bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of selection in the evolution of a transposable element
Authors: Dazenière Julie , Bousios Alexandros , Eyre-Walker Adam 
Published: March 2022

Abstract
Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a transposable element family from a single genome. We predict that the ratio of nonsynonymous to synonymous variants in the alignment should decrease as a function of the frequency of the variants, because elements with nonsynonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus long-terminal repeat retrotransposons that are abundant in maize and other plant species and show that nonsynonymous to synonymous variants declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of nonsynonymous to synonymous variants suggests that at least 85% of all nonsynonymous mutations in the transposable element reduce transposition. Crucially, these patterns in nonsynonymous to synonymous variants are only predicted to occur if the gene products from a particular transposable element insertion preferentially promote the transposition of the same insertion. Overall, by using large numbers of intact elements, this study sheds new light on the selective processes that act on transposable elements.
Paradoxically Greater Persistence of HIV RNA-Positive Cells in Lymphoid Tissue When ART Is Initiated in the Earliest Stage of Infection
Authors: Kroon Eugène , Chottanapund Suthat , Buranapraditkun Supranee , Sacdalan Carlo , Colby Donn J , Chomchey Nitiya , Prueksakaew Peeriya , Pinyakorn Suteeraporn , Trichavaroj Rapee , Vasan Sandhya , Manasnayakorn Sopark , Reilly Cavan , Helgeson Erika , Anderson Jodi , David Caitlin , Zulk Jacob , de Souza Mark , Tovanabutra Sodsai , Schuetz Alexandra , Robb Merlin L , Douek Daniel C , Phanuphak Nittaya , Haase Ashley , Ananworanich Jintanat , Schacker Timothy W 
Published: March 2022

Abstract
Starting antiretroviral therapy (ART) in Fiebig 1 acute HIV infection limits the size of viral reservoirs in lymphoid tissues, but does not impact time to virus rebound during a treatment interruption. To better understand why the reduced reservoir size did not increase the time to rebound we measured the frequency and location of HIV RNA+ cells in lymph nodes from participants in the RV254 acute infection cohort. HIV RNA+ cells were detected more frequently and in greater numbers when ART was initiated in Fiebig 1 compared to later Fiebig stages and were localized to the T-cell zone compared to the B-cell follicle with treatment in later Fiebig stages. Variability of virus production in people treated during acute infection suggests that the balance between virus-producing cells and the immune response to clear infected cells rapidly evolves during the earliest stages of infection.
Clinical Trials Registration: NCT02919306.
“Negotiated Coexistence”: Indian and Chinese Engagement in the Global Governance of Peacebuilding
Authors: Adhikari Monalisa 
Published: March 2022

AbstractA much-discussed theme in international relations is how emerging powers will engage with the declining liberal world order and its various governance regimes. This article examines the engagement of emergent powers with the regime of “peacebuilding.” Empirically, it examines the interaction between India and China, with liberal peacebuilding projects in the peace processes of Nepal and Myanmar respectively. Departing from the theory that emergent powers either displace, or converge with, the liberal world order, this article argues that emergent powers have a “negotiated coexistence” with liberal peacebuilders. Despite competing motivations, this “coexistence” of liberal peacebuilders and emergent powers is negotiated, first, by the agency of conflict-affected states, who invoke plural forms of international engagement, to gain strategic advantage, and secondly, by limited interaction between the two, given the differences in their priorities and modalities of engagement. The differences ensure that emergent powers operate in parallel, yet distinctly, from peacebuilders, rarely crossing each other's path. This limited interaction not only prevents this coexistence from degenerating into instances of potential contestation but also inhibits cooperation. Yet, when emergent powers view their economic and strategic interests being threatened by norms and practices of liberal peacebuilding projects, few instances of contestation emerge.
CancerBERT: a cancer domain-specific language model for extracting breast cancer phenotypes from electronic health records
Authors: Zhou Sicheng , Wang Nan , Wang Liwei , Liu Hongfang , Zhang Rui 
Published: March 2022

