gebhart/patrepeval huggingface dataset:
Smart bioconjugates (2003)

Many bioengineering technologies depend on communication between devices and cells or biomolecules. Effective communication in the device environment is based on controlling recognition events at the device interface. we are developing strategies to introduce "listening" capabilities into bioengineering technologies that provide sensitive and reversible control over biomolecular recognition events. Our approach utilizes "smart" polymers that can be used as molecular switches controlling (a) biorecognition processes (bioactivity switches) and(b) intracellular trafficking of biomolecules (membrane switches). Bioactivity switches are responsive polymer-engineered protein conjugates that can be stimulated to turn protein activity "on" and "off", or trigger release of bound ligand. Applications as "on-off" switches include affinity separations, diagnostics, drug targeting, and enzyme processes. Actions of bioactivity switches as triggered release systems include the delivery of biotinylated agents, affinity biomolecules, drugs, chemical agents, enzyme substrates, products or inhibitors, and signals. Membrane switches are pH-responsive polymer bioconjugates or complexes with drug carriers that disrupt endosomal membranes to enhance intracellular delivery of DNA or protein drugs. This action should increase the efficacies of gene, antisense oligonucleotide, and cancer therapies.
Efficiency of liquid tin(<scp>ii</scp>)<i>n</i>-alkoxide initiators in the ring-opening polymerization of<scp>l</scp>-lactide: kinetic studies by non-isothermal differential scanning calorimetry (2020)

Novel soluble liquid tin(ii) <i>n</i>-butoxide (Sn(O<i>n</i>C<sub>4</sub>H<sub>9</sub>)<sub>2</sub>), tin(ii) <i>n</i>-hexoxide (Sn(O<i>n</i>C<sub>6</sub>H<sub>13</sub>)<sub>2</sub>), and tin(ii) <i>n</i>-octoxide (Sn(O<i>n</i>C<sub>8</sub>H<sub>17</sub>)<sub>2</sub>) initiators were synthesized for use as coordination-insertion initiators in the bulk ring-opening polymerization (ROP) of l-lactide (LLA). In order to compare their efficiencies with the more commonly used tin(ii) 2-ethylhexanoate (stannous octoate, Sn(Oct)<sub>2</sub>) and conventional tin(ii) octoate/<i>n</i>-alcohol (SnOct<sub>2</sub>/<i>n</i>ROH) initiating systems, kinetic parameters derived from monomer conversion data were obtained from non-isothermal differential scanning calorimetry (DSC). In this work, the three non-isothermal DSC kinetic approaches including dynamic (Kissinger, Flynn-Wall, and Ozawa); isoconversional (Friedman, Kissinger-Akahira-Sunose (KAS) and Ozawa-Flynn-Wall (OFW)); and Borchardt and Daniels (B/D) methods of data analysis were compared. The kinetic results showed that, under the same conditions, the rate of polymerization for the 7 initiators/initiating systems was in the order of liquid Sn(O<i>n</i>C<sub>4</sub>H<sub>9</sub>)<sub>2</sub> > Sn(Oct)<sub>2</sub>/<i>n</i>C<sub>4</sub>H<sub>9</sub>OH > Sn(Oct)<sub>2</sub> ≅ liquid Sn(O<i>n</i>C<sub>6</sub>H<sub>13</sub>)<sub>2</sub> > Sn(Oct)<sub>2</sub>/<i>n</i>C<sub>6</sub>H<sub>13</sub>OH ≅ liquid Sn(O<i>n</i>C<sub>8</sub>H<sub>17</sub>)<sub>2</sub> > Sn(Oct)<sub>2</sub>/<i>n</i>C<sub>8</sub>H<sub>17</sub>OH. The lowest activation energies (<i>E</i> <sub>a</sub> = 52, 59, and 56 kJ mol<sup>-1</sup> for the Kissinger, Flynn-Wall, and Ozawa dynamic methods; <i>E</i> <sub>a</sub> = 53-60, 55-58, and 60-62 kJ mol<sup>-1</sup> for the Friedman, KAS, and OFW isoconversional methods; and <i>E</i> <sub>a</sub> = 76-84 kJ mol<sup>-1</sup> for the B/D) were found in the polymerizations using the novel liquid Sn(O<i>n</i>C<sub>4</sub>H<sub>9</sub>)<sub>2</sub> as the initiator, thereby showing it to be the most efficient initiator in the ROP of l-lactide.
Allosteric modifiers of hemoglobin. 1. Design, synthesis, testing, and structure-allosteric activity relationship of novel hemoglobin oxygen affinity decreasing agents (1991)

