bluuebunny/crossref_metadata_2025 huggingface dataset:
Immune features are associated with response to neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer
Authors: Beckabir Wolfgang , Zhou Mi , Lee Jin Seok , Vensko Steven P. , Woodcock Mark G. , Wang Hsing-Hui , Wobker Sara E. , Atassi Gatphan , Wilkinson Alec D. , Fowler Kenneth , Flick Leah M. , Damrauer Jeffrey S. , Harrison Michael R. , McKinnon Karen P. , Rose Tracy L. , Milowsky Matthew I. , Serody Jonathan S. , Kim William Y. , Vincent Benjamin G.
Published: May 2024

Neoadjuvant cisplatin-based chemotherapy is standard of care for muscle-invasive bladder cancer (MIBC). Immune checkpoint inhibition (ICI) alone, and ICI in combination with chemotherapy, have demonstrated promising pathologic response (<pT2) in the neoadjuvant setting. In LCCC1520 (NCT02690558), a phase 2 single-arm trial of neoadjuvant chemo-immunotherapy (gemcitabine and cisplatin plus pembrolizumab; NAC-ICI) for MIBC, 22/39 patients responded (pathologic downstaging as primary outcome), as previously described. Here, we report post-hoc correlative analyses. Treatment was associated with changes in tumor mutational profile, immune gene signatures, and RNA subtype switching. Clinical response was associated with an increase in plasma IL-9 from pre-treatment to initiation of cycle 2 of therapy. Tumors harbored diverse predicted antigen landscapes that change across treatment and are associated with APOBEC, tobacco, and other etiologies. Higher pre-treatment tumor PD-L1 and TIGIT RNA expression were associated with complete response. IL-8 signature and Stroma-rich subtype were associated with improved response to NAC-ICI versus neoadjuvant ICI (ABACUS trial, NCT02662309). Plasma IL-9 represents a potential predictive biomarker of NAC-ICI response, while tumor IL-8 signature and stroma-rich subtype represent potential predictive biomarkers of response benefit of NAC-ICI over neoadjuvant ICI. Future efforts must include additional independent biomarker discovery and validation, ultimately to improve the selection of patients for ICI-related treatments.
Multispecies deep learning using citizen science data produces more informative plant community models
Authors: Brun Philipp , Karger Dirk N. , Zurell Damaris , Descombes Patrice , de Witte Lucienne C. , de Lutio Riccardo , Wegner Jan Dirk , Zimmermann Niklaus E.
Published: May 2024

In the age of big data, scientific progress is fundamentally limited by our capacity to extract critical information. Here, we map fine-grained spatiotemporal distributions for thousands of species, using deep neural networks (DNNs) and ubiquitous citizen science data. Based on 6.7 M observations, we jointly model the distributions of 2477 plant species and species aggregates across Switzerland with an ensemble of DNNs built with different cost functions. We find that, compared to commonly-used approaches, multispecies DNNs predict species distributions and especially community composition more accurately. Moreover, their design allows investigation of understudied aspects of ecology. Including seasonal variations of observation probability explicitly allows approximating flowering phenology; reweighting predictions to mirror cover-abundance allows mapping potentially canopy-dominant tree species nationwide; and projecting DNNs into the future allows assessing how distributions, phenology, and dominance may change. Given their skill and their versatility, multispecies DNNs can refine our understanding of the distribution of plants and well-sampled taxa in general.
An inorganic-blended p-type semiconductor with robust electrical and mechanical properties
Authors: Meng You , Wang Weijun , Fan Rong , Lai Zhengxun , Wang Wei , Li Dengji , Li Xiaocui , Quan Quan , Xie Pengshan , Chen Dong , Shao He , Li Bowen , Wu Zenghui , Yang Zhe , Yip SenPo , Wong Chun-Yuen , Lu Yang , Ho Johnny C.
Published: May 2024

