Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the effects of acid deposition: refinements, adjustments and inclusion of nitrogen dynamics in the MAGIC model

Abstract. The MAGIC model of the responses of catchments to acidic deposition has been applied and tested extensively over a 15 year period at many sites and in many regions around the world. Overall, the model has proven to be robust, reliable and useful in a variety of scientific and managerial activities. Over the years, several refinements and additions to MAGIC have been proposed and/or implemented for particular applications. These adjustments to the model structure have all been included in a new version of the model (MAGIC7). The log aluminium – pH relationship now does not have to be fixed to aluminium trihydroxide solubility. Buffering by organic acids using a triprotic analog is now included. Dynamics of nitrogen retention and loss in catchments can now be linked to soil nitrogen and carbon pools. Simulation of short-term episodic response by mixing fractions of different water types is also possible. This paper presents a review of the conceptual structure of MAGIC7 relating to long-term simulation of acidification and recovery, describes the conceptual basis of the new nitrogen dynamics and provides a comprehensive update of the equations, variables, parameters and inputs for the model. Keywords: process-based model, acid deposition, recovery
Practical Application of Parallel Coordinates to Hurricane Trend Analysis

In climate studies, weather scientists are interested in discovering which environmental factors have the greatest influence on significant weather phenomena. Due to the destructiveness of recent hurricane seasons, some scientists are focusing their studies on discovering which environmental variables have the greatest impact on the intensity and frequency of seasonal storm activity using statistical regression techniques. Although complicated, such techniques are effective in screening data and providing quantitative associations. In conjunction with these statistical regression methods, researchers have relied on simple, yet effective, scatter plots or histograms which require several separate plots or layered plots to analyze multiple variables. However, these representation techniques suffer from several perceptual issues because they were not designed for rapid or accurate multidimensional analysis. In this type of study, researchers need visualization techniques that are specifically designed to accommodate the simultaneous display of a high number of variables in order to support exploratory visual analysis. We have applied and extended a highly successful multivariate information visualization technique, parallel coordinates [3], to the study of hurricane climate data and regression analysis. We analyzed several seasonal hurricane predictors that were provided by Mr. Phil Klotzbach of the Tropical Meteorology Project at Colorado State University. Using an advanced dynamic interaction model, we validated the notion that the parallel coordinates visualization technique enriches the scientists’ ability to rapidly discover and thoroughly analyze complex patterns and trends in climate data.
Bridging SCADA systems and GI systems

Supervisory Control and Data Acquisition (SCADA) systems are omnipresent in production operation worldwide. Failure detection within these systems remains a challenging task as the level of granularity in terms of location-based identification is low. The systems are able to identify and display failing components, but the situation becomes even more severe in case one of the failing components is not an electronic component but a structural component with a spatial extent such as a pipeline system. In consequence, the process of detection and repair of such components remains a time-consuming and cost-intensive task. To provide a generic solution for this kind of issues, the authors present a conceptualization and a software adapter bridging a SCADA system and a Geographic Information System (GIS). The authors employ international standards from both domains to enable an information exchange between these systems. The resulting autonomous software adapter and the corresponding prototypical implementation thus extends SCADA systems with GIS capabilities.
Message logging in mobile computing

Dependable mobile computing is enhanced by independent recovery, low power consumption and no dependence on stable storage at the mobile host. Existing recovery protocols proposed for mobile environments typically create consistent global checkpoints that do not guarantee independent recovery and low power consumption. This paper demonstrates the advantages of message logging by describing a receiver based logging protocol. Cheap pointing is utilized to limit log size and recovery latency. We compare the performance of our approach with that of existing mobile checkpointing and recovery algorithms in terms of failure free overhead and recovery time. We also describe a stable storage management scheme for mobile support stations. Garbage collection is achieved without direct participation of mobile hosts.
Integrated Visualization of Gene Network and Ontology Applying a Hierarchical Graph Visualization Technique

A gene network is constructed with genes as nodes, and interactions between genes as edges so as to reveal unknown gene functions and relationship. However, nodes and edges of gene networks are usually very numerous. Because of that, it may be difficult to understand relations between genomic functions and gene-gene interactions, if it is visualized by traditional techniques. This paper presents our technique on visualization of gene networks and gene ontology(GO), which summarizes gene functions and attributes. The technique represents the functions defined by GO as colors of nodes, and bundles edges depending on the gene functions to ease visual complication of the network.
Protein Calorie Malnutrition in Liver Cirrhosis

