bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating region memory management and tag-free generational garbage collection
Authors: ELSMAN MARTIN , HALLENBERG NIELS 
Published: February 2021

Abstract
We present a region-based memory management scheme with support for generational garbage collection. The scheme features a compile-time region inference algorithm, which associates values with logical regions, and builds on a region type system that deploys region types at runtime to avoid the overhead of write barriers and to support partly tag-free garbage collection. The scheme is implemented in the MLKit Standard ML compiler, which generates native x64 machine code. Besides demonstrating a number of important formal properties of the scheme, we measure the scheme’s characteristics, for a number of benchmarks, and compare the performance of the generated executables with the performance of executables generated with the MLton state-of-the-art Standard ML compiler and configurations of the MLKit with and without region inference and generational garbage collection enabled. Although region inference often serves the purpose of generations, combining region inference with generational garbage collection is shown often to be superior to combining region inference with non-generational collection despite the overhead introduced by a larger amount of memory waste, due to region fragmentation.
Assessment of regional and global right ventricular systolic function in children with repaired tetralogy of Fallot
Authors: Caris Elizabeth , Drant Stacey 
Published: February 2021

AbstractBackground:Echo assessment of right ventricular function is difficult due to its complex geometry and regional differences in wall motion. In patients with repaired tetralogy of Fallot, cardiac MRI is the gold standard for assessment of right ventricular function. There is scant data regarding the correlation of echo measures of right ventricular function with cardiac MRI right ventricular function in the paediatric population.Methods:Echocardiographic measures of regional and global right ventricular function were reviewed in 56 patients with repaired tetralogy of Fallot and 27 patients with structurally normal hearts. These measures were compared to global right ventricular ejection fraction by cardiac MRI.Results:Despite having the same right ventricular ejection fraction by cardiac MRI as normal controls, patients with repaired tetralogy of Fallot had significantly worse global and regional echocardiographic measures of right ventricular function. Right ventricular fractional area change and fractional shortening of the right ventricular outflow tract correlated best with global right ventricular function by MRI. Incorporation of these measures into a regression model allowed accurate prediction of global right ventricular function by cardiac MRI.Conclusion:Children with repaired tetralogy of Fallot have abnormal regional and global right ventricular function compared to patients with normal hearts. Despite the presence of patch material, the right ventricular outflow tract significantly contributes to global right ventricular function by cardiac MRI. When incorporated into a model that includes regional and global echocardiographic measures of right ventricular function, right ventricular outflow tract fractional shortening helps predict global right ventricular function by MRI.
Significance of herbicide order in sequential applications to target weeds in a sunn hemp living mulch
Authors: Bhaskar Vinay , Bellinder Robin R. , Reiners Stephen , Westbrook Anna S. , DiTommaso Antonio 
Published: February 2021

AbstractStriking a balance between the weed control capacity of living mulches and their competition with the main crop is complex. At rates that avoid severe injury to living mulch, herbicides may reduce their vigor while simultaneously contributing to weed control. In a 2-yr field study carried out in Freeville, NY, we evaluated the effects of various combinations consisting of two herbicides, applied sequentially at reduced rates, on the growth of a sunn hemp living mulch and weeds (including common lambsquarters, common purslane, hairy galinsoga, and Powell amaranth). When a herbicide with primarily POST activity (Type 1; e.g., rimsulfuron, 0.005 to 0.007 kg ai ha−1) was applied first, performance of sunn hemp (1700 to 3900 kg ha−1 dry biomass; 10% to 88% groundcover) was poor and weed growth (25% to 62% groundcover) was high, likely because sunn hemp was severely injured at a young growth stage and was outcompeted by weeds. A follow-up application (approximately 2 wk later) of a herbicide with primarily PRE and residual activities (Type 2; e.g., metribuzin, 0.05 to 0.15 kg ai ha−1), with a surfactant to enhance its POST activity, had little effect on established weeds. However, because sunn hemp was already 20 cm tall at weed emergence, applying a Type 2 herbicide first did not cause severe injury to sunn hemp and reduced weed pressure, thereby also enhancing sunn hemp performance (3,800 to 6,100 kg ha−1 dry biomass; 85% to 94% groundcover). Moreover, the follow-up application of a Type 1 herbicide affected the smaller weeds more (4% to 21% groundcover) than the better-established sunn hemp. Our results demonstrate that an appropriate sequence of herbicides at reduced rates may be important to control weeds while maintaining a healthy living mulch stand.
On the Ion Precipitation due to Field Line Curvature (FLC) and EMIC Wave Scattering and Their Subsequent Impact on Ionospheric Electrodynamics
Authors: Zhu Minghui , Yu Yiqun , Tian Xingbin , Shreedevi P. R. , Jordanova Vania K. 
Published: February 2021

