gebhart/patrepeval huggingface dataset:
DNA Condensation by Polyamines:  A Laser Light Scattering Study of Structural Effects (2001)

Polyamines such as spermidine and spermine are abundant in living cells and are believed to aid in the dense packaging of cellular DNA. DNA condensation is a prerequisite for the transport of gene vectors in living cells. To elucidate the structural features of polyamines governing DNA condensation, we studied the collapse of lambda-DNA by spermine and a series of its homologues, H2N(CH2)3NH(CH2)n=2-12NH(CH2)3NH2 (n = 4 for spermine), using static and dynamic light scattering techniques. All polyamines provoked DNA condensation; however, their efficacy varied with the structural geometry of the polyamine. In 10 mM sodium cacodylate buffer, the EC50 values for DNA condensation were comparable (4 +/- 1 microM) for spermine homologues with n = 4-8, whereas the lower and higher homologues provoked DNA condensation at higher EC50 values. The EC50 values increased with an increase in the monovalent ion (Na+) concentration in the buffer. The slope of a plot of log [EC50(polyamine4+)] against log [Na+] was approximately 1.5 for polyamines with even number values of n, whereas the slope value was approximately 1 for compounds with odd number values of n. Dynamic light scattering measurements showed the presence of compact particles with hydrodynamic radii (Rh) of about 40-50 nm for compounds with n = 3-6. Rh increased with further increase in methylene chain length separating the secondary amino groups of the polyamines (Rh = 60-70 nm for n = 7-10 and >100 nm for n = 11 and 12). Determination of the relative binding affinity of polyamines to DNA using an ethidium bromide displacement assay showed that homologues with n = 2 and 3 as well as those with n > 7 had significantly lower DNA binding affinity compared to spermine and homologues with n = 5 and 6. These data suggest that the chemical structure of isovalent polyamines exerts a profound influence on their ability to recognize and condense DNA, and on the size of the DNA condensates formed in aqueous solution.
Adaptive Local Window for Level Set Segmentation of CT and MRI Liver Lesions (2017)

We propose a novel method, the adaptive local window, for improving level set segmentation technique. The window is estimated separately for each contour point, over iterations of the segmentation process, and for each individual object. Our method considers the object scale, the spatial texture, and the changes of the energy functional over iterations. Global and local statistics are considered by calculating several gray level co-occurrence matrices. We demonstrate the capabilities of the method in the domain of medical imaging for segmenting 233 images with liver lesions. To illustrate the strength of our method, those lesions were screened by either Computed Tomography or Magnetic Resonance Imaging. Moreover, we analyzed images using three different energy models. We compared our method to a global level set segmentation, to a local framework that uses predefined fixed-size square windows and to a local region-scalable fitting model. The results indicate that our proposed method outperforms the other methods in terms of agreement with the manual marking and dependence on contour initialization or the energy model used. In case of complex lesions, such as low contrast lesions, heterogeneous lesions, or lesions with a noisy background, our method shows significantly better segmentation with an improvement of 0.25 ± 0.13 in Dice similarity coefficient, compared with state of the art fixed-size local windows (Wilcoxon, p < 0.001).
Minimizing Stress Shielding and Cement Damage in Cemented Femoral Component of a Hip Prosthesis through Computational Design Optimization (2017)

The average life expectancy of many people undergoing total hip replacement (THR) exceeds twenty-five years and the demand for implants that increase the load-bearing capability of the bone without affecting the short- or long-term stability of the prosthesis is high. Mechanical failure owing to cement damage and stress shielding of the bone are the main factors affecting the long-term survival of cemented hip prostheses and implant design must realistically adjust to balance between these two conflicting effects. In the following analysis we introduce a novel methodology to achieve this objective, the numerical technique combines automatic and realistic modeling of the implant and embedding medium, and finite element analysis to assess the levels of stress shielding and cement damage and, finally, global optimization, using orthogonal arrays and probabilistic restarts, were used. Applications to implants, fabricated using a homogeneous material and a functionally graded material, were presented.
Rapid Diagnostic Method for Detection of Mumps Virus Genome by Loop-Mediated Isothermal Amplification (2005)

