Miracle-dz/UniFAR-FTUs huggingface dataset:
Parametrising kinetic models of biological networks

Systems biology seeks to model biological networks dynamically. Two requirements need to be fulfilled for this to be possible. First, the interaction networks need to be known. Second, the dynamics of the interactions have to be revealed. Dynamics of interactions are described by rate laws using kinetics. These kinetics describe the interaction mechanism. For each single interaction occurring in a biological network parameters have to specified. They have to be measured by experiments. For enzyme catalysed reactions, for example, the parameters are measured by enzyme assays tracking the consumption of substrate. For many enzymes parameters and kinetic mechanism are not known. And existing data for parameters generally are of poor quality. After introducing kinetic modelling of metabolic networks we consider a published artificial genetic network that can either tend to a steady state or exhibit sustained oscillations depending on a critical parameter. This critical parameter is the Hill coefficient in the interaction from one gene with the other. For different parameter settings we examine at what value of the Hill coefficient a bifurcation occurs. At this point the network begins to oscillate. We thus assess the distribution of the critical values, a property that cannot be calculated analytically. We then go on to consider useful data sources for parmetrisation of kinetic models of metabolic networks and collect them in an electronical resource to make them electronically accessible and usable. This requires choosing standard references for the designation of components of biological networks. Finally we describe a workflow in which this data resource is used for automatic parametrisation of kinetic models of metabolic networks.
A new protein of adhesion plaques and ruffling membranes

A protein with a molecular weight on SDS polyacrylamide gels of 215,000 (referred to here as 215K) was purified from chicken gizzard smooth muscle. Antibodies against this protein localized it in fibroblasts to adhesion plaques (focal contacts), to regions underlying cell surface fibronectin, and to ruffling membranes. In the first two distributions it was similar to vinculin in cellular location, and this was confirmed by double-label immunofluorescence microscopy, but the concentration of 215K in membrane ruffles distinguished it from vinculin. There was no cross-reaction of the antibody against 215K with vinculin, and immunoprecipitation and antibody staining of SDS gels of whole cells revealed a single cross-reactive component with a molecular weight of 215,000. Immunoprecipitation from cultures labeled with [32P]phosphate revealed 215K to be a phosphoprotein. Transformation of rat or chicken fibroblasts by Rous sarcoma virus resulted in a reorganization of 215K, in some cases into complex intracellular structures. The localization of 215K where microfilament bundles terminate as well as in close relation to cell surface fibronectin and in membrane ruffles suggests that the protein has some function in the organization of actin filaments at or close to regions of actin-membrane attachment.
Concept for visualizing concealed objects to improve the driver's anticipation

Current advanced driver assistance systems (e.g. Emergency Brake Assistance, Lane Departure Warning, Lane Keeping Assistance and Blind Spot Detection) assist the driver in reacting to time-critical and unstable situations in a proper way. However, the anticipation of situations which are lying in the farer future is currently left primarily to the driver. In this paper, we present visualization concepts for concealed objects in order to support smart deceleration. Smart deceleration requires the anticipation of future traffic condition and the assistance of the driver in performing deceleration phases efficiently. In addition, safety is increased by reduction of potential criticality through the early deceleration phase. We have identified and categorized situations in which a broader anticipation is possible: situations with permanent obstacles, situations with temporarily stopped vehicles and situations with slower driving vehicles. An important issue when presenting information to the driver is the identification of the most suitable perspective. For visualizing the traffic situation in the surroundings of the driver’s car we established a virtual bird-eye perspective (VBEP), showing the traffic scene from a 3D viewpoint that is slightly raised above the driver and rigidly tethered to the car. This VBEP is a powerful concept to draw the driver’s attention to situations in the further future. On the basis of this concept we developed different visualizations and integrated them in the digital instrument cluster between the speedometer and the revolution counter.
Rhizobia with 16S rRNA and nifH Similar to Mesorhizobium huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae

New Zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, Carmichaelia, Clianthus and Montigena in the Carmichaelinae clade, tribe Galegeae, and Sophora, tribe Sophoreae, sub-family Papilionoideae. Ten bacterial strains isolated from NZ Carmichaelinae growing in natural ecosystems grouped close to the Mesorhizobium huakuii type strain in relation to their 16S rRNA and nifH gene sequences. However, the ten strains separated into four groups on the basis of their recA and glnII sequences: all groups were clearly distinct from all Mesorhizobium type strains. The ten strains separated into two groups on the basis of their nodA sequences but grouped closely together in relation to nodC sequences; all nodA and nodC sequences were novel. Seven strains selected and the M. huakuii type strain (isolated from Astragalus sinicus) produced functional nodules on Carmichaelia spp. , Clianthus puniceus and A. sinicus but did not nodulate two Sophora species. We conclude that rhizobia closely related to M. huakuii on the basis of 16S rRNA and nifH gene sequences, but with variable recA and glnII genes and novel nodA and nodC genes, are common symbionts of NZ Carmichaelinae.
Educational camp for children with asthma.

