bluuebunny/crossref_metadata_2025_split huggingface dataset:
A policy-based framework for the determination of management options to protect vulnerable marine ecosystems under the EU deep-sea access regulations
Authors: van Denderen P Daniël , Holah Helen , Robson Laura M , Hiddink Jan Geert , Menot Lénaick , Pedreschi Debbi , Kazanidis Georgios , Llope Marcos , Turner Phillip J , Stirling David , Murillo F Javier , Kenny Andrew , Campbell Neil , Allcock A Louise , Braga-Henriques Andreia , González-Irusta Jose M , Johnston Graham , Orejas Covadonga , Serrano Alberto , Xavier Joana R , Hopkins Peter , Kenchington Ellen , Nixon Eugene , Valanko Sebastian 
Published: November 2021

Abstract
Vulnerable marine ecosystems (VMEs) are particularly susceptible to bottom-fishing activity as they are easily disturbed and slow to recover. A data-driven approach was developed to provide management options for the protection of VMEs under the European Union “deep-sea access regulations.” A total of two options within two scenarios were developed. The first scenario defined VME closure areas without consideration of fishing activity. Option 1 proposed closures for the protection of VME habitats and likely habitat, while Option 2 also included areas where four types of VME geophysical elements were present. The second scenario additionally considered fishing. This scenario used VME biomass—fishing intensity relationships to identify a threshold where effort of mobile bottom-contact gears was low and unlikely to have caused significant adverse impacts. Achieving a high level of VME protection requires the creation of many closures (&gt; 100), made up of many small (∼50 km2) and fewer larger closures (&gt; 1000 km2). The greatest protection of VMEs will affect approximately 9% of the mobile fleet fishing effort, while closure scenarios that avoid highly fished areas reduce this to around 4–6%. The framework allows managers to choose the level of risk-aversion they wish to apply in protecting VMEs by comparing alternative strategies.
Dataset and method for deep learning-based reconstruction of 3D CAD models containing machining features for mechanical parts
Authors: Lee Hyunoh , Lee Jinwon , Kim Hyungki , Mun Duhwan 
Published: November 2021

ABSTRACT
Three-dimensional (3D) computer-aided design (CAD) model reconstruction techniques are used for numerous purposes across various industries, including free-viewpoint video reconstruction, robotic mapping, tomographic reconstruction, 3D object recognition, and reverse engineering. With the development of deep learning techniques, researchers are investigating the reconstruction of 3D CAD models using learning-based methods. Therefore, we proposed a method to effectively reconstruct 3D CAD models containing machining features into 3D voxels through a 3D encoder–decoder network. 3D CAD model datasets were built to train the 3D CAD model reconstruction network. For this purpose, large-scale 3D CAD models containing machining features were generated through parametric modeling and then converted into a 3D voxel format to build the training datasets. The encoder–decoder network was then trained using these training datasets. Finally, the performance of the trained network was evaluated through 3D reconstruction experiments on numerous test parts, which demonstrated a high reconstruction performance with an error rate of approximately 1%.
Radiation cancer risk at different dose rates: new dose-rate effectiveness factors derived from revised A-bomb radiation dosimetry data and non-tumor doses
Authors: Tanooka Hiroshi 
Published: November 2021

Abstract
The dose rate of atomic bomb (A-bomb) radiation to the survivors has still remained unclear, although the dose–response data of A-bomb cancers has been taken as a standard in estimating the cancer risk of radiation and the dose and dose-rate effectiveness factor (DDREF). Since the applicability of the currently used DDREF of 2 derived from A-bomb data is limited in a narrow dose-rate range, 0.25-75 Gy/min as estimated from analysis of DS86 dosimetry data in the present study, a non-tumor dose (Dnt) was applied in an attempt to gain a more universal dose-rate effectiveness factor (DREF), where Dnt is an empirical parameter defined as the highest dose at which no statistically significant tumor increase is observed above the control level and its magnitude depends on the dose rate. The new DREF values were expressed as a function of the dose rate at four exposure categories, i.e. partial body low LET, whole body low linear energy transfer (LET), partial body high LET and whole body high LET and provided a value of 14 for environmental level radiation at a dose rate of 10−9 Gy/min for whole body low LET.
Surgical management of locally invasive basaloid carcinoma of thymic gland
Authors: Lee Andy Chao Hsuan , Gorton Andrew , Tully Andy , Wu ShouJin , Podbielski Francis J 
Published: November 2021

