bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monthly Arctic sea ice prediction based on a data-driven deep learning model
Authors: Huan Xiaohe , Wang Jielong , Liu Zhongfang 
Published: October 2023

Abstract
There is growing interest in sub-seasonal to seasonal predictions of Arctic sea ice due to its potential effects on midlatitude weather and climate extremes. Current prediction systems are largely dependent on physics-based climate models. While climate models can provide good forecasts for Arctic sea ice at different timescales, they are susceptible to initial states and high computational costs. Here we present a purely data-driven deep learning model, UNet-F/M, to predict monthly sea ice concentration (SIC) one month ahead. We train the model using monthly satellite-observed SIC for the melting and freezing seasons, respectively. Results show that UNet-F/M has a good predictive skill of Arctic SIC at monthly time scales, generally outperforming several recently proposed deep learning models, particularly for September sea-ice minimum. Our study offers a perspective on sub-seasonal prediction of future Arctic sea ice and may have implications for forecasting weather and climate in northern midlatitudes.
Disorder unleashes panic in bitcoin dynamics
Authors: Alberto Javarone Marco , Di Antonio Gabriele , Valerio Vinci Gianni , Cristodaro Raffaele , Tessone Claudio J , Pietronero Luciano 
Published: October 2023

Abstract
The behaviour of Bitcoin owners is reflected in the structure and the number of bitcoin transactions encoded in the Blockchain. Likewise, the behaviour of Bitcoin traders is reflected in the formation of bullish and bearish trends in the crypto market. In light of these observations, we wonder if human behaviour underlies some relationship between the Blockchain and the crypto market. To address this question, we map the Blockchain to a spin-lattice problem, whose configurations form ordered and disordered patterns, representing the behaviour of Bitcoin owners. This novel approach allows us to obtain time series suitable to detect a causal relationship between the dynamics of the Blockchain and market trends of the Bitcoin and to find that disordered patterns in the Blockchain precede Bitcoin panic selling. Our results suggest that human behaviour underlying Blockchain evolution and the crypto market brings out a fascinating connection between disorder and panic in Bitcoin dynamics.
Long-range, time-varying statistical prediction of annual precipitation in a Mediterranean remote site
Authors: Diodato Nazzareno , Lanfredi Maria , Bellocchi Gianni 
Published: October 2023

Abstract
In the Mediterranean basin, climate change signals are often representative of atmospheric transients in precipitation patterns. Remote mountaintop rainfall stations are far from human influence and can more easily unveil climate signals to improve the accuracy of long-term forecasts. In this study, the world’s longest annual precipitation time-series (1884–2021) from a remote station, the Montevergine site (1284 m a.s.l.) in southern Italy, was investigated to explain its forecast performance in the coming decades, offering a representative case study for the central Mediterranean. For this purpose, a Seasonal AutoRegressive-exogenous Time Varying process with Exponential Generalised Autoregressive Conditional Heteroscedasticity (SARX(TVAR)-EGARCH) model was developed for the training period 1884–1991, validated for the interval 1992–2021, and used to make forecasts for the time-horizon 2022–2051, with the support of an exogenous variable (dipole mode index). Throughout this forecast period, the dominant feature is the emergence of an incipient and strong upward drought trend in precipitation until 2035. After this change-point, rainfall increases again, more slightly, but with considerable values towards the end of the forecast period. Although uncertainties remain, the results are promising and encourage the use of SARX(TVAR)-EGARCH in climate studies and forecasts in mountain sites.
The contribution of precipitation recycling to North American wet and dry precipitation extremes
Authors: Skinner Christopher B , Harrington Tyler S , Barlow Mathew , Agel Laurie 
Published: October 2023

