bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of sarcopenia in patients with gynecological cancer
Authors: Yamada Ryutaro , Todo Yukiharu , Minowa Kaoru , Minobe Shinichiro , Suzuki Yutaro , Kato Hidenori , Kurosu Hiroyuki , Mori Yoichi , Osanai Toshihisa 
Published: May 2022

Abstract

Background
The aim of the study was to investigate a prevalence of sarcopenia in patients with gynecological cancer in accordance with current diagnostic criteria of sarcopenia.

Methods
A series of 513 patients with gynecological cancer who were intended to newly receive initial or salvage treatment were recruited in a prospective study. Eligible patients were examined with dual energy X-ray absorptiometry and underwent handgrip strength test and the Short Physical Performance Battery before treatment. Sarcopenia was defined as both low skeletal muscle mass (skeletal muscle mass index) and low muscle strength (handgrip strength of &lt;18.0 kg) or both low skeletal muscle mass index and low physical performance (Short Physical Performance Battery score of ≤9).

Results
A total of 475 patients (92.6%) were completely assessed in this study. Eligible patients’ median age was 60 years (range: 29–89 years). Frequencies of patients with low skeletal muscle mass index, low hand grip strength and low Short Physical Performance Battery were 118 (24.8%), 70 (14.7%) and 80 (16.8%), respectively. Sarcopenia was finally identified in 45 patients (9.5%), which accounted for 38.1% of patients with low skeletal muscle mass index, 64.3% of the patients with low hand grip strength and 56.3% of the patients with low physical performance, respectively.

Conclusions
The prevalence of sarcopenia of 9.5% in patients with gynecological malignancy who were scheduled to newly receive an initial or a salvage treatment. A large-scale, nation-wide study might be planned to elucidate an accurate prevalence of sarcopenia among gynecologic cancer patients.
Ecology and responses to climate change of biocrust-forming mosses in drylands
Authors: Ladrón de Guevara Mónica , Maestre Fernando T 
Published: May 2022

Abstract
Interest in understanding the role of biocrusts as ecosystem engineers in drylands has substantially increased during the past two decades. Mosses are a major component of biocrusts and dominate their late successional stages. In general, their impacts on most ecosystem functions are greater than those of early-stage biocrust constituents. However, it is common to find contradictory results regarding how moss interactions with different biotic and abiotic factors affect ecosystem processes. This review aims to (i) describe the adaptations and environmental constraints of biocrust-forming mosses in drylands, (ii) identify their primary ecological roles in these ecosystems, and (iii) synthesize their responses to climate change. We emphasize the importance of interactions between specific functional traits of mosses (e.g. height, radiation reflectance, morphology, and shoot densities) and both the environment (e.g. climate, topography, and soil properties) and other organisms to understand their ecological roles and responses to climate change. We also highlight key areas that should be researched in the future to fill essential gaps in our understanding of the ecology and the responses to ongoing climate change of biocrust-forming mosses. These include a better understanding of intra- and interspecific interactions and mechanisms driving mosses’ carbon balance during desiccation–rehydration cycles.
Ethylene Insensitive 3-Like 2 is a Brassicaceae-specific transcriptional regulator involved in fine-tuning ethylene responses in Arabidopsis thaliana
Authors: Houben Maarten , Vaughan-Hirsch John , Mou Wangshu , Van de Poel Bram 
Published: May 2022

