gebhart/patrepeval huggingface dataset:
iSS-PC: Identifying Splicing Sites via Physical-Chemical Properties Using Deep Sparse Auto-Encoder (2017)

Gene splicing is one of the most significant biological processes in eukaryotic gene expression, such as RNA splicing, which can cause a pre-mRNA to produce one or more mature messenger RNAs containing the coded information with multiple biological functions. Thus, identifying splicing sites in DNA/RNA sequences is significant for both the bio-medical research and the discovery of new drugs. However, it is expensive and time consuming based only on experimental technique, so new computational methods are needed. To identify the splice donor sites and splice acceptor sites accurately and quickly, a deep sparse auto-encoder model with two hidden layers, called iSS-PC, was constructed based on minimum error law, in which we incorporated twelve physical-chemical properties of the dinucleotides within DNA into PseDNC to formulate given sequence samples via a battery of cross-covariance and auto-covariance transformations. In this paper, five-fold cross-validation test results based on the same benchmark data-sets indicated that the new predictor remarkably outperformed the existing prediction methods in this field. Furthermore, it is expected that many other related problems can be also studied by this approach. To implement classification accurately and quickly, an easy-to-use web-server for identifying slicing sites has been established for free access at: http://www.jci-bioinfo.cn/iSS-PC.
Simple method to evaluate coupling functions at antireflection-coated diode facets facing grating reflectors of long external cavities (1993)

The spectral content of the reflected light from a grating, positioned at a distance much longer than the diode length to form an external-cavity semiconductor laser, has been studied. The analytical expressions derived show that the coupling coefficient at the antireflection (AR)-coated diode facet facing the extended cavity can be divided into two factors, of which one is due to the off-overlapping between the centers of the diode mode and its reflected counterpart, and the other is due to the alteration of the wave vector after being dispersed by the grating.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High efficiency myogenic conversion of human fibroblasts by adenoviral vector-mediated MyoD gene transfer. An alternative strategy for ex vivo gene therapy of primary myopathies. (1998)

Ex vivo gene therapy of primary myopathies, based on autologous transplantation of genetically modified myogenic cells, is seriously limited by the number of primary myogenic cells that can be isolated, expanded, transduced, and reimplanted into the patient's muscles. We explored the possibility of using the MyoD gene to induce myogenic conversion of nonmuscle, primary cells in a quantitatively relevant fashion. Primary human and murine fibroblasts from skin, muscle, or bone marrow were infected by an E1-deleted adenoviral vector carrying a retroviral long terminal repeat-promoted MyoD cDNA. Expression of MyoD caused irreversible withdrawal from the cell cycle and myogenic differentiation in the majority (from 60 to 90%) of cultured fibroblasts, as defined by activation of muscle-specific genes, fusion into contractile myotubes, and appearance of ultrastructurally normal sarcomagenesis in culture. 24 h after adenoviral exposure, MyoD-converted cultures were injected into regenerating muscle of immunodeficient (severe combined immunodeficiency/beige) mice, where they gave rise to beta-galactosidase positive, centrally nucleated fibers expressing human myosin heavy chains. Fibers originating from converted fibroblasts were indistinguishable from those obtained by injection of control cultures of lacZ-transduced satellite cells. MyoD-converted murine fibroblasts participated to muscle regeneration also in immunocompetent, syngeneic mice. Although antibodies from these mice bound to adenoviral infected cells in vitro, no inflammatory infiltrate was present in the graft site throughout the 3-wk study period. These data support the feasibility of an alternative approach to gene therapy of primary myopathies, based on implantation of large numbers of genetically modified primary fibroblasts massively converted to myogenesis by adenoviral delivery of MyoD ex vivo.
SMC-mediated chromosome mechanics: a conserved scheme from bacteria to vertebrates? (1999)

