gebhart/patrepeval huggingface dataset:
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments (2007)

The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org.
Scratch input (2008)

We present Scratch Input, an acoustic-based input technique that relies on the unique sound produced when a fingernail is dragged over the surface of a textured material, such as wood, fabric, or wall paint. We employ a simple sensor that can be easily coupled with existing surfaces, such as walls and tables, turning them into large, unpowered and ad hoc finger input surfaces. Our sensor is sufficiently small that it could be incorporated into a mobile device, allowing any suitable surface on which it rests to be appropriated as a gestural input surface. Several example applications were developed to demonstrate possible interactions. We conclude with a study that shows users can perform six Scratch Input gestures at about 90% accuracy with less than five minutes of training and on wide variety of surfaces.
Clinical and preclinical photodynamic therapy (1995)

Photodynamic therapy (PDT) is a treatment modality that utilizes a photosensitizing drug activated by laser generated light, and is proving effective for oncologic and nononcologic applications. This report provides an overview of photosensitizers, photochemistry, photobiology, and the lasers involved in photodynamic therapy. Clinical and preclinical PDT studies involving Photofrin and various second generation photosensitizers are reviewed.
Effect of Butanol Challenge and Temperature on Lipid Composition and Membrane Fluidity of Butanol-Tolerant Clostridium acetobutylicum (1987)

The effect of butanol challenge (0, 1.0, 1.5% [vol/vol]) and growth temperature (22, 37, 42 degrees C) on the membrane composition and fluidity of Clostridium acetobutylicum ATCC 824 and a butanol-tolerant mutant, SA-2, was examined in chemically defined medium. Growth of strain ATCC 824 into the stationary phase coincided with a gradual increase in the percent saturated to percent unsaturated (SU) fatty acid ratio. When challenged with butanol at 22 and 37 degrees C, ATCC 824 demonstrated an immediate (within 30 min) dose-response increase in the SU ratio. This strain showed little additional change over a 48-h fermentation. Compared with ATCC 824, growth of SA-2 into the late stationary phase at 22 or 37 degrees C resulted in an overall greater increase in the SU ratio for both unchallenged and challenged cells. This effect was minimized when SA-2 was challenged at 42 degrees C, probably due to the combination of the membrane fluidizing effect of butanol and the elevated temperature. Growth at 42 degrees C resulted in an increase in longer acyl chain fatty acids at the expense of shorter acyl chains for both strains. The membrane fluidity exhibited by SA-2 remained essentially constant at various butanol challenge and temperature combinations, while that for the ATCC 824 strain increased with increasing butanol challenge. By synthesizing an increased amount of saturated fatty acids, the butanol-tolerant SA-2 strain has apparently developed a mechanism for maintaining a more stable membrane environment. Growth of the microorganism is necessary for butanol to fluidize the membrane. Incorporation of exogenous fatty acids (18:1) did not significantly improve the butanol tolerance of either strain. Since SA-2 was able to produce only trace amounts of either butanol or acetone, increased tolerance to butanol does not necessarily coincide with greater solvent yields in this strain.
Amino acid sequence at the reactive site of human alpha 1-antichymotrypsin. (1983)

The reactive site of human alpha 1-antichymotrypsin has been identified as encompassing a leucyl-seryl bond at the apparent P1 and P'1 positions. This has been determined by dissociation of complexes of the inhibitor with bovine alpha-chymotrypsin, followed by identification of new NH2-terminal sequences, as well as by proteolytic inactivation by porcine pancreatic elastase. The latter results in peptide bond cleavage between the apparent P5 and P4 positions of the inhibitor, yielding a fragment whose sequence overlaps with that obtained through complex dissociation. Some homology with the sequence obtained and that already reported for both antithrombin III and alpha 1-proteinase inhibitor can be noted.
Silicon on Sapphire (SOS) Device Technology (2004)

