bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting Flood Event Class Using a Novel Class Membership Function and Hydrological Modeling
Authors: Zhang Yongyong , Zhang Yongqiang , Zhai Xiaoyan , Xia Jun , Tang Qiuhong , Zhao Tongtiegang , Wang Wei
Published: June 2024

Predicting flood event classes aids in the comprehensive investigation of flood behavior dynamics and supports flood early warning and emergency plan development. Existing studies have mainly focused on historical flood event classification and the prediction of flood hydrographs or certain metrics (e.g., magnitude and timing) but have not focused on predicting flood event classes. Our study proposes a new approach for predicting flood event classes based on the class membership functions of flood regime metrics and hydrological modeling. The approach is validated using 1446 unimpacted flood events in 68 headstream catchments widely distributed across China. The new approach performs well, with class hit rates of 68.3% ± 0.4% for all events; 65.8% ± 0.6%, 56.8% ± 0.9%, and 69.5% ± 0.9% for the small, moderate and high spike flood event classes, respectively; and 82.5% ± 1.2% and 75.4% ± 1.1% for the moderate and high dumpy flood event classes, respectively. Furthermore, it performs better in the basins of northern China than in those of southern China, particularly for the small spike flood event class in the Songliao and Yellow River Basins, with hit rates of 80.0% ± 3.2% and 78.8% ± 3.2%, respectively. Our results indicate that the new approach will help improve the prediction performance of flood events and their corresponding classes, and provide deep insights into the comprehensive dynamic patterns of flood events for early warning and control management.
Quantifying the Impact of Internal Variability on the CESM2 Control Algorithm for Stratospheric Aerosol Injection
Authors: Connolly Charlotte , Prewett Emily , Barnes Elizabeth A. , Hurrell James W.
Published: June 2024

Earth system models are powerful tools to simulate the climate response to hypothetical climate intervention strategies, such as stratospheric aerosol injection (SAI). Recent simulations of SAI implement a tool from control theory, called a controller, to determine the quantity of aerosol to inject into the stratosphere to reach or maintain specified global temperature targets, such as limiting global warming to 1.5°C above pre‐industrial temperatures. This work explores how internal (unforced) climate variability can impact controller‐determined injection amounts using the Assessing Responses and Impacts of Solar climate intervention on the Earth system with Stratospheric Aerosol Injection (ARISE‐SAI) simulations. Since the ARISE‐SAI controller determines injection amounts by comparing global annual‐mean surface temperature to predetermined temperature targets, internal variability that impacts temperature can impact the total injection amount as well. Using an offline version of the ARISE‐SAI controller and data from Earth system model simulations, we quantify how internal climate variability and volcanic eruptions impact injection amounts. While idealized, this approach allows for the investigation of a large variety of climate states without additional simulations and can be used to attribute controller sensitivities to specific modes of internal variability.
The Global Biogeochemical Cycle of the Rare Earth Elements
Authors: Hatje V. , Schijf J. , Johannesson K. H. , Andrade R. , Caetano M. , Brito P. , Haley B. A. , Lagarde M. , Jeandel C.
Published: June 2024

To improve our understanding and guide future studies and applications, we review the biogeochemistry of the rare earth elements (REE). The REEs, which form a chemically uniform group due to their nearly identical physicochemical properties, include the lanthanide series elements plus scandium (Sc) and yttrium (Y). These elements, in conjunction with the neodymium isotopes, are powerful tools for understanding key oceanic, terrestrial, biological and even anthropogenic processes. Furthermore, their unique properties render them essential for various technological processes and products. Here, we delve into the characteristics of REE biogeochemistry and discuss normalization procedures and REE anomalies. We also examine the aqueous speciation of REEs, contributing to a better understanding of their behavior in aquatic settings, including the role of neodymium isotopes. We then focus on their environmental distribution, fractionation, and controlling processes in different environmental systems across the land‐ocean continuum. In addition, we analyze sinks, sources, and the mobility of REEs, providing insights into their behavior in these environments. We further investigate the sources of anthropogenic REEs and their bioavailability, bioaccumulation, and transfer along food webs. We also explore the potential effects of climate change on the cycling, mobility and bioavailability of REEs, underlining the importance of current research in this evolving field. In summary, we provide a comprehensive review of REE behavior in the environment, from their properties and roles to their distribution and anthropogenic impacts, offering valuable insights and pinpointing key knowledge gaps.
Tectonically Controlled Establishment of Modern‐Like Precipitation Patterns in East and Central Asia During the Early Late Miocene
Authors: Zhang Tao , Han Wenxia , Tian Qian , Zhang Jian , Kemp David B. , Wang Zhixiang , Yan Xinting , Mai Li , Fang Xiaomin , Ogg James
Published: June 2024

