gebhart/patrepeval huggingface dataset:
A novel peptide inhibits the influenza virus replication by preventing the viral attachment to the host cells (2009)

Avian influenza viruses (AIV), the causative agent of avian flu or bird flu, cause widespread morbidity and mortality in poultry. The symptoms of the disease range from mild flu like symptoms to death. These viruses possess two important surface glycoproteins, namely hemagglutinin (HA) and neuraminidase (NA) against which neutralizing antibodies are produced. Due to the highly mutative nature of the genes which encode these proteins, the viruses often confer resistance to the current anti-viral drugs making the prevention and treatment of infection challenging. In our laboratory, we have recently identified a novel anti-viral peptide (P1) against the AIV H9N2 from a phage displayed peptide library. This peptide inhibits the replication of the virus in ovo and in vitro by its binding to the HA glycoprotein. In the current study, we demonstrate that the peptide inhibits the virus replication by preventing the attachment to the host cell but it does not have any effect on the viral fusion. The reduction in the viral nucleoprotein (NP) expression inside the host cell has also been observed during the peptide (P1) treatment. This novel peptide may have the potential to be developed as a therapeutic agent for the treatment and control of avian influenza virus H9N2 infections.
Motor recovery monitoring in post acute stroke patients using wireless accelerometer and cross-correlation (2013)

Stroke is a major reason for physical immobility and death. For effective treatment of stroke, early diagnosis and aggressive medication in the form of thrombolytic drugs is shown to be essential. In order to provide proper care, the patient should be kept under continuous monitoring during the first few hours after subjecting thrombolytic drugs and based on the response of the patient to the medication, line of treatment should be changed. In our previous work [1], we have shown the proof of principle by monitoring the motor activity of the stroke patient using accelerometer fitted on patient's arms. Based on preliminary analysis, we proposed methods using resultant acceleration signal and showed its effectiveness in predicting National Institute of Health Stroke Scale (NIHSS) stroke index. In this paper, novel technique based on cross-correlation of accelerometer values along different axes is developed for predicting the NIHSS index. An overall increase in prediction accuracy by over 7% compared to the earlier method is obtained. A multi-class support vector machine (SVM) classifier for cross correlation features is also designed and an overall prediction accuracy of 93% is achieved.
Dual monoclonal antibody immunoassay for free prostate‐specific antigen (1996)

Prostate-specific antigen (PSA) is the most important tumor marker for early detection and monitoring of prostate cancer (PCa) patients. PSA is also elevated in many patients with benign prostatic hyperplasia (BPH). The study of the serum PSA forms, free PSA (f-PSA) and PSA complexed with α1-antichymotrypsin (PSA-ACT), may improve the discrimination between PCa and BPH. An immunoassay specific for f-PSA is reported with very low cross-reactivity (0.7%) to PSA-ACT. Serum specimens from BPH and PCa patients (determined by biopsy) with PSA levels from <1 to >100 ng/ml were tested. No f-PSA was detected in serum specimens from normal females (N = 50). Low levels (0–0.3 ng/ml) were detected in specimens from healthy males (N = 60). In specimens from PCa and BPH patients, the f-PSA to total PSA ratio (f/t) was found to range from 1% to higher than 60%. While maintaining an 80% sensitivity for cancer, the f/t ratio improved specificity to approximately 80%, as compared to 55% for total PSA alone. The receiver operating characteristics (ROC) curve analysis of the f/t ratio displayed a greater area under the plot (0.84) compared to total PSA alone (0.745). The results demonstrate that the f/t ratio significantly increases specificity for PCa detection compared to total PSA alone, showing the potential clinical value of the f-PSA immunoassay. © 1996 Wiley-Liss, Inc.
DEVELOPMENT OF NONLINEAR HARMONIC SENSORS FOR DETECTION OF MECHANICAL DAMAGE (2004)

