gebhart/patrepeval huggingface dataset:
The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification (2013)

Ubiquitylation is an essential posttranslational protein modification that is implicated in a diverse array of cellular functions. Although cells contain eight structurally distinct types of polyubiquitin chains, detailed function of several chain types including K29-linked chains has remained largely unclear. Current mass spectrometry (MS)-based quantification methods are highly inefficient for low abundant atypical chains, such as K29- and M1-linked chains, in complex mixtures that typically contain highly abundant proteins. In this study, we applied parallel reaction monitoring (PRM), a quantitative, high-resolution MS method, to quantify ubiquitin chains. The ubiquitin PRM method allows us to quantify 100attomole amounts of all possible ubiquitin chains in cell extracts. Furthermore, we quantified ubiquitylation levels of ubiquitin-proline-β-galactosidase (Ub-P-βgal), a historically known model substrate of the ubiquitin fusion degradation (UFD) pathway. In wild-type cells, Ub-P-βgal is modified with ubiquitin chains consisting of 21% K29- and 78% K48-linked chains. In contrast, K29-linked chains are not detected in UFD4 knockout cells, suggesting that Ufd4 assembles the K29-linked ubiquitin chain(s) on Ub-P-βgal in vivo. Thus, the ubiquitin PRM is a novel, useful, quantitative method for analyzing the highly complicated ubiquitin system.
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome (2017)

Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring. More broadly, our method can facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.
An 800 MHz 2$\,\times\,$1 Compact MIMO Antenna System for LTE Handsets (2011)

A compact size 2 × 1 multiple-input-multiple-output (MIMO) antenna system operating in the 800 MHz band is proposed for long term evolution (LTE) handsets. The fabricated MIMO system has a typical isolation of 12 dB and a maximum gain of 2.2 dBi. Two isolation enhancement methods are investigated; one that looks into the depth of the ground split separating the two antennas, the other introduces extra splits within the arms of the GND plane. It is found that introducing extra splits within the arms of the GND plane of the proposed geometry enhances the isolation by at least 3 dB. The proposed MIMO antenna system is based on meander line antennas, and covers the band from 760-886 MHz. The size of the antenna system is 40 × 50 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Merging Orthovoltage X-Ray Minibeams spare the proximal tissues while producing a solid beam at the target (2019)

Conventional radiation therapy of brain tumors often produces cognitive deficits, particularly in children. We investigated the potential efficacy of merging Orthovoltage X-ray Minibeams (OXM). It segments the beam into an array of parallel, thin (~0.3 mm), planar beams, called minibeams, which are known from synchrotron x-ray experiments to spare tissues. Furthermore, the slight divergence of the OXM array make the individual minibeams gradually broaden, thus merging with their neighbors at a given tissue depth to produce a solid beam. In this way the proximal tissues, including the cerebral cortex, can be spared. Here we present experimental results with radiochromic films to characterize the method's dosimetry. Furthermore, we present our Monte Carlo simulation results for physical absorbed dose, and a first-order biologic model to predict tissue tolerance. In particular, a 220-kVp orthovoltage beam provides a 5-fold sharper lateral penumbra than a 6-MV x-ray beam. The method can be implemented in arc-scan, which may include volumetric-modulated arc therapy (VMAT). Finally, OXM's low beam energy makes it ideal for tumor-dose enhancement with contrast agents such as iodine or gold nanoparticles, and its low cost, portability, and small room-shielding requirements make it ideal for use in the low-and-middle-income countries.
Line-scanning, stage scanning confocal microscope (2016)

We created a line-scanning, stage scanning confocal microscope as part of a new procedure: video assisted micrographic surgery (VAMS). The need for rapid pathological assessment of the tissue on the surface of skin excisions very large since there are 3.5 million new skin cancers diagnosed annually in the United States. The new design presented here is a confocal microscope without any scanning optics. Instead, a line is focused in space and the sample, which is flattened, is physically translated such that the line scans across its face in a direction perpendicular to the line its self. The line is 6mm long and the stage is capable of scanning 50 mm, hence the field of view is quite large. The theoretical diffraction-limited resolution is 0.7um lateral and 3.7um axial. However, in this preliminary report, we present initial results that are a factor of 5-7 poorer in resolution. The results are encouraging because they demonstrate that the linear array detector measures sufficient signal from fluorescently labeled tissue and also demonstrate the large field of view achievable with VAMS.
Responses to faecal microbiota transplantation in female and male patients with irritable bowel syndrome (2021)

There was no sex difference in the response to FMT among IBS patients with moderate-to-severe symptoms who had previously not responded to NICE-modified diet. However, female patients with IBS-D respond better and have higher reduction of symptoms than males after FMT.
Automatic Identification of Clinical Lead Dysfunctions (2005)

