gebhart/patrepeval huggingface dataset:
Reciprocity-based cognitive transmissions using a MU massive MIMO approach (2013)

Cognitive radio (CR) aims at enabling the coexistence between legacy systems called primary users (PU) and secondary users (SU), provided the SU do not (significantly) cause interference on PU links. Massive MIMO systems on the other hand yield significant performance and reliability enhancement. In this paper, we investigate the capacity of both PU and SU systems using multi-user (MU) massive MIMO and time division duplex (TDD). TDD indeed permits to estimate the channel state information (CSI) at the PU/SU transmitters to perform linear precoding, taking advantage of the channel reciprocity. The capacity is derived considering the CSI imperfections, the non-reciprocal radio frequency front-ends as well as antenna coupling effects. These impairments can be compensated using reciprocity calibration techniques we recently developed. Extending these techniques to MU massive MIMO, we evaluate interference cancellation precoders. Simulations reveal performance improvements using the massive MIMO reciprocity-based precoder in a CR approach.
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing (2012)

Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level. To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions.
Interleukin-12, an emerging anti-tumour cytokine. (1997)

Interleukin 12 is a multifunctional cytokine secreted by a wide variety of cells including macrophages and B cells and promotes cell-mediated immunity by its ability to selectively augment Th-1 type immune responses. This pleiotropic cytokine exerts numerous effects on T and NK cells, resulting in an enhancement of cytolytic activity and direct stimulation of IFN-gamma production and studies have demonstrated that this cytokine plays an important role in the promotion of the host resistance to infection by bacterial, fungal and protozoan pathogens. IL-12 has also been shown to cause tumour regression and reduce metastasis in animal models, due to both the promotion of antitumour immunity and also to the significant inhibition of angiogenesis and up-regulation of E-cadherin, a metastasis suppressor. Recent reports using local administration of IL-12 to the tumour site by retroviral vectors and 'gene gun' techniques have resulted in a significant reduction of tumour mass, with complete eradication occurring in several cases. The effects of IL-12 in patients with cancer are currently under investigation. Thus, interleukin-12 represents a cytokine with potent antitumour effects and may therefore be an attractive agent in anticancer therapy.
Enhanced Lycopene Productivity by Manipulation of Carbon Flow to Isopentenyl Diphosphate in Escherichia coli (2005)

Lycopene is a useful phytochemical that holds great commercial value. In our study the lycopene production pathway in E. coli originating from the precursor isopentenyl diphosphate (IPP) of the non-mevalonate pathway was reconstructed. This engineered strain of E. coli accumulated lycopene intracellularly under aerobic conditions. As a next step, the production of lycopene was enhanced through metabolic engineering methodologies. Various competing pathways at the pyruvate and acetyl-CoA nodes were inactivated to divert more carbon flux to IPP and subsequently to lycopene. It was found that the ackA-pta, nuo mutant produced a higher amount of lycopene compared to the parent strain. To further enhance lycopene production, a novel mevalonate pathway, in addition to the already existing non-mevalonate pathway, was engineered. This pathway utilizes acetyl-CoA as precursor, condensing it to form acetoacetyl-CoA and subsequently leading to formation of IPP. Upon the introduction of this new pathway, lycopene production increased by over 2-fold compared to the ackA-pta, nuo mutant strain.
ARTSCENE: A neural system for natural scene classification (2009)

How do humans rapidly recognize a scene? How can neural models capture this biological competence to achieve state-of-the-art scene classification? The ARTSCENE neural system classifies natural scene photographs by using multiple spatial scales to efficiently accumulate evidence for gist and texture. ARTSCENE embodies a coarse-to-fine Texture Size Ranking Principle whereby spatial attention processes multiple scales of scenic information, from global gist to local textures, to learn and recognize scenic properties. The model can incrementally learn and rapidly predict scene identity by gist information alone, and then accumulate learned evidence from scenic textures to refine this hypothesis. The model shows how texture-fitting allocations of spatial attention, called attentional shrouds, can facilitate scene recognition, particularly when they include a border of adjacent textures. Using grid gist plus three shroud textures on a benchmark photograph dataset, ARTSCENE discriminates 4 landscape scene categories (coast, forest, mountain, and countryside) with up to 91.85% correct on a test set, outperforms alternative models in the literature which use biologically implausible computations, and outperforms component systems that use either gist or texture information alone.
Substance P and immunoregulation. (1987)

