Miracle-dz/UniFAR-FTUs huggingface dataset:
Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria

Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacteria genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED). We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering – in which closely-related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering – such as competition between closely-related taxa, or convergent trait evolution in distantly-related taxa – in shaping particular traits in microbial communities.
LOCOMOTOR ACTIVITY AND NON‐PHOTIC INFLUENCES ON CIRCADIAN CLOCKS

Some of the main themes in this review are as follows. 1. The notion that non-photic zeitgebers are weak needs re-examining. Phase-shifts to some non-photic manipulations can be as large as those to light pulses. 2. As well as being able to phase-shift and entrain free-running rhythms, non-photic events have a number of other effects: these include after-effects of entrainment, period changes, and promotion of splitting. 3. The critical variable for non-photic shifting is unknown. Locomotor activity is more likely to be an index of some other necessary state rather than being causal itself. This index may be better when tendencies to move are channelled into easily measured behaviours like wheel-running. 4. Given ignorance about the critical variable, quantification of activity may be the best presently available measure of zeitgeber intensity. Therefore, the behaviour during non-photic manipulations must be examined as carefully as the shifts themselves. When no phase-shifting follows manipulations such as IGL lesions or serotonin depletion, if the animals are inactive, then little can be inferred. 5. Lack of information on the critical variable(s) for non-photic shifting makes it problematic to compare data from studies using different non-photic manipulations. However, the presence of locomotor activity (or its correlate) does appear to be necessary for triazolam to produce shifts. 6. Novelty-induced wheel-running in hamsters depends on the NPY projection from the IGL to SCN. It remains to be determined how important NPY is in other species or in clock-resetting by other manipulations, but methods are now available to study this. 7. Interactions between photic and non-photic zeitgebers remain virtually unexplored, but it is evident that photic and non-photic stimuli can attenuate the phase-shifting effects of each other. Interactions are not purely additive or predictable from PRCs. 8. The circadian system does more than synchronize free-running rhythms to the solar day. Its non-photic functions and their interactions with photic inputs probably account for some of the anatomical complexity of circadian circuitry.
Waves and turbulence on a beta-plane

Two-dimensional eddies in a homogeneous fluid at large Reynolds number, if closely packed, are known to evolve towards larger scales. In the presence of a restoring force, the geophysical beta-effect, this cascade produces a field of waves without loss of energy, and the turbulent migration of the dominant scale nearly ceases at a wavenumber kβ = (β/2U)½ independent of the initial conditions other than U, the r.m.s. particle speed, and β, the northward gradient of the Coriolis frequency. The conversion of turbulence into waves yields, in addition, more narrowly peaked wavenumber spectra and less fine-structure in the spatial maps, while smoothly distributing the energy about physical space. The theory is discussed, using known integral constraints and similarity solutions, model equations, weak-interaction wave theory (which provides the terminus for the cascade) and other linearized instability theory. Computer experiments with both finite-difference and spectral codes are reported. The central quantity is the cascade rate, defined as \[ T = 2\int_0^{\infty} kF(k)dk/U^3\langle k\rangle , \] where F is the nonlinear transfer spectrum and 〈k〉 the mean wavenumber of the energy spectrum. (In unforced inviscid flow T is simply U−1d〈k〉−1/dt, or the rate at which the dominant scale expands in time t.) T is shown to have a mean value of 3·0 × 10−2 for pure two-dimensional turbulence, but this decreases by a factor of five at the transition to wave motion. We infer from weak-interaction theory even smaller values for k [Lt ] kβ. After passing through a state of propagating waves, the homogeneous cascade tends towards a flow of alternating zonal jets which, we suggest, are almost perfectly steady. When the energy is intermittent in space, however, model equations show that the cascade is halted simply by the spreading of energy about space, and then the end state of a zonal flow is probably not achieved. The geophysical application is that the cascade of pure turbulence to large scales is defeated by wave propagation, helping to explain why the energy-containing eddies in the ocean and atmosphere, though significantly nonlinear, fail to reach the size of their respective domains, and are much smaller. For typical ocean flows, $k_{\beta}^{-1} = 70\,{\rm km} $, while for the atmosphere, $k_{\beta}^{-1} = 1000\,{\rm km}$. In addition the cascade generates, by itself, zonal flow (or more generally, flow along geostrophic contours).
HappyPermi: Presenting Critical Data Flows in Mobile Application to Raise User Security Awareness

