Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Patterns of Mating and Potential Hybridization from Pollinator Behavior

Hybridization in flowering plants is determined in part by the rate at which animal pollinators move between species and by the effectiveness of such movements in transferring pollen. Pollinator behavior can also influence hybrid fitness by determining receipt and export of pollen. We incorporated information on pollinator effectiveness and visitation behavior into a simulation model that predicts pollen transfer between Ipomopsis aggregata, Ipomopsis tenuituba, and hybrids. These predictions were compared with estimates of pollen transfer derived from movement of fluorescent dyes in experimental plant arrays. Interspecific pollen transfer was relatively uncommon in these arrays, whereas transfer between hybrids and the parental species was at least as common as conspecific transfer. Backcrossing was asymmetrical; I. aggregata flowers frequently received mixed loads of hybrid and conspecific pollen. The simulation suggests that these patterns of pollen transfer are largely explained by the visitation sequences of hummingbird and insect pollinators, with little contribution from mechanical isolation. Pollen receipt by hybrids exceeded that of both parental species in a year when pollinators preferred to visit F1 and F2 hybrids and was intermediate in another year when they preferred to visit I. aggregata. This suggests that natural variation in pollination may produce spatiotemporal variation in hybridization and hybrid fitness.
Condensins Promote Coorientation of Sister Chromatids During Meiosis I in Budding Yeast

The condensin complex is a key determinant of higher-ordered chromosome structure. We show here that the complex is also important for the correct alignment of chromosomes on the meiosis I spindle. Unlike during mitosis and meiosis II, when sister chromatids attach to microtubules emanating from opposite spindle poles (biorientation), accurate meiosis I chromosome segregation requires that sister chromatids attach to microtubules emanating from the same spindle pole (coorientation). The monopolin complex, consisting of Lrs4, Csm1, and the meiosis-specific component Mam1, brings about meiosis I coorientation. We find that in the absence of functional condensin complexes, a fraction of sister kinetochores biorient on the meiosis I spindle and association of the monopolin complex subunit Mam1 with kinetochores is decreased. Our studies uncover a new locus-specific effect of the condensin complex.
Anatomical substrates for the discriminative stimulus effects of methamphetamine in rats

Methamphetamine is a psychostimulant drug acting on central monoaminergic neurons to produce both acute psychomotor stimulation and long‐lasting behavioral effects including addiction and psychosis. Drug discrimination procedures have been particularly useful in characterizing subjective effects of addictive drugs. In the present study, to identify potential anatomical substrates for the discriminative stimulus effects of methamphetamine, we investigated the drug discrimination‐associated Fos expression in Sprague–Dawley rats trained to discriminate methamphetamine from saline under a two‐lever fixed ratio 20 (FR‐20) schedule of food reinforcement. The rats that fulfilled the criteria for learning the discrimination were anesthetized and perfused 2 h after the drug discrimination test, and Fos immunoreactivity was examined in 15 brain regions. Fos expression in the brains of rats that discriminate methamphetamine from saline was significantly increased in the nucleus accumbens (NAc) and the ventral tegmental area (VTA), but not in other areas including the cerebral cortex, caudate putamen, substantia nigra, hippocampus, amygdala and habenulla, as compared with the expression in control rats that were maintained under the FR‐20 schedule. The present findings suggest a role for the VTA and NAc as possible neuronal substrates in the discriminative stimulus effects of methamphetamine.
Examining Postsecondary Education Predictors and Participation for Students With Learning Disabilities

Given the history of poor postschool outcomes for students with disabilities, researchers repeatedly sought to demonstrate the links between predictor variables and postschool outcomes for students with disabilities. This secondary data analysis used the National Longitudinal Transition Study–2 to examine the relationship between postsecondary education–related transition services and postsecondary education participation for students with learning disabilities. Logistic regression analyses indicated receiving core content area instruction in the general education classroom was positively related to postsecondary education participation. Frequency distributions indicated students with learning disabilities attended 2-year college at higher rates than other postsecondary education programs. The results suggest educators should consider inclusion in general education classroom for core content area instruction for students with learning disabilities with postsecondary education goals to the extent permitted by their least restrictive environment.
Army Research Laboratory Aberdeen Proving Ground , MD 21005-5069 ARL-RP-340 September 2011 Phase Field Modeling of Twinning in Indentation of Transparent Crystals