AbstractObjectiveAccurate extraction of breast cancer patients’ phenotypes is important for clinical decision support and clinical research. This study developed and evaluated cancer domain pretrained CancerBERT models for extracting breast cancer phenotypes from clinical texts. We also investigated the effect of customized cancer-related vocabulary on the performance of CancerBERT models.Materials and MethodsA cancer-related corpus of breast cancer patients was extracted from the electronic health records of a local hospital. We annotated named entities in 200 pathology reports and 50 clinical notes for 8 cancer phenotypes for fine-tuning and evaluation. We kept pretraining the BlueBERT model on the cancer corpus with expanded vocabularies (using both term frequency-based and manually reviewed methods) to obtain CancerBERT models. The CancerBERT models were evaluated and compared with other baseline models on the cancer phenotype extraction task.ResultsAll CancerBERT models outperformed all other models on the cancer phenotyping NER task. Both CancerBERT models with customized vocabularies outperformed the CancerBERT with the original BERT vocabulary. The CancerBERT model with manually reviewed customized vocabulary achieved the best performance with macro F1 scores equal to 0.876 (95% CI, 0.873–0.879) and 0.904 (95% CI, 0.902–0.906) for exact match and lenient match, respectively.ConclusionsThe CancerBERT models were developed to extract the cancer phenotypes in clinical notes and pathology reports. The results validated that using customized vocabulary may further improve the performances of domain specific BERT models in clinical NLP tasks. The CancerBERT models developed in the study would further help clinical decision support.
A museum on the front line: The People’s Museum of Girona (1936–1938)
Authors: Domènech Casadevall Gemma 
Published: March 2022

Abstract
On 14 August 1937, at the height of the Spanish Civil War, Sir Frederic Kenyon, director of the British Museum, and James Mann, keeper of the Wallace Collection in London, visited the Catalan city of Girona, close to the border with France. They had been sent to Spain by the British government to ascertain at first hand the impact of the war on Spain’s artistic heritage, and to assess the efforts being made by the Republican government to protect it. During their visit, they devoted particular attention to the People’s Museum, on which the Catalan authorities had been working since the outbreak of the civil war, and which they planned to open in October of that year. At the time of the visit, the war had already been raging for a year.
Effect of amorphous carbon coating on the performance of liquid phase transmission electron microscopy (LP-TEM) and the dynamics of enclosed Pt nano-colloids
Authors: Li Xiaoguang , Mitsuishi Kazutaka , Takeguchi Masaki 
Published: March 2022

Abstract
Ultra-thin silicon nitride (SiN) membranes are critical in microfabrication-based liquid cells (LCs) for transmission electron microscopy (TEM). This study used a homemade LC with a 50-nm SiN membrane to study the dynamics of 2.58-nm platinum (Pt) nanoparticles (NPs) in approximately 200-nm-deep water. When a strong beam with electron flux ranging from 2.5 × 103 to 1.4 × 106 e−/(nm2 s) was applied to resolve the NPs, the beam caused NP aggregation and even drilled a hole on the top membrane. The hole drilling was prevented by coating a 1–4-nm-thick amorphous carbon layer on both sides of the membrane. The NP aggregation rate also decreased with increasing carbon thickness. After overcoming the aforementioned issues, lattice fringes of the Pt NPs were visible when the NPs were attached to the membrane of the 4-nm-carbon-coated LC containing a thin liquid layer. The effects of the electron beam and carbon on the LC and Pt NPs were investigated and discussed. This work provides a reference for LC-TEM research using strong electron beams.
Crying for Flicka: Boys, Young Men, and Emotion at the Cinema in Britain in the 1930s and 1940s
Authors: Tebbutt Melanie 
Published: March 2022

Abstract
This article re-visits contemporary surveys of the cinema in the 1930s and 1940s to explore the implications that the cinema’s role as an “emotional frontier” between everyday life and the imagination had on the emotional lives of boys and young men. It makes a novel contribution to the history of youth and emotions, arguing that for boys and young men who were disconnected from social life, the cinema was an “emotional refuge,” a space of heightened emotional encounter, in which conventional assumptions about masculinity could be fractured and “feminine” sensibilities otherwise difficult to express publicly could receive cathartic release.
Phenotypic variation in photosynthetic traits in wheat grown under field versus glasshouse conditions
Authors: Sales Cristina R G , Molero Gemma , Evans John R , Taylor Samuel H , Joynson Ryan , Furbank Robert T , Hall Anthony , Carmo-Silva Elizabete 
Published: March 2022

