Indecision Trees: Learning Argument-Based Reasoning under Quantified Uncertainty

Using Machine Learning systems in the real world can often be problematic, with inexplicable black-box models, the assumed certainty of imperfect measurements, or providing a single classification instead of a probability distribution. This paper introduces Indecision Trees, a modification to Decision Trees which learn under uncertainty, can perform inference under uncertainty, provide a robust distribution over the possible labels, and can be disassembled into a set of logical arguments for use in other reasoning systems.Comment: 12 pages, 1 figur

The connection between metallicity and metal-line kinematics in (sub-)damped Lyman-alpha systems

A correlation between the metallicity, [M/H], and rest-frame MgII equivalent width, EW, is found from 49 DLAs and strong sub-DLAs drawn from the literature over the redshift range 0.2<z_abs<2.6. The correlation is significant at 4.2 sigma and improves to 4.7 sigma when the mild evolution of [M/H] with redshift is taken into account. Even when including only the 26 DLAs (i.e. excluding sub-DLAs) which have Zn metallicities and EW>0.7A, the correlation remains at >3 sigma significance. Since the MgII2796 transition is predominantly saturated in DLAs (which always have EW greater than 0.3A), EW is far more sensitive to the kinematic spread of the metal velocity components across the absorption profile than it is to [M/H]. Thus, the observed [M/H]--EW correlation points to a strong link between the absorber metallicity and the mechanism for producing and dispersing the velocity components. We also note that approximately half of the 13 known molecular hydrogen absorbers have very high EW and very broad velocity structures which show characteristics usually associated with outflows. Follow-up ultraviolet- and blue-sensitive high-resolution spectra of high-EW systems, initially identified in low-resolution spectra, may therefore yield a large number of new H_2 discoveries.Comment: 9 pages, 2 figures (3 EPS files). Accepted by MNRA

Human Illnesses and Animal Deaths Associated with Freshwater Harmful Algal Blooms-Kansas

Citation: Trevino-Garrison, I., DeMent, J., Ahmed, F. S., Haines-Lieber, P., Langer, T., Menager, H., . . . Carney, E. (2015). Human Illnesses and Animal Deaths Associated with Freshwater Harmful Algal Blooms-Kansas. Toxins, 7(2), 353-366. doi:10.3390/toxins7020353Freshwater harmful algal bloom (FHAB) toxins can cause morbidity and mortality in both humans and animals, and the incidence of FHABs in the United States and Kansas has increased. In 2010, the Kansas Department of Health and Environment (KDHE) developed a FHAB policy and response plan. We describe the epidemiology of FHAB-associated morbidity and mortality in humans and animals in Kansas. Healthcare providers and veterinarians voluntarily reported FHAB-associated cases to KDHE. An investigation was initiated for each report to determine the source of exposure and to initiate public health mitigation actions. There were 38 water bodies with a confirmed FHAB in 2011. There were 34 reports of human and animal FHAB-associated health events in 2011, which included five dog deaths and hospitalization of two human case patients. Five confirmed human illnesses, two dog illnesses and five dog deaths were associated with one lake. Four human and seven dog cases were exposed to the lake after a public health alert was issued. Public health officials and FHAB partners must ensure continued awareness of the risks to the public, educate healthcare providers and veterinarians on FHAB-related health events and encourage timely reporting to public health authorities

Synchronous Symmetry Breaking in Neurons with Different Neurite Counts

As neurons develop, several immature processes (i.e., neurites) grow out of the cell body. Over time, each neuron breaks symmetry when only one of its neurites grows much longer than the rest, becoming an axon. This symmetry breaking is an important step in neurodevelopment, and aberrant symmetry breaking is associated with several neuropsychiatric diseases, including schizophrenia and autism. However, the effects of neurite count in neuronal symmetry breaking have never been studied. Existing models for neuronal polarization disagree: some predict that neurons with more neurites polarize up to several days later than neurons with fewer neurites, while others predict that neurons with different neurite counts polarize synchronously. We experimentally find that neurons with different neurite counts polarize synchronously. We also show that despite the significant differences among the previously proposed models, they all agree with our experimental findings when the expression levels of the proteins responsible for symmetry breaking increase with neurite count. Consistent with these results, we observe that the expression levels of two of these proteins, HRas and shootin1, significantly correlate with neurite count. This coordinated symmetry breaking we observed among neurons with different neurite counts may be important for synchronized polarization of neurons in developing organisms

Vascular endothelial growth factor C promotes cervical cancer metastasis via up-regulation and activation of RhoA/ROCK-2/moesin cascade

