gebhart/patrepeval huggingface dataset:
RCBA: An Efficient Annotation Tool for Community E-Learning (2011)

The topic of webpage content annotation has been an important research area in the field of human computer interaction. Annotation tools enable "value-adding" info to digital resources, by adding additional data in the form of provenances, understandings, references, comments and other types of remarks. They facilitate learners' and reviewers' understanding and remembering of information accessible over the Web, and make the collaborative learning easier. This paper describes an efficient annotation tool RCBA (Role Control Based Annotator), that we have developed which uses RBAC (Role Based Access Control) theory to identify and authenticate users and restrict their access to annotations stored on the database server, and enhance the knowledge sharing and reuse in communities' E-learning.
Screening for Glycosylphosphatidylinositol-Modified Cell Wall Proteins in Pichia pastoris and Their Recombinant Expression on the Cell Surface (2013)

Glycosylphosphatidylinositol (GPI)-anchored glycoproteins have various intrinsic functions in yeasts and different uses in vitro. In the present study, the genome of Pichia pastoris GS115 was screened for potential GPI-modified cell wall proteins. Fifty putative GPI-anchored proteins were selected on the basis of (i) the presence of a C-terminal GPI attachment signal sequence, (ii) the presence of an N-terminal signal sequence for secretion, and (iii) the absence of transmembrane domains in mature protein. The predicted GPI-anchored proteins were fused to an alpha-factor secretion signal as a substitute for their own N-terminal signal peptides and tagged with the chimeric reporters FLAG tag and mature Candida antarctica lipase B (CALB). The expression of fusion proteins on the cell surface of P. pastoris GS115 was determined by whole-cell flow cytometry and immunoblotting analysis of the cell wall extracts obtained by β-1,3-glucanase digestion. CALB displayed on the cell surface of P. pastoris GS115 with the predicted GPI-anchored proteins was examined on the basis of potential hydrolysis of p-nitrophenyl butyrate. Finally, 13 proteins were confirmed to be GPI-modified cell wall proteins in P. pastoris GS115, which can be used to display heterologous proteins on the yeast cell surface.
Formal Radical Cyclization onto Benzene Rings:  A General Method and Its Use in the Synthesis of <i>e</i><i>nt</i>-Nocardione A (2004)

An indirect method is described for effecting radical cyclization onto a benzene ring. Cross-conjugated dienones 6, which are readily prepared from phenols, undergo radical cyclization (6 --> 7 --> 8), and the products (8) are easily aromatized. The method has been applied to the synthesis of ent-nocardione A (21).
Pharmacokinetics of methylphenidate in hyperkinetic children. (1979)

1 Pharmacokinetic study has been carried out following oral administration of 10-20 mg of methylphenidate hydrochloride to four behaviorally disorders children. 2 It is indicated that the drug is metabolized to ritalinic acid with an apparent plasma half life of 2.5 h. 3 The variability in magnitude of plasma concentration seems to be due not to its metabolism to ritalinic acid but due to the variability in the apparent volume of distribution. 4 The brief half life of methylphenidate which parallels the short duration of action of methylphenidate in behaviorally disordered children may be explained in part by its low protein binding which results in high percentage of free drug being made available for metabolism to pharmacologically inactive metabolites.
Discovery of novel EGFR inhibitors: In silico study and 3D-pharmacophore model generation (2013)

In order to elucidate the essential structural features for Epidermal Gro wth Factor Receptor (EGFR) inhibitors, a ligand-based pharmacophore hypothesis was built on the basis of a set of twelve known EGFR inhibitors belonging to three different classes using Molecular Operatin g Environment (MOE) software. In a first step, three alignments, one for each group of compounds were generated. All of them were then submitted to MOE pharmacophore s earch in order to obtain a final pharmacophore model repr esentative of the whole dataset. A pharmacophore model including three features was developed comprising o ne hydrogen-donor (F1) and two aromatic/ hydrophobi c/ acceptor features (F2 and F3). The developed model was used to predict the activities of test set comp ounds by applying linear regression variable selection analy sis. The model exhibited excellent linearity with c orrelation coefficient (r) value, i.e., 0.943, and squared pre dictive correlation coefficient (r 2 ) of 0.889 between experimental and predicted activity values of test set compounds . Our model demonstrated good performance in a separate test set of 25 compounds: it accurately identified 67.7% of the compounds of medium and high inhibitory activities and misclassified only 28.5% of the compounds with low inhibitory activities. The results proved our pharm acophore model to be a filter of great sensitivity and specificity.
Antisense technology reveals the alpha2A adrenoceptor to be the subtype mediating the hypnotic response to the highly selective agonist, dexmedetomidine, in the locus coeruleus of the rat. (1996)

