gebhart/patrepeval huggingface dataset:
Redesigning the Coumarin Scaffold into Small Bright Fluorophores with Far-Red to Near-Infrared Emission and Large Stokes Shifts Useful for Cell Imaging (2017)

Among the palette of previously described fluorescent organic molecules, coumarins are ideal candidates for developing cellular and molecular imaging tools due to their high cell permeability and minimal perturbation of living systems. However, blue-to-cyan fluorescence emission is usually difficult in in vivo applications due to the inherent toxicity and poor tissue penetration of short visible light wavelengths. Here, we introduce a new family of coumarin-based fluorophores, nicknamed COUPY, with promising photophysical properties, including emission in the far-red/near-infrared (NIR) region, large Stokes shifts, high photostability, and excellent brightness. COUPY fluorophores were efficiently synthesized in only three linear synthetic steps from commercially available precursors, with the N-alkylation of a pyridine moiety being the key step at the end of the synthetic route, as it allows for the tuning of the photophysical properties of the resulting dye. Owing to their low molecular weights, COUPY dyes show excellent cell permeability and accumulate selectively in nucleoli and/or mitochondria of HeLa cells, as their far-red/NIR fluorescence emission is easily detected at a concentration as low as 0.5 μM after an incubation of only 20 min. We anticipate that these coumarin scaffolds will open a way to the development of novel coumarin-based far-red to NIR emitting fluorophores with potential applications for organelle imaging and biomolecule labeling.
A proposal for informative default priors scaled by the standard error\n of estimates (2020)

If we have an unbiased estimate of some parameter of interest, then its\nabsolute value is positively biased for the absolute value of the parameter.\nThis bias is large when the signal-to-noise ratio (SNR) is small, and it\nbecomes even larger when we condition on statistical significance; the winner's\ncurse. This is a frequentist motivation for regularization. To determine a\nsuitable amount of shrinkage, we propose to estimate the distribution of the\nSNR from a large collection or corpus of similar studies and use this as a\nprior distribution. The wider the scope of the corpus, the less informative the\nprior, but a wider scope does not necessarily result in a more diffuse prior.\nWe show that the estimation of the prior simplifies if we require that\nposterior inference is equivariant under linear transformations of the data. We\ndemonstrate our approach with corpora of 86 replication studies from psychology\nand 178 phase 3 clinical trials. Our suggestion is not intended to be a\nreplacement for a prior based on full information about a particular problem;\nrather, it represents a familywise choice that should yield better long-term\nproperties than the current default uniform prior, which has led to systematic\noverestimates of effect sizes and a replication crisis when these inflated\nestimates have not shown up in later studies.\n
(Z)-1-Methoxy-2-Methylseleno-1-(Trimethylsiloxy)Propene (2007)

[868617-71-4] C8H18O2SeSi (MW 253.27) InChI = 1S/C8H18O2SeSi/c1-7(11-3)8(9-2)10-12(4,5)6/h1-6H3/b8-7- InChIKey = YUIWJVQHUUQPBG-FPLPWBNLSA-N (reagent used as a nucleophile in asymmetric synthesis of organic compounds) Physical Data: bp 31 °C/0.4 mmHg; d 1.178 g cm−3. Solubility: sol alcohol, ether, and most organic solvents. Form Supplied in: a pale yellow oil; commercially unavailable. Analysis of Reagent Purity: IR (neat): 1724, 1655, 1439, 1252, 1221, 1178, 1132, 1097, 901, 843 cm−1; 1H NMR (C6D6): δ 3.30 (s, 3H), 2.13 (s, 3H), 1.87 (s, 3H), 0.30 (s, 9H); 13C NMR (C6D6): δ 152.8, 84.0, 56.0, 17.4, 4.5, 0.2; HR MS: calcd. for C8H18O2SeSi (M+) 254.0241, found 254.0240. Preparative Methods: (1) (eq 1; Step 1) To a suspension of selenium powder (7.0 g, 89 mmol) in THF (177 mL) at 0 °C was added methyllithium in ether (0.98 M, 98 mL, 96 mmol). After the reaction mixture had been stirred for 30 min at 0 °C, methyl 2-bromopropanoate (9.9 mL, 89 mmol) was added to the mixture at −78 °C. The reaction mixture was allowed to warm to room temperature and then saturated aqueous ammonium chloride was added. The mixture was extracted with diethyl ether, and the organic layer was washed with water and brine, dried over sodium sulfate. After filtration of the mixture and evaporation of the solvent, the crude product was purified by distillation to afford methyl 2-methylselenopropanoate (13.3 g, 82%) as a pale yellow oil: bp 82 °C/65 mmHg; IR (neat): 1730 cm−1;1H NMR (CDCl3): δ 3.68 (s, 3H), 3.41 (q, J = 7.3 Hz, 1H), 2.06 (s, 3H), 1.49 (d, J = 7.3 Hz, 3H); 13C NMR (CDCl3): δ 174.0, 52.0, 31.7, 16.9, 3.9; HR MS: calcd. for C5H10O2Se (M+) 181.9846, found 181.9843. (eq 1; Step 2) To a solution of diisopropylamine (1.8 mL, 12.8 mmol) in THF (15 mL) at 0 °C was added n-butyllithium in hexane (1.66 M, 7.8 mL, 12.9 mmol). After the reaction mixture had been stirred for 30 min at 0 °C, a solution of methyl 2-methylselenopropanoate (2.13 g, 11.8 mmol) in THF (10 mL) was added at −78 °C. The reaction mixture was stirred for 1 h at −78 °C and then chlorotrimethylsilane (3.0 mL, 23.7 mmol) was added. After the reaction mixture had been stirred for 1 h at room temperature, it was concentrated by evaporation of the solvent. Petroleum ether was added to the residue, and the suspension was filtered through a short pad of Celite under an argon atmosphere. After evaporation of the solvent, the crude product was purified by distillation to afford a mixture of (Z)- and (E)-1-methoxy-2-methylseleno-1-(trimethylsiloxy)propene (Z/E = 90/10, 2.22 g, 75%). Purification: usable after distillation. Handling, Storage, and Predictions: stable after distillation under argon or nitrogen atmosphere.
INVITED REVIEW Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants (2014)