The assembly of mitotic chromosomes is a fundamental cellular event that ensures the faithful segregation of genetic information during cell division. It involves two processes that are, in principle, mechanistically distinct. The first process, establishment of sister chromatid cohesion, occurs during or soon after chromosome duplication. The linkage between two sister chromatids is maintained throughout G2 phase and secures the bipolar attachment of each chromosome to the spindle apparatus from prometaphase through metaphase. The second process, chromosome condensation, can be visualized most dramatically at the onset of mitosis, converting the chromatids into physically strong, rod-shaped structures. The resulting metaphase chromosome consists of two condensed sister chromatids tightly paired at their centromeric regions as well as along their entire arms. At the onset of anaphase, the linkage between the sister chromatids is dissolved, allowing them to be pulled apart to opposite poles of the cell. This dynamic behavior of chromosomes had been described by cytologists long before the central role of DNA as the genetic material was recognized and long before the biochemical basis of cell cycle progression was elucidated. Nevertheless, the molecular mechanisms underlying these structural changes of chromosomes have remained poorly understood to date. A recent breakthrough in this field was the discovery of a novel family of chromosomal ATPases, the structural maintenance of chromosome (SMC) family. Genetic and biochemical studies have shown that in eukaryotes, two distinct classes of SMC protein complexes, condensins and cohesins, play central roles in chromosome condensation and sister-chromatid cohesion, respectively. Other SMC protein complexes are involved in chromosome-wide gene repression (dosage compensation) and recombinational repair. SMC proteins are also conserved among bacteria and archaea, and their functional characterization is just beginning to emerge. In this paper recent progress in the SMC field is discussed and an attempt is made to deduce a …
Synthetic Study on Selenocystine-Containing Peptides. (1993)

N-9-Fluorenylmethoxycarbonyl-Se-4-methoxybenzylselenocysteine++ + [Fmoc-Sec(MBzl)-OH] was synthesized from selenocystine and successfully applied to Fmoc-based solid-phase peptide synthesis. The stability and the deprotection conditions of the Se-MBzl group were examined. The diselenide bond of a peptide was directly and effectively established between Sec(MBzl) residues by treatment with iodine or the dimethyl sulfoxide-trifluoroacetic acid system. Reduction kinetics of diselenide and disulfide in model peptides by reduced glutathione were also studied comparatively.
Electrical Impedance Tomography (2012)

Electrical impedance tomography (EIT) produces cross-sectional images of an admittivity distribution inside an electrically conducting object. This chapter summarizes bioimpedance measurement methods, on which an EIT system is based, to acquire data for image reconstruction. Its forward problem is introduced in the context of a practically feasible measurement setting. Modeling of the forward problem and sensitivity analysis are the key to understanding and designing an inversion method. The chapter describes three kinds of EIT inverse problems, including static imaging, time-difference imaging and frequency-difference imaging. It focuses on robust image reconstructions that overcome the technical difficulties of the ill-posedness. After introducing the continuous Neumann-to-Dirichlet (NtD) data and some theoretical issues, the chapter formulates the discrete NtD data of an E-channel EIT system. It reviews mathematical theories of uniqueness and a direct reconstruction technique called the d-bar method. Controlled Vocabulary Terms electric impedance imaging
Mîr Dâmâd ve Metafiziği (2015)

Daha çok Mîr Dâmâd olarak bilinen Muhammed Bâkır Dâmâd(ö. 1631), İslam felsefesi tarihinde Safevî döneminin (16-18 yy) en önemlişahsiyetlerinden biridir. Kendisiyle tanındığı Üçüncü Muallim (el-Mu‘allimu’s-Sâlis)ünvanı,–İlk Muallim tartışmasız Aristoteles ve ikinci muallim Fârâbî’dir-, Şiiİran’ın felsefi dünyasında sahip olduğu tartışmasız büyük şöhretini kanıtlamaktadır.Bu, her şeyden daha çok onun hem yaşadığı dönemde hem de sonrasında nasılyüksek derecede bir İslam filozofu olduğunu göstermektedir.&amp;amp;nbsp;
NPSNET: Flight Simulation Dynamic Modeling Using Quaternions (1992)