Abstract
Recognition of the untapped potential of photosynthesis to improve crop yields has spurred research to identify targets for breeding. The CO2-fixing enzyme Rubisco is characterized by a number of inefficiencies, and frequently limits carbon assimilation at the top of the canopy, representing a clear target for wheat improvement. Two bread wheat lines with similar genetic backgrounds and contrasting in vivo maximum carboxylation activity of Rubisco per unit leaf nitrogen (Vc,max,25/Narea) determined using high-throughput phenotyping methods were selected for detailed study from a panel of 80 spring wheat lines. Detailed phenotyping of photosynthetic traits in the two lines using glasshouse-grown plants showed no difference in Vc,max,25/Narea determined directly via in vivo and in vitro methods. Detailed phenotyping of glasshouse-grown plants of the 80 wheat lines also showed no correlation between photosynthetic traits measured via high-throughput phenotyping of field-grown plants. Our findings suggest that the complex interplay between traits determining crop productivity and the dynamic environments experienced by field-grown plants needs to be considered in designing strategies for effective wheat crop yield improvement when breeding for particular environments.
Usefulness of AFP, PIVKA-II, and Their Combination in Diagnosing Hepatocellular Carcinoma Based on Upconversion Luminescence Immunochromatography
Authors: Zhang Song-gao , Huang Yi 
Published: March 2022

Abstract

Objectives
To evaluate the prognostic values of serum PIVKA-II (prothrombin induced by vitamin K absence–II) and α-fetoprotein (AFP) and the combination of these analytes for identifying hepatocellular carcinoma (HCC), and to analyze the correlation between biomarkers and clinicopathological features of HCC.

Methods
The levels of PIVKA-II and AFP in 331 case individuals were determined by upconverting phosphor technology-based immune lateral flow (UPT-LF) assay. We used the ROC curve to determine the diagnostic value; the relationships between the biomarkers and clinicopathological features of HCC also were analyzed.

Results
AFP and PIVKA-II have good diagnostic performance in the diagnosis of HCC; the best AUC was 0.76, 0.74. High levels of PIVKA-II were more advantageous than AFP in predicting tumor size, portal-vein embolism, and vascular invasion (all P &lt;.05).

Conclusion
Levels of PIVKA-II and AFP showed good diagnostic value for HCC, but the level of PIVKA-II was more closely related to the clinicopathological features of HCC.
Aligning Air Force Ground Surgical Team (GST) Training With the Deployment Experience
Authors: Edmonds Robert , Hansen Dallas 
Published: March 2022

ABSTRACT

Introduction
The Air Force Ground Surgical Team (GST) Phase 1 course is a two-week pre-deployment training for the Air Force’s conventional austere surgical care platform. Since the creation of the GST platform and associated training pipeline in 2017, course adjustments and improvements have relied on expert opinion and anecdote. To gain a more robust understanding of GST deployment clinical and operational activities, we conducted a survey of all surgeons who completed GST Phase 1 training from its inception in April 2017 to September 2020.

Materials and Methods
87 surgeons took the course from April 2017 to September 2020. 60 of those surgeons were still on active duty and were candidates to complete the survey sent from the Air Force Survey Office. 31 individuals responded and their identification was kept blinded. An IRB exemption was issued before study initiation.

Results
Of the 31 respondents, 9 took the GST Phase 1 course but never deployed, and were excluded. The remaining 22 surgeons deployed at some point from 2017 to 2020. Four surgeons reported providing no surgical care during their deployment. 68% of the surgeons deployed to an actual standalone GST platform, while the rest were retained at larger military treatment facilities (MTFs) or Role III facilities. The median number of surgeries performed was 2 for surgeons at standalone GSTs and 7 for those at larger MTFs/Role IIIs. A holding time of greater than 12 hours was reported for 15% of operative patients and 58% of nonoperative patients at standalone GSTs. 28% (n = 5) of surgeons reported taking care of patients in the Golden Hour of surgery, and 23% of teams reported a patient death. Two surgeons cared for a military working dog, and four surgeons cared for pediatric patients. 50% of surgeons had more than one patient present simultaneously for care. 50% of surgeons’ resupply were in the greater than 30 days or never received category.

