gebhart/patrepeval huggingface dataset:
The e (P4) outer membrane protein of Haemophilus influenzae: biologic activity of anti-e serum and cloning and sequencing of the structural gene (1991)

Outer membrane proteins of nontypeable (NT) Haemophilus influenzae are among the major candidates for inclusion in vaccines against these organisms. This article reports the purification of the e (P4) lipoprotein of H. influenzae and the subsequent production of antiserum directed against this protein. The anti-e polyclonal serum cross-reacted with e protein in multiple clinical NT H. influenzae isolates. Monoclonal antibody analysis of e protein showed at least one surface-exposed epitope to be conserved among NT H. influenzae strains. Anti-e serum also had bactericidal activity against multiple clinical isolates of NT H. influenzae. These results are in contrast to previous reports in the literature that purified P4 protein did not elicit biologically active antibodies. Anti-e antibodies exhibited synergistic bactericidal activity directed against NT H. influenzae when mixed with antibodies directed against another Haemophilus lipoprotein, PCP. This bactericidal synergy was observed against a variety of NT clinical isolates. We also report the cloning of the Haemophilus e lipoprotein, or hel, gene encoding the e protein and its expression and processing in Escherichia coli. The nucleotide sequence of the gene and deduced amino acid sequence of the protein are given. These results demonstrate that e protein is a viable candidate to be a component of a vaccine against NT H. influenzae.
Optical-fibre connector (1975)

A connector for joining plastics-coated, multimode fibres has low insertion loss and good environmental stability. The connector is suitable for field installation by a portable installation fixture and using simple tools.
Transactional memory introduction (2006)

Presents a collection of slides covering the following topics: Transactional Memory language construct; synchronised HashMap; transactional HashMap; Java; failure recovery; and parallel programming.
A Usable and Robust Continuous Authentication Framework Using Wearables (2020)

One-time login process in conventional authentication systems does not guarantee that the identified user is the actual user throughout the session. However, it is necessary to re-verify the user identity periodically throughout a login session, which is lacking in existing one-time login systems. Continuous authentication, which re-verifies the user identity without breaking the continuity of the session, can address this issue. However, existing methods for Continuous Authentication are either not reliable or not usable. In this paper, we introduce a usable and reliable Wearable-Assisted Continuous Authentication (WACA), which relies on the sensor-based keystroke dynamics and the authentication data is acquired through the built-in sensors of a wearable (e.g., smartwatch) while the user is typing. The acquired data is periodically and transparently compared with the registered profile of the initially logged-in user with one-way classifiers. With this, WACA continuously ensures that the current user is the user who logged-in initially. We implemented the WACA framework and evaluated its performance extensively on real devices with real users. The empirical evaluation of WACA reveals that WACA is feasible, and its error rate is as low as 1 percent with 30 seconds of processing time and 2-3 percent for 20 seconds. The computational overhead is minimal. Furthermore, WACA is capable of identifying insider threats with very high accuracy (99.2 percent) and also robust against powerful adversaries such as imitation and statistical attackers. We believe that this work has practical and far-reaching implications for the future of the usable authentication field.
Power dissipation in microwave-enhanced in situ transesterification of algal biomass to biodiesel (2012)

We investigated the effect of power dissipation on microwave-accelerated simultaneous extraction and transesterification of dry algal biomass (Nannochloropsis salina) to biodiesel. The response surface methodology (RSM) was applied to design the experiments and optimize the process parameters, including dry algae to methanol ratio, reaction time and catalyst concentrations, by evaluating their influences on the fatty acid methyl ester yield (FAME) under controlled microwave power conditions. The microwave energy utilization efficiency was estimated at various power levels to optimize the power dissipation, maximize FAME yields and minimize energy losses. The algal biomass characterization and algal biodiesel analysis were performed using various analytical instruments such as FTIR, SEM-EDS, TGA and GC-MS. The Nile Red method was applied for lipid localization in microalgae cells using confocal microscopy and fluorescence spectroscopy. The direct conversion technique has the potential to provide energy-efficient and economical routes for biodiesel production from algal biomass.
Hydrophobicity of transmembrane proteins: Spatially profiling the distribution (2003)

