bluuebunny/crossref_metadata_2025 huggingface dataset:
Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer
Authors: Ramaboli M. C. , Ocvirk S. , Khan Mirzaei M. , Eberhart B. L. , Valdivia-Garcia M. , Metwaly A. , Neuhaus K. , Barker G. , Ru J. , Nesengani L. T. , Mahdi-Joest D. , Wilson A. S. , Joni S. K. , Layman D. C. , Zheng J. , Mandal R. , Chen Q. , Perez M. R. , Fortuin S. , Gaunt B. , Wishart D. , Methé B. , Haller D. , Li J. V. , Deng L. , Swart R. , O’Keefe S. J. D.
Published: April 2024

Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.
Inkjet-printed optical interference filters
Authors: Jin Qihao , Zhang Qiaoshuang , Rainer Christian , Hu Hang , Chen Junchi , Gehring Tim , Dycke Jan , Singh Roja , Paetzold Ulrich W. , Hernández-Sosa Gerardo , Kling Rainer , Lemmer Uli
Published: April 2024

Optical interference filters (OIFs) are vital components for a wide range of optical and photonic systems. They are pivotal in controlling spectral transmission and reflection upon demand. OIFs rely on optical interference of the incident wave at multilayers, which are fabricated with nanometer precision. Here, we demonstrate that these requirements can be fulfilled by inkjet printing. This versatile technology offers a high degree of freedom in manufacturing, as well as cost-affordable and rapid-prototyping features from the micron to the meter scale. In this work, via rational ink design and formulation, OIFs were fully inkjet printed in ambient conditions. Longpass, shortpass, bandpass, and dichroic OIFs were fabricated, and precise control of the spectral response in OIFs was realized. Subsequently, customized lateral patterning of OIFs by inkjet printing was achieved. Furthermore, upscaling of the printed OIFs to A4 size (29.7 × 21.0 cm²) was demonstrated.
Orphan high field superconductivity in non-superconducting uranium ditelluride
Authors: Frank Corey E. , Lewin Sylvia K. , Saucedo Salas Gicela , Czajka Peter , Hayes Ian M. , Yoon Hyeok , Metz Tristin , Paglione Johnpierre , Singleton John , Butch Nicholas P.
Published: April 2024

Reentrant superconductivity is an uncommon phenomenon in which the destructive effects of magnetic field on superconductivity are mitigated, allowing a zero-resistance state to survive under conditions that would otherwise destroy it. Typically, the reentrant superconducting region derives from a zero-field parent superconducting phase. Here, we show that in UTe2 crystals extreme applied magnetic fields give rise to an unprecedented high-field superconductor that lacks a zero-field antecedent. This high-field orphan superconductivity exists at angles offset between 29o and 42o from the crystallographic b to c axes with applied fields between 37 T and 52 T. The stability of field-induced orphan superconductivity presented in this work defies both empirical precedent and theoretical explanation and demonstrates that high-field superconductivity can exist in an otherwise non-superconducting material.
Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes
Authors: Hauptfeld Ernestina , Pappas Nikolaos , van Iwaarden Sandra , Snoek Basten L. , Aldas-Vargas Andrea , Dutilh Bas E. , von Meijenfeldt F. A. Bastiaan
Published: April 2024

Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
Electrostatic steering of thermal emission with active metasurface control of delocalized modes
Authors: Siegel Joel , Kim Shinho , Fortman Margaret , Wan Chenghao , Kats Mikhail A. , Hon Philip W. C. , Sweatlock Luke , Jang Min Seok , Brar Victor Watson
Published: April 2024

We theoretically describe and experimentally demonstrate a graphene-integrated metasurface structure that enables electrically-tunable directional control of thermal emission. This device consists of a dielectric spacer that acts as a Fabry-Perot resonator supporting long-range delocalized modes bounded on one side by an electrostatically tunable metal-graphene metasurface. By varying the Fermi level of the graphene, the accumulated phase of the Fabry-Perot mode is shifted, which changes the direction of absorption and emission at a fixed frequency. We directly measure the frequency- and angle-dependent emissivity of the thermal emission from a fabricated device heated to 250 °C. Our results show that electrostatic control allows the thermal emission at 6.61 μm to be continuously steered over 16°, with a peak emissivity maintained above 0.9. We analyze the dynamic behavior of the thermal emission steerer theoretically using a Fano interference model, and use the model to design optimized thermal steerer structures.
Iterative SuFEx approach for sequence-regulated oligosulfates and its extension to periodic copolymers
Authors: Kim Min Pyeong , Kayal Swatilekha , Hwang Chiwon , Bae Jonghoon , Kim Hyunseok , Hwang Dong Gyu , Jeon Min Ho , Seo Jeong Kon , Ahn Dowon , Lee Wonjoo , Seo Sangwon , Chun Joong-Hyun , Yu Youngchang , Hong Sung You
Published: April 2024

