Miracle-dz/UniFAR-FTUs huggingface dataset:
Network analysis of time-lapse microscopy recordings

Multicellular organisms rely on intercellular communication to regulate important cellular processes critical to life. To further our understanding of those processes there is a need to scrutinize dynamical signaling events and their functions in both cells and organisms. Here, we report a method and provide MATLAB code that analyzes time-lapse microscopy recordings to identify and characterize network structures within large cell populations, such as interconnected neurons. The approach is demonstrated using intracellular calcium (Ca2+) recordings in neural progenitors and cardiac myocytes, but could be applied to a wide variety of biosensors employed in diverse cell types and organisms. In this method, network structures are analyzed by applying cross-correlation signal processing and graph theory to single-cell recordings. The goal of the analysis is to determine if the single cell activity constitutes a network of interconnected cells and to decipher the properties of this network. The method can be applied in many fields of biology in which biosensors are used to monitor signaling events in living cells. Analyzing intercellular communication in cell ensembles can reveal essential network structures that provide important biological insights.
THE VERTICAL LOBE AND TOUCH LEARNING IN THE OCTOPUS.

1. In this paper the effects of vertical and superior frontal lobe removal are considered in relation to touch learning and discussed in the light of findings from visual experiments. 2. Removal of the vertical and/or the median superior frontal lobe slows touch learning. The operated animals take nearly twice as many trials as controls to learn a simple tactile discrimination. Their performance is more variable than that of controls. 3. Removal of these parts increases the number, but does not alter the sign of errors made. Removal of the median superior frontal does not appear to add to the effect of removing the vertical lobe. 4. The pattern of errors made by controls and experimental animals is similar within groups of massed trials given in the course of training. 5. Once trained to a given standard of accuracy (75 or 85% correct responses) the operated animals remember for as long as controls. Retention tests show little difference in performance 5 and 10 days after the end of training; the difference between controls and experimentals cannot be attributed to more rapid forgetting by the latter. 6. In experiments involving reversal of learned discriminations controls learn in fewer trials than experimentals. 7. Octopuses operated after training show an immediate decline in performance that can, to a considerable extent, be compensated by further training. The operations do not entirely remove the effects of past experience. Again, the effects are quantitative, not qualitative. 8. Octopuses with the vertical lobes removed take about six times as long as controls to examine and reject an unfamiliar object. 9. These results are considered in relation to ( a ) the effects of lesions to the inferior frontal and subfrontal lobes, which are anatomically similar to the superior frontal and vertical, and ( b ) current theories of the function of the vertical lobe in visual experiments. 10. It is concluded that the vertical lobe produces quantitative increases in the effects of experience on subsequent actions. It remains unestablished whether it does this by amplifying the effects of events taking place elsewhere in the central nervous system or by adding further units to a pool of neurones alterable by experience. The latter seems more probable in view of experiments on the anatomically similar sub-frontal lobe, where a minimal number of cells must be present if the animals are to learn at all.
Entropy production minimisation of a compression-resorption heat pump

Waste heat recovery is essential to reduce energy consumption in industry. A heat pump can be used to upgrade waste heat to a temperature level that is suitable for process heat. This study concerns a compression-resorption heat pump. The goal is to optimise the heat pump energetically, while keeping the investment attractive. Entropy production is a measure for energy dissipation and therefore this will be used to quantify the exergetic losses of the cycle. To minimise entropy production is equivalent to optimising the energetic performance. A literature study is performed and two models are developed and applied to an example case from industry. For the example case the calculations showed that the COP can be increased by 26 % with respect to the currently installed pentane vapour-compression heat pump. The theory of non-equilibrium thermodynamics is applied to find the local entropy production distribution in the resorber. The calculations showed that especially in the beginning of the process the entropy production rate is high. Together the models are used to evaluate the economic performance of the system. To reduce the payback period new configurations of the heat exchanging process in the resorber are investigated using the criterion of equipartition of entropy production. These investigations show that distributing the inlet mass flow over the length of the heat exchanger does not decrease the required heat transfer area. Decreasing the cross-sectional area for the flow however, does cause a reduction of the heat transfer area.
HyDash: A Dashboard for Real-Time Business Intelligence based on the HyPer Main Memory Database System