Abstract
Thymic basaloid carcinoma is an extremely rare thymic tumor variant, and the most common presentations have been an incidental finding on a routine chest X-ray and dyspnea on exertion. Given its rarity, no treatment modalities have been demonstrated to improve survival. This rare case describes a patient with locally advanced thymic basaloid carcinoma treated by en bloc resection of phrenic nerve and left upper lobe with the tumor followed by adjuvant radiation therapy. Patient had no respiratory complaints at 10 months follow-up, and 10-month post-operative surveillance radiological study showed no objective sign of tumor recurrence.
Climate event classification based on historical meteorological records and its presentation on a Spatio-Temporal research platform
Authors: Huang Shi-Yun , Wu Shang-Yun , Chen You-Jun , Tsai Richard Tzong-Han , Fan I-Chun 
Published: November 2021

Abstract
Climate change has become a serious issue, and tracing climate events from historical records could be a solution to find a way to deal with it. This study conducted two experiments for classifying metrological text data—one unsupervised method for exploring a solution in the lack of labeled data and another supervised method for achieving high-performance classification. Both experiments took the meteorological text records as material in the early Qing Dynasty (1644 C.E. to 1795 C.E.) from the REACHES database. We also integrated the classification results to develop a Spatio-Temporal research platform with an instant response front-end interface to help humanity researchers access and analyze data according to the three dimensions of time, area, and event categories. With our Spatio-Temporal research platform, we had the ability with ease to analyze the meteorological records during 1650 C.E. to 1700 C.E., the late stage of the Little Ice Age, to investigate the phenomenon of climate change in the Qing Dynasty of China. We will continue to expand the capacity of the database and establish a mature Spatio-Temporal research platform in the future.
Sporotrichosis in a U.S. Army Basic Trainee
Authors: Wellington Trevor , Hauschild Jordan , Krauland Kevin J , Verwiebe Eric G , Markelz Ana E 
Published: November 2021

ABSTRACT
Lymphocutaneous sporotrichosis is a mycotic disease caused by traumatic inoculation of the dimorphic fungus Sporothrix schenckii, found ubiquitously in decaying vegetation. The potential for outbreaks, difficulty with timely diagnosis, as well as the prolonged treatment course and recovery from surgical intervention can have a substantial impact on the medical readiness of service members. Treatment with the antifungal therapy of choice, itraconazole, requires close patient monitoring for the duration of treatment for clinical response, drug tolerance, as well as therapeutic drug levels. We present a case of a U.S. Army enlistee with sporotrichosis contracted during basic training, highlighting the impact of delayed diagnosis and prolonged treatment course and recovery on medical readiness.
The SIBELIUS Project: E Pluribus Unum
Authors: Sawala Till , McAlpine Stuart , Jasche Jens , Lavaux Guilhem , Jenkins Adrian , Johansson Peter H , Frenk Carlos S 
Published: November 2021

ABSTRACT
We introduce ‘Simulations Beyond The Local Universe’ (SIBELIUS) that connect the Local Group (LG) to its cosmic environment. We show that introducing hierarchical small-scale perturbations to a density field constrained on large scales by observations provides an efficient way to explore the sample space of LG analogues. From more than 60 000 simulations, we identify a hierarchy of LG characteristics emanating from different scales: the total mass, orientation, orbital energy, and the angular momentum are largely determined by modes above λ = 1.6 comoving Mpc (cMpc) in the primordial density field. Smaller scale variations are mostly manifest as perturbations to the MW–M31 orbit, and we find that the observables commonly used to describe the LG – the MW–M31 separation and radial velocity – are transient and depend on specifying scales down to 0.2 cMpc in the primordial density field. We further find that the presence of M33/LMC analogues significantly affects the MW–M31 orbit and its sensitivity to small-scale perturbations. We construct initial conditions that lead to the formation of an LG whose primary observables precisely match the current observations.
xGASS: characterizing the slope and scatter of the stellar mass–angular momentum relation for nearby galaxies
Authors: Hardwick Jennifer A , Cortese Luca , Obreschkow Danail , Catinella Barbara , Cook Robin H W 
Published: November 2021

