gebhart/patrepeval huggingface dataset:
The Structure of Treponema pallidum Tp0751 (Pallilysin) Reveals a Non-canonical Lipocalin Fold That Mediates Adhesion to Extracellular Matrix Components and Interactions with Host Cells (2016)

Syphilis is a chronic disease caused by the bacterium Treponema pallidum subsp. pallidum. Treponema pallidum disseminates widely throughout the host and extravasates from the vasculature, a process that is at least partially dependent upon the ability of T. pallidum to interact with host extracellular matrix (ECM) components. Defining the molecular basis for the interaction between T. pallidum and the host is complicated by the intractability of T. pallidum to in vitro culturing and genetic manipulation. Correspondingly, few T. pallidum proteins have been identified that interact directly with host components. Of these, Tp0751 (also known as pallilysin) displays a propensity to interact with the ECM, although the underlying mechanism of these interactions remains unknown. Towards establishing the molecular mechanism of Tp0751-host ECM attachment, we first determined the crystal structure of Tp0751 to a resolution of 2.15 Å using selenomethionine phasing. Structural analysis revealed an eight-stranded beta-barrel with a profile of short conserved regions consistent with a non-canonical lipocalin fold. Using a library of native and scrambled peptides representing the full Tp0751 sequence, we next identified a subset of peptides that showed statistically significant and dose-dependent interactions with the ECM components fibrinogen, fibronectin, collagen I, and collagen IV. Intriguingly, each ECM-interacting peptide mapped to the lipocalin domain. To assess the potential of these ECM-coordinating peptides to inhibit adhesion of bacteria to host cells, we engineered an adherence-deficient strain of the spirochete Borrelia burgdorferi to heterologously express Tp0751. This engineered strain displayed Tp0751 on its surface and exhibited a Tp0751-dependent gain-of-function in adhering to human umbilical vein endothelial cells that was inhibited in the presence of one of the ECM-interacting peptides (p10). Overall, these data provide the first structural insight into the mechanisms of Tp0751-host interactions, which are dependent on the protein's lipocalin fold.
Unidirectional Key Distribution Across Time and Space with Applications to RFID Security. (2008)

We explore the problem of secret-key distribution in unidirectional channels, those in which a sender transmits information blindly to a receiver. We consider two approaches: (1) Key sharing across space, i.e., via simultaneously emitted values that may follow different data paths and (2) Key sharing across time, i.e., in temporally staggered emissions. Our constructions are of general interest, treating, for instance, the basic problem of constructing highly compact secret shares. Our main motivating problem, however, is practical key management in RFID (Radio-Frequency IDentification) systems. We describe the application of our techniques to RFID-enabled supply chains and a prototype privacy-enhancing system.
Thermochemical benefication of low rank coals (1986)

This patent describes a process for thermochemical beneficiation of carbonaceous solids. This process consists of introducing feed solids substantially free of surface liquids in sizes about 1/4 inch to about 4 inches in diameter to an upper portion of a pressurized wet carbonization reactor and maintaining the solids as moving packed bed within the wet carbonization reactor. Liquid is introduced to a lower portion of the wet carbonization reactor and passing the liquid upwardly in contact by countercurrent flow with the solids in the moving bed in an amount sufficient to flush product liquids. This liquid consists of dissolved and suspended products and make water from the moving bed; Within the moving packed bed a wet carbonization reaction zone at about 400/sup 0/ to about 650/sup 0/ F is maintained; An elevated pressure sufficient to prevent boiling of the liquid within the wet carbonization reactor is maintained. The solids in the wet carbonization reaction zone are maintained for an average residence time of about 10 to about 60 minutes to produce the dissolved and suspended products and make-water thereby beneficiating the solids. Product gases and product liquid from the upper portion of the wet carbonization reactor are withdrawn and beneficiatedmore » solids from the lower portion of the wet carbonization reactor are also withdrawn.« less
Multiepitope Synthetic Peptide and Recombinant Protein for the Detection of Antibodies to<i>Trypanosoma cruzi</i>in Patients with Treated or Untreated Chagas' Disease (2000)

A tetrapeptide and a recombinant protein, each representing 4 immunodominant epitopes of Trypanosoma cruzi, were tested by use of ELISA for the detection of serum antibodies. Sera from individuals with Chagas' disease, including persons untreated and successfully or unsuccessfully treated, were tested. These assays detected antibody in 100% of the parasitemias. The antibody reactivity decreased based on the success of treatment. Higher sensitivity was observed for tetrapeptide/recombinant protein assays than for lysate-based ELISA, and specificity was improved, particularly with Leishmania sera. The results indicate that multiepitope antigens provide a more sensitive and specific alternative to lysate for detection of anti-T. cruzi antibodies, as required for developing blood screening assays.
A Novel Method for Extending GPS to Underwater Applications (1991)