Business Intelligence (BI) is a set of techniques that help improve business decision making. From a technical point of view, BI relies on a set of tools which includes performance dashboards: layered services that combine monitoring, analysis, and reporting. However, most dashboard solutions today are based on data warehouses which face a problem of data staleness—a circumstance caused by the separation of transactional and analytical processing. Novel hybrid main memory database systems such as SAP’s HANA or HyPer overcome this issue and achieve best-of-breed transaction processing throughput and analytical query response times in one system in parallel on the same database state. In this work, we contribute HyDash, a web-based dashboard for real-time business intelligence. HyDash visualizes key performance indicators (KPIs) based on predefined SQL queries and provides an ad-hoc SQL query interface to dynamically extend the scope of the dashboard. HyDash relies on (i) hybrid main memory database systems and (ii) a push-based query result update mechanism based on the novel HTML5 WebSockets.
Repetitive control of underdamped linear oscillating motor

This paper presents a novel control method of linear oscillating motor in Linear-Driven Electro-Hydrostatic Actuator (LEHA). The tracking accuracy of linear oscillating motor is one of the key factors in the performance of LEHA. During the operation of LEHA, the linear oscillating motor is in the underdamped condition. The equivalent friction damping coefficient is defined in this paper to simplify PID tuning. Velocity and acceleration compensation is proposed here to construct the equivalent friction damping coefficient. In order to increase the oil flow rate in LEHA system, this strategy is combined with the repetitive control method which is capable to improve tracking accuracy. The repetitive controller with damping ratio compensation is also able to realize a high tracking quality under periodic loads.
Mutagenesis of specificity and toxicity regions of a Bacillus thuringiensis protoxin gene

Two different 30-nucleotide regions of the cryIAc insecticidal protoxin gene from Bacillus thuringiensis were randomly mutagenized. One region was within one of seven amphipathic helices believed to be important for the formation of ion channels. There was no loss of toxicity for three test insects by any of 27 mutants, a result similar to that obtained previously for mutations within another such helix. Only mutations within a region encoding the central helix have resulted in a substantial number of mutants with low or no toxicity. A second mutagenized region encodes amino acids which are unique to this toxin and are within one of the loops in a portion of the toxin important for specificity. Among 21 different mutations of these 10 residues, only changes of two adjacent serine residues resulted in decreased toxicity which was greater for Manduca sexta than for Heliothis virescens larvae. These mutant toxins bound poorly to the single M. sexta CryIAc vesicle-binding protein and to several of the multiple H. virescens-binding proteins. The loop containing these serines must be involved in the formation of a specific toxin recognition domain.
Optimizing color consistency in photo collections

With dozens or even hundreds of photos in today's digital photo albums, editing an entire album can be a daunting task. Existing automatic tools operate on individual photos without ensuring consistency of appearance between photographs that share content. In this paper, we present a new method for consistent editing of photo collections. Our method automatically enforces consistent appearance of images that share content without any user input. When the user does make changes to selected images, these changes automatically propagate to other images in the collection, while still maintaining as much consistency as possible. This makes it possible to interactively adjust an entire photo album in a consistent manner by manipulating only a few images. Our method operates by efficiently constructing a graph with edges linking photo pairs that share content. Consistent appearance of connected photos is achieved by globally optimizing a quadratic cost function over the entire graph, treating user-specified edits as constraints in the optimization. The optimization is fast enough to provide interactive visual feedback to the user. We demonstrate the usefulness of our approach using a number of personal and professional photo collections, as well as internet collections.
On the rising motion of a drop in stratified fluids