Three isomeric series of 2-(aryloxy)-2-methylpropionic acids were prepared and studied for their ability to decrease the oxygen affinity of human hemoglobin A. The isomeric aryloxy groups included 4-[[(aryloyl)amino]methyl]phenoxy, 4-(arylacetamido)phenoxy, and 4-[[(arylamino)carbonyl]methyl]phenoxy. A total of 20 compounds were synthesized and tested. Structure-activity relationships are presented. Several of the new compounds were found to be strong allosteric effectors of hemoglobin. The two most active compounds are 2-[4-[[(3,5-dichloroanilino)carbonyl]-methyl]phenoxy]- 2-methylpropionic acid and the corresponding 3,5-dimethyl derivative. The latter two compounds have been compared to other known potent allosteric effectors in the same assay and show greater activity. Both compounds also exhibit a right shift in the oxygen equilibrium curve when incubated with whole blood. The new compounds may be of interest in clinical or biological areas that require or would benefit from a reversal of depleted oxygen supply (i.e., ischemia, stroke, tumor radiotherapy, blood storage, blood substitutes, etc.). They are also structurally related to several marketed antilipidemic agents.
Electrochromic Sensor for Multiplex Detection of Metabolites Enabled by Closed Bipolar Electrode Coupling (2017)

Biosensors based on converting electrochemical signals into optical readouts are attractive candidates as low-cost, high-throughput sensor platforms. Here, we described a closed bipolar electrode (CBE)-based two-cell electrochromic device for sensing multiple metabolites, using the simultaneous detection of lactate, glucose, and uric acid as a model system. In the two-cell configuration, an analytical cell contains a redox mediator combined with a specific oxidase, e.g., lactate oxidase, glucose oxidase, or uricase, to form an electrochemical mediator-electrocatalyst pair that supports redox cycling. A closed bipolar electrode couples the electron transfer event in the analytical cell to an electrochromic reaction in a separate reporter cell, such that the magnitude of the color change is related to the concentration of metabolites in the analytical cell. To demonstrate multiplex operation, the CBE-based electrochromic detector is modified by integrating three sets of detection chemistries into a single device, in which simultaneous determination of glucose, lactate, and uric acid is demonstrated. Device sensitivity can be tuned by using reporter cells with different volumes. Furthermore, the analytical cell of this device can be fabricated as a disposable, paper-based carbon electrode without any pretreatment, demonstrating the potential to screen phenotypes that require multiple biomarkers in a point-of-care format.
Angle images for measuring heart motion from tagged MRI (2002)

This paper introduces a new image processing technique for rapid analysis and visualization of tagged cardiac magnetic resonance (MR) images. The method is based on the use of isolated spectral peaks in SPAMM-tagged magnetic resonance images. The authors call the phase of an image corresponding to just one of these peaks an angle image, and show that except for a phase-wrapping artifact, an angle image is linearly related to a component of the three-dimensional motion. Using one or more angle images, the authors show how to synthesize conventional tag lines, reconstruct displacement fields for small motions, calculate the optical flow between successive temporal images, and calculate two-dimensional strain. The authors demonstrate the performance of this approach on both real and simulated tagged MR images.
Integrated piezoelectric plate acoustic waves transducers (2008)

A piezoelectric film has been fabricated by a sol-gel spray technique directly onto an edge of a 2 mm-thick aluminium plate as an integrated ultrasonic transducer and used to detect line defects at a distance using mode converted symmetric and shear horizontal waves at 150°C.
A microwatt threshold Raman laser using a fiber-coupled high-Q micro-cavity (2002)