Deciphering how modern precipitation patterns became established in monsoon‐dominated East Asia and the arid interior Asia is crucial for predicting future precipitation trends under accelerated global warming and increased climate extremes. However, this effort is hindered by a scarcity of quantitative paleo‐precipitation data in this region. Here we reconstruct the pattern of Middle to Late Miocene paleo‐precipitation across an east‐to‐west transect from the summer monsoon‐dominated East Asian region through the transition zone and into interior Asia. Our work is based on a newly established precipitation calculation equation and quantitative pollen‐based precipitation conversion. Analysis indicates a common trend of precipitation across the studied region prior to ca, 11 Ma, followed by a clear divergence of precipitation variations between East and interior Asia since at least 11–9 Ma. This divergence is characterized by increasing precipitation in East Asia, but a coeval decrease in rainfall in the transition zone and interior Asia. The timing of this precipitation divergence was contemporaneous with intense tectonic activity in the northern Tibetan Plateau, which differentially affected the efficacy of water vapor transport into East and interior Asia. Modeling work using different topographic settings corroborates this tectonic influence. Our study demonstrates the early establishment of modern‐like precipitation patterns in East‐interior Asia at least in the early Late Miocene.
EMM EMUS Observations of FUV Aurora on Mars: Dependence on Magnetic Topology, Local Time, and Season
Authors: Chirakkil Krishnaprasad , Lillis Robert J. , Deighan Justin , Chaffin Michael S. , Jain Sonal K. , Brain David A. , Fillingim Matthew O. , Susarla Raghuram , Holsclaw Greg , Fang Xiaohua , Schneider Nick M. , AlMazmi Hoor , AlMatroushi Hessa , Gacesa Marko , El‐Kork Nayla , Thiemann Ed , Halekas Jasper S.
Published: June 2024

We present a comprehensive study of the nightside aurora phenomenon on Mars, utilizing observations from EMUS onboard Emirates Mars Mission. The oxygen emission at 130.4 nm is by far the brightest FUV auroral emission line observed at Mars. Our statistical analysis reveals geographic, solar zenith angle, local time, and seasonal dependencies of auroral occurrence. Higher occurrence of aurora is observed in regions of open magnetic topology, where crustal magnetic fields are either very weak or both strong and vertical. Aurora occurs more frequently closer to the terminator and is more likely on the dusk side than on the dawn side of the night hemisphere. A pronounced auroral feature appears close to midnight local times in the southern hemisphere, consistent with the spot of energetic electron fluxes previously identified in the Mars Global Surveyor data. This auroral spot is more frequent after midnight than before. Additionally, some regions on Mars are “aurora voids” where essentially no aurora occurs. Aurora exhibits a seasonal dependence, with a major enhancement near perihelion. Non–crustal field aurora additionally shows a secondary enhancement near Ls 30°. This seasonal variability is a combination of the variability in ionospheric photoelectrons and thermospheric atomic oxygen abundance. Auroral occurrence also shows an increase with the rise of Solar Cycle 25. The brightest auroral pixels are observed during space weather events such as Coronal Mass Ejections and Stream Interaction Regions. These observations not only shed light on where and when Martian aurora occurs, but also add to our understanding of Mars' magnetic environment and its interaction with the heliosphere.
Bringing Statistics to Storylines: Rare Event Sampling for Sudden, Transient Extreme Events
Authors: Finkel Justin , O’Gorman Paul A.
Published: June 2024

A leading goal for climate science and weather risk management is to accurately model both the physics and statistics of extreme events. These two goals are fundamentally at odds: the higher a computational model's resolution, the more expensive are the ensembles needed to capture accurate statistics in the tail of the distribution. Here, we focus on events that are localized in space and time, such as heavy precipitation events, which can start suddenly and decay rapidly. We advance a method for sampling such events more efficiently than straightforward climate model simulation. Our method combines elements of two existing approaches: adaptive multilevel splitting (AMS), a rare event algorithm that generates rigorous statistics but fails to enhance the sampling of sudden, transient extremes; and “ensemble boosting,” which generates physically plausible storylines of these events but not their statistics. We modify AMS by splitting trajectories well in advance of the event's onset, following the approach of ensemble boosting. Early splitting requires a rejection step that reduces efficiency, but it is critical for amplifying and diversifying simulated events in tests with the Lorenz‐96 model, for which we demonstrate improved sampling of extreme local energy fluctuations by approximately a factor of 10 relative to direct sampling. Our method is related to previous algorithms, including subset simulation and anticipated AMS, but is distinctly tailored to handle bursting events caused by chaotic traveling waves. Our work makes progress toward the goal of efficiently sampling such transient local extremes in atmospheric models.
The contract between NHS dentistry and communities and how this varies by neighbourhood types
Authors: Clark Stephen
Published: June 2024

Introduction There is a growing concern that the NHS's ability to deliver dental care is not keeping pace with population growth. Also, existing capacity may not be evenly distributed, potentially creating dental deserts in some neighbourhoods.

Aims This study aims to explore recent trends in NHS general practice dental capacity in England and analyse if these trends vary depending on neighbourhood context.