Malnutrition is prevalent in all forms of liver diseases. Protein calorie malnutrition (PCM) is associated with an increased risk of morbidity and mortality in patients with cirrhosis and occurs in 50% 90% of these patients. Although the pathogenesis of PCM is multifactorial, alterations in protein metabolism plays an important role. This article is based on a selective literature review of protein calorie malnutrition in liver cirrhosis. Malnutrition is prevalent in liver cirrhosis due to the presence of ascites, nausea, vomiting, insufficient food intake, malabsorption and metabolic disorders, poor dietary intake, malabsorption, increased intestinal protein losses, low protein synthesis, and hyper metabolism.
Investigation of Ocean Surface Wave Refraction Using TerraSAR-X Data

As a scientific and technological continuation of the X-band Synthetic Aperture Radar (X-SAR) and Shuttle Radar Topography Mission (SRTM) missions, the new X-SAR, namely, TerraSAR-X (TSX), was launched on June 15, 2007. Since then, it has provided numerous high-quality data over land and ocean operationally. In this paper, surface wave refraction and diffraction are investigated using TSX imagery acquired over the coast of Terceira island situated in the North Atlantic. Peak wavelength and wave direction are determined by SAR 2-D image spectra. They are compared to measurements of X-band marine radar and results of the WAve prediction Model (WAM). Significant wave height in the near-shore shallow water region is estimated from TSX Spotlight mode data following the wave refraction laws and using the developed XWAVE empirical algorithm. Image spectra of the TSX subscenes in the full-coverage region are given to investigate significant changes of wave direction and length. By analyzing another TSX image acquired in StripMap mode, a shadow zone in the lee side of Terceira island is identified. It is influenced jointly by wave refraction and diffraction. Furthermore, a cross-sea pattern revealed in the image spectra is investigated. The cross sea is generated by the diffracted wave rays from the northern and southern coasts of the island. Less wave directional spreading for the cross-sea situation is observed as well when compared to the image spectra at the origin of diffraction.
Modified Vector Control Algorithm for Increasing Partial-Load Efficiency of Fractional-Slot Concentrated-Winding Surface PM Machines

This paper presents a modified vector control algorithm for a fractional-slot concentrated-winding surface permanent magnet (SPM) machine that has been developed to maximize the machine's partial-load efficiency over a wide range of operating conditions. By increasing the amplitude of the negative d-axis current, the resulting increase in the stator copper losses can be more than offset by the reduction in the iron core losses achieved by lowering the stator d -axis flux amplitude. The effectiveness of this technique has been demonstrated using both analytical models and finite element analysis for a 55-kW (peak) SPM machine design developed for a demanding set of traction drive performance requirements. For this example, the modified control strategy increases the partial-load efficiency at 20% of rated torque by > 6% at 2000 r/min compared to the maximum torque/ampere algorithm, making the machine much more attractive for its intended application.
Polymer Nanocomposite Technology , Fundamentals of Barrier

The term “nanocomposite” is widely employed to describe an extremely broad range of materials, where one of the components has a dimension in the sub-micron scale. A better –and far more restrictive– definition would require that a true nanocomposite should be a fundamentally new material (hybrid) in which the nanometer scale component or structure gives rise to intrinsically new properties, which are not present in the respective macroscopic composites or the pure components. This latter definition necessitates that the nanostructure has dimensions smaller than a characteristic scale that underlies a physical property of the material. For example, for the electronic properties of a conductor or semi-conductor this scale would relate to the de Broglie wavelength of the electron (ranging from a few nanometers for a metal to hundreds of nanometers for a semiconductor), for the mechanical properties of a polymer it would relate to the size of the polymer coil or crystal (again ranging from a few nanometers to hundreds of nanometers), and for the thermodynamic properties of a polymer glass it would relate to the cooperativity length (a few nanometers). Here we shall restrict our discussion even further, focussing on one subclass of polymer/inorganic nanocomposites, where the inorganic component is a high aspectratio nanoscale filler. Particular emphasis will be given to principles that apply to pseudo-two-dimensional layered inorganic fillers (such as 2:1 alumino-silicates , from where most of our examples will be derived, and layered double hydroxides). In these systems, concurrent improvements across multiple properties are typically achieved –with simultaneous enhancement of barrier, mechanical, thermal, and thermomechanical response– in addition to ‘new’ properties –such as improved flammability and biodegradability, or antimicrobial activity– compared to the unfilled polymer. Consequently, the resulting nanocomposite material is better described by the term “hybrid” (denoting the large scale changes in multiple material characters) rather than polymer “composite” (a term traditionally associated with an incremental improvement of one or two key properties). ∗email: manias@psu.edu, fax: +1-814-865-2917, tel: +1-814-863-2980.
Benchmarks for IP forwarding tables