The need for accuracy, precision, and data registration in underwater positioning and navigation should be viewed as no less stringent than that existing on the surface or in the aerospace environment. This paper proposes a system that can be used to provide navigation service to free-ranging underwater users. This system uses buoys that act as roving pseudolites and translate GPS radio-based service to an acoustic-based service under water. Using this service, an unlimited number of users can independently locate themselves and navigate. Underwater extensions of Loran, Omega, or other radio-based navigation systems are also amenable to the technique.
<title>Raman detection of carotenoid pigments in the human retina</title> (2000)

We have used resonance Raman scattering as a novel, non- invasive, in-vivo optical technique to measure the concentration of carotenoid pigment in the human retina. Using argon laser excitation we are able to measure two strong carotenoid resonance Raman signals at 1159 and 1525 wave numbers, respectively. The required laser power levels are within the limits given by safety standards for ocular exposure. Of the approximately ten carotenoid pigment found in normal human serum, the species lutein and zeaxanthin are concentrated in high amounts in the cells of the human macula, which is an approximately 5 mm diameter area of the retina in which the visual acuity is highest. These carotenoids give the macula a characteristic yellow coloration, and it is speculated that these molecules function as filter to attenuate photochemical damage and/or image degradation under bright UV/blue light exposures. In addition, they are thought to act as free-radical scavenging antioxidants. Studies have shown that there may be a link between macular degenerative diseases, the leading cause of blindness in the elderly in the US, and the presence or absence of the carotenoids. We describe an instrument capable of measuring the macular carotenoids in human subjects in a non-invasive, rapid and quantitative way.
Localization in Optical Wireless Sensor Networks for IoT Applications (2019)

Optical wireless communications (OWC) and the internet of things (IoT) are two recent paradigms that are expected to be ubiquitous in the near future. In this paper, we introduce an early concept of how OWC can play a critical role in IoT applications in the context of real-time location-based services. OWC systems such as visible light communications (VLC) use light-emitting diodes (LED), already present in most user electronics as data transmission nodes. Studies on indoor OWC positioning generally assume that the location of the nodes, the LEDs that are connected to the backbone communications network, is provided to the user equipment (UE). In this paper, we consider a scenario where no a priori knowledge of the LED and UE locations is available, and the UE uses a single photodetector to measure the received optical intensity. We use these measurements to extract the distance between the UE and LEDs, and form geometric relations to find their locations. Once the LED locations have been found, we can track the UE using an extended Kalman filter. The joint source LED localization and UE tracking process is enhanced by using measurements that are collected by other members of the OWC-IoT network. Results show that the root mean square error of the LED localization can be decreased to 10 centimeters, and this leads to a user tracking accuracy better than 20 centimeters using the proposed method.
Direct laser fabrication of dense microlens arrays in semiconductor-doped glass (2000)

A direct laser writing technique in semiconductor-doped glasses is used to fabricate microlens arrays with fill factors exceeding the close-packing limit for circular microlenses. This is achieved by both structural and thermal interactions between adjacent lenses during fabrication, which result in the formation of microlenses shaped in accordance with the translational symmetry of the array. The effect of nearest-neighbor interaction on various time scales is studied and shown to be critical to the distortions observed.
FBA-AMNET: Foreground-Background Aware Atrous Multiscale Networks for Stereo Disparity Estimation (2020)

In this paper, we propose novel networks for stereo disparity estimation. First, deep features are extracted using efficient depthwise-separable convolutions. Next, the stereo matching costs are calculated from the deep features with a novel extended cost volume. Then, rich multiscale contextual information is aggregated with the proposed atrous multiscale network (AMNet). The proposed foreground-background aware network (FBA-AMNET) is trained with an iterative multi-task learning strategy to discriminate between foreground and background objects at multiple scales. The proposed networks advance the state of the art on challenging disparity estimation benchmarks, such as the KITTI 2012, KITTI 2015, Sceneflow, and Middlebury stereo benchmarks.
A bidirectional common polarization control method for coherent optical FDM transmission system (1990)

A bidirectional common polarization control method with a single polarization controller for a coherent optical FDM bidirectional transmission system is discussed. This method is promising for realizing a reliable and low-cost terminal in a coherent multichannel distribution system because the polarization controller can be placed in common only at a central office. Theoretical and experimental results show that the frequency separation delta f has to be 6*bit rate< delta f<120/ Delta tau (GHz) for FSK bidirectional transmission. The method is effective not only for reducing the complexity of the subscriber terminal but also for improving the reliability in a coherent CATV system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ion implanted passivated contacts for interdigitated back contacted solar cells (2015)

We describe work towards an interdigitated back contacted (IBC) solar cell utilizing ion implanted, passivated contacts. Formation of electron and hole passivated contacts to n-type CZ wafers using tunneling SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and ion implanted amorphous silicon (a-Si) are described. P and B were ion implanted into intrinsic amorphous Si films at several doses and energies. A series of post-implant anneals showed that the passivation quality improved with increasing annealing temperatures up to 900 °C. The recombination parameter, J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> , as measured by a Sinton lifetime tester, was J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> ~ 14 fA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for Si:P, and J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> ~ 56 fA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for Si:B contacts. The contact resistivity for the passivated contacts, as measured by TLM patterns, was 14 milliohm-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the n-type contact and 0.6 milliohm-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the p-type contact. These J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> and p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">contact</sub> values are encouraging for forming IBC cells using ion implantation to spatially define dopants.
Characteristics of Un doped and Europium-dopedSrI2 Scintillator Detectors (2012)

Abstract not provided
Video data acquisition accuracy for hand-held stereovision in image-guided surgery (2022)

Hand-held stereovision (HHS) has been implemented as an accurate, affordable, and non-ionizing method for image updating, and marker-less registration. Studies using HHS have collected images via individual snapshots. This study compares the accuracy of data acquisition from snapshots compared to a video stream data acquisition. An HHS system was calibrated via a tracked checkerboard to an accuracy of 0:88±0:24<i>mm</i>. A cadaver pig was used to measure accuracy of ducial locations with ducials placed on each spinous, and transverse process of L2 through L6. The system was then used to collect images of the surgical field. The images were collected 5 times. There was one snapshot image acquisition, and 4 video streams. After, the ducial locations were localized via a tracked stylus probe. The error was then computed between the stylus ducial locations and the ducial locations found on the stereovision depth map. The corresponding mean errors for the snapshots and 4 video acquisitions were as follows: 1:03 ± 0:24<i>mm</i>, 1:13 ± 0:34<i>mm</i>, 1:18 ± 0:59<i>mm</i>, 1:19 ± 0:47<i>mm</i>, and 3:23 ± 2:27<i>mm</i> respectively. While collecting the video streams the data were collected at what was perceived a constant speed. Each sequential video stream was collected at a higher speed. These speeds were calculated to be 7:22±1:95<i>mm</i>/s, 12:73±7:75<i>mm</i>/s, 19:19±12:74<i>mm</i>/s, and 30:14±13:33<i>mm</i>/s respectively. These data show that image acquisition via video streams at relatively low speeds have accuracy comparable to that of snapshot image acquisition.
On codes for optimal rebuilding access (2011)

MDS (maximum distance separable) array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with r redundancy nodes can correct any r erasures by accessing (reading) all the remaining information in both the systematic nodes and the parity (redundancy) nodes. However, in practice, a single erasure is the most likely failure event; hence, a natural question is how much information do we need to access in order to rebuild a single storage node? We define the rebuilding ratio as the fraction of remaining information accessed during the rebuilding of a single erasure. In our previous work we constructed array codes that achieve the optimal rebuilding ratio of 1/r for the rebuilding of any systematic node, however, all the information needs to be accessed for the rebuilding of the parity nodes. Namely, constructing array codes with a rebuilding ratio of 1/r for an arbitrary erasure was left as an open problem. In this paper, we solve this open problem and present array codes that achieve the lower bound of 1/r for rebuilding any single systematic or parity node.
Optical modelling of the gastric tissue to optimize the phototherapy efficacy against H. pylori infection (2016)

In the framework of the increasing phenomenon of antibiotic-resistant infections, those caused by Helicobacter pylori (Hp) have a particular significance, being worldwide diffused and associated with severe pathologies, among which gastric cancer. To overcome antibiotic-resistance, we propose the use of photodynamic therapy (PDT), based upon cytotoxic species production following bacteria illumination with visible light. In the case of Hp infection, this is due to the presence of endogenous light absorbers (porphyrins). To perform intra-gastric PDT, we have recently designed an illuminating ingestible device equipped with LED sources, where a crucial parameter is the choice of the emission wavelengths optimizing Hp photo-killing. For this purpose, both porphyrin absorption peaks and optical penetration in tissues have to be carefully accounted. By merging data on Hp porphyrin absorption spectrum with those coming by a Monte-Carlo optical modelling for illumination of the stomach wall surface, we have calculated the relative Hp photo-killing efficacy in three representative tissue models in the 400-650nm range. Results indicate that in thicker models, the red wavelengths are ultimately more effective than the blue-shifted ones, due to the greater penetration length in tissues despite a minor porphyrin absorption.
AUTOMATED DIAGNOSIS OF RETINOPATHY BY CONTENT-BASED IMAGE RETRIEVAL (2008)