Peptides released from peripheral nerve endings in mammals, including the tachykinin substance P (SP) and vasoactive intestinal polypeptide (VIP), are potent mediators of smooth muscle and vascular functions. Significant neurophysiological activities of SP and VIP include the transmission of nociceptive and interneuron excitatory signals, respectively. SP has been shown to modulate distinct immediate hypersensitivity responses by stimulating the generation of arachidonic acid-derived mediators from mucosal mast cells but not basophils. Functions of mononuclear and polymorphonuclear leukocytes that characterize the inflammatory response and that are altered by SP include chemotaxis, lysosomal enzyme release, and phagocytic activities. The effects of SP on cell-mediated immunity are largely stimulatory, in that synthesis of DNA, protein, and immunoglobulin by mature T and B lymphocytes, respectively, is significantly enhanced at nanomolar concentrations of the neuropeptide. Functionally relevant receptors for SP on T lymphocytes have been demonstrated by cell sorter and radioligand-binding techniques, and the lymphocyte membrane proteins that comprise the SP receptor are currently being isolated and purified to homogeneity. The characterization of the structure of the SP lymphocyte receptor and identification of the receptor gene will permit detailed analyses of the molecular interactions between the immune and nervous systems.
Neu-Protein Overexpression in Breast Cancer (1988)

Amplification of the neu proto-oncogene in breast cancer has been reported to correlate with the presence of lymph-node metastases and with a poor prognosis. We describe a method for the immunohistochemical detection of overexpression of neu protein on formalin-fixed paraffin-embedded tissue, with the use of two different monoclonal antibodies. In a group of tumors with a known neu-gene copy number, intense membrane staining of tumor cells was present in all tumors with neu-gene amplification. Of 189 tumors from patients with Stage II breast cancer, 27 (14 percent) had neu-membrane staining. Neu overexpression was associated with larger tumor size (P = 0.006) but not with lymph-node involvement. Neu-protein expression in lymph-node metastases was the same as its expression in primary tumors. Among the patients with neu overexpression (median follow-up, 37 months), disease-free survival was not significantly shorter; overall survival was reduced significantly in these patients (P = 0.042), but this reduction did not remain significant after adjustment for tumor size. Of 45 ductal carcinomas in situ, 19 (42 percent) had neu-membrane staining. These 19 were all of the large-cell, comedo growth type. None of 16 ductal carcinomas in situ of small-cell, papillary, or cribriform growth type had neu overexpression. We conclude that neu overexpression may be an early step in the development of a distinct histologic type of carcinoma of the breast, but we could find no association of overexpression with lymph-node status or tumor recurrence.
Cleavage at the Furin Consensus Sequence RAR/KR 109 and Presence of the Intervening Peptide of the Respiratory Syncytial Virus Fusion Protein Are Dispensable for Virus Replication in Cell Culture (2002)

Proteolytic processing of the respiratory syncytial virus F (fusion) protein results in the generation of the disulfide-linked subunits F1 and F2 and in the release of pep27, a glycopeptide originally located between the two furin cleavage sites FCS-1 (RKRR(136)) and FCS-2 (RAR/KR(109)). We made use of reverse genetics to study the importance of FCS-2 and of pep27 for BRSV replication in cell culture. Replacement of FCS-2 in the F protein of recombinant viruses by either of the sequences NANR(109), RANN(109) or SANN(109), respectively, abolished proteolytic processing at this position, whereas the cleavage of FCS-1 was not affected. All mutants replicated in calf kidney and Vero cells in the absence of exogenous trypsin, although somewhat higher titers of BRSV containing the NANR(109) or the RANN(109) motif were achieved in the presence of trypsin. The virus mutants showed a reduced cytopathic effect which was lowest in the case of the SANN(109) mutant. These findings demonstrate that cleavage at FCS-2 is dispensable for replication of respiratory syncytial virus in cell culture. A deletion mutant containing FCS-1 but lacking FCS-2 and most of pep27 replicated in cell culture as efficiently as the parental virus, indicating that this domain of the F protein is not essential for virus maturation and infectivity.
Fluorescence polarization immunoassay to determine aminoglycoside modifying enzymes activity. (1986)

The possible use of polarized-immunofluorescence to evaluate aminoglycoside-modifying enzyme activities has been investigated. The TDX instrument was used to determine the residual quantity of aminoglycoside following inactivation during the assay procedure. Through the spectrum of the modified aminoglycoside antibiotics the enzymes encoded on eleven R-factors from clinical isolates of Enterobacteriaceae have been identified.
Human RAD52 interactions with replication protein A and the RAD51 presynaptic complex (2017)

