bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manifolds with Odd Euler Characteristic and Higher Orientability
Authors: Hoekzema Renee S 
Published: June 2018

Abstract
It is well known that odd-dimensional manifolds have Euler characteristic zero. Furthermore, orientable manifolds have an even Euler characteristic unless the dimension is a multiple of $4$. We prove here a generalisation of these statements: a $k$-orientable manifold (or more generally Poincaré complex) has even Euler characteristic unless the dimension is a multiple of $2^{k+1}$, where we call a manifold $k$-orientable if the i-th Stiefel–Whitney class vanishes for all $0&lt;i&lt; 2^k$ ($k\geq 0$). More generally, we show that for a $k$-orientable manifold the Wu classes $v_l$ vanish for all $l$ that are not a multiple of $2^k$. For $k=0,1,2,3$, $k$-orientable manifolds with odd Euler characteristic exist in all dimensions $2^{k+1}m$, but whether there exists a 4-orientable manifold with an odd Euler characteristic is an open question.
High sensitivity mapping of cortical dopamine D2 receptor expressing neurons
Authors: Khlghatyan Jivan , Quintana Clémentine , Parent Martin , Beaulieu Jean-Martin 
Published: June 2018

AbstractCortical D2 dopamine receptor (Drd2) have mostly been examined in the context of cognitive function regulation and neurotransmission modulation of medial prefrontal cortex by principal neurons and parvalbumin positive, fast-spiking, interneurons in schizophrenia. Early studies suggested the presence of D2 receptors in several cortical areas, albeit with major technical limitations. We used combinations of transgenic reporter systems, recombinase activated viral vectors, quantitative translatome analysis and high sensitivity in situ hybridization to identify D2 receptor expressing cells and establish a map of their respective projections. Our results identified previously uncharacterized clusters of D2 expressing neurons in limbic and sensory regions of the adult mouse brain cortex. Characterization of these clusters by translatome analysis and cell type specific labeling revealed highly heterogeneous expression of D2 receptors in principal neurons and various populations of interneurons across cortical areas. Transcript enrichment analysis also demonstrated variable levels of D2 receptor expression and several orphan G-protein-coupled receptors co-expression in different neuronal clusters, thus suggesting strategies for genetic and therapeutic targeting of D2 expressing neurons in specific cortical areas. These results pave the way for a thorough reexamination of cortical D2 receptor functions, which could provide information about neuronal circuits involved in psychotic and mood disorders.
Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns
Authors: Tully Benjamin J 
Published: June 2018

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.
Toads and roads: transport infrastructure severely impacts dispersal regardless of life stage
Authors: Cayuela Hugo , Bonnaire Éric , Besnard Aurélien 
Published: June 2018

AbstractTransport infrastructure such as roads has been reported to negatively affect dispersal. Their effects on dispersal are thought to be complex, depending on the characteristics of the structure and the intensity of the traffic using it. In addition, individual factors, such as age, may strongly affect dispersal decisions and success when individuals are confronted with transport infrastructure. Despite the importance of this topic for wildlife conservation, few studies have investigated the effect of transport infrastructure on individuals’ dispersal decisions before and after sexual maturity. We examined the effects on two kinds of infrastructure, gravel tracks and paved roads, on the dispersal of an endangered amphibian, the yellow-bellied toad (Bombina variegata). We used capture-recapture data collected during a five-year period on a large, spatially structured population of B. variegata. Our study revealed that emigration rates increased with an individual’s age, while dispersal distance decreased. It also showed that both tracks and roads had negative effects on dispersal. The negative effect of roads was stronger than that of tracks. We additionally found that the effect of tracks on dispersal slightly decreased with a toad’s age. In contrast, the negative effect of roads was severe and relatively similar across age classes.
Effects of planting density on the growth and photosynthetic characteristics ofAlternanthera philoxeroidesunder different nutrient conditions
Authors: Li Ke , Chen Hao , Zhang Haijie , Huang Miansong , Quan Quan , Wang Tong , Liu Jian 
Published: June 2018

AbstractDensity and nutrient level are important factors that might affect the growth of invasive plants. To reveal the effects of plant density on the performance of invasive plantAlternanthera philoxeroidesunder different nutrient conditions, a greenhouse experiment was conducted in whichA. philoxeroideswas planted at three densities (low, medium and high) under three nutrient levels (low, medium and high). The results showed that both planting density and nutrient levels had significant effects on the growth of the plant. The biomass of individual plant and all plants in one pot under medium nutrient level were the highest while the photosynthetic rate and total chlorophyll content were the highest at the high nutrient level. Under different nutrient levels, the photosynthetic rate was the highest at medium planting density. The biomass of single plant decreased with the increase of population density, while the total biomass in the whole pot increased with the increase of density. These characteristics might contribute to the invasion ofA. philoxeroidesand help the plant to form monodominant community.
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics
Authors: Shimamura Teppei , Matsui Yusuke , Kajino Taisuke , Ito Satoshi , Takahashi Takashi , Miyano Satoru 
Published: June 2018

