Miracle-dz/UniFAR-FTUs huggingface dataset:
Diapycnal Mixing in a Coastal Regime - AESOP

Abstract : The long term goals are to identify the major processes producing mixing in the upper ocean and to understand their dynamics sufficiently well to permit accurate parameterization of mixing for use in numerical models. These measurements during August 2006 were the first attempt we know of to survey a coastal domain with sufficient coverage to assess how mixing levels vary across the domain. Previous measurements have been concentrated in sub-regions, often revealing particular mixing processes, but insufficient to represent mixing throughout a regional model. We ran lines of microstructure profiles 5-10 km long (Fig. 1), balancing needs for rapid temporal sampling against spatial windows containing at least some structure. Staying with each line for 12.5 hours resolved changes produced by the M2 twice-daily tide, and some lines were rerun at different phases of the monthly tide. As we began to understand patterns of tidal currents and mixing, the original set of lines was modified to reveal pulsing of water in and out of the large canyon splitting the bay down its middle. Powerful Doppler sonars installed on R/V Revelle by Rob Pinkel at Scripps, provided excellent velocity records, supplemented by a 300 kHz ADCP we installed on the bottom the bay? s southern half.
Mechanisms of Two Modulatory Actions of the Channel-binding Protein Slob on the Drosophila Slowpoke Calcium-dependent Potassium Channel

Slob57 is an ion channel auxiliary protein that binds to and modulates the Drosophila Slowpoke calcium-dependent potassium channel (dSlo). We reported recently that residues 1–39 of Slob57 comprise the key domain that both causes dSlo inactivation and shifts its voltage dependence of activation to more depolarized voltages. In the present study we show that removal of residues 2–6 from Slob57 abolishes the inactivation, but the ability of Slob57 to rightward shift the voltage dependence of activation of dSlo remains. A synthetic peptide corresponding in sequence to residues 1–6 of Slob57 blocks dSlo in a voltage- and dose-dependent manner. Two Phe residues and at least one Lys residue in this peptide are required for the blocking action. These data indicate that the amino terminus of Slob57 directly blocks dSlo, thereby leading to channel inactivation. Further truncation to residue Arg16 eliminates the modulation of voltage dependence of activation. Thus these two modulatory actions of Slob57 are independent. Mutation within the calcium bowl of dSlo greatly reduces its calcium sensitivity (Bian, S., I. Favre, and E. Moczydlowski. 2001. Proc. Natl. Acad. Sci. USA. 98:4776–4781). We found that Slob57 still causes inactivation of this mutant channel, but does not shift its voltage dependence of activation. This result confirms further the independence of the inactivation and the voltage shift produced by Slob57. It also suggests that the voltage shift requires high affinity Ca2+ binding to an intact calcium bowl. Furthermore, Slob57 inhibits the shift in the voltage dependence of activation of dSlo evoked by Ca2+, and this inhibition by Slob57 is greater at higher free Ca2+ concentrations. These results implicate distinct calcium-dependent and -independent mechanisms in the modulation of dSlo by Slob.
Three Colors Suffice: Conflict-Free Coloring of Planar Graphs

A conflict-free k-coloring of a graph assigns one of k different colors to some of the vertices such that, for every vertex v, there is a color that is assigned to exactly one vertex among v and v's neighbors. Such colorings have applications in wireless networking, robotics, and geometry, and are well-studied in graph theory. Here we study the natural problem of the conflict-free chromatic number χCF(G) (the smallest k for which conflict-free k-colorings exist), with a focus on planar graphs. For general graphs, we prove the conflict-free variant of the famous Hadwiger Conjecture: If G does not contain Kk+1 as a minor, then χCF(G) ≤ k. For planar graphs, we obtain a tight worst-case bound: three colors are sometimes necessary and always sufficient. In addition, we give a complete characterization of the algorithmic/computational complexity of conflict-free coloring. It is NP-complete to decide whether a planar graph has a conflict-free coloring with one color, while for outer-planar graphs, this can be decided in polynomial time. Furthermore, it is NP-complete to decide whether a planar graph has a conflict-free coloring with two colors, while for outerplanar graphs, two colors always suffice. For the bicriteria problem of minimizing the number of colored vertices subject to a given bound k on the number of colors, we give a full algorithmic characterization in terms of complexity and approximation for outerplanar and planar graphs.
Improved Geo-Spatial Resolution Using a Modified Approach to the Complex Ambiguity Function (CAF)

