gebhart/patrepeval huggingface dataset:
Towards an ultrathin multi-aperture microscope (2020)

Recent biomedical developments towards compact, mobile, decentralized and system-integrated diagnostic platforms require automated and miniaturized microscopy technologies. Reducing system dimensions by downsizing classical single aperture optics limits either the field of view (FOV) or resolution. However, arranging multiple miniaturized objectives in parallel allows overcoming this restraint by decoupling the system’s FOV from the axial system length. Based on this principle, we propose a thin multi-aperture microscope concept to image a large FOV with μm resolution. Due to a total optical system length of only 10 mm, the imaging optics can be integrated into conventional camera housings. The approach’s potential is demonstrated by introducing a first prototype specified by life science requirements. The final system enables for bright field and fluorescence imaging of (1) multiple separated object fields simultaneously (e.g. parallel monitoring in microfluidics applications) or (2) extended continuous object areas via sample scanning. Hence, the micro-objective array approach provides a microscopy solution for biomedical applications with tight space requirements like point-of-care diagnostic devices, cell incubator microscopes and organ/lab-on-chip long term monitoring.
Comparison of photo‐matching algorithms commonly used for photographic capture–recapture studies (2017)

Photographic capture-recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost-effectiveness. Recently, several computer-aided photo-matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state-of-the-art photo-matching algorithms prior to implementation in capture-recapture studies involving possibly thousands of images. Here, we compared the performance of four photo-matching algorithms; Wild-ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel-based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match "by eye" can be easily translated to accurate individual capture histories necessary for robust demographic estimates.
Protonated Molecule (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Cross‐talk between IL‐6 and TGF‐β signaling in hepatoma cells (2001)

Interleukin-6 (IL-6) is a multifunctional cytokine that plays important roles in the immune system, hematopoiesis, and acute phase reactions. Transforming growth factor-beta (TGF-beta) also has pleiotropy including the production of acute phase proteins in hepatocytes. To elucidate the cross-talk between IL-6 and TGF-beta signaling pathways in hepatic cells, we investigated the effects of TGF-beta on IL-6-induced signal transducer and activator of transcription-3 (STAT3) activation in a human hepatoma cell line, Hep3B. IL-6-induced activation of STAT3 activity and STAT3-mediated gene expression were augmented by TGF-beta in Hep3B cells. We provide evidence that these activities were due to physical interactions between STAT3 and Sma- and MAD-related protein-3, bridged by p300. These results demonstrate a molecular mechanism of a cross-talk between STAT3 and TGF-beta signaling pathways in hepatocytes.
Retrieval of Similar Scenes Based on Multimodal Distance Metric Learning in Soccer Videos (2019)

This paper presents a new method for retrieval of similar scenes based on multimodal distance metric learning in far-view soccer videos that broadly capture soccer fields and are not edited. We extract visual features and audio features from soccer video clips, and we extract text features from text data corresponding to these soccer video clips. In addition, distance metric learning based on Laplacian Regularized Metric Learning is performed to calculate the distances for each kind of features. Finally, by determining the final rank by integrating these distances, we realize successful multimodal retrieval of similar scenes from query scenes of soccer video clips. Experimental results show the effectiveness of our retrieval method.
Distribution of pemphigus and pemphigoid antigens, laminin, and type IV collagen in corneal epithelium. (1981)

Dog corneas were studied by indirect immunofluorescence with antibodies specific for pemphigus and pemphigoid antigens, laminin, and type IV collagen. The distribution of these antigens was similar to that observed in other squamous epithelia and skin. This study provides further evidence for close immunochemical similarities between these tissues.
Photo-labile BODIPY protecting groups for glycan synthesis (2022)

Protective groups that can be selectively removed under mild conditions are an essential aspect of carbohydrate chemistry. Groups that can be selectively removed by visible light are particularly attractive because carbohydrates are transparent to visible light. Here, different BODIPY protecting groups were explored for their utility during glycan synthesis. A BODIPY group bearing a boron difluoride unit is stable during glycosylations but can be cleaved with green light as illustrated by the assembly of a trisaccharide.
Pschorr–Hoppe Indole Synthesis (2016)