The Naval Postgraduate School (NPS) has actively explored the design and implementation of networked, real time, three-dimensional battlefield simulations on low-cost, commercially available graphics workstations. The most recent system, NPSNET, has improved in functionality to such an extent that it is considered a low-cost version of the Defense Advanced Research Project Agency's (DARPA) SIMNET system. To reach that level, it was necessary to economize in certain areas of the code so that real time performance occurred at an acceptable level. One of those areas was in aircraft dynamics. However, with “off-the-shelf” computers becoming faster and cheaper, real-time and realistic dynamics are no longer an expensive option. Realistic behavior can now be enhanced through the incorporation of an aerodynamic model. To accomplish this task, a prototype flight simulator was built that is capable of simulating numerous types of aircraft simultaneously within a virtual world. Besides being easily incorporated into NPSNET, such a simulator also provides the base functionality for the creation of a general purpose aerodynamic simulator that is particularly useful to aerodynamics students for graphically analyzing differing aircraft's stability and control characteristics. This system is designed for use on a Silicon Graphics workstation and uses the GL libraries. A key feature of the simulator is the use of quaternions for aircraft orientation representation to avoid singularities and high data rates associated with the more common Euler angle representation of orientation.
Identifying modules via concept analysis (1999)

Describes a general technique for identifying modules in legacy code. The method is based on concept analysis - a branch of lattice theory that can be used to identify similarities among a set of objects based on their attributes. We discuss how concept analysis can identify potential modules using both "positive" and "negative" information. We present an algorithmic framework to construct a lattice of concepts from a program, where each concept represents a potential module. We define the notion of a concept partition, present an algorithm for discovering all concept partitions of a given concept lattice, and prove the algorithm to be correct.
Surface-acoustic-wave pressure and temperature sensors (1976)

A sensitive sensor for the measurement of pressure and temperature is created by fabricating a surface-acoustic-wave (SAW) delay path on the surface of a thin diaphragm which, in turn, is in contact with the medium to be measured. The SAW delay path and associated electroacoustic transducers are utilized as the feedback circuit in a miniature electronic oscillator. Since the SAW time delay varies almost linearly with diaphragm temperature and pressure induced strain, the oscillator frequency is also a predominantly linear function of pressure and temperature. A frequency output sensor is desirable both for high-measurement resolution and for compatibility with digital data processors. Sensor configurations are discussed which can be optimized for independent measurement of either temperature or pressure.
Prevention of Mycoses in Immunocompromised Patients (1987)

Invasive fungal infections remain a major complication in immunocompromised hosts. The prognosis in these infections is poor, particularly for neutropenic patients with cancer. Candidiasis and aspergillosis are common in these patients, and numerous attempts have been made to evaluate potential prophylactic methods. Despite the fact that various agents (polyenes and/or imidazoles) and various formulations have been tested, the reported data on their effectiveness are still controversial. No single regimen can be recommended at this time for prevention of invasive candidiasis. The potential emergence of fungal strains resistant to the polyenes and the selection of Torulopsis glabrata by the imidazoles should also be taken into consideration. Aspergillosis, which is an airborne infection, may be prevented by isolation of patients at risk in rooms equipped with high-efficiency particulate air (HEPA) filters. In addition, the prophylactic administration of nasal sprays of amphotericin B has shown encouraging results, and this approach should be further investigated.
The dynamics of small molecules in intense laser fields (2004)

In the past decade, the understanding of the dynamics of small molecules in intense laser fields has advanced enormously. At the same time, the technology of ultra-short pulsed lasers has equally progressed to such an extent that femtosecond lasers are now widely available. This review is written from an experimentalist's point of view and begins by discussing the value of this research and defining the meaning of the word 'intense'. It continues with describing the Ti: sapphire laser, including topics such as pulse compression, chirped pulse amplification, optical parametric amplification, laser-pulse diagnostics and the absolute phase. Further aspects include focusing, the focal volume effect and space charge. The discussion of physics begins with the Keldysh parameter and the three regimes of ionization, i.e. multi-photon, tunnelling and over-the-barrier. Direct-double ionization (non-sequential ionization), high-harmonic generation, above-threshold ionization and attosecond pulses are briefly mentioned. Subsequently, a theoretical calculation, which solves the time-dependent Schrodinger equation, is compared with an experimental result. The dynamics of H-2(+) in an intense laser field is interpreted in terms of bond-softening, vibrational trapping (bond-hardening), below-threshold dissociation and laser-induced alignment of the molecular axis. The final section discusses the modified Franck-Condon principle, enhanced ionization at critical distances and Coulomb explosion of diatomic and triatomic molecules.
Effector Function of Resting T Cells: Activation of Synovial Fibroblasts (2001)