The history of the development of the Silicon on Sapphire (SOS) device technology is quite old, and dates back to the 1960s1). SOS devices are drawing a lot of attention as they are considered to be devices that are capable of performing high-speed operations while consuming low amounts of power. However, to form the silicon (Si) layer with only small crystallization defects has been extremely difficult as there is up to a maximum of 12.5% lattice unconformity between the crystal lattice of the sapphire (Al2O3), which is the supporting substrate of the SOS wafer and the Si crystal lattice, as shown in Figure 1. This remained a formidable obstacle for commercializing the SOS device products and restricted all activities to research and development.
ERK2 enters the nucleus by a carrier-independent mechanism (2002)

In stimulated cells, the mitogen-activated protein kinase ERK2 (extracellular signal-regulated kinase 2) concentrates in the nucleus. Evidence exists for CRM1-dependent, mitogen-activated protein kinase kinase-mediated nuclear export of ERK2, but its mechanism of nuclear entry is not understood. To determine requirements for nuclear transport, we tagged ERK2 with green fluorescent protein (GFP) and examined its nuclear uptake by using an in vitro import assay. GFP-ERK2 entered the nucleus in a saturable, time- and temperature-dependent manner. Entry of GFP-ERK2, like that of ERK2, required neither energy nor transport factors and was visible within minutes. The nuclear uptake of GFP-ERK2 was inhibited by wheat germ agglutinin, which blocks nuclear entry by binding to carbohydrate moieties on nuclear pore complex proteins. The nuclear uptake of GFP-ERK2 also was reduced by excess amounts of recombinant transport factors. These findings suggest that ERK2 competes with transport factors for binding to nucleoporins, which mediate the entry and exit of transport factors. In support of this hypothesis, we showed that ERK2 binds directly to a purified nucleoporin. Our data suggest that GFP-ERK2 enters the nucleus by a saturable, facilitated mechanism, distinct from a carrier- and energy-dependent import mechanism and involves a direct interaction with nuclear pore complex proteins.
Motivazione, impegno e fiducia in se stessi nelle regioni PON (2016)

Il rapporto internazionale PISA 2012 (OCSE, 2013) evidenzia come il rapporto tra insegnante e studente e il tipo di tecniche di insegnamento utilizzate abbiano un forte impatto sull’impegno e sui risultati in matematica. Gli insegnanti possono quindi contribuire alla formazione della motivazione, della perseveranza e dell’auto-efficacia dello studente attraverso opportune strategie di insegnamento, supportando ogni studente affinché possa avere alte aspettative. Non di secondaria importanza è il ruolo dei genitori nella motivazione degli studenti, che può essere alimentata riponendo su questi ultimi forti aspettative per i loro studi futuri e la loro carriera (OCSE, 2013). Infine, è interessante focalizzare l’attenzione su quelle categorie di studenti che ottengono risultati in matematica mediamente più bassi, ovvero le ragazze e gli studenti con basso stato socio-economico, per valutare se oltre a ottenere più bassi risultati hanno anche un atteggiamento più negativo verso l’apprendimento della matematica. In questo lavoro si analizzano diversi indicatori che descrivono l’atteggiamento degli studenti verso l’apprendimento. Inoltre, si considera il loro effetto sui risultati di matematica, le differenze esistenti di genere e di stato socio-economico in tale atteggiamento, nonché l’impatto di insegnanti e genitori su di esso. L’approccio di analisi scelto segue quello utilizzato nel rapporto internazionale PISA 2012 (OCSE, 2012). Il contributo di tale studio è nell’analisi di un particolare sotto-insieme di studenti italiani: gli studenti appartenenti alle regioni facenti parti del Programma Operativo Nazionale “Ricerca e competitività” (PON “R&C”). Tale sotto-insieme di studenti è molto importante, dato che questo programma è lo strumento attraverso il quale l’Unione Europea e l’Italia hanno condiviso una consistente quota delle risorse dei fondi strutturali europei per il sostegno delle attività di ricerca e innovazione nelle aree territoriali più svantaggiate del Paese, ovvero le quattro regioni dell’Obiettivo Convergenza rappresentate da Puglia, Calabria, Sicilia e Campania.
Stage-specific regulation of respiratory epithelial cell differentiation by Foxa1 (2005)

