gebhart/patrepeval huggingface dataset:
Automated Axon Segmentation from Highly Noisy Microscopic Videos (2015)

We present a novel method for automated segmentation of axons in extremely noisy videos obtained via two-photon microscopy in awake mice. We formulate segmentation as a pixel-wise classification problem in which a pixel is classified into "axon" or "non-axon" based on its feature vector. In order to deal with high levels of noise, the features of our classifier are derived from spatio-temporal Independent Component Analysis (stICA) which effectively isolates noise from signal components while leveraging temporal coherence from the video. We fit parametric models to represent the distribution of the extracted features and apply a probabilistic classifier over stICA components to determine the label of each pixel. Finally, we show compelling qualitative and quantitative results from very challenging two-photon microscopic, demonstrating the usefulness of our approach. An example time-series of two-photon images with our automated ROI extraction over layed is available with the supplemental materials.
Chirp parameter estimation from a sample covariance matrix (2001)

This paper considers the problem of estimating the bandwidth and the center frequency of a linear chirp signal. The nonstationarity property of chirp signals implies that the signal has high rank and reduces the applicability of subspace-based algorithms significantly. However, the special structure of the sample covariance matrix invites the use of regular frequency estimation algorithms. Herein, we show how subspace-type algorithms may be modified to provide accurate signal parameter estimates for linear chirp signals at reasonable complexity. The root-MUSIC algorithm is used as an example.
Optical detection of the spin state of a single nucleus in silicon (2004)

We propose a method to optically detect the spin state of a ${}^{31}\mathrm{P}$ nucleus embedded in a ${}^{28}\mathrm{Si}$ matrix. The nuclear-electron hyperfine splitting of the ${}^{31}\mathrm{P}$ neutral-donor ground state can be resolved via a direct frequency discrimination measurement of the ${}^{31}\mathrm{P}$-bound exciton photoluminescence using single-photon detectors. The measurement time is expected to be shorter than the optically modified lifetime of the nuclear spin at 4 K and 10 T.
Enzyme Immobilization Technologies and Industrial Applications (2023)

Enzymes play vital roles in diverse industrial sectors and are essential components of many industrial products. Immobilized enzymes possess higher resistance to environmental changes and can be recovered/recycled easily when compared to the free forms. The primary benefit of immobilization is protecting the enzymes from the harsh environmental conditions (e.g., elevated temperatures, extreme pH values, etc.). The immobilized enzymes can be utilized in various large-scale industries, e.g., medical, food, detergent, textile, and pharmaceutical industries, besides being used in water treatment plants. According to the required application, a suitable enzyme immobilization technique and suitable carrier materials are chosen. Enzyme immobilization techniques involve covalent binding, encapsulation, entrapment, adsorption, etc. This review mainly covers enzyme immobilization by various techniques and their usage in different industrial applications starting from 1992 until 2022. It also focuses on the multiscale operation of immobilized enzymes to maximize yields of certain products. Lastly, the severe consequence of the COVID-19 pandemic on global enzyme production is briefly discussed.
Delivery of Broadcast Services in 3G Networks (2007)

TV is regarded as a key service for mobile devices. In the past, Mobile TV was often associated with broadcast transmission. However, unicast technology is sufficient in many cases, especially since mobile users prefer to access content on-demand, rather than following a fixed schedule. In this paper we will focus on 3G mobile networks, which have been primarily optimized for unicast services. Based on a traffic model we will discuss the capacity limits of 3G networks for unicast distribution of Mobile TV. From the results it can be concluded that the capacity is sufficient for many scenarios. In order to address scenarios in which broadcast is a more appropriate technology, 3GPP has defined a broadcast extension, called Multimedia Broadcast Multicast Service (MBMS). MBMS introduces shared radio broadcast bearers and has thus the capabilities of a real broadcasting technology. We will give a short overview about MBMS including a discussion on MBMS capacity. Since MBMS is primarily a new transport technology, additional application and service layer technologies are required, like electronic service guide and service protection. These mechanisms are standardized by the Open Mobile Alliance (OMA) and are favorably combined with MBMS or 3G unicast distribution in order to create complete end-to-end solutions. In order to optimize a system for delivery of broadcast services over 3G networks, the advantages of broadcast and unicast should be combined. We argue that hybrid unicast-broadcast delivery offers the best system resource usage and also the best user experience, and is thus favorable not only for broadcast delivery in 3G networks, but actually also for non-cellular broadcast systems like DVB-H or DMB
Nup358/RanBP2 mediates HIV-1 docking at the nuclear pore. (2015)

