Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of a New Genotype of Crimean-Congo Hemorrhagic Fever Virus in Iran

Background and Aims: Crimean-Congo hemorrhagic fever (CCHF) is a fatal viral disease that occurs in approximately 30 countries. It has the most extensive geographic range among the tick-borne viruses that affect human health. CCHF viruses have a tripartite RNA genome consisting of large (L), medium (M) and small (S) segments. This study was undertaken to determine the genetic relationship of CCHF viruses in tick population of West Azerbaijan Province of Iran. Materials and Methods: In this study, RT-PCR method was used for detection of the CCHFV genome based on S segment. The phylogenetic relationship among the Iranian CCHF virus and also between these variants and those from other regions of the world was identified. Results: Two genotypes of CCHF virus were in circulation in Iran (Asia1& Europe 1). We were the first to demonstrate the presence of Europe 1 genotype of CCHF virus in Iran. Conclusion: Further epidemiologic studies including, CCHFV complete genome analysis and implementation of improved surveillance are urgently needed to better predict and respond to CCHF outbreaks in Iran and Middle East region.
Practitioner review: cognitive rehabilitation for children with acquired brain injury.

BACKGROUND The need to address acquired cognitive impairments is increasing in child populations seen across a range of settings. However, current clinical practice following brain injury in children does not necessarily incorporate the use of cognitive rehabilitation models or techniques. The aim of this paper is to review the literature in this area. METHODS All published interventions targeting the cognitive domains of attention, memory and/or executive function that could be identified were reviewed. Different cognitive rehabilitation techniques are briefly described and the clinical and research implications of the findings are discussed. RESULTS Eleven papers, involving 54 children and adolescents receiving intervention, were identified. This literature describes generalised cognitive rehabilitation programmes as well as more specific strategies targeting focal deficits. CONCLUSIONS There is an absence of randomised controlled trials and a very limited number of studies using other methodological approaches, providing at this time no conclusive evidence for the efficacy of cognitive rehabilitation for children with acquired brain injury, but a clear need to address a range of methodological difficulties in this field of enquiry.
Role of Flagellum and Motility in Pathogenesis of Vibrio vulnificus

ABSTRACT To assess the role of the flagellum which was detected by immunoscreening of surface proteins of Vibrio vulnificus, an flgE-deleted mutant was constructed and tested for its pathogenicity. The ability of this nonmotile mutant to adhere to INT-407 cells and its role in biofilm were decreased, as was its lethality to mice.
Arbuscular mycorrhizal fungal colonization. Factors involved in host recognition.

The arbuscular mycorrhizal (AM) symbiosis is the association between fungi of the order Glomales (Zygomycetes) and the roots of terrestrial plants ([Harley and Smith, 1983][1]). Conservative estimates suggest that this ancient symbiosis, dating back to the early Devonian age (398 million years ago
Patterns of cell behaviour underlying somitogenesis and notochord formation in intact vertebrate embryos

We have made a detailed analysis of cell behaviour using high resolution timelapse microscopy of the earliest cellular interactions taking place during morphogenesis of the notochord and somites in intact teleost embryos. Notochord formation is typified by active intercalation of paraxial mesenchyme cells into the lateral surfaces of the primordium. Following this recruitment phase, complete immiscibility develops between cells of the notochord and the presomitic mesenchyme. Dorso‐ventral and rostro‐caudal expansion of the notochord is characterised by translocation of cells within dorsoventral planes of section and is supported by elongation of the remaining cells and reduction in width across its latero‐medial axis. A lateral pallisading of paraxial mesenchyme against the lateral aspects of the notochord precedes overt segmentation. Intersomitic furrows form by localised de‐adhesion at small foci at the nascent intersomitic planes, which are consolidated by coalescence of such areas by de‐adhesion to produce the interface. It is not possible to predict precisely where cells would initiate de‐adhesion since there is a stochastic element to the phenomenon. Once formed, boundaries between somites are stable and provide no opportunity for mixing, except across the first formed furrow, which disintegrates at the 4‐6 somite stage. The first ten somites form at a constant rate of 2.3 somites/hr, during which time we recorded constant relative displacement of the segmental plate against the rostro‐caudally elongating notochord. Unlike teleost epiboly and gastrulation, no large‐scale movements of individual cells can be detected during elaboration of the embryonic axis. © 1994 Wiley‐Liss, Inc.
Relationship Development Intervention ® ( RDI ® ) as Evidence Based Practice for Autism Spectrum Disorders :

