bluuebunny/crossref_metadata_2025 huggingface dataset:
Pivotal role of the endoplasmic reticulum stress-related XBP1s/miR-22/SIRT1 axis in acute myeloid leukemia apoptosis and response to chemotherapy
Authors: Philippe Céline , Jaud Manon , Féral Kelly , Gay Alexandre , Van Den Berghe Loïc , Farce Manon , Bousquet Marina , Pyronnet Stéphane , Mazzolini Laurent , Rouault-Pierre Kevin , Touriol Christian
Published: June 2024

Malignant growth relies on rapid protein synthesis frequently leading to endoplasmic reticulum (ER) overload and accumulation of unfolded or misfolded protein in this cellular compartment. In the ER, protein homeostasis is finely regulated by a mechanism called the unfolded protein response (UPR), involving the activation of signalization pathways mediated by three transmembrane proteins, namely PERK, IRE1 and ATF6. IRE1 endoribonuclease activation leads in particular to the splicing of the cytosolic mRNA encoding the key UPR-specific transcription factor XBP1s. Our study shows that sustained activation of XBP1s expression in acute myeloid leukemia (AML) cells induces apoptosis in vitro and in vivo, whereas a moderate XBP1s expression sensitizes cells to chemotherapeutic treatments. ChIP-seq experiments identified specific XBP1s target genes including the MIR22HG lncRNA, the precursor transcript of microRNA-22-3p. miR-22-3p upregulation by XBP1s or forced expression of miR-22 significantly decreases cell’s viability and sensitizes leukemic cells to chemotherapy. We found that miR-22-3p intracellular effects result at least partially from the targeting of the mRNA encoding the deacetylase sirtuin-1 (SIRT1), a well-established pro-survival factor. Therefore, this novel XBP1s/miR-22/SIRT1 axis identified could play a pivotal role in the proliferation and chemotherapeutic response of leukemic cells.
Cardiac evaluation of patients with juvenile dermatomyositis
Authors: Akgün Gökmen , Sözeri Betül , Başar Eviç Zeynep , Şahin Nihal , Bayrak Yunus Emre , Ulu Kadir , Güngör Hüseyin Salih , Doğan Mustafa , Öner Taliha , Karacan Mehmet , Babaoğlu Kadir , Anık Yonca , Sönmez Hafize Emine
Published: June 2024

Background

The present study aims to evaluate possible cardiac involvement in juvenile dermatomyositis (JDM) patients by conventional methods and cardiac magnetic resonance imaging (MRI) along with a systematic review of the literature on cardiac features in JDM.

Methods

The study group consisted of JDM patients who underwent cardiac MRI. We conducted a systematic review of the published literature involving JDM patients with cardiac involvement.

Results

In the present study, although baseline cardiologic evaluations including electrocardiography and echocardiography were within normal limits, we showed late gadolinium enhancement on cardiac MRI in 3 of 11 JDM patients. In the literature review, we identified 25 articles related to cardiac involvement in JDM. However, none of them, except one case report, included cardiac MRI of JDM patients.

Conclusion

Cardiac abnormalities have been reported among the less frequent findings in patients with JDM. Cardiovascular complications during the long-term disease course are a leading cause of morbidity and mortality in these patients. Early detection of cardiac involvement by cardiac MRI in patients with JDM and aggressive treatment of them may improve the clinical course of these patients.

Impact

The myocardium in patients with JDM may be involved by inflammation.

Myocardial involvement may be evaluated by using contrast-enhanced cardiac MRI.

This is the first study evaluating cardiac involvement by cardiac MRI in JDM patients.

MRI may show early cardiac involvement in patients whose baseline cardiologic evaluations are within normal limits.

Early detection of cardiac involvement by cardiac MRI may improve the long-term prognosis of patients with JDM.
Treatment outcome according to genetic tumour alterations and clinical characteristics in digestive high-grade neuroendocrine neoplasms
Authors: Elvebakken Hege , Venizelos Andreas , Perren Aurel , Couvelard Anne , Lothe Inger Marie B. , Hjortland Geir O. , Myklebust Tor Å. , Svensson Johanna , Garresori Herish , Kersten Christian , Hofsli Eva , Detlefsen Sönke , Vestermark Lene W. , Knappskog Stian , Sorbye Halfdan
Published: June 2024

Background

Chemotherapy has limited efficacy in advanced digestive high-grade neuroendocrine neoplasms (HG-NEN) and prognosis is dismal. Predictive markers for palliative chemotherapy are lacking, and prognostic markers are limited.

Methods

Digestive HG-NEN patients (n = 229) were prospectively included 2013–2017. Pathological re-assessment revealed 188 neuroendocrine carcinomas (NEC) and 41 neuroendocrine tumours (NET G3). Tumour-DNA was sequenced across 360 cancer-related genes, assessing mutations (mut) and copy number alterations. We linked sequencing results to clinical information and explored potential markers for first-line chemotherapy efficacy and survival.