The synthesis of sequence-regulated oligosulfates has not yet been established due to the difficulties in precise reactivity control. In this work, we report an example of a multi-directional divergent iterative method to furnish oligosulfates based on a chain homologation approach, in which the fluorosulfate unit is regenerated. The oligosulfate sequences are determined by high resolution mass spectrometry of the hydrolyzed fragments, and polysulfate periodic copolymers are synthesized by using oligomeric bisfluorosulfates in a bi-directional fashion. The synthetic utility of this iterative ligation is demonstrated by preparing crosslinked network polymers as synthetic adhesive materials.
A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments
Authors: Zhang Yanmei , Hu Qifan , Pei Yuquan , Luo Hao , Wang Zixuan , Xu Xinxin , Zhang Qing , Dai Jianli , Wang Qianqian , Fan Zilian , Fang Yongcong , Ye Min , Li Binhan , Chen Mailin , Xue Qi , Zheng Qingfeng , Zhang Shulin , Huang Miao , Zhang Ting , Gu Jin , Xiong Zhuo
Published: April 2024

Cancer models play critical roles in basic cancer research and precision medicine. However, current in vitro cancer models are limited by their inability to mimic the three-dimensional architecture and heterogeneous tumor microenvironments (TME) of in vivo tumors. Here, we develop an innovative patient-specific lung cancer assembloid (LCA) model by using droplet microfluidic technology based on a microinjection strategy. This method enables precise manipulation of clinical microsamples and rapid generation of LCAs with good intra-batch consistency in size and cell composition by evenly encapsulating patient tumor-derived TME cells and lung cancer organoids inside microgels. LCAs recapitulate the inter- and intratumoral heterogeneity, TME cellular diversity, and genomic and transcriptomic landscape of their parental tumors. LCA model could reconstruct the functional heterogeneity of cancer-associated fibroblasts and reflect the influence of TME on drug responses compared to cancer organoids. Notably, LCAs accurately replicate the clinical outcomes of patients, suggesting the potential of the LCA model to predict personalized treatments. Collectively, our studies provide a valuable method for precisely fabricating cancer assembloids and a promising LCA model for cancer research and personalized medicine.
TAD boundary deletion causes PITX2-related cardiac electrical and structural defects
Authors: Baudic Manon , Murata Hiroshige , Bosada Fernanda M. , Melo Uirá Souto , Aizawa Takanori , Lindenbaum Pierre , van der Maarel Lieve E. , Guedon Amaury , Baron Estelle , Fremy Enora , Foucal Adrien , Ishikawa Taisuke , Ushinohama Hiroya , Jurgens Sean J. , Choi Seung Hoan , Kyndt Florence , Le Scouarnec Solena , Wakker Vincent , Thollet Aurélie , Rajalu Annabelle , Takaki Tadashi , Ohno Seiko , Shimizu Wataru , Horie Minoru , Kimura Takeshi , Ellinor Patrick T. , Petit Florence , Dulac Yves , Bru Paul , Boland Anne , Deleuze Jean-François , Redon Richard , Le Marec Hervé , Le Tourneau Thierry , Gourraud Jean-Baptiste , Yoshida Yoshinori , Makita Naomasa , Vieyres Claude , Makiyama Takeru , Mundlos Stephan , Christoffels Vincent M. , Probst Vincent , Schott Jean-Jacques , Barc Julien
Published: April 2024

While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.
A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery
Authors: Moine-Franel Alexandra , Mareuil Fabien , Nilges Michael , Ciambur Constantin Bogdan , Sperandio Olivier
Published: April 2024

This dataset represents a collection of pocket-centric structural data related to protein-protein interactions (PPIs) and PPI-related ligand binding sites. The dataset includes high-quality structural information on more than 23,000 pockets, 3,700 proteins on more than 500 organisms, and nearly 3500 ligands that can aid researchers in the fields of bioinformatics, structural biology, and drug discovery. It encompasses a diverse set of PPI complexes with more than 1,700 unique protein families including some with associated ligands, enabling detailed investigations into molecular interactions at the atomic level. This article introduces an indispensable resource designed to unlock the full potential of PPIs while pioneering a novel metric for pocket similarity for hypothesizing protein partners repurposing.
Chromosome-level genome assembly of marine diatom Skeletonema tropicum
Authors: Liu Shuya , Chen Nansheng
Published: April 2024

Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture. The assembled genome has a size of 78.78 Mb with a scaffold N50 of 3.17 Mb, anchored to 23 pseudo-chromosomes. In total, 20,613 protein-coding genes were predicted, of which 17,757 (86.14%) genes were functionally annotated. Collinearity analysis of the genomes of S. tropicum and S. marinoi revealed that these two genomes were highly homologous. This chromosome-level genome assembly of S. tropicum provides a valuable genomic platform for comparative analysis of mechanisms of ecological adaption.
The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis
Authors: Zhou Caibi , Tao Fang , Long Rupiao , Yang Xiaoting , Wu Xingli , Xiang Lan , Zhou Xiaolu , Girdthai Teerayoot
Published: April 2024

The chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.
Advanced mapping of inorganic treatments on porous carbonate stones by combined synchrotron radiation high lateral μXRPD and μXRF
Authors: Massinelli G. , Marinoni N. , Colombo C. , Gatta G. D. , Realini M. , Burghammer M. , Possenti E.
Published: April 2024

Understanding the effects of consolidating inorganic mineral treatments on carbonate stones of cultural heritage, and on the nature and distribution of newly formed products within the matrix, poses a significant challenge in Heritage Science and Conservation Science. Existing analytical methods often fail to deliver spatial and compositional insights into the newly formed crystalline phases with the appropriate high lateral resolution. In this study, we explore the capabilities and limitations of synchrotron radiation (SR) micro-X-ray powder diffraction (μXRPD) mapping combined with micro-X-ray fluorescence (μXRF) to give insight into compounds formed following the application of ammonium oxalate (AmOx) and diammonium phosphate-based (DAP) solutions on porous carbonate stone. Ultimately, the integration of μXRPD mapping and μXRF analysis proved itself a powerful asset in providing precise qualitative and quantitative data on the newly formed phases, in the case of both calcium oxalates (CaOxs) and calcium phosphates (CaPs), and their complex stratigraphic distribution, thus opening a new route for applications to a more comprehensive study of inorganic treatments applied to carbonate substrates.
Testcross performance and combining ability of early-medium maturing quality protein maize inbred lines in Eastern and Southern Africa
Authors: Mebratu Addisalem , Wegary Dagne , Teklewold Adefris , Tarekegne Amsal
Published: April 2024

Limited commercial quality protein maize (QPM) varieties with low grain yield potential are currently grown in Eastern and Southern Africa (ESA). This study was conducted to (i) assess the performance of single-cross QPM hybrids that were developed from elite inbred lines using line-by-tester mating design and (ii) estimate the general (GCA) and specific (SCA) combining ability of the QPM inbred lines for grain yield, agronomic and protein quality traits. One hundred and six testcrosses and four checks were evaluated across six environments in ESA during 2015 and 2016. Significant variations (P ≤ 0.01) were observed among environments, genotypes and genotype by environment interaction (GEI) for most traits evaluated. Hybrids H80 and H104 were the highest-yielding, most desirable, and stable QPM hybrids. Combining ability analysis showed both additive and non-additive gene effects to be important in the inheritance of grain yield. Additive effects were more important for agronomic and protein quality traits. Inbred lines L19 and L20 depicted desirable GCA effects for grain yield. Various other inbred lines with favorable GCA effects for agronomic traits, endosperm modification, and protein quality traits were identified. These inbred lines could be utilized for breeding desirable QPM cultivars. The QPM hybrids identified in this study could be commercialized after on-farm verification to replace the low-yielding QPM hybrids grown in ESA.
Coupled responses of thermomechanical waves in functionally graded viscoelastic nanobeams via thermoelastic heat conduction model including Atangana–Baleanu fractional derivative
Authors: Abouelregal Ahmed E. , Marin Marin , Foul Abdelaziz , Askar S. S.
Published: April 2024

