gebhart/patrepeval huggingface dataset:
MALT1 is deregulated by both chromosomal translocation and amplification in B-cell non-Hodgkin lymphoma (2003)

The MALT1 gene was identified through its involvement in t(11;18)(q21;q21), seen in 30% of cases of mucosa-associated lymphoid tissue (MALT) lymphoma. Here, we show that deregulated MALT1 expression may occur in B-cell non-Hodgkin lymphoma (B-NHL) of various histologic subtypes either through translocation to the immunoglobulin heavy chain (IGH) locus or by genomic amplification. First, 2 cases, one case of MALT lymphoma and another of aggressive marginal zone lymphoma (MZL) with t(14;18)(q32;q21), cytogenetically identical to the translocation involving BCL2, were shown by fluorescence in situ hybridization (FISH) to involve MALT1, which lies about 5 Mb centromeric of BCL2. Molecular cloning of both by long-distance inverse polymerase chain reaction showed breakpoints lying 1 to 2 kilobase (kb) centromeric of the first 5' MALT1 exon; both cases showed MALT1 overexpression at either RNA or protein levels. Second, we examined the structure and gene expression profile of genomic amplifications involving 18q21 in a panel of 40 B-NHL cell lines using comparative genomic hybridization to microarrays (array CGH) and gene expression profiling techniques. Using array CGH, 2 peaks of genomic amplification were observed, one centered around BCL2 and the other around MALT1. Ofthe 3 cell lines with MALT1 amplification, 2 showed MALT1 overexpression as assessed by gene profiling, quantitative reverse transcription-polymerase chain reaction (QRT-PCR), and Western blotting. To determine if comparable events occurred in primary MALT and splenic MZL tumors, 40 cases were analyzed by FISH or QRT-PCR; genomic amplification and MALT1 overexpression were seen in 2 cases. Together, these data implicate MALT1 as a dominant oncogene that may play a role in the pathogenesis of B-NHL.
Impression Cytology Study of Epithelial Phenotype of Ocular Surface Reconstructed by Preserved Human Amniotic Membrane (1997)

The success of conjunctival surface reconstruction correlated well with recovery of the conjunctival epithelial phenotype. The lack of corneal epithelial phenotype even on an avascular corneal stroma supports the concept that conjunctival transdifferentiation does not occur in vivo, and indicates that additional limbal stem cell transplantation is needed for effective corneal surface reconstruction in patients with limbal deficiency.
New cepstral representation using wavelet analysis and spectral transformation for robust speech recognition (2002)

The goal is to improve the speech recognition rate by optimisation of mel frequency cepstral coefficients (MFCCs): modifications concern the time-frequency representations used to estimate these coefficients. There are many ways to obtain a spectrum out of a signal which differ in the method itself (Fourier, wavelets,...), and in the normalisation. We show that we can obtain noise resistant cepstral coefficients, for speaker independent connected word recognition. The recognition system is based on a continuous whole word hidden Markov model. An error reduction rate of approximately 50% is achieved with word models.
B4, a human B lymphocyte-associated antigen expressed on normal, mitogen-activated, and malignant B lymphocytes. (1983)

The characterization of a new B cell-specific antigen (B4) is described in this report. With the use of a monoclonal antibody to B4, it was shown that B4 is present on B cells isolated from peripheral blood and lymphoid organs, on cell lines derived from normal and malignant B cells, and on tumor cells isolated from patients with B cell-derived neoplasms. B4, in contrast, was not detected on normal, activated, or malignant cells of T or myeloid origin. The B4 antigen is distinct from known B cell antigens, including sIg, Ia, B1, B2, Fc, and C3. Examination of mitogen-stimulated B lymphocytes suggests that the B4 antigen initially increases with B cell activation and then is lost at the terminal stage of B cell differentiation. Moreover, the observation that B4 is expressed on almost all early B cell tumors suggests that it may precede B1, CALLA, cytoplasmic mu, and B2 in early B cell ontogeny.
Epigenome Mapping in Normal and Disease States (2010)

