bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gallic acid inhibits Staphylococcus aureus RecA protein functions: Role in countering antibiotic resistance in bacteria
Authors: Kiran Kajal , Patil K Neelakanteshwar 
Published: October 2023

Abstract

Aim
Recombinase RecA and its homologs play a key role in homologous recombination DNA repair and revive stalled replication fork DNA synthesis. RecA plays an essential role in the evolution of antibiotic-resistant strains via stress-induced DNA repair mechanisms during the SOS response. Accordingly, RecA has become an attractive target to slow down antibiotic resistance rates and prevent mutations in pathogenic bacterial species.

Methods and results
We employed RecA conserved activities: DNA binding, displacement loop formation, strand exchange, ATP hydrolysis, and LexA cleavage, to elucidate the inhibitory role of gallic acid on Staphylococcus aureus RecA functions. Gallic acid inhibition of the SOS response by western blot analysis and its antibacterial activity were measured. The gallic acid inhibited all the canonical activities of S. aureus RecA protein.

Conclusion
The natural phenolic compound gallic acid interferes with RecA protein DNA complex formation and inhibits activities such as displacementloop formation, strand exchange reaction, ATP hydrolysis, and coprotease activity of S. aureus. Additionally, gallic acid can obstruct ciprofloxacin-induced RecA expression and eventually confer the inhibitory role of gallic acid in the SOS survival mechanism in S. aureus.
Using machine learning to develop smart reflex testing protocols
Authors: McDermott Matthew , Dighe Anand , Szolovits Peter , Luo Yuan , Baron Jason 
Published: October 2023

Abstract

Objective
Reflex testing protocols allow clinical laboratories to perform second line diagnostic tests on existing specimens based on the results of initially ordered tests. Reflex testing can support optimal clinical laboratory test ordering and diagnosis. In current clinical practice, reflex testing typically relies on simple “if-then” rules; however, this limits the opportunities for reflex testing since most test ordering decisions involve more complexity than traditional rule-based approaches would allow. Here, using the analyte ferritin as an example, we propose an alternative machine learning-based approach to “smart” reflex testing.

Methods
Using deidentified patient data, we developed a machine learning model to predict whether a patient getting CBC testing will also have ferritin testing ordered. We evaluate applications of this model to reflex testing by assessing its performance in comparison to possible rule-based approaches.

Results
Our underlying machine learning models performed moderately well in predicting ferritin test ordering (AUC=0.731 in reference to actual ordering) and demonstrated promising potential to underlie key clinical applications. In contrast, none of the many traditionally framed, rule-based, hypothetical reflex protocols we evaluated offered sufficient agreement with actual ordering to be clinically feasible. Using chart review, we further demonstrated that the strategic deployment of our model could avoid important ferritin test ordering errors.

Conclusions
Machine learning may provide a foundation for new types of reflex testing with enhanced benefits for clinical diagnosis.
Feeding level during the last week of gestation can influence performance of sows and their litters in the subsequent lactation
Authors: Bruun Thomas S , Eskildsen Maria , Hojgaard Camilla K , Nørskov Natalja P , Knudsen Knud Erik Bach , Theil Peter K , Feyera Takele 
Published: October 2023

Abstract
This study investigated the impact of feeding level during the last week of gestation on performance of sows and their litters in the subsequent lactation. A total of 48 sows were assigned to one of six feeding levels (1.8, 2.4, 3.1, 3.7, 4.3, or 5.0 kg/d) from day 108 of gestation until farrowing. Post-farrowing, all sows were fed similarly during lactation with a gradual increase in feed allowance in accordance with Danish recommendation until it reached the maximum allowance of 9 kg/d on day 17 of lactation. Plasma samples were collected from the sows during farrowing and lactation, and sow’s body weight and backfat thickness, and milk samples were taken during lactation. Litters were standardized to have 13 to 15 piglets each and weighed once weekly during lactation. Plasma concentrations of urea, acetate, and butyrate in sows linearly increased (P &lt; 0.001), while non-esterified fatty acids linearly decreased (P &lt; 0.001) during farrowing with increasing feeding level. Moreover, concentrations of triglycerides (P &lt; 0.001), acetate (P = 0.007), and succinate (P &lt; 0.001) were greater in plasma collected at the onset of farrowing compared to the end of farrowing. Conversely, concentrations of glucose, urea, and butyrate (P &lt; 0.001) were lower in plasma collected at the onset of farrowing than at the end. Sows fed 2.4 and 3.1 kg/d exhibited greater triglyceride concentrations than those fed 3.7 (P = 0.03) and 5.0 (P = 0.02) kg/d. Sows fed 1.8 kg/d during the last week of gestation had lower milk yield in wk 1 (P &lt; 0.001) and wk 2 (P = 0.001) of lactation compared to the other groups. Additionally, litter weight gain (P = 0.04) and litter weaning weight (P = 0.007) were lower in sows fed 1.8 kg/d compared to the other groups. The greatest milk yield, litter growth, and litter size were observed in sows fed 3.7 kg/d during the last week of gestation, whereas the estimate generated by the regression model revealed that sows should have been provided with 4.0 to 4.1 kg/d as an adequate feeding level to maximize these performances in the subsequent lactation. Interestingly, feeding level during the last week of gestation did not influence feed intake during lactation. In conclusion, this study highlights the significance of adequate feed supply (4.0 to 4.1 kg/d) during the last week of gestation in order to maximize performance of sows in the subsequent lactation.
New distribution ofReticulitermes speratus speratus(Blattodea: Rhinotermitidae) in Korea
Authors: Lee Hyo bin , Seo Min Seok , Lee Sang-Bin , Lee Wonhoon 
Published: October 2023

