bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Preacher’s Perspective
Authors: Honings Rick 
Published: April 2022

AbstractThis article presents a critical, postcolonial analysis of the travel accounts of the Dutch church minister Sytze Roorda van Eysinga (1773–1829), who travelled within the East Indies archipelago in the 1820s as ‘visitator’ of the churches and schools in the colony. Which elements are characteristic of the preacher’s perspective? What did he emphasize in his travel texts? How did he represent the indigenous people who had to be Christianized eventually? So far, only little attention has been paid to the preacher’s perspective in general and to the work of Sytze Roorda van Eysinga in particular. First, Roorda’s representation of the tropical landscape is analysed. Then, his ideas about the indigenous people are discussed, mainly using the theoretical framework of the bookMissionary discourses of difference. Negotiating Otherness in the British Empire, 1840–1900by Esme Cleall (2012).
NSF AI Institute for Research on Trustworthy AI in Weather, Climate, and Coastal Oceanography (AI2ES)
Authors: McGovern Amy , Bostrom Ann , Davis Phillip , Demuth Julie L. , Ebert-Uphoff Imme , He Ruoying , Hickey Jason , Gagne II David John , Snook Nathan , Stewart Jebb Q. , Thorncroft Christopher , Tissot Philippe , Williams John K. 
Published: April 2022

Abstract
We introduce the National Science Foundation (NSF) AI Institute for Research on Trustworthy AI in Weather, Climate, and Coastal Oceanography (AI2ES). This AI institute was funded in 2020 as part of a new initiative from the NSF to advance foundational AI research across a wide variety of domains. To date AI2ES is the only NSF AI institute focusing on environmental science applications. Our institute focuses on developing trustworthy AI methods for weather, climate, and coastal hazards. The AI methods will revolutionize our understanding and prediction of high-impact atmospheric and ocean science phenomena and will be utilized by diverse, professional user groups to reduce risks to society. In addition, we are creating novel educational paths, including a new degree program at a community college serving underrepresented minorities, to improve workforce diversity for both AI and environmental science.
Collision Fluctuations of Lucky Droplets with Superdroplets
Authors: Li Xiang-Yu , Mehlig Bernhard , Svensson Gunilla , Brandenburg Axel , Haugen Nils E. L. 
Published: April 2022

Abstract
It was previously shown that the superdroplet algorithm for modeling the collision–coalescence process can faithfully represent mean droplet growth in turbulent clouds. An open question is how accurately the superdroplet algorithm accounts for fluctuations in the collisional aggregation process. Such fluctuations are particularly important in dilute suspensions. Even in the absence of turbulence, Poisson fluctuations of collision times in dilute suspensions may result in substantial variations in the growth process, resulting in a broad distribution of growth times to reach a certain droplet size. We quantify the accuracy of the superdroplet algorithm in describing the fluctuating growth history of a larger droplet that settles under the effect of gravity in a quiescent fluid and collides with a dilute suspension of smaller droplets that were initially randomly distributed in space (“lucky droplet model”). We assess the effect of fluctuations upon the growth history of the lucky droplet and compute the distribution of cumulative collision times. The latter is shown to be sensitive enough to detect the subtle increase of fluctuations associated with collisions between multiple lucky droplets. The superdroplet algorithm incorporates fluctuations in two distinct ways: through the random spatial distribution of superdroplets and through the Monte Carlo collision algorithm involved. Using specifically designed numerical experiments, we show that both on their own give an accurate representation of fluctuations. We conclude that the superdroplet algorithm can faithfully represent fluctuations in the coagulation of droplets driven by gravity.
Comparison between Large-Scale Circulation Anomalies Associated with Interannual Variability and Decadal Change of Summer Arctic Sea Ice
Authors: Li Xinyu , Lu Riyu , Liu Jiping , Wang Shaoyin 
Published: April 2022

Abstract
Arctic sea ice in summer shows both interannual and long-term variations, and atmospheric circulation anomalies are known to play an important role. This study compares the summertime large-scale circulation anomalies associated with Arctic sea ice on interannual and decadal time scales. The results indicate that the circulation anomalies associated with decreased sea ice on an interannual time scale are characterized by a barotropic anticyclonic anomaly in the central Arctic, and the thermodynamic process is important for the circulation–sea ice coupling. On one hand, the descending adiabatic warming in low levels associated with the central Arctic anticyclonic anomaly leads to decreased sea ice by enhancing the downwelling longwave radiation. On the other hand, the anticyclonic anomaly also induces more moisture in low levels. The enhanced moisture and temperature (coupled with each other) further favor the reduction of sea ice by emitting more downwelling longwave radiation. By contrast, associated with the decadal sea ice decline, there is an anticyclonic anomaly over Greenland and a cyclonic anomaly over northern Siberia, and the wind-driven sea ice drift dominates the sea ice decline. The transpolar circulation anomalies between the anticyclonic and cyclonic anomalies promote transport of the ice away from the coasts of Siberia toward the North Pole, and drive the ice out of the Arctic Ocean to the North Atlantic. These circulation anomalies also induce sea ice decline through thermodynamic process, but it is not as significant as that on an interannual time scale.
The Effects of Uncorrelated Measurement Noise on SWOT Estimates of Sea Surface Height, Velocity, and Vorticity
Authors: Chelton Dudley B. , Samelson Roger M. , Farrar J. Thomas 
Published: April 2022

