bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Generic Pushbroom Sensor Model for Planetary Photogrammetry
Authors: Geng Xun , Xu Qing , Xing Shuai , Lan Chaozhen 
Published: March 2020

AbstractDifferent imaging instruments are designed in the planetary exploration missions, which require respective photogrammetric software modules to support the geometric processing of planetary remote sensing images. To decrease the cost of software development and maintenance, this paper presents a generic pushbroom sensor model for planetary photogrammetry. Thus, various coordinate transformations can be conducted in a unified and efficient way, without considering the specific camera and the optical distortion equations. In terms of implementation, the camera file and orientation data file designed for the airborne linear array camera ADS40 are used to manage the interior orientation and exterior orientation parameters of planetary images. The generic pushbroom sensor model supports the summing mode, varying exposure times within an image and image distortions, which are typical problems in need of a solution in planetary mapping. Furthermore, an alternative photogrammetric process based on extracting tie points on approximate orthophotos is developed. The geometric accuracy and computational efficiency of the generic pushbroom sensor model were compared with the popular planetary cartographic software—Integrated System for Imagers and Spectrometers (ISIS). The experimental results demonstrate that the proposed generic pushbroom sensor model can (1) deliver the same geometric accuracy as the ISIS pushbroom sensor model, (2) greatly improve the computational efficiency of orthophotos generation and tie points extraction, and (3) support various types of planetary remote sensing images. Moreover, the proposed generic pushbroom sensor model reduces the cost of software development because different types of planetary images share the same code base.
Stochastic Modeling as a Method of Arriving at Higher Frequencies: An Application to κ Estimation
Authors: Pikoulis Erion‐Vasilis , Ktenidou Olga‐Joan , Psarakis Emmanouil Z. , Abrahamson Norman A. 
Published: March 2020

AbstractWe present a framework for stochastically modeling the Fourier spectrum of the noisy seismic recording based on the fundamental assumption that the latter constitutes a random rather than a deterministic quantity. First we demonstrate (mathematically and through simulations) that, under the stochastic‐signal assumption, the periodogram ordinates of the noisy recording can be considered independent exponential random variables with a frequency‐dependent mean. Using this finding, the estimation of seismological parameters is translated into a well‐defined maximum likelihood (ML) problem, allowing a fast, accurate, and robust solution. Although the proposed ML methodology constitutes a general estimation framework that we believe can improve any spectral analysis, here we specifically apply it to the high‐frequency attenuation parameter (κ), crucial for understanding rock ground motion. Other seismological parameters could be estimated by appropriately adapting the theoretical model and frequency band used. The greatest advantage of the proposed method is its ability to account for the presence of noise rather than simply try to avoid it, as is the case with all conventional κ approaches and many other spectral analysis approaches. This means that the proposed technique achieves acceptable results even for very low signal‐to‐noise ratios (SNR), thus pushing the boundary of what can be considered usable recording quality. The technique's superior performance in estimation is demonstrated through a series of experiments involving both synthetic and real seismic recordings. Our results also indicate that, compared to this new “noise‐modeling” approach, conventional “noise‐avoiding” approaches are likely to systematically underestimate the “true” kappa value in recordings of moderate‐to‐low SNR.
Squirt Flow in Cracks with Rough Walls
Authors: Lissa Simón , Barbosa Nicolás D. , Caspari Eva , Alkhimenkov Yury , Quintal Beatriz 
Published: March 2020

AbstractWe explore the impact of roughness in crack walls on the P wave modulus dispersion and attenuation caused by squirt flow. For that, we numerically simulate oscillatory relaxation tests on models having interconnected cracks with both simple and intricate aperture distributions. Their viscoelastic responses are compared with those of models containing planar cracks but having the same hydraulic aperture as the rough wall cracks. In the absence of contact areas between crack walls, we found that three apertures affect the P wave modulus dispersion and attenuation: the arithmetic mean, minimum aperture, and hydraulic aperture. We show that the arithmetic mean of the crack apertures controls the effective P wave modulus at the low‐ and high‐frequency limits, thus representing the mechanical aperture. The minimum aperture of the cracks tends to dominate the energy dissipation process and, consequently, the characteristic frequency. An increase in the confining pressure is emulated by uniformly reducing the crack apertures, which allows for the occurrence of contact areas. The contact area density and distribution play a dominant role in the stiffness of the model, and in this scenario, the arithmetic mean is not representative of the mechanical aperture. On the other hand, for a low percentage of minimum aperture or in the presence of contact areas, the hydraulic aperture tends to control the characteristic frequency. Analyzing the local energy dissipation, we can more specifically visualize that a different aperture controls the energy dissipation process at each frequency, which means that a frequency‐dependent hydraulic aperture might describe the squirt flow process in cracks with rough walls.
Adherence to a Mediterranean-style eating pattern and risk of diabetes in a U.S. prospective cohort study
Authors: O’Connor Lauren E. , Hu Emily A. , Steffen Lyn M. , Selvin Elizabeth , Rebholz Casey M. 
Published: March 2020

Abstract
Background
A Mediterranean-style eating pattern is consistently associated with a decreased diabetes risk in Mediterranean and European populations. However, results in U.S. populations are inconsistent. The objective of this study was to assess whether a Mediterranean-style eating pattern would be associated with diabetes risk in a large, nationally representative U.S. cohort of black and white men and women.

Methods
Participants from the Atherosclerosis Risk in Communities study prospective cohort without diabetes, cardiovascular disease, or cancer at baseline (visit 1, 1987–1989; n = 11,991) were included (mean age 54 years, 56% female, 75% white). Alternate Mediterranean Diet scores (aMed) were calculated using the mean dietary intake self-reported at visit 1 and visit 3 (1993–1995) or visit 1 only for participants censored before visit 3. Participants were followed from visit 1 through 31 December 2016 for incident diabetes. We used Cox regression models to characterize associations of aMed (quintiles as well as per 1-point higher) with incident diabetes adjusted for energy intake, age, sex, race and study center, and education (Model 1) for all participants then stratified by race and body mass index (BMI). Model 2 included potential mediating behavioral and clinical measures associated with diabetes. Results are presented as hazard ratios and 95% confidence intervals.

Results
Over a median follow-up of 22 years, there were 4024 incident cases of diabetes. Higher aMed scores were associated with lower diabetes risk [Model 1: 0.83 (0.73–0.94) for Q5 vs Q1 (p-trend < 0.001) and 0.96 (0.95–0.98) for 1-point higher]. Associations were stronger for black vs white participants (interaction p < 0.001) and weaker for obese vs normal BMI (interaction p < 0.01). Associations were attenuated but statistically significant in Model 2.

Conclusions
An eating pattern high in fruits, vegetables, whole grains, legumes, nuts, and fish, and moderate in alcohol was associated with a lower risk of diabetes in a community-based U.S. population.
The intronic BRCA1 c.5407-25T>A variant causing partly skipping of exon 23—a likely pathogenic variant with reduced penetrance?
Authors: Høberg-Vetti Hildegunn , Ognedal Elisabet , Buisson Adrien , Vamre Tone Bøe Aaman , Ariansen Sarah , Hoover Jacqueline M. , Eide Geir Egil , Houge Gunnar , Fiskerstrand Torunn , Haukanes Bjørn Ivar , Bjorvatn Cathrine , Knappskog Per Morten 
Published: March 2020

