bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones
Authors: Zhao Rui , Zhang Irene H , Jayakumar Amal , Ward Bess B , Babbin Andrew R 
Published: April 2024

Abstract
Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the Scalindua genus, which represent most, if not all, of the anammox bacteria in the global ODZs. Metagenomic read-recruiting and comparison with historical data show that they are ubiquitously present in all three major ODZs. Beyond the core anammox metabolism, both organisms contain cyanase, and the more dominant one encodes a urease, indicating most ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. Molecular clock analysis suggests that the evolutionary radiation of these bacteria into ODZs occurred no earlier than 310 million years ago, ~1 billion years after the emergence of the earliest modern-type ODZs. Different strains of the ODZ Scalindua species are also found in benthic sediments, and the first ODZ Scalindua is likely derived from the benthos. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encodes genes for urea utilization but has lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to thrive in the global ODZ waters. Our findings expand the known metabolisms and evolutionary history of the bacteria controlling the global nitrogen budget.
Integrated multi-omics approach reveals novel associations in the rapeseed diet–microbiota–host axis in pigs
Authors: Onarman Umu Özgün C , Mydland Liv Torunn , Chen Chi , de Nanclares Marta Pérez , Shurson Gerald C , Urriola Pedro E , Sørum Henning , Øverland Margareth 
Published: April 2024

Abstract
Diet-mediated host–microbiota interplay is a key factor in optimizing the gut function and overall health of the host. Gaining insight into the biological mechanisms behind this relationship is fundamental to finding sustainable, environment-friendly feed solutions in livestock production systems. Here, we apply a multi-omics integration approach to elucidate sustainable diet-associated host–gut microbiota interactions in pigs and we demonstrate novel and biologically relevant host–microbe associations in the gut, driven by a rapeseed meal-based feed (RSF). Interestingly, RSF-diet promoted the abundance of segmented filamentous bacteria Candidatus Arthromitus that was associated with the maintenance of mucosal immunity in the ileum of pigs. In the colon, RSF diet affected host mRNA splicing functions, which may result in different host gene products, through host–microbiota associations, particularly with the Faecalibacterium population, and through the interaction of dietary components such as sinapic acid with the host cells. Moreover, telomere maintenance and organization functions that may determine the overall health of the host were upregulated and notably associated with Subdoligranulum population in the colon of RSF diet-fed pigs. This integrative multi-omics approach provides more insight into the diet–microbiota–host axis, and a better understanding of mechanisms and opportunities to find new strategies for modulating host health and potentially improving caloric and nutritional efficiency in animal production.
Integrated Multiplatform Analysis and Separation of Thirteen Flavonoids and Anthraquinones in Seven Medicinal Cassia Species
Authors: Girme Aboli , Saste Ganesh , Kureshi Azazahemad A , Jagtap Shubham , Kamble Siddhi , Wadye Saurabh D , Hingorani Lal 
Published: April 2024

Abstract

Background
Cassia (Family: Fabaceae) species are a large group of flowering plants rich in bioactive anthraquinone and flavonoids used in botanical supplements and nutraceuticals.

Objective
A simple and reliable high-performance liquid chromatography-photodiode array (HPLC-PDA) method was developed and validated for separating and quantifying 13 anthraquinone and flavonoids. These compounds were further confirmed using an LC-based electrospray ionization mass spectrometry (ESI-MS/MS) method in the leaves and flowers of selected Cassia species. A simple and rapid HPTLC method was developed for chemical fingerprint analysis of all Cassia species.

Method
All 13 compounds were chromatographically separated on a Zorbax TC18 (4.6 × 250, 5 μm particle size) analytical column, and 0.1% formic acid and acetonitrile as elution solvents at a flow rate of 0.8 mL/min with detection at 259 nm. For HPTLC fingerprinting, the mobile phase compositions of toluene, ethyl acetate, and formic acid (5.5:4.2:0.6, v/v/v) were optimized to separate and identify all compounds using silica gel 60F254 aluminum plates.

