gebhart/patrepeval huggingface dataset:
Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy (2016)

Two long-standing problems for superresolution (SR) fluorescence microscopy are high illumination intensity and long acquisition time, which significantly hamper its application for live-cell imaging. Reversibly photoswitchable fluorescent proteins (RSFPs) have made it possible to dramatically lower the illumination intensities in saturated depletion-based SR techniques, such as saturated depletion nonlinear structured illumination microscopy (NL-SIM) and reversible saturable optical fluorescence transition microscopy. The characteristics of RSFPs most critical for SR live-cell imaging include, first, the integrated fluorescence signal across each switching cycle, which depends upon the absorption cross-section, effective quantum yield, and characteristic switching time from the fluorescent "on" to "off" state; second, the fluorescence contrast ratio of on/off states; and third, the photostability under excitation and depletion. Up to now, the RSFPs of the Dronpa and rsEGFP (reversibly switchable EGFP) families have been exploited for SR imaging. However, their limited number of switching cycles, relatively low fluorescence signal, and poor contrast ratio under physiological conditions ultimately restrict their utility in time-lapse live-cell imaging and their ability to reach the desired resolution at a reasonable signal-to-noise ratio. Here, we present a truly monomeric RSFP, Skylan-NS, whose properties are optimized for the recently developed patterned activation NL-SIM, which enables low-intensity (∼100 W/cm(2)) live-cell SR imaging at ∼60-nm resolution at subsecond acquisition times for tens of time points over broad field of view.
Supplementary Figure 5 from <i>De Novo</i> Design of a Tumor-Penetrating Peptide (2023)

&lt;p&gt;PDF file - 590K, iNGR penetrates into extravascular tumor tissue&lt;/p&gt;
Sex steroids in human brain tumors and breast cancer (1990)

The concentrations of three sex steroids, estradiol, progesterone and testosterone, were analyzed by radioimmunoassay after celite chromatography in brain tumor and breast cancer tissues. The concentrations in malignant gliomas and breast cancers showed interindividual variations, especially evident with regard to estradiol. High estradiol concentrations were recorded in two patients with malignant astrocytoma. The concentrations of 1.00 pg/mg and 3.32 pg/mg were 10 to 30 times as high as in normal female brain. In five of ten astrocytomas the estradiol concentration was higher than the lowest breast cancer value. The distribution of progesterone seemed more even, and the level was significantly lower in brain tumors and breast cancers as compared with female brain, perhaps indicating an increased metabolism. Testosterone levels were somewhat higher in brain tumors, as compared with breast cancers, but not different from values in brain tissue. There were no significant age or sex correlation or differences in the concentrations of steroids in the brain tumors. The results suggest that manipulation of sex steroid metabolism in malignant brain tumors can be of beneficial therapeutic value as has been shown for breast cancer and prostatic carcinoma.
Solid-State NMR Study of Miscibility and Phase Separation in Blends and Semi-Interpenetrating Networks of 13C-Labeled Poly(styrene-co-acrylonitrile) and Poly(styrene-co-maleic anhydride) (1998)

Site-directed isotopic enrichment and solid-state 13C spin-diffusion NMR techniques were employed to characterize miscibility at the molecular level and phase separation in blends of amorphous polymers. Using 2D proton-driven spin-diffusion techniques on a mixture of 13C-labeled poly(styrene-co-maleic anhydride), [13CH2,13CO]SMA (27 wt % MA, Mw ∼ 4 × 104 g mol-1), and poly(styrene-co-acrylonitrile), [13CN]SAN (27 wt % ACN, Mw = 1.3 × 105 g mol-1), it is demonstrated that SMA and SAN are miscible on the molecular level. However, a specific orientation of the nitrile moieties in SAN with respect to the carbonyl groups in SMA is unlikely. This suggests that the miscibility of SAN and SMA copolymers is associated mainly with a decrease of intramolecular repulsion upon mixing, as opposed to a specific exothermic binary interaction. In addition, spin-diffusion experiments show that upon selective cross-linking of the SMA phase semi-interpenetrating networks are formed. Increasing the degree of cross-linking results in increasing degrees of phase separation.
A simple handheld pupillometer for chromatic Flicker studies (2014)

