bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and serological diagnosis of multiple bacterial zoonoses in febrile outpatients in Garissa County, north-eastern Kenya
Authors: Wainaina Martin , Lindahl Johanna F. , Mayer-Scholl Anne , Ufermann Christoph-Martin , Domelevo Entfellner Jean-Baka , Roesler Uwe , Roesel Kristina , Grace Delia , Bett Bernard , Al Dahouk Sascha 
Published: May 2024

AbstractBacterial zoonoses are diseases caused by bacterial pathogens that can be naturally transmitted between humans and vertebrate animals. They are important causes of non-malarial fevers in Kenya, yet their epidemiology remains unclear. We investigated brucellosis, Q-fever and leptospirosis in the venous blood of 216 malaria-negative febrile patients recruited in two health centres (98 from Ijara and 118 from Sangailu health centres) in Garissa County in north-eastern Kenya. We determined exposure to the three zoonoses using serological (Rose Bengal test for Brucella spp., ELISA for C. burnetti and microscopic agglutination test for Leptospira spp.) and real-time PCR testing and identified risk factors for exposure. We also used non-targeted metagenomic sequencing on nine selected patients to assess the presence of other possible bacterial causes of non-malarial fevers. Considerable PCR positivity was found for Brucella (19.4%, 95% confidence intervals [CI] 14.2–25.5) and Leptospira spp. (1.7%, 95% CI 0.4–4.9), and high endpoint titres were observed against leptospiral serovar Grippotyphosa from the serological testing. Patients aged 5–17 years old had 4.02 (95% CI 1.18–13.70, p-value = 0.03) and 2.42 (95% CI 1.09–5.34, p-value = 0.03) times higher odds of infection with Brucella spp. and Coxiella burnetii than those of ages 35–80. Additionally, patients who sourced water from dams/springs, and other sources (protected wells, boreholes, bottled water, and water pans) had 2.39 (95% CI 1.22–4.68, p-value = 0.01) and 2.24 (1.15–4.35, p-value = 0.02) times higher odds of exposure to C. burnetii than those who used unprotected wells. Streptococcus and Moraxella spp. were determined using metagenomic sequencing. Brucellosis, leptospirosis, Streptococcus and Moraxella infections are potentially important causes of non-malarial fevers in Garissa. This knowledge can guide routine diagnosis, thus helping lower the disease burden and ensure better health outcomes, especially in younger populations.
Adverse events reporting of XPO1 inhibitor - selinexor: a real-word analysis from FAERS database
Authors: Liu Yi , Yang Runyu , Feng Hui , Du Yue , Yang Bingyu , Zhang Mengyao , He Pengcheng , Ma Bohan , Niu Fan 
Published: May 2024

AbstractAs the world's first oral nuclear export inhibitor, selinexor is increasingly being used in clinical applications for malignant tumors. However, there is no extensive exploration on selinexor's adverse events (ADEs), necessitating a real-word assessment of its clinical medication safety. FAERS data (July 2019–June 2023) were searched for selinexor ADE reports across all indications. Use the system organ class (SOC) and preferred terms (PT) from the medical dictionary for regulatory activities (MedDRA) to describe, categorize, and statistic ADEs. Disproportionality analysis was employed through calculation of reporting odds ratio (ROR) and proportional reporting ratio (PRR). Based on total of 4392 selinexor related ADE reports as the primary suspect (PS), of which 2595 instances were severe outcomes. The predominant ADEs included gastrointestinal disorders, myelosuppression symptoms, and various nonspecific manifestations. 124 signals associated with selinexor ADE were detected, and 10 of these top 15 signals were not included into the instructions. Our study provides real-world evidence regarding the drug safety of selinexor, which is crucial for clinicians to safeguard patients’ health.
Sex- and cycle-dependent changes in spine density and size in hippocampal CA2 neurons
Authors: Jabra Sharif , Rietsche Michael , Muellerleile Julia , O’Leary Aet , Slattery David A. , Deller Thomas , Fellenz Meike 
Published: May 2024

