bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial attention enhances cortical tracking of quasi-rhythmic visual stimuli
Authors: Tabarelli D. , Keitel C. , Gross J. , Baldauf D. 
Published: July 2019

AbstractSuccessfully interpreting and navigating our natural visual environment requires us to track its dynamics constantly. Additionally, we focus our attention on behaviorally relevant stimuli to enhance their neural processing. Little is known, however, about how sustained attention affects the ongoing tracking of stimuli with rich natural temporal dynamics. Here, we used MRI-informed source reconstructions of magnetoencephalography (MEG) data to map to what extent various cortical areas track concurrent continuous quasi-rhythmic visual stimulation. Further, we tested how top-down visuo-spatial attention influences this tracking process. Our bilaterally presented quasi-rhythmic stimuli covered a dynamic range of 4 – 20Hz, subdivided into three distinct bands. As an experimental control, we also included strictly rhythmic stimulation (10 vs 12 Hz). Using a spectral measure of brain-stimulus coupling, we were able to track the neural processing of left vs. right stimuli independently, even while fluctuating within the same frequency range. The fidelity of neural tracking depended on the stimulation frequencies, decreasing for higher frequency bands. Both attended and non-attended stimuli were tracked beyond early visual cortices, in ventral and dorsal streams depending on the stimulus frequency. In general, tracking improved with the deployment of visuo-spatial attention to the stimulus location. Our results provide new insights into how human visual cortices process concurrent dynamic stimuli and provide a potential mechanism – namely increasing the temporal precision of tracking – for boosting the neural representation of attended input.
Metabolic Recovery and Compensatory Shell Growth of Juvenile Pacific Geoduck Panopea Generosa Following Short-Term Exposure to Acidified Seawater
Authors: Gurr Samuel J. , Vadopalas Brent , Roberts Steven B. , Putnam Hollie M. 
Published: July 2019

AbstractWhile acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 µatm) or elevated (~2400 µatm) pCO2 treatments and in common, ambient conditions, five months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories, however clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after five months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after five months in ambient conditions. Early exposure to low pH appears to trigger carry-over effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.Lay summaryCommercial shellfish hatcheries provide essential food security, but often production can be hampered by sensitivity of shellfish at early life stages. Repeated short-term exposures can increase tolerance and performance of the geoduck clam with implications for sustainable aquaculture.
Causal associations between potentially modifiable risk factors and the Alzheimer’s disease phenome: A Mendelian randomization study
Authors: Andrews Shea J , Fulton-Howard Brian , O’Reilly Paul , Farrer Lindsay A , Haines Jonathan L , Mayeux Richard , Naj Adam C , Pericak-Vance Margaret A , Schellenberg Gerard D , Wang Li-San , Marcora Edoardo , Goate Alison M 
Published: July 2019

AbstractObjectiveTo evaluate the causal association of 22 previously reported risk factors for Alzheimer’s disease (AD) on the “AD phenome”: AD, AD age of onset (AAOS), hippocampal volume, cortical surface area and thickness, cerebrospinal fluid (CSF) levels of Aβ42, tau, and ptau181, and the neuropathological burden of neuritic plaques, neurofibrillary tangles, and vascular brain injury (VBI).MethodsPolygenic risk scores (PRS) for the 22 risk factors were computed in 26,431 AD cases/controls and the association with AD was evaluated using logistic regression. Two-sample Mendelian randomization was used to evaluate the causal effect of risk factors on the AD phenome.ResultsPRS for increased education and diastolic blood pressure were associated with reduced risk for AD. PRS for increased total cholesterol and moderate-vigorous physical activity were associated with an increased risk of AD. MR indicated that only Education was causally associated with reduced risk of AD, delayed AAOS, and increased cortical surface area and thickness. Total-and LDL-cholesterol levels were causally associated with increased neuritic plaque burden, while diastolic blood pressure and pulse pressure are causally associated with increased risk of VBI. Furthermore, total cholesterol was associated with decreased hippocampal volume; smoking initiation and BMI with decreased cortical thickness; and sleep duration with increased cortical thickness.InterpretationOur comprehensive examination of the genetic evidence for the causal roles of previously reported risk factors in AD using PRS and MR, supports a causal role for education, blood pressure, cholesterol levels, smoking, and BMI with the AD phenome.
Tracking the mind’s eye: Primate gaze behavior during virtual visuomotor navigation reflects belief dynamics
Authors: Lakshminarasimhan Kaushik J , Avila Eric , Neyhart Erin , DeAngelis Gregory C , Pitkow Xaq , Angelaki Dora E 
Published: July 2019