Malicious Android applications can obtain user's private data and silently send it to a server. Android permissions are currently not sufficient enough to ensure the security of users' sensitive information. For a sufficient permission model it is important to account the target of the outgoing data flow. On the other hand, permission dialogues often contain relevant information, but most of the users generally do not understand the implications or the visualization fails to guide the user attention to it. It is important to empower users by providing applications that show them who can access their private data and who might send this data to the outside. In order to raise user awareness considering Android permissions, we developed HappyPermi, an application that visualizes which user information is accessible by the granted permissions. Our evaluation (n=20) shows that most users are not aware of the sensitive data that their installed applications have access to. Our results suggest how different users feel about accessing their sensitive data when they are aware of its outgoing destinations.
Superior colliculus encodes visual saliency before the primary visual cortex

Significance Theories of visual attention postulate the existence of a saliency map that guides attention/gaze toward the most visually conspicuous stimuli in complex scenes. This study compared saliency coding in the two dominant visual gateways: the primary visual cortex (V1) and the evolutionarily older visual system that exists in the midbrain superior colliculus. Our results show that neurons in the superficial visual layers of the superior colliculus (SCs) encoded saliency earlier and more robustly than V1 neurons. This was surprising, because the dominant input to the SCs arises from V1. This result is in line with models that place a feature processing stage (V1) before the feature-agnostic saliency map in SCs. Models of visual attention postulate the existence of a bottom-up saliency map that is formed early in the visual processing stream. Although studies have reported evidence of a saliency map in various cortical brain areas, determining the contribution of phylogenetically older pathways is crucial to understanding its origin. Here, we compared saliency coding from neurons in two early gateways into the visual system: the primary visual cortex (V1) and the evolutionarily older superior colliculus (SC). We found that, while the response latency to visual stimulus onset was earlier for V1 neurons than superior colliculus superficial visual-layer neurons (SCs), the saliency representation emerged earlier in SCs than in V1. Because the dominant input to the SCs arises from V1, these relative timings are consistent with the hypothesis that SCs neurons pool the inputs from multiple V1 neurons to form a feature-agnostic saliency map, which may then be relayed to other brain areas.
Methods for Quantification of Exposure to Cigarette Smoking and Environmental Tobacco Smoke: Focus on Developmental Toxicology

Active and passive smoking have been associated with an array of adverse effects on health. The development of valid and accurate scales of measurement for exposures associated with health risks constitutes an active area of research. Tobacco smoke exposure still lacks an ideal method of measurement. A valid estimation of the risks associated with tobacco exposure depends on accurate measurement. However, some groups of people are more reluctant than others to disclose their smoking status and exposure to tobacco. This is particularly true for pregnant women and parents of young children, whose smoking is often regarded as socially unacceptable. For others, recall of tobacco exposure may also prove difficult. Because relying on self-report and the various biases it introduces may lead to inaccurate measures of nicotine exposure, more objective solutions have been suggested. Biomarkers constitute the most commonly used objective method of ascertaining nicotine exposure. Of those available, cotinine has gained supremacy as the biomarker of choice. Traditionally, cotinine has been measured in blood, saliva, and urine. Cotinine collection and analysis from these sources has posed some difficulties, which have motivated the search for a more consistent and reliable source of this biomarker. Hair analysis is a novel, noninvasive technique used to detect the presence of drugs and metabolites in the hair shaft. Because cotinine accumulates in hair during hair growth, it is a unique measure of long-term, cumulative exposure to tobacco smoke. Although hair analysis of cotinine holds great promise, a detailed evaluation of its potential as a biomarker of nicotine exposure, is needed. No studies have been published that address this issue. Because the levels of cotinine in the body are dependent on nicotine metabolism, which in turn is affected by factors such as age and pregnancy, the characterization of hair cotinine should be population specific. This review aims at defining the sensitivity, specificity, and clinical utilization of different methods used to estimate exposure to cigarette smoking and environmental tobacco smoke.
Electrostatic Architecture of the Infectious Salmon Anemia Virus (ISAV) Core Fusion Protein Illustrates a Carboxyl-Carboxylate pH Sensor*