Abstract : The purpose of this thesis is to implement the CAF-Map method of geolocation in MATLAB. This method is a modification to the traditional Cross Ambiguity Function (CAF) based TDOA, FDOA geolocation where TDOA and FDOA are determined by locating the peak in the CAF plane and then the peak's information is fed to a Least Squares like geolocation tool to determine the emitters geolocation. This method omits the step in which the geolocation is determined with the "post processed" CAF peak information and instead maps the CAF surface directly to the earth's surface. In this thesis, the traditional CAF based geolocation is explained and the limitations are discussed. After this, the development of the CAF-Map method is explained and the algorithm is presented. This thesis explores the use of the CAF-Map method as a geolocation alternative to the traditional TDOA, FDOA methods and demonstrates its ability to geolocate co-channel emitters.
Pretreatment of rabbits with either hirudin, ancrod, or warfarin significantly reduces the immediate uptake of fibrinogen and platelets by the deendothelialized aorta wall after balloon-catheter injury in vivo.

Fibrinogen and platelets rapidly saturate the exposed subendothelium of a freshly deendothelialized aorta in vivo. As thrombin generated within the site of injury is largely responsible for fibrin(ogen) deposition, we questioned whether various anticoagulant treatments would inhibit uptake of both fibrinogen and platelets in vivo. Rabbits were anticoagulated by pretreatment with either Warfarin, Ancrod, or recombinant hirudin. Each anesthetized, anticoagulated (or saline-injected control) rabbit was injected i.v. with rabbit 51Cr-platelets and 125I-fibrinogen before a balloon-catheter deendothelializing (or sham) injury of the thoracic aorta. At 10 minutes after injury, the rabbit was exsanguinated and the aorta excised. Platelet adsorption by the deendothelialized aorta surface was substantially reduced in anticoagulated rabbits (controls, 2.2x10(5)/mm2; Warfarin-treated, 1.2x10(5)/mm2; Ancrod-treated, 5.3x10(4)/mm2; r-hirudin-treated [5 mg/kg], 5.3x10(4)/mm2), and a significant reduction of fibrinogen associated with the platelet layer (from 5.3 to 1 to 2 pmol/cm2) and within the underlying intima-media layer (from 16.9 to 5 to 6 pmol/cm2) was observed in the r-hirudin-and Warfarin-treated rabbits. The pattern of aorta-deposited 51Cr-platelets and 125I-fibrin in the anticoagulated rabbits corresponded well with an assessment by transmission electron microscopy of aortic tissue samples. We conclude that approximately 70% of fibrinogen uptake is thrombin dependent and that approximately 80% of platelet adsorption depends on codeposited fibrin(ogen) during the 10-minute interval after balloon injury. Pretreatment with an agent that interferes with either thrombin or fibrin production will inhibit the immediate interaction of fibrinogen and platelets with the freshly exposed subendothelium.
Latent affective mapping: a novel framework for the data-driven analysis of emotion in text

A necessary step in the generation of expressive speech synthesis is the automatic detection and classiﬁcation of emotions most likely to be present in textual input. We have recently advocated [1] a new emotion analysis strategy leveraging two separate semantic levels: one that encapsulates the foundations of the domain considered, and one that speciﬁcally accounts for the overall affective fabric of the language. This paper expands this premise into a more general framework, dubbed latent affective mapping , to expose the emergent relationship between these two levels. Such connection in turn advantageously in-forms the emotion classiﬁcation process. The beneﬁts gained though a richer description of the underlying affective space are illustrated via an empirical comparison of two different mapping instantiations ( latent affective folding and latent affective embedding ) with more conventional techniques based on expert knowledge of emotional keywords and keysets.
Towards User Modeling and Adaptive Systems for All (TUMAS-A 2009): Modeling and Evaluation of Accessible Intelligent Learning Systems