Continuum phase field theory is applied to study elastic twinning in calcite and sapphire single crystals subjected to indentation loading by wedge-shaped indenters. An order parameter is associated with the magnitude of stress-free twinning shear. Geometrically linear and nonlinear theories are implemented and compared, the latter incorporating neo-Hookean elasticity. Equilibrium configurations of deformed and twinned crystals are attained numerically via direct energy minimization. Results are in qualitative agreement with experimental observations: a long thin twin forms asymmetrically under one side of the indenter, the tip of the twin is sharp and the length of the twin increases with increasing load. Qualitatively similar results are obtained using isotropic and anisotropic elastic constants, though the difference between isotropic and anisotropic results is greater in sapphire than in calcite. Similar results are also obtained for nanometer-scale specimens and millimeter-scale specimens. Indentation forces are greater in the nonlinear model than the linear model because of the increasing tangent bulk modulus with increasing pressure in the former. Normalized relationships between twin length and indentation force are similar for linear and nonlinear theories at both nanometer and millimeter scales. Twin morphologies are similar for linear and nonlinear theories for indentation with a 90◦ wedge. However, in the nonlinear model, indentation with a 120◦ wedge produces a lamellar twin structure between the indenter and the long sharp primary twin. This complex microstructure is not predicted by the linear theory. (Some figures in this article are in colour only in the electronic version)
Term rewriting and its application to recognizing handwritten Hindu numerals

In this paper the theoretical basis is presented and the implementation of a term rewriting system based on algebraic specifications is described. The input to this system is represented by an algebraic specification language, which forms not only the set of axioms but also the sorts, variables, operators and terms of a specific simulated theory or application. Rewriting and matching mechanisms provide the formal methodology for evaluating terms and proving assertions in an algebraic theory. Specifications are evaluated by interpreting terms by means of rewrite rules. The rules are described by the axioms of the specifications where the finite termination and congruence properties are assumed. A term rewriting system to recognize handwritten Hindu numerals is introduced as a case study. Besides rewriting, a robust algorithm is proposed to segment the numeral's image into strokes based on feature points and to identify cavity features. A syntactic representation (term) of the input image is matched and rewritten against a set of rules. Experimental results proved that the proposed system is tolerant to recognize a variety of numeral shapes with 96% successful recognition rate.
Ly6h Regulates Trafficking of Alpha7 Nicotinic Acetylcholine Receptors and Nicotine-Induced Potentiation of Glutamatergic Signaling

α7 nAChRs are expressed widely throughout the brain, where they are important for synaptic signaling, gene transcription, and plastic changes that regulate sensory processing, cognition, and neural responses to chronic nicotine exposure. However, the mechanisms by which α7 nAChRs are regulated are poorly understood. Here we show that trafficking of α7-subunits is controlled by endogenous membrane-associated prototoxins in the Ly6 family. In particular, we find that Ly6h reduces cell-surface expression and calcium signaling by α7 nAChRs. We detect Ly6h in several rat brain regions, including the hippocampus, where we find it is both necessary and sufficient to limit the magnitude of α7-mediated currents. Consistent with such a regulatory function, knockdown of Ly6h in rat hippocampal pyramidal neurons enhances nicotine-induced potentiation of glutamatergic mEPSC amplitude, which is known to be mediated by α7 signaling. Collectively our data suggest a novel cellular role for Ly6 proteins in regulating nAChRs, which may be relevant to plastic changes in the nervous system including rewiring of glutamatergic circuitry during nicotine addiction.
The Protozoan Neospora caninum Directly Triggers Bovine NK Cells To Produce Gamma Interferon and To Kill Infected Fibroblasts

