Miracle-dz/UniFAR-FTUs huggingface dataset:
Disturbance size and frequency mediate the coexistence of benthic spatial competitors.

Disturbance plays a key role in structuring community dynamics and is central to conservation and natural resource management. However, ecologists continue to debate the importance of disturbance for species coexistence and biodiversity. Such disagreements may arise in part because few studies have examined variation across multiple dimensions of disturbance (e.g., size, frequency) and how the effects of disturbance may depend on species attributes (e.g., competitiveness, dispersal ability). In light of this gap in understanding and accelerating changes to disturbance regimes worldwide, we used spatial population models to explore how disturbance size and frequency interact with species attributes to affect coexistence between seagrass (Zostera marina) and colonial burrowing shrimp (Neotrypaea californiensis) that compete for benthic space in estuaries throughout the west coast of North America. By simulating population dynamics under a range of ecologically-relevant disturbance regimes, we discovered that intermediate disturbance (approximately 9-23% of landscape area per year) to short-dispersing, competitively-dominant seagrass can foster long-term stable coexistence with broad-dispersing, competitively-inferior burrowing shrimp via the spatial storage effect. When holding the total extent of disturbance constant, the individual size and annual frequency of disturbance altered landscape spatial patterns and mediated the dominance and evenness of competitors. Many small disturbances favored short-dispersing seagrass by hastening recolonization, whereas fewer large disturbances benefitted rapidly-colonizing burrowing shrimp by creating temporary refugia from competition. As a result, large, infrequent disturbances generally improved the strength and stability of coexistence relative to small, frequent disturbances. Regardless of disturbance size or frequency, the dispersal ability of the superior competitor (seagrass), the competitive ability the inferior competitor (burrowing shrimp), and the reproduction and survival of both species strongly influenced population abundances and coexistence. Our results show that disturbance size and frequency can promote or constrain coexistence by altering the duration of time over which inferior competitors can escape competitive exclusion, particularly when colonization depends on the spatial pattern of disturbance due to dispersal traits. For coastal managers and conservation practitioners, our findings indicate that reducing particularly large disturbances may help conserve globally-imperiled seagrass meadows and control burrowing shrimp colonies that can threaten the viability of oyster aquaculture.
Drosophila melanogaster: a simple system for understanding complexity

ABSTRACT Understanding human gene function is fundamental to understanding and treating diseases. Research using the model organism Drosophila melanogaster benefits from a wealth of molecular genetic resources and information useful for efficient in vivo experimentation. Moreover, Drosophila offers a balance as a relatively simple organism that nonetheless exhibits complex multicellular activities. Recent examples demonstrate the power and continued promise of Drosophila research to further our understanding of conserved gene functions. Summary: This Editorial outlines how research in Drosophila has and continues to help answer complex research questions in genetics, highlighting the value of this relatively simple model organism.
Multiplex fluorescence in situ hybridisation to detect anaplastic lymphoma kinase and ROS proto-oncogene 1 receptor tyrosine kinase rearrangements in lung cancer cytological samples

Aims Several predictive biomarkers of response to specific inhibitors have become mandatory for the therapeutic choice in non-small-cell lung cancer (NSCLC). In most lung cancer patients, the biological materials available to morphological and molecular diagnosis are exclusively cytological samples and minimum tumour wastage is necessary. Multiplex fluorescence in situ hybridisation (mFISH) to detect simultaneously ALK-rearrangement and ROS1-rearrangement on a single slide could be useful in clinical practice to save cytological samples for further molecular analysis. In this study, we aim to validate diagnostic performance of multiplex ALK/ROS1 fluorescence in situ hybridisation (FISH) approach in lung adenocarcinoma cytological series compared with classic single break apart probes. Methods We collected a series of 61 lung adenocarcinoma cytological specimens enriched in tumours harbouring ALK-rearrangement and ROS1-rearrangement. ALK and ROS1 status were previously assessed by classic FISH test using single break apart probes and immunohistochemistry. Study population was composed of 6 ALK-positive, 2 ROS1-positive and 53 ALK/ROS1-wild type. All specimens were analysed by multiplex FISH assay using FlexISH ALK/ROS1 DistinguISH Probe Zytovision. Results The dual ALK/ROS1 FISH probe test results were fully concordant with the results of previous single ALK and ROS1 FISH tests on two different slides. 6 ALK-positive and 2 ROS1-positive were confirmed through multiplex FISH test, without false-positive and false-negative results. Multiplex ALK/ROS1 FISH test results agreed with immunohistochemistry assay staining results. Conclusion Multiplex ALK/ROS1 FISH probe test is a useful tool to detect simultaneously ALK-rearrangement and ROS1-rearrangement on a single slide in cytological specimens with a small amount of biomaterial.
Influence of Polyurea Composite Coating on Selected Mechanical Properties of AISI 304 Steel