A portable pupillometer has been developed which is capable of performing accurate measurements of the pupil diameter during chromatic flicker stimulations. The handheld measuring system records the near-infrared image of the pupil at the rate of 25 fps and simultaneously stimulates the eye using a diffused flicker light generated by light emitting diodes (LEDs). Intensity, frequency and chromatic coordinates of the stimulus can be easily adjusted using a user-friendly graphical interface. Thanks to a chromatic monitoring of the stimulus close to the plane of the eye, photopically matched conditions can be easily achieved. The pupil diameter/area can be measured during flickering stimuli that are generated with frequency in a range of 0.1-20 Hz. The electronic unit, properly connected to the personal computer through a USB port, drives the optical unit, which can be easily held in a hand. The software interface controlling the system was developed in LabVIEW. This paper describes the instrument optical setup, front-end electronics and data processing. Moreover preliminary results obtained on a voluntary are reported.
Fabrication of ordered bi-metallic array with superstructure of gold micro-rings via templated-self-assembly procedure and its SERS application (2020)

Bi-metallic patterns with array of Pt discs decorated by Au rings were fabricated onto the substrate by a templated-self-assembly procedure in which multi-step self-assembly processes were involved. The original pattern was established by using the breath figure method. The bi-metallic sample with Au rings exhibited rather high sensitivity as well as great reproducibility within the array in surface-enhanced Raman scattering test.
Disruption of Microtubules Ablates the Specificity of Insulin Signaling to GLUT4 Translocation in 3T3-L1 Adipocytes (2005)

Although the cytoskeletal network is important for insulin-induced glucose uptake, several studies have assessed the effects of microtubule disruption on glucose transport with divergent results. Here, we investigated the effects of microtubule-depolymerizing reagent, nocodazole and colchicine, on GLUT4 translocation in 3T3-L1 adipocytes. After nocodazole treatment to disrupt microtubules, GLUT4 vesicles were dispersed from the perinuclear region in the basal state, and insulin-induced GLUT4 translocation was partially inhibited by 20-30%, consistent with other reports. We found that platelet-derived growth factor (PDGF), which did not stimulate GLUT4 translocation in intact cells, was surprisingly able to enhance GLUT4 translocation to approximately 50% of the maximal insulin response, in nocodazole-treated cells with disrupted microtubules. This effect of PDGF was blocked by pretreatment with wortmannin and attenuated in cells pretreated with cytochalasin D. Using confocal microscopy, we found an increased co-localization of GLUT4 and F-actin in nocodazole-treated cells upon PDGF stimulation compared with control cells. Furthermore, microinjection of small interfering RNA targeting the actin-based motor Myo1c, but not the microtubule-based motor KIF3, significantly inhibited both insulin- and PDGF-stimulated GLUT4 translocation after nocodazole treatment. In summary, our data suggest that 1) proper perinuclear localization of GLUT4 vesicles is a requirement for insulin-specific stimulation of GLUT4 translocation, and 2) nocodazole treatment disperses GLUT4 vesicles from the perinuclear region allowing them to engage insulin and PDGF-sensitive actin filaments, which can participate in GLUT4 translocation in a phosphatidylinositol 3-kinase-dependent manner.
Computerized detection and classification of lesions on breast ultrasound (2003)

We are developing a computerized method that detects suspicious areas on ultrasound images, and then distinguishes between malignant and benign-type lesions. The computerized scheme identifies potential lesions based on expected lesion shape and margin characteristics. All potential lesions are subsequently classified by a Bayesian neural net based on computer-extracted lesion features. The scheme was trained on a database of 400 cases (757 images) - consisting of complex cysts, benign and malignant lesions - and tested on a comparable database of 458 cases (1740 images) including 578 normal images. We investigated the performances of lesion detection and subsequent classification by a Bayesian neural net for two tasks. The first task was the distinction between actual lesions and false-positive (FP) detections, and the second task the distinction between actual malignant lesions and all detected lesion candidates. In training, the detection and classification method obtained an Az value of 0.94 in the distinction of false-positive detections from actual lesions, and an Az of 0.91 was obtained on the testing database. The task of distinguishing malignant lesions from all other detections (false-positives plus all benign type lesions) showed to be more challenging and Az values of 0.87 and 0.81 were obtained during training and testing, respectively. For the testing database, the combined detection and classification scheme correctly identified lesions in 82% (0.45 FP per image) of all the patients, and in 100% (0.43 FP malignancies per image) of the cancer patients.
Minimax sampling with arbitrary spaces (2005)

