julilili42/papers huggingface dataset:
Cyanodermella asteris sp. nov. (Ostropales) from the inflorescence axis of Aster tataricus
2017-04-27

An endophytic fungus isolated from the inflorescence axis of Aster tataricus is proposed as a new species. Phylogenetic analyses based on sequences from the ribosomal DNA cluster (the ITS1+5.8S+ITS2, 18S, and 28S regions) and the RPB2 gene revealed a relationship between the unknown fungus and the Stictidaceae lineage of the Ostropales. The new species, Cyanodermella asteris, grows in standard fungal growth media as a fluffy, pink filamentous fungus. Asexual and sexual sporulation has not yet been observed on media or in the plant.
The Entropy of Words&mdash;Learnability and Expressivity across More Than 1000 Languages
2017-04-27

The choice associated with words is a fundamental property of natural languages. It lies at the heart of quantitative linguistics, computational linguistics, and language sciences more generally. Information-theory gives us tools at hand to measure precisely the average amount of choice associated with words&amp;mdash;the word entropy. Here we use three parallel corpora&amp;mdash;encompassing ca. 450 million words in 1916 texts and 1259 languages&amp;mdash;to tackle some of the major conceptual and practical problems of word entropy estimation: dependence on text size, register, style and estimation method, as well as non-independence of words in co-text. We present three main results: 1) a text size of 50K tokens is sufficient for word entropies to stabilize throughout the text, 2) across languages of the world, word entropies display a unimodal distribution that is skewed to the right. This suggests that there is a trade-off between the learnability and expressivity of words across languages of the world. 3) There is a strong linear relationship between unigram entropies and entropy rates, suggesting that they are inherently linked. We discuss the implications of these results for studying the diversity and evolution of languages from an information-theoretic point of view.
Likelihood-based parameter estimation and comparison of dynamical cognitive models.
2017-04-27

Dynamical models of cognition play an increasingly important role in driving theoretical and experimental research in psychology. Therefore, parameter estimation, model analysis and comparison of dynamical models are of essential importance. Here we propose a maximum-likelihood approach for model analysis in a fully dynamical framework that includes time-ordered experimental data. Our methods can be applied to dynamical models for the prediction of discrete behavior (e.g., movement onsets), in particular, we use a dynamical model of saccade generation in scene viewing as a case study for our approach. For this model, the likelihood function can be computed directly by numerical simulation, which enables more efficient parameter estimation including Bayesian inference to obtain reliable estimates and corresponding credible intervals. Using hierarchical models inference is even possible for individual observers. Furthermore, our likelihood approach can be used to compare different models. In our example, the dynamical framework is shown to outperform non-dynamical statistical models. Additionally, the likelihood based evaluation differentiates model variants, which produced indistinguishable predictions on hitherto used statistics. Our results indicate that the likelihood approach is a promising framework for dynamical cognitive models.
Heterogeneous Contribution of Microdeletions in the Development of Common Generalized and Focal epilepsies
2017-04-27

ABSTRACT Background Microdeletions are known to confer risk to epilepsy, particularly at genomic rearrangement “hotspot” loci. However, deciphering their role outside hotspots and risk assessment by epilepsy sub-type has not been conducted. Methods We assessed the burden, frequency and genomic content of rare, large microdeletions found in a previously published cohort of 1,366 patients with Genetic Generalized Epilepsy (GGE) plus two sets of additional unpublished genome-wide microdeletions found in 281 Rolandic Epilepsy (RE) and 807 Adult Focal Epilepsy (AFE) patients, totaling 2,454 cases. These microdeletion sets were assessed in a combined analysis and in sub-type specific approaches against 6,746 ethnically matched controls. Results When hotspots are considered, we detected an enrichment of microdeletions in the combined epilepsy analysis (adjusted-P= 2.00×10 -7 ; OR = 1.89; 95%-CI: 1.51-2.35), where the implicated microdeletions overlapped with rarely deleted genes and those involved in neurodevelopmental processes. Sub-type specific analyses showed that hotspot deletions in the GGE subgroup contribute most of the signal (adjusted-P = 1.22×10 -12 ; OR = 7.45; 95%-CI = 4.20-11.97). Outside hotspot loci, microdeletions were enriched in the GGE cohort for neurodevelopmental genes (adjusted-P = 4.78×10 -3 ; OR = 2.30; 95%-CI = 1.42-3.70), whereas no additional signal was observed for RE and AFE. Still, gene content analysis was able to identify known ( NRXN1 , RBFOX1 and PCDH7 ) and novel ( LOC102723362 ) candidate genes affected in more than one epilepsy sub-type but not in controls. Conclusions Our results show a heterogeneous effect of recurrent and non-recurrent microdeletions as part of the genetic architecture of GGE and a minor to negligible contribution in the etiology of RE and AFE.
Tumor-targeted IL-12 combined with local irradiation leads to systemic tumor control via abscopal effects in vivo
2017-04-28

