bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of wind-speed profiles and optical turbulence above Gaomeigu and the Tibetan Plateau using ERA5 data
Authors: Han Yajuan , Yang Qike , Liu Nana , Zhang Kun , Qing Chun , Li Xuebin , Wu Xiaoqing , Luo Tao 
Published: October 2020

ABSTRACT
Appropriate knowledge of wind-speed distributions and optical turbulence at existing and potential astronomical observatories is crucial for siting ground-based telescopes and applying adaptive optics (AO) systems. In this paper, the wind-speed and optical-turbulence characteristics above Gaomeigu and the Tibetan Plateau are studied by employing the 20-yr (1999–2018) European Centre for Medium-Range Weather Forecasts’ fifth set of reanalysis data (ERA5). First, the meteorological parameters derived from ERA5 data are evaluated with coinciding radiosonde measurements. Results show that the meteorological parameters of ERA5 data in the free atmosphere have quite good reliability, with bias and root mean square error basically lower than 1.2 K in temperature and basically smaller than 2 m s−1 for wind speed. Then, vertical distributions and seasonal behaviour of the wind speed at Gaomeigu and Lhasa station above the Tibetan Plateau are analysed. Thirdly, the Richardson number (Ri) in the free atmosphere is calculated to provides us with a map of relative probability of different periods and regions of optical turbulence being developed above the two sites. In general, the atmospheric stability of Gaomeigu is higher than that of Lhasa station. Particularly in June, for Gaomeigu, the atmospheric stability within 6–30 km a.s.l. is basically superior or equal to the stable condition found at two mid-latitude sites: Oukaimeden and La Palma. Moreover, Lhasa station has a relative higher stability during June–September than other months. Furthermore, we provide the $( {C_n^2} )$ profiles using ERA5 data at Gaomeigu and Lhasa. The results indicate that the choice of an appropriate outer-scale model is crucial for revealing local turbulence characteristics.
Characterizing the possible interior structures of the nearby Exoplanets Proxima Centauri b and Ross-128 b
Authors: Herath Mahesh , Gunesekera Saraj , Jayaratne Chandana 
Published: October 2020

ABSTRACT
We developed a new numerical model to constrain the interior structure of rocky Exoplanets, and applied it to the nearby planets Proxima Centauri b and Ross-128 b. The recently measured elemental abundances of red dwarfs and Alpha Centauri were utilized to infer the bulk composition of each planet, and to measure their core mass fractions (CMFs). The results of our model predicted that the radius of Proxima b at its minimum mass may be 1.036 ± 0.040 R⊕, and if its mass is as high as 2 M⊕, 1.170 ± 0.040 R⊕. The radius of Ross-128 b at minimum mass may be 1.034 ± 0.040 R⊕, with its radius at an upper bound mass of 2 M⊕ being 1.150 ± 0.040 R⊕. Both planets may have thin mantles with similar conditions to Earth, but not convecting as vigorously. The CMFs might lie in the ranges of 20–59 per cent and 34–59 per cent for Proxima b and Ross-128 b, respectively, making it very likely they have massive iron cores. Their central temperatures may be high enough to partially melt the cores, and possibly generate magnetic fields. If they have magnetic fields at present, they are most likely to be multipolar in nature due to slow rotation speeds resulting from stellar tidal effects. The field strengths were predicted to have values of 0.06–0.23 G for Proxima b, and 0.07–0.14 G for Ross-128 b. If either planet contains more than 10 per cent of their mass in volatiles, magnetic fields would either be non-existent or very weak. The conditions of both planets may be hostile for habitability.
Unravelling the enigmatic ISM conditions in Minkowski’s object
Authors: Zovaro Henry R M , Sharp Robert , Nesvadba Nicole P H , Kewley Lisa , Sutherland Ralph , Taylor Philip , Groves Brent , Wagner Alexander Y , Mukherjee Dipanjan , Bicknell Geoffrey V 
Published: October 2020

