bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose
Authors: Brown Jennifer L , Perisin Matthew A , Swift Candice L , Benyamin Marcus , Liu Sanchao , Singan Vasanth , Zhang Yu , Savage Emily , Pennacchio Christa , Grigoriev Igor V , O'Malley Michelle A 
Published: November 2022

Abstract
A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established based on lactate cross-feeding to produce butyrate and butanol from plant biomass. Several co-culture formulations were assembled that consisted of anaerobic fungi (Anaeromyces robustus, Neocallimastix californiae, or Caecomyces churrovis) with the bacterium Clostridium acetobutylicum. Co-cultures were grown simultaneously (e.g., ‘one pot’), and compared to cultures where bacteria were cultured in fungal hydrolysate sequentially. Fungal hydrolysis of lignocellulose resulted in 7–11 mM amounts of glucose and xylose, as well as acetate, formate, ethanol, and lactate to support clostridial growth. Under these conditions, one-stage simultaneous co-culture of anaerobic fungi with C. acetobutylicum promoted the production of butyrate up to 30 mM. Alternatively, two-stage growth slightly promoted solventogenesis and elevated butanol levels (∼4–9 mM). Transcriptional regulation in the two-stage growth condition indicated that this cultivation method may decrease the time required to reach solventogenesis and induce the expression of cellulose-degrading genes in C. acetobutylicum due to relieved carbon-catabolite repression. Overall, this study demonstrates a proof of concept for biobutanol and bio-butyrate production from lignocellulose using an anaerobic fungal-bacterial co-culture system.
Challenging stylometry: The authorship of the baroque play La Segunda Celestina
Authors: Hernández-Lorenzo Laura , Byszuk Joanna 
Published: November 2022

Abstract
The aim of this study was to verify the possibility of Sor Juana Inés de la Cruz authoring the anonymous part of the baroque play La Segunda Celestina, commissioned to Agustín de Salazar, and left unfinished after his death. This is a first systematic stylometric study on this problem and a baroque hispanoamerican text. In our study, we faced building a balanced corpus from few available resources, and took extensive evaluation measures to deal with unclear stylometric signals. We use a variety of established attribution and verification methods, and introduce a novel evaluation procedure of examining historic texts with scarce corpora. The results support Sor Juana’s authorship, and unravel new connections between her and other authors of the time, showing, still undermined, powerful impact of her works on the epoch. The solutions adopted in solving methodological problems of such a complex task show how stylometry can overcome similar challenges.
A Bayesian approach for torque modelling of BeXRB pulsars with application to super-Eddington accretors
Authors: Karaferias A S , Vasilopoulos G , Petropoulou M , Jenke P A , Wilson-Hodge C A , Malacaria C 
Published: November 2022

ABSTRACT
In this study, we present a method to estimate posterior distributions for standard accretion torque model parameters and binary orbital parameters for X-ray binaries using a nested sampling algorithm for Bayesian parameter estimation. We study the spin evolution of two Be X-ray binary systems in the Magellanic Clouds, RX J0520.5−6932 and RX J0209−7427, during major outbursts, in which they surpassed the Eddington limit. Moreover, we apply our method to the recently discovered Swift J0243.6+6124, the only known Galactic pulsating ultra-luminous X-ray source. This is an excellent candidate for studying the disc evolution at super-Eddington accretion rates, because its luminosity spans several orders of magnitude during its outburst, with a maximum LX that exceeded the Eddington limit by a factor of ∼10. Our method, when applied to RX J0520.5−6932 and RX J0209−7427, is able to identify the more favourable torque model for each system, while yielding meaningful ranges for the NS and orbital parameters. Our analysis for Swift J0243.6+6124 illustrates that, contrary to the standard torque model predictions, the magnetospheric radius (Rm) and the Alfvén radius (RA) are not proportional to each other when surpassing the Eddington limit. Reported distance estimates of this source range between 5 and 7 kpc. Smaller distances require non-typical neutron star properties (i.e. mass and radius) and possibly lower radiative efficiency of the accretion column.
Metallicity profiles of ultradiffuse galaxies in NIHAO simulations
Authors: Cardona-Barrero S , Di Cintio A , Battaglia G , Macciò A V , Taibi S 
Published: November 2022