Alpha2 adrenergic agonists are used in the anesthetic management of the surgical patient for their sedative/hypnotic properties although the alpha2 adrenoceptor subtype responsible for these anesthetic effects is not known. Using a gene-targeting strategy, it is possible to specifically reduce the expression of the individual adrenoceptors expressed in the central nervous system and to thereby determine their role in hypnotic action. Stably transfected cell lines (PC 124D for rat alpha2A; NIH3T3 for rat alpha2C adrenoceptors) were exposed to 5 microM antisense oligodeoxynucleotides (ODNs) for alpha2A and alpha2C adrenergic receptor subtypes for 3 d. Individual receptor subtype expression, as determined by radiolabeled ligand binding, was selectively decreased only by the appropriate antisense ODNs and not by the "scrambled" ODNs. These antisense ODNs were then administered three times, on alternate days, into the locus coeruleus of chronically cannulated rats and their hypnotic response to dexmedetomidine (an alpha2 agonist) was determined. Only the alpha2A antisense ODNs significantly change the hypnotic response causing both an increase in latency to, and a decrease in duration of, the loss of righting reflex following dexmedetomidine; hypnotic response had normalized 8 d after stopping the ODNs. Therefore, the alpha2A adrenoceptor subtype is responsible for the hypnotic response to dexmedetomidine in the locus coeruleus of the rat.
Improving imaging through turbulence via aperture partitioning (2010)

Speckle imaging techniques make it possible to do high-resolution imaging through the turbulent atmosphere by collecting and processing a large number of short-exposure frames, each of which effectively freezes the atmosphere. In severe seeing conditions, when the characteristic scale of atmospheric fluctuations is much smaller than the diameter of the telescope, the reconstructed image is dominated by "turbulence noise" caused by redundant baselines in the pupil. I describe a generalization of aperture masking interferometry that dramatically improves imaging performance in this regime. The approach is to partition the aperture into annuli, form the bispectra of the focal plane images formed from each annulus, and recombine them into a synthesized bispectrum from which the object may be retrieved. This may be implemented using multiple cameras and special mirrors, or with a single camera and a suitable pupil phase mask. I report results from simulations as well as experimental results using telescopes at the Air Force Research Lab's Maui Space Surveillance Site.
Executive Summary: Heart Disease and Stroke Statistics—2013 Update (2013)

Each year, the American Heart Association (AHA), in conjunction with the Centers for Disease Control and Prevention, the National Institutes of Health, and other government agencies, brings together the most up-to-date statistics related to heart disease, stroke, and other cardiovascular and metabolic diseases and presents them in its Heart Disease and Stroke Statistical Update. The Statistical Update represents a critical resource for the lay public, policy makers, media professionals, clinicians, healthcare administrators, researchers, and others seeking the best available data on these conditions. Together, cardiovascular disease (CVD) and stroke produce immense health and economic burdens in the United States and globally. The Statistical Update brings together in a single document up-to-date information on the core health behaviors (including diet, physical activity [PA], smoking, and energy balance) and health factors (including blood pressure, cholesterol, and glucose) that define cardiovascular health; a range of major clinical disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, and peripheral arterial disease); and the associated outcomes (including quality of care, procedures, and economic costs). Since 2006, the annual versions of the Statistical Update have been cited >28 000 times in the literature. In 2014 alone, the various Statistical Updates were cited >5000 times. Each annual version of the Statistical Update undergoes major revisions to include the newest nationally representative data, add additional relevant published scientific findings, remove older information, add new sections or chapters, and increase the number of ways to access and use the assembled information. This year-long process, which begins as soon as the previous Statistical Update is published, is performed by the AHA Statistics Committee faculty volunteers and staff. For example, this year's edition includes new data on the monitoring and benefits of cardiovascular health in the population, new metrics to assess and monitor healthy diets, additional information in many chapters on the global CVD and stroke burden, new information on stroke in young adults, a new focus on underserved and minority populations, and further evidencebased approaches to changing behaviors, implementation strategies, and implications of the AHA's 2020 Impact Goals. Below are a few highlights from this year's Update.
In Vivo and In Vitro Starch Digestion: Are Current in Vitro Techniques Adequate? (2010)

