bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing Permafrost Monitoring With Autonomous Electrical Resistivity Tomography (A‐ERT): Low‐Cost Instrumentation and Open‐Source Data Processing Tool
Authors: Farzamian M. , Blanchy G. , McLachlan P. , Vieira G. , Esteves M. , de Pablo M. A. , Triantafilis J. , Lippmann E. , Hauck C. 
Published: March 2024

AbstractPermafrost is a widespread phenomenon in the cold regions of the globe and is under‐represented in global monitoring networks. This study presents a novel low‐cost, low‐power, and robust Autonomous Electrical Resistivity Tomography (A‐ERT) monitoring system and open‐source processing tools for permafrost monitoring. The processing workflow incorporates diagnostic and filtering tools and utilizes open‐source software, ResIPy, for data inversion. The workflow facilitates quick and efficient extraction of key information from large data sets. Field experiments conducted in Antarctica demonstrated the system's capability to operate in harsh and remote environments and provided high‐temporal‐resolution imaging of ground freezing and thawing dynamics. This data set and processing workflow allow for a detailed investigation of how meteorological conditions impact subsurface processes. The A‐ERT setup can complement existing monitoring networks on permafrost and is suitable for continuous monitoring in polar and mountainous regions, contributing to cryosphere research and gaining deeper insights into permafrost and active layer dynamics.
Machine Learning Analysis of Seismograms Reveals a Continuous Plumbing System Evolution Beneath the Klyuchevskoy Volcano in Kamchatka, Russia
Authors: Steinmann René , Seydoux Léonard , Journeau Cyril , Shapiro Nikolai M. , Campillo Michel 
Published: March 2024

AbstractVolcanoes produce a variety of seismic signals and, therefore, continuous seismograms provide crucial information for monitoring the state of a volcano. According to their source mechanism and signal properties, seismo‐volcanic signals can be categorized into distinct classes, which works particularly well for short transients. Applying classification approaches to long‐duration continuous signals containing volcanic tremors, characterized by varying signal characteristics, proves challenging due to the complex nature of these signals. That makes it difficult to attribute them to a single volcanic process and questions the feasibility of classification. In the present study, we consider the whole seismic time series as valuable information about the plumbing system (the combination of plumbing structure and activity distribution). The considered data are year‐long seismograms recorded at individual stations near the Klyuchevskoy Volcanic Group (Kamchatka, Russia). With a scattering network and a Uniform Manifold Approximation and Projection (UMAP), we transform the continuous data into a two‐dimensional representation (a seismogram atlas), which helps us to identify sudden and continuous changes in the signal properties. We observe an ever‐changing seismic wavefield that we relate to a continuously evolving plumbing system. Through additional data, we can relate signal variations to various state changes of the volcano including transitions from deep to shallow activity, deep reactivation, weak signals during quiet times, and eruptive activity. The atlases serve as a visual tool for analyzing extensive seismic time series, allowing us to associate specific atlas areas, indicative of similar signal characteristics, with distinct volcanic activities and variations in the volcanic plumbing system.
SARS-CoV-2 envelope protein impairs airway epithelial barrier function and exacerbates airway inflammation via increased intracellular Cl− concentration
Authors: Xu Jian-Bang , Guan Wei-Jie , Zhang Yi-Lin , Qiu Zhuo-Er , Chen Lei , Hou Xiao-Chun , Yue Junqing , Zhou Yu-Yun , Sheng Jie , Zhao Lei , Zhu Yun-Xin , Sun Jing , Zhao Jincun , Zhou Wen-Liang , Zhong Nan-Shan 
Published: March 2024

