gebhart/patrepeval huggingface dataset:
Biosynthesis and Characterization of Poly(3-hydroxydodecanoate) by β-Oxidation Inhibited Mutant of Pseudomonas entomophila L48 (2011)

A medium-chain-length (MCL) polyhydroxyalkanoates (PHAs) producer Pseudomonas entomophila L48 was investigated for microbial production of 3-hydroxydodecanote homopolymer. Pseudomonas entomophila L48 was found to produce MCL PHA consisting of 3-hydroxyhexanoate (3HHx), 3-hydroxyoctanoate (3HO), 3-hydroxydecanoate (3HD), and 3-hydroxydodecanoate (3HDD) from related carbon sources fatty acids. In this study, some of the genes encoding key enzymes in β-oxidation cycle of P. entomophila such as 3-hydroxyacyl-CoA dehydrogenase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase were deleted to study the relationship between β-oxidation and PHA synthesis in P. entomophila. Among the mutants constructed, P. entomophila LAC26 accumulated over 90 wt % PHA consisting of 99 mol % 3HDD. A fed-batch fermentation process carried out in a 6 L automatic fermentor produced 7.3 g L(-1) PHA consisting of over 97 mol % 3HDD fraction. Properties of MCL PHA were significantly improved along with increasing 3HDD contents. P(2.1 mol % 3HD-co-97.9 mol % 3HDD) produced by P. entomophila LAC25 had the widest temperature range between T(g) and T(m), which were -49.3 and 82.4 °C, respectively, in all MCL PHA reported so far. The new type of PHA also represented high crystallinity caused by side-chain crystallization compared with short side chain PHA. For the first time, P(3HDD) homopolymers were obtained.
The Optimum Pore Size for the Fixation of Porous-Surfaced Metal Implants by the Ingrowth of Bone (1980)

For a study on the effects of pore size variation on the rate of bone growth into porous-surfaced metallic implants and on the strength of fixation resulting from this ingrowth, 4 distinct pore size ranges were prepared on cobalt-base alloy implants with cobalt-base alloy powder particles of different dimensions. The porous implants were placed into canine femurs for periods of 4, 8, and 12 weeks. Mechanical tests were performed to measure the shear strength of fixation of the implants to cortical bone. For implants with powder-made porous surfaces, a pore size range of approximately 50 to 400 microns provided the optimum or maximum fixation strength (17 MPa) in the shortest time period (8 weeks).
Bi-directional Leaky-Wave Antennas with Independent Beam-Scanning Laws (2022)

A bi-directional periodic leaky-wave antenna (LWA) is presented for the millimeter-wave (mm-wave) band with suppressed stopband and independent beam-scanning laws for top and bottom sides of the antenna, respectively. The bi-directional slot-pair antenna is designed to radiate out-of-plane beams along two directions on each antenna face. The operation of this antenna is verified using full-wave simulations at a design frequency of 28 GHz. The antenna can be engineered to point high gain beam along specified angles, and can be adapted to provide precision control of the independent output beams in various frequency bands.
Tyrosine Kinase Inhibitors Only Partially Inhibit AKT-Dependent Signaling in Cells Expressing Oncogenic KIT, FLT3 or ABL Kinases. A Potential Model for Leukemia Cell Resistance to TKIs. (2007)

