gebhart/patrepeval huggingface dataset:
A Novel SRAM PUF Stability Improvement Method Using Ionization Irradiation (2020)

As one of the fundamental elements of the fingerprints of integrated circuit chips, static random-access memory based physical unclonable function (SRAM PUF) has been regarded as an attractive option for hardware security circuits. Commercial SRAM chips could be used as PUF chips for low cost systems. However, the mismatches existing in most commercial SRAM chips are quite small, which could result in poor stability of SRAM PUF. To address this issue, this paper proposes a novel SRAM PUF stability improvement method using total ionization dose (TID) effect for commercial SRAM chips. The principles of this new method are presented in detail and verified by simulations. Thereafter, the TID experiments are carried out on one kind of commercial SRAM chips and validate that this novel method could reduce the intra-chip hamming distance (HD_intra) by two orders of magnitude within the ionizing dose range of 40–100 Krad (SiO2), which is a significant stability improvement. Furthermore, considering the trade-offs of other performance factors, 40 Krad (SiO2) has been regarded as the recommended ionizing dose, which not only makes the stability and uniformity of SRAM PUF attain almost ideal values but also keeps the radiation-induced damage within a limited level.
Cortical Layer 1 and Layer 2/3 Astrocytes Exhibit Distinct Calcium Dynamics In Vivo (2008)

Cumulative evidence supports bidirectional interactions between astrocytes and neurons, suggesting glial involvement of neuronal information processing in the brain. Cytosolic calcium (Ca(2+)) concentration is important for astrocytes as Ca(2+) surges co-occur with gliotransmission and neurotransmitter reception. Cerebral cortex is organized in layers which are characterized by distinct cytoarchitecture. We asked if astrocyte-dominant layer 1 (L1) of the somatosensory cortex was different from layer 2/3 (L2/3) in spontaneous astrocytic Ca(2+) activity and if it was influenced by background neural activity. Using a two-photon laser scanning microscope, we compared spontaneous Ca(2+) activity of astrocytic somata and processes in L1 and L2/3 of anesthetized mature rat somatosensory cortex. We also assessed the contribution of background neural activity to the spontaneous astrocytic Ca(2+) dynamics by investigating two distinct EEG states ("synchronized" vs. "de-synchronized" states). We found that astrocytes in L1 had nearly twice higher Ca(2+) activity than L2/3. Furthermore, Ca(2+) fluctuations of processes within an astrocyte were independent in L1 while those in L2/3 were synchronous. Pharmacological blockades of metabotropic receptors for glutamate, ATP, and acetylcholine, as well as suppression of action potentials did not have a significant effect on the spontaneous somatic Ca(2+) activity. These results suggest that spontaneous astrocytic Ca(2+) surges occurred in large part intrinsically, rather than neural activity-driven. Our findings propose a new functional segregation of layer 1 and 2/3 that is defined by autonomous astrocytic activity.
Assessing the performance of rational spline-based empirical mode decomposition using a global annual precipitation dataset (2009)

Empirical mode decomposition (EMD), an adaptive data analysis methodology, has the attractive feature of robustness in the presence of nonlinear and non-stationary time series. Recently, in this journal, Pegram and co-authors ( Pegram et al . 2008 Proc. R. Soc. A 464 , 1483–1501), proposed a modification to the EMD algorithm whereby rational splines replaced cubic splines in the extrema envelope-fitting procedure. The modification was designed to reduce variance inflation, a feature frequently observed in cubic spline-based EMD components primarily due to spline overshooting, by introducing a spline tension parameter. Preliminary results there demonstrated the proof of concept that increasing the spline tension parameter reduces the variance of the resultant EMD components. Here, we assess the performance of rational spline-based EMD for a range of tension parameters and two end condition treatments, using a global dataset of 8135 annual precipitation time series. We found that traditional cubic spline-based EMD can produce decompositions that experience variance inflation and have orthogonality concerns. A tension parameter value of between 0 and 2 is found to be a good starting point for obtaining decomposition components that tend towards orthogonality, as measured by an orthogonality index (OI) metric. Increasing the tension parameter generally results in: (i) a decrease in the range of the OI, which is offset by slight increases in (ii) the median value of OI, (iii) the number of intrinsic mode function components, (iv) the average number of sifts per component, and (v) the degree of amplitude smoothing in the components. The two end conditions tested had little influence on the results, with the reflective case being slightly better than the natural spline case as indicated by the OI. The ability to vary the tension parameter to find an orthogonal set of components, without changing any sifting parameters, is a powerful feature of rational spline-based EMD, which we suggest is a significant improvement over cubic spline-based EMD.
Primary Extinction and Absorption: a Theoretical Approach Based on the Takagi-Taupin Equations. Application to Spherical Crystals (1998)

