Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of Croceibacter Bacteriophage P2559S

ABSTRACT Croceibacter atlanticus HTCC2559T, a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559T possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559T. Many genes predicted in the P2559S genome had their homologs in Bacteroides phages.
B4: experience with a globally-deployed software defined wan

We present the design, implementation, and evaluation of B4, a private WAN connecting Google's data centers across the planet. B4 has a number of unique characteristics: i) massive bandwidth requirements deployed to a modest number of sites, ii) elastic traffic demand that seeks to maximize average bandwidth, and iii) full control over the edge servers and network, which enables rate limiting and demand measurement at the edge. These characteristics led to a Software Defined Networking architecture using OpenFlow to control relatively simple switches built from merchant silicon. B4's centralized traffic engineering service drives links to near 100% utilization, while splitting application flows among multiple paths to balance capacity against application priority/demands. We describe experience with three years of B4 production deployment, lessons learned, and areas for future work.
Post - conflict land administration and its current status as facilitator of the post - conflict state building : case Mozambique

Mozambique suffered from a civil war, known as 16 years of war, which was officially over with the act of signing a General Peace Agreement (GPA) between FRELIMO government and RENAMO in Rome, Italy on 4 October 1992. In the GPA land issues are mentioned in relation to refugees and internally displaced persons (IDPs). During the war and some severed periods of droughts approximately 6 million people were displaced. One study showed that approximately 500.000 landmines were present primarily in the most fertile areas. After the GPA was signed, a process of returning of war displaced people started, and for these requirements and other land related issues the so-called Ad Hoc Land Commission was formed. Not a big number of IDPs and refugees came back to their homes. Some of their properties were occupied by secondary occupants soldiers and military staff. Others did not return because of the mine fields in the rural areas. IDPs and refugees settled in the bigger cities and locations near infrastructure, markets and transport.
Aphid specialism as an example of ecological–evolutionary divergence

Debate still continues around the definition of generalism and specialism in nature. To some, generalism is equated solely with polyphagy, but this cannot be readily divorced from other essential biological factors, such as morphology, behaviour, genetics, biochemistry, chemistry and ecology, including chemical ecology. Viewed in this light, and accepting that when living organisms evolve to fill new ecological–evolutionary niches, this is the primal act of specialisation, then perhaps all living organisms are specialist in the broadest sense. To illustrate the levels of specialisation that may be found in a group of animals, we here provide an overview of those displayed by a subfamily of hemipteran insects, the Aphididae, which comprises some 1600 species/subspecies in Europe alone and whose members are specialised in a variety of lifestyle traits. These include life cycle, host adaptation, dispersal and migration, associations with bacterial symbionts (in turn related to host adaptation and resistance to hymenopterous wasp parasitoids), mutualisms with ants, and resistance to insecticides. As with polyphagy, these traits cannot easily be separated from one another, but rather, are interconnected, often highly so, which makes the Aphididae a fascinating animal group to study, providing an informative, perhaps unique, model to illustrate the complexities of defining generalism versus specialism.
Neural and computational mechanisms of postponed decisions

We consider the mechanisms that enable decisions to be postponed for a period after the evidence has been provided. Using an information theoretic approach, we show that information about the forthcoming action becomes available from the activity of neurons in the medial premotor cortex in a sequential decision-making task after the second stimulus is applied, providing the information for a decision about whether the first or second stimulus is higher in vibrotactile frequency. The information then decays in a 3-s delay period in which the neuronal activity declines before the behavioral response can be made. The information then increases again when the behavioral response is required. We model this neuronal activity using an attractor decision-making network in which information reflecting the decision is maintained at a low level during the delay period, and is then selectively restored by a nonspecific input when the response is required. One mechanism for the short-term memory is synaptic facilitation, which can implement a mechanism for postponed decisions that can be correct even when there is little neuronal firing during the delay period before the postponed decision. Another mechanism is graded firing rates by different neurons in the delay period, with restoration by the nonspecific input of the low-rate activity from the higher-rate neurons still firing in the delay period. These mechanisms can account for the decision making and for the memory of the decision before a response can be made, which are evident in the activity of neurons in the medial premotor cortex.
Classification method for colored natural textures using Gabor filtering

The common methods of texture analysis are based on the gray levels of the texture image. However, the use of color information improves the classification accuracy of colored textures. In the classification of non-homogenous natural textures, human perception of texture and color are important. Therefore, the color space and texture analysis method should be selected to correspond to human vision. We present an effective method for the classification of colored natural textures. The natural textures are often non-homogeneous and directional, which makes them difficult to classify. In our method, multiresolution Gabor filtering is applied to the color components of the texture image in HSI color space. Using this method, the colored texture images can be classified in multiple scales and orientations. Experimental results show that the use of color information improves the classification of natural textures.
Bond Market Structure in the Presence of Marked Point Processes