AbstractThe regulation of transcription factor activity dynamically changes across cellular conditions and disease subtypes. The identification of biological modulators contributing to context-specific gene regulation is one of the challenging tasks in systems biology, which is necessary to understand and control cellular responses across different genetic backgrounds and environmental conditions. Previous approaches for identifying biological modulators from gene expression data were restricted to the capturing of a particular type of a three-way dependency among a regulator, its target gene, and a modulator; these methods cannot describe the complex regulation structure, such as when multiple regulators, their target genes, and modulators are functionally related. Here, we propose a statistical method for identifying biological modulators by capturing multivariate local dependencies, based on energy statistics, which is a class of statistics based on distances. Subsequently, our method assigns a measure of statistical significance to each candidate modulator through a permutation test. We compared our approach with that of a leading competitor for identifying modulators, and illustrated its performance through both simulations and real data analysis. Our method, entitled genome-wide identification of modulators using local energy statistical test (GIMLET), is implemented with R (≥ 3.2.2) and is available from github (https://github.com/tshimam/GIMLET).
Causal inference for spatial constancy across whole-body motion
Authors: Perdreau Florian , Cooke James , Koppen Mathieu , Medendorp W. Pieter 
Published: June 2018

AbstractThe brain can estimate the amplitude and direction of self-motion by integrating multiple sources of sensory information, and use this estimate to update object positions in order to provide us with a stable representation of the world. A strategy to improve the precision of the object position estimate would be to integrate this internal estimate and the sensory feedback about the object position based on their reliabilities. Integrating these cues, however, would only be optimal under the assumption that the object has not moved in the world during the intervening body displacement. Therefore, the brain would have to infer whether the internal estimate and the feedback relate to a same external position (stable object), and integrate and/or segregate these cues based on this inference – a process that can be modeled as Bayesian Causal inference. To test this hypothesis, we designed a spatial updating task across passive whole body translation in complete darkness, in which participants (n=11), seated on a vestibular sled, had to remember the world-fixed position of a visual target. Immediately after the translation, a second target (feedback) was briefly flashed around the estimated “updated” target location, and participants had to report the initial target location. We found that the participants’ responses were systematically biased toward the position of the second target position for relatively small but not for large differences between the “updated” and the second target location. This pattern was better captured by a Bayesian causal inference model than by alternative models that would always either integrate or segregate the internally-updated target position and the visual feedback. Our results suggest that the brain implicitly represents the posterior probability that the internally updated estimate and the sensory feedback come from a common cause, and use this probability to weigh the two sources of information in mediating spatial constancy across whole-body motion.Author SummaryA change of an object’s position on our retina can be caused by a change of the object’s location in the world or by a movement of the eye and body. Here, we examine how the brain solves this problem for spatial updating by assessing the probability that the internally-updated location during body motion and observed retinal feedback after the motion stems from the same object location in the world. Guided by Bayesian causal inference model, we demonstrate that participants’ errrors in spatial updating depend nonlinearly on the spatial discrepancy between internally-updated and reafferent visual feedback about the object’s location in the world. We propose that the brain implicitly represents the probability that the internally updated estimate and the sensory feedback come from a common cause, and use this probability to weigh the two sources of information in mediating spatial constancy across whole-body motion.
Biodiversity improves the ecological design of sustainable biofuel systems
Authors: Godwin Casey M. , Lashaway Aubrey R. , Hietala David C. , Savage Phillip E. , Cardinale Bradley J. 
Published: June 2018

