Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of silent cells, synchronization and modulatory activity in developing cellular networks

Developing networks in the immature nervous system and in cellular cultures are characterized by waves of synchronous activity in restricted clusters of cells. Synchronized activity in immature networks is proposed to regulate many different developmental processes, from neuron growth and cell migration, to the refinement of synapses, topographic maps, and the mature composition of ion channels. These emergent activity patterns are not present in all cells simultaneously within the network and more immature “silent” cells, potentially correlated with the presence of silent synapses, are prominent in different networks during early developmental periods. Many current network analyses for detection of synchronous cellular activity utilize activity‐based pixel correlations to identify cellular‐based regions of interest (ROIs) and coincident cell activity. However, using activity‐based correlations, these methods first underestimate or ignore the inactive silent cells within the developing network and second, are difficult to apply within cell‐dense regions commonly found in developing brain networks. In addition, previous methods may ignore ROIs within a network that shows transient activity patterns comprising both inactive and active periods. We developed analysis software to semi‐automatically detect cells within developing neuronal networks that were imaged using calcium‐sensitive reporter dyes. Using an iterative threshold, modulation of activity was tracked within individual cells across the network. The distribution pattern of both inactive and active, including synchronous cells, could be determined based on distance measures to neighboring cells and according to different anatomical layers. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 357–374, 2016
Statistical design space exploration for application-specific unit synthesis

The capability of performing semi-automated design space exploration is the main advantage of high-level synthesis with respect to RTL design. However, design space exploration performed during; high-level synthesis is limited in scope, since it provides promising solutions that represent good starting points for subsequent optimizations, but it provides no insight about the overall structure of the design space. In this work we propose unsupervised Monte-Carlo design exploration and statistical characterization to capture the key features of the design space. Our analysis provides insight on how various solutions are distributed over the entire design space. In addition, we apply extreme value theory (1997) to extrapolate achievable bounds from the sampling points.
Microvascular and Macrovascular Complications of Diabetes

Diabetes is a group of chronic diseases characterized by hyperglycemia. Modern medical care uses a vast array of lifestyle and pharmaceutical interventions aimed at preventing and controlling hyperglycemia. In addition to ensuring the adequate delivery of glucose to the tissues of the body, treatment of diabetes attempts to decrease the likelihood that the tissues of the body are harmed by hyperglycemia. The importance of protecting the body from hyperglycemia cannot be overstated; the direct and indirect effects on the human vascular tree are the major source of morbidity and mortality in both type 1 and type 2 diabetes. Generally, the injurious effects of hyperglycemia are separated into macrovascular complications (coronary artery disease, peripheral arterial disease, and stroke) and microvascular complications (diabetic nephropathy, neuropathy, and retinopathy). It is important for physicians to understand the relationship between diabetes and vascular disease because the prevalence of diabetes continues to increase in the United States, and the clinical armamentarium for primary and secondary prevention of these complications is also expanding. ### Diabetic retinopathy Diabetic retinopathy may be the most common microvascular complication of diabetes. It is responsible for ∼ 10,000 new cases of blindness every year in the United States alone.1 The risk of developing diabetic retinopathy or other microvascular complications of diabetes depends on both the duration and the severity of hyperglycemia. Development of diabetic retinopathy in patients with type 2 diabetes was found to be related to both severity of hyperglycemia and presence of hypertension in the U.K. Prospective Diabetes Study (UKPDS), and most patients with type 1 diabetes develop evidence of retinopathy within 20 years of diagnosis.2,3 Retinopathy may begin to develop as early as 7 years before the diagnosis of diabetes in patients with type 2 diabetes.1 There are several proposed pathological mechanisms by which diabetes may lead …
Chiral gravity in three dimensions