We present a pilot study, wherein annotators rated the quality of questions produced by our system and human tutors. This study has helped us to evaluate our tutorial dialog system’s question generation abilities and has aided us in identifying areas for further refinement of our dialog strategy. Moreover, this experiment has taught us several important lessons and highlighted critical issues related to running a question generation challenge.
The Role of the Phosphatidylinositol 4-Kinase PI4KA in Hepatitis C Virus-Induced Host Membrane Rearrangement

Background Hepatitis C virus (HCV), like other positive-sense RNA viruses, replicates on an altered host membrane compartment that has been called the “membranous web. ” The mechanisms by which the membranous web are formed from cellular membranes are poorly understood. Several recent RNA interference screens have demonstrated a critical role for the host phosphatidylinositol 4-kinase PI4KA in HCV replication. We have sought to define the function of PI4KA in viral replication. Methodology/Principal Findings Using a nonreplicative model of membranous web formation, we show that PI4KA silencing leads to aberrant web morphology. Furthermore, we find that PI4KA and its product, phosphatidylinositol 4-phosphate, are enriched on membranous webs and that PI4KA is found in association with NS5A in HCV-infected cells. While the related lipid kinase PI4KB also appears to support HCV replication, it does not interact with NS5A. Silencing of PI4KB does not overtly impair membranous web morphology or phosphatidylinositol 4-phosphate enrichment at webs, suggesting that it acts at a different point in viral replication. Finally, we demonstrate that the aberrant webs induced by PI4KA silencing require the activity of the viral NS3-4A serine protease but not integrity of the host secretory pathway. Conclusions/Significance PI4KA is necessary for the local enrichment of PI 4-phosphate at the HCV membranous web and for the generation of morphologically normal webs. We also show that nonreplicative systems of web formation can be used to order molecular events that drive web assembly.
Translating strategy into effective implementation: dispelling the myths and highlighting what works

Several reasons are frequently offered to explain (or to justify) failure to implement strategy. Some are valid but many have merely gained credibility from being repeated often. By discrediting the myths, we can more clearly look at a number of approaches that can greatly enhance the effectiveness of strategy implementation. There are seven key reasons for strategy failure. Unanticipated market changes – strategies can fail because the market conditions change before the strategy can take hold. Three preventative actions are cited: (1) effective competitor responses to strategy – to out‐perform the competition, competitive intelligence is a must; (2) too little investment – if insufficient resources are applied, the strategy will fail. Modeling will aid the executive to make smarter deployment of limited resources; and (3) failure of buy‐in – insufficient buy‐in to or understanding of the strategy among those who need to implement it will cause failure. Good strategic management is a function of people actively considering the strategy as they make day‐to‐day decisions in an ever‐changing world. Lack of focus – resources are wastefully dissipated if priorities are unclear. Put the strategy on one page: focus to execute. Poorly conceived business models – sometimes strategies are simply bad.
Using MODFLOW code to approach transient hydraulic head with a sharp‐interface solution