In a joint effort with Tuboscope Pipeline Services of Houston, Texas, Southwest Research Institute (SwRI) adapted its nonlinear harmonic (NLH) sensing technology for use on a new in-line inspection system (smart pig). Nonlinear harmonics, an AC magnetic method for detecting local anomalies of stress and plastic deformation, shows promise of improved characterization of mechanical damage defects such as gouged dents, even though the dents may have re-rounded. The SwRI-Tuboscope project produced a sensor design, electronic design, and sensor suspension design that are directly adaptable to a multitechnology ILI system. This report describes the NLH method, the sensor, circuit, and suspension designs, and shows results from the supporting laboratory work.
A New Performance Evaluation Metric for Radio Resource Management in Wireless Local Area Networks (2016)

In this paper, we propose Access Point Channel Capacity (ACC) as a Key Performance Indicator (KPI) for Radio Resource Management (RRM) algorithms in 802.11 Wireless Local Area Networks (WLANs). Introducing such a KPI is important especially for performance evaluation of 802.11 WLAN Self Organizing Networks (SON). ACC is a low complexity KPI that provides accurate per-AP estimate of the MAC layer potential throughput in the WLAN. The advantage of the proposed metric is that it can be derived directly from network statistics collected periodically from the access points. ACC is a vendor agnostic KPI since the required statistics are widely supported by all AP vendors and also TR-069 data model.
All-optical programmable shaping of narrow-band nanosecond pulses with picosecond accuracy by use of adapted chirps and quadratic nonlinearities (2001)

We experimentally demonstrate pure optical pulse picosecond shaping of narrow-bandwidth nanosecond pulses. The method used is based on the manipulation in the spectral domain of strongly chirped femtosecond pulses and on the use of either frequency addition or frequency difference.
Characterization of arbitrary femtosecond pulses using frequency-resolved optical gating (1993)

The frequency-resolved optical gating (FROG) technique for characterizing and displaying arbitrary femtosecond pulses is presented. The method is simple, general, broadband, and does not require a reference pulse. Using virtually any instantaneous nonlinear-optical effect, FROG involves measuring the spectrum of the signal pulse as a function of the delay between two input pulses. The resulting trace of intensity versus frequency and delay is related to the pulse's spectrogram a visually intuitive transform containing time and frequency information. It is proven using phase retrieval concepts that the FROG trace yields the full intensity I(t) and phase phi (t) of an arbitrary ultrashort pulse with no physically significant ambiguities. FROG appears to have temporal resolution limited only by the response of the nonlinear medium. The method is demonstrated by using self-diffraction through the electronic Kerr effect in BK-7 glass and 620-nm, linearly chirped, approximately 200-fs pulses of a few microjoules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On the Performance of a Simple Adaptive Relaying Protocol for Wireless Relay Networks (2008)

Distributed coding has been shown to be an effective scheme to explore cooperative spatial diversity in wireless relay networks. To date, the distributed coding schemes employ two major relaying protocols, decode and forward (DAF) and amplify and forward (AAF). They suffer from a disadvantage of either noise amplification or error propagation. In this paper, we propose a simple adaptive relaying protocol (ARP) for general relay networks. For the proposed approach, all relays are included into one of two relay groups, referred to as a DAF relay group and an AAF relay group. All relays, which decode correctly, are included in the DAF relay group, and other relays, which could not decode correctly, are included in the AAF relay group. Performance analysis of the proposed adaptive relaying protocol is carried out, and compared with other relaying protocols. It is shown that the proposed adaptive relaying protocol benefits from a significant coding gain contributed from the DAF relay group compared to a pure AAF relay protocol and simultaneously circumvent the detrimental effects of error propagation due to the imperfect decoding at relays in a DAF relay protocol, thus always outperforming both the AAF and DAF relaying protocols in all SNR regions.
Novel dental imaging using simultaneous photothermal radiometry and luminescence (2002)

Frequency-domain infrared photothermal radiometry is introduced as a dynamic dental diagnostic tool and its main features are compared with conventional laser luminescence for quantifying sound and defective (cracked) enamel or dentin. A high-spatial-resolution dynamic experimental imaging set-up, which can provide simultaneous measurements of laser-induced frequency-domain infrared photothermal radiometric and luminescence signals from defects in teeth, has been developed.
Simultaneous Analysis of Hop Bittering Components by High-Performance Liquid Chromatography. III. Development of On-Line Sample Enrichment by Precolumn Switching (1987)

