bluuebunny/crossref_metadata_2025_split huggingface dataset:
HYPHAEdelity: a quantitative image analysis tool for assessing peripheral whole colony filamentation
Authors: Britton Scott J , Rogers Lisa J , White Jane S , Maskell Dawn L 
Published: November 2022

Abstract
The yeast Saccharomyces cerevisiae, also known as brewer's yeast, can undergo a reversible stress-responsive transition from individual ellipsoidal cells to chains of elongated cells in response to nitrogen- or carbon starvation. Whole colony morphology is frequently used to evaluate phenotypic switching response; however, quantifying two-dimensional top-down images requires each pixel to be characterized as belonging to the colony or background. While feasible for a small number of colonies, this labor-intensive assessment process is impracticable for larger datasets. The software tool HYPHAEdelity has been developed to semi-automate the assessment of two-dimensional whole colony images and quantify the magnitude of peripheral whole colony yeast filamentation using image analysis tools intrinsic to the OpenCV Python library. The software application functions by determining the total area of filamentous growth, referred to as the f-measure, by subtracting the area of the inner colony boundary from the outer-boundary area associated with hyphal projections. The HYPHAEdelity application was validated against automated and manually pixel-counted two-dimensional top-down images of S. cerevisiae colonies exhibiting varying degrees of filamentation. HYPHAEdelity's f-measure results were comparable to areas determined through a manual pixel enumeration method and found to be more accurate than other whole colony filamentation software solutions.
Dynamic rupture simulations based on depth-dependent stress accumulation
Authors: Aochi H , Tsuda K 
Published: November 2022

SUMMARYThe depth variation in earthquake rupture behaviour is important for quantitative seismic hazard analysis. We discussed how to set up the initial stress on a fault before an earthquake based on the Mohr–Coulomb criterion considering depth variation. One can assume that the stress is uniformly loaded without exceeding the Coulomb criterion at any depth (stress-constrained condition); however, this implicitly induces a discontinuity of strain in a 1-D layered Earth model. We alternatively assumed that the strain in an upper layer does not exceed that in a lower layer (strain-constrained condition). We numerically demonstrated the dynamic rupture process through 3-D numerical simulations, particularly for the 2019 Mw 4.9 Le Teil (France) earthquake, showing a very shallow ruptured area with ground surface displacement. The rupture extent and seismogenic depth can be controlled by a limited layer at depth, which is favourably loaded in advance. The lateral extension of the rupture propagation at this layer is necessary to trigger the above layer but not enough to trigger the layers below. The depth variation of stress loading before an earthquake would be important for assessing the rupture size of moderate (magnitude 5–6) crustal earthquakes in particular.
The Prevalence of Symptomatic Congenital Cytomegalovirus Disease in Korea; A 15-Year Multicenter Study and Analysis of Big Data From National Health Insurance System
Authors: Choi Sae Rom , Kim Kyung-Ran , Son Sohee , Kim Dong Sub , Chang Yun Sil , Cho Eun Young , Chang Mea-Young , Kim Yun-Kyung , Jo Dae Sun , Kim Jin Kyu , Cho Hye-Kyung , Park Su Eun , Park Kyung Hee , Kim Hwang Min , Lee Byung-Kook , Kim Yae-Jean 
Published: November 2022

Abstract
The birth prevalence of symptomatic congenital cytomegalovirus (cCMV) disease among live birth in Korea from a multicenter study was 0.06% during 2001–2015 with increasing frequency. The administrative prevalence of cCMV infection by big-data analysis from the national health insurance system was 0.01% and the average healthcare cost was US$2010 per person.
Polysyllabic shortening in Modern Standard Arabic
Authors: Guba Mohammed Nour Abu , Mashaqba Bassil , Huneety Anas 
Published: November 2022

Abstract
This is the first study that investigates polysyllabic shortening in Arabic. It aims to find out the extent to which Modern Standard Arabic employs this phonetic mechanism, which is usually associated with stress-timed languages. Data were collected from 10 Jordanian speakers reading 6 sets of words representing the six monophthongs in Arabic in a carrier sentence. Based on the acoustic analysis of 180 vowels, it was found that the vowels in monosyllabic words were significantly longer than their counterparts in polysyllabic words. However, the differences between the vowels in disyllabic and trisyllabic words were much smaller. Findings suggest that polysyllabic shortening is not invoked as a mechanism to maintain the stress-timed rhythm of stress-timed languages. Rather, it seems to be a universal phonetic feature that applies in different degrees that are commensurate with the rhythm of the language in question.
Time-course transcriptome analysis reveals regulation of Arabidopsis seed dormancy by the transcription factors WOX11/12
Authors: Liao Jiakai , Deng Ban , Cai Xinyu , Yang Qixin , Hu Bangping , Cong Jiajing , Zhang Yuxiang , Wang Gang , Xin Guiliang , Li Yuting , Yang Li , Zhang Daizhen , Zhang Jin , Liu Bobin 
Published: November 2022