Results

In NEC given cis/carboplatin and etoposide (PE), TP53mut predicted inferior response rate in multivariate analyses (p = 0.009) and no BRAFmut NEC showed response. In overall assessment of PE-treated NEC, no genetic alterations were prognostic for OS. For small-cell NEC, TP53mut were associated with longer OS (p = 0.011) and RB1 deletions predicted lack of immediate-progression (p = 0.003). In non-small cell NEC, APC mut were associated with immediate-progression and shorter PFS (p = 0.008/p = 0.004). For NET G3, ATRXmut, ARID1A- and ERS1 deletions were associated with shorter PFS.

Conclusion

Correlations between genetic alterations and response/immediate-progression to PE were frequent in NEC but affected PFS or OS only when subdividing for cell-type. The classification of digestive NEC into large- and small-cell seems therefore molecularly and clinically relevant.
Interactomic exploration of LRRC8A in volume-regulated anion channels
Authors: Carpanese Veronica , Festa Margherita , Prosdocimi Elena , Bachmann Magdalena , Sadeghi Soha , Bertelli Sara , Stein Frank , Velle Angelo , Abdel-Salam Mostafa A. L. , Romualdi Chiara , Pusch Michael , Checchetto Vanessa
Published: June 2024

Ion channels are critical in enabling ion movement into and within cells and are important targets for pharmacological interventions in different human diseases. In addition to their ion transport abilities, ion channels interact with signalling and scaffolding proteins, which affects their function, cellular positioning, and links to intracellular signalling pathways. The study of “channelosomes” within cells has the potential to uncover their involvement in human diseases, although this field of research is still emerging. LRRC8A is the gene that encodes a crucial protein involved in the formation of volume-regulated anion channels (VRACs). Some studies suggest that LRRC8A could be a valuable prognostic tool in different types of cancer, serving as a biomarker for predicting patients’ outcomes. LRRC8A expression levels might be linked to tumour progression, metastasis, and treatment response, although its implications in different cancer types can be varied. Here, publicly accessible databases of cancer patients were systematically analysed to determine if a correlation between VRAC channel expression and survival rate exists across distinct cancer types. Moreover, we re-evaluated the impact of LRRC8A on cellular proliferation and migration in colon cancer via HCT116 LRRC8A-KO cells, which is a current topic of debate in the literature. In addition, to investigate the role of LRRC8A in cellular signalling, we conducted biotin proximity-dependent identification (BioID) analysis, revealing a correlation between VRAC channels and cell-cell junctions, mechanisms that govern cellular calcium homeostasis, kinases, and GTPase signalling. Overall, this dataset improves our understanding of LRRC8A/VRAC and explores new research avenues while identifying promising therapeutic targets and promoting inventive methods for disease treatment.
Realising a global One Health disease surveillance approach: insights from wastewater and beyond
Authors: Hill Richard , Stentiford Grant D. , Walker David I. , Baker-Austin Craig , Ward Georgia , Maskrey Benjamin H. , van Aerle Ronny , Verner-Jeffreys David , Peeler Edmund , Bass David
Published: June 2024

One Health is a recognition of the shared environment inhabited by humans, animals and plants, and the impact of their interactions on the health of all organisms. The COVID-19 pandemic highlighted the need for a framework of pathogen surveillance in a tractable One Health paradigm to allow timely detection and response to threats to human and animal health. We present case studies centered around the recent global approach to tackle antimicrobial resistance and the current interest in wastewater testing, with the concept of “one sample many analyses” to be further explored as the most appropriate means of initiating this endeavor.
TENT5-mediated polyadenylation of mRNAs encoding secreted proteins is essential for gametogenesis in mice
Authors: Brouze Michał , Czarnocka-Cieciura Agnieszka , Gewartowska Olga , Kusio-Kobiałka Monika , Jachacy Kamil , Szpila Marcin , Tarkowski Bartosz , Gruchota Jakub , Krawczyk Paweł , Mroczek Seweryn , Borsuk Ewa , Dziembowski Andrzej
Published: June 2024

Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of four TENT5 poly(A) polymerases in mouse fertility and gametogenesis. TENT5B and TENT5C play crucial yet redundant roles in oogenesis, with the double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display a gain-of-function infertility effect, with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, as shown by the sterility in males following the knockout of either gene. Finally, Tent5a knockout substantially lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through direct RNA sequencing, we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motif analysis and reporter mRNA assays reveal that the presence of an endoplasmic reticulum-leader sequence represents the primary determinant of TENT5-mediated regulation.
Observation of Mermin-Wagner behavior in LaFeO3/SrTiO3 superlattices
Authors: Kiaba M. , Suter A. , Salman Z. , Prokscha T. , Chen B. , Koster G. , Dubroka A.
Published: June 2024

