gebhart/patrepeval huggingface dataset:
Synthesis of [1α,2β,3α-2,3-bis(benzyloxymethyl)cyclobutyl]imidazol-5-amines: important precursors to cyclobut-A derivatives (1995)

A comparative study has been carried out on two different reaction sequences starting either from Feist's acid or ketene diethyl ketal and diethyl fumarate to prepare protected derivatives of (1α,2β,3α)-2,3-dihydroxycyclobutylamine. Difficulties were experienced upon reaction of the tert-butyldimethylsilyl-protected amine 13a with ethyl (Z)-N-(2-amino-l,2-dicyanovinyl)formimidate 6, but the dibenzoyl derivative 13b reacted smoothly to give the amidine 19 in high yield. The amidine is a useful intermediate for the synthesis of cyclobutane-based carbocyclic nucleosides. It can be readily converted by base treatment into the 4-cyanoimidazol-5-amine derivative 4b; a precursor to the dibenzoyl derivative of racemic Cyclobut-A and a new 1-amino-6-iminopurine derivative 25. Treatment of compound 19 with a catalytic amount of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) afforded the previously unknown 5-amino-4-(cyanoformimidoyl)imidazole derivative 20. This has been used to synthesize new 1,2-dihydropurine and 1-methyl derivatives of Cyclobut-A in good yields.
A novel Technique for Suppressing Undesired Coupling of LP01 Mode to Cladding Modes in Fiber Bragg Gratings (1996)

We propose a novel technique to suppress the undesired coupling of the fundamental mode to the cladding modes in a fiber grating by using a multimode grating fiber inserted between a pair of single mode fibers.
Automatic Pulmonary Artery-Vein Separation and Classification in Computed Tomography Using Tree Partitioning and Peripheral Vessel Matching (2015)

We present a method for automatic separation and classification of pulmonary arteries and veins in computed tomography. Our method takes advantage of local information to separate segmented vessels, and global information to perform the artery-vein classification. Given a vessel segmentation, a geometric graph is constructed that represents both the topology and the spatial distribution of the vessels. All nodes in the geometric graph where arteries and veins are potentially merged are identified based on graph pruning and individual branching patterns. At the identified nodes, the graph is split into subgraphs that each contain only arteries or veins. Based on the anatomical information that arteries and veins approach a common alveolar sag, an arterial subgraph is expected to be intertwined with a venous subgraph in the periphery of the lung. This relationship is quantified using periphery matching and is used to group subgraphs of the same artery-vein class. Artery-vein classification is performed on these grouped subgraphs based on the volumetric difference between arteries and veins. A quantitative evaluation was performed on 55 publicly available non-contrast CT scans. In all scans, two observers manually annotated randomly selected vessels as artery or vein. Our method was able to separate and classify arteries and veins with a median accuracy of 89%, closely approximating the inter-observer agreement. All CT scans used in this study, including all results of our system and all manual annotations, are publicly available at "http://www.w3.org/1999/xlink">http://arteryvein.grand-challenge.org".
REM sleep without atonia in middle‐aged and older psychiatric patients and Lewy body disease: a case series (2016)

Rapid eye movement sleep without atonia itself may be associated with specific clinical profiles, even when dream-enactment behavior is absent. Continued follow-up of the patients with MDD exhibiting RWA is warranted to determine if they represent the prodromal Parkinson's disease/dementia with Lewy bodies. Copyright © 2016 John Wiley & Sons, Ltd.
The common inversion of the Williams–Beuren syndrome region at 7q11.23 does not cause clinical symptoms (2008)

