julilili42/papers huggingface dataset:
Reverse Engineering Non-Linear Gene Regulatory Networks Based on the Bacteriophage &amp;#955; cI Circuit
2005-01-01

The ability to measure the transcriptional response of cells has drawn much attention to the underlying transcriptional networks. To untangle the network, numerous models with corresponding reverse engineering methods have been applied. In this work, we propose a non-linear model with adjustable degrees of complexity. The corresponding reverse engineering method uses a probabilistic scheme to reduce the reconstruction problem to subnetworks. Adequate models for gene regulatory networks must be anchored on sufficient biological knowledge. Here, the cI auto-inhibition circuit (cI circuit) is used to validate our reverse engineering method. Simulations of the cI circuit are used for the reconstruction, whereas a simplified cI circuit model assists the modeling phase. Several levels of complexity are evaluated, subsequently the reconstructed models show different properties. As a result, we reconstruct an abstract model, capturing the dynamic behavior of the cI circuit to a high degree.
Real-time Access of Magnetoencephalographic / -cardiographic Data: Technical Realization &amp;amp; Application to Online Fetal Heart Rate Recording
2005-01-01

Current standard magnetoencephalographic and -cardiographic systems do not allow real-time access to the measured data. We developed a software solution for real-time access and used it to create an online fetal heart rate monitor.
[Aristotle on the function of blood in the processes of life].
2005-01-01

This contribution explains some aspects of the Aristotelian conception of blood. According to Aristotle, blood is an homogeneous part of the body. It is producted in the heart of the warmest animals through the "cooking" of the nourishment, and then it is distributed all over the body, where it has non only the function to nourish the different organs and to induce their growth, but it also passes on the sense-data. Furthermore in the male creatures blood is the starting-point of the production - through a further "cooking" - of semen. On the contrary in the creatures of the female sex, whose body is colder such a tranformation of blood in semen doesn't happen. In the copulation the semen of the male works as bearer of the form and efficient cause, while the female blood acts as matter The outcome of the ag6n that takes place between the two factors determines for its part the sex of the offspring.
Bus-invert coding for LUT-based FPGAs
2005-01-01

We describe an approximative implementation of bus-invert coding for LUT-based FPGAs driving an external bus through dual-data-rate outputs. The majority voter circuit, typically implemented as a tree of full-adders, is the performance-limiting unit, and is replaced by an inexact interval logic. For a 16-bit bus, logic depth is limited to five stages of 4-input LUTs. Compared to an adder-tree implementation, propagation delay of the inexact majority voter is approximately one half. The disadvantage is that signal transition statistic is suboptimal, and the maximum number of simultaneous signal changes is increased to 10 in rare cases.
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations.
2005-01-01

Functional annotation of unknown proteins is a major goal in proteomics. A key step in this annotation process is the definition of a protein’s subcellular localization. As a consequence, numerous prediction techniques for localization have been developed over the years. These methods typically focus on a single underlying biological aspect or predict a subset of all possible subcellular localizations. There is a clear need for new methods that utilize and represent available protein specific biological knowledge from several sources, in order to improve accuracy and localization coverage for a wide range of organisms. Here we present a novel Support Vector Machine (SVM)-based approach for predicting protein subcellular localization, which integrates information about N-terminal targeting sequences, amino acid composition, and protein sequence motifs. An important step is taken towards emulating the protein sorting process by capturing and bringing together biologically relevant information. Our novel approach has been used to develop two new prediction methods, TargetLoc and MultiLoc. TargetLoc is restricted to analysis of proteins containing N-terminal targeting sequences, whereas MultiLoc covers all major eukaryotic subcellular localizations for animal, plant, and fungal proteins. Compared to similar methods, TargetLoc performs better than these. MultiLoc performs considerably better than comparable prediction methods predicting all major eukaryotic subcellular localizations, and shows better or comparable results to methods that are specialized on fewer localizations or for one organism.
Multidetector-Row CT for Detection of Noncalcified and Calcified Coronary Lesions
2005-01-01