ABSTRACT
Local examples of jet-induced star formation lend valuable insight into its significance in galaxy evolution and can provide important observational constraints for theoretical models of positive feedback. Using optical integral field spectroscopy, we present an analysis of the ISM conditions in Minkowski’s object (z = 0.0189), a peculiar star-forming dwarf galaxy located in the path of a radio jet from the galaxy NGC 541. Full spectral fitting with ppxf indicates that Minkowski’s object primarily consists of a young stellar population $\sim \! 10\, \rm Myr$ old, confirming that the bulk of the object’s stellar mass formed during a recent jet interaction. Minkowski’s object exhibits line ratios largely consistent with star formation, although there is evidence for a low level ($\lesssim \! 15 \, \rm per \, cent$) of contamination from a non-stellar ionizing source. Strong-line diagnostics reveal a significant variation in the gas-phase metallicity within the object, with $\log \left(\rm O / H \right) + 12$ varying by $\sim \! 0.5\, \rm dex$, which cannot be explained by in-situ star formation, an enriched outflow from the jet, or enrichment of gas in the stellar bridge between NGC 541 and NGC 545/547. We hypothesize that Minkowski’s object either (i) was formed as a result of jet-induced star formation in pre-existing gas clumps in the stellar bridge, or (ii) is a gas-rich dwarf galaxy that is experiencing an elevation in its star formation rate due to a jet interaction, and will eventually redden and fade, becoming an ultradiffuse galaxy as it is processed by the cluster.
H i deficiencies and asymmetries in HIPASS galaxies
Authors: Reynolds T N , Westmeier T , Staveley-Smith L 
Published: October 2020

ABSTRACT
We present an analysis of the sky distribution of neutral hydrogen (H i) deficiency and spectral asymmetry for galaxies detected by the H i Parkes All-Sky Survey (HIPASS) as a function of projected environment density. Previous studies of galaxy H i deficiency using HIPASS were sensitive to galaxies that are extremely H i rich or poor. We use an updated binning statistic for measuring the global sky distribution of H i deficiency that is sensitive to the average deficiencies. Our analysis confirms the result from previous studies that galaxies residing in denser environments, such as Virgo, are on average more H i deficient than galaxies at lower densities. However, many other individual groups and clusters are not found to be on average significantly H i poor, in contradiction to previous work. In terms of H i spectral asymmetries, we do not recover any significant trend of increasing asymmetry with environment density as found for other galaxy samples. We also investigate the correlation between H i asymmetry and deficiency, but find no variation in the mean asymmetry of galaxies that are H i rich, normal, or poor. This indicates that there is either no dependence of asymmetry on H i deficiency, or a galaxy’s H i deficiency only has a small influence on the measured H i asymmetry that we are unable to observe using only integrated spectra.
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses
Authors: Roux Simon , Páez-Espino David , Chen I-Min A , Palaniappan Krishna , Ratner Anna , Chu Ken , Reddy T B K , Nayfach Stephen , Schulz Frederik , Call Lee , Neches Russell Y , Woyke Tanja , Ivanova Natalia N , Eloe-Fadrosh Emiley A , Kyrpides Nikos C 
Published: October 2020

Abstract
Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
The international nucleotide sequence database collaboration
Authors: Arita Masanori , Karsch-Mizrachi Ilene , Cochrane Guy 
Published: October 2020

Abstract
The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been the core infrastructure for collecting and providing nucleotide sequence data and metadata for &gt;30 years. Three partner organizations, the DNA Data Bank of Japan (DDBJ) at the National Institute of Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have been collaboratively maintaining the INSDC for the benefit of not only science but all types of community worldwide.
The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity
Authors: Wolfe Aaron D , Li Shuxing , Goedderz Cody , Chen Xiaojiang S 
Published: October 2020

AbstractAPOBEC1 (APO1), a member of AID/APOBEC nucleic acid cytosine deaminase family, can edit apolipoprotein B mRNA to regulate cholesterol metabolism. This APO1 RNA editing activity requires a cellular cofactor to achieve tight regulation. However, no cofactors are required for deamination on DNA by APO1 and other AID/APOBEC members, and aberrant deamination on genomic DNA by AID/APOBEC deaminases has been linked to cancer. Here, we present the crystal structure of APO1, which reveals a typical APOBEC deaminase core structure, plus a unique well-folded C-terminal domain that is highly hydrophobic. This APO1 C-terminal hydrophobic domain (A1HD) interacts to form a stable dimer mainly through hydrophobic interactions within the dimer interface to create a four-stranded β-sheet positively charged surface. Structure-guided mutagenesis within this and other regions of APO1 clarified the importance of the A1HD in directing RNA and cofactor interactions, providing insights into the structural basis of selectivity on DNA or RNA substrates.
aYChr-DB: a database of ancient human Y haplogroups
Authors: Freeman Laurence , Brimacombe Conrad Stephen , Elhaik Eran 
Published: October 2020

