gebhart/patrepeval huggingface dataset:
The amino acid sequence of the aliphatic amidase from <i>Pseudomonas aeruginosa</i> (1987)

Amino acid sequence studies show that the aliphatic amidase (EC 3.5.1.4) from Pseudomonas aeruginosa PAC142 consists of a single polypeptide chain of 346 residues, giving an Mr of 38,400. The evidence from the amino acid studies is in complete agreement with that deduced from the DNA sequence of the amiE gene. Studies of the protein from Pseudomonas putida A87 show that it differs from the Ps. aeruginosa protein by about 30 amino acid substitutions. It now becomes possible to relate changes in the enzyme which result in altered specificity to structural changes in the protein.
Research and design of a BCI system model based on SVM (2008)

Brain-Computer Interface(BCI) is a communication system that connects the brain with computer and peripheral equipments.Brain-computer interface system is a new kind of computer application systems,which provides a communication and control channel between human and external devices by using BCI,without the normal output channel of periphery nerve and muscular,to replace the body movement or language,in order to implement the communication and control with the outside world.In this paper,after introducing the BCI2000 system,a BCI system design method is demonstrated based on SVM as the pattern classification method.The model primarily completes the application of controlling the direction of the concur movement by the classification of imaginary left and right hand movements of EEG.
An effective algorithm for parallelizing hash joins in the presence of data skew (2002)

A parallel hash join algorithm based on the concept of hierarchical hashing is proposed to address the problem data skew. The proposed algorithm adds an extra scheduling phase to the usual hash and join phases. During the scheduling phase, a heuristic optimization algorithm, using the output of the hash phase, attempts to balance the load across the multiple processors in the subsequent join phase. The algorithm naturally identifies the hash partitions with the largest skew elements, splits them up, and assigns each of them to an optimal number of processors. Assuming a Zipf-like distribution of the elements in the join column, the algorithm is shown to achieve good load balancing for the join phase in a CPU-bound environment, and it is shown to be fairly robust relative to the degree of data skew and the total number of processors. The overall speedup due to this algorithm is compared with conventional parallel hash join methods and the considerable advantage of the proposed method is demonstrated even when the additional scheduling phase is taken into account.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A practical depth-of-interaction PET/MR detector with dichotomous-orthogonal-symmetry decoding (2015)

Conventional dual-end depth-of-interaction (DOI) PET detector readout requires two 2D SiPM arrays; with top and bottom SiPM reading the same pixel, there is information redundancy. We proposed a dichotomous-orthogonal-symmetric (DOS) dual-end DOI readout to eliminate this redundancy to significantly reduce SiPM usage, electronic channels, and heat load. Reflecting films are used within the scintillator array to channel light exiting the top along the X-direction, while light exiting the bottom is channeled along the orthogonal Y-direction. Despite the unidirectional channeling on each end, the top readout can provide X-Y information using two 1-D SiPM arrays; similarly, the bottom readout also provides X-Y information with two 1-D SiPM arrays. Thus four 1-D SiPM arrays (4xN) are used to decode XYZ to replace two 2D SiPM arrays (2NxN); SiPM usage is reduced from 2N**2 to 4N. Monte Carlo simulations (GATE) were carried out to study the XY decoding accuracy, energy resolution, and DOI resolution. Coupling the DOS-DOI design with a channel-decoding scheme, an array of 15x15 LSO (2.4x2.4x20 mm pixels) can be decoded by 18 SiPMs (2 rows of nine 3x3mm SiPM) on top and 18 SiPMs at bottom, thus achieving a 10X reduction in SiPM usage, electronic channels and heat load. For BGO detectors, an 88 array (2.42.420 mm pixels) can be achieved with 6.4X reduction. Simulations show 5-6mm DOI resolution, 0.45-0.96mm XY decoding blurring, 20-24% energy resolution. This study shows the feasibility of the DOS-DOI design. Even comparing to non-DOI detectors, there is a 5X/3X SiPM reduction for LSO/BGO. The proposed detector may yield practical ultrahigh-resolution PET/MR systems with depth-of-interaction with a production cost below current non-DOI systems.
Detection of Herpes Simplex Virus DNA in Serum and Oral Secretions during Acute Recurrent Herpes Labialis (2002)