&lt;p&gt;(&lt;b&gt;A&lt;/b&gt;) Control and Nup214/CAN or Nup358/RanBP2 knock-down cells were infected at 5 days p.t with HIV-1 VSV-G and fixed at 6 h p.i. Cells were labelled with anti-p24 HIV-1 capsid antibody, stained with Hoechst, and observed by confocal fluorescence microscopy. An Acapella script was used to segment the nucleus and cytoplasm of each cell. Nuclear and cell membrane detection were derived from Hoechst staining and LV-encoded GFP expression, respectively. HIV-1 p24 capsid signals were automatically quantified within perinuclear or cytoplasmic regions using a spot detection algorithm, with an intensity threshold set on negative controls. Perinuclear spots, defined as those present within 2 pixels of the nuclear membrane (480 nm), are highlighted as coloured dots in right-hand panels. (&lt;b&gt;B&lt;/b&gt;) Quantification of Acapella-detected perinuclear p24 signal. Each point corresponds to one random cell and indicates the number of perinuclear capsid signals as a percentage of total cytoplasmic signal, representative of three independent experiments with mean +/− SEM. (&lt;b&gt;C&lt;/b&gt;) Control or LV-shRNA transduced cells were infected with HIV-1 VSV-G and fractionated at 6 hr p.i. At this early time point, reverse transcription is not completed and the majority of viral complexes is still in the cytoplasm: p24 capsid signal in the nuclear fraction corresponds to viruses docked at the nuclear membrane. Nuclear and cytoplasmic fractions were tested for p24 content by Western blotting. Actin, tubulin and lamin labelling were carried out on the same samples to test for protein loading and integrity of cytoplasmic and nuclear fractions, respectively. Numbers indicate sizes in kDa. (&lt;b&gt;D&lt;/b&gt;) Control and Nup358/RanBP2 knock-down cells were infected with HIV-1 VSV-G and fractionated at 6 hr p.i. Nuclei were labelled with anti-p24 and anti-Nup214 or -Nup358 antibodies, stained with Hoechst and placed on coverslips for microscopy observation using Apotome structured illumination (Zeiss). (&lt;b&gt;E&lt;/b&gt;) 2-LTR time points in control and Nup358/RanBP2 knock-down cells at 24 h, 48 h and 72 h p.i normalised for actin copy number, mean of triplicates +/− SD.&lt;/p&gt;
Ramp-Up Journey of New Hires: Tug of War of Aids and Impediments (2015)

Hiring top talent is essential for any software ￼￼company's success. After joining the company, new hires often spend weeks or months before making any major contribution and attaining the same productivity level as existing employees. We use the term ramp-up journey to refer to this transition of new hires from novice to experts. There can be several factors, such as lack of experience or lack of familiarity with processes unique to the new company, which influence the ramp-up journey. To understand such aids and impediments in the ramp-up journey, we conducted a study by analyzing data extracted from version control systems of eight large and popular product groups in Microsoft with several thousand software developers. In particular, we studied two aspects of the ramp-up journey. First, we studied time taken to make the first check-in into the version control system, an important milestone in the ramp-up journey indicating the first contribution. Second, we analyzed the time taken to reach the same productivity level as existing employees in terms of check-ins. We further augmented our quantitative study with qualitative results derived by surveying 411 professional developers. Our study produced promising results, including factors such as having a mentor, prior knowledge of required skill sets, and proactively asking questions, that could help reduce the ramp-up journey of new hires.
ChemInform Abstract: AN EFFICIENT SYNTHESIS OF 1α,25‐DIHYDROXY VITAMIN D3 (1985)