The probabilistic nature of content-based image retrieval permits us to make statistically relevant predictions regarding the presence, severity, and manifestations of common retinal diseases from digital images in an automated and deterministic manner.
Intraoperative Correction of Cochlear Implant Electrode Translocation (2021)

Scalar translocation of precurved CI electrodes can be corrected by removal and reinsertion. This significantly improves the perimodiolar positioning of these electrodes. There was a high rate of success (83%) in this cadaveric model as well as a successful in vivo attempt.
Poly(hydroxy amide ethers):  New High-Barrier Thermoplastics (1996)

The synthesis of a new class of high-barrier polymers, poly(hydroxy amide ethers), is described. The polymers are formed by the reactions of bisphenol-A diglycidyl ether, OCH2CHCH2OC6H4C(CH3)2C6H4OCH2CHCH2O, and amide-containing bisphenols of the general formula HOC6H4NHC(O)RC(O)NHC6H4OH [R = −(CH2)n−, −CH2C6H4CH2−, or −C6H4−] or HOC6H4NHC(O)C6H4OH at 140−160 °C in propylene glycol monophenyl ether solvent using ethyltriphenylphosphonium acetate as initiator. High-molecular-weight poly(hydroxy amide ethers) of the general structure [−CH2CH(OH)CH2OC6H4C(CH3)2C6H4OCH2CH(OH)CH2OC6H4NHC(O)RC(O)NHC6H4O−]n or [−CH2CH(OH)CH2OC6H4C(CH3)2C6H4OCH2CH(OH)CH2OC6H4NHC(O)C6H4O−]n are readily prepared. The amorphous thermoplastics have glass transition temperatures (Tg) of 90−133 °C and oxygen transmission rates (O2TR) which range from 0.7 to 4.6 cc·mil/100 in.2·atm·day (barrier units or BU) at 23 °C and 47−85% relative humidity. The effect that polymer structure has on oxygen barrier properties and Tg is described. The characterization, structure determination, and properties of the poly(hydroxy amide ethers), as well as the amide-containing bisphenol precursors, are also presented.
Distributed wavelet compression algorithms for wireless sensor networks (2006)

We address the problem of compression for wireless sensor networks from a signal processing point of view. Each of the sensors has limited power, and acquires data that should be sent to a central node. The final goal is to have a reconstructed version of the sampled field at the central node, with the sensors spending as little energy as possible. 
We propose two distributed wavelet compression algorithms for multihop, distributed sensor networks based on the lifting scheme. The first algorithm introduces extra transmissions in the network so as to give the nodes access to neighboring data, making it possible to compute the transform coefficients. The second algorithm exploits the natural data flow in the network to aggregate data by computing partial wavelet coefficients that are refined as the data flows towards the central node. We study the impact of quantization of partial data on the final distortion obtained, and propose a rule to determine how many bits should be used to quantize the partial information so as to achieve a target level of degradation, in the form of added distortion as compared to calculating coefficients without partially quantized data. We also introduce a framework where the network is represented as a graph, with sensors associated to nodes, transmission costs to edge weights, and different coding schemes associated to modes of operation. Dynamic programming techniques are used to optimize the network, assigning coding schemes to each of the nodes so that the overall energy cost is minimum. The proposed coding methods and optimization are extended to bidimensional networks, with irregular sensor deployment. In this scenario, our algorithm operates by first selecting a routing strategy through the network. Then, for each route, an optimal combination of data representation algorithms is selected. We then propose a simple heuristic to determine the data representation technique to use once path merges are taken into consideration.
Estimation of depletion or injection induced changes in reservoir stresses using time-lapse sonic data (2014)

A new technique uses time-lapse borehole sonic data acquired in a vertical borehole parallel to the X <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -axis to estimate changes in formation stresses caused by reservoir depletion or injection. A pre-production baseline survey acquires sonic data in an open or cased hole along with estimates of reservoir pressure, overburden and minimum horizontal stresses. After years of depletion or injection, a monitor survey acquires sonic data in an observation well. Both sonic datasets are processed to obtain the borehole Stoneley and cross-dipole dispersions. An inversion algorithm inverts the measured Stoneley dispersion to estimate the far-field shear modulus C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">66</sub> in the borehole cross-sectional plane. The shear moduli C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">44</sub> and C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">55</sub> in the two orthogonal borehole axial planes are obtained directly from the low-frequency asymptotes of the two cross-line flexural dispersions. Differences in the three shear moduli from the baseline survey yield the maximum horizontal stress magnitude and an acoustoelastic coefficient using the estimated pore pressure, overburden and minimum horizontal stresses. The three far-field shear moduli in the three orthogonal planes are also obtained from the subsequent monitor survey. This algorithm uses the acoustoelastic coefficient from the baseline survey and the three shear moduli after depletion or injection to estimate changes in the maximum and minimum horizontal stress magnitudes caused by reservoir pressure changes.