The primary-extinction problem for X-ray diffraction by perfect crystals is treated using the Becker–Coppens iterative procedure within the Takagi–Taupin equations. An analytical approximation for the primary-extinction factor yp describing both the effects of the X-ray multiple scattering and the absorption processes within the perfect crystal of an arbitrary shape is derived. The solution differs from the known expressions given by Zachariasen and Becker & Coppens on the basis of the Hamilton–Darwin intensity transfer equations and in the limiting case of a non-absorbing crystal it concurs with the Kato–Becker formula found in the Laue approximation of the dynamical theory. The theoretical results are consistent with experimental data of a number of reflections of Ge and Si single-crystal spheres measured at X-ray wavelengths λ = 0.56, 0.71 and 1.54 Å with a laboratory CAD-4 and a Huber four-circle diffractometer at HASYLAB, DESY, Hamburg, Germany. Two novel features are discussed. First, it is shown that by neglecting the X-ray absorption effect the calculated extinction factor yp is close to the value given by the Becker–Coppens formula. Second, it was found that for absorbing spherical crystals with μR ≥ 1 absorption effects cannot be treated separately from the primary-extinction phenomenon because of imaginary dispersion corrections to the atomic form factors. The experimental data are fitted to the Becker–Coppens and present theoretical models. The best fits are found to relate to the present model and produce relatively low R factors of 3 to 6% for the Bragg intensities measured in the cases of Si and Ge spherical crystals.
Alu PCR (2010)

Alu PCR is a rapid and easy-to-perform "DNA fingerprinting" technique based on the simultaneous analysis of many genomic loci flanked by Alu repetitive elements, which allows the detection of genetic polymorphisms and mutations in human and primate genomes. In the protocol described in the present chapter, two fluorochrome-labelled primers complementary to Alu sequences are used to perform the PCR, and the amplification products are then analysed by capillary electrophoresis. The resulting -complex electrophoretic pattern may show sample-to-sample variability due to insertion, deletion, or sequence change of Alu retrotransposons, or caused by length variation of the sequence interposed between two Alus.
CYP3A5 polymorphisms in renal transplant recipients: influence on tacrolimus treatment (2018)

Tacrolimus is a commonly used immunosuppressant after kidney transplantation. It has a narrow therapeutic range and demonstrates wide interindividual variability in pharmacokinetics, leading to potential underimmunosuppression or toxicity. Genetic polymorphism in CYP3A5 enzyme expression contributes to differences in tacrolimus bioavailability between individuals. Individuals carrying one or more copies of the wild-type allele *1 express CYP3A5, which increases tacrolimus clearance. CYP3A5 expressers require 1.5 to 2-fold higher tacrolimus doses compared to usual dosing to achieve therapeutic blood concentrations. Individuals with homozygous *3/*3 genotype are CYP3A5 nonexpressers. CYP3A5 nonexpression is the most frequent phenotype in most ethnic populations, except blacks. Differences between <i>CYP3A5</i> genotypes in tacrolimus disposition have not translated into differences in clinical outcomes, such as acute rejection and graft survival. Therefore, although genotype-based dosing may improve achievement of therapeutic drug concentrations with empiric dosing, its role in clinical practice is unclear. <i>CYP3A5</i> genotype may predict differences in absorption of extended-release and immediate-release oral formulations of tacrolimus. Two studies found that CYP3A5 expressers require higher doses of tacrolimus in the extended-release formulation compared to immediate release. <i>CYP3A5</i> genotype plays a role in determining the impact of interacting drugs, such as fluconazole, on tacrolimus pharmacokinetics. Evidence conflicts regarding the impact of <i>CYP3A5</i> genotype on risk of nephrotoxicity associated with tacrolimus. Further study is required.
2,3-Dihydroxybenzoate pathway in <i>Pseudomonas putida</i>. 1H n.m.r. study on the ring-cleavage site (1981)