ABSTRACT Natural killer (NK) cells are considered to be key players in the early innate responses to protozoan infections, primarily indirectly by producing gamma interferon (IFN-γ) in response to cytokines, like interleukin 12 (IL-12). We demonstrate that live, as well as heat-inactivated, tachyzoites of Neospora caninum, a Toxoplasma-like protozoan, directly trigger production of IFN-γ from purified, IL-2-activated bovine NK cells. This response occurred independently of IL-12 but was increased by the addition of the cytokine. A similar IFN-γ response was measured in cocultures of NK cells and N. caninum-infected autologous fibroblasts. However, no NK cell-derived IFN-γ response was detected when cells were cultured with soluble antigens from the organism, indicating that intact tachyzoites or nonsoluble components are necessary for NK cell triggering. Furthermore, N. caninum-infected autologous fibroblasts had increased susceptibility to NK cell cytotoxicity compared to uninfected fibroblasts. This cytotoxicity was largely mediated by a perforin-mediated mechanism. The activating receptor NKp46 was involved in cytotoxicity against fibroblasts but could not explain the increased cytotoxicity against infected targets. Interestingly, N. caninum tachyzoites were able to infect cultured NK cells, in which tachyzoites proliferated inside parasitophorous vacuoles. Together, these findings underscore the role of NK cells as primary responders during a protozoan infection, describe intracellular protozoan infection of NK cells in vitro for the first time, and represent the first functional study of purified bovine NK cells in response to infection.
Large deletions and uniparental disomy detected by SNP arrays in adults with thoracic aortic aneurysms and dissections

Large Deletions and Uniparental Disomy Detected by SNP Arrays in Adults With Thoracic Aortic Aneurysms and Dissections Siddharth Prakash, Scott A. LeMaire, Molly Bray, Dianna M. Milewicz, and John W. Belmont* Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas Texas Heart Institute at St. Luke’s Episcopal Hospital, Houston, Texas Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
Evaluating Different Descriptors for Model Design of Antimicrobial Peptides with Enhanced Activity Toward P. aeruginosa

The number of isolated drug‐resistant pathogenic microbes has increased drastically over the past decades, demonstrating an urgent need for new therapeutic interventions. Antimicrobial peptides have for a long time been looked upon as an interesting template for drug optimization. However, the process of optimizing peptide antimicrobial activity and specificity, using large peptide libraries is both tedious and expensive. Here, we describe the construction of a mathematical model for prediction, prior to synthesis, of peptide antibacterial activity toward Pseudomonas aeruginosa. By use of novel descriptors quantifying the contact energy between neighboring amino acids in addition to a set of inductive and conventional quantitative structure–activity relationship descriptors, we are able to model the peptides antibacterial activity. Cross‐correlation and optimization of the implemented descriptor values have enabled us to build a model (Bac2a‐ #2) that was able to correctly predict the activity of 84% of the tested peptides, within a twofold deviation window of the corresponding IC50 values, measured earlier. The predictive power, is an average of 10 submodels, each predicting the activity of 20 randomly excluded peptides, with a predictive success of 16.7 ± 1.6 peptides. The model has also been proven significantly more accurate than a simpler model (Bac2a‐ #1), where the inductive and conventional quantitative structure–activity relationship descriptors were excluded.
Iron mobilization from crocidolite asbestos greatly enhances crocidolite-dependent formation of DNA single-strand breaks in phi X174 RFI DNA.

