gebhart/patrepeval huggingface dataset:
Retraction for Venkataraman et al., Selective cell death mediated by small conditional RNAs (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Hierarchical decentralized control strategy for demand-side primary frequency response (2016)

The Grid Friendly™ Appliance (GFA) controller was proposed to autonomously switch off appliances by detecting under-frequency events. In this paper, a new frequency responsive load (FRL) controller is proposed by extending the functionality of the existing GFA controller. The proposed FRL controller can autonomously switch on (or off) end-use loads by detecting over-frequency (or under-frequency) events through local frequency measurement. Using the proposed FRL controller, a hierarchical decentralized control strategy is also developed for engaging the end-use loads to provide primary frequency response. The developed control strategy consists of two decision making layers including supervisory and device layers, and has several desirable features for primary frequency control. The FRL controller at the device layer preserves the autonomous operation of the enduse loads. The coordinator at the supervisory layer coordinates autonomous response to overcome the stability issue associated with high penetration of FRLs. The simulation results illustrate the effectiveness of the developed hierarchical decentralized control strategy in providing primary frequency response with the proposed FRL controller.
Consideration of an autonomous compact source for high-power microwave applications (2000)

The use of explosively driven flux compressors as light and compact autonomous single-shot power supplies for high-power microwave applications requires special attention to be paid to the conditioning and matching elements of the overall system, due to the fast-rising high voltage output step that is needed. This paper addresses various schemes by which this may be achieved and, based on proven techniques, a practical approach using a high-voltage transformer is described in detail. In addition, it is shown that future developments in long conduction plasma opening switches and fast-pulse compressors will open the way to much more compact and higher performance systems, with characteristics that could also match the requirements of high-power lasers and ion-beam generators.
The transcript release factor PTRF augments ribosomal gene transcription by facilitating reinitiation of RNA polymerase I (2001)

Termination of murine rDNA transcription by RNA polymerase I (Pol I) requires pausing of Pol I by terminator-bound TTF-I (transcription termination factor for Pol I), followed by dissociation of the ternary complex by PTRF (Pol I and transcript release factor). To examine the functional correlation between transcription termination and initiation, we have compared transcription on terminator-containing and terminator-less rDNA templates. We demonstrate that terminated RNA molecules are more efficiently synthesized than run-off transcripts, indicating that termination facilitates reinitiation. Transcriptional enhancement is observed in multiple- but not single-round transcription assays measuring either promoter-dependent or promoter-independent Pol I transcription. Increased synthesis of terminated transcripts is observed in crude extracts but not in a PTRF-free reconstituted transcription system, indicating that PTRF-mediated release of pre-rRNA is responsible for transcriptional enhancement. Consistent with PTRF serving an important role in modulating the efficiency of rRNA synthesis, PTRF exhibits pronounced charge heterogeneity, is phosphorylated at multiple sites and fractionates into transcriptionally active and inactive forms. The results suggest that regulation of PTRF activity may be an as yet unrecognized means to control the efficiency of ribosomal RNA synthesis.
Composite Organic−Inorganic Nanoparticles (COINs) with Chemically Encoded Optical Signatures (2004)

To obtain a coding system for multiplex detection, we have developed a method to synthesize a new type of nanomaterial called composite organic-inorganic nanoparticles (COINs). The method allows the incorporation of a broad range of organic compounds into COINs to produce surface enhanced Raman scattering (SERS)-like spectra that are richer in variety than fluorescence-based signatures. Preliminary data suggest that COINs can be used as Raman tags for multiplex and ultrasensitive detection of biomolecules.
Epigenetic DNA Hypermethylation of the HERP Gene Promoter Induces Down‐regulation of Its mRNA Expression in Patients With Alcohol Dependence (2006)

To our knowledge, this is the first study evaluating HERP mRNA expression and its specific gene promoter methylation in alcoholic patients. As hypermethylation of DNA is an important epigenetic factor in the down-regulation of gene expression, and as HERP has been considered to play an essential role within the intracellular defense system, these findings may be useful in the understanding and treatment of different disease conditions associated with alcohol dependence.
Decreased Platelet Number and Function and Increased Fibrinolysis Contribute to Postoperative Bleeding in Cardiopulmonary Bypass Patients (1988)