1. Ring cleavage of 2,3-dihydroxybenzoate by cell-free extracts of Pseudomonas putida leads to 2-hydroxy-6-oxo-(2Z,4E)-hexa-2,4-dienoic acid and CO2. 2. The 1H n.m.r. spectrum of the ring-fission product obtained in a 2H2O solution suggests that the extra-diol cleavage occurs between C-3 and C-4.
A Review of Quantum Cybersecurity: Threats, Risks and Opportunities (2022)

The promise of quantum computing is not speeding up conventional computing rather delivering an exponential advantage for certain classes of problems, with profound implications for cybersecurity for instance. With the advent and development of quantum computers, cyberspace security can surely become the most critical problem for the Internet in near future. On contrary, prosaic quantum technology can be promising to transform cybersecurity. This research aims to synthesize basic and fundamental studies concerning quantum cybersecurity that can be emerged both as a threat and solution to critical cybersecurity issues based on a systematic study. We provide a comprehensive, illustrative description of the current state-of-the-art quantum computing and cybersecurity and present the proposed approaches to date. Findings in quantum computing cybersecurity suggest that quantum computing can be adopted for the betterment of cybersecurity threats while it poses the most unexpected threats to cybersecurity. The focus and depth of this systematic survey not only provide quantum and cybersecurity practitioners and researchers with a consolidated body of knowledge about current trends in this area but also underpins a starting point for further research in this field.
Pancam: In-Service Inspection of Locomotive Pantographs (2007)

Pancam is an inspection system for in-service monitoring of wear and damage to pantographs on electric locomotives. Damage and wear of pantographs can cause damage to the locomotive and overhead wiring with subsequent interruption of service. Pancam uses CCD cameras to capture side and top views of the pantographs of locomotives in normal service. The side view is analysed for wear and damage to the carbon current collectors while the top view is analysed for damage to the horns on the pantograph. Analysis results are reported to railway staff through a database with a thin-client Web interface. This paper presents an overview of the Pancam system and discusses some of the analysis techniques. Performance results are also presented.
A Cdk5 Inhibitor Enhances the Induction of Insulin Secretion by Exendin-4 Both in Vitro and in Vivo (2007)

Exendin-4 (Ex4) is a peptide found in the lizard Heloderma suspectum, and it has a high similarity to glucagon-like peptide 1 (GLP-1). It induces insulin secretion without the risk of hypoglycemic episodes. Cyclin-dependent kinase 5 (Cdk5) is a serine/threonine kinase that is predominantly expressed in neurons. Recent studies have shown that this kinase regulates glucose-stimulated insulin secretion. Cdk5 inhibition enhances insulin secretion under conditions of stimulation by high glucose, but not low glucose. In the present study, we examined whether R-roscovitine (R-ros), a Cdk5 inhibitor, enhances insulin secretion induced by Ex4. R-ros induced Ex4-dependent insulin secretion under conditions of high glucose, but not low glucose in MIN6B1 cells. The enhancement by R-ros was also observed in db/db mice, a mouse model of type 2 diabetes. Moreover, long-term treatment with Ex4 and R-ros significantly improved HbA1c compared with treatment using only Ex4. These results suggest that a co-application of R-ros and Ex4 may become a promising therapy for the treatment of type 2 diabetes.
Enzyme Activity Fingerprinting with Substrate Cocktails (2004)

In the postgenomic era, emphasis is shifting from protein identification to protein functional analysis. Enzyme function can be characterized by measuring activity across series of substrates, which generates an activity profile or fingerprint. Activity fingerprinting is particularly useful to differentiate closely related enzymes. Previously reported fingerprinting methods use series of parallel measurements, which are complex and difficult to reproduce. Here we report a new method for fingerprinting enzyme activities based on using mixtures of substrates, or substrate cocktails, in a single reaction that is then analyzed by HPLC. The fingerprints produced are highly reproducible and allow functional differentiation and classification of closely related enzymes, as demonstrated for a series of lipases and esterases. The method is practical, general, and flexible in terms of reaction conditions and can be adapted to any reaction type.
Growth of Narrowly Dispersed Porphyrin Nanowires and Their Hierarchical Assembly into Macroscopic Columns (2008)