The ability of the iron associated with asbestos to catalyze damage to phi X174 RFI DNA was determined and compared with iron mobilized from asbestos. Asbestos (1 mg/ml) suspended for 30 min in 50 mM NaCl containing 0.5 micrograms phi X174 RFI DNA, pH 7.5, did not catalyze detectable amounts of DNA single-strand breaks (SSB). However, addition of ascorbate (1 mM) resulted in 19, 26, 7 or 8% DNA with SSB for crocidolite, amosite, chrysotile or tremolite respectively. The percentage of DNA with SSB induced by each form of asbestos was directly related to its iron content. Inclusion of desferrioxamine B, which binds Fe(III) rendering it redox inactive, completely inhibited asbestos-dependent formation of DNA SSB, suggesting that iron was responsible for catalyzing the formation of DNA SSB. Mobilization of Fe(II) from crocidolite by citrate, EDTA or nitrilotriacetate (1 mM) in the absence of ascorbate resulted in 15, 33 or 63% DNA with SSB respectively. This activity was completely inhibited by compounds considered to be . OH scavengers, i.e. mannitol, 5,5-dimethyl-1-pyrroline N-oxide or salicylate (100 mM). Preincubation of crocidolite with citrate (1 mM) for 24 h resulted in mobilization of 52 microM iron and increased ascorbate-dependent induction of DNA SSB compared with crocidolite that was preincubated without citrate. Iron mobilized by citrate was entirely responsible for crocidolite-dependent formation of DNA SSB as evidenced by complete inhibition with desferrioxamine B. Therefore, the results of the present study strongly suggest that iron was responsible for asbestos-dependent generation of oxygen radicals, which resulted in the formation of DNA SSB. Mobilization of iron by chelators, followed by redox cycling, greatly enhanced crocidolite-dependent formation of DNA SSB. Thus, mobilization of iron in vivo by low mol. wt chelators may lead to the increased production of reactive oxygen species resulting in damage to biomolecules, such as DNA.
Fatty acid and phorbol ester-mediated interference of mitogenic signaling via novel protein kinase C isoforms in pancreatic beta-cells (INS-1).

It is possible that activation of protein kinase C (PKC) isoforms by free fatty acids (FFA) plays a role in the failure of pancreatic beta-cell mass expansion to compensate for peripheral insulin resistance in the pathogenesis of type-2 diabetes. The effect of lipid moieties on activation of conventional (PKC-alpha and -beta1), novel (PKC-delta) and atypical (PKC-zeta) PKC isoforms was evaluated in an in vitro assay, using biotinylated neurogranin as a substrate. Oleoyl-Coenzyme A (CoA) and palmitoyl-CoA, but not unesterified FFA, significantly increased the activity of all PKC isoforms (P< or =0.05), particularly that for PKC-delta. It was found that FFA (0.4 mM oleate/complexed to 0.5% bovine serum albumin) inhibited IGF-I-induced activation of protein kinase B (PKB) in the pancreatic beta-cell line (INS-1), but this was alleviated in the presence of the general PKC inhibitor (Gö6850; 1 microM). To further investigate whether conventional or novel PKC isoforms adversely affect beta-cell proliferation, the effect of phorbol ester (phorbol 12-myristate 13-acetate; PMA)-mediated activation of these PKC isoforms on glucose/IGF-I-induced INS-1 cell mitogenesis, and insulin receptor substrate (IRS)-mediated signal transduction was investigated. PMA-mediated activation of PKC (100 nM; 4 h) reduced glucose/IGF-I mediated beta-cell mitogenesis (>50%; P< or =0.05), which was reversible by the general PKC inhibitor Gö6850 (1 microM), indicating an effect of PKC and not due to a non-specific PMA toxicity. PMA inhibited IGF-I-induced activation of PKB, correlating with inhibition of IGF-I-induced association of IRS-2 with the p85 regulatory subunit of phosphatidylinositol-3 kinase. However, in contrast, PMA activated the mitogen-activated protein kinases, Erk1/2. Titration inhibition analysis using PKC isoform inhibitors indicated that these PMA-induced effects were via novel PKC isoforms. Thus, FFA/PMA-induced activation of novel PKC isoforms can inhibit glucose/IGF-I-mediated beta-cell mitogenesis, in part by decreasing PKB activation, despite an upregulation of Erk1/2. Thus, activation of novel PKC isoforms by long-chain acyl-CoA may well contribute to decreasing beta-cell mass in the pathogenesis of type-2 diabetes, similar to their inhibition of insulin signal transduction which causes insulin resistance.
On the effectiveness of weighted moving windows: Experiment on linear regression based software effort estimation

