gebhart/patrepeval huggingface dataset:
Scaled mining of environmental acoustic data from temperate to tropical forests, from ocean to tropical rivers: A convolutional feature learning approach (2015)

Scaled passive acoustic monitoring has recently been developed to assess changes in biodiversity. It is applied to monitor changes in fauna composition associated with anthropogenic impacts and to improve the management of species and habitat conservation. Under the auspices of the “Scaled Acoustic BIODiversity” SABIOD project (CNRS MI/GDR MADICS/JASON UTLN), interdisciplinary teams collaborate to develop new joint machine learning and signal processing bioacoustic analyses. Currently, terabytes of sounds are recorded monthly using the innovative open SABIOD autonomous sensor arrays, positioned within forests or deep in the ocean. The challenges associated with tropical biodiversity as the variety of sound sources and the complexity of acoustic paths are being addressed by optimizing strategies that couple features learning, convolutional neural net, and advanced passive acoustic localization/filtering. Applications are many, including the classification of one thousand Amazon bird species, whale song classification, automatic indexing forest soundscapes, passive acoustic 3D tracking of bats and cetaceans with our patented system, and offshore cetacean monitoring. We discuss the main difficulties encountered and summarize the promising steps and strategies that we intend to pursue in the future coupling scaled CNN with Deep Scattering Spectrum. Demo/details: http://sabiod.univ-tln.fr.
Characterization of composite aminodeoxyisochorismate synthase and aminodeoxyisochorismate lyase activities of anthranilate synthase. (1993)

Anthranilate synthase [chorismate pyruvatelyase (amino-accepting), E.C.4.1.3.27] catalyzes the formation of anthranilate (o-aminobenzoate) and pyruvic acid from chorismate and glutamine. A mutant form of the enzyme from Salmonella typhimurium accumulates a compound that we had isolated and identified as trans-6-amino-5-[(1-carboxyethenyl)-oxy]-1,3- cyclohexadiene-1-carboxylic acid, commonly called aminodeoxyisochorismate (ADIC). Here we report that ADIC is formed by a reversible, Mg(2+)-dependent ADIC synthase activity of anthranilate synthase that can be functionally uncoupled from a Mg(2+)-dependent ADIC lyase activity of the enzyme by single amino acid substitutions in the TrpE subunit of the anthranilate synthase complex of S. typhimurium. Both of the component activities of the enzyme are sensitive to feedback inhibition by L-tryptophan. Purified ADIC is quantitatively converted to anthranilate and pyruvic acid by the ADIC lyase activity of wild-type anthranilate synthase. ADIC also serves as a substrate for the formation of chorismate by the enzyme in the absence of glutamine and (NH4)2SO4. The rate of ADIC formation by the mutant enzyme and the steady-state parameters for ADIC utilization by the wild-type enzyme are consistent with a role for ADIC as an enzyme-bound intermediate that does not accumulate during the course of the anthranilate synthase reaction. The altered catalytic specificity of mutant anthranilate synthase enzymes suggests a potential role for ADIC in secondary metabolism.
Preparation of Electroactive Poly(p-phenylene) Film by Means of Electrochemical Oxidation and Reduction Methods (1997)

We triedto provethe merit ofelectrochemicalreductivepolymerization(ERP)origin＆1char段cter of which is to control polymerization site on the preparation of兀一conjugated polymer filn1，As the results，an electroactive】)01y(ρ・phenylene〉film formed by ERP demonstrated a reversible higher redox property and narrower energy band gap in comparison with the film￡ormed by electrochemical oxidative polymerization of biphenyl．So it is efficient to鳳se EPR＆s the film formation ofπ一conjugated polymer鑑m，
Microstructure of N‐face InN grown on Si (111) by plasma‐assisted MBE using a thin GaN–AlN buffer layer (2010)