This paper contains experimental results of mechanical testing of the AISI 304 steel with composite coatings. The main goal was to investigate the impact of the applied polyurea composite coating on selected mechanical properties: Adhesion, impact resistance, static behavior, and, finally, fatigue lifetime of notched specimens. In the paper the following configurations of coatings were tested: EP (epoxy resin), EP_GF (epoxy resin + glass fabric), EP_GF_HF (epoxy resin + glass fabric hemp fiber), EP_PUA (epoxy resin + polyurea) resin, EP_GF_PUA (epoxy resin + glass fabric + polyurea) resin, and EP_GF_HF_PUA (epoxy resin + glass fabric + hemp fiber + polyurea) resin. The highest value of force required to break adhesive bonds was observed for the EP_PUA coating, the smallest for the single EP coating. A tendency of polyurea to increase the adhesion of the coating to the base was noticed. The largest area of delamination during the impact test was observed for the EP_GF_HF coating and the smallest for the EP-coated sample. In all tested samples, observed delamination damage during the pull-off test was located between the coating and the metallic base of the sample.
Aqueous-Based Binary Sulfide Nanoparticle Inks for Cu2ZnSnS4 Thin Films Stabilized with Tin(IV) Chalcogenide Complexes

Cu2ZnSnS4 (CZTS) is a promising semiconductor material for photovoltaic applications, with excellent optical and electronic properties while boasting a nontoxic, inexpensive, and abundant elemental composition. Previous high-quality CZTS thin films often required either vacuum-based deposition processes or the use of organic ligands/solvents for ink formulation, which are associated with various issues regarding performance or economic feasibility. To address these issues, an alternative method for depositing CZTS thin films using an aqueous-based nanoparticle suspension is demonstrated in this work. Nanoparticles of constituent binary sulfides (CuxS and ZnS) are stabilized in an ink using tin(IV)-based, metal chalcogenide complexes such as [Sn2S6]4−. This research paper provides a systematic study of the nanoparticle synthesis and ink formulation via the enabling role of the tin chalcogenide complexing power, the deposition of high-quality CZTS thin films via spin coating and annealing under sulfur vapor atmosphere, their structural characterization in terms of nanocrystal phase, morphology, microstructure, and densification, and their resultant optoelectronic properties.
Characterizing the PRRSV nsp2 Deubiquitinase Reveals Dispensability of Cis-Activity for Replication and a Link of nsp2 to Inflammation Induction