We investigate the term structure of zero coupon bonds when interest rates are driven by a general marked point process as well as by a Wiener process. Developing a theory that allows for measure–valued trading portfolios, we study existence and uniqueness of a martingale measure. We also study completeness and its relation to the uniqueness of a martingale measure. For the case of a finite jump spectrum we give a fairly general completeness result and for a Wiener–Poisson model we prove the existence of a time–independent set of basic bonds. We also give sufficient conditions for the existence of an affine term structure.
Changes in Risk Factors and Exercise Capacity After Cardiac Rehabilitation and Its Effect on Hospital Readmission

Background: Despite the positive outcomes reported with cardiac rehabilitation (CR), its impacts have been reported to be different from a region or country to another, which may be due to the different contents of rehabilitation programs. Objectives: To investigate the effect of CR on cardiovascular risk factors. Patients and Methods: This is a retrospective cohort study on the data from Imam Ali Cardiac Rehabilitation Center in Kermanshah province, Iran from 2001 to 2008. We used paired t-test to evaluate the effect of CR on cardiovascular risk factors. Logistic regression or t-test (unequal variance) were used to assess the factors influencing re-admission (due to cardiac problems). The relationship between different variables and death was studied using univariate cox proportional hazard. P values < 0.05 were considered significant for all analyses. Results: Out of 504 patients who completed rehabilitation, a total of 499 were analyzed. These 499 patients consisted of 383 men and 116 women. All anthropometric measurements, blood lipids (except HDL cholesterol), systolic and diastolic blood pressure, depression, anxiety and exercise capacity improved after rehabilitation (P < 0.05 for all cases). The improvement was observed in both sexes. A total of 39 patients were re-admitted to hospital after rehabilitation. Being female (OR = 2.40; 95%CI: 1.22-4.68) and history of diabetes (OR = 2.04; 95%CI: 1.04-4.02) increased the risk of re-admission significantly. Patients who were readmitted had higher anthropometric measurements at the beginning and the end of the program. Moreover, the initial exercise capacity of readmitted patients was lower than those who were not readmitted. After a maximal follow-up period of 6.3 years (median = 2.99 years), only eight patients expired (survival rate: 97.5%; 95%CI: 94.7-98.8). None of the variables in our study was significantly related to the survival rate. Conclusions: The comprehensive CR program in Imam Ali Center efficiently reduces cardiovascular risk factors and improves exercise capacity.
Antiallergic Function of KR62980, a Peroxisome Proliferator-Activated Receptor-γ Agonist, in a Mouse Allergic Rhinitis Model

Purpose Peroxisome proliferator-activated receptor γ (PPAR-γ) has been shown to play an important role in the control of inflammatory responses acting on macrophages, mast cells, T cells and eosinophils. A novel PPAR-γ ligand, KR62980 have been recently focused on due to the lower undesirable effects than other PPAR-γ ligands such as rosiglitazone and pioglitazone. The present study was aimed to investigate the effects of KR62980 on nasal symptoms and immunopathological profiles in allergic nasal mucosa in murine allergic rhinitis model. Methods BALB/c mice were sensitized and challenged intranasally with ovalbumin (OVA). KR62980 was administered intraperitoneally or orally 3 hours before each intranasal OVA challenge. Results Administration of KR62980 significantly decreased the number of nasal rubbing, nasal sneezing, ova-specific IgE and total IgE in serum, secretion of Interleukin (IL)-4, IL-5, and IL-17 from the spleen and eosinophilic infiltration in the nasal mucosa. KR62980 decreased the expression of IL-4, IL-5 and IL-10 mRNAs in the nasal mucosal tissue, while, it elevated the level of IL-10 and IFN-γ in splenocyte culture. KR62980 seemed to decrease IL-17 level in local and systemic level even though it did not reach to statistical significance. The anti-inflammatory effect was more definite when the KR62980 was administered intraorally than intraperitoneally. Conclusions A novel PPAR-γ ligand, KR62980 can attenuate OVA-induced allergic inflammation in mice mainly through modulation of Th2 cytokines. This finding suggests that PPAR-γ might have a role in the treatment of allergic rhinitis.
Simple visual self-localization for indoor mobile robots using single video camera

In this paper, we present a simple method for visual localization of indoor mobile robots based on a natural landmark model. Only two natural lines and an intersection point are used for localization to take the advantage of fast detection. To track the landmark model, Lucas-Kanade optical flow algorithm is applied by using gradient descent. Then, by adopting reasonable assumption for indoor environments, a quick localization method for mobile robots from correspondent landmark is proposed in a linear technique. Experimental results that demonstrate the robustness of the method with respect to image illumination and noises are also presented. The performance in indoor environments shows the feasibility of the proposed localization algorithm in real-time.
Synthetic-lethal interactions identify two novel genes, SLA1 and SLA2, that control membrane cytoskeleton assembly in Saccharomyces cerevisiae