Abstract
The Ka-band Radar Interferometer (KaRIn) on the Surface Water and Ocean Topography (SWOT) satellite will revolutionize satellite altimetry by measuring sea surface height (SSH) with unprecedented accuracy and resolution across two 50-km swaths separated by a 20-km gap. The original plan to provide an SSH product with a footprint diameter of 1 km has changed to providing two SSH data products with footprint diameters of 0.5 and 2 km. The swath-averaged standard deviations and wavenumber spectra of the uncorrelated measurement errors for these footprints are derived from the SWOT science requirements that are expressed in terms of the wavenumber spectrum of SSH after smoothing with a filter cutoff wavelength of 15 km. The availability of two-dimensional fields of SSH within the measurement swaths will provide the first spaceborne estimates of instantaneous surface velocity and vorticity through the geostrophic equations. The swath-averaged standard deviations of the noise in estimates of velocity and vorticity derived by propagation of the uncorrelated SSH measurement noise through the finite difference approximations of the derivatives are shown to be too large for the SWOT data products to be used directly in most applications, even for the coarsest footprint diameter of 2 km. It is shown from wavenumber spectra and maps constructed from simulated SWOT data that additional smoothing will be required for most applications of SWOT estimates of velocity and vorticity. Equations are presented for the swath-averaged standard deviations and wavenumber spectra of residual noise in SSH and geostrophically computed velocity and vorticity after isotropic two-dimensional smoothing for any user-defined smoother and filter cutoff wavelength of the smoothing.
The Impact of Mean-State Moisture Biases on MJO Skill in the Navy ESPC
Authors: Rushley Stephanie S. , Janiga Matthew A. , Ridout James A. , Reynolds Carolyn A. 
Published: April 2022

Abstract
The Madden–Julian oscillation (MJO) is a key source of predictability in the subseasonal time scale (weeks to months) and influences a wide range of weather and climate phenomena. Although there have been enormous gains in simulating the MJO, many climate and forecast models still have biases in MJO behavior and structure. In this study, we examine the MJO in the Navy Earth System Prediction Capability (Navy ESPC) forecasts performed for the Subseasonal Experiment (SubX) using process-based diagnostics and a moisture budget analysis that uses wavenumber–frequency filtering to isolate the MJO. The MJO in the Navy ESPC is too strong in both boreal winter and summer. This amplitude bias is driven by biases in the vertical moisture advection in the Navy ESPC, which is too strong and deep, driven by a more bottom-heavy vertical motion profile and too steep lower-tropospheric vertical moisture gradient. Additionally, the convective moisture adjustment time scale in the Navy ESPC is faster than observed, such that for a given moisture anomaly the precipitation response is greater than observed. In the Navy ESPC, the MJO propagation shows strong agreement with observations in the Indian Ocean, followed by too rapid propagation east of the Maritime Continent in both seasons. This MJO acceleration east of the Maritime Continent is linked to an acceleration of moisture anomalies driven by biases in anomalous moisture tendency. The mechanisms that drive this bias have seasonal differences, with excess evaporation in the western Pacific dominating in boreal winter and horizontal moisture advection dominating in boreal summer.
Anatomical parameters of sustentaculum Tali screw placement in the Asian population: A retrospective radio-anatomical study
Authors: Liao Li-qing , Feng Zi-yu , Li Yi-kai 
Published: April 2022