Abstract
Ethylene signaling directs a pleiotropy of developmental processes in plants. In Arabidopsis, ethylene signaling converges at the master transcription factor Ethylene Insensitive 3 (EIN3), which has five homologs, EIN3-like 1–5 (EIL1–EIL5). EIL1 is most fully characterized and operates similarly to EIN3, while EIL3–5 are not involved in ethylene signaling. EIL2 remains less investigated. Our phylogenetic analysis revealed that EIL2 homologs have only been retrieved in the Brassicaceae family, suggesting that EIL2 diverged to have specific functions in the mustard family. By characterizing eil2 mutants, we found that EIL2 is involved in regulating ethylene-specific developmental processes in Arabidopsis thaliana, albeit in a more subtle way compared with EIN3/EIL1. EIL2 steers ethylene-triggered hypocotyl elongation in light-grown seedlings and is involved in lateral root formation. Furthermore, EIL2 takes part in regulating flowering time as eil2 mutants flower on average 1 d earlier and have fewer leaves. A pEIL2:EIL2:GFP translational reporter line revealed that EIL2 protein abundance is restricted to the stele of young developing roots. EIL2 expression, and not EIL2 protein stability, is regulated by ethylene in an EIN3/EIL1-dependent way. Despite EIL2 taking part in several developmental processes, the precise upstream and downstream regulation of this ethylene- and Brassicaceae-specific transcription factor remains to be elucidated.
Cytokinin oxidase/dehydrogenase inhibitors: outlook for selectivity and high efficiency
Authors: Nisler Jaroslav , Pěkná Zuzana , Končitíková Radka , Klimeš Pavel , Kadlecová Alena , Murvanidze Nino , Werbrouck Stefaan P O , Plačková Lenka , Kopečný David , Zalabák David , Spíchal Lukáš , Strnad Miroslav 
Published: May 2022

Abstract
Inhibitors of cytokinin oxidase/dehydrogenase (CKX) reduce the degradation of cytokinins in plants, and this effect can be exploited in agriculture and in plant tissue culture. In this study, we examine the structure–activity relationship of two series of CKX inhibitors based on diphenylurea. The compounds of Series I were derived from the recently published CKX inhibitors 3TFM-2HM and 3TFM-2HE, and we identified key substituents with increased selectivity for maize ZmCKX1 and ZmCKX4a over AtCKX2 from Arabidopsis. Series II contained compounds that further exceled in CKX inhibitory activity as well as in the ease of their synthesis. The best inhibitors exhibited half-maximal inhibitory concentration (IC50) values in low nanomolar ranges with ZmCKX1 and especially with ZmCKX4a, which is generally more resistant to inhibition. The activity of the key compounds was verified in tobacco and lobelia leaf-disk assays, where N6-isopentenyladenine was protected from degradation and promoted shoot regeneration. All the prepared compounds were further tested for toxicity against Caenorhabditis elegans, and the assays revealed clear differences in toxicity between compounds with and without a hydroxyalkyl group. In a broader perspective, this work increases our understanding of CKX inhibition and provides a more extensive portfolio of compounds suitable for agricultural and biotechnological research.
A dual-function transcription factor, SlJAF13, promotes anthocyanin biosynthesis in tomato
Authors: Chen Yunzhu , Kim Pyol , Kong Lingzhe , Wang Xin , Tan Wei , Liu Xin , Chen Yuansen , Yang Jianfei , Chen Bowei , Song Yuxin , An Zeyu , Min Phyon Jong , Zhang Yang , Ding Bing , Kawabata Saneyuki , Li Yuhua , Wang Yu 
Published: May 2022

Abstract
Unlike modern tomato (Solanum lycopersicum) cultivars, cv. LA1996 harbors the dominant Aft allele, which is associated with anthocyanin synthesis in tomato fruit peel. However, the control of Aft anthocyanin biosynthesis remains unclear. Here, we used ethyl methanesulfonate-induced and CRISPR/Cas9-mediated mutation of LA1996 to show, respectively, that two class IIIf basic helix–loop–helix (bHLH) transcription factors, SlJAF13 and SlAN1, are involved in the control of anthocyanin synthesis. These transcription factors are key components of the MYB–bHLH–WD40 (MBW) complex, which positively regulates anthocyanin synthesis. Molecular and genetic analyses showed that SlJAF13 functions as an upstream activation factor of SlAN1 by binding directly to the G-Box motif of its promoter region. On the other hand, SlJAZ2, a JA signaling repressor, interferes with formation of the MBW complex to suppress anthocyanin synthesis by directly binding these two bHLH components. Unexpectedly, the transcript level of SlJAZ2 was in turn repressed in a SlJAF13-dependent manner. Mechanistically, SlJAF13 interacts with SlMYC2, inhibiting SlMYC2 activation of SlJAZ2 transcription, thus constituting a negative feedback loop governing anthocyanin accumulation. Taken together, our findings support a sophisticated regulatory network, in which SlJAF13 acts as an upstream dual-function regulator that fine tunes anthocyanin biosynthesis in tomato.
An investigation of the magnetic activity of HD 134319 based on TESS photometry and ground-based spectroscopy
Authors: Xu Fukun , Gu Shenghong , Ioannidis Panogiotis 
Published: May 2022