Two-dimensional magnetic materials can exhibit new magnetic properties due to the enhanced spin fluctuations that arise in reduced dimension. However, the suppression of the long-range magnetic order in two dimensions due to long-wavelength spin fluctuations, as suggested by the Mermin-Wagner theorem, has been questioned for finite-size laboratory samples. Here we study the magnetic properties of a dimensional crossover in superlattices composed of the antiferromagnetic LaFeO3 and SrTiO3 that, thanks to their large lateral size, allowed examination using a sensitive magnetic probe — muon spin rotation spectroscopy. We show that the iron electronic moments in superlattices with 3 and 2 monolayers of LaFeO3 exhibit a static antiferromagnetic order. In contrast, in the superlattices with single LaFeO3 monolayer, the moments do not order and fluctuate to the lowest measured temperature as expected from the Mermin-Wagner theorem. Our work shows how dimensionality can be used to tune the magnetic properties of ultrathin films.
Distinct basal ganglia contributions to learning from implicit and explicit value signals in perceptual decision-making
Authors: Balsdon Tarryn , Pisauro M. Andrea , Philiastides Marios G.
Published: June 2024

Metacognitive evaluations of confidence provide an estimate of decision accuracy that could guide learning in the absence of explicit feedback. We examine how humans might learn from this implicit feedback in direct comparison with that of explicit feedback, using simultaneous EEG-fMRI. Participants performed a motion direction discrimination task where stimulus difficulty was increased to maintain performance, with intermixed explicit- and no-feedback trials. We isolate single-trial estimates of post-decision confidence using EEG decoding, and find these neural signatures re-emerge at the time of feedback together with separable signatures of explicit feedback. We identified these signatures of implicit versus explicit feedback along a dorsal-ventral gradient in the striatum, a finding uniquely enabled by an EEG-fMRI fusion. These two signals appear to integrate into an aggregate representation in the external globus pallidus, which could broadcast updates to improve cortical decision processing via the thalamus and insular cortex, irrespective of the source of feedback.
MethPhaser: methylation-based long-read haplotype phasing of human genomes
Authors: Fu Yilei , Aganezov Sergey , Mahmoud Medhat , Beaulaurier John , Juul Sissel , Treangen Todd J. , Sedlazeck Fritz J.
Published: June 2024

The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser.
Tunable translation-level CRISPR interference by dCas13 and engineered gRNA in bacteria
Authors: Kim Giho , Kim Ho Joon , Kim Keonwoo , Kim Hyeon Jin , Yang Jina , Seo Sang Woo
Published: June 2024

Although CRISPR-dCas13, the RNA-guided RNA-binding protein, was recently exploited as a translation-level gene expression modulator, it has still been difficult to precisely control the level due to the lack of detailed characterization. Here, we develop a synthetic tunable translation-level CRISPR interference (Tl-CRISPRi) system based on the engineered guide RNAs that enable precise and predictable down-regulation of mRNA translation. First, we optimize the Tl-CRISPRi system for specific and multiplexed repression of genes at the translation level. We also show that the Tl-CRISPRi system is more suitable for independently regulating each gene in a polycistronic operon than the transcription-level CRISPRi (Tx-CRISPRi) system. We further engineer the handle structure of guide RNA for tunable and predictable repression of various genes in Escherichia coli and Vibrio natriegens. This tunable Tl-CRISPRi system is applied to increase the production of 3-hydroxypropionic acid (3-HP) by 14.2-fold via redirecting the metabolic flux, indicating the usefulness of this system for the flux optimization in the microbial cell factories based on the RNA-targeting machinery.
A photocatalytic redox cycle over a polyimide catalyst drives efficient solar-to-H2O2 conversion
Authors: Chi Wenwen , Dong Yuming , Liu Bing , Pan Chengsi , Zhang Jiawei , Zhao Hui , Zhu Yongfa , Liu Zeyu
Published: June 2024

Circumventing the conventional two-electron oxygen reduction pathway remains a great problem in enhancing the efficiency of H2O2 photosynthesis. A promising approach to achieve outstanding photocatalytic activity involves the utilization of redox intermediates. Here, we engineer a polyimide aerogel photocatalyst with photoreductive carbonyl groups for non-sacrificial H2O2 production. Under photoexcitation, carbonyl groups on the photocatalyst surface are reduced, forming an anion radical intermediate. The produced intermediate is oxidized by O2 to produce H2O2 and subsequently restores the carbonyl group. The high catalytic efficiency is ascribed to a photocatalytic redox cycle mediated by the radical anion, which not only promotes oxygen adsorption but also lowers the energy barrier of O2 reduction reaction for H2O2 generation. An apparent quantum yield of 14.28% at 420 ± 10 nm with a solar-to-chemical conversion efficiency of 0.92% is achieved. Moreover, we demonstrate that a mere 0.5 m2 self-supported polyimide aerogel exposed to natural sunlight for 6 h yields significant H2O2 production of 34.3 mmol m−2.
Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries
Authors: de Oliveira Lino Felipe Senne , Garg Shilpa , Li Simone S. , Misiakou Maria-Anna , Kang Kang , Vale da Costa Bruno Labate , Beyer-Pedersen Tobias Svend-Aage , Giacon Thamiris Guerra , Basso Thiago Olitta , Panagiotou Gianni , Sommer Morten Otto Alexander
Published: June 2024

