bluuebunny/crossref_metadata_2025 huggingface dataset:
New findings of Decapoda (Crustacea) in the Callovian of the Ryazan region (Central European Russia)
Authors: Dadykin Ivan A. , Shmakov Alexey S.
Published: December 2023

The decapod crustaceans of Central European Russia have been the subject of studies since the nineteenth century, and the only species, Eryma quadriverrucatum Trautschold, 1866 (Erymidae), has been found in the Callovian to the Oxfordian of that region. The present paper discusses the new exceptional findings of Solenoceridae, Glypheidae, and Mecochiridae from the upper Callovian sites of the Ryazan Region. The previously reported presence of Archeosolenocera sp. is confirmed in detail; Glypheopsis aff. G. etalloni (Oppel, 1861) and Eumorphia sp. are noticed for the first time for this area. Modern identification of erymids is reported: Eryma aff. E. ventrosum (von Meyer, 1835), E. ornatum (Quenstedt, 1858), and Stenodactylina insignis (Oppel, 1862) are noted in addition to E. quadriverrucatum. These findings address the gaps in the fragmented knowledge about the decapod fauna of Central European Russia and exhibit a differentiation of the local Russian decapod assemblage from those of Western Europe. The decapod community of the Ryazan region is considered to be associated with soft substrates of upper sublittoral zone.
Raids, Resistance, and Retribution: South Africa's Cato Manor Killings, 1960–1
Authors: Kynoch Gary
Published: December 2023

On 24 January 1960 nine police were killed in the African settlement of Cato Manor when residents turned on officers conducting a liquor patrol. On 5 September 1961, nine men convicted of the killings were hanged in Pretoria's Central Prison. These deaths produced contrasting narratives, one by the apartheid state and then decades later, another by the current African National Congress government. Apartheid police and judicial authorities vilified the accused as the worst kind of killers who wantonly slaughtered the representatives of law and order. Sixty years later, these murderers of the apartheid period were resurrected as martyrs and their remains were interred at Heroes Arch, a resting place for many antiapartheid activists. Moving past these binary versions allows us to consider a more mundane story that underscores the South African state's commitment to a model of policing that generated an unmatched degree of persecution in colonial Africa.
Gastrointestinal parasite assemblages from the wild rodent capybara (Hydrochoerus hydrochaeris) inhabiting a natural protected area from Argentina
Authors: Tietze E. , Bellusci A. , Cañal V. , Cringoli G. , Beltrame M.O.
Published: December 2023

Knowledge about parasitic diseases of wildlife will help us to understand the dynamics of parasites and their effects on host populations. The capybara (Hydrochoerus hydrochaeris) is the largest living rodent in the world, and its distribution is associated with the presence of tropical and subtropical wetlands in South America. The Los Padres Lake Integral Reserve (LPLIR) is an important conservation zone in the pampean region of Argentina. One of the emblematic species found within the reserve is the capybara. The objective of this study was to determine the gastrointestinal parasites present in wild capybaras of the LPLIR and to compare different coprological methodologies. Free-ranging capybara fresh feces from 57 individuals were randomly collected from the area of LPLIR in the summer of 2022. Three different techniques were applied: spontaneous sedimentation technique (SS), INTA modified McMaster technique (MM), and Mini-FLOTAC (MF) technique. Fifty-six samples from all samples analysed (56/57, 98%) were found to be positive for gastrointestinal parasites. Two species of Strongylida,Protozoophaga obesa,Echinocoleus hydrochaeris, one unidentified nematode, one unidentified spirurid, and at least two morphotypes ofEimeriaspp. oocysts were recorded. There were found significant differences in the proportion of positive samples and in richness by technique, but no significant differences were found in parasite counting. In conclusion, the choice of methodology depends on the specific objectives of the study. This is the first parasitological study of capybaras from the LPLIR and represents an exploration of parasite communities present in these wild rodents at their southernmost distribution.
Maternal social support during and after pregnancy and child cognitive ability: examining timing effects in two cohorts
Authors: Lähdepuro Anna , Räikkönen Katri , Pham Hung , Thompson-Felix Tara , Eid Rand S. , O'Connor Thomas G. , Glover Vivette , Lahti Jari , Heinonen Kati , Wolford Elina , Lahti-Pulkkinen Marius , O'Donnell Kieran J.
Published: December 2023

Background

Maternal anxiety, depression, and stress during and after pregnancy are negatively associated with child cognitive development. However, the contribution of positive maternal experiences, such as social support, to child cognitive development has received less attention. Furthermore, how maternal experience of social support during specific developmental periods impacts child cognitive development is largely unknown.

Methods

Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC; n = 5784) and the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction study (PREDO; n = 420), we investigated the associations between maternal perceived social support during and after pregnancy and child's general cognitive ability at 8 years of age, assessed with the Wechsler Intelligence Scale for Children (WISC). Bayesian relevant life course modeling was used to investigate timing effects of maternal social support on child cognitive ability.

Results

In both cohorts, higher maternal perceived social support during pregnancy was associated with higher performance on the WISC, independent of sociodemographic factors and concurrent maternal symptoms of depression and anxiety. In ALSPAC, pregnancy emerged as a sensitive period for the effects of perceived social support on child cognitive ability, with a stronger effect of social support during pregnancy than after pregnancy on child cognitive ability.

Conclusions

Our findings, supported from two prospective longitudinal cohorts, suggest a distinct role of maternal perceived social support during pregnancy for cognitive development in children. Our study suggests that interventions aimed at increasing maternal social support during pregnancy may be an important strategy for promoting maternal and child well-being.
Cognates are advantaged over non-cognates in early bilingual expressive vocabulary development
Authors: MITCHELL Lori , TSUI Rachel Ka-Ying , BYERS-HEINLEIN Krista
Published: December 2023

Bilinguals need to learn two words for most concepts. These words are called translation equivalents, and those that also sound similar (e.g., banana–banane) are called cognates. Research has consistently shown that children and adults process and name cognates more easily than non-cognates. The present study explored if there is such an advantage for cognate production in bilinguals’ early vocabulary development. Longitudinal expressive vocabulary data were collected from 47 English–French bilinguals starting at 16–20 months up to 27 months (a total of 219 monthly administrations in both English and French). Children produced a greater proportion of cognates than non-cognates, and the interval between producing a word and its translation equivalent was about 10–15 days shorter for cognates than for non-cognates. The findings suggest that cognate learning is facilitated in early bilingual vocabulary development, such that phonological overlap supports bilinguals in learning phonologically similar words across their two languages.
“You’re Not Understood, and You’re Isolated”: A Narrative Account of Loneliness by Black Older Adults in Ontario, Canada
Authors: Ojembe Blessing , Kapiriri Lydia , Griffin Meridith , Schormans Ann Fudge
Published: December 2023

Loneliness among older adults is a leading health and social concern globally and in Canada, including racialized and minoritized groups. Although previous studies have explored loneliness among ethnic minoritized groups in Canada, little is known about the constellating factors contributing to loneliness among native-born and immigrant Black older adults (BOAs) in Canada and their unique ways of dealing with the experience. Our study explores the constellating factors shaping loneliness experiences among BOAs living in Ontario. Using a narrative approach, we purposively selected and interviewed 13 BOAs. Time as a driver of change, a sense of belonging reinforced through place identity, and challenges of making a new home were dominant themes. Our finding highlights the need for increased cultural sensitivity at the micro and macro levels, which will improve a sense of belonging and reduce loneliness among racialized immigrant older adults.
Pre-stimulus bioelectrical activity in light-adapted ERG under blue versus white background
Authors: Tsay Katherine , Safari Sara , Abou-Samra Abdullah , Kremers Jan , Tzekov Radouil
Published: December 2023

To compare the baseline signal between two conditions used to generate the photopic negative response (PhNR) of the full-field electroretinogram (ERG): red flash on a blue background (RoB) and white flash on a white background (LA3). The secondary purpose is to identify how the level of pre-stimulus signal affects obtaining an unambiguous PhNR component. A retrospective chart review was conducted on four cohorts of patients undergoing routine ERG testing. In each group, LA3 was recorded the same way while RoB was generated differently using various luminances of red and blue light. The background bioelectrical activity 30 ms before the flash was extracted, and the root mean square (RMS) of the signal was calculated and compared between RoB and LA3 using Wilcoxon test. Pre-stimulus noise was significantly higher under RoB stimulation versus LA3 in all four conditions for both right and left eyes (ratio RoB/LA3 RMS 1.70 and 1.57 respectively, p < 0.033). There was also no significant difference between the RMS of either LA3 or RoB across protocols, indicating that the baseline noise across cohorts were comparable. Additionally, pre-stimulus noise was higher in signals where PhNR was not clearly identifiable as an ERG component versus signals with the presence of unambiguous PhNR component under RoB in all four groups for both eyes (p < 0.05), whereas the difference under LA3 was less pronounced. Our study suggests that LA3 produces less background bioelectrical activity, likely due to decreased facial muscle activity. As it seems that the pre-stimulus signal level affects PhNR recordability, LA3 may also produce a better-quality signal compared to RoB. Therefore, until conditions for a comparable bioelectrical activity under RoB are established, we believe that LA3 should be considered at least as a supplementary method to evaluate retinal ganglion cell function by ERG.
Investigating the Impact of an Exsolved H2O‐CO2 Phase on Magma Chamber Growth and Longevity: A Thermomechanical Model
Authors: Scholz Kathryn , Townsend Meredith , Huber Christian , Troch Juliana , Bachmann Olivier , Coonin Allie N.
Published: December 2023

Magmatic volatiles drive pressure, temperature, and compositional changes in upper crustal magma chambers and alter the physical properties of stored magmas. Previous studies suggest that magmatic H2O content influences the growth and longevity of silicic chambers through regulating the size and frequency of eruptions and impacting the crystallinity‐temperature curve. However, there has been comparatively little exploration of how CO2 impacts the evolution of magma chambers despite the strong influence of CO2 on H2O solubility and the high concentrations of CO2 often present in mafic systems. In this study, we integrate the thermodynamic effects of dissolved and exsolved H2O and CO2 with the mechanics of open‐system magma chambers that interact thermally and mechanically with the crust. We applied this model to investigate how intrinsic variations in magmatic H2O‐CO2 content influence the growth and longevity of silicic and mafic magma chambers. Our findings indicate that even with a tenfold increase in CO2 content (up to 10,000 ppm), CO2 plays a minimal role in long‐term chamber growth and longevity. While CO2 content affects the magma compressibility, the resulting changes in eruption mass are balanced out by a commensurate change in eruption frequency so that the time‐averaged eruptive flux and long‐term chamber behavior remain similar. In contrast, H2O content strongly influences chamber growth and longevity. In silicic systems, high H2O contents hinder magma chamber growth by increasing the total eruptive flux and steepening the slope of the crystallinity‐temperature curve. In mafic systems, high H2O contents promote magma chamber growth by flattening the slope of the crystallinity‐temperature curve.
The Effect of Different Implementations of the Weak Temperature Gradient Approximation in Cloud Resolving Models
Authors: Wong N. Z. , Kuang Z.
Published: December 2023

The Weak Temperature Gradient (WTG) approximation is a popular method used to couple convection in limited‐area domain simulations with large‐scale dynamics. However, several different schemes have been created to implement this approximation, and these different WTG schemes show a wide range of different results in an idealized framework. Our investigation shows that different model behavior is caused by the treatment of the different baroclinic modes by the different WTG schemes. More specifically, we hypothesize that the relative strengths of the baroclinic modes plays a large role in these differences, and show that modifying these schemes such that they treat the baroclinic modes in a similar manner accounts for many of the significant differences observed.
Seismic Autocorrelation Analysis of Deep Mars
Authors: Deng Sizhuang , Levander Alan
Published: December 2023

The InSight mission deployed one seismic station on Mars, providing a chance to apply single‐station‐based autocorrelation analysis to investigate Martian subsurface structures. However, recent analysis indicated the low‐frequency autocorrelation signals may originate from quasi‐periodic high‐amplitude instrumental “glitches” rather than the reflection response of deep Mars. In this study, we detected and removed these high‐amplitude glitches in raw seismic data and employed autocorrelation on the clean vertical component waveforms filtered between 0.05 and 0.1 Hz. We observed signals at the expected times for the olivine‐wadsleyite transition and core‐mantle boundary (CMB) as estimated by other methods. This result suggests that the low‐frequency autocorrelation signals are the reflection response from the olivine‐wadsleyite transition in the mantle and the Martian CMB region, rather than a noise phenomena. A grid search method to fit the observed PcP waveform was used to identify a layer intermediate in velocity between the Martian mantle and core at the Martian CMB.
Tropical Origins of the Pacific Meridional Mode Associated With the Nonlinear Interaction of ENSO With the Annual Cycle
Authors: Jiang Feng , Zhang Wenjun , Boucharel Julien , Jin Fei‐Fei
Published: December 2023

The Pacific Meridional Mode (PMM) has long been associated with extra‐tropical air‐sea coupling processes, which are thought to influence the development of El Niño‐Southern Oscillation (ENSO). Here we show that the PMM on seasonal to interannual timescales is closely associated with a newly proposed tropical mode known as the ENSO Combination mode (C‐mode), which arises from the nonlinear interaction between ENSO and the background annual cycle in the deep tropics. The PMM exhibits a remarkable resemblance with the C‐mode in atmospheric patterns, spectral characteristics, and local impacts. Based on a simple Hasselmann‐type model, we further demonstrate that the C‐mode‐related atmospheric anomalies can effectively drive PMM‐like sea surface temperature anomalies. As the C‐mode captures seasonally modulated ENSO characteristics, the seasonal‐to‐interannual PMM variability could naturally establish a connection with ENSO, thereby offering an alternative explanation for the observed relationship between PMM and ENSO.
Anomalous Meltwater From Ice Sheets and Ice Shelves Is a Historical Forcing
Authors: Schmidt Gavin. A. , Romanou Anastasia , Roach Lettie A. , Mankoff Kenneth D. , Li Qian , Rye Craig D. , Kelley Maxwell , Marshall John C. , Busecke Julius J. M.
Published: December 2023

Recent mass loss from ice sheets and ice shelves is now persistent and prolonged enough that it impacts downstream oceanographic conditions. To demonstrate this, we use an ensemble of coupled GISS‐E2.1‐G simulations forced with historical estimates of anomalous freshwater, in addition to other climate forcings, from 1990 through 2019. There are detectable differences in zonal‐mean sea surface temperatures (SST) and sea ice in the Southern Ocean, and in regional sea level around Antarctica and in the western North Atlantic. These impacts mostly improve the model's representation of historical changes, including reversing the forced trends in Antarctic sea ice. The changes in SST may have implications for estimates of the SST pattern effect on climate sensitivity and for cloud feedbacks. We conclude that the changes are sufficiently large that model groups should strive to include more accurate estimates of these drivers in all‐forcing historical simulations in future coupled model intercomparisons.
Energy Conversion by a Twisted Magnetic Structure at Magnetopause Boundary Layer: MMS Observations
Authors: Du C. X. , Fu H. S. , Wang Z. , Cao J. B. , Liu Y. Y. , Fu W. D.
Published: December 2023

The Earth's magnetopause is an ion‐scale boundary that separates the magnetosphere from the shocked solar wind. At such boundary, energy‐conversion processes frequently occur. Previous studies suggested that such energy conversions are related to the magnetic reconnection process. Here, we report a new mechanism that the coaction between the twisted magnetic structure and lower‐hybrid waves can also drive energy conversion (J⋅ E, J is current density and E is electric field) at the magnetopause boundary layer, by using high‐resolution measurements of the four Magnetospheric Multiscale spacecraft. We find that such energy conversion is efficient (with magnitude up to 20 nW/m3) and is attributed to an intense current filament (j ≈ 3,800 nA/m2) and a fluctuating electric field driven by lower‐hybrid waves. With the help of the First‐Order Taylor Expansion method, we find that the intense current filament is driven by a twisted magnetic structure at electron scale. Our study improves the understanding of energy‐conversion processes at the Earth's magnetopause.
Cortical microstructural associations with CSF amyloid and pTau
Authors: Nir Talia M. , Villalón-Reina Julio E. , Salminen Lauren E. , Haddad Elizabeth , Zheng Hong , Thomopoulos Sophia I. , Jack Clifford R. , Weiner Michael W. , Thompson Paul M. , Jahanshad Neda ,   for the Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: December 2023

Diffusion MRI (dMRI) can be used to probe microstructural properties of brain tissue and holds great promise as a means to non-invasively map Alzheimer’s disease (AD) pathology. Few studies have evaluated multi-shell dMRI models such as neurite orientation dispersion and density imaging (NODDI) and mean apparent propagator (MAP)-MRI in cortical gray matter where many of the earliest histopathological changes occur in AD. Here, we investigated the relationship between CSF pTau181 and Aβ1–42 burden and regional cortical NODDI and MAP-MRI indices in 46 cognitively unimpaired individuals, 18 with mild cognitive impairment, and two with dementia (mean age: 71.8 ± 6.2 years) from the Alzheimer’s Disease Neuroimaging Initiative. We compared findings to more conventional cortical thickness measures. Lower CSF Aβ1–42 and higher pTau181 were associated with cortical dMRI measures reflecting less hindered or restricted diffusion and greater diffusivity. Cortical dMRI measures, but not cortical thickness measures, were more widely associated with Aβ1–42 than pTau181 and better distinguished Aβ+ from Aβ- participants than pTau+ from pTau- participants. dMRI associations mediated the relationship between CSF markers and delayed logical memory performance, commonly impaired in early AD. dMRI metrics sensitive to early AD pathogenesis and microstructural damage may be better measures of subtle neurodegeneration in comparison to standard cortical thickness and help to elucidate mechanisms underlying cognitive decline.
Feasibility of a novel wearable thermal device for management of bothersome hot flashes in patients with prostate cancer
Authors: Peeke Pamela , Billes Sonja K. , Vetter Andrew , Naghavi Nader , Le Diana , Smith Matthew , Morgans Alicia K.
Published: December 2023

Background

This single-arm prospective study evaluated the feasibility of a novel wrist-worn thermal device that applies cooling to the inside of the wrist for management of bothersome hot flashes in prostate cancer survivors.

Methods

57 individuals were enrolled and instructed to use the thermal device as needed for management of hot flashes for 4 weeks. The primary outcome was thermal device usage (hours and sessions per day). Additional outcomes included the change in Hot Flash Related Daily Interference Scale (HFRDIS, range 0–10) and Patient Reported Outcomes Measurement Information System Sleep Disturbance 4a (PROMIS SD T-score, range 0–100) and Sleep-Related Impairment 8a (PROMIS SRI T-score, range 0–100). Study procedures were conducted remotely from May to Dec 2021 in the US.

Results

44 participants completed the study and 39 had retrievable usage data. The mean ± SD age was 67 ± 6 years and 5 ± 5 years since cancer diagnosis. The baseline mean ± SD HFRDIS score of 4.3 ± 2.0 indicated moderate hot flash interference in this population. During the study, participants used the thermal device (mean ± SD) 3.2 ± 2.5 hours/day and 7.6 ± 3.6 sessions/day. Most (67%) participants reported using the device 7 days and 7 nights each week. Statistically significant improvements from baseline at Week 4 were observed for HFRDIS (mean ± SE change: −1.1 ± 0.3), PROMIS SD (−6.0 ± 1.0), and PROMIS SRI (−5.5 ± 1.2) scores (all p < 0.001). The majority (69%) of participants reported that the thermal device was effective at helping them manage hot flashes. No adverse events were reported.

Conclusions

Results support the feasibility of using the thermal device for management of bothersome hot flashes in prostate cancer survivors. Future randomized controlled studies are warranted to evaluate the impact of the thermal device on frequency and severity of hot flashes, sleep quality, fatigue, and overall quality of life.
Chlorpromazine affects glioblastoma bioenergetics by interfering with pyruvate kinase M2
Authors: Abbruzzese Claudia , Matteoni Silvia , Matarrese Paola , Signore Michele , Ascione Barbara , Iessi Elisabetta , Gurtner Aymone , Sacconi Andrea , Ricci-Vitiani Lucia , Pallini Roberto , Pace Andrea , Villani Veronica , Polo Andrea , Costantini Susan , Budillon Alfredo , Ciliberto Gennaro , Paggi Marco G.
Published: December 2023

Glioblastoma (GBM) is the most frequent and lethal brain tumor, whose therapeutic outcome - only partially effective with current schemes - places this disease among the unmet medical needs, and effective therapeutic approaches are urgently required. In our attempts to identify repositionable drugs in glioblastoma therapy, we identified the neuroleptic drug chlorpromazine (CPZ) as a very promising compound. Here we aimed to further unveil the mode of action of this drug. We performed a supervised recognition of the signal transduction pathways potentially influenced by CPZ via Reverse-Phase Protein microArrays (RPPA) and carried out an Activity-Based Protein Profiling (ABPP) followed by Mass Spectrometry (MS) analysis to possibly identify cellular factors targeted by the drug. Indeed, the glycolytic enzyme PKM2 was identified as one of the major targets of CPZ. Furthermore, using the Seahorse platform, we analyzed the bioenergetics changes induced by the drug. Consistent with the ability of CPZ to target PKM2, we detected relevant changes in GBM energy metabolism, possibly attributable to the drug’s ability to inhibit the oncogenic properties of PKM2. RPE-1 non-cancer neuroepithelial cells appeared less responsive to the drug. PKM2 silencing reduced the effects of CPZ. 3D modeling showed that CPZ interacts with PKM2 tetramer in the same region involved in binding other known activators. The effect of CPZ can be epitomized as an inhibition of the Warburg effect and thus malignancy in GBM cells, while sparing RPE-1 cells. These preclinical data enforce the rationale that allowed us to investigate the role of CPZ in GBM treatment in a recent multicenter Phase II clinical trial.
Competition and evolutionary selection among core regulatory motifs in gene expression control
Authors: Gyorgy Andras
Published: December 2023

Gene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that carry their own bioenergetic cost. By ensuring that regulators are only expressed when needed, we demonstrate that autoregulation generally offers an advantage in an environment combining mutation and time-varying selection. Whether positive or negative feedback emerges as dominant depends primarily on the demand for the target gene product, typically to ensure that the detrimental impact of inevitable mutations is minimized. While self-repression of the regulator curbs the spread of these loss-of-function mutations, self-activation instead facilitates their propagation. By analyzing the transcription network of multiple model organisms, we reveal that reduced bioenergetic cost may contribute to the preferential selection of autoregulation among transcription factors. Our results not only uncover how seemingly equivalent regulatory motifs have fundamentally different impact on population structure, growth dynamics, and evolutionary outcomes, but they can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits.
Global distribution and dynamics of muddy coasts
Authors: Hulskamp Romy , Luijendijk Arjen , van Maren Bas , Moreno-Rodenas Antonio , Calkoen Floris , Kras Etiënne , Lhermitte Stef , Aarninkhof Stefan
Published: December 2023

Muddy coasts provide ecological habitats, supply food and form a natural coastal defence. Relative sea level rise, changing wave energy and human interventions will increase the pressure on muddy coastal zones. For sustainable coastal management it is key to obtain information on the geomorphology of and historical changes along muddy areas. So far, little is known about the distribution and behaviour of muddy coasts at a global scale. In this study we present a global scale assessment of the occurrence of muddy coasts and rates of coastline change therein. We combine publicly available satellite imagery and coastal geospatial datasets, to train an automated classification method to identify muddy coasts. We find that 14% of the world’s ice-free coastline is muddy, of which 60% is located in the tropics. Furthermore, the majority of the world’s muddy coasts are eroding at rates exceeding 1 m/yr over the last three decades.
Crystal-facet-dependent surface transformation dictates the oxygen evolution reaction activity in lanthanum nickelate
Authors: Füngerlings Achim , Wohlgemuth Marcus , Antipin Denis , van der Minne Emma , Kiens Ellen Marijn , Villalobos Javier , Risch Marcel , Gunkel Felix , Pentcheva Rossitza , Baeumer Christoph
Published: December 2023

Electrocatalysts are the cornerstone in the transition to sustainable energy technologies and chemical processes. Surface transformations under operation conditions dictate the activity and stability. However, the dependence of the surface structure and transformation on the exposed crystallographic facet remains elusive, impeding rational catalyst design. We investigate the (001), (110) and (111) facets of a LaNiO3−δ electrocatalyst for water oxidation using electrochemical measurements, X-ray spectroscopy, and density functional theory calculations with a Hubbard U term. We reveal that the (111) overpotential is ≈ 30−60 mV lower than for the other facets. While a surface transformation into oxyhydroxide-like NiOO(H) may occur for all three orientations, it is more pronounced for (111). A structural mismatch of the transformed layer with the underlying perovskite for (001) and (110) influences the ratio of Ni2+ and Ni3+ to Ni4+ sites during the reaction and thereby the binding energy of reaction intermediates, resulting in the distinct catalytic activities of the transformed facets.
GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations
Authors: Song Tianci , Broadbent Charles , Kuang Rui
Published: December 2023

Spatially-resolved RNA profiling has now been widely used to understand cells’ structural organizations and functional roles in tissues, yet it is challenging to reconstruct the whole spatial transcriptomes due to various inherent technical limitations in tissue section preparation and RNA capture and fixation in the application of the spatial RNA profiling technologies. Here, we introduce a graph-guided neural tensor decomposition (GNTD) model for reconstructing whole spatial transcriptomes in tissues. GNTD employs a hierarchical tensor structure and formulation to explicitly model the high-order spatial gene expression data with a hierarchical nonlinear decomposition in a three-layer neural network, enhanced by spatial relations among the capture spots and gene functional relations for accurate reconstruction from highly sparse spatial profiling data. Extensive experiments on 22 Visium spatial transcriptomics datasets and 3 high-resolution Stereo-seq datasets as well as simulation data demonstrate that GNTD consistently improves the imputation accuracy in cross-validations driven by nonlinear tensor decomposition and incorporation of spatial and functional information, and confirm that the imputed spatial transcriptomes provide a more complete gene expression landscape for downstream analyses of cell/spot clustering for tissue segmentation, and spatial gene expression clustering and visualizations.
Topological structures and syntenic conservation in sea anemone genomes
Authors: Zimmermann Bob , Montenegro Juan D. , Robb Sofia M. C. , Fropf Whitney J. , Weilguny Lukas , He Shuonan , Chen Shiyuan , Lovegrove-Walsh Jessica , Hill Eric M. , Chen Cheng-Yi , Ragkousi Katerina , Praher Daniela , Fredman David , Schultz Darrin , Moran Yehu , Simakov Oleg , Genikhovich Grigory , Gibson Matthew C. , Technau Ulrich
Published: December 2023

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.
Hyperbolic exciton polaritons in a van der Waals magnet
Authors: Ruta Francesco L. , Zhang Shuai , Shao Yinming , Moore Samuel L. , Acharya Swagata , Sun Zhiyuan , Qiu Siyuan , Geurs Johannes , Kim Brian S. Y. , Fu Matthew , Chica Daniel G. , Pashov Dimitar , Xu Xiaodong , Xiao Di , Delor Milan , Zhu X-Y. , Millis Andrew J. , Roy Xavier , Hone James C. , Dean Cory R. , Katsnelson Mikhail I. , van Schilfgaarde Mark , Basov D. N.
Published: December 2023

Exciton polaritons are quasiparticles of photons coupled strongly to bound electron-hole pairs, manifesting as an anti-crossing light dispersion near an exciton resonance. Highly anisotropic semiconductors with opposite-signed permittivities along different crystal axes are predicted to host exotic modes inside the anti-crossing called hyperbolic exciton polaritons (HEPs), which confine light subdiffractionally with enhanced density of states. Here, we show observational evidence of steady-state HEPs in the van der Waals magnet chromium sulfide bromide (CrSBr) using a cryogenic near-infrared near-field microscope. At low temperatures, in the magnetically-ordered state, anisotropic exciton resonances sharpen, driving the permittivity negative along one crystal axis and enabling HEP propagation. We characterize HEP momentum and losses in CrSBr, also demonstrating coupling to excitonic sidebands and enhancement by magnetic order: which boosts exciton spectral weight via wavefunction delocalization. Our findings open new pathways to nanoscale manipulation of excitons and light, including routes to magnetic, nonlocal, and quantum polaritonics.
Grassland intensification effects cascade to alter multifunctionality of wetlands within metaecosystems
Authors: Guo Yuxi , Boughton Elizabeth H. , Bohlman Stephanie , Bernacchi Carl , Bohlen Patrick J. , Boughton Raoul , DeLucia Evan , Fauth John E. , Gomez-Casanovas Nuria , Jenkins David G. , Lollis Gene , Miller Ryan S. , Quintana-Ascencio Pedro F. , Sonnier Grégory , Sparks Jed , Swain Hilary M. , Qiu Jiangxiao
Published: December 2023

Sustainable agricultural intensification could improve ecosystem service multifunctionality, yet empirical evidence remains tenuous, especially regarding consequences for spatially coupled ecosystems connected by flows across ecosystem boundaries (i.e., metaecosystems). Here we aim to understand the effects of land-use intensification on multiple ecosystem services of spatially connected grasslands and wetlands, where management practices were applied to grasslands but not directly imposed to wetlands. We synthesize long-term datasets encompassing 53 physical, chemical, and biological indicators, comprising >11,000 field measurements. Our results reveal that intensification promotes high-quality forage and livestock production in both grasslands and wetlands, but at the expense of water quality regulation, methane mitigation, non-native species invasion resistance, and biodiversity. Land-use intensification weakens relationships among ecosystem services. The effects on grasslands cascade to alter multifunctionality of embedded natural wetlands within the metaecosystems to a similar extent. These results highlight the importance of considering spatial flows of resources and organisms when studying land-use intensification effects on metaecosystems as well as when designing grassland and wetland management practices to improve landscape multifunctionality.
Sex-dimorphic neuroprotective effect of CD163 in an α-synuclein mouse model of Parkinson’s disease
Authors: Ferreira Sara A. , Li Conghui , Klæstrup Ida H. , Vitic Zagorka , Rasmussen Rikke K. , Kirkegaard Asger , Toft Gitte U. , Betzer Cristine , Svendsen Pia , Jensen Poul H. , Luo Yonglun , Etzerodt Anders , Moestrup Søren K. , Romero-Ramos Marina
Published: December 2023

Alpha-synuclein (α-syn) aggregation and immune activation represent hallmark pathological events in Parkinson’s disease (PD). The PD-associated immune response encompasses both brain and peripheral immune cells, although little is known about the immune proteins relevant for such a response. We propose that the upregulation of CD163 observed in blood monocytes and in the responsive microglia in PD patients is a protective mechanism in the disease. To investigate this, we used the PD model based on intrastriatal injections of murine α-syn pre-formed fibrils in CD163 knockout (KO) mice and wild-type littermates. CD163KO females revealed an impaired and differential early immune response to α-syn pathology as revealed by immunohistochemical and transcriptomic analysis. After 6 months, CD163KO females showed an exacerbated immune response and α-syn pathology, which ultimately led to dopaminergic neurodegeneration of greater magnitude. These findings support a sex-dimorphic neuroprotective role for CD163 during α-syn-induced neurodegeneration.
In vitro production of cat-restricted Toxoplasma pre-sexual stages
Authors: Antunes Ana Vera , Shahinas Martina , Swale Christopher , Farhat Dayana C. , Ramakrishnan Chandra , Bruley Christophe , Cannella Dominique , Robert Marie G. , Corrao Charlotte , Couté Yohann , Hehl Adrian B. , Bougdour Alexandre , Coppens Isabelle , Hakimi Mohamed-Ali
Published: December 2023

Sexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described1,2. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. 1), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on Toxoplasma sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.
Dynamic behaviour restructuring mediates dopamine-dependent credit assignment
Authors: Tang Jonathan C. Y. , Paixao Vitor , Carvalho Filipe , Silva Artur , Klaus Andreas , da Silva Joaquim Alves , Costa Rui M.
Published: December 2023

Animals exhibit a diverse behavioural repertoire when exploring new environments and can learn which actions or action sequences produce positive outcomes. Dopamine release after encountering a reward is critical for reinforcing reward-producing actions1–3. However, it has been challenging to understand how credit is assigned to the exact action that produced the dopamine release during continuous behaviour. Here we investigated this problem in mice using a self-stimulation paradigm in which specific spontaneous movements triggered optogenetic stimulation of dopaminergic neurons. Dopamine self-stimulation rapidly and dynamically changes the structure of the entire behavioural repertoire. Initial stimulations reinforced not only the stimulation-producing target action, but also actions similar to the target action and actions that occurred a few seconds before stimulation. Repeated pairings led to a gradual refinement of the behavioural repertoire to home in on the target action. Reinforcement of action sequences revealed further temporal dependencies of refinement. Action pairs spontaneously separated by long time intervals promoted a stepwise credit assignment, with early refinement of actions most proximal to stimulation and subsequent refinement of more distal actions. Thus, a retrospective reinforcement mechanism promotes not only reinforcement, but also gradual refinement of the entire behavioural repertoire to assign credit to specific actions and action sequences that lead to dopamine release.
An integrated individual-level trait-based phytoplankton dataset from transitional waters
Authors: Laraib Maira , Titocci Jessica , Rosati Ilaria , Basset Alberto
Published: December 2023

Functional trait-based approaches have undergone an extraordinary expansion in phytoplankton ecology. Morpho-functional traits have been shown to vary both within and between populations and species, potentially affecting individual fitness and the network of inter-individual relationships. Here we integrate six fully harmonized phytoplankton morpho-functional trait datasets, characterized by a fine data grain, reporting individual-level data over a large biogeographical area. Datasets refer to transitional water ecosystems, from five biogeographical areas: Northern Atlantic Ocean (Scotland), South-Western Atlantic Ocean (Brazil), South-Western Pacific Ocean (Australia), Indo Pacific Ocean (Maldives) and Mediterranean Sea (Greece and Turkey). The integrated dataset includes 127311 individual phytoplankton records with sampling locations, taxonomic and morphometric information according to Darwin Core standards and semantic annotations. The six FAIR datasets are openly available in the LifeWatch Italy data portal. The datasets have already been used for morpho-functional analyses and hypothesis testing on phytoplankton guilds at different levels of data aggregation and scale, from local to global.
Towards understanding policy design through text-as-data approaches: The policy design annotations (POLIANNA) dataset
Authors: Sewerin Sebastian , Kaack Lynn H. , Küttel Joel , Sigurdsson Fride , Martikainen Onerva , Esshaki Alisha , Hafner Fabian
Published: December 2023

Despite the importance of ambitious policy action for addressing climate change, large and systematic assessments of public policies and their design are lacking as analysing text manually is labour-intensive and costly. POLIANNA is a dataset of policy texts from the European Union (EU) that are annotated based on theoretical concepts of policy design, which can be used to develop supervised machine learning approaches for scaling policy analysis. The dataset consists of 20,577 annotated spans, drawn from 18 EU climate change mitigation and renewable energy policies. We developed a novel coding scheme translating existing taxonomies of policy design elements to a method for annotating text spans that consist of one or several words. Here, we provide the coding scheme, a description of the annotated corpus, and an analysis of inter-annotator agreement, and discuss potential applications. As understanding policy texts is still difficult for current text-processing algorithms, we envision this database to be used for building tools that help with manual coding of policy texts by automatically proposing paragraphs containing relevant information.
Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica
Authors: Xu Zhe , Bai Jianyang , Zhang Yue , Li Lu , Min Mengru , Cao Jingyu , Cao Jingxin , Xu Yanchun , Li Fei , Ma Ling
Published: December 2023

The Asian spongy moth,Lymantria dispar asiatica, is one of the most devastating forestry defoliators. The absence of a high-quality genome limited the understanding of its adaptive evolution. Here, we conducted the first chromosome-level genome assembly ofL. dispar asiaticausing PacBio HIFI long reads, Hi-C sequencing reads and transcriptomic data. The total assembly size is 997.59 Mb, containing 32 chromosomes with a GC content of 38.91% and a scaffold N50 length of 35.42 Mb. The BUSCO assessment indicated a completeness estimate of 99.4% for this assembly. A total of 19,532 protein-coding genes was predicted. Our study provides a valuable genomics resource for studying the mechanisms of adaptive evolution and facilitate an efficient control ofL. dispar asiatica.
Epidemiological and clinical features of SARS-CoV-2 Omicron variant infection in Quanzhou, Fujian province: a retrospective study
Authors: Zhang Huatang , Weng Zhangyan , Zheng Yijuan , Zheng Minghui , Chen Wenhuang , He Haoyi , Ye Xiaoyi , Zheng Youxian , Xie Jianfeng , Zheng Kuicheng , Zhang Jiming , Zhuang Xibin , Su Zhijun , Zhou Yongjun , Yu Xueping
Published: December 2023

Epidemiological and clinical data of patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (BA.2) admitted to three designated hospitals in Quanzhou City, Fujian Province, China, were collected and analyzed. Overall, 2,541 patients infected with BA.2, comprising 1,060 asymptomatic, 1,287 mild, and 194 moderate infections, were enrolled. The percentage of moderate infections was higher in patients aged ≥ 60 years than in those aged < 18 years and 18–59 years. The median hospitalization duration was 17 days. Among the 2,541 patients, 43.52% had a clear history of close contact. The vaccination rate was 87.92%, and the percentage of asymptomatic infections was higher in vaccinated than in unvaccinated patients. Moreover, patients with underlying diseases, including hypertension and diabetes mellitus, had more moderate infections than those without underlying diseases. The three most common clinical manifestations were fever, dry cough, and sore throat. The albumin-to-globulin (A/G) ratio and lymphocyte count decreased in cases with mild and moderate infections, while procalcitonin, erythrocyte sedimentation rate, interleukin-6, D-dimer, and C4 levels increased. Advanced age, non-vaccination, and underlying comorbid diseases were high-risk factors for disease progression in patients. However, dynamic monitoring of blood routine parameters, A/G ratio, and inflammatory indicators facilitated the prediction of disease progression.
Inflammatory protein signatures in individuals with obesity and metabolic syndrome
Authors: Mir Fayaz Ahmad , Abdesselem Houari B. , Cyprian Farhan , Iskandarani Ahmad , Doudin Asmma , Samra Tareq A. , Alkasem Meis , Abdalhakam Ibrahem , Taheri Shahrad , Abou-Samra Abdul-Badi
Published: December 2023

There is variability in the metabolic health status among individuals presenting with obesity; some may be metabolically healthy, while others may have developed the metabolic syndrome, a cluster including insulin resistance, hypertension, dyslipidemia, and increased risk of cardiovascular disease and type 2 diabetes. The mechanisms contributing to this metabolic heterogeneity are not fully understood. To address this question, plasma samples from 48 individuals with BMI ≥ 35 kg/m2 were examined (27 with and 21 without metabolic syndrome). Fasting plasma samples were subjected to Olink proteomics analysis for 184 cardiometabolic and inflammation-enriched proteins. Data analysis showed a clear differentiation between the two groups with distinct plasma protein expression profiles. Twenty-four proteins were differentially expressed (DEPs) between the two groups. Pathways related to immune cell migration, leukocyte chemotaxis, chemokine signaling, mucosal inflammatory response, tissue repair and remodeling were enriched in the group with metabolic syndrome. Functional analysis of DEPs revealed upregulation of 15 immunological pathways. The study identifies some of the pathways that are altered and reflect metabolic health in individuals with obesity. This provides valuable insights into some of the underlying mechanisms and can lead to identification of therapeutic targets to improve metabolic health in individuals with obesity.