Foxa1 is a member of the winged helix family of transcription factors that is expressed in epithelial cells of the conducting airways and in alveolar type II cells of the lung. To determine the role of Foxa1 during lung morphogenesis, histology and gene expression were assessed in lungs from Foxa1-/- gene-targeted mice from embryonic day (E) 16.5 to postnatal day (PN) 13. Deletion of Foxa1 perturbed maturation of the respiratory epithelium at precise times during lung morphogenesis. While dilatation of peripheral lung saccules was delayed in Foxa1-/- mice at E16.5, sacculation was unperturbed later in development (E17.5-E18.5). At PN5, alveolarization was markedly delayed in Foxa1-/- mice; however, by PN13 lung histology was comparable to wild-type controls. Clara cell secretory protein (CCSP), prosurfactant protein (SP)-C, and SP-B protein content and immunostaining were decreased in Foxa1-/- mice between E16.5 and E18.5 but normalized after birth. Timing and sites of expression of thyroid transcription factor-1, Foxj1, and beta-tubulin were unaltered in lungs of Foxa1-/- mice. In vitro, Foxa1 regulated the activity of CCSP and SP-A, SP-B, SP-C, and SP-D promoters as assessed by luciferase reporter assays in HeLa, H441, and MLE15 cells. Although Foxa1 regulates respiratory epithelial differentiation and structural maturation of the lung at precise developmental periods, the delay in maturation is subsequently compensated at times to enable respiratory function and restore normal lung structure after birth.
JC Polyomavirus Infection Is Strongly Controlled by Human Leucocyte Antigen Class II Variants (2014)

JC polyomavirus (JCV) carriers with a compromised immune system, such as in HIV, or subjects on immune-modulating therapies, such as anti VLA-4 therapy may develop progressive multifocal leukoencephalopathy (PML) which is a lytic infection of oligodendrocytes in the brain. Serum antibodies to JCV mark infection occur only in 50-60% of infected individuals, and high JCV-antibody titers seem to increase the risk of developing PML. We here investigated the role of human leukocyte antigen (HLA), instrumental in immune defense in JCV antibody response. Anti-JCV antibody status, as a surrogate for JCV infection, were compared to HLA class I and II alleles in 1621 Scandinavian persons with MS and 1064 population-based Swedish controls and associations were replicated in 718 German persons with MS. HLA-alleles were determined by SNP imputation, sequence specific (SSP) kits and a reverse PCR sequence-specific oligonucleotide (PCR-SSO) method. An initial GWAS screen displayed a strong HLA class II region signal. The HLA-DRB1*15 haplotype was strongly negatively associated to JCV sero-status in Scandinavian MS cases (OR = 0.42, p = 7×10(-15)) and controls (OR = 0.53, p = 2×10(-5)). In contrast, the DQB1*06:03 haplotype was positively associated with JCV sero-status, in Scandinavian MS cases (OR = 1.63, p = 0.006), and controls (OR = 2.69, p = 1×10(-5)). The German dataset confirmed these findings (OR = 0.54, p = 1×10(-4) and OR = 1.58, p = 0.03 respectively for these haplotypes). HLA class II restricted immune responses, and hence CD4+ T cell immunity is pivotal for JCV infection control. Alleles within the HLA-DR1*15 haplotype are associated with a protective effect on JCV infection. Alleles within the DQB1*06:03 haplotype show an opposite association. These associations between JC virus antibody response and human leucocyte antigens supports the notion that CD4+ T cells are crucial in the immune defence to JCV and lays the ground for risk stratification for PML and development of therapy and prevention.
Expression of inflammatory chemokines combined with local tumor destruction enhances tumor regression and long-term immunity. (2003)

