gebhart/patrepeval huggingface dataset:
Effects of TGF-beta and TGF-beta neutralizing antibodies on fibroblast-induced collagen gel contraction: implications for proliferative vitreoretinopathy. (1994)

Density-functional theory is used to study the geometric and electronic structure of cationic Si(16)(+) clusters with a Ti, V, or Cr dopant atom. Through unbiased global geometry optimization based on the basin-hopping approach, we confirm that a Frank-Kasper polyhedron, with the metal atom at the center, represents the ground-state isomer for all three systems. The endohedral cage geometry is thus stabilized even though only VSi(16)(+) achieves electronic shell closure within the prevalent spherical potential model. Our analysis of the electronic structure traces this diminished role of shell closure for the stabilization back to the adaptive capability of the metal-Si bonding, which is more the result of a complex hybridization than the originally proposed mere formal charge transfer. The resulting flexibility of the metal-Si bond can also help to stabilize "non-magic" cage-dopant combinations, which suggests that a wider range of materials may eventually be cast into this useful geometry for cluster-assembled materials.
Bias-voltage-controlled interlayer exchange coupling (1999)

We propose a new system whose magnetization direction can be controlled by an applied bias voltage without an external magnetic field. The system consists of a four layered structure F/sub 1//S/I/F/sub 2/ (F/sub 1/,F/sub 2/:ferromagnets, S:spacer, I:insulator). An analytic expression for bias-voltage-controlled interlayer exchange coupling in this system is developed within a simple free-electron-like, one-dimensional approximation. According to the approach, the magnetic configurations of the two magnetic layers oscillate from antiferromagnetic to ferromagnetic with applied bias voltage. This implies that we can switch/rotate the magnetization direction without an external magnetic field. Possible applications of such a system are also discussed.
Vascular endothelial cell adhesion and spreading promoted by the peptide REDV of the IIICS region of plasma fibronectin is mediated by integrin alpha 4 beta 1. (1992)

We have recently reported the attachment and spreading of human umbilical vein endothelial cells (HUVECs) upon substrates containing covalently grafted Arg-Glu-Asp-Val (REDV) peptide (Hubbell, J. A., Massia, S. P., Desai, N. P., and Drumheller, P. D. (1991) Bio/Technology 9, 568-572). This peptide has been reported to be the minimal active sequence within the CS5 site of the alternatively spliced type III connecting segment (IIICS) region of fibronectin, and the integrin alpha 4 beta 1 has been identified as the receptor on melanoma cells for this site. The integrin alpha 4 beta 1 has also been identified as the receptor for the CS1 site in the IIICS region on cells of neural crest origin, melanoma cells, lymphocytes, and hematopoietic stem cells. In this study, we demonstrate that this integrin also serves as a receptor on HUVECs for the peptide REDV from the CS5 site. The alpha 4 subunit was shown to be expressed upon HUVEC membranes by whole-cell enzyme-linked immunosorbent assay. Antifunctional antibodies directed against integrin subunits alpha 4 and beta 1 inhibited cell adhesion on REDV-grafted substrates, but not on RGD-grafted substrates. The alpha 4 subunit localized into fibrillar structures within spread cells on the REDV-grafted substrates, but not within spread cells on RGD-grafted substrates. Two proteins (144 and 120 kDa) were isolated from HUVEC extracts by REDV ligand affinity chromatography and were demonstrated by immunoprecipitation and Western blot to be the integrin subunits alpha 4 (144 kDa) and beta 1 (120 kDa); furthermore, the immunoprecipitation analyses demonstrated that the subunits formed a complex. HUVEC binding to REDV-grafted substrates was inhibited by both soluble REDV and RGD, demonstrating that adhesion was biospecific and that the REDV peptide is RGD-like. In this report we demonstrate for the first time that alpha 4 is present in the endothelial cell membrane, in contrast to previous reports by others, and that integrin alpha 4 beta 1 is the receptor for REDV-mediated adhesion to the IIICS region of region of plasma fibronectin.
Altered amino acid excretion in children with autism (2008)

Autism is a complex and life-long behavioural disorder of unknown aetiology. Recent reports have indicated the involvement of digestive tract dysfunction and possible complications from inadequate nutrition. In this study, 34 autistic children (12 untreated and 22 receiving therapeutic treatments related to digestive function and nutritional uptake) and 29 control subjects (all 5-15 years of age) were investigated to determine whether there were any anomalies in the urinary excretion of amino acids, glucose, sucrose, arabinose and tartaric acid using GC/FID and GC/MS analysis techniques. Significantly lower relative urinary levels of essential amino acids were revealed for both the untreated (mean +/- SEM, 32.53 +/- 3.09%) and treated (31.98 +/- 2.87%) autistic children compared with the controls (37.87 +/- 1.50%). There were no significant differences in measured excretions of sugars or tartaric acid. It was concluded that the untreated autistic children had evidence of altered metabolic homeostasis.
VHH selected against the viral spike protein can protect mice against lethal rabies virus challenge (2011)

VHH are polypeptides (15 kDa) derived from the variable domain of single heavy-chain antibodies of Camelidae. They represent the smallest antigen-binding fragment of an antibody (human IgG = 150 kDA). VHH are currently being explored for a number of applications.

Anti-rabies virus VHH were cloned from lymphocytes of vaccinated llamas and selected for their affinity with the viral spike glycoprotein G and neutralizing potency in a cellular infection assay. Linkage of two VHH allowed recognition of two identical or different epitopes and increased the neutralizing potency in cells more than a hundred-fold. Next, we examined the protection efficiency of these bimeric VHH in vivo.

Contrary to irrelevant control VHH, pre-incubation of the virus with anti-G VHH fully protected mice against disease and mortality upon inoculation of the virus-VHH mix in the nose, muscle or brain. Preventive administration of anti-G VHH in the nose, 24 hours prior to intranasal virus challenge, also almost completely prevented disease and lethal infection. This suggests that VHH remain sufficiently active for at least 24 hours at the site of administration in the nose to neutralize a significant part of the invading virus. Post exposure prophylaxis (PEP) by injection of anti-G VHH in the left quadriceps muscle 10 minutes after virus challenge in the right quadriceps muscle reduced mortality by 50%. Treatment 24 hours after virus challenge was however no longer effective, most likely because the virus had already reached the central nervous system and was no longer exposed to locally administered VHH.

Our results show that anti-G VHH can neutralize rabies virus in an Fc-independent way. VHH probably hinder the recognition of cellular receptors or interfere with the fusion of viral and cellular membranes. The bimeric constructs proved protective in different challenge models, but that protection in the PEP model was weak. This might be due to the short half-life of the used VHH. Considering that prolongation of the half-life of VHH is feasible by different approaches, VHH technology may offer perspectives as an alternative to antibodies for PEP. VHH have a low production cost, not contaminated by blood-borne pathogenic agents and are less likely to evoke allergic or immunopathological reactions. They have good thermal stability, which is an advantage in developing countries, where the cold chain for distribution and preservation can not always be guaranteed.
HLA-E and HLA-G Expression in Classical HLA Class I-Negative Tumors Is of Prognostic Value for Clinical Outcome of Early Breast Cancer Patients (2010)

Nonclassical HLAs, HLA-E and HLA-G, are known to affect clinical outcome in various tumor types. We examined the clinical impact of HLA-E and HLA-G expression in early breast cancer patients, and related the results to tumor expression of classical HLA class I. Our study population (n = 677) consisted of all early breast cancer patients primarily treated with surgery in our center between 1985 and 1995. Tissue microarray sections of arrayed tumor and normal control material were immunohistochemically stained for HLA-E and HLA-G. For evaluation of HLA-E and HLA-G and the combined variable, HLA-EG, a binary score was used. Expression of classical HLA class I molecules was determined previously. HLA-E, HLA-G, and HLA-EG on breast tumors were classified as expression in 50, 60, and 23% of patients, respectively. Remarkably, only in patients with loss of classical HLA class I tumor expression, expression of HLA-E (p = 0.027), HLA-G (p = 0.035), or HLA-EG (p = 0.001) resulted in a worse relapse-free period. An interaction was found between classical and nonclassical HLA class I expression (p = 0.002), suggestive for a biological connection. We have demonstrated that, next to expression of classical HLA class I, expression of HLA-E and HLA-G is an important factor in the prediction of outcome of breast cancer patients. These results provide further evidence that breast cancer is immunogenic, but also capable of evading tumor eradication by the host's immune system, by up- or downregulation of HLA class Ia and class Ib loci.
Antireflective Photoanode Made of TiO2 Nanobelts and a ZnO Nanowire Array (2010)

We fabricated an antireflective hybrid nanostructure using anatase TiO2 nanobelts synthesized by an alkaline hydrothermal route and a ZnO nanowire array grown via a low-temperature solution-phase process. The replacement of TiO2 nanoparticles with TiO2 nanobelts improved the electron transport in the TiO2 porous film. Importantly, rigorous coupled-wave analysis and reflectance measurements indicate that the well-designed composite of TiO2 nanobelt−ZnO nanowire array acted as an efficient antireflection coating. The photoanode made of this hybrid nanostructure may enhance the performance of dye-sensitized solar cells by minimizing the electron−hole recombination-related and reflection-induced energy loss.
Dielectrophoretic Sorting of Particles and Cells in a Microsystem (1998)

There are highly sensitive analytical techniques for probing cellular and molecular events in very small volumes. The development of microtools for effective sample handling and separation in such volumes remains a challenge. Most devices developed so far use electrophoretic and chromatographic separation methods. We show that forces generated by ac fields under conditions of negative dielectrophoresis (DEP) can also be used. Miniaturized electrode arrays are housed in a microchannel and driven with high-frequency ac. A laminar liquid flow carries particles past the electrodes. Modification of the ac drive changes the particle trajectories. We have handled latex particles of micrometer size and living mammalian cells in a device which consists of the following four elements: a planar funnel which concentrates particles from a 1-mm-wide stream to a beam of about 50-micron width, an aligner which narrows the beam further and acts to break up particle aggregates, a field cage which can be used to trap particles, and a switch which can direct particles into one of two output channels. The electrodes are made from platinum/titanium and indium tin oxide (ITO) on glass substrates. Particle concentration and switching could be achieved for linear flow velocities up to about 10 mm s-1. The combination of this new method with high-performance optical detection offers prospects for miniaturized flow cytometry.
The Chemorepulsive Activity of the Axonal Guidance Signal Semaphorin D Requires Dimerization (1998)

The axonal guidance signal semaphorin D is a member of a large family of proteins characterized by the presence of a highly conserved semaphorin domain of about 500 amino acids. The vertebrate semaphorins can be divided into four different classes that contain both secreted and membrane-bound proteins. Here we show that class III (SemD) and class IV semaphorins (SemB) form homodimers linked by intermolecular disulfide bridges. In addition to the 95-kDa form of SemD (SemD(95k)), proteolytic processing of SemD creates a 65-kDa isoform (SemD(65k)) that lacks the 33-kDa carboxyl-terminal domain. Although SemD(95k) formed dimers, the removal of the carboxyl-terminal domain resulted in the dissociation of SemD homodimers to monomeric SemD(65k). Mutation of cysteine 723, one of four conserved cysteine residues in the 33-kDa fragment, revealed its requirement both for the dimerization of SemD and its chemorepulsive activity. We suggest that dimerization is a general feature of sema- phorins which depends on class-specific sequences and is important for their function.
Synthetic gut microbiome: Advances and challenges (2020)

An exponential rise in studies regarding the association among human gut microbial communities, human health, and diseases is currently attracting the attention of researchers to focus on human gut microbiome research. However, even with the ever-growing number of studies on the human gut microbiome, translation into improved health is progressing slowly. This hampering is due to the complexities of the human gut microbiome, which is composed of >1,000 species of microorganisms, such as bacteria, archaea, viruses, and fungi. To overcome this complexity, it is necessary to reduce the gut microbiome, which can help simplify experimental variables to an extent, such that they can be deliberately manipulated and controlled. Reconstruction of synthetic or established gut microbial communities would make it easier to understand the structure, stability, and functional activities of the complex microbial community of the human gut. Here, we provide an overview of the developments and challenges of the synthetic human gut microbiome, and propose the incorporation of multi-omics and mathematical methods in a better synthetic gut ecosystem design, for easy translation of microbiome information to therapies.
Hepoxilin A3 is the endogenous lipid mediator opposing hypotonic swelling of intact human platelets. (1993)

When human blood platelets are exposed to hypotonic medium they swell first but, shortly thereafter, revert toward their original volume in a process termed regulatory volume decrease (RVD). RVD is the result of an enhanced efflux of K+ and Cl- ions and associated water. Platelet RVD is controlled by a short-lived lipoxygenase-derived product (LP). By using a combination of high-performance liquid chromatography, gas chromatography-mass spectrometry, and RVD reconstitution bioassay, we show that LP is identical with hepoxilin A3. In addition we demonstrate that authentic hepoxilin A3 possesses the same biological properties on RVD reconstitution as LP and that the activity of both compounds is amplified through epoxide hydrolase inhibition with 3,3,3-trichloropropene-1,2-oxide. Therefore, we report here that volume expansion causes the formation and release of hepoxilin A3 from intact human platelets and that this hepoxilin plays a major role in volume regulation.
Numerical recipes in C (1994)

Note: Includes bibliographical references, 3 appendixes and 2 indexes.- Diskette v 2.06, 3.5''[1.44M] for IBM PC, PS/2 and compatibles [DOS] Reference Record created on 2004-09-07, modified on 2016-08-08
Single-Step Multiplex Conventional and Real-Time Reverse Transcription Polymerase Chain Reaction Assays for Simultaneous Detection and Subtype Differentiation of Influenza A Virus in Swine (2010)

Because pigs are considered intermediate hosts for the emergence of novel influenza virus reassortants with associated zoonotic potential, monitoring and characterization of circulating influenza viruses in pigs are important for adequate control of infection. For this, rapid molecular diagnostic methods other than immunoassays are needed. Three novel single-step multiplex reverse transcription polymerase chain reaction (RT-PCR) assays were developed in the current study for simultaneous detection and subtype differentiation of Influenza A virus in pigs. A conventional single-step pentaplex RT-PCR was designed for concomitant detection of the generic matrix (M) gene, hemagglutinin H1 and H3, and neuraminidase N1 and N2 genes of Swine influenza virus (SIV). In the other 2 single-step tetraplex real-time RT-PCR assays, the primers and fluorescent probes were targeted for the simultaneous detection of common M, H1, H3, and N2 SIV genes (first assay), and for M, H1, and H3 SIV genes and the H5 gene of highly pathogenic avian influenza virus of Eurasian lineage (second assay). The real-time RT-PCR assays had detection sensitivity limits ranging from 10(1) to 10(3) copies of respective in vitro RNA transcripts of M, H1, H3, H5, and N2 genes. The multiplex assays were evaluated by using SIV isolates, clinical specimens, and the appropriate synthetic template. The recent H1N1 pandemic strain isolated from pigs also was tested in simplex RT-PCR and real-time RT-PCR assays with the H1 primers and probes. The efficacy of the multiplex RT-PCR and real-time RT-PCR shows the suitability of multiplex RT-PCR and real-time RT-PCR for rapid subtype identification and monitoring in North American pigs of Influenza A virus.
Independent two-color optogenetic excitation of neural populations (2013)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2013.
Nonlinearities identification using the LMS Volterra filter (2005)

Abstract:- Nonlinear adaptive filtering techniques, based on the Volterra model, are widely used for the nonlinearities identification in many applications. This paper proposes a new implementation of the third order LMS Volterra filter. A third order nonlinear system with memory is identified using the new LMS algorithm implementation for the Volterra kernels estimation. The accuracy of the proposed algorithm is appreciated by comparing the estimated third order kernel with the real kernel. It is demonstrated that the adaptive algorithm gives satisfactory convergence in different conditions of noise. The extension of the LMS algorithm implementation to higher order Volterra filters is also possible and involves a few simple changes. Key-Words:- Volterra kernels estimation, LMS algorithm, Nonlinear filter identification.
INDUCED RESISTANCE OF TOMATO TO WHITEFLIES AND PYTHIUM WITH THE PGPR BACILLUS SUBTILIS IN A SOILLESS CROP GROWN UNDER GREENHOUSE CONDITIONS (2007)

ISHS VIII International Symposium on Protected Cultivation in Mild Winter Climates: Advances in Soil and Soilless Cultivation under Protected Environment INDUCED RESISTANCE OF TOMATO TO WHITEFLIES AND PYTHIUM WITH THE PGPR BACILLUS SUBTILIS IN A SOILLESS CROP GROWN UNDER GREENHOUSE CONDITIONS
Standardized Extensions of High Efficiency Video Coding (HEVC) (2013)

This paper describes extensions to the High Efficiency Video Coding (HEVC) standard that are active areas of current development in the relevant international standardization committees. While the first version of HEVC is sufficient to cover a wide range of applications, needs for enhancing the standard in several ways have been identified, including work on range extensions for color format and bit depth enhancement, embedded-bitstream scalability, and 3D video. The standardization of extensions in each of these areas will be completed in 2014, and further work is also planned. The design for these extensions represents the latest state of the art for video coding and its applications.
Fibrillar β-Amyloid-stimulated Intracellular Signaling Cascades Require Vav for Induction of Respiratory Burst and Phagocytosis in Monocytes and Microglia (2006)

Microglial interaction with extracellular beta-amyloid fibrils (fAbeta) is mediated through an ensemble of cell surface receptors, including the B-class scavenger receptor CD36, the alpha(6)beta(1)-integrin, and the integrin-associated protein/CD47. The binding of fAbeta to this receptor complex has been shown to drive a tyrosine kinase-based signaling cascade leading to production of reactive oxygen species and stimulation of phagocytic activity; however, little is known about the intracellular signaling cascades governing the microglial response to fAbeta. This study reports a direct mechanistic link between the fAbeta cell surface receptor complex and downstream signaling events responsible for NADPH oxidase activation and phagosome formation. The Vav guanine nucleotide exchange factor is tyrosine-phosphorylated in response to fAbeta peptides as a result of the engagement of the microglia fAbeta cell surface receptor complex. Co-immunoprecipitation studies demonstrate an Abeta-dependent association between Vav and both Lyn and Syk kinases. The downstream target of Vav, the small GTPase Rac1, is GTP-loaded in an Abeta-dependent manner. Rac1 is both an essential component of the NADPH oxidase and a critical regulator of microglial phagocytosis. The direct role of Vav in fAbeta-stimulated intracellular signaling cascades was established using primary microglia obtained from Vav(-/-) mice. Stimulation of Vav(-/-) microglia with fAbeta failed to generate NADPH oxidase-derived reactive oxygen species and displayed a dramatically attenuated phagocytic response. These findings directly link Vav phosphorylation to the Abeta-receptor complex and demonstrate that Vav activity is required for fAbeta-stimulated intracellular signaling events upstream of reactive oxygen species production and phagosome formation.
Implementing telemedicine services in northern Norway: Barriers and facilitators (2003)

Telemedicine is not simply a technology - it also involves processes. The use of telemedicine is influenced by many factors. Our intention was to examine what conditions promote the use of telemedicine between general practitioners (GPs) and hospitals. Qualitative interviews were undertaken with 16 GPs in northern Norway. The extent to which GPs were using the services was limited, although some used them fairly frequently. The most widely used service was teledermatology. The GPs saw advantages of the services in general and saw clear benefits for their patients. The services were considered to be time-consuming, and the lack of adequate government remuneration for the time involved in teleconsultations was seen as a barrier to their use. The GPs focused on their own ability to handle new technology and expressed a need to practise more.
Genes and Signals (2001)

Genes & Signals analyzes gene regulation from a new perspective. The first chapter describes mechanisms found in bacteria, and two subsequent chapters discuss which of these is most highly exploited in higher organisms. A final chapter relates these molecular strategies to other enzymatic processes, including those involving kinases, RNA splicing enzymes, proteases, and others. A general theme emerges, one that proposes how a rather restricted set of signals and enzymatic functions has been used in evolution to generate complex life forms of different types.