Epigenomes are comprised, in part, of all genome-wide chromatin modifications, including DNA methylation and histone modifications. Unlike the genome, epigenomes are dynamic during development and differentiation to establish and maintain cell type-specific gene expression states that underlie cellular identity and function. Chromatin modifications are particularly labile, providing a mechanism for organisms to respond and adapt to environmental cues. Results from studies in animal models clearly demonstrate that epigenomic variability leads to phenotypic variability, including susceptibility to disease that is not recognized at the DNA sequence level. Thus, capturing epigenomic information is invaluable for comprehensively understanding development, differentiation, and disease. Herein, we provide a brief overview of epigenetic processes, how they are relevant to human health, and review studies using technologies that enable epigenome mapping. We conclude by describing feasible applications of epigenome mapping, focusing on epigenome-wide association studies (eGWAS), which have the potential to revolutionize current studies of human diseases and will likely promote the discovery of novel diagnostic, preventative, and treatment strategies.
Activity of CD4-Pseudomonas exotoxin against cells expressing diverse forms of the HIV and SIV envelope glycoproteins. (1992)

CD4(178)-PE40 is a genetically engineered hybrid toxin containing a portion of human CD4 linked to the translocation and ADP-ribosylation domains of Pseudomonas exotoxin A. In vitro, the molecule has been shown to selectively kill cells expressing the envelope glycoproteins of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV), and to inhibit HIV spread. In this report we examine the activity of the hybrid toxin against cells expressing diverse forms of the HIV and SIV envelope glycoproteins, encoded by recombinant vaccinia virus vectors. The activity of CD4(178)-PE40 was found to be unaffected by mutations in the HIV-1 or HIV-2 envelope glycoprotein genes, which prevent normal proteolytic processing of the corresponding gp160 precursor molecules. Cells expressing a mutant HIV-1 envelope glycoprotein lacking most of the cytoplasmic tail of the gp41 transmembrane subunit were also sensitive to the hybrid toxin. Most interestingly, HIV-1, HIV-2, and SIVmac envelope glycoprotein molecules known to have widely differing affinities for CD4 were found to be comparably effective at mediating sensitivity to CD4(178)-PE40. By virtue of its ability to kill infected cells, the hybrid toxin inhibited the spread of SIVmac in vitro. These results indicate that CD4(178)-PE40 is active against cells expressing HIV and SIV envelope glycoproteins with a diverse array of structural differences.
Different Functionalization of the Internal and External Surfaces in Mesoporous Materials for Biosensing Applications Using “Click” Chemistry (2010)

We report the use of copper(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC) to selectively functionalize the internal and external surfaces of mesoporous materials. Porous silicon rugate filters with narrow line width reflectivity peaks were employed to demonstrate this selective surface functionalization approach. Hydrosilylation of a dialkyne species, 1,8-nonadiyne, was performed to stabilize the freshly fabricated porous silicon rugate filters against oxidation and to allow for further chemical derivatization via "click" CuAAC reactions. The external surface was modified through CuAAC reactions performed in the absence of nitrogen-based Cu(I)-stabilizing species (i.e., ligand-free reactions). To subsequently modify the interior pore surface, stabilization of the Cu(I) catalyst was required. Optical reflectivity measurements, water contact angle measurements, Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) were used to demonstrate the ability of the derivatization approach to selectively modify mesoporous materials with different surface chemistry on the exterior and interior surfaces. Furthermore, porous silicon rugate filters modified externally with the cell-adhesive peptide Gly-Arg-Gly-Asp-Ser (GRGDS) allowed for cell adhesion via formation of focal adhesion points. Results presented here demonstrate a general approach to selectively modify mesoporous silicon samples with potential applications for cell-based biosensing.
Toward Visual Voice Activity Detection for Unconstrained Videos (2019)