Abstract
Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018–2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB—a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.
scAIDE: clustering of large-scale single-cell RNA-seq data reveals putative and rare cell types
Authors: Xie Kaikun , Huang Yu , Zeng Feng , Liu Zehua , Chen Ting 
Published: October 2020

Abstract
Recent advancements in both single-cell RNA-sequencing technology and computational resources facilitate the study of cell types on global populations. Up to millions of cells can now be sequenced in one experiment; thus, accurate and efficient computational methods are needed to provide clustering and post-analysis of assigning putative and rare cell types. Here, we present a novel unsupervised deep learning clustering framework that is robust and highly scalable. To overcome the high level of noise, scAIDE first incorporates an autoencoder-imputation network with a distance-preserved embedding network (AIDE) to learn a good representation of data, and then applies a random projection hashing based k-means algorithm to accommodate the detection of rare cell types. We analyzed a 1.3 million neural cell dataset within 30 min, obtaining 64 clusters which were mapped to 19 putative cell types. In particular, we further identified three different neural stem cell developmental trajectories in these clusters. We also classified two subpopulations of malignant cells in a small glioblastoma dataset using scAIDE. We anticipate that scAIDE would provide a more in-depth understanding of cell development and diseases.
Property Regimes
Authors: Canfield Matthew 
Published: October 2020

AbstractProperty regimes refer to the political, legal, and economic systems through which societies order their relationships between people with respect to valued things. Anthropologists and legal scholars have long been engaged in a dynamic dialogue about the organization and practice of property regimes. However, whereas legal theory has been uniquely concerned with ownership and private property as a system for allocating scarce goods and resources, anthropologists have investigated how property is constructed and shaped by everyday practice, illuminating how the distinctions between law and practice mutually constitute power relations. This chapter reviews how anthropologists have attended to aporias of property theory by ethnographically analysing conflicts and transformations between property regimes. It surveys anthropological insights into three continuing processes of property regime transformation: decolonization, privatization, and enclosure. In addition, it analyses two emergent processes around which property claims are being reconfigured: dematerialization and rematerialization. The dematerialization of property through informational and financial capitalism is occurring at a time when industrial modes of carbon-dependent accumulation are facing ecological limits brought on by climate change. However, technologies of informationalization and financialization are also rematerializing property regimes by constructing new calculative devices and global markets for increasingly limited natural resources. How these emerging regimes shape social relations between people, the distribution of social entitlements, and the boundaries between persons and things offers an important field of ethnographic enquiry.
An open-source research tool to study triaxial inertial sensors for monitoring selected behaviors in sheep
Authors: dos Reis Barbara R , Fuka Daniel R , Easton Zachary M , White Robin R 
Published: October 2020

Abstract
The use of automated systems for monitoring animal behavior provides information on individual animal behavior and can be used to enhance animal productivity. However, the advancement of this industry is hampered by technology costs, challenges with power supplies, limited data accessibility, and inconsistent testing approaches for confirming the detection of livestock behaviors. Development of open-source research tools similar to commercially available wearable technologies may contribute to the development of more-efficient and affordable technologies. The objective of this study was to demonstrate an open-source, microprocessor-based sensor designed to monitor and enable differentiation among selected behaviors of adult wethers. The sensor was comprised of an inexpensive espressif ESP-32-WROOM-32 microprocessor with Bluetooth communication, a generic MPU92/50 motion sensor that contains a three-axis accelerometer, three-axis magnetometer, a three-axis gyroscope, and a 5-V rechargeable lithium-ion battery. The open-source Arduino IDE software was used to program the microprocessor and to adjust the frequency of sampling, the data packet to send, and the operating conditions. For demonstration purposes, sensors were placed on six housed sheep for three 1-h increments with concurrent visual behavioral observation. Sensor readings (x-, y-, and z-axis) were summarized (mean and SD) within a minute and compared to animal behavior observations (also on a by-minute basis) using a linear mixed-effect model with animal as a random effect and behavioral classifier as a fixed effect. This analysis demonstrated the basic utility of the sensor to differentiate among animal behaviors based on sensed data (P &lt; 0.001). Although substantial additional work is needed for algorithm development, power source testing, and network optimization, this open-source platform appears to be a promising strategy to research wearable sensors in a generalizable manner.
Are Patient Outcomes Affected by the Presence of a Fellow or Resident in Lumbar Decompression Surgery?
Authors: Divi Srikanth N. , Goyal Dhruv K.C. , Galetta Matthew S. , Guzek Ryan , Kaye Ian David , Kurd Mark F. , Woods Barrett I. , Radcliff Kristen E. , Rihn Jeffrey A. , Anderson David Greg , Hilibrand Alan S. , Kepler Christopher K. , Vaccaro Alexander R. , Schroeder Gregory D. 
Published: October 2020

Study Design.
Retrospective cohort study.

