gebhart/patrepeval huggingface dataset:
A<i>Caenorhabditis elegans</i>Mass Spectrometric Resource for Neuropeptidomics (2018)

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. Graphical Abstract ᅟ.
Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy (2015)

The epileptic network is characterized by pathologic, seizure-generating 'foci' embedded in a web of structural and functional connections. Clinically, seizure foci are considered optimal targets for surgery. However, poor surgical outcome suggests a complex relationship between foci and the surrounding network that drives seizure dynamics. We developed a novel technique to objectively track seizure states from dynamic functional networks constructed from intracranial recordings. Each dynamical state captures unique patterns of network connections that indicate synchronized and desynchronized hubs of neural populations. Our approach suggests that seizures are generated when synchronous relationships near foci work in tandem with rapidly changing desynchronous relationships from the surrounding epileptic network. As seizures progress, topographical and geometrical changes in network connectivity strengthen and tighten synchronous connectivity near foci-a mechanism that may aid seizure termination. Collectively, our observations implicate distributed cortical structures in seizure generation, propagation and termination, and may have practical significance in determining which circuits to modulate with implantable devices.
Preclinical evaluation of influenza vaccines based on replication-deficient poxvirus vector MVA (2011)

The zoonotic transmissions of highly pathogenic avian influenza viruses of the H5N1 subtype hat occur since 1997 have sparked the development of novel influenza vaccines. The advent of reverse genetics technology, cell culture production techniques and novel adjuvants has improved the vaccine strain preparation, the production process and the immunogenicity of the vaccines respectively and would accelerated the availability of pandemic influenza vaccines. However, there is still room for improvement and alternative vaccine preparations are explored such as recombinant antigens (e.g. baculovirus expression) and viral vectors. Modified Vaccinia virus Ankara (MVA), originally developed as a safe smallpox vaccine can be exploited as a viral vector. It has favourable properties, which makes it an attractive candidate as a pandemic influenza vaccine (for review see reference [1]). Recently we have evaluated a MVA-based vaccine for highly pathogenic influenza virus of the H5N1 subtype in mice and macaques. To this end, recombinant MVA was constructed expressing the gene encoding the hemagglutinin of H5N1 influenza virus A/Vietnam/1194/04 (clade 1) (MVA-HA-VN/04) and used to immunize C57BL/6 mice and cynomolgus macaques (macaca fascicularis). Two immunizations induced strong virus specific antibody responses in both species and protected the animals from the development of severe disease observed in control animals inoculated with empty MVA vector or PBS after challenge infection with the homologous or the antigenically distinct influenza virus A/Indonesia/5/05 (clade 2.1). In vaccinated animals virus replication in the respiratory tract was not detectable and the development of histopathological changes in the lungs was prevented. Furthermore, a MVA-based 2009 pandemic H1N1 vaccine protected against severe disease in a pH1N1 ferret model. The preclinical evaluation of MVA-based candidate vaccines indicated that they have potential as vaccines against highly pathogenic H5N1 and pH1N1 influenza viruses. The MVA-based vaccines proved to be immunogenic and induced broad-protective immune responses. MVA has favourable properties for the production, storage and use as a pandemic influenza vaccine and further clinical development seems warranted.
Supplemental Table 2 from Intratumoral CD14&lt;sup&gt;+&lt;/sup&gt; Cells and Circulating CD14&lt;sup&gt;+&lt;/sup&gt;HLA-DR&lt;sup&gt;lo/neg&lt;/sup&gt; Monocytes Correlate with Decreased Survival in Patients with Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;Supplemental Table 2. Univariate and multivariable associations of CD14 expression with death from RCC for 375 patients with ccRCC&lt;/p&gt;
Characteristics of Ice Impedance Recorded From a Ring Electrode Placed at the Anterior Surface of the Cryoballoon (2018)

Impedance rise of 500 Ω at <90 seconds with freeze time of 90 seconds resulted in 100% PVI. Impedance measurements from the nose of the balloon is a direct measure of ice formation on the balloon. It provides real-time feedback on the quality of the ablation and defines the cryoapplication termination time based on ice formation, limiting ice expansion to extracardiac tissues.
Adaptive hemodynamic response function to optimize differential temporal information of hemoglobin signals in functional near-infrared spectroscopy (2012)