AbstractRare sequence variants in the non-coding part of the BRCA genes are often reported as variants of uncertain significance (VUS), which leave patients and doctors in a challenging position. The aim of this study was to determine the pathogenicity of the BRCA1 c.5407-25T>A variant found in 20 families from Norway, France and United States with suspected hereditary breast and ovarian cancer. This was done by combining clinical and family information with allele frequency data, and assessment of the variant’s effect on mRNA splicing. Mean age at breast (n = 12) and ovarian (n = 11) cancer diagnosis in female carriers was 49.9 and 60.4 years, respectively. The mean Manchester score in the 20 families was 16.4. The allele frequency of BRCA1 c.5407-25T>A was 1/64,566 in non-Finnish Europeans (gnomAD database v2.1.1). We found the variant in 1/400 anonymous Norwegian blood donors and 0/784 in-house exomes. Sequencing of patient-derived cDNA from blood, normal breast and ovarian tissue showed that BRCA1 c.5407-25T>A leads to skipping of exon 23, resulting in frameshift and protein truncation: p.(Gly1803GlnfsTer11). Western blot analysis of transiently expressed BRCA1 proteins in HeLa cells showed a reduced amount of the truncated protein compared with wild type. Noteworthily, we found that a small amount of full-length transcript was also generated from the c.5407-25T>A allele, potentially explaining the intermediate cancer burden in families carrying this variant. In summary, our results show that BRCA1 c.5407-25T>A leads to partial skipping of exon 23, and could represent a likely pathogenic variant with reduced penetrance.
Dissecting the role of PfAP2-G in malaria gametocytogenesis
Authors: Josling Gabrielle A. , Russell Timothy J. , Venezia Jarrett , Orchard Lindsey , van Biljon Riëtte , Painter Heather J. , Llinás Manuel 
Published: March 2020

AbstractIn the malaria parasite Plasmodium falciparum, the switch from asexual multiplication to sexual differentiation into gametocytes is essential for transmission to mosquitos. The transcription factor PfAP2-G is a key determinant of sexual commitment that orchestrates this crucial cell fate decision. Here we identify the direct targets of PfAP2-G and demonstrate that it dynamically binds hundreds of sites across the genome. We find that PfAP2-G is a transcriptional activator of early gametocyte genes, and identify differences in PfAP2-G occupancy between gametocytes derived via next-cycle and same-cycle conversion. Our data implicate PfAP2-G not only as a transcriptional activator of gametocyte genes, but also as a potential regulator of genes important for red blood cell invasion. We also find that regulation by PfAP2-G requires interaction with a second transcription factor, PfAP2-I. These results clarify the functional role of PfAP2-G during sexual commitment and early gametocytogenesis.
2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations
Authors: Trzaska Carole , Amand Séverine , Bailly Christine , Leroy Catherine , Marchand Virginie , Duvernois-Berthet Evelyne , Saliou Jean-Michel , Benhabiles Hana , Werkmeister Elisabeth , Chassat Thierry , Guilbert Romain , Hannebique David , Mouray Anthony , Copin Marie-Christine , Moreau Pierre-Arthur , Adriaenssens Eric , Kulozik Andreas , Westhof Eric , Tulasne David , Motorin Yuri , Rebuffat Sylvie , Lejeune Fabrice 
Published: March 2020

AbstractNonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2′-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations.
Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair
Authors: Ghodke Harshad , Ho Han Ngoc , van Oijen Antoine M. 
Published: March 2020

AbstractIn the model organism Escherichia coli, helix distorting lesions are recognized by the UvrAB damage surveillance complex in the global genomic nucleotide excision repair pathway (GGR). Alternately, during transcription-coupled repair (TCR), UvrA is recruited to Mfd at sites of RNA polymerases stalled by lesions. Ultimately, damage recognition is mediated by UvrA, followed by verification by UvrB. Here we characterize the differences in the kinetics of interactions of UvrA with Mfd and UvrB by following functional, fluorescently tagged UvrA molecules in live TCR-deficient or wild-type cells. The lifetimes of UvrA in Mfd-dependent or Mfd-independent interactions in the absence of exogenous DNA damage are comparable in live cells, and are governed by UvrB. Upon UV irradiation, the lifetimes of UvrA strongly depended on, and matched those of Mfd. Overall, we illustrate a non-perturbative, imaging-based approach to quantify the kinetic signatures of damage recognition enzymes participating in multiple pathways in cells.
NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance
Authors: Pak Joseph S. , DeLoughery Zachary J. , Wang Jing , Acharya Nischal , Park Yeonwoo , Jaworski Alexander , Özkan Engin 
Published: March 2020