Williams-Beuren syndrome (WBS) is caused by a approximately 1.5 million base pair deletion at 7q11.23. A common inversion of the region, WBSinv-1, exists as a polymorphism but was also found in individuals with WBS-like features but no deletion, suggesting it could cause clinical symptoms. We performed a full clinical, developmental and genetic assessment of two previously reported individuals with clinical symptoms and WBSinv-1 but no 7q11.23 deletion. We also examined expression of genes at 7q11.23 in individuals in the general population who have WBSinv-1. We show that individuals with clinical symptoms and WBSinv-1 do not show significant clinical or psychological overlap with individuals with WBS. In addition, a 1.3 Mb duplication of part of the velocardiofacial syndrome region on chromosome 22q11.2 was found in one participant with WBSinv-1 and clinical symptoms. We also demonstrate that individuals with WBSinv-1 show normal expression of genes from the WBS region. These results suggest that WBSinv-1 does not cause clinical symptoms and we advise caution when diagnosing individuals with atypical presentation of rare syndromes. Whole genome analysis may reveal previously unidentified copy number variants that could contribute to syndromic features.
Analysis of a genomic segment of white spot syndrome virus of shrimp containing ribonucleotide reductase genes and repeat regions (2000)

White spot syndrome is a worldwide disease of penaeid shrimp. The disease agent is a bacilliform, enveloped virus, white spot syndrome virus (WSSV), with a double-stranded DNA genome that probably contains well over 200 kb. Analysis of a 12.3 kb segment of WSSV DNA revealed eight open reading frames (ORFs), including the genes for the large (RR1) and small (RR2) subunits of ribonucleotide reductase. The rr1 and rr2 genes were separated by 5760 bp, containing several putative ORFs and two domains with multiple sequence repeats. The first domain contained six direct repeats of 54 bp and is part of a coding region. The second domain had one partial and two complete direct repeats of 253 bp at an intergenic location. This repeat, located immediately upstream of rr1, has homologues at several other locations on the WSSV genome. Phylogenetic analysis of RR1 and RR2 indicated that WSSV belongs to the eukaryotic branch of an unrooted parsimonious tree and, further, seems to suggest that WSSV and baculoviruses probably do not share an immediate common ancestor. The present analysis of WSSV favours the view that this virus is either a member of a new genus (Whispovirus) within the Baculoviridae or a member of an entirely new virus family.
Methods for metabolic evaluation of prostate cancer cells using proton and 13C HR‐MAS spectroscopy and [3‐13C] pyruvate as a metabolic substrate (2009)

Prostate cancer has been shown to undergo unique metabolic changes associated with neoplastic transformation, with associated changes in citrate, alanine, and lactate concentrations. (13)C high resolution-magic angle spinning (HR-MAS) spectroscopy provides an opportunity to simultaneously investigate the metabolic pathways implicated in these changes by using (13)C-labeled substrates as metabolic probes. In this work, a method to reproducibly interrogate metabolism in prostate cancer cells in primary culture was developed using HR-MAS spectroscopy. Optimization of cell culture protocols, labeling parameters, harvesting, storage, and transfer was performed. Using [3-(13)C] pyruvate as a metabolic probe, (1)H and (13)C HR-MAS spectroscopy was used to quantify the net amount and fractional enrichment of several labeled metabolites that evolved in multiple cell samples from each of five different prostate cancers. Average enrichment across all cancers was 32.4 +/- 5.4% for [3-(13)C] alanine, 24.5 +/- 5.4% for [4-(13)C] glutamate, 9.1 +/- 2.5% for [3-(13)C] glutamate, 25.2 +/- 5.7% for [3-(13)C] aspartate, and 4.2 +/- 1.0% for [3-(13)C] lactate. Cell samples from the same parent population demonstrated reproducible fractional enrichments of alanine, glutamate, and aspartate to within 12%, 10%, and 10%, respectively. Furthermore, the cells produced a significant amount of [4-(13)C] glutamate, which supports the bioenergetic theory for prostate cancer. These methods will allow further characterization of metabolic properties of prostate cancer cells in the future. Magn Reson Med, 2009. (c) 2009 Wiley-Liss, Inc.
Nanostructures Self-Assembled in Polymer Solutions Confined in Cylindrical Nanopores (2009)

