gebhart/patrepeval huggingface dataset:
Differential regulation of adherens junction dynamics during apical–basal polarization (2011)

Adherens junctions (AJs) in epithelial cells are constantly turning over to modulate adhesion properties under various physiological and developmental contexts, but how such AJ dynamics are regulated during the apical-basal polarization of primary epithelia remains unclear. Here, we used new and genetically validated GFP markers of Drosophila E-cadherin (DE-cadherin, hereafter referred to as DE-Cad) and β-catenin (Armadillo, Arm) to quantitatively assay the in vivo dynamics of biosynthetic turnover and membrane redistribution by fluorescence recovery after photobleaching (FRAP) assays. Our data showed that membrane DE-Cad and Arm in AJs of polarizing epithelial cells had much faster biosynthetic turnover than in polarized cells. Fast biosynthetic turnover of membrane DE-Cad is independent of actin- and dynamin-based trafficking, but is microtubule-dependent. Furthermore, Arm in AJs of polarizing cells showed a faster and diffusion-based membrane redistribution that was both quantitatively and qualitatively different from the slower and exchange-based DE-Cad membrane distribution, indicating that the association of Arm with DE-Cad is more dynamic in polarizing cells, and only becomes stable in polarized epithelial cells. Consistently, biochemical assays showed that the binding of Arm to DE-Cad is weaker in polarizing cells than in polarized cells. Our data revealed that the molecular interaction between DE-Cad and Arm is modulated during apical-basal polarization, suggesting a new mechanism that might be crucial for establishing apical-basal polarity through regulating the AJ dynamics.
Electrochemical atomic layer deposition of Pt nanostructures on carbon paper and Ni foam; poster (2012)

SA-Korea Hydrogen fuel cell workshop, Zebula Lodge, Bela Bela South Africa, 11-12 July 2012
Design and characterization of a dual-stage, thermally actuated nanopositioner (2005)

A nanopositioner is presented that has two stages for independent coarse and fine position control. Thermal microactuators operate both stages. The first stage includes a bistable mechanism: it travels 52 µm between two discrete positions. The second stage is mounted on the first stage and moves continuously through an additional 8 µm in the same direction as the first stage. Three approaches to the control of the second stage were evaluated in terms of accuracy and manufacturability, and one was selected for the design of the nanopositioner. The device was surface micromachined in a two-layer polysilicon process. Experiments were performed to characterize the resolution, repeatability, hysteresis and thermal drift of the second stage of the nanopositioner with open-loop control. Position measurements were obtained from scanning electron micrographs by a numerical procedure, which is described in detail. The nanopositioner demonstrated 170 nm resolution and repeatability within 124 nm. The hysteresis of the second stage was 6% of its full range. The nanopositioner drifted 25 nm in the first 60 min of operation with a time constant of about 6 min. The dual-stage nanopositioner may be useful for applications such as variable optical attenuators or wavelength-specific add–drop devices.
Initiation of adenovirus DNA replication in vitro requires a specific DNA sequence. (1983)

Initiation of adenovirus DNA replication in vitro occurs on a linearized plasmid DNA containing 3,327 base pairs of the adenovirus terminal sequence. Various deletions have been constructed in the plasmid DNA and their template activities examined. Deletions from an internal restriction enzyme cleavage site that retain only 20 base pairs or more of the adenovirus terminal sequence support initiation and limited chain elongation, whereas deletions that leave 14 base pairs or less of the terminal sequence do not. On the other hand, all deletions extending from the very terminus of the adenovirus DNA destroy the template activity. The terminal 20 base pairs of adenovirus DNA contain a sequence A-T-A-A-T-A-T-A-C-C, which is perfectly conserved in the DNAs from different serotypes of human adenovirus. Base changes within the conserved sequence greatly reduce the template activity. These results suggest that the terminal 20 base pairs constitute a functional origin for the initiation of adenovirus DNA replication in vitro.
Tracking Language Mobility in the Twitter Landscape (2016)

