gebhart/patrepeval huggingface dataset:
A Cost-Effective Distributed Acoustic Sensor Using a Commercial Off-the-Shelf DFB Laser and Direct Detection Phase-OTDR (2015)

We propose and experimentally demonstrate the use of cyclic pulse coding for enhanced performance in distributed acoustic sensing based on a phase-sensitive optical time-domain reflectometry (φ-OTDR) using direct detection. First, we present a theoretical analysis showing that to make cyclic pulse coding effective in φ-OTDR, the laser linewidth and stability must be optimized to simultaneously guarantee intrapulse coherence and interpulse incoherence. We then confirm that commercial off-the-shelf distributed feedback (DFB) lasers can satisfy these conditions, providing coding gain consistent with theoretical predictions. By externally modulating such lasers with cyclic pulse coding, we demonstrate a distributed acoustic sensor capable of measuring vibrations of up to 500 Hz over 5 km of standard single-mode fiber with 5-m spatial resolution with ~9-dB signal-to-noise ratio (SNR) improvement compared with the single-pulse equivalent. We also show that the proposed solution offers sensing performances that are comparable to similar sensors employing highly coherent and stabilized external cavity lasers and a single-pulse φ-OTDR.
A Novel in vitro Human Macrophage Model to Study the Persistence of Mycobacterium tuberculosis Using Vitamin D3 and Retinoic Acid Activated THP-1 Macrophages (2011)

Mycobacterium tuberculosis (Mtb) replicates within the human macrophages and we investigated the activating effects of retinoic acid (RA) and vitamin D(3) (VD) on macrophages in relation to the viability of intracellular Mtb. A combination of these vitamins (RAVD) enhanced the levels of DC-SIGN and mannose receptors on THP-1 macrophages that increased mycobacterial uptake but inhibited the subsequent intracellular growth of Mtb by inducing reactive oxygen species and autophagy. RAVD also enhanced antigen presenting and chemotactic receptors on THPs suggesting an activated phenotype for RAVD activated THPs. RAVD mediated activation was also associated with a marked phenotypic change in Mtb infected THPs that fused with adjacent THPs to form multinucleated giant cells (MNGCs). Typically, MNGCs occurred over 30 days of in vitro culture and contained non-replicating persisting Mtb for more than 60 days in culture. Latent tuberculosis occurs in over a third of mankind and we propose that RAVD mediated induction of persistent Mtb within human macrophages provides a novel model to develop therapeutic approaches and investigate pathogenesis of latency.
Learning disease relationships from clinical drug trials (2016)

The agreement of our results with other sources indicates that our premise regarding latent expert knowledge holds. The disease relationships unique to our network may be used to generate hypotheses for future biological and clinical research as well as drug repurposing and design. Our results provide an example of using experimental data on humans to generate biologically useful information and point to a set of new and promising strategies to link clinical outcomes data back to biological research.
Inhibition of West Nile Virus Multiplication in Cell Culture by Anti-Parkinsonian Drugs (2016)

West Nile virus (WNV) is a mosquito-borne flavivirus maintained in a transmission cycle between mosquitoes and birds, but it can also infect other vertebrates, including humans, in which it can cause neuroinvasive diseases. To date, no licensed vaccine or therapy for human use against this pathogen is yet available. A recent approach to search for new antiviral agent candidates is the assessment of long-used drugs commonly administered by clinicians to treat human disorders in drug antiviral development. In this regard, as patients with West Nile encephalitis frequently develop symptoms and features of parkinsonism, and cellular factors altered in parkinsonism, such as alpha-synuclein, have been shown to play a role on WNV infection, we have assessed the effect of four drugs (L-dopa, Selegiline, Isatin, and Amantadine), that are used as therapy for Parkinson's disease in the inhibition of WNV multiplication. L-dopa, Isatin, and Amantadine treatments significantly reduced the production of infectious virus in all cell types tested, but only Amantadine reduced viral RNA levels. These results point to antiparkinsonian drugs as possible therapeutic candidates for the development of antiviral strategies against WNV infection.
High-rate Viterbi processor: a systolic array solution (1990)

The main part of the Viterbi algorithm (VA) is a nonlinear feedback loop, the ACS recursion (add-compare-select recursion), which presents a bottleneck for high-speed implementations and cannot be circumvented by standard means. Because the two operations of the loop form an algebraic structure called semiring, it is shown that the ACS recursion of the Viterbi algorithm can therefore be written as a linear vector recursion. This allows the authors to employ the powerful techniques of parallel processing and pipelining, known for conventional linear systems, to achieve high throughput rates. Since the VA can be written as a linear vector recursion, it can be implemented by systolic arrays. For the class of shuffle exchange codes to be decoded by the Viterbi algorithm hardware-efficient code-optimized arrays are presented. It is shown that carry-save arithmetic can be used for the operations of ACS recursion, allowing each word-level operation to be pipelined and carried out by an efficient bit-level systolic array.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes (2021)

We intend to identify marker genes with differential gene expression (DEG) and RGC subtypes in cultures of human-induced pluripotent stem cell (iPSC)-derived retinal ganglion cells. Single-cell sequencing was performed on mature and functional iPSC-RGCs at day 40 using Chromium Single Cell 3' V3 protocols (10X Genomics). Sequencing libraries were run on Illumina Novaseq to generate 150 PE reads. Demultiplexed FASTQ files were mapped to the hg38 reference genome using the STAR package, and cluster analyses were performed using a cell ranger and BBrowser2 software. QC analysis was performed by removing the reads corresponding to ribosomal and mitochondrial genes, as well as cells that had less than 1X mean absolute deviation (MAD), resulting in 4705 cells that were used for further analyses. Cells were separated into clusters based on the gene expression normalization via PCA and TSNE analyses using the Seurat tool and/or Louvain clustering when using BBrowser2 software. DEG analysis identified subsets of RGCs with markers like <i>MAP2</i>, <i>RBPMS</i>, <i>TUJ1</i>, <i>BRN3A</i>, <i>SOX4</i>, <i>TUBB3</i>, <i>SNCG</i>, <i>PAX6</i> and <i>NRN1</i> in iPSC-RGCs. Differential expression analysis between separate clusters identified significant DEG transcripts associated with cell cycle, neuron regulatory networks, protein kinases, calcium signaling, growth factor hormones, and homeobox transcription factors. Further cluster refinement identified RGC diversity and subtype specification within iPSC-RGCs. DEGs can be used as biomarkers for RGC subtype classification, which will allow screening model systems that represent a spectrum of diseases with RGC pathology.
Diffusion tensor imaging during recovery from severe traumatic brain injury and relation to clinical outcome: a longitudinal study (2007)

Diffusion tensor imaging (DTI) has been proposed as a sensitive biomarker of traumatic white matter injury, which could potentially serve as a tool for prognostic assessment and for studying microstructural changes during recovery from traumatic brain injury (TBI). However, there is a lack of longitudinal studies on TBI that follow DTI changes over time and correlate findings with long-term clinical outcome. We performed a prospective longitudinal study of 30 adult patients admitted for subacute rehabilitation following severe traumatic brain injury. DTI and conventional MRI were acquired at mean 8 weeks (5-11 weeks), and repeated in 23 of the patients at mean 12 months (9-15 months) post-trauma. Using a region-of-interest-based approach, DTI parameters were compared to those of healthy matched controls, scanned during the same time period and rescanned with a similar interval as that of patients. At the initial scan, fractional anisotropy was reduced in all the investigated white matter regions in patients compared to controls (P <or= 0.01) due to decreased diffusivity parallel (lambda(parallel)) and increased diffusivity perpendicular (lambda(perpendicular)) to axonal fibre direction. Fractional anisotropy in the cerebral peduncle correlated with approximately 1 year Glasgow outcome scale score (r = 0.60, P<0.001) and in this sample predicted dichotomized outcome with 76% accuracy when taken alone, and with 100% accuracy in combination with clinical evaluation by functional independence measure at the time of the first scan. At follow-up DTI, fractional anisotropy in patients had increased in the internal capsule and in centrum semiovale (P <or= 0.01) due to an interval increase of lambda(parallel) with unchanged lambda(perpendicular). In these regions, fractional anisotropy and lambda( parallel) reached normal or supranormal levels, primarily in patients with favourable outcome. In the cerebral peduncle and in corpus callosum, lambda(parallel) and lambda(perpendicular) both increased during the scan interval and, particularly in patients with unfavourable outcome, fractional anisotropy remained depressed. No significant DTI parameter changes over time were found in controls, or in CSF of patients. These findings support that DTI is a clinically relevant biomarker in TBI, which may have prognostic value and also might serve as a tool for revealing changes in the neural tissue during recovery.
Speckle imaging with the PAPA detector (1985)

A new 2-D photon-counting camera, the PAPA (precision analog photon address) detector has been built, tested, and used successfully for the acquisition of speckle imaging data. The camera has 512 × 512 pixels and operates at count rates of at least 200,000/sec. In this paper we present technical details on the camera and include some of the laboratory and astronomical results which demonstrate the detector's capabilities.
How to diagnose diastolic heart failure (1998)

European Study Group on Diastolic Heart Failure* Because of the frequent occurrence of diastolic left ventricular dysfunction in patients with systolic left ventricular dysfunction and congestive cardiomyopathy A frequently used criterion As left ventricular relaxation depends on end-systolic load and volume
Alkyd Resins (2003)