Most mumps patients are clinically diagnosed without any virological examinations, but some diagnosed cases of mumps may be caused by other pathogens or secondary vaccine failure (SVF). To clarify these issues, a sensitive, specific, and rapid diagnostic method is required. We obtained 60 salivary swabs from 34 patients with natural infection during the course of the illness, 10 samples from patients with vaccine-associated parotitis, and 5 samples from patients with SVF. Total RNA was extracted and subjected to reverse transcription-PCR (RT-PCR) and loop-mediated isothermal amplification (LAMP) for genome amplification. We detected mumps virus RNA corresponding to 0.1 PFU by LAMP within 60 min after RNA extraction, with the same sensitivity as RT-nested PCR. Mumps virus was isolated in 30 of 33 samples within day 2, and mumps virus genome was amplified by LAMP in 32 of them. The quantity of virus titer was calculated by monitoring the time to reach the threshold of turbidity. The viral load decreased after day 3 and was lower in patients serologically diagnosed as having SVF with milder illness. Accuracy of LAMP for the detection of mumps virus genome was confirmed; furthermore, it is of benefit for calculating the viral load, which reflects disease pathogenesis.
Equilibria in data injection attacks (2014)

Data injection attacks are studied in a game theoretic setting. Assuming that the network operator acquires the state variables via generalized least squares (GLS) estimation, different attack performance metrics are proposed. The scenarios defined by the performance metrics are then analyzed. In particular, closed form expressions for best response functions and Nash equilibria (NEs) are given. First the case in which the attack vector can be constructed without energy constraints is studied. It is shown that for unconstrained attacks infinitely many optimal attack vectors exist and that the construction requires knowledge of the state variables in the grid. Alternatively, when energy constraints are included, the attack vector construction does not depend on the state variables. As a consequence, the optimal energy constrained attack strategy follows a correlated multivariate Gaussian distribution. It is shown that for unconstrained attacks infinitely many NEs exist and that in the constrained case at least one NE exists.
The Price of Reliable Accessibility (2014)

The literature on induced demand suggests that transportation system interventions that improve travel time not only result in short-term responses by travelers to shift modes, times of travel and routes, but also include longer-term inﬂuences on land use outcomes that further affect travel demand. This literature has not explored, however, whether improvements in travel time reliability might generate long-term impacts on real estate markets. Even the casual observer would likely agree that unreliable travel time to work is problematic, and a growing body of research has begun to measure the degree to which travelers value travel time reliability by analyzing their route or mode choices. To the authors' knowledge, however, no one has yet addressed the question of whether travel time reliability has longer-term effects beyond daily travel decisions, by inﬂuencing real estate market outcomes. Is travel time reliability valued enough by individuals, households, and ﬁrms to be capitalized into higher real estate prices and rents in locations with more reliable accessibility? Does reliability have enough value to inﬂuence long-term choices of households or ﬁrms regarding where they rent or purchase real estate? These are the questions explored in this research.
Sample Grading Method of Estimating Gas Reserves (1952)