Abstract Activating mutations of the KIT, FLT3 and ABL tyrosine kinases (TKs) are found in association with hematologic malignancies including subsets of acute leukemias, systemic mastocytosis, and chronic myelogenous leukemia. TK inhibitors (TKIs) have proven clinical activity for treatment of these diseases, but responses are largely partial or incomplete. We and others have previously demonstrated that the small molecule TKIs imatinib (KIT, BCR/ABL), dasatinib (KIT, BCR/ABL), sunitinib (KIT, FLT3), and tandutinib (KIT, FLT3) are potent inhibitors of oncogenic kinases relevant to hematologic malignancies. We now report that inhibition of TK phosphorylation (a surrogate for kinase activation), potently silences STAT and MAPK1/2 signaling - but incompletely inhibits activation of the AKT pathway: Using mastocytosis, leukemia and hematopoietic cell lines with endogenous or exogenous mutant KIT (V560G, D816V), FLT3 (ITD, D835V) or BCR/ABL isoforms, oncogenic TK-dependent downstream pathways were evaluated by immunoblotting. In addition, we determined the effect of treatment with specific TKIs +/– rapamycin on cellular proliferation and the induction of apoptosis. (Auto)phosphorylation of KIT, FLT3 or BCR/ABL results in activation of downstream pathways important for cell viability and cell survival. This includes the MAP Kinase (MAPK), STAT and PI3K/AKT pathways. All tested TKIs were able to potently decrease phosphorylation of members of the MAPK1/2, STAT3 and AKT pathways in cells harboring a corresponding TKI-sensitive oncogenic kinase. Notably, TKI treatment abolished phosphorylation of AKT at the Ser-473 site, whereas the Thr-308 phospho-site remained constitutively phosphorylated. This partial inhibition of AKT activity was insufficient to completely inhibit downstream kinases, such as p70S6Kinase, a known substrate of mTOR (Target Of Rapamycin). The addition of low nanomolar doses of rapamycin completely abrogated p70S6K phosphorylation alone or in combination with TK-inhibition. To determine the biological effect of more completely inhibiting AKT-dependent signaling, we tested TKI in physiological concentrations in combination with low dosage rapamycin (5–20nM). While rapamycin had only weak anti-proliferative effects when administered as monotherapy, combining rapamycin with each TKI demonstrated a strong additive to synergistic inhibitory potency with an up to 4 fold increase of antiproliferative as well as enhanced pro-apoptotic effects when compared to TKI monotherapy. We conclude that TKI inhibition of mutant KIT, FLT3 or ABL signaling is insufficient to globally silence AKT-driven pathways that may contribute to therapy failure. The addition of inhibitors targeting the AKT pathway, such as rapamycin, may improve clinical efficacy of TKI.
Localized Harris-FAST interest point detector (2016)

Simultaneous Localization and Mapping (SLAM) requires both rotation and scale invariant features. Few algorithms have been developed with rotation and scale invariant features with few limitations. Thus, an algorithm has been proposed to address rotation and scaling invariance. Proposed algorithm Harris-FAST interest point detector is a fusion of Harris and FAST interest point detectors. The detector is optimized by localizing the interest point detector to preferred area, from which the execution time of the algorithm reduced to the order of one fourth. The results of the proposed algorithm are compared with available feature detectors for its performance. Localized-Harris-FAST algorithm has been developed with an interest point detector for use in real time applications like SLAM on a mobile robot, which have limited computational resources.
Toxoplasma gondii Activates Hypoxia-inducible Factor (HIF) by Stabilizing the HIF-1α Subunit via Type I Activin-like Receptor Kinase Receptor Signaling (2010)

Toxoplasma gondii is an intracellular protozoan parasite that can cause devastating disease in fetuses and immune-compromised individuals. We previously reported that the alpha subunit of the host cell transcription factor, hypoxia-inducible factor-1 (HIF-1), is up-regulated by infection and necessary for Toxoplasma growth. Under basal conditions, HIF-1alpha is constitutively expressed but rapidly targeted for proteasomal degradation after two proline residues are hydroxylated by a family of prolyl hydroxylases (PHDs). The PHDs are alpha-ketoglutarate-dependent dioxygenases that have low K(m) values for oxygen, making them important cellular oxygen sensors. Thus, when oxygen levels decrease, HIF-1alpha is not hydroxylated, and HIF-1 is activated. How Toxoplasma activates HIF-1 under normoxic conditions remains unknown. Here, we report that Toxoplasma infection increases HIF-1alpha stability by preventing HIF-1alpha prolyl hydroxylation. Infection significantly decreases PHD2 abundance, which is the key prolyl hydroxylase for regulating HIF-1alpha. The effects of Toxoplasma on HIF-1alpha abundance and prolyl hydroxylase activity require activin-like receptor kinase signaling. Finally, parasite growth is severely diminished when signaling from this family of receptors is inhibited. Together, these data indicate that PHD2 is a key host cell factor for T. gondii growth and represent a novel mechanism by which a microbial pathogen subverts host cell signaling and transcription to establish its replicative niche.
Defocus Incorporated Multiple Segments Spectacle Lenses Changed the Relative Peripheral Refraction: A 2-Year Randomized Clinical Trial (2020)