Abstract Die Synthese der Titelverbindung (IX) erfolgt ausgehend vom Cholesterin‐Derivat (I) in einer Gesamtausb.
Identification of profilin as an IgE‐binding component in latex from Hevea brasiliensis: clinical implications (1995)

Considering the high occurrence of profilin as an allergen in many plant species, the assumption was made that profilin might be an allergen in Hevea brasiliensis, a member of the latex producing Euphorbiaceae family. Using IgE-binding inhibition by purified profilins we demonstrated that profilin is an IgE-binding component in the cytosolic fraction of natural latex and, to a lower extent, in the rubber fraction. Thirty-five out of 36 sera containing IgE to ragweed-profilin reacted with profilin from latex, indicating structural homologies between profilins from latex and ragweed. A large percentage (59%) of these sera were found to be positive in CAP latex assay. The preincubation of these sera with purified ragweed profilin greatly inhibited the CAP latex. Because profilin is also present in banana extract, it is likely to be involved in cross-sensitivity to banana and latex. In a group of 19 individuals allergic to latex only two had anti-profilin IgE antibodies. Profilin was barely detectable on glove extract immunoblots, whereas some sera from patients allergic to latex reacted with a 15 kDa allergen which was not profilin. Consequently, IgE antibodies to latex-profilin is a questionable factor for sensitization of occupationally-exposed patients; however, sensitization to profilin should be taken into account when interpreting the results of latex IgE antibody assays.
Longitudinal ellipsoid zone and subretinal fluid mapping following ocriplasmin injection in the prospective observational ORBIT trial (2019)

Ocriplasmin treatment resulted in VMT release, MH closure and visual acuity gains in a significant portion of eyes. EZ volume was significantly reduced at week 1, but recovered to baseline levels by final follow-up and was not associated with final visual acuity.
Adaptive optics sharpens multiphoton-microscope images (2005)

Originally developed for astronomy and military use, adaptive-optics is coming into its own for use in ­optical-sectioning microscopy techniques such as multiphoton microscopy.
Wafer-level quartz dry etching technology (2014)

Wafer-level quartz dry etching technology has been developed, which enables deep reactive ion etching (DRIE) for through-etch of ≥120-μm-thick crystal quartz wafers and an X-cut quartz DRIE. Our DRIE process employs direct wafer bonding of crystal quartz and silicon wafer by means of surface active bonding at room temperature and epoxy-based negative tone, i-line photoresist for the mask of the dry etching. Etching gases and DRIE parameters are optimized from the points of etching rate, mask selectivity, the angle of the sidewall and micro-loading effect. X-cut tuning fork resonator having folded arms has been fabricated by the wafer-level quartz dry etching technology.
Fine mapping of chromosome 3 in uveal melanoma: identification of a minimal region of deletion on chromosomal arm 3p25.1-p25.2. (2003)

To identify minimal common areas of allelic loss on chromosome 3, we have mapped both arms of the chromosome in 21 uveal melanomas that did not show monosomy 3 in our previous allelotype study. DNA was isolated from microdissected paraffin sections and amplified by PCR. In an initial screening, 14 microsatellite markers on chromosomal arm 3p and 13 on chromosomal arm 3q were used. Loss of heterozygosity for at least one marker was found in 9 of 21 tumors (43%) on 3p and 8 of 21 tumors (38%) on 3q. The initial analysis defined two common regions of allelic loss on 3p, a 7.3-Mb region between markers D3S1263 and D3S3510 spanning 3p25.3-24.3 and a larger region between markers D3S1578 and D3S1284. The two common regions of allelic loss were further mapped with an additional 14 microsatellite markers. A 1.4-Mb minimal region of allelic loss was identified between microsatellite markers D3S3610 and D3S1554 on 3p25.1-3p25.2. A total of 10 tumors had allelic loss in this region; 2 of these tumors had corresponding putative homozygous deletions. These homozygous deletions may further narrow the region of interest to 0.1 Mb. This 1.4-Mb minimum region of deletion includes several genes that might be involved in the carcinogenesis of uveal melanoma as well as other important tumor types.
A rapid field-use assay for mismatch number and location of hybridized DNAs (2010)