Bioethanol is a sustainable energy alternative and can contribute to global greenhouse-gas emission reductions by over 60%. Its industrial production faces various bottlenecks, including sub-optimal efficiency resulting from bacteria. Broad-spectrum removal of these contaminants results in negligible gains, suggesting that the process is shaped by ecological interactions within the microbial community. Here, we survey the microbiome across all process steps at two biorefineries, over three timepoints in a production season. Leveraging shotgun metagenomics and cultivation-based approaches, we identify beneficial bacteria and find improved outcome when yeast-to-bacteria ratios increase during fermentation. We provide a microbial gene catalogue which reveals bacteria-specific pathways associated with performance. We also show that Limosilactobacillus fermentum overgrowth lowers production, with one strain reducing yield by ~5% in laboratory fermentations, potentially due to its metabolite profile. Temperature is found to be a major driver for strain-level dynamics. Improved microbial management strategies could unlock environmental and economic gains in this US $ 60 billion industry enabling its wider adoption.
Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein
Authors: Du Wenjuan , Debski-Antoniak Oliver , Drabek Dubravka , van Haperen Rien , van Dortmondt Melissa , van der Lee Joline , Drulyte Ieva , van Kuppeveld Frank J. M. , Grosveld Frank , Hurdiss Daniel L. , Bosch Berend-Jan
Published: June 2024

Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
Long-term balancing selection for pathogen resistance maintains trans-species polymorphisms in a planktonic crustacean
Authors: Cornetti Luca , Fields Peter D. , Du Pasquier Louis , Ebert Dieter
Published: June 2024

Balancing selection is an evolutionary process that maintains genetic polymorphisms at selected loci and strongly reduces the likelihood of allele fixation. When allelic polymorphisms that predate speciation events are maintained independently in the resulting lineages, a pattern of trans-species polymorphisms may occur. Trans-species polymorphisms have been identified for loci related to mating systems and the MHC, but they are generally rare. Trans-species polymorphisms in disease loci are believed to be a consequence of long-term host-parasite coevolution by balancing selection, the so-called Red Queen dynamics. Here we scan the genomes of three crustaceans with a divergence of over 15 million years and identify 11 genes containing identical-by-descent trans-species polymorphisms with the same polymorphisms in all three species. Four of these genes display molecular footprints of balancing selection and have a function related to immunity. Three of them are located in or close to loci involved in resistance to a virulent bacterial pathogen, Pasteuria, with which the Daphnia host is known to coevolve. This provides rare evidence of trans-species polymorphisms for loci known to be functionally relevant in interactions with a widespread and highly specific parasite. These findings support the theory that specific antagonistic coevolution is able to maintain genetic diversity over millions of years.
Divergent and gram-scale syntheses of (–)-veratramine and (–)-cyclopamine
Authors: Hou Wenlong , Lin Hao , Wu Yanru , Li Chuang , Chen Jiajun , Liu Xiao-Yu , Qin Yong
Published: June 2024

Veratramine and cyclopamine, two of the most representative members of the isosteroidal alkaloids, are valuable molecules in agricultural and medicinal chemistry. While plant extraction of these compounds suffers from uncertain supply, efficient chemical synthesis approaches are in high demand. Here, we present concise, divergent, and scalable syntheses of veratramine and cyclopamine with 11% and 6.2% overall yield, respectively, from inexpensive dehydro-epi-androsterone. Our synthesis readily provides gram quantities of both target natural products by utilizing a biomimetic rearrangement to form the C-nor-D-homo steroid core and a stereoselective reductive coupling/(bis-)cyclization sequence to establish the (E)/F-ring moiety.
A benchmarking study of quantum algorithms for combinatorial optimization
Authors: Sankar Krishanu , Scherer Artur , Kako Satoshi , Reifenstein Sam , Ghadermarzy Navid , Krayenhoff Willem B. , Inui Yoshitaka , Ng Edwin , Onodera Tatsuhiro , Ronagh Pooya , Yamamoto Yoshihisa
Published: June 2024

We study the performance scaling of three quantum algorithms for combinatorial optimization: measurement-feedback coherent Ising machines (MFB-CIM), discrete adiabatic quantum computation (DAQC), and the Dürr–Høyer algorithm for quantum minimum finding (DH-QMF) that is based on Grover’s search. We use MaxCut problems as a reference for comparison, and time-to-solution (TTS) as a practical measure of performance for these optimization algorithms. For each algorithm, we analyze its performance in solving two types of MaxCut problems: weighted graph instances with randomly generated edge weights attaining 21 equidistant values from −1 to 1; and randomly generated Sherrington–Kirkpatrick (SK) spin glass instances. We empirically find a significant performance advantage for the studied MFB-CIM in comparison to the other two algorithms. We empirically observe a sub-exponential scaling for the median TTS for the MFB-CIM, in comparison to the almost exponential scaling for DAQC and the proven $$\widetilde{{{{\mathcal{O}}}}}\left(\sqrt{{2}^{n}}\right)$$

