bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site and land-use associations of soil bacteria and fungi define core and indicative taxa
Authors: Gschwend Florian , Hartmann Martin , Mayerhofer Johanna , Hug Anna-Sofia , Enkerli Jürg , Gubler Andreas , Meuli Reto G , Frey Beat , Widmer Franco 
Published: December 2021

ABSTRACTSoil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
Gap-com: general model selection criterion for sparse undirected gene networks with nontrivial community structure
Authors: Kuismin Markku , Dodangeh Fatemeh , Sillanpää Mikko J 
Published: December 2021

Abstract
We introduce a new model selection criterion for sparse complex gene network modeling where gene co-expression relationships are estimated from data. This is a novel formulation of the gap statistic and it can be used for the optimal choice of a regularization parameter in graphical models. Our criterion favors gene network structure which differs from a trivial gene interaction structure obtained totally at random. We call the criterion the gap-com statistic (gap community statistic). The idea of the gap-com statistic is to examine the difference between the observed and the expected counts of communities (clusters) where the expected counts are evaluated using either data permutations or reference graph (the Erdős-Rényi graph) resampling. The latter represents a trivial gene network structure determined by chance. We put emphasis on complex network inference because the structure of gene networks is usually nontrivial. For example, some of the genes can be clustered together or some genes can be hub genes. We evaluate the performance of the gap-com statistic in graphical model selection and compare its performance to some existing methods using simulated and real biological data examples.
Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification
Authors: O’Halloran Damien M 
Published: December 2021

Abstract
Glutamate-gated chloride channels belong to the Cys-loop receptor superfamily. Glutamate-gated chloride channels are activated by glutamate and form substrates for the antiparasitic drugs from the avermectin family. Glutamate-gated chloride channels are pentameric, and each subunit contains an N-terminal extracellular domain that binds glutamate and 4 helical transmembrane domains, which contain binding sites for avermectin drugs. In order to provide more insight into phylum-wide patterns of glutamate-gated chloride subunit gene expansion and sequence diversity across nematodes, we have developed a database of predicted glutamate-gated chloride subunit genes from 125 nematode species. Our analysis into this dataset described assorted patterns of species-specific glutamate-gated chloride gene counts across different nematodes as well as sequence diversity in key residues thought to be involved in avermectin binding.
Triple Linking Numbers and Heegaard Floer Homology
Authors: Gorsky Eugene , Lidman Tye , Liu Beibei , Moore Allison H 
Published: December 2021

AbstractWe establish some new relationships between Milnor invariants and Heegaard Floer homology. This includes a formula for the Milnor triple linking number from the link Floer complex, detection results for the Whitehead link and Borromean rings, and a structural property of the $d$-invariants of surgeries on certain algebraically split links.
Evolution and emergence: higher order information structure in protein interactomes across the tree of life
Authors: Klein Brennan , Hoel Erik , Swain Anshuman , Griebenow Ross , Levin Michael 
Published: December 2021

Abstract
The internal workings of biological systems are notoriously difficult to understand. Due to the prevalence of noise and degeneracy in evolved systems, in many cases the workings of everything from gene regulatory networks to protein–protein interactome networks remain black boxes. One consequence of this black-box nature is that it is unclear at which scale to analyze biological systems to best understand their function. We analyzed the protein interactomes of over 1800 species, containing in total 8 782 166 protein–protein interactions, at different scales. We show the emergence of higher order ‘macroscales’ in these interactomes and that these biological macroscales are associated with lower noise and degeneracy and therefore lower uncertainty. Moreover, the nodes in the interactomes that make up the macroscale are more resilient compared with nodes that do not participate in the macroscale. These effects are more pronounced in interactomes of eukaryota, as compared with prokaryota; these results hold even after sensitivity tests where we recalculate the emergent macroscales under network simulations where we add different edge weights to the interactomes. This points to plausible evolutionary adaptation for macroscales: biological networks evolve informative macroscales to gain benefits of both being uncertain at lower scales to boost their resilience, and also being ‘certain’ at higher scales to increase their effectiveness at information transmission. Our work explains some of the difficulty in understanding the workings of biological networks, since they are often most informative at a hidden higher scale, and demonstrates the tools to make these informative higher scales explicit.
Rifabutin versus rifampicin bactericidal and antibiofilm activities against clinical strains of Staphylococcus spp. isolated from bone and joint infections
Authors: Thill Pauline , Robineau Olivier , Roosen Gabrielle , Patoz Pierre , Gachet Benoit , Lafon-Desmurs Barthélémy , Tetart Macha , Nadji Safia , Senneville Eric , Blondiaux Nicolas 
Published: December 2021

