Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel system for spatial and temporal imaging of intrinsic plant water use efficiency

Instrumentation and methods for rapid screening and selection of plants with improved water use efficiency are essential to address current issues of global food and fuel security. A new imaging system that combines chlorophyll fluorescence and thermal imaging has been developed to generate images of assimilation rate (A), stomatal conductance (g s), and intrinsic water use efficiency (WUEi) from whole plants or leaves under controlled environmental conditions. This is the first demonstration of the production of images of WUEi and the first to determine images of g s from themography at the whole-plant scale. Data are presented illustrating the use of this system for rapidly and non-destructively screening plants for alterations in WUEi by comparing Arabidopsis thaliana mutants (OST1-1) that have altered WUEi driven by open stomata, with wild-type plants. This novel instrument not only provides the potential to monitor multiple plants simultaneously, but enables intra- and interspecies variation to be taken into account both spatially and temporally. The ability to measure A, g s, and WUEi progressively was developed to facilitate and encourage the development of new dynamic protocols. Images illustrating the instrument’s dynamic capabilities are demonstrated by analysing plant responses to changing photosynthetic photon flux density (PPFD). Applications of this system will augment the research community’s need for novel screening methods to identify rapidly novel lines, cultivars, or species with improved A and WUEi in order to meet the current demands on modern agriculture and food production.
MicroRNA-182 prevents vascular smooth muscle cell dedifferentiation via FGF9/PDGFRβ signaling

The abnormal phenotypic transformation of vascular smooth muscle cells (SMCs) causes various proliferative vascular diseases. MicroRNAs (miRNAs or miRs) have been established to play important roles in SMC biology and phenotypic modulation. This study revealed that the expression of miR-182 was markedly altered during rat vascular SMC phenotypic transformation in vitro. We aimed to investigate the role of miR-182 in the vascular SMC phenotypic switch and to determine the potential molecular mechanisms involved. The expression of miR-182 gene was significantly downregulated in cultured SMCs during dedifferentiation from a contractile to a synthetic phenotype. Conversely, the upregulation of miR-182 increased the expression of SMC-specific contractile genes, such as α-smooth muscle actin, smooth muscle 22α and calponin. Additionally, miR-182 overexpression potently inhibited SMC proliferation and migration under both basal conditions and under platelet-derived growth factor-BB stimulation. Furthermore, we identified fibroblast growth factor 9 (FGF9) as the target gene of miR-182 for the phenotypic modulation of SMCs mediated through platelet-derived growth factor receptor β (PDGFRβ) signaling. These data suggest that miR-182 may be a novel SMC phenotypic marker and a modulator that may be used to prevent SMC dedifferentiation via FGF9/PDGFRβ signaling.
TESNA : A Tool for Detecting Coordination Problems

Detecting problems in coordination can prove to be very difficult. This is especially true in large globally distributed environments where the Software Development can quickly go out of the Project Manager’s control. In this paper we outline a methodology to analyse the socio-technical coordination structures. We also show how this can be made easier with the help of a tool called TESNA that we have developed.
Semidefinite Relaxations for MIMO Transmissions With High-Order QAM Constellations

In this letter, simple semidefinite relaxations are proposed for the detection of high-order quadrature amplitude modulations in multiple-input–multiple-output systems. The detector is based on the addition of several convex and concave quadratic inequality constraints into the maximum-likelihood detector before relaxing the problem into a convex one. Combined with a randomized sampling procedure, it is shown that the performance and worst-case computational complexity of the proposed approach makes it very competitive against existing detectors in large problem sizes.
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).
Unconventional futures: anticipation, materiality, and the market in oil shale development