Three dimensional Einstein gravity with negative cosmological constant ? 1/? 2 deformed by a gravitational Chern-Simons action with coefficient 1/? is studied in an asymptotically AdS3 spacetime. It is argued to violate unitary or positivity for generic ? due to negative-energy massive gravitons. However at the critical value ? = 1, the massive gravitons disappear and BTZ black holes all have mass and angular momentum related by ? M = J. The corresponding chiral quantum theory of gravity is conjectured to exist and be dual to a purely right-moving boundary CFT with central charges (cL,? cR) = (0,? 3? /G).
Integrated System and Process Crash Recovery in the Loris Storage Stack

In this paper, we look at two important failure classes in the storage stack: system crashes, where the whole system shuts down unexpectedly, and process crashes, where a part of the storage stack software fails due to an implementation bug. We investigate these two problems in the context of the Loris storage stack. We show how restoring metadata consistency can provide a common first step for recovery from both types of crashes. In addition, we present fine-grained and corruption-resistant data resynchronization as the second step for system crash recovery, and an in-memory roll-forward log that can provide strong guarantees as the second step for process crash recovery in a microkernel setting. We implement our findings in our Loris prototype, and implement a new crash-resistant on-device layout as part of our proof of concept. The evaluation shows that our approach provides increased reliability at a reasonable performance cost.
Scaling law and enhancement of lift generation of an insect-size hovering flexible wing

We report a comprehensive scaling law and novel lift generation mechanisms relevant to the aerodynamic functions of structural flexibility in insect flight. Using a Navier–Stokes equation solver, fully coupled to a structural dynamics solver, we consider the hovering motion of a wing of insect size, in which the dynamics of fluid–structure interaction leads to passive wing rotation. Lift generated on the flexible wing scales with the relative shape deformation parameter, whereas the optimal lift is obtained when the wing deformation synchronizes with the imposed translation, consistent with previously reported observations for fruit flies and honeybees. Systematic comparisons with rigid wings illustrate that the nonlinear response in wing motion results in a greater peak angle compared with a simple harmonic motion, yielding higher lift. Moreover, the compliant wing streamlines its shape via camber deformation to mitigate the nonlinear lift-degrading wing–wake interaction to further enhance lift. These bioinspired aeroelastic mechanisms can be used in the development of flapping wing micro-robots.
Multi-K Machine Learning Ensembles

Ensemble machine learning models often surpass single models in classification accuracy at the expense of higher computational requirements during training and execution. In this paper we present a novel ensemble algorithm called Multi-K which uses unsupervised clustering as a form of dataset preprocessing to create component models that lead to effective and efficient ensembles. We also present a modification of Multi-K that we call Multi-KX that incorporates a metalearner to help with ensemble classifications. We compare our algorithms to several existing algorithms in terms of classification accuracy and computational speed.
Evolutionary potential of (beta/alpha)8-barrels: in vitro enhancement of a "new" reaction in the enolase superfamily.