Accurately characterizing the thermomechanical parameters of nanoscale systems is essential for understanding their performance and building innovative nanoscale technologies due to their distinct behaviours. Fractional thermal transport models are commonly utilized to correctly depict the heat transfer that occurs in these nanoscale systems. The current study presents a novel mathematical thermoelastic model that incorporates a new fractional differential constitutive equation for heat conduction. This heat equation is useful for understanding the effects of thermal memory. An application of a fractional-time Atangana–Baleanu (AB) derivative with a local and non-singular kernel was utilized in the process of developing the mathematical model that was suggested. To deal with effects that depend on size, nonlocal constitutive relations are introduced. Furthermore, in order to take into consideration, the viscoelastic behaviour of the material at the nanoscale, the fractional Kelvin–Voigt model is utilized. The proposed model is highly effective in properly depicting the unusual thermal conductivity phenomena often found in nanoscale devices. The study also considered the mechanical deformation, temperature variations, and viscoelastic characteristics of the functionally graded (FG) nanostructured beams. The consideration was made that the material characteristics exhibit heterogeneity and continuous variation across the thickness of the beam as the nanobeam transitions from a ceramic composition in the lower region to a metallic composition in the upper region. The complicated thermomechanical features of simply supported viscoelastic nanobeams that were exposed to harmonic heat flow were determined by the application of the model that was constructed. Heterogeneity, nonlocality, and fractional operators are some of the important variables that contribute to its success, and this article provides a full study and illustration of the significance of these characteristics. The results that were obtained have the potential to play a significant role in pushing forward the design and development of tools, materials, and nanostructures that have viscoelastic mechanical characteristics and graded functions.
Synthesis, biofilm formation inhibitory, and inflammation inhibitory activities of new coumarin derivatives
Authors: Ahmed Ghada E. , Elshahid Zeinab A. , El-Sawy Eslam Reda , Abdel-Aziz Mohamed S. , Abdel-Aziem Anhar
Published: April 2024

Coumarins are heterocycles of great interest in the development of valuable active structures in chemistry and biological domains. The ability of coumarins to inhibit biofilm formation of Gram positive bacterium (Staphylococcus aureus), Gram negative bacterium (Escherichia coli) as well as the methicillin-resistant S. aureus (MRSA) has been previously described. In the present work, new hybrid coumarin-heterocycles have been synthesized via the reaction of coumarin-6-sulfonyl chloride and 6-aminocoumarin with different small heterocycle moieties. The biological efficacy of the new compounds was evaluated towards their ability to inhibit biofilm formation and their anti-inflammatory properties. The antimicrobial activities of the newly synthesized compounds were tested against Gram positive bacterium (S. aureus ATCC 6538), Gram negative bacterium (E. coli ATCC 25922), yeast (Candida albicans ATCC 10231) and the fungus (Aspergillus niger NRRL-A326). Compounds 4d, 4e, 4f, 6a and 9 showed significant MIC and MBC values against S. aureus, E. coli, C. albicans, and methicillin-resistant S. aureus (MRSA) with especial incidence on compound 9 which surpasses all the other compounds giving MIC and MBC values of (4.88 and 9.76 µg/mL for S. aureus), (78.13 and 312.5 µg/mL for E. coli), (9.77 and 78.13 µg/mL for C. albicans), and (39.06 and 76.7 µg/mL for MRSA), respectively. With reference to the antibiofilm activity, compound 9 exhibited potent antibiofilm activity with IC50 of 60, 133.32, and 19.67 µg/mL against S. aureus, E. coli, and MRSA, (respectively) considering the reference drug (neomycin). Out of all studied compounds, the anti-inflammatory results indicated that compound 4d effectively inhibited nitric oxide production in lipopolysaccharide-(LPS-) stimulated RAW264.7 macrophage cells, giving NO% inhibition of 70% compared to Sulindac (55.2%)
Hypergraph regularized nonnegative triple decomposition for multiway data analysis
Authors: Liao Qingshui , Liu Qilong , Razak Fatimah Abdul
Published: April 2024

Tucker decomposition is widely used for image representation, data reconstruction, and machine learning tasks, but the calculation cost for updating the Tucker core is high. Bilevel form of triple decomposition (TriD) overcomes this issue by decomposing the Tucker core into three low-dimensional third-order factor tensors and plays an important role in the dimension reduction of data representation. TriD, on the other hand, is incapable of precisely encoding similarity relationships for tensor data with a complex manifold structure. To address this shortcoming, we take advantage of hypergraph learning and propose a novel hypergraph regularized nonnegative triple decomposition for multiway data analysis that employs the hypergraph to model the complex relationships among the raw data. Furthermore, we develop a multiplicative update algorithm to solve our optimization problem and theoretically prove its convergence. Finally, we perform extensive numerical tests on six real-world datasets, and the results show that our proposed algorithm outperforms some state-of-the-art methods.
Salvage prostate intensity modulated radiation therapy after cryotherapy failure
Authors: Perennec Tanguy , Rogé Maximilien , Hetet Jean-François , Colls Philippe , Guimas Valentine , Rio Emmanuel , Vaugier Loïg , Supiot Stéphane
Published: April 2024