Abstract A technique is presented by which well samples and core plugs of dolomiteformations are classified by microscopic examination into seven differentporosity grades. Quantitative values of porosity and permeability aredetermined for each grade by a statistical correlation of the core plug testdata with the porosity grading system. These quantitative values are applieddirectly to the grades exhibited in the well samples for the purpose ofestimating the reservoir void space for wells that were not cored. The procedure is described for estimating the gas reserves per unit area forthe South Hugoton gas field, but a reserve estimate for the field is notgiven. Introduction The miscroscopic examination of well samples and the graphic recording oftheir lithologic qualities and other distinguishing characteristics of variousgeologic formations drilled is both a science and an art of long standing andwide application. Usually the primary objective of a geologist who "sits onthe well" and examines the samples are: to identify the formation beingdrilled, determine the total depth, casing point, and completion interval. Inmost cases the porosity is described, if done at all, in general terms, suchas: trace, scattered, fine, poor, fair, medium, good, excellent, or in someother relative terms. In fields where various geologists have examined samplesand recorded observations on many wells considerable variations in lithologicterms and porosity descriptions occur unless there is primary effort toestablish uniformity of logging observations and standards of recordingobservable porosity. When an estimate of the pore volume of a reservoir is made a geologicconcept of the processes that control the magnitudes of porosity andpermeability is developed by microscopic examination of well samples. Thecharacteristics and appearances are then mentally related to rather generalquantitative units of porosity based on physical core data from the samereservoir or on such data or experience in other reservoirs that have similarqualities. The reliability of such estimates depends largely on the variationsof the lithology of the formations, the geometric properties of its voidsystem, the extent of comparisons of sample appearances with porosity data, aswell as the uniform recording of all relevant characteristics. This statementis particularly significant for dolomitized limestone formations of substantialthicknesses and heterogeneity such as the Permian Dolomites of the Hugoton gasfield. T.P. 3374
IRGC1, a testis-enriched immunity related GTPase, is important for fibrous sheath integrity and sperm motility in mice (2022)

Immunity-related GTPases (IRGs), also known as p47 GTPases, are a family of interferon-inducible proteins that play roles in immunity defense against intracellular pathogens. Although the molecular functions of IRGs have been well studied, the function of the family member, IRGC1, remains unclear. IRGC1 is unique among IRGs because its expression is not induced by interferon and it is expressed predominantly in the testis. Further, IRGC1 is well conserved in mammals unlike other IRGs. Here, we knocked out (KO) Irgc1 in mice using the CRISPR/Cas9 system and found that the fertility of Irgc1 KO males was severely impaired because of abnormal sperm motility. Further analyses with a transmission electron microscope revealed that the fibrous sheath (FS), an accessory structure of the sperm tail, was disorganized in Irgc1 KO mice. In addition, IRGC1 was detected in the sperm tail and fractionated with FS proteins. These results suggest that IRGC1 is a component of the FS and is involved in the correct formation of the FS.
Plasminogen Enhances Neuritogenesis on Laminin-1 (2009)

Proteins of the plasminogen activation system are broadly expressed throughout the nervous system, and key roles for these proteins in neuronal function have been demonstrated. Recent reports have established that plasminogen is synthesized in neuroendocrine tissues, making this protein and the proteolytic activity of the product of its activation, plasmin, available at sites separated anatomically from circulating, hepatocyte-derived plasminogen. Results with plasminogen-deficient humans and mice suggest a role for plasminogen in neuritogenesis. To elucidate the role of the plasminogen activation system in these processes, the function of plasminogen during neuritogenesis and neurite outgrowth was studied. It is shown here that plasminogen participates in neuritogenesis, as plasmin inhibitors reduced both neurite outgrowth and neurite length in PC-12 cells. The addition of exogenous plasminogen enhanced neurite outgrowth and neurite length in both PC-12 cells and primary cortical neurons. The proteolytic activity of plasmin was required, since mutation of the catalytic serine residue completely abolished the stimulatory activity. Furthermore, mutation of the lysine binding site within kringle 5 of the plasminogen molecule also reduced the neuritogenic activity of plasminogen. Additionally, we demonstrate that plasminogen specifically bound to laminin-1, the interaction resulted in increased plasminogen activation by tissue-type plasminogen activator, and was dependent on a functional lysine binding site within plasminogen kringle 5. Moreover, during NGF-induced neuritogenesis, laminin-1 was degraded, and this cleavage was catalyzed by plasmin. This study provides the first direct evidence that plasminogen participates in neurite outgrowth and also suggests that laminin-1 degradation by plasmin contributes to the process of neuritogenesis.
Giant tunability of microwave responses for current-driven skyrmions in a tapered nanostructure with notches (2023)

