gebhart/patrepeval huggingface dataset:
Experimental Protocol for Biodiesel Production with Isolation of Alkenones as Coproducts from Commercial <em>Isochrysis</em> Algal Biomass (2016)

The need to replace petroleum fuels with alternatives from renewable and more environmentally sustainable sources is of growing importance. Biomass-derived biofuels have gained considerable attention in this regard, however first generation biofuels from edible crops like corn ethanol or soybean biodiesel have generally fallen out of favor. There is thus great interest in the development of methods for the production of liquid fuels from domestic and superior non-edible sources. Here we describe a detailed procedure for the production of a purified biodiesel from the marine microalgae Isochrysis. Additionally, a unique suite of lipids known as polyunsaturated long-chain alkenones are isolated in parallel as potentially valuable coproducts to offset the cost of biodiesel production. Multi-kilogram quantities of Isochrysis are purchased from two commercial sources, one as a wet paste (80% water) that is first dried prior to processing, and the other a dry milled powder (95% dry). Lipids are extracted with hexanes in a Soxhlet apparatus to produce an algal oil ("hexane algal oil") containing both traditional fats (i.e., triglycerides, 46-60% w/w) and alkenones (16-25% w/w). Saponification of the triglycerides in the algal oil allows for separation of the resulting free fatty acids (FFAs) from alkenone-containing neutral lipids. FFAs are then converted to biodiesel (i.e., fatty acid methyl esters, FAMEs) by acid-catalyzed esterification while alkenones are isolated and purified from the neutral lipids by crystallization. We demonstrate that biodiesel from both commercial Isochrysis biomasses have similar but not identical FAME profiles, characterized by elevated polyunsaturated fatty acid contents (approximately 40% w/w). Yields of biodiesel were consistently higher when starting from the Isochrysis wet paste (12% w/w vs. 7% w/w), which can be traced to lower amounts of hexane algal oil obtained from the powdered Isochrysis product.
Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors (2017)

The oral microbiota plays a critical role in both local and systemic inflammation. Metabolic syndrome (MetS) is characterized by low-grade inflammation, and many studies have been conducted on the gut microbiota from stool specimens. However, the etiological role of the oral microbiota in the development of MetS is unclear. In this study, we analyzed the oral and gut microbiome from 228 subgingival plaque and fecal samples from a Korean twin-family cohort with and without MetS. Significant differences in microbial diversity and composition were observed in both anatomical niches. However, a host genetic effect on the oral microbiota was not observed. A co-occurrence network analysis showed distinct microbiota clusters that were dependent on the MetS status. A comprehensive analysis of the oral microbiome identified <i>Granulicatella</i> and <i>Neisseria</i> as bacteria enriched in subjects with MetS and <i>Peptococcus</i> as bacteria abundant in healthy controls. Validation of the identified oral bacteria by quantitative PCR (qPCR) showed that healthy controls possessed significantly lower levels of <i>G</i>. <i>adiacens</i> (<i>p</i> = 0.023) and a higher ratio of <i>Peptococcus</i> to <i>Granulicatella</i> (<i>p</i> < 0.05) than MetS subjects. Our results support that local oral microbiota can be associated with systemic disorders. The microbial biomarkers identified in this study would aid in determination of which individuals develop chronic diseases from their MetS and contribute to strategic disease management.
Perception-based Personalization of Hearing Aids using Gaussian Processes and Active Learning (2014)

Personalization of multi-parameter hearing aids involves an initial fitting followed by a manual knowledge-based trial-and-error fine-tuning from ambiguous verbal user feedback. The result is an often suboptimal HA setting whereby the full potential of modern hearing aids is not utilized. This article proposes an interactive hearing-aid personalization system that obtains an optimal individual setting of the hearing aids from direct perceptual user feedback. Results obtained with ten hearing-impaired subjects show that ten to twenty pairwise user assessments between different settings-equivalent to 5-10 min-is sufficient for personalization of up to four hearing-aid parameters. A setting obtained by the system was significantly preferred by the subject over the initial fitting, and the obtained setting could be reproduced with reasonable precision. The system may have potential for clinical usage to assist both the hearing-care professional and the user.
Production of Man5GlcNAc2-type sugar chain by the methylotrophic yeast<i>Ogataea minuta</i> (2006)