Design This research employs a descriptive analysis of time trends.

Materials and methods The study uses data on NHS-contracted capacity in England, measured in units of dental activity (UDAs). These UDAs are geo-located to neighbourhood types using practice postcodes. Changes in the populations of these neighbourhoods provide context for the capacity trends.

Results Some trends remain stable over time, albeit at insufficient levels. Rural areas continue to have the lowest capacity for NHS dental treatments. Additionally, areas with previously generous provision are experiencing significant percentage decreases in capacity.

Discussion To prevent the formation of dental deserts, two critical issues require attention: firstly, the accessibility of NHS treatment and how it varies across urban/suburban and rural neighbourhoods; secondly, balancing supply and demand by matching the supply of dental care with the demand, conditioned by socio-economic and socio-demographic factors within different neighbourhoods.
RANKL/RANK signaling recruits Tregs via the CCL20–CCR6 pathway and promotes stemness and metastasis in colorectal cancer
Authors: Ouyang Jing , Hu Shuang , Zhu Qingqing , Li Chenxin , Kang Tingting , Xie Wenlin , Wang Yun , Li Yan , Lu Yingsi , Qi Junhua , Xia Ming , Chen Jinrun , Yang Yingqian , Sun Yazhou , Gao Tianshun , Ye Liping , Liang Qian , Pan Yihang , Zhu Chengming
Published: June 2024

TNF receptor superfamily member 11a (TNFRSF11a, RANK) and its ligand TNF superfamily member 11 (TNFRSF11, RANKL) are overexpressed in many malignancies. However, the clinical importance of RANKL/RANK in colorectal cancer (CRC) is mainly unknown. We examined CRC samples and found that RANKL/RANK was elevated in CRC tissues compared with nearby normal tissues. A higher RANKL/RANK expression was associated with a worse survival rate. Furthermore, RANKL was mostly produced by regulatory T cells (Tregs), which were able to promote CRC advancement. Overexpression of RANK or addition of RANKL significantly increased the stemness and migration of CRC cells. Furthermore, RANKL/RANK signaling stimulated C-C motif chemokine ligand 20 (CCL20) production by CRC cells, leading to Treg recruitment and boosting tumor stemness and malignant progression. This recruitment process was accomplished by CCL20–CCR6 interaction, demonstrating a connection between CRC cells and immune cells. These findings suggest an important role of RANKL/RANK in CRC progression, offering a potential target for CRC prevention and therapy.
ALKBH4 impedes 5-FU Sensitivity through suppressing GSDME induced pyroptosis in gastric cancer
Authors: Jiang Xin , Zhu Zhiman , Ding Lina , Du Wenqi , Pei Dongsheng
Published: June 2024

5-Fluorouracil (5-FU) is the primary treatment option for advanced gastric cancer. However, the current challenge lies in the absence of validated biomarkers to accurately predict the efficacy and sensitivity of 5-FU in individual patients. It has been confirmed that 5-FU can regulate tumor progression by promoting gasdermin E (GSDME, encoded by DFNA5) cleavage to induce pyroptosis. Lysine demethylase ALKBH4 has been shown to be upregulated in a variety of tumors to promote tumor progression. However, its role in gastric cancer is not clear. In this study, we observed a significant upregulation of ALKBH4 expression in gastric cancer tissues compared to adjacent normal tissues, indicating its potential as a predictor for the poor prognosis of gastric cancer patients. On the contrary, GSDME exhibits low expression levels in gastric cancer and demonstrates a negative correlation with poor prognosis among patients diagnosed with gastric cancer. In addition, we also found that high expression of ALKBH4 can inhibit pyroptosis and promote the proliferation of gastric cancer cells. Mechanistically, ALKBH4 inhibits GSDME activation at the transcriptional level by inhibiting H3K4me3 histone modification in the GSDME promoter region, thereby reducing the sensitivity of gastric cancer cells to 5-FU treatment. These findings provide further insight into the regulatory mechanisms of ALKBH4 in the progression of gastric cancer and underscore its potential as a prognostic marker for predicting the sensitivity of gastric cancer cells to 5-FU treatment.
Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation
Authors: Stewart Rebeccah K. , Nguyen Patrick , Laederach Alain , Volkan Pelin C. , Sawyer Jessica K. , Fox Donald T.
Published: June 2024

Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.
Simultaneous enhancement of multiple functional properties using evolution-informed protein design
Authors: Fram Benjamin , Su Yang , Truebridge Ian , Riesselman Adam J. , Ingraham John B. , Passera Alessandro , Napier Eve , Thadani Nicole N. , Lim Samuel , Roberts Kristen , Kaur Gurleen , Stiffler Michael A. , Marks Debora S. , Bahl Christopher D. , Khan Amir R. , Sander Chris , Gauthier Nicholas P.
Published: June 2024

