Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Management, Risk and the Ecosystem Approach to Fisheries

Modern-day discussions of fishery governance and management revolve around a number of key ingredients – the goals of sustainability and resilience, the widespread presence of uncertainty and complexity, the corresponding directions of a precautionary approach and an ecosystem approach, and implementation of these through avenues such as robust management. This paper explores the links among these many ingredients. In particular, robust management mechanisms aim for reasonable success in meeting societal objectives of sustainability and resilience, even given high levels of uncertainty, limited understanding of the fishery and an imperfect capability to control exploitation. This draws on both a precautionary approach and an ecosystem approach, in what is, in fact, a form of risk management: risk is reduced through design measures that shift fisheries to become more robust to the inherent structural uncertainty. Managing risk, through robust management, is a key element of fishery governance in the context of the emerging Ecosystem Approach to Fisheries (EAF), and its joint pursuit of ecosystem health, sustainable resource use and human well-being.
Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.
Full-Wave Analysis of Periodic Dielectric Frequency-Selective Surfaces Under Plane Wave Excitation

A novel full-wave method for the modal characterization of dielectric electromagnetic band-gap structures under oblique plane wave excitation is presented, showing the dielectric lattice periodicity in both the longitudinal and the transverse propagation directions. In this method, an eigenvalue problem is obtained in terms of the generalized ABCD matrix of the periodic cell, whose solution provides not only the propagation constant of the fundamental Floquet mode, but also of the higher order modes of the global periodic structure. The proposed analysis technique has been successfully validated with a commercial software based on the frequency domain finite element method. The transmittance of a finite periodic material with a finite number of unit cells has also been successfully verified through comparisons with other theoretical results reported in the technical literature. Then, our new algorithm has been used to study band-gap materials made of rectangular dielectric parallel rods, investigating the variation of the dispersion diagram and the transmission and reflection transfer functions when modifying both geometrical and electrical parameters of this structure. Finally, the response differences when a periodical defect is considered in a finite periodic arrangement have also been highlighted.
Lactococcus lactis: high‐level expression of tetanus toxin fragment C and protection against lethal challenge

To determine if the food‐grade bacterium Lactococcus lactis holds promise as a vaccine antigen delivery vector we have investigated whether this bacterium can be made to produce high levels of a heterologous protein antigen. A regulated expression system has been developed which may be generally suitable for the expression of foreign antigens (and other proteins) In L. lactis. The system utilizes the fast‐acting T7 RNA polymerase to transcribe target genes, and provides the first example of the successful use of this polymerase in a Gram‐positive bacterium. When the performance of the expression system was characterized using tetanus toxin fragment C (TTFC) up to 22% of soluble cell protein was routinely obtained as TTFC. Mice immunized subcutaneously with L. lactis expressing TTFC were protected from lethal challenge with tetanus toxin. These results show for the first time that L. lactis is able to express substantial quantities of a heterologous protein antigen and that this organism can present this antigen to the Immune system in an immunogenic form.
The advantage of arthroscopic anterior cruciate ligament reconstruction with autograft from the tendons of the semitendinosus - gracilis muscles for the recovery of the stability of the knee.

UNLABELLED Anterior cruciate ligament (ACL) injuries remain a common orthopaedic disease, particularly in young adults. The treatment of choice for ACL injuries is ACL reconstruction (ligamentoplasty). ACL reconstruction is the surgical intervention used to replace the damaged ACL with a bone-patella tendon-bone (BTB) graft or with soft parts (semitendinosus - gracilis muscles (ST-G) - a method more frequently used nowadays). MATERIALS AND METHOD In the Clinic of Orthopedics and Traumatology of the University Emergency Hospital of Bucharest, during the period 01.01. 2009 - 01.03. 2011, a number of 37 arthroscopic ACL reconstructions with ST-G were studied, performed to treat ACL isolated injuries or injuries associated with complex trauma of the knee. RESULTS Clinical studies have shown that ACL reconstruction is highly superior to ACL repair (suturing). Arthroscopy was the main method of diagnosis in 28 cases, whereas the remaining ACL injuries were diagnosed using the MRI. CONCLUSIONS The rehabilitation of the patients who underwent arthroscopic ACL reconstructions with ST-G was easier and faster in comparison with that following the surgical interventions performed with BTB graft during the previous years.
In Vivo Imaging Reveals an Essential Role for Neutrophils in Leishmaniasis Transmitted by Sand Flies

