Miracle-dz/UniFAR-FTUs huggingface dataset:
Iterative projected clustering by subspace mining

Irrelevant attributes add noise to high-dimensional clusters and render traditional clustering techniques inappropriate. Recently, several algorithms that discover projected clusters and their associated subspaces have been proposed. We realize the analogy between mining frequent itemsets and discovering dense projected clusters around random points. Based on this, we propose a technique that improves the efficiency of a projected clustering algorithm (DOC). Our method is an optimized adaptation of the frequent pattern tree growth method used for mining frequent itemsets. We propose several techniques that employ the branch and bound paradigm to efficiently discover the projected clusters. An experimental study with synthetic and real data demonstrates that our technique significantly improves on the accuracy and speed of previous techniques.
Natural Allelic Variation Defines a Role for ATMYC1: Trichome Cell Fate Determination

The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein–protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants.
Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H

ABSTRACT Human APOBEC3H belongs to the APOBEC3 family of cytidine deaminases that potently inhibit exogenous and endogenous retroviruses. The impact of single nucleotide polymorphisms (SNP) and alternative splicing on the antiretroviral activity of human APOBEC3H is currently unknown. In this study, we show that APOBEC3H transcripts derived from human peripheral blood mononuclear cells are polymorphic in sequence and subject to alternative splicing. We found that APOBEC3H variants encoding a SNP cluster (G105R, K121D and E178D, hapII-RDD) restricted human immunodeficiency virus type 1 (HIV-1) more efficiently than wild-type APOBEC3H (hapI-GKE). All APOBEC3H variants tested were resistant to HIV-1 Vif, the viral protein that efficiently counteracts APOBEC3G/3F activity. Alternative splicing of APOBEC3H was common and resulted in variants with distinct C-terminal regions and variable antiretroviral activities. Splice variants of hapI-GKE displayed a wide range of antiviral activities, whereas similar splicing events in hapII-RDD resulted in proteins that uniformly and efficiently restricted viral infectivity (>20-fold). Site-directed mutagenesis identified G105R in hapI-GKE and D121K in hapII-RDD as critical substitutions leading to an average additional 10-fold increase in antiviral activity. APOBEC3H variants were catalytically active and, similarly to APOBEC3F, favored a GA dinucleotide context. HIV-1 mutagenesis as a mode of action for APOBEC3H is suggested by the decrease of restriction observed with a cytidine deaminase domain mutant and the inverse correlation between G-to-A mutations and infectivity. Thus, the anti-HIV activity of APOBEC3H seems to be regulated by a combination of genomic variation and alternative splicing. Since prevalence of hapII-RDD is high in populations of African descent, these findings raise the possibility that some individuals may harbor effective as well as HIV-1 Vif-resistant intracellular antiviral defense mechanisms.
Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens

Pathogens have evolved diverse strategies to maximize their transmission fitness. Here we investigate these strategies for directly transmitted pathogens using mathematical models of disease pathogenesis and transmission, modeling fitness as a function of within- and between-host pathogen dynamics. The within-host model includes realistic constraints on pathogen replication via resource depletion and cross-immunity between pathogen strains. We find three distinct types of infection emerge as maxima in the fitness landscape, each characterized by particular within-host dynamics, host population contact network structure, and transmission mode. These three infection types are associated with distinct non-overlapping ranges of levels of antigenic diversity, and well-defined patterns of within-host dynamics and between-host transmissibility. Fitness, quantified by the basic reproduction number, also falls within distinct ranges for each infection type. Every type is optimal for certain contact structures over a range of contact rates. Sexually transmitted infections and childhood diseases are identified as exemplar types for low and high contact rates, respectively. This work generates a plausible mechanistic hypothesis for the observed tradeoff between pathogen transmissibility and antigenic diversity, and shows how different classes of pathogens arise evolutionarily as fitness optima for different contact network structures and host contact rates.
Rapid precipitation in an Al0.5CrFeCoNiCu high entropy alloy

Abstract The effect of cooling rate on the microstructural evolution of Al0.5CrFeCoNiCu has been studied using differential scanning calorimetry and scanning electron microscopy. As cast Al0.5CrFeCoNiCu contained three phases; Cr–Fe–Co–Ni solid solution dendrites, Cu rich interdendritic material and L12 precipitates. During cooling at rates between 10 and 50°C min−1, an additional exothermic event, at ∼1010°C, was observed in the heat flow curves. Microstructural examination after cooling revealed the presence of two distinct populations of intragranular precipitates not present in the as cast material. Energy dispersive X-ray spectroscopy indicated that Cu rich precipitates formed within the dendrites, while a Cr–Fe–Co rich phase formed in the interdendritic constituent. Precipitation during cooling at rates approaching 1°C s−1 indicates that the diffusion kinetics of Al0.5CrFeCoNiCu is not, as previously suggested, sluggish.
Turning on stem cell cardiogenesis with extremely low frequency magnetic fields