The prevalent audio-based Voice Activity Detection (VAD) systems are challenged by the presence of ambient noise and are sensitive to variations in the type of the noise. The use of information from the visual modality, when available, can help overcome some of the problems of audio-based VAD. Existing visual-VAD systems however do not operate directly on the whole image but require intermediate face detection, face landmark detection and subsequent facial feature extraction from the lip region. In this work we present an end-to-end trainable Hierarchical Context Aware (HiCA) architecture for visual-VAD for videos obtained in unconstrained environments which can be trained with videos as input and audio speech labels as output. The network is designed to account for local and global temporal information in a video sequence. In contrast to existing visual-VAD systems our proposed approach does not rely on face detection and subsequent facial feature extraction. It can obtain a VAD accuracy of 66% on a dataset of Hollywood movie videos just with visual information. Further analysis of the representations learned from our visual-VAD system shows that the network learns to localize on human faces, and sometimes speaking human faces specifically. Our quantitative analysis of the effectiveness of face localization shows that our system performs better than sound-localization networks designed for unconstrained videos.
Novel multiple access scheme for wireless sensor network employing unmanned aerial vehicle (2010)

This paper proposes a new MAC protocol applied for a new kind of data collection applications that use a wireless sensor network employed with one unmanned aerial vehicle (WSN-UAV). In this protocol, the sensors are classified in different groups based on priorities and communicate with the UAV by a CDMA-based transmission scheme. The Prioritized Frame Selection based CDMA MAC protocol (PFSC-MAC <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> ) incorporates not only the value, but also the variation trend of the receiving power of the beacon signals. This protocol provides a low rate of failed packet due to the mobility of the UAV, which is the most critical metric in these types of applications. In addition, an optimal number of priority groups have also been introduced to guarantee a minimal transmission interval and a lowest failed packet ratio. Numerical results have also shown the efficient energy compared with the other protocol that is based on TDMA. This protocol is simple but promising for various applications that collect data from a large area sensor network.
Interleukin-2 fusion protein: An investigational therapy for interleukin-2 receptor expressing malignancies (1997)

DAB389IL-2 is an interleukin-2 receptor (IL-2R) specific fusion protein with a molecular weight of 58 kD containing the enzymatic and translocation domains of diphtheria toxin (DT) and human IL-2. This fusion protein is able to direct the cytocidal action of the DT enzymatic region only to cells which bear the IL-2R. The human IL-2R exists in three forms: low, intermediate and high affinity. The high-affinity form is believed to be the biologically relevant form on mature, activated T-lymphocytes, B-lymphocytes and monocytes. DAB389IL-2 is able to bind selectively to the high-affinity IL-2R in a concentration-dependent manner, and once bound is internalised via receptor-mediated endocytosis. Upon acidification of the formed vesicle, the enzymatic portion of the fusion protein is believed to pass into the cytosol where it ultimately inhibits protein synthesis by inactivation of elongation factor-2, resulting in cell death. The constitutive expression of the IL-2R on certain leukaemic and lymphomatous cells of T and B cell origin has been reported to occur in patients with chronic lymphocytic leukaemia, cutaneous T cell lymphoma (CTCL), Hodgkin's disease and non-Hodgkin's lymphomas (NHLs). A multicentre DAB389IL-2 dose-escalation study of patients with IL-2R expressing lymphomas has been conducted. A 10-fold range of doses were evaluated on a five-daily dose schedule. Patients received up to six courses, with an additional two courses permitted for patients with partial responses that appeared to be still improving after six courses. Most adverse experiences were transient and mild. Preliminary assessment of response indicated five complete responses (CR, duration ongoing at 20, 11, 7, 5 and 4 months) and seven partial responses (PR, duration 3-20 months) in the 35 patients with CTCL. One CR (duration > 20 months) in a patient with NHL (Lennett's lymphoma) and two PR (duration 9 and 2 months) in 17 patients with B-cell NHL have been observed. Based on the mode of action of DAB389IL-2, its safety profile, and the patient responses associated with the phase I/II clinical trials, a phase III programme in CTCL patients has been initiated and plans for additional trials in NHL patients are targeted for 1996.
Influence of the hinge region on complement activation, C1q binding, and segmental flexibility in chimeric human immunoglobulins. (1990)