OBJECTIVE To evaluate the impact of a 5-day educational camp program for children with asthma in terms of improving their knowledge of asthma and enhancing their performance in the use of inhaled medication and in physical activities. METHODS Every day, the children received 20-min interactive educational sessions, the technique for using the metered-dose inhaler was reviewed, two peak flow readings were recorded, and the children performed physical activities that included breathing and relaxation exercises. A questionnaire regarding knowledge of asthma, as well as asthma triggers, asthma medications, misconceptions regarding asthma, and the use of spacers, was administered before and after the intervention. Correct use of inhaled medication and exercise-related symptoms were also evaluated before and after the intervention. RESULTS A total of 37 children with asthma, aged 8-10 years (15 females and 22 males), were included in this study. Of those, 25% showed an improvement in the level of knowledge of asthma after the educational camp program, as evidenced by the greater number of correct answers on three of the twelve questions analyzed (p < 0.05). The exercise-related dyspnea scores decreased significantly (p < 0.05). The ability to use inhaled medication correctly was significantly improved after the intervention (p < 0.05). CONCLUSIONS The asthma educational camp program can improve knowledge about specific questions, encourage participation in physical activities, and improve the asthma management skills of children.
ACC/AHA Guideline Update on Perioperative Cardiovascular Evaluation for Noncardiac Surgery

Raymond J. Gibbons, MD, FACC, Chair Elliott M. Antman, MD, FACC, Vice Chair Peter B. Berger, MD, FACC Hugh Calkins, MD, FACC Bernard R. Chaitman, MD, FACC Gordon A. Ewy, MD, FACC Kirsten E. Fleischmann, MD, MPH, FACC Lee A. Fleisher, MD, FACC James B. Froehlich, MD, FACC Richard J. Gusberg, MD, FACS Jeffrey A. Leppo, MD, FACC Thomas Ryan, MD, FACC Robert C. Schlant, MD, FACC William L. Winters, Jr, MD, MACC
Magnetic correlations in the two-dimensional Anderson-Hubbard model

The two dimensional Hubbard model in the presence of diagonal and off-diagonal disorder is studied at half filling with a finite temperature quantum Monte Carlo method. Magnetic correlations as well as the electronic compressibility are calculated to determine the behavior of local magnetic moments, the stability of antiferromagnetic long range order (AFLRO), and properties of the disordered phase. The existence of random potentials (diagonal or ``site'' disorder) leads to a suppression of local magnetic moments which eventually destroys AFLRO. Randomness in the hopping elements (off-diagonal disorder), on the other hand, does not significantly reduce the density of local magnetic moments. For this type of disorder, at half-filling, there is no ``sign-problem'' in the simulations as long as the hopping is restricted between neighbor sites on a bipartite lattice. This allows the study of sufficiently large lattices and low temperatures to perform a finite-size scaling analysis. For off-diagonal disorder AFLRO is eventually destroyed when the fluctuations of antiferromagnetic exchange couplings exceed a critical value. The disordered phase close to the transition appears to be incompressible and shows an increase of the uniform susceptibility at low temperatures.
Activity-Dependent Release of Endogenous Brain-Derived Neurotrophic Factor from Primary Sensory Neurons Detected by ELISAIn Situ

To define activity-dependent release of endogenous brain-derived neurotrophic factor (BDNF), we developed an in vitromodel using primary sensory neurons and a modified ELISA, termed ELISAin situ. Dissociate cultures of nodose-petrosal ganglion cells from newborn rats were grown in wells precoated with anti-BDNF antibody to capture released BDNF, which was subsequently detected using conventional ELISA. Conventional ELISA alone was unable to detect any increase in BDNF concentration above control values following chronic depolarization with 40 mm KCl for 72 hr. However, ELISA in situ demonstrated a highly significant increase in BDNF release, from 65 pg/ml in control to 228 pg/ml in KCl-treated cultures. The efficacy of the in situ assay appears to be related primarily to rapid capture of released BDNF that prevents BDNF binding to the cultured cells. We therefore used this approach to compare BDNF release from cultures exposed for 30 min to either continuous depolarization with elevated KCl or patterned electrical field stimulation (50 biphasic rectangular pulses of 25 msec, at 20 Hz, every 5 sec). Short-term KCl depolarization was completely ineffective at evoking any detectable release of BDNF, whereas patterned electrical stimulation increased extracellular BDNF levels by 20-fold. In addition, the magnitude of BDNF release was dependent on stimulus pattern, with high-frequency bursts being most effective. These data indicate that the optimal stimulus profile for BDNF release resembles that of other neuroactive peptides. Moreover, our findings demonstrate that BDNF release can encode temporal features of presynaptic neuronal activity.
Pattern Avoidance and Young Tableaux

This paper extends Lewis's bijection (J. Combin. Theorey Ser. A 118, 2011) to a bijection between a more general class $\mathcal{L}(n,k,I)$ of permutations and the set of standard Young tableaux of shape $\langle (k+1)^n\rangle$, so the cardinality \[ |\mathcal{L}(n,k,I)|=f^{\langle (k+1)^n\rangle}, \] is independent of the choice of $I\subseteq [n]$. As a consequence, we obtain some new combinatorial realizations and identities on Catalan numbers. In the end, we raise a problem on finding a bijection between $\mathcal{L}(n,k,I)$ and $\mathcal{L}(n,k,I')$ for distinct $I$ and $I'$.
Optimal Distributed Voltage Regulation for Secondary Networks With DGs

An algorithm for the optimal voltage regulation of distribution secondary networks with distributed generators (DGs) is proposed in the paper. Based on the ε decomposition of the sensitivity matrix (inverse of Jacobian) obtained from the solution of the Newton-Raphson power flow problem, a large secondary network is divided into several small subnetworks. From the ε decomposition, the range of influence of each DG on the voltage of the entire network is determined. When voltage at particular nodes exceeds normal operating limits, the nearest DGs can be located and commanded to control the voltage. The control action can be coordinated using communications in a small-size subnetwork. The voltage regulation is achieved by solving a small linear programming optimization problem with an objective function that makes every DG to optimize its generation. The algorithm is tested with a model of a real heavily-meshed secondary network. The results show that the algorithm proposed in this paper can effectively control the voltage in a distributed manner. It is also discussed in the paper how to choose the value of ε for the system decomposition.
Lifelogging: Just a Technology-enabled Behavioral Fad or an Enduring Form of Human Behavior in a Computerized World?

According to Dodge and Kitchin (2007, p. 431), lifelogging can be defined as “(…) a form of pervasive computing consisting of a unified digital record of the totality of an individual's experiences, captured multimodally through digital sensors and stored permanently as a personal multimedia archive. ”. Hence, lifelogging can be understood as a form of self-tracking that could present researchers from various disciplines, such as HCI and IS, with valuable individual-level data. Against this background, in this paper we discuss whether lifelogging is just another technological and/or technology-enabled fad (see, for example, Steininger et al. 2009), or whether it is more of the sort of an enduring form of human behavior. A way to structure the discussion on the state of the art of emerging technologies has been presented by Moor (2005). In his framework, he discusses criteria that should be considered when assessing the societal impact of information technologies. The framework consists of three main stages, two of which a technology has to move through (i.e., “Introduction” and “Permeation” stage) until it becomes widely accepted (i.e., “Power” stage), and seven criteria are used to assess the stage in which a technology is. In this paper, we use Moor’s (2005) framework to determine the current stage of lifelogging. Our assessment is based on evaluation of the seven criteria. However, as some criteria overlap in their content, we grouped these criteria into three wider categories.
Computational Time-Division and Code-Division Channel Access Scheduling in Ad Hoc Networks

Using two-hop neighborhood information, we present the hybrid activation multiple access (HAMA) protocol for time-division channel access scheduling in ad hoc networks with omni-directional antennas. Different from other approaches, HAMA is a node-activation channel access protocol that also maximizes the chance of link activations using time- and code-division schemes. The throughput and delay characteristics of HAMA in randomly-generated multihop wireless networks are studied by analyses and simulations. The results of the analyses show that HAMA achieves higher channel utilization in ad hoc networks than previous similar works, namely, the node activation multiple access (NAMA), the link activation multiple access (LAMA) and pair-wise link activation multiple access (PAMA). In addition, HAMA achieves better throughout than an existing scheduling algorithm based on complete topology information, and much higher throughout than the ideal CSMA and CSMA/CA protocols. The main contribution of this work is to computationally derive channel access schedules according to local network topology information instead of on-demand negotiations or static global coordinations.
Body dysmorphic disorder: some key issues for DSM‐V

