1,068 research outputs found

    GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

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    BACKGROUND: The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. RESULTS: GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. CONCLUSIONS: GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment is already installed in the system

    The Hypothalamus in Alzheimer’s Disease: A Golgi and Electron and Microscope Study

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    Alzheimer’s disease is a progressive irreversible neurodegenerative disorder, characterized by gradual decline of mental faculties including learning capacity, emotional and behavioral alterations, serious decline of motor skills, and dysfunction of the autonomic nervous system with disruption of circadian rhythms. Among the potential modifiable risk factors diabetes and obesity may play a considerable role in the pathogenetic background of the disease. We describe some of the morphological alterations of the hypothalamic nuclei in early cases of Alzheimer’s disease, using silver impregnation techniques and electron microscopy. The morphological and morphometric study revealed substantial decrease of the neuronal population, which was particularly marked in the suprachiasmatic, the supraoptic and the paraventricular nuclei of the hypothalamus. The silver staining demonstrated an obvious shortage of the dendritic arborization of neurons, associated with marked spinal pathology and axonal dystrophy. It must be underlined that Alzheimer’s pathology, such as neuritic plaques and neurofibrillary degeneration was minimal in hypothalamus in comparison with other areas of the brain. Mitochondrial alterations and fragmentation of Golgi complex were observed by electron microscopy in a substantial number of neurons and astrocytes in the hypothalamic nuclei. The hypothalamic pathology may be related to instability of autonomic regulation which occurs gradually in Alzheimer’s disease

    Towards Understanding Photodegradation Pathways in Lignins:The Role of Intramolecular Hydrogen Bonding in Excited States

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    The photoinduced dynamics of the lignin building blocks syringol, guaiacol, and phenol were studied using time-resolved ion yield spectroscopy and velocity map ion imaging. Following irradiation of syringol and guaiacol with a broad-band femtosecond ultraviolet laser pulse, a coherent superposition of out-of-plane OH torsion and/or OMe torsion/flapping motions is created in the first excited 1ππ* (S1) state, resulting in a vibrational wavepacket, which is probed by virtue of a dramatic nonplanar → planar geometry change upon photoionization from S1 to the ground state of the cation (D0). Any similar quantum beat pattern is absent in phenol. In syringol, the nonplanar geometry in S1 is pronounced enough to reduce the degree of intramolecular H bonding (between OH and OMe groups), enabling H atom elimination from the OH group. For guaiacol, H bonding is preserved after excitation, despite the nonplanar geometry in S1, and prevents O–H bond fission. This behavior affects the propensities for forming undesired phenoxyl radical sites in these three lignin chromophores and provides important insight into their relative “photostabilities” within the larger biopolymer

    Identifying the Occurrence Time of the Destructive Kahramanmaraş-Gazientep Earthquake of Magnitude M7.8 in Turkey on 6 February 2023

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    Here, we employ natural time analysis of seismicity together with non-extensive statistical mechanics aiming at shortening the occurrence time window of the Kahramanmaraş-Gazientep M7.8 earthquake. The results obtained are in the positive direction pointing to the fact that after 3 February 2023 at 11:05:58 UTC, a strong earthquake was imminent. Natural time analysis also reveals a minimum fluctuation of the order parameter of seismicity almost three and a half months before the M7.8 earthquake, pointing to the initiation of seismic electrical activity. Moreover, before this earthquake occurrence, the detrended fluctuation analysis of the earthquake magnitude time-series reveals random behavior. Finally, when applying earthquake nowcasting, we find average earthquake potential score values which are compatible with those previously observed before strong (M≥7.1) earthquakes. The results obtained may improve our understanding of the physics of crustal phenomena that lead to strong earthquakes