ABSTRACT
We present a detailed study of the stellar mass versus specific angular momentum (AM) relation (Fall relation) for a representative sample of 564 nearby galaxies in the eXtended GALEX Arecibo SDSS Survey (xGASS). We focus on the dependence of the Fall relation’s slope on galaxy type and the galaxy properties regulating its scatter. Stellar specific AM is determined by combining single-dish H i velocity widths and stellar mass profiles for all H i detections in the xGASS sample. At fixed morphology (or bulge-to-total ratio), we find that the power-law slope of the Fall relation is consistent with 2/3. However, when all galaxy types are combined, we recover a much shallower slope of ∼0.47. We show that this is a consequence of the change in galaxy morphology as a function of mass, highlighting that caution should be taken when using the slope of the Fall relation to constrain galaxy formation models without taking sample selection into account. We quantify the Fall relations scatter and show that H i gas fraction is the strongest correlated parameter for low stellar masses (Spearman correlation: ρs = 0.61), while the bulge-to-total ratio becomes slightly more dominant at higher masses (ρs = −0.29). Intriguingly, when only the disc components of galaxies are considered, H i gas fraction remains the strongest correlated parameter with the scatter of the relation (regardless of disc stellar mass). Our work provides one of the best characterizations of the Fall relation for a representative sample of galaxies in the local Universe.
Completeness of the Gaia verse – V. Astrometry and radial velocity sample selection functions in Gaia EDR3
Authors: Everall Andrew , Boubert Douglas 
Published: November 2021

ABSTRACT
We risk reaching false scientific conclusions if we test our physical theories against subsets of the Gaia catalogue without correcting for the biased process by which stars make it into our sample. In this paper, we produce selection functions for three Gaia science samples to enable the community to correct for this bias. We estimate the probability that a source in Gaia EDR3 will have (i) a reported parallax and proper motion, (ii) an astrometric renormalized unit weight error below 1.4, or (iii) a reported radial velocity. These selectionfunctions are estimated as a function of G-band apparent magnitude and position on the sky, with the latter two also being dependent on G − GRP colour. The inferred selection functions have a non-trivial dependence on these observable parameters, demonstrating the importance of empirically estimating selection functions. We also produce a simple estimate for the selection function of the full Gaia EDR3 source catalogue to be used with the subset selection functions. We make all of our selection functions easily accessible through the GitHub repository selectionfunctions.
Kepler binary stars in NGC 6791 open cluster: KIC 2437060, KIC 2437149, and KIC 2438490
Authors: Çakırlı Ömür , Hoyman Barış 
Published: November 2021

ABSTRACT
The study of detached eclipsing binaries in open clusters can provide powerful tests of theoretical stellar evolutionary models. These models must simultaneously fit the masses, radii, and radiative properties of the eclipsing stars with essentially the same distance, age, and initial composition. In this way, clusters are ideal test benches for verification of the stellar evolution theory. To fully exploit this potential, we present a detailed analysis of three spectroscopic binaries that are members of NGC 6791. Measurements of the radial velocities were combined with Kepler photometry, to provide a full set of orbital and physical parameters. We applied a standard analysis to disentangle the spectra of each binary system and to determine the temperatures and metallicities for each component in binaries. High-precision analysis affords us the opportunity to define the evolutionary status of the components. We also derived the distances to the systems. Finally, we report on the detection of solar-like oscillation signals in a member in data from the Kepler mission.
A map of diffuse radio emission at 182 MHz to enhance epoch of reionization observations in the Southern hemisphere
Authors: Byrne Ruby , Morales Miguel F , Hazelton Bryna , Sullivan Ian , Barry Nichole , Lynch Christene , Line Jack L B , Jacobs Daniel C 
Published: November 2021