AbstractSex hormones affect structural and functional plasticity in the rodent hippocampus. However, hormone levels not only differ between males and females, but also fluctuate across the female estrous cycle. While sex- and cycle-dependent differences in dendritic spine density and morphology have been found in the rodent CA1 region, but not in the CA3 or the dentate gyrus, comparable structural data on CA2, i.e. the hippocampal region involved in social recognition memory, is so far lacking. In this study, we, therefore, used wildtype male and female mice in diestrus or proestrus to analyze spines on dendritic segments from identified CA2 neurons. In basal stratum oriens, we found no differences in spine density, but a significant shift towards larger spine head areas in male mice compared to females. Conversely, in apical stratum radiatum diestrus females had a significantly higher spine density, and females in either cycle stage had a significant shift towards larger spine head areas as compared to males, with diestrus females showing the larger shift. Our results provide further evidence for the sexual dimorphism of hippocampal area CA2, and underscore the importance of considering not only the sex, but also the stage of the estrous cycle when interpreting morphological data.
Annual rhythm in immune functions of blood leucocytes in an ophidian, Natrix piscator
Authors: Singh Alka , Singh Ramesh , Parganiha Arti , Tripathi Manish Kumar 
Published: May 2024

AbstractAnnual variations in animal’s physiological functions are an essential strategy to deal with seasonal challenges which also vary according to the time of year. Information regarding annual adaptations in the immune-competence to cope with seasonal stressors in reptiles is scarce. The present research plan was designed to analyze the presence of circannual immune rhythms in defense responses of the leucocytes in an ophidian, Natrix piscator. Peripheral blood leucocytes were obtained, counted, and superoxide anion production, neutrophil phagocytosis, and nitrite release were tested to assess the innate immune functions. Peripheral blood lymphocytes were separated by centrifugation (utilizing density gradient) and the cell proliferation was measured. The Cosinor rhythmometry disclosed the presence of significant annual rhythms in the number of leucocytes, superoxide anion production, nitric oxide production, and proliferation of stimulated lymphocytes. The authors found that respiratory burst activity and proliferative responses of lymphocytes were crucial immune responses that showed the annual rhythm. It was summarized that the immune function of the N. piscator is a labile attribute that makes the animal competent to cope with the seasonal stressor by adjustment in the potency of response.
Development of label-free electrochemical OMP-DNA probe biosensor as a highly sensitive system to detect of citrus huanglongbing
Authors: Kazemzadeh-Beneh Hashem , Safarnejad Mohammad Reza , Norouzi Parviz , Samsampour Davood , Alavi Seyed Mehdi , Shaterreza Davood 
Published: May 2024

AbstractThe fabrication of the first label-free electrochemical DNA probe biosensor for highly sensitive detection of Candidatus Liberibacter asiaticus (CLas), as the causal agent of citrus huanglongbing disease, is conducted here. An OMP probe was designed based on the hybridization with its target-specific sequence in the outer membrane protein (OMP) gene of CLas. The characterization of the steps of biosensor fabrication and hybridization process between the immobilized OMP-DNA probe and the target ssDNA oligonucleotides (OMP-complementary and three mismatches OMP or OMP-mutation) was monitored using cyclic voltammetry and electrochemical impedance spectroscopy based on increasing or decreasing in the electron transfer in [Fe (CN)6]3−/4− on the modified gold electrode surface. The biosensor sensitivity indicated that the peak currents were linear over ranges from 20 to 100 nM for OMP-complementary with the detection limit of 0.026 nM (S/N = 3). The absence of any cross-interference with other biological DNA sequences confirmed a high selectivity of fabricated biosensor. Likewise, it showed good specificity in discriminating the mutation oligonucleotides from complementary target DNAs. The functional performance of optimized biosensor was achieved via the hybridization of OMP-DNA probe with extracted DNA from citrus plant infected with CLas. Therefore, fabricated biosensor indicates promise for sensitivity and early detection of citrus huanglongbing disease.
Enzymatization of mouse monoclonal antibodies to the corresponding catalytic antibodies
Authors: Hifumi Emi , Ito Yuina , Tsujita Moe , Taguchi Hiroaki , Uda Taizo 
Published: May 2024

AbstractCatalytic antibodies possess a dual function that enables both antigen recognition and degradation. However, their time-consuming preparation is a significant drawback. This study developed a new method for quickly converting mice monoclonal antibodies into catalytic antibodies using site-directed mutagenesis. Three mice type monoclonal antibodies targeting hemagglutinin molecule of influenza A virus could be transformed into the catalytic antibodies by deleting Pro95 in CDR-3 of the light chain. No catalytic activity was observed for monoclonal antibodies and light chains. In contrast, the Pro95-deleted light chains exhibited a catalytic activity to cleave the antigenic peptide including the portion of conserved region of hemagglutinin molecule. The affinity of the Pro95-deleted light chains to the antigen increased approximately 100-fold compared to the wild-type light chains. In the mutants, three residues (Asp1, Ser92, and His93) come closer to the appropriate position to create the catalytic site and contributing to the enhancement of both catalytic function and immunoreactivity. Notably, the Pro95-deleted catalytic light chains could suppress influenza virus infection in vitro assay, whereas the parent antibody and the light chain did not. This strategy offers a rapid and efficient way to create catalytic antibodies from existing antibodies, accelerating the development for various applications in diagnostic and therapeutic applications.
Using isometric log-ratio in compositional data analysis for developing a groundwater pollution index
Authors: Oh Junseop , Kim Kyoung-Ho , Kim Ho-Rim , Park Sunhwa , Yun Seong-Taek 
Published: May 2024

Abstract
This study introduces a novel groundwater pollution index (GPI) formulated through compositional data analysis (CoDa) and robust principal component analysis (RPCA) to enhance groundwater quality assessment. Using groundwater quality monitoring data from sites impacted by the 2010–2011 foot-and-mouth disease outbreak in South Korea, CoDa uncovers critical hydrochemical differences between leachate-influenced and background groundwater. The GPI was developed by selecting key subcompositional parts (NH4
+-N, Cl-, and NO3--N) using RPCA, performing the isometric log-ratio (ILR) transformation, and normalizing the results to environmental standards, thereby providing a more precise and accurate assessment of pollution. Validated against government criteria, the GPI has shown its potential as an alternative assessment tool, with its reliability confirmed by receiver operating characteristic curve analysis. This study highlights the essential role of CoDa, especially the ILR -transformation, in overcoming the limitations of traditional statistical methods that often neglect the relative nature of hydrochemical data. Our results emphasize the utility of the GPI in significantly advancing groundwater quality monitoring and management by addressing a methodological gap in the quantitative assessment of groundwater pollution.
Discovery of seed germinating fungi (Mycetinis scorodonius) from Gastrodia elata Bl. f. glauca S. chow in Changbai Mountain and examination of their germination ability
Authors: Yang Xinyu , Gao Yugang , Li Zhaochun , Zang Pu , Zhao Yan , Liu Qun 
Published: May 2024

AbstractMulti-generational asexual reproduction of Gastrodia elata Bl. will cause seedling species degeneration. Sexual reproduction of Gastrodia elata Bl. seed is an effective method to solve the problem of degeneration. The development of Gastrodia elata Bl. seeds cannot be separated from the germination fungus. However, there are few strains of germination fungus in production, and there is also the problem of species degradation in application for many years. It is very important for the sexual reproduction of Gastrodia elata Bl. to isolate more new strains of excellent germination fungus from the origin. This study used the Gastrodia elata Bl. f. glauca S. chow seeds germination vegetative propagation corms capture method to isolate its symbiotic germination fungus, and comprehensively identified the species of germination fungus by colony morphology, ITS, sporocarps regeneration and germination function, and compared the growth characteristics and germination ability with other germination fungus (Mycena purpureofusca, Mycena dendrobii and Mycena osmundicola). The germination fungus was isolated from the vegetative propagation corms of Gastrodia elata Bl. f. glauca S. chow seeds and named GYGL-1. After comprehensive identification, GYGL-1 was Mycetinis scorodonius. Compared with other germination fungus, GYGL-1 has fast germination speed, vigorous growth, and high germination ability for Gastrodia elata Bl. f. glauca S. chow seeds. Innovated the isolation method of Gastrodia elata Bl. seeds germination fungus, obtained the regenerated sporocarps of the germination fungus, and discovered that Mycetinis scorodonius has a new function of germinating Gastrodia elata Bl. f. glauca S. chow seeds, enriching the resource library of Gastrodia elata Bl. germination fungus.
Metabolic plasticity drives mismatches in physiological traits between prey and predator
Authors: Affinito Flavio , Kordas Rebecca L. , Matias Miguel G. , Pawar Samraat 
Published: May 2024

AbstractMetabolic rate, the rate of energy use, underpins key ecological traits of organisms, from development and locomotion to interaction rates between individuals. In a warming world, the temperature-dependence of metabolic rate is anticipated to shift predator-prey dynamics. Yet, there is little real-world evidence on the effects of warming on trophic interactions. We measured the respiration rates of aquatic larvae of three insect species from populations experiencing a natural temperature gradient in a large-scale mesocosm experiment. Using a mechanistic model we predicted the effects of warming on these taxa’s predator-prey interaction rates. We found that species-specific differences in metabolic plasticity lead to mismatches in the temperature-dependence of their relative velocities, resulting in altered predator-prey interaction rates. This study underscores the role of metabolic plasticity at the species level in modifying trophic interactions and proposes a mechanistic modelling approach that allows an efficient, high-throughput estimation of climate change threats across species pairs.
Epitope binning for multiple antibodies simultaneously using mammalian cell display and DNA sequencing
Authors: Lin Ning , Miyamoto Kotaro , Ogawara Takumi , Sakurai Saki , Kizaka-Kondoh Shinae , Kadonosono Tetsuya 
Published: May 2024

AbstractEpitope binning, an approach for grouping antibodies based on epitope similarities, is a critical step in antibody drug discovery. However, conventional methods are complex, involving individual antibody production. Here, we established Epitope Binning-seq, an epitope binning platform for simultaneously analyzing multiple antibodies. In this system, epitope similarity between the query antibodies (qAbs) displayed on antigen-expressing cells and a fluorescently labeled reference antibody (rAb) targeting a desired epitope is analyzed by flow cytometry. The qAbs with epitope similar to the rAb can be identified by next-generation sequencing analysis of fluorescence-negative cells. Sensitivity and reliability of this system are confirmed using rAbs, pertuzumab and trastuzumab, which target human epidermal growth factor receptor 2. Epitope Binning-seq enables simultaneous epitope evaluation of 14 qAbs at various abundances in libraries, grouping them into respective epitope bins. This versatile platform is applicable to diverse antibodies and antigens, potentially expediting the identification of clinically useful antibodies.
Global climate modeling of the Jupiter troposphere and effect of dry and moist convection on jets
Authors: Boissinot Alexandre , Spiga Aymeric , Guerlet Sandrine , Cabanes Simon , Bardet Deborah 
Published: May 2024

Aims. The atmosphere of Jupiter is characterized by banded jets, including an equatorial super-rotating jet, by an intense moist con-vective activity, and by perturbations exerted by vortices, waves, and turbulence. Even after space exploration missions to Jupiter and detailed numerical modeling of Jupiter, questions remain about the mechanisms underlying the banded jets and the role played by dry and moist convection in maintaining these jets.
Methods. We report three-dimensional simulations of the Jupiter weather layer using a global climate model (GCM) called Jupiter-DYNAMICO, which couples hydrodynamical integrations on an icosahedral grid with detailed radiative transfer computations. We added a thermal plume model for Jupiter that emulates the effect of mixing of heat, momentum, and tracers by dry and moist convec-tive plumes that are left unresolved in the GCM mesh spacing with a physics-based approach.
Results. Our Jupiter-DYNAMICO global climate simulations show that the large-scale Jovian flow, in particular the jet structure, could be highly sensitive to the water abundance in the troposphere and that an abundance threshold exists at which equatorial super-rotation develops. In contrast to our dry (or weakly moist) simulations, simulations that include the observed amount of tropospheric water exhibit a clear-cut super-rotating eastward jet at the equator and a dozen eastward mid-latitude jets that do not migrate poleward. The magnitudes agree with the observations. The convective activity simulated by our thermal plume model is weaker in the equatorial regions than in mid to high latitudes, as indicated by lightning observations. Regardless of whether they are dry or moist, our simulations exhibit the observed inverse energy cascade from small (eddies) to large scales (jets) in a zonostrophic regime.
Quasi-periodic oscillation analysis for a sample of blazars at the optical band
Authors: Chen Zhao-Hao , Jiang Yunguo 
Published: May 2024

Context. Quasi-periodic behavior in the light curves of blazars can help us understand the physics. The identification of the supermassive black hole binary (SMBHB) is an active topic, and the periodicity analysis of light curves is a powerful method for searching for these sources.
Aims. In this work, we aim to identify quasi-periodic oscillations (QPOs) in the optical band light curves in our sample and discuss the possible physical origins behind these targets.
Methods. In this study, we collected 155 optical band light curves from three different monitoring programs. We searched for QPOs in our sample using the generalised Lomb-Scargle (GLS) and weighted wavelet Z-transform (WWZ) methods. We simulated 104 artificial light curves and evaluated the significance of the results using the Monte Carlo method.
Results. Our work reveals that 18 targets show QPOs with timescales ranging from 200 days to 1400 days. These QPOs could be explained by three scenarios, including the SMBHB, instability of thick disks and jet precession. Since the frequencies corresponding to QPOs are in the nHz regime, our work provides candidates of SMBHBs for further verification.
Dynamics and emission properties of flux ropes from two-temperature GRMHD simulations with multiple magnetic loops
Authors: Jiang Hong-Xuan , Mizuno Yosuke , Dihingia Indu K. , Nathanail Antonios , Younsi Ziri , Fromm Christian M. 
Published: May 2024

Context. Flux ropes erupting in the vicinity of a black hole are thought to be a potential model for the flares observed in Sagittarius A*.
Aims. In this study, we examine the radiative properties of flux ropes that emerged in the vicinity of a black hole.
Methods. We performed three-dimensional two-temperature general relativistic magnetohydrodynamic (GRMHD) simulations of magnetized accretion flows with alternating multiple magnetic loops and general relativistic radiation transfer (GRRT) calculations. In the GRMHD simulations, we implemented two different sizes of initial magnetic loops.
Results. In the small loop case, magnetic dissipation leads to a weaker excitement of magneto-rotational instability inside the torus, which generates a lower accretion rate compared to the large loop case. However, the small loop case generates more flux ropes due to frequent reconnection by magnetic loops with different polarities. By calculating the thermal synchrotron emission, we found that the variability of light curves and the emitting region are tightly related. At 230 GHz and higher, the emission from the flux ropes is relatively stronger compared to the background, which is responsible for the filamentary structure in the images. At lower frequencies (e.g., 43 GHz), emission comes from more extended regions, which have a less filamentary structure in the image.
Conclusions. Our study shows that self-consistent electron temperature models are essential for the calculation of thermal synchrotron radiation and the morphology of the GRRT images. Flux ropes contribute considerable emission at frequencies ≳230 GHz.
The satellite galaxy plane of NGC 4490 in light of ΛCDM
Authors: Pawlowski Marcel S. , Müller Oliver , Taibi Salvatore , Júlio Mariana P. , Kanehisa Kosuke Jamie , Heesters Nick 
Published: May 2024

Context. The system of galaxies around NGC 4490 was recently highlighted to display a flattened, kinematically correlated structure reminiscent of planes of satellite galaxies around other hosts.
Aims. Since known satellite planes are in tension with expectations from cosmological simulations in the Λ cold dark matter (ΛCDM) model, we aim to quantitatively assess for the first time the tension posed by the NGC 4490 system.
Methods. We measured the on-sky flattening as the major-to-minor axis ratio b/a of the satellite distribution and their line-of-sight kinematic correlation. Analogs to the system were selected in the TNG50 simulation and their flattening and correlation were similarly measured.
Results. We confirm the strong kinematic coherence of all 12 observed satellite objects with available line-of-sight velocities (of 14 in total): the northern ones approach and the southern ones recede relative to the host. The spatial distribution of all 14 objects is substantially flattened with b/a = 0.38 (0.26 considering only the 12 objects with available velocities). Such extreme arrangements are rare in the ΛCDM simulation, at a level of 0.21 to 0.35%. This fraction of analogs would drop further if at least one of the two satellite objects without velocities is confirmed to follow the kinematic trend, and would become zero if both are rejected as non-members. We also identify a likely galaxy pair in the observed system, and find a similar pair in the best-matching simulated analog.
Conclusions. Our measurements establish NGC 4490 as another strong example of a satellite plane in the Local Volume. This emphasizes that planes of satellites are a more general issue faced by ΛCDM also beyond the Local Group. The tension with typical systems drawn from simulations suggests that the observed one requires a specific formation scenario, potentially connected to the larger-scale galaxy alignment in its vicinity. The presence of galaxy pairs in the observed and a simulated system hints at the importance such groupings may have to understand satellite planes.