This thesis offers a political geography of unconventional energy development through a study of a particular fossil fuel resource called oil shale. Having long occupied a critical place in the politics and economy of certain states, most notably in Estonia, oil shale is now widely known as an ‘unconventional’ resource that is yet to become technically possible, commercially viable and socially acceptable to exploit. Following the movement through which oil shale becomes both unconventional and conventional, the thesis traces the resource through a series of geo-scientific, economic and political interventions. This study is based on analysis of technical literature and policy documents along with ethnographic fieldwork, interviews, and site visits conducted in Estonia, Colorado, Utah, Jordan, London and Brussels. Drawing together relational accounts of natural resources in political ecology and economic geography with insights from Science and Technology Studies, this project both contributes to critical research on the carbon economy and to recent debates on the concepts of materiality, anticipation, and marketization in social sciences. The thesis proposes a relational conceptualization of resource materiality, situating oil shale in multiple and conflicting forms which derive from geographically disparate practices in both resource assessment and technological development. The future of oil shale exploitation is not pre-determined by the process of global resource decline, nor is it precluded by international demands to move towards lower-carbon futures. Rather, it is determined through the conjunction of different future-oriented economic and political calculations that are entangled with resource materials and associated technological systems. Developing a non-essentialist account of markets as socio-technically distributed arrangements, the thesis argues that these rival calculations influence the design of market rules for both energy and emissions trading. The thesis concludes that what counts as ‘unconventional’ is not given, but continues to be both created and contested at the same time as it is ‘conventionalized’.
10 x 30 GHz pulse train generation from semiconductor amplifier fiber ring laser

A multiwavelength, fiber ring laser source, is demonstrated. It generates 10 wavelength channels, simultaneously mode-locked and synchronized at 30 GHz, each producing 7-ps pulses. The mode-locking technique relies on the gain saturation of the semiconductor amplifier from an external optical pulse train to impose the simultaneous mode-locking of the 10 wavelengths.
The effect of decoupling olfactory and visual stimuli on the foraging behavior of Manduca sexta

SUMMARY Within an appetitive context, Manduca sexta, a nectivorous nocturnal hawkmoth, can be attracted by a range of stimuli including floral volatiles and visual display, carbon dioxide and water vapor. Several studies on this and other flower-visiting insects have shown how olfactory and visual stimulation play (or do not play) a role in attraction and feeding. Nevertheless, these studies have consistently manipulated stimuli in a `presence–absence' manner. Here, we experimentally decoupled the presentation of both stimuli spatially and temporally in a wind tunnel, rather than entirely eliminating either one, and found that the decision-making process based on these stimuli is more flexible and complex than previously asserted. Manduca sexta was most responsive when both cues were present and emanated from the same source. When stimuli were spatially separated, responsiveness levels were comparable to those elicited by a single stimulus. However, transient olfactory stimulation either before or after visually guided approach (temporal decoupling) enhanced responsiveness to an odorless visual target. Additionally, searching times were increased by either a transient olfactory stimulation before take-off or by having the flower model spatially separated from the odor source tracked by the moths. Finally, in a dual-choice experiment, moths showed a strong bias for the visual display over the odor plume, suggesting the former to be the ultimate indicator of a nectar source. Our manipulation of floral cues shows that the feeding behavior of M. sexta, and probably of other nectivorous insects, is based not only on the sensory stimulation per se but also on the temporal and spatial pattern in which these stimuli are perceived.
Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo

Background The eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed.
Optimal planning for optical transport networks

In optical transport networks, recent development of new technologies has led to highly accelerated (‘disruptive’) increases in the capacity associated with a given investment cost. As a result, there have been dramatic decreases in the cost per unit of transport. We describe a nonlinear mixed–integer planning model that assumes both the continuous emergence of new systems and a constant–elasticity demand function. Optimization of the model with respect to price and technology acquisitions over time suggests that, with high elasticity and steeply dropping technology costs, a carrier will maximize net present value by frequently deploying new systems. This conclusion is in sharp contrast to the analogous results for voice networks, where demand is much less elastic and the rate of technology change is much slower.
An experimental investigation on elliptical instability of a strongly asymmetric vortex pair in a stable density stratification