Relationship Development Intervention® (RDI®) is a cost effective, research guided, intervention approach for remediating Autism Spectrum Disorders (ASD). The purpose of RDI® is to develop intersubjectivity, the agreed upon core of autism’s social and communicative deficits (Baron-Cohen, 2000). Intersubjectivity encompasses joint attention, social referencing, theory of mind, social reciprocity, and communication for experience sharing purposes. RDI® has a foundation of research and theoretical support, and a growing body of empirical evidence for its practices.
Isolation of mouse N‐CAM‐related cDNA: detection and cloning using monoclonal antibodies.

Clones coding for the mouse neural cell adhesion molecule (N‐CAM) were isolated from a cDNA library prepared in the expression vector lambda gt 11 from mRNA extracted from a mouse neuroblastoma cell line. This library was screened with two anti‐N‐CAM monoclonal antibodies directed against different sites on the molecule and with rabbit anti‐N‐CAM serum. Two clones were identified with the first monoclonal antibody, three with the second one, none reacted with both. The relevance of these cDNA clones to N‐CAM was confirmed by several observations. First, cDNA sequences detected with one monoclonal antibody cross‐hybridized with those identified by the other antibody. Second, the different fusion proteins all bound the rabbit serum in addition to one monoclonal antibody. Finally, the probes hybridized to discrete mRNA species of sufficient lengths to code for the very large N‐CAM polypeptides in RNA preparations from N‐CAM‐expressing, but not from N‐CAM‐negative cells. An additional mRNA species not seen in embryonic brain was expressed in adult mouse brain. Genomic blot experiments indicated that sequences corresponding to one of our probes are present only a few times in the mouse genome.
Consumption-based accounting of CO2 emissions

CO2 emissions from the burning of fossil fuels are the primary cause of global warming. Much attention has been focused on the CO2 directly emitted by each country, but relatively little attention has been paid to the amount of emissions associated with the consumption of goods and services in each country. Consumption-based accounting of CO2 emissions differs from traditional, production-based inventories because of imports and exports of goods and services that, either directly or indirectly, involve CO2 emissions. Here, using the latest available data, we present a global consumption-based CO2 emissions inventory and calculations of associated consumption-based energy and carbon intensities. We find that, in 2004, 23% of global CO2 emissions, or 6.2 gigatonnes CO2, were traded internationally, primarily as exports from China and other emerging markets to consumers in developed countries. In some wealthy countries, including Switzerland, Sweden, Austria, the United Kingdom, and France, >30% of consumption-based emissions were imported, with net imports to many Europeans of >4 tons CO2 per person in 2004. Net import of emissions to the United States in the same year was somewhat less: 10.8% of total consumption-based emissions and 2.4 tons CO2 per person. In contrast, 22.5% of the emissions produced in China in 2004 were exported, on net, to consumers elsewhere. Consumption-based accounting of CO2 emissions demonstrates the potential for international carbon leakage. Sharing responsibility for emissions among producers and consumers could facilitate international agreement on global climate policy that is now hindered by concerns over the regional and historical inequity of emissions.
Microorganism detection and identification using amplified single molecule detection

Using an amplified single molecule detection platform based on padlock probe and proximity ligation, detection of very low amounts of nucleic acid or protein molecules is achieved. Protein and nucleic acid analyses are performed in a similar fashion using circularizing DNA probes, rolling circle amplification and fluorescence-based counting of single reporter molecules. This allows a single system to be used for detection and identification of different types of biological threats, such as bacteria, bacterial spores, viruses, and toxins.
Design of photonic crystal devices