The papain-like cysteine protease 2 (PLP2) within the N-terminus of the porcine reproductive and respiratory syndrome virus (PRRSV) nsp2 replicase protein specifies a deubiquitinating enzyme (DUB), but its biochemical properties and the role in infection have remained poorly defined. By using in vitro assays, we found that the purified PLP2 could efficiently cleave K63 and K48 linked polyubiquitin chains Ub3-7 in vitro although displaying a differential activity in converting the respective ubiquitin dimers to monomer. The subsequent mutagenesis analyses revealed that the requirement for PLP2 DUB activity surprisingly resembled that for cis-cleavage activity, as several mutations (e.g., D91R, D85R, etc.) that largely ablated the DUB function also blocked the cis- but not trans-proteolytic cleavage of nsp2/3 polyprotein. Moreover, the analyses identified key mutations that could differentiate DUB from PLP2 cis- and trans-cleavage activities. Further reverse genetics analyses revealed the following findings: (i) mutations that largely blocked the DUB activity were all lethal to the virus, (ii) a point mutation T88G that selectively blocked the cis-cleavage activity of PLP2 did not affect viral viability in cell culture, and (iii) an E90Q mutation that did not affect either of the PLP2 activities led to rescue of WT-like virus but displayed significantly reduced ability to induce TNF-α production. Our findings support the possibility that the PLP2 DUB activity, but not cis-cleavage activity, is essential for PRRSV replication. The data also establish a strong link of nsp2 to pro-inflammatory cytokine induction during infection that operates in a manner independent of PLP2 DUB activity.
Securing Data in Transit using Two Channel Communication

Securing data in transit is critically important to the Department of Defense in todays contested environments. While encryption is often the preferred method to provide security, there exist applications for which encryption is too resource intensive, not cost-effective or simply not available. In this thesis, a two-channel communication system is proposed in which the message being sent can be intelligently and dynamically split over two or more channels to provide a measure of data security either when encryption is not available, or perhaps in addition to encryption. This data spiting technique employs multiple wireless channels operating at the physical layer, allowing traditional layers above to run seamlessly over it. Eight data splitting policies are developed with preliminary evaluation of their effectiveness in combating three common cyber security threat scenarios to include eavesdropping, jamming and man-in-the-middle attacks. These policies are then implemented in a simple proof-of-concept communication system simulation. Moreover, a framework is proposed for measuring and classifying the level of integrity, confidentiality and availability that is provided by each policy. While additional discussions present and evaluate potential packet structure, more possibilities for dynamic tunability of the developed policies and any potential vulnerabilities introduced by these data splitting schemes. Lastly, a simulation test-bed is constructed to allow for implementation and testing of future policies. These data splitting techniques could provide additional options to increase data-in-transit security for unencrypted systems operating in contested environments.
The multi-step reconstruction for arbitrarily high order finite volume schemes on the unstructured grids with compact stencils

In the present paper, a multi-step reconstruction procedure is proposed for the development of high order finite volume schemes on unstructured grids using compact stencil. A recursive algorithm is proposed which can eventually provide sufficient relations for high order reconstruction in a multi-step procedure. Two key elements of this procedure are the partial inversion technique and the continuation technique. The partial inversion can be used not only to obtain lower order reconstruction based on existing reconstruction relations, but also to regularize the existing reconstruction relations to provide new relations for higher order reconstructions. The continuation technique is to extend the regularized relations on the face-neighboring cells to current cell as additional reconstruction relations. This multi-step procedure is operationally compact since in each step only the relations defined on a compact stencil are used. In the present paper, the third and fourth order finite volume schemes based on two-step quadratic and three-step cubic reconstructions are studied.
Micro-patch and community scale spatial distribution of herbaceous cover in a grazed eucalypt woodland

This study described changes in spatial distribution of herbaceous cover in experimental paddocks in a eucalypt woodland of northern Australia after 5 years of different grazing pressures and drought. Herbaceous cover was irregularly distributed, with high cover zones in distinct bands across slopes on paddocks in stable and degrading condition, and irregular patches in a degraded paddock. Size and density of these zones declined with paddock condition, as native perennial tussock grasses were lost and replaced by an exotic stoloniferous grass. Describing disturbance responses of herbaceous cover in this community requires sampling at multiple spatial scales. Crown Copyright r 2004 Published by Elsevier Ltd. All rights reserved.
The Simulation Analysis on Neck Injure in Rear-end Crash by Predicting Occupant Injury Severity Using Support Vector Machine

