gebhart/patrepeval huggingface dataset:
High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis (2020)

Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.
Direct Bonding and Debonding Approach of Ultrathin Glass Substrates for High Temperature Devices (2017)

The advent of flexible thin-film electronic devices on ultrathin substrates is driven by the need to develop alternative handling methods fully compatible with front-end and backend processes. The purpose of this work is to present a new handling approach for ultrathin glass substrates based on direct glass-glass bonding and peel-off debonding at room temperature. This concept is evaluated through the realization of thin-film batteries (<;20μm) on ultrathin glass substrates (<;100μm). In order to bond, the ultrathin glass is laminated on thick carrier glass (>500μm) without intermediate layer. The stack of thin film battery is fabricated using sequential physical vapor depositions at temperature values up to 400°C. The debond process is completed at room temperature by mechanical peel-off of the encapsulation film laminated on thin film battery. As the results, there is no sign of any crack of the ultrathin glass (<;100μm) after debonding. Furthermore, the Electrochemical Impedance Spectroscopy (EIS) and galvanostatic cycling carried out before and after debonding process reveal that the device performances are slightly stable.
Sub-diffraction error mapping for localisation microscopy images (2021)

Assessing the quality of localisation microscopy images is highly challenging due to the difficulty in reliably detecting errors in experimental data. The most common failure modes are the biases and errors produced by the localisation algorithm when there is emitter overlap. Also known as the high density or crowded field condition, significant emitter overlap is normally unavoidable in live cell imaging. Here we use Haar wavelet kernel analysis (HAWK), a localisation microscopy data analysis method which is known to produce results without bias, to generate a reference image. This enables mapping and quantification of reconstruction bias and artefacts common in all but low emitter density data. By avoiding comparisons involving intensity information, we can map structural artefacts in a way that is not adversely influenced by nonlinearity in the localisation algorithm. The HAWK Method for the Assessment of Nanoscopy (HAWKMAN) is a general approach which allows for the reliability of localisation information to be assessed.
Training data selection by detecting predictability in non-stationary time series by a surrogate-cumulant based approach (2002)

We introduce a nonparametric cumulant based statistical approach for detecting linear and nonlinear statistical dependences in nonstationary time series. The statistical dependence is detected by measuring the predictability which tests the null hypothesis of statistical independence, expressed in Fourier-space, by the surrogate method. Therefore, the predictability is defined as a higher-order cumulant based significance discriminating between the original data and a set of scrambled surrogate data which correspond to the null hypothesis of a noncausal relationship between past and present. Information about the predictability can be used for example to select regions where a temporal structure is visible in order to select data for training a neural network for prediction. The regions where only a noisy behavior is observed are therefore ignored, avoiding in this fashion the learning of irrelevant noise which normally spoils the generalization characteristics of the neural network. We present an example of nonstationarity given by the chaotic time series of Henon (1976) perturbed with linearly increasing additive Gaussian noise. Nonlinear structures are tested in financial time series, like the Dollar-DM Tick exchange rate.
Uteroglobin gene expression in the rabbit uterus throughout gestation and in the fetal lung. Relationship between uteroglobin and eicosanoid levels in the developing fetal lung. (1995)

Uteroglobin (UG) gene encodes a cytokine-like, multifunctional, antiinflammatory protein, with potent phospholipase A2-inhibitory activity. It has been suggested that during implantation this protein protects the embryos from maternal immunological assault, facilitates the maintenance of quiescence in the uterus throughout pregnancy, prevents the onset of premature labor, and helps maintain an inflammation-free respiratory organ. This latter function of UG is suggested to be accomplished by preventing hydrolysis of surfactant phospholipids by a lung-specific phospholipase A2. Using reverse transcription polymerase chain reaction, in situ hybridization, immunofluorescence, and radioimmunoassay, we studied UG gene expression in the rabbit uterus throughout gestation and in the fetal lung. Here, we report that: (a) contrary to previous reports, UG gene expression in the rabbit uterus occurs throughout gestation with a precipitous decline just before parturition; (b) this gene expression is dramatically increased in the fetal lung with increasing gestational age; and (c) while there is an inverse relationship between the levels of UG, PGE2, and PGF2 alpha, a positive correlation was found in that of UG and leukotriene C4 in the fetal lung. Our results raise the possibility that dysregulation of UG gene expression, at least in part, may contribute to the onset of premature labor and the development of inflammatory lung disease in premature neonates.
O3–Na<sub>x</sub>Mn<sub>1/3</sub>Fe<sub>2/3</sub>O<sub>2</sub>as a positive electrode material for Na-ion batteries: structural evolutions and redox mechanisms upon Na<sup>+</sup>(de)intercalation (2015)