A hallmark of soluble globular protein tertiary structure is a hydrophobic core and a protein exterior populated predominantly by hydrophilic residues. Recent hydrophobic moment profiling of the spatial distribution of 30 globular proteins of diverse size and structure had revealed features of this distribution that were comparable. Analogous profiling of the hydrophobicity distribution of the alpha-helical buried bundles of several transmembrane proteins, as the lipid/protein interface is approached from within the bilayer, reveals spatial hydrophobicity profiles that contrast with those obtained for the soluble proteins. The calculations, which enable relative changes of hydrophobicity to be simply identified over the entire spatial extent of the multimer within the lipid bilayer, show the accumulated zero-order moments of the bundles to be mainly inverted with respect to that found for the soluble proteins. This indicates a statistical increase in the average residue hydrophobic content as the lipid bilayer is approached. This result differs from that of a relatively recent calculation and qualitatively agrees with earlier calculations involving lipid exposed and buried residues of the alpha-helices of transmembrane proteins. Spatial profiling, over the entire spatial extent of the multimer with scaled values of residue hydrophobicity, provides information that is not available from calculations using lipid exposure alone.
Simultaneous PCR detection of Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus types 1 and 2 from genital ulcers (1996)

A multiplex PCR (M-PCR) assay with colorimetric detection was devised for the simultaneous amplification of DNA targets from Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus (HSV) types 1 and 2. By using target-specific oligonucleotides in a microwell format, 298 genital ulcer swab specimens collected in New Orleans during three intervals from 1992 through 1994 were evaluated. The results of the M-PCR assay were compared with the results of dark-field microscopy and H. ducreyi culture on two different culture media. HSV culture results were available for 99 specimens collected during the third interval. Confirmatory PCR assays targeting different gene sequences for each of the three organisms were used to validate the M-PCR results. Specimens were resolved as positive for the determination of sensitivity if the reference diagnostic test was positive or if the results of both the M-PCR and the confirmatory PCR were positive. The resolved sensitivities of M-PCR for HSV, H. ducreyi, and T. pallidum were 100, 98.4, and 91%, respectively. The resolved sensitivities of HSV culture, H. ducreyi culture, and dark-field microscopy were 71.8, 74.2, and 81%, respectively. These results indicate that the M-PCR assay is more sensitive than standard diagnostic tests for the detection of HSV, H. ducreyi, and T. pallidum from genital ulcers.
Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in <i>Comamonas</i> sp. Strain NCIMB 9872 and Biotransformations Effected by <i>Escherichia coli</i> -Expressed Cyclopentanone 1,2-Monooxygenase (2002)

Cyclopentanone 1,2-monooxygenase, a flavoprotein produced by Pseudomonas sp. strain NCIMB 9872 upon induction by cyclopentanol or cyclopentanone (M. Griffin and P. W. Trudgill, Biochem. J. 129:595-603, 1972), has been utilized as a biocatalyst in Baeyer-Villiger oxidations. To further explore this biocatalytic potential and to discover new genes, we have cloned and sequenced a 16-kb chromosomal locus of strain 9872 that is herein reclassified as belonging to the genus COMAMONAS: Sequence analysis revealed a cluster of genes and six potential open reading frames designated and grouped in at least four possible transcriptional units as (orf11-orf10-orf9)-(cpnE-cpnD-orf6-cpnC)-(cpnR-cpnB-cpnA)-(orf3-orf4 [partial 3' end]). The cpnABCDE genes encode enzymes for the five-step conversion of cyclopentanol to glutaric acid catalyzed by cyclopentanol dehydrogenase, cyclopentanone 1,2-monooxygenase, a ring-opening 5-valerolactone hydrolase, 5-hydroxyvalerate dehydrogenase, and 5-oxovalerate dehydrogenase, respectively. Inactivation of cpnB by using a lacZ-Km(r) cassette resulted in a strain that was not capable of growth on cyclopentanol or cyclopentanone as a sole carbon and energy source. The presence of sigma(54)-dependent regulatory elements in front of the divergently transcribed cpnB and cpnC genes supports the notion that cpnR is a regulatory gene of the NtrC type. Knowledge of the nucleotide sequence of the cpn genes was used to construct isopropyl-beta-thio-D-galactoside-inducible clones of Escherichia coli cells that overproduce the five enzymes of the cpn pathway. The substrate specificities of CpnA and CpnB were studied in particular to evaluate the potential of these enzymes and establish the latter recombinant strain as a bioreagent for Baeyer-Villiger oxidations. Although frequently nonenantioselective, cyclopentanone 1,2-monooxygenase was found to exhibit a broader substrate range than the related cyclohexanone 1,2-monooxygenase from Acinetobacter sp. strain NCIMB 9871. However, in a few cases opposite enantioselectivity was observed between the two biocatalysts.
Class specific inhibition of house dust mite proteinases which cleave cell adhesion, induce cell death and which increase the permeability of lung epithelium (1998)

1. House dust mite (HDM) allergens with cysteine and serine proteinase activity are risk factors for allergic sensitization and asthma. A simple method to fractionate proteinase activity from HDM faecal pellets into cysteine and serine class activity is described. 2. Both proteinase fractions increased the permeability of epithelial cell monolayers. The effects of the serine proteinase fraction were inhibited by 4-(2-aminoethyl)-benzenesulphonyl fluoride hydrochloride (AEBSF) and soybean trypsin inhibitor (SBTI). The effects of the cysteine proteinase fraction could be inhibited by E-64. No reciprocity of action was found. 3. Treatment of epithelial monolayers with either proteinase fraction caused breakdown of tight junctions (TJs). AEBSF inhibited TJ breakdown caused by the serine proteinase fraction, whereas E-64 inhibited the cysteine proteinase fraction. 4. Agarose gel electrophoresis revealed that the proteinases induced DNA cleavage which was inhibited by the matrix metalloproteinase inhibitor BB-250. Compound E-64 inhibited DNA fragmentation caused by the cysteine proteinase fraction, but was without effect on the serine proteinase fraction. Staining of proteinase-treated cells with annexin V (AV) and propidium iodide (PI) revealed a diversity of cellular responses. Some cells stained only with AV indicating early apoptosis, whilst others were dead and stained with both AV and PI. 5. HDM proteinases exert profound effects on epithelial cells which will promote allergic sensitization; namely disruption of intercellular adhesion, increased paracellular permeability and initiation of cell death. Attenuation of these actions by proteinase inhibitors leads to the conclusion that compounds designed to be selective for the HDM enzymes may represent a novel therapy for asthma.
A Photonic Deep Neural Network Processor on a Single Chip with Optically Accelerated Training (2023)

We report an end-to-end photonic deep neural network processor, fabricated in a commercial CMOS process, that integrates optical matrix algebra and nonlinear function units onto a single chip and implements all-optical DNN inference and training.
Ultra-Dense Networks in 5G: Interference Management via Non-Orthogonal Multiple Access and Treating Interference as Noise (2017)

We propose a method for interference mitigation in an ultra-dense wireless network scenario in 5G, where a group of transmit points (TPs) intend to serve multiple user equipments (UEs) using the same wireless resource. The proposed UE scheduling subroutine may schedule a single UE or multiple UEs for each TP, where multiple UEs can be served via non-orthogonal multiple-access (NOMA). Afterwards, the link scheduling subroutine utilizes an extended form of the optimality conditions for treating interference as noise in single-user networks for the case where NOMA is also involved. This subroutine determines an activation/deactivation pattern of TPs while maintaining fairness among competing users and minimizing the level of interference among concurrent transmissions. We show that our proposed interference management scheme can improve over the benchmark schemes both in terms of sum-throughput and coverage, striking the right trade-off between these two performance metrics.
Tensor Transmission-Line Metamaterials (2010)

Transmission-line (TL) metamaterials possessing effective material parameters that are diagonal in the Cartesian basis have been previously studied. In this paper, TL metamaterials with arbitrary full tensors are introduced and analyzed. An approximate tensor analysis of the proposed metamaterials is first developed. Bloch analysis is then used to verify the approximate analysis and derive exact dispersion equations and impedance relations. Finally, simulation results are presented that validate the analysis and show the utility of this new class of metamaterials. The ability to design tensor metamaterials such as these is crucial to the practical implementation of novel devices derived through transformational optics/electromagnetics.
A Pipelined Memristive Neural Network Analog-to-Digital Converter (2020)