AbstractBoth field line curvature (FLC) and electromagnetic ion cyclotron (EMIC) wave scattering are believed to be associated with energetic ion precipitation, but their relative contributions to ionospheric ion precipitation and subsequent effects are still unclear. In this study, by using a kinetic ring current model, we investigate their impact on the ionosphere from two aspects: the global distribution of ion precipitation and resulting ionospheric conductance. Our results show that the intensity and coverage of ion precipitation due to EMIC waves are larger than that due to FLC scattering, while the latter mostly contributes to ion precipitation in outer regions (L > 4–5). We then estimate the conductance with empirical models using the simulated ion precipitation energy flux. When the EMIC wave associated proton precipitation is included, the conductance is significantly enhanced in the dusk‐to‐midnight sector and has a wide magnetic latitude (MLAT) range from around 52° to 62°, considerably altering the electric potential in the dusk sector, which further influences particle dynamics in the magnetosphere. On the contrary, the proton precipitation caused by FLC scattering only occurs at higher latitudes above MLAT = 60° and the corresponding conductance is slightly enhanced at midnight, with negligible influence on the convective electric potential. Although electron precipitation‐associated conductance is predominant globally, the results show that proton precipitation can also play an important role in ionospheric electrodynamics, especially when EMIC wave‐associated precipitating proton energy flux exceeds that of electrons in the dusk sector, a region where many subauroral coupling processes occur.
Dispersion of Buoyant and Sinking Particles in a Simulated Wind‐ and Wave‐Driven Turbulent Coastal Ocean
Authors: Thoman Todd X. , Kukulka Tobias , Gamble Kathleen 
Published: February 2021

AbstractIn shallow coastal oceans, turbulent flows driven by surface winds and waves and constrained by a solid bottom disperse particles. This work examines the mechanisms driving horizontal and vertical dispersion of buoyant and sinking particles for times much greater than turbulent integral time scales. Turbulent fields are modeled using a wind‐stress driven large eddy simulation (LES), incorporating wave‐driven Langmuir turbulence, surface breaking wave turbulent kinetic energy inputs, and a solid bottom boundary. A Lagrangian stochastic model is paired to the LES to incorporate Lagrangian particle tracking. Within a subset of intermediate buoyant rise velocities, particles experience synergistic vertical mixing in which breaking waves (BW) inject particles into Langmuir downwelling velocities sufficient to drive deep mixing. Along‐wind dispersion is controlled by vertical shear in mean along‐wind velocities. Wind and bottom friction‐driven vertical shear enhances dispersion of buoyant and sinking particles, while energetic turbulent mixing, such as from BW, dampens shear dispersion. Strongly rising and sinking particles trapped at the ocean surface and bottom, respectively, experience no vertical shear, resulting in low rates of along‐wind dispersion. Crosswind dispersion is shaped by particle advection in wind‐aligned fields of counter‐rotating Langmuir and Couette roll cells. Langmuir cells enhance crosswind dispersion in neutrally to intermediately buoyant particles through enhanced cell hopping. Surface trapping restricts particles to Langmuir convergence regions, strongly inhibiting crosswind dispersion. In shallow coastal systems, particle dispersion depends heavily on particle buoyancy and wave‐dependent turbulent effects.
Observations of the Impacts of Millimeter‐ to Centimeter‐Scale Heterogeneities on Relative Permeability and Trapping in Carbonate Rocks
Authors: Manoorkar Sojwal , Jackson Samuel J. , Krevor Samuel 
Published: February 2021