Inorganic semiconductors typically have limited p-type behavior due to the scarcity of holes and the localized valence band maximum, hindering the progress of complementary devices and circuits. In this work, we propose an inorganic blending strategy to activate the hole-transporting character in an inorganic semiconductor compound, namely tellurium-selenium-oxygen (TeSeO). By rationally combining intrinsic p-type semimetal, semiconductor, and wide-bandgap semiconductor into a single compound, the TeSeO system displays tunable bandgaps ranging from 0.7 to 2.2 eV. Wafer-scale ultrathin TeSeO films, which can be deposited at room temperature, display high hole field-effect mobility of 48.5 cm2/(Vs) and robust hole transport properties, facilitated by Te-Te (Se) portions and O-Te-O portions, respectively. The nanosphere lithography process is employed to create nanopatterned honeycomb TeSeO broadband photodetectors, demonstrating a high responsibility of 603 A/W, an ultrafast response of 5 μs, and superior mechanical flexibility. The p-type TeSeO system is highly adaptable, scalable, and reliable, which can address emerging technological needs that current semiconductor solutions may not fulfill.
Deleting the mitochondrial respiration negative regulator MCJ enhances the efficacy of CD8+ T cell adoptive therapies in pre-clinical studies
Authors: Wu Meng-Han , Valenca-Pereira Felipe , Cendali Francesca , Giddings Emily L. , Pham-Danis Catherine , Yarnell Michael C. , Novak Amanda J. , Brunetti Tonya M. , Thompson Scott B. , Henao-Mejia Jorge , Flavell Richard A. , D’Alessandro Angelo , Kohler M. Eric , Rincon Mercedes
Published: May 2024

Mitochondrial respiration is essential for the survival and function of T cells used in adoptive cellular therapies. However, strategies that specifically enhance mitochondrial respiration to promote T cell function remain limited. Here, we investigate methylation-controlled J protein (MCJ), an endogenous negative regulator of mitochondrial complex I expressed in CD8 cells, as a target for improving the efficacy of adoptive T cell therapies. We demonstrate that MCJ inhibits mitochondrial respiration in murine CD8+ CAR-T cells and that deletion of MCJ increases their in vitro and in vivo efficacy against murine B cell leukaemia. Similarly, MCJ deletion in ovalbumin (OVA)-specific CD8+ T cells also increases their efficacy against established OVA-expressing melanoma tumors in vivo. Furthermore, we show for the first time that MCJ is expressed in human CD8 cells and that the level of MCJ expression correlates with the functional activity of CD8+ CAR-T cells. Silencing MCJ expression in human CD8 CAR-T cells increases their mitochondrial metabolism and enhances their anti-tumor activity. Thus, targeting MCJ may represent a potential therapeutic strategy to increase mitochondrial metabolism and improve the efficacy of adoptive T cell therapies.
Highly porous metal-organic framework liquids and glasses via a solvent-assisted linker exchange strategy of ZIF-8
Authors: Xue Wen-Long , Kolodzeiski Pascal , Aucharova Hanna , Vasa Suresh , Koutsianos Athanasios , Pallach Roman , Song Jianbo , Frentzel-Beyme Louis , Linser Rasmus , Henke Sebastian
Published: May 2024

By combining the porosity of crystalline metal-organic frameworks (MOFs) with the unique processability of the liquid state, melt-quenched MOF glasses offer exciting opportunities for molecular separation. However, progress in this field is limited by two factors. Firstly, only very few MOFs melt at elevated temperatures and transform into stable glasses upon cooling the corresponding MOF liquid. Secondly, the MOF glasses obtained thus far feature only very small porosities and very small pore sizes. Here, we demonstrate solvent-assisted linker exchange (SALE) as a versatile method to prepare highly porous melt-quenched MOF glasses from the canonical ZIF-8. Two additional organic linkers are incorporated into the non-meltable ZIF-8, yielding high-entropy, linker-exchanged ZIF-8 derivatives undergoing crystal-to-liquid-to-glass phase transitions by thermal treatment. The ZIF-8 glasses demonstrate specific pore volumes of about 0.2 cm3g–1, adsorb large amounts of technologically relevant C3 and C4 hydrocarbons, and feature high kinetic sorption selectivities for the separation of propylene from propane.
H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours
Authors: Dibitetto Diego , Liptay Martin , Vivalda Francesca , Dogan Hülya , Gogola Ewa , González Fernández Martín , Duarte Alexandra , Schmid Jonas A. , Decollogny Morgane , Francica Paola , Przetocka Sara , Durant Stephen T. , Forment Josep V. , Klebic Ismar , Siffert Myriam , de Bruijn Roebi , Kousholt Arne N. , Marti Nicole A. , Dettwiler Martina , Sørensen Claus S. , Tille Jean-Christophe , Undurraga Manuela , Labidi-Galy Intidhar , Lopes Massimo , Sartori Alessandro A. , Jonkers Jos , Rottenberg Sven
Published: May 2024

