Miracle-dz/UniFAR-FTUs huggingface dataset:
Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity

Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity.
Writer Identification Using an Alphabet of Contour Gradient Descriptors

This paper presents a new method for writer identification, which emulates the approach taken by forensic document examiners. It combines a novel feature, which uses contour gradients to capture local shape and curvature, with character segmentation to create a pseudo-alphabet for a given handwriting sample. A distance metric is then defined between elements of these alphabets that captures character similarity between two handwriting samples. This approach achieves a Top-1 identification rate of 96.5% on the benchmark IAM dataset, reducing the error rate of previous approaches by 50%.
Sharp Retrenchment , Modulated Refinement and Punctured Simulation

Sharp retrenchment is introduced and briefly justified informally, as a liberalisation of refinement. In sharp retrenchment the relationship between an abstract operation and its concrete counterpart is mediated by extra predicates, allowing most particularly the description of nonrefinement-like properties, and the mixing of I/O and state aspects in the passage between levels of abstraction. Sharp retrenchments are briefly contrasted with unsharp ones. Sharp retrenchments are shown to have a natural law of composition, and the way in which refinements may be viewed as sharp retrenchments is discussed. Modulated refinement is introduced as a version of refinement allowing mixing of I/O and state aspects, in order to facilitate comparison between sharp retrenchment and refinement, and various notions of simulation are considered in this context, specifically: stepwise simulation, the ability of simulator to mimic a sequence of execution steps of the simulatee; strong simulation, in which states and step labels are mapped independently between simulatee and simulator; and the refinement notion itself. Special cases of sharp retrenchment are shown to possess various subsets of these simulation properties, and the extent to which sharp retrenchments contain refinements within them is addressed. Punctured simulation is introduced to cover cases where a concrete execution contains steps not simulable by the abstract system, and a number of maximality results about such punctured simulations are proved. The details of the theory are worked out for the B-Method, though the applicability of the underlying ideas is not limited to just that formalism.
SmartTunnel : A Multipath Approach to Achieving Reliability in the Internet

Reliability is critical to a variety of network applications. Unfortunately, due to lack of QoS support across ISP boundaries, it is difficult to achieve even two 9s (99%) reliability in today’s Internet. In this paper, we propose SmartTunnel, an end-to-end approach to achieving reliability. A SmartTunnel is a logical point-to-point tunnel between two end points that spans multiple physical network paths. It achieves reliability by strategically allocating traffic onto multiple paths and performing FEC coding. Such an end-to-end approach requires no explicit QoS support from intermediate ISPs, and is therefore easy to deploy in today’s Internet. To fully realize the potential of SmartTunnel, we analytically derive the near-optimal traffic allocation schemes that minimize loss rates. We extensively evaluate our approach using trace-driven simulations, ns-2 simulations, and experiments on PlanetLab. Our results clearly demonstrate that SmartTunnel is effective in achieving high reliability.
Kenyan coffee sector outlook : a framework for policy analysis

This paper examines recent trends in the Kenyan coffee sub-sector and evaluates production and export prospects for Kenyan coffee under several scenarios. In evaluating the long-term prospects for the Kenyan coffee subsector, scenarios with respect to important factors such as the potential yields and adoption rates of a new high-yielding variety and forecasts of international coffee prices have been considered. Secifically, the paper describes recent trends in Kenyan coffee production, consumption, exports, stocks, yields and prices and compares the performances of the estate and smallholder sectors within that context. It further describes the characteristics of coffee production in the estate and smallholder sectors, covering topics such as costs of production, quality differentials and government policies. The report also models coffee production in the estate and smallholder sectors using the vintage capital approach and describes projections of Kenyan coffee production from them. In that vein, the report examines the prospects for Kenya's coffee exports with the focus on the International Coffee Agreement and, in particular, the outlook for the Agreement's export quota system and Kenya's likely quota allotment.
Multicenter evaluating of a commercially available PCR assay for diagnosing enterovirus infection in a panel of cerebrospinal fluid specimens