Implantable cardioverter defibrillators (ICD) lead dysfunctions can cause inappropriate shocks. Current ICDs store lead diagnostics and detected episodes. This stored information with intracardiac electrograms (EGM) and sensed RR interval patterns may characterize the ICD lead performance. The aim of this analysis was to determine the sensitivity and positive predictive value (PPV) of an automatic lead dysfunction identification algorithm. This algorithm uses RR and EGM data to distinguish noncardiac oversensing (OS), for example, due to conductor fracture, and cardiac OS, for example, T-wave OS, from detected episodes. The algorithm also uses lead diagnostics: sensing integrity counter trends (e.g., RR intervals <140 ms), nonsustained tachyarrhythmias episodes with a mean RR <200 ms and impedance trends to identify lead fractures. The PPV was determined using the stored memory from 1,756 ICD patients enrolled in a 13-center long-term lead study with an average follow-up of 18.3 patient-months. Sensitivity was determined in 35 patients who presented with OS or lead fracture-related adverse events confirmed by stored ICD diagnostics. The algorithm sensitivity was 97.1% (34/35). There were 43 additional patients identified by the algorithm without an adverse event. Stored ICD diagnostics confirmed lead dysfunctions in 32 of 43 patients corresponding with an 85.7% PPV (66/77). ICD memory diagnostics and episodes with intracardiac EGM may be used to identify ICD lead dysfunctions with high sensitivity and PPV. This algorithm may be implemented in postprocessing ICD environments (e.g., remote server, programmer) to rapidly identify lead dysfunction prior its clinical manifestation.
Comparison of Methods Used for the Removal of Dmso following Cryopreservation and the Development of an Automated Protocol (1997)

Current methods of islet isolation are limited, thus requiring islets to be pooled from multiple donors to provide sufficient islet mass to permit insulin independence following islet transplantation. Low temperature banking is one approach used to pool islet preparations. Recently, we developed a method for bulk cryopreservation of islets in a single freezer bag system that is less labor-intensive and more readily kept sterile. As a further improvement to this bulk cryopreservation protocol we examined islet survival following slow-step dilution or our standard sucrose dilution protocol. Known numbers of canine islets were cryopreserved in DMSO by slow cooling to -40°C, storing at -196°C, and rapid thawing. When islets were frozen and thawed in glass tubes the recovery of islets after 48 h of tissue culture was significantly higher when the DMSO was removed using either a slow step (71.7 + 2.7%) or a modified slow step (75.7 + 3.9%) protocol as compared with the standard sucrose dilution protocol (65.7 + 3.0%) (p < 0.05, unpaired t-test). Insulin secretion in vitro and in vivo graft function was similar between the experimental groups. Similarly, when islets were frozen then thawed in freezer bags, islet recovery following 48 h postcryopreser-vation tissue culture at 37° C was 74.8 + 2.4% for slow-step dilution compared with 66.2 + 2.7% for the standard sucrose dilution group (p < 0.05, unpaired t-test). Islets thawed in the freezer bag using the modified slow-step dilution protocol showed equivalent functional viability during static incubation to nonfrozen controls. Bulk cryopreservation of isolated islets in single blood freezer bags is a practical alternative to cryopreservation in glass tubes. Development of an automated protocol for the slow stepwise removal of the cryoprotectant from islets in freezer bags will facilitate low temperature tissue banking of islets.
Development of an In-Situ Curemeter (1993)

Abstract An in-situ curemeter has been developed to follow the cure of thick articles during molding, by measuring continuously the dynamic mechanical properties (shear modulus and loss angle). It is a small-scale version of the Oscillating Disk Rheometer, designed to operate through the mold wall. An approximate theoretical treatment has been developed to relate the observed torque and loss angle to the dynamic properties of the rubber compound. Experiments were carried out with both unfilled and carbon-black-filled natural rubber compounds. Cure times measured by the curemeter were about the same as those obtained with the Oscillating Disk Rheometer. Modulus values inferred from the measured torques were compared with directly-measured values obtained from load-deflection curves for fully-cured specimens. Good agreement was found.
A set of mutually watermarked halftone images (2004)

In this paper, we propose a method called, modified stochastic error diffusion (MSED), to hide an invisible binary visual pattern in a set of error diffused halftone images. MSED can embed a dithered watermark in multiple halftone images while preserving the visual quality of each halftone image. When any of these images overlapping with any others, the watermark will appear. In case that many of these image overlapped together, the contrast of watermark becomes clearer.
Integration of Silver Nanoparticle-impregnated Polyelectrolyte Multilayers Into Murine-Splinted Cutaneous Wound Beds (2013)