The methylotrophic yeast Ogataea minuta IFO 10746 was selected as a suitable strain for producing human-compatible glycoproteins by means of analyses of its cell-wall mannoproteins. First, the OmURA3 gene encoding an orotidine-5'-phosphate decarboxylase was cloned and disrupted to generate a host strain with a uracil auxotrophic marker. Second, both the promoters and the terminators from the OmAOX1 gene encoding an alcohol oxidase for an inducible promoter, or those from the OmTDH1 gene encoding a glyceraldehyde-3-phosphate dehydrogenase for a constitutive promoter, were isolated to construct an expression vector system for heterologous genes. Next, the OmOCH1 gene encoding a starting enzyme with alpha-1,6-mannosyltransferase activity to form a backbone of the N-linked outer sugar chain peculiar to yeast was disrupted, and an alpha-1,2-mannosidase gene from Aspergillus saitoi with an endoplasmic reticulum retention signal (HDEL) under the control of the OmAOX1 promoter was introduced to convert the sugar chain to Man5GlcNAc2 in O. minuta. As a result, we succeeded in breeding a new methylotrophic yeast, O. minuta, producing a Man5GlcNAc2-high-mannose-type sugar chain as a prototype of a human-compatible sugar chain. We also elucidate here the usefulness of the strategy for producing human-compatible sugar chains in yeast.
Evaluation of RGB, Color-Infrared and Multispectral Images Acquired from Unmanned Aerial Systems for the Estimation of Nitrogen Accumulation in Rice (2018)

Unmanned aerial system (UAS)-based remote sensing is one promising technique for precision crop management, but few studies have reported the applications of such systems on nitrogen (N) estimation with multiple sensors in rice (Oryza sativa L.). This study aims to evaluate three sensors (RGB, color-infrared (CIR) and multispectral (MS) cameras) onboard UAS for the estimation of N status at individual stages and their combination with the field data collected from a two-year rice experiment. The experiments were conducted in 2015 and 2016, involving different N rates, planting densities and rice cultivars, with three replicates. An Oktokopter UAS was used to acquire aerial photography at early growth stages (from tillering to booting) and field samplings were taken at a near date. Two color indices (normalized excess green index (NExG), and normalized green red difference index (NGRDI)), two near infrared vegetation indices (green normalized difference vegetation index (GNDVI), and enhanced NDVI (ENDVI)) and two red edge vegetation indices (red edge chlorophyll index (CIred edge), and DATT) were used to evaluate the capability of these three sensors in estimating leaf nitrogen accumulation (LNA) and plant nitrogen accumulation (PNA) in rice. The results demonstrated that the red edge vegetation indices derived from MS images produced the highest estimation accuracy for LNA (R2: 0.79–0.81, root mean squared error (RMSE): 1.43–1.45 g m−2) and PNA (R2: 0.81–0.84, RMSE: 2.27–2.38 g m−2). The GNDVI from CIR images yielded a moderate estimation accuracy with an all-stage model. Color indices from RGB images exhibited satisfactory performance for the pooled dataset of the tillering and jointing stages. Compared with the counterpart indices from the RGB and CIR images, the indices from the MS images performed better in most cases. These results may set strong foundations for the development of UAS-based rice growth monitoring systems, providing useful information for the real-time decision making on crop N management.
Properties of normal-dispersion femtosecond fiber lasers (2008)