Thirteen laboratories participated in blind tests of a panel of 20 coded cerebrospinal fluid specimens (7 uninfected samples, 3 samples infected with 1 50% tissue culture infective dose [TCID50]/0.1 ml [nonenterovirus strains], and 10 samples infected with 10, 1, or 0.1 TCID50/0.1 ml [three different enterovirus serotypes]) on the Amplicor enterovirus PCR assay (Roche Diagnostic Systems). The panel was also evaluated by in-house PCR (two nested-PCR and three one-step PCR assay) or tissue culture (eight laboratories). The viral load was shown to influence greatly the sensitivity of the assay. The average sensitivity of the Amplicor test ranged from 67 to 98% for viral titers of 1 to 10 TCID50/0.1 ml, respectively; titers of 0.1 TCID50/0.1 ml resulted in a sensitivity of only 16%. The overall specificity of the Amplicor test was 98%. The Amplicor assay compared favorably to the five in-house PCR tests (no significant difference in either sensitivity or specificity) and was much more sensitive than tissue culture (P < 0.001), even for high viral loads. It was easy to perform, rapid (about 6 h), well-standardized, and appeared to be suitable for the diagnosis of enterovirus meningitis on a routine basis in laboratories trained in molecular biology techniques.
NCAM Is Essential for Axonal Growth and Fasciculation in the Hippocampus

The neural cell adhesion molecule (NCAM), probably the best characterized and most abundant cell adhesion molecule on neurons, is thought to be a major regulator of axonal growth and pathfinding. Here we present a detailed analysis of these processes in mice deficient for all NCAM isoforms, generated by gene targeting. The hippocampal mossy fiber tract shows prominent expression of polysialylated NCAM and the generation of new axonal projections throughout life. Focusing on this important intrahippocampal connection, we demonstrate that in the absence of NCAM, fasciculation and pathfinding of these axons are strongly affected. In addition we show alterations in the distribution of mossy fiber terminals. The phenotype is more severe in adult than in young animals, suggesting an essential role for NCAM in the maintenance of plasticity in the mature nervous system.
A new factorization and structure for cosine modulated filter banks with variable system delay

A new design method for biorthogonal modulated filter banks is presented. It is based on a cascade of simple matrices, and it has some properties that have not been reported before. It represents filter banks with arbitrary overall system delay and filter length, it is shown that almost all cosine modulated filter banks can be described by this structure, and that it leads to a more efficient implementation than previous structures. Imposing certain symmetries on the matrices can be used to design low delay filter banks with identical (except for the sign) baseband impulse responses for the analysis and synthesis filter bank.
Binding of Equine Infectious Anemia Virus Rev to an Exon Splicing Enhancer Mediates Alternative Splicing and Nuclear Export of Viral mRNAs

ABSTRACT In addition to facilitating the nuclear export of incompletely spliced viral mRNAs, equine infectious anemia virus (EIAV) Rev regulates alternative splicing of the third exon of thetat/rev mRNA. In the presence of Rev, this exon of the bicistronic RNA is skipped in a fraction of the spliced mRNAs. In this report, the cis-acting requirements for exon 3 usage were correlated with sequences necessary for Rev binding and transport of incompletely spliced RNA. The presence of a purine-rich exon splicing enhancer (ESE) was required for exon 3 recognition, and the addition of Rev inhibited exon 3 splicing. Glutathione-S-transferase (GST)-Rev bound to probes containing the ESE, and mutation of GAA repeats to GCA within the ESE inhibited both exon 3 recognition in RNA splicing experiments and GST-Rev binding in vitro. These results suggest that Rev regulates alternative splicing by binding at or near the ESE to block SR protein-ESE interactions. A 57-nucleotide sequence containing the ESE was sufficient to mediate Rev-dependent nuclear export of incompletely spliced RNAs. Rev export activity was significantly inhibited by mutation of the ESE or bytrans-complementation with SF2/ASF. These results indicate that the ESE functions as a Rev-responsive element and demonstrate that EIAV Rev mediates exon 3 exclusion through protein-RNA interactions required for efficient export of incompletely spliced viral RNAs.
BLOOD COAGULATION INITIATION BY A COMPLEMENT-MEDIATED PATHWAY

