gebhart/patrepeval huggingface dataset:
Conformational changes affecting the V3 and CD4-binding domains of human immunodeficiency virus type 1 gp120 associated with env processing and with binding of ligands to these sites (1993)

Two neutralizing human monoclonal antibodies (HuMAbs) directed against epitopes located near the tip of the V3 loop of human immunodeficiency virus type 1 env protein recognized solubilized gPr160, but not gp120, in radioimmunoprecipitation assays. Efficient immunoprecipitation of solubilized gp120 by these antibodies did occur in the presence of HuMAb 1125H, directed against a conformational epitope overlapping the CD4-binding site, or its F(ab')2 fragment. In contrast to the inability of the anti-V3 antibodies to immunoprecipitate solubilized gp120, these HuMAbs did bind to gp120 in intact virions; this level of binding increased severalfold in the presence of the F(ab')2 fragment of 1125H. These results demonstrate that neutralization epitopes in the V3 loop are sequestered in soluble gp120 but partly exposed in gPr160 and in virion-associated gp120 and that binding of antibodies to the discontinuous CD4-binding site leads to conformational changes that result in the exposure of V3 epitopes in soluble gp120 and their enhanced accessibility in gPr160 and in virion-associated gp120. Enhanced binding of suboptimal concentrations of 1125H to soluble gp120 was also induced by the presence of an anti-V3 HuMAb, indicating the occurrence of reciprocal allosteric interactions between the V3 loop and the CD4-binding site. It is likely that these effects contribute to the synergistic neutralization of human immunodeficiency virus type 1 previously reported for antibodies directed against these two regions.
Active Flow Control for Trailing Edge Flap Separation (2018)

Active flow control (AFC) in the form of sweeping jet (SWJ) excitation and discrete steady jet excitation is used to control the flow separation on an NACA 0015 semispan wing with a deflected, simple-hinged, trailing edge flap. This geometry has been the focus of several recent publications that investigated methods to improve the efficiency of sweeping jet actuators. In the current study, the interaction of the AFC excitation with the separated flowfields present at several flap deflection angles was examined. Previous studies with this model have been limited to a maximum flap deflection angle of 40. The flap deflection range was extended to 60! because systems studies have indicated that a high-lift system with simple-hinged flaps may require larger flap deflections than the Fowler flaps found on most high-lift systems. The results obtained at flap deflection angles of 20, 40, and 60 are presented and compared. Force and moment data, Particle Image Velocimetry (PIV) data, and steady and unsteady surface pressure data are used to describe the flowfield with and without AFC. With a flap deflection of 60, increasing the SWJ actuator momentum at the flap shoulder increased lift due to an increase in circulation but did not completely eliminate the recirculation region above the flap surface. AFC using the discrete steady jet actuators of this study increased lift as well but required more mass flow than the SWJ actuators and had a detrimental effect on lift at the highest mass flow level tested. PIV results showed that the angle between the excitation and the flap surface was not optimal for attaching the separated shear layer.
The effect of first-hop wireless bandwidth allocation on end-to-end network performance (2002)

With the increasing popularity of handheld devices and wireless local area networks (LANs), real-time applications such as Internet telephony are poised to become ubiquitous. While there has been a substantial amount of research on quality of service problems in the Internet, most end-to-end bandwidth allocation approaches, such as RSVP, have had limited success due to scalability and deployment issues. Starting with the observation that reserving bandwidth in the Internet backbone requires substantial infrastructure support, but reserving bandwidth in the first hop does not, we only focus on the first-hop reservation. We evaluate several first hop allocation schemes and determine their effectiveness in improving end-to-end performance. Since utilization of the reserved first-hop bandwidth depends on the remaining Internet path throughput, we characterize this throughput using traces collected from a popular Web site. Our analysis shows that different clients experience widely different throughputs, and that a significant portion of the clients receive very low throughput (e.g. less than 20 Kbps). We then evaluate several bandwidth allocation schemes for various congestion scenarios. Our results show that the scheme which takes into account of both the application data rate and available Internet path bandwidth yields the best performance. Moreover, the scheme performs even better if it adapts to the changing path properties. We discuss how path bandwidth can be measured without active probing, how frequently it needs to be measured, and how this measurement is incorporated into the first-hop bandwidth allocation algorithm.
Microwave Imaging of Conductivity Distribution of Silicon Wafers (2003)

Conductivity of silicon wafers was measured using the amplitude of the reflection coefficient of a microwave signal. A network analyzer was used to generate the microwave signal fed to a sensor and to measure the amplitude of the reflection coefficient. An open-ended coaxial line sensor was used to increase the spatial resolution and the sensitivity of the measurement. By microwave imaging, the distribution of the conductivity of a silicon wafer was mapped.
Incorporation of Axial System Response in Iterative Reconstruction from Axially Compressed Data of a Cylindrical Scanner using On-the-Fly Computing (2006)