The rising dynamics of a deformable drop in a linearly stratified fluid is numerically obtained using a finite-volume/front-tracking method. Our results show that the drag coefficient of a spherical drop in a stratified fluid enhances as Cd,s/Cd,h−1∼Frd−2.86 for drop Froude numbers in the range of 4 < Frd < 16. The role of the deformability of the drop on the temporal evolution of the motion is investigated along with stratification and inertial effects. We also present the important role of stratification on the transient rising motion of the drop. It is shown that a drop can levitate in the presence of a vertical density gradient. The drop undergoes a fading oscillatory motion around its neutrally buoyant position except for high viscosity ratio drops where the oscillation occurs around a density level lighter than the neutral buoyancy level. In addition, a detailed characterization of the flow signature of a rising drop in a linearly stratified fluid including the buoyancy induced vortices and the resu.
A linear-centric simulation framework for parametric fluctuations

The relative tolerances for interconnect and device parameter variations have not scaled with feature sizes which have brought about significant performance variability. As we scale toward 10 nm technologies, this problem will only worsen. New circuit families and design methodologies will emerge to facilitate construction of reliable systems from unreliable nanometer scale components. Such methodologies require new models of performance which accurately capture the manufacturing realities. Recently, one step toward this goal was made via a new variational reduced order interconnect model that efficiently captures large scale fluctuations in global parameter values. Using variational calculus the linear interconnect systems are represented by analytical models that include the global variational parameters explicitly. In this work we present a framework which extends the previous work to a linear-centric simulation methodology with accurate nonlinear device models and their fluctuations. The framework is applied to generate path delay distributions under nonlinear and linear parameter fluctuations.
Network design for rate adaptive media streams

Rate adaptive multimedia streams offer significant system and client benefits over nonadaptive streams. These benefits come at the price of increased complexity in providing adequate network support and difficulty in understanding how rate adaptation protocols affect client perceived QoS. In this paper we define quality of service in terms of the mean rate seen by the client. We identify an intuitive optimal adaptation policy that maximizes QoS. We suggest an appropriate scaling regime for rate adaptive streams and identify asymptotic QoS for large capacity networks under the optimal adaptation policy. Implementation of the optimal adaptation policy presents several obstacles that render it infeasible. We define a multiclass admission control policy that achieves asymptotically equivalent QoS to that achieved under the optimal adaptation policy, but without the need for dynamic adaptation. Our work carries implications for network designers and content providers.
A Model Driven Domain Engineering Method

This paper proposes an approach of organizing the development of a large software system. By domain analysis and design the method can provide a domain meta-model (DMM) based on the MOF model and a flexible and customizable domain specific software architecture (DSSA). In late domain implementation phase it can make use of DMM and DSSA to generate domain software. The method provides a good paradigm for automating software development that has flexibility, reusability, agility and productivity across the software life cycle. It can rapidly generate a new domain application without code programming when requirements changing. So the method can generate a domain software family, not only a single application. A major benefit of this approach to software development, as compared to the usual sequential "waterfall model" is the speed with which products can be brought to market.
Sum secrecy rate in multicarrier DF relay beamforming

In this paper, we study sum secrecy rate in multi-carrier decode-and-forward relay beamforming. We obtain the optimal source power and relay weights on each subcarrier which maximize the sum secrecy rate. For a given total power on a given subcarrier k, P<sup>k</sup><sub>0</sub>, we reformulate the optimization problem by relaxing the rank-1 constraint on the complex positive semidefinite relay weight matrix, and solve using semidefinite programming. We analytically prove that the solution to the relaxed optimization problem is indeed rank 1. We show that the subcarrier secrecy rate, R<sub>s</sub>(P<sup>k</sup><sub>0</sub>), is a concave function in total power P<sup>k</sup><sub>0</sub> if R<sub>s</sub>(P<sup>k</sup><sub>0</sub>) > 0 for any P<sup>k</sup><sub>0</sub> > 0. Numerical results show that the sum secrecy rate with optimal power allocation across subcarriers is more than the sum secrecy rate with equal power allocation. We also propose a low complexity suboptimal power allocation scheme which outperforms equal power allocation scheme.
Probabilistic estimates of attribute statistics and match likelihood for people entity resolution