Microsphere resonators are unsurpassed in terms of their ability to confine light for relatively long durations and within small modal volumes. These properties make high-Q microspheres ideally suited for studies of nonlinear physics within a resonant system. Early work by Chang and Campillo [1] demonstrated Raman oscillation in micro-droplets of CS2 at a record-low pump-power level. However, micro-droplets are not suitable for long term fundamental studies (and practical devices). In this work, we report on the observation of ultra-efficient Raman oscillation in a high-Q microsphere with record low pump threshold in the microwatt range and differential quantum efficiency of 36% [2]. The combination of a high-Q silica microresonator and fiber-taper coupling [3] results in a highly efficient system coupled directly to an optical fiber. As such, this system may naturally lend itself to further studies of the physics of nonlinear systems especially where ultra-low loss is a critical requirement.
Trajectory sampling for direct traffic observation (2001)

Traffic measurement is a critical component for the control and engineering of communication networks. We argue that traffic measurement should make it possible to obtain the spatial flow of traffic through the domain, i.e., the paths followed by packets between any ingress and egress point of the domain. Most resource allocation and capacity planning tasks can benefit from such information. Also, traffic measurements should be obtained without a routing model and without knowledge of network state. This allows the traffic measurement process to he resilient to network failures and state uncertainty. We propose a method that allows the direct inference of traffic flows through a domain by observing the trajectories of a subset of all packets traversing the network. The key advantages of the method are that (1) it does not rely on routing state; (2) its implementation cost is small; and (3) the measurement reporting traffic is modest and can be controlled precisely. The key idea of the method is to sample packets based on a hash function computed over the packet content. Using the same hash function will yield the same sample set of packets in the entire domain, and enables us to reconstruct packet trajectories.
Detection of ultrasound-modulated photons in diffuse media using the photorefractive effect (2004)

Ultrasound-modulated optical tomography is a dual-wave sensing technique in which diffusive light in a turbid medium interacts with an imposed acoustic field. A phase-modulated photon field emanates from the interaction region and carries with it information about the optomechanical properties of the medium. We present a technique for detection of ultrasound-induced optical phase modulation using an adaptive, photorefractive-crystal-based interferometry system. Experimental results are presented demonstrating detection of ultrasound-modulated signals in highly scattering media by use of pulsed ultrasound insonation.
High resolution cortical bone thickness measurement from clinical CT data (2010)

The distribution of cortical bone in the proximal femur is believed to be a critical component in determining fracture resistance. Current CT technology is limited in its ability to measure cortical thickness, especially in the sub-millimetre range which lies within the point spread function of today's clinical scanners. In this paper, we present a novel technique that is capable of producing unbiased thickness estimates down to 0.3mm. The technique relies on a mathematical model of the anatomy and the imaging system, which is fitted to the data at a large number of sites around the proximal femur, producing around 17,000 independent thickness estimates per specimen. In a series of experiments on 16 cadaveric femurs, estimation errors were measured as -0.01+/-0.58mm (mean+/-1std.dev.) for cortical thicknesses in the range 0.3-4mm. This compares with 0.25+/-0.69mm for simple thresholding and 0.90+/-0.92mm for a variant of the 50% relative threshold method. In the clinically relevant sub-millimetre range, thresholding increasingly fails to detect the cortex at all, whereas the new technique continues to perform well. The many cortical thickness estimates can be displayed as a colour map painted onto the femoral surface. Computation of the surfaces and colour maps is largely automatic, requiring around 15min on a modest laptop computer.
Ultrafast fiber lasers based on self-similar pulse evolution: a review of current progress (2015)

Self-similar fiber oscillators are a relatively new class of mode-locked lasers. In these lasers, the self-similar evolution of a chirped parabolic pulse in normally-dispersive passive, active, or dispersion-decreasing fiber (DDF) is critical. In active (gain) fiber and DDF, the novel role of local nonlinear attraction makes the oscillators fundamentally different from any mode-locked lasers considered previously. In order to reconcile the spectral and temporal expansion of a pulse in the self-similar segment with the self-consistency required by a laser cavity's periodic boundary condition, several techniques have been applied. The result is a diverse range of fiber oscillators which demonstrate the exciting new design possibilities based on the self-similar model. Here, we review recent progress on self-similar oscillators both in passive and active fiber, and extensions of self-similar evolution for surpassing the limits of rare-earth gain media. We discuss some key remaining research questions and important future directions. Self-similar oscillators are capable of exceptional performance among ultrashort pulsed fiber lasers, and may be of key interest in the development of future ultrashort pulsed fiber lasers for medical imaging applications, as well as for low-noise fiber-based frequency combs. Their uniqueness among mode-locked lasers motivates study into their properties and behaviors and raises questions about how to understand mode-locked lasers more generally.
Repair and reconstruction of common bile duct by poly(lactide) stent (2010)