The unprecedented data explosion has drastically changed the data science landscape. At the same time, Big Data analytics have reshaped the design and implementation of the applications that analyse the data. In this paper, we explore the use of Big Data tools for extracting value from Twitter data. We acquire a large set of Twitter data (10TB in size) and process it by relying on Spark DataFrame. The purpose of our analytics pipeline is to study the mobility of languages as captured by the Twitter signal. We study the evolution of languages from both a temporal and a spatial perspective, by applying density-based clustering and Self-Organising Maps techniques. The analysis enabled the detection of tourism trends and real-world events, as perceived through the Twitter lens.
Synthesis of bulky .beta.-lactams for inhibition of cell surface .beta.-lactamase activity (1993)

Procedures are described for the preparation of a series of compounds consisting of methicillin linked to beta-cyclodextrin through variable hydrophilic linkers. beta-Cyclodextrin was coupled to the antibiotic methicillin to prevent the antibiotic from permeating the outer membranes of bacteria. Stoichiometric oxidation of the beta-cyclodextrin with sodium metaperiodate provided a functional group for coupling to the linker. Methicillin was coupled to the linker via its carboxyl group. These compounds were tested for activity toward purified beta-lactamase. The length of the spacer arm between beta-cyclodextrin and methicillin was crucial in binding beta-lactamase and inhibiting activity. Compounds with longer spacers were effective inhibitors of beta-lactamase. We have deduced that the length of the spacer should be greater than 16 A for optimum inhibition of beta-lactamase.
Assessment of Clinician Diagnostic Concordance With Video Telemedicine in the Integrated Multispecialty Practice at Mayo Clinic During the Beginning of COVID-19 Pandemic From March to June 2020 (2022)

This diagnostic study of video telemedicine visits yielded a high degree of diagnostic concordance compared with in-person visits for most new clinical concerns. Some specific clinical circumstances over video telemedicine were associated with a lower diagnostic concordance, and these patients may benefit from timely in-person follow-up.
Analysis and Design of DC System Protection Using Z-Source Circuit Breaker (2015)

A modified Z-source breaker topology is introduced to minimize the reflected fault current drawn from a source while retaining a common return ground path. Conventional Z-source breaker topologies do not provide steady-state overload protection and can only guard against extremely large transient faults. The Z-source breaker can be designed for considerations affecting both rate of fault current rise and absolute fault current level, analogous in some respects to a thermal-magnetic breaker. Detailed analysis and design equations are presented to provide a framework for sizing components in the Z-source breaker topology. In addition, the proposed manual tripping mechanism enables protection against both instantaneous current surges and longer-term overcurrent conditions. The fault operation intervals of the proposed Z-source breaker topologies are both demonstrated in SPICE simulation and validated in experimental characterization.
Pituitary Adenylate Cyclase-Activating Polypeptide Relaxes Rat Gastrointestinal Smooth Muscle (1992)

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a new member of the secretin/glucagon peptides family, being most homologous to vasoactive intestinal peptide (VIP). The present study was designed to investigate a possible effect of PACAP on the rat gastrointestinal smooth muscle in vitro. We demonstrated that 1) PACAP reduced basal smooth-muscle contractions in all portions of the gastrointestinal tract, but the effect of VIP was region-specific. The inhibitory effect of PACAP in midcolon was approximately 100 times greater than that of VIP. 2) PACAP significantly inhibited smooth-muscle contractions induced by acetylcholine or carbachol. The inhibitory effect of PACAP was not affected by hexamethonium and was additive to the inhibitory effect of atropine and pirenzepine. 3) PACAP inhibited smooth-muscle contractions induced by substance P, cholecystokinin, and galanin, even after atropine treatment. Although the exact mechanism of the inhibitory action of PACAP remains to be clarified, PACAP appears to exert its effect in the rat at a site other than muscarinic receptors, probably through a direct effect on gastrointestinal smooth muscle in vitro.
Does the Wake-sleep Algorithm Produce Good Density Estimators? (1995)

