gebhart/patrepeval huggingface dataset:
Virtual Fluorescence Color Channels by Selective Photobleaching in Digital PCR Applied to the Quantification of KRAS Point Mutations (2021)

Multiplexing of analyses is essential to reduce sample and reagent consumption in applications with large target panels. In applications such as cancer diagnostics, the required degree of multiplexing often exceeds the number of available fluorescence channels in polymerase chain reaction (PCR) devices. The combination of photobleaching-sensitive and photobleaching-resistant fluorophores of the same color can boost the degree of multiplexing by a factor of 2 per channel. The only additional hardware required to create virtual fluorescence color channels is a low-cost light-emitting diode (LED) setup for selective photobleaching. Here, we present an assay concept for fluorescence color multiplexing in up to 10 channels (five standard channels plus five virtual channels) using the mediator probe PCR with universal reporter (UR) fluorogenic oligonucleotides. We evaluate the photobleaching characteristic of 21 URs, which cover the whole spectral range from blue to crimson. This comprehensive UR data set is employed to demonstrate the use of three virtual channels in addition to the three standard channels of a commercial dPCR device (blue, green, and red) targeting cancer-associated point mutations (<i>KRAS</i> G12D and G12V). Moreover, a LOD (limit of detection) analysis of this assay confirms the high sensitivity of the multiplexing method (<i>KRAS</i> G12D: 16 DNA copies/reaction in the standard red channel and <i>KRAS</i> G12V: nine DNA copies/reaction in the virtual red channel). Based on the presented data set, optimal fluorogenic reporter combinations can be easily selected for the application-specific creation of virtual channels, enabling a high degree of multiplexing at low optical and technical effort.
Efficacy of Lifestyle Modification for Long‐Term Weight Control (2004)

Abstract A comprehensive program of lifestyle modification induces loss of ∼10% of initial weight in 16 to 26 weeks, as revealed by a review of recent randomized controlled trials, including the Diabetes Prevention Program. Long‐term weight control is facilitated by continued patient‐therapist contact, whether provided in person or by telephone, mail, or e‐mail. High levels of physical activity and the consumption of low‐calorie, portion‐controlled meals, including liquid meal replacements, can also help maintain weight loss. Additional studies are needed of the effects of macronutrient content (e.g., low‐fat vs. low‐carbohydrate diets) on long‐term changes in weight and health. Research also is needed on effective methods of providing comprehensive weight loss control to the millions of Americans who need it.
ISOLATION AND IDENTIFICATION OF TRACHOMA AND INCLUSION CONJUNCTIVITIS AGENTS IN MELBOURNE, 1966 TO 1972 (1973)

Conjunctival scrapings from 262 adults with conjunctivitis were examined for chlamydia, viruses and bacteria. As well as the expected types of pathogenic bacteria cultured from the 415 specimens, seven isolates of chlamydia, four of herpes simplex and one of vaccinia were obtained. Eye secretions and serum from the 2 patients tested had chlamydial antibodies detected by the indirect immunofluorescent test. Chlamydia were also obtained from the eyes of 3 babies with neonatal non-bacterial conjunctivitis. Biological properties of all 10 chlamydia showed that they were trachoma-inclusion conjunctivitis agents.
Approximating Aggregation Queries in Peer-to-Peer Networks (2006)

Peer-to-peer databases are becoming prevalent on the Internet for distribution and sharing of documents, applications, and other digital media. The problem of answering large scale, ad-hoc analysis queries ― e.g., aggregation queries ― on these databases poses unique challenges. Exact solutions can be time consuming and difficult to implement given the distributed and dynamic nature of peer-to-peer databases. In this paper we present novel sampling-based techniques for approximate answering of ad-hoc aggregation queries in such databases. Computing a high-quality random sample of the database efficiently in the P2P environment is complicated due to several factors ― the data is distributed (usually in uneven quantities) across many peers, within each peer the data is often highly correlated, and moreover, even collecting a random sample of the peers is difficult to accomplish. To counter these problems, we have developed an adaptive two-phase sampling approach, based on random walks of the P2P graph as well as block-level sampling techniques. We present extensive experimental evaluations to demonstrate the feasibility of our proposed solutio
de novo MAPT mutation G335A causes severe brain atrophy, 3R and 4R PHF-tau pathology and early onset frontotemporal dementia (2020)