Abstract The article contains sections titled: 1. Introduction 2. Production 2.1. Raw Materials 2.2. Polymerization Theory 2.3. Formulation and Process Types; Laboratory Processing 2.4. Manufacture 3. Film Formation by Coatings Based on Alkyd Resins 4. Modified Alkyds 5. Low‐Solvent Coatings 6. Markets and End Uses
On the importance of configuration and closure of nerve cuff electrodes for recording (2002)

The extraction of neural information for feedback in functional electrical stimulation is limited by the poor signal to noise ratio (SNR) in the nerve recordings. Cuff electrodes have been successful in improving the SNR, but many parameters such as cuff dimensions, configurations and closing methods affect the obtainable SNR. In the present work we studied the effect of the monopolar and tripolar configuration on signal and noise in cuff recordings. Further, we compared two different cuff closures, the slit closure and the closure using interdigitating tubes. The cuff recordings were performed with an artificial nerve fiber set-up, and the results showed that the tripolar configuration gave a 2.4 times higher SNR than the monopolar configuration. A slit closure with a flap resulted in a 6% reduction of the nerve signal amplitude whereas the closure using interdigitating tubes reduced the signal with 19%.
Manifestation of intrinsic defects in optical properties of self-organized opal photonic crystals (2000)

Self-organized synthetic opals possessing a face centered cubic (fcc) lattice are promising for fabrication of a three-dimensional photonic crystal with a full photonic band gap in the visible. The fundamental limiting factor of this method is the large concentration of lattice defects and, especially, planar stacking faults, which are intrinsic to self-assembling growth of colloidal crystal. We have studied the influence of various types of defects on photonic band structure of synthetic opals by means of optical transmission, reflection and diffraction along different crystallographic directions. We found that in carefully chosen samples the stacking probability alpha can be as high as 0.8-0.9 revealing the strong preference of fcc packing sequence over the hexagonal close-packed (hcp). It is shown that scattering on plane stacking faults located perpendicular to the direction of growth results in a strong anisotropy of diffraction pattern as well as in appearance of a pronounced doublet structure in transmission and reflection spectra taken from the directions other than the direction of growth. This doublet is a direct manifestation of the coexistence of two crystallographic phases--pure fcc and strongly faulted. As a result the inhomogeneously broadened stop-bands overlap over a considerable amount of phase space. The latter, however, does not mean the depletion of the photonic density of states since large disordering results in filling of the partial gaps with both localized and extended states.
Predicting Network Activity from High Throughput Metabolomics (2013)

The functional interpretation of high throughput metabolomics by mass spectrometry is hindered by the identification of metabolites, a tedious and challenging task. We present a set of computational algorithms which, by leveraging the collective power of metabolic pathways and networks, predict functional activity directly from spectral feature tables without a priori identification of metabolites. The algorithms were experimentally validated on the activation of innate immune cells.
Short-Range Sensor for Underwater Robot Navigation using Line-lasers and Vision (2015)

This paper investigates a minimalistic laser-based range sensor, used for underwater inspection by Autonomous Underwater Vehicles (AUV). This range detection system system comprise two lasers projecting vertical lines, parallel to a camera's viewing axis, into the environment. Using both lasers for distance estimation, the sensor offers three dimensional interpretation of the environment. This is obtained by triangulation of points extracted from the image using the Hough Transform. We evaluate the system in simulation and by physical proof-of-concept experiments on an OpenROV platform.
Synthesis, Structure, and Applications of α-Cationic Phosphines (2016)

In α-cationic phosphines, at least one of the three substituents on phosphorus corresponds to a cationic (normally, but not always heteroaromatic) group, which is attached without any spacer to the phosphorus atom by a relatively inert P-C bond. This unique architecture confers to the resulting ligand strong acceptor properties, which frequently surpass those of traditional acceptor ligands such as phosphites or polyfluorinated phosphines. In addition, the fine-tuning of the stereoelectronic properties of α-cationic phosphines is also possible by judicious selection of the number and nature of the cationic groups. The opportunities offered in catalysis by α-cationic ligands arise from this ability to deplete electron density from the metals they coordinate. Thus, if in a hypothetical catalytic cycle the step that determines the rate is facilitated by an increase of the Lewis acidity at the metal center, then an acceleration of the whole process is expected by their use as ancillary ligands. Interestingly, this situation is found more frequently than one might think; many common elementary steps involved in catalytic cycles, such as reductive eliminations, coordination of substrates to metals, or attack of nucleophiles to coordinated substrates, belong to this category and are often fostered by electron poor metal centers. In this regard, our group has observed remarkable ligand acceleration effects by the employment of α-cationic phosphines in Au(I)- and Pt(II)-promoted hydroarylation and cycloisomerization reactions. These results seem to be general in π-acid catalysis when the nucleophile used is not especially electron rich because then their attack to the activated alkene or alkyne is normally rate determining. On the other hand, the use of cationic phosphines also presents drawbacks that limit their range of application. As a general rule, the reduced σ-donation from the phosphine is not compensated by the increased π-back-donation from the metal making the resulting phosphorus-metal bond weaker, and the corresponding catalysts more prone to decomposition. This can be critical when di- or tricationic ancillary ligands are used. In addition, the positively charged groups occasionally participate in undesired side reactions, with either the metal or the substrate, which are not present when their neutral congeners are used. Stimulated by both the fundamental questions regarding bonding and their valuable applications in catalysis, the chemistry of α-cationic phosphines has experienced an enormous growth during the last years. This Account describes our group's efforts and those of others to understand their coordination behavior, study their reactivity, and further develop their range of applications in catalysis.
Neutralizing Monoclonal Antibodies to Bovine Viral Diarrhoea Virus Bind to the 56K to 58K Glycoprotein (1988)