Although herpes simplex virus (HSV) has been detected in the peripheral blood of immunocompromised patients and in neonates with disseminated disease, the extent to which the virus may be present in the blood during a localized infection in otherwise healthy patients is still unknown. Literature on patterns of HSV shedding into the oral cavity at the prodromal stage of the disease, during recurrences, and also during asymptomatic periods is still lacking. The present study aims at the detection of HSV DNA in the serum and oral secretions during acute herpes labialis using a highly sensitive technique, the polymerase chain reaction (PCR). The study included 10 patients with acute herpes labialis and five healthy controls. Using PCR, herpes simplex virus DNA was detected in the serum of seven patients (70%) and in the saliva of nine patients (90%). One of the control cases showed positive HSV DNA in the saliva (20%). There was good statistical agreement between the presence of HSV DNA in the serum and saliva. Frequency of attacks, patient's age, and gender had no statistically significant effect on the presence of the virus in serum or in saliva. It is concluded that HSV viremia during attacks of recurrent herpes simplex is more frequent than previously appreciated.
How many numbers are required to specify sequence‐dependent properties of polynucleotides? (1992)

Abstract There are 10 unique dinucleotides of double‐stranded DNA, but only 8 independent nearest‐neighbor energies that occur in circular DNA, as shown by D. M. Gray and I. Tinoco [(1970) Biopolymers 9 , 223–244]. We extend that analysis to include end effects, and show that the number of unique dinuoleotide pairs (including ends) is 14. but there are only 12 independent energies. We discuss how these 12 energies (or spectra or any other pairwise additive property) can be measured and displayed, and how they should and should not be compared between experimenters. As an example, we analyzed the recently reported melting curves [M. J. Doktycz et al. (1992) Biopolymers , 32 , 849–864] of 16 DNA dumbbells in two different Na + environments. This analysis reveals a new means for evaluating end effects and the emergence of longer than nearest‐neighbor interactions at low salt concentration. © 1992 John Wiley & Sons, Inc.
“One-Step” Detection of Matrix Metalloproteinase Activity Using a Fluorogenic Peptide Probe-Immobilized Diagnostic Kit (2010)

Matrix metalloproteinases (MMPs) have been shown to be abundant in pathological conditions such as cancer, osteoarthritis (OA), and rheumatoid arthritis (RA). The extent of MMPs detected in biological samples provides important clinical information for diagnosis, prognosis, and therapeutic monitoring of various diseases relating with MMPs. Herein, we developed a new high-throughput MMP diagnostic kit (MMP-D-KIT) based on a 96-well plate by immobilizing MMP-13 specific fluorogenic peptide probes (MMP peptide probe), which is a pair consisting of a near-infrared (NIR) fluorophore (Cy5.5) and a quencher (BHQ-3), onto the biocompatible glycol chitosan (GC) polymer anchored 96-well plate. When MMP enzymes were simply added and incubated in a MMP-D-KIT, the fluorescence of each well was recovered and the fluorescence intensity showed distinct difference within minutes through NIR fluorescence imaging system. The fluorescence was recovered not only by MMP-13 activity, but also by other MMPs activity. Furthermore, recovery of NIR fluorescent signals in MMP-D-KIT was proportional to concentrations of immobilized MMP peptide probe-GC conjugates and, importantly, MMP concentration. The MMP-D-KIT is most specific for target MMP, compared with other enzymes including caspase-3 and 20s proteasome. Additionally, the MMP-D-KIT was used to detect MMP activity in biological samples such as synovial fluid from 12 OA patients (grades 1-4 based on the Kellgren-Lawrence grading scale). It was found that the fluorescence intensity measured using MMP-D-KIT decidedly correlates with the progression of OA. The MMP-D-KIT could be applicable in detecting MMP activities in various biological samples and evaluating the effects of MMP inhibitors in a rapid and easy fashion.
Monitoring <i>PIK3CA</i> mutant allele fraction (AF) in cell-free DNA (cfDNA) in metastatic breast cancer (MBC) patients treated with PI3Kα–inhibitor plus letrozole (L) or exemestane (E). (2014)

