gebhart/patrepeval huggingface dataset:
Navigation in laparoscopy – prototype research platform for improved image‐guided surgery (2008)

The manipulation of the surgical field in laparoscopic surgery, through small incisions with rigid instruments, reduces free sight, dexterity, and tactile feedback. To help overcome some of these drawbacks, we present a prototype research and development platform, CustusX, for navigation in minimally invasive therapy. The system can also be used for planning and follow-up studies. With this platform we can import and display a range of medical images, also real-time data such as ultrasound and X-ray, during surgery. Tracked surgical tools, such as pointers, video laparoscopes, graspers, and various probes, allow surgeons to interactively control the display of medical images during the procedure. This paper introduces navigation technologies and methods for laparoscopic therapy, and presents our software and hardware research platform. Furthermore, we illustrate the use of the system with examples from two pilots performed during laparoscopic therapy. We also present new developments that are currently being integrated into the system for future use in the operating room. Our initial results from pilot studies using this technology with preoperative images and guidance in the retroperitoneum during laparoscopy are promising. Finally, we shortly describe an ongoing multicenter study using this surgical navigation system platform.
Dry spinning polymeric nano/microfiber arrays using glass micropipettes with controlled porosities and fiber diameters (2007)

We present a method for dry spinning polymeric nano/microfiber arrays. In this technique polymer solution is continuously ejected from a stationary glass micropipette and the fibers are deposited as continuous arrays in parallel and complex geometrical configurations on a rotating substrate mounted on to a translation stage. As the polymer solution exits the glass micropipette, ambient air is used to evaporate the solvent, thus solidifying the fiber which is then deposited on the rotating substrate. For a given polymer, altering the processing and material parameters allows depositing fiber arrays with highly tunable porosities and uniform fiber diameters. The fiber array porosity is observed to decrease with increasing angular velocity of the rotating substrate at a constant translational stage velocity. Fiber array breaking strength experiments as a function of porosity show higher loads required to break low porosity arrays, which is critical in designing stronger materials. Additionally, single and double layered biological scaffolds fabricated using this technique are seeded with mouse C2C12 cells and cellular dynamics of adhesion, migration and proliferation is investigated.
The "capture effect": a new self-organizing network for "adaptive resolution" clustering in changing environments (2002)

In this paper two open questions in pattern recognition are addressed: learning data clusters appearing naturally at various scales (or resolutions); and online learning (or learning in changing environments). These problems are faced using self-organizing neural networks. In particular, a new mechanism is presented, called "capture effect", concerning an adaptive recruitment of neurons and local modulation of the neural receptive fields. The network is able, as shown in the experiments, to discriminate and code data clusters at a scale adapted to local data density, and to perform it online, accepting new input information without damaging previously encoded patterns. However, the network is also able to "forget", by releasing previously recruited neurons which are no longer "refreshed" by input patterns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Altitude considerations in HVAC equipment selection (1997)

One of the major sources of misunderstanding among designers who live and work at elevations above 2,000 ft is how and why you adjust HVAC equipment performance for altitude. Of course, there are some pieces of HVAC equipment performance for altitude. Of course, there are some pieces of HVAC equipment that do not need to have their performance derated for altitude: refrigeration compressors, water-cooled condensing units, evaporative condensers, pumps, and water-cooled chillers. However, the performance of much of the equipment selected for HVAC systems is affected by changes in the altitude at which the equipment is installed. The system designer must be aware of this to determine whether the selected equipment meets the actual demands of the project. Selecting equipment using unadjusted catalog data can result in undersized equipment and a disgruntled client.
Internal Hydraulic Loss in a Seal‐less Centrifugal Gyro Pump (1994)