We consider non-ideal sampling and reconstruction schemes in which the sampling and reconstruction spaces as well as the input signal can be arbitrary. To obtain a good reconstruction of the signal in the reconstruction space, from arbitrary samples, we suggest processing the samples prior to reconstruction with a linear transformation that is designed to minimize the worst-case squared-norm error between the reconstructed signal, and the best possible (but usually unattainable) approximation of the signal in the reconstruction space. We show both theoretically and through a simulation that if the input signal does not lie in the reconstruction space, then this method can outperform the consistent reconstruction method previously proposed for this problem.
Spatial Modulation in the Underwater Acoustic Channel (2004)

Multiple-input multiple-output (MIMO) communication channels are an active area of research for terrestrial wireless applications. The natural bandwidth limitations of the underwater acoustic channel (UAC) combined with the potential for a rich spatial propagation structure suggest the ocean may be another useful application area for MIMO techniques. An underwater acoustic communications experiment was conducted in the waters surrounding Elba, Italy, using spatially modulated signals. Two frequency regimes (9.5-14.5 kHz and 25-35 kHz) were explored over ranges up to 5 km using vertical line arrays suspended from drifting ships. The UAC had an average depth of 100 m. One-way communication links were established at two sites with one site having a rocky (reverberant) bottom and the other having a muddy (absorbent) bottom. The waveform comprised a single data stream with concatenated codes providing error control. The inner code was a high rate BCH code Trellis-coded modulation was used as the basis for the outer code. Successive coded symbols were multiplexed across the available transducer elements. This coding approach effectively maintains the inherent bandwidth efficiency of MIMO signaling. The receiver was an adaptive recursively updated multichannel decision feedback equalizer operating in conjunction with a digital phase-locked loop A packet-based, transport architecture was used and included a training sequence. A Viterbi algorithm was integrated with the equalizer that supported simultaneous tap-weight update and trellis transversal, thereby affording the decision-directed update partial error control. Using appropriate assumptions, channel capacity using a single transducer was estimated to be 5.4 bits/channel use at the soft bottom site. Capacity was maximized at 15.9 bits/channel use using four transducers. More detailed results will be presented along with performance predictions based on both propagation models and measured channel transfer functions7
Controlled clinical trial of canine therapy versus usual care to reduce patient anxiety in the emergency department (2019)

Exposure to therapy dogs plus handlers significantly reduced anxiety in ED patients.
MiPanda: A Resource for Analyzing and Visualizing Next-Generation Sequencing Transcriptomics Data (2018)

The Michigan Portal for the Analysis of NGS data portal (http://mipanda.org) is an open-access online resource that provides the scientific community with access to the results of a large-scale computational analysis of thousands of high-throughput RNA sequencing (RNA-seq) samples. The portal provides access to gene expression profiles, enabling users to interrogate expression of genes across myriad normal and cancer tissues and cell lines. From these data, tissue- and cancer-specific expression patterns can be identified. Gene-gene coexpression profiles can also be interrogated. The current portal contains data for over 20,000 RNA-seq samples and will be continually updated.
Confinement on energy transfer between luminescent centers in nanocrystals (2003)