Purpose: To compare changes in relative peripheral refraction (RPR) associated with myopia progression in myopic children wearing Defocus Incorporated Multiple Segments (DIMS) lenses and single vision (SV) spectacle lenses over 2 years. Methods: A 2-year double-blind, randomized controlled trial was conducted on 183 myopic children. Subjects were allocated to either wearing DIMS (n = 93) or SV spectacle lenses (n = 90). Peripheral refraction at 10°, 20°, and 30° of the nasal (10N, 20N, 30N) and temporal (10T, 20T, 30T) retinal eccentricities, central refraction, and axial length after cycloplegia were monitored every 6 months. Results: DIMS group showed symmetrical peripheral myopic shifts between the nasal and temporal retina (comparing myopic shifts between the nasal and temporal retina, the difference between the corresponding eccentricities were nonclinically significance). SV group showed asymmetrical peripheral myopic shifts between the nasal and temporal retina, with more myopic shifts (all P ≤ 0.001) at 10T (−0.32 ± 0.62 diopters [D]), at 20T (−0.69 ± 0.95 D), and 30T (−0.85 ± 1.52 D). No significant changes in RPR spherical equivalent (M) were noted in the DIMS group, whereas significant increases (all P < 0.0001) in hyperopic RPR M were observed at 10N (0.27 ± 0.45 D), 20N (0.75 ± 0.72 D), and 30N (0.98 ± 0.76 D) in the SV group. Conclusions: Wearing DIMS lenses resulted in a significantly different peripheral refraction profile and RPR changes, as well as significant myopia control effects when compared with SV lenses. Myopia control adopting myopic defocus in the midperiphery influenced peripheral refraction and slowed central myopia progression, most likely through alteration of overall retinal shape.
P235 Epigenetic landscape of the asthmatic airways (2016)

The airway epithelium of asthmatics exhibits distinct genomic and phenotypic characteristics. However the mechanisms underlying the establishment and chronicity of these characteristics remains unknown. We investigated if epigenetic changes underpin the genomic characteristics of the asthmatic airways by determining the chromatin landscape of bronchial epithelial cells (BECs) in healthy and asthmatic adults. We employed ChIP-seq of histone H3 acetylation (H3K27ac) to determine the chromatin landscape in e<i>x vivo</i> cultured BECs from healthy and allergic-atopic asthmatics (n = 3 donors each). Regions of differential enrichment were identified (MEDIPS) and associated genes and pathways determined (GREAT). Gene expression profiles were investigated by microarray (Illumina) and differential analysis conducted (Partek Genome Suite). Super enhancers (SEs) were identified (ROSE) and enrichment of transcription factor motifs (MEME) and their tissue distribution (protienatlas.org) determined. We identified 33,744 differentially enriched regions (DERs) of H3K27ac between asthma and healthy BECs. DERs were associated with genes (e.g. SERPINB2, TSLP) and pathways (e.g. leukotriene synthesis, antiviral response) previously implicated in asthma and had little overlap with known glucocorticoid receptor binding sites (1.7% of total). DERs occurred up to 100kb from gene promoters and gain or loss of H3K27ac was associated with increased and decreased gene expression in asthmatics respectively. Using a comparative approach, we identified SEs that were common (i.e., present across all donors) and distinct to health and asthma. In addition to established asthma genes (e.g. CLCA1) and transcription factors (e.g. TP63), asthma-SEs encompassed non-coding RNAs (up to 32% of genes) and epithelial-specific transcription factors (e.g. GCM2) previously unreported in asthma. Our data indicates that asthma influences the chromatin landscape of BECs and suggests the genomic differences observed in the asthmatic airway epithelium are underpinned by established epigenetic mechanisms.
LOW TEMPERATURE CHARACTERISTIC OF GaAlAs TEMPERATURE SENSOR DIODE (2001)

We have measured the forward characteristics of a GaAlAs temperature sensor diode (Lake Shore) in the temperature range 10–70 K and for fixed current values between 10 nA to 500 μA. On the basis of certain extrapolations, we suggest that these diodes can be used for temperature measurement at at ultra low temperatures.
An objective technique for evaluating doubletalk detectors in acoustic echo cancelers (1999)

