bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breadth versus depth of knowledge: the need for new model trematode species
Authors: Poulin R. 
Published: January 2025

Abstract
The growth of knowledge and research practices in any discipline is characterised by a trade-off between depth and breadth: we can either invest efforts to learn a little about many things, or learn a lot about few things. In parasitology, breadth of knowledge corresponds to research on biodiversity and taxonomy: the discovery and description of an increasing number of new species. In contrast, depth of knowledge comes from focused research on a few model species, about which we accumulate much detailed information. Breadth and depth of knowledge are equally important for progress in parasitology. In this essay, focusing on trematodes, I demonstrate that current research is rapidly broadening our knowledge (high rate of new trematode species being discovered) but not deepening that knowledge at a comparable rate. The use of model species, with caveats, appears to offer a promising avenue for deeper knowledge. I present a case study illustrating how it is possible to develop new model trematode species at low cost to increase the depth of our understanding in areas including host-parasite ecological dynamics, co-evolution, and responses to environmental and climatic changes. The take-home message serves as a call to action to parasitologists, emphasising the need to focus as much effort on depth of knowledge as we currently invest in breadth of knowledge.
Gender Diversity and Inclusion in Canadian Security Studies
Authors: Duncombe Constance , von Hlatky Stéfanie , Nuñez-Mietz Fernando G. , Rublee Maria Rost , Saideman Stephen M. 
Published: January 2025

ABSTRACTAlthough much research confirms a gender gap in political science and its subfields internationally, only recently have scholars analyzed country-specific conditions for women within the field. Our study contributes to this national-level examination of gender diversity and inclusion by examining the extent to which a gender gap within the subfield of security studies, identified in the international literature, also is present in Canada. Research on gender representation and gendered experiences mostly centers on the academic workforce in the United States. However, in this article, we share the results of a multi-method investigation into the state of gender diversity in Canadian security studies—a national context in which the university sector has signaled a strong commitment to diversity and the government has actively promoted gender equality in official policy. By analyzing data collected from an online survey of security studies scholars in Canada and a document analysis of Canadian security-related journals and selected security studies syllabi, this contribution provides evidence that women are underrepresented in Canadian security studies and experience the subfield in less positive ways. We discuss the implications of these findings for the security studies subfield and suggest paths for future research and key recommendations.
Statistics of Depressions Covering the Northern Gulf of Mexico Salt‐Minibasin Province: Drivers and Strength of Bathymetric Self‐Organization
Authors: Reece J. Kevin , Straub Kyle M. 
Published: January 2025

AbstractThe bathymetry of the northern Gulf of Mexico is strongly influenced by diapirism of subsurface salt. A competition between salt dynamics and the depositional mechanics of sediment laden density flows over geological timescales controls the scale of seafloor depressions, which are the dominant bathymetric features of the margin. Salt domes create topographic highs, and salt removal to the domes creates topographic lows, with sediment deposition driving the gravitational dynamics. The strength of bathymetric self‐organization into depressions is inferred through analysis of a vast bathymetric data set made public by the U.S. Bureau of Ocean and Energy Management. Depression geometric scales follow Pareto distributions, and their tail indexes aid inference of the strength of bathymetric self‐organization, with lower tail indexes linked to greater self‐organization. A comparison is made of margin subregions defined by pseudo‐flow drainage density maps, which inversely relates to the pre‐deformation thickness of subsurface salt. Tail indexes of distributions decrease with the thickness of the underlying salt. This is linked to the merger of depressions, which is enhanced when depressions can grow wider and deeper, as occurs over thick salt fields, and the development of salt structure. The manner of self‐organization results in most of the margin's ponded sediment accommodation residing in relatively few depressions that have reliefs exceeding 100 m. This relief is sufficient to induce sedimentation from even the thickest turbidity currents, which can further drive gravitational dynamics. The bathymetric complexity of depressions is also greatest over regions with the thickest salt, further supporting enhanced self‐organization.
A Cluster‐Based Data Assimilation Approach to Generate New Daily Gridded Time Series Precipitation Data in the Himalayan River Basins
Authors: Singh Japjeet , Singh Vishal , Ojha Chandra Shekhar Prasad 
Published: January 2025