In 1910 Robert Pschorr and Gerhard Hoppe reported the synthesis of indole via the reaction of o-nitrophenylace-tonitrile with tin foil and concentrated hydrochloric acid to give initially o-aminophenylacetonitrile. Subsequent treatment with sodium in boiling ethanol afforded indole. Although this simple synthesis of indole is first attributed to Pschorr and Hoppe, it was Makosza who greatly extended it by means of his vicarious nucleophilic substitution (VNS) of hydrogen as an efficient route to the prerequisite o-nitrophenylacetonitriles. Steven in 1925, in the context of a new aldehyde synthesis, prepared indole in 55% yield from o-nitrophenylacetonitrile using anhydrous stannous chloride and gaseous hydrogen chloride. Walker first used catalytic hydrogenation in the Pschorr-Hoppe indolization to prepare 5,6-dimethoxyindoles. With four moles of H2, ammonia is liberated, but with three moles of H2 the product retains the 2-amino group.
Differential induction of quinone reductase by phytoestrogens and protection against oestrogen-induced DNA damage (2004)

Quinone reductase (QR) is a phase II detoxification enzyme that plays an important role in detoxifying quinones and may help maintain the antioxidant function of the cell. We have previously observed that QR is up-regulated by anti-oestrogens, but not oestrogen, in breast cancer cells via ERbeta (oestrogen receptor beta) transactivation. Such QR induction appears to protect breast cells against oestrogen-induced oxidative DNA damage, most likely by reducing reactive oestrogen metabolites termed catecholestrogen-quinones back to the hydroxy-catecholestrogens which may be conjugated. We now report that the phytoestrogens biochanin A, genistein and resveratrol also up-regulate QR expression in breast cancer cells. We observe that regulation can occur at the transcriptional level, preferentially through ERbeta transactivation at the electrophile response element of the QR gene promoter. By chromatin immunoprecipitation analysis, we show binding of ERalpha and ERbeta to the QR promoter, with increased ERbeta binding in the presence of resveratrol. Functional studies show that biochanin A and resveratrol, but not genistein, can significantly protect against oestrogen-induced oxidative DNA damage in breast cancer cells. Antisense technology was used to determine whether such protection was dependent on ERbeta or QR. Our results with resveratrol are consistent with our hypothesis that the protective ability of resveratrol is partially dependent on the presence of ERbeta and QR. In conclusion, we postulate that phytoestrogen-mediated induction of QR may represent an additional mechanism for breast cancer protection, although the effects may be specific for a given phytoestrogen.
<b>Percutaneous Mechanical Mitral Commissurotomy with the Metallic Valvulotome:</b> Detailed Technical Aspects and Overview of the Results of the Multicenter Registry on 882 Patients (2000)

Percutaneous mechanical mitral commissurotomy (PMMC) is a new technique that has been developed over the last 3 years for the treatment of mitral stenosis. The device used opens the commissures by a direct action of two parallel bars located in a metallic head screwed at the distal end of a 13Fr catheter. Opening of the bars is obtained with the use of activating pliers attached at the proximal end of the catheter. The metallic dilator and the pliers can be safely reused after sterilization. The device and the direrent steps of the procedure are detailed in this article. The results of an international registry including 882 patients are reported here. PMMC could be achieved in 863 (98%) cases. Maximal opening of the bars was 40 mm in 90% of the cases. The technique resulted in an increase of the mitral valve area from 0.94 ± 0.2 cm 2 to 2.12 ± 0.4 cm 2 . Bilateral splitting of the commissures was achieved in 85% of the cases. Complications occurred in 33 (3.7%) patients: pericardial tamponade in 1.4% (12 cases, one death), mitral regurgitation &gt; grade 2 in 2.1% (18 cases, surgery required in 4), and transient stroke in 0.3% (3 patients). The role of the learning curve in the occurrence of complications has been clearly demonstrated. The cost of the procedure has been markedly decreased in developing countries due to multiple reuses of the device after sterilization.
Three novel patient‐derived BCR/ABL mutants show different sensitivity to second and third generation tyrosine kinase inhibitors (2012)