    The Hypothalamus in Alzheimer’s Disease

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    Alzheimer’s disease is a progressive, irreversible neurodegenerative disorder, characterized by gradual decline of mental faculties, including learning capacity, emotional and behavioral alterations, serious decline of motor skills, and dysfunction of the autonomic nervous system with disruption of circadian rhythms. Among the potential modifiable risk factors, diabetes and obesity may play a considerable role in the pathogenetic background of the disease. We describe some of the morphological alterations of the hypothalamic nuclei in early cases of Alzheimer’s disease, using silver impregnation techniques and electron microscopy. The morphological and morphometric study revealed substantial decrease of the neuronal population, which was particularly marked in the suprachiasmatic, the supraoptic, and the paraventricular nuclei of the hypothalamus. The silver staining demonstrated an obvious shortage of the dendritic arborization of neurons, associated with marked spinal pathology and axonal dystrophy. It must be underlined that Alzheimer’s pathology, such as neuritic plaques and neurofibrillary degeneration, was minimal in the hypothalamus in comparison with other cortical and subcortical areas of the brain. Mitochondrial alterations and fragmentation of Golgi complex were observed by electron microscopy in a substantial number of neurons and astrocytes in the hypothalamic nuclei. The hypothalamic pathology may be related to instability of autonomic regulation which occurs gradually in Alzheimer’s disease

    Risk of postoperative hypoxemia in ambulatory orthopedic surgery patients with diagnosis of obstructive sleep apnea: a retrospective observational study

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    <p>Abstract</p> <p>Background</p> <p>It is unclear when it is safe to discharge patients with a diagnosis of Obstructive Sleep Apnea (OSA) after ambulatory surgical procedures due to concern for postoperative respiratory compromise and hypoxemia. Our OSA patients undergoing ambulatory-type orthopedic procedures are monitored overnight in the PACU, thus we reviewed patient records to determine incidence of complications.</p> <p>Methods</p> <p>Two hundred and six charts of patients with preoperative diagnosis of OSA based on ICD-9 codes were reviewed for outcomes including episodes of hypoxemia. Univariate analysis followed by logistic regression and propensity analysis was performed to determine independent risk factors for hypoxemia and association with adverse outcomes.</p> <p>Results</p> <p>The majority of patients had regional anesthesia (95%). Thirty four percent of patients had hypoxemia in the PACU. Initial risk factors for hypoxemia identified by univariate analysis were BMI ≥ 35, increased age, history of COPD, upper extremity procedure, and use of peripheral nerve block. Independent risk factors identified by logistic regression were history of COPD (OR 3.64 with 95% CI 1.03-12.88) and upper extremity procedure (2.53, 1.36-4.68). After adjustment with propensity scores, adverse events were rare, and unplanned hospital admission after PACU stay was not increased with hypoxemia (11% vs 16%)</p> <p>Conclusions</p> <p>Episodes of postoperative hypoxemia in OSA patients undergoing ambulatory surgery with regional anesthesia are not associated with increased adverse outcomes or unplanned hospital admission.</p

    SLR Station Recovery, Center of Frame Motion, and Time Varying Gravity

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    Weekly station position estimates, beginning with 1993, are derived from the ITRF2008-based SLR processing of up to four satellites: Lageos 1, Lageos2, Starlette, and Stella. Helmert parameters obtained from c omparison of weekly SLR station positions and the a-priori SLRF2008 station complement are evaluated for geocenter motion and scale. Two me thods for modeling time varying gravity are employed in the SLR satel lite POD processing, with GGM03S serving as the static gravity field. Both methods forward model atmosphere gravity derived from 6-hour ECM WF pressure data. The standard approach applies an annual 20x20 field estimated from 4 years of GRACE data, and the IERS2003 recommended linear rates for C20, C30, C40, C21, and S21. The alternate approach us es a new set of low-order/degree 4x4 coefficients estimated weekly fr om SLR & DORIS processing to 10 satellites from 1993-2012. This exper imental tvg4x4 model has been shown to improve the TOPEX, Jason-1, and Jason-2 altimeter satellite orbits,. In this paper we apply the more detailed time-variable gravity modeling to the SLR satellite POD pro cessing and subsequent reference frame analyses. For this study we will evaluate the orbit differences (periodic and secular) for the satel lites concerned, characterize the impact on the station coordinate solutions, and the impact on reference frame parameters (geocenter and s cale)
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