The quality of images reconstructed by statistical iterative methods depends on an accurate model of the relationship between image space and projection space. Fast reconstruction is also an important aspect in the clinical environment. In previous work, we incorporated measured and modeled system response into iterative reconstruction. Since axial compression (span) was used in projection data, axial blurring was depth-dependent. We use pre-computed and stored axial components for a scanner without translation axial symmetry. For a scanner with translation symmetry, a fast line-of-response (LOR) line integral projector is available. In this case, axial blurring due to both geometrical and physics effects is implemented differently. Forward projection of axially blurred images is performed on-the-fly into LOR space, followed by axial compression of LOR data into scanner projection data formats. Our LOR projector is based on Joseph's method. The translation symmetry of the scanner is essential for its efficient and fast computing performance. LOR projection and span assembling are performed independently for each azimuthal angle and result in small additional memory allocation. Results show that an acceleration of the computing of the axial blurring is achievable without any component storage but with similar image quality.
Chronic SSRI Treatment Exacerbates Serotonin Deficiency in Humanized <i>Tph2</i> Mutant Mice (2012)

Selective serotonin reuptake inhibitors (SSRIs) are a major class of antidepressants that act by blocking inward transport of serotonin (5-HT) into presynaptic neurons mediated by the serotonin transporter (SERT). Both reuptake and ongoing synthesis are essential in supporting intraneuronal serotonin concentrations in serotonergic neurons. A rare mutation in tryptophan hydroxylase 2 (Tph2), the rate limiting enzyme for 5-HT synthesis, was identified in several patients with major depression, and knock-in mice expressing the analogous mutation (R439H Tph2 KI) show 80% reduction in 5-HT synthesis and tissue levels. Chronic treatment with SSRIs (fluoxetine and paroxetine) resulted in a dramatic further depletion of 5-HT tissue levels in R439H Tph2 KI mice (down to 1-3% of wild type levels) while having little effects in wild-type controls. Treatment with the 5-HT precursor 5-hydroxytryptophan (5-HTP) restored 5-HT tissue content in mutant mice, and cotreatment with 5-HTP and fluoxetine essentially prevented the depleting effect of a chronic SSRI. These data demonstrate that chronic SSRI treatment could further exacerbate the 5-HT deficiency in Tph2 mutation carriers, and this can be prevented by 5-HTP supplementation.
Wide-View and Broadband Circular Polarizers for Transflective Liquid Crystal Displays (2008)

A simple wide-view and broadband circular polarizer comprising of a linear polarizer and two uniaxial films is proposed to enhance the viewing angle of transflective liquid crystal displays (LCDs). For the transmissive mode, over the entire 90deg viewing cone, the normalized light leakage from two stacked circular polarizers is suppressed to below 1.5times10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , and contrast ratio over 10:1 is obtained using a normally black vertically aligned transflective LCD. At the same time, this configuration warrants a broadband operation and reasonably good viewing angle (10:1 contrast ratio is over 40 at all directions) for the reflective mode. The physical mechanisms for achieving broadband operation and wide viewing angle are discussed.
Decentralized Optimal Dispatch of Photovoltaic Inverters in Residential Distribution Systems (2014)

Decentralized methods for computing optimal real and reactive power setpoints for residential photovoltaic (PV) inverters are developed in this paper. It is known that conventional PV inverter controllers, which are designed to extract maximum power at unity power factor, cannot address secondary performance objectives such as voltage regulation and network loss minimization. Optimal power flow techniques can be utilized to select which inverters will provide ancillary services, and to compute their optimal real and reactive power setpoints. Leveraging advances in semidefinite relaxation techniques and sparsity-promoting regularizations, such problems can be solved with reduced computational burden and with optimality guarantees. To enable large-scale implementation, a novel algorithmic framework is introduced - based on the so-called alternating direction method of multipliers - by which the optimal power flow problem in this setting can be systematically decomposed into sub-problems that can be solved in a decentralized fashion by the utility and customer-owned PV systems with limited exchanges of information. Since the computational burden is shared among multiple devices and the requirement of all-to-all communication can be circumvented, the proposed optimization approach scales to large distribution networks.
A High-Performance Controlled-Current Inverter Drive (1980)

A production variable-frequency drive is described which uses an induction motor and a controlled-current inverter. The control loops of the drive have been arranged so that the performance of the drive is extended to zero speed and to the theoretical upper limit speed. Operating modes include torque smoothing by programmed dc link current, pulsewidth modulated (PWM) current shaping, and flux-controlled constant horsepower operation.
Multi-modality optical neural imaging using coherence control of VCSELs (2011)