AbstractCarbonate rock reservoirs are dominated by heterogeneity across a large and continuous range of spatial scales. We study the impact of heterogeneities on relative permeability and residual trapping for three carbonate rocks selected for their distinct spatial scales of rock texture. The Indiana limestone comprises millimeter‐scale heterogeneities, the Estaillades limestone consists of half‐centimeter‐scale heterogeneities, and the Edwards dolomite includes decimeter‐scale heterogeneity. Along with routine characterization of rock samples, steady‐state N2–deionized water drainage relative permeability measurements are made for each rock at two distinct total flow rates, at least 1 order of magnitude apart. The variation in flow potential across the core results in observations of fluid distribution, core‐average relative permeability, and residual trapping obtained for a range of continuum‐scale capillary number . The relative permeability curves for all rocks shift to the right of the water saturation axis with increasing flow potential; the nitrogen relative permeability increases while the water relative permeability decreases. However, the magnitude of the shift depends on the spatial scale of heterogeneity. An inspection of 3D saturation distributions in the cores and estimation of the capillary numbers of flow shows that the rock with the largest heterogeneity is capillary flow dominated throughout the range of injection rates tested; observations in the Indiana and Estaillades carbonates traverse capillary to viscous dominated flow regimes, with commensurate flow rate dependence in the relative permeability. In all cases, residual trapping is poorly described by the Land model.
Exciton diffusion exceeding 1 µm: run, exciton, run!
Authors: Dursun Ibrahim , Guzelturk Burak 
Published: February 2021

AbstractExciton diffusion lengths reaching the micrometer length scale have long been desired in solution-processed semiconductors but have remained unattainable using conventional materials to date. Now halide perovskite nanocrystal films show unprecedented exciton migration with diffusion lengths approaching 1 µm owing to the efficient combination of radiative and nonradiative energy transfer.
Addiction as a brain disease revised: why it still matters, and the need for consilience
Authors: Heilig Markus , MacKillop James , Martinez Diana , Rehm Jürgen , Leggio Lorenzo , Vanderschuren Louk J. M. J. 
Published: February 2021

AbstractThe view that substance addiction is a brain disease, although widely accepted in the neuroscience community, has become subject to acerbic criticism in recent years. These criticisms state that the brain disease view is deterministic, fails to account for heterogeneity in remission and recovery, places too much emphasis on a compulsive dimension of addiction, and that a specific neural signature of addiction has not been identified. We acknowledge that some of these criticisms have merit, but assert that the foundational premise that addiction has a neurobiological basis is fundamentally sound. We also emphasize that denying that addiction is a brain disease is a harmful standpoint since it contributes to reducing access to healthcare and treatment, the consequences of which are catastrophic. Here, we therefore address these criticisms, and in doing so provide a contemporary update of the brain disease view of addiction. We provide arguments to support this view, discuss why apparently spontaneous remission does not negate it, and how seemingly compulsive behaviors can co-exist with the sensitivity to alternative reinforcement in addiction. Most importantly, we argue that the brain is the biological substrate from which both addiction and the capacity for behavior change arise, arguing for an intensified neuroscientific study of recovery. More broadly, we propose that these disagreements reveal the need for multidisciplinary research that integrates neuroscientific, behavioral, clinical, and sociocultural perspectives.
Reconfigurable all-dielectric metalens with diffraction-limited performance
Authors: Shalaginov Mikhail Y. , An Sensong , Zhang Yifei , Yang Fan , Su Peter , Liberman Vladimir , Chou Jeffrey B. , Roberts Christopher M. , Kang Myungkoo , Rios Carlos , Du Qingyang , Fowler Clayton , Agarwal Anuradha , Richardson Kathleen A. , Rivero-Baleine Clara , Zhang Hualiang , Hu Juejun , Gu Tian 
Published: February 2021