O3–Na<sub>0.77</sub>Mn<sub>1/3</sub>Fe<sub>2/3</sub>O<sub>2</sub>was studied by<italic>in situ</italic>XRPD. The system undergoes several structural transitions from 1.5 V to 4.3 V: O′3 → O3 → P3 → “X”.
In Vitro Antiproliferative Activity of Isothiocyanates and Nitriles Generated by Myrosinase-Mediated Hydrolysis of Glucosinolates from Seeds of Cruciferous Vegetables (2000)

A comparison of the effect of isothiocyanates and nitriles derived from some glucosinolates, namely, epi-progoitrin, sinalbin, glucotropaeolin, glucocheirolin, and glucoraphenin, on human erythroleukemic in vitro cultured cells was studied. Many studies have in fact evidenced that a consumption of vegetable containing glucosinolates could reduce the development of colorectal cancer. In the experimental conditions used, the production of isothiocyanates and nitriles from glucosinolates is almost quantitative as confirmed by HPLC or GC-MS analysis. The obtained results demonstrated that in general nitriles are considerably less potent than the corresponding isothiocyanates in inhibiting cancer cell growth. Particularly, the isothiocyanates inhibitory activity on K562 cells growth is higher in the case of products derived from epi-progoitrin, glucotropaeolin, glucoraphenin, and glucocheirolin; while for nitriles the higher activity in inhibiting K562 cells growth is showed by sinalbin-derived product. Considering the antiproliferative activity found for isothiocyanates and nitriles, further studies will be aimed to the possible application of glucosinolate-derived products as chemopreventive cancer agents for the reduction of colorectal cancer.
Device Identification via Analog Signal Fingerprinting: A Matched Filter Approach (2006)

As part of the Detecting Intrusions at Layer ONe (DILON) project, we show that Ethernet devices can be uniquely identified and tracked—using as few as 25 Ethernet frames—by analyzing variations in their analog signal caused by hardware and manufacturing inconsistencies. An optimal detector, the matched filter, is utilized to create signal profiles, which aid in identifying the device the signal originated from. Several non-traditional applications of the filter are presented in order to improve its ability to discriminate between signals from seemingly identical devices of the same manufacturing lot. The experimental results of applying these filters to three different models of Ethernet cards, totaling 16 devices, are presented and discussed. Important applications of this technology include intrusion detection (discovering node impersonation and network tampering), authentication (preventing unauthorized access to the physical network), forensic data collection (tying a physical device to a specific network incident), and assurance monitoring (determining whether a device will or is in the process of failing). 1.
Novel Mitogenic Effect of Adenosine on Coronary Artery Smooth Muscle Cells (2005)

Adenosine is a vascular endothelial cell mitogen, but anti-mitogenic for aortic smooth muscle cells and fibroblasts when acting via the A2B adenosine receptor. However, we show that adenosine increases porcine coronary artery smooth muscle cell (CASMC) number, cellular DNA content, protein synthesis, and PCNA staining. RT-PCR analysis indicates that porcine CASMC express A1, A2A, A3, and barely detectable levels of A2B receptor mRNAs. The mitogenic effect of adenosine is mimicked by NECA, CCPA, and R-PIA, but not by CGS21680and 2-Cl-IB-MECA, and is inhibited by DPCPX, indicating a prominent role for the A1 receptor. This interpretation is supported by the finding that adenosine- and CCPA-induced DNA synthesis is significantly inhibited by pertussis toxin, but substantially potentiated by PD81723, an allosteric enhancer of the A1 receptor. When a cDNA encoding the porcine A1 receptor was cloned and expressed in COS-1 cells, A1 receptor pharmacology is confirmed. Anti-sense oligonucleotides to the cloned sequence dramatically suppress the mitogenic effect of adenosine and CCPA. Conversely, over-expression of the cloned A1 receptor in CASMC increases adenosine- and CCPA-induced DNA synthesis. Furthermore, stimulation with adenosine or CCPA of intact coronary arteries in an organ culture model of vascular disease increases cellular DNA synthesis, which was abolished by DPCPX. We conclude that adenosine acts as a novel mitogen in porcine CASMC that express the A1 adenosine receptor, possibly contributing to the development of coronary artery disease.
Long-term Risk of Melanoma-Related Mortality for Patients With Uveal Melanoma Treated With Proton Beam Therapy (2015)

In this large series of patients with ocular melanoma treated conservatively with proton beam irradiation, the cumulative melanoma-related mortality rates continued to increase up to 23 years after treatment. Annual rates decreased considerably (to <1%) 14 years after treatment. Information regarding the long-term risk of dying of uveal melanoma may be useful to clinicians when counseling patients.
Wine consumption and dementia in the elderly: a prospective community study in the Bordeaux area. (1997)