For big data practitioners, data integration/entity resolution/record linkage is one of the key challenges we face from day to day. Entity resolution/record linkage with high precision and recall on a large graph with billions of nodes, and hundreds of times more edges poses significant scalability challenges. Similarity based graph partition is still the most scalable method available. This paper presents a probabilistic method to approximate the match likelihood of a pair of records by incorporating values of different attributes and their aggregates/statistics. The quality of the approximates depend on the accuracy of the estimates of the aggregated values. The paper adapts the GTM model described in [1] to obtain the estimates. We present experimental results based on real world commercial data sources to show that the estimates obtained via GTM model is better than the baseline. Our experimental results also showed that the approximate match likelihood can improve the recall of the similarity function.
Design and analysis of dual band integrated hexagonal shaped microstrip UWB antenna

<span class="s22">In this paper, we proposed a hexagonal shaped </span><span class="s22">microstrip</span><span class="s22"> ultra-wideband (UWB) antenna integrated with dual band applications. The antenna design consists of a hexagonal shape patch with two folded Capacitive Loaded Line Resonators (CLLRs) on the left edge of the patch antenna. This hexagonal structure is used to implement UWB applications (3.1-10.6 GHz). A rectangular ground</span><span class="s22">,</span><span class="s22"> and two CLLR are also used on t</span><span class="s22">he bottom of antenna to obtain</span><span class="s22"> the extra dual resonant frequency at 2.4 GHz and 9.1 GHz for </span><span class="s22">B</span><span class="s22">luetooth and radar applications respectively. The proposed design is implemented using FR4 epoxy substrate. The relative permittivity of the substrate is 4</span><span class="s22">. 4. The overall size of designing</span><span class="s22"> antenna is 26 × 30 mm2 with 1.6 mm as thickness and fed by standard feed line of 50 Ω </span><span class="s22">microstrip</span><span class="s22">. The results obtained from the simulation indicate that the designed antenna attains a good bandwidth from 1.1 GHz – 10.69 GHz with VSWR < 2 and return loss < -10 </span><span class="s22">dB. </span><span class="s22"> The proposed geometry is s</span><span class="s22">imulated by using the </span><span class="s22">Ansoft</span><span class="s22"> HFSS </span><span class="s22">simulator working on the principle of FEM and results are also analyzed. </span>
Cdk 1 phosphorylation of BubR 1 controls spindle checkpoint arrest and Plk 1-mediated formation of the 3 F 3 / 2 epitope

Mitosis is controlled by precise temporal and spatial regulation of protein kinases and ubiquitin ligases (Murray, 2004). The activity of the Cdk1/cyclin B kinase is activated at mitotic entry and remains high until anaphase onset, during which destruction of cyclin B, mediated by the anaphase-promoting complex/ cyclosome (APC/C), inactivates Cdk1. The timing of APC/C activation and subsequent chromosome segregation is controlled by the spindle checkpoint, which delays the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. The absence of microtubule attachment or tension at kinetochores activates the checkpoint and arrests cells in mitosis. Protein phosphorylation mediated by checkpoint kinases, such as monopolar spindle 1 (Mps1), Aurora B, Bub1, BubR1, and polo-like kinase 1 (Plk1), plays an essential role in checkpoint signaling on kinetochores. In fact, unattached or untense kinetochores are hyperphosphorylated (Gorbsky and Ricketts, 1993; Nicklas et al., 1998), and the lack of tension promotes the formation of a kinetochore phosphoepitope recognized by the 3F3/2 monoclonal antibody (Cyert et al., 1988). We and others have recently identifi ed Plk1/Xenopus laevis polo-like kinase 1 (Plx1) as the 3F3/2 kinase (Ahonen et al., 2005; Wong and Fang, 2005). Despite the extensive efforts of over a decade, the molecular identity of the kinetochore protein harboring the physiological 3F3/2 epitope remains unknown. We report here that the checkpoint protein BubR1 is the kinetochore 3F3/2 antigen phosphorylated by Plx1. Furthermore, we show that formation of the BubR1 3F3/2 epitope requires a priming phosphorylation by Cdk1/cyclin B on Thr 605 and that this phosphorylation is required for checkpoint arrest.
Postoperative changes in the brain: MR imaging findings in patients without neoplasms.