We simultaneously evaluated platelet and fibrinolytic parameters to assess their individual and combined contributions to postoperative blood loss in cardiopulmonary (CP) bypass patients. Platelet count, platelet aggregability, hematocrit, plasminogen (PLG) concentration, alpha 2-antiplasmin (AP) concentration, free protease activity (fPA), and antithrombin-III (AT-III) were measured in nine patients undergoing surgery using cardiopulmonary bypass. Chest tube drainage was used as the measure of postoperative blood loss. Hematocrit, platelet count, PLG, AP, and AT-III all decreased during CP bypass, with PLG and AT-III decreasing much more than dilution. During CP bypass, platelet aggregability to ADP did not change significantly from pre-bypass, but aggregability to arachidonic acid (AA) decreased significantly. Following protamine administration there was a large increase (83%) in fPA, the platelet count showed a further drop (from 61% to 50% of pre-bypass levels), and platelet aggregability decreased significantly (from 95% to 34% of pre-bypass levels for ADP, and from 55% to 11.9% for AA). Chest tube drainage during the first four postoperative hours correlated positively (p less than 0.05) with the combination of increase in free protease activity and decrease in platelet count. The total chest tube drainage correlated significantly with the combination of decrease in platelet count and the decrease in platelet aggregability. These combinations of changes correlated significantly with postoperative blood loss whereas the individual changes did not.(ABSTRACT TRUNCATED AT 250 WORDS)
Bandwidth estimation: metrics, measurement techniques, and tools (2003)

In a packet network, the terms bandwidth and throughput often characterize the amount of data that the network can transfer per unit of time. Bandwidth estimation is of interest to users wishing to optimize end-to-end transport performance, overlay network routing, and peer-to-peer file distribution. Techniques for accurate bandwidth estimation are also important for traffic engineering and capacity planning support. Existing bandwidth estimation tools measure one or more of three related metrics: capacity, available bandwidth, and bulk transfer capacity. Currently available bandwidth estimation tools employ a variety of strategies to measure these metrics. In this survey we review the recent bandwidth estimation literature focusing on underlying techniques and methodologies as well as open source bandwidth measurement tools.
A Local-to-Global Approach to Multi-modal Movie Scene Segmentation (2020)

Scene, as the crucial unit of storytelling in movies, contains complex activities of actors and their interactions in a physical environment. Identifying the composition of scenes serves as a critical step towards semantic understanding of movies. This is very challenging -- compared to the videos studied in conventional vision problems, e.g. action recognition, as scenes in movies usually contain much richer temporal structures and more complex semantic information. Towards this goal, we scale up the scene segmentation task by building a large-scale video dataset MovieScenes, which contains 21K annotated scene segments from 150 movies. We further propose a local-to-global scene segmentation framework, which integrates multi-modal information across three levels, i.e. clip, segment, and movie. This framework is able to distill complex semantics from hierarchical temporal structures over a long movie, providing top-down guidance for scene segmentation. Our experiments show that the proposed network is able to segment a movie into scenes with high accuracy, consistently outperforming previous methods. We also found that pretraining on our MovieScenes can bring significant improvements to the existing approaches.
Hemodynamic response to anesthesia in pregnant and nonpregnant ICR mice. (1998)

