bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water
Authors: Jarrige Domitille , Haridas Sajeet , Bleykasten-Grosshans Claudine , Joly Muriel , Nadalig Thierry , Sancelme Martine , Vuilleumier Stéphane , Grigoriev Igor V , Amato Pierre , Bringel Françoise 
Published: October 2022

Abstract
The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56 Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.
Application of six-component ambient seismic noise data for high-resolution imaging of lateral heterogeneities
Authors: Tang Le , Fang Xinding 
Published: October 2022

SUMMARY
We develop a novel approach for imaging subsurface lateral heterogeneities using six-component (6C) ambient seismic noise data, consisting of three translational components and three rotational components. We first derive the 6C cross-correlation functions (CCFs) from ambient seismic noise data for surface waves and then apply the modified frequency Bessel (MF-J) transform to the 6C CCFs for surface wave dispersion curves. The phase velocities of Rayleigh and Love waves can be directly calculated from the 6C CCFs of a single pair of stations. Traditional array-based surface wave methods derive the surface wave phase velocity based on the presumption of a horizontally layered model. When this assumption breaks down due to the presence of, for example, dipping layer or heterogeneities, the resulting phase velocity can be severely smeared. By contrast, the proposed approach is not limited by the layered model assumption because it relies on single-point measurements to calculate the localized dispersion relations of the formation right beneath a receiver. Our numerical modelling results demonstrate that this approach is applicable to heterogeneous models and can image small-scale subsurface anomalies with very high lateral resolution.
Populist peacemaking: Trump's peace initiatives in the Middle East and the Balkans
Authors: Landau Dana M , Lehrs Lior 
Published: October 2022

Abstract
With the rise of populist leaders around the world, populism's impact on foreign policy and international affairs has come into focus. Adding to this literature, we propose the concept of ‘populist peacemaking’, in which key tenets of populism, in style and substance, are projected onto the sphere of international mediation. We offer an analytical framework for understanding populist peacemaking consisting of three features. Firstly, populist peacemaking is characterized by a rejection of the ‘peacemaking elites’ and their established rules and practices, including international norms, a refutation of context-specific knowledge, and a clean-slate approach that disregards past peacemaking attempts and alienates other international mediators. Secondly, populist peacemaking employs aggrandized rhetoric and symbolism that puts the mediator—rather than the conflict parties—in the spotlight, thus integrating domestic politics into peacemaking. Finally, populist peacemaking frames the process as representing the volonté générale, i.e. serving the interests of the ‘pure people’ in the conflict-affected context. We illustrate this phenomenon empirically with a case-study of United States' peacemaking efforts during the Trump era, tracing initiatives pursued by US envoys in the Israeli–Palestinian and Kosovo–Serbia conflicts. From this analysis, populist peacemaking emerges as a distinct phenomenon, not to be subsumed under the heading of ‘illiberal peacemaking’.
Distance in the International Criminal Court’s Relations with the ‘Local’
Authors: Lugano Geoffrey 
Published: October 2022

ABSTRACT∞
The literature on the International Criminal Court’s (ICC) relations with the local broadly falls under the rubric of either acceptance of or resistance to the Court. This article provides contrasting insights on the binaries in equal measure, revealing complex and dynamic processes of continuous negotiations of the parameters of the Court’s reach among the local. The article introduces the state of flux as a spatio-temporal account of how local actors order ‘distance’ in their relations with the ICC by invoking metaphorical kinship in ways that enable their oscillations between approval and hostility to the Court over time and space. In so doing, the article builds on the agency of a section of Kenya’s political elite, who have demonstrated the most dramatic trends of the state of flux since the Court’s establishment. The state of flux calls for the ICC’s continuous engagement with the local as a mitigation for its distancing.
In vitro evaluation of efficacy of nonstarch polysaccharides enzymes on wheat by simulating the avian digestive tract
Authors: Yang Xiaojie , Li Xi , Xu Weihan , Wang Heng , Liu Chuang , Wang Wence , Yang Lin , Zhu Yongwen 
Published: October 2022

