gebhart/patrepeval huggingface dataset:
Practical Issues with TLS Client Certificate Authentication (2014)

The most widely used secure Internet communication standard TLS (Transport Layer Security) has an optional client certificate authentication feature that in theory has significant security advantages over HTML form-based password authentication.In this paper we discuss practical security and usability issues related to TLS client certificate authentication stemming from the server-side and browser implementations.In particular, we analyze Apache's mod_ssl implementation on the server side and the most popular browsers -Mozilla Firefox, Google Chrome and Microsoft Internet Explorer on the client side.We complement our paper with a measurement study performed in Estonia where TLS client certificate authentication is widely used.We present our recommendations to improve the security and usability of TLS client certificate authentication.
Haptic gait retraining for knee osteoarthritis treatment (2010)

In this paper we introduce haptic gait retraining as a new method for treating early stage medial compartment knee osteoarthritis and for reducing risk of the disease in individuals who may be susceptible. The hardware and software for implementation are presented including rotational skin stretch and vibration haptic devices used to inform subjects of alterations in gait movements. We also present a method based on real-time motion analysis for predicting new subject-specific gaits tailored to change knee joint loading. This approach uses correlation data between gait parameters and knee loading as well as a localized linearization technique to compute a final combined-parameter gait with minimum change from the subject's original, unaltered gait. Finally, we validate the haptic gait retraining system with a user experiment and show that, for the duration of the experiment, the user is able to positively change knee joint loading to approximately the same degree as HTO surgery.
Intraspinal and behavioral consequences of nerve growth factor‐induced nociceptive sprouting and nerve growth factor‐induced hyperalgesia compared in adult rats (1999)

Intraspinal and behavioral events were studied in adult rats with nociceptive nerves that were undergoing collateral sprouting into adjacent denervated skin. This sprouting, which is driven by endogenous nerve growth factor (NGF), did not cause hyperalgesia. For comparison, we studied an exogenous NGF administration that induced hyperalgesia but was too brief to evoke sprouting. When nociceptive nerves sprouted in skin, back-labeling with wheat germ agglutinin-conjugated horseradish peroxidase revealed that their projections sprouted in the cord. The sprouted peripheral nerves now activated more c-Fos-containing interneurons, which stimulus-response studies showed was not due to an increased afferent discharge. We attribute the interneuron recruitment to synaptogenesis following the intraspinal sprouting. Nociceptive stimulation of dorsal skin reflexly activates underlying cutaneous trunci muscle (CTM). When a nociceptive field expanded by nerve sprouting, so did the area of the evoked CTM reflex: this implies a recruitment of CTM motoneurons. We interpret this “matching” of response to stimulus as an adaptive phenomenon ensured by an adaptive intraspinal sprouting of the nociceptive projections. Neither the intraspinal changes nor the reflex changes occurred if peripheral sprouting was blocked by systemic anti-NGF treatment, indicating that the role of endogenous NGF was only in that sprouting. No comparable adaptive events occurred during NGF-induced hyperalgesia. Neither nociceptive fields nor CTM reflexes were affected; however there was a recruitment of c-Fos-expressing interneurons. This recruitment was not explained by peripheral sensitization, and, because sprouting was not involved here, we attribute the recruitment to “synaptic unmasking,” i.e., an increased effectiveness of the preexisting excitatory circuitry. J. Comp. Neurol. 410:73–89, 1999. © 1999 Wiley-Liss, Inc.
Involvement of angiotensin II in glomerulosclerosis of stroke-prone spontaneously hypertensive rats. (1996)

Renal plasma flow (RPF), glomerular filtration rate (GFR), glomerular pathology and glomerular TGF-beta gene expression were examined in 12- and 24-week-old stroke-prone spontaneously hypertensive rats (SHRSP) and Wistar Kyoto rats (WKY). These parameters were also examined in SHRSP treated with equihypotensive doses of angiotensin II receptor antagonist (CV-11974:CV) and hydralazine (Hyd) for 12 weeks. Twelve-week-old SHRSP showed a decrease in RPF and GFR, and an increase in filtration fraction (FF) and urinary protein excretion (UP) compared to WKY. CV normalized these parameters, whereas although Hyd showed improved levels they were not to the levels achieved by the WKY. Glomerular TGF-beta expression was increased 2.0-fold in 12- and 24-week-old SHRSP, and CV, but not Hyd, decreased it to the control levels of WKY. At 24 weeks old, SHRSP showed a higher glomerulosclerosis index (GI) than WKY. CV, but not Hyd, lowered the GI to the level of the WKY controls. These data indicate that renal hemodynamic changes are closely associated with an increased TGF-beta expression in SHRSP and that this condition is caused by angiotensin II.
Structure of <i>Acinetobacter </i>Strain ADP1 Protocatechuate 3,4-Dioxygenase at 2.2 Å Resolution:  Implications for the Mechanism of an Intradiol Dioxygenase (2000)