ABSTRACT
Supernovae feedback driven expansion has proven to be a viable mechanism to explain the average properties, such as size, colour, mass, and internal kinematics, of a large fraction of ultradiffuse galaxies (UDGs). Here, we explore the origin of stellar metallicity gradients in feedback driven simulated UDGs from the NIHAO project and compare them with the observed distribution of metallicity gradients of both Local Group (LG) dwarfs as well as of the recently observed UDG DF44. Simulated UDGs display a large variety of metallicity profiles, showing flat to negative gradients, similarly to what is observed in LG dwarfs, while DF44 data suggest a flat to positive gradient. The variety of metallicity gradients in simulations is set by the interplay between the radius at which star formation occurs and the subsequent supernovae feedback driven stellar redistribution: rotation supported systems tend to have flat metallicity profiles while dispersion supported galaxies show negative and steep profiles. Our results suggest that UDGs are not peculiar in what regards their metallicity gradients, when compared to regular dwarfs. We predict that UDGs formed via SNae feedback should have flat-to-negative metallicity profiles: desirably, a larger observational sample of UDGs’ gradients shall be available in the future, in order to test our predictions.
WALLABY pre-pilot and pilot survey: The Tully Fisher relation in Eridanus, Hydra, Norma, and NGC4636 fields
Authors: Courtois Hélène M , Said Khaled , Mould Jeremy , Jarrett T H , Pomarède Daniel , Westmeier Tobias , Staveley-Smith Lister , Dupuy Alexandra , Hong Tao , Guinet Daniel , Howlett Cullan , Deg Nathan , For Bi-Qing , Kleiner Dane , Koribalski Bärbel , Lee-Waddell Karen , Rhee Jonghwan , Spekkens Kristine , Wang Jing , Wong O I , Bigiel Frank , Bosma Albert , Colless Matthew , Davis Tamara , Holwerda Benne , Karachentsev Igor , Kraan-Korteweg Renée C , McQuinn Kristen B W , Meurer Gerhardt , Obreschkow Danail , Taylor Edward 
Published: November 2022

ABSTRACT
The WALLABY pilot survey has been conducted using the Australian SKA Pathfinder (ASKAP). The integrated 21-cm H i line spectra are formed in a very different manner compared to usual single-dish spectra Tully–Fisher measurements. It is thus extremely important to ensure that slight differences (e.g. biases due to missing flux) are quantified and understood in order to maximise the use of the large amount of data becoming available soon. This article is based on four fields for which the data are scientifically interesting by themselves. The pilot data discussed here consist of 614 galaxy spectra at a rest wavelength of 21 cm. Of these spectra, 472 are of high enough quality to be used to potentially derive distances using the Tully–Fisher relation. We further restrict the sample to the 251 galaxies whose inclination is sufficiently close to edge-on. For these, we derive Tully–Fisher distances using the deprojected WALLABY velocity widths combined with infrared (WISE W1) magnitudes. The resulting Tully–Fisher distances for the Eridanus, Hydra, Norma, and NGC4636 clusters are 21.5, 53.5, 69.4, and 23.0 Mpc, respectively, with uncertainties of 5–10 per cent, which are better or equivalent to the ones obtained in studies using data obtained with giant single dish telescopes. The pilot survey data show the benefits of WALLABY over previous giant single-dish telescope surveys. WALLABY is expected to detect around half a million galaxies with a mean redshift of $z = 0.05 (200\, \mathrm{Mpc})$. This study suggests that about 200 000 Tully–Fisher distances might result from the survey.
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Authors: Olson Robert D , Assaf Rida , Brettin Thomas , Conrad Neal , Cucinell Clark , Davis James J , Dempsey Donald M , Dickerman Allan , Dietrich Emily M , Kenyon Ronald W , Kuscuoglu Mehmet , Lefkowitz Elliot J , Lu Jian , Machi Dustin , Macken Catherine , Mao Chunhong , Niewiadomska Anna , Nguyen Marcus , Olsen Gary J , Overbeek Jamie C , Parrello Bruce , Parrello Victoria , Porter Jacob S , Pusch Gordon D , Shukla Maulik , Singh Indresh , Stewart Lucy , Tan Gene , Thomas Chris , VanOeffelen Margo , Vonstein Veronika , Wallace Zachary S , Warren Andrew S , Wattam Alice R , Xia Fangfang , Yoo Hyunseung , Zhang Yun , Zmasek Christian M , Scheuermann Richard H , Stevens Rick L 
Published: November 2022

AbstractThe National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.
Database resources of the National Center for Biotechnology Information in 2023
Authors: Sayers Eric W , Bolton Evan E , Brister J Rodney , Canese Kathi , Chan Jessica , Comeau Donald C , Farrell Catherine M , Feldgarden Michael , Fine Anna M , Funk Kathryn , Hatcher Eneida , Kannan Sivakumar , Kelly Christopher , Kim Sunghwan , Klimke William , Landrum Melissa J , Lathrop Stacy , Lu Zhiyong , Madden Thomas L , Malheiro Adriana , Marchler-Bauer Aron , Murphy Terence D , Phan Lon , Pujar Shashikant , Rangwala Sanjida H , Schneider Valerie A , Tse Tony , Wang Jiyao , Ye Jian , Trawick Barton W , Pruitt Kim D , Sherry Stephen T 
Published: November 2022