Mean arterial blood pressure (BP) and heart rate (HR) during and after recovery from anesthesia in pregnant and nonpregnant ICR mice were evaluated. Mice were evaluated during mechanical ventilation, from 15 to 60 min after induction of anesthesia. The anesthetic protocols were pentobarbital (80 mg/kg, given intraperitoneally [i.p.]); two low doses of ketamine and xylazine (90 mg/kg, 7.5 mg/kg, respectively, i.p., with a second dose given 20 min after the initial dose); and a single high dose of ketamine and xylazine (150 mg/kg, 12.5 mg/kg, respectively, i.p.). The BP was measured in the right carotid artery, using a fluid-filled catheter connected to a chamber containing a solid-state pressure transducer. Mechanical ventilation was performed via tracheotomy, using a normalized minute ventilation of 3.5 ml*min-1*g-1 for nonpregnant mice and 3.0 ml*min-1*g-1 for pregnant mice. Mean BP was lower and HR was higher in pregnant than in nonpregnant mice for each anesthetic protocol. Pentobarbital induced significantly greater tachycardia and hypotension than did the other protocols. The average BP and HR were similar between two low doses and a single high dose of ketamine and xylazine. During spontaneous breathing from 30 to 180 min after recovery from anesthesia by use of a single low dose, ketamine and xylazine induced similar HR profiles, but mean BP in pregnant mice recovered earlier than did that in nonpregnant mice. These results suggest that ketamine and xylazine induced adequate anesthesia for superficial surgical procedures in pregnant and nonpregnant mice while inducing small changes in HR and BP, and pregnancy resulted in a different hemodynamic reaction in response to ketamine and xylazine. These data will be useful for the design and interpretation of physiologic protocols using pregnant and nonpregnant genetically targeted mice.
In vivo reflectance of blood and tissue as a function of light wavelength (1990)

Light reflectance from soft tissue has been utilized in noninvasive clinical measurement devices such as the photoplethysmograph and the reflectance pulse oximeter. Incident light on the skin travels into the underlying layers and is in part reflected back to the surface. This paper describes the reflectance of light from in vivo tissue for wavelengths in the range from 420 to 940 nm, based on photon diffusion theory and on experimental results from studies of 17 subjects. The results show a minimum reflectance and a peak sensitivity to the blood pulsations in the wavelength range from 510 to 590 nm. Skin pigmentation is seen to attenuate reflectance rather than altering the character of the modulation spectra. Based on the model introduced in this paper, the dependence of modulation spectra on mean blood fractional volume as well as wavelength is also described theoretically, and corroborated by further experimental data at 570 and 630 nm. At these latter wavelengths, the signal-to-noise ratio was calculated for the blood volume pulsation signal in the presence of physiological noise. The median for calculated ratios of reflectance modulation by blood pulsation and ratios of signal to noise between the two wavelengths were 13.1 and 7.5, respectively, for 93 sites in nine subjects. These results are seen to be consistent with the theory.
A broadening view of recombinational DNA repair in bacteria (1998)

Recombinational DNA repair is both the most complex and least understood of DNA repair pathways. In bacterial cells grown under normal laboratory conditions (without a DNA damaging treatment other than an aerobic environment), a substantial number (10-50%) of the replication forks originating at oriC encounter a DNA lesion or strand break. When this occurs, repair is mediated by an elaborate set of recombinational DNA repair pathways which encompass most of the enzymes involved in DNA metabolism. Four steps are discussed: (i) The replication fork stalls and/or collapses. (ii) Recombination enzymes are recruited to the location of the lesion, and function with nearly perfect efficiency and fidelity. (iii) Additional enzymatic systems, including the phiX174-type primosome (or repair primosome), then function in the origin-independent reassembly of the replication fork. (iv) Frequent recombination associated with recombinational DNA repair leads to the formation of dimeric chromosomes, which are monomerized by the XerCD site-specific recombination system.
Functional characterization of Kv channel beta‐subunits from rat brain. (1996)