A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely necessitates numerous primary sequence changes, and novel methods are needed to accurately predict combinations of mutations that maintain or enhance function. Models of sequence co-variation (e.g., EVcouplings), which leverage extensive information about various protein properties and activities from homologous protein sequences, have proven effective for many applications including structure determination and mutation effect prediction. We apply EVcouplings to computationally design variants of the model protein TEM-1 β-lactamase. Nearly all the 14 experimentally characterized designs were functional, including one with 84 mutations from the nearest natural homolog. The designs also had large increases in thermostability, increased activity on multiple substrates, and nearly identical structure to the wild type enzyme. This study highlights the efficacy of evolutionary models in guiding large sequence alterations to generate functional diversity for protein design applications.
In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer
Authors: Martinez Sebastien , Wu Shifei , Geuenich Michael , Malik Ahmad , Weber Ramona , Woo Tristan , Zhang Amy , Jang Gun Ho , Dervovic Dzana , Al-Zahrani Khalid N. , Tsai Ricky , Fodil Nassima , Gros Philippe , Gallinger Steven , Neely G. Gregory , Notta Faiyaz , Sendoel Ataman , Campbell Kieran , Elling Ulrich , Schramek Daniel
Published: June 2024

Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNFα, TGF-β and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.
Increasing control over biomineralization in conodont evolution
Authors: Shirley Bryan , Leonhard Isabella , Murdock Duncan J. E. , Repetski John , Świś Przemysław , Bestmann Michel , Trimby Pat , Ohl Markus , Plümper Oliver , King Helen E. , Jarochowska Emilia
Published: June 2024

Vertebrates use the phosphate mineral apatite in their skeletons, which allowed them to develop tissues such as enamel, characterized by an outstanding combination of hardness and elasticity. It has been hypothesized that the evolution of the earliest vertebrate skeletal tissues, found in the teeth of the extinct group of conodonts, was driven by adaptation to dental function. We test this hypothesis quantitatively and demonstrate that the crystallographic order increased throughout the early evolution of conodont teeth in parallel with morphological adaptation to food processing. With the c-axes of apatite crystals oriented perpendicular to the functional feeding surfaces, the strongest resistance to uniaxial compressional stress is conferred along the long axes of denticles. Our results support increasing control over biomineralization in the first skeletonized vertebrates and allow us to test models of functional morphology and material properties across conodont dental diversity.
Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide
Authors: Serrano Guillermo , Berastegui Nerea , Díaz-Mazkiaran Aintzane , García-Olloqui Paula , Rodriguez-Res Carmen , Huerga-Dominguez Sofia , Ainciburu Marina , Vilas-Zornoza Amaia , Martin-Uriz Patxi San , Aguirre-Ruiz Paula , Ullate-Agote Asier , Ariceta Beñat , Lamo-Espinosa Jose-Maria , Acha Pamela , Calvete Oriol , Jimenez Tamara , Molero Antonieta , Montoro Maria Julia , Díez-Campelo Maria , Valcarcel David , Solé Francisco , Alfonso-Pierola Ana , Ochoa Idoia , Prósper Felipe , Ezponda Teresa , Hernaez Mikel
Published: June 2024

While myelodysplastic syndromes with del(5q) (del(5q) MDS) comprises a well-defined hematological subgroup, the molecular basis underlying its origin remains unknown. Using single cell RNA-seq (scRNA-seq) on CD34+ progenitors from del(5q) MDS patients, we have identified cells harboring the deletion, characterizing the transcriptional impact of this genetic insult on disease pathogenesis and treatment response. Interestingly, both del(5q) and non-del(5q) cells present similar transcriptional lesions, indicating that all cells, and not only those harboring the deletion, may contribute to aberrant hematopoietic differentiation. However, gene regulatory network (GRN) analyses reveal a group of regulons showing aberrant activity that could trigger altered hematopoiesis exclusively in del(5q) cells, pointing to a more prominent role of these cells in disease phenotype. In del(5q) MDS patients achieving hematological response upon lenalidomide treatment, the drug reverts several transcriptional alterations in both del(5q) and non-del(5q) cells, but other lesions remain, which may be responsible for potential future relapses. Moreover, lack of hematological response is associated with the inability of lenalidomide to reverse transcriptional alterations. Collectively, this study reveals transcriptional alterations that could contribute to the pathogenesis and treatment response of del(5q) MDS.
Guiding antibiotics towards their target using bacteriophage proteins
Authors: Zhao Xinghong , Zhong Xinyi , Yang Shinong , Deng Jiarong , Deng Kai , Huang Zhengqun , Li Yuanfeng , Yin Zhongqiong , Liu Yong , Viel Jakob H. , Wan Hongping
Published: June 2024