The wake-sleep algorithm (Hinton, Dayan, Frey and Neal 1995) is a relatively efficient method of fitting a multilayer stochastic generative model to high-dimensional data.In addition to the top-down connections in the generative model, it makes use of bottom-up connections for approximating the probability distribution over the hidden units given the data, and it trains these bottom-up connections using a simple delta rule.We use a variety of synthetic and real data sets to compare the performance of the wake-sleep algorithm with Monte Carlo and mean field methods for fitting the same generative model and also compare it with other models that are less powerful but easier to fit. COMPETITORSWe compare the wake-sleep algorithm with six other density estimation methods.All data units are binary and can take on values d k = 1 (on) and d k = 0 (off).Gzip.Gzip (Gailly, 1993) is a practical compression method based on Lempel-Ziv coding.This sequential data compression technique encodes future segments of data by transmit-
Meta‐Analyses Support Previous and Novel Autism Candidate Genes: Outcomes of an Unexplored Brazilian Cohort (2019)

Large genomic databases of neurodevelopmental disorders (NDD) are helpful resources of genomic variations in complex and heterogeneous conditions, as Autism Spectrum Disorder (ASD). We evaluated the role of rare copy number variations (CNVs) and exonic de novo variants, in a molecularly unexplored Brazilian cohort of 30 ASD trios (n = 90), by performing a meta-analysis of our findings in more than 20,000 patients from NDD cohorts. We identified three pathogenic CNVs: two duplications on 1q21 and 17p13, and one deletion on 4q35. CNVs meta-analysis (n = 8,688 cases and n = 3,591 controls) confirmed 1q21 relevance by identifying duplications in other 16 ASD patients. Exome analysis led the identification of seven de novo variants in ASD genes (SFARI list): three loss-of-function pathogenic variants in CUL3, CACNA1H, and SHANK3; one missense pathogenic variant in KCNB1; and three deleterious missense variants in ATP10A, ANKS1B, and DOCK1. From the remaining 12 de novo variants in non-previous ASD genes, we prioritized PRPF8 and RBM14. Meta-analysis (n = 13,754 probands; n = 2,299 controls) identified six and two additional patients with validated de novo variants in PRPF8 and RBM14, respectively. By comparing the de novo variants with a previously established mutational rate model, PRPF8 showed nominal significance before multiple test correction (P = 0.039, P-value adjusted = 0.079, binomial test), suggesting its relevance to ASD. Approximately 60% of our patients presented comorbidities, and the diagnostic yield was estimated in 23% (7/30: three pathogenic CNVs and four pathogenic de novo variants). Our uncharacterized Brazilian cohort with tetra-hybrid ethnic composition was a valuable resource to validate and identify possible novel candidate loci. Autism Res 2020, 13: 199-206. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: We believed that to study an unexplored autistic population, such as the Brazilian, could help to find novel genes for autism. In order to test this idea, with our limited budget, we compared candidate genes obtained from genomic analyses of 30 children and their parents, with those of more than 20,000 individuals from international studies. Happily, we identified a genetic cause in 23% of our patients and suggest a possible novel candidate gene for autism (PRPF8).
WACCO and LOKO: Strong Consistency at Global Scale (2015)

Motivated by a vision for future global-scale services supporting frequent updates and widespread concurrent reads, we propose a scalable object-sharing system called WACCO offering strong consistency semantics. WACCO propagates read responses on a tree-based topology to satisfy broad demand and migrates objects dynamically to place them close to that demand. To demonstrate WACCO, we use it to develop a service called LOKO that could roughly encompass the current duties of the DNS and simultaneously support fine-grained status updates (e.g., Currently preferred routes) in a future Internet. We evaluate LOKO, including the performance impact of updates, migration, and fault tolerance, using a trace of DNS queries served by Akamai.
Selective darkening of the windshield using high speed video analysis for driving assistance (2012)

The paper presents the concept of a new visual based driving assistance system for increasing the safety and comfort in traffic. Using a high speed camera observing the vehicle's driver, an embedded image analysis module and a selective darkening panel attached to the windshield, the system is able to detect the appropriate area to be darkened in order to shade the driver's eyes and avoid the dazzling effect. The driver has a better view over the scene, since the rest of the windshield stays in high transparent mode. In this contribution, the main structure of the algorithm is presented. A patent is pending.
Total Synthesis of (±)-Welwitindolinone A Isonitrile (2006)