Infection with the obligate intracellular protozoan Leishmania is thought to be initiated by direct parasitization of macrophages, but the early events following transmission to the skin by vector sand flies have been difficult to examine directly. Using dynamic intravital microscopy and flow cytometry, we observed a rapid and sustained neutrophilic infiltrate at localized sand fly bite sites. Invading neutrophils efficiently captured Leishmania major (L.m.) parasites early after sand fly transmission or needle inoculation, but phagocytosed L.m. remained viable and infected neutrophils efficiently initiated infection. Furthermore, neutrophil depletion reduced, rather than enhanced, the ability of parasites to establish productive infections. Thus, L.m. appears to have evolved to both evade and exploit the innate host response to sand fly bite in order to establish and promote disease.
Methods for the efficient measurement of phased mission system reliability and component importance

An increasing number of systems operate over a number of consecutive time periods, in which their reliability structure and the consequences of failure differ, in order to perform some overall operation. Each distinct time period is known as a phase and the overall operation is known as a phased mission. Generally, a phased mission fails immediately if the system fails at any point and is considered a success only if all phases are completed without failure. The work presented in this thesis provides efficient methods for the prediction and optimisation of phased mission reliability. A number of techniques and methods for the analysis of phased mission reliability have been previously developed. Due to the component and system failure time dependencies introduced by the phases, the computational expense of these methods is high and this limits the size of the systems that can be analysed in reasonable time frames on modern computers. Two importance measures, which provide an index of the influence of each component on the system reliability, have also been previously developed. This is useful for the optimisation of the reliability of a phased mission, however a much larger number have been developed for non-phased missions and the different perspectives and functions they provide are advantageous. This thesis introduces new methods as well as improvements and extensions to existing methods for the analysis of both non-repairable and repairable systems with an emphasis on improved efficiency in the derivation of phase and mission reliability. New importance measures for phased missions are also presented, including interpretations of those currently available for non-phased missions. These provide a number of interpretations of component importance, allowing those most suitable in a given context to be employed and thus aiding in the optimisation of mission reliability. In addition, an extensive computer code has been produced that implements and tests the majority of the newly developed techniques and methods.
A new model for Context-Oriented Programs

Context-oriented programming (COP) is a new technique for programming that allows changing the context in which commands execute as a program executes. Compared to object-oriented programming (aspect-oriented programming), COP is more flexible (modular and structured). This paper presents a precise syntax-directed operational semantics for context-oriented programming with layers, as realized by COP languages like ContextJ* and ContextL. Our language model is built on Java enriched with layer concepts and activation and deactivation of layer scopes. The paper also presents a static type system that guarantees that typed programs do not get stuck. Using the means of the proposed semantics, the mathematical correctness of the type system is presented in the paper.
Interconversion of aflatoxin B1 and aflatoxicol by several fungi

Four fungal strains, namely, Aspergillus niger, Eurotium herbariorum, a Rhizopus sp. , and non-aflatoxin (AF)-producing Aspergillus flavus, which could convert AF-B1 to aflatoxicol (AFL), could also reconvert AFL to AF-B1. The interconversion of AF-B1 to AFL and of AFL to AF-B1 was ascertained to occur during proliferation of the fungi. These reactions were distinctly observed in cell-free systems obtained from disrupted mycelia of A. flavus and the Rhizopus sp. , but they were not observed in culture filtrates from intact (nondisrupted) mycelia of the same strains. The interconversion activities of AF-B1 and AFL were not observed when the cell-free systems were preheated at 100 degrees C. These findings strongly suggest that the interconversion of AF-B1 and AFL is mediated by intracellular enzymes of A. flavus and the Rhizopus sp. In addition, the isomerization of AFL-A to AFL-B observed in culture medium was also found to occur by the lowering of the culture pH.
Convergent multi-path routing