International audience
Tumor Therapy With Proteasome Inhibitor Bortezomib (Velcade, PS-341) Plus Death Receptor (DR5) Agonist Antibody MD5.1 (2005)

s: Abstracts for the 20th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer (Primary Authors are Italicized): NEW AGENTS IN DEVELOPMENT
1,3-Dichloropropenes – in the preparation of thiazole derivatives – 2-chloro-5-chloromethylthiazole and 5-hydroxymethylthiazole (2001)

1,3-Dichloropropene (a mixture of cis and trans isomers) has been used to synthesize thiazole derivatives by starting its reaction with sodium thiocyanate to give 3-chloro-2propenylthiocyanate. This thiocyanate on heating undergoes thermal [3,3]-sigmatropic rearrangement to give the isothiocyanate derivative, 3-chloro-1-propenylisothiocyanate. This mixture of cis and trans isomers of isothiocyanate on chlorination gave 2-chloro-5chloromethylthiazole. 5-Hydroxymethylthiazole is made from 2-chloro-5-chloromethyl thiazole in two steps, first by displacement of the aliphatic halogen with formate anion followed by hydrolysis of the formate ester and hydrodehalogenation of the aromatic halogen using hydrogen and palladium on carbon catalyst.
Multi Access Data Network Connectivity and IP Flow Mobility in Evolved Packet System &#40;EPS&#41; (2010)

Release-8 (Rel-8) EPS (Evolved Packet System) introduced a multi access 3GPP system where different heterogeneous access systems are connected to a common core network. However, in the system, the subscriber cannot communicate using multiple accesses simultaneously. Mobile devices with multiple interfaces are becoming commonly available and the set of applications running on the devices is diversifying with some applications suited to run over 3GPP access systems and other applications well suited to run over some other complementary access systems. In these circumstances, it has become important to allow dynamic allocation of different IP flows to different access systems as per their requirements, so that the user experience can be enhanced while the connectivity cost for the operator can be optimized. This paper has studied and analyzed the scenarios, requirements and solutions related to simultaneous connectivity to multiple access networks and IP flow mobility, and proposed necessary enhancements to existing 3GPP specifications for EPS.
γ-Alumina: The Essential and Unexpected Role of Water for the Structure, Stability, and Reactivity of “Defect” Sites (2012)

Combining experiments and DFT calculations, we show that tricoordinate Al(III) Lewis acid sites, which are present as metastable species exclusively on the major (110) termination of γ- and δ-Al(2)O(3) particles, correspond to the "defect" sites, which are held responsible for the unique properties of "activated" (thermally pretreated) alumina. These "defects" are, in fact, largely responsible for the adsorption of N(2) and the splitting of CH(4) and H(2). In contrast, five-coordinate Al surface sites of the minor (100) termination cannot account for the observed reactivity. The Al(III) sites, which are formed upon partial dehydroxylation of the surface (the optimal pretreatment temperature being 700 °C for all probes), can coordinate N(2) selectively. In combination with specific O atoms, they form extremely reactive Al,O Lewis acid-base pairs that trigger the low-temperature heterolytic splitting of CH(4) and H(2) to yield Al-CH(3) and Al-H species, respectively. H(2) is found overall more reactive than CH(4) because of its higher acidity, hence it also reacts on four-coordinate sites of the (110) termination. Water has the dual role of stabilizing the (110) termination and modifying (often increasing) both the Lewis acidity of the aluminum and the basicity of nearby oxygens, hence the high reactivity of partially dehyxdroxylated alumina surfaces. In addition, we demonstrate that the presence of water enhances the acidity of certain four-coordinate Al atoms, which leads to strong coordination of the CO molecule with a spectroscopic signature similar to that on Al(III) sites, thus showing the limits of this widely used probe for the acidity of oxides. Overall, the dual role of water translates into optimal water coverage, and this probably explains why in many catalyst preparations, optimal pretreatment temperatures are typically observed in the "activation" step of alumina.
Measuring Relevance (2001)