Novel therapeutic strategies against difficult-to-treat bacterial infections are desperately needed, and the faster and cheaper way to get them might be by repurposing existing antibiotics. Nanodelivery systems enhance the efficacy of antibiotics by guiding them to their targets, increasing the local concentration at the site of infection. While recently described nanodelivery systems are promising, they are generally not easy to adapt to different targets, and lack biocompatibility or specificity. Here, nanodelivery systems are created that source their targeting proteins from bacteriophages. Bacteriophage receptor-binding proteins and cell-wall binding domains are conjugated to nanoparticles, for the targeted delivery of rifampicin, imipenem, and ampicillin against bacterial pathogens. They show excellent specificity against their targets, and accumulate at the site of infection to deliver their antibiotic payload. Moreover, the nanodelivery systems suppress pathogen infections more effectively than 16 to 32-fold higher doses of free antibiotics. This study demonstrates that bacteriophage sourced targeting proteins are promising candidates to guide nanodelivery systems. Their specificity, availability, and biocompatibility make them great options to guide the antibiotic nanodelivery systems that are desperately needed to combat difficult-to-treat infections.
Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex
Authors: Riepl Daniel , Gamiz-Hernandez Ana P. , Kovalova Terezia , Król Sylwia M. , Mader Sophie L. , Sjöstrand Dan , Högbom Martin , Brzezinski Peter , Kaila Ville R. I.
Published: June 2024

Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
Multiple roles for hypoxia inducible factor 1-alpha in airway epithelial cells during mucormycosis
Authors: Kavaliauskas Povilas , Gu Yiyou , Hasin Naushaba , Graf Karen T. , Alqarihi Abdullah , Shetty Amol C. , McCracken Carrie , Walsh Thomas J. , Ibrahim Ashraf S. , Bruno Vincent M.
Published: June 2024

During pulmonary mucormycosis, inhaled sporangiospores adhere to, germinate, and invade airway epithelial cells to establish infection. We provide evidence that HIF1α plays dual roles in airway epithelial cells during Mucorales infection. We observed an increase in HIF1α protein accumulation and increased expression of many known HIF1α-responsive genes during in vitro infection, indicating that HIF1α signaling is activated by Mucorales infection. Inhibition of HIF1α signaling led to a substantial decrease in the ability of R. delemar to invade cultured airway epithelial cells. Transcriptome analysis revealed that R. delemar infection induces the expression of many pro-inflammatory genes whose expression was significantly reduced by HIF1α inhibition. Importantly, pharmacological inhibition of HIF1α increased survival in a mouse model of pulmonary mucormycosis without reducing fungal burden. These results suggest that HIF1α plays two opposing roles during mucormycosis: one that facilitates the ability of Mucorales to invade the host cells and one that facilitates the ability of the host to mount an innate immune response.
Hippocampal and orbitofrontal neurons contribute to complementary aspects of associative structure
Authors: Lin Huixin , Zhou Jingfeng
Published: June 2024

The ability to establish associations between environmental stimuli is fundamental for higher-order brain functions like state inference and generalization. Both the hippocampus and orbitofrontal cortex (OFC) play pivotal roles in this, demonstrating complex neural activity changes after associative learning. However, how precisely they contribute to representing learned associations remains unclear. Here, we train head-restrained mice to learn four ‘odor-outcome’ sequence pairs composed of several task variables—the past and current odor cues, sequence structure of ‘cue-outcome’ arrangement, and the expected outcome; and perform calcium imaging from these mice throughout learning. Sequence-splitting signals that distinguish between paired sequences are detected in both brain regions, reflecting associative memory formation. Critically, we uncover differential contents in represented associations by examining, in each area, how these task variables affect splitting signal generalization between sequence pairs. Specifically, the hippocampal splitting signals are influenced by the combination of past and current cues that define a particular sensory experience. In contrast, the OFC splitting signals are similar between sequence pairs that share the same sequence structure and expected outcome. These findings suggest that the hippocampus and OFC uniquely and complementarily organize the acquired associative structure.
Maize yield prediction and condition monitoring at the sub-county scale in Kenya: synthesis of remote sensing information and crop modeling
Authors: Kipkulei Harison K. , Bellingrath-Kimura Sonoko D. , Lana Marcos , Ghazaryan Gohar , Baatz Roland , Matavel Custodio , Boitt Mark K. , Chisanga Charles B. , Rotich Brian , Moreira Rodrigo M. , Sieber Stefan
Published: June 2024

Agricultural production assessments are crucial for formulating strategies for closing yield gaps and enhancing production efficiencies. While in situ crop yield measurements can provide valuable and accurate information, such approaches are costly and lack scalability for large-scale assessments. Therefore, crop modeling and remote sensing (RS) technologies are essential for assessing crop conditions and predicting yields at larger scales. In this study, we combined RS and a crop growth model to assess phenology, evapotranspiration (ET), and yield dynamics at grid and sub-county scales in Kenya. We synthesized RS information from the Food and Agriculture Organization (FAO) Water Productivity Open-access portal (WaPOR) to retrieve sowing date information for driving the model simulations. The findings showed that grid-scale management information and progressive crop growth could be accurately derived, reducing the model output uncertainties. Performance assessment of the modeled phenology yielded satisfactory accuracies at the sub-county scale during two representative seasons. The agreement between the simulated ET and yield was improved with the combined RS-crop model approach relative to the crop model only, demonstrating the value of additional large-scale RS information. The proposed approach supports crop yield estimation in data-scarce environments and provides valuable insights for agricultural resource management enabling countermeasures, especially when shortages are perceived in advance, thus enhancing agricultural production.
Bellybutton: accessible and customizable deep-learning image segmentation
Authors: Dillavou Sam , Hanlan Jesse M. , Chieco Anthony T. , Xiao Hongyi , Fulco Sage , Turner Kevin T. , Durian Douglas J.
Published: June 2024