The time evolution of the size distributions of (fully branched and debranched) starch molecules during in vivo and in vitro digestion was analyzed using size exclusion chromatography (SEC) and compared. In vivo digesta were collected from the small intestine of pigs fed with raw normal maize starch; in vitro digestion was carried out on the same diet fed to the pigs using a method simulating digestion in the mouth, stomach, and small intestine. A qualitative difference was observed between the in vitro and the in vivo digestion. The former showed a degradation of starch molecules to a more uniform size, whereas the in vivo digestion preserved the size distribution of native starch before producing a multimodal distribution, the heterogeneous nature of which current in vitro methods do not reproduce. The use of in vitro digestion to infer in vivo digestion patterns and, hence, potential nutrition benefits need to take account of this phenomenon.
Overview of a new carbapenem, panipenem/betamipron. (1994)

Carbapenems are beta-lactam antibiotics with a broad antibacterial spectrum and a potent bactericidal activity against both aerobic and anaerobic Gram-positive and Gram-negative organisms. They have been widely investigated in the past, and imipenem/cilastatin (IPM/CS), panipenem/betamipron (PAPM/BP), meropenem (MEPM) and biapenem (BIPM) are presently in clinical use or under trial. Of the carbapenems, imipenem is not readily hydrolysed by microbial beta-lactamase but is hydrolysed to open the beta-lactam ring by DHP-I from kidney and other tissues. In order to achieve greater stability to the enzyme and to prolong the action of the carbapenem in vivo, the co-administration of CS with IPM or the attainment of the chemical construction of the 1-beta methylcarbapenem derivatives in the case of MEPM and BIPM have been performed. However, some difference was found in the DHP-I activity with these carbapenems, but there was no significant difference in the pharmacokinetic parameters: AUC, CLtot, t1/2 and MRT except urinary clearance after administration of these compounds to humans. Considering that MRT as the amount of the antibiotics retained in the body is a clinically important parameter, the structural susceptibility of the carbapenems to the decomposition by DHP-I was suggested to have no clinically meaningful correlation with the pharmacokinetics of these compounds.
Performance modelling of the Orwell basic access mechanism (1987)

Orwell is a high speed slotted ring. Its protocol uses destination release of the slots. Because of this the carried load can be much larger than the transmission rate. A new analytical model of the Orwell basic access mechanism is presented in this paper. The model shows to be accurate and usable over a wide range of parameters. The performance analysis of the Orwell basic access mechanism is presented.
Localization of the insulin receptor binding sites for the SH2 domain proteins p85, Syp, and GAP. (1994)

The insulin receptor is known to interact with the SH2 domain proteins p85 (the regulatory subunit of phosphatidylinositol 3-kinase), Syp (a tyrosine phosphatase), and GAP (GTPase-activating protein). In this study, we mapped the insulin receptor binding sites for each of these proteins by examining the ability of phosphopeptides, corresponding to insulin receptor phosphorylation sites, and mutant insulin receptors to inhibit an insulin receptor-SH2 domain interaction. Precipitation of partially purified insulin receptors by glutathione S-transferase fusion proteins containing the N-terminal SH2 domains of p85 and GAP and both SH2 domains of Syp was demonstrated. The effect of the addition of each phosphopeptide on insulin receptor precipitation was tested. pY1322, the C-terminal insulin receptor peptide, inhibited insulin receptor precipitation by both p85- and Syp-GST. The NPXY internalization domain peptide inhibited insulin receptor precipitation by GAP-GST. These data were confirmed by mutant insulin receptor experiments. The insulin receptor C-terminal mutants, delta CT and Y/F2, were not precipitated by p85- or Syp-GST and the NPXY mutant insulin receptors, delta Ex16 and HI delta NPEY, were not precipitated by GAP-GST. Therefore, we conclude that p85 and Syp bind to the insulin receptor C terminus at tyrosine 1322 and GAP binds to the insulin receptor NPXY domain at tyrosine 960.
Aquaporin-4 deletion ameliorates hypoglycemia-induced BBB permeability by inhibiting inflammatory responses (2018)