The self-assembly of amphiphilic (porphyrin)Sn 1 in an aqueous Pluronic F127 media results in the formation of narrowly dispersed nanowires. Variation of aqueous Pluronic concentrations allows for a systematic variation of porphyrin nanowire lengths while keeping their widths constant. These nanowires can be further assembled into secondary macroscopic columns.
DOTS and DOTS‐Plus (2001)

Multidrug-resistant tuberculosis is already a global pandemic, with focal "hot spots" of ongoing transmission. Although DOTS (directly observed treatment, short course) chemotherapy is the goal of global tuberculosis control, short-course chemotherapy will not cure multidrug-resistant tuberculosis. In settings of high transmission of multidrug-resistant tuberculosis, "DOTS plus" (a complementary DOTS-based strategy with provisions for treating multidrug-resistant tuberculosis) is warranted. DOTS-plus project implementation to date reveals important clinical, epidemiological, and economic lessons. Community-based strategies designed to enhance local capacity are cost effective and make it possible to meet new medical challenges.
Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis (2011)

The mechanism of latent tuberculosis (TB) infection remains elusive. Several host factors that are involved in this complex process were previously identified. Micro RNAs (miRNAs) are endogenous ∼22 nt RNAs that play important regulatory roles in a wide range of biological processes. Several studies demonstrated the clinical usefulness of miRNAs as diagnostic or prognostic biomarkers in various malignancies and in a few nonmalignant diseases. To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers of this transition, we used human miRNA microarrays to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) in patients with active TB, latent TB infection (LTBI), and healthy controls. Using the software package BRB Array Tools for data analyses, 17 miRNAs were differentially expressed between the three groups (P<0.01). Hierarchical clustering of the 17 miRNAs expression profiles showed that individuals with active TB clustered independently of individuals with LTBI or from healthy controls. Using the predicted target genes and previously published genome-wide transcriptional profiles, we constructed the regulatory networks of miRNAs that were differentially expressed between active TB and LTBI. The regulatory network revealed that several miRNAs, with previously established functions in hematopoietic cell differentiation and their target genes may be involved in the transition from latent to active TB. These results increase the understanding of the molecular basis of LTBI and confirm that some miRNAs may control gene expression of pathways that are important for the pathogenesis of this infectious disease.
Protective vaccination in the horse against Streptococcus equi with recombinant antigens (2009)

Abstract Streptococcus equi subspecies equi ( S. equi ) is a clonal, equine host-adapted pathogen of global importance that causes a highly contagious suppurative lymphodendopathy of the head and neck, more commonly known as Strangles. The disease is highly prevalent, can be severe and spread easily by visibly infected animals or by carrier animals that show no clinical signs of disease. Antibiotic treatment is usually ineffective. However, the majority of horses develop immunity to re-infection, suggesting that vaccination should be a feasible way to prevent the infection. Live attenuated vaccine strains of S. equi are available but adverse reactions have been reported and they suffer from a short duration of immunity. Thus, a safe and effective vaccine against S. equi is highly desirable. In this report, Welsh mountain ponies vaccinated with a combination of seven recombinant S. equi proteins, were significantly protected from experimental infection by S. equi , resembling the spontaneous disease. The protective antigens consisted of five surface localized proteins and two IgG endopeptidases. The results from a second vaccination trial indicate that the endopeptidases were important for good protection. The similarity of S. equi to other pyogenic streptococci suggests that our findings have broader implications for the prevention of streptococcal infections.
Anthraquinone Oligomers as Anode-Active Material in Rechargeable Nickel/Oligomer Batteries with Aqueous Electrolyte (2018)