Abstract
In this study, the efficacy of different nonstarch polysaccharide (NSP) enzyme sources on wheat ingredients and wheat basal diets in vitro were evaluated by simulating the avian digestive tract. In Exp. 1, pH level was increased from 2.0 to 8.0 by simulating the avian digestive tract. The relative enzyme activities of xylanase A, B, and C and β-glucanase X at pH 3.0–3.5 were higher (P &lt; 0.05) than those at pH 2.0 or 7.0–8.0. The optimal pH levels of 3.5 and 7.0 were screened by simulating the proventriculus and small intestine, respectively to evaluate the efficacy of NSP enzyme on wheat sources. In Exp. 2, wheat 1 contained the highest content of NSP fractions and the lowest digestibility in vitro dry matter (IVDMD) and energy (IVED) in wheat samples. Therefore, wheat 1 was selected for hydrolysis research under different NSP enzyme sources and levels (1,500, 4,500, 13,500, 40,500, 121,500 U xylanase/kg and 250, 500, 1,000, 2,000, 4,000 U β-glucanase/kg) in vitro. The hydrolysis of wheat on the basis of the released reducing sugar content was determined by xylanase sources A &gt; B &gt; C (P &lt; 0.05) and β-glucanase sources of X &gt; Y (P &lt; 0.05). On the basis of the hydrolysis, the optimum dose of xylanase A and β-glucanase X were 40,500 U/kg and 2,000 U/kg, respectively. Subsequently, the completely randomized designs involving 2 NSP enzymes treatments × 2 endogenous digestive enzymes treatments (Exp. 3), as well as 2 wheat basal diets × 2 NSP enzymes treatments (Exp. 4) were used to evaluate the efficacy of NSP enzymes on dietary nutrient digestibility. The addition of NSP enzymes (40,500 U xylanase A/kg and 2,000 U β-glucanase X/kg) increased the IVDMD and IVED of wheat 1 without endogenous enzymes (P &lt; 0.05), while the IVDMD and IVED of wheat 1 with endogenous enzyme were only slightly increased (P &gt; 0.05). The addition of NSP enzymes could increase the IVDMD and IVED of corn–wheat–soybean meal diet (P &lt; 0.05), but had no effect on those of wheat–cottonseed meal rapeseed meal diet (P &gt; 0.05). In conclusion, xylanase and β-glucanase additions could effectively eliminate the adverse effects on wheat and wheat basal diets at the optimal pH levels of 3.5 and 7.0 by simulating the proventriculus and small intestine parts, respectively. The efficacy of NSP enzymes was influenced by the enzyme sources, dietary type, and the interaction of endogenous enzymes.
Is now the time for a Rubiscuit or Ruburger? Increased interest in Rubisco as a food protein
Authors: Pearce F Grant , Brunke Joel E 
Published: October 2022

Abstract
Much of the research on Rubisco aims at increasing crop yields, with the ultimate aim of increasing plant production to feed an increasing global population. However, since the identification of Rubisco as the most abundant protein in leaf material, it has also been touted as a direct source of dietary protein. The nutritional and functional properties of Rubisco are on a par with those of many animal proteins, and are superior to those of many other plant proteins. Purified Rubisco isolates are easily digestible, nutritionally complete, and have excellent foaming, gelling, and emulsifying properties. Despite this potential, challenges in efficiently extracting and separating Rubisco have limited its use as a global foodstuff. Leaves are lower in protein than seeds, requiring large amounts of biomass to be processed. This material normally needs to be processed quickly to avoid degradation of the final product. Extraction of Rubisco from the plant material requires breaking down the cell walls and rupturing the chloroplast. In order to obtain high-quality protein, Rubisco needs to be separated from chlorophyll, and then concentrated for final use. However, with increased consumer demand for plant protein, there is increased interest in the potential of leaf protein, and many commercial plants are now being established aimed at producing Rubisco as a food protein, with over US$60 million of funding invested in the past 5 years. Is now the time for increased use of Rubisco in food production as a nitrogen source, rather than just providing a carbon source?
Impact of Oral Ovulatory Induction Medications Among Female Military Members and Military Beneficiaries
Authors: Kim Ji Won , Grounds Benjamin E , Van Bokkem Kelsey C , Raiciulescu Sorana , Spitzer Trimble L 
Published: October 2022