Purpose: This study aimed to determine the anatomical parameters of successful Sustentaculum Tali (ST) screw placement in the Asian population. Method: CT scans of unilateral feet of 110 participants were reviewed, retrospectively. The 3 D reconstruction of the calcaneus and morphometric measurements were performed by Mimics Research 19.0 and 3-Matic Research 11.0. Finally, six cadaveric feet were used for verification of the accuracy of the measurements. Results: We discovered a method to help place ST screw successfully: (1) The entry point located at the middle section of the lateral wall of posterior talar articular surface (PTAS), and the perpendicular distance from the entry point to the lateral edge of PTAS (PDEL) was 10.78 mm, (2) Screw was perpendicular to the z-axis, 66.98° to the y-axis (the longitudinal axis of the foot), (3) The length of the ST screw should be approximately 44.74 mm in male and 41.14 mm in female, and (4) The diameter of the ST screw should be approximately 4.0 mm in male and 3.5 mm in female. With this new method, all screws in six cadaveric feet were placed successfully into the middle of ST. Conclusions: In this study, we discovered a general approach to safely place ST screws in the Asian population, which may potentially help surgeons improve their success rate in surgical practice.
Sex differences in outcome after thrombectomy for acute ischemic stroke. A propensity score-matched study
Authors: Casetta Ilaria , Fainardi Enrico , Pracucci Giovanni , Saia Valentina , Sallustio Fabrizio , da Ros Valerio , Nappini Sergio , Nencini Patrizia , Bigliardi Guido , Vinci Sergio , Grillo Francesco , Bracco Sandra , Tassi Rossana , Bergui Mauro , Cerrato Paolo , Saletti Andrea , De Vito Alessandro , Gasparotti Roberto , Magoni Mauro , Simonetti Luigi , Zini Andrea , Ruggiero Maria , Longoni Marco , Castellan Lucio , Malfatto Laura , Castellini Paola , Cosottini Mirco , Comai Alessio , Franchini Enrica , Lozupone Emilio , Della Marca Giacomo , Puglielli Edoardo , Casalena Alfonsina , Baracchini Claudio , Savio Daniele , Duc Enrica , Ricciardi Giuseppe , Cappellari Manuel , Chiumarulo Luigi , Petruzzellis Marco , Cavallini Anna , Cavasin Nicola , Critelli Adriana , Burdi Nicola , Boero Giovanni , Giorgianni Andrea , Versino Maurizio , Biraschi Francesco , Nicolini Ettore , Comelli Simone , Melis Maurizio , Padolecchia Riccardo , Tassinari Tiziana , Paolo Nuzzi Nunzio , Marcheselli Simona , Sacco Simona , Invernizzi Paolo , Gallesio Ivan , Ferrandi Delfina , Fancello Maria , Valeria Saddi Maria , Russo Monia , Pischedda Aldo , Baule Antonio , Mannino Marina , Florio Francesco , Inchingolo Vincenzo , Elena Flacco Maria , Romano Daniele , Silvagni Umberto , Inzitari Domenico , Mangiafico Salvatore , Toni Danilo ,   the Italian Registry of Endovascular Thrombectomy in Acute Stroke (IRETAS)
Published: April 2022

Background and purpose We sought to investigate whether there are gender differences in clinical outcome after stroke due to large vessel occlusion (LVO) after mechanical thrombectomy (EVT) in a large population of real-world patients. Methods From the Italian Registry of Endovascular Thrombectomy, we extracted clinical and outcome data of patients treated for stroke due to large vessel occlusion. We compared clinical and safety outcomes in men and women who underwent EVT alone or in combination with intravenous thrombolysis (IVT) in the total population and in a Propensity Score matched set. Results Among 3422 patients included in the study, 1801 (52.6%) were women. Despite older age at onset (mean 72.4 vs 68.7; p < 0.001), and higher rate of atrial fibrillation (41.7% vs 28.6%; p < 0.001), women had higher probability of 3-month functional independence (adjusted odds ratio-adjOR 1.19; 95% CI 1.02–1.38), of complete recanalization (adjOR 1.25; 95% CI 1.09–1.44) and lower probability of death (adjOR 0.75; 95% CI 0.62–0.90). After propensity-score matching, a well-balanced cohort comprising 1150 men and 1150 women was analyzed, confirming the same results regarding functional outcome (3-month functional independence: OR 1.25; 95% CI 1.04–1.51), and complete recanalization (OR 1.29; 95% CI 1.09–1.53). Conclusions Subject to the limitations of a non-randomized comparison, women with stroke due to LVO treated with mechanical thrombectomy had a better chance to achieve complete recanalization, and 3-month functional independence than men. The results could be driven by women who underwent combined treatment.
Risk factors for preoperative deep venous thrombosis in hip fracture patients: a meta-analysis
Authors: Wang Tao , Guo Junfei , Long Yubin , Yin Yingchao , Hou Zhiyong 
Published: April 2022

Abstract
Study design
A meta-analysis.

Background
Hip fracture (HF), as common geriatric fracture, is related to increased disability and mortality. Preoperative deep vein thrombosis (DVT) is one of the most common complications in patients with hip fractures, affecting 8–34.9% of hip fracture patients. The study aimed to assess the risk factors of preoperative DVT after hip fractures by meta-analysis.