Neural optical imaging can evaluate cortical hemodynamic fluctuations which reflect neural activity and disease state. We evaluate the use of vertical-cavity surface-emitting lasers (VCSELs) as illumination source for simultaneous imaging of blood flow and tissue oxygenation dynamics ex vivo and in vivo and demonstrate optical imaging of blood flow changes and oxygenation changes in response to induced ischemia. Using VCSELs we show a rapid switching from a single-mode to a special multi-mode rapid current sweep operation and noise values reduced to within a factor of 40% compared to non-coherent LED illumination. These VCSELs are promising for long-term portable continuous monitoring of brain dynamics in freely moving animals.
Myriad Functions of Stanniocalcin-1 (STC1) Cover Multiple Therapeutic Targets in the Complicated Pathogenesis of Idiopathic Pulmonary Fibrosis (IPF) (2015)

Idiopathic pulmonary fibrosis (IPF) is an intractable disease for which the pathological findings are characterized by temporal and spatial heterogeneity. The pathogenesis is composed of myriad factors, including repetitive injuries to epithelial cells, alterations in immunity, the formation of vascular leakage and coagulation, abnormal wound healing, fibrogenesis, and collagen accumulation. Therefore, the molecular target drugs that are used or attempted for treatment or clinical trials may not cover the myriad therapeutic targets of IPF. In addition, the complicated pathogenesis results in a lack of informative biomarkers to diagnose accurately the status of IPF. These facts point out the necessity of using a combination of drugs, that is, each single drug with molecular targets or a single drug with multiple therapeutic targets. In this review, we introduce a humoral factor, stanniocalcin-1 (STC1), which has myriad functions, including the maintenance of calcium homeostasis, the promotion of early wound healing, uncoupling respiration (aerobic glycolysis), reepithelialization in damaged tissues, the inhibition of vascular leakage, and the regulation of macrophage functions to keep epithelial and endothelial homeostasis, which may adequately cover the myriad therapeutic targets of IPF.
Angular-precision enhancement in free-space micromachined optical switches (1999)

Free-space micromachined optical-switching technology has emerged as a promising means of building the large-scale optical crossconnects that will be needed in future optical-transport networks. Although this technology has rapidly demonstrated promising optical performance, its ability to expand to the required port-count has yet to be demonstrated, In particular, the tight angular tolerances imposed by free-space interconnection present a significant challenge, In this letter, we demonstrate integrated mechanical structures that are capable of achieving better than 0.1/spl deg/ micromirror angular repeatability, thus opening the path to high-port-count optical crossconnects that live within cross-office optical-loss budgets.
Enzymatic Breaker System for Nondamaging Removal of Cellulose-Based Blocking Gels (1993)

ABSTRACT An external breaker system, consisting of a combination of enzymes, has been used to remove polymer damage at low to moderate temperatures. This enzyme mixture produces a stepwise breakdown of cellulose polymers at temperatures ranging from 60 °F to 140°F. The polymer is initially reduced to D-glucose and cellobiose. The complete hydrolysis of the cellobiose is subsequently afforded by the enzyme combination. The entire hydrolysis of the polymer occurs rapidly; therefore, the enzyme complex can be applied as an external breaker after the workover operations have been completed. Post workover injection of the enzyme complex allows blocking gels to retain maximum strength during operations. The enzyme combination is compatible with the brines used to prevent damage from swelling clays. The result is a blocking gel that is reduced to a clean non-viscous fluid that is easily recoverable.
Biomechanical Assessment of a V‐Shaped Semitendinosus Allograft Anterior Cable Reconstruction for Irreparable Rotator Cuff Tears (2021)

The VST may provide an option for treatment of irreparable MCTs with anterior rotator cable disruption.
Empirically detecting false test alarms using association rules (2015)

Applying code changes to software systems and testing these code changes can be a complex task that involves many different types of software testing strategies, e.g. system and integration tests. However, not all test failures reported during code integration are hinting towards code defects. Testing large systems such as the Microsoft Windows operating system requires complex test infrastructures, which may lead to test failures caused by faulty tests and test infrastructure issues. Such false test alarms are particular annoying as they raise engineer attention and require manual inspection without providing any benefit. The goal of this work is to use empirical data to minimize the number of false test alarms reported during system and integration testing. To achieve this goal, we use association rule learning to identify patterns among failing test steps that are typically for false test alarms and can be used to automatically classify them. A successful classification of false test alarms is particularly valuable for product teams as manual test failure inspection is an expensive and time-consuming process that not only costs engineering time and money but also slows down product development. We evaluating our approach on system and integration tests executed during Windows 8.1 and Microsoft Dynamics AX development. Performing more than 10,000 classifications for each product, our model shows a mean precision between 0.85 and 0.90 predicting between 34% and 48% of all false test alarms.
Correlation plenoptic imaging (2017)