A new index "loss factor Z" defined by Eq. 1 was introduced as the absolute expression of the mock loop resistance for testing a nonpulsatile pump. [formula: see text] where gamma is specific gravity of the fluid, g is the acceleration of gravity, delta P is total pressure head, and Q is flow. Z is expected to be constant, regardless of the pumping parameters. Z values obtained in the same mock loop but with different rotary blood pumps were almost identical and were defined as Z0. New methods of analysis of the flow-restrictive conditions of various rotary blood pumps are proposed in this paper: namely, differential loss factor delta Z, and loss factor sensitivity delta Z/delta A. The proposed Z-Q curves demonstrated better performance mapping than the conventional delta P-Q curves. Delta Z is the difference between the Z-Q curves of two different pumps. A is a design parameter of the pump; therefore delta Z/delta A is a quantitative expression of the effect of the design change on the hydraulic performance. These various indices were used to analyze the internal hydraulic loss of a centrifugal pump (Gyro pump). The relationship between its gap size (rotor casing) and hydraulic performance was assessed quantitatively by these indices. In this paper, the derivation processes and above-mentioned indices are described.
The CO-releasing molecule CORM-2 is a novel regulator of the inflammatory process in osteoarthritic chondrocytes (2008)

These data have opened new mechanisms of action for CORM-2, raising the prospect that CO-releasing molecules are an interesting strategy for the development of new treatments in articular conditions.
Thomson scattering measurements in low-density plasmas in the TST-2 spherical tokamak (2015)

Thomson scattering (TS) diagnostics have been widely used in fusion studies to measure profiles of electron temperature Te and electron density ne. In order to measure the low-density plasmas (ne ⩽ 1018 m−3) in TST-2, which is sustained by lower hybrid wave power, the signal-to-noise ratio in TS measurement has been improved by various means. For instance, optimization of the detecting system, accumulation of TS data obtained from reproducible discharges, and application of a coaxial multi-pass scheme were carried out. As a result, the profiles have been measured successfully and a peaked ne profile and a hollow Te profile were obtained. Additionally, isotropy of Te near the plasma center was confirmed by coaxial double-pass TS measurement.
Eliminating Positively Charged Lysine ε-NH<sub>3</sub><sup>+</sup> Groups on the Surface of Carbonic Anhydrase Has No Significant Influence on Its Folding from Sodium Dodecyl Sulfate (2005)

This study compares the folding of two polypeptides--bovine carbonic anhydrase (BCA) and peracetylated BCA (BCA-Ac(18))--having the same sequence of amino acids but differing by 18 formal units of charge, from a solution containing denaturing concentrations of sodium dodecyl sulfate (SDS). Acetylation of BCA with acetic anhydride converts all 18 lysine-epsilon-NH(3)(+) groups to lysine-epsilon-NHCOCH(3) groups and generates BCA-Ac(18). Both BCA and BCA-Ac(18) are catalytically active, and circular dichroism spectroscopy (CD) suggests that they have similar secondary and tertiary structures. SDS at concentrations above approximately 10 mM denatured both proteins. When the SDS was removed by dialysis, both proteins were regenerated in native form. This study suggests that large differences in the net charge of the polypeptide have no significant influence on the structure, the ability to refold, or the rate of refolding of this protein from solutions containing SDS. This study reinforces the idea that charged residues on the surface of BCA do not guide protein folding and raises the broader question of why proteins have charged residues on their surface, outside of the region of the active site.
Implementation of an efficient AC-DC converter for low voltage energy harvesting (2012)

In this paper, a new design methodology for low voltage electromagnetic energy harvesting systems consisting of a microgenerator and power processing circuit is introduced. The proposed converter consists of a boost converter in parallel with a buck-boost converter. The output DC bus is realized by using a single capacitor. The output capacitor is charged by the boost converter in the positive half cycle and by the buck-boost converter in the negative half cycle. Concerning the power efficiency, the effectiveness of the proposed converter is clarified by theoretical analysis. Furthermore, the validity of the circuit design is confirmed by simulations and experimental analysis.
Activation of Nrf2 Is Required for Normal and ChREBPα-Augmented Glucose-Stimulated β-Cell Proliferation (2018)