Body dysmorphic disorder (BDD), a distressing or impairing preoccupation with an imagined or slight defect in appearance, has been described for more than a century and increasingly studied over the past several decades. This article provides a focused review of issues pertaining to BDD that are relevant to DSM‐V. The review presents a number of options and preliminary recommendations to be considered for DSM‐V: (1) Criterion A may benefit from some rewording, without changing its focus or meaning; (2) There are both advantages and disadvantages to adding a new criterion to reflect compulsive BDD behaviors; this possible addition requires further consideration; (3) A clinical significance criterion seems necessary for BDD to differentiate it from normal appearance concerns; (4) BDD and eating disorders have some overlapping features and need to be differentiated; some minor changes to DSM‐IV's criterion C are suggested; (5) BDD should not be broadened to include body integrity identity disorder (apotemnophilia) or olfactory reference syndrome; (6) There is no compelling evidence for including diagnostic features or subtypes that are specific to gender‐related, age‐related, or cultural manifestations of BDD; (7) Adding muscle dysmorphia as a specifier may have clinical utility; and (8) The ICD‐10 criteria for hypochondriacal disorder are not suitable for BDD, and there is no empirical evidence that BDD and hypochondriasis are the same disorder. The issue of how BDD's delusional variant should be classified in DSM‐V is briefly discussed and will be addressed more extensively in a separate article. Depression and Anxiety, 2010. © 2010 Wiley‐Liss, Inc.
Near- and far-field model coupling methodology for wastewater discharges

The prediction of pollutant concentrations in the coastal waters is essential for water quality control. The description of physical processes and their implementation in computer models shows that there is neither a “complete model” including all important spatial and temporal scales of the dominant processes nor a standard procedure for the coupling of models. This is explained by deficiencies in either implementing dominant physical near-field processes into a far-field model and/or coupling the models to each other. Capabilities and limitations of modeling techniques applied to waste plume mixing and dispersion from submerged multiport discharges are discussed for environmental impact analysis. The recommended procedure combines the relative strengths of the near-field mixing zone model CORMIX and the Eulerian farfield flow and water quality models within Delft3D.
Modeling Incentives for Email Blocking Strategies

We consider the current arrangements whereby many users send their email via ISP \smarthosts" and model this system as an eco- nomic network. Some of these users will have insecurely conflgured ma- chines, which may be hijacked for the sending of spam. This can lead to other sites blocking all email from the smarthost, which will then afiect all of the ISP's users. We derive formulae that express when blocking is an appropriate action and show that the number of legitimate users at the ISP must be taken into account as well as the number of spam sources. We relate this formal model to real world behaviour and atti- tudes and generate some strategies that maximise utility for difierent sizes of ISP. We present some quantitative email data from a large ISP that indicates the likely range in which numerical solutions will lie. We also demonstrate that some of the present approaches to email blocking are irrational and counterproductive.
Do Reported Effects of Acute Aerobic Exercise on Subsequent Higher Cognitive Performances Remain if Tested against an Instructed Self-Myofascial Release Training Control Group? A Randomized Controlled Trial

A substantial body of evidence suggests positive effects of acute aerobic exercise (AAE) on subsequent higher cognitive functions in healthy young adults. These effects are widely understood as a result of the ongoing physiological adaptation processes induced by the preceding AAE. However, designs of published studies do not control for placebo, Hawthorne and subject expectancy effects. Therefore, these studies do not, at a high degree of validity, allow attributing effects of AEE on subsequent cognitive performance to exercise induced physical arousal. In the present study, we applied a randomized controlled blinded experiment to provide robust evidence for a physiological basis of exercise induced cognitive facilitation. Beyond that, the dose response relationship between AAE`s intensity and subsequent cognitive performances as well as a potentially mediating role of peripheral lactate in AAE induced cognitive facilitation was investigated. The 121 healthy young subjects who participated in this study were assigned randomly into 3 exercise groups and a self-myofascial release training control group. Exercise groups comprised a low, moderate and high intensity condition in which participants cycled on an ergometer at a heart rate corresponding to 45–50%, 65–70% and 85–90% of their individual maximum heart rate, respectively, for 35 minutes. Participants assigned to the control group completed a 35 minute instructed self-massage intervention using a foam roll. Before and after treatment, participants completed computer based versions of the Stroop task and the Trail Making Test as well as a free recall task. None of the applied exercise regimes exerted a significant effect on participants`performance at any of the applied cognitive testing procedure if compared to self-myofascial release training control group. Post hoc power analyses revealed no effect in the population of f = . 2 or larger at a risk of type II error (β) ≤. 183 for all measured variables. Our results, therefore, indicate that AAE induced cognitive facilitation is not (exclusively) based on physiological effects. Even if there is a substantial contribution of physiological adaptations to AAE in reported AAE induced cognitive facilitation, in this study, peripheral lactate could not be confirmed as such a factor. Peripheral lactate concentrations and cognitive testing performances after exercise showed rather small empirical and no significant associations. Our results suggest that other psychosocial aspects like expectations and social attention play an important role in AAE induced cognitive facilitation.