<p>Abstract</p> <p>Background</p> <p>The elevated expression of vascular endothelial growth factor C (VEGF-C) is correlated with clinical cervical cancer metastasis and patient survival, which is interpreted by VEGF-C functions to stimulate angiogenesis and lymphatic genesis. However, the direct impact of VEGF-C on cervical cancer cell motility remains largely unknown.</p> <p>Methods</p> <p>In this study, we investigated the effects of VEGF-C on actin cytoskeleton remodeling and on cervical cancer cell migration and invasion and how the actin-regulatory protein, moesin regulated these effects through RhoA/ROCK-2 signaling pathway.</p> <p>Results</p> <p>On cervical carcinoma cell line SiHa cells, exposure of VEGF-C triggered remodeling of the actin cytoskeleton and the formation of membrane ruffles, which was required for cell movement. VEGF-C significantly enhanced SiHa cells horizontal migration and three-dimensional invasion into matrices. These actions were dependent on increased expression and phosphorylation of the actin-regulatory protein moesin and specific moesin siRNA severely impaired VEGF-C stimulated-cell migration. The extracellular small GTPase RhoA/ROCK-2 cascade mediated the increased moesin expression and phosphorylation, which was discovered by the use of Y-27632, a specific inhibitor of Rho kinase and by transfected constitutively active, dominant-negative RhoA as well as ROCK-2 SiRNA. Furthermore, in the surgical cervical specimen from the patients with FIGO stage at cervical intra-epithelial neoplasia and I-II cervical squamous cell carcinoma, the expression levels of moesin were found to be significantly correlated with tumor malignancy and metastasis.</p> <p>Conclusions</p> <p>These results implied that VEGF-C promoted cervical cancer metastasis by upregulation and activation of moesin protein through RhoA/ROCK-2 pathway. Our findings offer new insight into the role of VEGF-C on cervical cancer progression and may provide potential targets for cervical cancer therapy.</p

Rabies Virus Infection Induces Type I Interferon Production in an IPS-1 Dependent Manner While Dendritic Cell Activation Relies on IFNAR Signaling

As with many viruses, rabies virus (RABV) infection induces type I interferon (IFN) production within the infected host cells. However, RABV has evolved mechanisms by which to inhibit IFN production in order to sustain infection. Here we show that RABV infection of dendritic cells (DC) induces potent type I IFN production and DC activation. Although DCs are infected by RABV, the viral replication is highly suppressed in DCs, rendering the infection non-productive. We exploited this finding in bone marrow derived DCs (BMDC) in order to differentiate which pattern recognition receptor(s) (PRR) is responsible for inducing type I IFN following infection with RABV. Our results indicate that BMDC activation and type I IFN production following a RABV infection is independent of TLR signaling. However, IPS-1 is essential for both BMDC activation and IFN production. Interestingly, we see that the BMDC activation is primarily due to signaling through the IFNAR and only marginally induced by the initial infection. To further identify the receptor recognizing RABV infection, we next analyzed BMDC from Mda-5−/− and RIG-I−/− mice. In the absence of either receptor, there is a significant decrease in BMDC activation at 12h post infection. However, only RIG-I−/− cells exhibit a delay in type I IFN production. In order to determine the role that IPS-1 plays in vivo, we infected mice with pathogenic RABV. We see that IPS-1−/− mice are more susceptible to infection than IPS-1+/+ mice and have a significantly increased incident of limb paralysis

Protein Expression Redirects Vesicular Stomatitis Virus RNA Synthesis to Cytoplasmic Inclusions

Positive-strand and double-strand RNA viruses typically compartmentalize their replication machinery in infected cells. This is thought to shield viral RNA from detection by innate immune sensors and favor RNA synthesis. The picture for the non-segmented negative-strand (NNS) RNA viruses, however, is less clear. Working with vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, we examined the location of the viral replication machinery and RNA synthesis in cells. By short-term labeling of viral RNA with 5′-bromouridine 5′-triphosphate (BrUTP), we demonstrate that primary mRNA synthesis occurs throughout the host cell cytoplasm. Protein synthesis results in the formation of inclusions that contain the viral RNA synthesis machinery and become the predominant sites of mRNA synthesis in the cell. Disruption of the microtubule network by treatment of cells with nocodazole leads to the accumulation of viral mRNA in discrete structures that decorate the surface of the inclusions. By pulse-chase analysis of the mRNA, we find that viral transcripts synthesized at the inclusions are transported away from the inclusions in a microtubule-dependent manner. Metabolic labeling of viral proteins revealed that inhibiting this transport step diminished the rate of translation. Collectively those data suggest that microtubule-dependent transport of viral mRNAs from inclusions facilitates their translation. Our experiments also show that during a VSV infection, protein synthesis is required to redirect viral RNA synthesis to intracytoplasmic inclusions. As viral RNA synthesis is initially unrestricted, we speculate that its subsequent confinement to inclusions might reflect a cellular response to infection

