gebhart/patrepeval huggingface dataset:
A JAK-STAT pathway regulates wing vein formation in Drosophila. (1996)

We present evidence that the JAK-STAT signal transduction pathway regulates multiple developmental processes in Drosophila. We screened for second-site mutations that suppress the phenotype of the hyperactive hopTum-1 Jak kinase, and recovered a mutation that meiotically maps to the known chromosomal position of D-Stat, a Drosophila stat gene. This hypomorphic mutation, termed statHJ contains a nucleotide substitution in the first D-Stat intron, resulting in a reduction in the number of correctly processed transcripts. Further, the abnormally processed mRNA encodes a truncated protein that has a dominant negative effect on transcriptional activation by the wild-type cDNA in cell culture. statHJ mutants exhibit patterning defects that include the formation of ectopic wing veins, similar to those seen in mutants of the epidermal growth factor/receptor pathway. Abnormalities in embryonic and adult segmentation and in tracheal development were also observed. The hopTum-1 and statHJ mutations can partially compensate for each other genetically, and Hop overexpression can increase D-Stat transcriptional activity in vitro, indicating that the gene products interact in a common regulatory pathway.
Finding the findings: identification of findings in medical literature using restricted natural language processing. (1996)

The ability to search the biomedical literature based on findings would provide enhanced access to information. We describe a computer program called FINDX which relies on the UMLS Metathesuaurus and restricted natural language processing to identify findings in free text. Such identification can serve as a filtering mechanism while selecting relevant papers. After discussing the salient characteristics of findings on which FINDX depends, we report on the results of an experiment in which we tested the program on a set of MEDLINE abstracts pertaining to the diagnosis of Parkinson Disease.
Functional Interactions of the Immunoglobulin Superfamily Member F11 Are Differentially Regulated by the Extracellular Matrix Proteins Tenascin-R and Tenascin-C (1999)

The axon-associated protein F11 is a GPI-anchored member of the immunoglobulin superfamily that promotes axon outgrowth and that shows a complex binding pattern toward multiple cell surface and extracellular matrix proteins including tenascin-R and tenascin-C. In this study, we demonstrate that tenascin-R and tenascin-C differentially modulate cell adhesion and neurite outgrowth of tectal cells on F11. While soluble tenascin-R increases the number of attached cells and the percentage of cells with neurites on immobilized F11, tenascin-C stimulates cell attachment to a similar extent but decreases neurite outgrowth. The cellular receptor interacting with F11 has been previously identified as NrCAM; however, in the presence of tenascin-R or tenascin-C cell attachment and neurite extension are independent of NrCAM. Antibody perturbation experiments indicate that beta(1) integrins instead of NrCAM function as receptor for neurite outgrowth of tectal cells on an F11.TN-R complex. Cellular binding assays support the possibility that the interaction of F11 to NrCAM is blocked in the presence of tenascin-R and tenascin-C. Furthermore, a sandwich binding assay demonstrates that tenascin-R and tenascin-C are able to form larger molecular complexes and to link F11 polypeptides by forming a molecular bridge. These results suggest that the molecular interactions of F11 might be regulated by the presence of tenascin-R and tenascin-C.
Nuclear Localization of KLF4 Is Associated with an Aggressive Phenotype in Early-Stage Breast Cancer (2004)

The results suggest that localization of KLF4 in the nucleus of breast cancer cells is a prognostic factor and identify KLF4 as a marker of an aggressive phenotype in early-stage infiltrating ductal carcinoma.
CHANGES IN AQUEOUS VASCULAR ENDOTHELIAL GROWTH FACTOR AND PIGMENT EPITHELIAL-DERIVED FACTOR LEVELS FOLLOWING INTRAVITREAL BEVACIZUMAB INJECTIONS FOR CHOROIDAL NEOVASCULARIZATION SECONDARY TO AGE-RELATED MACULAR DEGENERATION OR PATHOLOGIC MYOPIA (2008)

Intravitreal bevacizumab injections resulted in reduced aqueous VEGF and increased PEDF levels in patients with CNV secondary to age-related macular degeneration or pathologic myopia. These changes may be favorable for the inhibition of CNV angiogenesis.
The Phloem-Delivered RNA Pool Contains Small Noncoding RNAs and Interferes with Translation (2009)