Rad52 is a highly conserved protein involved in the repair of DNA damage. Human RAD52 has been shown to mediate single-stranded DNA (ssDNA) and is synthetic lethal with mutations in other key recombination proteins. For this study, we used single-molecule imaging and ssDNA curtains to examine the binding interactions of human RAD52 with replication protein A (RPA)-coated ssDNA, and we monitored the fate of RAD52 during assembly of the presynaptic complex. We show that RAD52 binds tightly to the RPA-ssDNA complex and imparts an inhibitory effect on RPA turnover. We also found that during presynaptic complex assembly, most of the RPA and RAD52 was displaced from the ssDNA, but some RAD52-RPA-ssDNA complexes persisted as interspersed clusters surrounded by RAD51 filaments. Once assembled, the presence of RAD51 restricted formation of new RAD52-binding events, but additional RAD52 could bind once RAD51 dissociated from the ssDNA. Together, these results provide new insights into the behavior and dynamics of human RAD52 during presynaptic complex assembly and disassembly.
An Improved, Practical, and Scalable Five-Step Synthesis of Psilocybin (2020)

Described herein is an improved synthesis of 3-[2-(dimethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate (psilocybin). The protocol outlines: synthesis of multigram quantities of psilocybin, identification of critical in-process parameters, and isolation of psilocybin without the use of chromatography, TLC, or aqueous workup. The synthesis furnishes psilocybin in five steps in 23% overall yield from an inexpensive acetoxyindole starting material. With specific focus on process control and impurity fate and removal, the improved procedure is amenable to providing high-quality psilocybin.
Demethylation of Promoter Regulatory Elements Contributes to Perforin Overexpression in CD4+ Lupus T Cells (2004)

Abstract Inhibiting DNA methylation in CD4+ T cells causes aberrant gene expression and autoreactive monocyte/macrophage killing in vitro, and the hypomethylated cells cause a lupus-like disease in animal models. Similar decreases in T cell DNA methylation occur in idiopathic lupus, potentially contributing to disease pathogenesis. The genes affected by DNA hypomethylation are largely unknown. Using DNA methylation inhibitors and oligonucleotide arrays we have identified perforin as a methylation-sensitive gene. Our group has also reported that DNA methylation inhibitors increase CD4+ T cell perforin by demethylating a conserved methylation-sensitive region that is hypomethylated in primary CD8+ cells, which express perforin, but is largely methylated in primary CD4+ cells, which do not. As lupus T cells also have hypomethylated DNA and promiscuously kill autologous monocytes/macrophages, we hypothesized that perforin may be similarly overexpressed in lupus T cells and contribute to the monocyte killing. We report that CD4+ T cells from patients with active, but not inactive, lupus overexpress perforin, and that overexpression is related to demethylation of the same sequences suppressing perforin transcription in primary CD4+ T cells and demethylated by DNA methylation inhibitors. Further, the perforin inhibitor concanamycin A blocks autologous monocyte killing by CD4+ lupus T cells, suggesting that the perforin is functional. We conclude that demethylation of specific regulatory elements contributes to perforin overexpression in CD4+ lupus T cells. Our results also suggest that aberrant perforin expression in CD4+ lupus T cells may contribute to monocyte killing.
Enrichment for Histone H3 Lysine 9 Methylation at Alu Repeats in Human Cells (2003)

The aim of this study was to identify in human cells common targets of histone H3 lysine 9 (H3-Lys9) methylation, a modification that is generally associated with gene silencing. After chromatin immunoprecipitation using an H3-Lys9 methylated antibody, we cloned the recovered DNA and sequenced 47 independent clones. Of these, 38 clones (81%) contained repetitive elements, either short interspersed transposable element (SINE or Alu elements), long terminal repeat (LTR), long interspersed transposable element (LINE), or satellite region (ALR/Alpha) DNA, and three additional clones were near Alu elements. Further characterization of these repetitive elements revealed that 32 clones (68%) were Alu repeats, corresponding to both old Alu (23 clones) and young Alu (9 clones) subfamilies. Association of H3-Lys9 methylation was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. In addition, we randomly selected 5 Alu repeats from the recovered clones and confirmed association with H3-Lys9 by PCR using primer sets flanking the Alu elements. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine rapidly decreased the level of H3-Lys9 methylation in the Alu elements, suggesting that H3-Lys9 methylation may be related to the suppression of Alu elements through DNA methylation. Thus H3-Lys9 methylation is enriched at human repetitive elements, particularly Alu elements, and may play a role in the suppression of recombination by these elements.
OX40 Costimulation Promotes Persistence of Cytomegalovirus-Specific CD8 T Cells: A CD4-Dependent Mechanism (2007)