We present a protocol for maintaining multiple paths to each destination in a network of processes. For each destination, each process in the network maintains a set of neighbors which are used as next-hops to reach the destination. This set is known as the successor set. Collectively, the successor sets from all processes in the network with respect to a given destination form a spanning, destination, and acyclic graph, whose only sink is the given destination. The protocol we present has two interesting properties. First the graph is maintained acyclic at all times, even though the successor set is dynamic. Second, the protocol tolerates all types of transient faults, even those which may not be detected. Therefore, if the protocol is started from an arbitrary initial state, it will converge to a normal operating state in which a spanning, directed, and acyclic graph is obtained and subsequently maintained.
Astrocytes and blood vessels define the foveal rim during primate retinal development.

PURPOSE To investigate the relationship between development of the perifoveal blood vessels and formation of the foveal depression. METHODS Retinal sections and flatmounts from monkeys aged between fetal day (Fd)80 and 2 years of age were double labeled using antisera to CD31 or von Willebrand factor to detect vascular endothelial cells and antiserum to glial fibrillary acidic protein to detect astrocytes. Sections were studied by fluorescence or confocal microscopy. RESULTS From Fd88 to 115, vessels on the horizontal meridian were found only at the level of the ganglion cell layer (GCL)-inner plexiform layer (IPL) border where they form the ganglion cell layer plexus (GCP). Stellate astrocytes accompany GCP vessels and extend closer to the fovea than vessels. The foveal avascular zone was present within the GCP at Fd101, and at Fd105 a shallow foveal depression encircled by the GCP was present. The GCP foveal margin had the same dimensions as the adult foveal pit. Both blood vessels and astrocytes were excluded from the emerging fovea throughout development. After Fd140, capillary plexuses in the outer retina anastomosed with the GCP on the foveal slope to form a perifoveal plexus, but this plexus did not mature until a month or more after birth. After Fd142, astrocytes rapidly disappeared from the GCP and most of central retina. CONCLUSIONS An avascular area is outlined by the GCP before the foveal pit begins to form, suggesting that molecular factors in this region exclude both vessels and astrocytes. These factors may also guide neuronal migration to form the pit. Because the perifoveal plexus is formed during late gestation, both capillary growth and foveal development may be affected adversely by prematurity.
Detection of Glycomic Alterations Induced by Overexpression of P-Glycoprotein on the Surfaces of L1210 Cells Using Sialic Acid Binding Lectins

P-glycoprotein (P-gp) overexpression is the most frequently observed cause of multidrug resistance in neoplastic cells. In our experiments, P-gp was expressed in L1210 mice leukemia cells (S cells) by selection with vincristine (R cells) or transfection with the gene encoding human P-gp (T cells). Remodeling of cell surface sugars is associated with P-gp expression in L1210 cells as a secondary cellular response. In this study, we monitored the alteration of cell surface saccharides by Sambucus nigra agglutinin (SNA), wheat germ agglutinin (WGA) and Maackia amurensis agglutinin (MAA). Sialic acid is predominantly linked to the surface of S, R and T cells via α-2,6 branched sugars that tightly bind SNA. The presence of sialic acid linked to the cell surface via α-2,3 branched sugars was negligible, and the binding of MAA (recognizing this branch) was much less pronounced than SNA. WGA induced greater cell death than SNA, which was bound to the cell surface and agglutinated all three L1210 cell-variants more effectively than WGA. Thus, the ability of lectins to induce cell death did not correlate with their binding efficiency and agglutination potency. Compared to S cells, P-gp positive R and T cells contain a higher amount of N-acetyl-glucosamine on their cell surface, which is associated with improved WGA binding. Both P-gp positive variants of L1210 cells are strongly resistant to vincristine as P-gp prototypical drug. This resistance could not be altered by liberalization of terminal sialyl residues from the cell surface by sialidase.
Photogrammetry and Laser Altimetry