A panel of murine monoclonal antibodies (MAbs) against the two major glycoproteins of bovine viral diarrhoea virus (BDV) was produced and assayed by serum neutralization, radioimmunoprecipitation (RIP) and immunoblotting. Based on their viral polypeptide specificity and on their ability to neutralize viral infectivity, the MAbs in the panel were divided into three classes: Class 1 MAbs reacted with the 56K to 58K glycoprotein and neutralized the virus, class 2 MAbs recognized the 56K to 58K glycoprotein but were not neutralizing, and class 3 MAbs reacted with the 48K glycoprotein and did not neutralize the virus. These results identify the 56K to 58K protein as one of the envelope glycoproteins of BDV. Evidence was obtained indicating that it is responsible for the induction of neutralizing antibodies. No large uncleaved precursors of the 56K to 58K protein could be identified unequivocally by RIP of infected cell extracts, suggesting that this polypeptide is proteolytically processed cotranslationally. A subset of MAbs that reacted with BDV isolates of the noncytopathic biotypes yielded similar results, indicating that these findings are applicable to both biotypes of BDV.
Attracting, preparing, and retaining under-represented populations in rural and remote Alberta-North communities (2011)

<p>For several years, the government of the western Canadian province of Alberta has drafted policies and conducted research on the problem of populations under-represented in adult education. This Alberta-North and Athabasca University study, funded by the Alberta government’s Innovation Fund, uses the advice and educational experiences of northern former and present students, and of other community members, to identify ways of better attracting, preparing, and retaining under-represented populations in northern Alberta communities through provision and training in the use of distance delivery methods.</p><p>The research reported here commences with a review of the literature to investigate the following: 1) the contribution distance education makes globally to learning access in remote areas (and resulting economic growth for under-served populations); 2) how support is provided to retain isolated students; and 3) the help needed to assist remote students to complete distance programs. Community consultations with social service and education agencies in three communities were conducted in order to obtain their perspectives about what helps to attract and support students to educational programs and the barriers students typically encounter, which might be mitigated by distance methods. Finally, a survey was designed and distributed in 87 Alberta-North communities in northern Alberta and across Canada’s Northwest Territories to add perspective to the consultation results.</p>
Effect of <i>Mentha spicata</i> essential oil on chemical, microbial, and sensory properties of minced camel meat during refrigerated storage (2017)

Abstract The aim of the present study was incorporation of Mentha spicata essential oil (MSO) at three different concentrations (0.5, 1, and 1.5% vol/wt) into raw minced camel meat to extend shelf life and evaluate its antibacterial activity against Listeria monocytogenes for 12 days at refrigerated temperature. Final microbial population (total mesophilic and psychrotrophic bacteria, Pseudomonas spp., Enterobacteriaceae, and L. monocytogenes ) decreased approximately 1–4 log CFU/g in treated samples compared to control. The initial total volatile base nitrogen was 8.86 ± 0.33 mg/100 g and after 12 days reached to 39.2 ± 0.13 mg/100 g in control, while it was lower than 25 mg/100 g for treated samples with 1 and 1.5% MSO. At the end of storage time in control samples peroxide value reached to 2.57 ± 0.01 meq peroxide/1,000 g lipid, while the values for the treated samples remained lower than 2 meq peroxide/1,000 g lipid. Moreover, during 12 days of storage, odor, color and also appearance of the minced camel meat treated with 0.5% MSO were superior. Practical applications Today as people tend to consume natural foods due to health concerns, the use of natural preservatives such as essential oils is increasing. Around the different parts of Iran Mentha spicata plant is known as a popular flavoring ingredient in home food making. In the present study, M. spicata essential oil as a natural substance could successfully extend the shelf life and control Listeria monocytogenes in fresh minced camel meat stored at refrigerated temperature for 12 days of storage. M. spicata essential oil can be used as a replacement to synthetic preservatives as well as synthetic flavorings in minced camel meat.