Methods
An extensive search of the literature was performed in the English databases of PubMed, Embase, and the Cochrane Library; and the Chinese databases of CNKI and WAN FANG. We collected possible predictors of preoperative DVT from included studies, and data analysis was conducted with RevMan 5.3 and STATA 12.0.

Results
A total of 26 English articles were included, and the rate of DVT was 16.6% (1627 of 9823 patients) in our study. Our findings showed that advanced age [p = 0.0003, OR = 0.13 95% CI (0.06, 0.21)], female patients [p = 0.0009, OR = 0.82 95% CI (0.72, 0.92)], high-energy injury [p = 0.009, OR = 0.58 95% CI (0.38, 0.87)], prolonged time from injury to admission [p < 0.00001, OR = 0.54 95% CI (0.44, 0.65)], prolonged time from injury to surgery [p < 0.00001, OR = 2.06, 95% CI (1.40, 2.72)], hemoglobin [p < 0.00001, OR = − 0.32 95% CI (− 0.43, − 0.21)], coronary heart disease [p = 0.006, OR = 1.25 95% CI (1.07, 1.47)], dementia [p = 0.02, OR = 1.72 95% CI (1.1, 2.67)], liver and kidney diseases [p = 0.02, OR = 1.91 95% CI (1.12, 3.25)], pulmonary disease [p = 0.02, OR = 1.55 95% CI (1.07, 2.23)], smoking [p = 0.007, OR = 1.45 95% CI (1.11, 1.89)], fibrinogen [p = 0.0005, OR = 0.20 95% CI (0.09, 0.32)], anti-platelet drug [p = 0.01, OR = 0.51 95% CI (0.30, 0.85)], C-reactive protein [p = 0.02, OR = 5.95 95% CI (1.04, 10.85)], < 35 g/l albumin [p = 0.006, OR = 1.42 95% CI (1.1, 1.82)], and thrombosis history [p < 0.00001, OR = 5.28 95% CI (2.85, 9.78)] were risk factors for preoperative DVT.

Conclusions
Many factors, including advanced age, female patients, high-energy injury, prolonged time from injury to admission, prolonged time from injury to surgery, patients with a history of coronary heart disease, dementia, liver and kidney diseases, pulmonary disease, smoking, and thrombosis, fibrinogen, C-reactive protein, and < 35 g/l albumin, were found to be associated with preoperative DVT. Our findings suggested that the patient with above characteristics might have preoperative DVT.
Level of evidence: Level III.
Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line
Authors: Lewerentz Jacob , Johansson Anna-Mia , Larsson Jan , Stenberg Per 
Published: April 2022

AbstractBackgroundImmortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of aDrosophila melanogastercell line (S2-DRSC) with a complex genome structure.ResultsUsing a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (> 80% of SVs), withGypsyretrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in otherD. melanogastercell lines.ConclusionsThe S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.
Comprehensive analysis of lncRNA-mRNAs co-expression network identifies potential lncRNA biomarkers in cutaneous squamous cell carcinoma
Authors: Hu Yu , Li Rong , Chen Hongyin , Chen Lihao , Zhou Xuyue , Liu Linxi , Ju Mei , Chen Kun , Huang Dan 
Published: April 2022

Abstract
Background
Cutaneous squamous cell carcinoma (cSCC) is the second most common type of skin cancer, the prognosis for patients with metastatic cSCC remains relatively poor. Thus, there is an urgent need to identify new diagnostic, prognostic, and therapeutic targets and pathways in cSCC.

Results
It detected a total of 37,507 lncRNA probes and 32,825 mRNA probes and found 3593 differentially expressed lncRNAs and 3236 differentially expressed mRNAs. It has been found that mRNAs ACY3, NR1D1, MZB1 has co-expression relationship with six lncRNAs, GXYLT1P3, LINC00348, LOC101928131, A-33-p3340852, A-21-p0003442 and LOC644838.

Conclusions
The aim of this study is to identify cSCC-specific lncRNAs and indicated that six unstudied lncRNAs may serve an important role in endoplasmic reticulum stress apoptosis, autophagy and the progression of cSCC by modulating ACY3, NR1D1 and MZB1.
Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche
Authors: Weinroth Margaret D. , Clawson Michael L. , Arthur Terrance M. , Wells James E. , Brichta-Harhay Dayna M. , Strachan Norval , Bono James L. 
Published: April 2022

Abstract
Background
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing.

Results
Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters.

Conclusions
In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.
FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data
Authors: Shang Guan-Dong , Xu Zhou-Geng , Wan Mu-Chun , Wang Fu-Xiang , Wang Jia-Wei 
Published: April 2022

Abstract
Background
Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets.

Results
Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied.

Conclusion
FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user’s species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (https://bioconductor.org/packages/devel/bioc/html/FindIT2.html).