Abplp is a yeast cortical actin-binding protein that contains an SH3 domain similar to those found in signal transduction proteins that function at the membrane/cytoskeleton interface. Although no detectable phenotypes are associated with a disruption allele of ABP1, mutations that create a requirement for this protein have now been isolated in the previously identified gene SAC6 and in two new genes, SLA1 and SLA2. The SAC6 gene encodes yeast fimbrin, an actin filament-bundling protein. Null mutations in SLA1 and SLA2 cause temperature-sensitive growth defects. Sla1p contains three SH3 domains and is essential for the proper formation of the cortical actin cytoskeleton. The COOH terminus of Sla2p contains a 200 amino acid region with homology to the COOH terminus of talin, a membrane cytoskeletal protein which is a component of fibroblast focal adhesions. Sla2p is required for cellular morphogenesis and polarization of the cortical cytoskeleton. In addition, synthetic-lethal interactions were observed for double- mutants containing null alleles of SLA2 and SAC6. In total, the mutant phenotypes, sequences, and genetic interactions indicate that we have identified novel proteins that cooperate to control the dynamic cytoskeletal rearrangements that are required for the development of cell polarity in budding yeast.
A Tool-Supported Quality Smell Catalogue For Android Developers

Usual software development processes apply optimisation phases in late iterations. The developed artefacts are optimised regarding particular qualities. In this sense refactorings are executed since the existing behaviour is preserved while the artefact improves its quality properties. The problem is that it is hard for developers to detect model structures dissatisfying a certain quality requirement manually. Without a set of potential problems and their explicit relation to particular qualities it is not possible to detect quality-specific deficiencies automatically. Furthermore, without potential solutions the identified poor structures cannot be resolved by tools. To overcome these problems we introduce a new quality smell catalogue focussing the Android platform.
Calcium Signaling in Transgenic Mice Overexpressing Cardiac Na+-Ca2+ Exchanger

We have produced transgenic mice which overexpress cardiac Na+-Ca2+ exchange activity. Overexpression has been assessed by Western blot, Northern blot, and immunofluorescence. Functional overexpression was analyzed using membrane vesicles and isolated ventricular myocytes. In whole cell clamped myocytes dialyzed with 0.1–0.2 mM Fura-2, the magnitude of ICa and Ca2+ i -transient triggered by ICa or caffeine were not significantly different in transgenic vs. control myocytes. In transgenic myocytes, activation of ICa, however, was followed by a large slowly inactivating transient inward current representing INa-Ca. This current depended on Ca2+ release as it was abolished when sarcoplasmic reticulum (SR) Ca2+ was depleted using thapsigargin. Cai-transients triggered by rapid application of 5 mM caffeine, even though equivalent in control and transgenic myocytes, activated larger INa-Ca (∼5 pA/pF at −90 mV) in transgenic vs. control myocytes (1.5 pA/pF). The decay rate of caffeine-induced Ca2+ i -transient and INa-Ca was 2.5 times faster in transgenic than in control myocytes. 5 mM Ni2+ was equally effective in blocking INa-Ca in control or transgenic myocytes. In 9 out of 26 transgenic myocytes, but none of the controls, Ca2+ influx via the exchanger measured at +80 mV caused a slow rise in [Ca2+]i triggering rapid release of Ca2+ from the SR. SR Ca2+ release triggered by the exchanger at such potentials was accompanied by activation of transient current in the inward direction. In 2 mM Fura-2–dialyzed transgenic myocytes caffeine-triggered Cai-transients failed to activate INa-Ca, even though the kinetics of inactivation of ICa slowed significantly in caffeine-treated myocytes. In 0.1 mM Fura-2–dialyzed transgenic myocytes 100 μM Cd2+ effectively blocked ICa and suppressed Cai-transients at −10 or +50 mV. Our data suggests that in myocytes overexpressing the exchanger, the content of intracellular Ca2+ pools and the signaling of its release by the Ca2+ channel vis-à-vis the Na+-Ca2+ exchanger were not significantly altered despite an up to ninefold increase in the exchanger activity. We conclude that the exchanger remains functionally excluded from the Ca2+ microdomains surrounding the DHP/ryanodine receptor complex.
Melting Temperature Analysis as Quantitative Method for Detection of Point Mutations