517 Background: In tumors that harbor activating mutations, tumor-derived cfDNA extracted from patient plasma can be serially quantified by droplet digital PCR (ddPCR). Mutant AF may be predictive of target-directed therapy for initial response and evolving resistance. We report results of a correlative aim assessing serial mutant AF in a phase I study of a PI3Kα-inhibitor, BYL719, with L or E in MBC. Methods: PIK3CA status was mutant/wild-type/unknown in 8/5/1 pts as determined by molecular analysis of tumor. Plasma samples were collected at baseline and on day 1 of each 28 day cycle while on protocol. cfDNA was extracted using QIAamp Circulating NA kit and quantified by KAPA hgDNA qPCR. Allele specific assays for PIK3CA E542K, E545K, H1047R and H1047L mutations were designed for quantification on BioRad QX200 Droplet Digital PCR System. Mutant AF is determined from the counts for mutant as compared to wild-type. The detection limit for each assay is calculated from the number of events detected. All sample runs are replicated. Results: 5/8 pts with PIK3CA mutation were evaluable by ddPCR having received treatment for at least 2 cycles with the PI3Kα-inhibitor. In the plasma of 4 pts, we identified a brisk decrease in PIK3CA mutant AF at cycle 2, day 1(C2D1) ranging from 91.8 - 99.6% decrease from baseline. All 4 pts had stable or responding disease as best response. In 1 patient, later determined to have disease progression there was a small change (19% decrease) in PIK3CA mutant AF at C2D1 with a 16X increase in mutant AF at C3. Ongoing responses result in a persistent low (>98% decrease) or undetectable mutant allele. In 1 patient, with a transient response, the marked decrease in mutant AF at C2D1 was followed by an increase at C3 predicting her clinical progression. Conclusions: Targeted therapies directed towards specific oncogene mutations may be assessed serially by ddPCR to confirm mutant target sensitivity. Assessment for early tumor resistance may allow a more rapid treatment change with real-time monitoring of target mutant alleles. Serial assessment may be helpful in the exploration of best and better tolerated dosing schedules. Clinical trial information: NCT01870505.
Steering behaviour and control of fast wheeled robots (2002)

This paper is devoted to mechanical and control analysis of steering systems of fast wheeled robots. Steering performances are analysed by means of a formulation of a path-tracking control problem. The mechanical model takes into account the wheel-sliding and wheel-elasticity which are relevant to the steering behaviour. When the path is a straight line or a circular arc, the tracking offsets are small and the assigned velocity is constant, the proposed tracking scheme leads to a controller using direct state feedback and linear quadratic regulation approach. Four different steering ways are examined, they combine steer and drive actions on a four wheeled robots.
Tangle-Bearing Neurons Survive Despite Disruption of Membrane Integrity in a Mouse Model of Tauopathy (2009)

Neurofibrillary tangles (NFTs) are associated with neuronal loss and correlate with cognitive impairment in Alzheimer disease, but how NFTs relate to neuronal death is not clear. We studied cell death in Tg4510 mice that reversibly express P301L mutant human tau and accumulate NFTs using in vivo multiphoton imaging of neurofibrillary pathology, propidium iodide (PI) incorporation into cells, caspase activation, and DNA labeling. We first observed that in live mice, a minority of neurons were labeled with the caspase probe or with PI fluorescence. These markers of cell stress were localized in the same cells and appeared specifically within NFT-bearing neurons. Contrary to expectations, the PI-stained neurons did not die during a day of observation; the presence of Hoechst-positive nuclei in them on the subsequent day indicated that the NFT-associated membrane disruption, as suggested by PI staining, and caspase activation do not lead to immediate death of neurons in this tauopathy model. This unique combination of in vivo multiphoton imaging with markers of cell death and pathological alteration is a powerful tool for investigating neuronal damage associated with neurofibrillary pathology.
Development and validation of a particle-enhanced turbidimetric inhibition assay for urine albumin on the Dade aca® analyzer (1997)