Results
The validation data for the developed HPLC-PDA method for 13 compounds showed good linearity (r2 &gt;0.99) with a sensitive LOD (0.082–1.969 μg/mL), LOQ (0.250–5.967 μg/mL), and excellent recoveries (85.22–100.32%). The quantification results were found to be precise and accurate (&lt;5.0% and relative error), -0.77–0.44 with ESI-MS/MS confirmation in the Cassia samples. The novel HPTLC method was excellent separation for 13 compounds, with Rf values ranging between 0.12 and 0.61.

Conclusions
The developed HPLC-PDA method was simple and precise and could separate and quantify anthraquinones and flavonoids along with confirmation, using a novel LC-based ESI-MS/MS. The HPTLC method was found to be simple and precise, with excellent separation capabilities for these compounds.

Highlights
This novel multiplatform approach successfully identified and quantified 13 compounds simultaneously using an integration of data strategy in seven medicinally important Cassia species’ leaves and flowers.
Development of an Analytical Quality by Design RP-HPLC Method and Its Validation for Estimation of Gefitinib From Bulk, Tablet Dosage Form, and Complex Nanoformulation
Authors: More Mahesh P , Pardeshi Sagar R , Tade Rahul , Meshram Pawan D , Naik Jitendra B , Deshmukh Prashant K 
Published: April 2024

Abstract

Background
Estimation of the drug and development of the method is a critical aspect of formulation development and a critical factor for analytical scientists. Gefitinib is a poorly soluble anticancer drug.

Objective
The present research focuses on the topic of the development of innovative quality by design methods for the estimation of gefitinib (GF) from bulk, pharmaceutical tablet formulation, and complex nanoformulations.

Methods
To simplify the estimation of poorly soluble drugs such as GF, response surface methodology (RSM) was adopted with effective leverages to obtain precise computation design space using the Box-Behnken design (BBD) model. The major three mixed-effect independent factors (percentage of buffer, pH of buffer, and flow rate) were screened with three prominent dependent responses (viz., theoretical plate, retention time, and tailing factor) selected for optimal analysis. Furthermore, co-processed steps were employed for the estimation of the analyte from the complex formulation.

Results
The RP-HPLC method uses the quality by design (QbD) approach can effectively estimate the analyte concentration of less than 4.5 min. The developed method was economically robust and sensitive and shows a relative standard deviation (RSD, %) of less than 2% for all the selected validation parameters. The estimated design space suggests the highest desirability (R2—0.998) at 60% of buffer in the mobile phase, pH 4.25, and flow rate of 0.7 mL/min.

Conclusions
The QbD approach was used to design and develop the method by understanding the interaction between dependent and independent variables to get the optimum values. The developed method was validated successfully and can be useful for formulation scientists to estimate drug concentration and drug release profiles from complex nanoformulations.

Highlights
The analytical approach was designed and quantified using a quality-by-design approach to make the RP-HPLC method more robust and efficient for the estimation of analytes from complex nanoformulations. The method is also useful to eliminate the interfering molecule during estimation by employing co-processing steps. The developed method saves time and cost of solvent and employs QbD as a requirement of recent regulatory concern.
A two-year review of cocaine findings in impaired driving investigations in Ontario, Canada
Authors: Currie Zachary , Lamparter Christina , Gosselin Sophie , Watterson James 
Published: April 2024

Abstract
Drug-impaired driving is an increasing public safety concern across Canada, particularly due to the demonstrated increase in use of recreational drugs such as cocaine. Cocaine is a central nervous system stimulant drug; however, it can impair an individual’s driving ability in both the stimulant and crash phases. Despite the scientific consensus regarding cocaine’s potential for driving impairment, there is relatively little information available regarding blood concentrations and associated observations of impairment in suspected impaired drivers. Retrospective data analysis was performed to evaluate suspected impaired driving cases in which cocaine and/or benzoylecgonine were detected alone, or in combination with other drugs, in blood and urine samples submitted to the Toxicology Section of the Centre of Forensic Sciences with incident dates between 2021 and 2022. Cocaine and/or benzoylecgonine were detected in 46% (blood) and 66% (urine) of the total impaired driving samples submitted. In 41 cases where cocaine and/or benzoylecgonine were the only drug finding in blood, concentrations of cocaine and benzoylecgonine ranged from 0.0073 to 0.26 mg/L (mean 0.096 mg/L) and 0.13 to 5.3 mg/L (mean 2.1 mg/L), respectively. Driving observations reported by the arresting officer in cases where cocaine and/or benzoylecgonine were the only drug finding in blood and urine included the driver being involved in a collision, the vehicle leaving the roadway, erratic driving and the driver being asleep at the wheel; observations of drug impairment reported by the drug recognition expert at the time of driver evaluation included abnormal speech patterns, poor balance/incoordination, abnormal body movements and the individual falling asleep. The results provide concentrations of cocaine and benzoylecgonine observed in suspected impaired drivers, insight into observations that may be associated with prior cocaine use and additional information to inform on the effects of cocaine on driving.
Sorting nexin 27–dependent regulation of Lck and CD4 tunes the initial stages of T-cell activation
Authors: Rodriguez-Rodriguez Cristina , González-Mancha Natalia , Ochoa-Echeverría Ane , Mérida Isabel 
Published: April 2024