In plants, the vascular tissue contains the enucleated sieve tubes facilitating long-distance transport of nutrients, hormones, and proteins. In addition, several mRNAs and small interfering RNAs/microRNAs were shown to be delivered via sieve tubes whose content is embodied by the phloem sap (PS). A number of these phloem transcripts are transported from source to sink tissues and function at targeted tissues. To gain additional insights into phloem-delivered RNAs and their potential role in signaling, we isolated and characterized PS RNA molecules distinct from microRNAs/small interfering RNAs with a size ranging from 30 to 90 bases. We detected a high number of full-length and phloem-specific fragments of noncoding RNAs such as tRNAs, ribosomal RNAs, and spliceosomal RNAs in the PS of pumpkin (Cucurbita maxima). In vitro assays show that small quantities of PS RNA molecules efficiently inhibit translation in an unspecific manner. Proof of concept that PS-specific tRNA fragments may interfere with ribosomal activity was obtained with artificially produced tRNA fragments. The results are discussed in terms of a functional role for long distance delivered noncoding PS RNAs.
Characterization of burn injuries using terahertz time-domain spectroscopy (2011)

The accuracy rates of the clinical assessment techniques used in grading burn injuries remain significantly low for partial thickness burns. In this paper, we present experimental results from terahertz characterization of 2<sup>nd</sup> and 3<sup>rd</sup> degree burn wounds induced on a rat model. Reflection measurements were obtained from the surface of both burned and normal skin using pulsed terahertz spectroscopy. Signal processing techniques are described for interpretation of the acquired terahertz waveform and differentiation of burn wounds. Furthermore, the progression of burn injuries is shown by comparison between acute characterization and 72-hours survival studies. While the water content of healthy and desiccated skin has been considered as a source of terahertz signal contrast, it is demonstrated that other biological effects such as formation of post-burn interstitial edema as well as the density of the discrete scattering structures in the skin (such as hair follicles, sweat glands, etc.) play a significant role in the terahertz response of the burn wounds.
A 16-element, K-band monolithic active receive phased array antenna (2003)

Advances in the GaAs monolithic microwave integrated circuit (MMIC) technology in the SHF/EHF suggest the feasibility of very thin active phased arrays which are ideal for conformal applications. A 16-element subarray was utilized to demonstrate the evaluate the design, fabrication, and integration of the recommended array architecture and technology proposed in a study which defines a design approach for the K-band monolithic active receive array. The 1.08 in.*1.08in.*0.24 in array consists of radiating element cells arranged in a 4*4 matrix with a 0.27 in. spacing between adjacent cells. Each radiating cell consists of a cavity radiating element excited by a Lange coupler, a GaAs MMIC receiver chip, and a 3-bit phase shifter. All 16 radiation cells are connected to a power combining network. Performance results are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synchronized Chemoenzymatic Synthesis of Monodisperse Hyaluronan Polymers (2004)

The length of the hyaluronan (HA) polysaccharide chain dictates its biological effects in many cellular and tissue systems. Long and short HA polymers often appear to have antagonistic or inverse effects. However, no source of very defined, uniform HA polymers with sizes greater than 10 kDa is currently available. We present a method to produce synthetic HA with very narrow size distributions in the range of approximately 16 kDa to approximately 2 MDa. The Pasteurella HA synthase enzyme, pmHAS, catalyzes the synthesis of HA polymer utilizing monosaccharides from UDP-sugar precursors. Recombinant pmHAS will also elongate exogenously supplied HA oligosaccharide acceptors in vitro in a nonprocessive fashion. As a result of bypassing the slow initiation step in vitro, the elongation process is synchronized in the presence of acceptor; thus all of polymer products are very similar in length. In contrast, without the use of an acceptor, the final polymer size range is difficult to predict and the products are more polydisperse. HA polymers of a desired size are constructed by controlling the reaction stoichiometry (i.e. molar ratio of precursors and acceptor molecules). The use of modified acceptors allows the synthesis of HA polymers containing tags (e.g. fluorescent, radioactive). In this scheme, each molecule has a single foreign moiety at the reducing terminus. Alternatively, the use of radioactive UDP-sugar precursors allows the synthesis of uniformly labeled native HA polymers. Overall, synthetic HA reagents with monodisperse size distributions and defined structures should assist in the elucidation of the numerous roles of HA in health and disease.
Passive immunization with a human monoclonal antibody protects hu-PBL-SCID mice against challenge by primary isolates of HIV-1 (1997)