Abstract

Background
Staphylococci account for approximately 60% of periprosthetic joint infections (PJIs). Rifampicin (RMP) combination therapy is generally considered to be the treatment of choice for staphylococcal PJIs but carries an important risk of adverse events and drug–drug interactions. Rifabutin (RFB) shares many of the properties of rifampicin but causes fewer adverse events.

Objectives
To compare the minimal inhibitory concentration (MIC), the minimum bactericidal concentrations (MBC), and the minimum biofilm eradication concentrations (MBEC) of rifabutin and rifampicin for staphylococcal clinical strains isolated from PJIs.

Methods
132 clinical strains of rifampicin-susceptible staphylococci [51 Staphylococcus aureus (SA), 48 Staphylococcus epidermidis (SE) and 33 other coagulase-negative staphylococci (CoNS)] were studied. The MBC and the MBEC were determined using the MBEC® Assay for rifabutin and rifampicin and were compared.

Results
When compared with the rifampicin MIC median value, the rifabutin MIC median value was significantly higher for SA (P &lt; 0.05), but there was no statistically significant difference for SE (P = 0.25) and CoNS (P = 0.29). The rifabutin MBC median value was significantly higher than that of rifampicin for SA (P = 0.003) and was lower for SE (P = 0.003) and CoNS (P = 0.03). Rifabutin MBEC median value was statistically lower than that of rifampicin for all strains tested.

Conclusions
Using the determination of MBEC values, our study suggests that rifabutin is more effective than rifampicin against clinical strains of Staphylococcus spp. obtained from PJIs. Using MBECs instead of MICs seems to be of interest when considering biofilms. In vivo higher efficacy of rifabutin when compared with rifampicin needs to be confirmed.
Effect of Quorum Sensing Inducers and Inhibitors on Cytoplasmic Incompatibility Induced byWolbachia(Rickettsiales: Anaplasmataceae) in American Serpentine Leafminer (Diptera: Agromyzidae): Potential Tool for the Incompatible Insect Technique
Authors: Hidayanti Ardhiani Kurnia , Gazali Achmad , Tagami Yohsuke 
Published: December 2021

AbstractAgricultural crops around the world are attacked by approximately 3,000–10,000 species of pest insect. There is increasing interest in resolving this problem using environmentally friendly approaches. Wolbachia (Hertig), an insect endosymbiont, can modulate host reproduction and offspring sex through cytoplasmic incompatibility (CI). The incompatible insect technique (IIT) based on CI-Wolbachia is a promising biological control method. Previous studies have reported an association between CI and Wolbachia density, which may involve a quorum sensing (QS) mechanism. In this study, we investigated the effect of manipulating QS in Wolbachia using several chemicals including 3O-C12-HSL; C2HSL; spermidine (QS inducers), 4-phenylbutanoyl; and 4-NPO (QS inhibitors) on American serpentine leafminer (Liriomyza trifolii [Burgess]), an agricultural pest. The results showed that inducing QS with 3O-C12-HSL decreased the proportion of hatched eggs and increased Wolbachia density, whereas QS inhibition with 4-phenylbutanoyl had the opposite effects. Thus, manipulating QS in Wolbachia can alter cell density and the proportion of hatched eggs in the host L. trifolii, thereby reducing the number of insect progeny. These findings provide evidence supporting the potential efficacy of the IIT based on CI-Wolbachia for the environmentally friendly control of insect pest populations.
Spectral analysis of cool white dwarfs accreting from planetary systems: from the ultraviolet to the optical
Authors: Hollands M A , Tremblay P-E , Gänsicke B T , Koester D 
Published: December 2021

