellite. A survey of the associated technologies and their likely availability is also performed, as well as an analysis of the regulatory issues and the business perspectives towards this new market.
Optomechanical Self-Stability of Freestanding Photonic Metasurfaces (2021)

We develop an analytical framework for self-stabilizing optical manipulation of freestanding metasurfaces in three dimensions. Our framework reveals that the challenging problem of stabilization against translational and rotational perturbations in three dimensions is reduced to a simpler scattering analysis of the metasurface unit cell in two dimensions. We derive universal analytical stiffness coefficients applicable to arbitrary three-dimensional radial metasurfaces and radial beam-intensity profiles. The analytical nature of our framework facilitates highly efficient discovery of optimal optomechanical metasurfaces. Such use of metasurfaces for mechanical stabilization enables macroscale and long-range control in collimated, but otherwise unfocused light beams, and could open up avenues for manipulation beyond traditional optical tweezing and transport.
Related Editorial from Combination of Two Insulin-Like Growth Factor-I Receptor Inhibitory Antibodies Targeting Distinct Epitopes Leads to an Enhanced Antitumor Response (2023)

Related Editorial from Combination of Two Insulin-Like Growth Factor-I Receptor Inhibitory Antibodies Targeting Distinct Epitopes Leads to an Enhanced Antitumor Response
Electric-field-induced nematic-cholesteric transition and three-dimensional director structures in homeotropic cells (2005)

We study the phase diagram of director structures in cholesteric liquid crystals of negative dielectric anisotropy in homeotropic cells of thickness d which is smaller than the cholesteric pitch p. The basic control parameters are the frustration ratio d/p and the applied voltage U. Upon increasing U, the direct transition from completely unwound homeotropic structure to the translationally invariant configuration (TIC) with uniform in-plane twist is observed at small d/p < or = 0.5. Cholesteric fingers that can be either isolated or arranged periodically occur at 0.5 < or = d/p<1 and at the intermediate U between the homeotropic unwound and TIC structures. The phase boundaries are also shifted by (1) rubbing of homeotropic substrates that produces small deviations from the vertical alignment; (2) particles that become nucleation centers for cholesteric fingers; (3) voltage driving schemes. A novel reentrant behavior of TIC is observed in the rubbed cells with frustration ratios 0.6 < or = d/p < or = 0.75, which disappears with adding nucleation sites or using modulated voltages. In addition, fluorescence confocal polarizing microscopy (FCPM) allows us to directly and unambiguously determine the three-dimensional director structures. For the cells with strictly vertical alignment, FCPM confirms the director models of the vertical cross sections of four types of fingers previously either obtained by computer simulations or proposed using symmetry considerations. For rubbed homeotropic substrates, only two types of fingers are observed, which tend to align along the rubbing direction. Finally, the new means of control are of importance for potential applications of the cholesteric structures, such as switchable gratings based on periodically arranged fingers and eyewear with tunable transparency based on TIC.
ATRP for interfacial tailoring of Al(2)O(3) nanoparticles to be used in insulating materials (2011)

ATRP for interfacial tailoring of Al(2)O(3) nanoparticles to be used in insulating materials
MicroRNA-224 is implicated in lung cancer pathogenesis through targeting caspase-3 and caspase-7 (2015)

We recently reported that miR-224 was significantly up-regulated in non-small cell lung cancer (NSCLC) tissues, in particular in resected NSCLC metastasis. We further demonstrated that miR-224 functions as an oncogene in NSCLC by directly targeting TNFAIP1 and SMAD4. However, the biological functions of miR-224 in NSCLC are controversial and underlying mechanisms of miR-224 in the progression and metastasis of lung cancer remain to be further explored. Here we report that caspase3 (CASP3) and caspase7 (CASP7) are previously unidentified targets of miR-224 in NSCLC, and that miR-224 promotes lung cancer cells proliferation and migration in part by directly targeting CASP7 and down-regulating its expression. In addition, miR-224 attenuated TNF-α induced apoptosis by direct targeting of CASP3 resulting in reduction of cleaved PARP1 expression in lung cancer cells. Furthermore, the expression of miR-224 negatively correlates with the expression of CASP7 and CASP3 in tissue samples from patients with lung cancer. Finally, we found that activated NF-κB signaling is involved in the regulation of miR-224 expression in lung cancer. Our study provides new insight in understanding of oncogenic role of miR-224 in the lung cancer pathogenesis and suggests that NF-κB/miR-224/CASP3, 7 pathway could be a putative therapeutic target in lung cancer.
An active-node fault diagnosis system for CEBus networks (1995)