We report a systematic study of all-normal-dispersion mode-locked fiber lasers. Spectral filtering of a chirped pulse in the cavity is a major component of the pulse shaping in these lasers. We identify the nonlinear phase shift accumulated by the pulse, spectral filter bandwidth, and group-velocity dispersion as the key parameters that determine the behavior and properties of these lasers. Trends in the performance as these parameters are varied are summarized. A wide range of pulse shapes and evolutions can occur. Experimental results from Yb-doped all-normal-dispersion fiber lasers agree reasonably well with the results of numerical simulations.
Evidence that blood pressure reduction by serotonin antagonists is related to alpha receptor blockade in spontaneously hypertensive rats. (1983)

In vitro affinity for vascular 5HT2 and alpha receptors was determined for several compounds (spiperone, ketanserin, mianserin, trazodone, mepiprazole, benzoctamine, m-trifluoro-methylphenylpiperazine, m-chlorophenylpiperazine, and 1-(1-naphthyl)piperazine) known to interact with serotonin receptors. All compounds competitively inhibited 5HT2 and alpha receptors with differing degrees of selectively. Based on these observations, ketanserin, benzoctamine, and 1(1-naphthyl)piperazine were evaluated as antihypertensive agents in spontaneously hypertensive rats (SHR). Of these compounds, 1-(1-naphthyl)piperazine was a highly selective 5HT2 receptor antagonist with a ratio of 5HT2 to alpha receptor affinity of greater than 2000. The ratio of 5HT2 to alpha receptor affinity for ketanserin and benzoctamine was 63 and 16, respectively. However, the order of affinity toward 5HT2 receptors was ketanserin greater than 1-(1-naphthyl)piperazine greater than benzoctamine whereas the order of affinity toward alpha receptors was ketanserin greater than benzoctamine greater than 1-(1-naphthyl)piperazine. A similar order of potency toward both 5HT2 and alpha receptors was found in pithed SHR based on antagonism of the pressor response to serotonin and methoxamine, respectively. In the SHR, maximum blood pressure reduction at a dose of 10 mg/kg i.p. was approximately 65 and 30 mm Hg for ketanserin and benzoctamine, respectively; 1-(1-naphthyl)piperazine did not affect blood pressure. Thus, blood pressure reduction more closely paralleled the in vitro and in vivo potency of these agents toward vascular alpha rather than 5HT2 receptors.(ABSTRACT TRUNCATED AT 250 WORDS)
Innovative Peritoneal Dialysis (1999)

As the peritoneal dialysis (PD) patient's residual renal function declines, the dialysis dose must be increased. However, the options for increasing the dose are limited to increasing the number of exchanges and/or the volume of each exchange. A review of the literature indicates that the dialysis dose can be significantly increased by flow-through PD, wherein the dialysate flows continuously into the peritoneal cavity through one catheter and out another and/or by regenerating the spent dialysate, thereby, significantly increasing the dialysate flow rate. Flow-thru PD has been used with and without dialysate regeneration. Regeneration has been used with standard inflow/outflow PD. In nearly all cases, substantially increased clearances over standard PD were obtained with reported urea and creatinine clearances as high as 58 and 48 ml/min, respectively. Applying flow-thru to the PD patient would require two catheters or a dual lumen catheter, and to obtain optimum clearances, the dialysate should be pumped through the peritoneal cavity at a high flow rate. Regenerating the dialysate allows high dialysate flow rates while reducing the total amount of dialysate required. For the continuous ambulatory peritoneal dialysis (CAPD) patient, the unit would have to be wearable; whereas for the patient on automated PD, flow-thru and/or regeneration PD could be incorporated into the equipment. With sorbent regeneration, the protein in the spent PD could be purified and returned to the patient thereby minimizing protein loss, increasing ultrafiltration, and enhancing the removal of protein-bound metabolic toxins.
Multipoint diffraction strain sensor: an add-on to moire interferometer (2006)