To investigate the effect of repair of bioabsorbable poly(lactide) (PLA) biliary stent in common bile duct (CBD) transection injury in canine prior to the clinical application. Circular tubing CBD stent was prepared by melt extraction technique using PLA. A transection incision was made on CBD of the normal canine, and then closed the incision with laser welding followed the implantation of PLA tubular stent into it. The stent was obtained to determine degradation of PLA in vivo at postoperative week 1, 4, and 12, respectively. The changes of outer diameter and burst pressure of CBD were investigated. Furthermore, serum liver enzyme values and CBD histopathological analysis were examined in the animals. The results noted that the polymer stent exhibited the same biomedical functions as T tubes and no significant tissue response. Therefore, biodegradable PLA stent matches the requirements in repair and reconstruction of CBD to support the duct, guide bile drainage and reduce T-tube-related complications.
Corrections to “Thermoelectric Generation Based on Spin Seebeck Effects” [DOI: 10.1109/JPROC.2016.2535167] (2016)

Corrections were made to information presented in Figure 2 of "Thermoelectric generation based on spin Seebeck effects," by Uchida, F. et al., Proc. IEEE, 2016 (DOI: 10.1109/JPROC.2016.2535167).
Avidity maturation of γ9δ2T-cell receptor engineered T-cells by CDR3 modulation (162.37) (2012)

Abstract Immunotherapy with innate immune cells has recently evoked a broad interest as a novel treatment option for cancer patients. γ9δ2T-cells are an emerging innate cell population with strong anti-tumor-reactivity and a promising candidate for immune interventions. Especially γ9δ2T-cell receptors (TCR) which recognize a broad panel of tumor cells with high avidity are clinically attractive since αβT-cells can be efficiently redirected against a variety of tumor cells by introducing a γ9δ2TCR. Here we demonstrate that distinct γ9δ2TCRs mediate different functional avidities and present the concept of combinatorial-γδTCR-chain exchange (CTE) as an efficient method to create γ9δ2TCRs that mediate strong anti-tumor-responses. Thereby γ9- and δ2-chains derived from individual γ9δ2T-cell clones are newly combined allowing the design of γ9δ2TCRs that mediate a higher functional avidity against a broad tumor cell panel in vitro and in vivo when compared to a reference γ9δ2TCR. We furthermore demonstrate that this phenomenon is selectively caused by differences in the CDR3-domains of γ9- and δ2-chain. Accordingly, alanine-scanning-mutations were performed and elucidated important residues within the CDR3 sequence and stress the impact of the CDR3 length for optimal γ9δ2TCR function. This knowledge allowed improving tumor-control by engineered T-cells not only in vitro but also in vivo in a humanized mouse model.
Communication-efficient distributed mining of association rules (2001)

Mining for associations between items in large transactional databases is a central problem in the field of knowledge discovery. When the database is partitioned among several share-nothing machines, the problem can be addressed using distributed data mining algorithms. One such algorithm, called CD, was proposed by Agrawal and Shafer in [1] and was later enhanced by the FDM algorithm of Cheung, Han et al. [5]. The main problem with these algorithms is that they do not scale well with the number of partitions. They are thus impractical for use in modern distributed environments such as peer-to-peer systems, in which hundreds or thousands of computers may interact. In this paper we present a set of new algorithms that solve the Distributed Association Rule Mining problem using far less communication. In addition to being very efficient, the new algorithms are also extremely robust. Unlike existing algorithms, they continue to be efficient even when the data is skewed or the partition sizes are imbalanced. We present both experimental and theoretical results concerning the behavior of these algorithms and explain how they can be implemented in different settings.
All-vanadium dual circuit redox flow battery for renewable hydrogen generation and desulfurisation (2015)

All-vanadium dual circuit redox flow battery capable of converting surplus electricity into hydrogen and performing simultaneous desulfurization with high efficiency.
Headset removal for virtual and mixed reality (2017)