The design and implementation of an active-node fault diagnosis system for CEBus networks is described. The system uses an IBM PC with a user-friendly GUI to provide statistical information on network traffic and messages. The PC is linked to an active CEBus node which monitors the network and can initiate testing sequences controlled by the PC.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: Handles for Solid‐Phase Peptide Synthesis (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Selectivity estimation for range predicates using lightweight models (2019)

Query optimizers depend on selectivity estimates of query predicates to produce a good execution plan. When a query contains multiple predicates, today's optimizers use a variety of assumptions, such as independence between predicates, to estimate selectivity. While such techniques have the benefit of fast estimation and small memory footprint, they often incur large selectivity estimation errors. In this work, we reconsider selectivity estimation as a regression problem. We explore application of neural networks and tree-based ensembles to the important problem of selectivity estimation of multi-dimensional range predicates. While their straightforward application does not outperform even simple baselines, we propose two simple yet effective design choices, i.e., regression label transformation and feature engineering, motivated by the selectivity estimation context. Through extensive empirical evaluation across a variety of datasets, we show that the proposed models deliver both highly accurate estimates as well as fast estimation.
A trench-gate injection enhanced lateral IEGT on SOI (2002)

This paper reports, for the first time, that lateral IGBTs with an injection enhanced multiple trench gate structure (LIEGT) on SOI successfully achieved both a low forward voltage drop and a high switching speed. The current density of LIEGTs with two trench gates is more than twice as large as that of conventional lateral IGBTs on a 10 /spl mu/m SOI. Closely spaced deep trench gates result in carrier storage under the trench gates and enhance lateral carrier flow. Although the switching speed of 10 /spl mu/m SOI LIEGTs is as fast as that of LIGBTs, its switching loss can be reduced. Thus, the electrical characteristics of lateral trench gate IEGTs on SOI are quite good.
An abnormal signal transduction pathway in CD4−CD8− double‐negative lymph node cells of MRL lpr/lpr mice (1991)

We describe here a novel 26-kDa posphoprotein (p26), associated to the T cell receptor of CD4-CD8- lymph node cells of lpr/lpr mice, but not present in significant amounts in control mouse cells including polyclonally activated T cells. lpr p26 is constitutively phosphorylated on a tyrosyl residue. It is most likely a member of the G protein family and displays high GTP-binding and GTPase activities both unsensitive to interleukin 2. Bordetella pertussis toxin has no effect on the spontaneously enhanced GTP hydrolysis. The traits associated to p26 could contribute to the distinctive features of lpr/lpr double-negative cells.
Efficient Power Network Analysis Considering Multidomain Clock Gating (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, an efficient framework is proposed to analyze the worst case of voltage variation of power network considering multidomain clock gating. First, a frequency-domain-based simulation method is proposed to obtain the time-domain voltage response. With the vector fitting technique, the frequency-domain responses are approximated by a partial fraction expression, which can be easily converted to a time-domain waveform. Then, an algorithm is proposed to find the worst-case voltage variation and corresponding clock gating patterns, through superimposing the voltage responses caused by all domains working separately. The major computation of the whole framework is solving the frequency-domain equation system, whose complexity is about <formula formulatype="inline"> <tex Notation="TeX">$O(N^{\alpha}D\log f_{\max})$</tex></formula>, where <formula formulatype="inline"><tex Notation="TeX">$\alpha$</tex></formula> is between one and two if using an iterative solver from the PETSc library. <formula formulatype="inline"><tex Notation="TeX">$N$ </tex></formula> is the node number, <formula formulatype="inline"><tex Notation="TeX">$f_{\max}$</tex></formula> is the upper bound of frequency, and <formula formulatype="inline"><tex Notation="TeX">$D$</tex></formula> is the number of clock domains. Numerical results show that the proposed simulation method is up to several hundred times faster than commercial fast simulators, like HSPICE and MSPICE. In addition, the proposed method is able to analyze large-scale power networks that the commercial tools are not able to afford. </para>
Bobby Sox homology regulates odontoblast differentiation of human dental pulp stem cells/progenitors (2014)

Our results suggest that BBX plays an important role during the odontoblast differentiation of human DPSCs/progenitors.
Bacterial outer membrane vesicles engineered with lipidated antigens as a platform for Staphylococcus aureus vaccine (2019)