†Background Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic (‘niche-controlled’) or intrinsic regulatory mechanisms and are fundamentally important in plant development. †Scope This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. †Conclusions Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
An IDS Alert Fusion Approach Based on Happened Before Relation (2008)

Alert fusion is a process that analyzes the alerts produced by one or more intrusion detection systems and provides a more succinct and high-level view of security event or attempted intrusions. Unfortunately, the serialized alerts by detected or created time will hide the intrinsic order between alerts. It is a disadvantage to alert fusion. In this paper, we proposed an alert fusion method based on a happened before relation, which revealed the intrinsic order between alerts. Utilizing the happened before relation can improve the performance of alert correlation and reduce the interference with other correlation components. The experiment results show that our approach is effective in achieving alert reduction and aggregation.
Templated dewetting: designing entirely self-organized platforms for photocatalysis (2016)

Formation and dispersion of metal nanoparticles on oxide surfaces in site-specific or even arrayed configuration are key in various technological processes such as catalysis, photonics, electrochemistry and for fabricating electrodes, sensors, memory devices, and magnetic, optical, and plasmonic platforms. A crucial aspect towards an efficient performance of many of these metal/metal oxide arrangements is a reliable fabrication approach. Since the early works on graphoepitaxy in the 70s, solid state dewetting of metal films on patterned surfaces has been much explored and regarded as a most effective tool to form defined arrays of ordered metal particles on a desired substrate. While templated dewetting has been studied in detail, particularly from a mechanistic perspective on lithographically patterned Si surfaces, the resulting outstanding potential of its applications on metal oxide semiconductors, such as titania, has received only limited attention. In this perspective we illustrate how dewetting and particularly templated dewetting can be used to fabricate highly efficient metal/TiO<sub>2</sub> photocatalyst assemblies <i>e.g.</i> for green hydrogen evolution. A remarkable advantage is that the synthesis of such photocatalysts is completely based on self-ordering principles: anodic self-organized TiO<sub>2</sub> nanotube arrays that self-align to a highest degree of hexagonal ordering are an ideal topographical substrate for a second self-ordering process, that is, templated-dewetting of sputter-deposited metal thin films. The controllable metal/semiconductor coupling delivers intriguing features and functionalities. We review concepts inherent to dewetting and particularly templated dewetting, and outline a series of effective tools that can be synergistically interlaced to reach fine control with nanoscopic precision over the resulting metal/TiO<sub>2</sub> structures (in terms of <i>e.g.</i> high ordering, size distribution, site specific placement, alloy formation) to maximize their photocatalytic efficiency. These processes are easy to scale up and have a high throughput and great potential to be applied to fabricate not only (photo)catalytic materials but also a large palette of other functional nanostructured elements and devices.
Aerial Image Mosaicking with the Aid of Vector Roads (2012)