AbstractReticulitermes speratus (Kolbe) is economically important pest in East Asia including Korea, Japan, and China where they infest wooden structures in urban areas. Previously, it has been reported that R. speratus consists of 5 subspecies, R. speratus kyushuensis Morimoto, R. speratus speratus Kolbe, R. speratus leptolabralis Morimoto, R. speratus okinawanus Morimoto, R. speratus yaeyamanus Morimoto, while only R. speratus kyushuensis was recorded in Korea in the past. However, it remains elusive if different subspecies of R. speratus other than R. speratus kyushuensis are present in Korea. In this study, we report the first record of R. speratus speratus from Korea, which was verified using soldier morphology and molecular characteristics obtained from a mitochondrial gene. R. speratus speratus Kolbe, 1885 (Blattodea: Rhinotermitidae) are found in several provinces, mainly southern regions in Korea, whereas R. speratus kyushuensis are distributed throughout the country. Our morphological comparison showed that R. speratus speratus can be distinguishable from R. speratus kyushuensis by the ratio of the posterior postmentum width to length. In the molecular comparison, R. speratus speratus revealed genetic differences of 3.06% (range 2.60–4.10%) from R. speratus kyushuensis using cytochrome oxidase subunit II gene sequences.
Comparison of 3 DNA extraction methods for extracting DNA from an adult Culex quinquefasciatus (Diptera: Culicidae)
Authors: Firmansyah Nurhadi Eko , Thongseesuksai Thaksaporn , Boonmars Thidarut , Sungkar Saleha , Laummaunwai Porntip 
Published: October 2023

Abstract
The aim of this study was to compare 3 DNA extraction methods: the PureLink Genomic DNA kit, DNAzol Direct reagent, and a microwave-based method, for extracting DNA from an adult Culex quinquefasciatus by focusing on the quantity and purity of DNA, cost, and time required. Ten mosquitoes were individually used for DNA extraction by each method. Based on the results obtained, DNA was extracted from each method using specific primers, resulting in a polymerase chain reaction (PCR) product with a length of 274 bp. The DNA quantity extracted using the DNAzol Direct (179.08 ± 3.77 ng/µl) differs significantly from that of the commercial kit (115.98 ± 4.57 ng/µl) and a microwave-based method (119.26 ± 3.06 ng/µl). The absorbance ratio of DNA extracted using the PureLink Genomic DNA kit, the DNAzol Direct, and the microwave-based methods was 1.92 ± 0.02, 1.79 ± 0.01, and 1.87 ± 0.01, respectively. Among the 3 methods evaluated, the microwave-based method is simpler, less expensive, and more time efficient. This is the first evaluation of the microwave-based method for extracting DNA from an adult mosquito. This study provides a useful guide for alternative DNA extraction methods for PCR-based assays, especially in low-resource settings.
It is buzziness time: rearing, mating, and overwintering Bombus vosnesenskii (Hymenoptera: Apidae)
Authors: Christman Morgan E , Barkan N Pinar , Campion Claire , Heraghty Sam D , Keaveny Ellen C , Verble Kelton M , Waybright Sarah A , Dillon Michael E , Lozier Jeffrey D , Strange James P 
Published: October 2023