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection disrupts the epithelial barrier and triggers airway inflammation. The envelope (E) protein, a core virulence structural component of coronaviruses, may play a role in this process. Pathogens could interfere with transepithelial Cl− transport via impairment of the cystic fibrosis transmembrane conductance regulator (CFTR), which modulates nuclear factor κB (NF-κB) signaling. However, the pathological effects of SARS-CoV-2 E protein on airway epithelial barrier function, Cl− transport and the robust inflammatory response remain to be elucidated. Here, we have demonstrated that E protein down-regulated the expression of tight junctional proteins, leading to the disruption of the airway epithelial barrier. In addition, E protein triggered the activation of Toll-like receptor (TLR) 2/4 and downstream c-Jun N-terminal kinase (JNK) signaling, resulting in an increased intracellular Cl− concentration ([Cl−]i) via up-regulating phosphodiesterase 4D (PDE4D) expression in airway epithelial cells. This elevated [Cl−]i contributed to the heightened airway inflammation through promoting the phosphorylation of serum/glucocorticoid regulated kinase 1 (SGK1). Moreover, blockade of SGK1 or PDE4 alleviated the robust inflammatory response induced by E protein. Overall, these findings provide novel insights into the pathogenic role of SARS-CoV-2 E protein in airway epithelial damage and the ongoing airway inflammation during SARS-CoV-2 infection.
Decreased calcium permeability caused by biallelic TRPV5 mutation leads to autosomal recessive renal calcium-wasting hypercalciuria
Authors: Guleray Lafci Naz , van Goor Mark , Cetinkaya Semra , van der Wijst Jenny , Acun Melisa , Kurt Colak Fatma , Cetinkaya Arda , Hoenderop Joost 
Published: March 2024

AbstractHypercalciuria is the most common metabolic risk factor in people with kidney stone disease. Its etiology is mostly multifactorial, although monogenetic causes of hypercalciuria have also been described. Despite the increased availability of genetic diagnostic tests, the vast majority of individuals with familial hypercalciuria remain unsolved. In this study, we investigated a consanguineous pedigree with idiopathic hypercalciuria. The proband additionally exhibited severe skeletal deformities and hyperparathyroidism. Whole-exome sequencing of the proband revealed a homozygous ultra-rare variant in TRPV5 (NM_019841.7:c.1792G>A; p.(Val598Met)), which encodes for a renal Ca2+-selective ion channel. The variant segregates with the three individuals with hypercalciuria. The skeletal phenotype unique to the proband was due to an additional pathogenic somatic mutation in GNAS (NM_000516.7:c.601C>T; p.(Arg201Cys)), which leads to polyostotic fibrous dysplasia. The variant in TRPV5 is located in the TRP helix, a characteristic amphipathic helix that is indispensable for the gating movements of TRP channels. Biochemical characterization of the TRPV5 p.(Val598Met) channel revealed a complete loss of Ca2+ transport capability. This defect is caused by reduced expression of the mutant channel, due to misfolding and preferential targeting to the proteasome for degradation. Based on these findings, we conclude that biallelic loss of TRPV5 function causes a novel form of monogenic autosomal recessive hypercalciuria, which we name renal Ca2+-wasting hypercalciuria (RCWH). The recessive inheritance pattern explains the rarity of RCWH and underscores the potential prevalence of RCWH in highly consanguineous populations, emphasizing the importance of exploration of this disorder within such communities.
IKK2 controls the inflammatory potential of tissue-resident regulatory T cells in a murine gain of function model
Authors: Cardinez Chelisa , Hao Yuwei , Kwong Kristy , Davies Ainsley R. , Downes Morgan B. , Roberts Nadia A. , Price Jason D. , Hernandez Raquel A. , Lovell Jessica , Chand Rochna , Feng Zhi-Ping , Enders Anselm , Vinuesa Carola G. , Miraghazadeh Bahar , Cook Matthew C. 
Published: March 2024