ABSTRACT
We present a broad-band map of polarized diffuse emission at 167–198 MHz developed from data from the Murchison Widefield Array (MWA). The map is designed to improve visibility simulation and precision calibration for 21 cm Epoch of Reionization (EoR) experiments. It covers a large swath – 11 000 sq. deg. – of the Southern hemisphere sky in all four Stokes parameters and captures emission on angular scales of 1–9°. The band-averaged diffuse structure is pre-dominantly unpolarized but has significant linearly polarized structure near RA = 0 h. We evaluate the accuracy of the map by combining it with the GLEAM catalogue and simulating an observation from the MWA, demonstrating that the accuracy of the short baselines (6.1–50 wavelengths) now approaches the accuracy of the longer baselines typically used for EoR calibration. We discuss how to use the map for visibility simulation for a variety of interferometric arrays. The map has potential to improve calibration accuracy for experiments such as the Hydrogen Epoch of Reionization Array and the forthcoming Square Kilometre Array as well as the MWA.
The large-scale distribution of ionized metals in IllustrisTNG
Authors: Artale M Celeste , Haider Markus , Montero-Dorta Antonio D , Vogelsberger Mark , Martizzi Davide , Torrey Paul , Bird Simeon , Hernquist Lars , Marinacci Federico 
Published: November 2021

ABSTRACT
We study the intrinsic large-scale distribution and evolution of seven ionized metals in the IllustrisTNG magnetohydrodynamical cosmological simulation. We focus on the fractions of C ii, C iv, Mg ii, N v, Ne viii, O vi, and Si iv in different cosmic web structures (filaments, haloes, and voids) and gas phases (warm–hot intergalactic medium, hot, diffuse, and condensed gas) from z = 6 to z = 0. Our analysis provides a new perspective to the study of the distribution and evolution of baryons across cosmic time while offering new hints in the context of the well-known missing baryons problem. The cosmic web components are here identified using the local comoving dark matter density, which provides a simple but effective way of mapping baryons on large scales. Our results show that C ii and Mg ii are mostly located in condensed gas inside haloes in high-density and low-temperature star-forming regions ($\rho _{\rm gas}/\bar{\rho }_{\rm bar}\gtrsim 10^3$, and T ≲ 105 K). C iv and Si iv present similar evolution of their mass fractions in haloes and filaments across cosmic time. In particular, their mass budgets in haloes in condensed phase ($\rho _{\rm gas}/\bar{\rho }_{\rm bar}\gtrsim 10^3$, and T ≲ 105 K) are driven by gas cooling and star formation with a peak at z ∼ 2. Finally, our results confirm that O vi, Ne viii, and N v are good tracers of warm/hot and low-density gas at low redshift ($\rho _{\rm gas}/\bar{\rho }_{\rm bar}\lesssim 10^3$, and T ≳ 105 K), regions that are likely to contain most of the missing baryons in the local Universe.
A composite likelihood approach for inference under photometric redshift uncertainty
Authors: Rau M M , Morrison C B , Schmidt S J , Wilson S , Mandelbaum R , Mao Y-Y ,   LSST Dark Energy Science Collaboration, Alonso David , Hartley Will , Kirkby David , Kuusela Mikael , Lee Ann B 
Published: November 2021

ABSTRACTObtaining accurately calibrated redshift distributions of photometric samples is one of the great challenges in photometric surveys like LSST, Euclid, HSC, KiDS, and DES. We present an inference methodology that combines the redshift information from the galaxy photometry with constraints from two-point functions, utilizing cross-correlations with spatially overlapping spectroscopic samples, and illustrate the approach on CosmoDC2 simulations. Our likelihood framework is designed to integrate directly into a typical large-scale structure and weak lensing analysis based on two-point functions. We discuss efficient and accurate inference techniques that allow us to scale the method to the large samples of galaxies to be expected in LSST. We consider statistical challenges like the parametrization of redshift systematics, discuss and evaluate techniques to regularize the sample redshift distributions, and investigate techniques that can help to detect and calibrate sources of systematic error using posterior predictive checks. We evaluate and forecast photometric redshift performance using data from the CosmoDC2 simulations, within which we mimic a DESI-like spectroscopic calibration sample for cross-correlations. Using a combination of spatial cross-correlations and photometry, we show that we can provide calibration of the mean of the sample redshift distribution to an accuracy of at least 0.002(1 + z), consistent with the LSST-Y1 science requirements for weak lensing and large-scale structure probes.
A nationwide questionnaire survey on the prevalence of ankylosing spondylitis and non-radiographic axial spondyloarthritis in Japan
Authors: Matsubara Yuri , Nakamura Yosikazu , Tamura Naoto , Kameda Hideto , Otomo Kotaro , Kishimoto Mitsumasa , Kadono Yuho , Tsuji Shigeyoshi , Atsumi Tatsuya , Matsuno Hiroaki , Takagi Michiaki , Kobayashi Shigeto , Fujio Keishi , Nishimoto Norihiro , Okamoto Nami , Nakajima Ayako , Matsui Kiyoshi , Yamamura Masahiro , Nakashima Yasuharu , Kawakami Atsushi , Mori Masaaki , Tomita Tetsuya 
Published: November 2021