Abstract
Sorting nexin 27 is a unique member of the sorting nexin family of proteins that mediates the endosome-to-plasma membrane trafficking of cargos bearing a PSD95/Dlg1/ZO-1 (PDZ)–binding motif. In brain, sorting nexin 27 regulates synaptic plasticity, and its dysregulation contributes to cognitive impairment and neuronal degeneration. In T lymphocytes, sorting nexin 27 partners with diacylglycerol kinase ζ to facilitate polarized traffic and signaling at the immune synapse. By silencing sorting nexin 27 expression in a human T-cell line, we demonstrate that sorting nexin 27 is a key regulator of the early T-cell tyrosine-based signaling cascade. Sorting nexin 27 transcriptionally controls CD4 abundance in resting conditions and that of its associated molecule, Lck. This guarantees the adequate recruitment of Lck at the immune synapse, which is indispensable for subsequent activation of tyrosine phosphorylation-regulated events. In contrast, reduced sorting nexin 27 expression enhances NF-κB–dependent induction of CXCR4 and triggers production of lytic enzymes and proinflammatory cytokines. These results provide mechanistic explanation to previously described sorting nexin 27 function in the control of immune synapse organization and indicate that impaired sorting nexin 27 expression contributes to CD4 T-cell dysfunction.
Physiological and molecular mechanisms associated with potato tuber dormancy
Authors: Dogramaci Munevver , Dobry Emily P , Fortini Evandro A , Sarkar Dipayan , Eshel Dani , Campbell Michael A 
Published: April 2024

Abstract
Tuber dormancy is an important physiological trait that impacts post-harvest storage and end-use qualities of potatoes. Overall, dormancy regulation of potato tubers is a complex process driven by genetic as well as environmental factors. Elucidation of the molecular and physiological mechanisms that influence different dormancy stages of tubers has wider potato breeding and industry-relevant implications. Therefore, the primary objective of this review is to present current knowledge of the diversity in tuber dormancy traits among wild relatives of potatoes and discuss how genetic and epigenetic factors contribute to tuber dormancy. Advancements in understanding of key physiological mechanisms involved in tuber dormancy regulation, such as apical dominance, phytohormone metabolism, and oxidative stress responses, are also discussed. This review highlights the impacts of common sprout suppressors on the molecular and physiological mechanisms associated with tuber dormancy and other storage qualities. Collectively, the literature suggests that significant changes in expression of genes associated with the cell cycle, phytohormone metabolism, and oxidative stress response influence initiation, maintenance, and termination of dormancy in potato tubers. Commercial sprout suppressors mainly alter the expression of genes associated with the cell cycle and stress responses and suppress sprout growth rather than prolonging tuber dormancy.
Searching for planet-driven dust spirals in ALMA visibilities
Authors: Stevenson Edward T , Ribas Álvaro , Speedie Jessica , Booth Richard A , Clarke Cathie J 
Published: April 2024

ABSTRACT
Atacama Large Millimetre/submillimetre Array (ALMA) observations of the thermal emission from protoplanetary disc dust have revealed a wealth of substructures that could evidence embedded planets, but planet-driven spirals, one of the more compelling lines of evidence, remain relatively rare. Existing works have focused on detecting these spirals using methods that operate in image space. Here, we explore the planet detection capabilities of fitting planet-driven spirals to disc observations directly in visibility space. We test our method on synthetic ALMA observations of planet-containing model discs for a range of disc/observational parameters, finding it significantly outperforms image residuals in identifying spirals in these observations and is able to identify spirals in regions of the parameter space in which no gaps are detected. These tests suggest that a visibility-space fitting approach warrants further investigation and may be able to find planet-driven spirals in observations that have not yet been found with existing approaches. We also test our method on six discs in the Taurus molecular cloud observed with ALMA at 1.33 mm, but find no evidence for planet-driven spirals. We find that the minimum planet masses necessary to drive detectable spirals range from ≈0.03 to $0.5 \, M_{\text{Jup}}$ over orbital radii of 10–100 au, with planet masses below these thresholds potentially hiding in such disc observations. Conversely, we suggest that planets ≳0.5–1 MJup can likely be ruled out over orbital radii of ≈20–$60 \, \text{au}$ on the grounds that we would have detected them if they were present.
WISDOM Project – XIX. Figures of merit for supermassive black hole mass measurements using molecular gas and/or megamaser kinematics
Authors: Zhang Hengyue , Bureau Martin , Smith Mark D , Cappellari Michele , Davis Timothy A , Dominiak Pandora , Elford Jacob S , Liang Fu-Heng , Ruffa Ilaria , Williams Thomas G 
Published: April 2024

ABSTRACT
The mass (MBH) of a supermassive black hole (SMBH) can be measured using spatially resolved kinematics of the region where the SMBH dominates gravitationally. The most reliable measurements are those that resolve the smallest physical scales around the SMBHs. We consider here three metrics to compare the physical scales probed by kinematic tracers dominated by rotation: the radius of the innermost detected kinematic tracer Rmin normalized by the SMBH’s Schwarzschild radius (RSchw ≡ 2GMBH/c2, where G is the gravitational constant and c the speed of light), sphere-of-influence (SOI) radius ($R_\mathrm{SOI}\equiv GM_\mathrm{BH}/\sigma _\mathrm{e}^2$, where σe is the stellar velocity dispersion within the galaxy’s effective radius), and equality radius [the radius Req at which the SMBH mass equals the enclosed stellar mass, MBH = M*(Req), where M*(R) is the stellar mass enclosed within the radius R]. All metrics lead to analogous simple relations between Rmin and the highest circular velocity probed Vc. Adopting these metrics to compare the SMBH mass measurements using molecular gas kinematics to those using megamaser kinematics, we demonstrate that the best molecular gas measurements resolve material that is physically closer to the SMBHs in terms of RSchw but is slightly farther in terms of RSOI and Req. However, molecular gas observations of nearby galaxies using the most extended configurations of the Atacama Large Millimeter/submillimeter Array can resolve the SOI comparably well and thus enable SMBH mass measurements as precise as the best megamaser measurements.
Electron-capture supernovae in NS + He star systems and the double neutron star systems
Authors: Guo Yun-Lang , Wang Bo , Chen Wen-Cong , Li Xiang-Dong , Ge Hong-Wei , Jiang Long , Han Zhan-Wen 
Published: April 2024

ABSTRACT
Electron-capture-supernovae (EC-SNe) provide an alternative channel for producing neutron stars (NSs). They play an important role in the formation of double NS (DNS) systems and the chemical evolution of galaxies, and contribute to the NS mass distribution in observations. It is generally believed that EC-SNe originate from e-captures on $\rm ^{24}Mg$ and $\rm ^{20}Ne$ in the massive degenerate oxygen–neon (ONe) cores with masses close to the Chandrasekhar limit (MCh). However, the origin of EC-SNe is still uncertain. In this paper, we systematically studied the EC-SNe in NS + He star systems by considering the explosive oxygen burning that may occur in the near-MCh ONe core. We provided the initial parameter spaces for producing EC-SNe in the initial orbital period − initial He star mass (log$P_{\rm orb}^{\rm i}-M_{\rm He}^{\rm i}$) diagram, and found that both $M_{\rm He}^{\rm i}$ and minimum $P_{\rm orb}^{\rm i}$ for EC-SNe increase with metallicity. Then, by considering NS kicks added to the newborn NS, we investigated the properties of the formed DNS systems after the He star companions collapse into NSs, such as the orbital periods, eccentricities, and spin periods of recycle pulsars (Pspin), etc. The results show that most of the observed DNS systems can be produced by NS kicks of $\lesssim$50 km s−1. In addition, we found that NSs could accrete more material if the residual H envelope on the He star companions is considered, which can form the mildly recycled pulsars (Pspin ∼ 20 ms) in DNS systems.
A comprehensive analysis of pneumococcal two-component system regulatory networks
Authors: Pettersen Jens Sivkær , Nielsen Flemming Damgaard , Andreassen Patrick Rosendahl , Møller-Jensen Jakob , Jørgensen Mikkel Girke 
Published: April 2024

Abstract
Two-component systems are key signal-transduction systems that enable bacteria to respond to a wide variety of environmental stimuli. The human pathogen, Streptococcus pneumoniae (pneumococcus) encodes 13 two-component systems and a single orphan response regulator, most of which are significant for pneumococcal pathogenicity. Mapping the regulatory networks governed by these systems is key to understand pneumococcal host adaptation. Here we employ a novel bioinformatic approach to predict the regulons of each two-component system based on publicly available whole-genome sequencing data. By employing pangenome-wide association studies (panGWAS) to predict genotype-genotype associations for each two-component system, we predicted regulon genes of 11 of the pneumococcal two-component systems. Through validation via next-generation RNA-sequencing on response regulator overexpression mutants, several top candidate genes predicted by the panGWAS analysis were confirmed as regulon genes. The present study presents novel details on multiple pneumococcal two-component systems, including an expansion of regulons, identification of candidate response regulator binding motifs, and identification of candidate response regulator-regulated small non-coding RNAs. We also demonstrate a use for panGWAS as a complementary tool in target gene identification via identification of genotype-to-genotype links. Expanding our knowledge on two-component systems in pathogens is crucial to understanding how these bacteria sense and respond to their host environment, which could prove useful in future drug development.
Association between pro-inflammatory diet and abdominal pain: cross-sectional and case-control study from UK biobank and NHANES 2017–2020
Authors: Li Laifu , Zhuang Yan , Ran Yan , Chen Jiamiao , Wang Lianli , Lu Shiwei , Sun Yating , Ye Fangchen , Dai Fei 
Published: April 2024

Abstract

Background
There is a close association between diet and abdominal pain; however, relationship between inflammatory diet and characteristics of abdominal pain has not been characterized yet.

Methods
This study analyzed baseline data from the UK Biobank, 3-item DHQ-Abdominal Pain Questionnaire (DHQ-3Q), which including abdominal pain in the past 3 months, severity of abdominal pain, and frequency of abdominal pain, and data from the National Health and Nutrition Examination Survey (NHANES) from 2017 to 2020. Energy-adjusted Dietary Inflammatory Index (E-DII), constructed based on 26 or 27 nutrients, was analyzed using continuous or categorical methods. Logistic regression and restricted cubic spline analyses examined the association between E-DII and abdominal pain.

Results
In UK Biobank, compared to participants in the lowest quintile of E-DII, the adjusted ORs for the highest quintile were 1.12 (95% CI 1.02–1.24; P = .022), 1.05 (95% CI 1.00–1.09; P = .030), 1.26 (95% CI 1.17–1.36; P &lt; .001), and 1.10 (95% CI 1.00–1.20; P = .044) for chronic abdominal pain, abdominal pain in the past three months, severity of abdominal pain, and frequency of abdominal pain, respectively. In NHANES, compared to participants in the lowest quintile of E-DII, the adjusted ORs for the highest quintile were 1.46 (95% CI 1.20–1.77;P &lt; .001), 1.75 (95% CI 1.20–2.60; P = .005), 1.45 (95% CI 1.14–1.87; P = .003), and 1.18 (95% CI 0.82–1.72; P = .380) for abdominal pain in the past year, upper left abdominal pain, upper middle abdominal pain, and upper right abdominal pain. Additionally, there was a nonlinear correlation between E-DII score and DHQ-3Q (P nonlinear &lt;.001).

Conclusion
Following a pro-inflammatory diet is linked to a higher likelihood of experiencing abdominal pain, as well as increased severity and frequency of such pain. Therefore, further longitudinal studies are necessary to investigate this relationship.