AbstractRecent studies show variations in precipitation‐gridded data set accuracy with changing geographical parameters. Ensemble precipitation products, combining diverse data sets, offer global‐scale effectiveness, but applying them to regional studies, particularly in small to medium‐sized sub‐basins, presents challenges in addressing precipitation dependence on specific geographical conditions. Here, we present a newly developed Clusters Based‐Minimum Error approach to assimilate different open‐source gridded precipitation data sets for forming an accurate precipitation product over small to medium‐sized hilly terrain basins, with limited precipitation gauges. This methodology generates the New Gridded Precipitation Data Set (NGPD) from 1991 to 2022 for the Upper Ganga Basin in the western Himalaya, covering approximately 22,292 km2. The study utilizes nine open‐source gridded precipitation data sets and 11 observed precipitation gauges, NGPD is evaluated through station‐wise, grid‐wise, and elevation‐wise analyses using statistical parameters, quantile‐quantile plots, daily coefficient of determination, Rainfall Anomaly Index, and seasonality/precipitation pattern analyses. Results demonstrate the superior performance of NGPD compared to other gridded precipitation sources across various evaluation metrics. Nash‐Sutcliffe Efficiency (NSE), Coefficient of determination (R2), and Root mean squared error (RMSE) range from 0.67 to 0.90, 0.73–0.93, and 4.4–10.69 mm/day, respectively, w.r.t 11 observed precipitation gauges. NGPD outperforms the widely used IMD data set in India, exhibiting a monthly scale improvement of 18.47% and 17.7% in average NSE and R2 values, respectively. Additionally, the methodology is also successfully applied to the Tamor Basin in Nepal, proving its reliability for various Himalayan regions. This approach reliably creates accurate gridded precipitation data sets for hilly sub‐basins, especially in Himalayan regions with limited station data.
Changes in Snow Drought and the Impacts on Streamflow Across Northern Catchments
Authors: Han Juntai , Yang Yuting , Guo Yuhan , Li Changming , Liu Ziwei , Tu Zhuoyi , Xi Haiyang 
Published: January 2025

AbstractSnow drought, characterized by an anomalous reduction in snowpack, exerts profound hydrological and socioeconomic impacts in cold regions. Despite its significance, the influence of diverse snow drought types, including warm, dry, and warm‐and‐dry variants, on streamflow remains inadequately understood. Here we present the first hemispheric‐scale, observation‐based assessment of snow drought patterns and the impacts on seasonal and annual streamflow (Q) across 3049 northern catchments over 1950–2020. Our findings reveal that catchments with a lower mean annual snowfall fraction () exhibit a heightened prevalence and severity of warm and warm‐and‐dry snow droughts, whereas high‐ experience a more prevalent but less severe dry snow drought. This disparity arises from distinct sensitivities of snowpack to cold‐season precipitation and temperature. In addition, dry and warm‐and‐dry snow droughts induce a reduction in Q during both cold and warm seasons, culminating in a significant decrease in annual Q. Conversely, warm snow drought increases annual Q in catchments with but decreases annual Q in catchments with , attributable to a trade‐off between increased cold‐season streamflow (Qc) and decreased warm‐season streamflow (Qw). With ongoing climate warming, a continued reduction in snowfall is anticipated, which is expected to further increase the frequency and severity of warm and warm‐dry snow droughts. These circumstances, particularly impactful under low conditions, are poised to present formidable challenges for water resources management in cold regions globally.
ApoM maintains cellular homeostasis between mitophagy and apoptosis by affecting the stability of Nnt mRNA through the Zic3-ApoM-Elavl2-Nnt axis during neural tube closure
Authors: Liu Qing , Liu Dan , Wang Yuejiao , Wei Xiaowei , Ma Wei , Gu Hui , Jia Shanshan , He Yiwen , Luo Wenting , Cao Songying , Yang Zhonghua , Wu Anhua , Yuan Zhengwei 
Published: January 2025