Polymer nanostructures self-assembled from solutions confined in cylindrical nanopores were investigated via Monte-Carlo simulations. The nanostructures, including some novel ones, were self-assembled under a wide range of conditions. It is shown that the interactions of the segments with the wall, reflecting the wetting/dewetting by the polymer segments of the wall, constitute a crucial factor in the nanostructure formation. When there are attractive interactions between the segments of a homopolymer or between one kind of segment of a copolymer and the wall, short nanorods, long nanorods, and long nanorods containing channels are generated, and the diameters of the nanostructures are close to the diameter of the cylindrical nanopores. When the above interactions are repulsive, nanospheres, short nanorods, nanocapsules, long nanorods, and nanocylindroids are formed, and generally, the diameter of the nanostructure is smaller than the diameter of the cylindrical nanopores because of the formation of a depletion layer near the wall of the cylindrical nanopores. Our results also indicate that nanostructures that occupy the entire height of the nanopores are more easily generated in nanopores with larger diameters. It should be noted that the nanostructures formed from solutions are usually irregular and cannot be characterized by a unique diameter.
Developmental changes in contractility and sarcomeric proteins from the early embryonic to the adult stage in the mouse heart (2003)

Developmental changes in force-generating capacity and Ca2+ sensitivity of contraction in murine hearts were correlated with changes in myosin heavy chain (MHC) and troponin (Tn) isoform expression, using Triton-skinned fibres. The maximum Ca2+-activated isometric force normalized to the cross-sectional area (FCSA) increased mainly during embryogenesis and continued to increase at a slower rate until adulthood. During prenatal development, FCSA increased about 5-fold from embryonic day (E)10.5 to E19.5, while the amount of MHC normalized to the amount of total protein remained constant (from E13.5 to E19.5). This suggests that the development of structural organization of the myofilaments during the embryonic and the fetal period may play an important role for the improvement of force generation. There was an overall decrease of 0.5 pCa units in the Ca2+ sensitivity of force generation from E13.5 to the adult, of which the main decrease (0.3 pCa units) occurred within a short time interval, between E19.5 and 7 days after birth (7 days pn). Densitometric analysis of SDS-PAGE and Western blots revealed that the major switches between troponin T (TnT) isoforms occur before E16.5, whereas the transition points of slow skeletal troponin I (ssTnI) to cardiac TnI (cTnI) and of beta-MHC to alpha-MHC both occur around birth, in temporal correlation with the main decrease in Ca2+ sensitivity. To test whether the changes in Ca2+ sensitivity are solely based on Tn, the native Tn complex was replaced in fibres from E19.5 and adult hearts with fast skeletal Tn complex (fsTn) purified from rabbit skeletal muscle. The difference in pre-replacement values of pCa50 (-log([Ca2+] M-1)) required for half-maximum force development) between E19.5 (6.05 +/- 0.01) and adult fibres (5.64 +/- 0.04) was fully abolished after replacement with the exogenous skeletal Tn complex (pCa50 = 6.12 +/- 0.05 for both stages). This suggests that the major developmental changes in Ca2+ sensitivity of skinned murine myocardium originate primarily from the switch of ssTnI to cTnI.
Versatile Alligator Nanostructures for Quantum Networks with Solid-State Emitters (2020)

We report design and fabrication of novel “alligator” nanostructures as both a high-Q photonic crystal cavity that helps preserve NV centers’ optical coherence and a polarization-selective mirror for high-fidelity quantum state transfer.
Rank learning for factoid question answering with linguistic and semantic constraints (2010)

This work presents a general rank-learning framework for passage ranking within Question Answering (QA) systems using linguistic and semantic features. The framework enables query-time checking of complex linguistic and semantic constraints over keywords. Constraints are composed of a mixture of keyword and named entity features, as well as features derived from semantic role labeling. The framework supports the checking of constraints of arbitrary length relating any number of keywords. We show that a trained ranking model using this rich feature set achieves greater than a 20% improvement in Mean Average Precision over baseline keyword retrieval models. We also show that constraints based on semantic role labeling features are particularly effective for passage retrieval; when they can be leveraged, an 40% improvement in MAP over the baseline can be realized.
Group VIA Phospholipase A 2 Mediates Enhanced Macrophage Migration in Diabetes Mellitus by Increasing Expression of Nicotinamide Adenine Dinucleotide Phosphate Oxidase 4 (2014)

