bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrabacterial lipid inclusions in mycobacteria: unexpected key players in survival and pathogenesis?
Authors: Mallick Ivy , Santucci Pierre , Poncin Isabelle , Point Vanessa , Kremer Laurent , Cavalier Jean-François , Canaan Stéphane 
Published: May 2021

ABSTRACT
Mycobacterial species, including Mycobacterium tuberculosis, rely on lipids to survive and chronically persist within their hosts. Upon infection, opportunistic and strict pathogenic mycobacteria exploit metabolic pathways to import and process host-derived free fatty acids, subsequently stored as triacylglycerols in the form of intrabacterial lipid inclusions (ILI). Under nutrient-limiting conditions, ILI constitute a critical source of energy that fuels the carbon requirements and maintain redox homeostasis, promoting bacterial survival for extensive periods of time. In addition to their basic metabolic functions, these organelles display multiple other biological properties, emphasizing their central role in the mycobacterial life cycle. However, despite their importance, the dynamics of ILI metabolism and their contribution to mycobacterial adaptation/survival in the context of infection has not been thoroughly documented. Herein, we provide an overview of the historical ILI discoveries, their characterization and current knowledge regarding the microenvironmental stimuli conveying ILI formation, storage and degradation. We also review new biological systems to monitor the dynamics of ILI metabolism in extra- and intracellular mycobacteria and describe major molecular actors in triacylglycerol biosynthesis, maintenance and breakdown. Finally, emerging concepts regarding the role of ILI in mycobacterial survival, persistence, reactivation, antibiotic susceptibility and inter-individual transmission are also discussed.
Frequency-dependent anisotropy in partially saturated porous rock with multiple sets of mesoscale fractures
Authors: Pang Shuo , Stovas Alexey , Xing Huilin 
Published: May 2021

SUMMARY
Accurate modelling of the frequency-dependence of seismic wave velocity related to fracture system and fluid content is crucial to the quantitative interpretation of seismic data in fractured reservoirs. Both mesoscale fractures and patchy saturation effects can cause significant velocity dispersion and attenuation in the seismic frequency band due to wave-induced fluid flow (WIFF) mechanism. Considering the coupled impact of ‘mesoscale fractures’ and ‘patchy saturation’, we derive expressions for the frequency-dependent anisotropy in partially saturated porous rock containing two fracture sets with different orientations, sizes and connectivities. Especially, we simplify the rock-physics model as an orthorhombic (ORT) media by assuming the mesoscale fractures to be orthogonal and give the explicit expressions for frequency-dependent elastic constants. Finally, we give the expressions for the frequency-dependent phase velocity in patchy saturated and fractured ORT media and investigate the effect of patchy saturation on P-wave velocity at different polar and azimuth angles. In this paper, we investigate the effects of fluid saturation and fluid pressure on frequency-dependent velocities and Thomsen anisotropy parameters. Also, the effect of the relative permeability is very noticeable. The relaxation frequency can be lower in partially saturated fractured rocks compared with the fully saturated case, which makes the rock have a larger stiffness. The non-monotonic relationships between frequency-dependent anisotropy and fluid saturation add complexity to seismic forward modelling and inversion in reservoirs with complex fracture patterns.
Video Recording and Analysis of Avian Movements and Behavior: Insights from Courtship Case Studies
Authors: Janisch Judith , Mitoyen Clementine , Perinot Elisa , Spezie Giovanni , Fusani Leonida , Quigley Cliodhna 
Published: May 2021

Abstract
Video recordings are useful tools for advancing our understanding of animal movements and behavior. Over the past decades, a burgeoning area of behavioral research has put forward innovative methods to investigate animal movement using video analysis, which includes motion capture and machine learning algorithms. These tools are particularly valuable for the study of elaborate and complex motor behaviors, but can be challenging to use. We focus in particular on elaborate courtship displays, which commonly involve rapid and/or subtle motor patterns. Here, we review currently available tools and provide hands-on guidelines for implementing these techniques in the study of avian model species. First, we suggest a set of possible strategies and solutions for video acquisition based on different model systems, environmental conditions, and time or financial budget. We then outline the available options for video analysis and illustrate how different analytical tools can be chosen to draw inference about animal motor performance. Finally, a detailed case study describes how these guidelines have been implemented to study courtship behavior in golden-collared manakins (Manacus vitellinus).
The Stabilizing Function of the Tail During Arboreal Quadrupedalism
Authors: Young Jesse W , Chadwell Brad A , Dunham Noah T , McNamara Allison , Phelps Taylor , Hieronymus Tobin , Shapiro Liza J 
Published: May 2021

AbstractLocomotion on the narrow and compliant supports of the arboreal environment is inherently precarious. Previous studies have identified a host of morphological and behavioral specializations in arboreal animals broadly thought to promote stability when on precarious substrates. Less well-studied is the role of the tail in maintaining balance. However, prior anatomical studies have found that arboreal taxa frequently have longer tails for their body size than their terrestrial counterparts, and prior laboratory studies of tail kinematics and the effects of tail reduction in focal taxa have broadly supported the hypothesis that the tail is functionally important for maintaining balance on narrow and mobile substrates. In this set of studies, we extend this work in two ways. First, we used a laboratory dataset on three-dimensional segmental kinematics and tail inertial properties in squirrel monkeys (Saimiri boliviensis) to investigate how tail angular momentum is modulated during steady-state locomotion on narrow supports. In the second study, we used a quantitative dataset on quadrupedal locomotion in wild platyrrhine monkeys to investigate how free-ranging arboreal animals adjust tail movements in response to substrate variation, focusing on kinematic measures validated in prior laboratory studies of tail mechanics (including the laboratory data presented). Our laboratory results show that S. boliviensis significantly increase average tail angular momentum magnitudes and amplitudes on narrow supports, and primarily regulate that momentum by adjusting the linear and angular velocity of the tail (rather than via changes in tail posture per se). We build on these findings in our second study by showing that wild platyrrhines responded to the precarity of narrow and mobile substrates by extending the tail and exaggerating tail displacements, providing ecological validity to the laboratory studies of tail mechanics presented here and elsewhere. In conclusion, our data support the hypothesis that the long and mobile tails of arboreal animals serve a biological role of enhancing stability when moving quadrupedally over narrow and mobile substrates. Tail angular momentum could be used to cancel out the angular momentum generated by other parts of the body during steady-state locomotion, thereby reducing whole-body angular momentum and promoting stability, and could also be used to mitigate the effects of destabilizing torques about the support should the animals encounter large, unexpected perturbations. Overall, these studies suggest that long and mobile tails should be considered among the fundamental suite of adaptations promoting safe and efficient arboreal locomotion.
Understanding fishery interactions and stock trajectory of yellowfin tuna exploited by Iranian fisheries in the Sea of Oman
Authors: Eighani Morteza , Cope Jason M , Raoufi Paria , Naderi Reza Abbaspour , Bach Pascal 
Published: May 2021

Abstract
The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort to maintain sustainable stock levels. The yellowfin tuna (Thunnus albacares) fishery in the Sea of Oman has experienced intense increases in removals since 1980, with particularly high levels since the 1990s. Here, we apply a statistical catch-at-age model to time-series of catches and fishery-dependent length composition data to obtain a preliminary and general understanding of the population dynamics of this stock since the start of the fishery in 1950–2019. Despite limited data, population models consistently indicate a sharp decline in population status since the beginning of the time-series across a variety of assumptions on stock productivity and life history. The gillnet fishery takes almost exclusively immature individuals, with high fishing intensity and removal rates. Both reference models indicate the population is essentially at the same relative stock status in 2019 (10% of unfished), but with very different future projections and higher absolute stock size when recruitment is estimated. The yellowfin tuna population in 2019 is below estimated MSY reference points (based either on unfished size or spawning output at MSY) for current relative stock size, and over the fishing intensity at MSY, indicating current overfishing. Adjusting the interactions of that fishery with the population, while continuing to collected biological composition data representative of each fleet in the fishery, will help mitigate current stock decline and provide the ability to refine future population status determination and forecasts through more informed stock assessments.
Usability, inclusivity, and content evaluation of COVID-19 contact tracing apps in the United States
Authors: Blacklow Serena O , Lisker Sarah , Ng Madelena Y , Sarkar Urmimala , Lyles Courtney 
Published: May 2021

AbstractWe evaluated the usability of mobile COVID-19 contact tracing apps, especially for individuals with barriers to communication and limited digital literacy skills. We searched the Apple App Store, Google Play, peer-reviewed literature, and lay press to find contact tracing apps in the United States. We evaluated apps with a framework focused on user characteristics and user interface. Of the final 26 apps, 77% were on both iPhone and Android. 69% exceeded 9th grade readability, and 65% were available only in English. Only 12% had inclusive illustrations (different genders, skin tones, physical abilities). 92% alerted users of an exposure, 42% linked to a testing site, and 62% linked to a public health website within 3 clicks. Most apps alert users of COVID-19 exposure but require high English reading levels and are not fully inclusive of the U.S. population, which may limit their reach as public health tools.
Pyrosilviculture Needed for Landscape Resilience of Dry Western United States Forests
Authors: North M P , York R A , Collins B M , Hurteau M D , Jones G M , Knapp E E , Kobziar L , McCann H , Meyer M D , Stephens S L , Tompkins R E , Tubbesing C L 
Published: May 2021

AbstractA significant increase in treatment pace and scale is needed to restore dry western US forest resilience owing to increasingly frequent and severe wildfire and drought. We propose a pyrosilviculture approach to directly increase large-scale fire use and modify current thinning treatments to optimize future fire incorporation. Recommendations include leveraging wildfire’s “treatment” in areas burned at low and moderate severity with subsequent pyrosilviculture management, identifying managed wildfire zones, and facilitating and financing prescribed fire with “anchor,” “ecosystem asset,” and “revenue” focused thinning treatments. Pyrosilviculture would also expand prescribed-burn and managed-wildfire objectives to include reducing stand density, increasing forest heterogeneity, and selecting for tree species and phenotypes better adapted to changing climate and disturbance regimes. The potential benefits and limitations of this approach are discussed. Fire is inevitable in dry western US forests and pyrosilviculture focuses on proactively shifting more of that fire into managed large-scale burns needed to restore ecosystem resilience.
Transitory Trust: Falsified Passports, Circulars, and Other Speculations in Nineteenth-Century Cuba
Authors: Sartorius David 
Published: May 2021

Abstract
In nineteenth-century Cuba, the increasing and uneven use of passports for maritime travel generated confusion about their authority and encouraged their falsification. This essay explores the forgery and misuse of travel papers alongside the fabrications of an official colonial record that concealed the illegal transatlantic slave trade as it implemented documentary procedures for legal travel. Cuban officials pursued individuals who traveled without passports, with other people’s passports, or lacked other papers, with a disproportionate focus on the circulation of free people of African descent. At the same time, the limited reach of government decrees and policies complicated strict determinations of transgression. Rather than taking this as evidence of a broken system, recognizing how various actors created the conditions for a collective susceptibility both to the authority conferred by passports and to plausible falsehoods lets us view borders, individual identity, and Caribbean mobility in new light. The essay calls on historians to approach the archival record of passports and mobility by balancing our retrospective recognition of falsifications with an awareness of fluctuating estimations of documentary veracity in the past.
Case Report: Soldier With Latrodectism After Black Widow Spider Bite During a Field Training Exercise
Authors: Kubena Bryan E , Umar Mohamad A , Walker Jerimiah D , Harper Hillary 
Published: May 2021

ABSTRACT
Latrodectism from black widow spider (BWS) bites is rare in the United States. Latrodectism is a severe systemic manifestation of the envenomation that includes severe abdominal pain mimicking acute surgical abdomen and, in rare cases, could lead to acute myocarditis and rhabdomyolysis. The BWS typically inhabits dark, low-lying areas such as woodpiles, tree stumps, outdoor storage, outdoor furniture, outdoor toilets, and rock piles and is most active during warm weather months. Military service members often participate in field training exercises during warm weather in wooded areas littered with woodpiles and tree stumps; therefore, they are at an increased risk for bites by arachnids. We report the case of a 26-year-old active duty male soldier evacuated from field training with latrodectism and possible envenomation-induced myocarditis after a suspected BWS bite.
A binary with a δ Scuti star and an oscillating red giant: orbit and asteroseismology of KIC 9773821
Authors: Murphy Simon J , Li Tanda , Sekaran Sanjay , Bedding Timothy R , Yu Jie , Tkachenko Andrew , Colman Isabel , Huber Daniel , Hey Daniel , Baratashvili Tinatin , Janssens Soetkin 
Published: May 2021

ABSTRACT
We study the δ Scuti – red giant (RG) binary KIC 9773821, the first double-pulsator binary of its kind. It was observed by Kepler during its 4-yr mission. Our aims are to ascertain whether the system is bound, rather than a chance alignment, and to identify the evolutionary state of the RG via asteroseismology. An extension of these aims is to determine a dynamical mass and an age prior for a δ Sct star, which may permit mode identification via further asteroseismic modelling. We determine spectroscopic parameters and radial velocities (RVs) for the RG component using HERMES@Mercator spectroscopy. Light arrival-time delays from the δ Sct pulsations are used with the red-giant RVs to determine that the system is bound and to infer its orbital parameters, including the binary mass ratio. We use asteroseismology to model the individual frequencies of the red giant to give a mass of $2.10^{+0.20}_{-0.10}$ M⊙ and an age of $1.08^{+0.06}_{-0.24}$ Gyr. We find that it is a helium-burning secondary clump star, confirm that it follows the standard $\nu _{\rm max}$ scaling relation, and confirm its observed period spacings match their theoretical counterparts in the modelling code mesa. Our results also constrain the mass and age of the δ Sct star. We leverage these constraints to construct δ Sct models in a reduced parameter space and identify four of its five pulsation modes.
Experimental branching fractions, transition probabilities, and oscillator strengths in La i
Authors: Wang Xinghao , Xie Hongqiang , Di Haoran , Su Zihuai , Yu Qi 
Published: May 2021