ABSTRACT
The accretion of planetary debris into the atmospheres of white dwarfs leads to the presence of metal lines in their spectra. Cool metal-rich white dwarfs, which left the main sequence many Gyr ago, allow the study of the remnants of the oldest planetary systems. Despite their low effective temperatures (Teff), a non-negligible amount of their flux is emitted in the near-ultraviolet (NUV), where many overlapping metal lines can potentially be detected. We have observed three metal-rich cool white dwarfs with the Space Telescope Imaging Spectrograph (STIS) onboard the Hubble Space Telescope, and compare the results determined from the NUV data with those previously derived from the analysis of optical spectroscopy. For two of the white dwarfs, SDSS J1038−0036 and SDSS J1535+1247, we find reasonable agreement with our previous analysis and the new combined fit of optical and NUV data. For the third object, SDSS J0956+5912, including the STIS data leads to a 10 per cent lower Teff, though we do not identify a convincing explanation for this discrepancy. The unusual abundances found for SDSS J0956+5912 suggest that the accreted parent body was composed largely of water ice and magnesium silicates, and with a mass of up to ≃ 2 × 1025 g. Furthermore, SDSS J0956+5912 shows likely traces of atomic carbon in the NUV. While molecular carbon is not observed in the optical, we demonstrate that the large quantity of metals accreted by SDSS J0956+5912 can suppress the C2 molecular bands, indicating that planetary accretion can convert DQ stars into DZs (and not DQZs/DZQs).
Spectral and polarization properties of reflected X-ray emission from black hole accretion discs
Authors: Podgorný J , Dovčiak M , Marin F , Goosmann R , Różańska A 
Published: December 2021

ABSTRACTX-ray polarimetric missions planned for this decade will significantly enhance our knowledge of compact accreting sources. Observations of the X-ray polarization signal from active galactic nuclei (AGNs) or X-ray binary systems (XRBs) will bring new means to study inner accretion flow in these objects that, together with currently used spectroscopic and timing techniques, will help us to determine better their properties, such as their inclination, orientation, shape, and size of their corona as well as the black hole spin. In this work, we present a yet missing piece in the global polarization models of black hole accretion discs. We compute the reflected X-ray emission from the disc in a local co-moving frame using (1) the radiative transfer code titan to obtain the ionization structure of the disc and (2) the Monte Carlo code stokes that incorporates the physics of absorption, re-emission, and Compton scattering to produce a complete spectropolarimetric output. We present the final Stokes parameters I, Q, and U for a set of photon-indices of the incident primary power-law radiation, the disc ionization parameters, incident and emission angles, for three independent polarization states of the incident coronal X-ray photons with a sufficient resolution in energy to allow for sharp discussion of spectral and polarization properties. We show that the spectral component matches well literature predictions. The polarization degree and angle are in agreement with analytical approximations previously appearing in reflection models and we demonstrate that the polarized reflected X-ray emission can be, locally, quite large in the $2{\!-\!}12\,$ keV band.
Orbital precession of the S2 star in Scalar–Tensor–Vector Gravity
Authors: Della Monica Riccardo , de Martino Ivan , de Laurentis Mariafelicia 
Published: December 2021

ABSTRACT
We have obtained the first constraint of the parameter space of Scalar–Tensor–Vector Gravity using the motion of the S2-star around the supermassive black hole at the centre of the Milky Way, and we did not find any serious tension with General Relativity. We used the Schwarzschild-like metric of Scalar–Tensor–Vector Gravity to predict the orbital motion of S2-star, and to compare it with the publicly available astrometric data, which include 145 measurements of the positions, 44 measurements of the radial velocities of S2-star along its orbit, and only the inferred rate of precession, as the latest GRAVITY data are not yet public. We employed a Markov chain Monte Carlo algorithm to explore the parameter space, and constrained the only one additional parameter of Scalar–Tensor–Vector Gravity to α ≲ 0.662 at 99.7 ${{\ \rm per\ cent}}$ confidence level, where α = 0 reduces this modified theory of gravity to General Relativity.
Radio emission from outflow–cloud interaction and its constraint on tidal disruption event outflow
Authors: Mou Guobin , Wang Tinggui , Wang Wei , Yang Jingjing 
Published: December 2021

ABSTRACT
Tidal disruption event (TDE) can launch an ultrafast outflow. If the black hole is surrounded by large amounts of clouds, outflow–cloud interaction will generate bow shocks, accelerate electrons, and produce radio emission. Here, we investigate the interaction between a non-relativistic outflow and clouds in active galaxies, which is manifested as outflow–BLR (broad-line region) interaction, and can be extended to outflow–torus interaction. This process can generate considerable radio emission, which may account for the radio flares appearing a few months later after TDE outbursts. Benefitting from efficient energy conversion from outflow to shocks and the strong magnetic field, outflow–cloud interaction may play a non-negligible, or even dominating role in generating radio flares in a cloudy circumnuclear environment if the CNM density is no more than 100 times the Sgr A*-like one. In this case, the evolution of radio spectra can be used to directly constrain the properties of outflows.
Persistence, Magnitude, and Patterns of Postacute Symptoms and Quality of Life Following Onset of SARS-CoV-2 Infection: Cohort Description and Approaches for Measurement
Authors: Peluso Michael J , Kelly J Daniel , Lu Scott , Goldberg Sarah A , Davidson Michelle C , Mathur Sujata , Durstenfeld Matthew S , Spinelli Matthew A , Hoh Rebecca , Tai Viva , Fehrman Emily A , Torres Leonel , Hernandez Yanel , Williams Meghann C , Arreguin Mireya I , Ngo Lynn H , Deswal Monika , Munter Sadie E , Martinez Enrique O , Anglin Khamal A , Romero Mariela D , Tavs Jacqueline , Rugart Paulina R , Chen Jessica Y , Sans Hannah M , Murray Victoria W , Ellis Payton K , Donohue Kevin C , Massachi Jonathan A , Weiss Jacob O , Mehdi Irum , Pineda-Ramirez Jesus , Tang Alex F , Wenger Megan A , Assenzio Melissa T , Yuan Yan , Krone Melissa R , Rutishauser Rachel L , Rodriguez-Barraquer Isabel , Greenhouse Bryan , Sauceda John A , Gandhi Monica , Scheffler Aaron Wolfe , Hsue Priscilla Y , Henrich Timothy J , Deeks Steven G , Martin Jeffrey N 
Published: December 2021

Abstract

Background
There is mounting evidence for the presence of postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC), but there is limited information on the spectrum, magnitude, duration, and patterns of these sequelae as well as their influence on quality of life.

Methods
We assembled a cohort of adults with a documented history of SARS-CoV-2 RNA positivity at ≥2 weeks past onset of coronavirus disease 2019 (COVID-19) symptoms or, if asymptomatic, first positive test. At 4-month intervals, we queried physical and mental health symptoms and quality of life.

Results
Of the first 179 participants enrolled, 10 were asymptomatic during the acute phase of SARS-CoV-2 infection, 125 were symptomatic but not hospitalized, and 44 were symptomatic and hospitalized. During the postacute phase, fatigue, shortness of breath, concentration problems, headaches, trouble sleeping, and anosmia/dysgeusia were most common through 8 months of observation. Symptoms were typically at least somewhat bothersome and sometimes exhibited a waxing-and-waning course. Some participants experienced symptoms of depression, anxiety, and post-traumatic stress, as well as difficulties with performance of usual activities. The median visual analogue scale rating of general health was lower at 4 and 8 months compared with pre-COVID-19. Two clusters of symptom domains were identified.

Conclusions
Many participants report bothersome symptoms following onset of COVID-19 with variable patterns of persistence and impact on quality of life. The substantial variability suggests the existence of multiple subphenotypes of PASC. A rigorous approach to the prospective measurement of symptoms and functional manifestations sets the stage for the next phase of research focusing on the pathophysiologic causes of the various subgroups of PASC.
Abraham von Franckenberg and the Ancient Wisdom of Rebirth
Authors: Zuber Mike A. 
Published: December 2021

Abstract
This chapter shows how the Silesian nobleman Abraham von Franckenberg linked Jacob Boehme’s spiritual alchemy to the idea of ancient wisdom, as exemplified by the gnostic church father Valentinus. Franckenberg himself experienced a crisis of faith in 1617 and discovered the heterodox devotional literature of his day upon his religious awakening. In the early 1620s, he read many of Boehme’s works in manuscript and met with their author in person repeatedly. Soon after Boehme’s death, Franckenberg composed an epistolary treatise that defended Valentinus against his detractors and presented him as a model Christian who had experienced rebirth. Much like Boehme, Franckenberg described this as spiritual alchemy. In later writings, he frequently alluded to concepts of his spiritual alchemy yet never again presented it as fully as in his early Theophrastia Valentiniana.
Collaboration, Counterfeit, and Calumny in Amsterdam
Authors: Zuber Mike A. 
Published: December 2021

Abstract
This chapter proves that Friedrich Breckling considerably adulterated a text originally composed in the late sixteenth century and embedded aspects of spiritual alchemy within it. Accusations raised among religious dissenters, notably by prophet and poet Quirinus Kuhlmann, and within the republic of letters at large led some of those who owned exemplars of the resulting book, Bartholomaeus Sclei’s Theosophische-Schrifften of 1686, to annotate their copies with information on Breckling’s interventions. Based on three such copies and other sources, several other collaborators and heavily edited passages can be identified. Yet there is reason to believe that even such annotated exemplars considerably underestimated Breckling’s contribution. In particular, the book’s index draws attention to several passages in which spiritual alchemy figures prominently and its bodily consequences are discussed.
Agnes de Mille on Broadway: 1943–1945
Authors: Gennaro Liza 
Published: December 2021

Abstract
Examination of Agnes de Mille as a radical dance maker in her choreographic trifecta—Oklahoma! (1943), One Touch of Venus (1943), and Bloomer Girl (1944)—reveals an ideological shift in the production of dance on Broadway and the development of a paradigm for making dances in the musical theater. This chapter further explores de Mille’s ability to employ dance as a medium for presenting social commentary, developing character, and creating a space for female spectatorship. Her artistic project required dancers who were not merely technicians but rather actor-dancers capable of embodying character and expressing legible story through dance. Displacing the stable of Broadway chorus men and women, de Mille introduced the actor-dancer to the commercial stage, thereby developing some of the greatest dance talents of the twentieth century, including Joan McCracken, Bambi Linn, Sono Osato, and James Mitchell. Selected dances from One Touch of Venus (1943), Bloomer Girl (1944), and Carousel (1945) are analyzed.
Broadway Dance
Authors: Gennaro Liza 
Published: December 2021

Abstract
Acknowledging the 1980s HIV/AIDS crisis and the deaths of hundreds of would-be choreographers, this chapter explores the trauma experienced by the dance and theater communities as a defining moment in the history of Broadway dance. I examine the advent of Broadway outsiders, post-modernist Bill T. Jones (Spring Awakening [2006]) and physical theatre practitioner, Steven Hoggett (American Idiot [2010] [2012], Once [2012], The Last Ship [2014]) onto Broadway and assess the diminishment of systems created by de Mille and Robbins. I also analyze Broadway insiders Savion Glover (Bring In ‘Da Noise, Bring in ‘Da Funk [1996], Shuffle Along, The Making of the Musical Sensation of 1921 And All That Followed [2016]), Andy Blankenbuehler (In the Heights [2008], Hamilton [2015]), Sergio Trujillo (Memphis [2009], Hands on a Hardbody [2013]), and Lorin Latarro (Waitress [2016]). I investigate how these four negotiate the systems of Robbins and Fosse while at the same time absorbing the influx of ideas coming from physical theatre Finally, the chapter looks at contemporary dance choreographer Camille Brown, who possesses an exceptional ability to discover fresh interpretations of time-worn dance vocabularies and to tell stories with invented movement. I contend that Brown is the latest choreographer using Broadway as a vehicle for inventive dance and setting a new standard of dance excellence and innovation in musical theater.