Taken together, these observations identify iPLA2β and lysophosphatidic acid derived from its action as critical in regulating macrophage Nox4 activity and migration in the diabetic state in vivo and under similar conditions ex vivo.
Decentralized coordination of plug-in hybrid vehicles for imbalance reduction in a smart grid (2011)

Intelligent electricity grids, or 'Smart Grids', are being introduced at a rapid pace. Smart grids allow the management of new distributed power generators such as solar panels and wind turbines, and innovative power consumers such as plug-in hybrid vehicles. One challenge in Smart Grids is to fulfill consumer demands while avoiding infrastructure overloads. Another challenge is to reduce imbalance costs: after ahead scheduling of production and consumption (the socalled 'load schedule'), unpredictable changes in production and consumption yield a cost for repairing this balance.To cope with these risks and costs, we propose a decentralized, multi-agent system solution for coordinated charging of PHEVs in a Smart Grid. Essentially, the MAS utilizes an intention graph for expressing the flexibility of a fleet of PHEVs. Based on this flexibility, charging of PHEVs can be rescheduled in real-time to reduce imbalances.We discuss and evaluate two scheduling strategies for reducing imbalance costs: reactive scheduling and proactive scheduling. Simulations show that reactive scheduling is able to reduce imbalance costs by 14%, while proactive scheduling yields the highest imbalance cost reduction of 44%.
Experimental and numerical study of transient bubble-elastic membrane interaction (2006)

A study of the interaction between a membrane and a submerged oscillating bubble is presented. Though the behavior of such a bubble near an elastic (relatively thick) boundary has been studied by several authors, much less attention is focused on the behavior of such a bubble near a (thin) elastic membrane. For membranes, it is the curvature and not the deflection that is responsible for a pressure buildup in the fluid close to the bubble. Due to this difference in physics, it is not a certainty if the dynamics of bubbles near a deformable elastic boundary vis-a-vis a membrane would exhibit any similarity. Our intent is a systematic study on the latter, which can be exploited in future work (e.g., in biomedical applications where elastic membranes are often involved). Experimental observations of transient bubble interaction with a thin elastic membrane are presented and the dynamics of the bubble in the vicinity of the membrane are compared to the boundary element method simulations. The bubble is generated using a very low voltage (only 55V) in contrast to the relatively much higher voltages usually employed in reported works. This is very attractive from a safety viewpoint and accords great simplification of the setup. The comparisons show that the interaction between the transient bubble and the membrane induces a perturbation on the bubble surface that strengthens the bubble contraction and can lead to mushroom shape, bubble elongation, and bubble splitting. The influence of the two main parameters, namely, the distance between the bubble and the membrane and the elasticity of the membrane, are also discussed.
Probability of Satellite Interception by an Air Launched Pre-Guided Missile (1961)

The following note develops a simple computational model containing the timing, operational and mechanistic error parameters expected to be present in at tempts at satellite interception utilizing an aircraft launched, pre-guided missile. Such a model will introduce simplifying approximations, bu t its value lies in its ability to measure the relative importance of the various errors and to determine where improvement will be most rewarding. The approximations introduced are believed to be consistent with the precision of present instrument accuracies.
Synthesis of 1‐[11C]‐D,L‐homocysteine thiolactone: A potential tracer for myocardial ischemia using PET (1989)

Abstract The synthesis of 1‐[ 11 C]‐D,L‐homocysteine thiolactone, a potential tracer for PET imaging of ischemic heart regions, is described. The labelling is achieved by reaction of [ 11 C]carbon dioxide with α‐lithiated S‐(tetrahydropyran‐2‐yl)3‐thiopropylisonitrile. Deprotection of the mercapto group and lactonisation of the resulting thioamino acid is accomplished in an acid catalysed reaction. The radiochemical yield obtained is 10 to 15% and the synthesis time, including the HPLC purification is about 45 min.
ELECTRON-SPIN AND TUNNELING EFFUCTS IN THE MICROWAVE SPECTRUM OF $SO_{2}-O_{2}$ (1997)

