bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of skin pigmentation-associated variation in West Eurasia
Authors: Ju Dan , Mathieson Iain 
Published: December 2020

SignificanceSome of the genes responsible for the evolution of light skin pigmentation in Europeans show signals of positive selection in present-day populations. Recently, genome-wide association studies have highlighted the highly polygenic nature of skin pigmentation. It is unclear whether selection has operated on all of these genetic variants or just a subset. By studying variation in over a thousand ancient genomes from West Eurasia covering 40,000 y, we are able to study both the aggregate behavior of pigmentation-associated variants and the evolutionary history of individual variants. We find that the evolution of light skin pigmentation in Europeans was driven by frequency changes in a relatively small fraction of the genetic variants that are associated with variation in the trait today.
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
Authors: Marshall Jamie L. , Doughty Benjamin R. , Subramanian Vidya , Guckelberger Philine , Wang Qingbo , Chen Linlin M. , Rodriques Samuel G. , Zhang Kaite , Fulco Charles P. , Nasser Joseph , Grinkevich Elizabeth J. , Noel Teia , Mangiameli Sarah , Bergman Drew T. , Greka Anna , Lander Eric S. , Chen Fei , Engreitz Jesse M. 
Published: December 2020

Significance
Gene expression is precisely controlled across human cell types to control cellular functions and phenotypes. Here we present a technology to quantify the level of expression of genes in single cells, which will help to understand how genes are regulated in each cell type in the human body. We demonstrate that this technology improves upon existing tools to enable understanding how DNA regulatory elements control gene expression and mapping the frequencies of different cell types in tissues. This technology will enable new large-scale studies to understand gene control.
Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles
Authors: Yabukarski Filip , Biel Justin T. , Pinney Margaux M. , Doukov Tzanko , Powers Alexander S. , Fraser James S. , Herschlag Daniel 
Published: December 2020

Significance
Enzymes position catalytic and reactant groups in active sites, but motions are also integral to enzyme function. Decades of research have revealed static snapshots for many enzymes, but we know very little about the extents and directions of motions of the residues that make up enzymes and their active sites. We took advantage of emerging crystallographic approaches to provide information about protein conformational ensembles for the enzyme ketosteroid isomerase (KSI). Ensemble analyses indicated limited change in conformational heterogeneity through the enzyme’s reaction cycle and a balance of positioning and flexibility that allows KSI to efficiently catalyze multiple reaction steps. We tested KSI-specific and general models for enzyme catalysis, demonstrating the power of and need for “ensemble–function” interrogation of enzymes.
Axon morphology is modulated by the local environment and impacts the noninvasive investigation of its structure–function relationship
Authors: Andersson Mariam , Kjer Hans Martin , Rafael-Patino Jonathan , Pacureanu Alexandra , Pakkenberg Bente , Thiran Jean-Philippe , Ptito Maurice , Bech Martin , Bjorholm Dahl Anders , Andersen Dahl Vedrana , Dyrby Tim B. 
Published: December 2020

Significance
Axons, the brain’s communication cables, have been described as cylinders since their discovery in 1860. Their structure is linked to how fast they conduct signals and is thus indicative of brain health and function. Here, we demonstrate an interplay between the micromorphology of axons and other extra-axonal structures, showing that axons are noncylindrical and exhibit environment-dependent diameter and trajectory variations. The nonspecificity in diameter, and thus conduction velocity, challenges the current knowledge of how axons communicate signals. Diffusion magnetic resonance imaging can be used to measure axon diameter in the living brain in order to explore the brain network and detect potential biomarkers of disease, but we show here that the observed complex morphologies of axons bias these measurements.
Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE
Authors: Scott Ashley , Power Robert C. , Altmann-Wendling Victoria , Artzy Michal , Martin Mario A. S. , Eisenmann Stefanie , Hagan Richard , Salazar-García Domingo C. , Salmon Yossi , Yegorov Dmitry , Milevski Ianir , Finkelstein Israel , Stockhammer Philipp W. , Warinner Christina 
Published: December 2020

SignificanceHere we report the identification of staple and exotic food remains in Bronze and Early Iron Age dental calculus from the Southern Levant. The analysis of dietary plant microremains and proteins sheds new light on consumed exotic foods from South and East Asia during the second millennium BCE. We provide the earliest direct evidence in the Mediterranean to date for the consumption of sesame, soybean, probable banana, and turmeric. The recovery and identification of diverse foodstuffs using molecular and microscopic techniques enables a new understanding of the complexity of early trade routes and nascent globalization in the ancient Near East and raises questions about the long-term maintenance and continuity of this trade system into later periods.
Cryo-EM structure of the full-length WzmWzt ABC transporter required for lipid-linked O antigen transport
Authors: Caffalette Christopher A. , Zimmer Jochen 
Published: December 2020