Alcoholism is a possible cause of dementia, mainly through associated nutritional deficiencies and, rarely, through acute direct toxicity. However alcohol consumption was not found to be a risk factor in previous epidemiologic studies. We prospectively studied 3,777 community residents aged 65 and over, in the districts of Gironde and Dordogne. Average daily alcoholic consumption was recorded at baseline. Incident cases of dementia and Alzheimer's disease were screened at follow-up with explicit criteria. At 3 years, 2,273 subjects not demented at baseline were still available for follow-up. Wine was the only alcoholic beverage reported by more than 95 p. 100 of regular drinkers. In the 318 subjects drinking 3 to 4 standard glasses per day (> 250 and up to 500 ml), categorized as moderate drinkers, the crude odds ratio (OR) was 0.18 for incident dementia (p < 0.01) and 0.25 for Alzheimer's disease (p < 0.03), as compared to the 971 non-drinkers. After adjusting for age, sex, education, occupation, baseline MMSE and other possible confounders, the ORs were respectively 0.19 (p < 0.01) and 0.28 (p < 0.05). In the 922 mild drinkers (< 1 to 2 glasses per day) there was a negative association only with AD, after adjustment (OR = 0.55; p < 0.05). The inverse relationship between moderate wine drinking and incident dementia was explained neither by known predictors of dementia nor by medical, psychological or socio-familial factors. Considering also the well documented negative associations between moderate wine consumption and cardiovascular morbidity and mortality in this age group, it seems that there is no medical rationale to advise people over 65 to quit drinking wine moderately, as this habit carries no specific risk and may even be of some benefit for their health. Advising all elderly people to drink wine regularly for prevention of dementia would be however premature at this stage.
Structure of the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">L</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="normal">β</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>phases in a hydrated phosphatidylcholine multimembrane (1988)

We report x-ray measurements on well aligned, freely suspended films of stacked bilayer membranes of the phospholipid dimyristoyl-phosphatidylcholine in a continuously variable humidity- and temperature-controlled environment. Remarkably, the most commonly observed ${\mathrm{L}}_{\mathrm{\ensuremath{\beta}}\mathcal{'}}$ phase is in fact three distinct 2D phases where the phase transitions are driven by hydration forces and the phases are distinguished by the relation between the molecular tilt direction and the 2D bond direction.
Pharmaceuticals, Large‐Scale Synthesis (2005)

Abstract The capability to fulfill drug substance requirements in support of the various elements of pharmaceutical development is an essential component of the overall drug development process. The preparation of bulk materials for toxicology, formulation development, and clinical supplies can represent a significant challenge, depending on such factors as the molecular complexity of the drug candidate, the quantities of materials required, and the state of development of the synthetic process. As a drug candidate proceeds through the various stages of drug development and into commercial launch, the challenge of process development is to ensure the uninterrupted supply of drug substance without compromising the ability to ultimately supply a commercially viable chemical process. This chapter serves to provide a general overview of the issues and requirements associated with the development and scale‐up of chemical processes for bulk active drug substances. An account of the nevirapine process development efforts at Boehringer Ingelheim is also provided as an example of the evolution of a chemical process from the initial efforts in medicinal chemistry through to commercial‐scale operations.
EOS: Exactly-Once E-Service Middleware (2002)

Today&apos;s web-based E-services do not handle system fail-ures well. One of the most prominent examples is unin-tentional purchase of multiple copies of the same item (e.g., a DVD) in an online store. This may happen when the user sees a browser timeout for the final checkout (place order) request caused by a short outage or over-load of the network or the backend servers (typically dur-ing peak load). Whereas the request may have been suc-cessfully albeit slowly processed, the user may attempt to send the check-out request once again, e.g., by hitting the browser refresh button, unintentionally buying another copy of the same item.
An efficient numerical method to solve the non-uniform MTL equation including field coupling (2004)

A simple and accurate method to solve the non-uniform multi-conductor transmission line problem is presented. The solution of the telegrapher's equation for an n-conductor transmission line above ideal conducting ground is given by the solution of 2n+1 initial-value problems, treated by the method of Runge-Kutta. The per-unit-length parameters and distributed current and voltage sources which result from the incident electromagnetic fields are developed in cubical splines. Examples are presented and are compared to full-wave method of moments (MoM) solutions (electric field integral equation).
Cumulative effects of ultraviolet radiation on the skin: cancer and photoaging. (1990)