AbstractLoss-of-function mutations have provided crucial insights into the immunoregulatory actions of Foxp3+ regulatory T cells (Tregs). By contrast, we know very little about the consequences of defects that amplify aspects of Treg function or differentiation. Here we show that mice heterozygous for an Ikbkb gain-of-function mutation develop psoriasis. Doubling the gene dose (IkbkbGoF/GoF) results in dactylitis, spondylitis, and characteristic nail changes, which are features of psoriatic arthritis. IkbkbGoF mice exhibit a selective expansion of Foxp3 + CD25+ Tregs of which a subset express IL-17. These modified Tregs are enriched in both inflamed tissues, blood and spleen, and their transfer is sufficient to induce disease without conventional T cells. Single-cell transcriptional and phenotyping analyses of isolated Tregs reveal expansion of non-lymphoid tissue (tissue-resident) Tregs expressing Th17-related genes, Helios, tissue-resident markers including CD103 and CD69, and a prominent NF-κB transcriptome. Thus, IKK2 regulates tissue-resident Treg differentiation, and overactivity drives dose-dependent skin and systemic inflammation.
Hazardous explosive eruptions of a recharging multi-cyclic island arc caldera
Authors: Preine Jonas , Karstens Jens , Hübscher Christian , Druitt Tim , Kutterolf Steffen , Nomikou Paraskevi , Manga Michael , Gertisser Ralf , Pank Katharina , Beethe Sarah , Berthod Carole , Crutchley Gareth , McIntosh Iona , Ronge Thomas , Tominaga Masako , Clark Acacia , DeBari Susan , Johnston Raymond , Mateo Zenon , Peccia Ally , Jones Christopher , Kletetschka Günther , Metcalfe Abigail , Bernard Alexis , Chen Hehe , Chiyonobu Shun , Fernandez-Perez Tatiana , Joshi Kumar Batuk , Koukousioura Olga , McCanta Molly , Morris Antony , Polymenakou Paraskevi , Woodhouse Adam , Yamamoto Yuzuru , Wang Kuo-Lung , Lee Hao-Yang , Li Xiaohui , Papanikolaou Dimitrios 
Published: March 2024

AbstractCaldera-forming eruptions of silicic volcanic systems are among the most devastating events on Earth. By contrast, post-collapse volcanic activity initiating new caldera cycles is generally considered less hazardous. Formed after Santorini’s latest caldera-forming eruption of ~1600 bce, the Kameni Volcano in the southern Aegean Sea enables the eruptive evolution of a recharging multi-cyclic caldera to be reconstructed. Kameni’s eruptive record has been documented by onshore products and historical descriptions of mainly effusive eruptions dating back to 197 bce. Here we combine high-resolution seismic reflection data with cored lithologies from International Ocean Discovery Program Expedition 398 at four sites to determine the submarine architecture and volcanic history of intra-caldera deposits from Kameni. Our shore-crossing analysis reveals the deposits of a submarine explosive eruption that produced up to 3.1 km3 of pumice and ash, which we relate to a historical eruption in 726 ce. The estimated volcanic explosivity index of magnitude 5 exceeds previously considered worst-case eruptive scenarios for Santorini. Our finding that the Santorini caldera is capable of producing large explosive eruptions at an early stage in the caldera cycle implies an elevated hazard potential for the eastern Mediterranean region, and potentially for other recharging silicic calderas.
An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity
Authors: Ryan Daniel , Bornet Elise , Prezza Gianluca , Alampalli Shuba Varshini , Franco de Carvalho Taís , Felchle Hannah , Ebbecke Titus , Hayward Regan J. , Deutschbauer Adam M. , Barquist Lars , Westermann Alexander J. 
Published: March 2024

AbstractPlasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data—publicly available through the Theta-Base web browser (http://micromix.helmholtz-hiri.de/bacteroides/)—constitute a valuable resource for the microbiome community.
Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development
Authors: Dvoretskova Elena , Ho May C. , Kittke Volker , Neuhaus Florian , Vitali Ilaria , Lam Daniel D. , Delgado Irene , Feng Chao , Torres Miguel , Winkelmann Juliane , Mayer Christian 
Published: March 2024

AbstractThe mammalian telencephalon contains distinct GABAergic projection neuron and interneuron types, originating in the germinal zone of the embryonic basal ganglia. How genetic information in the germinal zone determines cell types is unclear. Here we use a combination of in vivo CRISPR perturbation, lineage tracing and ChIP–sequencing analyses and show that the transcription factor MEIS2 favors the development of projection neurons by binding enhancer regions in projection-neuron-specific genes during mouse embryonic development. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity toward the appropriate binding sites. In interneuron precursors, the transcription factor LHX6 represses the MEIS2–DLX5-dependent activation of projection-neuron-specific enhancers. Mutations of Meis2 result in decreased activation of regulatory enhancers, affecting GABAergic differentiation. We propose a differential binding model where the binding of transcription factors at cis-regulatory elements determines differential gene expression programs regulating cell fate specification in the mouse ganglionic eminence.
Warmer autumns and winters could reduce honey bee overwintering survival with potential risks for pollination services
Authors: Rajagopalan Kirti , DeGrandi-Hoffman Gloria , Pruett Matthew , Jones Vincent P. , Corby-Harris Vanessa , Pireaud Julien , Curry Robert , Hopkins Brandon , Northfield Tobin D. 
Published: March 2024