Bacterial outer membrane vesicles (OMVs) represent an interesting vaccine platform for their built-in adjuvanticity and simplicity of production process. Moreover, OMVs can be decorated with foreign antigens using different synthetic biology approaches. However, the optimal OMV engineering strategy, which should guarantee the OMV compartmentalization of most heterologous antigens in quantities high enough to elicit protective immune responses, remains to be validated. In this work we exploited the lipoprotein transport pathway to engineer OMVs with foreign proteins. Using 5 <i>Staphylococcus aureus</i> protective antigens expressed in <i>Escherichia coli</i> as fusions to a lipoprotein leader sequence, we demonstrated that all 5 antigens accumulated in the vesicular compartment at a concentration ranging from 5 to 20% of total OMV proteins, suggesting that antigen lipidation could be a universal approach for OMV manipulation. Engineered OMVs elicited high, saturating antigen-specific antibody titers when administered to mice in quantities as low as 0.2 μg/dose. Moreover, the expression of lipidated antigens in <i>E. coli</i> BL21(DE3)Δ<i>ompA</i>Δ<i>msbB</i>Δ<i>pagP</i> was shown to affect the lipopolysaccharide structure, with the result that the TLR4 agonist activity of OMVs was markedly reduced. These results, together with the potent protective activity of engineered OMVs observed in mice challenged with <i>S. aureus</i> Newman strain, makes the 5-combo-OMVs a promising vaccine candidate to be tested in clinics.
Antimicrobial properties of three lactic acid bacterial cultures and their cell free supernatants againstListeria monocytogenes (2012)

Control of Listeria monocytogenes in ready-to-eat (RTE) food products is a significant challenge and improved means for control are needed. In this study, the anti-listerial effects of three lactic acid bacteria (LAB) were investigated. Spot-on-lawn assays demonstrated the largest zones of inhibition against L. monocytogenes were produced by the Pediococcus acidilactici strain, with zone diameters ranging from 13 to 18 mm. Minimum inhibitory concentration (MIC) experiments using cell free supernatant (CFS) from the LAB revealed that while two of the strains were effective at inhibiting L. monocytogenes growth only up to a 1:4 dilution, P. acidilactici was able to inhibit growth up to a 1:256 dilution. Survival assays performed at 7°C determined that the P. acidilactici strain was capable of producing a 4.5 log reduction in L. monocytogenes counts and maintaining the reduction for 21 days. The effectiveness of P. acidilactici was reduced under log phase growth, autoclaving for longer than 15 min (121°C and 15 psi), and treatment with proteinase K (25 mg/mL).
Active noise control for headrests (2015)

This paper presents the active noise control (ANC) systems for creating quiet zone to cover the users' ears in headrests. The two-input two-output (TITO) ANC headrest system based on the multiple-channel adaptive feedback filtered-x least mean square (FXLMS) algorithm is proposed. In order to reduce system cost of the TITO ANC headrest system, the combined-input combined-output (CICO) ANC headrest system based on the single-channel adaptive feedback FXLMS algorithm is developed. The performance of the proposed ANC headrest systems are evaluated using the experimental setups. The real-time experiment results show that the CICO ANC headrest system achieves the satisfactory performance.
Diversifying Database Activity Monitoring with Bandits (2019)

Database activity monitoring (DAM) systems are commonly used by organizations to protect the organizational data, knowledge and intellectual properties. In order to protect organizations database DAM systems have two main roles, monitoring (documenting activity) and alerting to anomalous activity. Due to high-velocity streams and operating costs, such systems are restricted to examining only a sample of the activity. Current solutions use policies, manually crafted by experts, to decide which transactions to monitor and log. This limits the diversity of the data collected. Bandit algorithms, which use reward functions as the basis for optimization while adding diversity to the recommended set, have gained increased attention in recommendation systems for improving diversity. In this work, we redefine the data sampling problem as a special case of the multi-armed bandit (MAB) problem and present a novel algorithm, which combines expert knowledge with random exploration. We analyze the effect of diversity on coverage and downstream event detection tasks using a simulated dataset. In doing so, we find that adding diversity to the sampling using the bandit-based approach works well for this task and maximizing population coverage without decreasing the quality in terms of issuing alerts about events.
Measuring space-time curvature using maximally path-entangled quantum states (2022)

Experiments at the interface of quantum field theory and general relativity would greatly benefit theoretical research towards their unification. The gravitational aspects of quantum experiments performed so far can be explained either within Newtonian gravity or by Einstein's equivalence principle. Here, we describe a way to measure components of the Riemann curvature tensor with maximally path-entangled quantum states of light. We show that the entanglement-induced increase in sensitivity also holds for gravitationally-induced phases in Mach-Zehnder interferometers. As a result, the height difference between the two interferometer arms necessary to rule out flat space-time by measuring gravity gradients can be significantly reduced.
Enhancing Sensitivity of an Atomic Interferometer to the Heisenberg Limit Using Increased Quantum Noise (2018)

