bluuebunny/crossref_metadata_2025_split huggingface dataset:
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves
Authors: Cardoso Milena A , Rizzardi Luis E A , Kume Leonardo W , Groeneveld Clarice S , Trefflich Sheyla , Morais Diego A A , Dalmolin Rodrigo J S , Ponder Bruce A J , Meyer Kerstin B , Castro Mauro A A 
Published: November 2021

Abstract

Motivation
Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees.

Results
Here, we present TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy to represent tree diagrams with focus on the leaves. The TreeAndLeaf package combines force-directed graph and tree layout algorithms using a single visualization system, allowing projection of multiple layers of information onto a graph-tree diagram. The Supplementary Information provides two case studies that use breast cancer data from epidemiological and experimental studies.

Availability and implementation
TreeAndLeaf is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/TreeAndLeaf/ (version≥1.4.2).

Supplementary information
Supplementary data are available at Bioinformatics online.
Some Scheduling Problems With Job Rejection And A Learning Effect
Authors: Toksari M Duran , Atalay Berrin 
Published: November 2021

AbstractIn this paper, we examined single and parallel machine scheduling problems with a learning effect and job rejection simultaneously. In real life, job processing times decrease when there is a learning effect. In some cases, producers cannot process all the jobs and pay the penalty cost for these jobs that they do not process. In our study, learning effect and job rejection are considered at the same time. We examined four different objective functions. Our objectives for single-machine scheduling problems are makespan and rejection cost minimization, total completion time and rejection cost minimization and total absolute deviation of completion times (TADC) and rejection cost minimization. Our objective for parallel machines is makespan and rejection cost minimization. The problems are solved by mathematical models, and four different algorithms are proposed for the problems. From these algorithms, the same results are obtained with single-machine makespan and rejection cost minimization, parallel machine makespan and rejection cost minimization and total completion time and rejection cost minimization. The accuracy for these models is obtained as 100%. The proposed algorithm for TADC and rejection cost minimization yielded close-to-optimal results. Mathematical model and algorithm results for 10 jobs, 20 jobs and 30 jobs are compared and the results are presented. The obtained solutions are obtained in polynomial time.
Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay
Authors: Kindler Gareth S , Wong Hon Lun , Larkum Anthony W D , Johnson Michael , MacLeod Fraser I , Burns Brendan P 
Published: November 2021

ABSTRACTThe present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich and hypersaline region of Blue Holes, Shark Bay. This was achieved via high-throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi group (11%) and Planctomycetes (10%). These mats were found to also harbour a diverse community of potentially novel microorganisms, including members from the DPANN, Asgard archaea and candidate phyla radiation, with highest diversity found in the lower regions (∼14–20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium- to high-quality metagenome-assembled genomes, viral defence mechanisms (CRISPR, BREX and DISARM), elemental transport, osmoprotection, heavy metal resistance and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.
Slowdown in Mortality Improvement in the Past Decade: A US/UK Comparison
Authors: Murphy Michael J , Grundy Emily M D 
Published: November 2021

Abstract

Objectives
To investigate the slowdown in mortality improvement in the United States, United Kingdom, and comparator countries observed in the first decade of the twenty-first century and critically evaluate proposed explanations.

Methods
Change-point analysis to identify the year of change in comparison of national mortality trends and linear spline models in the investigation of subnational differences using data from the Human Mortality Database, Global Burden of Disease cause-specific data, and, for the United Kingdom, national statistics data. Consideration of the impact of using different methods to estimate overall mortality is also concluded together with a review of methodological assumptions made in previous studies.

Results
The results confirm the slowdown in mortality improvement observed in the early twenty-first century but indicate that proposed explanations for this are inadequate on a range of counts.