Patients with both major forms of diabetes would benefit from therapies that increase β-cell mass. Glucose, a natural mitogen, drives adaptive expansion of β-cell mass by promoting β-cell proliferation. We previously demonstrated that a carbohydrate response element-binding protein (ChREBPα) is required for glucose-stimulated β-cell proliferation and that overexpression of ChREBPα amplifies the proliferative effect of glucose. Here we found that ChREBPα reprogrammed anabolic metabolism to promote proliferation. ChREBPα increased mitochondrial biogenesis, oxygen consumption rates, and ATP production. Proliferation augmentation by ChREBPα required the presence of ChREBPβ. ChREBPα increased the expression and activity of Nrf2, initiating antioxidant and mitochondrial biogenic programs. The induction of Nrf2 was required for ChREBPα-mediated mitochondrial biogenesis and for glucose-stimulated and ChREBPα-augmented β-cell proliferation. Overexpression of Nrf2 was sufficient to drive human β-cell proliferation in vitro; this confirms the importance of this pathway. Our results reveal a novel pathway necessary for β-cell proliferation that may be exploited for therapeutic β-cell regeneration.
A mechanistic pathogenetic model of myelodysplastic syndrome (2011)

Myelodysplastic Syndrome (MDS) is a set of bone marrow failure diseases that remain difficult to diagnose, classify, and treat. Some subtypes of MDS follow an aggressive course with short survival and a high rate of progression to a subset of acute myeloid leukemia (MDS-related or MDR-AML), while other subtypes have survival approaching that of age-matched peers, with infrequent or absent leukemic progression. There is no effective model of MDS as a group, of its subtypes, or of MDR-AML. Current models do not satisfactorily address available data, and have led to no progress in diagnosis or treatment in over a decade. A re-analysis of data on which these models is based leads to the conclusion that data may have been misinterpreted, with generation of faulty models of disease. In this manuscript we review data on which the models are based, and generate an alternative interpretation of data and a new model of MDS. This new model appears to correlate well with available data, leads to a modified classification of MDS, is testable, and if correct may lead to new approaches to diagnosis and treatment of MDS and MDR-AML. This new model should be tested.
An SH0 Lithium Niobate dispersive delay line for chirp compression-enabled low power radios (2017)

This paper presents the first demonstration of a shear-horizontal mode Lithium Niobate dispersive delay line, featuring a center frequency of 250 MHz, a delay-bandwidth (TB) product of 100, an electromechanical coupling (k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) in excess of 35%, and a low insertion loss of 10 dB. The high compression is attained via a large bandwidth of 125 MHz, centered at 250 MHz, and an extensive delay of 0.8 μS. The device shown herein has greatly outperformed the state of the art, namely surface acoustic wave delay lines which typically have an insertion loss over 25 dB for a comparable compression ratio. The attained performance can be attributed to the excellent piezoelectric coupling of lamb waves in a suspended Lithium Niobate X-cut thin film. A voltage gain of 3 has been demonstrated for instantaneously amplifying chirp-coded signals, a feature that can be harnessed to enhance signal to noise ratio in low power wake-up radios for Internet of Things (IoT) applications.
Araneus in the Era of XML (1999)

A large body of research has been recently motivated by the attempt to extend database manipulation techniques to data on the Web. Most of these research efforts -- which range from the definition of Web query languages and the related optimizations, to systems for Web site development and management, and to integration techniques -- started before XML was introduced, and therefore have strived for a long time to handle the highly heterogeneous nature of HTML pages. In the meanwhile, Web data sources have evolved from small, home-made collections of HTML pages into complex platforms for distributed data access and application development, and XML promises to impose itself as a more appropriate format for this new breed of Web sites. XML brings data on the Web closer to databases, since, differently from HTML, it is based on a clean distinction between the way the data, its logical structure (the DTD), and the chosen presentation (the stylesheet) are specified. By virtue of this, most of the early research proposals for data management on the Web are now being reconsidered in this new perspective. In this paper, we discuss the impact of XML on the research work conducted in the last few years by our group in the framework of the Araneus project. Araneus started as an attempt to investigate the chances of re-applying traditional database concepts and abstractions, such as the ones of data-model and query language, to data on the Web. In this spirit, we have developed several tools and techniques to handle both structured and semistructured data, in the Web style, as follows: (i) a data model called ADM for modeling Web documents and hypertexts; (ii) languages for wrapping and querying Web sites; (iii) tools and techniques for Web site design and implementation.
Effect of input phase modulation to a phase-sensitive optical amplifier (2016)