A fully automated method based on on-line sample enrichment by precolumn switching was developed for determination of the nine main hop bittering components in wort and beer. A combination of two columns was used: a tetramethylolmethanetriacrylate type for trapping and an octadecylated silica type for final separation. The on-line method was compared with the conventional method based on off-line sample enrichment (liquid-liquid extraction and concentration). Both methods showed nearly the same product recoveries for iso-α-acids, α-acids, and β-acids. This sample enrichment method—an automated high-performance liquid chromatography system—is distinguished by simple, rapid operation and by good reproducibility, and it is eminently suited for automated routine analysis in the brewery. This method was semiautomatically applied to the determination of hop bittering components in hops and hop products.
Erbium-Doped Fiber Amplifiers and the Next Generation of Lightwave Systems (1992)

Erbium-doped fiber amplifiers (EDFAs) promise to revolutionize lightwave technology, lowering system costs while enhancing network performance and reliability. The high gain (G > 40 decibels), high output power (P > 100 milliwatts), and near-ideal noise performance achieved by EDFAs, which operate in the 1550-nanometer telecommunications window, have been unparalleled by any competing amplifier technology. EDFAs are inherently fiber compatible, insensitive to polarization effects, and immune to crosstalk among wavelength-multiplexed channels. These remarkable attributes, and the ease with which they can be realized, have propelled EDFAs from their discovery in the research laboratory to commercial availability in less than three years. EDFAs may be used as power amplifiers to boost transmitter power, optical repeaters to amplify weak signals, and optical preamplifiers to increase receiver sensitivity. The success of EDFA system experiments and the decision to use EDFAs as repeaters in the next generation of transoceanic submarine lightwave systems demonstrate the practical benefits of EDFAs and their potential in future lightwave systems.
Induction of antibodies against seasonal allergy in foals by a novel peptide (2013)

Equine recurrent airway obstruction (RAO) is a type‐I immediate hypersensitivity response involving reaginic antibodies (IgE and IgG). Normally horses are protected from airway inflammation by secretoglobulins secreted by Clara Cells in airway epithelium. A peptide with 21 amino acids was developed from equine Clara Cell protein (CC10) and the objective of the study was to investigate the peptide's ability to induce antibody production in Shetland pony foals. The peptide has homology to common environmental allergens. The study was approved by IACUC of LSU. The age of the foals ranged from 4–6 months. The peptide was covalently conjugated with a large carrier protein, Keyhole Limpet Hemocyanin (KLH) and administered to one foal subcutaneously at a dose of 0.1 mg/kg body weight. Two more foals were given the conjugated peptide with an equal volume of Freund's incomplete adjuvant (IFA). Five ml of blood was collected before the injection of the peptide and post injection weekly for 42 days. The results of blood analysis indicated that the antibody titer increased exponentially with time in foals that received conjugated peptide with IFA. This finding suggests that the peptide has the potential to be used as a vaccine against seasonal allergic diseases such as RAO. The study was supported by funding from Equine Health Studies Program of LSU‐SVM.
Comparison of techniques of acoustically interrogating a fluid-filled pipe. (2010)

Through-transmission of sound in a fluid-filled pipe was experimentally investigated, with comparison to a one dimensional computational model. Pipe curvature is shown to be a contributor to deviations from the model, as is dynamical interaction between the finitely yielding pipe walls and the fluid contents. Various techniques of acoustically interrogating the system are considered. These include the different information which may be extracted via continuous-wave acoustical excitation, swept-frequency interferometry, and tone- and chirp-burst excitations. Each of these techniques has their advantages and disadvantages, especially in situations where short-time measurements must be made, and a version of the gain-bandwidth product must be taken into account. Some algorithms for automatically extracting fluid sound-speed are discussed, and it is shown that no one dominates under all circumstances. [This work was supported by Chevron USA.]
Monoclonal Antibodies for Combating Synthetic Opioid Intoxication (2019)