Immediately after the introduction of multidetector-row computed tomography (MDCT) scanners in 1998, one became aware that not only hyperdense but also hypodense areas within contrast-enhanced axial slices could be seen (see Fig. 1). The question to be answered was whether these areas are artifacts or atherosclerotic plaques.
Genetics of Atypical Parkinsonism
2005-01-01

Parkinson's disease (PD) is traditionally defined as a clinico-pathologic entity, characterized by a core syndrome of akinesia, rigidity, tremor, and postural instability, and pathologically by a more or less selective degeneration of dopaminergic neurons of the substantia nigra, leading to a deficiency of dopamine in the striatal projection areas of these neurons. Characteristic eosinophilic inclusions, the Lewy bodies (LBs), are found in surviving dopaminergic neurons but also, although less abundantly, in other parts of the brain in most cases ().
Laminin type 1 augments the transforming growth factor beta-induced expression of matrix metalloproteinase 3 in synovial fibroblasts
2005-01-01

Chaperonins have classically been thought of as intracellular molecules involved in the correct folding of proteins.Their expression is upregulated during times of stress such as heat (hence their common nomenclature as heat shock proteins [HSP]), anoxia, hypoglycaemia and reactive oxygen species [1].These are conditions found in infected tissues or in tissues with chronic inflammation such as the rheumatoid synovium.In their intracellular location they protect the cell from apoptotic death due to stress.Increasingly chaperonins have been recognised to subserve extracellular functions for which they have received the name 'chaperokines' since they bind to specific receptors on the cell surface and activate cells of the innate immune system to secrete inflammatory cytokines, chemokines and small molecular weight mediators such as prostaglandins [2].Indeed, an early event in inflammation is cell stress/necrosis leading to the release of HSP60 and HSP70 that binds via a CD14-mediated mechanism to Toll-like receptors 2 and 4 [2] as part of the 'danger' signal [3].The secretion of tumour necrosis factor alpha, IL-1, IL-12 and other chemokines prepares the environment for a TH1 adaptive immune response.It is now recognised that some chaperonins, such as BiP and HSP27, may activate the innate immune system to secrete anti-inflammatory cytokines, such as IL-10 [4,5] that may skew the adaptive immune response to TH2.Recent work by our group has shown that BiP can not only prevent but also treat ongoing collagen-induced arthritis in DBA/1 mice [6], suggesting that chaperonins may down modulate ongoing TH1 responses.Thus, it may be possible to suppress rheumatoid inflammation by administration of appropriate chaperonins such as BiP.Finally, chaperonins may be important system regulators determining the outcome between TH1 and Th2 immune responses.References 1.
Dopamine and Glutamate in Motor and Cognitive Symptoms of Parkinson’s Disease
2005-01-01

Parkinson's disease (PD) is characterized by motor and cognitive deficits. The main motor symptoms of PD are on the one hand hypokinetic signs, such as bradykinesia, akinesia, rigidity, and loss of postural reflexes, and on the other hand hyperkinetic signs, such as tremor, (see Chapter 21; ref. 1). Cognitive deficits in nondemented PD patients comprise deficits in sensitivity to reward (2), deficits in procedural and habit learning (3), and deficits in switching arbitrarily from one behavioral activity to another, possibly owing to a deficit in attentional set shifting (4). It has even been argued that PD patients are deficient in so-called executive functions of human mind (5,6). "Executive function is a neuropsychological construct that has been used to capture the highest order of cognitive abilities," e.g., flexibility of thought in the generation of solutions to novel problems (7,8). The reason why the cognitive aspects are not well perceived may be that in humans, the cognitive functions in PD are mainly unconscious; they are thus not experienced and cannot be explicitely communicated. Another reason that renders analysis of PD symptoms so difficult is that the diseased human brain is able to use (cortical) loops to bypass or compensate for basal ganglia (BG) dysfunctions, however, with the disadvantage of a loss of parallel processing and reduced velocity.
RESIDUAL CONFINEMENT IN HIGH-TEMPERATURE YANG-MILLS THEORY
2005-01-01

The infrared behavior of Landau gauge gluon and ghost propagators are investigated in Yang-Mills theory at non-vanishing temperatures. Self-consistent solutions are presented for temperatures below the presumed phase transition and in the infinite temperature limit. Gluon confinement is manifest in the infrared behavior of these propagators. As expected confinement prevails below the phase transition. In the infinite-temperature limit a qualitative change is observed: the chromoelectric sector exhibits a near-perturbative behavior while long-range chromomagnetic interactions, mediated by soft ghost modes, are still present. The latter behavior is in agreement with corresponding lattice results. It furthermore implies that part of the gluons are still confined.
Predicting Single Genes Related to Immune-Relevant Processes
2005-01-01

In this paper we address the problem of predicting gene activities by finding gene regulatory dependencies in experimental DNA microarray data. Only few approaches to infer the dependencies of complete gene interconnectivity networks can be found in the literature. Due to the limited number of available data, the inferring problem is under-determined and ambiguous. Therefore, we introduce a new algorithm to infer relationships only between selected genes and the unknown gene network. This method is able to predict gene activation by mathematical modeling of the network and its simulation. The parameters of the mathematical model are determined by optimization with evolutionary algorithms. In this paper we will show that our approach is able to correctly predict gene responses in immune related regulatory processes and correctly identify some of the true genomic relationships of these genes.
Die Kristallstruktur von 1,3-Dicyclohexyl- 4,5-dimethylimidazolium- Dicyanomethylid / The Crystal Structure of 1,3-Dicyclohexyl-4,5- dimethylimidazolium Dicyanomethylide
2005-01-01

The crystal structure of 1,3-dicyclohexyl-4,5-dimethylimidazolium dicyanomethylide (6, [ImH][HC(CN) 2 ]), obtained from the carbene Im and malodinitrile, reveals the presence of ion pairs connected by NHC hydrogen bonds.
Multidetector-Row CT vs Intravascular Ultrasound for Coronary Plaque Characterization
2005-01-01

Coronary artery disease (CAD) constitutes a major clinically relevant disease in the Western industrialized world, causing 600,000 deaths annually (1). The underlying pathophysiological mechanism seems to be coronary plaque disruption, subsequent thrombosis, and acute myocardial infarction. Fifty percent of afflicted patients experience this potentially life-threatening condition without experiencing prior symptoms (2). Therefore, direct visualization of epicardial coronary arteries is necessary to assess the focal severity and clinical relevance of the vessel wall alterations. The visualization of plaque has two different clinical focal points. On the one hand, obstructive coronary artery disease causing chronic ischemia to the vessel-dependent myocardial tissue needs to be assessed to determine an adequate revascularization strategy (condition of stable angina pectoris). On the other hand, precursors of the already mentioned unheralded plaque rupture causing unstable angina, myocardial infarction, or sudden death should be assessed to take preventive measures to avoid these acute coronary syndromes.
Spontaneous windows file sharing via virtual groups
2005-01-01

Although file and printer sharing services have been deployed almost ubiquitously for a long time as part of Microsoft Windows, only recent peer-to-peer applications popularized file-sharing on a global scale. As the Windows CIFS protocol was designed for local area networks, its use has been confined to relatively small environments. We propose a mechanism to set up spontaneous virtual groups that allow to use legacy Windows file and printer sharing globally in virtual LANs.
Commander S — The shell as a browser
2005-01-01

Commander S is a new approach to interactive Unix shells based on interpretation of command output and cursor-oriented termi-nal programs. The user can easily refer to the output of previous commands when composing new command lines or use interactive viewers to further explore the command results. Commander S is extensible by plug-ins for parsing command output and for view-ing command results interactively. The included job control avoids garbling of the terminal by informing the user in a separate widget and running background processes in separate terminals. Comman-der S is also an interactive front-end to scsh, the Scheme Shell, and it closely integrates Scheme evaluation with command execution. The paper also shows how Commander S employs techniques from object-oriented programming, concurrent programming, and func-tional programming techniques. 1.
A pointillism style for the non-photorealistic display of augmented reality scenes
2005-01-01

The ultimate goal of augmented reality is to provide the user with a view of the surroundings enriched by virtual objects. Practically all augmented reality systems rely on standard real-time rendering methods for generating the images of virtual scene elements. Although such conventional computer graphics algorithms are fast, they often fail to produce sufficiently realistic renderings. The use of simple lighting and shading methods, as well as the lack of knowledge about actual lighting conditions in the real surroundings, cause virtual objects to appear artificial.
Turning cool star X-ray spectra upside down
2005-01-01

H1504+65 is a young white dwarf with Teff=200 000 K and is the hottest post‐AGB star ever analysed with detailed model atmospheres. Chandra LETG+HRC‐S spectra have revealed the richest X‐ray absorption line spectrum recorded from a stellar photosphere to date. The line forming regions in this extremely hot photosphere produce many transitions in absorption that are also observed in emission in cool star coronae. We have performed a detailed comparison of Chandra spectra of H1504+65 with those of Procyon and α Cen A and B. NLTE model spectra for the white dwarf have enabled us to identify a wealth of absorption lines from highly ionised O, Ne and Mg. In turn, these features have allowed us to identify coronal lines whose origins were hitherto unknown.
UHECR observation from space and the ESA Cosmic Vision Programme
2005-01-01

The astrophysical and physical processes at the very end of the known energy spectrum, in the region of the so-called Ultra High Energies (UHE), have been the subject of an intense debate in the last years. UHE particles are nucleons, nuclei, photons, and neutrinos or even new particles predicted by theory, but not discovered yet, with energies from a few 10(18) eV, where fluxes of cosmic neutrinos are expected from "standard" physics and astrophysics, to beyond the decade of 10(20) eV, where radiation is thought to be produced under the most extreme physical conditions in the Universe. The understanding of the nature, origin, propagation to Earth of such UHE particles would provide entire new information on the sources and the astrophysical mechanisms that could produce them. Moreover, observations at UHE, would, possibly, allow us to test high energy physics beyond the limit of existing and next generation accelerators as well as Lorentz invariance at extreme energies. The ground-based Pierre Auger Observatory, whose southern site is currently being completed in Argentina, -will surely provide, in the near future, more solid observational bases for the understanding of what is today the UHE puzzle. However, in any post-Auger scenario, only space-based observatories can reach the collecting power necessary to fully explore the LTHE Universe, establishing then "Particle Astronomy" as a new observational window. Building on the studies conducted for the ESA-led Mission EUSO, we summarize here: 1. the science goals of an ESA "Cosmic Vision 20152025" mission for UHE search; 2. Its scientific requirements; 3. The necessary R&amp;amp;D preliminary to any further development of such a challenging innovative mission.
Exact representations for tumour incidence for some density‐dependent models
2005-01-01

Carcinogenesis is a multistage random process involving generic changes and stochastic proliferation and differentiation of normal cells and genetically altered stem cells. In this paper, we present the probability of time to tumour onset for a carcinogenesis model wherein the cells grow according to a birth and death process with density‐dependent birth and death rates. This is achieved by transforming the underlying system of difference equations which results in a continued fraction. This continued fraction approach helps us to find the complete solutions. The popular Moolgavkar‐Venzon‐Knudson (MVK) model assumes constant birth, death, and transition rates.
Bose–Einstein condensates in tailored micro potentials
2005-01-01

A combination of a large scaled 'carrier chip' and micron scaled 'atom-optics chips' is used for phase coherent manipulation Bose–Einstein condensates. Diffraction of condensates from a magnetic lattice potential is observed up to the fifth order.
Ocular Flutter—A Sign of Brain-Stem Pathology as Rare Consequence of Cyclosporin A Treatment
2005-01-01

Cyclosporin A is a widely used immunosuppressive drug. While neurotoxic side effects are frequent and manifold, oculomotor disturbances have hardly ever been noted. Here, we report the case of a 56-year-old woman, suffering from acute myeloid leukemia (AML) and treated with allogeneic peripheral blood stem-cell transplantation (PBSCT) and supporting cyclosporin, who developed neurological deficits consisting of ocular flutter, severe ataxia, and tremor of trunk and extremities within a few days. Whereas MRI scans of the neurocranium and spinal cord, Doppler ultrasound of the extracranial brain-supplying blood vessels, and the standard repertoire of electrophysiological examinations of the peripheral nerves were inconclusive, a cerebrospinal fluid tap showed an elevated cell count with leukemic blasts documenting leukemic meningitis. As soon as the cyclosporin medication, which had been initiated after the PBSCT 13 weeks earlier, was terminated, the aforementioned disturbances promptly subsided, well before treatment of the meningeosis was commenced. This temporal relationship indicates that ocular flutter as well as ataxia and tremor were caused by cyclosporin-associated neurotoxicity rather than by meningeosis. The isolated oculomotor abnormality of ocular flutter in the absence of typical cerebellar oculomotor disturbances suggests that ocular flutter might be a consequence of brain-stem dysfunction rather than reflecting cerebellar disturbances.
Anticoagulation during continuous renal replacement therapy with lepirudin in patients with heparin-induced thrombocytopenia
2005-01-01

Introduction Community-acquired pneumonia remains a common condition worldwide.It is associated with significant morbidity and mortality.The aim of this study was to evaluate conditions that could predict a poor outcome.Design Retrospective analyse of 69 patients admitted to the ICU from 1996 to 2003.Demographic data included age, sex and medical history.Etiologic agents, multiorgan dysfunction, nosocomial infections, SAPS II and PORT scores were recorded for each patient.For statistical analysis we used a t test, chi-square test and Mann-Whitney U test on SPSS ® .A value of P less than 0.05 was considered significant.Results Forty-seven patients were male and 22 patients were female.Mean age was 52 years.Sixty-seven percent had serious pre-morbid conditions including pulmonary disease (34.8%), cardiac problems (36.2%),diabetes (13%) and chronic liver disease (5.8%); 40.6% were smokers, drug abusers or alcohol dependents.Sixtyeight patients required invasive mechanical ventilation.The average length of ventilation was 13.5 days, median 8 days.The mean SAPS II score was 40.14 and the mean PORT score was 141.The mortality rate was 27.5% (SAPS II estimated mortality, 35%).Complications reported were ARDS (40.6%), septic shock (34.8%), acute renal failure (2.9%), cardiac arrest (8.7%) and nosocomial infeccions (46.4%).Mortality rates were higher for previous hepatic (75%) and metabolic (33%) diseases.We found a close association between crude mortality and SAPS II score (P = 0.003) and development of complications (P = 0.0028).Respiratory dysfunction (P = 0.006) and septic shock (P = 0.022) were most significantly related to mortality.No significant differences were founded regarding age, comorbidities, PORT score, etiologic agents, nosocomial infections and length of invasive mechanical ventilation.Conclusions Previous hepatic chronic disease was strictly related to higher mortality as well as isolation of MRSA.ARDS and septic shock predicted a poor outcome.SAPS II score was the best severity indicator of mortality. P2
Ternary Fission Induced by Polarized Neutrons
2005-01-01

\\nTernary fission of (e,e) U- and Pu- isotopes induced by cold polarized neutrons discloses some new facets of the process. In the so-called ROT effect shifts in the angular distributions of ternary particles relative to the fission fragments show up. In the so-called TRI effect an asymmetry in the emission of ternary particles relative to a plane formed by the fragment momentum and the spin of the neutron appear. The two effects are shown to be linked to the components of angular momentum perpendicular and parallel to the fission axis at the saddle point of fission. Based on theoretical models the spectroscopic properties of the collective transitional states at the saddle point are inferred from experiment.\\n