ABSTRACT
We present an analysis of the starspot properties and chromospheric activity on HD 134319 using high-precision photometry by Transiting Exoplanet Survey Satellite (TESS) in sectors 14–16 (T1) and 21–23 (T2) and high-resolution spectroscopy by the ELODIE spectrograph on 1.93-m telescope of Observatoire de Haute-Provence (OHP/ELODIE) and the High Resolution Echelle Spectrometer on Keck 10-m telescope of W. M. Keck Observatory (Keck/HIRES) during the years 1995–2013. We applied a two-spot model with generalized Lomb–Scargle (GLS) periodogram determined period of P = 4.436391 ± 0.00137 d to model chunks sliding over TESS light curve. We also measured the relative equivalent widths of Ca ii H and K, Hβ and Hα emissions by subtracting the overall spectrum from individual spectra. It was found that a two-spot configuration, namely a primary, slowly evolving and long-lasting spot (P) plus a secondary, rapidly evolving spot (S), was capable of explaining the data, although the actual starspot distribution cannot be derived from the collected data. Despite the spot radius–latitude degeneracy revealed in the best-fitting solutions, a sudden alternation between P and S radii followed by a gradual decrease of S in T1 and a decrease of both P and S from T1 to T2 were significant, corresponding to the evolution of magnetic activity. In addition, S revealed rotation and an oscillatory longitude migration synchronized to P in T1, but had a much larger migration than P in T2. This might indicate the evolution of the internal magnetic configuration. Chromospheric activity indicators were found to be tightly correlated with each other and revealed rotational modulation as well as a long-term decrease of emissions, implying the existence and evolution of magnetic activity on HD 134319.
The optical depth of foregrounds for the highest redshift 21 cm signals
Authors: Seitova Daniya , Pober Jonathan 
Published: May 2022

ABSTRACT
Foreground emission makes it difficult to detect the highly redshifted cosmological 21 cm signal at any frequency. However, at low frequencies, foregrounds are likely to become optically thick, which would make it completely impossible to see a 21 cm signal behind them. To find out which regions of the sky might be optically thick for the highest redshifts of the 21 cm signal, we fit the measurements from LWA1 and the Haslam 408 MHz map with a two-component spectral model and calculate the frequency-dependent foreground optical depth point-by-point across the sky. Limitations of the current data prevent us from making any strong conclusions at high statistical significance, but there is suggestive evidence (∼1σ) that as much as 25 per cent of the sky could be obscured for the highest redshift 21 cm signals.
Cosmic void baryon acoustic oscillation measurement: Evaluation of sensitivity to selection effects
Authors: Forero-Sánchez Daniel , Zhao Cheng , Tao Charling , Chuang Chia-Hsun , Kitaura Francisco-Shu , Variu Andrei , Tamone Amélie , Kneib Jean-Paul 
Published: May 2022

Abstract
Cosmic voids defined as a subset of Delaunay Triangulation (DT) circumspheres have been used to measure the Baryon Acoustic Oscillations (BAO) scale; providing tighter constraints on cosmological parameters when combined with matter tracers. These voids are defined as spheres larger than a given radius threshold, which is constant over the survey volume. However, the response of these void tracers to observational systematics has not yet been studied. In this work we analyse the response of void clustering to selection effects. We find for the case of moderate (&lt;20 per cent) incompleteness, void selection based on a constant radius cut yields robust measurements. This is particularly true for BAO-reconstructed galaxy samples, where large-scale void exclusion effects are mitigated. Moreover, we observe for the case of severe (up to 90 per cent) incompleteness – such as can be found at the edges of the radial selection function – that an accurate estimation of the void distribution is necessary for unbiased clustering measurements. In addition, we find that without reconstruction, using a constant threshold under these conditions produces a stronger void exclusion effect that can affect the clustering on large scales. A new void selection criteria dependent on the (local) observed tracer density that maximises the BAO peak significance prevents the aforementioned exclusion features from contaminating the BAO signal. Finally, we verify, with large simulations including light cone evolution, that both void sample definitions (local and constant) yield unbiased and consistent BAO scale measurements.
Eccentricity evolution in gaseous dynamical friction
Authors: Szölgyén Ákos , MacLeod Morgan , Loeb Abraham 
Published: May 2022