The repertoire of reactions in the mechanistically diverse enolase superfamily is the result of divergent evolution that conserved enolization of a carboxylate anion substrate but allowed different overall reactions using different substrates. Details of the pathways for the natural evolutionary process are unknown, but the events reasonably involve (1) incremental increases in the level of the "new" reaction that would provide a selective advantage and (2) an accompanying loss of the "old" reaction catalyzed by the progenitor. In an effort to better understand the molecular processes of divergent evolution, the D297G mutant of the l-Ala-d/l-Glu epimerase (AEE) from Escherichia coli was designed so that it could bind the substrate for the o-succinylbenzoate synthase (OSBS) reaction and, as a result, catalyze that reaction [Schmidt, D. M. Z. , Mundorff, E. C. , Dojka, M. , Bermudez, E. , Ness, J. E. , Govindarajan, S. , Babbitt, P. C. , Minshull, J., and Gerlt, J. A. (2003) Biochemistry 42, 8387-8393]. The AEE progenitor did not catalyze the OSBS reaction, but the D297G mutant catalyzed a low level of the OSBS reaction (k(cat), 0.013 s(-)(1); K(m), 1.8 mM; k(cat)/K(m), 7.4 M(-)(1) s(-)(1)) that was sufficient to permit anaerobic growth by an OSBS-deficient strain of E. coli; the level of the progenitor's natural AEE reaction was significantly diminished. Using random mutagenesis and an anaerobic metabolic selection, we now have identified the I19F substitution as an additional mutation that enhances both growth of the OSBS-deficient strain and the kinetic constants for the OSBS reaction (k(cat), 0.031 s(-)(1); K(m), 0.34 mM; k(cat)/K(m), 90 M(-)(1) s(-)(1)). Several other substitutions for Ile 19 also enhanced the level of the OSBS reaction. All of the substitutions substantially decreased the level of the AEE reaction from that possessed by the D297G progenitor. The changes in the kinetic constants for both the OSBS and AEE reactions are attributed to a readjustment of substrate specificity so that the substrate for the OSBS reaction is more productively presented to the conserved acid/base catalysts in the active site. These observations support our hypothesis that evolution of "new" functions in the enolase superfamily can occur simply by changes in specificity-determining residues.
Phosphorylation of Mixed Lineage Leukemia 5 by Cdc2 Affects Its Cellular Distribution and Is Required for Mitotic Entry*

The human mixed lineage leukemia-5 (MLL5) gene is frequently deleted in myeloid malignancies. Emerging evidence suggests that MLL5 has important functions in adult hematopoiesis and the chromatin regulatory network, and it participates in regulating the cell cycle machinery. Here, we demonstrate that MLL5 is tightly regulated through phosphorylation on its central domain at the G2/M phase of the cell cycle. Upon entry into mitosis, the phosphorylated MLL5 delocalizes from condensed chromosomes, whereas after mitotic exit, MLL5 becomes dephosphorylated and re-associates with the relaxed chromatin. We further identify that the mitotic phosphorylation and subcellular localization of MLL5 are dependent on Cdc2 kinase activity, and Thr-912 is the Cdc2-targeting site. Overexpression of the Cdc2-targeting MLL5 fragment obstructs mitotic entry by competitive inhibition of the phosphorylation of endogenous MLL5. In addition, G2 phase arrest caused by depletion of endogenous MLL5 can be compensated by exogenously overexpressed full-length MLL5 but not the phosphodomain deletion or MLL5-T912A mutant. Our data provide evidence that MLL5 is a novel cellular target of Cdc2, and the phosphorylation of MLL5 may have an indispensable role in the mitotic progression.
Getting Things Done on Computational RFIDs with Energy-Aware Checkpointing and Voltage-Aware Scheduling

Computational RFIDs (CRFIDs) provide flexible, general-purpose computation on a microcontroller via energy that is harvested and stored in capacitors rather than batteries. Our contributions include a definition of CRFIDs, a framework for energy management in CRFIDs, and the preliminary design of Mementos, a medley of compile-time and run-time techniques to achieve effective forward progress of computation on CRFIDs by using energy-aware computational checkpoints and voltage-aware program reordering that maintains program semantics. Our preliminary measurements indicate that Mementos will enable CRFIDs to complete long-running computations despite constant interruptions to power.
A Probabilistic Generative Model for an Intermediate Constituency-Dependency Representation

We present a probabilistic model extension to the Tesniere Dependency Structure (TDS) framework formulated in (Sangati and Mazza, 2009). This representation incorporates aspects from both constituency and dependency theory. In addition, it makes use of junction structures to handle coordination constructions. We test our model on parsing the English Penn WSJ treebank using a re-ranking framework. This technique allows us to efficiently test our model without needing a specialized parser, and to use the standard evaluation metric on the original Phrase Structure version of the treebank. We obtain encouraging results: we achieve a small improvement over state-of-the-art results when re-ranking a small number of candidate structures, on all the evaluation metrics except for chunking.
Interference in DNA Replication Can Cause Mitotic Chromosomal Breakage Unassociated with Double-Strand Breaks