Abstract The investigation of the gigahertz dynamics of a skyrmion—a topologically protected chiral spin texture, offers several applications in high-frequency magnonic devices. In this work, we have investigated the motion and microwave resonant dynamics of skyrmions in an engineered nanostructure using micromagnetic simulations. The structure is a tapered ferromagnetic/heavy metal bilayer with notches to stabilize the skyrmion for dynamic studies. The skyrmion is moved along the nanostructure via current-induced spin–orbit torques. Multiple stable skyrmion states were demonstrated in the structure, where a remarkable tunability of 6 GHz is observed between the initial and the final state. This large shift in the resonant frequency has been attributed to the variation in the size of the skyrmion at various locations in the engineered nanostructure. The dependency of the skyrmion velocity and their microwave responses on the DzyalosnDzyaloshinskii–Moriya interaction strength and the perpendicular magnetic anisotropy is described. The calculation of the skyrmion Hall angle shed light on the motion and stability of the skyrmion in the structure.
Tyrosine kinases regulate chondrocyte hypertrophy: promising drug targets for Osteoarthritis (2021)

Osteoarthritis (OA) is a major health problem worldwide that affects the joints and causes severe disability. It is characterized by pain and low-grade inflammation. However, the exact pathogenesis remains unknown and the therapeutic options are limited. In OA articular chondrocytes undergo a phenotypic transition becoming hypertrophic, which leads to cartilage damage, aggravating the disease. Therefore, a therapeutic agent inhibiting hypertrophy would be a promising disease-modifying drug. The therapeutic use of tyrosine kinase inhibitors has been mainly focused on oncology, but the Food and Drug Administration (FDA) approval of the Janus kinase inhibitor Tofacitinib in Rheumatoid Arthritis has broadened the applicability of these compounds to other diseases. Interestingly, tyrosine kinases have been associated with chondrocyte hypertrophy. In this review, we discuss the experimental evidence that implicates specific tyrosine kinases in signaling pathways promoting chondrocyte hypertrophy, highlighting their potential as therapeutic targets for OA.
Preparation and characterization of conjugates of recombinant CD4 and deglycosylated ricin A chain using different cross-linkers (1990)

In a previous study, we have demonstrated that conjugates containing soluble, recombinant human CD4 (rCD4) and the deglycosylated form of ricin A chain (dgA) (rCD4-dgA) effectively kill a human T cell line infected with the human immunodeficiency virus (HIV) in vitro. In contrast, such conjugates are 100-1000-fold less toxic to uninfected cells. In order to use a rCD4-dgA conjugate effectively in vivo, it was important to demonstrate that (1) it binds to and kills HIV-infected, but not uninfected, human cells, (2) it is stable in the circulation, and (3) it has an optimal therapeutic index (toxicity to animals versus toxicity to target cells). A major factor affecting the efficacy of such conjugates in vitro and in vivo is the nature of the cross-linker between the ligand (rCD4) and the toxin (dgA). In this report, we have prepared rCD4-dgA conjugates using three different cross-linkers. Different methods of purification have been compared by determining the optimal yield, purity, and retention of biological activity (i.e., binding to gp120 and dgA chain activity). The structure of these conjugates as well as their cytotoxicity to target cells in vitro has been analyzed. Finally, we have compared their pharmacokinetics, tissue localization, and toxicity in mice.
Danger of Overwarming Blood by Microwave (1971)

Microwave blood warmers have a number of advantages over the currently used plastic coils immersed in water. A single warmer may be used to service several operating rooms simultaneously and the blood is warmed within a matter of minutes. Although three independent studies indicate that the red blood cells are not altered when subjected to microwaves, we have experienced difficulties. Five units of blood were obviously overheated and hemolyzed in spite of our observing recommended precautions. Four units were transfused to three patients.
Initial characteristics of pressure sensors (2015)