Background: The infectious salmon anemia virus (ISAV) fusion (F) protein displays pH-dependent host fusion activity. Results: Thermal stability of ISAV F is inversely correlated with pH. Conclusion: ISAV F exhibits class I viral fusion architecture that is stabilized at fusion pH by carboxyl-carboxylate electrostatics. Significance: This analysis contributes new model principles to our understanding of the diversity of viral entry strategies. Segment 5, ORF 1 of the infectious salmon anemia virus (ISAV) genome, encodes for the ISAV F protein, which is responsible for viral-host endosomal membrane fusion during a productive ISAV infection. The entry machinery of ISAV is composed of a complex of the ISAV F and ISAV hemagglutinin esterase (HE) proteins in an unknown stoichiometry prior to receptor engagement by ISAV HE. Following binding of the receptor to ISAV HE, dissociation of the ISAV F protein from HE, and subsequent endocytosis, the ISAV F protein resolves into a fusion-competent oligomeric state. Here, we present a 2.1 Å crystal structure of the fusion core of the ISAV F protein determined at low pH. This structure has allowed us to unambiguously demonstrate that the ISAV entry machinery exhibits typical class I viral fusion protein architecture. Furthermore, we have determined stabilizing factors that accommodate the pH-dependent mode of ISAV transmission, and our structure has allowed the identification of a central coil that is conserved across numerous and varied post-fusion viral glycoprotein structures. We then discuss a mechanistic model of ISAV fusion that parallels the paramyxoviral class I fusion strategy wherein attachment and fusion are relegated to separate proteins in a similar fashion to ISAV fusion.
Diagnostic Approaches for the Detection of Bovine Viral Diarrhea (BVD) Virus and Related Pestiviruses

teritis in piglets associated with Aujeszky’s disease virus infection. Vet Pathol 21:450-452. 14. Patel JR, Edington N, Mumford JA: 1982, Variation in cellular tropism between isolates of equine herpesvirus-1 in foals. Arch Virol 74:41-51. 15. Sambrook J, Fritsch EF, Maniatis T: 1989, Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory’ Press, Cold Spring Harbor, NY. 16. Studdert MJ: 1983, Restriction endonuclease DNA fingerprinting of respiratory, foetal and perinatal foal isolates of equine herpesvirus type 1. Arch Virol 77:249-258. 17. Studdert MJ, Simpson T, Roizman B: 1981, Differentiation of respiratory and abortigenic isolates of equine herpesvirus 1 by restriction endonucleases. Science 214:562-564. 18. Whitwell KE, Blunden AS: 1992, Pathological findings in horses dying during an outbreak of the paralytic form of equid herpesvirus type 1 (EHV1) infection. Equine Vet J 24: 13-19. 19. Yeargan MR, Allen GP, Bryans JT: 1985, Rapid subtyping of equine herpesvirus 1 with monoclonal antibodies. J Clin Microbiol 21:694-697.
Secondary Embedding of Peritoneal Dialysis Catheters

2006; 26:671–6. 5. Verger C, Duman M, Durand PY, Veniez G, Fabre E, Ryckelynck JP. Influence of autonomy and type of home assistance on the prevention of peritonitis in assisted automated peritoneal dialysis patients. An analysis of data from the French Language Peritoneal Dialysis Registry. Nephrol Dial Transplant 2007; 22:1218–23. 6. Winkelmayer WC, Glynn RJ, Mittleman MA, Levin R, Pliskin JS, Avorn J. Comparing mortality of elderly patients on hemodialysis versus peritoneal dialysis: a propensity score approach. J Am Soc Nephrol 2002; 13:2353–62. 7. Termorshuizen F, Korevaar JC, Dekker FW, Van Manen JG, Boeschoten EW, Krediet RT; The Netherlands Cooperative Study on the Adequacy of Dialysis Study Group. Hemodialysis and peritoneal dialysis: comparison of adjusted mortality rates according to the duration of dialysis: analysis of the Netherlands Cooperative Study on the Adequacy of Dialysis 2. J Am Soc Nephrol 2003; 14:2851–60. 8. Bargman JM. Is there more to living than not dying? A reflection of survival studies in dialysis. Semin Dial 2007; 20:49–51. 9. Oliver MJ, Hunt KD, Lodberg LA, Pham TT, Quinn RR. Home care assisted peritoneal dialysis: risk of invasive procedures to maintain access [Abstract]. Perit Dial Int 2007; 27(Suppl 3):S23. 10. Quinn RR, Hunt KD, Lodberg LA, Pham TT, Oliver MJ. Home care assisted PD: the impact of expanding eligibility for peritoneal dialysis on the risk of hospitalization [Abstract]. Perit Dial Int 2007; 27(Suppl 3):S18.
Breaking the language barrier: an emergentist coalition model for the origins of word learning.

Abstract I. What Does it Take to Learn a Word? II. The Emergentist Coalition Model. III. The Interactive Intermodal Preferential Looking Paradigm: Camille Rocroi (Johns Hopkins University). IV. Learning Novel Nouns: Children use Multiple Cues: Rebecca J. Brand (University of Oregon). V. What Does it Take for 12-Month-Olds to Learn a Word? : Elizabeth Hennon (Temple University), He Len Chung (Temple University), and Ellie Brown (Haverford College). VI. IS 12-Month-Old Word Learning Domain-General, Socially Determined, or Emergent? VII. General Discussion. References. Acknowledgments. Commentary: Pushing the Limits on Theories of Word Learning: Lois Bloom (Columbia University). Contributors. Statement of Editorial Policy.
Big Data and Cloud Computing: Trends and Challenges