Abstract
Research on the aetiology of neural tube defects (NTDs) has made progress in recent years. However, the molecular mechanism of apolipoproteins underlying NTDs development remains unclear. This study aimed to investigate the function of apolipoprotein M (ApoM) in the pathogenesis of NTDs and its underlying mechanisms. We demonstrated that ApoM expression was reduced in the spinal cord samples of rat models and human fetuses with NTDs respectively. Specifically, lack of ApoM resulted in reduced cytosolic localization of Elavl2 and caused Nnt mRNA degradation, which further led to impaired cell homeostasis by suppressing PINK1-PRKN-mediated mitophagy and promoting apoptosis and subsequent NTDs formation. Moreover, Zic3 directly interacted with the promoter of ApoM and activated its transcription. Lastly, intra-amniotic delivery of adenoviral recombinant Zic3 or ApoM could promote mitophagy and alleviate apoptosis in spinal cords of NTDs. Collectively, these findings highlight the important role of the Zic3-ApoM-Elavl2-Nnt axis in cellular homeostasis during neural tube development, thereby revealing an intracellular molecular regulatory mechanism of ApoM, providing a mechanistic basis for understanding embryonic neural development, and offering experimental evidence for potential therapeutic targets for NTDs.
Kinship clustering within an ecologically diverse killer whale metapopulation
Authors: Baumgartner Chérine D. , Jourdain Eve , Bonhoeffer Sebastian , Borgå Katrine , Heide-Jørgensen Mads P. , Karoliussen Richard , Laine Jan T. , Rosing-Asvid Aqqalu , Ruus Anders , Tavares Sara B. , Ugarte Fernando , Samarra Filipa I. P. , Foote Andrew D. 
Published: January 2025

Abstract
Metapopulation dynamics can be shaped by foraging ecology, and thus be sensitive to shifts in prey availability. Genotyping 204 North Atlantic killer whales at 1346 loci, we investigated whether spatio-temporal population structuring is linked to prey type and distribution. Using population-based methods (reflecting evolutionary means), we report a widespread metapopulation connected across ecological groups based upon nuclear genome SNPs, yet spatial structuring based upon mitogenome haplotypes. These contrasting patterns of markers with maternal and biparental inheritance are consistent with matrilineal site fidelity and philopatry, and male-mediated gene flow among demes. Connectivity between fish-eating and ‘mixed-diet’ (eating both fish and mammal prey) killer whales, marks a deviation within a species renowned for its marked structure associated with ecology. However, relatedness estimates suggest distinct spatial clusters, and heterogeneity in recent gene flow between them. The contrasting patterns between inference of structure and inference of relatedness suggest that gene flow has been partially restricted over the past two to three generations (50–70 years). This coincides with the collapse of North Atlantic herring stocks in the late 1960s and the subsequent cessation of their seasonal connectivity. Statistically significant association between diet types and assignment of Icelandic killer whales to relatedness-based clusters indicated limited gene flow was maintained through Icelandic ‘mixed-diet’ whales when herring-mediated connectivity was diminished. Thus, conservation of dietary variation within this metapopulation is critical to ensure genetic health. Our study highlights the role of resource dynamics and foraging ecology in shaping population structure and emphasises the need for transnational management of this widespread migratory species and its prey.
Cryo-electron tomography pipeline for plasma membranes
Authors: Sun Willy W. , Michalak Dennis J. , Sochacki Kem A. , Kunamaneni Prasanthi , Alfonzo-Méndez Marco A. , Arnold Andreas M. , Strub Marie-Paule , Hinshaw Jenny E. , Taraska Justin W. 
Published: January 2025

Abstract
Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with subtomogram averaging and employs a genetically encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cellular environment. The pipeline provides efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of mammalian cells.
Non-linear enhancement of ultrafast X-ray diffraction through transient resonances
Authors: Kuschel Stephan , Ho Phay J. , Al Haddad Andre , Zimmermann Felix F. , Flueckiger Leonie , Ware Matthew R. , Duris Joseph , MacArthur James P. , Lutman Alberto , Lin Ming-Fu , Li Xiang , Nakahara Kazutaka , Aldrich Jeff W. , Walter Peter , Young Linda , Bostedt Christoph , Marinelli Agostino , Gorkhover Tais 
Published: January 2025