Abstract The structural properties of 2 µm thick N‐face InN film, grown on Si (111) by plasma source molecular beam epitaxy after the initial deposition of 20 nm AlN and 40 nm GaN, were examined by transmission electron microscopy. The lattice mismatched GaN/AlN and InN/GaN interfaces limited the propagation of threading dislocations (TDs). Dislocation annihilation interactions occurred in the first ∼200 nm of the InN film and reduced the TD density. However, the density of screw and mixed type TDs was four times higher than edge type ones. This was attributed to the observed GaN/InN interfacial roughness, which was introduced by terminating TDs from the GaN/AlN buffer layer. Strain measurements showed that the InN film, as well as both buffer layers, was relaxed.
Modeling and rendering waves: wave-tracing using beta-splines and reflective and refractive texture mapping. (1987)

The graphical simulation of a certain subset of hydrodynamics phenomena is examined. New algorithms for both modeling and rendering these complex phenomena are presented. The modeling algorithms deal with wave refraction in an ocean. Waves refract in much the same way as light. In both cases, the equation that controls the change in direction is Snell's law. Ocean waves are continuous but can be discretely decomposed into wave rays or wave orthogonals . These wave orthogonals are wave-traced in a manner similar to the rendering algorithm of ray-tracing. The refracted wave orthogonals are later traversed and their height contributions to the final surface are calculated using a sinusoidal shape approximation and the principle of wave superposition. The surface is then represented by Beta-splines , using the tension (or β2) shape parameter to easily add more complexity to the surface. The rendering algorithms are based on the use of texture maps and Fresnel's law of reflection. In each algorithm, two texture maps are used to simulate reflection and refraction . Based on surface normal orientation and Fresnel's law, a weighting is calculated that determines what fractions of reflected color and refracted color are assigned to a point. These algorithms are more efficient, though less accurate, alternatives to standard ray-tracing techniques.
EPR Spectroscopic Characterization of Neuronal NO Synthase (1996)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionEPR Spectroscopic Characterization of Neuronal NO SynthaseChris Galli, Ryan MacArthur, Husam M. Abu-Soud, Pamela Clark, Dennis J. Stuehr, and Gary W. BrudvigCite this: Biochemistry 1996, 35, 22, 7298Publication Date (Web):June 4, 1996Publication History Published online4 June 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/bi965003whttps://doi.org/10.1021/bi965003wcorrectionACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views246Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (69 KB) Get e-Alertsclose Get e-Alerts
Response surface methodology optimization for extraction of phenolics and antioxidant capacity in defatted dabai parts (2013)

This study aimed to determine the total phenolics and antioxidant capacity of defatted dabai parts based on liquid extraction and optimized using response surface methodology (RSM). A two-level factorial design was applied to determine the effect of two independent variables (extraction time: X1 and % methanol: X2) on three response variables (total phenolic content: Y1, total flavonoid/anthocyanin content: Y2 and Trolox equivalent antioxidant capacity: Y3). The optimum conditions for extraction time and percent methanol were 36 min or 1 min and 62.25% or 53% for the defatted dabai pulp or peel, respectively. The RSM optimized extraction was compared with sonication-assisted extraction. Optimization results showed that defatted dabai parts had high total phenolic content and antioxidant capacity. Sonication-assisted extraction utilized the optimized extraction conditions had further increased the total phenolic content and antioxidant capacity of defatted dabai peel, but not in the pulp. Therefore, optimization of different extraction methods for the defatted fruit parts is recommended for future studies.
Rapid Injection Linear Dichroism for Studying the Kinetics of Biological Processes (2012)