With the advent of high-speed, high-precision, and low-power mixed-signal systems, there is an ever-growing demand for accurate, fast, and energy-efficient analog-to-digital (ADCs) and digital-to-analog converters (DACs). Unfortunately, with the downscaling of CMOS technology, modern ADCs trade off speed, power and accuracy. Recently, memristive neuromorphic architectures of four-bit ADC/DAC have been proposed. Such converters can be trained in real-time using machine learning algorithms, to break through the speed-power-accuracy trade-off while optimizing the conversion performance for different applications. However, scaling such architectures above four bits is challenging. This paper proposes a scalable and modular neural network ADC architecture based on a pipeline of four-bit converters, preserving their inherent advantages in application reconfiguration, mismatch self-calibration, noise tolerance, and power optimization, while approaching higher resolution and throughput in penalty of latency. SPICE evaluation shows that an 8-bit pipelined ADC achieves 0.18 LSB INL, 0.20 LSB DNL, 7.6 ENOB, and 0.97 fJ/conv FOM. This work presents a significant step towards the realization of large-scale neuromorphic data converters.
MicroRNA Let-7i Is a Promising Serum Biomarker for Blast-Induced Traumatic Brain Injury (2012)

Blast-induced traumatic brain injury (TBI) is of significant concern in soldiers returning from the current conflicts in Iraq and Afghanistan. Incidents of TBI have increased significantly in the current conflicts compared to previous wars, and a majority of these injuries are caused by improvised explosive devices. Currently, no specific technique or biomarker is available for diagnosing TBI when no obvious clinical symptoms are present. Micro-RNAs are small RNA (~ 22nts) molecules that are expressed endogenously and play an important role in regulating gene expression. MicroRNAs have emerged as novel serum diagnostic biomarkers for various diseases. In this study, we studied the effect of blast overpressure injury on the microRNA signatures in the serum of rats. Rats were exposed to three serial 120-kPa blast overpressure exposures through a shockwave tube. Blood and cerebrospinal fluid were collected at various time points after injury, and microRNA modulation was analyzed using real-time PCR. Five microRNAs were significantly modulated in the serum samples of these animals at three time points post-injury. Further, we also found that the levels of microRNA let-7i are also elevated in cerebrospinal fluid post-blast wave exposure. The presence of microRNA in both serum and cerebrospinal fluid immediately after injury makes microRNA let-7i an ideal candidate for further studies of biomarkers in TBI.
Cloning and characterization of the gene for amylosucrase from Neisseria polysaccharea: production of a linear alpha-1,4-glucan (1997)

The gene for the amylosucrase from Neisseria polysaccharea (ATCC 43768) was cloned by use of a functional expression system in Escherichia coli XL1-Blue. The deduced amino acid sequence of the protein has homology to the sequences of the alpha-amylase class of enzymes, with the highest similarities being found to the sequences of the trehalose synthase from Pimelobacter sp. strain R48 (17) and amylomaltase from Thermotoga maritima (11). However, the regions of highest homology within the alpha-amylase class of enzymes, which are essential for the catalytic activity, are only scarcely found in the sequence of amylosucrase. By using the enzyme isolated from culture supernatants of transformed E. coli cells, it is possible to synthesize linear alpha-1,4-glucans from sucrose, indicating that the enzyme is not capable of producing alpha-1,6-glycosidic linkages on its own.
Upper-Extremity Stroke Therapy Task Discrimination Using Motion Sensors and Electromyography (2008)