Cryotherapy is an ablative therapy that can be used to treat localized prostate cancer. In case of recurrence, treatment options are not well-defined, and their outcomes are unknown. We therefore collected all patients treated with radiotherapy after cryotherapy for prostate cancer recurrence in Nantes (France) between 2012 and 2019. We identified ten patients. After a median follow-up of 5 years, two patients presented late grade 3 toxicities; one patient presented a grade 3 rectal hemorrhage, and one had a grade 3 hematuria. Two patients relapsed at 61 and 62 months, and three patients died of other causes. Radiotherapy to treat local prostate cancer recurrence after cryotherapy seems feasible and effective in local control. These results do not allow us to recommend this technique in current practice but are encouraging for the conduct of prospective trials.
Effects and prediction of cognitive load on encoding model of brain response to auditory and linguistic stimuli in educational multimedia
Authors: Asaadi Amir Hosein , Amiri S. Hamid , Bosaghzadeh Alireza , Ebrahimpour Reza
Published: April 2024

Multimedia is extensively used for educational purposes. However, certain types of multimedia lack proper design, which could impose a cognitive load on the user. Therefore, it is essential to predict cognitive load and understand how it impairs brain functioning. Participants watched a version of educational multimedia that applied Mayer’s principles, followed by a version that did not. Meanwhile, their electroencephalography (EEG) was recorded. Subsequently, they participated in a post-test and completed a self-reported cognitive load questionnaire. The audio envelope and word frequency were extracted from the multimedia, and the temporal response functions (TRFs) were obtained using a linear encoding model. We observed that the behavioral data are different between the two groups and the TRFs of the two multimedia versions were different. We saw changes in the amplitude and latencies of both early and late components. In addition, correlations were found between behavioral data and the amplitude and latencies of TRF components. Cognitive load decreased participants’ attention to the multimedia, and semantic processing of words also occurred with a delay and smaller amplitude. Hence, encoding models provide insights into the temporal and spatial mapping of the cognitive load activity, which could help us detect and reduce cognitive load in potential environments such as educational multimedia or simulators for different purposes.
DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes
Authors: Ledesma-Dominguez Leonardo , Carbajal-Degante Erik , Moreno-Hagelsieb Gabriel , Pérez-Rueda Ernesto
Published: April 2024

Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. In this work, we propose a hybrid model to identify transcription factors (TFs) among prokaryotic and eukaryotic protein sequences, named Deep Regulation (DeepReg) model. Two architectures were used in the DL model: a convolutional neural network (CNN), and a bidirectional long-short-term memory (BiLSTM). DeepReg reached a precision of 0.99, a recall of 0.97, and an F1-score of 0.98. The quality of our predictions, the bias-variance trade-off approach, and the characterization of new TF predictions were evaluated and compared against those produced by DeepTFactor, as well as against experimental data from three model organisms. Predictions based on our DLM tended to exhibit less variance and bias than those from DeepTFactor, thus increasing reliability and decreasing overfitting.
From sensor fusion to knowledge distillation in collaborative LIBS and hyperspectral imaging for mineral identification
Authors: Lopes Tomás , Capela Diana , Guimarães Diana , Ferreira Miguel F. S. , Jorge Pedro A. S. , Silva Nuno A.
Published: April 2024

Multimodal spectral imaging offers a unique approach to the enhancement of the analytical capabilities of standalone spectroscopy techniques by combining information gathered from distinct sources. In this manuscript, we explore such opportunities by focusing on two well-known spectral imaging techniques, namely laser-induced breakdown spectroscopy, and hyperspectral imaging, and explore the opportunities of collaborative sensing for a case study involving mineral identification. In specific, the work builds upon two distinct approaches: a traditional sensor fusion, where we strive to increase the information gathered by including information from the two modalities; and a knowledge distillation approach, where the Laser Induced Breakdown spectroscopy is used as an autonomous supervisor for hyperspectral imaging. Our results show the potential of both approaches in enhancing the performance over a single modality sensing system, highlighting, in particular, the advantages of the knowledge distillation framework in maximizing the potential benefits of using multiple techniques to build more interpretable models and paving for industrial applications.
Effects of environmental exposure to iron powder on healthy and elastase-exposed mice
Authors: Galli Thiago Tafarel , de Campos Elaine Cristina , do Nascimento Camargo Leandro , Fukuzaki Silvia , dos Santos Tabata Marayama , Hamaguchi Sara Sumie Sobral , Bezerra Suellen Karoline Moreira , Silva Fabio José Alencar , Rezende Bianca Goulart , dos Santos Lopes Fernanda Tenório Quirino , Olivo Clarice Rosa , Saraiva-Romanholo Beatriz Mangueira , Prado Carla Máximo , Leick Edna Aparecida , Bourotte Christine Laure Marie , Benseñor Isabela Judith Martins , Lotufo Paulo Andrade , Righetti Renato Fraga , Tibério Iolanda Fátima Lopes Calvo
Published: April 2024