Many optical applications depend on amplitude modulating optical beams using devices such as acousto-optical modulators (AOMs) or optical choppers. Methods to add amplitude modulation (AM) often inadvertently impart phase modulation (PM) onto the light as well. While this PM is of no consequence to many phase-insensitive applications, phase-sensitive processes can be affected. Here we study the effects of input phase and amplitude modulation on the output of a quantum-noise limited phase-sensitive optical amplifier (PSA) realized in hot <sup>85</sup>Rb vapor. We investigate the dependence of PM on AOM alignment and demonstrate a novel approach to quantifying PM by using the PSA as a diagnostic tool. We then use this method to measure the alignment-dependent PM of an optical chopper which arises due to diffraction effects as the chopper blade passes through the optical beam.
Trichloroethylene oxidation by purified toluene 2-monooxygenase: products, kinetics, and turnover-dependent inactivation (1997)

Trichloroethylene is oxidized by several types of nonspecific bacterial oxygenases. Toluene 2-monooxygenase from Burkholderia cepacia G4 is implicated in trichloroethylene oxidation and is uniquely suggested to be resistant to turnover-dependent inactivation in vivo. In this work, the oxidation of trichloroethylene was studied with purified toluene 2-monooxygenase. All three purified toluene 2-monooxygenase protein components and NADH were required to reconstitute full trichloroethylene oxidation activity in vitro. The apparent Km and Vmax were 12 microM and 37 nmol per min per mg of hydroxylase component, respectively. Ten percent of the full activity was obtained when the small-molecular-weight enzyme component was omitted. The stable oxidation products, accounting for 84% of the trichloroethylene oxidized, were carbon monoxide, formic acid, glyoxylic acid, and covalently modified oxygenase proteins that constituted 12% of the reacted [14C]trichloroethylene. The stable oxidation products may all derive from the unstable intermediate trichloroethylene epoxide that was trapped by reaction with 4-(p-nitrobenzyl)pyridine. Chloral hydrate and dichloroacetic acid were not detected. This finding differs from that with soluble methane monooxygenase and cytochrome P-450 monooxygenase, which produce chloral hydrate. Trichloroethylene-dependent inactivation of toluene 2-monooxygenase activity was observed. All of the protein components were covalently modified during the oxidation of trichloroethylene. The addition of cysteine to reaction mixtures partially protected the enzyme system against inactivation, most notably protecting the NADH-oxidoreductase component. This suggested the participation of diffusible intermediates in the inactivation of the oxidoreductase.
A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm (2005)

PERL (ActivePerl, version 5.8) is available at activestate.com; the PERLMagick libraries are available at imagemagick.org, and IMAJIN_COLOC, the source code and user documentation can be downloaded from http://www.fda.gov/cber/research/imaging/imageanalysis.htm.
A multiply-add engine with monolithically integrated 3D memristor crossbar/CMOS hybrid circuit (2017)