AbstractActive metasurfaces, whose optical properties can be modulated post-fabrication, have emerged as an intensively explored field in recent years. The efforts to date, however, still face major performance limitations in tuning range, optical quality, and efficiency, especially for non-mechanical actuation mechanisms. In this paper, we introduce an active metasurface platform combining phase tuning in the full 2π range and diffraction-limited performance using an all-dielectric, low-loss architecture based on optical phase change materials (O-PCMs). We present a generic design principle enabling binary switching of metasurfaces between arbitrary phase profiles and propose a new figure-of-merit (FOM) tailored for reconfigurable meta-optics. We implement the approach to realize a high-performance varifocal metalens operating at 5.2 μm wavelength. The reconfigurable metalens features a record large switching contrast ratio of 29.5 dB. We further validate aberration-free and multi-depth imaging using the metalens, which represents a key experimental demonstration of a non-mechanical tunable metalens with diffraction-limited performance.
Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis
Authors: Song Won-Min , Agrawal Praveen , Von Itter Richard , Fontanals-Cirera Barbara , Wang Minghui , Zhou Xianxiao , Mahal Lara K. , Hernando Eva , Zhang Bin 
Published: February 2021

AbstractMelanoma is the most lethal skin malignancy, driven by genetic and epigenetic alterations in the complex tumour microenvironment. While large-scale molecular profiling of melanoma has identified molecular signatures associated with melanoma progression, comprehensive systems-level modeling remains elusive. This study builds up predictive gene network models of molecular alterations in primary melanoma by integrating large-scale bulk-based multi-omic and single-cell transcriptomic data. Incorporating clinical, epigenetic, and proteomic data into these networks reveals key subnetworks, cell types, and regulators underlying melanoma progression. Tumors with high immune infiltrates are found to be associated with good prognosis, presumably due to induced CD8+ T-cell cytotoxicity, via MYO1F-mediated M1-polarization of macrophages. Seventeen key drivers of the gene subnetworks associated with poor prognosis, including the transcription factor ZNF180, are tested for their pro-tumorigenic effects in vitro. The anti-tumor effect of silencing ZNF180 is further validated using in vivo xenografts. Experimentally validated targets of ZNF180 are enriched in the ZNF180 centered network and the known pathways such as melanoma cell maintenance and immune cell infiltration. The transcriptional networks and their critical regulators provide insights into the molecular mechanisms of melanomagenesis and pave the way for developing therapeutic strategies for melanoma.
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika
Authors: Fischer C. , Koblmüller S. , Börger C. , Michelitsch G. , Trajanoski S. , Schlötterer C. , Guelly C. , Thallinger G. G. , Sturmbauer C. 
Published: February 2021

AbstractWith more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes ofTropheus moorii(TM) andPetrochromis trewavasae(PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH,SMO,WNT9A) and the BMP and GLI families.
Single-cell RNA sequencing reveals developmental heterogeneity among Plasmodium berghei sporozoites
Authors: Ruberto Anthony A. , Bourke Caitlin , Merienne Nicolas , Obadia Thomas , Amino Rogerio , Mueller Ivo 
Published: February 2021

AbstractIn the malaria-causing parasite’s life cycle, Plasmodium sporozoites must travel from the midgut of a mosquito to the salivary glands before they can infect a mammalian host. However, only a fraction of sporozoites complete the journey. Since salivary gland invasion is required for transmission of sporozoites, insights at the molecular level can contribute to strategies for malaria prevention. Recent advances in single-cell RNA sequencing provide an opportunity to assess sporozoite heterogeneity at a resolution unattainable by bulk RNA sequencing methods. In this study, we use a droplet-based single-cell RNA sequencing workflow to analyze the transcriptomes of over 8000 Plasmodium berghei sporozoites derived from the midguts and salivary glands of Anopheles stephensi mosquitoes. The detection of known marker genes confirms the successful capture and sequencing of samples composed of a mixed population of sporozoites. Using data integration, clustering, and trajectory analyses, we reveal differences in gene expression profiles of individual sporozoites, and identify both annotated and unannotated markers associated with sporozoite development. Our work highlights the utility of a high-throughput workflow for the transcriptomic profiling of Plasmodium sporozoites, and provides new insights into gene usage during the parasite’s development in the mosquito.
Spatial distribution of physiologic 12-lead QRS complex
Authors: Hnatkova Katerina , Andršová Irena , Toman Ondřej , Smetana Peter , Huster Katharina M. , Šišáková Martina , Barthel Petra , Novotný Tomáš , Schmidt Georg , Malik Marek 
Published: February 2021