AbstractAxon pathfinding is critical for nervous system development, and it is orchestrated by molecular cues that activate receptors on the axonal growth cone. Robo family receptors bind Slit guidance cues to mediate axon repulsion. In mammals, the divergent family member Robo3 does not bind Slits, but instead signals axon repulsion from its own ligand, NELL2. Conversely, canonical Robos do not mediate NELL2 signaling. Here, we present the structures of NELL-Robo3 complexes, identifying a mode of ligand engagement for Robos that is orthogonal to Slit binding. We elucidate the structural basis for differential binding between NELL and Robo family members and show that NELL2 repulsive activity is a function of its Robo3 affinity and is enhanced by ligand trimerization. Our results reveal a mechanism of oligomerization-induced Robo activation for axon guidance and shed light on Robo family member ligand binding specificity, conformational variability, divergent modes of signaling, and evolution.
Low-temperature paddlewheel effect in glassy solid electrolytes
Authors: Smith Jeffrey G. , Siegel Donald J. 
Published: March 2020

AbstractGlasses are promising electrolytes for use in solid-state batteries. Nevertheless, due to their amorphous structure, the mechanisms that underlie their ionic conductivity remain poorly understood. Here, ab initio molecular dynamics is used to characterize migration processes in the prototype glass, 75Li2S–25P2S5. Lithium migration occurs via a mechanism that combines concerted motion of lithium ions with large, quasi-permanent reorientations of PS43−anions. This latter effect, known as the ‘paddlewheel’ mechanism, is typically observed in high-temperature crystalline polymorphs. In contrast to the behavior of crystalline materials, in the glass paddlewheel dynamics contribute to Lithium-ion mobility at room temperature. Paddlewheel contributions are confirmed by characterizing spatial, temporal, vibrational, and energetic correlations with Lithium motion. Furthermore, the dynamics in the glass differ from those in the stable crystalline analogue, γ-Li3PS4, where anion reorientations are negligible and ion mobility is reduced. These data imply that glasses containing complex anions, and in which covalent network formation is minimized, may exhibit paddlewheel dynamics at low temperature. Consequently, these systems may be fertile ground in the search for new solid electrolytes.
Optical spin-orbit torque in heavy metal-ferromagnet heterostructures
Authors: Choi Gyung-Min , Oh Jung Hyun , Lee Dong-Kyu , Lee Seo-Won , Kim Kun Woo , Lim Mijin , Min Byoung-Chul , Lee Kyung-Jin , Lee Hyun-Woo 
Published: March 2020

AbstractSpin current generation through the spin-orbit interaction in non-magnetic materials lies at the heart of spintronics. When the generated spin current is injected to a ferromagnet, it produces spin-orbit torque and manipulates magnetization efficiently. Optically generated spin currents are expected to be superior to their electrical counterparts in terms of the manipulation speed. Here we report optical spin-orbit torques in heavy metal/ferromagnet heterostructures. The strong spin-orbit coupling of heavy metals induces photo-excited carriers to be spin-polarized, and their transport from heavy metals to ferromagnets induces a torque on magnetization. Our results demonstrate that heavy metals can generate spin-orbit torque not only electrically but also optically.
Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides
Authors: Miller Rebecca L. , Guimond Scott E. , Schwörer Ralf , Zubkova Olga V. , Tyler Peter C. , Xu Yongmei , Liu Jian , Chopra Pradeep , Boons Geert-Jan , Grabarics Márkó , Manz Christian , Hofmann Johanna , Karlsson Niclas G. , Turnbull Jeremy E. , Struwe Weston B. , Pagel Kevin 
Published: March 2020