Saltwater intrusion problems have been usually tackled through analytical models because of its simplicity, easy implementation and low computational cost. Most of these models are based on the sharp‐interface approximation and the Ghyben–Herzberg relation, which neglects mixing of fresh water and seawater and implicitly assumes that salt water remains static. This paper provides insight into the validity of a sharp‐interface approximation defined from a steady state solution when applied to transient seawater intrusion problems. The validation tests have been performed on a 3D unconfined synthetic aquifer, which include spatial and temporal distribution of recharge and pumping wells. Using a change of variable, the governing equation of the steady state sharp‐interface problem can be written with the same structure of the steady confined groundwater flow equation as a function of a single potential variable (ϕ). We propose to approach also the transient problem solving a single potential equation (using also the ϕ variable) with the same structure of the confined groundwater flow equation. It will allow solving the problem by using the classical MODFLOW code. We have used the parameter estimation model PEST to calibrate the parameters of the transient sharp‐interface equation. We show how after the calibration process, the sharp‐interface approach may provide accurate enough results when applied to transient problems and improve the steady state results, thus avoiding the need of implementing a density‐dependent model and reducing the computational cost. This has been proved by comparing results with those obtained using the finite difference numerical code SEAWAT for solving the coupled partial differential equations of flow and density‐dependent transport. The comparison was performed in terms of piezometric heads, seawater penetration, transition zone width and critical pumping rates. Copyright © 2014 John Wiley & Sons, Ltd.
Diagnosis of Autism Spectrum Disorders Using Temporally Distinct Resting‐State Functional Connectivity Networks

Resting‐state functional magnetic resonance imaging (R‐fMRI) is dynamic in nature as neural activities constantly change over the time and are dominated by repeating brief activations and deactivations involving many brain regions. Each region participates in multiple brain functions and is part of various functionally distinct but spatially overlapping networks. Functional connectivity computed as correlations over the entire time series always overlooks interregion interactions that often occur repeatedly and dynamically in time, limiting its application to disease diagnosis.
Effect of Bafilomycin A1 and Nocodazole on Endocytic Transport in HeLa Cells: Implications for Viral Uncoating and Infection

ABSTRACT Bafilomycin A1 (baf), a specific inhibitor of vacuolar proton ATPases, is commonly employed to demonstrate the requirement of low endosomal pH for viral uncoating. However, in certain cell types baf also affects the transport of endocytosed material from early to late endocytic compartments. To characterize the endocytic route in HeLa cells that are frequently used to study early events in viral infection, we used 35S-labeled human rhinovirus serotype 2 (HRV2) together with various fluid-phase markers. These virions are taken up via receptor-mediated endocytosis and undergo a conformational change to C-antigenic particles at a pH of <5.6, resulting in release of the genomic RNA and ultimately in infection (E. Prchla, E. Kuechler, D. Blaas, and R. Fuchs, J. Virol. 68:3713–3723, 1994). As revealed by fluorescence microscopy and subcellular fractionation of microsomes by free-flow electrophoresis (FFE), baf arrests the transport of all markers in early endosomes. In contrast, the microtubule-disrupting agent nocodazole was found to inhibit transport by accumulating marker in endosomal carrier vesicles (ECV), a compartment intermediate between early and late endosomes. Accordingly, lysosomal degradation of HRV2 was suppressed, whereas its conformational change and infectivity remained unaffected by this drug. Analysis of the subcellular distribution of HRV2 and fluid-phase markers in the presence of nocodazole by FFE revealed no difference from the control incubation in the absence of nocodazole. ECV and late endosomes thus have identical electrophoretic mobilities, and intraluminal pHs of <5.6 and allow uncoating of HRV2. As bafilomycin not only dissipates the low endosomal pH but also blocks transport from early to late endosomes in HeLa cells, its inhibitory effect on viral infection could in part also be attributed to trapping of virus in early endosomes which might lack components essential for uncoating. Consequently, inhibition of viral uncoating by bafilomycin cannot be taken to indicate a low pH requirement only.
Dietary Factors Impact on the Association between CTSS Variants and Obesity Related Traits