ABSTRACT
We analyse how drag forces modify the orbits of objects moving through extended gaseous distributions. We consider how hydrodynamic (surface area) drag forces and dynamical friction (gravitational) drag forces drive the evolution of orbital eccentricity. While hydrodynamic drag forces cause eccentric orbits to become more circular, dynamical friction drag can cause orbits to become more eccentric. We develop a semi-analytic model that accurately predicts these changes by comparing the total work and torque applied to the orbit at periapse and apoapse. We use a toy model of a radial power-law density profile, ρ ∝ r−γ, to determine that there is a critical γ = 3 power index, which separates the eccentricity evolution in dynamical friction: orbits become more eccentric for γ &lt; 3 and circularize for γ &gt; 3. We apply these findings to the infall of a Jupiter-like planet into the envelope of its host star. The hydrostatic envelopes of stars are defined by steep density gradients near the limb and shallower gradients in the interior. Under the influence of gaseous dynamical friction, an infalling object’s orbit will first decrease in eccentricity and then increase. The critical separation that delineates these regimes is predicted by the local density slope and is linearly dependent on polytropic index. More broadly, our findings indicate that binary systems may routinely emerge from common envelope phases with non-zero eccentricities that were excited by the dynamical friction forces that drove their orbital tightening.
The 2021 outburst of the recurrent nova RS Ophiuchi observed in X-rays by the Neil Gehrels Swift Observatory: a comparative study
Authors: Page K L , Beardmore A P , Osborne J P , Munari U , Ness J-U , Evans P A , Bode M F , Darnley M J , Drake J J , Kuin N P M , O’Brien T J , Orio M , Shore S N , Starrfield S , Woodward C E 
Published: May 2022

ABSTRACT
On 2021 August 8, the recurrent nova RS Ophiuchi (RS Oph) erupted again, after an interval of 15.5 yr. Regular monitoring by the Neil Gehrels Swift Observatory began promptly, on August 9.9 (0.37 d after the optical peak), and continued until the source passed behind the Sun at the start of November, 86 d later. Observations then restarted on day 197, once RS Oph emerged from the Sun constraint. This makes RS Oph the first Galactic recurrent nova to have been monitored by Swift throughout two eruptions. Here we investigate the extensive X-ray data sets between 2006 and 2021, as well as the more limited data collected by the European X-ray Observatory Satellite (EXOSAT) in 1985. The hard X-rays arising from shock interactions between the nova ejecta and red giant wind are similar following the last two eruptions. In contrast, the early supersoft source (SSS) in 2021 was both less variable and significantly fainter than in 2006. However, 0.3–1 keV light curves from 2021 reveal a 35 s quasi-periodic oscillation consistent in frequency with the 2006 data. The Swift X-ray spectra from 2021 are featureless, with the soft emission typically being well parametrized by a simple blackbody, while the 2006 spectra showed much stronger evidence for superimposed ionized absorption edges. Considering the data after day 60 following each eruption, during the supersoft phase the 2021 spectra are hotter, with smaller effective radii and lower wind absorption, leading to an apparently reduced bolometric luminosity. We explore possible explanations for the gross differences in observed SSS behaviour between the 2006 and 2021 outbursts.
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning
Authors: Rodrigues Carlos H M , Ascher David B 
Published: May 2022

AbstractRecent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational approaches have been proposed to explore potential biological interactions, they have been limited to specific interactions, and have not been readily accessible for non-experts or use in bioinformatics pipelines. Here we present CSM-Potential, a geometric deep learning approach to identify regions of a protein surface that are likely to mediate protein-protein and protein–ligand interactions in order to provide a link between 3D structure and biological function. Our method has shown robust performance, outperforming existing methods for both predictive tasks. By assessing the performance of CSM-Potential on independent blind tests, we show that our method was able to achieve ROC AUC values of up to 0.81 for the identification of potential protein-protein binding sites, and up to 0.96 accuracy on biological ligand classification. Our method is freely available as a user-friendly and easy-to-use web server and API at http://biosig.unimelb.edu.au/csm_potential.
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions
Authors: Tang Li , Zhong Zhizhou , Lin Yisheng , Yang Yifei , Wang Jun , Martin James F , Li Min 
Published: May 2022

Abstract
Long distance enhancers can physically interact with promoters to regulate gene expression through formation of enhancer-promoter (E-P) interactions. Identification of E-P interactions is also important for profound understanding of normal developmental and disease-associated risk variants. Although the state-of-art predictive computation methods facilitate the identification of E-P interactions to a certain extent, currently there is no efficient method that can meet various requirements of usage. Here we developed EPIXplorer, a user-friendly web server for efficient prediction, analysis and visualization of E-P interactions. EPIXplorer integrates 9 robust predictive algorithms, supports multiple types of 3D contact data and multi-omics data as input. The output from EPIXplorer is scored, fully annotated by regulatory elements and risk single-nucleotide polymorphisms (SNPs). In addition, the Visualization and Downstream module provide further functional analysis, all the output files and high-quality images are available for download. Together, EPIXplorer provides a user-friendly interface to predict the E-P interactions in an acceptable time, as well as understand how the genome-wide association study (GWAS) variants influence disease pathology by altering DNA looping between enhancers and the target gene promoters. EPIXplorer is available at https://www.csuligroup.com/EPIXplorer.
ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence
Authors: Tsybulskyi Volodymyr , Meyer Irmtraud M 
Published: May 2022

Abstract
There is an increased interest in the determination of RNA structures in vivo as it is now possible to probe them in a high-throughput manner, e.g. using SHAPE protocols. By now, there exist a range of computational methods that integrate experimental SHAPE-probing evidence into computational RNA secondary structure prediction. The state-of-the-art in this field is currently provided by computational methods that employ the minimum-free energy strategy for prediction RNA secondary structures with SHAPE-probing evidence. These methods, however, rely on the assumption that transcripts in vivo fold into the thermodynamically most stable configuration and ignore evolutionary evidence for conserved RNA structure features. We here present a new computational method, ShapeSorter, that predicts RNA structure features without employing the thermodynamic strategy. Instead, ShapeSorter employs a fully probabilistic framework to identify RNA structure features that are supported by evolutionary and SHAPE-probing evidence. Our method can capture RNA structure heterogeneity, pseudo-knotted RNA structures as well as transient and mutually exclusive RNA structure features. Moreover, it estimates P-values for the predicted RNA structure features which allows for easy filtering and ranking. We investigate the merits of our method in a comprehensive performance benchmarking and conclude that ShapeSorter has a significantly superior performance for predicting base-pairs than the existing state-of-the-art methods.
Detecting TAD-like domains from RNA-associated interactions
Authors: Zhang Yu Wei , Chen Lingxi , Li Shuai Cheng 
Published: May 2022

Abstract
Topologically associated domains (TADs) are crucial chromatin structural units. Evidence has illustrated that RNA–chromatin and RNA–RNA spatial interactions, so-called RNA-associated interactions (RAIs), may be associated with TAD-like domains (TLDs). To decode hierarchical TLDs from RAIs, we proposed SuperTLD, a domain detection algorithm incorporating imputation. We applied SuperTLD on four RAI data sets and compared TLDs with the TADs identified from the corresponding Hi-C datasets. The TLDs and TADs share a moderate similarity of hierarchies ≥ 0.5312 and the finest structures ≥ 0.8295. Comparison between boundaries and domains further demonstrated the novelty of TLDs. Enrichment analysis of epigenetic characteristics illustrated that the novel TLDs exhibit an enriched CTCF by 0.6245 fold change and H3 histone marks enriched within domains. GO analysis on the TLD novel boundaries exhibited enriched diverse terms, revealing TLDs’ formation mechanism related closely to gene regulation.