A variety of complement-activating substances, including inulin, immunoglobulin aggregates, bacterial endotoxins, and staphylococcal protein A, were found to initiate blood coagulation through a complement-mediated pathway. These substances markedly accelerated blood coagulation in normal rabbit blood. That this clot-promoting activity requires an intact complement system was demonstrated by an almost total lack of effect on blood from rabbits with an inherited deficiency of the sixth component of complement (C6). Small amounts of isolated C6 conferred to C6-deficient blood the ability to respond with accelerated coagulation upon activation of the complement system. In addition, it was determined that activation of complement through the previously described C3 activator system resulted in the initiation of blood coagulation. The participation of C1, C2, and C4 was not necessary.
Comparison of SQL Injection Detection and Prevention Tools based on Attack Type and Deployment Requirements

SQL injection is a type of attack which the attacker adds Structured Query Language code to a web form input box to gain access or make changes to data. SQL injection vulnerability allows an attacker to flow commands directly to a web application's underlying database and destroy functionality or confidentiality. Researchers have proposed different tools to detect and prevent this vulnerability. In this paper we present all SQL injection attack types and also different tools which can detect or prevent these attacks. Finally we compared these tools against attack types and deployment requirements. Keyword: SQL Injection Attacks, detection, prevention, tool, comparison.
Towards Automating Class-Splitting Using Betweenness Clustering

Large, unwieldy classes are a significant maintenance problem. Programmers dislike them because the fundamental logic is often obscured, making them hard to understand and modify. This paper proposes a solution - a semi-automatic technique for splitting large classes into smaller, more cohesive ones. The core of the technique is the use of betweenness clustering to identify the best way of partitioning a class. This turned a tedious manual process into a quick and simple semi-automated one in roughly one third of the cases we examined.
Entry Barriers , Reallocation , and Productivity Growth : Evidence from Japanese manufacturing firms MURAO

This paper investigates the effect of exogenous entry barriers on productivity growth, using an R&D-based endogenous growth model. Previous theoretical and empirical literature has emphasized the role of two types of reallocation on productivity growth, namely, reallocation of market shares among incumbent firms (selection channel) and firm turnover (entry/exit channel). When firms have heterogeneous innovation efficiency levels, we find that a reduction in entry costs may reduce the selection pressure on inefficient incumbents while it stimulates the entry of new firms. We incorporate entry cost and free entry condition into the model proposed by Lentz and Mortensen (2008) and estimate entry cost and other structural parameters using Japanese firm-level data. A counterfactual simulation of the reduced entry cost suggests that positive effect of stimulated entry on productivity growth outweighs the negative one of reduced selection. We also show quantitatively that increased R&D tax credits enhance productivity growth through both reallocation channels.
Affine registration with multi-scale autoconvolution

In this paper we propose a novel method for the recovery of affine transformation parameters between two images. Registration is achieved without separate feature extraction by directly utilizing the intensity distribution of the images. The method can also be used for matching point sets under affine transformations. Our approach is based on the same probabilistic interpretation of the image function as the recently introduced multi-scale autoconvolution (MSA) transform. Here we describe how the framework may be used in image registration and present two variants of the method for practical implementation. The proposed method is experimented with binary and grayscale images and compared with other non-feature-based registration methods. The experiments show that the new method can efficiently align images of isolated objects and is relatively robust.
Ý(4ôbÍ$5_@_È | ¤−"Â © h¿Âql DESIGN OF FUZZY ADAPTIVE OUTPUT-FEEDBACK CONTROLLERS AND CHAIN OBSERVERS FOR A CLASS OF SISO NONLINEAR DELAYED SYSTEMS

In this thesis, a fuzzy adaptive output feedback controllers and chain observers for a class of nonlinear delayed systems is proposed. The proposed approach do not need the availability of the state variables. The linearization approach is used to transform a nonlinear system into a linear system through Lie derivative method. We adopt an fuzzy adaptive chain observer in which no strictly positive real (SPR) condition is needed. Further, we combine a self-structuring scheme with an on-line estimation of the fuzzy parameters to reduce the dynamic order of the adaptive output-feedback fuzzy control system. The proposed observer consists of a chain of observation algorithm to reconstruct the system states at different delayed time instants (chain observer) for state prediction. Based on the Lyapunov synthesis approach, a global uniform ultimate boundedness property (UUB) of the state estimation errors and tracking errors in the closed-loop system can be achieved. According to some conditions, global exponential convergence to a bounded value for the observation error is ensured for any given delay in the measurements. Finally, an inverted pendulum system is used to illustrate the effectiveness of the proposed method.
Limited feedback designs for two-way relaying systems with physical network coding