Echo cancelers commonly employ a doubletalk detector (DTD), which is essential to keep the adaptive filter from diverging in the presence of near-end speech and other disruptive noise. There have been numerous algorithms to detect doubletalk in an acoustic echo canceler (AEC). In those applications, typically, the threshold is chosen only by some heuristic method and the performance evaluation is very subjective. In this study, we develop a way to objectively evaluate DTD algorithms based on the standard statistical methods of detection theory. A receiver operating characteristic (ROC) is derived to characterize DTD performance. Several DTD algorithms are examined and simulated under typical real-world operating conditions using measured room responses and signals taken from a digital speech database. The DTD methods are then evaluated and compared using the ROC metric.
Comparative Performance of Several Flexible Docking Programs and Scoring Functions:  Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets (2007)

Virtual screening by molecular docking has become a widely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three widely used docking programs (Glide, GOLD, and DOCK) for virtual database screening is studied when they are applied to the same protein target and ligand set. Comparisons of the docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The Glide XP methodology is shown to consistently yield enrichments superior to the two alternative methods, while GOLD outperforms DOCK on average. The study also shows that docking into multiple receptor structures can decrease the docking error in screening a diverse set of active compounds.
EXPRESSION PROFILING OF THE MANNURONAN C5‐EPIMERASE MULTIGENIC FAMILY IN THE BROWN ALGA LAMINARIA DIGITATA (PHAEOPHYCEAE) UNDER BIOTIC STRESS CONDITIONS1 (2008)

The aim of this study was to profile expression of mannuronan C5-epimerase (ManC5-E) genes of Laminaria digitata (Huds.) J. V. Lamour. under treatment with brown alga cell wall components known to induce defense reaction in this organism. After determining that incubation in the presence of homo-guluronates increased the accumulation of ManC5-E transcripts, we cloned a number of partial ManC5-E genes from nonelicited and elicited specimens. In addition to these fragments, previously identified genes from sporophyte and protoplast cDNA libraries were considered for a clustering analysis. Several groups of ManC5-E genes were observed, including groups containing sequences specific from nonelicited and elicited sporophytes, and sequences isolated from protoplasts. Quantitative real-time PCR experiments were then carried out using genes representative of different groups. Results of transcript accumulation during protoplast regeneration and sporophyte elicitation supported the hypothesis that specific C5-epimerase genes are recruited under pathogen attack, enabling L. digitata to modify its cell wall in response to environmental stimuli.
Constitutively solvent‐tolerant Pseudomonas taiwanensis VLB120∆C∆ttgV supports particularly high‐styrene epoxidation activities when grown under glucose excess conditions (2019)

Solvent-tolerant bacteria represent an interesting option to deal with the substrate and product toxicity in bioprocesses. Recently, constitutive solvent tolerance was achieved for Pseudomonas taiwanensis VLB120 via knockout of the regulator TtgV, making tedious adaptation unnecessary. Remarkably, ttgV knockout increased styrene epoxidation activities of P. taiwanensis VLB120Δ C. With the aim to characterize and exploit the biocatalytic potential of P. taiwanensis VLB120Δ C and VLB120Δ CΔ ttgV, we investigated and correlated growth physiology, native styrene monooxygenase (StyAB) gene expression, whole-cell bioconversion kinetics, and epoxidation performance. Substrate inhibition kinetics was identified but was attenuated in two-liquid phase bioreactor setups. StyA fusion to the enhanced green fluorescent protein enabled precise enzyme level monitoring without affecting epoxidation activity. Glucose limitation compromised styAB expression and specific activities (30-40 U/g <sub>CDW</sub> for both strains), whereas unlimited batch cultivation enabled specific activities up to 180 U/g <sub>CDW</sub> for VLB120Δ CΔ ttgV strains, which is unrivaled for bioreactor-based whole-cell oxygenase biocatalysis. These extraordinarily high specific activities of constitutively solvent-tolerant P. taiwanensis VLB120∆ C∆ ttgV could be attributed to its high metabolic capacity, which also enabled high expression levels. This, together with the high product yields on glucose and biomass obtained qualifies the VLB120∆ ttgV strain as a highly attractive tool for the development of ecoefficient oxyfunctionalization processes and redox biocatalysis in general.
Association of travel distance and cerebral aneurysm treatment (2017)

Patients who must travel further to receive advanced neurovascular care are more likely to receive treatment for their aneurysms only after they rupture. Further inquiry is needed to determine how to better provide neurosurgical treatment to patients living in underserved areas.
The proposed APHIS regulation modernization could enhance agriculture biotechnology research and development in the USA (2020)