NHS-IL12 is an immunocytokine, a fusion protein of IL12's functional domains and a necrosis-targeting antibody, which has shown significant effects against human rhabdomyosarcoma xenografts in a humanized tumor model, including terminal growth arrest and differentiation of the tumor cells. Here, we locally irradiated the tumors, increasing necrosis and consequently intratumoral immune cytokine availability, and asked whether this effect may surmount efficacy of single treatment modality. Humanized mice bearing bilateral rhabdomyosarcoma xenografts were evaluated for tumor burden and survival after irradiation, systemic NHS-IL12 therapy or a combination of both. Intratumoral immune compartments were characterized by immunohistochemistry and molecular methods. T<sub>H</sub>1-cytokine dependency of underlying effector mechanisms were investigated <i>in vitro</i> in several human tumor cell lines. NHS-IL12 when combined with irradiation terminally arrested tumor growth and significantly improved survival. Combination treatment induced dense intratumoral T-cell infiltrates, clonal epitope-specific T-cell expansions, expression of cytotoxins, decreased pro-tumorigenic cytokines and induced senescence and differentiation in the cancer cells. Senescence and differentiation were reproduced <i>in vitro</i> and confirmed to be dependent on T<sub>H</sub>1 cytokines IFNγ and TNF-α. NHS-IL12 and irradiation together induced broad intratumoral T<sub>H</sub>1 biased NK and T-cell compartments, established antitumoral cytokine profiles and irreversibly growth arrested tumor cells, leading to systemic cancer control and improved survival. For the first time, we describe immune-induced senescence as a novel mechanism resulting from a treatment regimen combining irradiation with immunotherapy.
Biosynthesis of the β‐Lactone Proteasome Inhibitors Belactosin and Cystargolide
2017-04-28

Abstract Belactosins and cystargolides are natural product proteasome inhibitors from Actinobacteria. Both feature dipeptidic backbones and a unique β‐lactone building block. Herein, we present a detailed investigation of their biosynthesis. Identification and analysis of the corresponding gene clusters indicated that both compounds are assembled by rare single‐enzyme amino acid ligases. Feeding experiments with isotope‐labeled precursors and in vitro biochemistry showed that the formation of the β‐lactone warhead is unprecedented and reminiscent of leucine biosynthesis, and that it involves the action of isopropylmalate synthase homologues.
A Reaction Cycle for Octahedral Tungsten Iodide Clusters
2017-04-28

A reaction cycle is shown for octahedral tungsten iodide compounds. The thermal transformation of W<sub>6</sub>I<sub>16</sub> (W<sub>6</sub>I<sub>12</sub>·2I<sub>2</sub>) via release of iodine proceeds via the new W<sub>6</sub>I<sub>13</sub> (W<sub>6</sub>I<sub>12</sub>·xI<sub>2</sub> with 0 < x ≤ 1/2) to yield a new modification of W<sub>6</sub>I<sub>12</sub>, denoted as α-W<sub>6</sub>I<sub>12</sub>. When heated, α-W<sub>6</sub>I<sub>12</sub> is converted into the known (β-)W<sub>6</sub>I<sub>12</sub>. The reaction of (β-)W<sub>6</sub>I<sub>12</sub> with I<sub>2</sub> leads to the formation of the starting compound W<sub>6</sub>I<sub>16</sub>. The new compounds W<sub>6</sub>I<sub>13</sub> (W<sub>6</sub>I<sub>12</sub>·xI<sub>2</sub> with 0 < x ≤ 1/2) and α-W<sub>6</sub>I<sub>12</sub> are structurally characterized by powder and single-crystal X-ray diffraction techniques. The thermal decomposition of W<sub>6</sub>I<sub>16</sub> and the monotropic phase transition of α-W<sub>6</sub>I<sub>12</sub> into β-W<sub>6</sub>I<sub>12</sub> are examined by differential scanning calorimetry measurements.
Interaction effects in a microscopic quantum wire model with strong spin–orbit interaction
2017-04-28