Significance
Gram-negative bacteria employ cell surface polysaccharides to evade host immune responses, enhance survival in extreme environments, and protect themselves against antimicrobial agents. The outer membrane of gram-negatives is rich in lipopolysaccharide (LPS), comprising the endotoxin lipid A, a short oligosaccharide, and a long terminal polysaccharide known as the O antigen. O antigens extend the cellular envelope creating a barrier that obscures the cell membrane to protect it from complement component deposition and insertion, thereby evading the innate immune response of the host. Understanding O antigen biosynthesis and how the specialized ABC transporter WzmWzt translocates the O antigen for assembly of mature LPS provides a molecular basis for manipulating this fundamental process in gram-negative pathogens.
Satellites can reveal global extent of forced labor in the world’s fishing fleet
Authors: McDonald Gavin G. , Costello Christopher , Bone Jennifer , Cabral Reniel B. , Farabee Valerie , Hochberg Timothy , Kroodsma David , Mangin Tracey , Meng Kyle C. , Zahn Oliver 
Published: December 2020

Significance
Forced labor in fisheries is increasingly recognized as a human rights crisis. Until recently, its extent was poorly understood and no tools existed for systematically detecting forced labor risk on individual fishing vessels on a global scale. Here we use satellite data and machine learning to identify these high-risk vessels and find widespread risk of forced labor in the world’s fishing fleet. This information provides new opportunities for unique market, enforcement, and policy interventions. This also provides a proof of concept for how remotely sensed dynamic individual behavior can be used to infer forced labor abuses.
Mechanistic insights into the synergistic activation of the RXR–PXR heterodimer by endocrine disruptor mixtures
Authors: Delfosse Vanessa , Huet Tiphaine , Harrus Deborah , Granell Meritxell , Bourguet Maxime , Gardia-Parège Caroline , Chiavarina Barbara , Grimaldi Marina , Le Mével Sébastien , Blanc Pauline , Huang David , Gruszczyk Jakub , Demeneix Barbara , Cianférani Sarah , Fini Jean-Baptiste , Balaguer Patrick , Bourguet William 
Published: December 2020

Significance
Many environmental pollutants act as endocrine disruptors that interfere with normal endocrine regulation and promote adverse effects in humans. As a major target of xenobiotics, the pregnane X receptor (PXR) is known to play opposite roles by both facilitating their clearance and mediating their toxic effects. Here, we use structural and functional approaches to describe two converging mechanisms leading to a robust synergistic stimulation of the PXR pathway by mixtures of three chemicals exhibiting very low efficacy when administered separately. This “cocktail effect” relies on two cooperative binding processes that enhance both ligand binding affinity and recruitment of transcriptional coactivators. Our findings show how chemical mixtures may alter physiology and homeostasis at concentrations where individual components are considered safe.
Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
Authors: Abas Lindy , Kolb Martina , Stadlmann Johannes , Janacek Dorina P. , Lukic Kristina , Schwechheimer Claus , Sazanov Leonid A. , Mach Lukas , Friml Jiří , Hammes Ulrich Z. 
Published: December 2020

Significance
The plant hormone auxin regulates many aspects of plant life and has the unique ability to flow throughout the plant in defined directions, as observed by Darwin over a century ago. The chemical NPA inhibits this directional flow, thereby severely affecting plant growth. In studying the specific effects of NPA, researchers have also uncovered general principles underlying plant development. Exactly how NPA inhibits directional auxin flow is unclear. NPA interacts with proteins that can transport auxin, such as ABCB transporters, and we show here that NPA also associates with and inhibits the major transporters that specialize in directional auxin flow—PINs. This explanation of NPA action will guide future research and may help reveal how PINs perform auxin transport.
Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein
Authors: Flower Thomas G. , Buffalo Cosmo Z. , Hooy Richard M. , Allaire Marc , Ren Xuefeng , Hurley James H. 
Published: December 2020

Significance
The structure of the SARS-CoV-2 ORF8 protein reveals two novel intermolecular interfaces layered onto an ORF7 fold. One is mediated by a disulfide bond, the other is noncovalent, and both are novel with respect to SARS-CoV. The structural analysis here establishes a molecular framework for understanding the rapid evolution of ORF8, its contributions to COVID-19 pathogenesis, and the potential for its neutralization by antibodies.
Optomechanically induced optical responses with non-rotating wave approximation
Authors: Yan Xiao-Bo 
Published: December 2020