AbstractHoney bees and other pollinators are critical for food production and nutritional security but face multiple survival challenges. The effect of climate change on honey bee colony losses is only recently being explored. While correlations between higher winter temperatures and greater colony losses have been noted, the impacts of warmer autumn and winter temperatures on colony population dynamics and age structure as an underlying cause of reduced colony survival have not been examined. Focusing on the Pacific Northwest US, our objectives were to (a) quantify the effect of warmer autumns and winters on honey bee foraging activity, the age structure of the overwintering cluster, and spring colony losses, and (b) evaluate indoor cold storage as a management strategy to mitigate the negative impacts of climate change. We perform simulations using the VARROAPOP population dynamics model driven by future climate projections to address these objectives. Results indicate that expanding geographic areas will have warmer autumns and winters extending honey bee flight times. Our simulations support the hypothesis that late-season flight alters the overwintering colony age structure, skews the population towards older bees, and leads to greater risks of colony failure in the spring. Management intervention by moving colonies to cold storage facilities for overwintering has the potential to reduce honey bee colony losses. However, critical gaps remain in how to optimize winter management strategies to improve the survival of overwintering colonies in different locations and conditions. It is imperative that we bridge the gaps to sustain honey bees and the beekeeping industry and ensure food and nutritional security.
Economic feasibility study of organic and conventional fish farming systems of Indian major carps
Authors: Beg Mirza Masum , Roy Subha M. , Moulick Sanjib , Mandal Basudev , Kim Taeho , Mal Bimal C. 
Published: March 2024

AbstractOrganic aquaculture is a new approach in the modern farming system. As the capital investment is higher for setting up the organic aquaculture, it is essential to conduct an economic feasibility study with compare the conventional farming system. In the current study, economic feasibility of culturing Indian major carps (IMC) using conventional culture system and organic culture system (OCS) were evaluated. IMC was cultured for three consecutive years from 2017 to 2019 in experimental ponds of 0.015 hectare (ha) area each. The crude protein content of the organic and conventional feed was maintained at the same iso-nitrogenous level (32% crude protein) but the highest production to the tune of 19 tons per ha was obtained in OCS. Further, in case of OCS, apart from fish production, vermicomposting to the tune of 45,000 kg ha−1 in the first year, and 90,000 kg ha−1 from second year onward is achievable by installing a vermicomposting unit of 200 tons annual capacity. Economic analysis of the culture systems assuming a project period of 10 years showed that the highest net present value (NPV) of 1.06 million USD, a payback period of one year and nine months and an internal rate of return (IRR) of 51% are achievable per ha of fish culture pond for OCS. Sensitivity analysis of various costs performed for OCS revealed that profitability of the organic fish farming investment is most sensitive to the total fish production and sale price of the organic fishes. In terms of production of fish and economics of organic culture system is proved to be the best available technique.
Efficient quantum algorithms for set operations
Authors: Elgendy Rehab , Younes Ahmed , Abu-Donia H. M. , Farouk R. M. 
Published: March 2024

AbstractAnalyzing the relations between Boolean functions has many applications in many fields, such as database systems, cryptography, and collision problems. This paper proposes four quantum algorithms that use amplitude amplification techniques to perform set operations, including Intersection, Difference, and Union, on two Boolean functions in $$\mathcal {O}(\sqrt{\mathcal {N}} )$$

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time complexity. The proposed algorithms employ two quantum amplitude amplification techniques divided into two stages. The first stage uses the Younes et al. algorithm for quantum searching via entanglement and partial diffusion to prepare incomplete superpositions of the truth set of the first Boolean function. In the second stage, a modified version of Arima’s algorithm, along with an oracle that represent the second Boolean function, is employed to handle the set operations. The proposed algorithms have a higher probability of success in more general and comprehensive applications when compared with relevant techniques in literature.
Semen proteome and transcriptome of the endangered black-footed ferret (Mustela nigripes) show association with the environment and fertility outcome
Authors: Ali Nadya , Amelkina Olga , Santymire Rachel M. , Koepfli Klaus-Peter , Comizzoli Pierre , Vazquez Juan M. 
Published: March 2024