Linear dichroism is defined as the differential absorbance of linearly polarized light oriented in two orthogonal directions by an aligned sample. The measurement of a linear dichroism (LD) spectrum of a sample provides two key pieces of structural information. First, that the sample and the chromophores within the sample are able to align. Second, given knowledge of the transition polarization directions of the chromophores, the orientation of the chromophores within the aligned sample can be resolved. It has been shown that LD can provide unique information on the structure of some of the more challenging biomolecular complexes. This has included macromolecular protein and peptide fibers such as actin, tubulin, and amyloids as well as protein-membrane complexes and DNA-protein complexes. Much of this work has been enabled by the development of a low volume Couette flow cell that efficiently aligns long molecules in solution. However, the current Couette system is inherently complex to assemble for each experiment and hence not suited to measurement of rapid reactions. In this paper we detail the development of the first rapid injection LD cell. The system utilizes a conventional stopped-flow injection system coupled to a modified low volume Couette cell, where a narrow bore capillary replaces the normal solid central rod. The system is shown to have similar optical characteristics to the conventional LD Couette flow cell but with the added benefit of a much shorter dead time (0.60 s compared to ~60). The rapid injection Couette cell has been used to measure the degradation of DNA by DNA exonuclease I, providing data that would not be available using a conventional system.
Abstract LB208: Obesity is associated with lower tumor oxidative phosphorylation (OXPhos) in metastatic melanoma (MM) (2021)

Abstract Immune checkpoint inhibitors (ICI) and BRAF targeted therapies improve overall survival (OS) for patients (pts) with MM, but treatment responses are heterogeneous. Recent data strongly implicates host factors in response and resistance to these agents. We and others have shown that overweight/obese BMI [OW/OB: body mass index (BMI≥25)] is associated with improved OS with both ICI and BRAF targeted therapies in MM pts. The biologic basis for this association is unknown. Thus, we examined the molecular and immune correlates of BMI in MM. In melanoma TCGA regionally metastatic specimens with available BMI (n=202), BMI was not associated with DNA mutations or copy number variations, nor with protein expression. To assess for associations with gene expression, we performed a gene set enrichment analysis (GSEA) on pooled data for cohorts of MM patients with RNAseq and BMI data (TCGA, n=202; MDACC, n=61; MIA, n=68; UCLA, n=26). Following batch correction, GSEA identified downregulation of OXPHOS and adipogenesis in tumors from OW/OB pts compared to normal (NL) BMI (BMI&amp;lt;25). Mass spectrometry of 36 MM specimens from the TCGA cohort confirmed downregulation of the TCA cycle intermediates citrate (p=0.01) and succinate (p&amp;lt;0.05) in OW/OB MM. Immunohistochemistry for key immune cell populations and checkpoints in the MIA and MDACC cohorts did not identify significant differences by BMI, consistent with the lack of difference in inflammatory pathways by gene expression. Finally, we evaluated associations of BMI with gut microbiome features in MM pts (n=272). OW/OB was associated with lower microbial alpha diversity vs. NL BMI (p=0.02), but no significant differences were observed in the composition of individual species. As increased microbiome diversity has been associated with improved outcomes with ICI in MM, this finding supports that changes in the microbiome are unlikely to explain the improved outcomes seen with ICI in OW/OB pts. In sum, our findings suggest that host energy balance influences tumor metabolism in MM, with downregulation of OXPHOS in MM from OB/OW pts, which may influence outcomes with targeted and immune therapies. These hypothesis generating findings suggest one possible mechanism underlying the obesity paradox observed in MM pts. Citation Format: Andrew W. Hahn, Mingchu Xu, Jun Li, Lauren E. Haydu, M.A. Wadud Khan, Tuba N. Gide, Alexander M. Menzies, Courtney W. Hudgens, Theodore S. Nowicki, Jeffrey E. Gershenwald, Antoni Ribas, Michael T. Tetzlaff, Alexander J. Lazar, James Willmott, Jennifer Wargo, Andrew Futreal, Jianhua Zhang, Michael A. Davies, Jennifer L. McQuade. Obesity is associated with lower tumor oxidative phosphorylation (OXPhos) in metastatic melanoma (MM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB208.
Medicinal Chemistry Insights in the Discovery of Novel LSD1 Inhibitors (2015)