Discussion
Mortality improvement slowed down in the early twenty-first century but the explanations advanced, such as opioid use in the United States or influenza epidemics and austerity programs in the United Kingdom, seem unlikely to account for this. Further research considering longer-term life course and cohort influences is needed.
A spectral element approach to computing normal modes
Authors: Kemper J , van Driel M , Munch F , Khan A , Giardini D 
Published: November 2021

SUMMARYWe introduce a new approach to the computation of gravito-elastic free oscillations or normal modes of spherically symmetric bodies based on a spectral element discretization of the radial ordinary differential equations. Our method avoids numerical instabilities often encountered in the classical method of radial integration and root finding of the characteristic function. To this end, the code is built around a sparse matrix formulation of the eigenvalue problem taking advantage of state-of-the-art parallel iterative solvers. We apply the method to toroidal, spheroidal and radial modes and we demonstrate its versatility in the presence of attenuation, fluid layers and gravity (including the purely elastic case, the Cowling approximation, and full gravity). We demonstrate higher-order convergence and verify the software by computing seismograms and comparing these to existing numerical solutions. Finally, to emphasize the general applicability of our code, we show spectra and eigenfunctions of Earth, Mars and Jupiter’s icy moon Europa and discuss the different types of modes that emerge.
Subvalvular tissue mimicking valve detachment-like pathology by vertical aneurysm in Takayasu’s arteritis
Authors: Kiryu Kentaro , Igarashi Itaru , Wada Takuya , Yamamoto Hiroshi 
Published: November 2021

Abstract
A 74-year-old woman with Takayasu’s arteritis previously underwent aortic valve replacement at 59 years old. She was initially diagnosed with aortic valve stenosis and valve detachment. Moreover, preoperative computed tomography revealed ∼40 mm distance between the coronary artery ostium and the prosthetic valve (PV) and an aneurysm at the sinus of Valsalva. A Bentall procedure was subsequently performed. Intraoperative findings revealed no detachment of the PV. Following PV removal, the subvalvular tissue was noted to protrude into the left ventricular outflow tract. Subsequently, it was revealed that the tissue could have interfered with the PV; however, the PV appeared to have been detached considering the imaging findings.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)–Specific Memory B Cells From Individuals With Diverse Disease Severities Recognize SARS-CoV-2 Variants of Concern
Authors: Lyski Zoe L , Brunton Amanda E , Strnad Matt I , Sullivan Peter E , Siegel Sarah A R , Tafesse Fikadu G , Slifka Mark K , Messer William B 
Published: November 2021

AbstractThe unprecedented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has called for substantial investigations into the capacity of the human immune system to protect against reinfection and keep pace with the evolution of SARS-CoV-2. We evaluated the magnitude and durability of the SARS-CoV-2–specific antibody responses against parental WA-1 SARS-CoV-2 receptor-binding domain (RBD) and a representative variant of concern (VoC) RBD using antibodies from 2 antibody compartments: long-lived plasma cell–derived plasma antibodies and antibodies encoded by SARS-CoV-2–specific memory B cells (MBCs). Thirty-five participants naturally infected with SARS-CoV-2 were evaluated; although only 25 of 35 participants had VoC RBD–reactive plasma antibodies, 34 of 35 (97%) participants had VoC RBD–reactive MBC-derived antibodies. Our finding that 97% of previously infected individuals have MBCs specific for variant RBDs provides reason for optimism regarding the capacity of vaccination, prior infection, and/or both, to elicit immunity with the capacity to limit disease severity and transmission of VoCs as they arise and circulate.
Coronary artery bypass graft for stent occlusion in a patient with essential thrombocythemia
Authors: Al-Sarraf Nael 
Published: November 2021

Abstract
Essential thrombocythemia (ET) is a rare myeloproliferative disorder characterized by pathologic expansion of the megakaryocytic elements in the bone marrow leading to persistent thrombocytosis and platelet dysfunction. The incidence of coronary artery disease can reach 9.4% and this is accompanied by high incidence of acute myocardial infractions. There are no clear guidelines for best management approach to these patients when cardiac surgery is planned. A case of ET required coronary artery bypass graft surgery for stent occlusion is presented with careful preoperative planning leading to full recovery with no complications.
On the fragility of Alfvén waves in a stratified atmosphere
Authors: Cally Paul S 
Published: November 2021