Histone H2AX plays a key role in DNA damage signalling in the surrounding regions of DNA double-strand breaks (DSBs). In response to DNA damage, H2AX becomes phosphorylated on serine residue 139 (known as γH2AX), resulting in the recruitment of the DNA repair effectors 53BP1 and BRCA1. Here, by studying resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient mammary tumours, we identify a function for γH2AX in orchestrating drug-induced replication fork degradation. Mechanistically, γH2AX-driven replication fork degradation is elicited by suppressing CtIP-mediated fork protection. As a result, H2AX loss restores replication fork stability and increases chemoresistance in BRCA1/2-deficient tumour cells without restoring homology-directed DNA repair, as highlighted by the lack of DNA damage-induced RAD51 foci. Furthermore, in the attempt to discover acquired genetic vulnerabilities, we find that ATM but not ATR inhibition overcomes PARP inhibitor (PARPi) resistance in H2AX-deficient tumours by interfering with CtIP-mediated fork protection. In summary, our results demonstrate a role for H2AX in replication fork biology in BRCA-deficient tumours and establish a function of H2AX separable from its classical role in DNA damage signalling and DSB repair.
Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae
Authors: Puginier Camille , Libourel Cyril , Otte Juergen , Skaloud Pavel , Haon Mireille , Grisel Sacha , Petersen Malte , Berrin Jean-Guy , Delaux Pierre-Marc , Dal Grande Francesco , Keller Jean
Published: May 2024

Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.
High-power electrically pumped terahertz topological laser based on a surface metallic Dirac-vortex cavity
Authors: Liu Junhong , Xu Yunfei , Li Rusong , Sun Yongqiang , Xin Kaiyao , Zhang Jinchuan , Lu Quanyong , Zhuo Ning , Liu Junqi , Wang Lijun , Cheng Fengmin , Liu Shuman , Liu Fengqi , Zhai Shenqiang
Published: May 2024

Topological lasers (TLs) have attracted widespread attention due to their mode robustness against perturbations or defects. Among them, electrically pumped TLs have gained extensive research interest due to their advantages of compact size and easy integration. Nevertheless, limited studies on electrically pumped TLs have been reported in the terahertz (THz) and telecom wavelength ranges with relatively low output powers, causing a wide gap between practical applications. Here, we introduce a surface metallic Dirac-vortex cavity (SMDC) design to solve the difficulty of increasing power for electrically pumped TLs in the THz spectral range. Due to the strong coupling between the SMDC and the active region, robust 2D topological defect lasing modes are obtained. More importantly, enough gain and large radiative efficiency provided by the SMDC bring in the increase of the output power to a maximum peak power of 150 mW which demonstrates the practical application potential of electrically pumped TLs.
Contractile injection systems facilitate sporogenic differentiation of Streptomyces davawensis through the action of a phage tapemeasure protein-related effector
Authors: Nagakubo Toshiki , Nishiyama Tatsuya , Yamamoto Tatsuya , Nomura Nobuhiko , Toyofuku Masanori
Published: May 2024

Contractile injection systems (CISs) are prokaryotic phage tail-like nanostructures loading effector proteins that mediate various biological processes. Although CIS functions have been diversified through evolution and hold the great potential as protein delivery systems, the functional characterisation of CISs and their effectors is currently limited to a few CIS lineages. Here, we show that the CISs of Streptomyces davawensis belong to a unique group of bacterial CISs distributed across distant phyla and facilitate sporogenic differentiation of this bacterium. CIS loss results in decreases in extracellular DNA release, biomass accumulation, and spore formation in S. davawensis. CISs load an effector, which is a remote homolog of phage tapemeasure proteins, and its C-terminal domain has endonuclease activity responsible for the CIS-associated phenotypes. Our findings illustrate that CISs can contribute to the reproduction of bacteria through the action of the effector and suggest an evolutionary link between CIS effectors and viral cargos.
Profiling complex repeat expansions in RFC1 in Parkinson’s disease
Authors: Alvarez Jerez Pilar , Daida Kensuke , Miano-Burkhardt Abigail , Iwaki Hirotaka , Malik Laksh , Cogan Guillaume , Makarious Mary B. , Sullivan Roisin , Vandrovcova Jana , Ding Jinhui , Gibbs J. Raphael , Markham Androo , Nalls Mike A. , Kesharwani Rupesh K. , Sedlazeck Fritz J. , Casey Bradford , Hardy John , Houlden Henry , Blauwendraat Cornelis , Singleton Andrew B. , Billingsley Kimberley J.
Published: May 2024