Abstract
Bombus vosnesenskii Radowszkowski, 1862 is one of three bumble bee species commercially available for pollination services in North America; however, little is documented about B. vosnesenskii colony life cycle or the establishment of ex situ rearing, mating, and overwintering practices. In this study, we documented nest success, colony size, and gyne production; recorded the duration of mating events; assessed overwintering survival of mated gynes; and evaluated second-generation nest success for colonies established from low- and high-elevation wild-caught B. vosnesenskii gynes. Of the 125 gynes installed, 62.4% produced brood cells (nest initiation) and 43.2% had at least 1 worker eclose (nest establishment). High-elevation B. vosnesenskii gynes had significantly higher nest initiation and establishment success than low-elevation gynes. However, low-elevation colonies were significantly larger with queens producing more gynes on average. Mating was recorded for 200 low-elevation and 37 high-elevation gynes, resulting in a mean duration of 62 and 51 min, respectively. Mated gynes were then placed into cold storage for 54 days to simulate overwintering, which resulted in 59.1% of low-elevation gynes surviving and 91.9% of high-elevation gynes surviving. For second-generation low-elevation gynes, 26.4% initiated nesting and 14.3% established nesting. Second-generation high-elevation gynes did not initiate nesting despite CO2 narcosis treatments. Overall, these results increase our understanding of B. vosnesenskii nesting, mating, and overwintering biology from 2 elevations. Furthermore, this study provides information on successful husbandry practices that can be used by researchers and conservationists to address knowledge gaps and enhance the captive rearing of bumble bees.
The “Risks of Routine Tests” and Analogical Reasoning in Assessments of Minimal Risk
Authors: Kwek Adrian 
Published: October 2023

Abstract
Research risks have to meet minimal risk requirements in order for the research to qualify for expedited ethics review, to be exempted from ethics review, or to be granted consent waivers. The definition of “minimal risk” in the Common Rule (45 CFR 46) relies on the risks-of-daily-life and risks-of-routine-tests as comparators against which research activities are assessed to meet minimal risk requirements. While either or both comparators have been adopted by major ethics codes, they have also been criticized. In response to criticisms, elaborations, and alternative comparators have been proposed. In this paper, I approach the search for workable comparators from the point of view that ethical reasoning about minimal risk involves analogical reasoning using comparators. In this regard, I develop two necessary conditions for an adequate minimal risk conception, which I use to assess three comparators. I conclude that the risks-of-routine-tests best fits the analogical reasoning operating in minimal risk assessments.
“My professor said, ‘You can have this great career in mathematics if you go into statistics’”: Interview with Robert Santos
Authors: Britten Anna , Tarran Brian 
Published: October 2023

Abstract
Robert Santos became director of the US Census Bureau in January 2022, the first person of colour in the role. At this year’s Joint Statistical Meetings in Toronto, Brian Tarran and Anna Britten interviewed him and top-ranking Bureau colleagues
‘This app is evil forest true true’: metaphor-based metadiscursive evaluations of Twitter by Nigerians
Authors: Inya Onwu 
Published: October 2023

Abstract
Previous linguistic studies on Nigeria-based Twitter discourse have investigated radicalist, terrorist, campaign, and electioneering discourses. These previous studies focus on discourses produced on Twitter, and not metadiscursive reflections about the social media space itself, and the discursive practice of dragging, in the context of celebrity–newcomer socialization, drawing theoretical insights from metaphoric conceptualizations. This article examines metaphor-based metadiscursive evaluations of the microblogging space by Nigerians. The data for the study comprise tweets retrieved from the Twitter account of a Nigerian celebrity new to Twitter, and subjected to metaphor scenario analysis. It was found that the metaphoric concepts of EVIL FOREST, STREET AS CULTURE/HIGHWAY, and DRAG/TIGER GENERATOR provide frames for characterizing, and evaluating Twitter, and the practice of dragging, respectively. Such user-based metadiscursive metaphoric reflections about the digital space, and culture grant access to the conceptual, and ideological structures that underscore participation in cyberspace. This article has implications for understanding the conceptual and ideological structures that underscore participation on Twitter NG, and the (dis)affiliative stance towards online bullying inherent in the practice of dragging.
The 2021 mutual phenomena involving the Galilean satellites of Jupiter and the inner satellite Thebe
Authors: Catani L M , Assafin M , Morgado B E , Santos-Filho S , Braga-Ribas F , Vieira-Martins R , Arcas-Silva J , Milone A C , Lima I J , Botelho R B 
Published: October 2023

ABSTRACT
Astrometric studies and orbital modelling of planetary moons have contributed significantly to advancing our understanding of their orbital dynamics. These studies require precise positions measured over extended periods. In this paper, we present the results of the 2021 Brazilian Jovian mutual phenomena campaign. The data correspond to eight events between Galilean satellites, in addition to a rare eclipse of Thebe, an inner satellite, totalling nine events. A geometric model along with the DE440/JUP365 ephemerides was used to reproduce the events and simulate the light curves. A Monte Carlo method and chi-squared statistics were used to fit the simulated light curves to the observations. The reflectance model adopted for our simulations was the complete version of the Oren–Nayer model. The average uncertainty of the relative positions of the Galilean satellites was 5 mas (15 km) and for the inner Thebe satellite 32 mas (96 km). The seven mutual events (nine independent observations) here analysed represent an addition of 17 per cent events (10 per cent light curves) with respect to the 2021 international mutual phenomena campaign. Furthermore, our result of Thebe eclipse is only the second measurement published to date. Our results contribute to the ephemeris data base, being fundamental to improving satellite orbits and thus minimizing their uncertainties.
Double black hole mergers in nuclear star clusters: eccentricities, spins, masses, and the growth of massive seeds
Authors: Chattopadhyay Debatri , Stegmann Jakob , Antonini Fabio , Barber Jordan , Romero-Shaw Isobel M 
Published: October 2023

ABSTRACT
We investigate the formation of intermediate mass black holes (IMBHs) through hierarchical mergers of stellar origin black holes (BHs), as well as BH mergers formed dynamically in nuclear star clusters. Using a semi-analytical approach that incorporates probabilistic mass-function-dependent double BH (DBH) pairing, binary-single encounters, and a mass-ratio-dependent prescription for energy dissipation in hardening binaries, we find that IMBHs with masses of $\mathcal {O}(10^2)$–$\mathcal {O}(10^4)\, \rm M_\odot$ can be formed solely through hierarchical mergers in time-scales of a few 100 Myrs to a few Gyrs. Clusters with escape velocities ≳400 km s−1 inevitably form high-mass IMBHs. The spin distribution of IMBHs with masses ≳ 103 M⊙ is strongly clustered at χ ∼ 0.15; while for lower masses, it peaks at χ ∼ 0.7. Eccentric mergers are more frequent for equal-mass binaries containing first- and/or second-generation BHs. Metal-rich, young, dense clusters can produce up to 20 per cent of their DBH mergers with eccentricity ≥0.1 at $10\, \rm Hz$, and ∼2–9 per cent of all in-cluster mergers can form at &gt;10 Hz. Nuclear star clusters are therefore promising environments for the formation of highly eccentric DBH mergers, detectable with current gravitational-wave detectors. Clusters of extreme mass (∼108 M⊙) and density (∼108 M⊙ pc−3) can have about half of all of their DBH mergers with primary masses ≥100 M⊙. The fraction of in-cluster mergers increases rapidly with increasing cluster escape velocity, being nearly unity for vesc ≳ 200 km s−1. Cosmological merger rate of DBHs from nuclear clusters varies ⪅0.01–1 Gpc−3 yr−1, where the large error bars come from uncertainties in the cluster initial conditions, number density distribution, and redshift evolution of nucleated galaxies.
Multiple imaging of the quasar 2005 + 403 formed by anisotropic scattering
Authors: Koryukova T A , Pushkarev A B , Kiehlmann S , Readhead A C S 
Published: October 2023

ABSTRACT
We report on the low Galactic latitude (b = 4${_{.}^{\circ}}$3) quasar 2005 + 403, the second active galactic nuclei, in which we detected a rare phenomenon of multiple imaging induced by refractive-dominated scattering. The manifestation of this propagation effect is revealed at different frequencies (≲ 8 GHz) and epochs of Very Long Baseline Array (VLBA) observations. The pattern formed by anisotropic scattering is stretched out along the line of constant Galactic latitude with a local position angle, PA ≈ 40° showing 1–2 sub-images, often on either side of the core. Analysing the multifrequency VLBA data ranging from 1.4 to 43.2 GHz, we found that both the angular size of the apparent core component and the separation between the primary and secondary core images follow a wavelength squared dependence, providing convincing evidence for a plasma scattering origin for the multiple imaging. Based on the Owens Valley Radio Observatory long-term monitoring data at 15 GHz obtained for 2005 + 403, we identified the characteristic flux density excursions occurred in 2019 April and May and attributed to an extreme scattering event (ESE) associated with the passage of a plasma lens across the line of sight. Modelling the ESE, we determined that the angular size of the screen is 0.4 mas and it drifts with the proper motion of 4.4 mas yr−1. Assuming that the scattering screen is located in the highly turbulent Cygnus region, the transverse linear size and speed of the lens with respect to the observer are 0.7 au and 37 km s−1, respectively.
Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty
Authors: Togkousidis Anastasis , Kozlov Oleksiy M , Haag Julia , Höhler Dimitri , Stamatakis Alexandros 
Published: October 2023

Abstract
Phylogenetic inferences under the maximum likelihood criterion deploy heuristic tree search strategies to explore the vast search space. Depending on the input dataset, searches from different starting trees might all converge to a single tree topology. Often, though, distinct searches infer multiple topologies with large log-likelihood score differences or yield topologically highly distinct, yet almost equally likely, trees. Recently, Haag et al. introduced an approach to quantify, and implemented machine learning methods to predict, the dataset difficulty with respect to phylogenetic inference. Easy multiple sequence alignments (MSAs) exhibit a single likelihood peak on their likelihood surface, associated with a single tree topology to which most, if not all, independent searches rapidly converge. As difficulty increases, multiple locally optimal likelihood peaks emerge, yet from highly distinct topologies. To make use of this information, we introduce and implement an adaptive tree search heuristic in RAxML-NG, which modifies the thoroughness of the tree search strategy as a function of the predicted difficulty. Our adaptive strategy is based upon three observations. First, on easy datasets, searches converge rapidly and can hence be terminated at an earlier stage. Second, overanalyzing difficult datasets is hopeless, and thus it suffices to quickly infer only one of the numerous almost equally likely topologies to reduce overall execution time. Third, more extensive searches are justified and required on datasets with intermediate difficulty. While the likelihood surface exhibits multiple locally optimal peaks in this case, a small proportion of them is significantly better. Our experimental results for the adaptive heuristic on 9,515 empirical and 5,000 simulated datasets with varying difficulty exhibit substantial speedups, especially on easy and difficult datasets (53% of total MSAs), where we observe average speedups of more than 10×. Further, approximately 94% of the inferred trees using the adaptive strategy are statistically indistinguishable from the trees inferred under the standard strategy (RAxML-NG).
Alternative splicing of BCL-x is controlled by RBM25 binding to a G-quadruplex in BCL-x pre-mRNA
Authors: Le Sénéchal Ronan , Keruzoré Marc , Quillévéré Alicia , Loaëc Nadège , Dinh Van-Trang , Reznichenko Oksana , Guixens-Gallardo Pedro , Corcos Laurent , Teulade-Fichou Marie-Paule , Granzhan Anton , Blondel Marc 
Published: October 2023

Abstract
BCL-x is a master regulator of apoptosis whose pre-mRNA is alternatively spliced into either a long (canonical) anti-apoptotic Bcl-xL isoform, or a short (alternative) pro-apoptotic Bcl-xS isoform. The balance between these two antagonistic isoforms is tightly regulated and overexpression of Bcl-xL has been linked to resistance to chemotherapy in several cancers, whereas overexpression of Bcl-xS is associated to some forms of diabetes and cardiac disorders. The splicing factor RBM25 controls alternative splicing of BCL-x: its overexpression favours the production of Bcl-xS, whereas its downregulation has the opposite effect. Here we show that RBM25 directly and specifically binds to GQ-2, an RNA G-quadruplex (rG4) of BCL-x pre-mRNA that forms at the vicinity of the alternative 5′ splice site leading to the alternative Bcl-xS isoform. This RBM25/rG4 interaction is crucial for the production of Bcl-xS and depends on the RE (arginine-glutamate-rich) motif of RBM25, thus defining a new type of rG4-interacting domain. PhenDC3, a benchmark G4 ligand, enhances the binding of RBM25 to the GQ-2 rG4 of BCL-x pre-mRNA, thereby promoting the alternative pro-apoptotic Bcl-xS isoform and triggering apoptosis. Furthermore, the screening of a combinatorial library of 90 putative G4 ligands led to the identification of two original compounds, PhenDH8 and PhenDH9, superior to PhenDC3 in promoting the Bcl-xS isoform and apoptosis. Thus, favouring the interaction between RBM25 and the GQ-2 rG4 of BCL-x pre-mRNA represents a relevant intervention point to re-sensitize cancer cells to chemotherapy.