AbstractThe induction of seed dormancy and its release involve a finely regulated genetic program controlled by various environmental and developmental cues that are critical for plant survival and population expansion. Light plays a key role in seed dormancy and germination, but the molecular mechanisms underlying the control of dormancy are unclear. In the present study, high-resolution temporal RNA-seq in Arabidopsis identified WOX11 as encoding a hub transcription factor during the seed dormancy induction and release stages. This gene might have evolved from gymnosperms and expanded in angiosperms with highly conserved expression patterns in seeds. WOX11 and its homolog WOX12 were highly expressed from 2 d after pollination, and mRNA abundance was greatly increased during the seed dormancy induction and release stages. Further, we found that WOX11 plays a role in the regulation of seed dormancy downstream of phytochrome B (PHYB)-mediated red-light signaling during the induction stage, indicating that WOX11/12 are newly identified components of red-light signaling transduction. Taken together, our results suggest that WOX11/12-mediated PHYB signaling regulates seed dormancy in Arabidopsis, and provide insights into the developmental regulation and evolutionary adaptation of plants to changes in the light environment.
Discovery and properties of ultra-high redshift galaxies (9 &lt; z &lt; 12) in the JWST ERO SMACS 0723 Field
Authors: Adams N J , Conselice C J , Ferreira L , Austin D , Trussler J A A , Juodžbalis I , Wilkins S M , Caruana J , Dayal P , Verma A , Vijayan A P 
Published: November 2022

ABSTRACT
We present a reduction and analysis of the James Webb Space Telescope (JWST) SMACS 0723 field using new post-launch calibrations to conduct a search for ultra-high-redshift galaxies (z &gt; 9) present within the Epoch of Reionization. We conduct this search by modelling photometric redshifts in several ways for all sources and by applying conservative magnitude cuts (mF200W &lt; 28) to identify strong Lyman breaks greater than 1 mag. We find four z &gt; 9 candidate galaxies which have not previously been identified, with one object at z = 11.5, and another which is possibly a close pair of galaxies. We measure redshifts for candidate galaxies from other studies and find the recovery rate to be only 23 per cent, with many being assigned lower redshift, dusty solutions in our work. Most of our z &gt; 9 sample show evidence for Balmer-breaks, or extreme emission lines from H β and [O iii], demonstrating that the stellar populations could be advanced in age or very young depending on the cause of the F444W excess. We discuss the resolved structures of these early galaxies and find that the Sérsic indices reveal a mixture of light concentration levels, but that the sizes of all our systems are exceptionally small (&lt;0.5 kpc). These systems have stellar masses M* ∼ 109.0 M⊙, with our z ∼ 11.5 candidate a dwarf galaxy with a stellar mass M* ∼ 107.8–108.2 M⊙. These candidate ultra high-redshift galaxies are excellent targets for future NIRSpec observations aimed to better understand their physical nature.
The infrared features and full rotational constant catalogue of the newly detected MgC2 astromolecule
Authors: Watrous Alexandria G , Fortenberry R C 
Published: November 2022

ABSTRACT
The recent radioastronomical detection of magnesium dicarbide (MgC2) towards the carbon-rich star IRC+10216 leads to questions about whether this molecule can be observed in other wavelengths, especially with the wealth of IR data being produced by JWST. This present, theoretical spectral characterization, unfortunately, implies that mid-IR observations of MgC2 are unlikely due to small IR transition intensities, overlap with polycyclic aromatic hydrocarbon IR features, low frequencies/long wavelengths, or the relatively small column densities. In spite of this, the full set of fundamental anharmonic vibrational frequencies are provided for each of the 24Mg, 25Mg, and 26Mg isotopologues as are the complete rotational constants for the same set for additional laboratory characterization. Most notably and with regards to 24MgC2, the B0 and C0 (11452.7 and 9362.7 MHz) rotational constants are uniquely provided for the first time. The experimentally derived A0, (B + C)/2, and (B − C)/4 values are within 0.7 % of the presently computed anharmonic results implying similar accuracy for the remaining spectroscopic constants.
Local gravitational instability of stratified rotating fluids: three-dimensional criteria for gaseous discs
Authors: Nipoti Carlo 
Published: November 2022

ABSTRACTFragmentation of rotating gaseous systems via gravitational instability is believed to be a crucial mechanism in several astrophysical processes, such as formation of planets in protostellar discs, of molecular clouds in galactic discs, and of stars in molecular clouds. Gravitational instability is fairly well understood for infinitesimally thin discs. However, the thin-disc approximation is not justified in many cases, and it is of general interest to study the gravitational instability of rotating fluids with different degrees of rotation support and stratification. We derive dispersion relations for axisymmetric perturbations, which can be used to study the local gravitational stability at any point of a rotating axisymmetric gaseous system with either barotropic or baroclinic distribution. Three-dimensional (3D) stability criteria are obtained, which generalize previous results and can be used to determine whether and where a rotating system of given 3D structure is prone to clump formation. For a vertically stratified gaseous disc of thickness hz (defined as containing ≈70% of the mass per unit surface), a sufficient condition for local gravitational instability is $Q_{\rm 3D}\equiv (\sqrt{\kappa ^2+\nu ^2}+c_{\rm s}h_z^{-1})/{\sqrt{4\pi G\rho }}\ \lt\ 1$, where ρ is the gas volume density, κ the epicycle frequency, cs the sound speed, and $\nu ^2\equiv \rho ^{\prime }_zp^{\prime }_z/\rho ^2$, where $\rho ^{\prime }_z$ and $p^{\prime }_z$ are the vertical gradients of, respectively, gas density and pressure. The combined stabilizing effects of rotation (κ2) and stratification (ν2) are apparent. In unstable discs, the conditions for instability are typically met close to the mid-plane, where the perturbations that are expected to grow have characteristic radial extent of a few hz.
Living in solitude or building reefs: ecophenotypic variation of the vermetid Petaloconchus varians revealed by mitochondrial DNA analysis
Authors: Breves André , de Paula Thiago Silva , Spotorno Paula , Fernandes Maurício Romulo , Lôbo-Hajdu Gisele , Pimenta Alexandre Dias 
Published: November 2022

Abstract
This study aimed to investigate whether the marine snails Petaloconchus varians (d'Orbigny, 1839) and Petaloconchus myrakeenae Absalão & Rios, 1987 from southeastern Brazil are conspecific. Both species were described from Rio de Janeiro, and they diverge mainly in their growth forms (i.e. gregarious for P. varians and solitary for P. myrakeenae). Examination of shell features, operculum, radula and anatomic details revealed no differences between the species. Analysis of partial cytochrome c oxidase subunits I (CO1) sequences showed that all Petaloconchus samples from Rio de Janeiro clustered into a single clade, which included specimens from the Caribbean (Venezuela). In addition, a genetic differentiation test showed that the analysed populations are structured and the species likely originated in the Caribbean and has undergone significant population expansion. We conclude that P. myrakeenae is a junior synonym of P. varians and provide a morphological redescription of the latter. Furthermore, we argue that different growth forms of P. varians are ecophenotypes, apparently influenced by wave action and water temperature. Tests should be conducted to confirm this hypothesis and to evaluate the impact of other parameters on the plasticity of growth forms, such as food supply and habitat heterogeneity.
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
Authors: Hernández-Plaza Ana , Szklarczyk Damian , Botas Jorge , Cantalapiedra Carlos P , Giner-Lamia Joaquín , Mende Daniel R , Kirsch Rebecca , Rattei Thomas , Letunic Ivica , Jensen Lars J , Bork Peer , von Mering Christian , Huerta-Cepas Jaime 
Published: November 2022

Abstract
The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.
dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes
Authors: Zheng Jinfang , Hu Boyang , Zhang Xinpeng , Ge Qiwei , Yan Yuchen , Akresi Jerry , Piyush Ved , Huang Le , Yin Yanbin 
Published: November 2022

Abstract
Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.
Primordial black holes and dark matter mass spectra
Authors: Kitabayashi Teruyuki 
Published: November 2022

Abstract
Because primordial black holes (PBHs) evaporate into all particle species in nature, PBHs may emit several dark matter (DM) particle species with specific mass spectra. We assume that PBHs are the only source of DMs, and DMs only interact with the standard model particles gravitationally. We show a relation between the number of DM particle species NDM and initial PBH density β and mass $M_{\rm BH}^{\rm in}$. β–$M_{\rm BH}^{\rm in}$ curves for different NDM tend to overlap with each other for heavy initial PBHs. We also show the allowed region of DM masses for multiple DMs.
Are CLO Collateral and Tranche Ratings Disconnected?
Authors: Griffin John M , Nickerson Jordan 
Published: November 2022

Abstract
Between March and August 2020, S&P and Moody’s downgraded approximately 25$\%$ of collateral feeding into CLOs and only 2$\%$ of tranche values, with rating actions concentrating in junior tranches. Both S&P and Moody’s modeling indicate that the impacts should have been considerably larger, especially for higher-rated tranches. Neither changes in correlation nor the accumulation of pre-COVID-19 protective cushions can explain the downgrade asymmetry on upper tranches. Instead, CLO managers repositioned their collateral pools to dampen the negative credit shock and rating agencies incorporated qualitative adjustments in their CLO ratings. Important potential policy and market implications from these findings are discussed.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Rheumatoid arthritis macrophages are primed for inflammation and display bioenergetic and functional alterations
Authors: Hanlon Megan M , McGarry Trudy , Marzaioli Viviana , Amaechi Success , Song Qingxuan , Nagpal Sunil , Veale Douglas J , Fearon Ursula 
Published: November 2022

Abstract

Objectives
Myeloid cells with a monocyte/macrophage phenotype are present in large numbers in the RA joint, significantly contributing to disease; however, distinct macrophage functions have yet to be elucidated. This study investigates the metabolic activity of infiltrating polarized macrophages and their impact on pro-inflammatory responses in RA.

Methods
CD14+ monocytes from RA and healthy control (HC) bloods were isolated and examined ex vivo or following differentiation into ‘M1/M2’ macrophages. Inflammatory responses and metabolic analysis ± specific inhibitors were quantified by RT-PCR, western blot, Seahorse XFe technology, phagocytosis assays and transmission electron microscopy along with RNA-sequencing (RNA-seq) transcriptomic analysis.

Results
Circulating RA monocytes are hyper-inflammatory upon stimulation, with significantly higher expression of key cytokines compared with HC (P &lt; 0.05) a phenotype which is maintained upon differentiation into mature ex vivo polarized macrophages. This induction in pro-inflammatory mechanisms is paralleled by cellular bioenergetic changes. RA macrophages are highly metabolic, with a robust boost in both oxidative phosphorylation and glycolysis in RA along with altered mitochondrial morphology compared with HC. RNA-seq analysis revealed divergent transcriptional variance between pro- and anti-inflammatory RA macrophages, revealing a role for STAT3 and NAMPT in driving macrophage activation states. STAT3 and NAMPT inhibition results in significant decrease in pro-inflammatory gene expression observed in RA macrophages. Interestingly, NAMPT inhibition specifically restores macrophage phagocytic function and results in reciprocal STAT3 inhibition, linking these two signalling pathways.

Conclusion
This study demonstrates a unique inflammatory and metabolic phenotype of RA monocyte-derived macrophages and identifies a key role for NAMPT and STAT3 signalling in regulating this phenotype.
Diagnosis and Management of Functional Pouch Disorders: A Systematic Review
Authors: Roussel Breton N. , Shah Samir A. 
Published: November 2022

BACKGROUND:
Functional disorders impart significant morbidity in patients with inflammatory bowel disease who undergo restorative proctocolectomy.

OBJECTIVE:
This systematic review aimed to summarize the management strategies for various functional disorders of the pouch.

DATA SOURCES:
A database search of PubMed was conducted to identify relevant clinical studies assessing the management of various functional disorders in patients who underwent restorative proctocolectomy.

STUDY SELECTION:
Published clinical studies investigating a functional disorder of the pouch in patients who previously underwent a colectomy with ileal pouch-anal anastomosis.

INTERVENTIONS:
Restorative proctocolectomy was completed in patients with inflammatory bowel disease or other indications such as a diagnosis of familial adenomatous polyposis.

MAIN OUTCOME MEASURES:
The primary outcomes described in this review include the prevalence of functional disorders of the pouch in patients undergoing restorative proctocolectomy and the relevant management strategies.

RESULTS:
Ten clinical studies were identified using the predetermined search terms and screened for relevancy to patients with inflammatory bowel disease who previously underwent colectomy with ileal pouch-anal anastomosis. A qualitative summary was developed on the basis of data from these studies and from current guidelines developed for the management of inflammatory bowel disease.

LIMITATIONS:
This systematic review is limited by the small number and low quality of the clinical studies included as well as the nonquantitative summary of the findings.

CONCLUSIONS:
Functional disorders of the pouch are likely underdiagnosed. Although a source of significant morbidity, these diseases require additional clinical studies to better elucidate effective management strategies.