Abstract Different methods have been devised to detect point mutations. Some are very sensitive, detecting mutations even in a background of normal tissue, but none provide information about the percentage of cells with mutant DNA. Here we describe an easy, fast and reliable method, melting temperature analysis, which not only detects point mutations but also provides quantitative information on the percentage of cells with mutant DNA. By this method we detected a G-A transition in codon 12 of the K-ras gene in DNA of subjects with colorectal cancer. The K-ras mutation was found in 9/10 bowel cancers and 8/10 normal adjacent samples. It was also detected in 4/7 stool samples from the same patients. In colorectal cancers, the proportion of K-ras mutant cells was variable: in two the mutant/wild-type DNA ratio was 30/70, in three 50/50, and in four 70/30. Melting temperature analysis was sensitive for the detection of point mutations in bowel cancer and also in apparently normal tissue, providing quantitative information about the percentage of cells with mutant DNA.
A case-based reasoning approach for detection of salient regions in images

Automatic salient region detection in an image is useful for image compression, image cropping for resizing on smaller displays, object recognition and tracking. In this paper case-based reasoning is used to make a system learn the relevant attributes of a salient region, based on global and local color contrast. CIELab colorspace is used as it is perceptually uniform and matches the human visual perception. The parameters used are background colors at the boundary, color distance, spatial variance, size of the connected components of salient color and dominant colors. Intensity values are used to deal with images containing black and white shades. Exemplar images are presented to the system to categorize the cases. The method is tested on a large image database.
Critical Aspects of Supervised Pattern Recognition Methods for Interpreting Compositional Data

A lot of multivariate data sets of interest to scientists are called compositional or "closed" data sets, and consists essentially of relative proportions. A recent search on the web by entering "chemical compositional data", led to more than 2,730,000 results within different fields and disciplines, but specially, agricultural and food sciences (August 2011 using Google searcher). The driving causes for the composition of foods lie on four factors (Gonzalez, 2007): Genetic factor (genetic control and manipulation of original specimens), Environmental factor (soil, climate and symbiotic and parasite organisms), Agricultural factor (cultures, crop, irrigation, fertilizers and harvest practices) and Processing factor (post-harvest manipulation, preservation, additives, conversion to another food preparation and finished product). But the influences of these factors are hidden behind the analytical measurements and only can be inferred and uncover by using suitable chemometric procedures.
Comparison of stochastic parameterization approaches in a single-column model By

We discuss and test the potential usefulness of single-column models (SCMs) for the testing of stochastic physics schemes that have been proposed for use in general circulation models (GCMs). We argue that although single column tests cannot be definitive in exposing the full behaviour of a stochastic method in the full GCM, and although there are differences between SCM testing of deterministic and stochastic methods, SCM testing remains a useful tool. It is necessary to consider an ensemble of SCM runs produced by the stochastic method. These can be usefully compared to deterministic ensembles describing initial condition uncertainty and also to combinations of these (with structural model changes) into poor man’s ensembles. The proposed methodology is demonstrated using an SCM experiment recently developed by the GCSS (GEWEX Cloud System Study) community, simulating transitions between active and suppressed periods of tropical convection.
Distributed Adaptive Learning of Graph Signals

The aim of this paper is to propose distributed strategies for adaptive learning of signals defined over graphs. Assuming the graph signal to be bandlimited, the method enables distributed reconstruction, with guaranteed performance in terms of mean-square error, and tracking from a limited number of sampled observations taken from a subset of vertices. A detailed mean-square analysis is carried out and illustrates the role played by the sampling strategy on the performance of the proposed method. Finally, some useful strategies for distributed selection of the sampling set are provided. Several numerical results validate our theoretical findings, and illustrate the performance of the proposed method for distributed adaptive learning of signals defined over graphs.
CHI ten year view: creating and sustaining common ground

● What will be the state of the CHI community in the year 2006? What kind of work will the members of that community be doing? What will they consider to be the key issues and research questions of the day? What will be the nature of the social and technological context in which their work will occur? What kind of educational preparation and work experience will characterize a successful CHI professional? What body of knowledge and set of skills will form the common ground of the field? These scenarios will then be used to address the question: How can the CHI community create and sustain common ground today that will help it thrive and and make important contributions in 2006 and beyond?
“They Moved to City Areas, Abroad”: Views of the Elderly on the Implications of Outmigration for the Middle Hills of Western Nepal

Massive outmigration from the Hill Region of Nepal has various implications for the older people left behind. This article assesses their situation and the challenges they face. To capture older people's experiences and views on the effects of outmigration on their living conditions, I applied a livelihoods perspective. This study, based on in-depth qualitative interviews and group discussions carried out in 3 mountain villages, found that outmigration has had a profound effect on local economic and social conditions. Economic effects have included reduction and in some cases abandonment of agricultural land due to lack of labor. Socially, the elderly have experienced disrespect and neglect from the young, and they lament the demise of traditional Nepalese norms and values in society and in the family. Outmigration in combination with shifting demographics has created entirely new life situations for the elderly and has made their lives more difficult. This article contributes to an underresearched topic relevant to the mountain regions of the global South and draws attention to a social group that has frequently been overlooked in both development and migration research.