AbstractThe ex situ population of the endangered black-footed ferret (Mustela nigripes) has been experiencing declines in reproductive success over the past 30 years of human-managed care. A potential cause may be environmental-dependent inbreeding depression with diet being one of the contributing factors since ferrets are not fed their natural diet of prairie dogs. Here, we generated and analyzed semen proteome and transcriptome data from both wild and ex situ ferrets maintained on various diets. We identified 1757 proteins across all samples, with 149 proteins unique to the semen of wild ferrets and forming a ribosomal predicted protein–protein interaction cluster. Wild ferrets also differed from ex situ ferrets in their transcriptomic profile, showing enrichment in ribosomal RNA processing and potassium ion transport. Successful fertility outcomes documented for ex situ ferrets showed the strongest association with the semen transcriptome, with enrichment in genes involved in translation initiation and focal adhesion. Fertility also synergized with the effect of diet on differentially expressed transcriptomes, mainly affecting genes enriched in mitochondrial function. Our data and functional networks are important for understanding the causes and mechanisms of declining fertility in the ex situ ferret population and can be used as a resource for future conservation efforts.
Treatment satisfaction with disease-modifying therapy is the only predictor of Adherence among multiple sclerosis patients from Upper Egypt
Authors: Khedr Eman M. , Mahmoud Doaa M. , Hussein Hussein B. , Malky Islam E. L. , Mostafa Sarah S. , Gamea Ayman 
Published: March 2024

AbstractDespite the proven efficacy of the disease-modifying therapy (DMT) for multiple sclerosis (MS), the rates of non-adherence are frequently high. We aimed to evaluate the rate of non-adherence to the first DMT in Upper Egypt and identify different contributing factors. Out of 310 patients, ninety-seven adult patients with RRMS were recruited from three MS units located in Upper Egypt and were subjected to the following: complete clinical history, expanded disability status score (EDSS), Eight-item Morisky Medication Adherence Scale (MMAS-8), abbreviated Treatment Satisfaction Questionnaire for Medication-9 (TSQM-9), Hamilton depression scale, Fatigue Severity Scale (FSS) and the Pittsburgh Sleep Quality Index (PSQI). According to MMAS-8 scores, 63 (64.9%) of patients were non-adherent to their first DMT. Non-adherent patients are more likely to have longer disease duration (p = 0.002), longer duration on first DMT (p = 0.030), first DMT-start date before 2019 (p = 0.040), and lower treatment satisfaction scores (p = 0.016). However, there was no significant relation with physical disability, depression, fatigue, or sleep quality. On the regression analysis model, a lower treatment satisfaction score was the only predictor of DMT non-adherence (p = 0.012). Despite expanding DMT options, non-adherence among MS patients in Upper Egypt is high. Treatment satisfaction with DMT is the only predictor of adherence among MS patients of Upper Egypt. Adherence and satisfaction with the prescribed DMT should be assessed carefully to maximize DMT benefits.
Positive affect and heart rate variability: a dynamic analysis
Authors: Beatton Tony , Chan Ho Fai , Dulleck Uwe , Ristl Andrea , Schaffner Markus , Torgler Benno 
Published: March 2024

AbstractTraditional survey methods can provide noisy data arising from recall, memory and other biases. Technological advances (particularly in neuroscience) are opening new ways of monitoring physiological processes through non-intrusive means. Such dense continuous data provide new and fruitful avenues for complementing self-reported data with a better understanding of human dynamics and human interactions. In this study, we use a survey to collect positive affect (feelings) data from more than 300 individuals over a period of 24 h, and at the same time, map their core activities (5000 recorded activities in total) with measurements of their heart rate variability (HRV). Our results indicate a robust correlation between the HRV measurements and self-reported affect. By drawing on the neuroscience and wellbeing literature we show that dynamic HRV results are what we expect for positive affect, particularly when performing activities like sleep, travel, work, exercise and eating. This research provides new insights into how to collect HRV data, model and interpret it.