The cumulative effects of solar exposure are skin cancer and photoaging. This relationship has been established by epidemiological, clinical, and pathological investigation. Understanding of the mechanisms of skin cancer and photoaging requires the study of model systems. For example, the study of cancerprone xeroderma pigmentosum patients has indicated that effective DNA repair is a major defence mechanism against skin cancer. However, there are few human models. The hairless albino mouse has been shown to be a good model for both photocarcinogenesis by ultraviolet radiation (UVR) alone and UVR in association with 8-methoxypsoralen and photoaging and may provide much information on mechanistic aspects. The use of sunscreens is often advocated as a means of preventing the cumulative effects of solar exposure. Animal data support this approach but such data must be interpreted with caution.
FROM GRAPHENE AND TOPOLOGICAL INSULATORS TO WEYL SEMIMETALS (2015)

This paper was presented at the 11th International School on Theoretical Physics Rzeszow, Poland, 1 – 6 September 2014. This work was published in HILLS, R.D.Y. ...et al., 2015. From graphene and topological insulators to Weyl semimetals. IN: Dugaev, V., Wal, A. and Barnas, J. (eds.) Symmetry, Spin Dynamics and the Properties of Nanostructures, pp. 277-315. Copyright @ 2015 with permission from World Scientific Publishing Co. Pte. Ltd.
Determination of Phosphorus-, Copper-, and Zinc-Containing Human Brain Proteins by LA-ICPMS and MALDI-FTICR-MS (2005)

Human brain proteins containing phosphorus, copper, and zinc were detected directly in protein spots in gels of a human brain sample after separation by two-dimensional gel electrophoresis using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). A powerful laser ablation system with cooled laser ablation chamber was coupled to a double-focusing sector field ICPMS. The separated protein spots in 2D gels were fast screened using the optimized microanalytical LA-ICPMS technique measured at medium mass resolution with a focused laser beam (wavelength, 213 nm; diameter of laser crater, 50 mum; and laser power density, 3 x 10(9) W cm(-2)) with respect to selected three essential elements. Of 176 protein spots in 2D gel from a human brain sample, phosphorus, copper, and zinc were detected in 31, 43, and 49 protein spots, respectively. For the first time, uranium as a naturally occurring radioactive element was found in 20 selected protein spots. The detection limits for P, S, Cu, Zn and U were determined in singular protein spots with 0.0013, 1.29, 0.029, 0.063, and 0.000 01 mg g(-1), respectively. A combination of LA-ICPMS with matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS) was applied for the identification of selected protein spots from human brain protein separated by 2D gel electrophoresis. Combining MALDI-FTICR-MS for the structure analysis of metal- and phosphorus-containing human brain proteins with LA-ICPMS, the direct analysis of heteroelements on separated proteins in 2D gels can be performed. For quantification of analytical LA-ICPMS data, the number of sulfur atoms per protein (and following the sulfur concentration) determined by MALDI-FTICR-MS was used for internal standardization. From the known sulfur concentration in protein, the concentration of other heteroelements was calculated. In addition, the number of phosphorylation and the phosphorylation sites of phosphorylated proteins in the human brain sample detected by LA-ICPMS were determined by MALDI-FTICR-MS. This technique allows the study of posttranslational modifications in human brain proteins.
Bone Generation in the Reconstruction of a Critical Size Calvarial Defect in an Experimental Model† (2007)

rhBMP2 but not PRP accelerated calvarial regeneration in 3 months. The DBM in the rhBMP2 groups were substituted by new trabecular bone. Shape molding was good with both metal and resorbable plate.
A proline‐rich protein, verprolin, involved in cytoskeletal organization and cellular growth in the yeast <i>Saccharomyces cerevisiae</i> (1993)

A gene (VRP1) encoding a novel proline-rich protein (verprolin) has been isolated from the yeast Saccharomyces cerevisiae as a result of its hybridization to a chick vinculin cDNA probe. The deduced protein sequence contains 24% proline residues present as proline-rich motifs throughout the verprolin sequence. Several of these motifs resemble recently identified sequences shown to bind Src homology 3 (SH3) domains in vitro. Replacement of the wild-type VRP1 allele with a mutant allele results in strains that grow slower than wild-type strains and are temperature sensitive. The vrp1 mutants are impaired in both cell shape and size and display aberrant chitin and actin localization. We propose that verporlin is involved in the maintenance of the yeast actin cytoskeleton, through interactions with other proteins, possibly containing SH3 domains.
Transposon induced chimeras show that <i>floricaula</i>, a meristem identity gene, acts non-autonomously between cell layers (1995)

Flower meristems comprise several distinct cell layers. To understand the role of cell interactions between and within these layers, we have generated plants chimeric for a key floral homeotic gene, floricaula (flo). These chimeras arose in Antirrhinum by excision of a transposon, restoring flo gene function. Activity of flo in a subset of cell layers gives fertile flowers with an abnormal morphology. This shows that flo can act non-autonomously between layers, although some aspects of its function are impaired. In addition, we show that flo exhibits some cell-autonomy within layers.