Multipoint Diffraction Strain Sensor has been developed based on a normal moire interferometer, with the novel feature of whole field strain determination, along with the possibility of rotation and tilt determination. This unique feature has been implemented by simultaneous tracking of sampled wavefront diffracted from the component under test. In this sensor a high-frequency diffraction grating is bonded on the specimen, which is illuminated by two symmetric collimated laser beams, as in a typical moire interferometer. The first orders of diffracted beams impinge on a CCD camera, via a microlens array. The lens array serves a dual purpose - to sample the diffracted wavefront and to focus the wavefront to a number of spots on the CCD. The deviation of the individual spots generated by both of the beams is directly proportional to the normal strain and a component of the shear strain. Simultaneous strain measurement at more than a thousand points can be readily obtained and is demonstrated. This novel technique is expected to be very valuable in numerous industrial metrology applications.
Bilayer Segmentation of Live Video (2006)

This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs nonmotion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing groundtruth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Foreground/ background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video.
<title>Three-dimensional vision system for peanut pod maturity</title> (1991)

A machine vision system was designed. for determining the peanut pod ripeness color after the outer hull layer of the pod had been removed. Pods were fed from a vibratory bowl feeder through a singulation chute to a measurement chamber where they entered free-fall. An IR detector sensed the presence of the peanut pod leaving the singulation chute and triggered a B/W CCD camera to capture the image. A ring strobe surrounding the camera lens illuminated the peanut. Algorithms were developed to determine the pod ripeness color for three views of the pod. 1.
Distinct roles for the small GTPases Cdc42 and Rho in endothelial responses to shear stress (1999)

Shear stress, the tangential component of hemodynamic forces, plays an important role in endothelial remodeling. In this study, we investigated the role of Rho family GTPases Cdc42 and Rho in shear stress-induced signal transduction and cytoskeleton reorganization. Our results showed that shear stress induced the translocation of Cdc42 and Rho from cytosol to membrane. Although both Cdc42 and Rho were involved in the shear stress-induced transcription factor AP-1 acting on the 12-O-tetradecanoyl-13-phorbol-acetate-responsive element (TRE), only Cdc42 was sufficient to activate AP-1/TRE. Dominant-negative mutants of Cdc42 and Rho, as well as recombinant C3 exoenzyme, attenuated the shear stress activation of c-Jun NH2-terminal kinases (JNKs), suggesting that Cdc42 and Rho regulate the shear stress induction of AP-1/TRE activity through JNKs. Shear stress-induced cell alignment and stress fiber formation were inhibited by the dominant-negative mutants of Rho and p160ROCK, but not by the dominant-negative mutant of Cdc42, indicating that the Rho-p160ROCK pathway regulates the cytoskeletal reorganization in response to shear stress.
In Vitro and in Vivo Models of Cartilage Injury (2001)

D'Lima, Darryl D. MD; Hashimoto, Sanshiro MD; Chen, Peter C. PhD; Lotz, Martin K. MD; Colwell, Clifford W. Jr. MD Author Information
AMBIQUAL - a full reference objective quality metric for ambisonic spatial audio (2018)

Streaming spatial audio over networks requires efficient encoding techniques that compress the raw audio content without compromising quality of experience. Streaming service providers such as YouTube need a perceptually relevant objective audio quality metric to monitor users' perceived quality and spatial localization accuracy. In this paper we introduce a full reference objective spatial audio quality metric, AMBIQUAL, which assesses both Listening Quality and Localization Accuracy. In our solution both metrics are derived directly from the B-format Ambisonic audio. The metric extends and adapts the algorithm used in ViSQOLAudio, a full reference objective metric designed for assessing speech and audio quality. In particular, Listening Quality is derived from the omnidirectional channel and Localization Accuracy is derived from a weighted sum of similarity from B-format directional channels. This paper evaluates whether the proposed AMBIQUAL objective spatial audio quality metric can predict two factors: Listening Quality and Localization Accuracy by comparing its predictions with results from MUSHRA subjective listening tests. In particular, we evaluated the Listening Quality and Localization Accuracy of First and Third-Order Ambisonic audio compressed with the OPUS 1.2 codec at various bitrates (i.e. 32, 128 and 256, 512kbps respectively). The sample set for the tests comprised both recorded and synthetic audio clips with a wide range of time-frequency characteristics. To evaluate Localization Accuracy of compressed audio a number of fixed and dynamic (moving vertically and horizontally) source positions were selected for the test samples. Results showed a strong correlation (PCC=0.919; Spearman=0.882 regarding Listening Quality and PCC=0.854; Spearman=0.842 regarding Localization Accuracy) between objective quality scores derived from the B-format Ambisonic audio using AMBIQUAL and subjective scores obtained during listening MUSHRA tests. AMBIQUAL displays very promising quality assessment predictions for spatial audio. Future work will optimise the algorithm to generalise and validate it for any Higher Order Ambisonic formats.
Synthesis by Spray Pyrolysis of Mesoporous NbRu<sub><i>y</i></sub>O<sub><i>z</i></sub> as Electrocatalyst Supports in Fuel Cells (2009)