The subject of this PhD thesis is the study of pho tonic crystal waveguides that incorporate discontinuities or stru ctural fabrication-induced variations. For the numerical study of these device s th mode matching (MM) method is proposed. The comparison of the MM method with the couple mode theory (CMT) showed that the CMT can provide only a first approximation to the perturbation-induced scattering in photonic cry stal waveguides. Additionally it was investigated the propagation of optical pulses in photonic crystal waveguides near the edge of the guided band , where the group velocity of the pulse is minimized.
Bimodal Control of Fear-Coping Strategies by CB1 Cannabinoid Receptors

To maximize their chances of survival, animals need to rapidly and efficiently respond to aversive situations. These responses can be classified as active or passive and depend on the specific nature of threats, but also on individual fear coping styles. In this study, we show that the control of excitatory and inhibitory brain neurons by type-1 cannabinoid (CB1) receptors is a key determinant of fear coping strategies in mice. In classical fear conditioning, a switch between initially predominant passive fear responses (freezing) and active behaviors (escape attempts and risk assessment) develops over time. Constitutive genetic deletion of CB1 receptors in CB1−/− mice disrupted this pattern by favoring passive responses. This phenotype can be ascribed to endocannabinoid control of excitatory neurons, because it was reproduced in conditional mutant mice lacking CB1 receptors from cortical glutamatergic neurons. CB1 receptor deletion from GABAergic brain neurons led to the opposite phenotype, characterized by the predominance of active coping. The CB1 receptor agonist Δ9-tetrahydrocannabinol exerted a biphasic control of fear coping strategies, with lower and higher doses favoring active and passive responses, respectively. Finally, viral re-expression of CB1 receptors in the amygdala of CB1−/− mice restored the normal switch between the two coping strategies. These data strongly suggest that CB1 receptor signaling bimodally controls the spontaneous adoption of active or passive coping strategies in individuals. This primary function of the endocannabinoid system in shaping individual behavioral traits should be considered when studying the mechanisms of physiological and pathological fear.
Integrative Analysis of the Physical Transport Network into Australia

Effective biosecurity is necessary to protect nations and their citizens from a variety of threats, including emerging infectious diseases, agricultural or environmental pests and pathogens, and illegal wildlife trade. The physical pathways by which these threats are transported internationally, predominantly shipping and air traffic, have undergone significant growth and changes in spatial distributions in recent decades. An understanding of the specific pathways and donor-traffic hotspots created by this integrated physical transport network is vital for the development of effective biosecurity strategies into the future. In this study, we analysed the physical transport network into Australia over the period 1999–2012. Seaborne and air traffic were weighted to calculate a “weighted cumulative impact” score for each source region worldwide, each year. High risk source regions, and those source regions that underwent substantial changes in risk over the study period, were determined. An overall risk ranking was calculated by integrating across all possible weighting combinations. The source regions having greatest overall physical connectedness with Australia were Singapore, which is a global transport hub, and the North Island of New Zealand, a close regional trading partner with Australia. Both those regions with large amounts of traffic across multiple vectors (e.g., Hong Kong), and those with high levels of traffic of only one type (e.g., Bali, Indonesia with respect to passenger flights), were represented among high risk source regions. These data provide a baseline model for the transport of individuals and commodities against which the effectiveness of biosecurity controls may be assessed, and are a valuable tool in the development of future biosecurity policy.
Biologically Inspired Security as a Service for Service-Oriented Middleware

Service-Oriented computing is a new programming paradigm based on service-oriented architecture that uses web services as its basic building block. Service-Oriented Middleware is a middleware layer that was developed to support service-oriented computing by allowing the flexible integration and operation of web services within the service-oriented computing environment. With the wide adoption of service-oriented computing, web service applications are no longer contained within tightly controlled environments, and thus could be subjected to malicious attacks, such as Denial of Service attacks. In this paper, we propose a generic security service that protects web services against denial of service attacks at the service-oriented middleware layer. Our security service draws on a bio-inspired framework that was developed to counteract denial of service at the network layer. To evaluate our work we have developed a prototype that showed that our proposed security service was able to detect denial of service attacks targeting a web service.
IOP-induced lamina cribrosa deformation and scleral canal expansion: independent or related?