We investigate the effect of strong interactions on the spectral properties\\nof quantum wires with strong Rashba spin-orbit interaction in a magnetic field,\\nusing a combination of Matrix Product State and bosonization techniques.\\nQuantum wires with strong Rashba spin-orbit interaction and magnetic field\\nexhibit a partial gap in one-half of the conducting modes. Such systems have\\nattracted wide-spread experimental and theoretical attention due to their\\nunusual physical properties, among which are spin-dependent transport, or a\\ntopological superconducting phase when under the proximity effect of an s-wave\\nsuperconductor. As a microscopic model for the quantum wire we study an\\nextended Hubbard model with spin-orbit interaction and Zeeman field. We obtain\\nspin resolved spectral densities from the real-time evolution of excitations,\\nand calculate the phase diagram. We find that interactions increase the pseudo\\ngap at and thus also enhance the Majorana-supporting phase and\\nstabilize the helical spin order. Furthermore, we calculate the optical\\nconductivity and compare it with the low energy spiral Luttinger Liquid result,\\nobtained from field theoretical calculations. With interactions, the optical\\nconductivity is dominated by an excotic excitation of a bound\\nsoliton-antisoliton pair known as a breather state. We visualize the\\noscillating motion of the breather state, which could provide the route to\\ntheir experimental detection in e.g. cold atom experiments.\\n
Fused thia-heterocycles via isothiocyanates. Part I. Facile synthesis of some new 1-benzothiopyran- 4-one derivatives
2017-04-28

Abstract A selected set of new 4 H -benzothiopyran-4-one derivatives 6a–h has been prepared by a one-pot reaction involving deprotonated methyl 3-oxo-3(2′,4′,5′-trichlorophenyl)propanoate 5 and the appropriate aryl or alkyl isothiocyanate. 2,4,5-Trichloroacetophenone 4 , required for the synthesis of 5 , is successfully prepared by Friedel–Craft’s acetylation of 1,2,4-trichlorobenzene in 82% yield. The structures of the new compounds 5 and 6a–h are based on microanalytical and spectral (NMR, MS(EI), and HRMS) data.
0693 VARIATION IN ACTIGRAPHY-ESTIMATED REST-ACTIVITY PATTERNS BY DEMOGRAPHIC FACTORS
2017-04-28

Rest-activity patterns provide an indication of circadian rhythmicity in the free-living setting. We aimed to describe the distributions of rest-activity patterns in a convenience sample of adults and children across demographic variables using parametric and non-parametric analytical methods. A sample of adults (N=590) and children (N=58) wore an actigraph on their non-dominant wrist for 7 days and nights. Cosinor regression methods were applied to the accelerometer count data to calculate MESOR, acrophase and amplitude. Non-parametric methods were used to calculate the intra-daily stability, inter-daily variability, most active 10 hour period, least active 5 hour period, and relative amplitude. Demographic variables examined included age, sex, race, education, marital status, and household income. Linear mixed effects models were used to test for demographic differences in rest-activity patterns. Adolescents, compared to younger children, had later timing of peak activity (β=1.1 hours [95%CI: 0.4, 1.2] and peak inactivity (β=1.6 hours [95%CI: 0.9, 2.3]), lower activity levels during their least and most active periods (β=0.4 ln counts [95%CI: 0.1, 0.6] and β=-709 counts [95%CI: -1003, -416]), and less regular rest-activity patterns. Adults (i.e. ages 40 to 49 years), compared to younger adults (ages 18 to 29 years), had earlier timings of peak activity and peak inactivity (β=-1.0 hours [95%CI: -1.6, -0.4] and β=-0.7 hours [95%CI: -1.2, -0.2]), and their rest-activity patterns were more regular. Adult females and whites had more stable rest-activity patterns compared to African Americans and adult males. Higher educated adults had a later timing of their peak activities (β= 0.8 hours [95%CI: 0.4, 1.2]) and also showed less stable rest-activity patterns. Rest-activity patterns vary across the lifespan, and differ by race, sex and education. Understanding population variation in these patterns provides a foundation for further elucidating the health implications of rest-activity patterns across the lifespan. This work was supported by NIH grants U01-CA116850, U54-CA155496, U54-CA155626, U54-CA155435 and U54-CA155850 and 1R01-CA164993. JM, CRM, PJ were supported by NIH grants K01-HL123612, 1F31-CA183125 and K99-CA201542, respectively. MQ was supported by a scholarship from the Tuebinger Program for the Advancement of Women in Science.
Ring opening of cyclobutane in 1,3-dimethyl-5-methylenebarbituric acid dimer by various nucleophiles
2017-04-28