We have characterized a series of genetically engineered chimeric human IgG3 and IgG4 anti-dansyl (DNS) antibodies with identical antibody-combining sites but different hinge region amino acid compositions to determine how the hinge region influences Fab fragment segmental flexibility, C1q binding, and complement activation. Our data support the correlation between "upper hinge" length and Fab segmental flexibility; moreover, we confirm that a hinge region is essential for C1q binding and complement activation. However, the hinge length by itself is not sufficient for complement activity in IgG molecules. We have demonstrated that the IgG4 hinge, which imparts restricted segmental flexibility, reduces the ability of IgG3 molecules to activate complement. We also find that the IgG3 hinge region, which imparts greater segmental motion, is not sufficient to create complement activation activity in IgG4 anti-DNS antibodies. Finally, we conclude that (i) segmental motion is correlated with "upper hinge" length, (ii) hinge length and segmental flexibility is not enough to alter complement binding and activation, and (iii) segmental flexibility does not correlate with proficiency to activate the complement cascade.
Joint position sense and vibration sense: anatomical organisation and assessment (2002)

Clinical examination of joint position sense and vibration sense can provide important information concerning specific cutaneous sensory receptors, peripheral nerves, dorsal roots, and central nervous system pathways and should be included as a regular component of the neurological examination. Although these sensory modalities share a spinal cord and brainstem pathway, they arise in different receptors and terminate in separate distributions within the thalamus and cerebral cortex. Consequently, both modalities should be tested as part of the neurological examination. Clinical testing of these modalities requires simultaneous stimulation of tactile receptors; hence this review will include information about the receptors and pathways responsible for tactile sensation.
'Go or Grow': the key to the emergence of invasion in tumour progression? (2010)

Uncontrolled proliferation and abnormal cell migration are two of the main characteristics of tumour growth. Of ultimate importance is the question what are the mechanisms that trigger the progression from benign neoplasms (uncontrolled/autonomous proliferation) to malignant invasive tumours (high migration). In the following, we challenge the currently prevailing view that the emergence of invasiveness is mainly the consequence of acquired cancer cell mutations. To study this, we mainly focus on the 'glioblastoma multiforme' (GBM) tumour which is a particularly aggressive and invasive tumour. In particular, with the help of a simple growth model, we demonstrate that the short time required for the recurrence of a GBM tumour after a gross total resection cannot be deduced solely from a mutation-based theory. We propose that the transition to invasive tumour phenotypes can be explained on the basis of the microscopic 'Go or Grow' mechanism (migration/proliferation dichotomy) and the oxygen shortage, i.e. hypoxia, in the environment of a growing tumour. We test this hypothesis with the help of a lattice-gas cellular automaton. Finally, we suggest possible therapies that could help prevent the progression towards malignancy and invasiveness of benign tumours.
Rational Design of DNA Vaccines for the Induction of Human Papillomavirus Type 16 E6- and E7-Specific Cytotoxic T-Cell Responses (2012)

Many DNA vaccine candidates have been developed for the treatment of human papillomavirus type 16 (HPV16)-induced malignancies. Most of these vaccines consist of a fusion of E7 with a "carrier-protein" that functions to increase the potency of the vaccine. The nature of these carrier-proteins varies widely, and the mechanisms proposed to explain the enhanced immunogenicity of such fusions are often linked to the biological function of the carrier-protein. However, the potentiating effect of these carrier-proteins might also be explained by more general mechanisms, such as the provision of CD4+ T-cell help, increased antigen stability, or altered subcellular localization of the antigen. To assess whether these more generic mechanisms could suffice to generate highly immunogenic DNA vaccines, we evaluated a series of modular HPV16 E7 DNA vaccines in which the presence of CD4+ T-cell help, the presence of an endogenous carrier-protein, and the subcellular localization of the antigen could be systematically altered. Using this approach, we demonstrate that the addition of an element that provides CD4+ T-cell help, elements that enforce endoplasmic reticulum (ER) localization/retention are both necessary and sufficient to create markedly effective HPV16 E7-directed DNA vaccines. Importantly, the resulting design rules also apply to an HPV16 E6-directed DNA vaccine. The developed "HELP(ER)" HPV DNA vaccines encode only very limited additional sequences besides the antigen, thereby reducing the risk of antigenic competition and/or autoimmunity.
Guidelines for the treatment of gout: a Swiss perspective (2016)