Silver is a commonly used topical antimicrobial. However, technologies to immobilize silver at the wound surface are lacking, while currently available silver-containing wound dressings release excess silver that can be cytotoxic and impair wound healing. We have shown that precise concentrations of silver at lower levels can be immobilized into a wound bed using a polyelectrolyte multilayer attachment technology. These silver nanoparticle-impregnated polyelectrolyte multilayers are noncytotoxic yet bactericidal in vitro, but their effect on wound healing in vivo was previously unknown. The purpose of this study was to determine the effect on wound healing of integrating silver nanoparticle/polyelectrolyte multilayers into the wound bed. A full-thickness, splinted, excisional murine wound healing model was employed in both phenotypically normal mice and spontaneously diabetic mice (healing impaired model). Gross image measurements showed an initial small lag in healing in the silver-treated wounds in diabetic mice, but no difference in time to complete wound closure in either normal or diabetic mice. Histological analysis showed modest differences between silver-treated and control groups on day 9, but no difference between groups at the time of wound closure. We conclude that silver nanoparticle/polyelectrolyte multilayers can be safely integrated into the wound beds of both normal and diabetic mice without delaying wound closure, and with transient histological effects. The results of this study suggest the feasibility of this technology for use as a platform to affect nanoscale wound engineering approaches to microbial prophylaxis or to augment wound healing.
Query Processing Using Distance Oracles for Spatial Networks (2010)

The popularity of location-based services and the need to do real-time processing on them has led to an interest in performing queries on transportation networks, such as finding shortest paths and finding nearest neighbors. The challenge here is that the efficient execution of spatial operations usually involves the computation of distance along a spatial network instead of "as the crow flies," which is not simple. Techniques are described that enable the determination of the network distance between any pair of points (i.e., vertices) with as little as O(n) space rather than having to store the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> distances between all pairs. This is done by being willing to expend a bit more time to achieve this goal such as O(log n) instead of O(1), as well as by accepting an error ε in the accuracy of the distance that is provided. The strategy that is adopted reduces the space requirements and is based on the ability to identify groups of source and destination vertices for which the distance is approximately the same within some ε. The reductions are achieved by introducing a construct termed a distance oracle that yields an estimate of the network distance (termed the ε-approximate distance) between any two vertices in the spatial network. The distance oracle is obtained by showing how to adapt the well-separated pair technique from computational geometry to spatial networks. Initially, an e-approximate distance oracle of size O(n/(ε <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> )) is used that is capable of retrieving the approximate network distance in O(log n) time using a B-tree. The retrieval time can be theoretically reduced further to O(1) time by proposing another e-approximate distance oracle of size O((n log n)/(ε <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> )) that uses a hash table. Experimental results indicate that the proposed technique is scalable and can be applied to sufficiently large road networks. For example, a 10-percentapproximate oracle (ε = 0.1) on a large network yielded an average error of 0.9 percent with 90 percent of the answers having an error of 2 percent or less and an average retrieval time of 68 μ seconds. The fact that the network distance can be approximated by one value is used to show how a number of spatial queries can be formulated using appropriate SQL constructs and a few built-in primitives. The result is that these operations can be executed on almost any modern database with no modifications, while taking advantage of the existing query optimizers and query processing strategies.
Modulating the Properties of Fe(III) Macrocyclic MRI Contrast Agents by Appending Sulfonate or Hydroxyl Groups (2020)

Complexes of Fe(III) that contain a triazacyclononane (TACN) macrocycle, two pendant hydroxyl groups, and a third ancillary pendant show promise as MRI contrast agents. The ancillary group plays an important role in tuning the solution relaxivity of the Fe(III) complex and leads to large changes in MRI contrast enhancement in mice. Two new Fe(III) complexes, one with a third coordinating hydroxypropyl pendant, Fe(L2), and one with an anionic non-coordinating sulfonate group, Fe(L1)(OH<sub>2</sub>), are compared. Both complexes have a deprotonated hydroxyl group at neutral pH and electrode potentials representative of a stabilized trivalent iron center. The r<sub>1</sub> relaxivity of the Fe(L1)(OH<sub>2</sub>) complex is double that of the saturated complex, Fe(L2), at 4.7 T, 37 °C in buffered solutions. However, variable-temperature <sup>17</sup>O-NMR experiments show that the inner-sphere water of Fe(L1)(OH<sub>2</sub>) does not exchange rapidly with bulk water under these conditions. The pendant sulfonate group in Fe(L1)(OH<sub>2</sub>) confers high solubility to the complex in comparison to Fe(L2) or previously studied analogues with benzyl groups. Dynamic MRI studies of the two complexes showed major differences in their pharmacokinetics clearance rates compared to an analogue containing a benzyl ancillary group. Rapid blood clearance and poor binding to serum albumin identify Fe(L1)(OH<sub>2</sub>) for development as an extracellular fluid contrast agent.
Wireless access test-bed through visible light and dimming compatible OFDM (2015)