LSD1 is an epigenetic modulator associated with transcriptional regulation of genes involved in a broad spectrum of key cellular processes, and its activity is often altered under pathological conditions. LSD1 inhibitors are considered to be candidates for therapy of cancer, viral diseases and neurodegeneration. Many LSD1 inhibitors with various scaffolds have been disclosed, and a few potent molecules are in different stages of clinical development. In this review, we summarize recent biological findings on the roles of LSD1 and the current understanding of the clinical significance of LSD1, and focus on the medicinal chemistry strategies used in the design and development of LSD1 inhibitors as drug-like epigenetic modulators since 2012, including a brief consideration of structure-activity relationships.
Making serine integrases work for us (2017)

DNA site-specific recombinases are enzymes (often associated with mobile DNA elements) that catalyse breaking and rejoining of DNA strands at specific points, thereby bringing about precise genetic rearrangements. Serine integrases are a group of recombinases derived from bacteriophages. Their unusual properties, including directionality of recombination and simple site requirements, are leading to their development as efficient, versatile tools for applications in experimental biology, biotechnology, synthetic biology and gene therapy. This article summarizes our current knowledge of serine integrase structure and mechanism, then outlines key factors that affect the performance of these phage recombination systems. Recently published studies, that have expanded the repertoire of available systems and reveal system-specific characteristics, will help us to choose the best integrases for envisaged applications.
An Efficient Destination Prediction Approach Based on Future Trajectory Prediction and Transition Matrix Optimization (2018)

Destination prediction is an essential task in various mobile applications and up to now many methods have been proposed. However, existing methods usually suffer from the problems of heavy computational burden, data sparsity, and low coverage. Therefore, a novel approach named DestPD is proposed to tackle the aforementioned problems. Differing from an earlier approach that only considers the starting and current location of a partial trip, DestPD first determines the most likely future location and then predicts the destination. It comprises two phases, the offline training and the online prediction. During the offline training, transition probabilities between two locations are obtained via Markov transition matrix multiplication. In order to improve the efficiency of matrix multiplication, we propose two data constructs, Efficient Transition Probability (ETP) and Transition Probabilities with Detours (TPD). They are capable of pinpointing the minimum amount of needed computation. During the online prediction, we design Obligatory Update Point (OUP) and Transition Affected Area (TAA) to accelerate the frequent update of ETP and TPD for recomputing the transition probabilities. Moreover, a new future trajectory prediction approach is devised. It captures the most recent movement based on a query trajectory. It consists of two components: similarity finding through Best Path Notation (BPN) and best node selection. Our novel BPN similarity finding scheme keeps track of the nodes that induces inefficiency and then finds similarity fast based on these nodes. It is particularly suitable for trajectories with overlapping segments. Finally, the destination is predicted by combining transition probabilities and the most probable future location through Bayesian reasoning. The DestPD method is proved to achieve one order of cut in both time and space complexity. Furthermore, the experimental results on real-world and synthetic datasets have shown that DestPD consistently surpasses the state-of-the-art methods in terms of both efficiency (approximately over 100 times faster) and accuracy.
ChemInform Abstract: BASE‐CATALYZED REARRANGEMENTS INVOLVING YLIDE INTERMEDIATES. PART 12. THE PREPARATION AND REACTIONS OF 2‐OXIDOANILINIUM YLIDES (1981)

Abstract Die Titelverbindungen (II) wurden aus den entsprechenden quaternären Salzen (I) dargestellt und bilden beim Erhitzen die Produkte (III) durch [1,4]‐Umlagerungen.
Trafficking of Leishmania donovani promastigotes in non-lytic compartments in neutrophils enables the subsequent transfer of parasites to macrophages (2007)