Abstract The reactivity of cyclobutane moiety in 1,3-dimethyl-5-methylenebarbituric acid dimer ( 5 ) towards different nucleophiles was investigated. New derivatives of 5-(substituted methyl)-1,3-dimethylbarbiturate 6–13 were prepared in good yields using various aliphatic amines, cyanide anion, and Ph 3 P, Ph 3 As, Ph 3 Sb. Chemical structures of synthesized products were characterized using NMR, MS, and elemental analysis. The reaction of thiophenoxide and thiocyanate nucleophiles with 5 did not give any new products.
10-Month-Old Infants Are Sensitive to the Time Course of Perceived Actions: Evidence From a Study Combining Eye-tracking and EEG
2017-04-28

Abstract Research has shown that infants are able to track a moving target efficiently – even if it is transiently occluded from sight. This basic ability allows prediction of when and where events happen in everyday life. Yet, it is unclear whether, and how, infants internally represent the time course of ongoing movements to derive predictions. In this study, 10-month-old crawlers observed the video of a same-aged crawling baby that was transiently occluded and reappeared in either a temporally continuous or non-continuous manner (i.e., delayed by 500 ms vs. forwarded by 500 ms relative to the real-time movement). Eye movement and rhythmic neural brain activity (EEG) were measured simultaneously. Eye movement analyses showed that infants were sensitive to slight temporal shifts in movement continuation after occlusion. Furthermore, brain activity related to sensorimotor rather than mnemonic processing differed between observation of continuous and non-continuous movements. Early sensitivity to an action’s timing may hence be explained within the internal real-time simulation account of action observation. Overall, the results support the hypothesis that 10-month-old infants are well prepared for internal representation of the time course of observed movements that are within the infants’ current motor repertoire.
0967 BARRIERS TO HEALTHY SLEEP AND THE ACCEPTABILITY OF A SMARTPHONE APP FOR IMPROVING SLEEP IN AT-RISK ADOLESCENTS
2017-04-28

Deficient sleep is highly prevalent in adolescents and contributes to a range of adverse health and behavioral outcomes. Smartphone apps provide inexpensive and readily accessible platforms for engaging adolescents in sleep health promoting interventions, particularly with populations at increased risk of short sleep such as ethnic/racial minority teens. Designing effective apps, however, requires better understanding of the reasons for poor sleep among adolescents as well as their readiness to use sleep health apps. We conducted three focus groups (N=27 total, age 14 to 18 years) in adolescents living in low- and middle-income racially/ethnically diverse Boston (MA) neighborhoods. We also interviewed 10 participants who provided specific feedback on two commercially available sleep promoting smartphone apps, one of which each participant had used for 2 weeks preceding the interviews. Focus group discussions and interviews were audio-recorded, transcribed and thematically analyzed. Reasons for deficient sleep that were common across all groups were: academic demands; disrupted circadian rhythms; environmental, emotional and cognitive factors; and use of stimulants and electronic devices. Reluctance to follow scheduled sleep routines on weekends and feelings of dependency on personal electronic devices emerged as important barriers to the adoption of sleep hygiene recommendations for a majority of the participants. While participants expressed potential interest in an app-based sleep intervention, they were doubtful about successfully adopting sleep hygiene practices, especially on weekends. The overall feedback on two commercial sleep apps was positive, with a good adherence and engagement rate (80% reported usage of 5 days and more per week), and perceived health benefits (70%). This qualitative research highlights the challenges in addressing aspects of sleep hygiene such as consistency of sleep schedule and use of electronics. The positive responses to use of apps suggest that with appropriate content and design they may be leveraged to promote healthy sleep in adolescents. This study was funded by an American Sleep Medicine Foundation Focused Project Award. MQ was supported by a scholarship from the Tuebinger Program for the Advancement of Women in Science.
Absence of ppGpp Leads to Increased Mobilization of Intermediately Accumulated Poly(3-Hydroxybutyrate) in Ralstonia eutropha H16
2017-04-29