Speaking at a Born Digital meeting in San Francisco, University of British Columbia professor John Willinsky noted "a sense among academics of the increasing irrelevance of the library to the creation and transmission of knowledge." In response, Willinsky advocates the creation of an exchange economy among research libraries that would sponsor the online, refereed publication of the scholarship (journals, dissertations, databases, archives, etc.) associated with their faculty members. He sees the increasing privatization of public knowledge as a potentially dangerous trend. He challenged librarians who are trained information specialists to become the center of a public knowledge exchange society. 1
Photo-alignment of Low-molecular Mass Nematic Liquid Crystals on Photochemically Bifunctional Chalcone-epoxy Film by Irradiation of a Linearly Polarized UV Light (2002)

Photocrosslinkable chalcone-epoxy compound comprising 1,3-bis-(4-hydroxy-phenyl)-propenone was synthe-sized for fabricating the photo-alignment layer of liquid crystals. Chalcone group was introduced into the main chain unit of the epoxy oligomer. We observed a photodimerization behavior and an optical anisotropy of this material by irradiation of a linearly polarized UV(LP-UV) light. With a trace amount of cationic photoinitiator (TRS-HFA), polymerization of epoxy groups was also conducted at the similar wavelength range used for photodimerization. Linearly polarized UV irradiation on the chalcone-epoxy films with cationic photoinitiator induced optical anisotropy of the film and the resultant film can be used for alignment layers for low molecular weight nematic liquid crystals.
Etching Reactivity of Negative Ions Generated in Cl2Downstream Plasma (2003)

Etching reactivity of negative ions is studied in the downstream region of inductively coupled Cl2 plasma. Negative ions are confirmed by a quadrupole mass and energy analyzer, and Cl- ions are found to be the dominant species and to show a maximum density at 30 mTorr pressure. The Si etch rate is examined in two ways; one is by direct exposure to the plasma with a certain DC bias and the other is by using a specially designed electrode box which enables independent ion irradiation by eliminating electrons magnetically. A higher etch rate is observed at the positive bias, especially at a pressure higher than 30 mTorr, while at the negative bias, the etching closely depends on pressure and is not observed at pressures higher than 10 mTorr. The Si etch rate obtained by the electrode box with the positive DC bias was maximum at 30 mTorr, being consistent with the result of the mass analysis and revealing that the etching is due to negative ions. It is concluded that the higher etch rate at the positive bias is due to the negative Cl- ions whose reactivity is higher than that of the positive Cl2+ ions. An in situ X-ray photoelectron spectroscopy (XPS) observation of the etched Si surface showed that the depth of the SiCl layer was thinner at the positive bias than at the negative bias, confirming that the negative ions have the higher etching reactivity.
An ontology-driven context aware framework for smart traffic monitoring (2017)

In this paper, we present a comprehensive methodology to support IoT based semantic traffic monitoring in smart cities to derive the status of traffic on a road segment in order to optimize traffic flow during rush hours. Smart traffic monitoring involves real-time traffic scene analysis from CCTV cameras to detect and identify stalled vehicles and measure traffic density on roads. The scene analysis essentially necessitates tracking and counting the number of moving and stopped vehicles as they progress along the image sequence by utilizing computer vision techniques. The obtained features along with manually annotated traffic data are translated to a higher level information using semantic web technologies, thus providing a common platform to exchange the information. As the perceptual modelling of traffic data involves media patterns so we have employed Multimedia Web Ontology Language (MOWL) for the semantic interpretation and to tackle inherent uncertainties involved in these media documents. MOWL supports hierarchical probabilistic reasoning framework and utilizes time-varying Dynamic Bayesian Networks (DBN) to perform semantic comparison and predict the evolution of changing situations. In this paper, we discuss the key tasks of vision and probabilistic reasoning components that provide a feasible solution to identify the cause of traffic jam. The proposed approach can be used to trigger an automatic warning or alerts to traffic authorities in case any anomalous activity is encountered and guide users to take some different route to avoid jam. The experimental results shows effectiveness of real-time vehicle monitoring to assess congestion on road and offer user an assistive environment to operate.
Evaluation of p53 mutation as a predictive biomarker for outcome to chemotherapy in ovarian cancer. (2011)