Morphological analysis of mitotic chromosomes is used to detect mutagenic chemical compounds and to estimate the dose of ionizing radiation to be administered. It has long been believed that chromosomal breaks are always associated with double-strand breaks (DSBs). We here provide compelling evidence against this canonical theory. We employed a genetic approach using two cell lines, chicken DT40 and human Nalm-6. We measured the number of chromosomal breaks induced by three replication-blocking agents (aphidicolin, 5-fluorouracil, and hydroxyurea) in DSB-repair-proficient wild-type cells and cells deficient in both homologous recombination and nonhomologous end-joining (the two major DSB-repair pathways). Exposure of cells to the three replication-blocking agents for at least two cell cycles resulted in comparable numbers of chromosomal breaks for RAD54−/−/KU70−/− DT40 clones and wild-type cells. Likewise, the numbers of chromosomal breaks induced in RAD54−/−/LIG4−/− Nalm-6 clones and wild-type cells were also comparable. These data indicate that the replication-blocking agents can cause chromosomal breaks unassociated with DSBs. In contrast with DSB-repair-deficient cells, chicken DT40 cells deficient in PIF1 or ATRIP, which molecules contribute to the completion of DNA replication, displayed higher numbers of mitotic chromosomal breaks induced by aphidicolin than did wild-type cells, suggesting that single-strand gaps left unreplicated may result in mitotic chromosomal breaks.
Local observability and controllability of nonlinear discrete-time fractional order systems based on their linearisation

ABSTRACT The concepts of local controllability and observability of nonlinear discrete-time systems with the Caputo-, Riemann–Liouville- and Grünwald–Letnikov-type h-difference fractional order operators are studied. The Implicit Function Theorem is used in order to show that the nonlinear systems are locally observable or controllable in a finite number of steps if their linear approximations are observable or controllable, respectively, in the same number of steps.
Application of Support Vector Machine to Predicting Mechanical Properties of TC4

On the basis of numerous experimental results the effect of heat treatment on mechanical properties of TC4 alloy is studied. A computer model expressing the relationships between heat treatment and mechanical properties has been established with supported vector machine method. The input parameters were determined by the heating temperature and heating time which are important factors of the mechanical performance, and the output parameters are tensile and yield strength and elongation. The model is established by libsvm with RBF kernel function, e-SVR and proper parameters. Experimental results show that prediction accuracy made by using support vector machine reached over 95%, and the model has good learning precision and generalization and it can be used for predicting the mechanical properties of TC4 alloy.
Understanding the structure/property/processing inter-relationships in organic semiconducting blends

Over the last few years organic semiconductors have seen a dramatic rise in interest from both academia and industry alike. This has been largely due to their promise of low-cost, highthroughput manufacture, combined with many other positive attributes including their: flexibility; semi-transparency and light-weight nature. This combination of factors show that organic semiconductors hold strong potential to compete with inorganic technologies in a number of existing and emerging applications. More specifically, blends comprised of a number organic semiconductors offer significant promise for devices such as organic photovoltaics (OPVs) and organic light emitting diodes (OLEDs), as tuning the chemical nature of the constituting materials can influence the blend’s optoelectronic properties. However, during processing, such as blending, complex mixture of phases are formed which renders understanding these systems challenging. This thesis examines the relationships between the three critical aspects that affect organic semiconducting blends, namely: the processing route selected, the resulting microstructure and, as a consequence, the induced optoelectronic properties. A more comprehensive understanding is developed of how the processing route (solution casting from common solvent vs. bilayer fabrication via lamination) can affect the structural formation processes in organic semiconductor systems, such as crystallisation, vitrification etc. Additionally, this thesis elucidates how the structural formation processes influence the mixture of phases that evolve and discusses how the microstructure that is created affects the photo-physical processes such as exciton quenching and charge generation, within these systems. The results within this thesis highlight the sensitive interplay between the three areas of structure, property and processing. Clear insights into how to manipulate these aspects to positively impact the photo-physical processes are conferred. The findings discussed here give, thus, clear guidelines as to how to further enhance understanding and terminally improve the performance of devices such as organic solar cells.
Fate agent evolutionary algorithms with self-adaptive mutation