Abstract. We investigate the elliptical instability of a strongly asymmetric vortex pair in a stratified fluid, generated by the acceleration and deceleration of the rotation of a single flap. The dominant parameter is the Froude number, Fr = U/(NR) , based on the maximum azimuthal velocity, U , and corresponding radius, R , of the strongest vortex, i.e. the principal vortex, and buoyancy frequency N . For Fr >1, both vortices are elliptically unstable while the instability is suppressed for Fr
Production Forecasting of Coalbed Methane Wells Based on Type-2 Fuzzy Logic System

Coal bed methane (CBM) reservoir production is controlled by a large set of parameters: geology, tectonics, reservoir, completion and operation. Its simulation process is complicated, relative information is difficult to be obtained, so it is necessary to analyze accurately coal bed gas potential production capacity by adopting other mathematics methods in case of incomplete information. Regarding this problem, a new type-2 fuzzy logic system (T2FLS) method to predict CBM production capacity is proposed in this paper. Methods analyze and assess input parameters of T2FLS by integrating qualitative analysis method and quantitative assessment method (Fuzzy cluster analysis and grey correlation degree analysis). Output parameters include cumulative average gas production, peak gas rate and time to achieve a peak rate. T2FLS production forecast method is applied to CBM wells of Hancheng mine and verification results show that such prediction results are highly consistent with the variation of the CBM well production. The proposed method required less data. The comparison of this method with the existed method (ANN, T1FLS) shows that the proposed method has notable advantage in generalization, stability and consistency.
Bank-Firm Relationships and the Survival of Non-Financial Firms During the Financial Crisis 2008-2009

Utilising a unique data set with annual accounts from around 37,000 Danish non-financial firms spanning almost one and a half decade, we offer microeconometric evidence on bankfirm relationships and the survival of firms during the financial crisis 2008-9. Within the framework of accounting-based credit-scoring models we find that the probability of default during the crisis was significantly higher for firms with a JEL Classification: E44, G21, G33
Mapping Tasks to Processors in Heterogeneous Multiprocessor Architectures: The MATEHa Algorithm

An automatic task-to-processor mapping algorithm is analyzed in parallel systems that run over loosely coupled distributed architectures. This research is based on the TTIGHa model that allows predicting parallel application performance running over heterogeneous architectures. In particular, the heterogeneity of both processors and communications is taken into consideration. From the results obtained with the TTIGHa model, the MATEHa algorithm for task-to-processors assignment is presented and its implementation is analyzed. Experimental results working on subsets of two-cluster heterogeneous machines are presented, analyzing the resulting mapping scheme with MATEHa and two previous mapping methods: MATE and HEFT. Finally, the algorithm robustness is considered based on the variation of model parameters: inter-process communication times and processing times.
Systems Based Study of the Therapeutic Potential of Small Charged Molecules for the Inhibition of IL-1 Mediated Cartilage Degradation

Inflammatory cytokines are key drivers of cartilage degradation in post-traumatic osteoarthritis. Cartilage degradation mediated by these inflammatory cytokines has been extensively investigated using in vitro experimental systems. Based on one such study, we have developed a computational model to quantitatively assess the impact of charged small molecules intended to inhibit IL-1 mediated cartilage degradation. We primarily focus on the simplest possible computational model of small molecular interaction with the IL-1 system—direct binding of the small molecule to the active site on the IL-1 molecule itself. We first use the model to explore the uptake and release kinetics of the small molecule inhibitor by cartilage tissue. Our results show that negatively charged small molecules are excluded from the negatively charged cartilage tissue and have uptake kinetics in the order of hours. In contrast, the positively charged small molecules are drawn into the cartilage with uptake and release timescales ranging from hours to days. Using our calibrated computational model, we subsequently explore the effect of small molecule charge and binding constant on the rate of cartilage degradation. The results from this analysis indicate that the small molecules are most effective in inhibiting cartilage degradation if they are either positively charged and/or bind strongly to IL-1α, or both. Furthermore, our results showed that the cartilage structural homeostasis can be restored by the small molecule if administered within six days following initial tissue exposure to IL-1α. We finally extended the scope of the computational model by simulating the competitive inhibition of cartilage degradation by the small molecule. Results from this model show that small molecules are more efficient in inhibiting cartilage degradation by binding directly to IL-1α rather than binding to IL-1α receptors. The results from this study can be used as a template for the design and development of more pharmacologically effective osteoarthritis drugs, and to investigate possible therapeutic options.
Real-time scheduling interfaces and contracts for the design of distributed embedded systems