Plenoptic Imaging (PI) is a novel optical technique for achieving tridimensional imaging in a single shot. In conventional PI, a microlens array is inserted in the native image plane and the sensor array is moved behind the microlenses. On the one hand, the microlenses act as imaging pixels to reproduce the image of the scene; on the other hand, each microlens reproduces on the sensor array an image of the camera lens, thus providing the angular information associated with each imaging pixel. The recorded propagation direction is exploited, in post- processing, to computationally retrace the geometrical light path, thus enabling the refocusing of different planes within the scene, the extension of the depth of field of the acquired image, as well as the 3D reconstruction of the scene. However, a trade-off between spatial and angular resolution is built in the standard plenoptic imaging process. We demonstrate that the second-order spatio-temporal correlation properties of light can be exploited to overcome this fundamental limitation. Using two correlated beams, from either a chaotic or an entangled photon source, we can perform imaging in one arm and simultaneously obtain the angular information in the other arm. In fact, we show that the second order correlation function possesses plenoptic imaging properties (i.e., it encodes both spatial and angular information), and is thus characterized by a key re-focusing and 3D imaging capability. From a fundamental standpoint, the plenoptic application is the first situation where the counterintuitive properties of correlated systems are effectively used to beat intrinsic limits of standard imaging systems. From a practical standpoint, our protocol can dramatically enhance the potentials of PI, paving the way towards its promising applications.
Total Synthesis of (−)‐Dictyostatin: Confirmation of Relative and Absolute Configurations (2004)

Will the real dictyostatin please stand up? There were five finalists as stereostructures for the potent anticancer agent dictyostatin; ten, if one were to include enantiomers. A total synthesis of (−)-dictyostatin (1) has ended the decade-old masquerade and identified the winner as a structure recently proposed by Paterson and Wright. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z460593_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
sodC-Based Real-Time PCR for Detection of Neisseria meningitidis (2011)

Real-time PCR (rt-PCR) is a widely used molecular method for detection of Neisseria meningitidis (Nm). Several rt-PCR assays for Nm target the capsule transport gene, ctrA. However, over 16% of meningococcal carriage isolates lack ctrA, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, sodC, is found in Nm but not in other Neisseria species. To better identify Nm, regardless of capsule genotype or expression status, a sodC-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (C(t)) value of 35, with 100% average reaction efficiency and an average R(2) of 0.9925. 99.7% (624/626) of Nm isolates tested were sodC-positive, with a range of average C(t) values from 13.0 to 29.5. The mean sodC C(t) value of these Nm isolates was 17.6±2.2 (±SD). Of the 626 Nm tested, 178 were nongroupable (NG) ctrA-negative Nm isolates, and 98.9% (176/178) of these were detected by sodC rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, sodC detected 25/157 Nm or 4 additional specimens compared to ctrA and 24 more than culture. Among 582 carriage specimens, sodC detected Nm in 1 more than ctrA and in 4 more than culture. This sodC rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes.
Development of Soldier Conformable Antennae Using Conducting Polymers (2010)

Abstract : A conducting polymer based camouflaged antenna has been developed for use by soldiers in theater. The antenna is built using polypyrrole strips fabricated using a custom built instrument capable of cutting fiber strips with varying widths, thicknesses and up to 10m long. These fibers have been woven into a patch form and their radiating properties are studied. We have also demonstrated that this antenna can transmit and receive information at distances up to 2.75 km in an urban environment.
A Mobile Food Record For Integrated Dietary Assessment (2016)

This paper presents an integrated dietary assessment system based on food image analysis that uses mobile devices or smartphones. We describe two components of our integrated system: a mobile application and an image-based food nutrient database that is connected to the mobile application. An easy-to-use mobile application user interface is described that was designed based on user preferences as well as the requirements of the image analysis methods. The user interface is validated by user feedback collected from several studies. Food nutrient and image databases are also described which facilitates image-based dietary assessment and enable dietitians and other healthcare professionals to monitor patients dietary intake in real-time. The system has been tested and validated in several user studies involving more than 500 users who took more than 60,000 food images under controlled and community-dwelling conditions.
Image restoration from non-uniform magnetic field influence for direct Fourier NMR imaging (1984)

A new technique is proposed for NMR image restoration from the influence of main magnetic field non-uniformities. This technique is applicable to direct Fourier NMR imaging. The mathematical basis and details of this technique are fully described. Modification to include image restoration from non-linear field gradient influence is also presented. Computer simulation demonstrates the effectiveness of this technique for both Fourier zeugmatography and spin-warp imaging.