Molecular dielectrophoresis (DEP) is employed to rapidly (<ms) trap ssDNA molecules in a flowing solution to a cusp-shaped nanocolloid assembly on a chip with a locally amplified AC electric field gradient. By tuning AC field frequency and DNA DEP mobility relative to its electrophoretic mobility due to electrostatic repulsion from like-charged nanocolloids, mismatch-specific binding of DNA molecules at the cusp is achieved by the converging flow, with a concentration factor about 6 orders of magnitude higher than the bulk, thus allowing fluorescent quantification of concentrated DNAs at the singularity in a generic buffer, at room temperature within a minute. Optimum flow rate and the corresponding hybridization rate change by nearly a factor of 2 with a single mismatch in the 26 base docking sequence and are also sensitive to the mismatch location. This dielectrophoresis and shear enhanced pico-molar sensitivity and SNP selectivity can hence be used for field-use DNA detection/identification.
Stable Lanthanide Luminescence Agents Highly Emissive in Aqueous Solution: Multidentate 2-Hydroxyisophthalamide Complexes of (2003)

Applications such as high throughput assays (drug development,genomic screening, and clinical diagnostic assays) or fluorescencemicroscopy require highly sensitive detection of low concentrationanalytes, with many analyses performed in a short period of timeand without preliminary purification of the sample.
Inactive Gingipains from P. gingivalis Selectively Skews T Cells toward a Th17 Phenotype in an IL-6 Dependent Manner (2017)

Gingipain cysteine proteases are considered key virulence factors of <i>Porphyromonas gingivalis</i>. They significantly influence antibacterial and homeostatic functions of macrophages, neutrophils, the complement system, and cytokine networks. Recent data indicate the role of <i>P. gingivalis</i> in T cell differentiation; however, the involvement of gingipains in this process remains elusive. Therefore, the aim of this study was to investigate the contribution of danger signals triggered by the gingipains on the generation of Th17 cells, which play a key role in protection against bacterial diseases but may cause chronic inflammation and bone resorption. To this end we compared the effects of the wild-type strain of <i>P. gingivalis</i> (W83) with its isogenic mutant devoid of gingipain activity (ΔKΔRAB), and bacterial cells pretreated with a highly-specific inhibitor of gingipains activity (KYTs). Antigen presenting cells (APCs), both professional (dendritic cells), and non-professional (gingival keratinocytes), exposed to viable bacteria expressed high amounts of cytokines (IL-6, IL-21, IL-23). These cytokines are reported to either stimulate or balance the Th17-dependent immune response. Surprisingly, cells infected with <i>P. gingivalis</i> devoid of gingipain activity showed increased levels of all tested cytokines compared to bacteria with fully active enzymes. The effect was dependent on both the reduction of cytokine proteolysis and the lack of cross-talk with other bacterial virulence factors, including LPS and fimbriae that induce <i>de novo</i> synthesis of cytokines. The profile of lymphocyte T differentiation from naive T cells showed enhanced generation of Th17 in response to bacteria with inactive gingipains. Moreover, we found that gingipain-dependent induction of Th17 cells was highly specific, since other T cell-subsets remained unchanged. Finally, inhibition of IL-6 signaling in dendritic cells led to a significant depletion of the Th17 population. Cumulatively, this study revealed a previously undisclosed role of gingipain activity in the process of Th17 differentiation reliant on blocking signaling through IL-6. Since inactivation of gingipains accelerates the skewing of T cells toward Th17 cells, which are detrimental in periodontitis, IL-6 signaling may serve as an attractive target for treatment of the disease.
Conformational Properties of the Unnatural Amino Acid .beta.-Methylphenylalanine in a Linear Octapeptide System; Correlations of 13C-NMR Chemical Shifts with the Side-Chain Stereochemistry of These Amino Acid Residues (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational Properties of the Unnatural Amino Acid .beta.-Methylphenylalanine in a Linear Octapeptide System; Correlations of 13C-NMR Chemical Shifts with the Side-Chain Stereochemistry of These Amino Acid ResiduesKatalin E. Kover, Ding Jiao, Sunan Fang, and Victor J. HrubyCite this: J. Org. Chem. 1994, 59, 5, 991–998Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/jo00084a014https://doi.org/10.1021/jo00084a014research-articleACS PublicationsRequest reuse permissionsArticle Views87Altmetric-Citations20LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Zur Energiedelle von Diradikalen, IV[1]. 2‐Methylen‐1,4‐cyclohexadiyl (1993)