The luminescence dynamics of optical centers in nanocrystals depends critically on the phonon density of states (PDOS), which is quite distinct from that of bulk materials. It is shown that energy transfer (ET) in nanocrystals is confined by discrete PDOS as well as direct size restriction. Temperature-, concentration-, and size-dependence of the fluorescence decay from the S3/24 state of Er3+ in Y2O2S nanocrystals have been investigated using laser spectroscopic experiments and computational simulations. A set of microscopic rate equations that govern the evolution of the excitation probability Pi(t) are solved iteratively using a Monte Carlo method. The simulations of ET based on a theoretical model with five parameters are in good agreement with the experimental results. It is shown that phonon-assisted ET processes in Er3+:Y2O2S nanocrystals contribute partly to the fluorescence decay at 295 K, and is negligible at 5 K. For applications, the nanoconfinement effects on ET may significantly reduce the efficiency of sensitized or upconversion luminescence due to the lack of low-frequency phonon modes and restricted excitation migration in nanophosphors.
The pH dependent reactions of graphene oxide with small molecule thiols (2018)

Graphene oxide (GO) is a heterogenous 2D carbon-based material composed of sp<sup>2</sup> and sp<sup>3</sup> hybridized carbon atoms and oxygen containing functionalities, <i>i.e.</i>, alcohols and epoxides. Thus, the chemical reactivity of GO is complex and both complimentary and contrasting to the reactivity of corresponding small molecules (<i>e.g.</i>, tertiary alcohols, epoxides, and alkenes). Understanding the reactivity of GO under different conditions and with different reagents will ensure the chemical composition can be controlled and thus electronic and optical properties dictated, and solubility tuned for desired applications. Reaction of GO nanosheets towards a variety of reagents has been reported, however controlling the reaction pathway of GO nanosheets with a single nucleophile by simple alternation of the reaction medium has not been realized. This ability to tune the reaction by modification of solution pH, for example, would aid in understanding the reactivity of GO. Herein, we report that GO undergoes two distinct reaction pathways with ethane thiol depending on the pH of the reaction media: under aprotic basic conditions GO nanosheets undergo functionalization with minimal reduction, and under superacidic conditions GO nanosheets are reduced with no functionalization.
Cycloadditions. 24. Addition of dichloroketene to silyl enol ethers. Synthesis of functionalized cyclobutanones (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloadditions. 24. Addition of dichloroketene to silyl enol ethers. Synthesis of functionalized cyclobutanonesLarry R. Krepski and Alfred HassnerCite this: J. Org. Chem. 1978, 43, 16, 3173–3179Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/jo00410a017https://doi.org/10.1021/jo00410a017research-articleACS PublicationsRequest reuse permissionsArticle Views853Altmetric-Citations29LEARN 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
On the pH-Dependent Quenching of Quantum Dot Photoluminescence by Redox Active Dopamine (2012)

We investigated the charge transfer interactions between luminescent quantum dots (QDs) and redox active dopamine. For this, we used pH-insensitive ZnS-overcoated CdSe QDs rendered water-compatible using poly (ethylene glycol)-appended dihydrolipoic acid (DHLA-PEG), where a fraction of the ligands was amine-terminated to allow for controlled coupling of dopamine-isothiocyanate onto the nanocrystal. Using this sample configuration, we probed the effects of changing the density of dopamine and the buffer pH on the fluorescence properties of these conjugates. Using steady-state and time-resolved fluorescence, we measured a pronounced pH-dependent photoluminescence (PL) quenching for all QD-dopamine assemblies. Several parameters affect the PL loss. First, the quenching efficiency strongly depends on the number of dopamines per QD-conjugate. Second, the quenching efficiency is substantially increased in alkaline buffers. Third, this pH-dependent PL loss can be completely eliminated when oxygen-depleted buffers are used, indicating that oxygen plays a crucial role in the redox activity of dopamine. We attribute these findings to charge transfer interactions between QDs and mainly two forms of dopamine: the reduced catechol and oxidized quinone. As the pH of the dispersions is changed from acidic to basic, oxygen-catalyzed transformation progressively reduces the dopamine potential for oxidation and shifts the equilibrium toward increased concentration of quinones. Thus, in a conjugate, a QD can simultaneously interact with quinones (electron acceptors) and catechols (electron donors), producing pH-dependent PL quenching combined with shortening of the exciton lifetime. This also alters the recombination kinetics of the electron and hole of photoexcited QDs. Transient absorption measurements that probed intraband transitions supported those findings where a simultaneous pronounced change in the electron and hole relaxation rates was measured when the pH was changed from acidic to alkaline.
Assignment of apolipoprotein H (APOH: beta-2-glycoprotein I) to human chromosome 17q23→qter; determination of the major expression site (1992)