Brain injury resulting from stroke often causes upper-extremity motor deficits that limit activities of daily living. Several therapies being developed for motor rehabilitation after stroke focus on increasing time spent using the extremity to promote motor relearning. Providing a novel system for user-worn therapy may increase the amount and rate of functional motor recovery. A user-worn system comprising accelerometers, gyroscopes, and electromyography amplifiers was used to wirelessly transmit motion and muscle activity from normal and stroke subjects to a computer as they completed five upper-extremity rehabilitation tasks. An algorithm was developed to automatically detect the therapy task a subject performed based on the gyroscope and electromyography data. The system classified which task a subject was attempting to perform with greater than 80% accuracy despite the fact that those with severe impairment produced movements that did not resemble the goal tasks and were visually indistinguishable from different tasks. This developed system could potentially be used for home-therapy compliance monitoring, real-time patient feedback and to control therapy interventions.
The SYSTERS protein sequence cluster set (2000)

The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and hierarchically into superfamily and subfamily clusters. The cluster set can be searched with a sequence using the SSMAL search tool or a traditional database search tool like BLAST or FASTA. Additionally a multiple alignment is generated for each cluster and annotated with domain information from the Pfam database of protein domain families. A taxonomic overview of the organisms covered by a cluster is given based on the NCBI taxonomy. The cluster set is available for querying and browsing at http://www.dkfz-heidelberg. de/tbi/services/cluster/systersform
Generalized compliant motion with sensor fusion (1991)

A task execution primitive has been developed which merges compliant motion with the fusion of real and virtual sensory data for execution of general manipulation tasks. The behavior of the primitive is specified by an input parameter set. Motion can be caused by a variety of inputs including a Cartesian trajectory generator, a wrist force-torque sensor, dither waveforms, virtual springs, virtual joint limiting force fields, and 6 degree of freedom hand controllers. The primitive has been been used for a variety of autonomous and shared control tasks in the JPL telerobot testbed. The primitive provides autonomous control, compliant teleoperation, and shared control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>MODTRAN2: suitability for remote sensing</title> (1993)

MODTRAN2 (1992) is the most recent version of MODTRAN, the Moderate Resolution Atmospheric Radiance and Transmittance Model, first released by the Geophysics Directorate, Phillips Laboratory, in 1990. It encompasses all the capabilities of LOWTRAN 7, the historic 20 cm<SUP>-1</SUP> resolution radiance code, but incorporates a much more sensitive molecular band model with 2 cm<SUP>-1</SUP> resolution. For inversion algorithm applications, MODTRAN2 must prove to be sufficiently accurate when calculating layer- specific perturbations. First steps in establishing this capability have recently been accomplished. DREV (Defence Research Establishment Valcartier, Canada), in conjunction with the Geophysics Directorate, has taken measurements with a surface-based Bomem interferometer (approximately 1 cm<SUP>-1</SUP> resolution), with full supporting sonde profiles (z, T, p, and relative humidity). This suggests that the derivative matrices, typically required for inversion algorithms, may be readily (and rapidly) calculated using MODTRAN whenever its spectral resolution is adequate.
Ultra-high-rate modulation of high-Q optical cavities (2010)

By modulating the output coupler of a microcavity, the traditional limits in resonant modulators and laser modulation can be circumvented. High-Q microcavity modulators and lasers can be ultra- high-speed, low-power, and compact.
Silicon Nitride Boundary Lubrication: Effect of Phosphorus-Containing Organic Compounds (1996)

The boundary lubricating characteristics of phosphorus-containing compounds on silicon nitride, were studied using a ball-on-three-flat wear tester. The compounds were tested at 1% by weight in a pure paraffin oil under a mean pressure of about 2 GPa. The compounds are effective in reducing wear. Continuous surface films were observed in and around the wear scars for most of the phosphorus compounds. These, films are complex mixtures containing phosphorus and silicon. A detailed study on a zinc, dithiophosphate (ZDP) surface, film revealed high concentrations of zinc and phosphorus, but very little sulfur. This is in direct contrast to surface analysis results on steel systems in which sulfur-containing species are found on the worn surface. This suggests different chemical reaction pathways for phosphorus compounds on steel and silicon nitride surfaces.
Randomly Disordered Glass-Air Optical Fiber Imaging Based on Deep Learning (2018)

We demonstrate that images can be reconstructed for objects away from the imaging plane without any distal optics by combining deep neural networks with meter-long glass-air disordered optical fibers. This imaging system is bending-independent.