Visible light communications (VLC) technology has a potential to complement the RF wireless technology for indoor coverage. It promises concurrent illumination control and wireless data transmission capabilities. The potential of advanced multi-carrier modulation techniques, i.e. orthogonal frequency-division multiplexing (OFDM), introduces new challenges in the development of driver circuits. The reverse polarity optical OFDM (RPO-OFDM) is a recent approach to realize compatibility between the analog OFDM signal and the industry well-known pulse-width modulation (PWM) for dimming control. In this paper, we present the implementation of a wireless access test-bed through visible light and dimming compatible RPO-OFDM. A driver topology capable of driving a string of light-emitting diodes (LEDs) using a RPO-OFDM signal is proposed. The driver alleviates the nonlinearity of LEDs by proper biasing and maintaining a quasi-linear range of operation, i.e. minimizes the OFDM signal clipping. Using a software defined radio (SDR) platform for online modulation and demodulation, and a range of un-coded quadrature amplitude modulation (QAM) constellations, the experimentally obtained measurements demonstrate linear wide-range dimming while independently maintaining a bit-error performance below the forward error correction (FEC). Error free bit-error rate (BER) performance without symbol level equalization is obtained for binary phase shift keying (BPSK) and 4-QAM.
Recombinant Myxoma Virus Expressing Walleye Dermal Sarcoma Virus orfC Is Attenuated in Rabbits (2020)

The poxvirus, myxoma virus (MYXV) has shown efficacy as an oncolytic virus (OV) in some cancer models. However, MYXV replication within murine cancer models and spontaneous canine sarcomas is short-lived. In mice, successful treatment of tumors requires frequent injections with MYXV. We hypothesize that treatment of cancer with a recombinant MYXV that promotes apoptosis could improve the efficacy of MYXV. The orfC gene of walleye dermal sarcoma virus (WDSV), which induces apoptosis, was recombined into the MYXV genome (MYXVorfC). A marked increase in apoptosis was observed in cells infected with MYXVorfC. To ensure that expression of WDSV orfC by MYXV does not potentiate the pathogenesis of MYXV, we evaluated the effects of MYXVorfC inoculation in the only known host of MYXV, New Zealand white rabbits. Virus dissemination in rabbit tissues was similar for MYXVorfC and MYXV. Virus titers recovered from tissues were lower in MYXVorfC-infected rabbits as compared to MYXV-infected rabbits. Importantly, rabbits infected with MYXVorfC had a delayed onset of clinical signs and a longer median survival time than rabbits infected with MYXV. This study indicates that MYXVorfC is attenuated and suggests that MYXVorfC will be safe to use as an OV therapy in future studies.
All-optical phase and amplitude regeneration of DPSK signals based on phase-sensitive amplification (2006)

All-optical regeneration of differential phase-shift keyed signals by an interferometric phase-sensitive amplifier is described theoretically and demonstrated experimentally. Measurements reveal simultaneous reduction of both phase and amplitude noise when the device functions as a limiting amplifier
Spacecraft Architecture for Disturbance-Free Payload (2002)

A novel spacecraft architecture that provides a solution to the combined problems of payload pointing and isolation from spacecraft vibrations is presented. In this architecture, payload and spacecraft are separate bodiesthat fly in close-proximity formation and interact through noncontact sensors and actuators to achieve precision payload control and isolation from spacecraft disturbances. Vibration isolation is provided down to zero frequency and isolation performance is not limited by sensor characteristics. The proposed concept has far-reaching implications for space missions with stringent pointing control and stability requirements, allowing faster slews and uninterrupted missions during momentum dumping. The applicability of the proposed concept to future missions is discussed. Analysis and simulation results are presented for a large space telescope and provide a first demonstration of the concept. The results show more than two orders of magnitude performance improvement over state-of-the-art pointing and isolation systems.
High-resolution bistable nematic liquid crystal device realized on orientational surface patterns (2003)

The four-fold symmetry of a checkerboard-like surface alignment consisted of square domains arrived at the macroscopic orientational bistability of nematic liquid crystals. Switching between the two orientations took place with an appropriate electric field. Here the threshold field of bistable switching decreased as temperature increased, and the light could heat only the selected region in the cell including a light-absorbing medium. Irradiating the laser concurrently with an electric field, we addressed a selected region in the alignment pattern without the disturbance of neighboring regions. Extending this process, we realized an extremely fine bistable device of nematic liquid crystal with a pixel size down to about 2 μm.