SUMMARYTo take the best actions, we often need to maintain and update beliefs about variables that cannot be directly observed. To understand the principles underlying such belief updates, we need tools to uncover subjects’ belief dynamics from natural behaviour. We tested whether eye movements could be used to infer subjects’ beliefs about latent variables using a naturalistic, visuomotor navigation task. We observed eye movements that appeared to continuously track the goal location even when no visible target was present there. Accurate goal-tracking was associated with improved task performance, and inhibiting eye movements in humans impaired navigation precision. By using passive stimulus playback and manipulating stimulus reliability, we show that subjects’ eye movements are likely voluntary, rather than reflexive. These results suggest that gaze dynamics play a key role in action-selection during challenging visuomotor behaviours, and may possibly serve as a window into the subject’s dynamically evolving internal beliefs.
Leveraging peptide substrate libraries to design inhibitors of bacterial Lon protease
Authors: Babin Brett M. , Kasperkiewicz Paulina , Janiszewski Tomasz , Yoo Euna , Drąg Marcin , Bogyo Matthew 
Published: July 2019

AbstractLon is a widely-conserved housekeeping protease found in all domains of life. Bacterial Lon is involved in the recovery from various types of stress, including tolerance to fluoroquinolone antibiotics, and is linked to pathogenesis in a number of organisms. However, detailed functional studies of Lon have been limited by the lack of selective, cell-permeable inhibitors. Here we describe the use of positional scanning libraries of hybrid peptide substrates to profile the primary sequence specificity of bacterial Lon. In addition to identifying optimal natural amino acid binding preferences, we identified several non-natural residues that were leveraged to develop optimal peptide substrates as well as a potent peptidic boronic acid inhibitor of Lon. Treatment ofE. coliwith this inhibitor promotes UV-induced filamentation and reduces tolerance to ciprofloxacin, phenocopying establishedlon-deletion phenotypes. It is also non-toxic to mammalian cells due to its increased selectivity for Lon over the proteasome. Our results provide new insight into the primary substrate specificity of Lon and identify substrates and an inhibitor that will serve as useful tools for dissecting the diverse cellular functions of Lon.
Evidence that inconsistent gene prediction can mislead analysis of algal genomes
Authors: Chen Yibi , González-Pech Raúl A. , Stephens Timothy G. , Bhattacharya Debashish , Chan Cheong Xin 
Published: July 2019

AbstractComparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.
Regulation of nucleolar dominance inDrosophila melanogaster
Authors: Warsinger-Pepe Natalie , Li Duojia , Yamashita Yukiko M. 
Published: July 2019

AbstractIn eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon, whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e. non-hybrid contexts). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms (SNPs) between X rDNA vs. Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development ofD. melanogaster. We demonstrate that nucleolar dominance is a developmentally-regulated program, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g. X/Y, X/X, X/X/Y) and a chromosome rearrangement, we show that Y chromosome rDNA likely containsciselements that dictate its dominance over the X chromosome rDNA. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation/silencing in nucleolar dominance.
Challenges in the calibration of large-scale ordinary differential equation models
Authors: Kapfer Eva-Maria , Stapor Paul , Hasenauer Jan 
Published: July 2019

AbstractMathematical models based on ordinary differential equations have been employed with great success to study complex biological systems. With soaring data availability, more and more models of increasing size are being developed. When working with these large-scale models, several challenges arise, such as high computation times or poor identifiability of model parameters. In this work, we review and illustrate the most common challenges using a published model of cellular metabolism. We summarize currently available methods to deal with some of these challenges while focusing on reproducibility and reusability of models, efficient and robust model simulation and parameter estimation.
Phase variation of a signal transduction system controlsClostridioides difficilecolony morphology, motility, and virulence
Authors: Garrett Elizabeth M. , Sekulovic Ognjen , Wetzel Daniela , Jones Joshua B. , Edwards Adrianne N. , Vargas-Cuebas Germán , McBride Shonna M. , Tamayo Rita 
Published: July 2019

AbstractRecent work has revealed thatClostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. ManyC. difficilestrains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show thatC. difficilereversibly differentiates into rough and smooth colony morphologies, and that bacteria derived from the isolates display opposing surface and swimming motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein CmrRST, which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of Type IV pili, suggesting a novel mechanism of surface expansion inC. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration. In a hamster model of acuteC. difficiledisease, colony morphology correlates with virulence, and the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressingC. difficile. Our findings indicate thatC. difficileemploys phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis.Significance StatementPhenotypic heterogeneity within a genetically clonal population allows many mucosal pathogens to survive within their hosts, balancing the need to produce factors that promote colonization and persistence with the need to avoid the recognition of those factors by the host immune system. Recent work suggests that the human intestinal pathogenClostridium difficileemploys phase variation during infection to generate a heterogeneous population differing in swimming motility, toxin production, and more. This study identifies a signal transduction system that broadly impactsC. difficilephysiology and behaviorin vitroand in an animal model. Phase variation of this system is therefore poised to modulate the coordinated expression of multiple mechanisms influencingC. difficiledisease development.
Species‐specific strategies increase unpredictability of escape flight in eared moths
Authors: Hügel Theresa , Goerlitz Holger R. 
Published: July 2019

Abstract

Many prey species overlap in time and space and are hunted by the same predators. A common anti‐predator behaviour is using evasive manoeuvres to escape an attacking predator. The escape‐tactic diversity hypothesis postulates that species‐specific differences in evasive behaviour will increase the overall unpredictability experienced by predators within a predator–prey community. Evolutionary, escape‐tactic diversity would be driven by the enhanced predator protection for each prey individual in the community. However, escape‐tactic diversity could also be a functional consequence of morphological differences that correlate with evasive capabilities.

Echolocating bats and eared moths are a textbook example of predator–prey interactions. Moths exhibit evasive flight with diverse tactics; however, the variability of their evasive flight within and between species and individuals has never been quantified systematically. In addition, moth species show variation in size, which correlates with their flight capability.

We recorded flight strength during tethered flight of eight sympatric moth species in response to the same level of simulated bat predation. Our method allowed us to record kinematic parameters that are correlated with evasive flight in a controlled way to investigate species‐specific differences in escape tactics.

We show species‐specific and size‐independent differences in both overall flight strength and change of flight strength over time, supporting the escape‐tactic diversity hypothesis for eared moths. Additionally, we show strong interindividual differences in evasive flight within some species. This diversity in escape tactic between eared moths increases the overall unpredictability of evasive flight experienced by bat predators, likely providing increased protection against predatory bats for the single individual.
Some remarks on Q‐compensated sparse deconvolution without knowing the quality factor Q
Authors: Chai Xintao , Peng Ronghua , Tang Genyang , Chen Wei , Li Jingnan 
Published: July 2019