10522 Background: There is increasing evidence that patients (pts) with wild type p53 have higher response rates to single agent carboplatin and may gain no benefit from the addition of paclitaxel chemotherapy. We tested two hypotheses in the context of a controlled clinical trial: 1) Tumours with wild-type p53 are more sensitive to platinum based chemotherapy than those with mutant p53, so will survive longer; 2) Pts whose tumours have mutant p53 benefit from the addition of paclitaxel to treatment, whilst those with wild type p53 do not. Methods: We collected 265 archival diagnostic tissue samples from pts that took part in the UK Medical Research Council ICON3 ovarian cancer trial comparing carboplatin or CAP (cyclophosphamide, doxorubicin, cisplatin) vs carboplatin plus paclitaxel. We examined the tissue for p53 mutations by genomic DNA sequencing of the coding exons and adjacent splice sites. Overall survival (OS) was updated for this study. A Cox regression model was applied in the analysis. Results: Mutations of p53 were detected in 130/265 (49.1%) pts tumour samples. With a median follow up of 12 years, a total of 214 (84%) pts had died. In univariate analysis, the presence of p53 mutations was associated with worse OS for pts who received single agent carboplatin [HR (95%CI)=1.72(1.14-2.60), p=0.0099, n=121] and p53 status retained independent prognostic significance after adjusting for age, stage, residual bulk, grade and histology [HR (95% CI)=1.89 (1.20-2.93), p=0.0059]. For the second hypothesis (n=265), pts whose tumours had mutant p53 showed greater benefit from the addition of paclitaxel to their treatment [HR (95%CI)=0.64(0.43-0.95) p=0.027] compared to patients with wild-type p53 tumours [HR (95%CI)=1.02(0.68-1.54) p=0.92]. Conclusions: We conclude that p53 is an independent prognostic biomarker for OS in ovarian cancer, particularly for patients receiving single agent carboplatin. Furthermore, the addition of paclitaxel shows OS benefit for pts with p53 mutant tumours, but not for those with wild-type p53 tumours.
SCIG Based Wind Energy Integrated Multiterminal MMC-HVDC Transmission Network (2020)

Modular multilevel converter (MMC) based HVDC system for renewable energy integration has attracted the researcher’s interest nowadays. This paper proposes a control strategy for MMC based multiterminal HVDC system for grid integration of squirrel cage induction generator (SCIG) based wind energy systems. Unlike the average model, this work models the MMC using the aggregate model and develops multiterminal HVDC transmission network in MATLAB/Simulink. It further develops the MMC multiterminal HVDC transmission network in real time digital simulator (RTDS). Instead of simplified current source, the proposed network considers the complete dynamics of SCIG based wind source from generation to integration. It employs field-oriented control for optimum wind energy tracking and forms isolated AC grids using feed forward controller. The proposed MMC controller performance has been tested under severe balanced and unbalanced disturbances. The results from aggregate model based MMC network in MATLAB/Simulink and those of the experimental MMC network in RTDS are in full agreement. The results confirm optimum wind energy tracking, fulfill grid code requirements, and improve low voltage ride through capability.
Dynamics of Thin Liquid Films with Nonsoluble Surfactants:  Weakly Nonlinear Analysis (2000)

Amplitude equations for Turing instabilities for two models describing dynamics of thin liquid films with nonsoluble surfactants are derived. Analytical expressions for the film rupture time were obtained, and the comparison with the results of previous numerical simulations was performed. It was shown that the Marangoni effect due to insoluble surfactants cannot prevent the film rupture.
Outbreak of a beta-lactam resistant non-typeable Haemophilus influenzae sequence type 14 associated with severe clinical outcomes (2015)

This report illustrates the existence of non-typeable H. influenzae with high virulence, and furthermore emphasizes the importance of continuous surveillance of possible outbreaks in health care facilities and prompt measures when outbreaks occur.
1.3 Octave Supercontinuum Generation in Highly Ge-doped Photonic Crystal Fiber (2016)

We present a flat, visible 1.3-octave supercontinuum generated in a GeO2-doped photonic crystal fiber owing to an overlap of the modulation instability and Raman gain regions resulting in efficient energy transfer to new frequency components
“Rescue” regimens after Helicobacter pylori treatment failure (2008)