-This analysis study aims at investigating the connection between occupant injury severity level and occupant, vehicle, roadway, and factors on the environmental basis of support vector machine (SVM) model. The multi-layer perception (MLP) neural network model was the benchmark for evaluating the performance of SVM model. Historical crash data from 1994 to 2012 were used as the data source. The best SVM model provided an overall classification accuracy of 63.4% and 58.6% for the testing group datasets and training group datasets respectively. The performance of SVM model was compared with those of MLP models, SVM model gave satisfactory result with less datasets over-fitting. Therefore, SVM model is capable of predicting occupant injury severity levels in a rear-end crash. The finite element model of the rear-end crash simulation was determined with commercial code ANSYS/LS-DYNA. The seats and dummies were imported from software LS-PREPOST which was implemented in the model. The effects of passenger posture and distance between dummy head and headrest on neck injury were thoroughly analyzed. Results show that the two factors have certain influence on neck injury. Shorten the gap between the dummy head and headrest helps to reduce the neck injury and neck moment.
Assessing the Impact of Dominant Sequencing-Based Gene Expression Profiling Techniques ( SGEPTs ) on Phytopathogenic Fungi

The application of transcriptomics for the selection of candidate genes responsible for fungal pathogenicity or fungal-plant interactions is one of the main methods for studying the aetiology of fungal pathogenesis. The major challenge for researchers is to choose an effective technique for the analysis of transcriptomes. Sequencing-based gene expression profiling techniques (SGEPTs) are powerful tools that are used for this purpose. The analytical SGEPTs, which are well-known as extensive sequencing expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS), and a revolutionary tool known as RNA sequencing (RNA-seq) have accelerated our understanding of the molecular mechanism of fungal pathogenesis. In this review, we systematically present the methodology and technique considerations of each dominant SGEPT, highlight the application of these techniques in phytopathogenic fungal studies, and briefly consider the future sequencing platform for RNA-seq and the potential application of RNA-seq techniques in phytopathogenic fungi.
A pr 2 01 3 Phase Transition and Strong Predictability

The statistical mechanical interpretation of algorithmic information theory (AIT, for short) was introduced and developed in our former work [K. Tadaki, Local Proceedings of CiE 2008, pp.425–434, 2008], where we introduced the notion of thermodynamic quantities into AIT. These quantities arereal functions of temperature T > 0. The values of all the thermodynamic quantities diverge whenT exceeds1. This phenomenon corresponds to phase transition in statistical mechanics. In this paper we introduce the notion of strong predictability for an infinite binary sequence and then apply it to the partition function Z(T ), which is one of the thermodynamic quantities in AIT. We then reveal a new computational aspect of the phase transiti on in AIT by showing the critical difference of the behavior of Z(T ) betweenT = 1 and T < 1 in terms of the strong predictability for the base-two expansion ofZ(T ).
Municipal Separate Storm Sewer System ( MS 4 ) Practices Assessment Phase III – Reclaimed Water Areas Final Report

The Florida Stormwater Association (FSA) is acknowledged for all their efforts in facilitating the Phase III project with FDEP as well as the recruitment and management of each of the 12 Florida participating MS4s. Each of the participating MS4s is acknowledged for all of their efforts and time, many of whom were participants in the previous Phase II project. The FDEP is acknowledged for their consideration and interest in addressing the questions that were raised from Phase II and has allowed Phase II and Phase III to be the comprehensive investigation of particulate matter and nutrient recovery by common maintenance practices in the United States to date. This project would not have been possible without the efforts, interest and common vision of the FSA, FDEP and participating MS4s.
RTL Design and Implementation of Erasure Code for RAID system

Erasure codes is Error Correction scheme that converts data into codes . It is used primarily in distributed storage system for the failure of disks and its recovery. For a set of „n‟ data symbols you can have anywhere from 1 to „k‟ erasure codes generated. The value of „k‟ determines how many failures can be tolerated while still ensuring that no data is lost. Erasure codes are extended version of RAID 6 operation, which is supported through 4 input block descriptor. A study of throughput for raid engine supports Erasure codes for max 10 input buffers and 6 output buffers is optimal. Difference between RAID 6 and erasure code is that Raid 6 has 2 output parities and max 4 input sources whereas the erasure codes has 6 output parities and max 10 input sources. Erasure code is generated in turn using Galois Field (GF) Polynomial Multiplier equation of x8+x4+x3+x2+1and this gives us a prime polynomial of 0x11d. A fully symmetric erasure code allows for as many erasure tokens as data tokens. A “10 of 16” erasure code is synthesized using cadence RTL compiler for RAID system. Keywords— Erasure code, RTL, GF Multiplier, RAID system, Cadence IES Simulator,SimVison
Vehicle Re-identification in video