Expression of chemokines within tumors can be used to recruit immature dendritic cells (DCs) for the initiation of antitumor T-cell responses. Here, we describe the chemokine receptor expression on murine bone marrow-derived immature DCs. On the basis of these receptor studies, we chose to express the chemokines CCL3 (Mip-1alpha) or CCL20 (Mip-3alpha) in tumors. We show that expression of these chemokines in the colorectal tumor model CMT93 significantly decreases tumorigenesis. This decrease is associated with an increase in CD8 T cells, natural killer cells, and Class II DCs in the tumor within the first 24 h. Furthermore, studies in immunodeficient mice show that both natural killer cells and T cells are required for this decrease in immunogenicity. CCL3 and CCL20 expression alone did not significantly inhibit the development of the B16 melanoma tumor. However, coexpression of the Herpes Simplex Virus thymidine kinase gene (HSVtk) and CCL20, cured large established tumors where HSVtk expression alone was not sufficient. Finally, coexpression of HSVtk with either CCL3 or CCL20 was able to significantly increase protection against subsequent tumor rechallenge.
Behavioral Effects of Neural Transplantation (1992)

Considerable evidence suggests that transplantation of fetal neural tissue ameliorates the behavioral deficits observed in a variety of animal models of CNS disorders. However, it is also becoming increasingly clear that neural transplants do not necessarily produce behavioral recovery, and in some cases have either no beneficial effects, magnify existing behavioral abnormalities, or even produce a unique constellation of deficits. Regardless, studies demonstrating the successful use of neural transplants in reducing or eliminating behavioral deficits in these animal models has led directly to their clinical application in human neurodegenerative disorders such as Parkinson's disease. This review examines the beneficial and deleterious behavioral consequences of neural transplants in different animal models of human diseases, and discusses the possible mechanisms by which neural transplants might produce behavior recovery.
Exchangeability of the flagellin (FliC) and the cap protein (FliD) among different species in flagellar assembly (2012)

Flagellar filament self-assembles from the component protein, flagellin or FliC, with the aid of the capping protein, HAP2 or FliD. Depending on the helical parameters of filaments, flagella from various species are divided into three groups, family I, II, and III. Each family coincides with the traditional classification of flagella, peritrichous flagella, polar flagella, and lateral flagella, respectively. To elucidate the physico-chemical properties of flagellin to separate families, we chose family I flagella and family II flagella and examined how well the exchangeability of a combination of FliC and/or FliD from different families is kept in filament formation. FliC or FliD of Salmonella enterica serovar Typhimurium (Salty; family I) were exchanged with those of Escherichia coli (Escco; family I) or Pseudomonas aeruginosa (Pseae; family II). In a Salty fliC deletion mutant, Escco FliC formed short filaments, but Pseae FliC did not form filaments. In a Salty fliD deletion mutant, both Escco FliD and Pseae FliD allowed Salty FliC to polymerize into short filaments. In conclusion, FliC can be exchanged among the same family but not between different families, while FliD serves as the cap protein even in different families, confirming that FliC is essential for determining families, but FliD plays a subsidiary role in filament formation.
Sample adaptive offset for HEVC (2011)

A new video coding tool, sample adaptive offset (SAO), is introduced in this paper. SAO has been adopted into the Working Draft of the new video coding standard, High-Efficiency Video Coding (HEVC). The SAO is located after deblocking in the video coding loop. The concept of SAO is to classify reconstructed pixels into different categories and then reduce the distortion by simply adding an offset for each category of pixels. The pixel intensity and edge properties are used for pixel classification. To further improve the coding efficiency, a picture can be divided into regions for localization of offset parameters. Simulation results show that SAO can achieve on average 2% bit rate reduction and up to 6% bit rate reduction. The run time increases for encoders and decoders are only 2%.
cDNA cloning and primary structure of a white-face hornet venom allergen, antigen 5. (1988)