IPv4 and IPv6 route tables are ever changing and a subject of constant study. The Network Processing Forum (NPF) required a parameterized selection of IPv4/IPv6 route tables, real and synthetic, to enable benchmarking the performance of systems that include network processors and search engines (co-processors). The benchmarks have scalable parameters, and are to be run in a standard way, as specified in the NPF IP Forwarding Implementation Agreement. A synthetic traffic generator was also required to implement the benchmarks. Requirements were collected, and a freely available software toolkit was created. The kit has two sets of components - one set which generates IPv4 forwarding tables in the range of 1000 to 1 million prefixes, along with IPv6 tables of size 400 to 1200 prefixes, and another set which generates synthetic traffic patterns for the benchmarks. The toolkit's programs can be used for NPF benchmark certification, or as a suite of helpful table and traffic generation tools. This paper explains the empirical schemes devised to create IPv4 and IPv6 route tables in line with these requirements, along with the algorithms used to implement the schemes. It also describes the problem of generating traffic to exercise the route tables produced using the previous schemes. The results obtained by running this software to generate route tables are presented and evaluated.
FORMATION, SURVIVAL, AND DESTRUCTION OF VORTICES IN ACCRETION DISKS

Two-dimensional hydrodynamical disks are nonlinearly unstable to the formation of vortices. Once formed, these vortices essentially survive forever. What happens in three dimensions? We show with incompressible shearing box simulations that in three dimensions, a vortex in a short box forms and survives just as in two dimensions. But a vortex in a tall box is unstable and is destroyed. In our simulation, the unstable vortex decays into a transient turbulent-like state that transports angular momentum outward at a nearly constant rate for hundreds of orbital times. The three-dimensional instability that destroys vortices is a generalization of the two-dimensional instability that forms them. We derive the conditions for these nonlinear instabilities to act by calculating the coupling between linear modes, and thereby derive the criterion for a vortex to survive in three dimensions as it does in two dimensions: the azimuthal extent of the vortex must be larger than the scale height of the accretion disk. When this criterion is violated, the vortex is unstable and decays. Because vortices are longer in azimuthal than in radial extent by a factor that is inversely proportional to their excess vorticity, a vortex with given radial extent will only survive in a three-dimensional disk if it is sufficiently weak. This counterintuitive result explains why previous three-dimensional simulations always yielded decaying vortices: their vortices were too strong. Weak vortices behave two-dimensionally even if their width is much less than their height because they are stabilized by rotation, and behave as Taylor–Proudman columns. We conclude that in protoplanetary disks, weak vortices can trap dust and serve as the nurseries of planet formation. Decaying strong vortices might be responsible for the outward transport of angular momentum that is required to make accretion disks accrete.
Airflow and optic flow mediate antennal positioning in flying honeybees

To maintain their speeds during navigation, insects rely on feedback from their visual and mechanosensory modalities. Although optic flow plays an essential role in speed determination, it is less reliable under conditions of low light or sparse landmarks. Under such conditions, insects rely on feedback from antennal mechanosensors but it is not clear how these inputs combine to elicit flight-related antennal behaviours. We here show that antennal movements of the honeybee, Apis mellifera, are governed by combined visual and antennal mechanosensory inputs. Frontal airflow, as experienced during forward flight, causes antennae to actively move forward as a sigmoidal function of absolute airspeed values. However, corresponding front-to-back optic flow causes antennae to move backward, as a linear function of relative optic flow, opposite the airspeed response. When combined, these inputs maintain antennal position in a state of dynamic equilibrium. DOI: http://dx.doi. org/10.7554/eLife.14449. 001
Gutsy moves in mice: cellular and molecular dynamics of endoderm morphogenesis

Despite the importance of the gut and its accessory organs, our understanding of early endoderm development is still incomplete. Traditionally, endoderm has been difficult to study because of its small size and relative fragility. However, recent advances in live cell imaging technologies have dramatically expanded our understanding of this tissue, adding a new appreciation for the complex molecular and morphogenetic processes that mediate gut formation. Several spatially and molecularly distinct subpopulations have been shown to exist within the endoderm before the onset of gastrulation. Here, we review findings that have uncovered complex cell movements within the endodermal layer, before and during gastrulation, leading to the conclusion that cells from primitive endoderm contribute descendants directly to gut.
Traffic violation alert and management