BCR/ABL (Breakpoint Cluster Region protein/Abelson tyrosine-protein kinase 1) kinase domain (KD) mutations represent the most frequently described mechanism of resistance to the treatment with tyrosine kinase inhibitors (TKI) in patients with chronic myeloid leukemia (CML). Mutations may impair TKI activity by directly or indirectly impairing the drug binding to the protein. We report the discovery of three new BCR/ABL mutations, L248R, T315V, and F317R identified in two patients with CML (L248R and T315V) and in one patient with Ph+ acute lymphoblastic leukemia (ALL) (F317R). Mutations were screened against second-generation (bosutinib, nilotinib, and dasatinib), as well as third-generation TKIs (ponatinib/AP-24534 and DCC-2036). Furthermore, the activity profile of ponatinib and DCC-2036 against a panel of 24 clinically relevant BCR/ABL mutants is presented and compared to the other TKIs. The IC50 values for each TKI against the mutants and the IC50 increase over wild type BCR/ABL (relative resistance, RR) were calculated to define four resistance levels: sensitive (RR ≤ 2), moderately resistant (2 < RR ≤ 4), resistant (4 < RR ≤ 10), or highly resistant (RR > 10). L248R and T315V showed high resistance to imatinib, bosutinib, dasatinib, and nilotinib, intermediate resistance to ponatinib, but were sensitive to DCC-2036. Interestingly, F317R showed a moderate resistance to imatinib and nilotinib, but is resistant/highly resistant to dasatinib, bosutinib, ponatinib, and DCC-2036. The availability of drugs activity profiles may become a useful tool for clinicians dealing with the treatment of drug-resistant CML patients.
Electron-Transfer Reagent Anion Formation via Electrospray Ionization and Collision-Induced Dissociation (2006)

A strategy is described and demonstrated for the formation of reagent anions via electrospray ionization (ESI) for electron-transfer dissociation (ETD). To circumvent difficulties associated with formation of high mass-to-charge ratio (m/z) reagent anions, it is desirable to form ETD reagents via means other than those that require reagent molecule vaporization. ESI is a candidate method, but anions that are generally generated efficiently by ESI tend to react with multiply protonated polypeptides via proton transfer. The strategy described herein involves the use of a precursor reagent molecule that ionizes efficiently via electrospray ionization and that can subsequently be converted to an ETD reagent via gas-phase dissociation. The approach is demonstrated with arenecarboxylic acids that yield strong signals associated with the deprotonated molecule and that subsequently undergo collision-induced dissociation (CID) by loss of CO(2). In the present work, triply protonated KGAILKGAILR served as a test substrate for the CID product ions to give rise to ETD. Several precursor molecules were shown to be capable of generating ETD reagents via ESI followed by CID. These included 9-anthracenecarboxylic acid, 2-fluoro-5-iodobenzoic acid, and 2-(fluoranthene-8-carbonyl)benzoic acid. The latter molecule has the most attractive set of characteristics as a precursor for a relatively high m/z ratio ETD reagent.
Automated Power Assessment for Helicopter Turboshaft Engines (2008)

An accurate indication of available power is required for helicopter mission planning purposes. Available power is currently estimated on U.S. Army Blackhawk helicopters by performing a Maximum Power Check (MPC), a manual procedure performed by maintenance pilots on a periodic basis. The MPC establishes Engine Torque Factor (ETF), an indication of available power. It is desirable to replace the current manual MPC procedure with an automated approach that will enable continuous real-time assessment of available power utilizing normal mission data. This report presents an automated power assessment approach which processes data currently collected within helicopter Health and Usage Monitoring System (HUMS) units. The overall approach consists of: 1) a steady-state data filter which identifies and extracts steady-state operating points within HUMS data sets; 2) engine performance curve trend monitoring and updating; and 3) automated ETF calculation. The algorithm is coded in MATLAB (The MathWorks, Inc.) and currently runs on a PC. Results from the application of this technique to HUMS mission data collected from UH-60L aircraft equipped with T700-GE-701C engines are presented and compared to manually calculated ETF values. Potential future enhancements are discussed.
Potentiation of left ventricular function at a reduced exercise level: Assessment by radionuclide ventriculography (1984)