How well antibodies can protect against disease due to HIV-1 infection remains a pivotal but unresolved issue with important implications for vaccine design and the use of prophylactic antibody to prevent infection after accidental exposure to the virus and to interrupt transmission of virus from mother to child. Strong doubts about the possible utility of antibodies in vivo have been raised because of the relative resistance of primary viruses to antibody neutralization in vitro. Primary viruses are likely to be close to the viruses transmitted during natural infection in humans. Vaccine studies have been of little value in assessing antibody efficacy in vivo because none of the strategies described to date have elicited significant neutralizing antibody responses to primary viruses. Passive immunization studies are similarly hindered by the paucity of reagents able to neutralize primary viruses effectively and a single study has suggested some benefit. Here we describe experiments to explore the ability of passive antibody to protect against primary virus challenge in hu-PBL-SCID mice. In this model, severe combined immunodeficient (SCID) mice are populated with human peripheral blood mononuclear cells (PBMCs) and infected with HIV-1. We find that the potent neutralizing human monoclonal antibody IgG1b12 at high dose is able to completely protect even when given several hours after viral challenge. The results are encouraging for antibody-based postexposure prophylaxis and support the notion that antibody induction could contribute to an effective vaccine.
Inhibition of interferon-inducible MxA protein expression by hepatitis B virus capsid protein. (1999)

Chronic hepatitis B treatment has been significantly improved by interferon (IFN) treatment. However, some studies have suggested that hepatitis B virus (HBV) might have a direct effect on the resistance to IFN. Defective particles, generated by spliced HBV RNA and associated with chronic hepatitis B, have been previously characterized; expression of these particles leads to cytoplasmic accumulation of the capsid protein. The aim of this study was to investigate the role of these defective genomes in IFN resistance. The global antiviral activity of IFN was studied by virus yield reduction assays, the expression of three IFN-induced antiviral proteins was analysed by Western blotting and confocal microscopy, and the regulation of MxA gene expression was studied by Northern blotting and the luciferase assay, in Huh7 cells transfected with a complete or the defective HBV genome. Results showed that the expression of the defective genome reduces the antiviral activity of IFN and that this modulation involves a selective inhibition of MxA protein induction by the HBV capsid protein. Our results also show the trans-suppressive effect of the HBV capsid on the MxA promoter, which might participate in this phenomenon. In conclusion, this study shows a direct interplay between the IFN-sensitive pathway and the capsid protein and might implicate this defective HBV genome in virus persistence.
Anthocyanins of Crowberry, Empetrum nigrum coll. (1984)

ABSTRACT Anthocyanins of northern crowberry ( Empetrum nigrum ssp. hermaphroditum (Hagerup) Böcker) were extracted from the berry with acidified ethanol and purified with solvent extractions and ion exchange chromatography. Separation of anthocyanins and analysis of aglycones were carried out with HPLC. Glycosidic units were analyzed with GLC‐MS. Twelve nonacylated monosides were found: glucoside, galactoside and arabinoside of delphinidin and petunidin, and galactoside and arabinoside of cyanidin, peonidin and malvidin. Three main anthocyanins were galactosides of cyanidin, dolphinidin and malvidin which formed about 60% of total anthocyanins.
Nucleic acid-triggered catalytic drug release (2000)

We propose a concept for the rational design and synthesis of highly selective chemotherapeutic agents that makes direct use of genetic information about the disease state. The key idea is to use the mRNA or DNA specific to the disease state to trigger the catalytic release of a cytotoxic drug by promoting the association of a prodrug with a catalyst capable of releasing the drug. We demonstrate the feasibility of such an approach in vitro with a model system that is based on the hydrolysis of p-nitrophenyl esters by imidazole. In our model system, the catalytic component consists of an imidazole group linked to the 5' end of a 15-mer that is complementary to the 5' end of the triggering oligodeoxynucleotide. The corresponding prodrug component consists of a p-nitrophenol ester linked to the 3' end of an 8-mer oligodeoxynucleotide that is complementary to the 3' end of the triggering sequence. We show that this system efficiently releases p-nitrophenol in the presence of all three components and that the reaction is catalytic and undergoes multiple turnovers. We also show that the complex between the catalytic component and the triggering oligodeoxynucleotide behaves like an enzyme and follows Michaelis-Menten kinetics, with a K(M) of 22 microM and a k(cat) of 0.018 min(-1). Most importantly, we show that catalytic release of p-nitrophenol is sensitive to the presence of a single base-pair mismatch.
DNA binding of .DELTA.- and .LAMBDA.-[Ru(phen)2DPPZ]2+ (1993)

Linear dichroism (LD) spectroscopy and steady-state as well as time-resolved luminescence spectroscopy have been used to investigate the interaction of the DELTA and LAMBDA enantiomers of Ru(phen)2DPPZ2+ (phen = 1,10-phenanthroline; DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) with DNA. The pure enantiomers, which were difficult to separate by traditional resolving methods, were synthesized via a chiral precursor. Changes in luminescence, isotropic absorption and excited state lifetimes upon binding, and the LD observed in flow-oriented DNA systems provide detailed information about the DNA binding of the enantiomers. Flow LD shows that both enantiomers bind to DNA in a well-defined manner with an orientation of the dipyridophenazine chromophore consistent with intercalation of this moiety between base-pairs. Both enantiomers are found to show luminescence in the presence of DNA to which they bind very strongly (K almost-equal-to 10(8) M-1); however, the relative luminescence quantum yield of the bound DELTA enantiomer is 6-10 times larger than that of the bound LAMBDA enantiomer. Furthermore, for each enantiomer two distinct excited state lifetimes are found in varying proportions depending on the binding ratio. The large difference in luminescence quantum yield between the enantiomers is interpreted in terms of slightly different intercalation geometries of the dipyridophenazine ligand, resulting in different protections from quenching by solvent water and diastereomeric differences in the interactions between enantiomers bound in contigue on DNA.
Loss calculation and design of arbitrarily curved integrated-optic waveguides (1983)

Radiation losses in arbitrarily curved integrated-optic waveguides are computed numerically by means of the beam-propagation method. From the results obtained, design rules for bends and S-shaped curves connecting two straight waveguides are derived.
Biodistribution of monoclonal antibodies: scale-up from mouse to human using a physiologically based pharmacokinetic model. (1995)

The efficacy of a novel diagnostic or therapeutic agent depends on its selective localization in a target tissue. Biodistribution studies are expensive and difficult to carry out in humans, but such data can be obtained easily in rodents. We have developed a physiologically based pharmacokinetic model for scaling up data from mice to humans, the first such model for genetically engineered macromolecules that bind to their targets in vivo, such as mAbs. The mathematical model uses physiological parameters including organ volumes, blood flow rates, and vascular permeabilities; the compartments (organs) are connected anatomically. This allows the use of scale-up techniques to predict antibody distribution in humans. The model was tested with data obtained in human patients for the biodistribution of a mAb against carcinoembryonic antigen. The model was further tested for a two-step protocol: bifunctional antibodies and radiolabeled hapten, which compared favorably with data in both mice and humans. The model was useful for optimization of treatment parameters, such as dose and time interval of injections, binding affinities, and choice of molecular carrier. This framework may be applicable to other genetically engineered molecules (e.g., growth factors, antisense oligonucleotides, and gene-carrying vectors).
Rapamycin Protects against Neuron Death inIn VitroandIn VivoModels of Parkinson's Disease (2010)

We report that rapamycin, an allosteric inhibitor of certain but not all actions of the key cellular kinase mammalian target of rapamycin (mTOR), protects neurons from death in both cellular and animal toxin models of Parkinson's disease (PD). This protective action appears to be attributable to blocked translation of RTP801/REDD1/Ddit4, a protein that is induced in cell and animal models of PD and in affected neurons of PD patients and that causes neuron death by leading to dephosphorylation of the survival kinase Akt. In support of this mechanism, in PD models, rapamycin spares phosphorylation of Akt at a site critical for maintenance of its survival-promoting activity. The capacity of rapamycin to provide neuroprotection in PD models appears to arise from its selective suppression of some but not all actions of mTOR, as indicated by the contrasting finding that Torin1, a full catalytic mTOR inhibitor, is not protective and induces Akt dephosphorylation and neuron death.
Accel: A Corrective Fusion Network for Efficient Semantic Segmentation\n on Video (2018)

We present Accel, a novel semantic video segmentation system that achieves\nhigh accuracy at low inference cost by combining the predictions of two network\nbranches: (1) a reference branch that extracts high-detail features on a\nreference keyframe, and warps these features forward using frame-to-frame\noptical flow estimates, and (2) an update branch that computes features of\nadjustable quality on the current frame, performing a temporal update at each\nvideo frame. The modularity of the update branch, where feature subnetworks of\nvarying layer depth can be inserted (e.g. ResNet-18 to ResNet-101), enables\noperation over a new, state-of-the-art accuracy-throughput trade-off spectrum.\nOver this curve, Accel models achieve both higher accuracy and faster inference\ntimes than the closest comparable single-frame segmentation networks. In\ngeneral, Accel significantly outperforms previous work on efficient semantic\nvideo segmentation, correcting warping-related error that compounds on datasets\nwith complex dynamics. Accel is end-to-end trainable and highly modular: the\nreference network, the optical flow network, and the update network can each be\nselected independently, depending on application requirements, and then jointly\nfine-tuned. The result is a robust, general system for fast, high-accuracy\nsemantic segmentation on video.\n
Consensus Statement for the Prevention and Management of Pain in the Newborn (2001)

Management of pain must be considered an important component of the health care provided to all neonates, regardless of their gestational age or severity of illness.
Truly Quantitative XPS Characterization of Organic Monolayers on Silicon: Study of Alkyl and Alkoxy Monolayers on H−Si(111) (2005)

The quantitative characterization of the chemical composition (bonding at grafted and ungrafted sites, surface coverage) is a key issue for the application of silicon-organic monolayer hybrid interfaces. The primary purpose of this article is to demonstrate that X-ray photoelectron spectroscopy (XPS) requires to be truly quantitative to deal with two main questions. The first one is accounting for X-ray photodiffraction (XPD), a well-known phenomenon that is responsible for azimuthal variations of the XPS signal intensity. A simple procedure is proposed to account for XPD in angle-resolved measurements. The second critical point concerns the choice of photoelectron attenuation lengths (AL). This article demonstrates that n-alkanethiol self-assembled monolayers on Au(111) can be used as a reference system to derive the effective monolayer thickness on silicon substrates and that one may use the empirical relationship established by Laibinis and co-workers to calculate the relevant ALs (Laibinis, P. E.; Bain, C. D.; Whitesides, G. M. J. Phys. Chem. 1991, 95, 7017). A self-consistent approach is presented to justify the above assertions and to give a complete compositional description of alkyl and alkoxy monolayers directly grafted on atomically flat H-Si(111) surfaces. Direct evidences are provided that a Si-C and a Si-O-C linkage is formed, respectively, after reaction with decene and decanol and that the ungrafted sites remain saturated with H atoms. Moreover, the quantitative spectra analysis of satellite peaks at fixed polar angle and three independent angle-resolved Si2p and C1s spectra all give the same surface coverage very close to its theoretical limit.
Somatostatin inhibition of fructose-induced hypertension. (1989)

The role of insulin resistance and hyperinsulinemia in the etiology of fructose-induced hypertension was studied in male Sprague-Dawley rats. Rats consumed a fructose-enriched diet (containing 66% of total calories as fructose) for 11 days and were infused continuously during the last 7 days with either a somatostatin analogue or vehicle. At the end of this period, rats receiving the somatostatin analogue had a lower plasma insulin concentration (52 +/- 4 vs. 70 +/- 6 microunits/ml, p less than 0.01) and a lower blood pressure (133 +/- 2 vs. 150 +/- 2 mm Hg) than did the rats infused with the control solution. In addition, the increase in plasma triglyceride concentration in response to the fructose-enriched diet was significantly attenuated (p less than 0.001) in the rats infused with somatostatin. These data provide further support that the increase in blood pressure that occurs when normal rats are fed a high fructose diet is dependent on the ability of this intervention to cause insulin resistance and hyperinsulinemia.