Big data is currently one of the most critical emerging technologies. Big Data are used as a concept that refers to the inability of traditional data architectures to efficiently handle the new data sets. The 4V’s of big data – volume, velocity, variety and veracity makes the data management and analytics challenging for the traditional data warehouses. It is important to think of big data and analytics together. Big data is the term used to describe the recent explosion of different types of data from disparate sources. Analytics is about examining data to derive interesting and relevant trends and patterns, which can be used to inform decisions, optimize processes, and even drive new business models. Cloud computing seems to be a perfect vehicle for hosting big data workloads. However, working on big data in the cloud brings its own challenge of reconciling two contradictory design principles. Cloud computing is based on the concepts of consolidation and resource pooling, but big data systems (such as Hadoop) are built on the shared nothing principle, where each node is independent and selfsufficient. The integrating big data with cloud computing technologies, businesses and education institutes can have a better direction to the future. The capability to store large amounts of data in different forms and process it all at very large speeds will result in data that can guide businesses and education institutes in developing fast. Nevertheless, there is a large concern regarding privacy and security issues when moving to the cloud which is the main causes as to why businesses and educational institutes will not move to the cloud. This paper introduces the characteristics, trends and challenges of big data. In addition to that, it investigates the benefits and the risks that may rise out of the integration between big data and cloud computing.
Interaction Screening: Efficient and Sample-Optimal Learning of Ising Models

We consider the problem of learning the underlying graph of an unknown Ising model on p spins from a collection of i.i. d. samples generated from the model. We suggest a new estimator that is computationally efficient and requires a number of samples that is near-optimal with respect to previously established information-theoretic lower-bound. Our statistical estimator has a physical interpretation in terms of "interaction screening". The estimator is consistent and is efficiently implemented using convex optimization. We prove that with appropriate regularization, the estimator recovers the underlying graph using a number of samples that is logarithmic in the system size p and exponential in the maximum coupling-intensity and maximum node-degree.
Exuberant growth and synapse formation of olfactory sensory neuron axonal arborizations

Neural connections in the adult nervous system are established with a high degree of precision. Several examples throughout the nervous system indicate that this precision is achieved by first establishing an initial exuberant immature pattern of connectivity that is then sculpted into the adult pattern via pruning. This often emerges as an activity‐dependent process. In the olfactory system, sensory axons from neurons expressing the same odorant receptor project with high precision to specific glomerular structures in the olfactory bulb. This process undergoes maturation‐dependent refinements that are not fully understood. Due to technical impediments that have made it difficult to focus on single axons, it is unknown whether olfactory sensory projections are established in an exuberant fashion. Here we developed a novel technique of electroporation that allowed us to simultaneously label single olfactory sensory neuron (OSN) axonal arbors and their presynaptic specializations. Using this method we were able to incorporate plasmids into OSNs at an immature stage, thereby allowing a time‐course study of axonal arbor development and synapse formation in single olfactory sensory axons. We observed that the number of branch points, the total branch length, and the number and density of presynaptic specializations peaked at postnatal day 8 and decreased afterwards. Our data demonstrate that olfactory sensory axons develop in an exuberant way, both in terms of branch growth and synaptic composition. We hypothesize that exuberant branches and synapses are eliminated to achieve the mature pattern in a process likely to be regulated by neural activity. J. Comp. Neurol.519:3713‐3726, 2011. © 2011 Wiley‐Liss, Inc.
Effect of soaking on the nutritional quality of pequi (Caryocar brasiliense Camb.) peel flour

Pequi peel comprises 76% of the whole fruit and it is discarded during consumption. Thus, pequi peel has been considered a solid residue, although it has potential for use in various applications. Limitations in the use of this material are mainly due to the lack of information of its nutritional composition, especially about the toxic or antinutritional factors. Soaking is often used to prepare complementary foods and has been reported to be beneficial for enhancing nutritive value. The effect of soaking on the nutritional quality of pequi peel flour was determined by measuring changes in chemical composition, antinutritional factors, total phenols and in vitro protein and starch digestibility. The results showed that 24 h of maceration increases the content of lipids (200%), protein (28.3%) and dietary fibber (31%), while carbohydrate and ash content decreases. There were no haemagglutination activity or α-amylase inhibitors, but it was detected the presence of phytic acid (0.4 g 100 g-1). The soaking reduced 8.5% phenols and 19.0% tannins, 6.2% protein digestibility, and was also effective to eliminate trypsin inhibitors, and increase starch digestibility (24.2%). Soaking was efficient to improve nutritional characteristics of the pequi peel flour, opening up possibilities for its use in food formulations.