O

̃

2

n

scaling for DH-QMF. We conclude that the MFB-CIM outperforms DAQC and DH-QMF in solving MaxCut problems.
Fitness effects of synthetic and natural diet preservatives on the edible insect Bombyx mori
Authors: Lei Xiaoyu , Qian Zhaoyi , Zhu Xinyue , Zhang Nan , He Jintao , Xiao Jian , Shen Xiaoqiang , Muhammad Abrar , Sun Chao , Shao Yongqi
Published: June 2024

Silkworm pupae as widely consumed insect products are good biosources of protein and micronutrients. Silkworm rearing throughout the year can be achieved by feeding them an artificial diet instead of native plants, facilitating extensive pupa production. However, artificial diets are prone to spoilage caused by bacterial contamination. Here, we evaluated the antiseptic effect of ethylparaben (EP, chemical preservative) and medium-chain fatty acids (MCFA, natural preservative) in a silkworm artificial diet. Results showed that both preservatives effectively inhibited pathogenic bacterial growth. Furthermore, the addition of EP or MCFA did not negatively impact the production capacity of silkworms and the homeostasis of gut microbiota. However, the expression of genes involved in detoxification such as Ugt2, and immune response such as Cecropin B, were upregulated after EP consumption. Therefore, natural preservative MCFA emerges as a suitable option from a safety perspective. These findings highlight future directions for improving insect artificial diet formulation.
CODC-v1: a quality-controlled and bias-corrected ocean temperature profile database from 1940–2023
Authors: Zhang Bin , Cheng Lijing , Tan Zhetao , Gouretski Viktor , Li Fuchao , Pan Yuying , Yuan Huifeng , Ren Huanping , Reseghetti Franco , Zhu Jiang , Wang Fan
Published: June 2024

High-quality ocean in situ profile observations are fundamental for ocean and climate research and operational oceanographic applications. Here we describe a new global ocean subsurface temperature profile database named the Chinese Academy of Science (CAS) Oceanography Data Center version 1 (CODC-v1). This database contains over 17 million temperature profiles between 1940–2023 from all available instruments. The major data source is the World Ocean Database (WOD), but CODC-v1 also includes some data from some Chinese institutes which are not available in WOD. The data are quality-controlled (QC-ed) by a new QC system that considers the skewness of local temperature distributions, topographic barriers, and the shift of temperature distributions due to climate change. Biases in Mechanical Bathythermographs (MBTs), eXpendable Bathythermographs (XBTs), and Bottle data (OSD) are all corrected using recently proposed correction schemes, which makes CODC-v1 a bias-corrected dataset. These aspects ensure the data quality of the CODC-v1 database, making it suitable for a wide spectrum of ocean and climate research and applications.
CN+: Vehicular Dataset at Traffic Light Regulated Intersection in Bremen, Germany
Authors: Karunathilake Thenuka , Zongo Meyo , Amarawardana Dinithi , Förster Anna
Published: June 2024

Vehicular Ad-Hoc Networks (VANETs) were introduced to avoid vehicular-related accidents and to improve the safety of both vehicular passengers and other road users. In VANETs, the vehicles are expected to communicate with neighbouring vehicles to increase awareness about the surrounding by using V2V (vehicle-to-vehicle) communication links. Since the introduction of VANETs, much research has focused on developing state-of-the-art algorithms to increase safety. However, real-world testing of these developed algorithms has become challenging due to the required high cost and multiple practical reasons. Therefore, simulation-based testing is commonly used for VANETs related applications. Using real datasets inside a simulation can significantly increase the results’ accuracy and help to achieve realistic results. In this study, we present a dataset called ’CN+’, which consists of more than 25,000 vehicles collected over 32 hours at a signalized intersection in Bremen, Germany. paper
An EEG & eye-tracking dataset of ALS patients & healthy people during eye-tracking-based spelling system usage
Authors: Ngo Thi Duyen , Kieu Hai Dang , Nguyen Minh Hoa , Nguyen The Hoang-Anh , Can Van Mao , Nguyen Ba Hung , Le Thanh Ha
Published: June 2024

This research presents a dataset consisting of electroencephalogram and eye tracking recordings obtained from six patients with amyotrophic lateral sclerosis (ALS) in a locked-in state and one hundred seventy healthy individuals. The ALS patients exhibited varying degrees of disease progression, ranging from partial mobility and weakened speech to complete paralysis and loss of speech. Despite these physical impairments, the ALS patients retained good eye function, which allowed them to use a virtual keyboard for communication. Data from ALS patients was recorded multiple times at their homes, while data from healthy individuals was recorded once in a laboratory setting. For each data recording, the experimental design involved nine recording sessions per participant, each corresponding to a common human action or demand. This dataset can serve as a valuable benchmark for several applications, such as improving spelling systems with brain-computer interfaces, investigating motor imagination, exploring motor cortex function, monitoring motor impairment progress in patients undergoing rehabilitation, and studying the effects of ALS on cognitive and motor processes.
A Military Audio Dataset for Situational Awareness and Surveillance
Authors: Kim June-Woo , Yoon Chihyeon , Jung Ho-Young
Published: June 2024