1. The potassium channel beta-subunit from rat brain, Kv beta 1.1, is known to induce inactivation of the delayed rectifier channel Kv1.1 and Kv1.4 delta 1-110. 2. Kv beta 1.1 was co-expressed in Xenopus oocytes with various other potassium channel alpha-subunits. Kv beta 1.1 induced inactivation in members of the Kv1 subfamily with the exception of Kv 1.6; no inactivation of Kv 2.1, Kv 3.4 delta 2-28 and Kv4.1 channels could be observed. 3. The second member of the beta-subunit subfamily, Kv beta 2, had a shorter N-terminal end, accelerated inactivation of the A-type channel Kv 1.4, but did not induce inactivation when co-expressed with delayed rectifiers of the Kv1 channel family. 4. To test whether this subunit co-assembles with Kv alpha-subunits, the N-terminal inactivating domains of Kv beta 1.1 and Kv beta 3 were spliced to the N-terminus of Kv beta 2. The chimaeric beta-subunits (beta 1/ beta 2 and beta 3/ beta 2) induced fast inactivation of several Kv1 channels, indicating that Kv beta 2 associates with these alpha-subunits. No inactivation was induced in Kv 1.3, Kv 1.6, Kv2.1 and Kv3.4 delta 2-28 channels. 5. Kv beta 2 caused a voltage shift in the activation threshold of Kv1.5 of about -10 mV, indicating a putative physiological role. Kv beta 2 had a smaller effect on Kv 1.1 channels. 6. Kv beta 2 accelerated the activation time course of Kv1.5 but had no marked effect on channel deactivation.
Effect of primary selective laser trabeculoplasty on tonographic outflow facility: a randomised clinical trial (2010)

Primary SLT significantly increased the tonographic outflow facility and decreased IOP in patients with primary open angle glaucoma and ocular hypertension but no statistically significant differences were found between the 360° and 180° groups. The level of IOP reduction due to primary SLT treatment could not be explained by the increase in tonographic outflow facility alone. Clinical trial registration ISRCTN66330584, Current Controlled Trials. 1/11/2006.
The conserved N-terminal region of Sendai virus nucleocapsid protein NP is required for nucleocapsid assembly (1993)

Sendai virus nucleocapsid protein NP synthesized in the absence of other viral components assembled into nucleocapsid-like particles. They were identical in density and morphology to authentic nucleocapsids but were smaller in size. The reduction in size was probably due to the fact that they contained RNA only 0.5 to 2 kb in length. Nucleocapsid assembly requires NP-NP and NP-RNA interactions. To identify domains on NP protein involved in nucleocapsid formation, 29 NP protein mutants were tested for the ability to assemble. Any deletion between amino acid residues 1 and 399 abolished formation of nucleocapsid-like particles, but mutants within this region exhibited two different phenotypes. Deletions between positions 83 and 384 completely abolished all interactions. Deletions between residues 1 and 82 and between residues 385 and 399, at the N- and C-terminal ends of the region from 1 to 399, resulted in unstructured aggregates of NP protein, indicating only a partial loss of function. Deletions within the C-terminal 124 amino acids were the only ones that did not affect assembly. The results suggest that NP protein can be divided into at least two separate domains which function independently of each other. Domain I (residues 1 to 399) seems to contain all of the structural information necessary for assembly, while domain II (residues 400 to 524) is not involved in nucleocapsid formation.
Cannabinoid Receptors and Endocannabinoids: Role in Neuroinflammatory and Neurodegenerative Disorders (2010)

The G-protein coupled receptors for Δ⁹-tetrahydrocannabinol, the major psychoactive principle of marijuana, are known as cannabinoid receptors of type 1 (CB₁) and 2 (CB₂) and play important functions in degenerative and inflammatory disorders of the central nervous system. Whilst CB₁ receptors are mostly expressed in neurons, where they regulate neurotransmitter release and synaptic strength, CB₂ receptors are found mostly in glial cells and microglia, which become activated and over-express these receptors during disorders such as Alzheimer's disease, multiple sclerosis, amyotropic lateral sclerosis, Parkinson's disease, and Huntington's chorea. The neuromodulatory actions at CB₁ receptors by endogenous agonists ('endocannabinoids'), of which anandamide and 2-arachidonoylglycerol are the two most studied representatives, allows them to counteract the neurochemical unbalances arising during these disorders. In contrast, the immunomodulatory effects of these lipophilic mediators at CB₂ receptors regulate the activity and function of glia and microglia. Indeed, the level of expression of CB₁ and CB₂ receptors or of enzymes controlling endocannabinoid levels, and hence the concentrations of endocannabinoids, undergo time- and brain region-specific changes during neurodegenerative and neuroinflammatory disorders, with the initial attempt to counteract excitotoxicity and inflammation. Here we discuss this plasticity of the endocannabinoid system during the aforementioned central nervous system disorders, as well as its dysregulation, both of which have opened the way to the use of either direct and indirect activators or blockers of CB₁ and CB₂ receptors for the treatment of the symptoms or progression of these diseases.
Characterization of a human melanoma-associated ganglioside antigen defined by a monoclonal antibody, 4.2. (1982)