Abstract
The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases. New resources include the Comparative Genome Resource (CGR) and the BLAST ClusteredNR database. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, IgBLAST, GDV, RefSeq, NCBI Virus, GenBank type assemblies, iCn3D, ClinVar, GTR, dbGaP, ALFA, ClinicalTrials.gov, Pathogen Detection, antimicrobial resistance resources, and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.
HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method
Authors: Choi Youngseok , Ahn Sojin , Park Myeongkyu , Lee SaetByeol , Cho Seoae , Kim Heebal 
Published: November 2022

Abstract
HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.
Very large hidden genetic diversity in one single tumor: evidence for tumors-in-tumor
Authors: Chen Bingjie , Wu Xianrui , Ruan Yongsen , Zhang Yulin , Cai Qichun , Zapata Luis , Wu Chung-I , Lan Ping , Wen Haijun 
Published: November 2022

Abstract
Despite the concern of within-tumor genetic diversity, this diversity is in fact limited by the kinship among cells in the tumor. Indeed, genomic studies have amply supported the ‘Nowell dogma’ whereby cells of the same tumor descend from a single progenitor cell. In parallel, genomic data also suggest that the diversity could be &gt;10-fold larger if tumor cells are of multiple origins. We develop an evolutionary hypothesis that a single tumor may often harbor multiple cell clones of independent origins, but only one would be large enough to be detected. To test the hypothesis, we search for independent tumors within a larger one (or tumors-in-tumor). Very high density sampling was done on two cases of colon tumors. Case 1 indeed has 13 independent clones of disparate sizes, many having heavy mutation burdens and potentially highly tumorigenic. In Case 2, despite a very intensive search, only two small independent clones could be found. The two cases show very similar movements and metastasis of the dominant clone. Cells initially move actively in the expanding tumor but become nearly immobile in late stages. In conclusion, tumors-in-tumor are plausible but could be very demanding to find. Despite their small sizes, they can enhance the within-tumor diversity by orders of magnitude. Such increases may contribute to the missing genetic diversity associated with the resistance to cancer therapy.
Theoretical Approaches in Digital Religion Studies
Authors: Evolvi Giulia 
Published: November 2022

Abstract
This chapter provides an overview of theoretical frameworks employed to study digital religion from the beginning of the field in the 1990s to its current theoretical developments and possible future directions. It is divided in four parts: first, it explores four waves of digital religion studies and the definitions used to describe religion and the Internet; second, it presents the three theoretical frameworks of mediation, mediatization, and religious-social shaping of technology; third, it describes some of the recently developed theories in the field (third spaces, hypermediation, mediatized religious design, religious digital creatives, and the technological apologetic); and fourth, it reflects on the possible future directions of the field, highlighting the need to focus on global perspectives, sociocultural issues connected with religion, and the development of new platforms and technologies.
DNA Hyper-methylation Associated With Schizophrenia May Lead to Increased Levels of Autoantibodies
Authors: Wei Hui , Yuan Yanbo , Zhu Caiyun , Ma Mingjie , Yang Fude , Lu Zheng , Wang Chuanyue , Deng Hong , Zhao Jingping , Tian Runhui , Zhu Wanwan , Shen Yan , Yu Xin , Xu Qi 
Published: November 2022

Abstract

Background and Hypothesis
Environmental stressors may influence immune surveillance in B lymphocytes and stimulate autoimmune responses via epigenetic DNA methylation modifications in schizophrenia (SCZ).

Study Design
A total of 2722, Chinese Han origin subjects were recruited in this study (2005–2011), which included a discovery follow-up cohort with 40 remitters of SCZ (RSCZ), 40 nonremitters of SCZ (NRSCZ), and 40 controls (CTL), and a replication follow-up cohort (64 RSCZ, 16 NRSCZ, and 84 CTL), as well as a case-control validation cohort (1230 SCZ and 1208 CTL). Genomic DNA methylation, target gene mRNA transcripts, and plasma autoantibody levels were measured across cohorts.

Study Results
We found extensive differences in global DNA methylation profiles between RSCZ and NRSCZ groups, wherein differential methylation sites (DMS) were enriched with immune cell maturation and activation in the RSCZ group. Out of 2722 participants, the foremost DMS cg14341177 was hyper-methylated in the SCZ group and it inhibited the alternative splicing of its target gene BICD2 and may have increased its autoantigen exposure, leading to an increase in plasma anti-BICD2 IgG antibody levels. The levels of cg14341177 methylation and anti-BICD2 IgG decreased significantly in RSCZ endpoint samples but not in NRSCZ endpoint samples. There are strong positive correlations between cg14341177 methylation, anti-BICD2 IgG, and positive and negative syndrome scale (PANSS) scores in the RSCZ groups, but not in the NRSCZ groups.

Conclusions
These data suggest that abnormal DNA methylation could affect autoreactive responses in SCZ, and that cg14341177 methylation and anti-BICD2 IgG levels may potentially serve as useful biomarkers.
P020 Polysomnographic titration of non-invasive ventilation in motor neurone disease (3TLA): Study protocol for a randomised controlled trial
Authors: Berlowitz D , Rowe D , Howard M , Piper A , Graco M , Braat S , Singh B , Sousa T , Lannin N , Sawyer A ,   TLA Trial Group
Published: November 2022

Abstract

Introduction
The benefits of using non-invasive ventilation (NIV) on survival in motor neurone disease (MND) are well-established. Recent MND cohort studies have extended this finding to suggest that adherence with NIV of &gt;4 hours/day improves survival more than &lt;4 hours/day, and that any use increases survival more than no use at all. Despite these data, only approximately 19% of Australians with MND start NIV. Our team has recently demonstrated that specific and individualised NIV titration using polysomnography (PSG) leads to better NIV usage in MND. However, for this clinical practice model to result in sustained benefits, evidence of effectiveness across multiple sites, as well as culture and practice change must occur. The primary aim of this randomised controlled trial (RCT) is to determine if the proportion of participants using NIV for &gt;4 hours/day during the 7-week post-randomisation period is higher in the PSG (Intervention) than the Control group.

Methods
A two-arm, individual participant, assessor-blinded RCT in 7 MND care centres across Australia. Eligible participants will be randomised (1:1) to either the Intervention (PSG assisted optimization of NIV) or a Control group (sham PSG). Respiratory, sleep and patient-reported outcome measures will be collected at baseline and follow-up 7 weeks after the PSG. An implementation science program, health economic evaluation and 12-month cohort follow-up will be undertaken.
Data collection is underway.

Trial Registration
ClinicalTrials.gov (#CT05136222).
P092 Risk factors for obstructive sleep apnea: A scoping review of systematic reviews
Authors: Qian Y , Dharmage S , Hamilton G , Senaratna C , Perret J 
Published: November 2022

Abstract

Introduction
The high prevalence of obstructive sleep apnea (OSA) challenges public health and health care significantly. Summarizing the evidence and identifying research gaps on risk factors for OSA could focus efforts to reduce the disease burden.

Methods
We performed a scoping review to map the current evidence of OSA-related risk factors. Medline was searched systematically for systematic reviews/meta-analyses including observational and interventional studies, excluding reviews limited to paediatric populations.

Results
Of 974 abstracts, 49 eligible systematic reviews were retrieved, covering six major categories of risk factors, namely demographic(n=9), lifestyle(n=9), genetic(n=11), comorbidity-related(n=10), environmental(n=2), and other(e.g., protein level, surgery, n=12). Obesity/BMI and increasing age were major risk factors for OSA, however, longitudinal obesity trajectories or weight changes were not explored. Smoking was inconsistently associated with OSA. Alcohol consistently increased OSA severity(n=5). 5-HT2A(5-hydroxy-tryptamine), tumor necrosis factor- α, and angiotensin converting enzyme activity were associated with increased risk of OSA(n=4 for each). Comorbidity-related risk factors were identified including asthma, hypothyroidism, gastroesophageal reflux disease, depression while allergic rhinitis and Parkinson’s disease had null and negative effects, respectively. Menopause, ethnicity, and enlarged adenoids/tonsils are yet to be systematically synthesized.
Overall, there was no review analyzing any longitudinal risk factor for OSA in the general population.

Discussion
Although this review supports the potential benefit of reducing OSA and its severity from weight loss and/or quitting smoking among the general population, there is an absence of data on longitudinal risk factor trajectories, which could help guide and strengthen public health policy.
Exit from periodic joint-tenancy: what “bare trust”, exactly?
Authors: Chan Alex Chun Hei , Leung Samuel Yee Ching 
Published: November 2022

Abstract
The commercial world runs itself through an intricacy of legal relationships amongst which a tenancy may be one of the most common. The statutory law of the United Kingdom superimposes a trust over every tenancy so that each co-tenant is deemed to be a trustee of each other. Can a co-tenant then ditch his/her cohorts and extinguish a periodic tenancy only to re-contract with the landlord over the very property without committing a breach of trust? This was considered not long ago in Procter v Procter [2022] EWHC 1202 (Ch) and most recently in Pile v Pile [2022] EWHC 2036 (Ch). We trace back to what had been adjudicated by the House of Lords in Hammersmith and Fulham London Borough Council v Monk [1992] 1 AC 478 (HL) three decades ago, scrutinize the sufficiency of a line of authorities developed since then and as they were applied in Procter and Pile, and venture to suggest that the statutory trust is one of its own kind deserving wider and deeper study beyond traditional trust analysis and why.