Opioid abuse in the United States has been declared a national crisis and is exacerbated by an inexpensive, readily available, and illicit supply of synthetic opioids. Specifically, fentanyl and related analogues such as carfentanil pose a significant danger to opioid users due to their high potency and rapid acting depression of respiration. In recent years these synthetic opioids have become the number one cause of drug-related deaths. In our research efforts to combat the public health threat posed by synthetic opioids, we have developed monoclonal antibodies (mAbs) against the fentanyl class of drugs. The mAbs were generated in hybridomas derived from mice vaccinated with a fentanyl conjugate vaccine. Guided by a surface plasmon resonance (SPR) binding assay, we selected six hybridomas that produced mAbs with 10<sup>-11</sup> M binding affinity for fentanyl, yet broad cross-reactivity with related fentanyl analogues. In mouse antinociception models, our lead mAb (6A4) could blunt the effects of both fentanyl and carfentanil in a dose-responsive manner. Additionally, mice pretreated with 6A4 displayed enhanced survival when subjected to fentanyl above LD<sub>50</sub> doses. Pharmacokinetic analysis revealed that the antibody sequesters large amounts of these drugs in the blood, thus reducing drug biodistribution to the brain and other tissue. Lastly, the 6A4 mAb could effectively reverse fentanyl/carfentanil-induced antinociception comparable to the opioid antagonist naloxone, the standard of care drug for treating opioid overdose. While naloxone is known for its short half-life, we found the half-life of 6A4 to be approximately 6 days in mice, thus monoclonal antibodies could theoretically be useful in preventing renarcotization events in which opioid intoxication recurs following quick metabolism of naloxone. Our results as a whole demonstrate that monoclonal antibodies could be a desirable treatment modality for synthetic opioid overdose and possibly opioid use disorder.
Performance of a Catalyzed Diesel Particulate Filter System During Soot Accumulation and Regeneration (2003)

<div class="htmlview paragraph">The trapping and regeneration behaviors of a diesel particulate filter (DPF), including particle size, are examined via engine dynamometer testing. The exhaust system consists of two active lean NO<sub>x</sub> (ALN) catalysts in series followed by a catalyzed DPF. Forced regenerations are accomplished by injecting diesel fuel into the exhaust in front of the ALN catalysts to generate an exotherm sufficient to induce soot oxidation. Results are reported for two diesel fuels, one with 340 ppm sulfur, and the other with 4 ppm sulfur, and as a function of DPF regeneration temperature. The results show the DPF to be very effective at removing particulate matter, &gt;99% efficiency. The &lt;1% of particles that escape trapping exhibit a size distribution very similar to engine out soot. During regeneration, particle emissions remain well below engine out levels for the low sulfur fuel, but exhibit a temporary nucleation mode of about ten times the engine out level for the high sulfur fuel. The regeneration rate increases exponentially with temperature, and the fastest regenerations suffer the lowest fuel economy penalty.</div>
Genetic and pharmacological evidence for more than one human steroid 5 alpha-reductase. (1992)

The enzyme steroid 5 alpha-reductase catalyzes the conversion of testosterone into the more potent androgen, dihydrotestosterone, and impairment of this reaction causes a form of male pseudohermaphroditism in which genetic males differentiate predominantly as phenotypic females. We previously isolated cDNA clones that encode a human steroid 5 alpha-reductase enzyme. Here, we report molecular and genetic studies demonstrating that the gene encoding this cDNA is normal in subjects with the genetic disease steroid 5 alpha-reductase deficiency. We further show that in contrast to the major steroid 5 alpha-reductase in the prostate and cultured skin fibroblasts, the cDNA-encoded enzyme exhibits a neutral to basic pH optima and is much less sensitive to inhibition by the 4-aza steroid, finasteride (MK-906). The results provide genetic, biochemical, and pharmacological support for the existence of at least two steroid 5 alpha-reductase isozymes in man.
<i>n</i>-indium tin oxide/<i>p</i>-indium phosphide solar cells (1977)

n-indium tin oxide/p-indium phosphide (n-ITO/p-InP) solar cells have been prepared by ion-beam deposition of indium tin oxide on p-InP single-crystal substrates. The cells have a solar power conversion efficiency of 14.4% at air mass 2 (AM2) when provided with antireflection coatings.
Expression of the antiapoptotic baculovirus p35 gene in tomato blocks programmed cell death and provides broad-spectrum resistance to disease (2002)