The conversion of raw images into quantifiable data can be a major hurdle and time-sink in experimental research, and typically involves identifying region(s) of interest, a process known as segmentation. Machine learning tools for image segmentation are often specific to a set of tasks, such as tracking cells, or require substantial compute or coding knowledge to train and use. Here we introduce an easy-to-use (no coding required), image segmentation method, using a 15-layer convolutional neural network that can be trained on a laptop: Bellybutton. The algorithm trains on user-provided segmentation of example images, but, as we show, just one or even a sub-selection of one training image can be sufficient in some cases. We detail the machine learning method and give three use cases where Bellybutton correctly segments images despite substantial lighting, shape, size, focus, and/or structure variation across the regions(s) of interest. Instructions for easy download and use, with further details and the datasets used in this paper are available at pypi.org/project/Bellybuttonseg.
Artificial intelligence-driven assessment of salt caverns for underground hydrogen storage in Poland
Authors: Derakhshani Reza , Lankof Leszek , GhasemiNejad Amin , Zaresefat Mojtaba
Published: June 2024

This study explores the feasibility of utilizing bedded salt deposits as sites for underground hydrogen storage. We introduce an innovative artificial intelligence framework that applies multi-criteria decision-making and spatial data analysis to identify the most suitable locations for storing hydrogen in salt caverns. Our approach integrates a unified platform with eight distinct machine-learning algorithms—KNN, SVM, LightGBM, XGBoost, MLP, CatBoost, GBR, and MLR—creating rock salt deposit suitability maps for hydrogen storage. The performance of these algorithms was evaluated using various metrics, including Mean Squared Error (MSE), Mean Absolute Error (MAE), Mean Absolute Percentage Error (MAPE), Root Mean Square Error (RMSE), and Correlation Coefficient (R2), compared against an actual dataset. The CatBoost model demonstrated exceptional performance, achieving an R2 of 0.88, MSE of 0.0816, MAE of 0.1994, RMSE of 0.2833, and MAPE of 0.0163. The novel methodology, leveraging advanced machine learning techniques, offers a unique perspective in assessing the potential of underground hydrogen storage. This approach is a valuable asset for various stakeholders, including government bodies, geological services, renewable energy facilities, and the chemical/petrochemical industry, aiding them in identifying optimal locations for hydrogen storage.
Reactions of wintering passerines to male calls of the European cuckoo Cuculus canorus
Authors: Tryjanowski Piotr , Golawski Artur , Jankowiak Łukasz , Møller Anders Pape
Published: June 2024

The reaction of birds to the nest parasite, the European cuckoo Cuculus canorus, has been the subject of extensive testing in various aspects. However, while the cuckoo is a long-distance migrant, some of its hosts are sedentary species. In this study, we aimed to investigate whether species, primarily hosts, react to the presence of the cuckoo also in the winter season. This behaviour may involve an attempt to drive the parasite away from locations that will subsequently become their breeding sites. During playback experiments conducted in the winter of 2021/2022 in Poland, we demonstrated that numerous bird species react to the male cuckoo calls in winter. These calls may be perceived as a source of danger, particularly by cuckoo hosts, who responded to this call more frequently than non-hosts and the control species (pigeon). Nonetheless, the birds’ reactions were not strong, as they did not approach the source of the call. However, our results are constrained by the limited number of cuckoo host species wintering in Poland. To better evaluate the intensity of bird responses to the male cuckoo’s call during the non-breeding season, further studies should be conducted in regions where a greater variety of species, especially those most susceptible to parasitism, overwinter.
Automated hearing loss type classification based on pure tone audiometry data
Authors: Kassjański Michał , Kulawiak Marcin , Przewoźny Tomasz , Tretiakow Dmitry , Kuryłowicz Jagoda , Molisz Andrzej , Koźmiński Krzysztof , Kwaśniewska Aleksandra , Mierzwińska-Dolny Paulina , Grono Miłosz
Published: June 2024