This article proposes a novel approach for using vector roads for the generation of seamline networks for aerial image mosaicking. A representative seamline is extracted as follows. First, the straight skeleton of the overlapping area of adjacent images is extracted. Second, vector roads in the overlapping regions are overlaid with the extracted skeleton to build a weighted graph G and the lowest-cost path is considered as a seamline candidate. Finally, the seamline candidate is refined by considering its surrounding pixels. The refined seamline is employed as the final seamline. The resultant seamlines commonly follow the centerlines of roads as much as possible and the mosaic image appears more seamless. Moreover, the vector-based approach is typically more efficient than the existing raster-based approaches: the vector-based approach is nearly ten times faster than a raster-based representative.
Feature Selection Using Salp Swarm Algorithm with Chaos (2018)

The performance of classification algorithms is highly sensitive to the data dimensionality. High dimensionality may cause many problems to a classifier like overfitting and high computational time. Feature selection (FS) is a key solution to both problems. It aims to reduce the number of features by removing the irrelevant, redundant and noisy data, while trying to keep an acceptable classification accuracy. FS can be formulated as an optimization problem. Metaheuristic algorithms have shown superior performance in solving this type of problems. In this work, a chaotic version of Salp Swarm Algorithm (SSA) is proposed, which is considered one of the recent metaheuristic algorithms. The proposed approach is applied for the first time on feature selection problems. Four different chaotic maps are used to control the balance between the exploration and exploitation in the proposed approach. The proposed approaches are evaluated using twelve real datasets. The comparative results shows that the chaotic maps significantly enhances the performance of the SSA algorithm and outperforms other similar approaches in the literature.
NOTE ON THE STRONTIUM-90 FALLOUT (1959)

A revision is reported of an estimate made previously of the mean residence time of Sr-90 in the stratosphere from data recently made available by Libby. It is assumed that stratospheric fallout is uniformly distributed over the earth's surface and that the tropospheric fallout is confined about the latitude of the explosion. The mean stratospheric residence time is found to be between 6 and 7 1/2 years. The previous estimate made in RM-1956, Note on the Sr- 90 Hazard, determined this value to be between 4 and 6 years. (auth)
Aspects of Distributed Computer Systems (1980)

From the Publisher:
Distributed processing has become a mainstream systems style. This volume describes the state-of-the-art, and explores the underlying issues (and controversies) of distributed computer systems. Contains new material on recent developments in software, hardware, and systems design--and expanded chapters on network protocols, distributed data, distributed database, and software structure. Also discusses the costs of distributed computer systems, and the effects of distributed processing on management styles.
FRAUNHOFER HHI AT TRECVID 2004: SHOT BOUNDARY DETECTION SYSTEM (2004)

This paper describes the shot boundary detection and determination system developed at the Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, used for the evaluation at TRECVID 2004. The system detects and determines the position of hard cuts, dissolves, fades, and wipes. It is very fast and has proved to have a very good detection performance. As input for our system, we use luminance pixel values of sub-sampled video data. The hard cut detector uses pixel and edge differences with an adaptive thresholding scheme. Flash detection and slow motion detection lower the false positive rate. Dissolve and fade detection is done with edge energy statistics, pixel and histogram differences, and a linearity measure. Wipe detection works with an evenness factor and double Hough transform. The difference between the submitted runs is basically only different threshold settings in the detectors, resulting in different recall and precision values. 1.
Single-cell RNA sequencing unveils intestinal eosinophil development and specialization (2021)

Eosinophils are an integral part of the gastrointestinal (GI) immune system that contribute to homeostatic and inflammatory processes. Here, we investigated the existence of functional subsets that carry out specialized tasks in health and disease. We used single-cell transcriptomics and high-dimensional flow cytometry to delineate murine eosinophil subpopulations and their ontogenetic relationship in the steady state and during infection and inflammation. Profiling of eosinophils from bone marrow, blood, spleen and several GI tissues revealed five distinct subsets representing consecutive developmental and maturation stages across organs, each controlled by a specific set of transcription factors. Furthermore, we discovered a highly adapted PD-L1 + CD80 + eosinophil subset in the GI tract, characterized by its immune regulatory properties, bactericidal activity upon challenge infection and tissue-protective function during inflammation. Our data provide a framework for the characterization of eosinophil subsets in GI diseases and highlight their crucial contribution to homeostasis, immune regulation and host defense.
New Precision Metrics for Contrast Sensitivity Testing (2017)