The Energy‐Well of Diradicals, IV [1] . – 2‐Methylene‐1,4‐cyclohexadiyl The energy surface of the title compound 2 is derived from the kinetics of its precursors 5, 6, 7 , and 8 , the oxygen dependance of its trapping rate, and heat of hydrogenation measurements of 5, 6, 7 , and 15 . These data lead to a heat of formation for the diradical 2 of 69.8 kcal/mol and an energy well of 8.2 kcal mol –1 . From the Curie plot of the ESR spectrum and oxygen trapping experiments a singlet‐triplet splitting of 1.4 kcal mol –1 is indicated, with the triplet being the ground state.
ChemInform Abstract: MODIFICATION OF DNA WITH POTENT MUTACARCINOGENIC 2‐AMINO‐6‐METHYLDIPYRIDO(1,2‐A:3′,2′‐D)IMIDAZOLE ISOLATED FROM A GLUTAMIC ACID PYROLYSATE: STRUCTURE OF THE MODIFIED NUCLEIC ACID BASE AND INITIAL CHEMICAL EVENT CAUSED BY THE MUTAGEN (1983)

Abstract Die Titelverbindung (Ia) (Glu‐P‐l ), ein aus dem Pyrolysat von Glutaminsäure isoliertes wirksames Mutacarcinogen, reagiert mit DNA in vitro und in vivo; die Struktur (II) (Gua‐Glu‐P‐l )der modifizierten Nucleinsäure‐Base wird anhand unabhängiger Synthese bestimmt.
Simultaneous activation and hepatocyte growth factor activator inhibitor 1-mediated inhibition of matriptase induced at activation foci in human mammary epithelial cells (2005)

Activation of single-chain, latent matriptase, a type II transmembrane serine protease, depends on the weak proteolytic activity of its own zymogen as well as its cognate inhibitor, hepatocyte growth factor activator inhibitor 1 (HAI-1). Oligomerization of matriptase zymogens and HAI-1, and probably its interaction with other proteins, has been proposed to occur during matriptase activation. In the present study, we examined the cellular events associated with matriptase activation triggered either by the physiological inducer sphingosine 1-phosphate (S1P) or by a chemical inducer, the polyanionic compound suramin. S1P-induced matriptase translocation to cell-cell contacts, where it is activated, is an F-actin polymerization-dependent process. Conversely, suramin-induced matriptase accumulation and activation at vesicle-like structures is an F-actin polymerization-independent process. While matriptase activation can occur at different subcellular locations, both S1P- and suramin-induced matriptase accumulation form unique subcellular structures, termed activation foci, where oligomerization of matriptase zymogens and HAI-1 may occur, promoting matriptase activation. Furthermore, matriptase activation may be regulated by intracellular signaling, because Ro 31-8220, a bisindolylmaleimide protein kinase C inhibitor, inhibited both S1P- and suramin-induced activation. The requirement of HAI-1 for matriptase activation and the coincidence of HAI-1 and matriptase in activation foci apparently provide rapid access of HAI-1 for the inhibition of matriptase immediately after its activation. Indeed, all activated matriptase was detected in complexes with HAI-1 only 5 min after suramin stimulation. The close temporospatial coupling of matriptase activation with its inhibition suggests that the proteolytic activity of this enzyme must be well controlled and that the proteolysis of matriptase substrates may be tightly regulated by this mechanism.
The Total Synthesis of (+)-Palitantin (1992)

An asymmetric synthesis of (+)-palitantin [1; (2R,3R,5S,6R)-5-(1,3-heptadienyl)-2,3-dihydroxy-6-hydroxymethyl-cyclohexanone] is described, starting from the homochiral alcohol (-)-3 [(1S,2S,3R)-2,3-isopropylidenedioxycyclohexanol], obtained via lipase-mediated resolution. Key steps include a regioselective dehydration and stereoselective cuprate addition.