PURPOSE To study the association between the intraocular pressure (IOP)-induced anterior-posterior lamina cribrosa deformation (LCD) and scleral canal expansion (SCE). METHODS 3D eye-specific models of the lamina and sclera of the eyes of three normal monkeys were constructed. Morphing techniques were used to produce 768 models with controlled variations in geometry and materials. Finite element analysis was used to predict the LCD and SCE resulting from an increase in IOP. We analyzed the association between LCD and SCE for the population as a whole, and for subsets. RESULTS For some conditions, such as deep and stiff lamina, the association between LCD and SCE was strong and consistent with the concept of "the sclera pulls the lamina taut" as IOP increases. For other conditions, such as shallow and compliant lamina, there was no association. Further, for other conditions, such as for thin and stiff sclera, the association was opposite to the tautening. Although most of the models had similar response to IOP, some cases had peculiarly large LCD and SCE. The properties of the lamina cribrosa (LC) greatly influenced its response to variations in IOP; for example, deep laminas tended to displace anteriorly, whereas shallow LCs displaced little or posteriorly. CONCLUSIONS The association between LCD and SCE varied greatly depending on the properties of the lamina and sclera, which shows that it is critical to consider the characteristics of the population when interpreting measurements of LCD and SCE. This work is the first systematic analysis of the relationship between LCD and SCE.
Gene-targeting approaches in the study of cellular processes involved in growth or differentiation. Advances in the analysis of oncogenes, tumour-suppressor genes, cytokine/receptor systems and developmental control genes.

Recent advances in embryonic stem cell (ES) technology have made it possible to introduce mutations into the mouse genome by homologous recombination and thereby selectively generate mutant mice. Genetically manipulated mutant mice have contributed enormously to our understanding of the molecular functions of isolated genes and the mechanisms of cell growth and differentiation, as well as increasing our understanding of diseases such as cancer. Here, we will briefly summarise the recent advances in gene-targeting studies with particular emphasis on growth factors and their receptors, oncogenes, tumour-suppressor genes and developmental control genes.
Heme oxygenase-1: molecular mechanisms of gene expression in oxygen-related stress.

Disturbances of intracellular redox equilibrium may alter eukaryotic gene expression patterns in the manifestation of an adaptive stress response. The inducible heme oxygenase-1 gene, ho-1, responds dramatically to changes in cellular redox potential provoked by multiple agents (oxidants, xenobiotics, reactive oxygen species, nitric oxide, and ultraviolet-A radiation) as well as deviations in oxygen tension in excess or deficit of normal physiological levels. This dual response to hyperoxic and hypoxic states renders ho-1 an intriguing model system for studying oxygen-regulated gene expression. The complexation or depletion of reduced glutathione apparently represents an underlying mechanism by which oxidants trigger the response. Chelatable iron levels also influence the induction of ho-1 as evidenced by the inhibitory effects of iron-chelating compounds. Redox-sensitive protein kinase cascades (e.g., mitogen-activated protein kinases) participate in ho-1 regulation. Recent progress in understanding ho-1 transcription has identified two distal enhancer regions (E1, E2) in the mouse ho-1 gene that mediate the response to many inducing conditions. This review will examine the potential roles of iron, glutathione, and reactive oxygen species in the upstream events leading to ho-1 activation following oxygen related stress.
Ca2+ influx shutdown in neutrophils induced by Fas (CD95) cross‐linking

In neutrophils, as in most other cell types, Ca2+ signalling is important for a number of cellular activities. Although inositol(1,4,5)trisphosphate‐mediated release of Ca2+ from intracellular stores is a necessary prelude, it is the Ca2+ influx that is responsible for many of the neutrophil responses. We report here that although elevations of cytosolic Ca2+ do not accompany Fas‐mediated apoptosis in neutrophils, the Ca2+ influx component of the response to N‐formyl‐methionyl‐leucyl‐phenylalanine (FMLP) becomes selectively inactived as the neutrophils progress towards accelerated apoptosis induced by Fas (CD95) cross‐linking. After 4 hr incubation at 37°, untreated neutrophils display an exaggerated Ca2+ influx phase in response to FMLP. This was absent in neutrophils that had been Fas‐activated at the same time. No Ca2+ influx component was demonstrable by the removal of extracellular Ca2+ or by Ca2+ channel blockade with Ni2+ and no Mn2+ influx was detectable. The defect could not be attributed to a decrease in receptor sensitivity, receptor coupling or receptor number because the release of stored Ca2+ remained constant during incubation and was unaffected by Fas activation. Ca2+ influx became uncoupled from store release before detectable gross morphological changes or phosphatidyl serine externalization and was also insensitive to caspase 3 and 8 inhibitors. These results suggest a mechanism other than caspase‐mediated proteolytic damage to components important for Ca2+ influx.
[Clinicopathologic features and prognostic factors of cervical lymph node metastasis in oral squamous cell carcinoma].

BACKGROUND & OBJECTIVE The cervical lymphatic meta-static rate of oral squamous carcinoma is 50%-59%. The management of cervical lymphatic metastasis relates with prognosis of patients with oral squamous carcinoma. This study was to investigate the clinicopathologic features and prognosis factors of cervical lymph node metastasis in oral squamous cell carcinoma. METHODS Clinicopathologic data of 191 patients with oral squamous cell carcinoma were retrospectively reviewed. The relationship between histopathologic factors and cervical lymph node metastasis was evaluated by univariate Chi(2) test. Cox regression model was used to analyze impacts of pathologic factors of cervical lymph nodes, such as metastatic status, size and number of positive neck nodes,levels of positive nodes, the lowest involved nodal level, on prognosis. RESULTS The overall 5-year survival rate of the 191 patients was 48.7%. Univariate Chi(2) test confirmed that only depth of primary tumor infiltration correlated to cervical lymph node metastasis. Cox regression analysis revealed that clinical N stage, cervical lymphatic metastatic status, number of involved levels, and the lowest involved nodal level affected prognosis of patients, the most significant prognostic factors of cervical lymph node were clinical N stage, and the lowest involved nodal level. CONCLUSIONS Cervical lymph node metastasis is a significant prognostic factor of oral squamous cell carcinoma. The identification of metastatic patterns of cervical lymph nodes, and the management targeting pathologic factors of cervical lymph node affecting survival are critical for improving the treatment effect on oral squamous cell carcinoma.
FINE-GRAINED CRITICAL PATH ANALYSIS AND OPTIMIZATION FOR AREA-TIME EFFICIENT REALIZATION OF MULTIPLE CONSTANT MULTIPLICATIONS

In this paper, a set of operators suitable for digit-serial FIR filtering is presented. The canonical and inverted forms are studied. In each of these structures both the symmetrical and antisymmetrical particular cases are also covered. In last two decades, many efficient algorithms and architectures have been introduced for the design of low complexity bit-parallel Multiple Constant Multiplications (MCM) operation which dominates the complexity of many digital signal processing systems. On the other hand, little attention has been given to the digit-serial MCM design that offers alternative low complexity MCM operations at the cost of an increased delay. In this topic, we address the problem of optimizing the gate-level area in digit -serial MCM designs and introduce high level synthesis algorithms, design architectures, and a computer aided design tool. The proposed optimization algorithms for the digit-serial MCM architectures in the design of digit-serial MCM operations and finite impulse response filters yields better performance compared with multiple Constant multipliers using Common Sub-expression Elimination (CSE) algorithm with high efficiency.
Neither constant nor a fallacy

Mohammed and colleagues doubt the value of hospital standardised mortality ratios.1 They describe a possibility of increased bias consequent on a “constant risk fallacy” occurring if the effects of risk factors used in model adjustment process are assumed to be constant across hospitals in the subsequent hospital grouping, when they are not. Using data from four UK hospitals, Mohammed and colleagues showed …