This paper considers a limited feedback system for two-way wireless relaying channels with physical network coding (PNC). For full feedback systems, the optimal structure with the PNC has already been studied where a modulo operation is employed. In this case, phase and power of two end node channels are adjusted to maximize the minimum distance. Based on this result, we design new quantization methods for the phase and the power in the limited feedback system. By investigating the minimum distance of the received constellation, we present a codebook design to maximize the worst minimum distance. Especially, for quantization of the power for 16-QAM, a new power quantization scheme is proposed to maximize the performance. Also, utilizing the characteristics of the minimum distance observed in our code-book design, we present a power allocation method which does not require any feedback information. Simulation results confirm that our proposed scheme outperforms conventional systems with reduced complexity.
Improving EFL learners Interpretation Skills through Translation as a Teaching Technique: A Case Study of Secondary Schools , El-Gurashi Locality, Gezira State, Sudan

Translation enables learners to differentiate between L1 and L2 meanings and so it facilities language learning. This study aims at integrate translation for facilitating EFL teaching and learning, solve the problems of understanding the difficult terms and help teachers use translation in EFL classroom when the need arises. The study adopted the descriptive analytical method. The data for the study were collected by means of a questionnaire. (50) teachers from El Hasaheisa secondary schools responded to the questionnaire. Then it were analyzed by the SPSS program . The analysis the questionnaire lead to the following results: Using translation enables students to communicate meanings between the L1 and L2 culture, using translation develops learners’ interpretation, translation solves the problems of understanding L2 concepts, translation helps in memorizing L2 words and structures, translation enhances motivation to learn English, translation improves EFL learners translation skills, using translation develops learners’ fluency and through translation EFL learners can understand difficult terms and some grammatical points. Based on the previous finding, the study 5 recommends the following: Using translation should develop learners’ fluency, translation should be used for understanding only difficult concepts, translation should be practiced for understanding the accurate meaning of the contexts, using L1 in EFL classes should save class time, EFL learners should gain translation skills and translation should help learners in memorizing L2 words and structure
An efficient space partitioning technique based on linear kd-trees for collision culling

We present an efficient “broad phase” algorithm for selecting candidate collision pairs in N-body simulation. As our technique is derived from kd-trees, we first introduce some background kdtree concepts and their geometrical interpretation. Then we cover the construction of a linear kd-tree and its use in N-body simulation. We finally study its time and memory complexity, and compare the performance of an implementation with that of other algorithms (namely Sweep and Prune and Delaunay triangulation). Preliminary tests show that the linear kd-tree performs more than fifty times faster than the other methods on conventional computers, for highly dynamic simulations with a few thousand elements or more. We also conclude that simulations of several million elements are feasible on a single processor in less than five seconds per time step.
Lancaster University Management School Working Paper 2000/005 a New Look at Gender Effects in Participation and Occupation Choice a New Look at Gender Effects in Participation and Occupation Choice

©Didier Soopramanien and Geraint Johnes All rights reserved. Short sections of text, not to exceed two paragraphs, may be quoted without explicit permission, provided that full acknowledgement is given. ABSTRACT The growth in female labour particpation and occupational attainment represents the most dramatic feature of labour markets in the second half of the twentieth century. This has been due in part to developments in social attitudes and the consequent changes in the prices attached to womens' characteristics, and in part to changes in those characteristics themselves. This paper analyses these issues by constructing models of participation and occupational choice for the years 1970 and 1990, and then by evaluating which participation and occupation regimes would have been selected by respondents with the characteristics of women observed in 1970 had they faced the coefficients which obtained in 1990. It is established that changing prices accounts for a substantial part of the improvement in womens' fortunes in the labour market. To provide a basis of comparison, the model is also estimated for men. Choices concerning occupational and labour market participation are modelled using both the standard multinomial logit and the nested logit techniques. The latter, which has not previously been employed in the present context, alleviates problems due to the strong assumption in simpler models of the independence of irrelevant alternatives, and provides much additional useful information.