The measurement of urine albumin now has a well-established role in the monitoring of patients with diabetes mellitus. We have developed a particle-enhanced immunoturbidimetric inhibition assay for urine albumin on the Dade aca analyzer. The inhibition approach removes any of the potential antigen excess difficulties that could be expected from the wide clinical range of urine albumin, but retains the sensitivity advantages of latex-enhanced immunoturbidimetry. Human serum albumin (HSA) is covalently attached to 40-nm poly(chloromethyl)styrene-modified latex particles. This reagent, along with monoclonal antibody to HSA, is aliquoted into the aca reagent pack along with polyethylene glycol 8000 in a tablet form (giving a final reaction concentration of 15 g/L). A 150 mmol/L phosphate buffer, pH 7.8, is used to fill the reagent pack in the instrument and the agglutination reaction is monitored at 340 nm. The sample volume is 100 microL and the calibration curve covers the range 2-250 mg/L. Evaluation of commercial scale reagents against the Beckman Array nephelometric immunoassay system gave a Deming regression correlation of aca = 0.87 x Beckman + 8.5, r = 0.995, n = 145. Mean analytical recovery was 104+/-4.5%, n = 20, and there was no evidence of a lack of parallelism. Interassay precision was 8.8% at 10.0 mg/L and <2.5% at >65 mg/L. Calibrator stability was in excess of 60 days. A small reference range study (24-h urine collections, n = 27) gave a mean of 5.6 mg/L with a range of 0.5-16.2 mg/L. Analytical sensitivity (2.5 SD from zero) was 0.40 mg/L.
Low-molecular-weight proteinuria in insulin-dependent diabetes mellitus: a study of the urinary excretion of beta 2-microglobulin and retinol-binding protein in alkalinized patients with and without microalbuminuria. (1989)

The urinary excretion of two low-molecular-weight proteins (beta 2-microglobulin and retinol-binding protein) was measured in 12 insulin-dependent diabetic patients with persistent microalbuminuria and an equal number with normal albumin excretion; reference ranges for the excretion of beta 2-microglobulin (beta 2M) and retinol-binding protein (RBP) were also obtained in 40 non-diabetic subjects. To ensure the stability of beta 2M in urine a urinary pH greater than or equal to 7 was achieved by giving oral sodium bicarbonate. beta 2M and RBP excretion was significantly higher in the diabetics than in the controls (p less than 0.01), but no higher in microalbuminuric than non-albuminuric diabetics. In the diabetics as a group a significant correlation was found between the excretion of beta 2M and RBP (r = 0.53, p less than 0.01), but more patients had an abnormal excretion of beta 2M than RBP (p less than 0.001). No significant correlation was found between the urinary excretion of either low-molecular-weight protein and duration of diabetes, insulin dose, HbA1, urinary glucose excretion or systemic blood pressure. Measured under appropriate alkaline conditions beta 2M appears to be more sensitive than RBP in detecting an abnormality of the renal proximal tubule which may be an early feature of diabetic renal involvement not characterized by microalbuminuria; microalbuminuria may have glomerular and tubular components.
Cost Projection of State of the Art Lithium-Ion Batteries for Electric Vehicles Up to 2030 (2017)

The negative impact of the automotive industry on climate change can be tackled by changing from fossil driven vehicles towards battery electric vehicles with no tailpipe emissions. However their adoption mainly depends on the willingness to pay for the extra cost of the traction battery. The goal of this paper is to predict the cost of a battery pack in 2030 when considering two aspects: firstly a decade of research will ensure an improvement in material sciences altering a battery’s chemical composition. Secondly by considering the price erosion due to the production cost optimization, by maturing of the market and by evolving towards to a mass-manufacturing situation. The cost of a lithium Nickel Manganese Cobalt Oxide (NMC) battery (Cathode: NMC 6:2:2 ; Anode: graphite) as well as silicon based lithium-ion battery (Cathode: NMC 6:2:2 ; Anode: silicon alloy), expected to be on the market in 10 years, will be predicted to tackle the first aspect. The second aspect will be considered by combining process-based cost calculations with learning curves, which takes the increasing battery market into account. The 100 dollar/kWh sales barrier will be reached respectively between 2020-2025 for silicon based lithium-ion batteries and 2025–2030 for NMC batteries, which will give a boost to global electric vehicle adoption.
Distributed Dynamic Spectrum Management for Digital Subscriber Lines (2007)