Objective.
The aim of this study was to determine whether the presence of a fellow or resident (F/R) compared to a physician assistant (PA) affected surgical variables or short-term patient outcomes.

Summary of Background Data.
Although orthopedic spine fellows and residents must participate in minimum number of decompression surgeries to gain competency, the impact of trainee presence on patient outcomes has not been assessed.

Methods.
One hundred and seventy-one patients that underwent a one- to three-level lumbar spine decompression procedure at a high-volume academic center were retrospectively identified. Operative reports from all cases were examined and patients were placed into one of two groups based on whether the first assist was a F/R or a PA. Univariate analysis was used to compare differences in total surgery duration, 30-day and 90-day readmissions, infection and revision rates, patient-reported outcome measures (Short Form-12 Physical Component Score and Mental Component Score, Oswestry Disability Index, Visual Analog Scale [VAS] Back, VAS Leg) between groups. Multiple linear regression was used to assess change in each patient reported outcome and multiple binary logistic regression was used to determine significant predictors of revision, infection, and 30- or 90-day readmission.

Results.
Seventy-eight patients were included in the F/R group compared to 93 patients in the PA group. There were no differences between groups for total surgery time, 30-day or 90-day readmissions, infection, or revision rates. Using univariate analysis, there were no differences between the two groups pre- or postoperatively (P > 0.05). Using multivariate analysis, presence of a surgical trainee did not significantly influence any patient reported outcome and did not affect infection, revision, or 30- and 90-day readmission rates.

Conclusion.
This is one of the first studies to show that the presence of an orthopedic spine fellow or resident does not affect patient short-term outcomes in lumbar decompression surgery.

Level of Evidence: 3
A Novel Clinical Scoring System for Perioperative Morbidity in Metastatic Spinal Tumor Surgery
Authors: De la Garza Ramos Rafael , Benton Joshua A. , Gelfand Yaroslav , Echt Murray , Hamad Mousa K. , Kinon Merritt D. , Yanamadala Vijay , Yassari Reza 
Published: October 2020

Study Design.
Retrospective cohort study.

Objective.
To evaluate a scoring system to predict morbidity for patients undergoing metastatic spinal tumor surgery (MSTS).

Summary of Background Data.
Multiple scoring systems exist to predict survival for patients with spinal metastasis. The potential benefits and risks of surgery need to be evaluated for patients with disseminated cancer and limited life expectancy. Few scoring systems exist to predict perioperative morbidity after MSTS.

Methods.
We reviewed records of patients who underwent MSTS at our institution between 2013 and 2019. All perioperative complications occurring within 30 days were recorded. A clinical scoring system consisting of five variables (age ≥ 70 yr, hypoalbuminemia, poor preoperative functional status [Karnofsky ≤ 40], Frankel Grade A-C, and multilevel disease ≥2 continuous vertebral bodies) was evaluated as a predictive tool for morbidity; every parameter was assigned a value of 0 if absent or 1 if present (total possible score = 5). The effect of the scoring system on morbidity was evaluated using stepwise multiple logistic regression. Model accuracy was calculated by receiver operating characteristic analysis.

Results.
One hundred and five patients were identified, with a male prevalence of 58.1% and average age at surgery of 61 years. The overall 30-day complication rate was 36.2%. The perioperative morbidity was 4.6%, 30.0%, 53.9%, and 64.7% for patients with scores of 0, 1, 2, and ≥3 points, respectively (P < 0.001). On multiple logistic regression analysis controlling for covariates not present in the model, the scoring system was significantly associated with 30-day morbidity (OR 3.11; 95% CI, 1.72–5.59; P < 0.001). The model's accuracy was estimated at 0.75.

Conclusion.
Our proposed model was found to accurately predict perioperative morbidity after MSTS. The Spine Oncology Morbidity Assessment (SOMA) score may prove useful for risk stratification and possibly decision-making, though further validation is needed.

Level of Evidence: 4