In construction of an effort estimation model, it seems effective to use a window of training data so that the model is trained with only recent projects. Considering the chronological order of projects within the window, and weighting projects according to their order within the window, may also affect estimation accuracy. In this study, we examined the effects of weighted moving windows on effort estimation accuracy. We compared weighted and non‐weighted moving windows under the same experimental settings. We confirmed that weighting methods significantly improved estimation accuracy in larger windows, although the methods also significantly worsened accuracy in smaller windows. This result contributes to understanding properties of moving windows. Copyright © 2014 John Wiley & Sons, Ltd.
Reduced L-type calcium current in ventricular myocytes from pigs with hyperdynamic septic shock*

Objective: To hypothesize that reduced L-type calcium current with consequent shortening of cardiac repolarization is present in a clinically relevant porcine model of hyperdynamic septic shock. Myocardial depression is a well-recognized manifestation of sepsis and septic shock. Reduction of L-type calcium current was demonstrated to contribute to the myocardial depression in endotoxemic rodents. Design: Laboratory animal experiments. Setting: Animal research laboratory at a university. Subjects: Twenty-two domestic pigs of either gender. Interventions: In anesthetized, mechanically ventilated, and instrumented pigs, sepsis was induced by bacteremia (central venous infusion of live Pseudomonas aeruginosa) and continued for 22 hrs. Measurements and Main Results: Electrocardiogram was recorded before and 22 hrs after induction of bacteremia. RR, QT, and QTc intervals were significantly shortened by sepsis. In vitro, action potentials were recorded in right ventricular trabeculae. Action potential durations were shortened in septic preparations. Tumor necrosis factor-&agr; did not influence action potential durations. L-type calcium current was measured in isolated ventricular myocytes. Peak L-type calcium current density was reduced in myocytes from septic animals (8.3 ± 0.4 pA/pF vs. 11.2 ± 0.6 pA/pF in control). The voltage dependence of both L-type calcium current activation and inactivation was shifted to more negative potentials in myocytes from septic animals. Action potential-clamp experiments revealed that the contribution of L-type calcium current to the septic action potential was significantly diminished. In cardiac myocytes incubated with tumor necrosis factor-&agr;, L-type calcium current was not further affected. Conclusions: In a clinically relevant porcine model, hyperdynamic septic shock induced shortening of ventricular repolarization and reduction of L-type calcium current. The contribution of L-type calcium current to the action potential in septic ventricular myocytes was significantly diminished. Tumor necrosis factor-&agr; probably did not contribute to this effect.
Transcriptional profile in afferent lymph cells following vaccination with liposomes incorporating CpG

Vaccine formulations incorporating innate immune stimulants are highly immunogenic; however, the biological signals that originate in the peripheral tissues at the site of injection and are transmitted to the local lymph node to induce immunity remain unclear. By directly cannulating the ovine afferent lymphatic vessels, we have previously shown that it takes 72 hr for mature antigen‐loaded dendritic cells and monocytes to appear within afferent lymph following injection of a liposomal formulation containing the Toll‐like receptor ligand CpG. In this present study, we characterize the global transcriptional signatures at this time‐point in ovine afferent lymph cells as they migrate from the injection site into the lymphatics following vaccination with a liposome antigen formulation incorporating CpG. We show that at 72 hr post vaccination, liposomes alone induce no changes in gene expression and inflammatory profiles within afferent lymph; however, the incorporation of CpG drives interferon, antiviral and cytotoxic gene programmes. This study also measures the expression of key genes within individual cell types in afferent lymph. Antiviral gene signatures are most prominent in lymphocytes, which may play a significant and unexpected role in sustaining the immune response to vaccination at the site of injection. These findings provide a comprehensive analysis of the in vivo immunological pathways that connect the injection site with the local draining lymph node following vaccination.