Prolonged exposure to iron powder and other mineral dusts can threaten the health of individuals, especially those with COPD. The goal of this study was to determine how environmental exposure to metal dust from two different mining centers in Brazil affects lung mechanics, inflammation, remodeling and oxidative stress responses in healthy and elastase-exposed mice. This study divided 72 male C57Bl/6 mice into two groups, the summer group and the winter group. These groups were further divided into six groups: control, nonexposed (SAL); nonexposed, given elastase (ELA); exposed to metal powder at a mining company (SAL-L1 and ELA-L1); and exposed to a location three miles away from the mining company (SAL-L2 and ELA-L2) for four weeks. On the 29th day of the protocol, the researchers assessed lung mechanics, bronchoalveolar lavage fluid (BALF), inflammation, remodeling, oxidative stress, macrophage iron and alveolar wall alterations (mean linear intercept-Lm). The Lm was increased in the ELA, ELA-L1 and ELA-L2 groups compared to the SAL group (p < 0.05). There was an increase in the total number of cells and macrophages in the ELA-L1 and ELA-L2 groups compared to the other groups (p < 0.05). Compared to the ELA and SAL groups, the exposed groups (ELA-L1, ELA-L2, SAL-L1, and SAL-L2) exhibited increased expression of IL-1β, IL-6, IL-10, IL-17, TNF-α, neutrophil elastase, TIMP-1, MMP-9, MMP-12, TGF-β, collagen fibers, MUC5AC, iNOS, Gp91phox, NFkB and iron positive macrophages (p < 0.05). Although we did not find differences in lung mechanics across all groups, there were low to moderate correlations between inflammation remodeling, oxidative stress and NFkB with elastance, resistance of lung tissue and iron positive macrophages (p < 0.05). Environmental exposure to iron, confirmed by evaluation of iron in alveolar macrophages and in air, exacerbated inflammation, initiated remodeling, and induced oxidative stress responses in exposed mice with and without emphysema. Activation of the iNOS, Gp91phox and NFkB pathways play a role in these changes.
Tumor growth-arrest effect of tetrahydroquinazoline-derivative human topoisomerase II-alpha inhibitor in HPV-negative head and neck squamous cell carcinoma
Authors: Sarogni Patrizia , Brindani Nicoletta , Zamborlin Agata , Gonnelli Alessandra , Menicagli Michele , Mapanao Ana Katrina , Munafò Federico , De Vivo Marco , Voliani Valerio
Published: April 2024

Oral malignancies continue to have severe morbidity with less than 50% long-term survival despite the advancement in the available therapies. There is a persisting demand for new approaches to establish more efficient strategies for their treatment. In this regard, the human topoisomerase II (topoII) enzyme is a validated chemotherapeutics target, as topoII regulates vital cellular processes such as DNA replication, transcription, recombination, and chromosome segregation in cells. TopoII inhibitors are currently used to treat some neoplasms such as breast and small cells lung carcinomas. Additionally, topoII inhibitors are under investigation for the treatment of other cancer types, including oral cancer. Here, we report the therapeutic effect of a tetrahydroquinazoline derivative (named ARN21934) that preferentially inhibits the alpha isoform of human topoII. The treatment efficacy of ARN21934 has been evaluated in 2D cell cultures, 3D in vitro systems, and in chick chorioallantoic membrane cancer models. Overall, this work paves the way for further preclinical developments of ARN21934 and possibly other topoII alpha inhibitors of this promising chemical class as a new chemotherapeutic approach for the treatment of oral neoplasms.
Seismic response analysis of subway station under obliquely incident SV waves
Authors: Zhu Hui , Yan Songhong , Sun Weiyu , Zhang Rongling , Ou Erfeng , Liang Qingguo
Published: April 2024