ABSTRACTThe subsurface media are not perfectly elastic, thus anelastic absorption, attenuation and dispersion (aka Q filtering) effects occur during wave propagation, diminishing seismic resolution. Compensating for anelastic effects is imperative for resolution enhancement. Q values are required for most of conventional Q‐compensation methods, and the source wavelet is additionally required for some of them. Based on the previous work of non‐stationary sparse reflectivity inversion, we evaluate a series of methods for Q‐compensation with/without knowing Q and with/without knowing wavelet. We demonstrate that if Q‐compensation takes the wavelet into account, it generates better results for the severely attenuated components, benefiting from the sparsity promotion. We then evaluate a two‐phase Q‐compensation method in the frequency domain to eliminate Q requirement. In phase 1, the observed seismogram is disintegrated into the least number of Q‐filtered wavelets chosen from a dictionary by optimizing a basis pursuit denoising problem, where the dictionary is composed of the known wavelet with different propagation times, each filtered with a range of possible values. The elements of the dictionary are weighted by the infinity norm of the corresponding column and further preconditioned to provide wavelets of different values and different propagation times equal probability to entry into the solution space. In phase 2, we derive analytic solutions for estimates of reflectivity and Q and solve an over‐determined equation to obtain the final reflectivity series and Q values, where both the amplitude and phase information are utilized to estimate the Q values. The evaluated inversion‐based Q estimation method handles the wave‐interference effects better than conventional spectral‐ratio‐based methods. For Q‐compensation, we investigate why sparsity promoting does matter. Numerical and field data experiments indicate the feasibility of the evaluated method of Q‐compensation without knowing Q but with wavelet given.
Predicting the fundamental thermal niche of crop pests and diseases in a changing world: A case study on citrus greening
Authors: Taylor Rachel A. , Ryan Sadie J. , Lippi Catherine A. , Hall David G. , Narouei‐Khandan Hossein A. , Rohr Jason R. , Johnson Leah R. 
Published: July 2019

Abstract

Predicting where crop pests and diseases can occur, both now and in the future under different climate change scenarios, is a major challenge for crop management. One solution is to estimate the fundamental thermal niche of the pest/disease to indicate where establishment is possible. Here, we develop methods for estimating and displaying the fundamental thermal niche of pests and pathogens and apply these methods to Huanglongbing (HLB), a vector‐borne disease that is currently threatening the citrus industry worldwide.

We derive a suitability metric based on a mathematical model of HLB transmission between tree hosts and its vector Diaphorina citri, and incorporate the effect of temperature on vector traits using data from laboratory experiments performed at different temperatures. We validate the model using data on the historical range of HLB.

Our model predicts that transmission of HLB is possible between 16 and 33°C with peak transmission at ~25°C. The greatest uncertainty in our suitability metric is associated with the mortality of the vectors at peak transmission, and fecundity at the edges of the thermal range, indicating that these parameters need further experimental work.

We produce global thermal niche maps by plotting how many months each location is suitable for establishment of the pest/disease. This analysis reveals that the highest suitability for HLB occurs near the equator in large citrus‐producing regions, such as Brazil and South‐East Asia. Within the Northern Hemisphere, the Iberian peninsula and California are HLB suitable for up to 7 months of the year and are free of HLB currently.

Policy implications. We create a thermal niche map which indicates the places at greatest risk of establishment should a crop disease or pest enter these regions. This indicates where surveillance should be focused to prevent establishment. Our mechanistic method can be used to predict new areas for Huanglongbing transmission under different climate change scenarios and is easily adapted to other vector‐borne diseases and crop pests.
Lisbon After the Crisis: From Credit‐fuelled Suburbanization to Tourist‐driven Gentrification
Authors: Lestegás Iago 
Published: July 2019

AbstractThis article examines Lisbon's post‐crisis transition from a once dominant process of suburban expansion enabled by abundant credit to one of ongoing gentrification of its historic centre. In my research, I draw on quantitative and qualitative data to illustrate the remarkable growth of the metropolitan area's population and dwelling stock until the global financial crisis—which affected the Portuguese economy in the course of a process of financialization that relied heavily on the housing industry—and the intensity of urban rehabilitation in subsequent years. However, there is evidence that the latter has not halted nor reduced the loss of long‐term residents in the historic centre, as tourists and other international gentrifiers occupy the upgraded dwelling stock amid an escalation of house prices and rents. The specific contribution of this research lies in the link that it establishes between Lisbon's ongoing process of inner‐city gentrification and the lack of suburban expansion after 2007. By showing that the credit crunch triggered a shift in the geographic location of real‐estate capital that materialized in a new urban development model, this research adds an empirical layer to the study of the spatial effects of the crisis and contributes to the literature on the subsequent restructuring of southern European housing markets.