Abstract The USDA’s Animal and Plant Health Inspection Service (APHIS) is one of three agencies that govern the importation, interstate movement, or environmental release of certain genetically engineered (GE) organisms. APHIS regulations are in 7 CFR part 340, originally issued in 1987 ( https://www.aphis.usda.gov/biotechnology/downloads/7_cfr_340.pdf ) and based on the premise that a GE crop could pose a plant pest risk. A major revision was proposed June 6, 2019 ( https://www.aphis.usda.gov/brs/fedregister/BRS_20190606.pdf ), with public comments accepted for 60 d. Members of the Society for In Vitro Biology (SIVB)—especially within the plant section—are impacted by the current rules and will be impacted by changes. Therefore, the public policy committee studied the changes and prepared a response that was reviewed by the board of directors and submitted to APHIS. APHIS received 6186 comments overall. In general, the SIVB welcomes the proposed revisions, which recognize established scientific guidelines and principles for plant pest risk assessment. In addition, they recognize the safety record accumulated over multiple decades of current GE mechanisms of action (MOA), so the proposed rules include an exemption for new events with established MOA’s in a previously reviewed crop. Further, the proposed rules focus on DNA function and impact rather than its source organism with regulatory review triggered by potential for increased plant pest risk. Most importantly, the proposed revisions codify a light regulatory approach for many applications of genome editing, because these applications result in plants that could otherwise have been developed through traditional breeding techniques or found in nature. If implemented appropriately in the final rule, we find these changes remove many current barriers, and thus are likely to stimulate university and business “startup” innovation. The SIVB recognizes the need for exemption for further model species and gene delivery organisms. Such concerns were adequately expressed by the submitted response. Remaining hurdles for innovative plant incorporated protectants are still problematic. Nevertheless, the SIVB applauds the efforts to update APHIS rules in a scientifically defensible manner. The detailed response is shared below.
An optimised fuzzy logic controller (2002)

An optimal fuzzy logic controller (FLC) tuning algorithm is reported in this paper. With the aid of genetic algorithms (GA), optimal rules of a fuzzy logic controller are designed. This is achieved by deriving a tailor-made encoding scheme, initialisation, crossover and mutation of rule table into chromosomes. The genetic algorithm incorporates as much existing knowledge of the system as possible to increase the speed of optimisation. For a linear system, the proposed algorithm shows a significant improvement in convergence. For a nonlinear system, the algorithm attempted the truck and truck-and-tailer backing up problems for the whole plan. It is concluded that the proposed algorithm can be applied effectively to solve variety of problems and can accommodate different performance criterion.
Ecobilan de divers itinéraires d'entretien du sol (2007)

La reconquete de la qualite des eaux est aujourd'hui un enjeu environnementol majeur. Pour repondre a cet objectif, la profession viticole a lance fin 2004 un plan d'action interprofessionnel baptise «plan eau». Sa mise en place sur le terrain se traduit par un bouleversement des techniques d'entretien des sols dont les objectifs sont de reduire l'utilisation des produits herbicides et de limiter les transferts vers les milieux naturels. Mois si la preservation de la qualite de l'eau est bien sur prioritaire dans notre demarche de progres, les solutions alternatives proposees ne doivent pas deplacer les problemes vers d'autres compartiments de l'environnement. Une evaluation globale et multicriteres de l'ensemble des impacts environnementaux lies a nos pratiques actuelles et futures doit donc etre systematiquement realisee. Cet article vous propose une premiere analyse comparative des ecobilans realises sur differents itineraires techniques d'entretien du sol.
Development of Spark Plug for Ion Current Misfire Detection System (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;In this paper, the authors introduce the spark plug for misfire detection system by ion current. In order to realize high accuracy misfire detection, the signal of ion current must be larger than that of noise. For maintaining ion signal in all designed lifetime, the configuration and initial condition of spark position are derived by an experiment and consideration about degradation in use. Additionally, the cause of noise is determined by an observation and a theoretical study, and we indicate the method to inhibit noise efficiently. Finally, effect of the methods found by these two approaches is confirmed with an engine, and we propose specifications of spark plug satisfying the condition that realize high accuracy detection by ion current.&lt;/div&gt;&lt;/div&gt;