Abstract
Diffraction-before-destruction imaging with ultrashort X-ray pulses can visualize non-equilibrium processes, such as chemical reactions, with sub-femtosecond precision in the native environment. Here, a nanospecimen diffracts a single X-ray flash before it disintegrates. The sample structure can be reconstructed from the coherent diffraction image (CDI). State-of-the-art X-ray snapshots lack high spatial resolution because of weak diffraction signal. Bleaching effects from photo-ionization significantly restrain image brightness scaling. We find that non-linear transient ion resonances can overcome this barrier if X-ray laser pulses are shorter than in most experiments. We compared snapshots from individual ≈ 100 nm Xe nanoparticles as a function of pulse duration and incoming X-ray fluence. Our experimental results and Monte Carlo simulations suggest that transient resonances can increase ionic scattering cross sections significantly beyond literature values. This provides a novel avenue towards substantial improvement of the spatial resolution in CDI in combination with sub-femtosecond temporal precision at the nanoscale.
Validation of a multiplexed immunoassay for immunological analysis of pre erythrocytic malaria vaccines
Authors: Stockdale L. K. , Provstgaard-Morys S. , Bellamy D. , Woods D. , Rapi K. , Bajer A. , Hollingdale B. , Muñoz O. , Malik S. , Hill A. V. S. , Ewer K. J. 
Published: January 2025

Abstract
The primary immunological readout for clinical trials of R21/MatrixM™ malaria vaccine, is total IgG antibody specific to the central four amino acid NANP repeat region of the circumsporozoite protein. A multiplexed assay, which includes NANP, was developed and validated for four antigens representing components of the R21 immunogen. Initial assay optimisation included validation of the HBsAg international standard. Further validation performed in Oxford covered intra and inter-assay, and inter-operator variability, accuracy of QC and standard curve material, and included bridging to a singleplex NANP6 ELISA. The assay was shown to be robust and specific, with a broad dynamic range. We report a strong linear relationship between NANP6 IgG as measured by the singleplex ELISA and the multiplexed assay with rho values of 0.89 and 0.88 for two separate clinical trials (both p < 0.0005). This assay can be used to measure antibodies specific to the CSP NANP repeat region, CSP C-term region, full length R21 and HBsAg.
Dichotomy retreat and aqueous alteration on Noachian Mars recorded in highland remnants
Authors: McNeil Joseph D. , Fawdon Peter , Balme Matthew R. , Coe Angela L. , Cuadros Javier , Turner Stuart M. R. 
Published: January 2025

Abstract
The Mawrth Vallis region is a plateau situated on the highland side of Mars’ hemispheric dichotomy boundary. It has a >200-m-thick phyllosilicate-bearing stratigraphic succession that indicates extensive aqueous alteration between 4.1 Ga and 3.7 Ga, during the Noachian Period. In addition, thousands of kilometre-scale isolated mounds in the lowlands north and west of Mawrth Vallis have been identified. Here we use geomorphological and spectroscopic analyses to show that the mounds are erosional remnants that formed through retreat of the highland plateau in the Noachian. Consequently, the escarpment that marks the surface expression of the dichotomy must have receded south-southeast by hundreds of kilometres in this area. Lateral and stratigraphic geochemical variation in the mounds show that widespread, multiphase aqueous alteration occurred in situ across this region in surface and subsurface environments. The mound succession is underlain by a pyroxene-rich unit that represents unaltered material below the regional phyllosilicate-bearing sequence and is unconformably overlain by a thin capping unit that marks the end of large-scale regional aqueous activity. Thus, the mounds contain a stratigraphic record of the onset, evolution and cessation of Noachian aqueous conditions in this region, detailing the environment and climate of Mars at its most habitable.
Mapping the cellular etiology of schizophrenia and complex brain phenotypes
Authors: Duncan Laramie E. , Li Tayden , Salem Madeleine , Li Will , Mortazavi Leili , Senturk Hazal , Shahverdizadeh Naghmeh , Vesuna Sam , Shen Hanyang , Yoon Jong , Wang Gordon , Ballon Jacob , Tan Longzhi , Pruett Brandon Scott , Knutson Brian , Deisseroth Karl , Giardino William J. 
Published: January 2025