Human apolipoprotein H (APOH) is associated with lipoprotein present in plasma. It has been shown that APOH has structural similarities with the regulation of complement activation (RCA) protein superfamily and is involved in phospholipid binding interactions on platelets and as an autoantigen in complex with anionic phospholipids. Nevertheless, additional functional studies are necessary to establish the physiological role of APOH. By hybridizing a cDNA probe for APOH to a panel of somatic cell hybrids, we show that the structural locus for this protein maps to 17q23----qter and is therefore not part of the RCA cluster on chromosome 1. The site of biosynthesis for APOH was established by Northern blot analysis. Hybridization of the APOH cDNA probe to total liver RNA identified a transcript of approximately 1.5 kb.
Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants (2023)

Emerging SARS-CoV-2 variants have accrued mutations within the spike protein rendering most therapeutic monoclonal antibodies against COVID-19 ineffective. Hence there is an unmet need for broad-spectrum mAb treatments for COVID-19 that are more resistant to antigenically drifted SARS-CoV-2 variants. Here we describe the design of a biparatopic heavy-chain-only antibody consisting of six antigen binding sites recognizing two distinct epitopes in the spike protein NTD and RBD. The hexavalent antibody showed potent neutralizing activity against SARS-CoV-2 and variants of concern, including the Omicron sub-lineages BA.1, BA.2, BA.4 and BA.5, whereas the parental components had lost Omicron neutralization potency. We demonstrate that the tethered design mitigates the substantial decrease in spike trimer affinity seen for escape mutations for the hexamer components. The hexavalent antibody protected against SARS-CoV-2 infection in a hamster model. This work provides a framework for designing therapeutic antibodies to overcome antibody neutralization escape of emerging SARS-CoV-2 variants.
Dense wavelength-division multiplexed transmission in "zero-dispersion" dsf by means of hybrid Raman/erbium-doped fiber amplifiers (1999)

Transmission of 25 and 50 equally 100-GHz and 50-GHz spaced 10-Gb/s (OC-192) channels on the ITU grids is demonstrated over eight and four 83.8-km long spans, respectively, of DSF with the zero-dispersion wavelength within the signal wavelength band. Significant performance improvements are obtained with a pump power of only 440 mW with 55-/spl mu/m/sup 2/ dispersion-shifted fibers because of their relatively high Raman efficiency.
Serologic Evidence of Infection with Eaton Agent in Lower Respiratory Illness in Childhood (1960)

THE agent isolated in cotton rats, hamsters or embryonated hen's eggs by Eaton et al.1 2 3 from patients with cold-agglutinin-positive atypical pneumonia has been the subject of considerable controversy. This agent could be propagated in embryonated eggs and produced pneumonic lesions in hamsters and cotton rats after intranasal inoculation. The results of neutralization tests in hamsters or cotton rats that suggested the development of antibody to this agent during convalescence from atypical pneumonia have not been accepted by certain workers since the challenge inoculum did not produce pneumonitis in all inoculated animals. In addition, the question of latent agents in cotton . . .
ChemInform Abstract: THERMAL SIGMATROPIC REARRANGEMENTS OF VINYLALLENES LEADING TO 11‐CIS‐RETINOIDS AND THE NOVEL PROPERTIES OF 9‐CIS,11‐CIS,13‐CIS‐RETINAL AND 11‐CIS,13‐CIS‐RETINAL (1983)

Abstract Das aus der Cuprat‐Spezies (IV) und der Verbindung (I) [‐+ (Va)] nach Behandlung v.on (Va) mit Tetrabutylammoniumfluorid/THF zugängliche Vinylallen (Vb) liefert bei der Thermolyse ein Gemisch der isomerenRetinoide(VIa) + (VIb) + (VIIa) sowie infolge Weiterreaktion des instabilen vierten Isomeren (VIIb) die tricyclische Verbindung (VIII).