A major allergen of white-face hornet (Dolichovespula maculata) venom is antigen 5 (also designated Dol m V). We have determined the primary structures of two forms of this protein by cDNA and protein sequencings. These two forms with 204 and 205 amino acid residues differ in 23% of their sequences but they are antigenically similar. Both forms have sequence similarity with a pathogenesis-related protein of tobacco leaf. In a 130-residue overlap of these proteins, 35-39 residues were identical. Hornet antigen 5 cDNAs were isolated from an expression library in lambda gt11 phage using antibody probes. Several of the cDNAs were not full length, but the fusion fragments expressed were immunoreactive. These results suggest that antigenic determinants of the sequential type are distributed throughout the entire molecule of antigen 5. After subcloning, antigen 5 was also expressed in pKK233-2 plasmid.
Health outcomes following treatment for six months with once daily tiotropium compared with twice daily salmeterol in patients with COPD (2003)

Exacerbations of COPD and health resource usage were positively affected by daily treatment with tiotropium. With the exception of the number of hospital days associated with all causes, salmeterol twice daily resulted in no significant changes compared with placebo. Tiotropium also improved health related quality of life, dyspnoea, and lung function in patients with COPD.
Plasticity-related Gene 5 (PRG5) Induces Filopodia and Neurite Growth and Impedes Lysophosphatidic Acid– and Nogo-A–mediated Axonal Retraction (2009)

Members of the plasticity-related gene (PRG1-4) family are brain-specific integral membrane proteins and implicated in neuronal plasticity, such as filopodia formation and axon growth after brain lesion. Here we report on the cloning of a novel member of the PRG family, PRG5, with high homologies to PRG3. PRG5 is regulated during brain and spinal cord development and is exclusively allocated within the nervous system. When introduced in neurons, PRG5 is distributed in the plasma membrane and induces filopodia as well as axon elongation and growth. Conversely, siRNA mediated knockdown of PRG5 impedes axon growth and disturbs filopodia formation. Here we show that PRG5 induces filopodia growth independently of Cdc42. Moreover, axon collapse and RhoA activation induced by LPA and myelin-associated neurite inhibitor Nogo-A is attenuated in the presence of PRG5, although direct activation of the RhoA-Rho-PIP5K kinase pathway abolishes PRG5 -formed neurites. Thus, we describe here the identification of a novel member of the PRG family that induces filopodia and axon elongation in a Cdc42-independent manner. In addition, PRG5 impedes brain injury-associated growth inhibitory signals upstream of the RhoA-Rho kinase pathway.
Induction of Sesquiterpenoid Biosynthesis in Tobacco Cell Suspension Cultures by Fungal Elicitor (1987)

Large amounts of the sesquiterpenoid capsidiol accumulated in the media of tobacco (Nicotiana tabacum L. cv KY14) cell suspension cultures upon addition of fungal elicitor. Capsidiol accumulation was proportional to the amount of elicitor added. The accumulation of capsidiol was preceded by a transient increase in the capsidiol de novo synthesis rate as measured by the incorporation of exogenous [(14)C]acetate. Changes in 3-hydroxy-3-methylglutaryl-CoA reductase activity (HMGR; EC 1.1.1.34), an enzyme of general isoprenoid metabolism, paralleled the changes in [(14)C]acetate incorporation into capsidiol. Incubation of the cell cultures with mevinolin, a potent in vitro inhibitor of the tobacco HMGR enzyme activity, inhibited the elicitor-induced capsidiol accumulation in a concentration dependent manner. [(14)C]Acetate incorporation into capsidiol was likewise inhibited by mevinolin treatment. Unexpectedly, [(3)H] mevalonate incorporation into capsidiol was also partially inhibited by mevinolin, suggesting that mevinolin may effect secondary sites of sesquiterpenoid biosynthesis in vivo beyond HMGR. The data indicated the importance of the induced HMGR activity for capsidiol production in elicitor-treated tobacco cell suspension cultures.