A notion of interfaces based on regular languages for modelling and verification of real-time scheduling constraints was proposed in [5]. This initial notion considers task sets running on single resources, and simple deadline requirements. We extend the approach to enable support for complex task models running on systems with multiple resources. We show that this extension preserves all properties of the original notion. In addition, this extension gives rise to the application of our interfaces in the design of more complex systems, where components can be spread over distributed architectures. The work is complemented by an initial implementation that performs scheduling analysis for a relevant class of real-time interfaces. It actually constructs an interface for a system model if it satisfies a set of given real-time requirements.
Multi-view gait recognition based on tensor analysis

In this paper, we have proposed a tensor analysis method for multi-view gait recognition. Gait Energy Image (GEI) is used for gait feature and then 4-order tensor is composed. Using a generalized singular value decomposition method-HOSVD, this tensor is decomposed to person subspace, series subspace, view subspace and feature subspace. In person subspace we finish the multi-view gait recognition. Lastly, we perform recognition by using a simple nearest neighbor rule. Experimental results on the widely used CASIA-B gait database demonstrate the effectiveness of the proposed method.
Multi-App Security Analysis with FUSE: Statically Detecting Android App Collusion

Android's popularity has given rise to myriad application analysis techniques to improve the security and robustness of mobile applications, motivated by the evolving adversarial landscape. These techniques have focused on identifying undesirable behaviors in individual applications, either due to malicious intent or programmer error. We present a collection of tools that provide a static information flow analysis across a set of applications, showing a holistic view of all the applications destined for a particular device. The techniques we present include a static binary single-app analysis, a security lint tool to mitigate the limits of static binary analysis, a multi-app information flow analysis, and an evaluation engine to detect information flows that violate specified security policies. We show that our single-app analysis is comparable with the leading approaches on the DroidBench benchmark suite; we present a brief listing of lint-like heuristics used to show the limits of the single-app analysis in the context of an application; we present a multi-app analysis, and demonstrate information flows that cannot be detected by single-app analyses; and we present a policy evaluation engine to automatically detect violations in collections of Android apps.
Assessing Elementary School Students' Conceptions of Engineering and Technology

As our society becomes increasingly dependent on engineering and technology, it is more important than ever that our citizens are technologically literate. There are many possible ways to develop technological literacy—one of the most wide-reaching is through K-12 schools. The Museum of Science, Boston is working to create curricular materials and professional development for K-12 students and teachers. However, previous research in science has evinced that responsible curriculum development draws upon and is shaped by students’ conceptions and misconceptions (Posner, Strike, Hewson, & Gertzog, 1982).
Critically loaded k-limited polling systems with switch-over times

We consider a two-queue polling model with switch-over times and k-limited service (serve at most ki customers during one visit period to queue i) in each queue. The major benefit of the k-limited service discipline is that it - besides bounding the cycle time - effectuates prioritization by assigning different service limits to different queues. System performance is studied in the heavy-traffic regime, in which one of the queues becomes critically loaded with the other queue remaining stable. By using a singular-perturbation technique, we rigorously prove heavy-traffic limits for the joint queue-length distribution. Moreover, it is observed that an interchange exists among the first two moments in service and switch-over times such that the HT limits remain unchanged.