AbstractFor algal biofuels to become a commercially viable and sustainable means of decreasing greenhouse gas emissions, growers are going to need to design feedstocks that achieve at least three characteristics simultaneously as follows: attain high yields; produce high quality biomass; and remain stable through time. These three qualities have proven difficult to achieve simultaneously under the ideal conditions of the laboratory, much less under field conditions (e.g., outdoor culture ponds) where feedstocks are exposed to highly variable conditions and the crop is vulnerable to invasive species, disease, and grazers. Here, we show that principles from ecology can be used to improve the design of feedstocks and to optimize their potential for “multifunctionality.” We performed a replicated experiment to test these predictions under outdoor conditions. Using 80 ponds of 1,100 L each, we tested the hypotheses that polycultures would outperform monocultures in terms of the following functions: biomass production, yield of biocrude from biomass, temporal stability, resisting population crashes, and resisting invasions by unwanted species. Overall, species richness improved stability, biocrude yield, and resistance to invasion. While this suggests that polycultures could outperform monocultures on average, invasion resistance was the only function where polycultures outperformed the best single species in the experiment. Due to tradeoffs among different functions that we measured, no species or polyculture was able to maximize all functions simultaneously. However, diversity did enhance the potential for multifunctionality—the most diverse polyculture performed more functions at higher levels than could any of the monocultures. These results are a key finding for ecological design of sustainable biofuel systems because they show that while a monoculture may be the optimal choice for maximizing short‐term biomass production, polycultures can offer a more stable crop of the desired species over longer periods of time.
Regulation of
Aspergillus nidulans
CreA-Mediated Catabolite Repression by the F-Box Proteins Fbx23 and Fbx47
Authors: de Assis Leandro José , Ulas Mevlut , Ries Laure Nicolas Annick , El Ramli Nadia Ali Mohamed , Sarikaya-Bayram Ozlem , Braus Gerhard H. , Bayram Ozgur , Goldman Gustavo Henrique 
Published: June 2018

ABSTRACT

The attachment of one or more ubiquitin molecules by SCF (
S
kp–
C
ullin–
F
-box) complexes to protein substrates targets them for subsequent degradation by the 26S proteasome, allowing the control of numerous cellular processes. Glucose-mediated signaling and subsequent carbon catabolite repression (CCR) are processes relying on the functional regulation of target proteins, ultimately controlling the utilization of this carbon source. In the filamentous fungus
Aspergillus nidulans
, CCR is mediated by the transcription factor CreA, which modulates the expression of genes encoding biotechnologically relevant enzymes. Although CreA-mediated repression of target genes has been extensively studied, less is known about the regulatory pathways governing CCR and this work aimed at further unravelling these events. The Fbx23 F-box protein was identified as being involved in CCR and the Δ
fbx23
mutant presented impaired xylanase production under repressing (glucose) and derepressing (xylan) conditions. Mass spectrometry showed that Fbx23 is part of an SCF ubiquitin ligase complex that is bridged via the GskA protein kinase to the CreA-SsnF-RcoA repressor complex, resulting in the degradation of the latter under derepressing conditions. Upon the addition of glucose, CreA dissociates from the ubiquitin ligase complex and is transported into the nucleus. Furthermore, casein kinase is important for CreA function during glucose signaling, although the exact role of phosphorylation in CCR remains to be determined. In summary, this study unraveled novel mechanistic details underlying CreA-mediated CCR and provided a solid basis for studying additional factors involved in carbon source utilization which could prove useful for biotechnological applications.

IMPORTANCE
The production of biofuels from plant biomass has gained interest in recent years as an environmentally friendly alternative to production from petroleum-based energy sources. Filamentous fungi, which naturally thrive on decaying plant matter, are of particular interest for this process due to their ability to secrete enzymes required for the deconstruction of lignocellulosic material. A major drawback in fungal hydrolytic enzyme production is the repression of the corresponding genes in the presence of glucose, a process known as carbon catabolite repression (CCR). This report provides previously unknown mechanistic insights into CCR through elucidating part of the protein-protein interaction regulatory system that governs the CreA transcriptional regulator in the reference organism
Aspergillus nidulans
in the presence of glucose and the biotechnologically relevant plant polysaccharide xylan.
Kinematic sensitivity analysis of a novel micro-mechanism for displacement amplification
Authors: Iqbal Sohail , Malik Afzaal , Shakoor Rana I 
Published: June 2018

This research article presents the design and analysis of a displacement amplification mechanism based on a microelectromechanical system (MEMS). The mechanism, compared to generic displacement mechanisms, is smaller and capable of amplifying input displacement by a factor of 6.8. Finite element analysis (FEA) is performed with commercial software Intellisuite using the extended finite element method (XFEM) technique to verify the analytical results from mathematical models. Kinematic response and kinematic sensitivity analysis of the amplification mechanism are computationally carried out to predict the effect of different geometric parameters on the performance of the proposed mechanism. The analysis predicts that length and angle of flexure are the two key geometric parameters significantly affecting the amplification factor (AF), with length having a direct relationship and angle of flexure having an inverse relationship. A significant increase in the AF is seen for a flexure length up to 550 μm and angle below 5°. Based on the sensitivity analysis, the design is optimized, and geometric parameters are finalized. Modal analysis and dynamic simulations, including direct-integration transient and steady-state modal analysis, are performed on the mechanism under the application of 25 g. The mechanism can be integrated with any conventional actuating mechanism in a microsystem where the amplification of a small displacement at the output is desired.
Microbiological Etiologies of Pneumonia Complicating Stroke
Authors: Kishore Amit K. , Vail Andy , Jeans Adam R. , Chamorro Angel , Di Napoli Mario , Kalra Lalit , Langhorne Peter , Roffe Christine , Westendorp Willeke , Nederkoorn Paul J. , Garau Javier , van de Beek Diederik , Montaner Joan , Woodhead Mark , Meisel Andreas , Smith Craig J. ,   on behalf of Pneumonia in Stroke Consensus (PISCES) Group
Published: June 2018

Background and Purpose—
Identifying the causal pathogens of pneumonia complicating stroke is challenging, and antibiotics used are often broad spectrum, without recourse to the microbiological cause. We aimed to review existing literature to identify organisms responsible for pneumonia complicating stroke, before developing a consensus-based approach to antibiotic treatment.

Methods—
A systematic literature review of multiple electronic databases using predefined search criteria was undertaken, in accordance with Cochrane and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidance. Published studies of hospitalized adults with ischemic stroke, intracerebral hemorrhage, or both, which identified microbiological etiologies for pneumonia complicating stroke up to January 1, 2017, were considered. Analysis included summary statistics and random-effects meta-analysis where appropriate.

Results—

Fifteen studies (40% ischemic stroke, 60% ischemic stroke and intracerebral hemorrhage) involving 7968 patients were included. Reported occurrence of pneumonia varied considerably between studies (2%–63%) with a pooled frequency of 23% (95% confidence interval, 14%–34%;
I
2
=99%). Where reported (60%), the majority of pneumonia occurred within 1 week of stroke (78%). Reported frequency of positive culture data (15%–88%) varied widely. When isolated, aerobic Gram-negative bacilli (38%) and Gram-positive cocci (16%) were most frequently cultured; commonly isolated organisms included
Enterobacteriaceae
(21.8%:
Klebsiella pneumoniae
, 12.8% and
Escherichia coli
, 9%),
Staphylococcus aureus
(10.1%),
Pseudomonas aeruginosa
(6%),
Acinetobacter baumanii
(4.6%), and
Streptococcus pneumoniae
(3.5%). Sputum was most commonly used to identify pathogens, in isolation (40%) or in conjunction with tracheal aspirate (15%) or blood culture (20%).

Conclusions—
Although the analysis was limited by small and heterogeneous study populations, limiting determination of microbiological causality, this review suggests aerobic Gram-negative bacilli and Gram-positive cocci are frequently associated with pneumonia complicating stroke. This supports the need for appropriately designed studies to determine microbial cause and a consensus-based approach in antibiotic usage and further targeted antibiotic treatment trials for enhanced antibiotic stewardship.
From Christian Polemic to a Jewish-Converso Dialogue
Authors: Yisraeli Yosi 
Published: June 2018

Abstract
This article presents a new reading of the polemical strategies and arguments embodied in the “anti-Jewish” tractate by the converted bishop of Burgos, Pablo de Santa María (c.1352–1435), the Scrutinium scripturarum (c.1432). It suggests the Scrutinium reflected a unique polemical dynamic that emerged between converts and Jews following the mass conversions of 1391 and the early fifteenth century, regarding the spiritual assimilation of converts to their new faith. Grappling with the new challenges faced by converts, the Scrutinium articulated a Christian approach toward rabbinic traditions and Jewish skepticism that differed dramatically from the scholastic–polemical traditions that were employed at the disputation of Tortosa. Its introduction of rabbinic esotericism provided its Latin-reading audience new historical and theological grounds for the integration of rabbinic authority within Christian scholarship and history. In doing so, it embodied what could be considered a distinct “converso voice,” which challenged the customary religious boundaries between Judaism and Christianity.
Apologetic Glosses—Venues for Encounters: Annotations on Abraham in the Latin Translations of the Qurʾān
Authors: Starczewska Katarzyna K. 
Published: June 2018

Abstract
The aim of this article is to present a set of glosses to the Qurʾān written by the sixteenth-century Spanish convert Juan Gabriel and to analyze them in the context of apologetic argumentation. The glosses come from a translation commissioned by Egidio da Viterbo (1518). I present here the index of topics covered by the glosses and argue for their conciliatory character. I also select glosses that focus on the identity of Abraham and compare them with annotations that appear in other Latin translations of the Qurʾān. The conclusion of this study is that, although there was a tradition in Latin Europe of glossing the Qurʾān in particular places, for example in passages where biblical figures are mentioned, Juan Gabriel used this tradition to present Islam as compatible with Christianity rather than a heresy.