bluuebunny/crossref_metadata_2025_split huggingface dataset:
A32 PHAGE TREATMENT DELAYS ONSET OF CROHN’S-ASSOCIATED E. COLI DRIVEN COLITIS IN MICE COLONIZED WITH A DEFINED MICROBIOTA
Authors: Jackson K , Galipeau H , Hann A , Coombes B , Hosseinidoust Z , Verdu E 
Published: March 2023

Abstract

Background
Opportunistic pathogens have been postulated to drive dysregulated inflammation in inflammatory bowel disease (IBD). Indeed, adherent-invasive Escherichia coli (AIEC) isolated from IBD patients have pathobiont and pro-inflammatory characteristics. Current treatments for IBD suppress the immune response and do not target key microbial drivers, therefore novel strategies are required.

Purpose
Our aim was to determine whether bacteriophage therapy targeted against AIEC could reduce the severity of E. coli-driven colitis in gnotobiotic mice.

Method
Adult germ-free C57BL/6 mice were colonized with altered Schaedler-like flora (ASF) and E. coli NRG857c, a Crohn’s disease-associated bacterial isolate. Three weeks later, mice were treated with daily phage (selected by killing curves bioassays against E. coli NRG857c) or PBS for 2 weeks (n=6/group). Mice were then exposed to low-dose dextran sulfate sodium (2%; DSS) in drinking water for 5 days, followed by 2 days of water. PBS-treated mice (n=6) that received no DSS were used as additional negative controls. Mice were monitored daily for weight, stool consistency, and occult blood. At sacrifice, colon tissue was collected for histological analysis and fecal contents were cultured to determine bacterial load. In separate experiments, C57BL/6NTac-Il10em8Tac (IL-10-/-) mice were colonized with ASF-like microbiota and E. coli NRG857c. Three weeks later, mice (n=5) were treated with weekly phage or PBS (n=5) for 7 weeks. Mice were monitored weekly as described above.

Result(s)
Daily phage treatment reduced the severity of clinical symptoms induced by acute DSS administration (p &lt; 0.001 vs. DSS-PBS treated mice). At endpoint, phage treatment was associated with lower histological scores as compared with DSS-PBS controls (p &lt; 0.0001). A 1-log reduction in AIEC bacterial load was observed in phage treated mice as compared with DSS-PBS controls (p &lt; 0.001). In IL-10-/- mice, weekly phage treatment delayed the spontaneous onset of colitis (p &lt; 0.0001 vs. PBS-treated mice). At endpoint, mice treated with phage had lower colitis scores. Reduced weekly AIEC bacterial load was observed in phage-treated mice.

Conclusion(s)
Lytic phages, targeting a known AIEC pathobiont isolated from Crohn’s disease patients, ameliorate acute intestinal injury and delay onset of spontaneous colitis. Future work will investigate the mechanisms by which phage therapy prevents and treats colitis, to better inform clinical trial design.

Disclosure of Interest
None Declared
Is salt the solution? Interactions between trace-metal uptake and salinity in the freshwater crabPotamonautes warreniCalman, 1918 (Decapoda: Brachyura: Potamonautidae)
Authors: Glendinning Susan K , Vosloo Andre 
Published: March 2023

AbstractCrustaceans inhabiting freshwater are more vulnerable to increased loading with dissolved trace metals than those from more saline conditions for both physicochemical and physiological reasons. Potamonautes warreni (Calman, 1918) is a true freshwater crab inhabiting rivers in proximity to mining activities in South Africa. In order to assess whether the uptake of zinc (Zn2+) and cadmium (Cd2+) were associated with Na+- and Ca2+-uptake routes, individuals of P. warreni were acclimated to different Na+ or Ca2+ concentrations before measuring trace-metal uptake into the haemolymph and tissues in an intermediate freshwater. Cd2+ uptake into the haemolymph was elevated following acclimation to ‘Na+ replete’ conditions, when compared with ‘Na+ deplete’ conditions, indicating that a physiological response to the acclimation salinity had influenced Cd2+ uptake. Zn2+ uptake by the whole body was elevated in P. warreni individuals from the ‘Na+ replete’ group when compared with crabs acclimated to Na+ free water. A general change in permeability may have occurred and indeed, the apparent water permeability (water efflux) of P. warreni was increased in elevated Na+ and Ca2+ concentrations compared with that in softer water. A comparison of the osmoregulatory ability between P. warreni and the catadromous crab Eriocheir sinensisH. Milne Edwards, 1853 highlighted the greater permeability of the latter. Lower Zn2+ and Cd2+ uptake rates were measured in P. warreni in comparison to those measured in E. sinensis by other authors, indicating that the more well adapted a species is to life in freshwater, the less susceptible they will be to metal uptake. Future investigations to understand further the mechanisms influencing Zn2+ and Cd2+ uptake are required to understand the role that salinity can play in protecting a species from trace-metals released into the environment.
Laboratory evaluations of biodegradable boric acid hydrogel baits for the control of Argentine ant (Hymenoptera: Formicidae)
Authors: Le Benning , Park Hoeun , Campbell Kathleen , Rust Michael K , Lee Chow-Yang , Choe Dong-Hwan 
Published: March 2023

AbstractDue to their mutualistic relationship with plant pests, the Argentine ant is considered a major pest in subtropical fruit orchards and vineyards. Besides insecticide sprays, liquid baiting has been demonstrated as an effective method to suppress the Argentine ant populations. To improve the economic feasibility of liquid baiting, hydrogel materials have been recently tested as a carrier for liquid baits containing various insecticidal active ingredients. Here, we tested boric acid as a toxicant in the aqueous sugar bait delivered in a biodegradable calcium alginate hydrogel. Laboratory tests demonstrated that boric acid (1%) liquid bait incorporated in the calcium alginate hydrogel effectively killed Argentine ant workers. Potassium sorbate (0.25%) added to the liquid bait as a preservative did not impact the efficacy of boric acid even though it significantly reduced the degree of swelling of the hydrogel beads in the bait solution. Testing with 2-month-old bait suggested that long-term storage might impact bait efficacy even with potassium sorbate preservative.
A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)
Authors: Winter Sven , Meißner René , Greve Carola , Ben Hamadou Alexander , Horin Petr , Prost Stefan , Burger Pamela A 
Published: March 2023

Abstract
The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.
The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly
Authors: Pinto Brendan J , Gamble Tony , Smith Chase H , Keating Shannon E , Havird Justin C , Chiari Ylenia 
Published: March 2023

Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.
A direct numerical simulation method for solid-solid collision and coupling with fluid
Authors: Yang Ming , Liu Jubao , Ding Yuqi , Yue Qianbei , Zhang Qiang 
Published: March 2023

AbstractThe collision between solids in fluid is common in engineering, but the numerical simulation method is less studied. A direct numerical simulation method combining the sharp interface immersed boundary method and the finite element method based on penalty function was established for solid–solid collision and coupling with fluid. The lubrication model for cylinder structures with and without fluid flow was developed using the data regression method. The partitioned coupling algorithm was used to realize the coupling solution between the fluid and solid domains. Four numerical examples were presented to demonstrate the validity of the established method. The numerical simulation of the vortex-induced collisions between two side-by-side cylinders showed the capabilities of the proposed method.
‘Refugee Education Is Our Responsibility’: How Governance Shapes the Politics of Bridging the Humanitarian—Development Divide
Authors: Carvalho Shelby , Haybano Alebachew Kemisso 
Published: March 2023

Abstract
Reforms striving to bridge the humanitarian–development divide in refugee-hosting countries can alter the status quo related to refugee management and service provision. Such changes can result in obstacles to sustainable refugee inclusion when they challenge vested interests. In this paper, we propose a theoretical framework outlining the conditions under which government bureaucracies are likely to cooperate in donor-initiated refugee integration reforms as well as when and how they resist with a focus on the role of governance structures. We draw on archival data, observation, and key informant interviews to apply our framework to the case of Ethiopia as the government and international partners engage in reform efforts to include refugees in the national education system and to move from a humanitarian- to development-oriented model of financing. In this case, we find that reforms backed by international donors fundamentally challenged the vested interests of existing bureaucracies and that the resulting resistance substantially narrowed the original policy goals and will likely have implications for bridging the humanitarian–development divide going forward.
Association between priapism and HIV disease and treatment
Authors: Mulloy Evan , Li Shufeng , Belladelli Federico , Del Giudice Francesco , Glover Frank , Eisenberg Michael L 
Published: March 2023

AbstractBackgroundPriapism, a urologic emergency, has known associations with certain medical conditions. Many cases are idiopathic, suggesting an opportunity to identify novel risk factors.AimWe sought to identify medical conditions and pharmaceutical treatments that are associated with priapism using data-mining techniques.MethodsUsing deidentified data in a large insurance claims database, we identified all men (age ≥20 years) with a diagnosis of priapism from 2003 to 2020 and matched them to cohorts of men with other diseases of male genitalia: erectile dysfunction, Peyronie disease, and premature ejaculation. All medical diagnoses and prescriptions used prior to first disease diagnosis were examined. Predictors were selected by random forest, and conditional multivariate logistic regressions were applied to assess the risks of each predictor.OutcomesWe identified novel relationships of HIV and some HIV treatments with priapism and confirmed existing associations.ResultsAn overall 10 459 men with priapism were identified and matched 1:1 to the 3 control groups. After multivariable adjustment, men with priapism had high associations of hereditary anemias (odds ratio [OR], 3.99; 95% CI, 2.73-5.82), use of vasodilating agents (OR, 2.45; 95% CI, 2.01-2.98), use of HIV medications (OR, 1.95; 95% CI, 1.36-2.79), and use of antipsychotic medications (OR, 1.90; 95% CI, 1.52-2.38) as compared with erectile dysfunction controls. Similar patterns were noted when compared with premature ejaculation and Peyronie disease controls.Clinical ImplicationsHIV and its treatment are associated with priapism, which may affect patient counseling.Strengths and LimitationsTo our knowledge, this is the first study to identify risk factors for priapism utilizing machine learning. All men in our series were commercially insured, which limits the generalizability of our findings.ConclusionUsing data-mining techniques, we confirmed existing associations with priapism (eg, hemolytic anemias, antipsychotics) and identified novel relationships (eg, HIV disease and treatment).
Oil of Gladness and the Immortal High Priest in Hebrews
Authors: Duff Justin 
Published: March 2023

Abstract
The anointment of Jesus with the ‘oil of gladness’ in Hebrews 1 is a puzzling feature of Hebrews’ argument. The anointment—which is drawn from Psalm 45 and connected to Christ’s messianic enthronement—is often regarded as a royal investiture that transpired after the death of Christ. The relationship with royal messianism and heavenly enthronement, however, may overshadow another significant function of the oil of gladness: high priestly consecration and bodily immortalization. In this article, the function of Christ’s anointment is explored against uses of Psalm 45 in early Judaism and Greco-Roman and Second Temple traditions that depict heavenly oil as an agent of bodily transformation. These traditions suggest that Jesus’ anointment in Hebrews may signify a priestly consecration that transforms and immortalizes the human body for the heavenly realms. The anointment of Jesus in Hebrews may therefore be connected to the incarnate Son’s inheritance of ‘indestructible life’ (7:16) and clarifies when Jesus ‘became’ a royal-priestly Messiah ‘for the ages’.
A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activation of defence responses in Arabidopsis
Authors: Piovesana Maiara , Wood Ana K M , Smith Daniel P , Deery Michael J , Bayliss Richard , Carrera Esther , Wellner Nikolaus , Kosik Ondrej , Napier Johnathan A , Kurup Smita , Matthes Michaela C 
Published: March 2023

Abstract
Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. However, despite their prominence, their biological roles have remained largely elusive so far. In this study we report the characterization of an Arabidopsis mutant named crk10-A397T in which alanine 397 has been replaced by a threonine in the αC helix of the kinase domain of CRK10, known to be a crucial regulatory module in mammalian kinases. The crk10-A397T mutant is a dwarf that displays collapsed xylem vessels in the root and hypocotyl, whereas the vasculature of the inflorescence develops normally. In situ phosphorylation assays with His-tagged wild type and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of autophosphorylation, with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Transcriptomic analysis of wild type and crk10-A397T mutant hypocotyls revealed that biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant, and a root-infection assay with the vascular pathogen Fusarium oxysporum demonstrated that the mutant has enhanced resistance to this pathogen compared with wild type plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10, the first such mutant to have been identified for a CRK in Arabidopsis.
Evaluation of Vitamin D Status and the Analysis of Risk Factors of Vitamin D Deficiency in Twin Pregnancies
Authors: Le Juan , Lv Zhi-Hua , Peng Rui , Li Yan , Wang Shao-Ting 
Published: March 2023

Abstract

Objective
Optimization of maternal vitamin D (VD) status has beneficial effects on pregnancies, but little is known about it of twin pregnancies (TP). Our aim was to promote the current understanding of VD status and its associated factors in TP.

Methods
We performed liquid chromatography-tandem mass spectrometry to quantify 25-hydroxyvitamin D [25(OH)D] and used the enzyme-linked immunosorbent assay method to detect vitamin D binding protein (VDBP) in 218 singleton pregnancies (SP) and 236 TP.

Results
Levels of 25(OH)D and VDBP were higher in TP than SP. The 25(OH)D, free 25(OH)D, C-3 epimer of 25-hydroxyvitamin D [epi-25(OH)D], and VDBP all increased with gestational progress. Age, body &#x2028;mass index, and hemoglobin level were associated with VD deficiency (VDD). Analysis of covariance demonstrated that the 25(OH)D and VDBP of TP and SP still showed differences after adjusting for the above associated factors.

Conclusion
Differences in VD status were found in SP and TP, suggesting that the assessment of VD status in TP should be treated with caution. High VDD prevalence is observed among pregnant Chinese women, and it is recommended to promote evaluation for VDD.
Tissue-Like 3D Standard and Protocols for Microscope Quality Management
Authors: Abrams Benjamin , Pengo Thomas , Wee Tse-Luen , Deagle Rebecca C , Vuillemin Nelly , Callahan Linda M , Smith Megan A , Kubow Kristopher E , Girard Anne-Marie , Rappoport Joshua Z , Bayles Carol J , Cameron Lisa A , Cole Richard , Brown Claire M 
Published: March 2023

AbstractThis article outlines a global study conducted by the Association of Biomedical Resource Facilities (ABRF) Light Microscopy Research Group (LMRG). The results present a novel 3D tissue-like biologically relevant standard sample that is affordable and straightforward to prepare. Detailed sample preparation, instrument-specific image acquisition protocols and image analysis methods are presented and made available to the community. The standard consists of sub-resolution and large well characterized relative intensity fluorescence microspheres embedded in a 120 µm thick 3D gel with a refractive index of 1.365. The standard allows the evaluation of several properties as a function of depth. These include the following: 1) microscope resolution with automated analysis of the point-spread function (PSF), 2) automated signal-to-noise ratio analysis, 3) calibration and correction of fluorescence intensity loss, and 4) quantitative relative intensity. Results demonstrate expected refractive index mismatch dependent losses in intensity and resolution with depth, but the relative intensities of different objects at similar depths are maintained. This is a robust standard showing reproducible results across laboratories, microscope manufacturers and objective lens types (e.g., magnification, immersion medium). Thus, these tools will be valuable for the global community to benchmark fluorescence microscopes and will contribute to improved scientific rigor and reproducibility.
Hunting for C-rich long-period variable stars in the Milky Way’s bar-bulge using unsupervised classification ofGaiaBP/RP spectra
Authors: Sanders Jason L , Matsunaga Noriyuki 
Published: March 2023

ABSTRACTThe separation of oxygen- and carbon-rich asymptotic giant branch sources is crucial for their accurate use as local and cosmological distance and age/metallicity indicators. We investigate the use of unsupervised learning algorithms for classifying the chemistry of long-period variables from Gaia DR3’s BP/RP spectra. Even in the presence of significant interstellar dust, the spectra separate into two groups attributable to O-rich and C-rich sources. Given these classifications, we utilize a supervised approach to separate O-rich and C-rich sources without blue and red photometers (BP/RP) spectra but instead given broadband optical and infrared photometry finding a purity of our C-rich classifications of around 95 per cent. We test and validate the classifications against other advocated colour–colour separations based on photometry. Furthermore, we demonstrate the potential of BP/RP spectra for finding S-type stars or those possibly symbiotic sources with strong emission lines. Although our classification suggests the Galactic bar-bulge is host to very few C-rich long-period variable stars, we do find a small fraction of C-rich stars with periods $\gt 250\, \mathrm{day}$ that are spatially and kinematically consistent with bar-bulge membership. We argue the combination of the observed number, the spatial alignment, the kinematics, and the period distribution disfavour young metal-poor star formation scenarios either in situ or in an accreted host, and instead, these stars are highly likely to be the result of binary evolution and the evolved versions of blue straggler stars already observed in the bar-bulge.
Using the star-forming main sequence to explore quiescent galaxies across cosmic time
Authors: Houston Tyler , Croton Darren J , Sinha Manodeep 
Published: March 2023

ABSTRACT
In this letter, we explore the quiescent lives of central galaxies using the Semi-Analytical Galaxy Evolution galaxy model and Uchuu dark matter simulation. We ask three questions: (1) How much of a galaxy’s life is spent in quiescence? (2) How often do galaxies transit off the main sequence? (3) What is the typical duration of a quiescent phase? We find that the low- and high-mass galaxies spend the highest fraction of their lives in quiescence: 45 ± 19 per cent for log10(Mstar) &lt; 9.0 (3.68 ± 1.80 Gyr) and 26 ± 25 per cent for log10(Mstar) &gt; 11.5 (3.46 ± 3.30 Gyr), falling to 7 ± 13 per cent for galaxies in-between (0.82 ± 1.57 Gyr). Low-mass galaxies move in and out of quiescence frequently, 2.8 ± 1.3 times on average, though only for short periods, 1.49 ± 1.04 Gyr. This can be traced to the influence of supernova feedback on their quite stochastic evolution. Galaxies of higher mass have fewer quiescent periods, ∼0.7 ± 0.9, and their length increases with mass, peaking at 1.97 ± 2.27 Gyr. However, our high-mass population comprises star-forming and quiescent galaxies with diverging evolutionary paths, so the actual time may be even longer. These high-mass trends are driven by radio-mode feedback from supermassive black holes, which, once active, tend to remain active for extended periods.