In this paper an approach to the vehicle re-identification problem in a multiple camera system is presented. We focused on the re-identification itself assuming that the vehicle detection problem is already solved including extraction of a full-fledged 3D bounding box. The re-identification problem is solved by using color histograms, histograms of oriented gradients by a linear regressor. The features are used in separate models in order to get the best results in the shortest CPU computation time. The proposed method works with a high accuracy (60 % true positives retrieved with 10 % false positive rate on a challenging subset of the test data) in 85 milliseconds of the CPU (Core i7) computation time per one vehicle re-identification assuming the fullHD resolution video input. The applications of this work include finding important parameters like travel time, traffic flow, or traffic information in a distributed traffic surveillance and monitoring system.
Unsupervised Activity Learning and Parsing Learned Action 1 : Selected Visual Atoms : Selected Language Atoms

Human communication typically has an underlying structure. This is reflected in the fact that in many user generated videos, a starting point, ending, and certain objective steps between these two can be identified. In this paper, we propose a method for parsing a video into such semantic steps in an unsupervised way. The proposed method is capable of providing a “semantic storyline” of the video composed of its objective steps. We accomplish this using both visual and language cues in a joint generative model. The proposed method can also provide a textual description for each of the identified semantic steps. We evaluate this method on a large number of complex YouTube videos and show results of unprecedented quality for this intricate and impactful problem.
AU THE EFFECT OF CLIMATE CHANGES VERSUS EMISSION CHANGES ON FUTURE ATMOSPHERIC LEVELS OF POPS AND Hg IN THE ARCTIC

We have investigated how predicted future changes in climate and emissions will affect atmospheric transport to the Arctic and environmental fate within the Arctic of persistent organic pollutants and mercury. We have furthermore studied the importance of the three major source areas: Europe, Asia and North America as well the importance of re-emissions from previously deposited compounds. Overall the effect of climate change on the atmospheric transport and fate of POPs and Hg to the Arctic appears to be moderate under the studied climate scenario.
Effects of Recombinant Myostatin Propeptide on Fracture Repair in a Fibula Osteotomy Model

INTRODUCTION Myostatin (GDF-8) suppresses muscle growth, development, and regeneration, and mice lacking myostatin show a significant increase in muscle mass. We have found that the receptor for myostatin, ActRIIB, is expressed in bone marrow derived stem cells, and mice lacking myostatin show increased bone density and strength. It is also known that myostatin is expressed in the fracture callus early (<48 hrs) in the healing process, but the role of myostatin in fracture repair is not clear. 3 Myostatin can circulate in an inactive form, bound to a propeptide from which it must be cleaved to form an active ligand. A recombinant myostatin propeptide effectively inhibits active myostatin in vitro and in vivo. We used a fibula osteotomy model in mice to test the hypothesis that blocking active myostatin with systemic injections of a recombinant myostatin propeptide would improve bone repair.
Predictive Analytics on Data Streams

The growing amounts of data brought about the need for transition from offline to online data processing. In our thesis, we explored the utilization of incremental and online data processing in power engineering domain, where this need is imminent because of ongoing introduction of smart metering. We designed two stream processing power demand forecasting methods, which addressed the main requirements of stream mining, i.e., accuracy, timeliness and adaptability. The third requirement relates to changes that occur in stream data over time, i.e., concept drifts. We studied two ways of adaptation of prediction model to the drifts – informed and blind, which differ in incorporation of an explicit change detection mechanism. We proposed incremental forecasting method with informed adaptation and online method with blind adaptation. Both of our approaches equaled the standard batch approaches in accuracy with less computing resources.