In this study, spray pyrolysis was used to produce two mesoporous powders, niobium oxide and niobium oxide with 12% ruthenium (by weight, metal basis, based on precursor mixture), as potential catalytic supports in fuel cells. Niobium oxide and ruthenium-modified niobium oxide powders displayed spherical particle morphology with internal mesoporosity introduced by surfactant templating, providing surface areas as high as 183 and 167 m2/g, respectively, after postprocessing that included an acid etch and calcination. The incorporation of ruthenium into niobium oxide, coupled with appropriate postsynthesis treatment, resulted in a material with electrical resistance that was reduced by roughly 5 orders of magnitude relative to unmodified niobium oxide. The structure and properties of these two materials subject to different postprocessing treatments were extensively characterized, and dynamic factors related to aerosol and subsequent thermal processing of these materials are discussed. Cyclic voltammetry showed that the ruthenium-modified material possessed activity for methanol oxidation in a basic environment.
Composition and Potency Characterization of Mycobacterium avium subsp. paratuberculosis Purified Protein Derivatives (2016)

Mycobacterium avium subsp. paratuberculosis (MAP) purified protein derivatives (PPDs) are immunologic reagents prepared from cultured filtrates of the type strain. Traditional production consists of floating culture incubation at 37°C, organism inactivation by autoclaving, coarse filtration, and protein precipitation. Three traditional production PPDs were used in this study including lot 9801, which served as a reference and has been used in the field for decades. Alternative production PPDs (0902A and 0902B), in which the autoclaving step was removed, were also analyzed in this study. SDS-PAGE analysis revealed protein smearing in traditional PPDs, but distinct bands were observed in the alternative PPD preparations. Antibody bound distinct protein bands in the alternative PPDs by immunoblot analysis, whereas an immunoreactive smear was observed with the traditional PPDs. Mass spectrometry identified 194 proteins among three PPD lots representing the two different production methods, ten of which were present in all PPDs examined. Selected proteins identified by mass spectrometry were recombinantly expressed and purified from E. coli and evaluated by the guinea pig potency test. Seven recombinant proteins showed greater erythema as compared to the reference PPD lot 9801 in paired guinea pigs and were able to stimulate interferon-gamma production in blood from Johne's positive animals. These results suggest that autoclaving culture suspensions is not a necessary step in PPD production and specific proteins could supplant the PPD antigen for intradermal skin testing procedures and for use as in-vitro assay reagents.
Improving the Stability and Catalyst Lifetime of the Halogenase RebH By Directed Evolution (2014)

We previously reported that the halogenase RebH catalyzes selective halogenation of several heterocycles and carbocycles, but product yields were limited by enzyme instability. Here, we use directed evolution to engineer an RebH variant, 3-LR, with a Topt over 5 °C higher than that of wild-type, and 3-LSR, with a Tm 18 °C higher than that of wild-type. These enzymes provided significantly improved conversion (up to fourfold) for halogenation of tryptophan and several non-natural substrates. This initial evolution of RebH not only provides improved enzymes for immediate synthetic applications, but also establishes a robust protocol for further halogenase evolution.