ABSTRACT

Introduction
Twelve percent of reproductive aged females in the United States have utilized fertility services, and it is estimated that 25% of infertility patients have ovulatory dysfunction. Clomiphene and letrozole are currently first-line treatment options for ovulatory dysfunction. These are both disqualifying medications in the U.S. Navy and Air Force for duties that involve flying. These medication restrictions could reduce the likelihood of female aviators seeking infertility treatment. This pilot study seeks to evaluate the severity of common side effects in order to provide recommendations to the current aeromedical guidelines.

Materials and Methods
An anonymous survey was provided to all active duty and dependent patients who presented to the infertility clinic at a single military medical center for a mid-cycle scan from February 2021 to February 2022. The survey included demographic, treatment cycle, medication type, medication dose, and the presence and severity of common adverse reactions. The provider additionally recorded the number of dominant follicles that were noted at the time of ultrasound. The Kruskal–Wallis test was used to analyze the severity of adverse effects, and chi-square analysis was used to compare the difference in symptoms from previous cycles.

Results
A total of 569 surveys were collected. Of the participants, 45.4% were military members and 3.5% worked in the field of aviation. Letrozole was prescribed to 88.7% of the patients. Less than 3% reported severe or debilitating side effects. There was no difference in presence or severity when comparing the cycle number.

Conclusions
The majority of side effects for oral ovulation induction medications were described as slight or mild. Therefore, this study provides evidence-based data of severity side effects that could be used to guide the waiver process and improve readiness for female aviators in the military.
Standardization of Pulmonary Embolism Evaluation and Management Through Implementation of a Pulmonary Embolism Response Team: A Single-Center Experience at Brooke Army Medical Center
Authors: Tunzi Matthew , Boster Joshua , Godar Cassandra , Yugawa Craig , Prichard Ian , Walter Robert , Anderson Jess 
Published: October 2022

ABSTRACT

Introduction
Pulmonary embolism (PE) is associated with significant rates of morbidity and mortality. Management of PE is complex, and adverse patient events are not uncommon. Brooke Army Medical Center (BAMC) is among several select institutions that have implemented multidisciplinary pulmonary embolism response teams (PERTs) to improve PE outcomes. PERT structure varies among institutions and often involves specialty expertise from a variety of departments within the hospital. PE response teams aim to improve the diagnosis and treatment for patients with acute PE. Here, we report our initial experience with this intervention.

Materials and Methods
We developed a multidisciplinary PERT and implemented a standardized algorithm to guide the evaluation, management, and disposition of patients with acute PE. Patients with PE were identified in the pre-PERT period (2015-2017) and the post-PERT period (2020-2021). A retrospective analysis of clinical characteristics, management strategies, and outcomes was performed for both cohorts.

Results
A total of 68 patients with acute PE were analyzed, 38 patients before PERT adoption, and 30 patients post-PERT. Baseline characteristics between the two cohorts were similar. A statistically significant increase in the evaluation for right ventricle dysfunction was noted in the post-PERT cohort, with 80% of patients having pro-brain natriuretic peptide labs obtained compared to 47% in the pre-PERT cohort (P = .005). Furthermore, 97% of patients in the post-PERT cohort had a transthoracic echocardiogram compared to 55% in the pre-PERT cohort (P = .0001). Six patients in the pre-PERT cohort underwent catheter-directed thrombolysis, compared to zero in the post-PERT cohort (P = .006). There were no differences in other treatment modalities. There was no statistically significant difference in length of stay between the two cohorts.