Abstract
Slow light propagation is an important phenomenon in quantum optics. Here, we theoretically study the properties of slow light in a simple optomechanical system considering an effect of non-rotating wave approximation (NRWA) that was ignored in previous related works. With the NRWA effect, the ultraslow light can be easily achieved at the window of optomechanically induced transparency, especially in unresolved sideband regime. From the theoretical results, we find the upper bound of the time delay is exactly the mechanical ringdown time which can last for several minutes (mHz linewidth) in recent experiments. Additionally, the interesting phenomena of the perfect optomechanically induced transmission and absorption are studied in the system with the NRWA effect. We believe the results can be used to control optical transmission in modern optical networks.
Numerical simulations of hydrogen interstitial diffusion and ferroelectricity degradation in lead titanate films
Authors: You Jeong Ho , Zhu Lin , Gray Cooper , Wang Zhi , Yeo Chang-Dong 
Published: December 2020

Abstract
Numerical simulations have been performed to study hydrogen interstitial diffusion and ferroelectric degradation in lead titanate films. The computational method consists of two parts: hydrogen diffusion property calculations using density functional theory (DFT) and ferroelectric property calculations using molecular dynamics (MD) simulations. The hydrogen interstitial diffusion path and the activation energy have been obtained using DFT calculations. With the obtained diffusion properties, the distributions of hydrogen impurities have been calculated using Fick’s second law and used as input to MD simulations, with various diffusion times and hydrogen surface concentrations. It has been found that magnitudes of remnant polarization and coercive electric fields decrease with increasing the diffusion time and the hydrogen surface concentration. The distribution of hydrogen impurities is another critical factor to ferroelectric responses. Compared to a uniform distribution of hydrogen impurities, the nonuniform distribution diminishes the ferroelectric properties more severely. A heavily defective region due to the nonuniform hydrogen distribution reduces the effective film thickness and induces the in-plane ferroelectric domain formations.
Experimental and numerical studies on kV scattered x-ray imaging for real-time image guidance in radiation therapy
Authors: Huang Yanqi , Yang Kai , Lai Youfang , Liu Huan , Shen Chenyang , Zhong Yuncheng , Shao Yiping , Li Xinhua , Liu Bob , Jia Xun 
Published: December 2020

Abstract
Motion management is a critical component of image guided radiotherapy for lung cancer. We previously proposed a scheme using kV scattered x-ray photons for marker-less real-time image guidance in lung cancer radiotherapy. This study reports our recent progress using the photon counting detection technique to demonstrate potential feasibility of this method and using Monte Carlo (MC) simulations and ray-tracing calculations to characterize the performance. In our scheme, a thin slice of x-ray beam was directed to the target and we measured the outgoing scattered photons using a photon counting detector with a parallel-hole collimator to establish the correspondence between detector pixels and scatter positions. Image corrections of geometry, beam attenuation and scattering angle were performed to convert the raw image to the actual image of Compton attenuation coefficient. We set up a MC simulation system using an in-house developed GPU-based MC package modeling the image formation process. We also performed ray-tracing calculations to investigate the impacts of imaging system geometry on resulting image resolution. The experiment demonstrated feasibility of using a photon counting detector to measure scattered x-ray photons and generate the proposed scattered x-ray image. After correction, x-ray scattering image intensity and Compton scattering attenuation coefficient were linearly related, with R
2 greater than 0.9. Contrast to noise ratios of different objects were improved and the values in experimental results and MC simulation results agreed with each other. Ray-tracing calculations revealed the dependence of image resolution on imaging geometry. The image resolution increases with reduced source to object distance and increased collimator height. The study demonstrated potential feasibility of using scattered x-ray imaging as a real-time image guidance method in radiation therapy.
A hierarchical model of abdominal configuration changes extracted from golden angle radial magnetic resonance imaging
Authors: Zhang Yuhang , Kashani Rojano , Cao Yue , Lawrence Theodore S , Johansson Adam , Balter James M 
Published: December 2020

Abstract
Abdominal organs are subject to a variety of physiological forces that superimpose their effects to influence local motion and configuration. These forces not only include breathing, but can also arise from cyclic antral contractions and a range of slow configuration changes. To elucidate each individual motion pattern as well as their combined effects, a hierarchical motion model was built for characterization of these 3 motion modes (characterized as deformation maps between states) using golden angle radial MR signals. Breathing motions are characterized first. Antral contraction states are then reconstructed after breathing motion-induced deformation are corrected; slow configuration change states are further extracted from breathing motion-corrected image reconstructions. The hierarchical model is established based on these multimodal states, which can be either individually shown or combined to demonstrate any arbitrary composited motion patterns. The model was evaluated using 20 MR scans acquired from 9 subjects. Poor reproducibility of breathing motions both within as well as between scan sessions was observed, with an average intra-subject difference of 1.6 cycles min−1 for average breathing frequencies of 12.0 cycles min−1. Antral contraction frequency distributions were more stable than breathing, but also presented poor reproducibility between scans with an average difference of 0.3 cycles min−1 for average frequencies of 3.2 cycles min−1. The magnitudes of motions beyond breathing were found to be significant, with 14.4 and 33.8 mm maximal motions measured from antral contraction and slow configuration changes, respectively. Hierarchical motion models have potential in multiple applications in radiotherapy, including improving the accuracy of dose delivery estimation, providing guidance for margin creation, and supporting advanced decisions and strategies for immobilization, treatment monitoring and gating.
Near-threshold production of antihydrogen positive ion in positronium–antihydrogen collision
Authors: Yamashita Takuma , Kino Yasushi , Hiyama Emiko , Jonsell Svante , Froelich Piotr 
Published: December 2020