Hearing problems are commonly diagnosed with the use of tonal audiometry, which measures a patient’s hearing threshold in both air and bone conduction at various frequencies. Results of audiometry tests, usually represented graphically in the form of an audiogram, need to be interpreted by a professional audiologist in order to determine the exact type of hearing loss and administer proper treatment. However, the small number of professionals in the field can severely delay proper diagnosis. The presented work proposes a neural network solution for classification of tonal audiometry data. The solution, based on the Bidirectional Long Short-Term Memory architecture, has been devised and evaluated for classifying audiometry results into four classes, representing normal hearing, conductive hearing loss, mixed hearing loss, and sensorineural hearing loss. The network was trained using 15,046 test results analysed and categorised by professional audiologists. The proposed model achieves 99.33% classification accuracy on datasets outside of training. In clinical application, the model allows general practitioners to independently classify tonal audiometry results for patient referral. In addition, the proposed solution provides audiologists and otolaryngologists with access to an AI decision support system that has the potential to reduce their burden, improve diagnostic accuracy, and minimise human error.
Target reliability-based design optimization studies on cohesive soil amended with chitosan and casein for liner applications
Authors: Rasheed Romana Mariyam , Moghal Arif Ali Baig , Basha B. Munwar , Almajed Abdullah
Published: June 2024

The current study investigated the primary and secondary compressibility characteristics of organic clay with two biopolymers, Chitosan (Dch) and Casein (Dca) at dosages of 0.5%, 1%, 2%, and 4%. The primary compression index (Cc) values were reduced by 18% and 59% at dosage (Dch and Dca) of 4% at a consolidation pressure of 800 kPa. The secondary compression indices of chitosan and casein-treated soils fell below the normal range specified for organic soils and lay in the range of 0.01–0.017. The biopolymers also accelerated the consolidation process at all dosages (Dch) and 2% Dca. The hydraulic conductivity increased for all dosages of chitosan whereas it declined for all dosages of casein compared to untreated soil. The reliability analysis was conducted for biopolymer-treated soils and presented a rational approach toward the selection of a suitable liner. Chitosan failed to achieve a target reliability index of 3 whereas casein-amended samples attained values equal to and greater than 3 at all dosages and consolidation pressures at COV of Kmax = 20%. At all dosages, the casein-treated soils exhibited reliability index values greater than 3 up to COV of Kmax = 40% indicating the higher stability of casein mixes as a liner material.
Temporal trajectories of artificial radiocaesium 137Cs in French rivers over the nuclear era reconstructed from sediment cores
Authors: Eyrolle Frédérique , Chaboche Pierre-Alexis , Lepage Hugo , Gouin Valérie Nicoulaud , Boyer Patrick , De Vismes Anne , Seignemartin Gabrielle , Badariotti Dominique , Chabaux François , Chastanet Maxime , Claval David , Copard Yoann , Coynel Alexandra , Debret Maxime , Delus Claire , Euzen Cassandra , Gardes Thomas , Giner Franck , Gurriaran Rodolfo , Grenz Christian , Grosbois Cécile , Lestel Laurence , Losson Benoît , Mansuy-Huault Laurence , Montarges-Pelletier Emmanuelle , Morereau Amandine , Mourier Brice , Mourier David , Ollive Vincent , Papillon Laure , Schafer Jorg , Schmitt Laurent , Sempere Richard , Winiarski Thierry , Zebracki Mathilde , Evrard Olivier
Published: June 2024

137Cs is a long-lived man-made radionuclide introduced in the environment worldwide at the early beginning of the nuclear Era during atmospheric nuclear testing’s followed by the civil use of nuclear energy. Atmospheric fallout deposition of this major artificial radionuclide was reconstructed at the scale of French large river basins since 1945, and trajectories in French nuclearized rivers were established using sediment coring. Our results show that 137Cs contents in sediments of the studied rivers display a large spatial and temporal variability in response to the various anthropogenic pressures exerted on their catchment. The Loire, Rhone, and Rhine rivers were the most affected by atmospheric fallout from the global deposition from nuclear tests. Rhine and Rhone also received significant fallout from the Chernobyl accident in 1986 and recorded significant 137Cs concentrations in their sediments over the 1970–1985 period due to the regulatory releases from the nuclear industries. The Meuse River was notably impacted in the early 1970s by industrial releases. In contrast, the Seine River display the lowest 137Cs concentrations regardless of the period. All the rivers responded similarly over time to atmospheric fallout on their catchment, underlying a rather homogeneous resilience capacity of these river systems to this source of contamination.
An improved approach for automated cervical cell segmentation with PointRend
Authors: Zhang Baocan , Wang Wenfeng , Zhao Wei , Jiang Xiaolu , Patnaik Lalit Mohan
Published: June 2024