Modulation of stem cell differentiation is an important assignment for cellular engineering. Embryonic stem (ES) cells can differentiate into cardiomyocytes, but the efficiency is typically low. Here, we show that exposure of mouse ES cells to extremely low frequency magnetic fields triggered the expression of GATA‐4 and Nkx‐2.5, acting as cardiac lineage‐promoting genes in different animal species, including humans. Magnetic fields also enhanced prodynorphin gene expression, and the synthesis and secretion of dynorphin B, an endorphin playing a major role in cardiogenesis. These effects occurred at the transcriptional level and ultimately ensued into a remarkable increase in the yield of ES‐derived cardiomyocytes. These results demonstrate the potential use of magnetic fields for modifying the gene program of cardiac differentiation in ES cells without the aid of gene transfer technologies and may pave the way for novel approaches in tissue engineering and cell therapy.
Evolution strategies applied to perturbed objective functions

We investigate the behavior of evolution strategies on noisy objective functions. We show for the simple sphere model that convergence velocity is not reduced as long as the noise level is small compared to the function value. If the noise level reaches a certain threshold, a size of the parent population greater than 1 improves the convergence precision significantly. Convergence reliability is tested for two nonconvex functions. Again the search process seems to be not influenced by low level noise. Interpreting the impact of noise purely as a modification of the selection process gives new insight into the role of selection in evolution strategies. <<ETX>>
PUMA: Planning Under Uncertainty with Macro-Actions

Planning in large, partially observable domains is challenging, especially when a long-horizon lookahead is necessary to obtain a good policy. Traditional POMDP planners that plan a different potential action for each future observation can be prohibitively expensive when planning many steps ahead. An efficient solution for planning far into the future in fully observable domains is to use temporally-extended sequences of actions, or "macro-actions. " In this paper, we present a POMDP algorithm for planning under uncertainty with macro-actions (PUMA) that automatically constructs and evaluates open-loop macro-actions within forward-search planning, where the planner branches on observations only at the end of each macro-action. Additionally, we show how to incrementally refine the plan over time, resulting in an anytime algorithm that provably converges to an epsilon-optimal policy. In experiments on several large POMDP problems which require a long horizon lookahead, PUMA outperforms existing state-of-the art solvers.
In ovo application of antagomiRs indicates a role for miR-196 in patterning the chick axial skeleton through Hox gene regulation

Patterning of the vertebrate axial skeleton requires precise spatial and temporal control of Hox gene expression during embryonic development. MicroRNAs (miRNAs) are recently described modulators of gene activity, and members of the miR-196 and miR-10 families have been shown to target several Hox genes in vivo. Testing miRNA function in mice is complicated by potential redundancy between family members. To circumvent this, we have developed protocols for introducing modified antisense oligonucleotides (antagomiRs) in ovo during chick development. Using this approach, we identify a layer of regulatory control provided by the miR-196 family in defining the boundary of Hox gene expression along the anterior-posterior (A-P) embryonic axis. Following knockdown of miR-196, we observe a homeotic transformation of the last cervical vertebrae toward a thoracic identity. This phenotypic alteration is, in part, due to an anterior expansion of Hoxb8 gene expression and consolidates the in vivo relevance of post-transcriptional Hox gene regulation provided by miRNAs in the complex hierarchies governing axial pattering.
Learning maps in 3D using attitude and noisy vision sensors

In this paper, we address the problem of learning 3D maps of the environment using a cheap sensor setup which consists of two standard web cams and a low cost inertial measurement unit. This setup is designed for lightweight or flying robots. Our technique uses visual features extracted from the web cams and estimates the 3D location of the landmarks via stereo vision. Feature correspondences are estimated using a variant of the PROSAC algorithm. Our mapping technique constructs a graph of spatial constraints and applies an efficient gradient descent-based optimization approach to estimate the most likely map of the environment. Our approach has been evaluated in comparably large outdoor and indoor environments. We furthermore present experiments in which our technique is applied to build a map with a blimp.
First Characterization of CTX-M-15-Producing Escherichia coli ST131 and ST405 Clones Causing Community-Onset Infections in South America

ABSTRACT CTX-M-15-producing Escherichia coli has emerged worldwide as an important pathogen associated with community-onset infections, but in South America reports are scarce. We document the presence of CTX-M-15-producing E. coli of the international ST131 and ST405 clones in Colombia and present the first molecular characterization of these isolates in South America.
Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate

Di-myo-inositol 1,1′-phosphate (DIP) is a major osmoprotecting metabolite in a number of hyperthermophilic species of archaea and bacteria. Although the DIP biosynthesis pathway was previously proposed, genes encoding only two of the four required enzymes, inositol-1-phosphate synthase and inositol monophosphatase, were identified. In this study we used a comparative genomic analysis to predict two additional genes of this pathway (termed dipA and dipB) that remained missing. In Thermotoga maritima both candidate genes (in an originally misannotated locus TM1418) form an operon with the inositol-1-phosphate synthase encoding gene (TM1419). A predicted inositol-mono-phosphate cytidylyltransferase activity was directly confirmed for the purified product of T. maritima gene dipA cloned and expressed in Escherichia coli. The entire DIP pathway was reconstituted in E. coli by cloning of the TM1418–TM1419 operon in pBAD expression vector and confirmed to function in the crude lysate. 31P NMR and MS analysis revealed that DIP synthesis proceeds via a phosphorylated DIP intermediate, P-DIP, which is generated by the dipB-encoded enzyme, now termed P-DIP synthase. This previously unknown intermediate is apparently converted to the final product, DIP, by an inositol monophosphatase-like phosphatase. These findings allowed us to revise the previously proposed DIP pathway. The genomic survey confirmed its presence in the species known to use DIP for osmoprotection. Among several newly identified species with a postulated DIP pathway, Aeropyrum pernix was directly proven to produce this osmolyte.
Decoupling congestion control and bandwidth allocation policy with application to high bandwidth-delay product networks

In this dissertation, we propose a new architecture for Internet congestion control that decouples the control of congestion from the bandwidth allocation policy. We show that the new protocol, called XCP, enables very large per-flow throughput (e.g., more than 1 Gb/s), which is unachievable using current congestion control. Additionally, we show via extensive simulations that XCP significantly improves the overall performance, reducing drop rate by three orders of magnitude, increasing utilization, decreasing queuing delay, and attaining fairness in a few RTTs. Using tools from control theory, we model XCP and demonstrate that, in steady state, it is stable for any capacity, delay, and number of sources. XCP does not maintain any per-flow state in routers and requires only a few CPU cycles per packet making it implementable in high-speed routers. Its flexible architecture facilitates the design and implementation of quality of service, such as guaranteed and proportional bandwidth allocations. Finally, XCP is amenable to gradual deployment. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Morbid obesity and metabolic syndrome in Ossabaw miniature swine are associated with increased platelet reactivity

Background: Metabolic syndrome (MetS) and type 2 diabetes mellitus in humans are associated with increased platelet activation and hyperreactivity of platelets to various agonists. Ossabaw swine develop all the hallmarks of MetS including obesity, insulin resistance, hypertension, dyslipidemia, endothelial dysfunction, and coronary artery disease when being fed excess calorie atherogenic diet. We hypothesized that Ossabaw swine with MetS would exhibit increased platelet reactivity compared with lean pigs without MetS. Materials and methods: Ossabaw swine were fed high caloric, atherogenic diet for 44 weeks to induce MetS (n = 10) and were compared with lean controls without MetS that had been fed normal calorie standard diet (n = 10). Light transmittance aggregometry was performed using adenosine diphosphate (ADP), collagen, thrombin, and arachidonic acid (AA) at different concentrations. Dose response curves and EC50 were calculated. Glucose tolerance testing and intravascular ultrasound study of coronary arteries were performed. Results: MetS pigs compared with lean controls were morbidly obese, showed evidence of arterial hypertension, elevated cholesterol, low-density lipoprotein/high-density lipoprotein, and triglycerides, and insulin resistance. Platelets from MetS pigs were more sensitive to ADP-induced platelet aggregation than leans (EC50: 1.83 ± 1.3 μM vs 3.64 ± 2.2 μM; P = 0.02). MetS pigs demonstrated higher platelet aggregation in response to collagen than lean pigs (area under the curve: 286 ± 74 vs 198 ± 123; P = 0.037) and a trend for heightened response to AA (AUC: 260 ± 151 vs 178 ± 145; P = 0.13). No significant difference was found for platelet aggregation in response to thrombin. Conclusions: MetS in Ossabaw swine is associated with increased reactivity of platelets to ADP and collagen. The Ossabaw swine may be a practical, large animal model for the study of certain aspects of platelet pathophysiology and examine vascular devices in a metabolic environment comparable to humans with MetS.
Observations of damage modes as a function of microstructure during NACE TM0177-96 tensile testing of API 5L grade X60 linepipe steels

The mechanisms of sulfide stress cracking (SSC) of grade X60 Iinepipe steels produced by thermomechanical controlled processing (TMCP) have been investigated by applying acoustic emission testing to the NACE TM0177-96 method A tensile test. This method enables the interruption of the test before failure, allowing the observation of the development of subcritical damage as a function of microstructure. The results are interpreted in terms of a correlation between local failure mode and microstructural features, with cracking obeying the kinetics described by acoustic emission. Apart from the successful application of acoustic emission testing to the NACE TM0177-96 method A tensile test, this test method has also been shown to reveal Stress-Oriented Hydrogen Induced Cracking (SOHIC) in susceptible microstructure.
Boosting monte carlo rendering by ray histogram fusion