This paper investigates the dynamic spectrum management problem for digital subscriber lines. Two new distributed dynamic spectrum management algorithms, which improve upon the existing iterative water-filling algorithm, are proposed. Unlike the iterative water-filling algorithm, in which crosstalk interference is reduced by using adaptive power backoff, the new algorithms employ full power and mitigate crosstalk interference by shifting one user's spectrum away from the other's. Simulation results show that the new algorithms achieve significant performance gains over the iterative water-filling algorithm in mixed central office/remote terminal (CO/RT) deployment asymmetric digital subscriber line (ADSL) and upstream very-high bit-rate digital subscriber line (VDSL).
Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States (2013)

Together, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.
Outdoor Localization and Distance Estimation Based on Dynamic RSSI Measurements in LoRa Networks: Application to Cattle Rustling Prevention (2019)

In this paper, we propose an RSSI-based distance estimation scheme for localization of cattle collars communicating with long-range LoRa radios. Cattle localization is designed to prevent theft in livestock. The proposed solution decreases the cost of cattle localization by minimizing the number of collars with GPS and allows accurate localization of collars without GPS. We propose an RSSI-based distance estimation using realtime adjustment of RSSI-distance mapping, taking advantage of communication between collar nodes and gateway. Log-distance path-loss model is also used as a rescue when the map does not provide accurate correspondence. Experimentation results show the validity of the approach with highly accurate localization of non-GPS collars.
Once again on the Hieroglyphic Luwian sign *19 〈á〉 (2013)

The theory of Kloekhorst about the phonetic interpretation of the Hieroglyphic Luwian sign *19 〈á〉 as a glottal stop + a (etymologically matching Proto- Indo-European *h1) was seriously criticized by several scholars. This paper gives a critical assessment of the views published until now and provides additional evidence. It will be argued that evidence from seal inscriptions that use this - and only this sign - for the transcription of the glottal stop and present cases where only the assumption of a glottal stop leads to regular spellings confirm the interpretation as a glottal stop, which is further corroborated by Cuneiform Luwian and etymological evidence.
Effectiveness of hand hygiene teaching on knowledge and compliance of hand washing among the students at a selected school in Mugalivakkam village, Kancheepuram District (2014)

Background: One of the major health problems in our country is unsanitary conditions especially poor hand hygiene leads to a rigorous public health hazard to children in the school. Children are not aware of important of hand hygiene at school level. Health education is considered necessary for better knowledge.
Reactivity Relationships between Chiral Cyclic Amido and Imine Tungsten(II) Complexes (2006)

Reaction of [Tp‘W(CO)2(PhC⋮CMe)][OTf] (1) (Tp‘ = hydridotris(3,5-dimethylpyrazolyl)borate) with excess pyrrolidine affords the chiral tungsten(II) amido complex (2a). The corresponding η1-imine complex (3a) is prepared by oxidation of amido complex 2a with elemental iodine in the presence of base. The 2-methyl-1-pyrroline complex (3b) is synthesized directly by 2-methyl-1-pyrroline addition to the labile tungsten complex 1. Only one pair of enantiomers (SWRC/RWSC) of 2-methylpyrrolidine amido complex (2b) is detected when 2b is prepared by direct reaction of tungsten complex 1 with deprotonated 2-methylpyrrolidine. An alternative route to this amido complex is available through addition of MeMgBr to cationic imine complex 3a. In this case the same diastereomer predominates as in the ligand substitution route to 2b. The opposite diastereomer, SWSC/RWRC, is obtained as the major product of hydride addition to the cationic 2-methyl-1-pyrroline complex 3b. Deuteride addition to imine complex 3a yields the amido complex 2a-d1 with a high diastereoselectivity ratio as determined by 2H NMR. Protonation of amido complex 2a using [H(OEt2)2][BAr‘4] gives the cationic pyrrolidine complex (4a).
Glycosaminoglycan-degrading enzymes in porcine aortic heart valves: implications for bioprosthetic heart valve degeneration. (2003)

The combined action of active GAG-degrading enzymes and the failure of GA to stabilize GAGs towards enzymatic digestion may contribute significantly to bioprosthetic heart valve degeneration and subsequent structural failure.
Gearbox Modeling and Load Simulation of a Baseline 750-kW Wind Turbine Using State-of-the-Art Simulation Codes (2009)

This report discusses the causes for premature wind turbine gearbox failure and determining a method for revealing the missing loading conditions relevant to the gearbox design process.