The sphinganine analog mycotoxin, AAL-toxin, induces a death process in plant and animal cells that shows apoptotic morphology. In nature, the AAL-toxin is the primary determinant of the Alternaria stem canker disease of tomato, thus linking apoptosis to this disease caused by Alternaria alternata f. sp. lycopersici. The product of the baculovirus p35 gene is a specific inhibitor of a class of cysteine proteases termed caspases, and naturally functions in infected insects. Transgenic tomato plants bearing the p35 gene were protected against AAL-toxin-induced death and pathogen infection. Resistance to the toxin and pathogen co-segregated with the expression of the p35 gene through the T3 generation, as did resistance to A. alternata, Colletotrichum coccodes, and Pseudomonas syringae pv. tomato. The p35 gene, stably transformed into tomato roots by Agrobacterium rhizogenes, protected roots against a 30-fold greater concentration of AAL-toxin than control roots tolerated. Transgenic expression of a p35 binding site mutant (DQMD to DRIL), inactive against animal caspases-3, did not protect against AAL-toxin. These results indicate that plants possess a protease with substrate-site specificity that is functionally equivalent to certain animal caspases. A biological conclusion is that diverse plant pathogens co-opt apoptosis during infection, and that transgenic modification of pathways regulating programmed cell death in plants is a potential strategy for engineering broad-spectrum disease resistance in plants.
Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma (2021)

In the field of circulating cell-free DNA, most of the studies have focused on short DNA molecules (e.g., <500 bp). The existence of long cell-free DNA molecules has been poorly explored. In this study, we demonstrated that single-molecule real-time sequencing allowed us to detect and analyze a substantial proportion of long DNA molecules from both fetal and maternal sources in maternal plasma. Such molecules were beyond the size detection limits of short-read sequencing technologies. The proportions of long cell-free DNA molecules in maternal plasma over 500 bp were 15.5%, 19.8%, and 32.3% for the first, second, and third trimesters, respectively. The longest fetal-derived plasma DNA molecule observed was 23,635 bp. Long plasma DNA molecules demonstrated predominance of A or G 5' fragment ends. Pregnancies with preeclampsia demonstrated a reduction in long maternal plasma DNA molecules, reduced frequencies for selected 5' 4-mer end motifs ending with G or A, and increased frequencies for selected motifs ending with T or C. Finally, we have developed an approach that employs the analysis of methylation patterns of the series of CpG sites on a long DNA molecule for determining its tissue origin. This approach achieved an area under the curve of 0.88 in differentiating between fetal and maternal plasma DNA molecules, enabling the determination of maternal inheritance and recombination events in the fetal genome. This work opens up potential clinical utilities of long cell-free DNA analysis in maternal plasma including noninvasive prenatal testing of monogenic diseases and detection/monitoring of pregnancy-associated disorders such as preeclampsia.
A Novel Recurrent Neural Network Architecture for Classification of Atrial Fibrillation Using Single-lead ECG (2019)

Atrial Fibrillation (AF) is a type of abnormal heart rhythm which may lead to a stroke or cardiac arrest. In spite of numerous research works, developing an automatic mechanism for accurate detection of AF remains a popular yet unsolved problem. In this paper, we propose a deep neural network architecture for classification of AF using single-lead Electrocardiogram (ECG) signals of short duration. We define a novel Recurrent Neural Network (RNN) structure, comprising two Long-Short Term Memory (LSTM) networks for temporal analysis of RR intervals and PR intervals in an ECG recording. Output states of the two LSTMs are merged at the dense layer along with a set of hand-crafted statistical features, related to the measurement of heart rate variability (HRV). The proposed architecture is proven on the open access PhysioNet Challenge 2017 dataset, containing more than 8500 single-lead ECG recordings. Results show that our methodology yields sensitivity of 0.93, specificity of 0.98 and F1-score of 0.89 in classifying AF, which is better than the existing accuracy scores, reported on the dataset.
Paper-based rapid detection of pork and chicken using LAMP–magnetic bead aggregates (2016)

Magnetic beads (MBs) have been widely used for DNA quantification.