Specific Roles of Akt iso Forms in Apoptosis and Axon Growth Regulation in Neurons

Akt is a member of the AGC kinase family and consists of three isoforms. As one of the major regulators of the class I PI3 kinase pathway, it has a key role in the control of cell metabolism, growth, and survival. Although it has been extensively studied in the nervous system, we have only a faint knowledge of the specific role of each isoform in differentiated neurons. Here, we have used both cortical and hippocampal neuronal cultures to analyse their function. We characterized the expression and function of Akt isoforms, and some of their substrates along different stages of neuronal development using a specific shRNA approach to elucidate the involvement of each isoform in neuron viability, axon development, and cell signalling. Our results suggest that three Akt isoforms show substantial compensation in many processes. However, the disruption of Akt2 and Akt3 significantly reduced neuron viability and axon length. These changes correlated with a tendency to increase in active caspase 3 and a decrease in the phosphorylation of some elements of the mTORC1 pathway. Indeed, the decrease of Akt2 and more evident the inhibition of Akt3 reduced the expression and phosphorylation of S6. All these data indicate that Akt2 and Akt3 specifically regulate some aspects of apoptosis and cell growth in cultured neurons and may contribute to the understanding of mechanisms of neuron death and pathologies that show deregulated growth

Neutron-proton pairing in the N=Z radioactive fp-shell nuclei 56Ni and 52Fe probed by pair transfer

The isovector and isoscalar components of neutron-proton pairing are investigated in the N=Z unstable nuclei of the \textit{fp}-shell through the two-nucleon transfer reaction (p,$^3$He) in inverse kinematics. The combination of particle and gamma-ray detection with radioactive beams of $^{56}$Ni and $^{52}$Fe, produced by fragmentation at the GANIL/LISE facility, made it possible to carry out this study for the first time in a closed and an open-shell nucleus in the \textit{fp}-shell. The transfer cross-sections for ground-state to ground-state (J=0$^+$,T=1) and to the first (J=1$^+$,T=0) state were extracted for both cases together with the transfer cross-section ratios $\sigma$(0$^+$,T=1) /$\sigma$(1$^+$,T=0). They are compared with second-order distorted-wave born approximation (DWBA) calculations. The enhancement of the ground-state to ground-state pair transfer cross-section close to mid-shell, in $^{52}$Fe, points towards a superfluid phase in the isovector channel. For the "deuteron-like" transfer, very low cross-sections to the first (J=1$^+$,T=0) state were observed both for \Ni\phe\, and \Fe\phe\, and are related to a strong hindrance of this channel due to spin-orbit effect. No evidence for an isoscalar deuteron-like condensate is observed.Comment: 7 pages, 4 figure

Streptococcus pneumoniae Serotype 1 Capsular Polysaccharide Induces CD8+CD28− Regulatory T Lymphocytes by TCR Crosslinking

Zwitterionic capsular polysaccharides (ZPS) of commensal bacteria are characterized by having both positive and negative charged substituents on each repeating unit of a highly repetitive structure that has an α-helix configuration. In this paper we look at the immune response of CD8+ T cells to ZPSs. Intraperitoneal application of the ZPS Sp1 from Streptococcus pneumoniae serotype 1 induces CD8+CD28− T cells in the spleen and peritoneal cavity of WT mice. However, chemically modified Sp1 (mSp1) without the positive charge and resembling common negatively charged polysaccharides fails to induce CD8+CD28− T lymphocytes. The Sp1-induced CD8+CD28− T lymphocytes are CD122lowCTLA-4+CD39+. They synthesize IL-10 and TGF-β. The Sp1-induced CD8+CD28− T cells exhibit immunosuppressive properties on CD4+ T cells in vivo and in vitro. Experimental approaches to elucidate the mechanism of CD8+ T cell activation by Sp1 demonstrate in a dimeric MHC class I-Ig model that Sp1 induces CD8+ T cell activation by enhancing crosslinking of TCR. The expansion of CD8+CD28− T cells is independent, of direct antigen-presenting cell/T cell contact and, to the specificity of the T cell receptor (TCR). In CD8+CD28− T cells, Sp1 enhances Zap-70 phosphorylation and increasingly involves NF-κB which ultimately results in protection versus apoptosis and cell death and promotes survival and accumulation of the CD8+CD28− population. This is the first description of a naturally occurring bacterial antigen that is able to induce suppressive CD8+CD28− T lymphocytes in vivo and in vitro. The underlying mechanism of CD8+ T cell activation appears to rely on enhanced TCR crosslinking. The data provides evidence that ZPS of commensal bacteria play an important role in peripheral tolerance mechanisms and the maintenance of the homeostasis of the immune system