Abstract
Over the course of a season, a location’s precipitation is comprised of moisture sourced from a diverse set of geographic regions. Seasonal extremes in precipitation may arise from changes in the contribution of one or several of these sources. Here, we use the Community Earth System Model with numerical water tracers to quantify the contribution of locally sourced, known as precipitation recycling, versus remotely sourced precipitation to seasonal wet and dry extremes across North America. The greatest impact of recycling on both wet and dry extremes is found in the Interior West of the United States where changes to recycling contribute as much as 25%–30% of drought deficit and pluvial surplus. Recycling contributions are smaller across the eastern U.S., generally less than 8%, highlighting the greater role of imported moisture for explaining hydroclimate extremes in these regions. Robust contributions of precipitation recycling to drought and pluvials across the Interior West are driven by consistent changes to local evaporation and the conversion of local evaporation to local precipitation during extreme hydroclimate conditions. The results are consistent with an energy-limited and water-limited evaporation framework and provide a new estimate of the role of local processes in shaping hydroclimate extremes.
Development of a human glioblastoma model using humanized DRAG mice for immunotherapy
Authors: Srivastava Rashmi , Labani-Motlagh Alireza , Chen Apeng , Bohorquez Jose Alejandro , Qin Bin , Dodda Meghana , Yang Fan , Ansari Danish , Patel Sahil , Ji Honglong , Trasti Scott , Chao Yapeng , Patel Yash , Zou Han , Hu Baoli , Yi Guohua 
Published: October 2023

Abstract
Glioblastoma (GBM) is the most common and lethal primary brain tumor. The development of alternative humanized mouse models with fully functional human immune cells will potentially accelerate the progress of GBM immunotherapy. We successfully generated humanized DRAG (NOD.Rag1KO.IL2RγcKO) mouse model by transplantation of human DR4+ hematopoietic stem cells (hHSCs), and effectively grafted GBM patient-derived tumorsphere cells to form xenografted tumors intracranially. The engrafted tumors recapitulated the pathological features and the immune cell composition of human GBM. Administration of anti-human PD-1 antibodies in these tumor-bearing humanized DRAG mice decreased the major tumor-infiltrating immunosuppressive cell populations, including CD4+PD-1+ and CD8+PD-1+ T cells, CD11b+CD14+HLA-DR+ macrophages, CD11b+CD14+HLA-DR−CD15− and CD11b+CD14−CD15+ myeloid-derived suppressor cells, indicating the humanized DRAG mice as a useful model to test the efficacy of GBM immunotherapy. Taken together, these results suggest that the humanized DRAG mouse model is a reliable preclinical platform for studying brain cancer immunotherapy and beyond.
Use of Elasticsearch-based business intelligence tools for integration and visualization of biological data
Authors: Scott-Boyer Marie-Pier , Dufour Pascal , Belleau François , Ongaro-Carcy Regis , Plessis Clément , Périn Olivier , Droit Arnaud 
Published: October 2023

Abstract
The emergence of massive datasets exploring the multiple levels of molecular biology has made their analysis and knowledge transfer more complex. Flexible tools to manage big biological datasets could be of great help for standardizing the usage of developed data visualizations and integration methods. Business intelligence (BI) tools have been used in many fields as exploratory tools. They have numerous connectors to link numerous data repositories with a unified graphic interface, offering an overview of data and facilitating interpretation for decision makers. BI tools could be a flexible and user-friendly way of handling molecular biological data with interactive visualizations. However, it is rather uncommon to see such tools used for the exploration of massive and complex datasets in biological fields. We believe that two main obstacles could be the reason. Firstly, we posit that the way to import data into BI tools are not compatible with biological databases. Secondly, BI tools may not be adapted to certain particularities of complex biological data, namely, the size, the variability of datasets and the availability of specialized visualizations. This paper highlights the use of five BI tools (Elastic Kibana, Siren Investigate, Microsoft Power BI, Salesforce Tableau and Apache Superset) onto which the massive data management repository engine called Elasticsearch is compatible. Four case studies will be discussed in which these BI tools were applied on biological datasets with different characteristics. We conclude that the performance of the tools depends on the complexity of the biological questions and the size of the datasets.
SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra
Authors: Han Xu , Wang Wanli , Ma Li-Hua , AI-Ramahi Ismael , Botas Juan , MacKenzie Kevin , Allen Genevera I , Young Damian W , Liu Zhandong , Maletic-Savatic Mirjana 
Published: October 2023

Abstract

Motivation
Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challenges faced when analyzing NMR data and identifies metabolites in a sample with high accuracy.

Results
As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e. the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates. To assess SPA-STOCSY’s efficiency and accuracy, we applied it to synthesized spectra and spectra acquired on Drosophila melanogaster tissue and human embryonic stem cells. In the synthesized spectra, SPA outperformed Statistical Recoupling of Variables (SRV), an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the biological data, SPA-STOCSY performed comparably to the operator-based Chenomx analysis while avoiding operator bias, and it required &lt;7 min of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. It may thus accelerate the use of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.