It has been nearly twenty years since functional near-infrared spectroscopy (fNIRS) was first applied to assessing human brain functions. It has now become widely accepted as a common functional imaging modality with more than 100 publications of fNIRS-related scientific literature annually. However, universal analytical methods for fNIRS data have yet to be established. Although not frequently mentioned, temporal analysis of fNIRS data also poses a technical challenge: how oxygenated and deoxygenated hemoglobin (Hb) signals should be treated. With its analogy to fMRI, a general linear model (GLM) with regression to a canonical hemodynamic response function (HRF) has often been used. However, the Hb parameters do not necessarily follow the same behavior as the BOLD signal: rather, we often encounter different temporal profiles for the two Hb signals. Here we introduce adaptive methods to find the optimal HRF for temporal analysis of fNIRS data. Application of the GLM with regression to a temporally optimized HRF on the functional activation data during an overt confrontation naming task revealed different temporal structures for oxy-Hb and deoxy-Hb signals, with the latter having substantial temporal delay. However, when the temporally optimized HRF was used, the two parameters yielded reasonably compatible activation patterns including activation in classical language-related areas of the left hemisphere. These results suggest the potential use of the GLM with regression to an adaptive HRF to fully utilize temporal information of both Hb parameters.
Efficient Advert Assignment (2014)

We develop a framework for the analysis of large-scale Ad-auctions where adverts are assigned over a continuum of search types. For this pay-per-click market, we provide an efficient mechanism that maximizes social welfare. In particular, we show that the social welfare optimization can be solved in separate optimizations conducted on the time-scales relevant to the search platform and advertisers. Here, on each search occurrence, the platform solves an assignment problem and, on a slower time-scale, each advertiser submits a bid which matches its demand for click-throughs with supply. Importantly, knowledge of global parameters, such as the distribution of search terms, is not required when separating the problem in this way. Exploiting the information asymmetry between the platform and advertiser, we describe a simple mechanism which incentivizes truthful bidding and has a unique Nash equilibrium that is socially optimal, and thus implements our decomposition. Further, we consider models where advertisers adapt their bids smoothly over time, and prove convergence to the solution that maximizes social welfare. Finally, we describe several extensions which illustrate the flexibility and tractability of our framework.
OCT study of fellow eyes of macular holes. (2000)

The aim of this study was to examine the vitreomacular interface in symptom-free fellow eyes of macular holes using optical coherence tomography (OCT) to add information to the pathogenesis of macular holes and to refine prognostic factors for bilateral involvement. Sixty-six patients with a full thickness macular hole in one eye and a symptom-free fellow eye were included in the study between 01/98-05/99. The finding on OCT that a perifoveal vitreous detachment can result in a foveal cyst and subsequently a macular hole confirms the theory of Gass of vitreous traction. Symptom-free fellow eyes with a foveal cyst on OCT represent an elevated risk (55%) for macular hole development. Vitreofoveal separation is probably a good prognostic sign.
A monoclonal antibody to a differentiation antigen present on mature human macrophages and absent from monocytes. (1985)

A monoclonal antibody is described that has been generated in the mouse against cultured human blood monocytes/macrophages. The antibody, designated 25F9, belongs to the IgG1 subclass, detects antigens of m.w. 86,000, and does not react with freshly isolated blood monocytes but reacts with monocytes after 3 days of culture. The expression of the 25F9 antigen on macrophages increases with culture time. Furthermore, the antibody is negative on platelets, granulocytes, lymphocytes, and a large number of human cell lines except the two melanoma lines MeWo and Mel 57. In cryostat sections of normal human tissue (skin, lung, liver, thymus) and of inflammatory or neoplastic tissue (cutaneous lymphoma, eczema, BCG-granuloma, and melanoma), the antibody reacts with scattered macrophages in the dermis but not with epidermal Langerhans cells, with alveolar macrophages, with liver Kupffer cells, and with scattered macrophages in the cortex and medulla of thymus. In eczema, BCG-granuloma, and cutaneous lymphoma, only a few infiltrating macrophages were stained. On the other hand, a large number of macrophages and melanophages reacted positively in melanoma. In some cases melanoma cells also stained weakly positive. Thus, the antibody detects a differentiation antigen preferentially expressed on mature, tissue-fixed macrophages and absent from blood monocytes.
PARALLELISM IN XPRS (2000)

This paper discusses the approach being taken by XPRS, a software data base machine being built at Berkeley, toward intra-query parallelism. There are two components to our design. The first is a unique two-dimensional file system called FTD which automatically balances arm activity among multiple disks. The second component is the novel way that we construct parallel plans by making use of information about available main memory and the load average per processor. Both components are described in this paper.
Renal vasoconstriction with U-46,619; role of arachidonate metabolites. (1994)