AbstractDespite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a “Shotgun” Ion Mobility Mass Spectrometry Sequencing (SIMMS2) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS2 analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS2 thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation.
Exfoliated near infrared fluorescent silicate nanosheets for (bio)photonics
Authors: Selvaggio Gabriele , Chizhik Alexey , Nißler Robert , Kuhlemann llyas , Meyer Daniel , Vuong Loan , Preiß Helen , Herrmann Niklas , Mann Florian A. , Lv Zhiyi , Oswald Tabea A. , Spreinat Alexander , Erpenbeck Luise , Großhans Jörg , Karius Volker , Janshoff Andreas , Pablo Giraldo Juan , Kruss Sebastian 
Published: March 2020

AbstractImaging of complex (biological) samples in the near-infrared (NIR) is beneficial due to reduced light scattering, absorption, phototoxicity, and autofluorescence. However, there are few NIR fluorescent materials known and suitable for biomedical applications. Here we exfoliate the layered pigment CaCuSi4O10 (Egyptian Blue, EB) via ball milling and facile tip sonication into NIR fluorescent nanosheets (EB-NS). The size of EB-NS can be tailored to diameters <20 nm and heights down to 1 nm. EB-NS fluoresce at 910 nm and the fluorescence intensity correlates with the number of Cu2+ ions. Furthermore, EB-NS display no bleaching and high brightness compared with other NIR fluorophores. The versatility of EB-NS is demonstrated by in-vivo single-particle tracking and microrheology measurements in Drosophila melanogaster embryos. EB-NS can be uptaken by plants and remotely detected in a low-cost stand-off detection setup. In summary, EB-NS have the potential for a wide range of bioimaging applications.
Electricity-powered artificial root nodule
Authors: Lu Shengtao , Guan Xun , Liu Chong 
Published: March 2020

AbstractRoot nodules are agricultural-important symbiotic plant-microbe composites in which microorganisms receive energy from plants and reduce dinitrogen (N2) into fertilizers. Mimicking root nodules using artificial devices can enable renewable energy-driven fertilizer production. This task is challenging due to the necessity of a microscopic dioxygen (O2) concentration gradient, which reconciles anaerobic N2 fixation with O2-rich atmosphere. Here we report our designed electricity-powered biological|inorganic hybrid system that possesses the function of root nodules. We construct silicon-based microwire array electrodes and replicate the O2 gradient of root nodules in the array. The wire array compatibly accommodates N2-fixing symbiotic bacteria, which receive energy and reducing equivalents from inorganic catalysts on microwires, and fix N2 in the air into biomass and free ammonia. A N2 reduction rate up to 6.5 mg N2 per gram dry biomass per hour is observed in the device, about two orders of magnitude higher than the natural counterparts.
Increased male susceptibility to Mycobacterium tuberculosis infection is associated with smaller B cell follicles in the lungs
Authors: Hertz David , Dibbern Jannike , Eggers Lars , von Borstel Linda , Schneider Bianca E. 
Published: March 2020

AbstractTuberculosis prevalence is significantly higher among men than women. We have previously revealed an increased susceptibility of male C57BL/6 mice towards Mycobacterium tuberculosis (Mtb) H37Rv. In the current study, we confirm the male bias for infection with the Beijing strain HN878. Males succumbed to HN878 infection significantly earlier than females. In both models, premature death of males was associated with smaller B cell follicles in the lungs. Analysis of homeostatic chemokines and their receptors revealed differences between H37Rv and HN878 infected animals, indicating different immune requirements for follicle formation in both models. However, expression of IL-23, which is involved in long-term containment of Mtb and lymphoid follicle formation, was reduced in male compared to female lungs in both models. Our study reveals sex differences in the formation of B cell follicles in the Mtb infected lung and we propose that impaired follicle formation is responsible for accelerated disease progression in males.