bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fermentation of araticum, baru, and pequi by-products by probiotic strains: effects on microorganisms, short-chain fatty acids, and bioactive compounds
Authors: de Oliveira Fellipe Lopes , Morzelle Maressa Caldeira , Moretti Marcia Maria de Souza , Casarotti Sabrina Neves 
Published: August 2023

Abstract
Fruit by-products, due to their unique chemical composition containing dietary fibers and bioactive compounds, may favor the growth of probiotic strains. This study evaluated the fermentation of araticum, baru, and pequi by-products using Lactobacillus acidophilus (La-5, LA3, and NCFM) and Bifidobacterium animalis subsp. lactis (Bb-12) probiotic strains. We assessed probiotic viability, short-chain fatty acid levels, and bioactive compound levels after 48 h of fermentation. Araticum and pequi by-products led to counts higher than 6 log CFU/mL after 48-h fermentation for all Lactobacillus strains, but only the araticum by-product supported the growth of the Bb-12 strain. Fermentation of araticum by-product resulted in greater amounts of acetate (39.97 mM for LA3 and 39.08 mM for NCFM) and propionate (0.20 mM for NCFM), while baru by-product showed greater amounts of butyrate (0.20 mM for La-5 and Bb-12). Fermentation of araticum and baru by-products resulted in an increase in bioactive compounds, with the latter showing total phenolic compounds and antioxidant activity from 1.4 to 1.7 and from 1.3 to 3.1 times higher, respectively, than the negative control treatment. Araticum by-product exhibited a higher potential for prebiotic effects, and fermentation by the tested probiotic strains is essential to increase bioactive compound levels.
Association of adverse effects with high serum posaconazole concentrations
Authors: Jensen Kelsey , Saleh Omar Abu , Chesdachai Supavit , Jannetto Paul J , Mara Kristin C , Yetmar Zachary A , Rivera Christina G 
Published: August 2023

Abstract
Posaconazole therapeutic drug monitoring (TDM) is widely utilized to assess therapeutic efficacy and safety; however, clinical effects of very high serum concentrations are unknown. A retrospective review of 90 patients receiving posaconazole for treatment or prophylaxis of invasive fungal infections with serum concentrations ≥3000 ng/mL from 1/1/2019 to 4/30/2021 evaluated the incidence and type of adverse drug reactions (ADRs). Symptomatic ADRs were very common in patients with posaconazole concentrations of ≥5000 ng/mL and 3000–4999 ng/mL (80% vs. 58.8%; P = 0.31). Posaconazole TDM should be performed for both treatment and prophylaxis indications and dose decrease for serum concentrations &gt;3000 ng/mL should be considered.
Chemical abundance analysis of symbiotic giants. Metallicity and CNO abundance patterns in 14 northern S-type systems
Authors: Gałan Cezary , Mikołajewska Joanna , Hinkle Kenneth H , Joyce Richard R 
Published: August 2023

ABSTRACT
In previous works, we computed abundances for the red giant in nearly four dozen S-type symbiotic systems (SySt). The abundances provide information about metallicity, evolutionary status, and possible memberships in Galactic stellar populations. Here, we extend our studies with a northern hemisphere sample of SySt. This northern sample is dominated by Galactic disc/halo objects, whereas our previous southern sample is heavily biased toward the bulge population. Spectrum synthesis of high-resolution (R ∼ 50 000), near-IR spectra using standard LTE analysis and atmospheric models have been used to measure abundances of CNO and elements around the iron peak (Fe, Ti, Ni, and Sc) in the atmospheres of the red giant component. The SySt sample shows generally slightly sub-solar metallicity, as expected for an older disc population, with a median at [Fe/H]  ∼ −0.2 dex. Enhanced 14N, depleted 12C, and decreased 12C/13C, indicate that all these giants have experienced the first dredge-up. Comparison with theoretical predictions indicates that additional mixing processes had to occur to explain the observed C and N abundances. Relative O and Fe abundances agree with those represented by Galactic disc and bulge giant populations in the APOGEE data, with a few cases that can be attributed to membership in the extended thick-disc/halo. As an interesting byproduct of this study, we observed a blue-shifted additional component on the wings of absorption lines in the spectra of AG Peg, which could be connected with accretion on to the hot component.
Another look at the dayside spectra of WASP-43b and HD 209458b: Are there scattering clouds?
Authors: Taylor Jake , Parmentier Vivien 
Published: August 2023

ABSTRACT
The search for clouds on the dayside of hot Jupiters has been disadvantaged due to the limited number of high quality space-based observations of their dayside. To date, retrieval studies have found no evidence for grey clouds on the dayside, however none of these studies explored the impact of scattering clouds. In this study we reanalyse the dayside emission spectrum of the hot Jupiter WASP-43b considering the different Spitzer data in the literature. We find that, in 2 of the 4 data sets explored, retrieving with a model that contains a scattering cloud is favoured over a cloud free model by a confidence of 3.13 - 3.36 σ. The other 2 data sets finds no evidence for scattering clouds. We find that the retrieved H2O abundance is consistent regardless of the Spitzer data used and is consistent with literature values. We perform the same analysis for the hot Jupiter HD 209458b and find no evidence for dayside clouds, consistent with previous studies.
Magnetic fields and rotation periods of M dwarfs from SPIRou spectra
Authors: Donati J-F , Lehmann L T , Cristofari P I , Fouqué P , Moutou C , Charpentier P , Ould-Elhkim M , Carmona A , Delfosse X , Artigau E , Alencar S H P , Cadieux C , Arnold L , Petit P , Morin J , Forveille T , Cloutier R , Doyon R , Hébrard G ,   the Collaboration SLS
Published: August 2023

ABSTRACT
We present near-infrared spectropolarimetric observations of a sample of 43 weakly to moderately active M dwarfs, carried with SPIRou at the Canada–France–Hawaii Telescope in the framework of the SPIRou Legacy Survey from early 2019 to mid-2022. We use the 6700 circularly polarised spectra collected for this sample to investigate the longitudinal magnetic field and its temporal variations for all sample stars, from which we diagnose, through quasi-periodic Gaussian process regression, the periodic modulation and longer-term fluctuations of the longitudinal field. We detect the large-scale field for 40 of our 43 sample stars, and infer a reliable or tentative rotation period for 38 of them, using a Bayesian framework to diagnose the confidence level at which each rotation period is detected. We find rotation periods ranging from 14 to over 60 d for the early-M dwarfs, and from 70 to 200 d for most mid- and late-M dwarfs (potentially up to 430 d for one of them). We also find that the strength of the detected large-scale fields does not decrease with increasing period or Rossby number for the slowly rotating dwarfs of our sample as it does for higher-mass, more active stars, suggesting that these magnetic fields may be generated through a different dynamo regime than those of more rapidly rotating stars. We also show that the large-scale fields of most sample stars evolve on long time-scales, with some of them globally switching sign as stars progress on their putative magnetic cycles.
Tensions with the flat ΛCDM model from high-redshift cosmography
Authors: Bargiacchi G , Dainotti M G , Capozziello S 
Published: August 2023

ABSTRACT
The longstanding search for the cosmological model that best describes the Universe has been made more intriguing since the recent discovery of the Hubble constant, H0, tension observed between the value of H0 from the Cosmic Microwave Background and from type Ia supernovae (SNe Ia). Hence, the commonly trusted flat Λ cold dark matter (ΛCDM) model is under investigation. In this scenario, cosmography is a very powerful technique to investigate the evolution of the Universe without any cosmological assumption, thus revealing tensions between observational data and predictions from cosmological models in a completely model-independent way. We here employ a robust cosmographic technique based on an orthogonal logarithmic polynomial expansion of the luminosity distance to fit quasars (QSOs) alone and QSOs combined with Gamma-Ray Bursts (GRBs), SNe Ia, and Baryon Acoustic Oscillations. To apply QSOs and GRBs as probes we use, respectively, the Risaliti–Lusso relation between ultraviolet and X-ray luminosities and the ‘Dainotti GRB 3D relation’ among the rest-frame end time of the X-ray plateau emission, its corresponding luminosity, and the peak prompt luminosity. We also correct QSOs and GRBs for selection biases and redshift evolution and we employ both the traditional Gaussian likelihood and the newly discovered best-fitting likelihoods for each probe investigated. This comprehensive analysis reveals a strong tension ($\gt 4 \, \sigma$) between our data sets and the flat ΛCDM model proving the power of both the cosmographic approach and high-redshift sources, such as QSOs and GRBs, which can probe the Universe at early epochs.
JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom
Authors: Sreedasyam Avinash , Plott Christopher , Hossain Md Shakhawat , Lovell John T , Grimwood Jane , Jenkins Jerry W , Daum Christopher , Barry Kerrie , Carlson Joseph , Shu Shengqiang , Phillips Jeremy , Amirebrahimi Mojgan , Zane Matthew , Wang Mei , Goodstein David , Haas Fabian B , Hiss Manuel , Perroud Pierre-François , Jawdy Sara S , Yang Yongil , Hu Rongbin , Johnson Jenifer , Kropat Janette , Gallaher Sean D , Lipzen Anna , Shakirov Eugene V , Weng Xiaoyu , Torres-Jerez Ivone , Weers Brock , Conde Daniel , Pappas Marilia R , Liu Lifeng , Muchlinski Andrew , Jiang Hui , Shyu Christine , Huang Pu , Sebastian Jose , Laiben Carol , Medlin Alyssa , Carey Sankalpi , Carrell Alyssa A , Chen Jin-Gui , Perales Mariano , Swaminathan Kankshita , Allona Isabel , Grattapaglia Dario , Cooper Elizabeth A , Tholl Dorothea , Vogel John P , Weston David J , Yang Xiaohan , Brutnell Thomas P , Kellogg Elizabeth A , Baxter Ivan , Udvardi Michael , Tang Yuhong , Mockler Todd C , Juenger Thomas E , Mullet John , Rensing Stefan A , Tuskan Gerald A , Merchant Sabeeha S , Stacey Gary , Schmutz Jeremy 
Published: August 2023

Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability
Authors: Liu Wenpeng , Polaczek Piotr , Roubal Ivan , Meng Yuan , Choe Won-chae , Caron Marie-Christine , Sedgeman Carl A , Xi Yu , Liu Changwei , Wu Qiong , Zheng Li , Masson Jean-Yves , Shen Binghui , Campbell Judith L 
Published: August 2023

Abstract
FANCD2 protein, a key coordinator and effector of the interstrand crosslink repair pathway, is also required to prevent excessive nascent strand degradation at hydroxyurea-induced stalled forks. The RAD51 recombinase has also been implicated in regulation of resection at stalled replication forks. The mechanistic contributions of these proteins to fork protection are not well understood. Here, we used purified FANCD2 and RAD51 to study how each protein regulates DNA resection at stalled forks. We characterized three mechanisms of FANCD2-mediated fork protection: (1) The N-terminal domain of FANCD2 inhibits the essential DNA2 nuclease activity by directly binding to DNA2 accounting for over-resection in FANCD2 defective cells. (2) Independent of dimerization with FANCI, FANCD2 itself stabilizes RAD51 filaments to inhibit multiple nucleases, including DNA2, MRE11 and EXO1. (3) Unexpectedly, we uncovered a new FANCD2 function: by stabilizing RAD51 filaments, FANCD2 acts to stimulate the strand exchange activity of RAD51. Our work biochemically explains non-canonical mechanisms by which FANCD2 and RAD51 protect stalled forks. We propose a model in which the strand exchange activity of FANCD2 provides a simple molecular explanation for genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.
The induction of p53 correlates with defects in the production, but not the levels, of the small ribosomal subunit and stalled large ribosomal subunit biogenesis
Authors: Eastham Matthew John , Pelava Andria , Wells Graeme Raymond , Lee Justine Katherine , Lawrence Isabella Rachel , Stewart Joshua , Deichner Maria , Hertle Regina , Watkins Nicholas James , Schneider Claudia 
Published: August 2023

Abstract
Ribosome biogenesis is one of the biggest consumers of cellular energy. More than 20 genetic diseases (ribosomopathies) and multiple cancers arise from defects in the production of the 40S (SSU) and 60S (LSU) ribosomal subunits. Defects in the production of either the SSU or LSU result in p53 induction through the accumulation of the 5S RNP, an LSU assembly intermediate. While the mechanism is understood for the LSU, it is still unclear how SSU production defects induce p53 through the 5S RNP since the production of the two subunits is believed to be uncoupled. Here, we examined the response to SSU production defects to understand how this leads to the activation of p53 via the 5S RNP. We found that p53 activation occurs rapidly after SSU production is blocked, prior to changes in mature ribosomal RNA (rRNA) levels but correlated with early, middle and late SSU pre-rRNA processing defects. Furthermore, both nucleolar/nuclear LSU maturation, in particular late stages in 5.8S rRNA processing, and pre-LSU export were affected by SSU production defects. We have therefore uncovered a novel connection between the SSU and LSU production pathways in human cells, which explains how p53 is induced in response to SSU production defects.
Three-way contact analysis characterizes the higher order organization of the Tcra locus
Authors: Dai Ranran , Zhu Yongchang , Li Zhaoqiang , Qin Litao , Liu Nan , Liao Shixiu , Hao Bingtao 
Published: August 2023

Abstract
The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2–TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.
Single-worm long-read sequencing reveals genome diversity in free-living nematodes
Authors: Lee Yi-Chien , Ke Huei-Mien , Liu Yu-Ching , Lee Hsin-Han , Wang Min-Chen , Tseng Yung-Che , Kikuchi Taisei , Tsai Isheng Jason 
Published: August 2023

Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
LIPID TRANSFER PROTEIN4 regulates cotton ceramide content and activates fiber cell elongation
Authors: Duan Yujia , Shang Xiaoguang , He Qingfei , Zhu Lijie , Li Weixi , Song Xiaohui , Guo Wangzhen 
Published: August 2023

Abstract
Cell elongation is a fundamental process for plant growth and development. Studies have shown lipid metabolism plays important role in cell elongation; however, the related functional mechanisms remain largely unknown. Here, we report that cotton (Gossypium hirsutum) LIPID TRANSFER PROTEIN4 (GhLTP4) promotes fiber cell elongation via elevating ceramides (Cers) content and activating auxin-responsive pathways. GhLTP4 was preferentially expressed in elongating fibers. Over-expression and down-regulation of GhLTP4 led to longer and shorter fiber cells, respectively. Cers were greatly enriched in GhLTP4-overexpressing lines and decreased dramatically in GhLTP4 down-regulating lines. Moreover, auxin content and transcript levels of indole-3-acetic acid (IAA)-responsive genes were significantly increased in GhLTP4-overexpressing cotton fibers. Exogenous application of Cers promoted fiber elongation, while NPA (N-1-naphthalic acid, a polar auxin transport inhibitor) counteracted the promoting effect, suggesting that IAA functions downstream of Cers in regulating fiber elongation. Furthermore, we identified a basic helix-loop-helix transcription factor, GhbHLH105, that binds to the E-box element in the GhLTP4 promoter region and promotes the expression of GhLTP4. Suppression of GhbHLH105 in cotton reduced the transcripts level of GhLTP4, resulting in smaller cotton bolls and decreased fiber length. These results provide insights into the complex interactions between lipids and auxin-signaling pathways to promote plant cell elongation.
CHLORIDE CHANNEL-b mediates vacuolar nitrate efflux to improve low nitrogen adaptation in Arabidopsis
Authors: Shi Yujiao , Liu Dong , He Yiqi , Tang Jing , Chen Haifei , Gong Pan , Luo Jin-Song , Zhang Zhenhua 
Published: August 2023

Abstract
The vacuole is an important organelle for nitrate storage, and the reuse of vacuolar nitrate under nitrate starvation helps plants adapt to low-nitrate environments. CHLORIDE CHANNEL-b (CLC-b) in the vacuolar membrane is a nitrate transporter; however, its regulation and effects on nitrate efflux have not been established. Here, we evaluated CLC-b expression and its effects on physiological parameters under low nitrate conditions. CLC-b expression increased significantly in the roots of wild-type Arabidopsis (Arabidopsis thaliana) Col-0 under nitrate starvation. Under low nitrate, clcb mutants showed reductions in chlorophyll content and xylem sap nitrate concentration, shoot/root nitrate ratios, shoot/root total N ratios, and biomass. CLC-b-overexpression yielded opposite phenotypes and increased nitrogen use efficiency. CLC-b mutants showed elevated chlorate tolerance and an increased proportion of vacuolar nitrate relative to the total protoplast nitrate content as compared to the wild type. Yeast 1-hybrid, EMSA, and chromatin immunoprecipitation (ChIP) experiments showed that HRS1 HOMOLOG2 (HHO2), the expression of which is downregulated under low nitrate, binds directly to the promoter of CLC-b. clcb/hho2 double mutants and HHO2-overexpressing clcb plants had similar phenotypes under low nitrate to those of clcb single mutants. Thus, CLC-b mediates vacuolar nitrate efflux and is negatively regulated by HHO2, providing a theoretical basis for improving plant adaptability to low nitrate.
The impact of administrative disciplinary proceedings on military police officers in São Paulo
Authors: Cruz Fernanda Novaes , Rodrigues de Oliveira André , Castelo Branco Frederico , Cubas Viviane de Oliveira 
Published: August 2023

Abstract
Studies on police institutions have argued that the internal treatment given to agents contributes to define how these agents will treat the communities to which they provide services. Brazil’s main police force has a military structure and formal ties with the Armed Forces. These military characteristics include career structure, regulations, manuals, and disciplinary regiments either copied or adapted from the Army. In this work, we analyse data from a survey applied to 298 military police officers stationed in the city of São Paulo. Using Structural Equation Modelling, we analysed whether, among the police officers who answered a Disciplinary Administrative Proceeding, their evaluation of having been granted the right to speak, treated with respect during the process, and a fair outcome at the end impact their perceptions about their relationship with peers, superiors, and their views on organizational justice. Our findings reveal that respectful treatment during the proceeding was more important than a favourable outcome, and the perception of having been treated with respect during the Disciplinary Administrative Proceeding positively impacts their views about their superiors and organizational justice. These findings help us to reflect on the impacts of the militarization of Public Security on internal relationships as well as the importance of procedural justice within this context.