Audio classification related to military activities is a challenging task due to the high levels of background noise and the lack of suitable and publicly available datasets. To bridge this gap, this paper constructs and introduces a new military audio dataset, named MAD, which is suitable for training and evaluating audio classification systems. The proposed MAD dataset is extracted from various military videos and contains 8,075 sound samples from 7 classes corresponding to approximately 12 hours, exhibiting distinctive characteristics not presented in academic datasets typically used for machine learning research. We present a comprehensive description of the dataset, including its acoustic statistics and examples. We further conduct a comprehensive sound classification study of various deep learning algorithms on the MAD dataset. We are also releasing the source code to make it easy to build these systems. The presented dataset will be a valuable resource for evaluating the performance of existing algorithms and for advancing research in the field of acoustic-based hazardous situation surveillance systems.
Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus
Authors: Ren Xianyun , Sun Dongfang , Lv Jianjian , Gao Baoquan , Jia Shaoting , Bian Xueqiong , Zhao Kuangcheng , Li Jitao , Liu Ping , Li Jian
Published: June 2024

Recent conservation efforts to protect rare and endangered aquatic species have intensified. Nevertheless, the ornate spiny lobster (Panulirus ornatus), which is prevalent in the Indo-Pacific waters, has been largely ignored. In the absence of a detailed genomic reference, the conservation and population genetics of this crustacean are poorly understood. Here, We assembled a comprehensive chromosome-level genome for P. ornatus. This genome—among the most detailed for lobsters—spans 2.65 Gb with a contig N50 of 51.05 Mb, and 99.11% of the sequences with incorporated to 73 chromosomes. The ornate spiny lobster genome comprises 65.67% repeat sequences and 22,752 protein-coding genes with 99.20% of the genes functionally annotated. The assembly of the P. ornatus genome provides valuable insights into comparative crustacean genomics and endangered species conservation, and lays the groundwork for future research on the speciation, ecology, and evolution of the ornate spiny lobster.
Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis
Authors: Edelbroek Bart , Kjellin Jonas , Jerlström-Hultqvist Jon , Koskiniemi Sanna , Söderbom Fredrik
Published: June 2024

Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926–2013)
Authors: Heleno Ruben , Costa José M. , Covelo Filipe , Santos Joaquim , Lopes Pedro , Gouveia António C. , Matos Arménio , Salgado Agostinho , Girão da Cruz M. Teresa , Farminhão João , Horta Marta , Barreto Guilherme , Marques Ana V. , Craveiro Leonardo , Pinto Patrícia , Santos Matilde , Nunes Bárbara , Barreiro Margarida , Dias André , Rodrigues Gabriel , Esteves Leonor , Wanderley Marina , Santos Inês , Artiaga José Pedro , Veríssimo João , Vilhena Inês , Moniz Lucas , Leão Arthur , Couras Marta , Mendes Sara B. , Nereu Mauro , Dias da Silva Ana Margarida , Sales Fátima , Gonçalves M. Teresa , Coutinho António , Freitas Helena , Silva Joaquim S. , Ramos Jaime , Marchante Elizabete , Timóteo Sérgio
Published: June 2024

Species phenology - the timing of key life events - is being altered by ongoing climate changes with yet underappreciated consequences for ecosystem stability. While flowering is generally occurring earlier, we know much less about other key processes such as the time of fruit ripening, largely due to the lack of comprehensive long-term datasets. Here we provide information on the exact date and site where seeds of 4,462 taxa were collected for the Index Seminum (seed exchange catalogue) of the Botanic Garden of the University of Coimbra, between 1926 and 2013. Seeds were collected from spontaneous and cultivated individuals across Portugal, including both native and introduced taxa. The database consists of 127,747 curated records with information on the species, or infraspecific taxa (including authority), and the day and site where seeds were collected. All records are georeferenced and provided with a confidence interval for the collection site. Taxonomy was first curated manually by in-house botanists and then harmonized according to the GBIF backbone taxonomy.
Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity
Authors: Pechlivanis Nikos , Karakatsoulis Georgios , Kyritsis Konstantinos , Tsagiopoulou Maria , Sgardelis Stefanos , Kappas Ilias , Psomopoulos Fotis
Published: June 2024

Despite recent research efforts to explore the co-occurrence patterns of diverse microbes within soil microbial communities, a substantial knowledge-gap persists regarding global climate influences on soil microbiota behaviour. Comprehending co-occurrence patterns within distinct geoclimatic groups is pivotal for unravelling the ecological structure of microbial communities, that are crucial for preserving ecosystem functions and services. Our study addresses this gap by examining global climatic patterns of microbial diversity. Using data from the Earth Microbiome Project, we analyse a meta-community co-occurrence network for bacterial communities. This method unveils substantial shifts in topological features, highlighting regional and climatic trends. Arid, Polar, and Tropical zones show lower diversity but maintain denser networks, whereas Temperate and Cold zones display higher diversity alongside more modular networks. Furthermore, it identifies significant co-occurrence patterns across diverse climatic regions. Central taxa associated with different climates are pinpointed, highlighting climate’s pivotal role in community structure. In conclusion, our study identifies significant correlations between microbial interactions in diverse climatic regions, contributing valuable insights into the intricate dynamics of soil microbiota.
Twenty-nine newly sequenced genomes and a comprehensive genome dataset for the insect endosymbiont Buchnera
Authors: Lu Congcong , Zou Tianmin , Liu Qian , Huang Xiaolei
Published: June 2024

Most phloem-feeding insects face nutritional deficiency and rely on their intracellular symbionts to provide nutrients, and most of endosymbiont genomes have undergone reduction. However, the study of genome reduction processes of endosymbionts has been constrained by the limited availability of genome data from different insect lineages. The obligate relationship between aphids and Buchnera aphidicola (hereafter Buchnera) makes them a classic model for studying insect-endosymbiont interaction. Here, we report 29 newly sequenced Buchnera genomes from 11 aphid subfamilies, and a comprehensive dataset based on 90 Buchnera genomes from 14 aphid subfamilies. The dataset shows a significant genomic difference of Buchnera among different aphid lineages. The dataset exhibits a more balanced distribution of Buchnera (from 14 aphid subfamilies) genome sizes, ranging from 400 kb to 600 kb, which can illustrate the genome reduction process of Buchnera. The new genome data provide valuable insights into the microevolutionary processes leading to genomic reduction of insect endosymbionts.
In vitro photothermal therapy of pancreatic cancer mediated by immunoglobulin G-functionalized silver nanoparticles
Authors: Nedelcu Andreea , Mocan Teodora , Sabau Lavinia Ioana , Matea Cristian Tudor , Tabaran Flaviu , Pop Teodora , Delcea Cristian , Mosteanu Ofelia , Mocan Lucian
Published: June 2024

Pancreatic cancer is one of the most aggressive forms of cancer, and treatment options are limited. One therapeutic approach is to use nanoparticles to deliver the active agent directly to pancreatic cancer cells. Nanoparticles can be designed to specifically target cancer cells, minimizing damage to healthy tissues. Silver nanoparticles have the unique ability to absorb light, especially in the near-infrared (NIR) region. In this study, silver nanoparticles functionalized with IgG molecules were synthesized and administered to pancreatic cancer cell lines. Subsequently, the cells were photo-excited using a 2 W 808 nm laser and further examined in PANC-1 pancreatic cancer cell lines. Flow cytometry and confocal microscopy combined with immunochemical staining were used to examine the interaction between photo-excited silver nanoparticles and pancreatic cancer cells. The photothermal therapy based on IgG-functionalized silver nanoparticles in pancreatic cancer induces dysfunction in the Golgi apparatus, leading to the activation of the caspase-3 apoptotic pathway and ultimately resulting in cellular apoptosis. These findings suggest that our proposed IgG nanoparticle laser treatment could emerge as a novel approach for the therapy of pancreatic cancer.
Driving selective upcycling of mixed polyethylene waste with table salt
Authors: Shaker Mohamed , Hamdani Syeda Shamila , Muzata Tanyaradzwa S. , Rabnawaz Muhammad
Published: June 2024

Advanced recycling offers a unique opportunity for the circular economy, especially for mixed and contaminated plastics that are difficult to recycle mechanically. However, advanced recycling has barriers such as poor selectivity, contaminant sensitivity, and the need for expensive catalysts. Reported herein is a simple yet scalable methodology for converting mixed polyethylene (high-density and low-density polyethylene recycled polyethylene) into upcycled waxes with up to 94% yield. This high yield was possible by performing the reaction at a mild temperature and was enabled by using inexpensive and reusable table salt. Without table salt, in otherwise identical conditions, the plastic remained essentially undegraded. These upcycled waxes were used as prototypes for applications such as water- and oil-resistant paper, as well as rheology modifiers for plastics. Their performance is similar to that of commercial wax as well as rheology modifiers. A preliminary economic analysis shows that the upcycled waxes obtained by this table salt-catalyzed approach offer three times more revenue than those reported in the literature. This pioneering discovery opens the door for a circular economy of plastics in general and polyolefins in particular.
Number of steady states of quantum evolutions
Authors: Amato Daniele , Facchi Paolo
Published: June 2024

We prove sharp universal upper bounds on the number of linearly independent steady and asymptotic states of discrete- and continuous-time Markovian evolutions of open quantum systems. We show that the bounds depend only on the dimension of the system and not on the details of the dynamics. A comparison with similar bounds deriving from a recent spectral conjecture for Markovian evolutions is also provided.
First-night effect reduces the beneficial effects of sleep on visual plasticity and modifies the underlying neurochemical processes
Authors: Tamaki Masako , Yamada Takashi , Barnes-Diana Tyler , Wang Zhiyan , Watanabe Takeo , Sasaki Yuka
Published: June 2024

Individuals experience difficulty falling asleep in a new environment, termed the first night effect (FNE). However, the impact of the FNE on sleep-induced brain plasticity remains unclear. Here, using a within-subject design, we found that the FNE significantly reduces visual plasticity during sleep in young adults. Sleep-onset latency (SOL), an indicator of the FNE, was significantly longer during the first sleep session than the second session, confirming the FNE. We assessed performance gains in visual perceptual learning after sleep and increases in the excitatory-to-inhibitory neurotransmitter (E/I) ratio in early visual areas during sleep using magnetic resonance spectroscopy and polysomnography. These parameters were significantly smaller in sleep with the FNE than in sleep without the FNE; however, these parameters were not correlated with SOL. These results suggest that while the neural mechanisms of the FNE and brain plasticity are independent, sleep disturbances temporarily block the neurochemical process fundamental for brain plasticity.
X-ray Thomson scattering absolute intensity from the f-sum rule in the imaginary-time domain
Authors: Dornheim T. , Döppner T. , Baczewski A. D. , Tolias P. , Böhme M. P. , Moldabekov Zh. A. , Gawne Th. , Ranjan D. , Chapman D. A. , MacDonald M. J. , Preston Th. R. , Kraus D. , Vorberger J.
Published: June 2024

We present a formally exact and simulation-free approach for the normalization of X-ray Thomson scattering (XRTS) spectra based on the f-sum rule of the imaginary-time correlation function (ITCF). Our method works for any degree of collectivity, over a broad range of temperatures, and is applicable even in nonequilibrium situations. In addition to giving us model-free access to electronic correlations, this new approach opens up the intriguing possibility to extract a plethora of physical properties from the ITCF based on XRTS experiments.
Factors affecting the expression and stability of full-length and truncated SRSF3 proteins in human cancer cells
Authors: Sue Sung-How , Liu Shu-Ting , Huang Shih-Ming
Published: June 2024

Alternative splicing plays a crucial role in increasing the diversity of mRNAs expressed in the genome. Serine/arginine-rich splicing factor 3 (SRSF3) is responsible for regulating the alternative splicing of its own mRNA and ensuring that its expression is balanced to maintain homeostasis. Moreover, the exon skipping of SRSF3 leads to the production of a truncated protein instead of a frameshift mutation that generates a premature termination codon (PTC). However, the precise regulatory mechanism involved in the splicing of SRSF3 remains unclear. In this study, we first established a platform for coexpressing full-length SRSF3 (SRSF3-FL) and SRSF3-PTC and further identified a specific antibody against the SRSF3-FL and truncated SRSF3 (SRSF3-TR) proteins. Next, we found that exogenously overexpressing SRSF3-FL or SRSF3-PTC failed to reverse the effects of digoxin, caffeine, or both in combination on this molecule and its targets. Endoplasmic reticulum-related pathways, transcription factors, and chemicals such as palmitic acid and phosphate were found to be involved in the regulation of SRSF3 expression. The downregulation of SRSF3-FL by palmitic acid and phosphate was mediated via different regulatory mechanisms in HeLa cells. In summary, we provide new insights into the altered expression of the SRSF3-FL and SRSF3-TR proteins for the identification of the functions of SRSF3 in cells.
Using NaOH@Graphene oxide-Fe3O4 as a magnetic heterogeneous catalyst for ultrasonic transesterification; experimental and modelling
Authors: Haghighi Sepideh Moradi , Hemmati Alireza , Moghadamzadeh Hamidreza , Ghaemi Ahad , Raoofi Nahid
Published: June 2024

Burning fossil fuels causes toxic gas emissions to increase, therefore, scientists are trying to find alternative green fuels. One of the important alternative fuels is biodiesel. However, using eco-friendly primary materials is a main factor. Sustainable catalysts should have high performance, good activity, easy separation from reaction cells, and regenerability. In this study, to solve the mentioned problem NaOH@Graphene oxide-Fe3O4 as a magnetic catalyst was used for the first time to generate biodiesel from waste cooking oil. The crystal structure, functional groups, surface area and morphology of catalyst were studied by XRD, FTIR, BET, and FESEM techniques. The response surface methodology based central composite design (RSM-CCD) was used for biodiesel production via ultrasonic technique. The maximum biodiesel yield was 95.88% in the following operation: 10.52:1 molar ratio of methanol to oil, a catalyst weight of 3.76 wt%, a voltage of 49.58 kHz, and a time of 33.29 min. The physiochemical characterization of biodiesel was based to ASTM standard. The magnetic catalyst was high standstill to free fatty acid due to the five cycle’s regeneration. The kinetic study results possess good agreement with first-order kinetics as well as the activation energy and Arrhenius constant are 49.2 kJ/min and 16.47 * 1010 min−1, respectively.