ABSTRACTComplete asymptotic expansions are developed for slow, Alfvén, and fast magnetohydrodynamic waves at the base of an isothermal 3D plane stratified atmosphere. Together with existing convergent Frobenius series solutions about z = ∞, matchings are numerically calculated that illuminate the fates of slow and Alfvén waves injected from below. An Alfvén wave in a two-dimensional model is 2.5D in the sense that the wave propagates in the plane of the magnetic field but its polarization is normal to it in an ignorable horizontal direction, and the wave remains an Alfvén wave throughout. The rotation of the plane of wave propagation away from the vertical plane of the magnetic field pushes the plasma displacement vector away from horizontal, thereby coupling it to stratification. It is shown that potent slow–Alfvén coupling occurs in such 3D models. It is found that about 50 per cent of direction-averaged Alfvén wave flux generated in the low atmosphere at frequencies comparable to or greater than the acoustic cut-off can reach the top as Alfvén flux for small magnetic field inclinations θ, and this increases to 80 per cent or more with increasing θ. On the other hand, direction-averaged slow waves can be 40 per cent effective in converting to Alfvén waves at small inclination, but this reduces sharply with increasing θ and wave frequency. Together with previously explored fast–slow and fast–Alfvén couplings, this provides valuable insights into which injected transverse waves can reach the upper atmosphere as Alfvén waves, with implications for solar and stellar coronal heating and solar/stellar wind acceleration.
Galactic H ii region IRAS 17149 − 3916 – a multiwavelength study
Authors: Potdar Ajay , Das Swagat R , Issac Namitha , Tej Anandmayee , Vig Sarita , Chandra C H Ishwara 
Published: November 2021

ABSTRACT
This paper presents a multiwavelength investigation of the Galactic H ii region IRAS 17149 − 3916. Using the Giant Meterwave Radio Telescope, India, first low-frequency radio continuum observations at 610 and 1280 MHz for this region are presented. The ionized gas emission displays an interesting cometary morphology, which is likely powered by the early-type source, E4 (IRS-1). The origin of the cometary morphology is discussed under the framework of the widely accepted bow shock, champagne flow, and clumpy cloud mechanisms. The mid- and far-infrared data from Spitzer-GLIMPSE and Herschel-Hi-GAL reveal a complex network of pillars, clumps, bubble, filaments, and arcs suggesting the profound influence of massive stars on the surrounding medium. Triggered star formation at the tip of an observed pillar structure is reported. High-resolution ALMA continuum data show a string of cores detected within the identified clumps. The core masses are well explained by thermal Jeans fragmentation and support the hierarchical fragmentation scenario. Four ‘super-Jeans’ cores are identified which, at the resolution of the present data set, are suitable candidates to form high-mass stars.
Orbital dynamics of two circumbinary planets around misaligned eccentric binaries
Authors: Chen Cheng , Lubow Stephen H , Martin Rebecca G 
Published: November 2021

ABSTRACT
We investigate the orbital dynamics of circumbinary planetary systems with two planets around a circular or eccentric orbit binary. The orbits of the two planets are initially circular and coplanar to each other, but misaligned with respect to the binary orbital plane. The binary–planet and planet–planet interactions result in complex planet tilt oscillations. We use analytical models and numerical simulations to explore the effects of various values of the planet semimajor axes, binary eccentricity, and initial inclination. Around a circular orbit binary, secular tilt oscillations are driven by planet–planet interactions and are periodic. In that case, planets undergo mutual libration if close together and circulation if far apart with an abrupt transition at a critical separation. Around an eccentric orbit binary, secular tilt oscillations are driven by both planet–planet interactions and binary–planet interactions. These oscillations generally display more than one frequency and are generally not periodic. The transition from mutual planet libration to circulation is not sharp and there is a range of separations for which the planets are on orbits that are sometimes mutually librating and sometimes circulating. In addition, at certain separations, there are resonances for which tilt oscillations are complicated but periodic. For planets that are highly misaligned with respect to an eccentric orbit binary, there are stationary (non-oscillating) tilt configurations that are generalizations of polar configurations for the single planet case. Tilt oscillations of highly inclined planets occur for initial tilts that depart from the stationary configuration.
Testing planet formation from the ultraviolet to the millimetre
Authors: Choksi Nick , Chiang Eugene 
Published: November 2021

ABSTRACT
Gaps imaged in protoplanetary discs are suspected to be opened by planets. We compute the present-day mass accretion rates $\dot{M}_{\rm p}$ of seven hypothesized gap-embedded planets, plus the two confirmed planets in the PDS 70 disc. The accretion rates are based on disc gas surface densities Σgas from C18O observations, and planet masses Mp from simulations fitted to observed gaps. Assuming accretion is Bondi-like, we find in eight out of nine cases that $\dot{M}_{\rm p}$ is consistent with the time-averaged value given by the current planet mass and system age, Mp/tage. As system ages are comparable to circumstellar disc lifetimes, these gap-opening planets may be undergoing their last mass doublings, reaching final masses of $M_{\rm p} \sim 10\rm{\!-\!}10^2 \, M_\oplus$ for the non-PDS 70 planets, and $M_{\rm p} \sim 1\!-\!10 \, M_{\rm J}$ for the PDS 70 planets. For another 15 gaps without C18O data, we predict Σgas by assuming their planets are accreting at their time-averaged $\dot{M}_{\rm p}$. Bondi accretion rates for PDS 70b and c are orders of magnitude higher than accretion rates implied by measured U-band and H α fluxes, suggesting most of the accretion shock luminosity emerges in as yet unobserved wavebands, or that the planets are surrounded by dusty, highly extincting, quasi-spherical circumplanetary envelopes. Thermal emission from such envelopes or from circumplanetary discs, on Hill sphere scales, peaks at wavelengths in the mid-to-far-infrared and can reproduce observed mm-wave excesses.
HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs
Authors: Yang Yang , Zhang Liwei , Xiong Chaoyang , Chen Jun , Wang Li , Wen Zengqi , Yu Juan , Chen Ping , Xu Yanhui , Jin Jingji , Cai Yong , Li Guohong 
Published: November 2021

Abstract
Histone variants have been implicated in regulating chromatin dynamics and genome functions. Previously, we have shown that histone variant H3.3 actively marks enhancers and cooperates with H2A.Z at promoters to prime the genes into a poised state in mouse embryonic stem cells (mESCs). However, how these two important histone variants collaboratively function in this process still remains elusive. In this study, we found that depletion of different components of HIRA complex, a specific chaperone of H3.3, results in significant decreases of H2A.Z enrichment at genome scale. In addition, CUT&Tag data revealed a genomic colocalization between HIRA complex and SRCAP complex. In vivo and in vitro biochemical assays verified that HIRA complex could interact with SRCAP complex through the Hira subunit. Furthermore, our chromatin accessibility and transcription analyses demonstrated that HIRA complex contributed to preset a defined chromatin feature around TSS region for poising gene transcription. In summary, our results unveiled that while regulating the H3.3 incorporation in the regulatory regions, HIRA complex also collaborates with SRCAP to deposit H2A.Z onto the promoters, which cooperatively determines the transcriptional potential of the poised genes in mESCs.
Mutation enrichment in human DNA samples via UV-mediated cross-linking
Authors: Leong Ka Wai , Yu Fangyan , Makrigiorgos G Mike 
Published: November 2021

Abstract
Detection of low-level DNA mutations can reveal recurrent, hotspot genetic changes of clinical relevance to cancer, prenatal diagnostics, organ transplantation or infectious diseases. However, the high excess of wild-type (WT) alleles, which are concurrently present, often hinders identification of salient genetic changes. Here, we introduce UV-mediated cross-linking minor allele enrichment (UVME), a novel approach that incorporates ultraviolet irradiation (∼365 nm UV) DNA cross-linking either before or during PCR amplification. Oligonucleotide probes matching the WT target sequence and incorporating a UV-sensitive 3-cyanovinylcarbazole nucleoside modification are employed for cross-linking WT DNA. Mismatches formed with mutated alleles reduce DNA binding and UV-mediated cross-linking and favor mutated DNA amplification. UV can be applied before PCR and/or at any stage during PCR to selectively block WT DNA amplification and enable identification of traces of mutated alleles. This enables a single-tube PCR reaction directly from genomic DNA combining optimal pre-amplification of mutated alleles, which then switches to UV-mediated mutation enrichment-based DNA target amplification. UVME cross-linking enables enrichment of mutated KRAS and p53 alleles, which can be screened directly via Sanger sequencing, high-resolution melting, TaqMan genotyping or digital PCR, resulting in the detection of mutation allelic frequencies of 0.001–0.1% depending on the endpoint detection method. UV-mediated mutation enrichment provides new potential for mutation enrichment in diverse clinical samples.
Alcohol and Vaporized Nicotine Co-exposure During Adolescence Contribute Differentially to Sex-Specific Behavioral Effects in Adulthood
Authors: Ruffolo Jessica , Frie Jude A , Thorpe Hayley H A , Talhat Malik Asfandyaar , Khokhar Jibran Y 
Published: November 2021

Abstract

Introduction
Co-occurrence of e-cigarette use and alcohol consumption during adolescence is frequent. Here, we examined whether adolescent co-exposure to alcohol drinking and vaporized nicotine would impact reward- and cognition-related behaviors in adult male and female rats during adulthood.

Aims and Methods
Four groups of male and female Sprague Dawley rats (n = 8–11/group/sex) received either nicotine (JUUL 5% nicotine pods) or vehicle vapor for 10 minutes daily between postnatal days 30–46, while having continuous voluntary access to ethanol and water during this time in a two-bottle preference design. Upon reaching adulthood, all rats underwent behavioral testing (ie, Pavlovian conditioned approach testing, fear conditioning and a two-bottle alcohol preference).

Results
A sex-dependent effect, not related to adolescent nicotine or alcohol exposure, on alcohol drinking in adulthood was found, such that females had a higher intake and preference for alcohol compared to males; both male and female adult rats also had greater alcohol preference compared to their alcohol preference as adolescents. Male rats exposed to vaporized nicotine with or without alcohol drinking during adolescence exhibited altered reward-related learning in adulthood, evidenced by enhanced levels of sign-tracking behavior. Male rats that drank alcohol with or without nicotine vapor in adolescence showed deficits in associative fear learning and memory as adults. In contrast, these effects were not seen in female rats exposed to alcohol and nicotine vapor during adolescence.

Conclusions
The present study provides evidence that co-exposure to alcohol and vaporized nicotine during adolescence in male, but not female, rats produces long-term changes in reward- and cognition-related behaviors.

Implications
These findings enhance our understanding of the effects of alcohol drinking and nicotine vapor exposure in adolescence. Moreover, they highlight potential sex differences that exist in the response to alcohol and nicotine vapor, underscoring the need for follow-up studies elucidating the neurobiological mechanisms that drive these sex differences, as well as the long-term effects of alcohol and nicotine vapor use.
Morphological and Molecular Characterization of Sclerotinia sclerotiorum on Sugar Beet in Montana, U.S.A.
Authors: Khan M. F. R. , Bhuiyan M. Z. R. , Lakshman Dilip K. , Mosher P. , Cymbaluk Timothy , Peters Duane 
Published: November 2021

In this contribution, we report on a survey of leaf blight on sugar beet in the Sidney factory district of Montana caused by the soilborne fungus Sclerotinia sclerotiorum. In addition to morphological and pathological characterization of the pathogen on sugar beet, we confirmed the molecular identity of the fungus by DNA sequence analysis of the ribosomal internal transcribed spacer region. Our findings are significant because the sugar beet production in south-central and eastern Montana contributes more than $100 million in economic activities. The incidence of this emerging disease will require changes in conventional disease management.