bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory processing remains sensitive to environmental experience during adolescence
Authors: Anbuhl Kelsey L. , Yao Justin D. , Hotz Robert A. , Mowery Todd M. , Sanes Dan H. 
Published: April 2021

AbstractDevelopment is a time of great opportunity. A heightened period of neural plasticity contributes to dramatic improvements in perceptual, motor, and cognitive skills. However, developmental plasticity poses a risk: greater malleability of neural circuits exposes them to environmental factors that may impede behavioral maturation. While these risks are well-established prior to sexual maturity (i.e., critical periods), the degree of neural vulnerability during adolescence remains uncertain. To address this question, we induced a transient period of hearing loss (HL) spanning adolescence in the gerbil, confirmed by assessment of circulating sex hormones, and asked whether behavioral and neural deficits are diminished. Wireless recordings were obtained from auditory cortex neurons during perceptual task performance, and within-session behavioral and neural sensitivity were compared. We found that a transient period of adolescent HL caused a significant perceptual deficit (i.e., amplitude modulation detection thresholds) that could be attributed to degraded auditory cortex processing, as confirmed with both single neuron and population-level analyses. In contrast, perceptual deficits did not occur when HL of the same duration was induced in adulthood. To determine whether degraded auditory cortex encoding was attributable to an intrinsic change, we obtained auditory cortex brain slices from adolescent HL animals, and recorded synaptic and discharge properties from auditory cortex pyramidal neurons. There was a clear and novel phenotype, distinct from critical period HL: excitatory postsynaptic potential amplitudes were elevated in adolescent HL animals, whereas inhibitory postsynaptic potentials were unchanged. This is in contrast to critical period deprivation, where there are large changes to synaptic inhibition. Taken together, these results show that diminished adolescent sensory experience can cause long-lasting behavioral deficits that originate, in part, from a dysfunctional cortical circuit.Abstract FigureSummary of experimental design and main findings.
Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics
Authors: Quinn Andrew J. , Lopes-dos-Santos Vítor , Huang Norden , Liang Wei-Kuang , Juan Chi-Hung , Yeh Jia-Rong , Nobre Anna C. , Dupret David , Woolrich Mark W. 
Published: April 2021

AbstractNon-sinusoidal waveform is emerging as an important feature of neuronal oscillations. However, the role of single cycle shape dynamics in rapidly unfolding brain activity remains unclear. Here, we develop an analytical framework that isolates oscillatory signals from time-series using masked Empirical Mode Decomposition to quantify dynamical changes in the shape of individual cycles (along with amplitude, frequency and phase) using instantaneous frequency. We show how phase-alignment, a process of projecting cycles into a regularly sampled phase-grid space, makes it possible to compare cycles of different durations and shapes. ‘Normalised shapes’ can then be constructed with high temporal detail whilst accounting for differences in both duration and amplitude. We find that the instantaneous frequency tracks non-sinusoidal shapes in both simulated and real data. Notably, in local field potential recordings of mouse hippocampal CA1, we find that theta oscillations have a stereotyped slow-descending slope in the cycle-wise average, yet exhibiting high variability on a cycle-by-cycle basis. We show how Principal Components Analysis allows identification of motifs of theta cycle waveform that have distinct associations to cycle amplitude, cycle duration and animal movement speed. By allowing investigation into oscillation shape at high temporal resolution, this analytical framework will open new lines of enquiry into how neuronal oscillations support moment-by-moment information processing and integration in brain networks.
Borf: Improved ORF prediction inde-novoassembled transcriptome annotation
Authors: Signal Beth , Kahlke Tim 
Published: April 2021

ABSTRACTORF prediction inde-novoassembled transcriptomes is a critical step for RNA-Seq analysis and transcriptome annotation. However, current approaches do not appropriately account for factors such as strand-specificity and incompletely assembled transcripts. Strand-specific RNA-Seq libraries should produce assembled transcripts in the correct orientation, and therefore ORFs should only be annotated on the sense strand. Additionally, start site selection is more complex than appreciated as sequences upstream of the first start codon need to be correctly annotated as 5’ UTR in completely assembled transcripts, or part of the main ORF in incomplete transcripts. Both of these factors influence the accurate annotation of ORFs and therefore the transcriptome as a whole. We generated fourde-novotranscriptome assemblies of well annotated species as a gold-standard dataset to test the impact strand specificity and start site selection have on ORF prediction in real data. Our results show that prediction of ORFs on the antisense strand in data from stranded RNA libraries results in false-positive ORFs with no or very low similarity to known proteins. In addition, we found that up to 23% of assembled transcripts had no stop codon upstream and in-frame of the first start codon, instead comprising a sequence of upstream codons. We found the optimal length cutoff of these upstream sequences to accurately classify these transcripts as either complete (upstream sequence is 5’ UTR) or 5’ incomplete (transcript is incompletely assembled and upstream sequence is part of the ORF). Here, we present Borf, the better ORF finder, specifically designed to minimise false-positive ORF prediction in stranded RNA-Seq data and improve annotation of ORF start-site prediction accuracy. Borf is written in Python3 and freely available athttps://github.com/betsig/borf.
Marine food webs are more complex but less stable in sub-Antarctic than in Antarctic regions
Authors: Rodriguez Iara Diamela , Marina Tomás Ignacio , Schloss Irene Ruth , Saravia Leonardo Ariel 
Published: April 2021

AbstractFood web structure plays an important role in determining ecosystem stability against perturbations. High-latitude marine ecosystems are being affected by environmental stressors and biological invasions. In the West Antarctic Peninsula these transformations are mainly driven by climate change, while in the sub-Antarctic region by anthropogenic activities. Understanding the differences between these areas is necessary to monitor the changes that are expected to occur in the upcoming decades. Here, we compared the structure and stability of Antarctic (Potter Cove) and sub-Antarctic (Beagle Channel) marine food webs. We compiled species trophic interactions (predator-prey) and calculated complexity, structure and stability metrics. Even if both food webs presented the same connectance, we found important differences between them. The Beagle Channel food web is more complex, but less stable and sensitive to the loss of its most connected species, while the Potter Cove food web presented lower complexity and greater stability against perturbations.
Many ways to stick the landing: novel righting strategies allow spotted lanternfly nymphs to land on diverse substrates
Authors: Kane Suzanne Amador , Bien Theodore , Contreras-Orendain Luis , Ochs Michael F. , Hsieh S. Tonia 
Published: April 2021

AbstractUnlike large animals, insects and other very small animals are so unsusceptible to impact-related injuries that they can use falling for dispersal and predator evasion. Reorienting to land upright can mitigate lost access to resources and predation risk. Such behaviors are critical for the spotted lanternfly (SLF) (Lycorma delicatula), an invasive, destructive insect pest spreading rapidly in the US. High-speed video of SLF nymphs released under different conditions showed that these insects self-right using both active midair righting motions previously reported for other insects, and novel post-impact mechanisms that take advantage of their ability to experience near-total energy loss on impact. Unlike during terrestrial self-righting, in which an animal initially at rest on its back uses appendage motions to flip over, SLF nymphs impacted the surface at varying angles and then self-righted during the rebound using coordinated body rotations, foot-substrate adhesion, and active leg motions. These previously-unreported strategies were found to promote disproportionately upright, secure landings on both hard, flat surfaces and tilted, compliant host plant leaves. Our results highlight the importance of examining biomechanical phenomena in ecologically-relevant contexts, and show that, for small animals, the post-impact bounce period can be critical for achieving an upright landing.
Plasticity of the gastrocnemius elastic system in response to decreased work and power demand during growth
Authors: Cox SM , DeBoef A , Salzano MQ , Katugam K , Piazza SJ , Rubenson J 
Published: April 2021

AbstractElastic energy storage and release can enhance performance that would otherwise be limited by the force-velocity constraints of muscle. While functional influence of a biological spring depends on tuning between components of an elastic system (the muscle, spring, driven mass, and lever system), we do not know whether elastic systems systematically adapt to functional demand. To test whether altering work and power generation during maturation alters the morphology of an elastic system, we prevented growing guinea fowl (Numida Meleagris) from jumping. At maturity, we compared the jump performance of our treatment group to that of controls and measured the morphology of the gastrocnemius elastic system. We found that restricted birds jumped with lower jump power and work, yet there were no significant between-group differences in the components of the elastic system. Further, subject-specific models revealed no difference in energy storage capacity between groups, though energy storage was most sensitive to variations in muscle properties (most significantly operating length and least dependent on tendon stiffness). We conclude that the gastrocnemius elastic system in the guinea fowl displays little to no plastic response to decreased demand during growth and hypothesize that neural plasticity may explain performance variation.
The Bouma law accounts for crowding in fifty observers
Authors: Kurzawski Jan W. , Burchell Augustin , Thapa Darshan , Winawer Jonathan , Majaj Najib J. , Pelli Denis G. 
Published: April 2021

AbstractCrowdingis the failure to recognize an object due to surrounding clutter. Our visual crowding survey measured 13 crowding distances (or “critical spacings”) twice in each of 50 observers. The survey included three eccentricities (0, 5, and 10 deg), four cardinal meridians, two orientations (radial and tangential), and two fonts (Sloan and Pelli). The survey also tested foveal acuity, twice. Remarkably, fitting a two-parameter model, the well- known Bouma law — crowding distance grows linearly with eccentricity — explains 82% of the variance for all 13 × 50 measured log crowding distances, cross-validated. An enhanced Bouma law, with factors for meridian, crowding orientation, target kind, and observer, explains 94% of the variance, again cross-validated. These additional factors reveal several asymmetries, consistent with previous reports, which can be expressed as crowding- distance ratios: 0.62 horizontal:vertical, 0.79 lower:upper, 0.78 right:left, 0.55 tangential:radial, and 0.78 Sloan font:Pelli font. Across our observers, peripheral crowding is independent of foveal crowding and acuity. Evaluation of the Bouma factorb(the slope of the Bouma law) as a biomarker of visual health would be easier if there were a way to compare results across crowding studies that use different methods. We define astandardized Bouma factor b’that corrects for differences from Bouma’s 25 choice alternatives, 75% threshold criterion, and linearly symmetric flanker placement. For radial crowding on the right meridian, the standardized Bouma factorb’is 0.24 for this study, 0.35 for Bouma (1970), and 0.30 for the geometric mean across five representative modern studies, including this one, showing good agreement across labs, including Bouma’s. We found that guaranteeing fixation by gaze-contingent display halved the standard deviation across observers of the estimated logb. The reduction in standard deviation is explained by a “peeking” model in which the observer looked near an anticipated target location in 50% ofunmonitored-fixation trials. Individual differences are robust, as evidenced by the much larger 0.08 SD of logbacross observers than the 0.03 SD of test-retest within observers. Crowding’s ease of measurement enhances its promise as a biomarker for dyslexia and visual health.
Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation
Authors: Walker Caleb , Dien Bruce , Giannone Richard J. , Slininger Patricia , Thompson Stephanie R. , Trinh Cong T. 
Published: April 2021

ABSTRACTYarrowia lipolyticais an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticatedY. lipolyticaclade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504, which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing non-preferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer inY. lipolytica. To fill this knowledge gap, we analyzed the genetic diversity of five undomesticatedY. lipolyticastrains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticatedY. lipolyticastrains to complex phenotypes of superior growth, sugar utilization, lipid accumulation and degradation in biomass hydrolysates.IMPORTANCEYarrowia lipolyticais an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates. Our investigation into the genetic diversity of undomesticatedY. lipolyticastrains, coupled with detailed strain characterization and proteomic analysis, revealed metabolic processes and regulatory elements conferring desirable phenotypes for growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates by these natural variants. This study provides a better understanding of the robust metabolism ofY. lipolyticaand suggests potential metabolic engineering strategies to enhance its performance.
Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles
Authors: Gaulke Christopher A , Schmeltzer Emily R , Dasenko Mark , Tyler Brett M. , Thurber Rebecca Vega , Sharpton Thomas J 
Published: April 2021

ABSTRACTShotgun metagenomic sequencing has transformed our understanding of microbial community ecology. However, preparing metagenomic libraries for high-throughput DNA sequencing remains a costly, labor-intensive, and time-consuming procedure, which in turn limits the utility of metagenomes. Several library preparation procedures have recently been developed to offset these costs, but it is unclear how these newer procedures compare to current standards in the field. In particular, it is not clear if all such procedures perform equally well across different types of microbial communities, or if features of the biological samples being processed (e.g., DNA amount) impact the accuracy of the approach. To address these questions, we assessed how five different shotgun DNA sequence library preparation methods, including the commonly used Nextera®Flex kit, perform when applied to metagenomic DNA. We measured each method’s ability to produce metagenomic data that accurately represents the underlying taxonomic and genetic diversity of the community. We performed these analyses across a range of microbial community types (e.g., soil, coral-associated, mouse-gut-associated) and input DNA amounts. We find that the type of community and amount of input DNA influence each method’s performance, indicating that careful consideration may be needed when selecting between methods, especially for low complexity communities. However, cost-effective preparation methods we assessed are generally comparable to the current gold standard Nextera®DNA Flex kit for high-complexity communities. Overall, the results from this analysis will help expand and even facilitate access to metagenomic approaches in future studies.IMPORTANCEMetagenomic library preparation methods and sequencing technologies continue to advance rapidly, allowing researchers to characterize microbial communities in previously underexplored environmental samples and systems. However, widely-accepted standardized library preparation methods can be cost-prohibitive. Newly available approaches may be less expensive, but their efficacy in comparison to standardized methods remains unknown. In this study, we compared five different metagenomic library preparation methods. We evaluated each method across a range of microbial communities varying in complexity and quantity of input DNA. Our findings demonstrate the importance of considering sample properties, including community type, composition, and DNA amount, when choosing the most appropriate metagenomic library preparation method.
HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics
Authors: Durso-Cain Karina , Kumberger Peter , Schälte Yannik , Fink Theresa , Dahari Harel , Hasenauer Jan , Uprichard Susan L. , Graw Frederik 
Published: April 2021

AbstractHepatitis C virus (HCV) is capable of spreading within a host by two different transmission modes: cell-free and cell-to-cell. Although viral dissemination and diffusion of viral particles facilitates the infection of distant cells, direct cell-to-cell transmission to uninfected neighboring cells is thought to shield the virus from immune recognition. However, the contribution of each of these transmission mechanisms to HCV spread is unknown. To dissect the contribution of these different transmission modes to HCV spread, we measured HCV lifecycle kinetics and used an in vitro spread assay to monitor HCV spread kinetics after low multiplicity of infection in the absence and presence of a neutralizing antibody that blocks cell-free spread. By analyzing these data with a spatially-explicit mathematical model that describes viral spread on a single-cell level, we quantified the contribution of cell-free and cell-to-cell spread to the overall infection dynamics and show that both transmission modes act synergistically to enhance the spread of infection. Thus, the simultaneous occurrence of both transmission modes likely represents an advantage for HCV that may contribute to the efficient establishment of chronic infection. Notably, the relative contribution of each viral transmission mode appeared to vary dependent on different experimental conditions and suggests that viral spread is optimized according to the environment. Together, our analyses provide insight into the transmission dynamics of HCV and reveal how different transmission modes impact each other.ImportanceHepatitis C Virus can spread within a host by diffusing viral particles or direct cell-to-cell transfer of viral material between infected and uninfected cells. To which extend these cell-free and cell-to-cell transmission modes contribute to HCV spread, establishment of chronicity and antiviral escape is still unknown. By combiningin vitroexperimental HCV spread data with a multi-scale mathematical model we have disentangled the contribution and interplay of cell-free and cell-to-cell transmission modes during HCV infection. Our analysis revealed synergistic effects between the two transmission modes, with the relative contribution of each transmission mode varying dependent on the experimental conditions. This highlights the adaptability of the virus and suggests that transmission modes might be optimized dependent on the environment, which could contribute to viral persistence.