Laser altimetry has, and is continuing to have a profound impact on photogrammetry. This paper discusses the interrelationship between the two fields, identifies problems, and suggests a common research agenda. Surface reconstruction is an important application in photogrammetry. DTMs, for example, are as much an end result as an intermediate step for orthophoto generation and for object recognition. The quality control is a central issue, regardless how the surface is obtained. The paper analyzes the effect of systematic errors of laser ranging systems on the reconstructed surface. To keep these effects as small as possible, rigorous calibration methods are necessary, including suitable test surfaces and proper error modeling. In a more complex setting, better results are achieved if laser ranging is combined with stereopsis. The combination of different surface measurements is a challenging fusion problem. At the sensor level, the systems, such as camera and laser, can be tightly integrated to the degree that the laser footprint is recorded by the camera. On the feature level, extracted features from imagery and laser ranging must be combined in a way that accounts for the different error models. Finally, on the symbolic level, a combined surface must explain the measurements resulting from the different sources.
An ensemble based system for Chlorophyll-a estimation using MODIS imagery over Southern Quebec inland waters

The purpose of this study was to enhance the performance of the Adaptive-model (AM) for Chlorophyll-a (Chl-a) concentration estimation using MODIS-imagery. The AM is based on the combination of spectral response classification and three semi-empirical estimators. Most critical step in Chl-a estimation when using the AM is the estimator selection. A wrong selection could lead to an over- or underestimation and induces a staircase effect in Chl-a modelization. Ensemble based systems (EBS) development can be in interesting solution. One of the most used techniques to develop an EBS is bagging-algorithm. However, its main weakness is time consumption. The Gaussian-quadrature (GQ) formula has the potential to handle this kind of problems. The objective of this study is to develop a mixed ensemble based system for Chl-a estimation in Quebec inland waters using GQ formula. Statistical indexes evaluation was satisfied, relative-RMSE=15% and R2=0.98 whereas matrix-confusion results were 0.92 and 0.8 for global-success and Kappa-index, respectively.
Experience applying the SPIN model checker to an industrial telecommunications system

Model checking has for years been advertised as a way of ensuring the correctness of complex software systems. However, there exist surprisingly few critical studies of the application of model checking to industrial-scale software systems by people other than the model checker's own authors. In this paper we report our experience in applying the Spin model checker to the validation of the failover protocols of a commercial telecommunications system. While we conclude that model checking is not yet ready for such applications, we find that current research in the model checking community is working to address the difficulties we encountered.
Multiple Resistance at No Cost: Rifampicin and Streptomycin a Dangerous Liaison in the Spread of Antibiotic Resistance

Evidence is mounting that epistasis is widespread among mutations. The cost of carrying two deleterious mutations, or the advantage of acquiring two beneficial alleles, is typically lower that the sum of their individual effects. Much less is known on epistasis between beneficial and deleterious mutations, even though this is key to the amount of genetic hitchhiking that may occur during evolution. This is particularly important in the context of antibiotic resistance: Most resistances are deleterious, but some can be beneficial and remarkably rifampicin resistance can emerge de novo in populations evolving without antibiotics. Here we show pervasive positive pairwise epistasis on Escherichia coli fitness between beneficial mutations, which confer resistance to rifampicin, and deleterious mutations, which confer resistance to streptomycin. We find that 65% of double resistant strains outcompete sensitive bacteria in an environment devoid of antibiotics. Weak beneficial mutations may therefore overcome strong deleterious mutations and can even render double mutants strong competitors.
Undoing Appropriateness: Raciolinguistic Ideologies and Language Diversity in Education

In this article, Nelson Flores and Jonathan Rosa critique appropriateness-based approaches to language diversity in education. Those who subscribe to these approaches conceptualize standardized linguistic practices as an objective set of linguistic forms that are appropriate for an academic setting. In contrast, Flores and Rosa highlight the raciolinguistic ideologies through which racialized bodies come to be constructed as engaging in appropriately academic linguistic practices. Drawing on theories of language ideologies and racialization, they offer a perspective from which students classified as long-term English learners, heritage language learners, and Standard English learners can be understood to inhabit a shared racial positioning that frames their linguistic practices as deficient regardless of how closely they follow supposed rules of appropriateness. The authors illustrate how appropriateness-based approaches to language education are implicated in the reproduction of racial normativity by exp.