Abstract
Near-threshold production of antihydrogen ion (

H

̄

+

) in positronium–antihydrogen collisions is predicted by a rigorous four-body scattering calculation. The convergence of the cross sections for the rearrangement and for all competing reactions (elastic scattering, de/excitation and de/polarization of positronium) is carefully examined against partial waves. The multi-channel scattering solutions are composed of functions that diagonalize the four-body Hamiltonian, and scattering functions that satisfy the correct asymptotic boundary conditions. The production rates of

H

̄

+

show large discrepancies compared to more approximate calculations.
Understanding the conceptual frameworks and methods of the food–energy–water nexus at the household level for development-oriented policy support: a systematic review
Authors: Itayi Chirenje Leonard , Mohan Geetha , Saito Osamu 
Published: December 2020

Abstract
This paper undertakes a systematic review of the literature to understand current trends in the food–energy–water (FEW) nexus for development-oriented policy support. The paper follows three steps: (a) a bibliometric analysis of FEW nexus research, (b) a content analysis of FEW nexus research, and (c) development of a framework that fills existing gaps in FEW nexus research. The review found that FEW nexus approaches have gained ground in academia as a resource management tool and policy guide; however, the process does not have a robust conceptualization. The current FEW nexus approaches focus on national, regional, and international scales of analysis to understand the three sectors’ interactions. Further, these approaches underline the nexus processes, which have been researched in detail, including synergies and tradeoffs. However, research on the FEW nexus has not adequately explored the social factors that form part of the nexus, especially at the local household scale. Factors such as the gender dynamics of resource ownership, work roles at different scales, household incomes, and culture are essential components that are yet to be explored in FEW nexus research. Most of the existing frameworks on the FEW nexus overemphasize models and the quantitative measurement of processes while paying limited attention to social aspects. Still, these social aspects are crucial, especially on the household scale; therefore, to overcome these gaps, this paper proposes a FEW nexus framework at the local household scale that includes socio-economic determinants.
Ecological and forestry features of broad leaved forest and their role in the conservation of biodiversity in the Novgorod region
Authors: Smirnov I A , Nikonov M V 
Published: December 2020

Abstract
The article provides information on the distribution and condition of broad leaved forest in the Novgorod region. A semi-landscape distribution of broad leaved forest sections is presented. Based on the data of 143 sample plots, the biological diversity of broad leaved forest was estimated.
Patch shape and size effect on performance of in-situ scarf patch repair in aircraft panel
Authors: Dwivedi Kishan , Pathak Himanshu 
Published: December 2020

Abstract
Patch repairing technique is effective and efficient approach to enhance structural performance of aged aircraft panels. The presented work emphases on studying the patch shape and size effect on scarf composite patch repair of aluminium aircraft panel under thermal, thermo-elastic and mechanical load. In this work, patched repaired structural member has been simulated by ABAQUS software to find out the performance of patch repair in term of patch thickness and patch shape. Five different patch shapes are chosen to analysis: circular, square, hexagonal, rectangular and trapezoidal with different patch thickness 1, 2, 3, 4, 5 mm. The Heat transfer and coupled temp-displacement analysis has been performed under cure temperature 394 K for in-situ patch repair model. The analysis of the critical von-Mises stress and heat flux load distribution in composite patch repair system allows us to estimate performance in composite patch repair system. The results show that patch shape and size has significant effect on magnitude of heat flux load and induced von-Mises stress. Trapezoidal shape of composite patch repair has lower value of von-Mises stress and heat flux load as compared to all four shapes of composite patches.
Modeling and Simulation of a Semi-active Vehicle Suspension system using PID Controller
Authors: Narwade Prashant , Deshmukh Ravindra , Nagarkar Mahesh , Bankar Milind 
Published: December 2020

Abstract
In this article, the numerical simulation of Magneto-rheological (MR) damper has been done using PID controller in Matlab-Simulink software to compare between the regular Macpherson strut and semi active suspension systems. The Magneto-rheological damper is a control device filled with Magneto-rheological fluid which changes damping force by changing property of viscosity on application of magnetic field. The results show that proportional integral derivative (PID) controller used to control damper in semi-active suspension is more efficient to reduce road disturbances than the regular suspension using Macpherson strut. Vehicle chassis displacement and acceleration can be reduced within milliseconds of time.