ABSTRACT
The branching fraction (BF) determinations were performed for 87 La i lines from 290.963 to 1078.646 nm based on the emission spectra of hollow cathode lamps recorded using the 1.0 m Fourier transform spectrometer (FTS) and are available from the digital library of National Solar Observatory on Kitt Peak, USA (http://diglib.nso.edu/). Furthermore, by combining the determined BFs with reliable lifetime values reported in literature, the transition probabilities and absolute oscillator strengths for these lines were derived.
Predicting electromagnetic counterparts using low-latency gravitational-wave data products
Authors: Stachie Cosmin , Coughlin Michael W , Dietrich Tim , Antier Sarah , Bulla Mattia , Christensen Nelson , Essick Reed , Landry Philippe , Mours Benoit , Schianchi Federico , Toivonen Andrew 
Published: May 2021

ABSTRACT
Searches for gravitational-wave counterparts have been going in earnest since GW170817 and the discovery of AT2017gfo. Since then, the lack of detection of other optical counterparts connected to binary neutron star or black hole–neutron star candidates has highlighted the need for a better discrimination criterion to support this effort. At the moment, low-latency gravitational-wave alerts contain preliminary information about binary properties and hence whether a detected binary might have an electromagnetic counterpart. The current alert method is a classifier that estimates the probability that there is a debris disc outside the black hole created during the merger as well as the probability of a signal being a binary neutron star, a black hole–neutron star, a binary black hole, or of terrestrial origin. In this work, we expand upon this approach to both predict the ejecta properties and provide contours of potential light curves for these events, in order to improve the follow-up observation strategy. The various sources of uncertainty are discussed, and we conclude that our ignorance about the ejecta composition and the insufficient constraint of the binary parameters by low-latency pipelines represent the main limitations. To validate the method, we test our approach on real events from the second and third Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO)–Virgo observing runs.
The Worldwide Invasion ofDrosophila suzukiiIs Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions
Authors: Mérel Vincent , Gibert Patricia , Buch Inessa , Rodriguez Rada Valentina , Estoup Arnaud , Gautier Mathieu , Fablet Marie , Boulesteix Matthieu , Vieira Cristina 
Published: May 2021

AbstractTransposable elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo and found that TEs occupy 47% of the genome and are mostly located in gene-poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied the variation of TE abundance in genomic data from 16 invasive and six native populations of D. suzukii. We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θw^ a proxy of effective population size. We did not find any correlation between TE contents and bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g., transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.
Genetic Origins and Sex-Biased Admixture of the Huis
Authors: Ma Xixian , Yang Wenjun , Gao Yang , Pan Yuwen , Lu Yan , Chen Hao , Lu Dongsheng , Xu Shuhua 
Published: May 2021

Abstract
The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west–east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, that is, excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.
Optimizing protein V untranslated region sequence in M13 phage for increased production of single-stranded DNA for origami
Authors: Lee Bo-Young , Lee Jaewon , Ahn Dong June , Lee Seungwoo , Oh Min-Kyu 
Published: May 2021

Abstract
DNA origami requires long scaffold DNA to be aligned with the guidance of short staple DNA strands. Scaffold DNA is produced in Escherichia coli as a form of the M13 bacteriophage by rolling circle amplification (RCA). This study shows that RCA can be reconfigured by reducing phage protein V (pV) expression, improving the production throughput of scaffold DNA by at least 5.66-fold. The change in pV expression was executed by modifying the untranslated region sequence and monitored using a reporter green fluorescence protein fused to pV. In a separate experiment, pV expression was controlled by an inducer. In both experiments, reduced pV expression was correlated with improved M13 bacteriophage production. High-cell-density cultivation was attempted for mass scaffold DNA production, and the produced scaffold DNA was successfully folded into a barrel shape without compromising structural quality. This result suggested that scaffold DNA production throughput can be significantly improved by reprogramming the RCA in E. coli.