The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.
Structures and Properties of Sago Starches with Low and High Viscosities on Amylography (1989)

ABSTRACT Both amyloses and amylopectins from sago starches with low (280 BU, low‐v) and high (735 BU, high‐v) viscosities on amylography differed in molecular structures. The low‐v amylopectin (average chain length, c.I., 22) was a smaller molecule with a slightly higher amount of long chains than the high‐v amylopectin (c.I., 22). The number‐and weight‐average degrees of polymerization of the low‐v amylose were 2490 and 5090, respectively, which were half those of the high‐v amylose. The low‐v amylose had a lower molar fraction of branched molecules with a shorter inner chain length than the high‐v amylose, but both branched molecules had a similar number (17–19) of chains on the average. Both starch granules had the same crystalline type (C a ) and amylose content (24%).
Mutation Testing to Validate Networks Protocols (2020)

As networks continue to grow in complexity using wired and wireless technologies, efficient testing solutions should accommodate such changes and growth. Network simulators provide a network-independent environment to provide different types of network testing. This paper is motivated by the observation that, in many cases in the literature, the success of developed network protocols is very sensitive to the initial conditions and assumptions of the testing scenarios. Network services are deployed in complex environments; results of testing and simulation can vary from one environment to another and sometimes in the same environment at different times. Our goal is to propose mutation-based integration testing that can be deployed with network protocols and serve as Built-in Tests (BiT).This paper proposes an integrated mutation testing framework to achieve systematic test cases' generation for different scenario types. Scenario description and variables' setting should be consistent with the protocol specification and the simulation environment. We focused on creating test cases for critical scenarios rather than preliminary or simplified scenarios. This will help users to report confident simulation results and provide credible protocol analysis. The criticality is defined as a combination of network performance metrics and critical functions' coverage. The proposed solution is experimentally proved to obtain accurate evaluation results with less testing effort by generating high-quality testing scenarios. Generated test scenarios will serve as BiTs for the network simulator. The quality of the test scenarios is evaluated from three perspectives: (i) code coverage, (ii) mutation score and (iii) testing effort. In this work, we implemented the testing framework in NS2, but it can be extended to any other simulation environment.
Design and validation of distributed control with decentralized intelligence in process industries: A survey (2008)

This paper presents an overview of the works on design and validation of distributed control in process industry. Due to the significant market demand for distributed reconfigurable systems, not just in manufacturing industry but also in process industry, several researches are undertaken to look at the design techniques in implementation of such a decentralized control approach. It has shown that a distributed control can bring benefits such as flexibility, reconfigurability and software reusability. International standards such as IEC61499 and IEC61804 are established for such distributed application with newly introduced Function Block (FB) concepts. Intelligent control and multi-agents approach are emerging techniques for distributed control application. In particular, a process control system is generally considered as a hybrid system because it usually contains both discrete and continuous dynamics. Therefore when handling validation of distributed systems, hybrid verification and simulation will have an important role.
Cerebral microenvironment influences expression of the vitronectin gene in astrocytic tumors (1995)

Expression of the vitronectin gene was detected in advanced human astrocytoma by in situ hybridization, whereas vitronectin mRNA was undetectable in low grade tumors or in normal adult brain, indicating that vitronectin is a marker of malignant astrocytoma. We established a model of human astrocytoma by transplanting U-251MG human astrocytoma cells intracerebrally into acid mice (C.B.17 severe combined immunodeficient mice). In this model, tumors progressed rapidly and vitronectin mRNA was preferentially detected at the invading tumor margins, i.e. where tumor cells were adjacent to the normal brain tissue. Surprisingly, when U-251MG cells were injected subcutaneously into scid mice, vitronectin mRNA was undetectable throughout the tumor. Moreover, vitronectin mRNA or protein could not be detected among these cells in culture under a wide variety of growth conditions. These findings demonstrate that the cerebral microenvironment influences the expression of the vitronectin gene in malignant astrocytoma. Importantly, the vitronectin binding integrins alpha v beta 3 and alpha v beta 5 localized to distinct sites within these tumors, with beta 3 mRNA synthesized among invading cells, and alpha v and beta 5 mRNAs detected throughout the tumor. In vitro, both of these receptors were capable of promoting adhesion and invasion of astrocytoma cells on a vitronectin substratum. These findings implicate the expression of the vitronectin gene as a contributing factor to the biological behavior of astrocytomas within the cerebral microenvironment.
Physical Bounds to the Entropy-Depolarization Relation in Random Light Scattering (2005)