A highly stereoselective total synthesis of the alkaloid natural product welwitindolinone A isonitrile has been completed. The synthesis utilizes a chloronium ion mediated semi-pinacol rearrangement to simultaneously install the C10 quaternary center and neopentyl chlorine and a novel anionic cyclization to construct the spiro-oxindole with complete stereocontrol.
THE 2009 LABROSA PRETRAINED AUDIO CHORD RECOGNITION SYSTEM (2009)

Our pre-trained audio chord recognition system relies on labeled data to train Gaussian models of each chord class, based on a beat-synchronous chroma representation developed for cover song detection [1]. All chord models are based on two prototype models, one for major chords and one for minor, which are trained on all available examples, suitably transposed to align their tonality. Chord recognition is accomplished with a hidden Markov model using the perchord Gaussians to calculate observation likelihoods [4]. The system estimates a single key for each track, based on a single Gaussian full-covariance model of the chroma distribution, then transposing the track’s chroma representation to maximize its likelihood under this model. This key model was trained using ground-truth labels for each track as reported in the Allan Pollack annotations [3]. Recognition
Highly Excretable Gold Supraclusters for Translatable In Vivo Raman Imaging of Tumors (2022)

ABSTRACT Raman spectroscopy provides excellent specificity for in vivo preclinical imaging through a readout of fingerprint-like spectra. To achieve sufficient sensitivity for in vivo Raman imaging, metallic gold nanoparticles larger than 10 nm were employed to amplify Raman signals via surface-enhanced Raman scattering (SERS). However, the inability to excrete such large gold nanoparticles has restricted the translation of Raman imaging. Here we present Raman-active metallic gold supraclusters that are biodegradable and excretable as nanoclusters. Although the small size of the gold nanocluster building blocks compromises the electromagnetic field enhancement effect, the supraclusters exhibit bright and prominent Raman scattering comparable to that of large gold nanoparticle-based SERS nanotags due to high loading of NIR-resonant Raman dyes and much suppressed fluorescence background by metallic supraclusters. The bright Raman scattering of the supraclusters was pH-responsive, and we successfully performed in vivo Raman imaging of acidic tumors in mice. Furthermore, in contrast to large gold nanoparticles that remain in the liver and spleen, the supraclusters dissociated into small nanoclusters, and 73% of the administered dose to mice was excreted over 4 months. The highly excretable Raman supraclusters demonstrated here offer great potential for clinical applications of in vivo Raman imaging by replacing non-excretable large gold nanoparticles.
Electrochemical studies of porphyrin-appended dendrimers (2006)

The electrochemical properties of porphyrin-appended dendrimers containing 2-, 4-, 8-, 16-, 32- and 64-porphyrin macrocycles in their free-base and zinc(II) forms have been investigated. Both series gave diffusional based voltammetric responses in dichloromethane. There was minimal effect of dendrimer generation on the redox potentials. Multiple pi-cation and anion radicals as well as dications and dianions were formed on the surface of the dendrimers on oxidation or reduction as appropriate, with each cyclic voltammetric wave representing electron transfer to or from multiple non-interacting porphyrin sites. Electrostatic interactions in the higher generation dendrimers result in kinetic effects being observed for the highly charged species generated when each porphyrin unit is doubly or triply oxidised. The number of electrons transferred on reduction or oxidation of the dendrimers was evaluated using steady-state microelectrode voltammetry. For the lower generations of species a good correlation was observed between numbers of electrons transferred and number of porphyrin entities per molecule; for the dendrimers containing 32 and 64 units, however, slight negative deviations were observed, possibly due to electrostatic interactions as the porphyrins become closer packed.
Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time (2020)