AbstractThe normal physiologic range of QRS complex duration spans between 80 and 125 ms with known differences between females and males which cannot be explained by the anatomical variations of heart sizes. To investigate the reasons for the sex differences as well as for the wide range of normal values, a technology is proposed based on the singular value decomposition and on the separation of different orthogonal components of the QRS complex. This allows classification of the proportions of different components representing the 3-dimensional representation of the electrocardiographic signal as well as classification of components that go beyond the 3-dimensional representation and that correspond to the degree of intricate convolutions of the depolarisation sequence. The technology was applied to 382,019 individual 10-s ECG samples recorded in 639 healthy subjects (311 females and 328 males) aged 33.8 ± 9.4 years. The analyses showed that QRS duration was mainly influenced by the proportions of the first two orthogonal components of the QRS complex. The first component demonstrated statistically significantly larger proportion of the total QRS power (expressed by the absolute area of the complex in all independent ECG leads) in females than in males (64.2 ± 11.6% vs 59.7 ± 11.9%, p < 0.00001—measured at resting heart rate of 60 beats per minute) while the second component demonstrated larger proportion of the QRS power in males compared to females (33.1 ± 11.9% vs 29.6 ± 11.4%, p < 0.001). The analysis also showed that the components attributable to localised depolarisation sequence abnormalities were significantly larger in males compared to females (2.85 ± 1.08% vs 2.42 ± 0.87%, p < 0.00001). In addition to the demonstration of the technology, the study concludes that the detailed convolution of the depolarisation waveform is individual, and that smoother and less intricate depolarisation propagation is the mechanism likely responsible for shorter QRS duration in females.
Complex biology of constitutional ring chromosomes structure and (in)stability revealed by somatic cell reprogramming
Authors: Nikitina T. V. , Kashevarova A. A. , Gridina M. M. , Lopatkina M. E. , Khabarova A. A. , Yakovleva Yu. S. , Menzorov A. G. , Minina Yu. A. , Pristyazhnyuk I. E. , Vasilyev S. A. , Fedotov D. A. , Serov O. L. , Lebedev I. N. 
Published: February 2021

AbstractHuman ring chromosomes are often unstable during mitosis, and daughter cells can be partially or completely aneuploid. We studied the mitotic stability of four ring chromosomes, 8, 13, 18, and 22, in long-term cultures of skin fibroblasts and induced pluripotent stem cells (iPSCs) by GTG karyotyping and aCGH. Ring chromosome loss and secondary aberrations were observed in all fibroblast cultures except for r(18). We found monosomy, fragmentation, and translocation of indexed chromosomes. In iPSCs, aCGH revealed striking differences in mitotic stability both between iPSC lines with different rings and, in some cases, between cell lines with the same ring chromosome. We registered the spontaneous rescue of karyotype 46,XY,r(8) to 46,XY in all six iPSC lines through ring chromosome loss and intact homologue duplication with isoUPD(8)pat occurrence, as proven by SNP genotype distribution analysis. In iPSCs with other ring chromosomes, karyotype correction was not observed. Our results suggest that spontaneous correction of the karyotype with ring chromosomes in iPSCs is not universal and that pluripotency is compatible with a wide range of derivative karyotypes. We conclude that marked variability in the frequency of secondary rearrangements exists in both fibroblast and iPSC cultures, expanding the clinical significance of the constitutional ring chromosome.