Thromboxane A2 (TxA2) or its stable mimetic U-46,619 can increase the generation of arachidonate metabolites. Therefore, these studies were designed to investigate the role of prostaglandins, TxA2, and leukotrienes in the renal vascular response to U-46,619. Anesthetized rats were studied during a basal period and during an intra-aortic infusion of vehicle or U-46,619 (1 micrograms/kg per minute). U-46,619 reduced the GFR and the RBF without changing the mean arterial pressure or the femoral vascular resistance. All of the effects of U-46,619 were blocked by pretreatment with the TxA2/prostaglandin H2 receptor antagonist SQ-29,548. Pretreatment with the cyclo-oxygenase inhibitor indomethacin did not modify the renal vascular response to U-46,619. However, pretreatment with the TxA2 synthesis inhibitor UK-38,485 or with the leukotriene D4/E4 antagonist LY-163,443 markedly blunted the U-46,619-induced increase in renal vascular resistance and the decrease in GFR. These results indicate that the renal vascular response to U-46,619 is receptor mediated and is promoted by TxA2 and leukotriene D4/E4.
Dynamic Intervertebral Foramen Narrowing During Simulated Rear Impact (2006)

Extrapolation of the present results indicated that the highest potential for ganglia compression injury was at the lower cervical spine, C5-C6 and C6-C7. Acute ganglia compression may produce a sensitized neural response to repeat compression, leading to chronic radiculopathy following rear impact.
<sup/> A 3D Tissue-Printing Approach for Validation of Diffusion Tensor Imaging in Skeletal Muscle (2017)

The ability to noninvasively assess skeletal muscle microstructure, which predicts function and disease, would be of significant clinical value. One method that holds this promise is diffusion tensor magnetic resonance imaging (DT-MRI), which is sensitive to the microscopic diffusion of water within tissues and has become ubiquitous in neuroimaging as a way of assessing neuronal structure and damage. However, its application to the assessment of changes in muscle microstructure associated with injury, pathology, or age remains poorly defined, because it is difficult to precisely control muscle microstructural features in vivo. However, recent advances in additive manufacturing technologies allow precision-engineered diffusion phantoms with histology informed skeletal muscle geometry to be manufactured. Therefore, the goal of this study was to develop skeletal muscle phantoms at relevant size scales to relate microstructural features to MRI-based diffusion measurements. A digital light projection based rapid 3D printing method was used to fabricate polyethylene glycol diacrylate based diffusion phantoms with (1) idealized muscle geometry (no geometry; fiber sizes of 30, 50, or 70 μm or fiber size of 50 μm with 40% of walls randomly deleted) or (2) histology-based geometry (normal and after 30-days of denervation) containing 20% or 50% phosphate-buffered saline (PBS). Mean absolute percent error (8%) of the printed phantoms indicated high conformity to templates when "fibers" were >50 μm. A multiple spin-echo echo planar imaging diffusion sequence, capable of acquiring diffusion weighted data at several echo times, was used in an attempt to combine relaxometry and diffusion techniques with the goal of separating intracellular and extracellular diffusion signals. When fiber size increased (30-70 μm) in the 20% PBS phantom, fractional anisotropy (FA) decreased (0.32-0.26) and mean diffusivity (MD) increased (0.44 × 10<sup>-3</sup> mm<sup>2</sup>/s-0.70 × 10<sup>-3</sup> mm<sup>2</sup>/s). Similarly, when fiber size increased from 30 to 70 μm in the 50% PBS diffusion phantoms, a small change in FA was observed (0.18-0.22), but MD increased from 0.86 × 10<sup>-3</sup> mm<sup>2</sup>/s to 1.79 × 10<sup>-3</sup> mm<sup>2</sup>/s. This study demonstrates a novel application of tissue engineering to understand complex diffusion signals in skeletal muscle. Through this work, we have also demonstrated the feasibility of 3D printing for skeletal muscle with relevant matrix geometries and physiologically relevant tissue characteristics.
Performance of scheduling algorithms in optical packet switches with limited-range wavelength converters (2005)

This paper evaluates the performance of an optical packet switching architecture that uses the wavelength conversion technique to solve the packet contention problem. The architecture, referred to as shared per node (SPN), is equipped with limited-range wavelength converters shared per node. We evaluate for this architecture the performance of the optimum scheduling algorithm by resolving an integer linear programming problem. Unfortunately the optimum scheduling algorithm has a high time complexity and it cannot be adopted for optical packet switches requiring packet scheduling time in the order of 10/100 ns. For this reason we propose some scheduling algorithms allowing the best optimum scheduling performance to be reached in low computation time. In particular an algorithm, based on heuristic rules, is proposed able to reach good performance with a complexity O(M),M being the number of wavelengths used
Herriott cell interferometer for unsteady density measurements in small length scale thruster plasmas (2000)