This article proposes a new multiscale filter accelerating Monte Carlo renderer. Each pixel in the image is characterized by the colors of the rays that reach its surface. The proposed filter uses a statistical distance to compare with each other the ray color distributions associated with different pixels, at each scale. Based on this distance, it decides whether two pixels can share their rays or not. This simple and easily reproducible algorithm provides a psnr gain of 10 to 15 decibels, or equivalently accelerates the rendering process by using 10 to 30 times fewer samples without observable bias. The algorithm is consistent, does not assume a particular noise model, and is immediately extendable to synthetic movies. Being based on the ray color values only, it can be combined with all rendering effects.
On a Bernoulli problem with geometric constraints

A Bernoulli free boundary problem with geometrical constraints is studied. The domain Ω is constrained to lie in the half space determined by x1 ≥ 0 and its boundary to contain a segment of the hyperplane {x1 =0 } where non-homogeneous Dirichlet conditions are imposed. We are then looking for the solution of a partial differential equation satisfying a Dirichlet and a Neumann boundary condition simultaneously on the free boundary. The existence and uniqueness of a solution have already been addressed and this paper is devoted first to the study of geometric and asymptotic properties of the solution and then to the numerical treatment of the problem using a shape optimization formulation. The major difficulty and originality of this paper lies in the treatment of the geometric constraints.
The Tree of Experience in the Forest of Information: Overweighing Experienced Relative to Observed Information

Standard economic models assume that the weight given to information from different sources depends exclusively on its diagnosticity. In this paper we study whether the same piece of information is weighted more heavily simply because it arose from direct experience rather than from observation. We investigate this possibility by conducting repeated game experiments in which groups of players are randomly rematched on every round and receive feedback about the actions and outcomes of all players. We find that participants' actions are influenced more strongly by the behavior of players they directly interact with than by those they only observe.
Astrocytic Inos-dependent Enhancement of Synaptic Release in Mouse Neocortex Slice Preparation and Recording

Buskila Y, Amitai Y. Astrocytic iNOS-dependent enhancement of synaptic release in mouse neocortex. Nitric oxide (NO) has been recognized as an atypical neuronal messenger affecting synaptic transmission, but its cellular source has remained unresolved as the neuronal NO synthase isoform (nNOS) in brain areas such as the neocortex is expressed only by a small subset of inhibitory neurons. The involvement of the glial NOS isoform (iNOS) in modulating neuronal activity has been largely ignored because it has been accepted that this enzyme is regulated by gene induction following detrimental stimuli. Using acute brain slices from mouse neocortex and electrophysiology, we found that selective inhibition of iNOS reduced both spontaneous and evoked synaptic release. Moreover, iNOS inhibition partially prevented and reversed the potentiation of excitatory synapses in layer 2/3 pyramidal neurons. NOS enzymatic assay confirmed a small but reliable Ca 2ϩ-independent activity fraction, consistent with the existence of functioning iNOS in the tissue. Together these data point to astrocytes as a source for the nitrosative regulation of synaptic release in the neocortex. Nitric oxide (NO) has direct neural effects and has been defined as neurotransmitter (Boehning and Snyder 2003). It has been largely assumed that a neuronal Ca 2ϩ /calmodulin-regulated NO synthase isoform (nNOS) consists the principal source of NO acting as a retrograde messenger in the brain to regulate synaptic release (e.g., Arancio et al. 1996; Micheva et al. 2003; Prast and Philippu 2001). Accordingly, the potentia-tion of certain excitatory synaptic pathways in the neocortex exhibits a NO-mediated presynaptic component (Feldman 2009; Hardingham and Fox 2006; Sjostrom et al. 2007). However, puzzling information points to lack of nNOS expression by pyramidal neurons in the neocortex as only a small specific subset of GABAergic neuron express this enzyme (Gonchar and Burkhalter 1997; Vruwink et al. 2001). Another Ca 2ϩ /calmodulin-regulated NOS isoform is probably confined to endothelial cells (eNOS) to affect blood flow, though it has been proposed that NO produced by the cerebral vasculature affects nearby neurons (Garthwaite et al. 2006). A third NOS isoform is expressed only by glia cells (iNOS) and acts in a Ca 2ϩ-independent manner. The involvement of this isoform in modulating neuronal activity has been largely ignored as it has been well accepted that this enzyme is regulated by gene induction following detrimental events such as ischemia or inflammation. Nevertheless, several studies indicate a low constitutive expression of iNOS in various brain regions (Chan et …