Abstract Viral hemorrhagic fevers (VHFs) remain some of the most devastating human diseases, and recent outbreaks of Ebola virus disease (EVD) 1,2 and Lassa fever (LF) 3,4 highlight the urgent need for sensitive, field-deployable tests to diagnose them 5,6 . Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting Ebola virus (EBOV) and Lassa virus (LASV), with both fluorescent and lateral flow readouts. We demonstrate on laboratory and clinical samples the sensitivity of these assays and the capacity of the SHERLOCK platform to handle virus-specific diagnostic challenges. Our EBOV diagnostic detects both the L and NP genes, thereby eliminating the potential for false positive results caused by the rVSVΔG-ZEBOV-GP live attenuated vaccine. Our two LASV diagnostics together capture 90% of known viral diversity and demonstrate that CRISPR-RNAs (crRNAs) can be effectively multiplexed to provide greater coverage of known viral diversity. We performed safety testing to demonstrate the efficacy of our HUDSON protocol in heat-inactivating and chemically treating VHF viruses before SHERLOCK testing, eliminating the need for an extraction. We developed a user-friendly field protocol and mobile application (HandLens) to report results, facilitating SHERLOCK’s use in endemic regions. Finally, we successfully deployed our tests in Sierra Leone and Nigeria in response to recent outbreaks.
Revisiting alkaline aerobic lignin oxidation (2018)

Alkaline aerobic oxidation is an effective way to produce valuable aromatic chemicals from lignin.
Neural correlates of pre‐attentive processing of pattern deviance in professional musicians (2009)

Pre-attentive registration of aberrations in predictable sound patterns is attributed to the temporal cortex. However, electrophysiology suggests that frontal areas become more important when deviance complexity increases. To play an instrument in an ensemble, professional musicians have to rely on the ability to detect even slight deviances from expected musical patterns and therefore have highly trained aural skills. Here, we aimed to identify the neural correlates of experience-driven plasticity related to the processing of complex sound features. We used functional magnetic resonance imaging in combination with an event-related oddball paradigm and compared brain activity in professional musicians and non-musicians during pre-attentive processing of melodic contour variations. The melodic pattern consisted of a sequence of five tones each lasting 50 ms interrupted by silent interstimulus intervals of 50 ms. Compared to non-musicians, the professional musicians showed enhanced activity in the left middle and superior temporal gyri, the left inferior frontal gyrus and in the right ventromedial prefrontal cortex in response to pattern deviation. This differential brain activity pattern was correlated with behaviorally tested musical aptitude. Our results thus support an experience-related role of the left temporal cortex in fast melodic contour processing and suggest involvement of the prefrontal cortex.
Determination of Antibody Glycosylation by Mass Spectrometry (2012)

Immunoglobulin (Ig) G is formed by two antigen-binding moieties termed Fabs and a conserved Fc -portion, which interacts with components of the immune systems. Within the Fc, N-linked carbohydrates are attached to each conserved asparagine residue at position 297 within the CH2 domain. These oligosaccharide moieties introduce a higher degree of heterogeneity within the molecule, by influencing stability of the antibody and its mediated effector functions, such as antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity (CDC). The carbohydrate moieties can vary strongly depending on the production host and can be manipulated by different fermentation conditions, thereby influencing the function of the antibody. Therefore it is necessary to carefully monitor changes in the carbohydrate composition during cell line development and production processes. This chapter describes two different mass spectrometry based methods used for analyses of the carbohydrate moieties attached to the Fc-part of human IgG1. In the first approach, the glycans are released from the antibody by endoglycosidase (Peptide N Glycosidase F) digestion and monitored by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MS), whereas in the second method the carbohydrate structures, still attached to an enzymatically produced Fc-fragment, are analyzed by electrospray ionization mass spectrometry.
A 16 mm. Sound-on-Film Projector<!--<xref ref-type="other" rid="fn1-10.5594_J14755">*</xref>--> (1932)

A description is given of a talking picture equipment suitable for application in the non-theatrical field. The factors influencing the selection of a satisfactory form of film are pointed out, and a short review is presented of the problem involved in obtaining a sound record of good quality on this film.