The present paper presents an in-vehicle system for traffic violation alert and management. The system hardware consists of a combination of an on-board computer vision system for traffic sign detection and recognition with a data recorder device for traffic violation alert and management. At present, traffic violations are only focused on three signs: namely speed limit, stop sign, and forbidden turning. The system is designed to warn drivers about potential traffic violations by emitting acoustical messages through vehicle loudspeakers. These messages are issued with sufficient notice to provide the driver with enough time to react to the oncoming traffic situation. However, when a traffic violation is committed, the corresponding offence information such as vehicle speed, GPS location, and other driving parameters, are saved in a database for off-line analysis. In addition, an auxiliary application permits the registered traffic violations to be represented as a standard Google Earth map. The prototype was tested in a real scene under different lighting conditions and showed reasonable results.
PROBABILISTIC IMAGE SEGMENTATION FOR LOW-LEVEL MAP BUILDING IN ROBOT NAVIGATION

We propose a simple map building system for a mobile robot equipped with a single camera. The system is based on probabilistic segmentation of the ground area, which is safe to move on, from the rest of the scene, which is treated as obstacles. The slow convergence of MCMC methods often makes them poorly suited for practical image processing applications. We propose an efficient segment diffusion algorithm and certain approximations that make the MCMC approach applicable to real-time navigation.
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems

MOTIVATION Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses. RESULTS Here we present a flexible and widely applicable noise decomposition tool that allows us to calculate contributions of individual reactions to the total variability of a system's output. With the package it is, therefore, possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that the noise contributions resulting from individual reactions can be inferred from data experimental data along with Bayesian parameter inference. The method is based on the linear noise approximation, which is assumed to provide a reasonable representation of analyzed systems. AVAILABILITY AND IMPLEMENTATION http://sourceforge.net/p/stochdecomp/
Reconstructing the lost reality archaeological analysis and Transmedial Technologies for a perspective of Virtual Reality in the Etruscan city of Kainua

This paper presents the very first results of a three-year research program concerning the digital reconstruction of an entire Etruscan town, based on a philological analysis of archaeological data. The archaeological site and the adjacent museum will be then provided with suitable systems of perception and discovery of the archaeological reality, fully reconstructed due to innovative Transmedial Technologies based on Virtual Reality and, since this work is still in progress, studied through future digital models based on historic BIM process.
Functional redundancy between DNA ligases I and III in DNA replication in vertebrate cells

In eukaryotes, the three families of ATP-dependent DNA ligases are associated with specific functions in DNA metabolism. DNA ligase I (LigI) catalyzes Okazaki-fragment ligation at the replication fork and nucleotide excision repair (NER). DNA ligase IV (LigIV) mediates repair of DNA double strand breaks (DSB) via the canonical non-homologous end-joining (NHEJ) pathway. The evolutionary younger DNA ligase III (LigIII) is restricted to higher eukaryotes and has been associated with base excision (BER) and single strand break repair (SSBR). Here, using conditional knockout strategies for LIG3 and concomitant inactivation of the LIG1 and LIG4 genes, we show that in DT40 cells LigIII efficiently supports semi-conservative DNA replication. Our observations demonstrate a high functional versatility for the evolutionary new LigIII in DNA replication and mitochondrial metabolism, and suggest the presence of an alternative pathway for Okazaki fragment ligation.
Challenges Faced by Managers in Conducting Performance Appraisals in Organizations

The process of management involves a continuous judgment on the behavior and performance of staff whose one way of review is through a system of performance appraisal. It is important that members of the organization know exactly what is expected of them, and the yardsticks by which their performance and results is measured. A formalized and systematic appraisal scheme will enable a regular assessment of the individual’s performance, highlight potential, identify training and development needs, improve the future performance of staff and also form the basis of a review of financial rewards and planned career progression. Past researchers have contended that organizations face many problems in conducting performance appraisal ranging from legal issues, gender, race, rating instruments, organizational culture, politics, resources, knowledge, skills, standards as well as the appraisal process itself. This study aimed at investigating the challenges faced by Commercial banks in conducting effective performance appraisal. Both qualitative and quantitative approaches were used in the study, where top and middle management were randomly selected and interviewed by the researcher. Data collection was done through observation, interviews, and questionnaires that were divided into five parts (personal profile, performance appraisal implementation, evaluation of performance appraisal, feedback, and finally the recommendation). Keywords: Performance; performance appraisal; Organization.