Helicobacter pylori (H pylori) infection is the main cause of gastritis, gastroduodenal ulcer disease, and gastric cancer. After more than 20 years of experience in H pylori treatment, in my opinion, the ideal regimen to treat this infection is still to be found. Currently, apart from having to know first-line eradication regimens well, we must also be prepared to face treatment failures. Therefore, in designing a treatment strategy we should not focus on the results of primary therapy alone, but also on the final (overall) eradication rate. The choice of a "rescue" treatment depends on which treatment is used initially. If a clarithromycin-based regimen was used initially, a subsequent metronidazole-based treatment (quadruple therapy) may be used afterwards, and then a levofloxacin-based combination would be a third "rescue" option. Alternatively, it has recently been suggested that levofloxacin-based rescue therapy constitutes an encouraging second-line strategy, representing an alternative to quadruple therapy in patients with previous PPI-clarithromycin-amoxicillin failure, with the advantage of efficacy, simplicity and safety. In this case, a quadruple regimen may be reserved as a third-line rescue option. Finally, rifabutin-based rescue therapy constitutes an encouraging empirical fourth-line strategy after multiple previous eradication failures with key antibiotics such as amoxicillin, clarithromycin, metronidazole, tetracycline, and levofloxacin. Even after two consecutive failures, several studies have demonstrated that H pylori eradication can finally be achieved in almost all patients if several rescue therapies are consecutively given. Therefore, the attitude in H pylori eradication therapy failure, even after two or more unsuccessful attempts, should be to fight and not to surrender.
Pigment composition of 6 xanthophycean algae and Scenedesmus quadricauda (1994)

The pigment composition of 6 xanthophyceae algae (Goniochloris sculpta, Pleurochloris sp., Heterothrix mucicola, Heterothrix sp. 1-3) and Scenedesmus quadricauda (strain GREIFSWALD/15) was investigated. The pigments were analysed using HPLC. In investigated xanthophycean algae the following main pigments were found: neoxanthin (0.013-0.643 % of total dry mass), violaxanthin (0.011-0.662 % of total dry mass), antheraxanthin (0.013-0.596 % of total dry mass), lutein (0.113-3.340 % of total dry mass), zeaxanthin (0.085-0.401 % of total dry mass), chlorophyll a (0.372-3.221 of total dry mass) and beta-carotene (0.016-0.162 % of total dry mass). Expected presence of pigments diatoxanthin and diadinoxanthin in investigated xanthophycean algae was not confirmed. Chlorophyll b was found only in the green alga Scenedesmus quadricauda.
Influence of HDL on the formation of 6-keto-PGF1 alpha and TXB2 in vitro: the importance of the source of HDL. (1992)

The influence of HDL, isolated from normolipidemic human blood and blood of normo- and hyperlipidemic rabbits, on in vitro 6-keto-PGF1 alpha synthesis by rabbit aorta and on TXB2 synthesis by platelets of clotting human and rabbit blood was tested. The HDL fraction from normolipidemic subjects, when incubated with blood from normolipidemic humans or rabbits, inhibited TXB2 formation. The same fraction stimulated the formation of 6-keto-PGF1 alpha after incubation with rabbit aorta taken from normolipidemic animals. HDL taken from hyperlipidemic rabbits inhibited 6-keto-PGF1 alpha formation in rabbits and had no influence on TXB2 formation. These results support the hypothesis that not only is the absolute amount of HDL important for its influence on prostanoid formation, but also the origin and the composition of the HDL fraction.
Ultrahigh-average-power solid state laser (2002)

This work presents an improved disk laser concept, where a diode- pumped disk is hydrostatically clamped to a rigid substrate and continuously cooled by a microchannel heat exchanger. Effective reduction of thermo-optical distortions makes this laser suitable for continuous operation at ultrahigh-average power.
The prevention of atherosclerosis with antioxidants (1992)

Recent research findings have suggested a role for pharmacologic as well as nutritional antioxidants in the prevention of atherosclerosis. Data from animal studies as well as cell culture experiments have shown that the drug probucol, which has hypocholesterolemic and antioxidant properties, is able to prevent oxidative modification of low density lipoproteins (LDL). Such modification is now believed to play a major part in the initiation and progression of arterial lesions. Nutrients with antioxidant properties such as vitamins C and E, beta-carotene, and mono-unsaturated fatty acids (when they replace polyunsaturated fatty acids) can reduce the susceptibility of LDL to oxidation. Antioxidant therapy, if proven useful, should be considered an adjunct to lipid-lowering therapy in order to have the greatest impact on coronary heart disease.