Silicon (Si) based complementary metal-oxide semiconductor (CMOS) technology has been the driving force of the information-technology revolution. However, scaling of CMOS technology as per Moore's law has reached a serious bottleneck. Among the emerging technologies memristive devices can be promising for both memory as well as computing applications. Hybrid CMOS/memristor circuits with CMOL (CMOS + "Molecular") architecture have been proposed to combine the extremely high density of the memristive devices with the robustness of CMOS technology, leading to terabit-scale memory and extremely efficient computing paradigm. In this work, we demonstrate a hybrid 3D CMOL circuit with 2 layers of memristive crossbars monolithically integrated on a pre-fabricated CMOS substrate. The integrated crossbars can be fully operated through the underlying CMOS circuitry. The memristive devices in both layers exhibit analog switching behavior with controlled tunability and stable multi-level operation. We perform dot-product operations with the 2D and 3D memristive crossbars to demonstrate the applicability of such 3D CMOL hybrid circuits as a multiply-add engine. To the best of our knowledge this is the first demonstration of a functional 3D CMOL hybrid circuit.
Shadow Casting For Multiple-Valued Associative Logic (1986)

The operating characteristics of digital optical computers utilizing spatial light modulator based shadow casting are reviewed. The geometric and physical limitations of this method are examined. Because of the highly parallel nature of this approach, such systems are capable of truth-table processing. A detailed analysis of the relative advantages of both direct and associative truth table processing is presented. For each case, the use of binary or of multiple-valued logic is considered. The respective merits from the point of view of the number of computations per second and the energy required per computation are outlined. Switching energy considerations based on the use of multiple wavelengths in these systems are also discussed. The characteristic features of this type of optical logic are compared to those of electronic logic.
Changes in Oxidative Damage, Inflammation and [NAD(H)] with Age in Cerebrospinal Fluid (2014)

An extensive body of evidence indicates that oxidative stress and inflammation play a central role in the degenerative changes of systemic tissues in aging. However a comparatively limited amount of data is available to verify whether these processes also contribute to normal aging within the brain. High levels of oxidative damage results in key cellular changes including a reduction in available nicotinamide adenine dinucleotide (NAD(+)), an essential molecule required for a number of vital cellular processes including DNA repair, immune signaling and epigenetic processing. In this study we quantified changes in [NAD(H)] and markers of inflammation and oxidative damage (F2-isoprostanes, 8-OHdG, total antioxidant capacity) in the cerebrospinal fluid (CSF) of healthy humans across a wide age range (24-91 years). CSF was collected from consenting patients who required a spinal tap for the administration of anesthetic. CSF of participants aged >45 years was found to contain increased levels of lipid peroxidation (F2-isoprostanes) (p = 0.04) and inflammation (IL-6) (p = 0.00) and decreased levels of both total antioxidant capacity (p = 0.00) and NAD(H) (p = 0.05), compared to their younger counterparts. A positive association was also observed between plasma [NAD(H)] and CSF NAD(H) levels (p = 0.03). Further analysis of the data identified a relationship between alcohol intake and CSF [NAD(H)] and markers of inflammation. The CSF of participants who consumed >1 standard drink of alcohol per day contained lower levels of NAD(H) compared to those who consumed no alcohol (p<0.05). An increase in CSF IL-6 was observed in participants who reported drinking >0-1 (p<0.05) and >1 (p<0.05) standard alcoholic drinks per day compared to those who did not drink alcohol. Taken together these data suggest a progressive age associated increase in oxidative damage, inflammation and reduced [NAD(H)] in the brain which may be exacerbated by alcohol intake.
Gaussian-beam expansions for focused transducers (2003)

It is shown that a small set of Gaussian beams can efficiently represent the fields of ideal focused transducers. Each beam in the expression has two complex parameters related to the complex width and complex amplitude of the beam, i.e., four real parameters. For an N-beam expansion, a least-squares minimization algorithm chooses the 4N parameters to match the Gaussian-beam prediction to the data. One set of data is the pressure field calculated exactly with the Rayleigh integral for an unapodized transducer. As few as six beams give a very reasonable match to the data. The number of beams required for a good fit equals the number of lobes to be fit in the example. Another set of data is the pitch-catch voltage measured by two focused transducers facing each other at twice their focal distance and scanned past each other along a line perpendicular to their axes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>