We present a theoretical study of multimode scattering of light by optically random media, using the Mueller-Stokes formalism which permits us to encode all the polarization properties of the scattering medium in a real 4 x 4 matrix. From this matrix two relevant parameters can be extracted: the depolarizing power D(M) and the polarization entropy E(M) of the scattering medium. By studying the relation between E(M) and D(M), we find that all scattering media must satisfy some universal constraints. These constraints apply to both classical and quantum scattering processes. The results obtained here may be especially relevant for quantum communication applications, where depolarization is synonymous with decoherence.
cAMP increasing agents attenuate the generation of apoptosis by etoposide in promonocytic leukemia cells (1998)

Treatment of U-937 promonocytic cells with the DNA topoisomerase II inhibitor etoposide rapidly caused death by apoptosis, as determined by changes in chromatin structure, production of DNA breaks, nucleosome-sized DNA degradation, decrease in mitochondrial membrane potential and phosphatidyl serine translocation in the plasma membrane, and at the same time induced intracellular acidification. Both the execution of the apoptotic process and the intracellular acidification were reduced by the addition of forskolin plus theophylline or other cAMP increasing agents. These agents also attenuated the induction of apoptosis by camptothecin, heat-shock, cadmium chloride and X-radiation. Although etoposide slightly increased the production of reactive oxygen intermediates, this increase was not prevented by forskolin plus theophylline, and the addition of antioxidant agents failed to inhibit apoptosis. Etoposide caused a great increase in NF-(kappa)B binding activity, which was not prevented by forskolin plus theophylline, while AP-1 binding was little affected by the topoisomerase inhibitor. The treatments did not significantly alter the levels of Bcl-2 and Bax. By contrast, the expression of c-myc, which was very high in untreated U-937 cells and only partially inhibited by etoposide, was rapidly and almost totally abolished by the cAMP increasing agents. Finally, it was observed that etoposide caused a transient dephosphorylation of retinoblastoma (Rb), which was associated with cleavage of poly(ADP-ribose) polymerase (PARP). Both Rb dephosphorylation and PARP cleavage were inhibited by forskolin plus theophylline. The inhibition of Rb (type I) phosphatase and ICE/CED-3-like protease activities, and the abrogation of c-myc expression, are mechanisms which could explain the anti-apoptotic action of cAMP increasing agents in myeloid cells.
<i>Myxosoma cerebralis</i>: Isolation and Concentration from Fish Skeletal Elements — Sequential Enzymatic Digestions and Purification by Differential Centrifugation (1974)

An effective sequential procedure for recovery of Myxosoma cerebralis spores from infected trout was developed, and quantification of spores was carried out at each step of release and concentration. Methods are described for fresh and frozen material. Effective concentration of from 1100- to 9000-fold and an estimated efficiency of recovery of about 80% has been achieved. Tabular and graphic data are presented with recommendations for diagnostic applications. The immediate applications of these procedures are in implementing more effective detection and in preparing antigen for the immunologic studies that should provide the most sensitive detection.
Yeast ubiquitin-like genes are involved in duplication of the microtubule organizing center. (1996)

KAR1 is required for duplication of the Saccharomyces cerevisiae microtubule organizing center, the spindle pole body (SPB) (Rose, M.D., and G.R. Fink, 1987. Cell. 48:1047-1060). Suppressors of a kar1 allele defective for SPB duplication were isolated in two genes, CDC31 and DSK2 (Vallen, E.A., W.H., M. Winey, and M.D. Rose. 1994. Genetics. 137:407-422). To elucidate the role of DSK2 in SPB duplication, we cloned the gene and found it encodes a novel ubiquitin-like protein containing an NH2 terminus 36% identical to ubiquitin. The only other known yeast ubiquitin-like protein is encoded by the nucleotide excision repair gene RAD23 (Watkins, J.F.,P. Sung, L. Prakash, and S. Prakash. 1993. Mol. Cell. Bio. 13:7757-7765). Unlike ubiquitin, the NH2-terminal domain of Dsk2p is not cleaved from the protein, indicating that Dsk2p is not conjugated to other proteins. Although the DSK2-1 mutation alters a conserved residue in the Dsk2p ubiquitin-like domain, we detect no differences in Dsk2p or Cdc31p stability. Therefore, DSK2 does not act by interfering with ubiquitin-dependent protein degradation of these proteins. Although DSK2 is not essential, a strain deleted for both DSK2 and RAD23 is temperature sensitive for growth due to a block in SPB duplication. In addition, overexpression of DSK2 is toxic, and the DSK2-1 allele causes a block in SPB duplication. Therefore, DSK2 dosage is critical for SPB duplication. We determined that CDC31 gene function is downstream of DSK2 and KAR1. Dsk2p is a nuclear-enriched protein, and we propose that Dsk2p assists in Cdc31 assembly into the new SPB.
On the Capacity of Wideband 60GHz Channels with Antenna Directionality (2007)