Traditional interferometric techniques have been shown to lack the resolution needed to characterize the electron and neutral densities in the diffuse plasma of the Pulsed Plasma Thruster (PPT) exhaust. In the present work, a Herriott cell is added into a standard quadrature heterodyne interferometer to increase sensitivity for electron density measurements, and allow measurements of neutral densities amidst mechanical vibration. Measurements of electron and neutral density during and after the current pulse are sought for the purposes of modeling spacecraft contamination from PPTs. Testing is performed on the UIUC PPT-4, a coaxial electrothermal PPT pulsing at 20 J. Analytical and experimental analysis are conducted to determine the integrity of the phase front and the effect of multiple passes on the density measurements taken. Up to 18-passes through the plasma are accomplished using the Herriott cell, while maintaining sufficient phase-front quality for interferometric analysis. The advantage of the cell is obvious at late times when the external mechanical vibrations induce an apparent phase shift in the same direction as for neutral particles. Due to the same dependence on wavelength, 2 laser frequencies cannot be used to separate neutral and mechanical vibration contributions. The Herriott cell allows a density resolution increase linear with the number of passes that does not increase the mechanical vibrational component. Uncertainties from both mechanical vibrational sources and shot-to-shot variations of the thruster itself are investigated and characterized for this system. Due to variations in mechanical vibrations on a day to day basis, the cell is able to characterize the neutral density of the thruster only over short time periods. At 200 (is for single tests (-20 shots averaged) at 14 and 18 passes neutral density at the exit plane was shown to be no more than 1 *10 cm. Average peak electron density (4 jis) was shown to be 5.0 ± 1.1 *10 cm, however the single shot error due to the Herriott cell is±10 cm.
Υλοποίηση και πειραματική αξιολόγηση εργασιοκεντρικών κατανεμημένων αλγορίθμων στην πλατφόρμα YALPS (2012)

Διατριβή (Μεταπτυχιακή) -- Πανεπιστήμιο Κύπρου, Σχολή Θετικών και Εφαρμοσμένων Επιστημών, Τμήμα Πληροφορικής, 2012.
Conditional Access System Using Broadcasting for Narrow-band Mobile Broadcasting Systems (2007)

A conditional access system (CAS) is essential for controlling digital content usage in narrow-band broadcasting such as terrestrial 1-segment broadcasting and digital audio broadcasting.We assume that 'broadcasting receivers' refers not only to mobile phones but also to mobile receivers that do not have two-way communication functions.This would include mobile receivers for use in motor vehicles and portable receivers used in combination with personal digital assistants (PDAs) and portable game stations.A CAS provides a way of restricting broadcasting reception and content playback services to subscribers.To distinguish between subscribers and non-subscribers,contract information needs to be distributed to each receiver,and this needs to be done by broadcasting to mobile receivers.Conventional CASs,i.e.,those used for digital satellite broadcasting,broadcast contract information in this way.Doing this,however,requires a wide transmission band of about 300 kbps because contract information is transmitted to individual receivers.The current technology for distributing contract information on conventional CASs cannot therefore be applied to narrow-band broadcasting.In order to resolve this problem,we have developed a new CAS that is capable of transmitting contract information even in narrow-band broadcasting.We describe the scheme used to calculate the transmission rate of contract information.Furthermore,we have evaluated both the security and the implementation of the proposed CAS and determined that the proposed CAS can be applied to existing services.
High-rate Time-bin Quantum Key Distribution Using Quantum-controlled Measurement (2018)

We realize a time-bin qudit-based quantum key distribution system that uses two-photon interference for measuring the phase-basis states, allowing us to generate a secret key at a megabits-per-second rate.
Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival (2021)

Leiomyosarcomas (LMS) are genetically heterogeneous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site continues to dictate clinical management, the contribution of genetic factors to LMS subtype, origins, and timing are unknown. Here we analyze 70 genomes and 130 transcriptomes of LMS, including multiple tumor regions and paired metastases. Molecular profiling highlight the very early origins of LMS. We uncover three specific subtypes of LMS that likely develop from distinct lineages of smooth muscle cells. Of these, dedifferentiated LMS with high immune infiltration and tumors primarily of gynecological origin harbor genomic dystrophin deletions and/or loss of dystrophin expression, acquire the highest burden of genomic mutation, and are associated with worse survival. Homologous recombination defects lead to genome-wide mutational signatures, and a corresponding sensitivity to PARP trappers and other DNA damage response inhibitors, suggesting a promising therapeutic strategy for LMS. Finally, by phylogenetic reconstruction, we present evidence that clones seeding lethal metastases arise decades prior to LMS diagnosis.
Treatment of carcinoma of the breast by radiation therapy (1977)

One hundred and fifty patients with carcinoma of the breast were treated by radiation therapy without mastectomy. Seventy-seven patients had excisional biopsy of the breast mass while the remainder had incisional biopsy or needle biopsy. There has been 100% local control in patients with Stage I or Stage II disease. The local control rate in Stage III is 67.5%. Those patients who had excisional biopsy had a significantly lower incidence of local recurrence than did those in whom the tumor was left in situ. The cumulative survival probability at five years is 100% for Stage I, 65% for Stage II and 26% for Stage III. Recommendations are made concerning axillary node sampling and adjuvant chemotherapy for patients treated by this technique.