Our data suggest that AQP4 deletion protects BBB integrity by reducing inflammatory responses due to the upregulation of PPAR-γ expression and attenuation of proinflammatory cytokine release. Reduction in AQP4 may be protective in acute severe hypoglycemia.
RA-UNet: A Hybrid Deep Attention-Aware Network to Extract Liver and Tumor in CT Scans (2020)

Automatic extraction of liver and tumor from CT volumes is a challenging task due to their heterogeneous and diffusive shapes. Recently, 2D deep convolutional neural networks have become popular in medical image segmentation tasks because of the utilization of large labeled datasets to learn hierarchical features. However, few studies investigate 3D networks for liver tumor segmentation. In this paper, we propose a 3D hybrid residual attention-aware segmentation method, i.e., RA-UNet, to precisely extract the liver region and segment tumors from the liver. The proposed network has a basic architecture as U-Net which extracts contextual information combining low-level feature maps with high-level ones. Attention residual modules are integrated so that the attention-aware features change adaptively. This is the first work that an attention residual mechanism is used to segment tumors from 3D medical volumetric images. We evaluated our framework on the public MICCAI 2017 Liver Tumor Segmentation dataset and tested the generalization on the 3DIRCADb dataset. The experiments show that our architecture obtains competitive results.
Characterization of recent H5 subtype avian influenza viruses from US poultry (2004)

In the US, the isolation of H5 subtype avian influenza (AI) viruses has been uncommon in commercial chickens and turkeys, although sporadic isolations have been made from the live bird markets or its supply chain since 1986. In 2002, two different outbreaks of H5 AI occurred in commercial chicken or turkey operations. The first occurred in Texas and was identified as a H5N3 subtype AI virus. The second outbreak was caused by a H5N2 virus isolated from a turkey farm in California. In this study we analyzed recent H5 subtype AI viruses from different avian species and different sources in the US. Most recent H5 subtype isolates shared a high sequence identity and phylogenetically assorted into a separate clade from the Pennsylvania/83 lineage isolates. However, no established lineage was found within this clade and the recent H5 subtype isolates seemed to be the result of separate introductions from the wild bird reservoir. The Texas H5N3 isolate shared the lowest homology with the other recent isolates in the haemagglutinin gene and had a unique haemagglutinin cleavage site sequence of REKR/G (other recent isolates have the typical avirulent motif, RETR/G). Furthermore, this isolate had a 28 amino acid deletion in the stalk region of the neuraminidase protein, a common characteristic of chicken adapted influenza viruses, and may indicate that this virus had actually been circulating in poultry for an extended period of time before it was isolated. In agreement with genetic evidence, the Texas H5N3 isolate replicated better than other H5 isolates in experimentally infected chickens. The outbreak in Texas with a more chicken-adapted H5N3 virus underscores the importance of ongoing surveillance and control efforts regarding the H5 subtype AI virus in the US.
h-gamma: an RC delay metric based on a gamma distribution approximation of the homogeneous response (2002)