Fate Agent EAs form a novel flavour or subclass in EC. The idea is to decompose the main loop of traditional evolutionary algorithms into three independently acting forces, implemented by the so-called Fate Agents, and create an evolutionary process by injecting these agents into a population of candidate solutions. This paper introduces an extension to the original concept, adding a mechanism to self-adapt the mutation of the Breeder Agents. The method improves the behaviour of the original Fate Agent EA on dynamically changing fitness landscapes.
Iodine status in the Nordic countries – past and present

Background Adequate iodine nutrition is dependent on ground water content, seafood, and, as many countries use iodized cow fodder, dairy products. In most countries, salt fortification programs are needed to assure adequate iodine intake. Objectives The objectives are threefold: 1) to describe the past and present iodine situation in the Nordic countries, 2) to identify important gaps of knowledge, and 3) to highlight differences among the Nordic countries’ iodine biomonitoring and fortification policies. Design Historical data are compared with the current situation. The Nordic countries’ strategies to achieve recommended intake and urine iodine levels and their respective success rates are evaluated. Results In the past, the iodine situation ranged from excellent in Iceland to widespread goiter and cretinism in large areas of Sweden. The situation was less severe in Norway and Finland. According to a 1960 World Health Organization (WHO) report, there were then no observations of iodine deficiency in Denmark. In Sweden and Finland, the fortification of table salt was introduced 50–75 years ago, and in Norway and Finland, the fortification of cow fodder starting in the 1950s helped improve the population's iodine status due to the high intake of milk. In Denmark, iodine has been added to household salt and salt in bread for the past 15 years. The Nordic countries differ with regard to regulations and degree of governmental involvement. There are indications that pregnant and lactating women, the two most vulnerable groups, are mildly deficient in iodine in several of the Nordic countries. Conclusion The Nordic countries employ different strategies to attain adequate iodine nutrition. The situation is not optimal and is in need of re-evaluation. Iodine researchers, Nordic national food administrations, and Nordic governmental institutions would benefit from collaboration to attain a broader approach and guarantee good iodine health for all.
Physical activity classification using body-worn inertial sensors in a multi-sensor setup

Physical inactivity significantly impacts personal health, reduces quality of life, and often leads to mobility disorders, diabetes, and cardiovascular disease. Monitoring daily life activities by means of wearable inertial sensors can provide valuable feedback necessary to improve the quality of daily life and prevent the development of mobility disorders caused by physical inactivity. In this study, a physical activity classification (PAC) algorithm was developed and tested using an inertial sensor-based dataset. The dataset was acquired from multiple inertial sensors, each mounted at a different body location, and consists of various Activities of Daily Living (ADL). Data from nineteen healthy young subjects were analyzed. Time- and frequency-domain features from raw 3D accelerometer and 3D gyroscope signals were computed by performing windowing of the time series data. The K-nearest neighbors (KNN) pattern recognition algorithm was used to classify thirteen different ADLs and was evaluated by a 10-fold cross-validation. The proposed PAC algorithm outperformed the existing algorithm validated using the same dataset, with an overall mean classification rate (sensitivity) of 97.38%. This paper discusses the limitations of this study and proposes ways to overcome said limitations in order to make the PAC algorithm more effective in real-life conditions.
A risk-based contingency selection method for SPS applications

In current power system operations, transmission networks have been operated at their limits much more frequently and for much longer periods of time. Special protection systems (SPS) are attractive for increasing transmission capacity in a competitive market, but the installation costs and system reliability issues are important. In this letter, a risk-based method is proposed to take the uncertainty of contingency occurrence and impacts into account to provide an essential set of contingency cases for SPS implementation.