Many patients can't maintain peak workload (P) for prolonged imaging. The authors evaluated the effect of a reduced workload following maximal supine bicycle exercise on left ventricular ejection fraction (EF) and wall motion in 16 pts. with CAD (greater than or equal to50% stenosis in greater than or equal to1 major coronary artery) and 9 normals who underwent symptom-limited RVG. After acquisition of resting and maximal exercise LAO views, the pts. exercise level was decreased to 60% of the peak workload achieved. A repeat LAO view was then obtained at the reduced workload (post peak) (PP) 4-8 min. after the P. A significant increase in ejection fraction from Peak to PP was seen in the entire patient group, from 62-66% (p<.005). Pts. with CAD increased from 58% to 62% (p<.01), while normals tended to increase from 69% to 73% (p=.16). PP wall motion also tended to improve compared with Peak wall motion in 12 cases studied. PPEF-PEF was not significantly different between patients with CAD and normals. The PPEF-rest EF difference (PPEF-REF) was significantly different at 13.8 in normals and 7 in pts. with CAD (p<.015). The Peak EF-rest EF difference (PEF-REF) was 9.8 in normals and 2.3 in pts.more » with CAD (p<.02). PPEF-REF, PEF-REF, and the presence of CAD wre correlated with Peak exercise level in watts (r=.56-.68; p=<.03). Thus, the PPEF-REF and PEF-REF were related to both exercise level and presence of CAD in this series. Improved EF occurs with PP workloads in pts. with CAD and tends to occur in normals. Wall motion also tends to improve in both groups. These occurrences must be considered in interpreting RVGs obtained at reduced workloads after Peak exercise has been achieved.« less
Hyperpolarized pyruvate to measure the influence of PKM2 activation on glucose metabolism in the healthy kidney (2021)

The purpose of the current study was to investigate if hyperpolarized [1-<sup>13</sup> C]pyruvate can inform us on the metabolic consequences for the kidney glucose metabolism upon treatment with the pyruvate kinase M2 (PKM2) activator TEPP-46, which has shown promise as a novel therapeutic target for diabetic nephropathy. A healthy male Wistar rat model was employed to study the conversion of [1-<sup>13</sup> C]pyruvate to [1-<sup>13</sup> C]lactate in the kidney 2 and 4 h after treatment with TEPP-46. All rats were scanned with hyperpolarized [1-<sup>13</sup> C]pyruvate kidney MR and vital parameters and blood samples were taken after scanning. The PKM2 activator TEPP-46 increases the glycolytic activity in the kidneys, leading to an increased lactate production, as seen by hyperpolarized pyruvate-to-lactate conversion. The results are supported by an increase in blood lactate, a decreased blood glucose level and an increased pyruvate kinase (PK) activity. The metabolic changes observed in both kidneys following treatment with TEPP-46 are largely independent of renal function and could as such represent a new and extremely sensitive metabolic readout for future drugs targeting PKM2. These results warrant further studies in disease models to evaluate if [1-<sup>13</sup> C]pyruvate-to-[1-<sup>13</sup> C]lactate conversion can predict treatment outcome.
Engineering novel chemosensory proteins to respond to antiviral drugs (2021)

Cellular activities constantly change to precisely respond to their biological needs. In many cases, proteins carry out these activities because they can exhibit graded and dynamic responses to perform an array of cellular functions. To study these biological activities and to repurpose proteins for novel uses such as cell therapies, we must be able to control protein activity with synthetic inducers, such as chemical ligands. Multiple chemical inducers have been employed to achieve protein control, but there remains a need for inducer ligands that minimally interact with endogenous pathways, display high bioavailability, and are absent or minimally present from dietary sources. In this work, we control protein activities with the Hepatitis C virus cis-protease NS3 and its numerous clinically validated, highly specific inhibitors. First, we use NS3 to create a Ligand Inducible Connection (LInC) to chemically control gene expression, protein localization and cell signaling in mammalian cells. We then extend the use of catalytically inactive NS3 as a high affinity binder in conjunction with genetically encoded approaches to inhibit NS3, including peptides and RNA aptamers. Using catalytically inactive NS3, genetically encoded peptides, and small molecule drugs, we conditionally control peptide docking with antiviral drugs. We apply this concept to control mammalian gene expression, cell signaling, enzyme activity, and develop a new mechanism for allosteric regulation of Cre recombinase. Altogether, we have developed a new toolkit for controlling diverse protein activities with highly orthogonal, antiviral drugs.
Novel <i>THAP1</i> sequence variants in primary dystonia (2010)

A heterogeneous collection of THAP1 sequence variants is associated with varied anatomical distributions and onset ages of both familial and sporadic primary dystonia.
Peptide contour length determines equilibrium secondary structure in protein‐analogous micelles (2013)

This work advances bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates in which a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide contour length in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e., micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide contour length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and α-helical structure. Upon self-assembly in the crowded environment of a micellar corona, however, short peptides are prone to β-sheet structure and cylindrical micelle geometry while longer peptides remain helical in spheroidal micelles. The transition to β-sheets in short peptides is rapid, whereby amphiphiles first self-assemble with α-helical peptide structure, then transition to their equilibrium β-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide contour length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the time-dependent nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates.