gebhart/patrepeval huggingface dataset:
Machine Learning Approaches for Cognitive State Classification and Brain Activity Prediction: A Survey (2015)

The application of machine learning approaches to decode cognitive states through functional Magnetic Resonance Imaging (fMRI) is one of the emerging fields of research over the past decade. Multivoxel Pattern Analysis (MVPA) treats the activation of multiple voxels from the fMRI data as a pattern to decode the brain states using machine learning based classifiers. The potential in designing a classifier to accurately classify the discriminating cognitive states has attracted great attention from machine learning researchers. Interest has been evinced in particular to the application of such classifiers to study brain functions, diagnose mental diseases, detect deception and develop a brain-computer-interface. This paper surveys the recent development of machine learning approaches in cognitive state classification and brain activity prediction. Comparative studies of various techniques have been investigated to appreciate their merits and demerits. Furthermore, feature selection is discussed in this survey as an important preprocessing step in MVPA because it incorporates those features that will be integrated in the classification task of fMRI data, thereby improving the performance of the classifier. Features can be selected by restricting the analysis to specific anatomical regions or by computing univariate (voxel-wise) or multivariate statistics. Besides a summary and the future perspective of this field, an extensive list of bibliography is included for the community of interest. Keywords: Classification, feature selection, feature extraction, functional magnetic resonance imaging, brain activity prediction, machine learning.
Neural Stem Cells Are Uniquely Suited for Cell Replacement and Gene Therapy in the CNS (2000)

In recent years, it has become evident that the developing and even the adult mammalian CNS contain a population of undifferentiated, multipotent cell precursors, neural stem cells, the plastic properties of which might be of advantage for the design of more effective therapies for many neurological diseases. This article reviews the recent progress in establishing rodent and human clonal neural stem cell lines, their biological properties, and how these cells can be utilized to correct a variety of defects, with prospects for the near future to harness their behaviour for neural stem cell-based treatment of diseases in humans.
Ruthenium-catalyzed hydroborations of alkenes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRuthenium-catalyzed hydroborations of alkenesKevin Burgess and Marcel JasparsCite this: Organometallics 1993, 12, 10, 4197–4200Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/om00034a065https://doi.org/10.1021/om00034a065research-articleACS PublicationsRequest reuse permissionsArticle Views588Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Using Polarization Effects to Alter Chemical Reactivity:  A Simple Host Which Enhances Amine Nucleophilicity (2000)

The rational design of a bis(phosphine oxide) host which is capable of binding a benzylic amine is presented. The ability of this host to increase the rate of addition of 4-fluorobenzylamine to N-phenylmaleimide is rationalized in terms of the enhancement of the nucleophilicity of the benzylic amine.
<title>Fabrication of high-energy x-ray transmission gratings for the Advanced X-ray Astrophysics Facility (AXAF)</title> (1994)

The High Energy Transmission Grating spectrometer (HETG) on the Advanced X-ray Astrophysics Facility (AXAF) requires the fabrication and assembly of hundreds of large area (approximately equals 6 cm<SUP>2</SUP>), low-distortion, ultra-fine-period transmission gratings efficient in the 0.4-10 keV band ((lambda) equals 1.2-30 angstroms). The spectrometer requires two types of gratings: Medium Energy Gratings (MEG), which have a period of 0.4 micrometers and consist of gold bars 0.4 micrometers thick, and High Energy Gratings (HEG), which have a period of 0.2 micrometers and consist of gold bars 0.7 micrometers thick. Both types are supported by 0.5-1.0 micrometers -thick polyimide membranes. The gratings are fabricated using a variety of techniques including interference lithography, tri-level resist processing, reactive-ion etching, and gold microplating. An earlier approach which utilized x-ray lithography has been abandoned. Recent efforts have focussed on improving the yield and robustness of the many complicated fabrication steps, and improving the profile of the grating bars. We present details of the fabrication procedure and discuss the issues associated with developing an optimal fabrication process.
The link between fungi and severe asthma: a summary of the evidence (2006)

There is current evidence to demonstrate a close association between fungal sensitisation and asthma severity. Whether such an association is causal remains to be confirmed, but this is explored by means of a detailed literature review. There is evidence from two randomised controlled trials that, in the example of allergic bronchopulmonary aspergillosis (ABPA), treatment with systemic antifungal therapy can offer a therapeutic benefit to approximately 60% of patients. ABPA is only diagnosed if a combination of clinical and immunological criteria is achieved. It is not known whether such cases are a discrete clinical entity or part of a spectrum of the pulmonary allergic response to fungi or fungal products. This paper describes the epidemiological evidence that associates severity of asthma with fungi and discusses possible pathogenetic mechanisms. Many airborne fungi are involved, including species of Alternaria, Aspergillus, Cladosporium and Penicillium, and exposure may be indoors, outdoors or both. The potential for a therapeutic role of antifungal agents for patients with severe asthma and fungal sensitisation is also explored. Not only are many patients with severe asthma desperately disabled by their disease, but, in the UK alone, asthma accounts for 1,500 deaths per yr. The healthcare costs of these patients are enormous and any treatment option merits close scrutiny. Within this report, the case for the consideration of a new term related to this association is put forward. The current authors propose the term "severe asthma with fungal sensitisation". However, it is recognised that enhanced and precise definition of fungal sensitisation will require improvements in diagnostic testing.
The first 17 amino acids of Huntingtin modulate its sub-cellular localization, aggregation and effects on calcium homeostasis (2006)

A truncated form of the Huntington's disease (HD) protein that contains the polyglutamine repeat, Httex1p, causes HD-like phenotypes in multiple model organisms. Molecular signatures of pathogenesis appear to involve distinct domains within this polypeptide. We studied the contribution of each domain, singly or in combination, to sub-cellular localization, aggregation and intracellular Ca2+ ([Ca2+]i) dynamics in cells. We demonstrate that sub-cellular localization is most strongly influenced by the first 17 amino acids, with this sequence critically controlling Httex1p mitochondrial localization and also promoting association with the endoplasmic reticulum (ER) and Golgi. This domain also enhances the formation of visible aggregates and together with the expanded polyQ repeat acutely disrupts [Ca2+]i levels in glutamate-challenged PC12 cells. Isolated cortical mitochondria incubated with Httex1p resulted in uncoupling and depolarization of these organelles, further supporting the idea that Httex1p-dependent mitochondrial dysfunction could be instrumental in promoting acute Ca2+ dyshomeostasis. Interestingly, neither mitochondrial nor ER associations seem to be required to promote long-term [Ca2+]i dyshomeostasis.
Improved Cellular Activity of Antisense Peptide Nucleic Acids by Conjugation to a Cationic Peptide-Lipid (CatLip) Domain (2008)

Conjugation to cationic cell penetrating peptides (such as Tat, Penetratin, or oligo arginines) efficiently improves the cellular uptake of large hydrophilic molecules such as oligonucleotides and peptide nucleic acids, but the cellular uptake is predominantly via an unproductive endosomal pathway and therefore mechanisms that promote endosomal escape (or avoid the endosomal route) are required for improving bioavailability. A variety of auxiliary agents (chloroquine, calcium ions, or lipophilic photosensitizers) has this effect, but improved, unaided delivery would be highly advantageous in particular for future in vivo applications. We find that simply conjugating a lipid domain (fatty acid) to the cationic peptide (a CatLip conjugate) increases the biological effect of the corresponding PNA (CatLip) conjugates in a luciferase cellular antisense assay up to 2 orders of magnitude. The effect increases with increasing length of the fatty acid (C8-C16) but in parallel also results in increased cellular toxicity, with decanoic acid being optimal. Furthermore, the relative enhancement is significantly higher for Tat peptide compared to oligoarginine. Confocal microscopy and chloroquine enhancement indicates that the lipophilic domain increases the endosomal uptake as well as promoting significantly endosomal escape. These results provide a novel route for improving the (cellular) bioavailability of larger hydrophilic molecules.
Candida albicans Iff11, a Secreted Protein Required for Cell Wall Structure and Virulence (2007)

The Candida albicans cell wall is the immediate point of contact with the host and is implicated in the host-fungal interaction and virulence. To date, a number of cell wall proteins have been identified and associated with virulence. Analysis of the C. albicans genome has identified the IFF gene family as encoding the largest family of cell wall-related proteins. This family is also conserved in a range of other Candida species. Iff11 differs from other family members in lacking a GPI anchor, and we have demonstrated it to be O glycosylated and secreted in C. albicans. A null mutant lacking IFF11 was hypersensitive to cell wall-damaging agents, suggesting a role in cell wall organization. In a murine model of systemic infection the null mutant was highly attenuated in virulence, and survival-standardized infections suggest it is required to establish an infection. This work provides the first evidence of the importance of this gene family in the host-fungal interaction and virulence.
The Necessity and Quandaries of Dengue Vaccine Development (2011)

to dengue occur annually [19]. There is no specific, licensed anti-DENV therapeutic or preventative vaccine. The financial, social and individual cost of dengue is significant, underestimated, and underappreciated [20–25]. The strategic administration of a safe and efficacious dengue vaccine, in coordination with efforts to educate about personal protective measures and sustained vector control, is the best hope to reduce the global dengue burden. There are numerous dengue vaccine candidates in clinical development. Early efforts to develop a dengue vaccine date back more than 70 years, with attempts to prevent virus transmission using infectious human plasma treated with ox bile or virus grown in live mosquitoes
Production of proinflammatory cytokines and adhesion molecules in ex-vivo xenogeneic kidney perfusion (1994)

Xenogeneic transplantation of solid organs is limited due to hyperacute rejection. In concordant systems, the mechanisms of rejection can be studied due to cross-reactivity of mediators with anti-human monoclonal antibodies. The aim of this study was to obtain information about the kinetics of proinflammatory cytokines and production of soluble adhesion molecules in the acute phase of reperfusion, eight kidneys from rhesus monkeys were perfused ex-vivo with human blood (group B/0) for 1 hour in a closed system. Blood levels of IL-1b, IL-6, TNFalpha, soluble ICAM, and E-selectin were measured using an ELISA technique under steady-state conditions. Cytokine levels rose significantly within the 60-min interval (IL-1b, 6.1 +/- 2.6-161.1 +/- 98.5 pg/ml; IL-6, 30.2 +/- 7.7-274.2 +/- 75.8 pg/ml; TNFalpha, 544.2 +/- 363.6-1651.0 +/- 25.7 pg/ml; P < 0.05). Immediately after the beginning of reperfusion, soluble ICAM-1 and selectin levels were abnormally high and rose constantly throughout the observation period, reaching significance at 60 min. High levels of proinflammatory cytokines may lead to an induction of adhesion molecules, thus, upregulating the leukocyte-endothelial interaction in a complement-independent mechanism. Specific pretreatment with monoclonal antibodies against ICAM-1, LFA-1, or other soluble mediators may be useful in down-regulating hyperacute rejection in trans-species transplantation.
Enabling Communities of Knowledge Workers (2004)

The MITRE corporation is a geographicallydistributed company of knowledge workers workingon projects either related by the same customer or bythe problems and technologies being addressed.MITRE early on recognized the power of informationtechnology to enhance the effectiveness of each of itsstaff with knowledge sharing tools. Early deploymentof an Intranet with novel functions has promotedinformation sharing among the staff, enabling eachstaff member to effectively leverage the knowledge ofthe entire company. Specific examples, storagestructures, information spaces, search mechanisms andpolicy issues that have promoted sharing have revealedmany lessons for enabling the knowledge worker.
Use of PCR and PCR-SSP for detection of urinary donor-origin DNA in renal transplant recipients with acute rejection. (2003)

Presence of door specific DNA in the urine of the recipient is strongly associated with acute rejection. Analysis of DNA derived from donor cells in urine was an effective and accurate method for the diagnosis of acute rejection of a renal transplant.
What drives disease in multiple sclerosis: Inflammation or neurodegeneration? (2010)

Abstract Multiple sclerosis (MS) is defined as a chronic inflammatory disease of the central nervous system, which leads to focal inflammatory demyelinated lesions with secondary neurodegeneration. However, this concept has recently been challenged by several observations suggesting that in this disease neurodegeneration might occur independently of inflammation. Here, these new findings are critically discussed and evidence that active neurodegeneration in MS is invariably associated with inflammation is provided. The present review shows, however, that the inflammatory reaction is much more complex, as thought before, and that in the progressive stage of the disease it might become trapped in the central nervous system behind a repaired blood–brain barrier. Future therapeutic options for this disease are discussed on the basis of recent knowledge of the mechanisms of inflammation and neurodegeneration. (Clin. Exp. Neuroimmunol. doi: 10.1111/ j.1759‐1961.2009.00003.x, January 2010)
Site-directed mutagenesis in hemoglobin: Functional and structural study of the intersubunit hydrogen bond of threonine-38(C3).alpha. at the .alpha.1-.beta.2 interface in human hemoglobin (1993)

To clarify the functional and structural roles of Thr-38 alpha at the alpha 1-beta 2 interface, two artificial alpha-chain mutants, in which Thr-38 alpha is replaced by Ser (Hb T38 alpha S) or Val (Hb T38 alpha V), were prepared. Thr-38 alpha is one of the highly conserved amino acid residues in hemoglobins and forms a hydrogen bond to Asp-99 beta, which is a crucial residue to stabilize the T state, via a water molecule in the deoxygenated form. We investigated their oxygen binding properties together with structural consequences of the mutations by using various spectroscopic probes. Their oxygen equilibrium curves showed small changes in the oxygen binding properties. Structural probes such as ultraviolet-region derivative and oxy-minus-deoxy difference spectra, resonance Raman scattering, and 1H-NMR spectra also indicated that the oxy and deoxy forms of these mutants show spectra characteristic of the R and T states, respectively, and the R-T transition is not very disturbed. The present structural and functional data of the mutants imply that the hydrogen bond between Thr-38 alpha and Asp-99 beta does not play a key role in stabilizing the deoxy T structure, which is in sharp contrast to the role of the hydrogen bond between Tyr-42 alpha and Asp-99 beta, and suggest that the interactions via the intersubunit hydrogen bonds are highly site-specific, depending on the amino acid residue which participates in them.
Mutagenesis. (1995)

Choosing the right mutagen means selecting the right combination of mutagen efficiency and mutagen specificity. For mutagen efficiency, nothing beats EMS. It is extremely potent, it is easy to use, and its mutational specificity is well documented. If mutations other than G/C-->A/T transitions are desired, mutagens other than EMS must be used. Based on initial observations, ENU appears to be as efficient as EMS. Work with other organisms predicts that ENU will yield a wider variety of transitions and transversions than EMS. If this proves to be true, ENU will become an important mutagen for routine genetic analysis. For investigators wanting large multigene deletions, gamma irradiation, UV irradiation, formaldehyde, and DEO are the mutagens of choice. Gamma irradiation yields the highest frequency of events by far, but may also yield more complex rearrangements. Based on limited information, UV irradiation, formaldehyde, and DEO appear to be effective deletion mutagens. Of the three, UV appears to be the most efficient. For investigators wanting small intragenic deletions, TMP appears most effective. TMP is not very potent, but a large proportion of TMP-induced unc-22 mutations are small deletions. Hopefully this will be true of all genes. For investigators wanting other types of genome rearrangements (e.g., translocations, crossover suppressors), gamma irradiation (or possibly X irradiation) is effective. For transposon insertions, mut-2 (especially strain TR679) provides the highest possible frequency of events. Because mut-2 activates several families of transposons, it yields insertions in genes that are poor targets for Tc1. Manipulating a strain with such high frequencies of spontaneous mutations, however, can be problematical (see above). For Tc1-specific events, mut-6 (strain RW7097) is the best choice. It provides frequencies comparable to those of Bergerac, but its Tc1 copy number is much lower. A reasonable strategy for spontaneous mutagenesis is to use TR679 only if mutants are not obtained in strains with lower levels of activity (e.g., MT3126 or RW7097).
Developmental gene expression and tissue distribution of the CHIP28 water-channel protein. (1993)

The CHIP28 water channel is a major component of red cell and renal tubule membranes; however, its ontogeny and tissue distribution remain undefined. Three patterns of expression were identified when CHIP28 mRNA was surveyed by in situ hybridization histochemistry in rats between embryonic day 14 and maturity. (i) CHIP28 mRNA and protein were very abundant in hematopoietic tissue and kidneys of mature rats, but strong expression did not occur until after birth, when it appeared in renal proximal tubules and descending thin limbs, red pulp of the spleen, and membranes of circulating red cells. (ii) CHIP28 mRNA was abundant in choroid plexus epithelium throughout fetal development and maturity. (iii) CHIP28 mRNA was transiently observed in periosteum, heart, vascular endothelium, and cornea during fetal development. The ontogeny of kidney and red cell CHIP28 expression coincides with the ability of kidneys to concentrate urine, suggesting that CHIP28 promotes water reabsorption in the proximal nephron and provides red cell osmoregulation needed for passage through the hypertonic medulla. Its presence in the choroid plexus suggests that CHIP28-mediated water transport contributes to secretion of cerebrospinal fluid. The functional role of CHIP28 in developing bone, heart, and eye is unclear. These findings further establish the general physiologic role of CHIP28 as a water channel involved in reabsorption, osmoregulation, and secretion. The studies also suggest other possible functions during fetal development and predict that complex mechanisms will be needed for regulation of CHIP28 gene expression in diverse tissues at distinct points in development.
Biochemical and Functional Characterization of DNA Complexes Capable of Targeting Genes to Hepatocytes via the Asialoglycoprotein Receptor (1997)

Electrostatic binding of polycations or basic polypeptides to the DNA phosphate backbone has been previously described as a one-step process which results in uncontrolled aggregation and precipitation of the DNA in solution. We describe here a multistep process in which the condensation of DNA in the presence of poly-L-lysine can be controlled to produce particles of discrete size and shape suitable for receptor-mediated gene transfer in vivo and in vitro. The first step in this process involves the gradual accretion of poly-L-lysine onto the DNA phosphate backbone, until charges are neutralized. The addition of poly-L-lysine to a concentrated solution of DNA in this fashion prevents intermolecular aggregation of the DNA, presumably by promoting the formation of a nucleus of condensation along the length of each DNA molecule. The second stage of the process involves adjusting the ionic strength of the solvent to facilitate the solubilization of compact DNA.poly-L-lysine complexes. Several physical and biochemical parameters have been studied and correlated with the efficacy of DNA/ligand-poly-L-lysine particles in transferring genes to the liver of adult animals by receptor-mediated endocytosis.
R2D2, a Bridge Between the Initiation and Effector Steps of the Drosophila RNAi Pathway (2003)

The RNA interference (RNAi) pathway is initiated by processing long double-stranded RNA into small interfering RNA (siRNA). The siRNA-generating enzyme was purified from Drosophila S2cells and consists of two stoichiometric subunits: Dicer-2(DCR-2) and a previously unknown protein that we named R2D2. R2D2 is homologous to the Caenorhabditis elegans RNAi protein RDE-4. Association with R2D2 does not affect the enzymatic activity of DCR-2. Rather, the DCR-2/R2D2 complex, but not DCR-2 alone, binds to siRNA and enhances sequence-specific messenger RNA degradation mediated by the RNA-initiated silencing complex (RISC). These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC.
ChemInform Abstract: MEK Inhibitors: The Chemistry and Biological Activity of U0126, Its Analogues, and Cyclization Products. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.