This paper aims to investigate the dynamic response characteristics of subway station under earthquakes. To this end, seismic waves are transformed into equivalent nodal loads on viscoelastic artificial boundaries using theories and methods of wave motion. The calculation formulas for equivalent nodal loads of SV waves incident at any angle are established, and ANSYS' APDL program compiles to automatically generate the viscoelastic artificial boundary and input the seismic loads. A finite element model of soil-subway station interaction was established, and the seismic response characteristics of a two-story three-span subway station under different incidence angles of SV waves were investigated using the above seismic input method. The results indicate that the incidence angle of seismic waves has a significant impact on the seismic response of subway station. Inclined incidence of seismic waves causes non-uniform loading and deformation of the subway station. Specifically, a small angle leads to predominantly transverse shear deformation, while a large angle causes mainly vertical shear deformation. The inclined incidence of seismic waves significantly increases the vertical acceleration of the subway station, with the effect becoming more pronounced as the angle increases. Additionally, special attention should be given to the joints between the structural slab and the side wall, slab and center column, as well as the two ends of the center column as they are vulnerable areas during earthquakes and require careful consideration in seismic design.
Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease
Authors: Ren Mengting , Pan Hanghai , Zhou Xinxin , Yu Mosang , Ji Feng
Published: April 2024

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.
Lignin nanoparticles as a highly efficient adsorbent for the removal of methylene blue from aqueous media
Authors: Pourbaba Reza , Abdulkhani Ali , Rashidi Alimorad , Ashori Alireza
Published: April 2024

This work demonstrated enhanced adsorption capabilities of lignin nanoparticles (LNPs) synthesized via a straightforward hydrotropic method compared to pristine lignin (PL) powder for removing methylene blue dye from aqueous solutions. Kraft lignin was used as a precursor and p-toluenesulfonic acid as the hydrotrope to produce spherical LNPs with ~ 200 nm diameter. Extensive characterization by SEM, AFM, DLS, zeta potential, and BET verified successful fabrication of microporous LNPs with fourfold higher specific surface area (14.9 m2/g) compared to PL (3.4 m2/g). Significantly reduced particle agglomeration and rearranged surface chemistry (zeta potential of −13.3 mV) arising from the self-assembly of lignin fractions under hydrotropic conditions enabled the application of LNPs and superior adsorbents compared to PL. Batch adsorption experiments exhibited up to 14 times higher methylene blue removal capacity, from 20.74 for PL to 127.91 mg/g for LNPs, and ultrafast equilibrium uptake within 3 min for LNPs compared to 10 min for PL. Kinetic modeling based on pseudo-first-order and pseudo-second-order equations revealed chemisorption as the predominant mechanism, with a rate constant of 0.032825 g/mg·h for LNPs—over an order of magnitude higher than PL (0.07125 g/mg·h). Isotherm modeling indicated Langmuir monolayer adsorption behavior on relatively uniform lignin surface functional groups. The substantially augmented adsorption performance of LNPs arose from the increased surface area and abundance of surface functional groups, providing greater accessibility of chemically active binding sites for rapid dye uptake. Overall, this work demonstrates that tailoring lignin nanoparticle structure and surface chemistry via scalable hydrotropic synthesis is a simple and sustainable approach for producing highly efficient lignin-based nano-adsorbents for organic dye removal from industrial wastewater.
Classification of mental workload using brain connectivity and machine learning on electroencephalogram data
Authors: Safari MohammadReza , Shalbaf Reza , Bagherzadeh Sara , Shalbaf Ahmad
Published: April 2024

Mental workload refers to the cognitive effort required to perform tasks, and it is an important factor in various fields, including system design, clinical medicine, and industrial applications. In this paper, we propose innovative methods to assess mental workload from EEG data that use effective brain connectivity for the purpose of extracting features, a hierarchical feature selection algorithm to select the most significant features, and finally machine learning models. We have used the Simultaneous Task EEG Workload (STEW) dataset, an open-access collection of raw EEG data from 48 subjects. We extracted brain-effective connectivities by the direct directed transfer function and then selected the top 30 connectivities for each standard frequency band. Then we applied three feature selection algorithms (forward feature selection, Relief-F, and minimum-redundancy-maximum-relevance) on the top 150 features from all frequencies. Finally, we applied sevenfold cross-validation on four machine learning models (support vector machine (SVM), linear discriminant analysis, random forest, and decision tree). The results revealed that SVM as the machine learning model and forward feature selection as the feature selection method work better than others and could classify the mental workload levels with accuracy equal to 89.53% (± 1.36).
An exact algorithm to find a maximum weight clique in a weighted undirected graph
Authors: Rozman Kati , Ghysels An , Janežič Dušanka , Konc Janez
Published: April 2024