Abstract The mechanisms that regulate CMV-specific T cell responses in vivo are poorly understood. During murine CMV infection of B6 mice, primary responses in the spleen are dominated by CD8 T cells reactive with antigenic epitopes in M45, M57, and m139 murine CMV gene products. However, during the later persistent phase of infection, CD8 T cell responses to epitopes in m139 and M38 viral gene products predominate. The basis for this shift in CD8 T populations is unknown. In this study, we demonstrate that OX40, a TNFR superfamily member, specifically regulates the accumulation of CD8 T cells reactive with the persistent-phase epitopes. Defective CD8 T cell responses in OX40−/− mice were replicated in MHC class II−/− mice implying that CD4 T cells in part controlled the differentiation of the CD8 T cell clones responsive to these epitopes during persistent infection. Furthermore, treatment of infected mice with an agonist OX40 Ab induced expansion of protective primary virus-specific CD8 T cells independent of CD4 T cell help, but CD4 T cells were crucial for anti-OX40 to promote CD8 T cells reactive to the persistent dominant epitopes. Collectively, these results indicate manipulation of OX40 may be useful in improving cellular immunotherapy regimes for treatment of persistent virus infections.
Methane-Producing Microbial Community in a Coal Bed of the Illinois Basin (2008)

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.
Augmenting appearance-based localization and navigation using belief update (2010)

Appearance-based localization compares the current image taken from a robot's camera to a set of pre-recorded images in order to estimate the current location of the robot. Such techniques often maintain a graph of images, modeling the dynamics of the image sequence. This graph is used to navigate in the space of images.In this paper we bring a set of techniques together, including Partially-Observable Markov Decision Processes, hierarchical state representations, visual homing, human-robot interactions, and so forth, into the appearance-based approach. Our approach provides a complete solution to the deployment of a robot in a relatively small environment, such as a house, or a work place, allowing the robot to robustly navigate the environment after minimal training.We demonstrate our approach in two environments using a real robot, showing how after a short training session, the robot is able to navigate well in the environment.
ESD: a pervasive reliability concern for IC technologies (1993)

Several aspects of ESD are described from the point of view of the test, design, product, and reliability engineering. A review of the ESD phenomena along with the test methods, the appropriate on-chip protection techniques, and the impact of process technology advances from CMOS to BiCMOS on the ESD sensitivity of IC protection circuits are presented. The status of understanding in the field of ESD failure physics and the current approaches for modeling are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New heterogeneous catalysis for the synthesis of poly(ether polyol)s (2002)

Abstract Novel double‐metal cyanide (DMC) complex catalysts were prepared with various precursors of cobalt or nickel and zinc with potassium cyanide. In the presence of an alcohol initiator, but in the absence of an organic‐binding ligand, the catalysts were highly active for the polymerization of alkyl‐ or alkenyl‐substituted epoxides to produce poly(ether polyol)s. The polymer obtained from propylene oxide showed a more isotactic structure than did the polymer made from nonselective conventional catalysts. The influence of different reaction variables were examined, including the ratio of the initiator to the substrate, the presence of a protonic agent, the temperature, as well as the concentration of the catalyst and the solvent. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 1553–1557, 2002
Speech Acquisition in Meetings with an Audio-Visual Sensor Array (2005)

Close-talk headset microphones have been traditionally used for speech acquisition in a number of applications, as they naturally provide a higher signal-to-noise ratio - needed for recognition tasks than single distant microphones. However, in multi-party conversational settings like meetings, microphone arrays represent an important alternative to close-talking microphones, as they allow for localisation and tracking of speakers and signal-independent enhancement, while providing a non-intrusive, hands-free operation mode. In this article, we investigate the use of an audio-visual sensor array, composed of a small table-top microphone array and a set of cameras, for speaker tracking and speech enhancement in meetings. Our methodology first fuses audio and video for person tracking, and then integrates the output of the tracker with a beamformer for speech enhancement. We compare and discuss the features of the resulting speech signal with respect to that obtained from single close-talking and table-top microphones.
Performance improvement of 10 Gb/s standard fiber transmission systems by using the SPM effect in the dispersion compensating fiber (1996)

The use of dispersion compensating fibers (DCF's) has now emerged as the most practical technique to compensate for the chromatic dispersion in the long-haul, optically amplified standard fiber (1.3 μm zero dispersion) transmission systems. We investigated the effects of SPM in the standard fiber and the DCF in a repeaterless 10 Gb/s transmission system. We show that the SPM in the DCF reverses the spectral broadening in the standard fiber. We further show that the DCF length which offers the widest eye margin decreases as the launching power into the DCF is increased while the ISI penalty remains the same. This results in an increased signal-to-noise ratio (SNR) and hence improvement of the system performance.