In a conventional atomic interferometer employing $N$ atoms, the phase sensitivity is at the standard quantum limit: $1/\sqrt{N}$. Using spin-squeezing, the sensitivity can be increased, either by lowering the quantum noise or via phase amplification, or a combination thereof. Here, we show how to increase the sensitivity, to the Heisenberg limit of $1/N$, while increasing the quantum noise by $\sqrt{N}$, thereby suppressing by the same factor the effect of excess noise. The protocol uses a Schrodinger Cat state representing a superposition of two collective states of $N$ atoms, behaving as a single entity with an $N$-fold increase in Compton frequency. The resulting $N$-fold phase magnification is revealed by using atomic state detection instead of collective state detection. We also show how to realize an atomic clock based on such a Schrodinger Cat state, with an $N$-fold increase in the effective transition frequency. We discuss potential experimental constraints for implementing this scheme, using one axis twist squeezing employing the cavity feedback scheme, and show that the effects of cavity decay and spontaneous emission are highly suppressed. We find that the maximum improvement in sensitivity can be close to the ideal limit, for as many as ten million atoms.
Cardiolipin exposure on the outer mitochondrial membrane modulates α-synuclein (2018)

Neuronal loss in Parkinson's disease (PD) is associated with aberrant mitochondrial function and impaired proteostasis. Identifying the mechanisms that link these pathologies is critical to furthering our understanding of PD pathogenesis. Using human pluripotent stem cells (hPSCs) that allow comparison of cells expressing mutant SNCA (encoding α-synuclein (α-syn)) with isogenic controls, or SNCA-transgenic mice, we show that SNCA-mutant neurons display fragmented mitochondria and accumulate α-syn deposits that cluster to mitochondrial membranes in response to exposure of cardiolipin on the mitochondrial surface. Whereas exposed cardiolipin specifically binds to and facilitates refolding of α-syn fibrils, prolonged cardiolipin exposure in SNCA-mutants initiates recruitment of LC3 to the mitochondria and mitophagy. Moreover, we find that co-culture of SNCA-mutant neurons with their isogenic controls results in transmission of α-syn pathology coincident with mitochondrial pathology in control neurons. Transmission of pathology is effectively blocked using an anti-α-syn monoclonal antibody (mAb), consistent with cell-to-cell seeding of α-syn.
226 Engineered Lactobacilli as a System to Screen Potent RANTES Mutants Acting as Live CCR5 Antagonist HIV-1 Blockers (2011)

As AIDS preventatives, topical microbicides represent an alternative and complementary option to a vaccine, and CCR5 (the main HIV-1 coreceptor) is a target of major interest. The live microbicide concept, based on the engineering of commensal bacteria to deliver anti-HIV-1 agents in vivo and in situ, is the landscape in which this work has been envisaged and devised. The successful production of the wild type chemokine RANTES (a natural ligand of CCR5) and the C1C5 RANTES mutant (a CCR5 antagonist) in lactobacilli and the evidence for a superior expression/folding by lactobacilli, as compared to mammalian cells, set the standards for lactobacilli as a platform to integrate design and selection of conceptually novel full-length RANTES derivatives with potent anti-HIV-1 activity and CCR5 antagonism (crucial to avoid pro-inflammatory activity). Two lactobacilli strains have been implemented, providing vaginal and intestinal applicability, respectively. Hot spot mutations spanning through RANTES aa sequence were retrieved or designed ex novo to achieve CCR5 antagonism and potent anti-HIV-1 activity. The lactobacilli-induced partial proteolytic cleavage occurring between RANTES aa positions 12 and 13 is also being resolved by mutagenesis. Lactobacilli codon-optimized cDNAs encoding for RANTES mutants were inserted into vectors suitable for lactobacilli protein secretion. Protein quantity and forms secreted by engineered lactobacilli were analyzed by ELISA and Western blot, respectively. Qualitative anti-HIV-1 activity was tested by acute infection assays on partially purified proteins. These procedures flowed in iterative cycles, with a stepwise integration of successful mutations in single CCR5 antagonist RANTES derivatives. The system is designed to collectively yield a small number of lead compounds presenting ideal features as live microbicides. The most effective leads will be purified and accurately tested for: i) CCR5 antagonism, ii) anti-HIV-1 activity, iii) protein full-length, and iv) correct disulphide bonding.
[Acquisition of the sequence of a new subclass of human alpha- satellite DNA, localized in the centromere regions of two pairs of acrocentric chromosomes]. (1989)

The results are presented in the paper on obtaining of a clone of sub-group of alpha-satellite human DNA localized in heterochromatin regions of two pairs of acrocentric chromosomes. The obtained repeated DNA sequence is represented in a genome by some 20,000 copies. Using of the blot-hybridization method made it possible to show the polymorphic restriction variant distribution being preserved in different individuals genomes. Intergenomic structural heterogeneity in this alpha-satellite DNA sub-group has been found only by using restriction endonuclease BamHI.
Glossary (2011)

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