Virtual Reality (VR) has advanced significantly in recent years and allows users to explore novel environments (both real and imaginary), play games, and engage with media in a way that is unprecedentedly immersive. However, compared to physical reality, sharing these experiences is difficult because the user's virtual environment is not easily observable from the outside and the user's face is partly occluded by the VR headset. Mixed Reality (MR) is a medium that alleviates some of this disconnect by sharing the virtual context of a VR user in a flat video format that can be consumed by an audience to get a feel for the user's experience.
Expansion and Length-Dependent Fragility of CTG Repeats in Yeast (1998)

Expansion of DNA trinucleotide repeats (TNRs) is the causative mutation in a growing number of human genetic diseases. Large expansions of a CTG tract were obtained and shown by genetic and physical assays to be length-dependent sites of chromosome breakage in Saccharomyces cerevisiae. Deletion of RAD27, which encodes a nuclease involved in Okazaki fragment processing, caused length-dependent destabilization of CTG tracts and a substantial increase in expansion frequency. The genetic assay described here can be used to evaluate other factors that induce TNR expansion or chromosome fragility in humans.
Effect of reactive species on surface crosslinking of plasma-treated polymers investigated by surface force microscopy (2006)

Polymer surface modification by ions, uncharged particles, and photons of inductively coupled Ar plasma was investigated with a surface force microscope. Optical windows consisting of crystals with different cutoff wavelengths and a metal shield were used to deconvolute the effects of the various plasma species on the modification of the surface nanomechanical properties of polyethylene. The extent of surface crosslinking was related to the frictional energy dissipated during nanoscratching. It is shown that surface crosslinking is primarily due to the simultaneous effects of uncharged particles and vacuum ultraviolet photons, while the ion bombardment effect is secondary.
Insecticidal toxins from the bacterium<i>Photorhabdus luminescens</i>: gene cloning and toxin histopathology (1999)

Four toxin complexes, Tca, Tcb, Tcc and Tcd from the culture broth of Photorhabdus luminescens have been purified and the four toxin complex encoding loci, tca, tcb, tcc and tcd, cloned. Genetic knockout of either tca or tcd reduced oral toxicity to Manduca sexta, and knockout of both loci eliminated activity. Purified Tca specifically affected the insect midgut, despite its putative normal delivery directly into the insect haemocel. These Photorhabdus toxins may form useful alternatives to other orally active bacterial protein toxins such as those from Bacillus thuringiensis.
Polarization-Time Code and 4$\,\times\,$4 Equalizer-Decoder for Coherent Optical Transmission (2012)

A linear polarization-time code in conjunction with an adaptive multi-tap 4 4 joint equalizer-decoder is proposed to average the effects of polarization-dependent impairments on two polarizations. For the first time in the context of polarization-time coding, there is no assumption of polarization-dependent loss (PDL) of knowledge at the receiver. This method compensates the performance loss penalty due to polarization-dependent impairments in polarization division multiplexed coherent optical single-carrier systems. Using the proposed method, a 1.25-dB optical signal-to-noise ratio gain is achieved in the presence of 6-dB PDL. The proposed 44 joint equalizer-decoder has twice the complexity of conventional time-domain equalizers. Further changes at the receiver including the demodulator are not required. Since the outputs of the equalizer are noisy quadrature phase shift keying signals, adoption of the method to work with both hard and soft forward error corrections is straightforward.
Speaker-Invariant Training Via Adversarial Learning (2018)

We propose a novel adversarial multi-task learning scheme, aiming at actively curtailing the inter-talker feature variability while maximizing its senone discriminability so as to enhance the performance of a deep neural network (DNN) based ASR system. We call the scheme speaker-invariant training (SIT). In SIT, a DNN acoustic model and a speaker classifier network are jointly optimized to minimize the senone (tied triphone state) classification loss, and simultaneously mini-maximize the speaker classification loss. A speaker-invariant and senone-discriminative deep feature is learned through this adversarial multi-task learning. With SIT, a canonical DNN acoustic model with significantly reduced variance in its output probabilities is learned with no explicit speaker-independent (SI) transformations or speaker-specific representations used in training or testing. Evaluated on the CHiME-3 dataset, the SIT achieves 4.99% relative word error rate (WER) improvement over the conventional SI acoustic model. With additional unsupervised speaker adaptation, the speaker-adapted (SA) SIT model achieves 4.86% relative WER gain over the SA SI acoustic model.