Regular screening for cervical cancer is one of the best tools to reduce cancer incidence. Automated cell segmentation in screening is an essential task because it can present better understanding of the characteristics of cervical cells. The main challenge of cell cytoplasm segmentation is that many boundaries in cell clumps are extremely difficult to be identified. This paper proposes a new convolutional neural network based on Mask RCNN and PointRend module, to segment overlapping cervical cells. The PointRend head concatenates fine grained features and coarse features extracted from different feature maps to fine-tune the candidate boundary pixels of cell cytoplasm, which are crucial for precise cell segmentation. The proposed model achieves a 0.97 DSC (Dice Similarity Coefficient), 0.96 TPRp (Pixelwise True Positive Rate), 0.007 FPRp (Pixelwise False Positive Rate) and 0.006 FNRo (Object False Negative Rate) on dataset from ISBI2014. Specially, the proposed method outperforms state-of-the-art result by about$$3\%$$3%on DSC,$$1\%$$1%on TPRp and$$1.4\%$$1.4%on FNRo respectively. The performance metrics of our model on dataset from ISBI2015 are slight better than the average value of other approaches. Those results indicate that the proposed method could be effective in cytological analysis and then help experts correctly discover cervical cell lesions
Ambient air pollution exposure and COVID-19 related hospitalizations in Santiago, Chile
Authors: Dales Robert , Lukina Anna O. , Romero-Meza Rafael , Blanco-Vidal Claudia , Cakmak Sabit
Published: June 2024

Morbidity and mortality from several diseases are increased on days of higher ambient air pollution. We carried out a daily time-series analysis with distributive lags to study the influence of short-term air pollution exposure on COVID-19 related hospitalization in Santiago, Chile between March 16 and August 31, 2020. Analyses were adjusted for temporal trends, ambient temperature, and relative humidity, and stratified by age and sex. 26,579 COVID-19 hospitalizations were recorded of which 24,501 were laboratory confirmed. The cumulative percent change in hospitalizations (95% confidence intervals) for an interquartile range increase in air pollutants were: 1.1 (0.2, 2.0) for carbon monoxide (CO), 0.30 (0.0, 0.50) for nitrogen dioxide (NO2), and 2.7 (1.9, 3.0) for particulate matter of diameter ≤ 2.5 microns (PM2.5). Associations with ozone (O3), particulate matter of diameter ≤ 10 microns (PM10) and sulfur dioxide (SO2) were not significant. The observed effect of PM2.5 was significantly greater for females and for those individuals ≥ 65 years old. This study provides evidence that daily increases in air pollution, especially PM2.5, result in a higher observed risk of hospitalization from COVID-19. Females and the elderly may be disproportionately affected.
High prevalence and low intensity of Echinophthirius horridus infection in seals revealed by high effort sampling
Authors: Herzog Insa , Siebert Ursula , Lehnert Kristina
Published: June 2024

Seal lice (Echinophthirius horridus) are bloodsucking ectoparasites of phocid seals and vectors of pathogens like the heartworm, Acanthocheilonema spirocauda. Grey and harbour seal populations are recovering in German waters and wildlife health surveillance is crucial for wildlife conservation. A new, high effort sampling protocol for seal lice was applied for grey and harbour seals along the German North- and Baltic Sea coast. Freshly dead seals were systematically sampled within a health monitoring of stranded seals over 12 months. Prevalence, intensity and distribution patterns of seal lice were analysed. 58% of harbour seals (n = 71) and 70% of grey seals (n = 10) were infected with seal lice. A majority of harbour seals displayed mild levels of infection, while three were moderately and two were severely infected. The head was the preferred predilection site, indicating that E. horridus prefers body areas with frequent access to atmospheric oxygen. Nits and different developmental stages were recorded in all age classes in grey and harbour seals in all seasons. For the first time, copulating specimens of E. horridus were recorded on a dead harbour seal, highlighting that E. horridus reproduces throughout the year on seals of all age classes in German waters.
Modulation of the glycaemic index value of shortbread cookies by the use of erythritol and fruit pomace
Authors: Raczkowska Ewa , Bienkiewicz Maciej , Gajda Robert
Published: June 2024

Fruit pomace, as a by-product of fruit and vegetable processing, is a cheap and easily accessible material for further processing that can replace selected recipe ingredients, most often flour. In addition, their advantage is their high health-promoting potential. The aim of this study was to evaluate the effect of the simultaneous use of erythritol (100% sucrose substitution) and the addition of varying amounts of blackcurrant, chokeberry and apple pomace (0%, 10%, 30% and 50% by weight of flour) on the glycaemic response after consumption of shortbread cookies in an in vivo study with humans (ISO 26642:2010). It was shown that an increase in the addition of each type of pomace reduced the glycaemic index value of the cookies. The pomace and sucrose-sweetened cookies were classified in the medium and low GI group. For each type of pomace, an increase in its share in the recipe of cookies was associated with a reduction in GI values (pomace: apple 49.1–37.2%, blackcurrant 56.4–41.0%, chokeberry 59.4–35.5%). Similar correlations were shown for the use of erythritol (pomace: apple 39.5–29.1%, blackcurrant 43.9–31.9%, chokeberry 34.6–20.7%). A significant effect of pomace addition on the GI values of shortbread cookies, was only observed for sucrose-sweetened products. The results obtained allow the conclusion that there is potential for the use of waste raw materials in the production of functional foods.