We introduce a new algorithm MaxCliqueWeight for identifying a maximum weight clique in a weighted graph, and its variant MaxCliqueDynWeight with dynamically varying bounds. This algorithm uses an efficient branch-and-bound approach with a new weighted graph coloring algorithm that efficiently determines upper weight bounds for a maximum weighted clique in a graph. We evaluate our algorithm on random weighted graphs with node counts up to 10,000 and on standard DIMACS benchmark graphs used in a variety of research areas. Our findings reveal a remarkable improvement in computational speed when compared to existing algorithms, particularly evident in the case of high-density random graphs and DIMACS graphs, where our newly developed algorithm outperforms existing alternatives by several orders of magnitude. The newly developed algorithm and its variant are freely available to the broader research community at http://insilab.org/maxcliqueweight, paving the way for transformative applications in various research areas, including drug discovery.
Graphsene as a novel porous two-dimensional carbon material for enhanced oxygen reduction electrocatalysis
Authors: Hosseini Mohammadreza , Soleimani Maryam , Shojaei Fazel , Pourfath Mahdi
Published: April 2024

Graphene allotropes with varied carbon configurations have attracted significant attention for their unique properties and chemical activities. This study introduces a novel two-dimensional carbon-based material, termed Graphsene (GrS), through theoretical study. Comprising tetra-, penta-, and dodeca-carbon rings, GrS’s cohesive energy calculations demonstrate its superior structural stability over existing graphene allotropes, including graphyne and graphdiyne families. Phonon dispersion analysis confirms GrS’s dynamic stability and its relatively low thermal conductivity. All calculated GrS elastic constants meet the Born criteria, ensuring mechanical stability. Ab-initio molecular dynamic simulations show GrS maintains its structure at 300 K. HSE06 calculations reveal a narrow electronic bandgap of 20 meV, with the electronic band structure featuring a highly anisotropic Dirac-like cone due to its intrinsic structural anisotropy along armchair and zigzag directions. Notably, GrS is predicted to offer exceptional catalytic performance for the oxygen reduction reaction, favoring the four-electron reduction pathway with high selectivity under both acidic and alkaline conditions. This discovery opens promising avenues for developing metal-free catalyst materials in clean energy production.
Sequence based model using deep neural network and hybrid features for identification of 5-hydroxymethylcytosine modification
Authors: Khan Salman , Uddin Islam , Khan Mukhtaj , Iqbal Nadeem , Alshanbari Huda M. , Ahmad Bakhtiyar , Khan Dost Muhammad
Published: April 2024

RNA modifications are pivotal in the development of newly synthesized structures, showcasing a vast array of alterations across various RNA classes. Among these, 5-hydroxymethylcytosine (5HMC) stands out, playing a crucial role in gene regulation and epigenetic changes, yet its detection through conventional methods proves cumbersome and costly. To address this, we propose Deep5HMC, a robust learning model leveraging machine learning algorithms and discriminative feature extraction techniques for accurate 5HMC sample identification. Our approach integrates seven feature extraction methods and various machine learning algorithms, including Random Forest, Naive Bayes, Decision Tree, and Support Vector Machine. Through K-fold cross-validation, our model achieved a notable 84.07% accuracy rate, surpassing previous models by 7.59%, signifying its potential in early cancer and cardiovascular disease diagnosis. This study underscores the promise of Deep5HMC in offering insights for improved medical assessment and treatment protocols, marking a significant advancement in RNA modification analysis.
Percutaneous ultrasound-guided versus open cut-down access to femoral vessels for the placement of a REBOA catheter
Authors: Grechenig Peter , Hallmann Barbara , Eibinger Nicolas Rene , Koutp Amir , Zajic Paul , Höfler Gerald , Puchwein Paul
Published: April 2024

Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) may be useful in treating exsanguinating trauma patients. This study seeks to compare rates of success, complications and time required for vascular access between ultrasound-guidance and surgical cut-down for femoral sheath insertion as a prospective observational case control study. Participating clinicians from either trauma surgery or anesthesiology were allocated to surgical cut-down or percutaneous ultrasound-guided puncture on a 1:1 ratio. Time spans to vessel identification, successful puncture, and balloon inflation were recorded. 80 study participants were recruited and allocated to 40 open cut-down approaches and 40 percutaneous ultrasound-guided approaches. REBOA catheter placement was successful in 18/40 cases (45%) using a percutaneous ultrasound guided technique and 33/40 times (83%) using the open cut-down approach (p < 0.001). Median times [in seconds] compared between percutaneous ultrasound-guided puncture and surgical cut-down were 36 (18–73) versus 117(56–213) for vessel visualization (p < 0.001), 136 (97–175) versus 183 (156–219) for vessel puncture (p < 0.001), and 375 (240–600) versus 288 (244–379) for balloon inflation (p = 0.08) overall. Access to femoral vessels for REBOA catheter placement is safer when performed by cut-down and direct visualization but can be performed faster by an ultrasound-guided technique when vessels can be identified clearly and rapidly.