ABSTRACT

Objective
This nationwide study aimed to reveal the prevalence of ankylosing spondylitis (AS), non-radiographic axial spondyloarthritis (nr-ax SpA), and the positivity rate of human leukocyte antigen (HLA) among such patients in Japan.

Methods
The first survey was conducted in 2221 randomly selected facilities (26.3%) in September 2018, where the patients with AS/nr-ax SpA were taken care of from January to December 2017. We estimated the total number of these patients using response and extraction rates. A second survey was conducted in 117 facilities (49.8%) to assess for HLA-B27 positivity rate and clinical features.

Results
The estimated total numbers of the patients with AS and nr-ax SpA were 3200 (95% confidence interval [CI]: 2400–3900) and 800 (530–1100), suggesting that the prevalence values of AS and nr-ax SpA in general population were 2.6/100,000 (0.0026%) and 0.6/100,000 (0.0006%), respectively. Although 55.5% (76/137) of patients with AS were HLA-B27-positive, those whose age of onset was estimated to be over 50 years tended to undergo less HLA-B27 testing.

Conclusion
This study revealed the lower prevalence of AS/nr-ax SpA in Japan, compared to those in other countries. Further studies are required to reveal the association of HLA-B27 with the clinical features.
Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis
Authors: Adefisayo Oyindamola O , Dupuy Pierre , Nautiyal Astha , Bean James M , Glickman Michael S 
Published: November 2021

Abstract
DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as Mycobacterium tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here, we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.
Cancer risk in patients with immunoglobulin A nephropathy: a Swedish population-based cohort study
Authors: Rehnberg Johanna , Ludvigsson Jonas F , Carrero Juan-Jesus , Emilsson Louise 
Published: November 2021

ABSTRACT

Background
IgA nephropathy (IgAN) is the most common primary glomerulonephritis affecting all ages and both sexes, but there is a lack of studies on its association with cancer and whether it is a paramalignant condition.

Methods
In a Swedish population-based cohort study we compared the risk of cancer among 3882 biopsy-verified IgAN patients diagnosed during 1974–2011 with 19 341 reference individuals and followed them until 2015. Cox regression was used to estimate hazard ratios (HRs) for cancer in IgAN patients versus controls and conditional logistic regression assessed the risk of cancer before the IgAN was confirmed.

Results
During a median follow-up of 12.6 years, 488 (12.6%) patients with IgAN and 1783 (9.2%) matched reference individuals were diagnosed with cancer {HR 1.70 [95% confidence interval (CI), 1.52–1.89]}. The increased risk was only seen in IgAN patients developing end-stage renal disease (ESRD), with an HR of 4.01 (95% CI 3.33–4.82) for any cancer and HR of 2.22 (95% CI 1.79–2.75) when excluding non-melanoma skin cancer (NMSC). Non-ESRD IgAN patients did not have an increased overall cancer risk [HR 1.13 (95% CI 0.99–1.30)]. There was no increased risk of cancer preceding an IgAN diagnosis [odds ratio 1.10 (95% CI 0.92–1.32)].

Conclusions
We found no support for IgAN being a paramalignant condition. There was an increased risk of cancer in IgAN patients, but only for those with ESRD. Our results indicate ∼6 extra cancer cases per 100 IgAN patients with ESRD per 10 years, or &gt;17 extra cases if including NMSC as well.