Conclusions
To our knowledge, this is the first report describing the successful implementation of a PERT at a military treatment facility to guide the evaluation, management, and treatment of PE. The implementation of the PERT improved the appropriate diagnostic evaluation for patients with intermediate-risk PE and reduced the use of non-guideline-based catheter-directed thrombolysis. This initiative serves as an example of what could be applied across other military treatment facilities within the Defense Health Agency.
Constraints on primordial magnetic fields from their impact on the ionization history with Planck 2018
Authors: Paoletti D , Chluba J , Finelli F , Rubiño-Martín J A 
Published: October 2022

ABSTRACT
We update and extend our previous cosmic microwave background anisotropy constraints on primordial magnetic fields through their dissipation by ambipolar diffusion and magnetohydrodynamic decaying turbulence effects on the post-recombination ionization history. We derive the constraints using the latest Planck 2018 data release which improves on the E-mode polarization leading to overall tighter constraints with respect to Planck 2015. We also use the low-multipole E-mode polarization likelihood obtained by the SROLL2 map making algorithm and we note how it is compatible with larger magnetic field amplitudes than the Planck 2018 baseline, especially for positive spectral indices. The 95 per cent confidence level constraints on the amplitude of the magnetic fields from the combination of the effects is $\sqrt{\langle B^2 \rangle } \lt 0.69 (\lt 0.72)$ nG for Planck 2018 (SROLL2) by marginalizing on the magnetic spectral index. We also investigate the impact of a damping scale allowed to vary and the interplay between the magnetic field effects and the lensing amplitude parameter.
An intergalactic medium temperature from a giant radio galaxy
Authors: Oei Martijn S S L , van Weeren Reinout J , Hardcastle Martin J , Vazza Franco , Shimwell Tim W , Leclercq Florent , Brüggen Marcus , Röttgering Huub J A 
Published: October 2022

ABSTRACT
The warm–hot intergalactic medium (warm–hot IGM, or WHIM) pervades the filaments of the Cosmic Web and harbours half of the Universe’s baryons. The WHIM’s thermodynamic properties are notoriously hard to measure. Here we estimate a galaxy group–WHIM boundary temperature using a new method. In particular, we use a radio image of the giant radio galaxy (giant RG, or GRG) created by NGC 6185, a massive nearby spiral. We analyse this extraordinary object with a Bayesian 3D lobe model and deduce an equipartition pressure Peq = 6 × 10−16 Pa – among the lowest found in RGs yet. Using an X-ray-based statistical conversion for Fanaroff–Riley II RGs, we find a true lobe pressure $P = 1.5\substack{+1.7\\ -0.4}\times 10^{-15}\ \mathrm{Pa}$. Cosmic Web reconstructions, group catalogues, and MHD simulations furthermore imply an Mpc–scale IGM density $1 + \delta _\mathrm{IGM} = 40\substack{+30\\ -10}$. The buoyantly rising lobes are crushed by the IGM at their inner side, where an approximate balance between IGM and lobe pressure occurs: PIGM ≈ P. The ideal gas law then suggests an IGM temperature $T_\mathrm{IGM} = 11\substack{+12\\-5} \times 10^6\ \mathrm{K}$, or $k_\mathrm{B}T_\mathrm{IGM} = 0.9\substack{+1.0\\-0.4}\ \mathrm{keV}$, at the virial radius – consistent with X-ray-derived temperatures of similarly massive groups. Interestingly, the method is not performing at its limit: in principle, estimates TIGM ∼ 4 × 106 K are already possible – rivalling the lowest X-ray measurements available. The technique’s future scope extends from galaxy group outskirts to the WHIM. In conclusion, we demonstrate that observations of GRGs in Cosmic Web filaments are finally sensitive enough to probe the thermodynamics of galaxy groups and beyond.
HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms
Authors: Shilo Asaf , Pegoraro Gianluca , Misteli Tom 
Published: October 2022

AbstractSplicing factors play an essential role in regulation of alternative pre-mRNA splicing. While much progress has been made in delineating the mechanisms of the splicing machinery, the identity of signal transduction pathways and upstream factors that regulate splicing factor activity is largely unknown. A major challenge in the discovery of upstream regulatory factors of pre-mRNA splicing is the scarcity of functional genomics screening methods to monitor splicing outcomes of endogenous genes. Here, we have developed HiFENS (high throughput FISH detection of endogenous splicing isoforms), a high-throughput imaging assay based on hybridization chain reaction (HCR) and used HiFENS to screen for cellular factors that regulate alternative splicing of endogenous genes. We demonstrate optimized detection with high specificity of endogenous splicing isoforms and multiplexing of probes for accurate detection of splicing outcomes with single cell resolution. As proof-of-principle, we perform an RNAi screen of 702 human kinases and identify potential candidate upstream splicing regulators of the FGFR2 gene. HiFENS should be a useful tool for the unbiased delineation of cellular pathways involved in alternative splicing regulation.
A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript
Authors: Sharma Shrikant , Pisignano Giuseppina , Merulla Jessica , Catapano Carlo V , Varani Gabriele 
Published: October 2022

Abstract
Transcription of E-cadherin, a tumor suppressor that plays critical roles in cell adhesion and the epithelial-mesenchymal transition, is regulated by a promoter-associated non-coding RNA (paRNA). The sense-oriented paRNA (S-paRNA) includes a functional C/A single nucleotide polymorphism (SNP rs16260). The A-allele leads to decreased transcriptional activity and increased prostate cancer risk. The polymorphic site is known to affect binding of a microRNA-guided Argonaute 1 (AGO1) complex and recruitment of chromatin-modifying enzymes to silence the promoter. Yet the SNP is distant from the microRNA-AGO1 binding domain in both primary sequence and secondary structure, raising the question of how regulation occurs. Here we report the 3D NMR structure of the 104-nucleotide domain of the S-paRNA that encompasses the SNP and the microRNA-binding site. We show that the A to C change alters the locally dynamic and metastable structure of the S-paRNA, revealing how the single nucleotide mutation regulates the E-cadherin promoter through its effect on the non-coding RNA structure.
G4Atlas: a comprehensive transcriptome-wide G-quadruplex database
Authors: Yu Haopeng , Qi Yiman , Yang Bibo , Yang Xiaofei , Ding Yiliang 
Published: October 2022

Abstract
RNA G-quadruplex (rG4) is a vital RNA tertiary structure motif that involves the base pairs on both Hoogsteen and Watson-Crick faces of guanines. rG4 is of great importance in the post-transcriptional regulation of gene expression. Experimental technologies have advanced to identify in vitro and in vivo rG4s across diverse transcriptomes. Building on these recent advances, here we present G4Atlas, the first transcriptome-wide G-quadruplex database, in which we have collated, classified, and visualized transcriptome rG4 experimental data, generated from rG4-seq, chemical profiling and ligand-binding methods. Our comprehensive database includes transcriptome-wide rG4s generated from 82 experimental treatments and 238 samples across ten species. In addition, we have also included RNA secondary structure prediction information across both experimentally identified and unidentified rG4s to enable users to display any potential competitive folding between rG4 and RNA secondary structures. As such, G4Atlas will enable users to explore the general functions of rG4s in diverse biological processes. In addition, G4Atlas lays the foundation for further data-driven deep learning algorithms to examine rG4 structural features.
A cap 0-dependent mRNA capture method to analyze the yeast transcriptome
Authors: Nowacka Martyna , Latoch Przemysław , Izert Matylda A , Karolak Natalia K , Tomecki Rafal , Koper Michał , Tudek Agnieszka , Starosta Agata L , Górna Maria W 
Published: October 2022

Abstract
Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes.