bluuebunny/crossref_metadata_2025 huggingface dataset:
Paradoxical restoration from complete and persistent atrioventricular block after surgical aortic valve replacement: a case report
Authors: Nishihara Ami , Okabe Yuta , Morizumi Sei , Enomoto Yoshiharu , Yoshida Kentaro
Published: October 2024

Background

One of the most important and relatively frequent complications of aortic valve replacement is atrioventricular block. It typically occurs by direct injury of the infranodal conduction system due to intra-operative manipulation and persists post-operatively, necessitating permanent pacemaker implantation in many cases.

Case summary

A 66-year-old man presented to our hospital after experiencing syncope while walking after drinking. He had experienced two episodes of alcohol-induced syncope several years earlier. His electrocardiogram (ECG) and transthoracic echocardiogram revealed complete atrioventricular block and severe aortic stenosis, respectively. He received a temporary pacemaker on the day of admission and underwent surgical aortic valve replacement on hospital Day 9. The native aortic valve was bicuspid. Unexpectedly, the ECG immediately after aortic valve replacement showed complete restoration of atrioventricular conduction during temporary atrial pacing. The atrioventricular block did not recur, and he was discharged to home on post-operative Day 13.

Discussion

This remarkably rare clinical course, complete restoration from complete and persistent atrioventricular block after surgical aortic valve replacement, can be explained by multifactorial mechanisms: (i) surgical removal of the aortic annulus calcification directly hindering the infranodal conduction system; (ii) relief from the ventricular pressure overload stressing the conduction system within the septum; and (iii) improvement of substantial autonomic dysregulation as manifested by alcohol-sensitive syncope in the present patient, which was a result of unloading of the intraventricular pressure affecting the left ventricular mechanoreceptor.
Evolution from mixed to fixed handedness in mirror-image flowers: insights from adaptive dynamics
Authors: Saltini Marco , Barrett Spencer C H , Deinum Eva E
Published: October 2024

Mirror-image flowers (enantiostyly) involve a form of sexual asymmetry in which a flower’s style is deflected either to the left or right side, with a pollinating anther orientated in the opposite direction. This curious floral polymorphism, which was known but not studied by Charles Darwin, occurs in at least 11 unrelated angiosperm families and represents a striking example of adaptive convergence in form and function associated with cross-pollination by insects. In several lineages, dimorphic enantiostyly (one stylar orientation per plant, both forms occurring within populations) has evolved from monomorphic enantiostyly, in which all plants can produce both style orientations. We use a modelling approach to investigate the emergence of dimorphic enantiostyly from monomorphic enantiostyly under gradual evolution. We show using adaptive dynamics that depending on the balance between inbreeding depression following geitonogamy, pollination efficiency, and plant density, dimorphism can evolve from an ancestral monomorphic population. In general, the newly emergent dimorphic population is stable against invasion of a monomorphic mutant. However, our model predicts that under certain ecological conditions, for example, a decline of pollinators, dimorphic enantiostyly may revert to a monomorphic state. We demonstrate using population genetics simulations that the observed evolutionary transitions are possible, assuming a plausible genetic architecture.
Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes
Authors: Mazur-Marzec Hanna , Andersson Anders F , Błaszczyk Agata , Dąbek Przemysław , Górecka Ewa , Grabski Michał , Jankowska Katarzyna , Jurczak-Kurek Agata , Kaczorowska Anna K , Kaczorowski Tadeusz , Karlson Bengt , Kataržytė Marija , Kobos Justyna , Kotlarska Ewa , Krawczyk Beata , Łuczkiewicz Aneta , Piwosz Kasia , Rybak Bartosz , Rychert Krzysztof , Sjöqvist Conny , Surosz Waldemar , Szymczycha Beata , Toruńska-Sitarz Anna , Węgrzyn Grzegorz , Witkowski Andrzej , Węgrzyn Alicja
Published: October 2024

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North–East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.
Validity of a visual analogue scale to measure and value the perceived level of sanitation: evidence from Ghana and Mozambique
Authors: Cheung Ho Hei , Adriano Zaida , Dwumfour-Asare Bismark , Nyarko Kwabena B , Scott Pippa , Nala Rassul , Brown Joe , Cumming Oliver , Ross Ian
Published: October 2024

Two billion people globally lack access to a basic toilet, and sanitation is a critical determinant of health and well-being. Evaluations of sanitation programmes typically measure disease or behaviour, and visual analogue scales (VASs) have not been used to measure users’ feelings about their level of sanitation. In this study, we assess the validity of a horizontal sanitation VAS numbered 0–10, with end anchors ‘best imaginable’ and ‘worst imaginable’ sanitation. In Kumasi, Ghana, we surveyed 291 participants before and after uptake of a container-based sanitation service. In Maputo, Mozambique, we surveyed 424 participants from treatment groups of a prior trial. We assessed construct validity by testing hypothesized associations between VAS scores and toilet characteristics and by respondents valuing three hypothetical sanitation states. We assessed responsiveness by comparing VAS with/without sanitation interventions. There was evidence (P < 0.05) for 60% of hypothesized associations in Ghana and 100% in Mozambique. For responsiveness, there was a 3.4-point increase (2.1 SD) in VAS 10 weeks post-intervention in Ghana and a 2.9 point difference (1.3 SD) in Mozambique. In valuation exercises, the mean was higher (P < 0.001) for the objectively better sanitation state. The sanitation VAS could be useful in economic evaluation to identify which improvements achieve quality-of-life gains most efficiently. For future studies, we recommend a vertical sanitation VAS numbered 0–100 with emojis at end anchors but retaining a 0–10 option for those who struggle with numeracy.
Circadian rhythms of microbial communities and their role in regulating nitrogen and phosphorus cycling in the rhizosphere of tea plants
Authors: Liu Miao , Wang Junhua , Li Zhengzhen , Li Xin , Korpelainen Helena , Li Chunyang
Published: October 2024

The circadian clock mediates metabolic functions of plants and rhythmically shapes structure and function of microbial communities in the rhizosphere. However, it is unclear how the circadian rhythm of plant hosts regulates changes in rhizosphere bacterial and fungal communities and nutrient cycles. In the present study, we measured diel changes in the rhizosphere of bacterial and fungal communities, and in nitrogen (N) and phosphorus (P) cycling in 20-year-old tea plantations. The fungal communities were more stable in their responses to circadian changes than bacterial communities in the rhizosphere of the cultivars LJ43 and ZC108. Nevertheless, fungal genera with circadian rhythms were more numerous and had a higher abundance at midnight. Organic P and N mineralization in the rhizosphere was more intensive in LJ43 under day–night alterations, while inorganic N and P cycling was more easily affected by circadian rhythms in ZC108. The rhizosphere denitrification encoded by the genes AOA and AOB was intensive in the morning, irrespective of tea cultivar. Genes related to rhizosphere N fixation (nifH) and denitrification (nosZ and nirK) expressed at greater levels in ZC108, and they reached a peak at midnight. Moreover, the diel rhythm of rhizosphere microbial communities in ZC108 largely regulated dial changes in N and P cycling. These results suggested that the bacterial and fungal communities in the rhizosphere respond differently to circadian rhythms, and they vary between tea cultivars. The timing of bacterial and fungal cycling largely regulates rhizosphere N and P cycling and their ecological functions.
CRISPR/Cas9-mediated CHS2 mutation provides a new insight into resveratrol biosynthesis by causing a metabolic pathway shift from flavonoids to stilbenoids in Vitis davidii cells
Authors: Lai Gongti , Fu Peining , He Liyuan , Che Jianmei , Wang Qi , Lai Pufu , Lu Jiang , Lai Chengchun
Published: October 2024

Resveratrol is an important phytoalexin that adapts to and responds to stressful conditions and plays various roles in health and medical therapies. However, it is only found in a limited number of plant species in low concentrations, which hinders its development and utilization. Chalcone synthase (CHS) and stilbene synthase (STS) catalyze the same substrates to produce flavonoids and resveratrol, respectively. However, it remains unclear how CHS and STS compete in metabolite synthesis. In this study, two CHS2 mutant cell lines (MT1 and MT2) were generated using CRISPR/Cas9 genome editing. These CHS2 mutant cell lines exhibited abundant mutations in CHS2, leading to the premature termination of protein translation and subsequent CHS2 knockout. Amplicon sequencing confirmed comprehensive CHS2 knockout in MT1, whereas the wild-type sequence remained predominant in the MT2 cell line. Transcriptome and RT-qPCR results showed a significant downregulation of genes involved in flavonoid biosynthesis, including CHS2, CHS3, F3H, F3’H, DFR, FLS, LDOX, among others, resulting in decreased flavonoid accumulation, such as anthocyanins, proanthocyanidins, quercetin, and kaempferol. Conversely, STS genes involved in stilbenoid biosynthesis were upregulated competing with the flavonoid pathway. Consequently, there was a marked increase in stilbenoids, including resveratrol, piceatannol, piceid, and pterostilbene, with a 4.1-fold increase in resveratrol and a 5.3-fold increase in piceid (a derivative of resveratrol) observed in CHS2 mutant cell lines. This research demonstrates that CHS2 mutation induces a shift from flavonoid biosynthesis towards stilbenoid biosynthesis, offering new insights into metabolite biosynthesis and regulation, as well as an alternative solution for natural resveratrol production, and a novel breeding approach for eliminating non-target agronomic traits using CRISPR-Cas9.
Resistance is reality: findings from the first Ukrainian cumulative antibiogram
Authors: Vodianyk Arkadii , Holovnia Oksana , Diomin Eugene , Letourneau Alyssa R , Poznansky Mark C , Shenoy Erica S , Turbett Sarah E
Published: October 2024

Background

Antimicrobial resistance is a global health threat resulting in significant morbidity and mortality worldwide. Until recently, in Ukraine, cumulative antibiograms (CuAbgms) have never been available.

Objectives

To describe the first CuAbgm developed in Ukraine.

Methods

We developed a CuAbgm for the Okhmatdyt National Specialized Children’s Hospital using data from WHONET. Antimicrobial susceptibility testing was performed per EUCAST guidelines. The CuAbgm was developed using guidance from CLSI.

Results

For Escherichia coli, 66% and 69% of isolates were susceptible to ceftazidime and ceftriaxone, respectively, and 99% were susceptible to meropenem. For Klebsiella pneumoniae, 26% and 27% of isolates were susceptible to ceftazidime and ceftriaxone, respectively, and only 59% were susceptible to meropenem. Of the carbapenem-resistant K. pneumoniae isolates that underwent additional susceptibility testing, only 38% were susceptible to ceftazidime/avibactam. For Pseudomonas aeruginosa, only 53% were susceptible to meropenem. Of those that were resistant to meropenem and underwent additional susceptibility testing, only 12% were susceptible to ceftazidime/avibactam. Similarly, for Acinetobacter spp., only 37% of isolates were susceptible to meropenem. Susceptibility to ampicillin/sulbactam was also low at 45%. The oxacillin susceptibility rate for Staphylococcus aureus was 99%.

Conclusions

In this first-ever CuAbgm developed in Ukraine, high levels of resistance were demonstrated among Gram-negative bacteria. CuAbgms should be prioritized in laboratories in Ukraine to guide empirical antimicrobial therapy, infection control and antimicrobial stewardship policies. This is of heightened relevance during wartime, when there is a need for healthcare systems to treat complex and infected penetrating and blast-related injuries.
Forsythoside B, the active component of Frosythiae fructuse water extract, alleviates Streptococcus pneumoniae virulence by targeting pneumolysin
Authors: Wang Zhongtian , Sun Yingying , Gu Kuan , Tong Yue , Liu Huanyu , Wang Lei , Tan Tianhui , Yang Fushuang , Ren Xiaoting , Ding Lizhong , Sun Liping , Wang Lie
Published: October 2024

Aims

To explore the therapeutic potential of Forsythoside B in treating Streptococcus pneumoniae (S. pneumoniae) infections, focusing on its ability to inhibit pneumolysin activity and protect cells from damage.

Methods and results

Hemolysis tests were used to evaluate Forsythoside B’s inhibitory effect on pneumolysin activity, while growth curve analysis assessed its impact on S. pneumoniae growth. Western blotting and oligomerization analysis were conducted to examine its influence on pneumolysin oligomerization. Cytotoxicity assays, including LDH release and live/dead cell staining, evaluated the protective effects of Forsythoside B against pneumolysin-induced damage in A549 cells. Additionally, a mouse model was employed to test the effects on survival rates, lung bacterial load, and inflammation. The results showed that Forsythoside B significantly inhibited pneumolysin activity, reduced its oligomerization, and protected A549 cells from damage without affecting bacterial growth. In the mouse model, it improved survival rates and reduced lung inflammation, indicating its potential as a therapeutic agent against S. pneumoniae infections.

Conclusions

Forsythoside B shows potential as a therapeutic agent for treating pneumonia, particularly in infections caused by S. pneumoniae.
Seminal plasma uterine priming alters uterine transcriptomics and negatively impacts embryo growth and uterine artery resistance but not offspring liver transcriptomics in beef cattle
Authors: Swanson Rebecca M , Messman Riley D , Dobbins Thomas W , Contreras-Correa Zully E , Arick Mark A , Sidelinger Darcie R , King Heath , Lemley Caleb O
Published: October 2024

Seminal plasma uterine priming is important for pregnancy and offspring phenotype in mice and swine; however, impacts on the uterus of the dam and her offspring in cattle are unknown. We sought to determine the effects of seminal plasma uterine priming at estrus on uterine transcriptomics, early gestation (days 35, 40, and 45) embryo morphometrics, mid- to late-gestation (days 140 to 220) uterine artery hemodynamics, birth morphometrics, and liver transcriptomics in offspring at 30 d of age. Multiparous Angus-based commercial beef cows were randomly assigned to receive treatment at estrus: 0.5 mL pooled seminal plasma in the uterine body (n = 31, seminal plasma primed) or no treatment (n = 31, control). Seven days later a subset of cows (n = 4/treatment) underwent uterine biopsies, and the remaining cows underwent embryo transfer. Embryo crown-rump length and uterine artery hemodynamics were measured during gestation using ultrasonography. Morphometrics of the calf were collected within 24 h of parturition. Liver biopsies were collected at 30 d of age. Data were analyzed by analysis of variance (ANOVA) in a completely randomized design for the effect of treatment. Myosin heavy chain I (JSP.1) was downregulated [Benjamin–Hochberg adj P (BH) ≤ 0.05] and ABO alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase (ABO) was upregulated (BH adj P ≤ 0.05) in the uterus of seminal plasma primed cows 7 d after treatment. Embryo crown-rump length was less (P < 0.05) in seminal plasma primed cows. Mid- to late-gestation (days 140 to 220) uterine artery resistance was increased (P < 0.05) in seminal plasma primed cows. Seminal plasma priming did not alter birth weights or curve-crown-rump length, but heart girth was increased (P < 0.05) in offspring from seminal plasma primed cows. There were no differentially expressed genes (BH adj P ≤ 0.05) in offspring liver at 30 d of age; however, myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) was absent in all liver samples from calves from seminal plasma primed cows. In contrast, vomeronasal 1 receptor bosTauV1R414 (BOSTAUV1R414) was present in 6 of the 7 liver samples from calves from seminal plasma primed cows. Seminal plasma uterine priming alters uterine transcriptomics, negatively impacts early gestation embryo growth, and mid- to late-gestation uterine artery resistance suggesting downstream vascular anomalies. However, these in utero conditions did not impact offspring from birth to 30 d of age.
Influence of sire plane of nutrition and targeted body weight gain on ewe lamb growth, glucose metabolism, and ovarian reserve
Authors: Bochantin-Winders Kerri A , Slavick Kathryn R , Jurgens Isabella M , Hurlbert Jennifer L , Menezes Ana Clara B , Kirsch James D , Borowicz Pawel P , Schauer Christopher S , Dahlen Carl R
Published: October 2024

Rambouillet rams were managed on either a positive (POS; gain 12% body weight [BW]; n = 8), maintenance (MAINT; maintain BW; n = 8), or negative (NEG; lose 12% BW; n = 8) plane of nutrition before breeding. Rams were bred to ewes (n = 10 per ram) that were managed similarly throughout gestation, and lambs were fed a common diet postnatally. Two ewe lambs (7.6 ± 0.02 mo of age, BW = 47.1 ± 1.17 kg) from each sire were selected and within-pair, randomly assigned to be managed for a moderate (MOD, 0.11 kg/d; n = 23) or accelerated (ACC, 0.20 kg/d; n = 22) rate of gain for 56 d. Ewe lamb BW was recorded on a weekly basis and blood was collected on days 0, 28, and 56 for analysis of insulin-like growth factor 1 (IGF-1), triiodothyronine (T3), thyroxine (T4), glucose, blood urea nitrogen (BUN), and non-esterified fatty acids (NEFA). Intravenous glucose tolerance tests (IVGTT) were conducted from days −7 to −4 and days 57 to 64. A unilateral ovariectomy was performed and ovarian follicles were staged and counted macro and microscopically. Sire treatment × day and ewe treatment × day interactions were present for BW (P ≤ 0.05), where POS had slower growth than MAINT and NEG, and tended (P = 0.10) to have reduced average daily gain (ADG) when managed at an accelerated rate of gain. By design, ACC had greater BW and ADG than MOD (P < 0.05). Concentrations of IGF-1 and T4 were greater in ACC than MOD (P ≤ 0.05), and NEG tended to have greater concentrations of IGF-1 than POS and MAINT (P = 0.08). At the first IVGTT, the concentration of insulin was influenced by a sire treatment × time interaction (P ≤ 0.05), suggesting impaired secretion in NEG-sires ewes, but no differences in area under the curve (AUC) for glucose, insulin, or their ratio (P ≥ 0.11). No interactive effects of sire and ewe treatment (P ≥ 0.52) were observed at the second IVGTT, but insulin and insulin:glucose ratio were influenced by sire treatment × time (P ≤ 0.02), as NEG had greater insulin concentration at 60 min than MAINT (P = 0.03) and greater AUC than POS and MAINT (P ≤ 0.04). No differences in ovary size, weight, or total counts of macro and microscopic follicles were observed (P ≥ 0.23). Ewes-fed ACC had a greater number of small surface follicles (P = 0.02), whereas MOD tended to have a greater number of large surface follicles and tertiary follicles (P < 0.06). These findings suggest that the paternal plane of nutrition influences female offspring physiology, particularly at varying growth rates.
Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi
Authors: Jacobs David K , Kinziger Andrew , Abrecht Mira , McCraney W Tyler , Hà Benjamin A , Spies Brenton T , Heath-Heckman Elizabeth , Marimuhtu Mohan P A , Nguyen Oanh , Fairbairn Colin W , Seligmann William E , Escalona Merly , Miller Courtney , Shaffer H Bradley
Published: October 2024

The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.
Past and current climate as a driver in shaping the distribution of the Longitarsus candidulus species group (Coleoptera: Chrysomelidae)
Authors: Biondi Maurizio , D’Alessandro Paola , Salvi Daniele , Berrilli Emanuele , Iannella Mattia
Published: October 2024

Longitarsus candidulus (Foudras) is a thermophilic flea beetle species widely distributed in the Mediterranean Basin and associated with Daphne gnidium L. and Thymelaea hirsuta (L.). Longitarsus laureolae Biondi and Longitarsus leonardii Doguet, phylogenetically closely related to L. candidulus, show together a peculiar and rare disjunct distribution along the central-southern Apennines and the Cantabrian-Pyrenean mountain system, respectively. Both are associated with Daphne laureola L. in mesophilic habitats. We used “ecological niche modeling” to infer the Pleistocene dynamics in the distribution of the three flea beetle species and their host plants. We interpreted their current distributions, paying particular attention to the presumed time of species divergence as inferred from recent studies. The differentiation of L. laureolae and L. leonardii from L. candidulus likely represents a response to the marked climatic changes during the Late Pliocene. Such a split was likely associated with a trophic niche shift of the laureolae/leonardii ancestor towards the typically mesophilic host plant D. laureola. The subsequent split between L. laureolae and L. leonardii, possibly due at first to the niche competition, was then boosted by an allopatric divergence during the Middle Pleistocene, likely caused by a large area of low environmental suitability for both species, mainly located between the northern Apennines and the south-western Alps.
Between Worlds: Ontological Security among Syrian Refugees in Germany and Turkey
Authors: Secen Sefa
Published: October 2024

Sometimes physical security may come at the cost of ontological security for refugees. They may struggle to develop stable narratives of identity and fail to situate themselves within their new social environments. States often prioritize addressing refugees’ physical security needs to facilitate their integration, but largely overlook the importance of identity security. This study argues that ontological security is crucial to integration processes, and refugees reestablish it by engaging in various forms of identity backlash, lowering their interest in the politics of the host country, and heightening their desire to return home. In other words, identity backlash, political disinterest, and an intensified desire to return home function as ontological security-seeking mechanisms and anxiety responses. The study contributes to ontological security theory (OST) by introducing a novel and nuanced framework that defines a set of indicators for the emotional and narrative-oriented aspects of ontological security among refugees. It takes a micro-level approach examining ontological security at the individual level for Syrian refugees in Turkey and Germany. The specific findings of this study are threefold. First, I find a significantly lower level of narrative-oriented security among Syrian refugees in Turkey than in Germany. Second, the results indicate that narrative-oriented ontological security among Syrian refugees is strongly associated with identity backlash, low political interest, and a willingness to return to the home country. Third, the results show that physical security and ontological security are not always correlated. Overall, this study demonstrates how OST can provide insights into the complex interplay between perceptions of security, identity backlash, political integration, and willingness to return among refugee communities.
Efficient statistical inference methods for assessing changes in species’ populations using citizen science data
Authors: Dennis Emily B , Diana Alex , Matechou Eleni , Morgan Byron J T
Published: October 2024

The global decline of biodiversity, driven by habitat degradation and climate breakdown, is a significant concern. Accurate measures of change are crucial to provide reliable evidence of species’ population changes. Meanwhile citizen science data have witnessed a remarkable expansion in both quantity and sources and serve as the foundation for assessing species’ status. The growing data reservoir presents opportunities for novel and improved inference but often comes with computational costs: computational efficiency is paramount, especially as regular analysis updates are necessary. Building upon recent research, we present illustrations of computationally efficient methods for fitting new models, applied to three major citizen science data sets for butterflies. We extend a method for modelling abundance changes of seasonal organisms, firstly to accommodate multiple years of count data efficiently, and secondly for application to counts from a snapshot mass-participation survey. We also present a variational inference approach for fitting occupancy models efficiently to opportunistic citizen science data. The continuous growth of citizen science data offers unprecedented opportunities to enhance our understanding of how species respond to anthropogenic pressures. Efficient techniques in fitting new models are vital for accurately assessing species’ status, supporting policy-making, setting measurable targets, and enabling effective conservation efforts.
Synchrotron self-Compton in a radiative-adiabatic fireball scenario: modelling the multiwavelength observations in some Fermi/LAT bursts
Authors: Fraija Nissim , Veres P , Betancourt Kamenetskaia B , Galvan-Gamez A , Dainotti M G , Dichiara Simone , Becerra R L
Published: October 2024

Energetic GeV photons expected from the closest and the most energetic Gamma-ray bursts (GRBs) provide a unique opportunity to study the very-high-energy emission as well as the possible correlations with lower energy bands in realistic GRB afterglow models. In the standard GRB afterglow model, the relativistic homogeneous shock is usually considered to be fully adiabatic, however, it could be partially radiative. Based on the external forward-shock scenario in both stellar wind and constant-density medium, we present a radiative-adiabatic analytical model of the synchrotron self-Compton (SSC) and synchrotron processes considering an electron energy distribution with a power-law index of $1\lt p\lt 2$ and $2\le p$. We show that the SSC scenario plays a relevant role in the radiative parameter $\epsilon$, leading to a prolonged evolution during the slow cooling regime. In a particular case, we derive the Fermi/LAT light curves together with the photons with energies $\ge 100$ MeV in a sample of nine bursts from the second Fermi/LAT GRB catalogue that exhibited temporal and spectral indices with $\gtrsim 1.5$ and $\approx 2$, respectively. These events can hardly be described with closure relations of the standard synchrotron afterglow model, and also exhibit energetic photons above the synchrotron limit. We have modelled the multiwavelength observations of our sample to constrain the microphysical parameters, the circumburst density, the bulk Lorentz factor, and the mechanism responsible for explaining the energetic GeV photons.
Constraints on the early luminosity history of the Sun: applications to the Faint Young Sun problem
Authors: Basinger Connor , Pinsonneault Marc , Bastelberger Sandra T , Gaudi B Scott , Domagal-Goldman Shawn D
Published: October 2024

Stellar evolution theory predicts that the Sun was fainter in the past, which can pose difficulties for understanding Earth’s climate history. One proposed solution to this Faint Young Sun (FYS) problem is a more luminous Sun in the past. In this paper, we address the robustness of the solar luminosity history using the yrec code to compute solar models including rotation, magnetized winds, and the associated mass-loss. We present detailed solar models, including their evolutionary history, which are in excellent agreement with solar observables. Consistent with prior standard models, we infer a high solar metal content. We provide predicted X-ray luminosities and rotation histories for usage in climate reconstructions and activity studies. We find that the Sun’s luminosity deviates from the standard solar model trajectory by at most 0.5 per cent during the Archean (corresponding to a radiative forcing of 0.849 W m$^{-2}$). The total mass-loss experienced by solar models is modest because of strong feedback between mass and angular momentum loss. We find a maximum mass-loss of $1.35 \times 10^{-3} \,{\rm M}_\odot$ since birth, at or below the level predicted by empirical estimates. The associated maximum luminosity increase falls well short of the level necessary to solve the FYS problem. We present compilations of paleotemperature and CO$_2$ reconstructions. One-dimensional ‘inverse’ climate models demonstrate a mismatch between the solar constant needed to reach high temperatures (e.g. 60–80 $^{\circ }$C) and the narrow range of plausible solar luminosities determined in this study. Maintaining a temperate Earth, however, is plausible given these conditions.
General relativistic self-gravitating equilibrium discs around rotating neutron stars
Authors: Kim Yoonsoo , Kim Jinho , Kim Hee Il , Lee Hyung Mok
Published: October 2024

In modelling a relativistic disc around a compact object, the self-gravity of the disc is often neglected while it needs to be incorporated for more accurate descriptions in several circumstances. Extending the Komatsu–Eriguchi–Hachisu self-consistent field method, we present numerical models of a rapidly rotating neutron star with a self-gravitating disc in stationary equilibrium. In particular, our approach allows us to obtain numerical solutions involving a massive disc with the rest mass $\mathcal {O}(10^{-1})-\mathcal {O}(10^0)\, \mathrm{ M}_\odot$ closely attached to a rotating neutron star, given that the disc is mainly supported by the relativistic electron degeneracy pressure. We also assess the impact of self-gravity on the internal structure of the disc and the neutron star. These axisymmetric, stationary solutions can be employed for simulations involving the neutron star–disc system in the context of high-energy transients and gravitational-wave emissions.
Evaluating the variance of individual halo properties in constrained cosmological simulations
Authors: Stiskalek Richard , Desmond Harry , Devriendt Julien , Slyz Adrianne
Published: October 2024

Constrained cosmological simulations play an important role in modelling the local Universe, enabling investigation of the dark matter content of local structures and their formation. We introduce an internal method for quantifying the extent to which the variance of individual halo properties is suppressed by the constraints imposed on the initial conditions. We apply it to the Constrained Simulations in BORG (CSiBORG) suite of 101 high-resolution realizations across the posterior probability distribution of initial conditions from the Bayesian Origin Reconstruction from Galaxies (BORG) algorithm. The method is based on the overlap of the initial Lagrangian patch of a halo in one simulation with those in another, measuring the degree to which the haloes’ particles are initially coincident. This addresses the extent to which the imposed large-scale structure constraints reduce the variance of individual halo properties. We find consistent reconstructions of $M\gtrsim 10^{14}~\mathrm{M}_\odot \, h^{-1}$ haloes, indicating that the constraints from the BORG algorithm are sufficient to pin down the masses, positions, and peculiar velocities of clusters to high precision, though we do not assess how well they reproduce observations of the local Universe. The effect of the constraints tapers off towards lower mass, and the halo spins and concentrations are largely unconstrained at all masses. We document the advantages of evaluating halo consistency in the initial conditions and describe how the method may be used to quantify our knowledge of the halo field given galaxy survey data analysed through the lens of probabilistic inference machines such as BORG.
Most extremely low mass white dwarfs with non-degenerate companions are inner binaries of hierarchical triples
Authors: Lagos-Vilches Felipe , Hernandez Mercedes , Schreiber Matthias R , Parsons Steven G , Gänsicke Boris T
Published: October 2024

Extremely low-mass white dwarfs (ELM WDs) with non-degenerate companions are believed to originate from solar-type main-sequence binaries undergoing stable Roche lobe overflow mass transfer when the ELM WD progenitor is at (or just past) the termination of the main-sequence. This implies that the orbital period of the binary at the onset of the first mass transfer phase must have been $\lesssim 3-5$ d. This prediction in turn suggests that most of these binaries should have tertiary companions since $\approx 90$ per cent of solar-type main-sequence binaries in that period range are inner binaries of hierarchical triples. Until recently, only precursors of this type of binaries have been observed in the form of EL CVn binaries, which are also known for having tertiary companions. Here, we present high-angular-resolution images of TYC 6992-827-1, an ELM WD with a sub-giant (SG) companion, confirming the presence of a tertiary companion. Furthermore, we show that TYC 6992-827-1, along with its sibling TYC 8394-1331-1 (whose triple companion was detected via radial velocity variations), are in fact descendants of EL CVn binaries. Both TYC 6992-827-1 and TYC 8394-1331-1 will evolve through a common envelope phase, which depending on the ejection efficiency of the envelope, might lead to a single WD or a tight double WD binary, which would likely merge into a WD within a few Gyr due to gravitational wave emission. The former triple configuration will be reduced to a wide binary composed of a WD (the merger product) and the current tertiary companion.
a-sloth reveals the nature of the first stars
Authors: Hartwig Tilman , Lipatova Veronika , Glover Simon C O , Klessen Ralf S
Published: October 2024

The first generation of stars (Pop III) are too dim to be observed directly and probably too short-lived to have survived for local observations. Hence, we rely on simulations and indirect observations to constrain the nature of the first stars. In this study, we calibrate the semi-analytical model a-sloth (Ancient Stars and Local Observables by Tracing Haloes), designed for simulating star formation in the early Universe, using a likelihood function based on nine independent observables. These observables span Milky Way-specific and cosmologically representative variables, ensuring a comprehensive calibration process. This calibration methodology ensures that a-sloth provides a robust representation of the early Universe’s star formation processes, aligning simulated values with observed benchmarks across a diverse set of parameters. The outcome of this calibration process is best-fitting values and their uncertainties for 11 important parameters that describe star formation in the early Universe, such as the shape of the initial mass function (IMF) of Pop III stars or escape fractions of ionizing photons. Our best-fitting model has a Pop III IMF with a steeper slope, dN/d$M \propto M^{-1.77}$, than the log-flat models often proposed in the literature, and also relatively high minimum and maximum masses, $M_{\rm min} = 13.6~\, \mathrm{M}_\odot$ and $M_{\rm max} = 197~\, \mathrm{M}_\odot$. However, we emphasize that the IMF-generating parameters are poorly constrained and, e.g. the IMF slope could vary from log-flat to Salpeter. We also provide data products, such as delay time distribution, bubble size distributions for ionizing and metal-enriched bubbles at high redshift, and correlation plots between all 11 input parameters. Our study contributes to understanding the formation of early stars through a-sloth, providing valuable insights into the nature of Pop III stars and the intricate processes involved in the early Universe’s star formation.
Indication of rapid magnetic field decay in X-ray dim isolated neutron star RX J0720.4−3125
Authors: Igoshev Andrei P , Popov Sergei B
Published: October 2024

Magnetic field evolution of neutron stars is a long-standing debate. The rate of magnetic field decay for isolated, non-accreting neutron stars can be quantified by measuring the negative second derivative of the spin period. Alternatively, this rate can be estimated by observing an excess of thermal emission with respect to the standard cooling without additional heating mechanisms involved. One of the nearby cooling isolated neutron stars – RX J0720.4−3125, – offers a unique opportunity to probe the field decay as for this source there are independent measurements of the surface X-ray luminosity, the second spin period derivative, and magnetic field. We demonstrate that the evolution rate of the spin period derivative is in correspondence with the rate of dissipation of magnetic energy of the dipolar field if a significant part of the released energy is emitted in X-rays. The instantaneous time-scale for the magnetic field decay is ${\sim} 10^4$ yr.
DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data
Authors: Kodama Yuichi , Ara Takeshi , Fukuda Asami , Tokimatsu Toshiaki , Mashima Jun , Kosuge Takehide , Tanizawa Yasuhiro , Tanjo Tomoya , Ogasawara Osamu , Fujisawa Takatomo , Nakamura Yasukazu , Arita Masanori
Published: October 2024

The Bioinformation and DNA Data Bank of Japan Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides public databases that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), the DDBJ Center accepts and distributes nucleotide sequence data ranging from raw reads to assembled and annotated sequences with the National Center for Biotechnology Information and the European Bioinformatics Institute. Besides INSDC databases, the DDBJ Center provides databases for functional genomics (Genomic Expression Archive), metabolomics (MetaboBank), human genetic variations (TogoVar-repository) and human genetic and phenotypic data (Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics supercomputer, which is also a platform for the DDBJ Group Cloud (DGC) services for sharing and analysis of pre-publication data among research groups. This paper reports recent updates on the databases and the services of the DDBJ Center, highlighting the DGC service.
Measurable disease as baseline criterion for response assessment in glioblastoma: A comparison of PET -based (PET RANO 1.0) and MRI-based (RANO) assessments
Authors: Müller Katharina J , Forbrig Robert , Reis Jonas , Wiegand Lilian , Barci Enio , Kunte Sophie C , Kaiser Lena , Schönecker Stephan , Schichor Christian , Harter Patrick N , Thon Niklas , von Baumgarten Louisa , Preusser Matthias , Albert Nathalie L
Published: October 2024

Background

Recently, criteria based on amino acid positron emission tomography (PET) have been proposed for response assessment in diffuse gliomas (PET RANO 1.0). In this study, we compare the prevalence of measurable disease according to PET RANO 1.0 with magnetic resonance imaging (MRI)-based Response Assessment in Neuro-Oncology (RANO) criteria in glioblastoma.

Methods

We retrospectively identified patients with newly diagnosed IDH-wild-type glioblastoma who underwent [18F] Fluoroethyltyrosine (FET) PET and MRI after resection or biopsy and before radio-/radiochemotherapy. Two independent investigators analyzed measurable disease according to PET RANO 1.0 or MRI-RANO criteria. Additionally, lesion size, congruency patterns, and uptake intensity on [18F]FET PET images were assessed.

Results

We evaluated 125 patients including 49 cases after primary resection and 76 cases after biopsy. Using PET criteria, 113 out of 125 patients (90.4%) had measurable disease, with a median PET-positive volume of 15.34 cm3 (8.83–38.03). With MRI, a significantly lower proportion of patients had measurable disease (57/125, 45.6%; P < .001) with a median sum of maximum cross-sectional diameters of 35.65 mm (26.18–45.98). None of the 12 patients without measurable disease on PET had measurable disease on MRI. Contrariwise, 56/68 patients (82.4%) without measurable disease on MRI exhibited measurable disease on PET. Clinical performance status correlated significantly with PET-positive volume and MRI-based sum of diameters (P < .0059, P < .0087, respectively).

Conclusions

[18F]FET PET identifies a higher number of patients with measurable disease compared to conventional MRI in newly diagnosed glioblastoma. PET-based assessment may serve as a novel baseline parameter for evaluating residual tumor burden and improving patient stratification in glioblastoma studies. Further validation in prospective trials is warranted.
LOMU Type Alkali Basalts in East Asia Sourced from Subduction Recycling of Multiple Ancient Crustal Components
Authors: Dey Bidisha , Shibata Tomoyuki , Yoshikawa Masako
Published: October 2024

The origin of alkali basalts with distinctive time-integrated low U/Pb (low μ, LOMU) from East Asia is controversial due to the complex geochemical and tectonic signatures reported from this region. We report new data on the petrology and geochemistry of the Higashi-Matsuura and Kita-Matsuura alkali basalts from Southwest Japan, which confirm the presence of a LOMU-type mantle component below the Japanese Islands, similar to East Asian intraplate volcanoes. We use whole rock geochemistry and mineral chemistry to determine mantle melting, magma evolution conditions and isotopic evolution of the LOMU mantle source. Petrological studies show that the Higashi-Matsuura alkali basalts (~3 Ma) were derived from a hydrous mantle source with ~880 μg/g H2O, at a pressure of 1.8 to 2.3 GPa at a mantle potential temperature of ~1300°C. Trace element modelling concludes that these basalts may have been generated through the hydrous upwelling and partial melting of the asthenospheric mantle containing ~15% dehydrated eclogitic component. Higashi-Matsuura alkali basalts show 206Pb/204Pb values of 17.72 to 18.04 which are among the lowest values from Southwest Japan. Relatively older (6–8 Ma) alkali basalts from the Kita-Matsuura area showing similar physicochemical characteristics, do not show LOMU-type isotopic trends. Trace element and Pb–Sr–Nd isotopic data indicate that the Higashi-Matsuura mantle component is similar to the extreme LOMU components reported from the Northeast China alkali basalts, as well as the recently discovered Petit Spot volcanoes on the Pacific Plate. We model the origin of the LOMU signature from the lowest reported Pb isotope ratios in East Asia, from intraplate alkali basalts in Northeast China. Our model suggests that at least two separate subduction events of marine sediments, at 1.8 and 2.2 Ga, are required to explain the observed Pb isotopic variation in the East Asian region. Other LOMU type basalts from East Asia, including Southwest Japan and Petit Spot, define a linear trend between the Xiaogulihe basalts and lithospheric mantle xenoliths, with 40% to 60% Pb in Higashi-Matsuura basalts being derived from the lithospheric mantle during upwelling. This suggests that the LOMU array in East Asia may have been formed by mixing between multiple ancient, subducted sediment components accumulated at the mantle transition zone for about 2 billion years, and its recent upwelling due to dehydration of the stagnant Pacific slab and related melting of the metasomatised asthenospheric mantle.
Rational Expectations Models with Higher-Order Beliefs
Authors: Huo Zhen , Takayama Naoki
Published: October 2024

We develop a method of solving rational expectations models with dispersed information and dynamic strategic complementarities. In these types of models, the equilibrium outcome hinges on an infinite number of higher-order expectations which require an increasing number of state variables to keep track of. Despite this complication, we prove that the equilibrium outcome always admits a finite-state representation when the signals follow finite ARMA processes. We also show that such a finite-state result may not hold with endogenous information aggregation. We further illustrate how to use the method to derive comparative statics, characterize equilibrium outcomes in HANK-type network games, reconcile with empirical evidence on expectations, and integrate incomplete information with bounded rationality in general equilibrium.