Background/Aims Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology–this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors–increased by high protein, glycemic index and energy diets. Methods Four tag SNPs (rs7511673, rs11576175, rs10888390 and rs1136774) were selected to capture all common variation in the CTSS region. Association between these four SNPs and several adiposity measurements (BMI, waist circumference, waist for given BMI and being a weight gainer–experiencing the greatest degree of unexplained annual weight gain during follow-up or not) given, where applicable, both as baseline values and gain during the study period (6–8 years) were tested in 11,091 European individuals (linear or logistic regression models). We also examined the interaction between the CTSS variants and dietary factors–energy density, protein content (in grams or in % of total energy intake) and glycemic index–on these four adiposity phenotypes. Results We found several associations between CTSS polymorphisms and anthropometric traits including baseline BMI (rs11576175 (SNP N°2), p = 0.02, β = −0.2446), and waist change over time (rs7511673 (SNP N°1), p = 0.01, β = −0.0433 and rs10888390 (SNP N°3), p = 0.04, β = −0.0342). In interaction with the percentage of proteins contained in the diet, rs11576175 (SNP N°2) was also associated with the risk of being a weight gainer (pinteraction = 0.01, OR = 1.0526)–the risk of being a weight gainer increased with the percentage of proteins contained in the diet. Conclusion CTSS variants seem to be nominally associated to obesity related traits and this association may be modified by dietary protein intake.
MIPAS ozone validation by stratospheric balloon and aircraft measurements

A number of in situ and remote sensing techniques for the measurement of upper tropospheric and stratospheric O3 content was employed during dedicated experiments of the ESABC programme, aiming at the validation of the ENVISAT chemistry payload. In this paper, we will be focusing on the validation of MIPAS off-line products, by presenting the results of the intercomparison between MIP AS O3 vertical profiles and aircraft and balloon correlative measurements. First priority is given to the validation of processor v4.61 data, but individual results of 2002 and 2003 balloon observations are also compared with MIPAS O3 non operational data. Some general remarks are finally expressed, along with specific recommendation to fully exploit the available ESABC validation dataset.
Insecticide resistance and cross-resistance development in Colorado potato beetle Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae) populations in Canada 2008-2011.

BACKGROUND A survey of insecticide resistance in over 150 Canadian populations of Colorado potato beetle was completed between 2008 and 2011. Three neonicotinoid and two anthranilic diamide insecticides were tested at a discriminating concentration (DC) with second-instar larvae in a leaf-disc bioassay. RESULTS The mean mortality for the imidacloprid (Admire) DC was 46-67% between 2008 and 2011 respectively. Over the 4 years, 10-46% and 26-40% of the populations were classified as resistant or showed reduced susceptibility to imidacloprid. The mean mortality for thiamethoxam (Actara) and clothianidin (Poncho/Titan) ranged from 56-76% in 2008 to 81-84% in 2010 for each insecticide respectively, indicating continuous susceptibility to clothianidin but reduced susceptibility to thiamethoxam. In 2008 and 2009, susceptibility to chlorantraniliprole (Coragen) was observed in 85% of populations. Similarly, cyantraniliprole (Cyazypyr) affected 93% of the 2009 and 74% of the 2010 populations. There was a significant (P < 0.05) and high positive correlation (R = 0.4-0.84) between the three neonicotinoids, indicating the potential for cross-resistance. CONCLUSIONS The trend observed in decreasing susceptibility for thiamethoxam and clothianidin will continue unless resistance management practices are followed.
Responsive Action-based Video Synthesis

We propose technology to enable a new medium of expression, where video elements can be looped, merged, and triggered, interactively. Like audio, video is easy to sample from the real world, but hard to segment into clean reusable elements. Reusing a video clip means non-linear editing, and compositing with novel footage. The new context dictates how carefully a clip must be prepared, so our end-to-end approach enables previewing and easy iteration. We convert static-camera videos into loopable sequences, synthesizing them in response to simple end-user requests. This is hard because a) users want essentially semantic-level control over the synthesized video content, and b) automatic loop-finding is brittle and leaves users limited opportunity to work through problems. We propose a human-in-the-loop system where adding effort gives the user progressively more creative control. Artists help us evaluate how our trigger interfaces can be used for authoring of videos and video-performances.