Inoculation of Leishmania (L.) spp. promastigotes in the dermis of mammals by blood-feeding sand flies can be accompanied by the rapid recruitment of neutrophils, inflammatory monocytes and dendritic cells. Despite the presence of these lytic leucocytes, parasitism is efficiently established. We show here that Leishmania donovani promastigotes are targeted to two different compartments in neutrophils. The compartments harbouring either damaged or non-damaged parasites were characterized at the electron microscopy (EM) level using the glucose 6-phosphatase cytochemistry and endosome-phagosome fusion assays. One involves the contribution of lysosomes leading to the formation of highly lytic compartments where parasites are rapidly degraded. The other is lysosome-independent and involves the contribution of a compartment displaying some features of the endoplasmic reticulum (ER) where parasites are protected from degradation. Using genetically modified parasites, we show that the promastigote surface lipophosphoglycan (LPG) is required to inhibit lysosome fusion and maintain parasites in neutrophil compartments displaying ER features. L. donovani-harbouring neutrophils that eventually enter apoptosis can be phagocytosed by macrophages enabling the stealth entry of parasites into their final replicative host cells. Thus, the ability of L. donovani to avoid trafficking into lysosomes-derived compartments in short-lived neutrophils constitutes a key process for the subsequent establishment of long-term parasitism.
Tetrodotoxin-resistant Na+currents and inflammatory hyperalgesia (1999)

Several mechanisms have been identified that may underlie inflammation-induced sensitization of high-threshold primary afferent neurons, including the modulation of voltage- and Ca2+-dependent ion channels and ion channels responsible for the production of generator potentials. One such mechanism that has recently received a lot of attention is the modulation of a tetrodotoxin (TTX)-resistant voltage-gated Na+ current. Evidence supporting a role for TTX-resistant Na+ currents in the sensitization of primary afferent neurons and inflammatory hyperalgesia is reviewed. Such evidence is derived from studies on the distribution of TTX-resistant Na+ currents among primary afferent neurons and other tissues of the body that suggest that these currents are expressed only in a subpopulation of primary afferent neurons that are likely to be involved in nociception. Data from studies on the biophysical properties of these currents suggest that they are ideally suited to mediate the repetitive discharge associated with prolonged membrane depolarizations. Data from studies on the effects of inflammatory mediators and antinociceptive agents on TTX-resistant Na+ currents suggest that modulation of these currents is an underlying mechanism of primary afferent neuron sensitization. In addition, the second-messenger pathways underlying inflammatory mediator-induced modulation of these currents appear to underlie inflammatory mediator-induced hyperalgesia. Finally, recent antisense studies have also yielded data supporting a role for TTX-resistant Na+ currents in inflammatory hyperalgesia. Although data from these studies are compelling, data presented at the Neurobiology of Pain colloquium raised a number of interesting questions regarding the role of TTX-resistant Na+ currents in inflammatory hyperalgesia; implications of three of these questions are discussed.
Trajectory tracking and formation flight of autonomous UAVs in GPS-denied environments using onboard sensing (2014)

In GPS-denied environments like in indoor applications, location systems based on Vicon cameras, infrared cameras or UWB techniques are generally employed to provide location information of multiple mobile robots. The location systems require expensive and external equipments, which limits the applicable range of micro unmanned aerial vehicles (UAVs) in GPS-denied environments. In the paper, efficient control schemes based on onboard commodity sensors are presented for autonomous UAVs in indoor applications, where the horizontal displacement of the platform is provided by an optical flow sensor. With the aid of lightweight onboard sensors, a complete 6-degree of freedom (DOF) state of the UAV can be estimated. Control strategies are presented for low-level stabilization as well as high-level tracking and formation control. Experiments illustrate that the UAVs with onboard sensing and computation can achieve autonomous trajectory tracking and distributed formation flight based on a leader-follower scheme.
Effects and Students' Perspectives of Blended Learning on English into Arabic Translation. (2019)

Translation constitutes a problem for many students worldwide and Arab students particularly due to the ineffective approaches to the teaching of translation. The current study aimed at measuring the effect of a proposed blended learning programme on developing Egyptian secondary students’ translation skills from English into Arabic; and exploring students’ perspectives on this proposed programme. Social constructivism informs this study as its theoretical framework. This study adopted a mixed-methods research design with quasi-experimental research design and semi-structured interviews. Participants were divided into experimental and control groups, 20 students each. Results showed that the blended learning programme proved statistically effective in developing the translation skills of the experimental group students. Moreover, students' perspectives on the benefits and challenges of using the blended learning programme were reported. Theoretical and pedagogical implications for the teaching of translation using blended learning are provided.