Conclusions
The GST Phase 1 course has a unique role in preparing students to provide austere surgical care. This includes both preparing to function in the operational military environment as well as applying sound in-garrison trauma surgical care techniques to the austere, resource variable environment. The results of this survey suggest that a broadening of content-specific deployment-related topics, the formalization of documentation education, incorporating formal evidence-based nontechnical skills training, and identifying optimal GST context-specific behaviors will strengthen the effectiveness of the course in preparing students for deployment.
Galactic tides and the Crater II dwarf spheroidal: a challenge to LCDM?
Authors: Borukhovetskaya Alexandra , Navarro Julio F , Errani Raphaël , Fattahi Azadeh 
Published: March 2022

ABSTRACT
The unusually low velocity dispersion and large size of Crater II pose a challenge to our understanding of dwarf galaxies in the Lambda cold dark matter (LCDM) cosmogony. The low velocity dispersion suggests either a dark halo mass much lower than the minimum expected from hydrogen cooling limit arguments or one that is in the late stages of extreme tidal stripping. The tidal interpretation has been favoured in recent work and is supported by the small pericentric distances consistent with available kinematic estimates. We use N-body simulations to examine this interpretation in detail, assuming a Navarro–Frenk–White (NFW) profile for Crater II’s progenitor halo. Our main finding is that, although the low velocity dispersion can indeed result from the effect of tides, the large size of Crater II is inconsistent with this hypothesis. This is because galaxies stripped to match the observed velocity dispersion are also reduced to sizes much smaller than the observed half-light radius of Crater II. Unless its size has been substantially overestimated, reconciling this system with LCDM requires that either (i) it is not bound and near equilibrium (unlikely, given its crossing time is shorter than the time elapsed since pericentre) or (ii) its progenitor halo deviates from the assumed NFW profile. The latter alternative may signal that baryons can affect the inner halo cusp even in extremely faint dwarfs or, more intriguingly, may signal effects associated with the intimate nature of the dark matter, such as finite self-interactions, or other such deviations from the canonical LCDM paradigm.
Streaming velocity effects on the post-reionization 21-cm baryon acoustic oscillation signal
Authors: Long Heyang , Givans Jahmour J , Hirata Christopher M 
Published: March 2022

ABSTRACTThe relative velocity between baryons and dark matter in the early Universe can suppress the formation of small-scale baryonic structure and leave an imprint on the baryon acoustic oscillation (BAO) scale at low redshifts after reionization. This ‘streaming velocity’ affects the post-reionization gas distribution by directly reducing the abundance of pre-existing mini-haloes ($\lesssim 10^7 {\rm M}_{\bigodot }$) that could be destroyed by reionization and indirectly modulating reionization history via photoionization within these mini-haloes. In this work, we investigate the effect of streaming velocity on the BAO feature in H i 21 cm intensity mapping after reionization, with a focus on redshifts 3.5 ≲ z ≲ 5.5. We build a spatially modulated halo model that includes the dependence of the filtering mass on the local reionization redshift and thermal history of the intergalactic gas. In our fiducial model, we find isotropic streaming velocity bias coefficients bv ranging from −0.0043 at z = 3.5 to −0.0273 at z = 5.5, which indicates that the BAO scale is stretched (i.e. the peaks shift to lower k). In particular, streaming velocity shifts the transverse BAO scale between 0.121 per cent (z = 3.5) and 0.35 per cent (z = 5.5) and shifts the radial BAO scale between 0.167 per cent (z = 3.5) and 0.505 per cent (z = 5.5). These shifts exceed the projected error bars from the more ambitious proposed hemispherical-scale surveys in H i (0.13 per cent at 1σ per Δz = 0.5 bin).
UX Ori stars eclipses by large-scale disc perturbations
Authors: Shulman S G , Grinin V P 
Published: March 2022