A monoclonal IgM antibody, 4.2, reacting with a surface antigen expressed on most human melanomas (Yeh, M.-I., Hellström, I., Abe, K., Hakomori, S., and Hellström, K. E. (1982) Int. J. Cancer, 29, 269-275) was shown to be directed to a ganglioside with the carbohydrate structure NeuAc alpha 2 leads to 8NeuAc alpha 2 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1Cer. The carbohydrate structure, established by enzymatic degradation and methylation analysis with mass spectrometry, is identical with that of brain GD3 ganglioside, but its ceramide is characterized by a predominance of longer chain fatty acids, in contrast to brain GD3 that has mainly C18:0 fatty acid. The antibody did not react with various other gangliosides, including those having the same terminal sugar sequence (NeuAc alpha 2 leads to 8NeuAc alpha 2 leads to 3Gal) as GD3, such as GT1a and GQ1b. Its specificity is therefore restricted to the NeuAc alpha 2 leads to 8NeuAc alpha 2 leads to 3Gal beta 1 leads to 4Glc leads to Cer sequence, including the innermost sugar, Glc residue.
Statins Activate Peroxisome Proliferator-Activated Receptor γ Through Extracellular Signal-Regulated Kinase 1/2 and p38 Mitogen-Activated Protein Kinase–Dependent Cyclooxygenase-2 Expression in Macrophages (2007)

Both statins and peroxisome proliferator-activated receptor (PPAR)gamma ligands have been reported to protect against the progression of atherosclerosis. In the present study, we investigated the effects of statins on PPARgamma activation in macrophages. Statins increased PPARgamma activity, which was inhibited by mevalonate, farnesylpyrophosphate, or geranylgeranylpyrophosphate. Furthermore, a farnesyl transferase inhibitor and a geranylgeranyl transferase inhibitor mimicked the effects of statins. Statins inhibited the membrane translocations of Ras, RhoA, Rac, and Cdc42, and overexpression of dominant-negative mutants of RhoA (DN-RhoA) and Cdc42 (DN-Cdc42), but not of Ras or Rac, increased PPARgamma activity. Statins induced extracellular signal-regulated kinase (ERK)1/2 and p38 mitogen-activated protein kinase (MAPK) activation. However, DN-RhoA and DN-Cdc42 activated p38 MAPK, but not ERK1/2. ERK1/2- or p38 MAPK-specific inhibitors abrogated statin-induced PPARgamma activation. Statins induced cyclooxygenase (COX)-2 expression and increased intracellular 15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) levels through ERK1/2- and p38 MAPK-dependent pathways, and inhibitors or small interfering RNA of COX-2 inhibited statin-induced PPARgamma activation. Statins also activate PPARalpha via COX-2-dependent increases in 15d-PGJ(2) levels. We further demonstrated that statins inhibited lipopolysaccharide-induced tumor necrosis factor alpha or monocyte chemoattractant protein-1 mRNA expression, and these effects by statins were abrogated by the PPARgamma antagonist T0070907 or by small interfering RNA of PPARgamma or PPARalpha. Statins also induced ATP-binding cassette protein A1 or CD36 mRNA expression, and these effects were suppressed by small interfering RNAs of PPARgamma or PPARalpha. In conclusion, statins induce COX-2-dependent increase in 15d-PGJ(2) level through a RhoA- and Cdc42-dependent p38 MAPK pathway and a RhoA- and Cdc42-independent ERK1/2 pathway, thereby activating PPARgamma. Statins also activate PPARalpha via COX-2-dependent pathway. These effects of statins may explain their antiatherogenic actions.
Allergy to ophthalmic preservatives (2009)

A large number of clinical and experimental studies reveal that preservatives in topical ophthalmic medications have been demonstrated to produce effects from inflammation/ hypersensitivity to permanent cytotoxic effects involving all structures of the eye.