PURPOSE To determine the time course of postoperative changes in the brain by using magnetic resonance (MR) imaging. MATERIALS AND METHODS Contrast material-enhanced MR images (32 preoperative, 161 postoperative) in 95 patients who underwent temporal lobectomy for treatment of nonneoplastic epilepsy were evaluated for enhancement pattern at the surgical margin and for the presence of dural enhancement, fluid, and air. Images were obtained 9 hours to 5.6 years after surgery. RESULTS Surgical margin contrast enhancement was present and increased from 20 hours to 29 days after surgery. The predominant early (days 0-5) pattern was thin linear enhancement (16 of 18 [89%] images). The later (days 6-29) pattern was thick linear or nodular (tumorlike appearance) (11 of 18 [61%] images). Surgical margin enhancement was absent after day 30, although few data were collected 1-5 months after surgery. Dural enhancement was seen on 96 of 97 (99%) postoperative MR images. Extraaxial fluid was seen on all 46 images obtained during the first 30 days and was absent by day 51. Intracranial air was present on 31 of 35 (89%) images obtained during the first 4 days but was absent after day 5. CONCLUSION Knowledge of the evolution of contrast enhancement patterns on postoperative MR images of the brain can help in differentiating benign from neoplastic changes.
Choice of Cell Source in Cell-Based Therapies for Retinal Damage due to Age-Related Macular Degeneration: A Review

Background. Age-related macular degeneration (AMD) is a complex disorder that affects primarily the macula involving the retinal pigment epithelium (RPE) but also to a certain extent the photoreceptor layer and the retinal neurons. Cell transplantation is a promising option for AMD and clinical trials are underway using different cell types. Methods. We hypothesize that instead of focusing on a particular cell source for concurrent regeneration of all the retinal layers and also to prevent exhaustive research on an array of cell sources for regeneration of each layer, the choice should depend on, precisely, which layer is damaged. Results. Thus, for a damage limited to the retinal pigment epithelial (RPE) layer, the choice we suggest would be RPE cells. When the damage extends to rods and cones, the choice would be bone marrow stem cells and when retinal neurons are involved, relatively immature stem cell populations with an inherent capacity to yield neuronal lineage such as hematopoietic stem cells, embryonic stem cells, or induced pluripotent stem cells can be tried. Conclusion. This short review will prove to be a valuable guideline for those working on cell therapy for AMD to plan their future directions of research and therapy for this condition.
Agent services for situation aware control of power systems with distributed generation

Electric Power system of Denmark exhibits some unique characteristics. An increasing part of the electricity is produced by distributed generators (DGs). Most of these DGs are connected to the network at the distribution level. At the same time the concept of vehicle to grid (V2G) is already in the process of realization. This situation has created an incentive in electric power industry to utilize modern information and communication technologies (ICT) for improving the distribution system automation. This paper describes our work on how significantly increased amount of distributed generation could be exploited for the robust control of electric power systems. In particular, we present our work on the implementation of a dynamic service oriented system, in which autonomous agents represent different components of low voltage grid. These agents could offer and utilize electric power control services. We present results from several experiments where agents offer and utilize services in order to achieve distributed and autonomous control for subgrid operation of a distribution system. Finally it is discussed how the service oriented architecture can be combined with knowledge based reasoning to implement situation awareness required in complex control situations.