Synovial tissue in rheumatoid arthritis is characterized by infiltration with large numbers of T lymphocytes and APCs as well as hyperplasia of synovial fibroblasts. Current understanding of the pathogenesis of RA includes the concept that synovial fibroblasts, which are essential to cartilage and bone destruction, are regulated by cytokines derived primarily from monocyte-macrophage cells. Recently it has been found that synovial fibroblasts can also function as accessory cells for T cell activation by superantigens and other stimuli. We have now found that highly purified resting T cells, even in the absence of T cell mitogens, induce activation of synovial fibroblasts when cocultured for 6-24 h. Such activation was evident by induction or augmentation of mRNA for stromelysin, IL-6, and IL-8, gene products important in joint inflammation and joint destruction. Furthermore, increased production of IL-6 and IL-8 was quantitated by intracellular cytokine staining and flow cytometry. This technique, previously used for analysis of T cell function, was readily adaptable for assays of synovial fibroblasts. Resting T cells also induced synovial fibroblasts to produce PGE(2), indicating activation of expression of the cyclooxygenase 2 gene. Synergy was observed between the effects of IL-17, a cytokine derived from stimulated T cells that activates fibroblasts, and resting T lymphocytes. Various subsets of T cells, CD4(+), CD8(+), CD45RO(+), and CD45RA(+) all had comparable ability to induce synovial fibroblast activation. These results establish an Ag-independent effector function for resting T cells that is likely to be important in inflammatory compartments in which large numbers of T lymphocytes and fibroblasts can come into direct contact with each other.
In Vivo Structural Activity and Optimization Studies of Folate−Tubulysin Conjugates (2009)

Herein we report on the potencies of 4 related folate-conjugated tubulysins constructed with either tubulysin B hydrazide (EC0305), tubulysin A hydrazide (EC0510), the N,O-acetal derivative of natural tubulysins (EC0317) or a tubulysin B ester (EC0302). Our results confirmed that EC0305 is the most favorable conjugate of the group due to its potent antitumor activity [100% cures at 1 micromol/kg, three times a week (TIW) for 2 weeks] and its favorably low toxicity profile. In contrast, the natural tubulysin B drug proved to be inactive against a human nasopharyngeal tumor model when administered at doses near to or greater than the maximum tolerated dose (MTD). When tested against more chemoresistant folate receptor expressing M109 and 4T1-cl2 tumors, EC0305 displayed superior antitumor activity over a previously disclosed folate conjugate of desacetylvinblastine monohydrazide (EC145). These studies demonstrate that EC0305 has significant antiproliferative activity against FR expressing tumors, including those which are generally more chemoresistant, and that EC0305 should be considered for development as a candidate for the treatment of advanced FR-expressing human cancers.
UK NHS pilot study on cell‐free DNA testing in screening for fetal trisomies: factors affecting uptake (2014)

This study has identified factors that can influence the decision of women undergoing combined screening in favor of or against CVS and in favor of or against cfDNA testing.
Protection from Lethal Gram-Positive Infection by Macrophage Scavenger Receptor–Dependent Phagocytosis (2000)

Infections with gram-positive bacteria are a major cause of morbidity and mortality in humans. Opsonin-dependent phagocytosis plays a major role in protection against and recovery from gram-positive infections. Inborn and acquired defects in opsonin generation and/or recognition by phagocytes are associated with an increased susceptibility to bacterial infections. In contrast, the physiological significance of opsonin-independent phagocytosis is unknown. Type I and II class A scavenger receptors (SR-AI/II) recognize a variety of polyanions including bacterial cell wall products such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), suggesting a role for SR-AI/II in innate immunity to bacterial infections. Here, we show that SR-AI/II-deficient mice (MSR-A(-/-)) are more susceptible to intraperitoneal infection with a prototypic gram-positive pathogen, Staphylococcus aureus, than MSR-A(+/+) control mice. MSR-A(-/-) mice display an impaired ability to clear bacteria from the site of infection despite normal killing of S. aureus by neutrophils and die as a result of disseminated infection. Opsonin-independent phagocytosis of gram-positive bacteria by MSR-A(-/-) macrophages is significantly decreased although their phagocytic machinery is intact. Peritoneal macrophages from control mice phagocytose a variety of gram-positive bacteria in an SR-AI/II-dependent manner. Our findings demonstrate that SR-AI/II mediate opsonin-independent phagocytosis of gram-positive bacteria, and provide the first evidence that opsonin-independent phagocytosis plays a critical role in host defense against bacterial infections in vivo.
Ferrous and Cobaltous Chlorides Bearing 2,8-Bis(imino)quinolines: Highly Active Catalysts for Ethylene Polymerization at High Temperature (2010)