Recently a probability interpretation of moments was proposed as a compromise between the Elmore delay and higher order moment matching for RC timing estimation (Kay and Pileggi, 1998). By modeling RC impulses as time-shifted incomplete gamma distribution function, the delays could be obtained via table lookup using a gamma integral table and the first three moments of the impulse response. However, while this approximation works well for many examples, it struggles with responses when the metal resistance becomes dominant, and produces results with impractical time shift values In this paper the probability interpretation is extended to the circuit homogeneous response, without requiring the time shift parameter. The gamma distribution is used to characterize the normalized homogeneous portion of the step response. For a generalized RC interconnect model (RC tree or mesh), the stability of the homogeneous-gamma distribution model is guaranteed. It is demonstrated that when a table model is carefully constructed, the h-gamma approximation provides for excellent improvement over the Elmore delay in terms of accuracy, with very little additional cost in terms of CPU time.
14-3-3 proteins and protein phosphatases are not reduced in tau-deficient mice (2007)

Tau is an axonal microtubule-associated protein, whose dysfunction causes neurodegenerative diseases such as Alzheimer's disease and other tauopathies. Earlier studies have shown the interactions of tau with glycogen synthase kinase-3beta, 14-3-3zeta, protein phosphatase 1 and protein phosphatase 2A. In this study, we compared the amounts of these tau-interacting proteins in brain microtubule-enriched fractions from wild-type and tau-deficient mice. Contrary to our expectation, we detected no difference in the amount of these proteins between wild-type and tau-deficient mice. Our findings indicate that only a small portion of tau-interacting proteins are bound to tau in vivo, and suggest the existence of other scaffolding proteins. We propose that tau-deficient mice are an ideal system for confirming the function of tau-interacting proteins.
Collision indicator charts for gantry‐couch position combinations for Siemens ONCOR and Elekta Infinity linacs (2013)

Noncoplanar radiation fields from a linear accelerator can be used to deliver radiation dose distributions that are superior to those delivered using coplanar radiation fields. Noncoplanar radiation field arrangements are especially valuable when delivering stereotactic body radiation therapy (SBRT). Noncoplanar radiation fields, however, are geometrically more challenging to deliver than coplanar radiation fields, and are associated with a greater risk of collisions between the gantry, treatment couch, and patient. Knowledge of which treatment couch offset, treatment couch angle, and gantry angle combinations provide a collision-free radiotherapy delivery is useful in the treatment planning process, as the risk of requiring replanning due to improperly selected treatment parameters can be minimized. Such tables are by default specific to the linear accelerator make and model used for treatment. In this work a set of plots is presented indicating which combination of treatment couch lateral offsets (-10 cm to 10 cm), couch angles (270° to 90°), and gantry angles (0° to 360°), will result in collision-free radiation delivery using Siemens ONCOR linear accelerators equipped with a 160-leaf multileaf collimator and a 550 TxT treatment table, and a Elekta Infinity linear accelerator with an MLCi2 and Elekta iBEAM evo Couchtop EP. The patient was assumed to have a width of 50 cm and a height of 25 cm.
Effect of endurance training on mRNA expression of uncoupling proteins 1, 2, and 3 in the rat (1998)

Endurance exercise training has been shown to decrease diet‐induced thermogenesis (DIT) in rats and humans. In rodents, most thermogenesis is thought to occur in brown adipose tissue via activation of the uncoupling protein‐1 (UCP1) and in skeletal muscle. Since the level of UCP1 mRNA in rat BAT was reported to be unmodified by exercise training, the newly described uncoupling proteins UCP2 and UCP3 could be responsible for the decreased DIT in trained rats. UCP3 mRNA levels in endurancetrained rats were found to be reduced by 76% and 59% in tibialis anterior and soleus muscles, respectively. UCP2 mRNA levels were also decreased in tibialis anterior and in heart by 54% and 41%, respectively. Neither white adipose tissue UCP2 nor brown adipose tissue UCP1, UCP2, and UCP3 mRNA levels were modified. The results of this study show that a need for a higher metabolic efficiency is associated with decreased mRNA expression of the uncoupling proteins in skeletal and heart muscles, which would decrease energy dissipation in these tissues. The down‐regulation of UCP3 and UCP2 expressions might also contribute to the rapid weight gain known to occur when exercise training ceased.—Boss, O., Samec, S., Desplanches, D., Mayet, M.‐H., Seydoux, J., Muzzin, P., Giacobino, J.‐P. Effect of endurance training on mRNA expression of uncoupling proteins 1, 2, and 3 in the rat. FASEB J . 12, 339–335 (1998)