Availability and implementation
The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.
Right coronary artery kinking after tricuspid valve annuloplasty: a case report
Authors: Florence Jeremy , Duband Benjamin , Souteyrand Géraud , Motreff Pascal 
Published: October 2023

Abstract

Background
Right coronary artery (RCA) injury is a rare complication of valvular surgery. However, complications should be considered, due to the significant clinical consequences. Identifying the coronary injury type and understanding the underlying pathophysiological mechanisms is essential to managing these complications.

Case summary
The case of a 59-year-old man who underwent conservative mitral valve surgery with tricuspid valve annuloplasty is presented. The early post-operative period was complicated by acute coronary syndrome with inferior persistent ST-segment elevation. A coronary angiogram confirmed critical RCA hazy lesions, raising the suspicion of coronary kinking. To confirm the underlying mechanism for these lesions and determine the best treatment strategy, endocoronary imaging was performed, revealing coronary kinking of the RCA. Based on the persistent acute ischaemia, a long-lasting drug-eluting stent (DES) was implanted in the lower and upper knees of the RCA. After angioplasty, electrocardiography showed regression of the ST-segment elevation. Ten days later, coronary angiography and optical coherence tomography showed good results. The patient recovered from his myocardial infarction.

Discussion
Only a few reports describe the use of endocoronary imaging for diagnosing coronary artery injury after tricuspid annuloplasty. The variety of lesion types that could underlie a single post-operative myocardial infarction makes endocoronary imaging a relevant technique to guide management strategy and optimize DES implantation.
Comorbidities in mild autonomous cortisol secretion and the effect of treatment: systematic review and meta-analysis
Authors: Pelsma Iris C M , Fassnacht Martin , Tsagarakis Stylianos , Terzolo Massimo , Tabarin Antoine , Sahdev Anju , Newell-Price John , Marina Ljiljana , Lorenz Kerstin , Bancos Irina , Arlt Wiebke , Dekkers Olaf M 
Published: October 2023

Abstract

Objective
To assess (1) comorbidities associated with and (2) treatment strategies for patients with adrenal incidentalomas and mild autonomous cortisol secretion (MACS; &gt; 1.8 µg/dL (&gt;50 nmol/L) cortisol level cut-off following the 1 mg dexamethasone suppression test).

Design
Systematic review and meta-analysis.

Methods
Seven databases were searched up to July 14, 2022. Eligible studies were (randomized) trials, cohort studies, and cross-sectional studies assessing comorbidities potentially attributable to cortisol excess or mortality in patients with adrenal incidentaloma with or without MACS or the effects of conservative or surgical management of MACS. Random-effects meta-analysis was performed to estimate pooled proportions (with 95% CIs).

Results
In 30 cross-sectional and 16 cohort studies (n = 17 156 patients in total), patients with MACS had a higher prevalence of diabetes (relative risk [RR] 1.44 [1.23-1.69]), hypertension (RR = 1.24 [1.16-1.32]), and dyslipidemia (RR = 1.23 [1.13-1.34]). All-cause mortality (adjusted for confounders) in patients with MACS, assessed in 4 studies (n = 5921), was increased (hazard ratio [HR] = 1.54 [1.27-1.81]). Nine observational studies (n = 856) and 2 randomized trials (n = 107) suggest an improvement in glucometabolic control (RR = 7.99 [2.95-21.90]), hypertension (RR = 8.75 [3.99-19.18]), and dyslipidemia (RR = 3.24 [1.19-8.82]) following adrenalectomy.

Conclusions
The present systematic review and meta-analysis highlight the relevance of MACS, since both cardiometabolic morbidities and mortality appeared to have increased in patients with MACS compared to patients with non-functioning incidentalomas. However, due to heterogeneous definitions, various outcomes, selective reporting, and missing data, the reported pooled estimates need to be interpreted with caution. The small number of patients in randomized trials prevents any strong conclusion on the causality between MACS and these comorbidities.
Larval plastic responses to warming and desiccation delay gonadal maturation in postmetamorphic spadefoot toads
Authors: Burraco Pablo , Torres-Montoro Juan Carlos , Gomez-Mestre Ivan 
Published: October 2023

Abstract
Developmental plasticity allows organisms to adjust life-history traits to varying environmental conditions, which can have concomitant effects across life stages. Many amphibians are suitable model systems to study plasticity because their larvae can adjust growth and differentiation under fluctuating environments. It is unknown, however, whether somatic and gonadal differentiation are equally affected by environmentally induced plasticity or whether their decoupling alters gonadal maturation postmetamorphosis, which may affect fitness. We tested if developmental acceleration in response to warming and desiccation risk results in shifts in gonadal maturation during metamorphosis and postmetamorphic growth in western spadefoot toads (Pelobates cultripes). We found additive effects of increased temperature and desiccation risk on development and growth at metamorphosis, which largely constrained gonadal maturation in metamorphic and postmetamorphic individuals of both sexes. Furthermore, the conditions experienced by larvae incurred sex-specific carryover effects on the gonadal maturation of juveniles 5 months after metamorphosis. In females, high temperature delayed ovarian maturation regardless of the water level. In males, exposure to high temperature and high water levels slightly delayed the testes’ maturation. These results highlight the relevance of larval plasticity in the gonadal maturation of species undergoing metamorphosis, which may have implications for population demographics and the evolution of life histories.
Striatal Dopamine Signals and Reward Learning
Authors: Bech Pol , Crochet Sylvain , Dard Robin , Ghaderi Parviz , Liu Yanqi , Malekzadeh Meriam , Petersen Carl C H , Pulin Mauro , Renard Anthony , Sourmpis Christos 
Published: October 2023

AbstractWe are constantly bombarded by sensory information and constantly making decisions on how to act. In order to optimally adapt behavior, we must judge which sequences of sensory inputs and actions lead to successful outcomes in specific circumstances. Neuronal circuits of the basal ganglia have been strongly implicated in action selection, as well as the learning and execution of goal-directed behaviors, with accumulating evidence supporting the hypothesis that midbrain dopamine neurons might encode a reward signal useful for learning. Here, we review evidence suggesting that midbrain dopaminergic neurons signal reward prediction error, driving synaptic plasticity in the striatum underlying learning. We focus on phasic increases in action potential firing of midbrain dopamine neurons in response to unexpected rewards. These dopamine neurons prominently innervate the dorsal and ventral striatum. In the striatum, the released dopamine binds to dopamine receptors, where it regulates the plasticity of glutamatergic synapses. The increase of striatal dopamine accompanying an unexpected reward activates dopamine type 1 receptors (D1Rs) initiating a signaling cascade that promotes long-term potentiation of recently active glutamatergic input onto striatonigral neurons. Sensorimotor-evoked glutamatergic input, which is active immediately before reward delivery will thus be strengthened onto neurons in the striatum expressing D1Rs. In turn, these neurons cause disinhibition of brainstem motor centers and disinhibition of the motor thalamus, thus promoting motor output to reinforce rewarded stimulus-action outcomes. Although many details of the hypothesis need further investigation, altogether, it seems likely that dopamine signals in the striatum might underlie important aspects of goal-directed reward-based learning.
Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses
Authors: Russell Nikki D , Jorde Lynn B , Chow Clement Y 
Published: October 2023

Abstract
Misfolded proteins in the endoplasmic reticulum (ER) elicit the ER stress response, a large transcriptional response driven by 3 well-characterized transcription factors (TFs). This transcriptional response is variable across different genetic backgrounds. One mechanism in which genetic variation can lead to transcriptional variability in the ER stress response is through altered binding and activity of the 3 main TFs: XBP1, ATF6, and ATF4. This work attempts to better understand this mechanism by first creating a computational pipeline to identify potential binding sites throughout the human genome. We utilized GTEx data sets to identify cis-eQTLs that fall within predicted TF binding sites (TFBSs). We also utilized the ClinVar database to compare the number of pathogenic vs benign variants at different positions of the binding motifs. Finally, we performed a cis-eQTL analysis on human cell lines experiencing ER stress to identify cis-eQTLs that regulate the variable ER stress response. The majority of these cis-eQTLs are unique to a given condition: control or ER stress. Some of these stress-specific cis-eQTLs fall within putative binding sites of the 3 main ER stress response TFs, providing a potential mechanism by which these cis-eQTLs might be impacting gene expression under ER stress conditions through altered TF binding. This study represents the first cis-eQTL analysis on human samples experiencing ER stress and is a vital step toward identifying the genetic components responsible for the variable ER stress response.
Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird
Authors: Zhang Hongkai , Lundberg Max , Tarka Maja , Hasselquist Dennis , Hansson Bengt 
Published: October 2023

Abstract
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10−9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10−9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.