Currently the 60 GHz band is being considered as the most attractive option for the design of very high rate (multi Gbps) short range communication systems. These systems will use antenna directionality to offset the high path loss and to achieve a higher degree of spatial reuse. Besides providing a power gain, directional antennas change the observed multipath. In this paper, we study different effects of the antenna directionality on the capacity of the 60GHz channel.
Electric-field-induced strain-mediated magnetoelectric effect in CoFeB-MgO magnetic tunnel junctions (2013)

Magnetoelectric coupling between magnetic and electric dipoles is one of the cornerstones of modern physics towards developing the most energy-efficient magnetic data storage. Conventionally, magnetoelectric coupling is achieved in single-phase multiferroics or in magnetoelectric composite nanostructures consisting of ferromagnetic and ferroelectric/piezoelectric materials. Here, we demonstrate an electric-field-induced strain-mediated magnetoelectric effect in ultrathin CoFeB/MgO magnetic tunnel junction employing non-piezoelectric material, which is a vitally important structure for spintronic devices, by using dynamical magnetoelectric and piezoresponse force microscopy measurement techniques. We show that the applied electric-field induces strain in a few atomic layers of dielectric MgO which is transferred to magnetostrictive CoFeB layer, resulting in a magnetoelectric effect of magnitude up to 80.8 V cm-1 Oe-1 under -0.5 V. The demonstrated strain-mediated magnetoelectric effect with an electric field in magnetic tunnel junctions is a significant step towards exploring magnetoelectrically controlled spintronic devices for low-power and high density magnetic data storage applications.
Tunneling Anisotropic Magnetoresistance and Spin-Orbit Coupling in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>Fe</mml:mi><mml:mo>/</mml:mo><mml:mi>GaAs</mml:mi><mml:mo>/</mml:mo><mml:mi>Au</mml:mi></mml:math>Tunnel Junctions (2007)

We report the observation of tunneling anisotropic magnetoresistance effect in the epitaxial metal-semiconductor system Fe/GaAs/Au. The observed twofold anisotropy of the resistance can be switched by reversing the bias voltage, suggesting that the effect originates from the interference of the spin-orbit coupling at the interfaces. Corresponding model calculations reproduce the experimental findings very well.
Optimization of the Selectivity of Pyrene Immunoaffinity Columns Prepared by the Sol−Gel Method (1997)

The sol−gel method opened a new path for synthesizing immunoaffinity column packing materials by encapsulating antibodies in the pores of a silica glass matrix. This paper describes different strategies for the optimization of the selectivity of pyrene immunoaffinity columns synthesized by encapsulating the immunoglobulin (IgG) fraction of an anti-pyrene antiserum in a porous silica glass. The selectivity of the columns which are designed for the determination of pyrene in aqueous samples is limited by the retention of cross-reacting and nonspecifically adsorbed polycyclic aromatic hydrocarbons (PAHs). An optimum in selectivity is achieved by a new method to wash the columns with a mixture of a high molecular weight polymer which blocks nonspecific adsorption sites and a surfactant which removes unwanted substances by inclusion into micelles. Optimal results were achieved by washing with 5% (v/v) Roti-Block in 10:90 acetonitrile−water (v/v). Roti-Block is the trade name for a mixture of a high molecular weight poly(vinylpyrrolidone) with a nonionic surfactant dissolved in PBS buffer.
The environment as our common heritage (2012)

What does it mean to say that the environment is our ‘common heritage’? On one level this is a simple statement of fact: when we are born, we come into a world that is not of our own making. The air we breathe, the water we drink, the natural resources on which our livelihoods depend, and the accumulated knowledge and information that underpin our ability to use these resources wisely – all these come to us as gifts of creation that have been passed on to us by preceding generations and enriched by their innovation and creativity. Yet once we take seriously – as I do – the proposition that this common heritage belongs in common and equal measure to us all, we move beyond a positive statement of facts to a normative declaration of ethics. We move beyond an understanding of what is to an assertion of what ought to be. To say that the environment belongs in common and equal measure to us all does not mean that we have inherited a free gift with no strings attached. For our common heritage carries with it a common responsibility: the responsibility to share the environment fairly among all who are alive today, and the responsibility to care for it wisely to ensure that our children, our grandchildren and the generations who follow will share fairly in our common heritage too.