A series of 2,8-bis(1-aryliminoethyl)quinolines [2,8-(2,6-R12-4-R2C6H2N═CCH3)2C9H5N (L), R1 = Me, Et, or i-Pr, R2 = H or Me] is synthesized and used in the reaction with ferrous or cobaltous chlorides. The corresponding complexes LMCl2 are limitedly formed with ligands containing ortho-methyl groups of the imino phenyl rings (R = H, M = Fe (Fe1), M = Co (Co1); R = Me, M = Fe (Fe2), M = Co (Co2). The X-ray diffraction study reveals a distorted pyramidal geometry of Co1 around the cobalt atom. These complexes, activated with methylaluminoxane (MAO), show unique properties toward ethylene polymerization: no activity observed at low temperature, but high activity achieved at temperatures higher than 80 °C (up to 7.61 × 106 g·mol−1·h−1 at 100 °C). Moreover, the polyethylenes obtained are high molecular weight with narrow molecular distribution. This is the first example of iron and cobalt procatalysts with high activity for ethylene polymerization at high temperature.
High hydrostatic pressure inactivated human tumour cells preserve their immunogenicity. (2004)

High hydrostatic pressure (HHP) is an established method to inactivate biomolecules and microoganisms. It is routinely used for the sterilization of foodstuff. Recently, new applications as inactivation of microorganisms and tumour cells for bone transplants or for cancer vaccines have emerged. Characterization of the HHP-induced cellular responses are a prerequisite for its clinical use. To this end, we investigated the fate of human cells after HHP by cytofluorometry. We observed that the induction by HHP of cell death is time- and pressure-dependent. Surprisingly, an HHP-treatment of 100 MPa did not reduce viability at any time point. Pressures from 150 to 250 MPa-induced programmed cell death in most cells. However, survivors were observed in long term culture experiments under these conditions. Pressures above 300 MPa immediately induced cell death by necrosis and completely inactivated the cells. In contrast to inactivation by other necrosis inducing treatments like heat, freeze/thaw, or chemical agents, HHP avoids generation of Maillard products and disintegration and lysis of the cells. Instead HHP generates a gelatinised mixture of antigens captured in a distinct and robust particle and maintains their humoral immunogenicity. The high viscosity of the internal matrix of a pressurised cell is reflected by the slow penetration of the low molecular compound propidium iodide and limits the bleeding of antigen before uptake by antigen presenting cells. Taken together, HHP is an alternative method for the inactivation of mammalian cells in clinical settings.
Herbicidal Potential of Rhizobitoxine (1973)

The bacterially produced phytotoxin 2-amino-4-(2-amino-3-hydroxypropoxy)- trans -3-butenoic acid (rhizobitoxine) was tested for herbicidal properties in comparison with 3-amino- s -triazole (amitrole) and 4-chloro-5-(dimethylamino)-2-( a,a,a ,-trifluro- m -tolyl)-3(2H)-pyridazinone (metflurazone). In postemergence tests with various plant seedlings, rhizobitoxine and amitrole were approximately equal in phytotoxicity on a weight basis, and both were generally much more phytotoxic than metflurazone. Phytotoxicity of rhizobitoxine varied markedly among grass species. Sorghum ( Sorghum bicolor (L.) Moench ‘Hegari’) was very sensitive to rhizobitoxine, large crabgrass ( Digitaria sanguinalis (L.) Scop.) was moderately sensitive, wheat ( Triticum aestivum L. ‘Thorne’) was tolerant, and Kentucky bluegrass ( Poa pratensis L.) was very tolerant. In contrast, amitrole was almost as phytotoxic to bluegrass as to large crabgrass, and metflurazone had little effect on either. In a preemergence test with mustard ( Brassica japonica (L.) Coss. ‘Southern Giant Curled’) rhizobitoxine was as effective as amitrole, when compared on a molar basis, in inhibiting chlorophyll synthesis and root growth and was superior in retarding overall growth and development.