ABSTRACT
We simulate the polarized radiative transfer in the vicinity of the UX Ori type stars during their minima. Our model of an eclipse by an extended disc perturbation generalizes the compact gas-dust cloud eclipse model. We apply the radiative transfer method based on enumeration using the directions grid to model the influence of the perturbation extensions along azimuth and radius on the eclipse depth and parameters of the linear polarization. We investigate eclipses both for the flared disc and for the disc with a puffing-up in the dust sublimation zone. The puffing-up is obtained by adding a dusty disc wind to the model. Comparison with a compact cloud eclipse model reveals that the eclipse by a large-scale azimuthally extended perturbation may be significantly deeper and show a greater linear polarization degree. We also demonstrate that the perturbation extension together with the disc puffing-up can strongly affect the degree of polarization and colour index of the star during the eclipse. The position angle of the linear polarization may also change markedly during and after an eclipse by a large-scale perturbation for the model with a puffed-up inner rim. Also, in this model, the maximum degree of the linear polarization can be achieved not at the brightness minimum but closer to the end of the eclipse. We discuss the modelling results in the context of the photopolarimetric observations of UX Ori stars.
Probing the dark Solar system: detecting binary asteroids with a space-based interferometric asteroid explorer
Authors: Sullivan Andrew G , Veske Doğa , Márka Zsuzsa , Bartos Imre , Márka Szabolcs 
Published: March 2022

ABSTRACTWith the inception of gravitational wave astronomy, astrophysical studies using interferometric techniques have begun to probe previously unknown parts of the Universe. In this work, we investigate the potential of a new interferometric experiment to study a unique group of gravitationally interacting sources within our Solar system: binary asteroids. We present the first study into binary asteroid detection via gravitational signals. We identify the interferometer sensitivity necessary for detecting a population of binary asteroids in the asteroid belt. We find that the space-based gravitational wave detector LISA will have negligible ability to detect these sources as these signals will be well below the LISA noise curve. Consequently, we propose a 4.6 au and a 1 au arm-length interferometer specialized for binary asteroid detection, targeting frequencies between 10−6 and 10−4 Hz. Our results demonstrate that the detection of binary asteroids with space-based gravitational wave interferometers is possible though very difficult, requiring substantially improved interferometric technology over what is presently proposed for space-based missions. If that threshold can be met, an interferometer may be used to map the asteroid belt, allowing for new studies into the evolution of our Solar system.
A MeerKAT-meets-LOFAR study of MS 1455.0 + 2232: a 590 kiloparsec ‘mini’-halo in a sloshing cool-core cluster
Authors: Riseley C J , Rajpurohit K , Loi F , Botteon A , Timmerman R , Biava N , Bonafede A , Bonnassieux E , Brunetti G , Enßlin T , Di Gennaro G , Ignesti A , Shimwell T , Stuardi C , Vernstrom T , van Weeren R J 
Published: March 2022

ABSTRACT
Radio mini-haloes are poorly understood, moderately extended diffuse radio sources that trace the presence of magnetic fields and relativistic electrons on scales of hundreds of kiloparsecs, predominantly in relaxed clusters. With relatively few confirmed detections to-date, many questions remain unanswered. This paper presents new radio observations of the galaxy cluster MS 1455.0+2232 performed with MeerKAT (covering the frequency range 872−1712 MHz) and LOFAR (covering 120−168 MHz), the first results from a homogeneously selected mini-halo census. We find that this mini-halo extends for ∼590 kpc at 1283 MHz, significantly larger than previously believed, and has a flatter spectral index (α = −0.97 ± 0.05) than typically expected. Our X-ray analysis clearly reveals a large-scale (254 kpc) sloshing spiral in the intracluster medium. We perform a point-to-point analysis, finding a tight single correlation between radio and X-ray surface brightness with a super-linear slope of $b_{\rm 1283\, MHz} = 1.16^{+0.06}_{-0.07}$ and $b_{\rm 145\, MHz} = 1.15^{+0.09}_{-0.08}$; this indicates a strong link between the thermal and non-thermal components of the intracluster medium. Conversely, in the spectral index/X-ray surface brightness plane, we find that regions inside and outside the sloshing spiral follow different correlations. We find compelling evidence for multiple sub-components in this mini-halo for the first time. While both the turbulent (re-)acceleration and hadronic scenarios are able to explain some observed properties of the mini-halo in MS 1455.0+2232, neither scenario is able to account for all the evidence presented by our analysis.