A biallelic (AAGGG) expansion in the poly(A) tail of an AluSx3 transposable element within the gene RFC1 is a frequent cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS), and more recently, has been reported as a rare cause of Parkinson’s disease (PD) in the Finnish population. Here, we investigate the prevalence of RFC1 (AAGGG) expansions in PD patients of non-Finnish European ancestry in 1609 individuals from the Parkinson’s Progression Markers Initiative study. We identified four PD patients carrying the biallelic RFC1 (AAGGG) expansion and did not identify any carriers in controls.
A negative feedback loop underlies the Warburg effect
Authors: Jaiswal Alok , Singh Raghvendra
Published: May 2024

Aerobic glycolysis, or the Warburg effect, is used by cancer cells for proliferation while producing lactate. Although lactate production has wide implications for cancer progression, it is not known how this effect increases cell proliferation and relates to oxidative phosphorylation. Here, we elucidate that a negative feedback loop (NFL) is responsible for the Warburg effect. Further, we show that aerobic glycolysis works as an amplifier of oxidative phosphorylation. On the other hand, quiescence is an important property of cancer stem cells. Based on the NFL, we show that both aerobic glycolysis and oxidative phosphorylation, playing a synergistic role, are required to achieve cell quiescence. Further, our results suggest that the cells in their hypoxic niche are highly proliferative yet close to attaining quiescence by increasing their NADH/NAD+ ratio through the severity of hypoxia. The findings of this study can help in a better understanding of the link among metabolism, cell cycle, carcinogenesis, and stemness.
BOLD: Blood-gas and Oximetry Linked Dataset
Authors: Matos João , Struja Tristan , Gallifant Jack , Nakayama Luis , Charpignon Marie-Laure , Liu Xiaoli , Economou-Zavlanos Nicoleta , S. Cardoso Jaime , Johnson Kimberly S. , Bhavsar Nrupen , Gichoya Judy , Celi Leo Anthony , Wong An-Kwok Ian
Published: May 2024

Pulse oximeters measure peripheral arterial oxygen saturation (SpO2) noninvasively, while the gold standard (SaO2) involves arterial blood gas measurement. There are known racial and ethnic disparities in their performance. BOLD is a dataset that aims to underscore the importance of addressing biases in pulse oximetry accuracy, which disproportionately affect darker-skinned patients. The dataset was created by harmonizing three Electronic Health Record databases (MIMIC-III, MIMIC-IV, eICU-CRD) comprising Intensive Care Unit stays of US patients. Paired SpO2 and SaO2 measurements were time-aligned and combined with various other sociodemographic and parameters to provide a detailed representation of each patient. BOLD includes 49,099 paired measurements, within a 5-minute window and with oxygen saturation levels between 70–100%. Minority racial and ethnic groups account for ~25% of the data – a proportion seldom achieved in previous studies. The codebase is publicly available. Given the prevalent use of pulse oximeters in the hospital and at home, we hope that BOLD will be leveraged to develop debiasing algorithms that can result in more equitable healthcare solutions.
Construction of high-quality genomes and gene catalogue for culturable microbes of sugarcane (Saccharum spp.)
Authors: Wu Liang , Lin Haidong , zhang Lijun , Kiet Ta Quang , Liu Peng , Song Jinkang , Duan Yong , Hu Chunyu , Yang Hao , Duan Weixing , Yang Xiping
Published: May 2024