Abstract
Psychiatric disorders are multifactorial and effective treatments are lacking. Probable contributing factors to the challenges in therapeutic development include the complexity of the human brain and the high polygenicity of psychiatric disorders. Combining well-powered genome-wide and brain-wide genetics and transcriptomics analyses can deepen our understanding of the etiology of psychiatric disorders. Here, we leverage two landmark resources to infer the cell types involved in the etiology of schizophrenia, other psychiatric disorders and informative comparison of brain phenotypes. We found both cortical and subcortical neuronal associations for schizophrenia, bipolar disorder and depression. These cell types included somatostatin interneurons, excitatory neurons from the retrosplenial cortex and eccentric medium spiny-like neurons from the amygdala. In contrast we found T cell and B cell associations with multiple sclerosis and microglial associations with Alzheimer’s disease. We provide a framework for a cell-type-based classification system that can lead to drug repurposing or development opportunities and personalized treatments. This work formalizes a data-driven, cellular and molecular model of complex brain disorders.
Alterations in genes associated with cytosolic RNA sensing in whole blood are associated with coronary microvascular disease in SLE
Authors: Huo Lihong , Naveen Kumar Arati , Tumurkhuu Gantsetseg , Bose Moumita , Berman Daniel S. , Wallace Daniel J. , Wei Janet , Ishimori Mariko , Bairey Merz C. Noel , Jefferies Caroline 
Published: January 2025

Abstract
Systemic lupus erythematosus (SLE) patients are 90% women and over three times more likely to die of cardiovascular disease than women in the general population. Chest pain with no obstructive cardiac disease is associated with coronary microvascular disease (CMD), where narrowing of the small blood vessels can lead to ischemia, and frequently reported by SLE patients. Using whole blood RNA samples, we asked whether gene signatures discriminate SLE patients with coronary microvascular dysfunction (CMD) on cardiac MRI (n = 4) from those without (n = 7) and whether any signaling pathway is linked to the underlying pathobiology of SLE CMD. RNA-seq analysis revealed 143 differentially expressed (DE) genes between the SLE and healthy control (HC) groups, with virus defense and interferon (IFN) signaling being the key pathways identified as enriched in SLE as expected. We next conducted a comparative analysis of genes differentially expressed in SLE–CMD and SLE–non-CMD relative to HC samples. Our analysis highlighted differences in IFN signaling, RNA sensing and ADP-ribosylation pathways between SLE–CMD and SLE–non-CMD. This is the first study to investigate possible gene signatures associating with CMD in SLE, and our data strongly suggests that distinct molecular mechanisms underly vascular changes in CMD and non-CMD involvement in SLE.
A chaotic digital signature algorithm based on a dynamic substitution box
Authors: Flores-Carapia Rolando , Silva-García Víctor Manuel , Cardona-López Manuel Alejandro , Villarreal-Cervantes Miguel Gabriel 
Published: January 2025

Abstract
Given the large volumes of sensitive information transmitted over the Internet, digital signatures are essential for verifying message authenticity and integrity. A key challenge is minimizing computationally intensive operations, such as modular inverses, without compromising security. In this research, we propose the DSADH
$$\pi$$
algorithm, which introduces a confusion step directly into the signature itself, rather than only applying it to the message, using a dynamic substitution box. It is generated with the number pi and changes with each signing. In addition, to enhance security, this work uses a 2048-bit prime, double the length frequently used. This proposal induces chaotic behavior in the signature, making it highly sensitive to any changes in the signer’s private key or message content, thereby enhancing authentication and integrity verification. Moreover, the proposed algorithm computes a single multiplicative modular inverse during verification and none during signing, unlike other approaches that require inverse computation in both stages. Since the required inverse is for the Diffie-Hellman session key, it always exists and can be precomputed per communication rather than per message. Consequently, DSADH
$$\pi$$
is on average 45 times faster than DSA. Additionally, we introduce a method to assess signature security by constructing images from signature bytes generated by slight changes to the signer’s private key and message. Then, their chaotic behavior is evaluated with cryptographic metrics.