Gout is a common condition and its management is suboptimal. A number of guidelines on the management of gout have been published in the last decade by professional societies with the aim of informing the physician of the recommended therapeutic strategies and the treatment options. We have tried to synthesize the current recommendations and to highlight some challenges that still need to be resolved in clinical practice in Switzerland.
Microbial Indicators of Oil-Rich Salt Marsh Sediments (1975)

Selected microbial parameters were monitored in sediments from a pristine and an oil-field salt marsh. Although numbers of hydrocarbonoclastic bacteria and fungi were significantly greater in the oil field, the values did not show a strong correlation with levels of hydrocarbons (r = 0.43 and r = 0.49, respectively). However, a high correlation was noted between ratios of hydrocarbonoclastic and total aerobic heterotrophic bacteria and levels of hydrocarbons as well as the relative concentration of hydrocarbons (ratio of hydrocarbons to chloroform extractables) (r = 0.87 and r = 0.77, respectively). Data suggest that this first ratio is a more valid microbial indicator of hydrocarbon abundance than other factors examined. Significant differences in the ratio of pigmented to total colony-forming units, the ratio of different to total colony-forming units, and the diversity index were noted between the natural and oil-field marsh. It is suggested that the presence of hydrocarbons alters the relative abundance of the most predominant aerobic heterotrophic bacteria.
Antitumour activity of oral E7080, a novel inhibitor of multiple tyrosine kinases, in human sarcoma xenografts (2011)

E7080 is an inhibitor of multiple tyrosine kinases, several of which have pro-angiogenic properties, including receptors for VEGF, FGF, SCF and PDGF. We undertook our study to evaluate the preclinical activity of E7080 in human sarcomas. The antitumour activity of orally administered E7080 was tested in ten human tumour xenografts representing different sarcoma histotypes. Concomitant changes in microvessel density were assayed by immunohistochemistry to CD31. Immunohistochemistry was also used to assess the expression of kinases that E7080 is known to inhibit. The MTS assay was applied to determine effects on tumour cell viability in vitro. At the Q1D5 × 2 schedule, E7080 (30 mg/kg) was active (T/C<40%) in 7/10 xenografts. The effects were accompanied by marked decrease in microvessel densities. Given at the Q1D5 × 4 schedule, E7080 (30, 10, 3 mg/kg) showed antitumour activity in a dose dependent manner in two different xenografts. E7080 growth inhibition did not correlate with the expression of VEGFR1-3, PDGFRA, PDGFRB, FGFR1 or KIT on tumour cells but was significantly correlated with expression of VEGFR2 on tumour microvessels. In vitro E7080 did not show potent effects on tumour cell viability in four different sarcoma cell lines, with IC50 values ≥ 10 μM. In conclusion, E7080 showed broad in vivo antitumour activity in sarcoma, mainly attributable to angiogenesis inhibition. E7080 was also active in xenografts resistant to one or more clinically relevant reference drugs given at MTD (doxorubicin, cisplatin or ifosfamide). The present results encourage further investigation of a potential role of E7080 in sarcoma therapy in the clinic.
Synthesis of Degradable Model Networks via ATRP and Click Chemistry (2006)

A simple scheme involving atom transfer radical polymerization (ATRP) from a bifunctional initiator, conversion of the bromine end groups of the resulting telechelic polymer to azides, and cross-linking of this azido-telechelic macromonomer with multi-acetylene functionalized small molecules via copper-catalyzed azide-alkyne cycloaddition was employed to prepare the first tert-butyl acrylate model networks. This general scheme is wide in scope, enabling synthesis of model networks possessing defined pore size from any monomer polymerizable by ATRP. Introduction of an olefin moiety into the ATRP initiator enabled degradation of the materials by ozonolysis to yield star polymer products bearing three or four arms depending on which cross-linker was employed in the parent network. Size-exclusion chromatography of the ozonolysis products confirmed the pore size of the parent network and yielded insight into the number of unreacted functionalities. Model networks derived from a trifunctional alkyne were found to be more completely cross-linked than those derived from a tetrafunctional alkyne, presumably due to less steric hindrance in the former system.