Author Institution: Optical Technology Division, National Institute of Standards and Technology; Faculty of Science, University of United Arab Emirates
Cep152 interacts with Plk4 and is required for centriole duplication (2010)

Centrioles are microtubule-based structures that organize the centrosome and nucleate cilia. Centrioles duplicate once per cell cycle, and duplication requires Plk4, a member of the Polo-like kinase family; however, the mechanism linking Plk4 activity and centriole formation is unknown. In this study, we show in human and frog cells that Plk4 interacts with the centrosome protein Cep152, the orthologue of Drosophila melanogaster Asterless. The interaction requires the N-terminal 217 residues of Cep152 and the crypto Polo-box of Plk4. Cep152 and Plk4 colocalize at the centriole throughout the cell cycle. Overexpression of Cep152 (1-217) mislocalizes Plk4, but both Cep152 and Plk4 are able to localize to the centriole independently of the other. Depletion of Cep152 prevents both normal centriole duplication and Plk4-induced centriole amplification and results in a failure to localize Sas6 to the centriole, an early step in duplication. Cep152 can be phosphorylated by Plk4 in vitro, suggesting that Cep152 acts with Plk4 to initiate centriole formation.
Increased Active OMI/HTRA2 Serine Protease Displays a Positive Correlation with Cholinergic Alterations in the Alzheimer’s Disease Brain (2018)

OMI/HTRA2 (high-temperature requirement serine protease A2) is a mitochondrial serine protease involved in several cellular processes, including autophagy, chaperone activity, and apoptosis. Few studies on the role of OMI/HTRA2 in Alzheimer's disease (AD) are available, but none on its relationship with the cholinergic system and neurotrophic factors as well as other AD-related proteins. In this study, immunohistochemical analyses revealed that AD patients had a higher cytosolic distribution of OMI/HTRA2 protein compared to controls. Quantitative analyses on brain extracts indicated a significant increase in the active form of OMI/HTRA2 in the AD brain. Activated OMI/HTRA2 protein positively correlated with stress-associated read-through acetylcholinesterase activity. In addition, α7 nicotinic acetylcholine receptor gene expression, a receptor also known to be localized on the outer membrane of mitochondria, showed a strong correlation with OMI/HTRA2 gene expression in three different brain regions. Interestingly, the activated OMI/HTRA2 levels also correlated with the activity of the acetylcholine-biosynthesizing enzyme, choline acetyltransferase (ChAT); with levels of the neurotrophic factors, NGF and BDNF; with levels of the soluble fragments of amyloid precursor protein (APP); and with gene expression of the microtubule-associated protein tau in the examined brain regions. Overall, the results demonstrate increased levels of the mitochondrial serine protease OMI/HTRA2, and a coherent pattern of association between the activated form of OMI/HTRA2 and several key proteins involved in AD pathology. In this paper, we propose a new hypothetical model to highlight the importance and needs of further investigation on the role of OMI/HTRA2 in the mitochondrial function and AD.
The issue of the cardiovascular safety of dihydropyridines (1996)

This review describes aspects of the calcium channel blocker controversy as it relates to hypertensive and coronary artery disease patients. Much of the controversy has occurred because of off-label use of short-acting calcium channel blockers that were never approved or recommended for use in patients with hypertension or acute myocardial infarction. A recent analysis of slow-onset, long-acting calcium channel blockers, which lack large peak-to trough fluctuations in drug levels, did not show a signal suggesting an increase in cardiovascular events.
Decentralised approaches for network management (1997)

Centralised network management has shown inadequacy for efficient management of large heterogenous networks. As a result, several distributed approaches have been adapted to overcome the problem. This paper is a review of decentralised network management techniques and technologies. We explain distributed architectures for network management, and discuss some of the most important implemented distributed network management systems. A comparison is made between these approaches to show the pitfalls and merits of each.