This work is an initial investigation of the possible use of redox-active anthraquinone as anode material in combination with Ni(OH)2 in a secondary battery with aqueous KOH electrolyte. Three different anode materials are investigated: an anthraquinone monomer and two different anthraquinone based oligomers. All batteries are rechargeable, and almost 100% of the theoretical capacity can be accessed in the first cycle, after which significant capacity loss occurs. The capacity loss is attributed mainly to swelling of the electrodes and solubility of anthraquinones in their charged (reduced) state because reduced anthraquinone is deprotonated and ionized in alkaline solutions. Nonetheless, batteries based on one of the oligomerized anthraquinones (oligo[benzene-1,4-dithiol-alt-(1,5- dichloroanthraquinone)] anode) show the best performance and retain almost 50% of the discharge capacity after 100 cycles. The better performance is attributed to the reduced solubility caused by the oligomerization. It is anticipated that measures to decrease the solubility further could lead to much improved capacity retention.
The role of the cytoskeleton in the viscoelastic properties of human articular chondrocytes (2003)

Biomechanical factors are believed to play an important role in regulating the metabolic activity of chondrocytes in articular cartilage. Previous studies suggest that cytoskeletal proteins such as actin, vimentin, and tubulin influence cellular mechanical properties, and may therefore influence the mechanical interactions between the chondrocyte and the surrounding tissue matrix. In this study, we investigated the role of specific cytoskeletal components on the mechanical properties of individual chondrocytes isolated from normal or osteoarthritic hip articular cartilage. Chondrocytes were exposed to a range of concentrations of chemical agents that disrupt the primary cytoskeletal elements (cytochalasin D for F-actin microfilaments, acrylamide for vimentin intermediate filaments, and colchicine for microtubules). Chondrocyte mechanical properties were determined using the micropipette aspiration technique coupled with a viscoelastic solid model of the cell. Chondrocyte stiffness (elastic modulus) was significantly increased with osteoarthritis. With increasing cytochalasin D treatment, chondrocyte stiffness decreased by up to 90% and apparent viscosity decreased by up to 80%. The effect of cytochalasin D was greater on normal chondrocytes than those isolated from osteoarthritic cartilage. Treatment with acrylamide also decreased the moduli and viscosity, but only at the highest concentration tested. No consistent changes in cell mechanical properties were observed with colchicine treatment. These findings suggest that microfilaments and possibly intermediate filaments provide the viscoelastic properties of the chondrocyte, and changes in the structure and properties of these cytoskeletal elements may reflect changes in the chondrocyte with osteoarthritis.
Use and Misuse of Cq in qPCR Data Analysis and Reporting (2021)

In the analysis of quantitative PCR (qPCR) data, the quantification cycle (C<sub>q</sub>) indicates the position of the amplification curve with respect to the cycle axis. Because C<sub>q</sub> is directly related to the starting concentration of the target, and the difference in C<sub>q</sub> values is related to the starting concentration ratio, the only results of qPCR analysis reported are often C<sub>q</sub>, ΔC<sub>q</sub> or ΔΔC<sub>q</sub> values. However, reporting of C<sub>q</sub> values ignores the fact that C<sub>q</sub> values may differ between runs and machines, and, therefore, cannot be compared between laboratories. Moreover, C<sub>q</sub> values are highly dependent on the PCR efficiency, which differs between assays and may differ between samples. Interpreting reported C<sub>q</sub> values, assuming a 100% efficient PCR, may lead to assumed gene expression ratios that are 100-fold off. This review describes how differences in quantification threshold setting, PCR efficiency, starting material, PCR artefacts, pipetting errors and sampling variation are at the origin of differences and variability in C<sub>q</sub> values and discusses the limits to the interpretation of observed C<sub>q</sub> values. These issues can be avoided by calculating efficiency-corrected starting concentrations per reaction. The reporting of gene expression ratios and fold difference between treatments can then easily be based on these starting concentrations.
Rapid urea broth test for yeasts (1978)

A rapid, miniaturized, urea broth test useful for detecting urease activity of yeasts was compared to Christensen urea agar. All urease-producing yeasts tested were positive on both media; however, 60% were reactive in the urea R broth within 30 min, and the remainder were reactive within 4 h. This urea multiwell test may be useful as a rapid screening method for detecting urease-producing yeasts recovered from clinical specimens and as an adjunct test with other rapid methods of yeast identification.