ABSTRACT In this study, we constructed a set of Ralstonia eutropha H16 strains with single, double, or triple deletions of the (p)ppGpp synthase/hydrolase ( spoT1 ), (p)ppGpp synthase ( spoT2 ), and/or polyhydroxybutyrate (PHB) depolymerase ( phaZa1 or phaZa3 ) gene, and we determined the impact on the levels of (p)ppGpp and on accumulated PHB. Mutants with deletions of both the spoT1 and spoT2 genes were unable to synthesize detectable amounts of (p)ppGpp and accumulated only minor amounts of PHB, due to PhaZa1-mediated depolymerization of PHB. In contrast, unusually high levels of PHB were found in strains in which the (p)ppGpp concentration was increased by the overexpression of (p)ppGpp synthase (SpoT2) and the absence of (p)ppGpp hydrolase. Determination of (p)ppGpp levels in wild-type R. eutropha under different growth conditions and induction of the stringent response by amino acid analogs showed that the concentrations of (p)ppGpp during the growth phase determine the amount of PHB remaining in later growth phases by influencing the efficiency of the PHB mobilization system in stationary growth. The data reported for a previously constructed Δ spoT2 strain (C. J. Brigham, D. R. Speth, C. Rha, and A. J. Sinskey, Appl Environ Microbiol 78:8033–8044, 2012, https://doi.org/10.1128/AEM.01693-12 ) were identified as due to an experimental error in strain construction, and our results are in contrast to the previous indication that the spoT2 gene product is essential for PHB accumulation in R. eutropha . IMPORTANCE Polyhydroxybutyrate (PHB) is an important intracellular carbon and energy storage compound in many prokaryotes and helps cells survive periods of starvation and other stress conditions. Research activities in several laboratories over the past 3 decades have shown that both PHB synthase and PHB depolymerase are constitutively expressed in most PHB-accumulating bacteria, such as Ralstonia eutropha . This implies that PHB synthase and depolymerase activities must be well regulated in order to avoid a futile cycle of simultaneous PHB synthesis and PHB degradation (mobilization). Previous reports suggested that the stringent response in Rhizobium etli and R. eutropha is involved in the regulation of PHB metabolism. However, the levels of (p)ppGpp and the influence of those levels on PHB accumulation and PHB mobilization have not yet been determined for any PHB-accumulating species. In this study, we optimized a (p)ppGpp extraction procedure and a high-performance liquid chromatography–mass spectrometry (HPLC-MS)-based detection method for the quantification of (p)ppGpp in R. eutropha . This enabled us to study the relationship between the concentrations of (p)ppGpp and the accumulated levels of PHB in the wild type and in several constructed mutant strains. We show that overproduction of the alarmone (p)ppGpp correlated with reduced growth and massive overproduction of PHB. In contrast, in the absence of (p)ppGpp, mobilization of PHB was dramatically enhanced.
Murine Lymphocyte Labeling by <sup>64</sup>Cu-Antibody Receptor Targeting for <em>In Vivo </em> Cell Trafficking by PET/CT
2017-04-29

This protocol illustrates the production of <sup>64</sup>Cu and the chelator conjugation/radiolabeling of a monoclonal antibody (mAb) followed by murine lymphocyte cell culture and <sup>64</sup>Cu-antibody receptor targeting of the cells. In vitro evaluation of the radiolabel and non-invasive in vivo cell tracking in an animal model of an airway delayed-type hypersensitivity reaction (DTHR) by PET/CT are described. In detail, the conjugation of a mAb with the chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) is shown. Following the production of radioactive <sup>64</sup>Cu, radiolabeling of the DOTA-conjugated mAb is described. Next, the expansion of chicken ovalbumin (cOVA)-specific CD4<sup>+</sup> interferon (IFN)-γ-producing T helper cells (cOVA-TH1) and the subsequent radiolabeling of the cOVA-TH1 cells are depicted. Various in vitro techniques are presented to evaluate the effects of <sup>64</sup>Cu-radiolabeling on the cells, such as the determination of cell viability by trypan blue exclusion, the staining for apoptosis with Annexin V for flow cytometry, and the assessment of functionality by IFN-γ enzyme-linked immunosorbent assay (ELISA). Furthermore, the determination of the radioactive uptake into the cells and the labeling stability are described in detail. This protocol further describes how to perform cell tracking studies in an animal model for an airway DTHR and, therefore, the induction of cOVA-induced acute airway DHTR in BALB/c mice is included. Finally, a robust PET/CT workflow including image acquisition, reconstruction, and analysis is presented. The <sup>64</sup>Cu-antibody receptor targeting approach with subsequent receptor internalization provides high specificity and stability, reduced cellular toxicity, and low efflux rates compared to common PET-tracers for cell labeling, e.g.<sup>64</sup>Cu-pyruvaldehyde bis(N4-methylthiosemicarbazone) (<sup>64</sup>Cu-PTSM). Finally, our approach enables non-invasive in vivo cell tracking by PET/CT with an optimal signal-to-background ratio for 48 h. This experimental approach can be transferred to different animal models and cell types with membrane-bound receptors that are internalized.