Visual sensitivity is comprehensively described by the contrast sensitivity function (CSF), but current routine clinical care does not include its assessment because of the time-consuming need to estimate thresholds for a large number of spatial frequencies. The quick CSF method, however, dramatically reduces testing times by using a Bayesian information maximization rule. We evaluate the test-retest variability of a tablet-based quick CSF implementation in a study with 100 subjects who repeatedly assessed their vision with and without optical correction. We first discuss two commonly used measures of repeatability, intraclass correlation and the Bland-Altman Coefficient of Repeatability, and show that they are vulnerable to artifacts. Instead, we propose to formulate precision as an information retrieval task: from all repeat test scores, can we retrieve a certain individual based on their first test score? We then use rank-based analyses such as mean average precision as a better measure to compare different test metrics, and show that the highest test-retest precision is achieved using a summary statistic, the area under the log CSF (AULCSF). This demonstrates the benefit of assessment of the whole CSF compared to sensitivity at individual spatial frequencies only. AULCSF also yields best discrimination performance (99.2%) between measurements that were taken with and without glasses, respectively, even better than CSF Acuity. The tablet-based quick CSF thus enables the rapid and reliable home monitoring of visual function, which has the potential to improve early diagnosis and treatment of ophthalmic pathologies such as diabetic retinopathy or age-related macular degeneration.
Compact Hash Tables for High-Performance Traffic Classification on Multi-core Processors (2014)

Traffic classification is one of the kernel applications in network management. Many Machine Learning (ML) traffic classification algorithms are based on decision-trees. While most of the existing implementations of decision-trees are hardware-based, a new trend in network applications is to use software-based solutions. The decision-tree used for traffic classification is highly unbalanced; it is challenging to achieve high performance on multi-core platforms. In this paper, we present a high-throughput and low-latency traffic classification engine on multi-core platforms. We convert the decision-tree used in the C4.5 algorithm into multiple compact tables. All the compact tables are searched in parallel; efficient hashing techniques are employed to reduce the processing latency. The outcomes from all the tables are merged into the final classification result. High throughput can be sustained even if we scale up (1) the number of concurrent traffic classifiers, (2) the number of decision-tree leaves and (3) the number of features examined during the classification process. We prototype our design on state-of-the-art AMD and Intel multi-core platforms. For a typical C4.5 decision-tree consisting of 92 leaf nodes and 7 flow-level features, we achieve 134.15 Million Lookups Per Second (MLPS) throughput and 238.53 ns processing latency per lookup. Even for highly unbalanced decision-trees or large decision-trees consisting of up to 2 K leaf nodes, our traffic classification engine sustains high throughput and low latency without sacrificing classification accuracy (≥ 98.15%). We achieve 2.7× throughput compared with the classic C4.5 decision-tree-based implementations, and at least 12× speed-up compared with the existing traffic classifiers on multi-core platforms.
Short- and Long-Term Effects of Sildenafil on Skin Flap Survival in Rats (2006)

These results suggest that PDE 5 inhibitors may play a more important role in early postoperative skin flap viability rather than at later time points and may be beneficial for skin flap viability as shown in the rat model. PDE 5 inhibitors may reduce the extent of necrosis after reconstructive surgeries.
Traumatic Brain Injury in the Elderly: Is it as Bad as we Think? (2012)

Traumatic brain injury in elderly patients is a neglected global disease burden. The main cause is fall, followed by motor vehicle accidents. This review article summarizes different aspects of geriatric traumatic brain injury, including epidemiology, pathology, and effects of comorbidities and pre-injury medications such as antiplatelets and anticoagulants. Functional outcome with or without surgical intervention, cognitive outcome, and psychiatric complications are discussed. Animal models are also reviewed in attempt to explain the relationship of aging and outcome, together with advances in stem cell research. Though elderly people in general did fare worse after traumatic brain injury, certain "younger elderly" people, aged 65-75 years, could have a comparable outcome to younger adults after minor to moderate head injury.
Risk of breast cancer recurrence in women initiating tamoxifen with CYP2D6 inhibitors (2009)

CRA508 The full, final text of this abstract will be available in Part II of the 2009 ASCO Annual Meeting Proceedings, distributed onsite at the Meeting on May 30, 2009, and as a supplement to the June 20, 2009, issue of the Journal of Clinical Oncology. [Table: see text]
Power level-dependent dual-operating mode LDMOS power amplifier for CDMA wireless base-station applications (2005)

The design and analysis of a dual-operating mode laterally diffused metal-oxide semiconductor (LDMOS) power amplifier for code-division multiple-access wireless communication base-station applications is presented in this paper. The amplifier structure consists of four parallelly located single-stage LDMOS amplifier array, the dual-mode input power divider, and output power combiner. In this dual-mode operation, the number of operating power amplifier (either one or four amplifiers) is controlled depending on the required power level. This results in significant improvement in efficiency performance of the amplifier by minimizing unnecessary dc power consumption. In addition to the enhancement of efficiency, the amplifier design approach also provides better overall linearity performance. The proposed dual-operating mode design technique was successfully demonstrated by designing, implementing, and testing an LDMOS power amplifier with Motorola MRF 21030 in this study.