DONET, i.e., the dense ocean-floor network system for earthquakes and tsunamis has started its operation in the Nankai Trough, SW Japan in the early of 2010. DONET in 20 observatories consists of various geophysical sensors such as broadband seismometer, seismic accelerometer, tsunami meter, and so on. The present study focuses on pressure sensors being used as tsunami meters measuring hydraulic pressure change. Pressure sensors specify their performance for both hysteresis and repeatability, however there is no specification about the long-term sensor's stability. In this study, we evaluate the initial sensor's stability in terms of the laboratory experiment and the in-situ measurements. The high accuracy pressure standard is used for the laboratory experiment. The present experiment has been done by applying 20 MPa hydro-static pressure to the pressure sensors, which is equivalent to approximately 2,000 m water depth under the constant temperature of 2 °C for duration of one month. As a result, our experiment suggests that sensor's drift vary among pressure sensors and the sensor's drift occurs 10 cm per month in maximum. On the other hand, we evaluate the sensor's drift since deployment into the deep-sea by removing tide component. The in-situ measurement indicates that the sensor's drift continues after the deployment. Some pressure sensor's drift in the initial stage from the in-situ measurement corresponds to that from the experiment for the direction and the rate.
Preoperative evaluation of abdominal aortic aneurysms: is there a need for aortography? (1981)

A comparison was made between angiography (AI), computer tomography (CT) and ultrasound (US) in the preoperative evaluation of 85 consecutive patients with abdominal aortic aneurysm. A total of 63 AI, 24 CT and 43 US were performed. It is concluded that the diagnostic accuracy in identifying aneurysms is higher for CT and US than for AI. AI and CT provide more correct data concerning the anatomy in the region of the renal arteries than US. We suggest that a non-invasive technique should be used for preoperative verification of the diagnosis. AI should only be used when the upper limit of the aneurysm and the relation to the renal arteries cannot be defined by non-invasive methods and, furthermore, in all cases with clinical signs of stenotic disease of the iliac arteries.
Investigation of water environments in a C18 bonded silica phase using 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy (2001)

High resolution 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra have been obtained on typical C18 bonded silicas used in chromatographic solid-phase extraction separations. It has been shown for the first time that water molecules distributed in distinct physico-chemical environments within the chromatographic system can be detected directly using a simple 1H MAS NMR measurement. The resonances assigned to water protons in differing physico-chemical environments have distinct chemical shifts, line widths, relaxation times (T1 and T2) and also exhibit temperature dependent coalescence behaviour. This novel MAS approach may lead to a better understanding of the environments of other analytes in mixtures during such separations.
A Novel Application of the Principles of Linear Elastic Fracture Mechanics (LEFM) to the Fatigue Behavior of Tendon Tissue (2004)

LEFM and other FM approaches may prove to be very valuable in advancing our understanding of damage accumulation in soft connective tissues.
Accuracy of history, physical examination, cardiac biomarkers, and biochemical variables in identifying dogs with stage B2 degenerative mitral valve disease (2021)

Our findings indicate accessible measurements could be used to screen dogs with preclinical DMVD. Encouraging at-risk dogs to seek further evaluation could result in a greater proportion of cases being appropriately managed.
FIBRE BRAGG SENSORS COMPARED WITH ELECTRICAL STRAIN GAUGES FOR USE IN FORCE MEASUREMENT - PROSPECTS AND POTENTIALS (2009)

Abstract − This article deals with the technical properties of fiber Bragg gratings with regard to their use as the strain-sensitive element in force transducers. Electrical strain gages are widely used in modern, precise force transducers. The electrical strain gage provides both outstanding technical properties and cost-effectiveness. Besides the electrical strain gage, the measurement principle of fiber Bragg-based sensors has recently become established. First applications in experimental mechanics have shown that this technology offers a lot of potential. Optical strain gauges are available on the marked since one year and are proofed in many applications. These sensors are mainly based on so-called fiber Bragg gratings. Such a Bragg grating uses a great many reflection points at regular spacing. At each of these points, part of the radiated light is reflected. The reflected light interferes (constructive interference) and generates a reflection peak. This peak shows a characteristic wavelength which is dependent on the spacing of the reflection points. The following sketch shows a Bragg grating in a fibre and its influence on the spectrum of the transmitted and reflected light. Reflected light τ This article presents the properties relevant to use in the manufacture of transducers such as: