bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying Canopy Snow in Subalpine Forests: A Comparative Study of Methods
Authors: Harvey Natasha , Burns Sean P. , Musselman Keith N. , Barnard Holly , Blanken Peter D.
Published: January 2025

The interception of snow by the canopy is an important process in the water and energy balance in cold‐region coniferous forests. Direct measurements of canopy snow interception are difficult at scales larger than individual trees, requiring indirect methods such as eddy covariance, time‐lapse photography, or modeling. At the Niwot Ridge Subalpine Forest AmeriFlux site in the Colorado Front Range, USA, we compared methods that estimate or simulate the presence of snow interception. Timelapse photography images were analyzed using thresholding analysis and used to train a Convolutional Neural Network (CNN) model to estimate canopy snow presence. Interception was also estimated from eddy covariance measurements above and below the canopy, as well as from model simulations. These methods were applied over January 2019, with binarized results compared to a “ground truth” of human labeled images to calculate the Balanced Accuracy Score. The highest accuracy was achieved by the CNN predictions. Based on the Balanced Accuracy Scores, select methods were extended to estimate the presence of canopy snow for the 2018/2019 winter. All methods provided insight into the process of interception in a subalpine forest but presented challenges, including differing flux footprints of the above‐ and below‐canopy eddy covariance measurements and the inability of red‐green‐blue imagery to monitor snow interception at night, during sunrise, and during sunset.
Solar Semidiurnal Variations in the Thermosphere and Ionosphere Forced From Above and From Below
Authors: Forbes Jeffrey M. , Zhang Xiaoli , Cullens Chihoko , Maute Astrid
Published: January 2025

The nature and origins of solar‐synchronous semidiurnal variations (SW2) in the thermosphere and ionosphere are explored through analysis of Thermosphere Ionosphere Electrodynamics General Circulation Model (TIEGCM) simulations that include and exclude forcing by tides at its 97‐km lower boundary derived from Ionospheric Connection (ICON) explorer data. SW2 consists of two components, one excited in‐situ () and one due to vertical propagation from below the thermosphere (). in turn consists of a part forced by heating due to absorption of solar radiation () and a part of “geomagnetic” origin () arising from magnetospheric coupling at high latitudes. At 300 km all three components achieve wind and temperature amplitudes of order 25 and 15–20 K within specific geographic domains and levels of solar activity. exhibits upward propagation from the lower thermosphere much like the symmetric component of , refraction toward the winter hemisphere by mean winds, modulation by the 27‐day solar rotation rate, and is estimated to exceed in general importance for F10.7 133 sfu. At solar flux levels 75 sfu F10.7 125 sfu, electron density perturbations are of order 10%–35% for and 15%–25% for . Vertical E B drifts are of order 5–8 for , 3–5 for , and 5–8 for , the latter extending to the equator at elevated magnetic activity, and suggesting the presence of penetrating electric fields and/or disturbance dynamo action.
Improved Correction of Extreme Precipitation Through Explicit and Continuous Nonstationarity Treatment and the Metastatistical Approach
Authors: Vidrio‐Sahagún Cuauhtémoc Tonatiuh , He Jianxun , Pietroniro Alain
Published: January 2025

Climate models simulate extreme precipitation under nonstationarity due to continuous climate change. However, systematic errors in local‐scale climate projections are often corrected using stationary or quasi‐stationary methods without explicit and continuous nonstationarity treatment, like quantile mapping (QM), detrended QM, and quantile delta mapping. To bridge this gap, we introduce nonstationary QM (NS‐QM) and its simplified version for consistent nonstationarity patterns (CNS‐QM). Besides, correction approaches for extremes often rely on limited extreme‐event records. To leverage ordinary‐event information while focusing on extremes, we propose integrating the simplified Metastatistical extreme value (SMEV) distribution into NS‐QM and CNS‐QM (NS‐QM‐SMEV and CNS‐QM‐SMEV). We demonstrate the superiority of NS‐ and CNS‐QM‐SMEV over existing methods through a simulation study and show several real‐world applications using high‐resolution‐regional and coarse‐resolution‐global climate models. NS‐QM and CNS‐QM reflect nonstationarity more realistically but may encounter challenges due to data limitations like estimation errors and uncertainty, particularly for the most extreme events. These issues, shared by existing approaches, are effectively mitigated using the SMEV distribution. NS‐ and CNS‐QM‐SMEV offer lower estimation error, approximate unbiasedness, reduced uncertainty, and improved representation of the entire distribution, especially for samples of ∼70 years, and greater superiority with larger samples. We show existing methods may perform competitively for short samples but exhibit substantial biases in quantile‐quantile matching due to bypassing nonstationarity modeling. NS‐ and CNS‐QM‐SMEV avoid these biases, adhering better to their theoretical functioning. Thus, NS‐ and CNS‐QM‐SMEV enhance the correction of extremes under nonstationarity. Yet, properly identifying nonstationarity patterns is crucial for reliable implementations.
Tree‐Ring Insights Into Past and Future Streamflow Variations in Beijing, Northern China
Authors: Cao Honghua , Chen Feng , Hu Mao , Hou Tiyuan , Zhao Xiaoen , Wang Shijie , Zhang Heli
Published: January 2025

As the largest city in northern China and the capital of China, the rapid increases in Beijing’s water consumption in recent years have made water resources provision an increasing problem. To rationally allocate water resources, it is important to obtain long‐term runoff information in Beijing. In this study we develop a 236‐year chronology of tree‐ring widths based on cores from Pinus tabuliformis from four sampling sites. The resulting regression model reconstructs December–July runoff of the Yongding River in Beijing, with 49.5% of the variance explained, back to 1786 CE. Among the last 236 years, 1868, 1956, 1991, 1998, 2018, and 2021 were extremely high runoff years; and 1900, 1906, 1999, and 2000 were extremely low runoff years. Comparison of the runoff reconstruction results with climate grid data demonstrated a large magnitude of climate change in North China during the study period. Linkage analysis between the reconstructed runoff and large‐scale water vapor indicated that the high runoff years occurred during negative phases of the Pacific Decadal Oscillation, which may be influenced by the East Asian Summer Monsoon. Projections indicate that the flow of the Yongding River will increase in the future. Supported by policies such as the Ecological Water Supply and South‐to‐North Water Diversion, regional vegetation productivity and Yongding River runoff have increased substantially since 2000. Vegetation growth interacts with runoff volume. It is unclear how long these increases will continue.
Discriminating circular polarization of light: Left or right?
Authors: Lee Wanhee , Cho Changsoon
Published: January 2025

Achiral dielectric nanostructures provide an efficient method for discriminating left- and right-circularly polarized photons, leveraging the photothermoelectric effect.
More than just a name? From magnetic to optical skyrmions and the topology of light
Authors: Chen Jian , Forbes Andrew , Qiu Cheng-Wei
Published: January 2025

Topology is usually perceived intrinsically immutable for a given object. We argue that optical topologies do not immediately enjoy such benefits. Using ‘optical skyrmions’ as an example, we show that they will exhibit varying textures and topological invariants (skyrmion numbers), depending on how to construct the skyrmion vector when projecting from real to parameter space. We demonstrate the fragility of optical skyrmions under a ubiquitous scenario--simple reflection off an optical mirror. Optical topology is not without benefit, but it must not be assumed.
Discoidin domain receptor 2 is an important modulator of BMP signaling during heterotopic bone formation
Authors: Wu Fashuai , Ge Chunxi , Pan Haichun , Han Yuanyuan , Mishina Yuji , Kaartinen Vesa , Franceschi Renny T.
Published: January 2025

Bone morphogenetic proteins are essential for bone regeneration/fracture healing but can also induce heterotopic ossification (HO). Understanding accessory factors modulating BMP signaling would provide both a means of enhancing BMP-dependent regeneration while preventing HO. This study focuses on the ability of the collagen receptor, discoidin domain receptor 2 (DDR2), to regulate BMP activity. As will be shown, induction of bone formation by subcutaneous BMP2 implants is severely compromised in Ddr2-deficient mice. In addition, Ddr2 deficiency attenuates HO in mice expressing the ACVR1 mutation associated with human fibrodysplasia ossificans progressiva. In cells migrating into BMP2 implants, DDR2 is co-expressed with GLI1, a skeletal stem cell marker, and DDR2/GLI1-positive cells participate in BMP2-induced bone formation where they contribute to chondrogenic and osteogenic lineages. Consistent with this distribution, conditional knockout of Ddr2 in Gli1-expressing cells inhibited bone formation to the same extent seen in globally Ddr2-deficient animals. This response was explained by selective inhibition of Gli1+ cell proliferation without changes in apoptosis. The basis for this DDR2 requirement was explored further using bone marrow stromal cells. Although Ddr2 deficiency inhibited BMP2-dependent chondrocyte and osteoblast differentiation and in vivo, bone formation, early BMP responses including SMAD phosphorylation remained largely intact. Instead, Ddr2 deficiency reduced the nuclear/cytoplasmic ratio of the Hippo pathway intermediates, YAP and TAZ. This suggests that DDR2 regulates Hippo pathway-mediated responses to the collagen matrix, which subsequently affect BMP responsiveness. In summary, DDR2 is an important modulator of BMP signaling and a potential therapeutic target both for enhancing regeneration and treating HO.
Vitamin D sensitizes cervical cancer to radiation-induced apoptosis by inhibiting autophagy through degradation of Ambra1
Authors: zhang Zhaoming , Yu Xinyue , Cheng Guanghui
Published: January 2025

Cervical cancer (CC) is becoming a major health issue globally, and radiotherapy plays a crucial role in its treatment. However, the prognosis of some patients remains poor due to tumor resistance to the therapy. This study aimed to explore whether vitamin D could confer a more radiosensitive phenotype in CC based on our previous findings and detection using the database. We found that vitamin D sensitized vitamin D receptor (VDR)-positive CC cells (Siha and Caski) to the cytotoxic effects of radiation in vivo and in vitro. We examined conventional radiation-induced cell death, such as DNA damage and cell cycle arrest, in vitamin D–treated cells to detect the underlying mechanism, but no association was observed between them. Subsequently, our proteome analysis exhibited that autophagy was reduced in irradiated CCs treated with vitamin D, and apoptosis displayed the opposite effect. Moreover, we confirmed that vitamin D-pretreated irradiated cells displayed reduced autophagy activity mediated by the Ambra1 downregulation, and the elevation of apoptosis was attributed to the activation of caspase 8. Importantly, the pharmacological inhibition of caspases or the Ambra1 overexpression could restore tumor proliferation under the vitamin D and radiation combination treatment. Hence, the aforementioned findings revealed the essential impact of vitamin D in terms of enhancing radiosensitivity in CC meditated by inhibiting autophagy and proposed the addition of vitamin D as a viable strategy to improve the therapeutic efficacy of VDR-positive CC.
Remodelling of the immune landscape by IFNγ counteracts IFNγ-dependent tumour escape in mouse tumour models
Authors: Lau Vivian W. C. , Mead Gracie J. , Varyova Zofia , Mazet Julie M. , Krishnan Anagha , Roberts Edward W. , Prota Gennaro , Gileadi Uzi , Midwood Kim S. , Cerundolo Vincenzo , Gérard Audrey
Published: January 2025

Loss of IFNγ-sensitivity by tumours is thought to be a mechanism enabling evasion, but recent studies suggest that IFNγ-resistant tumours can be sensitised for immunotherapy, yet the underlying mechanism remains unclear. Here, we show that IFNγ receptor-deficient B16-F10 mouse melanoma tumours are controlled as efficiently as WT tumours despite their lower MHC class I expression. Mechanistically, IFNγ receptor deletion in B16-F10 tumours increases IFNγ availability, triggering a remodelling of the immune landscape characterised by inflammatory monocyte infiltration and the generation of ‘mono-macs’. This altered myeloid compartment synergises with an increase in antigen-specific CD8+ T cells to promote anti-tumour immunity against IFNγ receptor-deficient tumours, with such an immune crosstalk observed around blood vessels. Importantly, analysis of transcriptomic datasets suggests that similar immune remodelling occurs in human tumours carrying mutations in the IFNγ pathway. Our work thus serves mechanistic insight for the crosstalk between tumour IFNγ resistance and anti-tumour immunity, and implicates this regulation for future cancer therapy.
Experimental identification of topological defects in 2D colloidal glass
Authors: Vaibhav Vinay , Bera Arabinda , Liu Amelia C. Y. , Baggioli Matteo , Keim Peter , Zaccone Alessio
Published: January 2025

Topological defects are singularities within a field that cannot be removed by continuous transformations. The definition of these irregularities requires an ordered reference configuration, calling into question whether they exist in disordered materials, such as glasses. However, recent work suggests that well-defined topological defects emerge in the dynamics of glasses, even if they are not evident in the static configuration. In this study, we reveal the presence of topological defects in the vibrational eigenspace of a two-dimensional experimental colloidal glass. These defects strongly correlate with the vibrational features and spatially correlate with each other and structural “soft spots”, more prone to plastic flow. This work experimentally confirms the existence of topological defects in disordered systems revealing the complex interplay between topology, disorder, and dynamics.
Gene-editing in patient and humanized-mice primary muscle stem cells rescues dysferlin expression in dysferlin-deficient muscular dystrophy
Authors: Escobar Helena , Di Francescantonio Silvia , Smirnova Julia , Graf Robin , Müthel Stefanie , Marg Andreas , Zhogov Alexej , Krishna Supriya , Metzler Eric , Petkova Mina , Daumke Oliver , Kühn Ralf , Spuler Simone
Published: January 2025

Dystrophy-associated fer-1-like protein (dysferlin) conducts plasma membrane repair. Mutations in the DYSF gene cause a panoply of genetic muscular dystrophies. We targeted a frequent loss-of-function, DYSF exon 44, founder frameshift mutation with mRNA-mediated delivery of SpCas9 in combination with a mutation-specific sgRNA to primary muscle stem cells from two homozygous patients. We observed a consistent >60% exon 44 re-framing, rescuing a full-length and functional dysferlin protein. A new mouse model harboring a humanized Dysf exon 44 with the founder mutation, hEx44mut, recapitulates the patients’ phenotype and an identical re-framing outcome in primary muscle stem cells. Finally, gene-edited murine primary muscle stem-cells are able to regenerate muscle and rescue dysferlin when transplanted back into hEx44mut hosts. These findings are the first to show that a CRISPR-mediated therapy can ameliorate dysferlin deficiency. We suggest that gene-edited primary muscle stem cells could exhibit utility, not only in treating dysferlin deficiency syndromes, but also perhaps other forms of muscular dystrophy.
Mitigating CaCO3 crystal nucleation and growth through continuous ion displacement via alternating electric fields
Authors: Liu Yiming , Xiao Minhao , Huang Xiaochuan , Park Jane , Hoffman Matthew E. , Feng Yuren , An Alicia Kyoungjin , Li Qilin , Hoek Eric M. V. , Jassby David
Published: January 2025

Mineral crystal formation poses a challenge on surfaces (e.g., heat exchangers, pipes, membranes, etc.) in contact with super-saturated fluids. Applying alternating currents (AC) to such surfaces can prevent surface crystallization under certain conditions. Here, we demonstrate that ion displacement induced by periodic charging and discharging of the electrical double layer (EDL) inhibits both heterogeneous and homogeneous nucleation (and crystal growth) of CaCO3. Titanium sheets (meant to simulate metallic heat exchanger surfaces) are immersed in super-saturated CaCO3 solutions with a saturation index >11. We show that at relatively high AC frequencies, incomplete EDL formation leads to an alternating electric field that propagates far into the bulk solution, inducing rapid ion migration that overwhelms the Brownian motion of ions. Electrochemical characterization reveals EDL charging/discharging under AC conditions that greatly inhibits precipitation. Operating at 4 Vpp, 0.1–10 Hz reduces turbidity by over 96% and reduces CaCO3 coverage on the metal plates by over 92%. Based on electrokinetic and crystallization models, the ion displacement velocity (exceeding the mean Brownian velocity) and displacement length disrupts ion collision and crystal nucleation. Overall, the technique has potential for preventing mineral crystal formation in heat exchangers and many other industrially relevant systems.
Deep learning and genome-wide association meta-analyses of bone marrow adiposity in the UK Biobank
Authors: Xu Wei , Mesa-Eguiagaray Ines , Morris David M. , Wang Chengjia , Gray Calum D. , Sjöström Samuel , Papanastasiou Giorgos , Badr Sammy , Paccou Julien , Li Xue , Timmers Paul R. H. J. , Timofeeva Maria , Farrington Susan M. , Dunlop Malcolm G. , Semple Scott I. , MacGillivray Tom , Theodoratou Evropi , Cawthorn William P.
Published: January 2025

Bone marrow adipose tissue is a distinct adipose subtype comprising more than 10% of fat mass in healthy humans. However, the functions and pathophysiological correlates of this tissue are unclear, and its genetic determinants remain unknown. Here, we use deep learning to measure bone marrow adiposity in the femoral head, total hip, femoral diaphysis, and spine from MRI scans of approximately 47,000 UK Biobank participants, including over 41,000 white and over 6300 non-white participants. We then establish the heritability and genome-wide significant associations for bone marrow adiposity at each site. Our meta-GWAS in the white population finds 67, 147, 134, and 174 independent significant single nucleotide polymorphisms, which map to 54, 90, 43, and 100 genes for the femoral head, total hip, femoral diaphysis, and spine, respectively. Transcriptome-wide association studies, colocalization analyses, and sex-stratified meta-GWASes in the white participants further resolve functional and sex-specific genes associated with bone marrow adiposity at each site. Finally, we perform a multi-ancestry meta-GWAS to identify genes associated with bone marrow adiposity across the different bone regions and across ancestry groups. Our findings provide insights into BMAT formation and function and provide a basis to study the impact of BMAT on human health and disease.
Immune correlates of early clearance of Mycobacterium tuberculosis among tuberculosis household contacts in Indonesia
Authors: Setiabudiawan Todia P. , Apriani Lika , Verrall Ayesha J. , Utami Fitria , Schneider Marion , Indrati Agnes R. , Halim Pauline P. , Kaplonek Paulina , Malca Hadar , Lee Jessica Shih-Lu , Moorlag Simone J. C. F. M. , de Bree L. Charlotte J. , Mourits Vera P. , Joosten Leo A. B. , Netea Mihai G. , Alisjahbana Bachti , McNamara Ryan P. , Alter Galit , van Laarhoven Arjan , Ussher James E. , Sharples Katrina , Koeken Valerie A. C. M. , Hill Philip C. , van Crevel Reinout
Published: January 2025

Some individuals, even when heavily exposed to an infectious tuberculosis patient, do not develop a specific T-cell response as measured by interferon-gamma release assay (IGRA). This could be explained by an IFN-γ-independent adaptive immune response, or an effective innate host response clearing Mycobacterium tuberculosis (Mtb) without adaptive immunity. In heavily exposed Indonesian tuberculosis household contacts (n = 1347), a persistently IGRA negative status was associated with presence of a BCG scar, and - especially among those with a BCG scar - with altered innate immune cells dynamics, higher heterologous (Escherichia coli-induced) proinflammatory cytokine production, and higher inflammatory proteins in the IGRA mitogen tube. Neither circulating concentrations of Mtb-specific antibodies nor functional antibody activity associated with IGRA status at baseline or follow-up. In a cohort of adults in a low tuberculosis incidence setting, BCG vaccination induced heterologous innate cytokine production, but only marginally affected Mtb-specific antibody profiles. Our findings suggest that a more efficient host innate immune response, rather than a humoral response, mediates early clearance of Mtb. The protective effect of BCG vaccination against Mtb infection may be linked to innate immune priming, also termed ‘trained immunity’.
A higher order PUF complex is central to regulation of C. elegans germline stem cells
Authors: Qiu Chen , Crittenden Sarah L. , Carrick Brian H. , Dillard Lucas B. , Costa Dos Santos Stephany J. , Dandey Venkata P. , Dutcher Robert C. , Viverette Elizabeth G. , Wine Robert N. , Woodworth Jennifer , Campbell Zachary T. , Wickens Marvin , Borgnia Mario J. , Kimble Judith , Hall Traci M. Tanaka
Published: January 2025

PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF binding elements (FBEs) in its 3′UTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established ‘canonical’ FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discoveries of the LST-1–FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predict an expanded regulatory repertoire of different assemblies of PUF-partner-RNA higher order complexes in nematode GSCs. This also suggests analogous PUF controls may await discovery in other biological contexts and organisms.
A simple model for Behavioral Time Scale Synaptic Plasticity (BTSP) provides content addressable memory with binary synapses and one-shot learning
Authors: Wu Yujie , Maass Wolfgang
Published: January 2025

Recent experimental studies in the awake brain have identified a rule for synaptic plasticity that is instrumental for the instantaneous creation of memory traces in area CA1 of the mammalian brain: Behavioral Time scale Synaptic Plasticity. This one-shot learning rule differs in five essential aspects from previously considered plasticity mechanisms. We introduce a transparent model for the core function of this learning rule and establish a theory that enables a principled understanding of the system of memory traces that it creates. Theoretical predictions and numerical simulations show that our model is able to create a functionally powerful content-addressable memory without the need for high-resolution synaptic weights. Furthermore, it reproduces the repulsion effect of human memory, whereby traces for similar memory items are pulled apart to enable differential downstream processing. Altogether, our results create a link between synaptic plasticity in area CA1 of the hippocampus and its network function. They also provide a promising approach for implementing content-addressable memory with on-chip learning capability in highly energy-efficient crossbar arrays of memristors.
Functional protein mining with conformal guarantees
Authors: Boger Ron S. , Chithrananda Seyone , Angelopoulos Anastasios N. , Yoon Peter H. , Jordan Michael I. , Doudna Jennifer A.
Published: January 2025

Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.
ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip
Authors: Lee John J. Y. , Tao Ran , You Zhen , Haldipur Parthiv , Erickson Anders W. , Farooq Hamza , Hendriske Liam D. , Abeysundara Namal , Richman Cory M. , Wang Evan Y. , Das Gupta Neha , Hadley Jennifer , Batts Melissa , Mount Christopher W. , Wu Xiaochong , Rasnitsyn Alex , Bailey Swneke , Cavalli Florence M. G. , Morrissy Sorana , Garzia Livia , Michealraj Kulandaimanuvel Antony , Visvanathan Abhi , Fong Vernon , Palotta Jonelle , Suarez Raul , Livingston Bryn G. , Liu Miao , Luu Betty , Daniels Craig , Loukides James , Bendel Anne , French Pim J. , Kros Johan M. , Korshunov Andrey , Kool Marcel , Chico Ponce de León Fernando , Perezpeña-Diazconti Mario , Lach Boleslaw , Singh Sheila K. , Leary Sarah E. S. , Cho Byung-Kyu , Kim Seung-Ki , Wang Kyu-Chang , Lee Ji-Yeoun , Tominaga Teiji , Weiss William A. , Phillips Joanna J. , Dai Shizhong , Zadeh Gelareh , Saad Ali G. , Bognár László , Klekner Almos , Pollack Ian F. , Hamilton Ronald L. , Ra Young-shin , Grajkowska Wieslawa A. , Perek-Polnik Marta , Thompson Reid C. , Kenney Anna M. , Cooper Michael K. , Mack Stephen C. , Jabado Nada , Lupien Mathieu , Gallo Marco , Ramaswamy Vijay , Suva Mario L. , Suzuki Hiromichi , Millen Kathleen J. , Huang L. Frank , Northcott Paul A. , Taylor Michael D.
Published: January 2025

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma ZIC1 mutants exhibit LOF phenotypes. Distinct ZIC1 mutations affect cells of the rhombic lip in diametrically opposed ways, suggesting that ZIC1 is a critical developmental transcriptional regulator in both the normal and transformed rhombic lip and identifying ZIC1 as an exquisitely context-dependent driver gene in medulloblastoma.
Exploring the effects of perceived social support and psychological distress through mediation and multigroup analyses in work-related quality of life
Authors: Yılmaz Sıdıka Ece , Çıtak Şenel
Published: January 2025

Work-related quality of life has emerged as a central focus in the field of occupational health due to its impact on individual well-being and overall quality of life. So, it is crucial to enhance the current theory by conducting a study on the concept across different sectors. Also, the specific mechanisms through which perceived social support influences work-related quality of life remain underexplored. The role of psychological distress as a potential mediator in this relationship has not been investigated. Thus, the study aimed to explore the mediating role of psychological distress in this relationship, while also examining potential gender differences. The study, conducted with 401 teachers through a questionnaire, utilized the AMOS program for data analysis. The findings supported the direct effects among the variables and the mediating role of psychological distress. Additionally, the impact of psychological distress on work-related quality of life was found to be higher for females, but no differences for other paths. The study contributes to the literature by addressing the gap in understanding the mechanisms regarding work-related quality of life. The results highlight the importance of considering psychological distress and gender differences in interventions aimed at improving work-related quality of life.
Harnessing CRISPR interference to resensitize laboratory strains and clinical isolates to last resort antibiotics
Authors: Frusteri Chiacchiera Angelica , Casanova Michela , Bellato Massimo , Piazza Aurora , Migliavacca Roberta , Batt Gregory , Magni Paolo , Pasotti Lorenzo
Published: January 2025

The global race against antimicrobial resistance requires novel antimicrobials that are not only effective in killing specific bacteria, but also minimize the emergence of new resistances. Recently, CRISPR/Cas-based antimicrobials were proposed to address killing specificity with encouraging results. However, the emergence of target sequence mutations triggered by Cas-cleavage was identified as an escape strategy, posing the risk of generating new antibiotic-resistance gene (ARG) variants. Here, we evaluated an antibiotic re-sensitization strategy based on CRISPR interference (CRISPRi), which inhibits gene expression without damaging target DNA. The resistance to four antibiotics, including last resort drugs, was significantly reduced by individual and multi-gene targeting of ARGs in low- to high-copy numbers in recombinant E. coli. Escaper analysis confirmed the absence of mutations in target sequence, corroborating the harmless role of CRISPRi in the selection of new resistances. E. coli clinical isolates carrying ARGs of severe clinical concern were then used to assess the robustness of CRISPRi under different growth conditions. Meropenem, colistin and cefotaxime susceptibility was successfully increased in terms of MIC (up to > 4-fold) and growth delay (up to 11 h) in a medium-dependent fashion. ARG repression also worked in a pathogenic strain grown in human urine, as a demonstration of CRISPRi-mediated re-sensitization in host-mimicking media. This study laid the foundations for further leveraging CRISPRi as antimicrobial agent or research tool to selectively repress ARGs and investigate resistance mechanisms.
Hypoxia traits imprinted in otolith δ13C from individual to global scales
Authors: Howard Evan M. , Deutsch Curtis A.
Published: January 2025

Hypoxia tolerance and its variation with temperature, activity, and body mass, are critical ecophysiological traits through which climate impacts marine ectotherms. To date, experimental determination of these traits is limited to a small subset of modern species. We leverage the close coupling of carbon and oxygen in animal metabolism to mechanistically relate these traits to the carbon isotopes in fish otoliths (δ13Coto). The model reproduces the major empirical patterns in δ13Coto at individual to global scales. The weak dependence on body size and strong, non-linear, dependence on temperature reflect the same balance between metabolism and ventilatory gas exchange that underlies organisms’ hypoxia tolerance. The global relationship between temperature and δ13Coto records both the fractionation by aragonite precipitation and the variation in hypoxia traits across ocean biomes. Because hypoxia tolerance is imprinted on both otolith geochemistry and species biogeography, the model allows the aerobic limits of species geographic ranges to be predicted from fish δ13Coto. This physiologically grounded model provides a foundation for the use of otolith chemistry to reconstruct modern spatial patterns and paleoceanographic changes in key traits that shape aerobic habitat of aquatic species.
Solution combustion synthesis of ZnO doped CuO nanocomposite for photocatalytic and sensor applications
Authors: Kumar A. Naveen , Balakrishna M. , Desai Usha , Rakshith R. , Ambika K. M. , Soumya P. , Ravikumar C. R. , Vadivu S. Senthil , Naik Nithesh
Published: January 2025

ZnO-doped CuO nanocomposites (CuO-ZnO NPs) of 1, 3, and 5 mol% were prepared by the solution combustion method using ODH as a fuel (Oxlyl-hydrazide) at 500 °C and calcining at 1000 °C for two hours and the Structural, photocatalytic, and electrochemical properties were investigated by experimental and theoretical methods. X-ray diffraction (XRD) patterns revealed a crystallite size (D) range of 25 to 31 nm for pure CuO and 1, 3, and 5 mol% CuO-ZnO NPs. According to calculations, the optical energy band gap (Eg) of the NPs is between 2.1 and 2.5 eV. Under UV light irradiation, the photocatalytic degradation of CuO + 3%ZnO NPs on Congo Red (CR) and Methylene Blue (MB) dye was assessed under the influence of UV light. The degradation efficiency increased with the catalyst dosage (10 − 60 mg L− 1). At a concentration of the catalyst of 60 mg, the degradation efficiency can even reached 70% after 120 min. The electrochemical properties of the prepared NPs were studied using cyclic voltammetry and electrochemical impedance spectroscopy (EIS). Solutions of glucose and ascorbic acid were effectively sensed using modified carbon paste electrodes. These innovative results can be considered for the expansion of novel resources to scale for dual applications in the areas of photocatalysis and sensors.
Enhancing betalains production and antioxidant activity in Celosia argentea cell suspension cultures using biotic and abiotic elicitors
Authors: Mueangnak Kanchanok , Kitwetcharoen Haruthairat , Thanonkeo Sudarat , Klanrit Preekamol , Apiraksakorn Jirawan , Klanrit Poramaporn , Klanrit Poramate , Thanonkeo Pornthap
Published: January 2025

Celosia argentea is a plant known for producing bioactive compounds, including betalains, which possess various biological and pharmaceutical properties. This study aimed to investigate the effect of biotic and abiotic elicitors on betalains production and their antioxidant activity in cell suspension cultures of C. argentea. Various concentrations of chitosan, yeast extract, salicylic acid, methyl jasmonate, copper sulfate (CuSO4), and cobalt chloride (CoCl2) were evaluated. The results revealed that chitosan, salicylic acid, methyl jasmonate, and CuSO4 significantly improved betalains production in the cell suspension cultures. Among these elicitors, chitosan at 5.0 mg/L and CuSO4 at 6.4 µM were the most effective in enhancing betalains production, yielding the highest concentrations of 4.65 and 4.99 mg/g dry weight, respectively. Notably, the betalains derived from the elicitor-treated cultures exhibited greater antioxidant activity compared to the control. These findings suggest that chitosan and CuSO4 are promising elicitors for sustainable in vitro production of betalains from C. argentea cell suspension cultures on a commercial scale, owing to their ability to enhance betalains production and antioxidant activity.
Exploring the catalytic hydrothermal liquefaction of Namibian encroacher bush
Authors: Cutz Luis , Bias Nikos , Al-Naji Majd , de Jong Wiebren
Published: January 2025

An urgent ecological issue is the threat posed by invasive species, which are becoming more widespread especially in Africa. These encroachments damage ecosystems, pose a threat to biodiversity, and outcompete local plants and animals. This article focuses on converting Acacia Mellifera from Namibia, commonly known as encroacher bush (EB) into high-quality drop-in intermediates for the chemical and transport industry via hydrothermal liquefaction (HTL). HTL tackles the growing need for sustainable energy carriers while simultaneously halting the spread of the invasive species. A surface response methodology was used to optimize the HTL process for the following operational conditions: temperature (250–340 °C), residence time (5–60 min) and catalyst loading (0–10 wt%). The catalyst of choice was determined after evaluating the energy recovery (ER) of four different catalysts (Zeolite, La2O3, Hydrotalcite, Ni/SiO2–Al2O3) under the same HTL operational conditions. The results indicate that the addition of hydrotalcite results in high yields of bio-crude oil (13–28 wt%), without compromising the high heating value (HHV, 26–31 MJ/kg), water content (0.47 wt%) or increasing the content of oxygenated compounds compared to the non-catalytic experiment. For the experimental conditions tested, we observed a global maximum in conversion in the 330 °C and 30 min range. Our findings indicate that the most significant factor on the conversion of EB into bio-crude oil was temperature, followed by the catalyst loading. Furthermore, biochars produced at 330 °C and 30 min show potential as solid biofuels with HHVs up to 28.30 MJ/kg.
Parasites specific to centipedes form a new major lineage of terrestrial gregarines
Authors: Miroliubova Tatiana S. , Mikhailov Kirill V. , Simdyanov Timur G. , Aleoshin Vladimir V. , Dũng Đinh Thế , Kudriavkina Aleksandra I.
Published: January 2025

Gregarines from the families Dactylophoridae and Trichorhynchidae parasitize exclusively centipedes and have a distinct morphology among other terrestrial eugregarines, but their evolutionary relationships have not yet been studied with molecular methods. Here we obtain rDNA operon sequences for the dactylophorids and trichorhynchids. We describe a new species Trichorhynchus efeykini sp. n. from a scutigeromorph Thereuopoda longicornis from Vietnam. Phylogenetic analyses with combined SSU, 5.8S and LSU rDNA dataset support the previously proposed separation of Trichorhynchus to the Trichorhynchidae based on morphology and recover the dactylophorids and trichorhynchids as sister groups in a monophyletic clade. This clade appears sister to the clade of the Actinocephaloidea and Stylocephaloidea, and represents a new major lineage of terrestrial gregarines that we designate as a new superfamily Dactylophoroidea.
Sex differences in aggression and its neural substrate in a cichlid fish
Authors: Jackson Lillian R. , Dumitrascu Mariam , Alward Beau A.
Published: January 2025

Aggression is ubiquitous among social species and can function to maintain social dominance hierarchies. The African cichlid fish Astatotilapia burtoni is an ideal study species for studying aggression due to their dominance hierarchy and robust behavioral repertoire. To further understand the potential sex differences in aggression in this species, we characterized aggression in male and female A. burtoni in a mirror assay. We then quantified neural activation patterns in brain regions of the social behavior network (SBN) to investigate if differences in behavior are reflected in the brain with immunohistochemistry by detecting the phosphorylated ribosome marker phospho-S6 ribosomal protein (pS6), a marker for neural activation. We found that A. burtoni perform both identical and sex-specific aggressive behaviors in response to a mirror assay. Females had greater pS6 immunoreactivity than males in the Vv (ventral part of the ventral telencephalon), a homolog of the lateral septum in mammals. Males but not females had higher pS6 immunoreactivity in the ATn after the aggression assay. The ATn (anterior tuberal nucleus) is a homolog of the ventromedial hypothalamus in mammals, which is strongly implicated in the regulation of aggression in males. Several regions also have higher pS6 immunoreactivity in negative controls than fish exposed to a mirror, implicating a role for inhibitory neural processes in suppressing aggression until a relevant stimulus is present. Male and female A. burtoni display both similar and different behavioral patterns in aggression in response to a mirror assay. There are also sex differences in the corresponding neural activation patterns in the SBN. In mirror males but not females, the ATn clusters with the POA, revealing a functional connectivity of these regions that is triggered in an aggressive context in males. These findings suggest that distinct neural circuitry underlie aggressive behavior in male and female A. burtoni, serving as a foundation for future work investigating the molecular and neural underpinnings of sex differences in behavior in this species to reveal fundamental insights into understanding aggression.
Genome-wide association studies in lettuce reveal the interplay of seed age, color, and germination under high temperatures
Authors: Oh Sookyung , Ahn Ezekiel , Shi Ainong , Mou Beiquan , Park Sunchung
Published: January 2025

Thermoinhibition, the suppression of seed germination by high temperatures, is an adaptive trait that ensures successful seedling establishment in natural environments. While beneficial for wild plants, thermoinhibition can adversely affect crop yields due to uneven and reduced germination rates, particularly in the face of climate change. To understand the genetic basis of thermoinhibition, we conducted a comprehensive genetic analysis of a diverse panel of Lactuca spp. accessions. Our findings revealed that L. serriola, a wild ancestor of cultivated lettuce, showed relaxed thermoinhibition response compared to cultivated lettuce, suggesting that this trait may have been positively selected during early domestication in the Mediterranean region with hot, dry summers. Additionally, we found that thermoinhibition intensified with seed age but was less pronounced in dark-colored seeds, which showed increased germination under high temperatures. Genome-wide association studies identified genomic regions associated with thermoinhibition, including genes involved in ethylene and ABA signaling. Interestingly, some of these regions were also linked to seed color, suggesting a potential genetic coupling between black seed color and reduced thermoinhibition. These results highlighted the complex interplay between thermoinhibition, seed color, and domestication in lettuce, indicating a complicated nature of thermoinhibition regulation. By elucidating the genetic architecture of thermoinhibition, our study provides a valuable foundation for breeding strategies to enhance lettuce resilience to climate change.
Determining optimum assembly zone for modular reconfigurable robots using multi-objective genetic algorithm
Authors: Pasumarthi Ravikiran , Samarakoon S. M. Bhagya P. , Elara Mohan Rajesh , Sheu Bing J.
Published: January 2025

Reconfigurable modular robots can be used in application domains such as exploration, logistics, and outer space. The robots should be able to assemble and work as a single entity to perform a task that requires high throughput. Selecting an optimum assembly position with minimum distance traveled by robots in an obstacle surrounding the environment is challenging. Therefore, this paper proposes a novel approach for optimizing the assembly zone of modular robots in heterogeneous obstacle environments. The method uses a multi-objective Genetic Algorithm (GA) to minimize total travel distance and individual distance disparities. Utilizing the A* algorithm for path planning ensures efficient navigation. A generic kinematic model enabling holonomic locomotion with any reconfiguration and a new modular robot design are also introduced. Hardware experiments have been conducted to validate the kinematic model’s applicability for holonomic navigation across different robot configurations. Simulations and physical experiments demonstrated the effectiveness of the proposed method in determining assembly zones, with GA outperforming multi-objective pattern search and random selection in terms of total distance and individual distances traveled by the robots.
Bio particle swarm optimization and reinforcement learning algorithm for path planning of automated guided vehicles in dynamic industrial environments
Authors: Lin Shiwei , Wang Jianguo , Huang Bomin , Kong Xiaoying , Yang Hongwu
Published: January 2025

Automated guided vehicles play a crucial role in transportation and industrial environments. This paper presents a proposed Bio Particle Swarm Optimization (BPSO) algorithm for global path planning. The BPSO algorithm modifies the equation to update the particles’ velocity using the randomly generated angles, which enhances the algorithm’s searchability and avoids premature convergence. It is compared with Particle Swarm Optimization (PSO), Genetic Algorithm (GA), and Transit Search (TS) algorithms by benchmark functions. It has great performance in unimodal optimization problems, and it gains the best fitness value with fewer iterations and average runtime than other algorithms. The Q-learning method is implemented for local path planning to avoid moving obstacles and combines with the proposed BPSO for the safe operations of automated guided vehicles. The presented BPSO-RL algorithm combines the advantages of the swarm intelligence algorithm and the Q-learning method, which can generate the globally optimal path with fast computational speed and support in dealing with dynamic scenarios. It is validated through computational experiments with moving obstacles and compared with the PSO algorithm for AGV path planning.
Kaolinite induces rapid authigenic mineralisation in unburied shrimps
Authors: Corthésy Nora , Saleh Farid , Antcliffe Jonathan B. , Daley Allison C.
Published: January 2025

Fossils preserving soft tissues and lightly biomineralized structures are essential for the reconstruction of past ecosystems and their evolution. Understanding fossilization processes, including decay and mineralisation, is crucial for accurately interpreting ancient morphologies. Here we investigate the decay of marine and freshwater shrimps deposited on the surface of three different clay beds. In experimental set ups containing kaolinite, cryogenic scanning electron microscopy shows a black film comprised of newly formed anhedral and cryptocrystalline aluminosilicates on marine shrimp cuticles, which stabilise the overall morphology. This is the first experimental evidence for the replication of arthropod lightly biomineralized structures in aluminosilicates shortly after death, while carcasses are not buried by sediments. The preservation of morphology through aluminosilicates could result in carcasses persisting on the seafloor for weeks without losing much external anatomical information. In this context, instantaneous burial capturing animals alive may not be a prerequisite for exceptional preservation as usually thought.