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies.
Compliance with the 24-h Movement Guidelines for Portuguese children: differences between boys and girls
Authors: Martins João , Tapia-Serrano Miguel Ángel , Nogueira Telma , Sanchéz-Miguel Pedro Antonio
Published: May 2024

The 24-h Movement Guidelines for children recommend at least 60 min per day of moderate-to-vigorous intensity physical activity (PA), ≤ 2 h/day of screen time, and 9–11 h/day of sleep for children. Since little information is available on the 24-h Movement Guidelines in Portuguese children, this research attempts to know the proportion of Portuguese children meeting individual and combinations of these 24-h Movement Guidelines. Another aim of this study is to test sex differences in compliance with 24-h Movement Guidelines. A final sample of 1351 Portuguese children (51.4% girls, aged 7.65 ± 1.21) participated in this cross-sectional study. PA, screen time and sleep duration were parent-reported through a questionnaire. Only 3.7% of children met all three 24-h Movement Guidelines, whereas 11.9% met none. Although boys showed greater compliance with PA recommendations and girls with screen time recommendations, no significant sex differences were found in the compliance of all three 24-h Movement Guidelines. Given that 96.3% of Portuguese children did not meet 24-h Movement Guidelines, promoting these three movement behaviours in both boys and girls is crucial to encouraging positive consequences early.
Transcriptome profiling and characterization of peritoneal metastasis ovarian cancer xenografts in humanized mice
Authors: Kang Sung Wan , Lee Ji-young , Kang Ok-Ju , Kim Yong-Man , Choi Eun Kyung , Lee Shin-Wha
Published: May 2024

Although immunotherapy has not yet been as successful in ovarian cancer (OC), it remains a potential therapeutic strategy. Preclinical models of OC are necessary to evaluate the efficacy of immuno-oncology (IO) drugs targeting human immune components but have been underutilized. Developing mouse models with a humanized (Hu) immune system can help understand the human immune response to IO drugs which have demonstrated limited effectiveness in OC patients. We established OC xenograft Hu-mouse models by intraperitoneally injecting luciferase-expressing SKOV-3 Luc and OVCAR-3 Luc OC cells into CD34+ Hu-mice. Tumor growth was monitored through bioluminescence imaging (BLI). In the SKOV-3 Luc Hu-mouse model, we assessed the efficacy of PD-1 blockade with pembrolizumab. We observed the presence of human lymphocyte and myeloid cell subsets within the tumors, lymph nodes, blood, and spleens in these models. Notably, these tumors exhibited a high prevalence of tumor-infiltrating macrophages. Furthermore, we identified HDAC class I target genes, and genes associated with epithelial-mesenchymal transition (EMT) and fibroblasts in the tumors of Hu-mice treated with pembrolizumab. Our xenograft Hu-mouse model of OC provides a valuable tool for investigating the efficacy of IO drugs. The insights gained from this model offer useful information to explore potential mechanisms associated with unresponsive anti-PD-1 treatment in OC.
Classification of artificial intelligence tools for civil engineering under the notion of complex fuzzy rough Frank aggregation operators
Authors: Emam Walid , Ahmmad Jabbar , Mahmood Tahir , ur Rehman Ubaid , Yin Shi
Published: May 2024

In recent days researchers have tried to handle the maximum information and use those techniques and methods in which there is no chance of data loss or loss of information is minimum. The structure like fuzzy set and complex fussy set cannot discuss the upper and lower approximations. Moreover, we can observe that a fuzzy rough set cannot discuss the second dimension and in this case, there is a chance of data loss. To cover all these issues in previous ideas, the notion of a complex fuzzy rough set in Cartesian form is the demand of the day because this structure can discuss the second dimension as well as upper and lower approximations. For this purpose, in this manuscript, we have developed the theory of complex fuzzy relation and complex fuzzy rough set in Cartesian form. Moreover, we have initiated the fundamental laws for complex fuzzy rough numbers based on Frank t-norm and t-conorm. The fundamental tools that can convert the overall input into a single output are called aggregation operators (AOs). So based on the characteristics of AOs, we have defined the notion of complex fuzzy rough Frank average and complex fuzzy rough Frank geometric AOs. The utilization of the developed theory is necessary to show the importance and validity of the delivered approach. So based on developed notions, we have defined an algorithm for this purpose along with an illustrative example. We have utilized the introduced structure for the classification of AI tools for civil engineering. Moreover, the comparative analysis of the delivered approach shows the advancement of the introduced structure as compared to existing notions.
Clustering swap prediction for image-text pre-training
Authors: Fayou Sun , Ngo Hea Choon , Sek Yong Wee , Meng Zuqiang
Published: May 2024

It is essential to delve into the strategy of multimodal model pre-training, which is an obvious impact on downstream tasks. Currently, clustering learning has achieved noteworthy benefits in multiple methods. However, due to the availability of open image-text pairs, it is challenging for multimodal with clustering learning. In this paper, we propose an approach that utilizes clustering swap prediction strategy to learn image-text clustering embedding space by interaction prediction between image and text features. Unlike existing models with clustering learning, our method (Clus) allows for an open number of clusters for web-scale alt-text data. Furthermore, in order to train the image and text encoders efficiently, we introduce distillation learning approach and evaluate the performance of the image-encoder in downstream visual tasks. In addition, Clus is pre-trained end-to-end by using large-scale image-text pairs. Specifically, both text and image serve as ground truth for swap prediction, enabling effective representation learning. Concurrently, extensive experiments demonstrate that Clus achieves state-of-the-art performance on multiple downstream fine-tuning and zero-shot tasks (i.e., Image-Text Retrieval, VQA, NLVR2, Image Captioning, Object Detection, and Semantic Segmentation).
Inhibitory effects of algal polysaccharide extract from Cladophora spp. against herpes simplex virus infection
Authors: Srisai Pitchayuth , Suriyaprom Sureeporn , Panya Aussara , Pekkoh Jeeraporn , Tragoolpua Yingmanee
Published: May 2024

Herpes simplex virus (HSV) is a causative agent of fever blister, genital herpes, and neonatal herpes. Nowadays, edible algae are recognized as health food due to high nutrition content and their many active compounds that are beneficial to health. The purpose of this study is to investigate the inhibitory effects of algal polysaccharide extract from Cladophora spp. against herpes simplex virus type 1 and type 2 on Vero cells. In this study, the structure of polysaccharide extract is presented as S=O and C–O–S of the sulfate group, as identified by the FT-IR technique. The toxicity of algal polysaccharide extract on Vero cells was determined by MTT assay. The algal extract showed low toxicity on the cells, with 50% cytotoxic concentration (CC50) value greater than 5000 µg mL−1. The inhibition of HSV infection by the algal extract was then evaluated on Vero cells using plaque reduction assay. The 50% effective concentration (EC50) values of algal extract exhibited antiviral activity against HSV-1 upon treatment before, during, and after viral adsorption with and without removal of the extract were 70.31, 15.17, > 5000 and 9.78 µg mL−1, respectively. Additionally, the EC50 values of algal extract against HSV-2 upon treatment before, during and after viral adsorption with, and without removal of the extract were 5.85, 2.57, > 5000 and 26.96 µg mL−1, respectively. Moreover, the algal extract demonstrated direct inactivation of HSV-1 and HSV-2 virions as well as inhibitory effect against HSV replication. Accordingly, algal polysaccharide extract containing sulfated polysaccharides showed strong activity against HSV. Therefore, it is proved to be useful to apply Cladophora spp. polysaccharide extract as an anti-HSV agent.
No strong support for a Dunning–Kruger effect in creativity: analyses of self-assessment in absolute and relative terms
Authors: Lebuda Izabela , Hofer Gabriela , Rominger Christian , Benedek Mathias
Published: May 2024

Competencies related to the evaluation of own cognitive processes, called metacognitive monitoring, are crucial as they help decide whether to persist in or desist from cognitive efforts. One of the most well-known phenomena in this context—the Dunning–Kruger effect—is that less skilled people tend to overestimate their performance. This effect has been reported for various kinds of performance including creativity. More recently, however, it has been suggested that this phenomenon could be a statistical artifact caused by the better-than-average effect and by regression toward the mean. Therefore, we examined the Dunning–Kruger effect in the context of creative thinking performance (i.e., divergent thinking ability) across two studies (Study 1: N = 425; Study 2: N = 317) and applied the classical quartile-based analysis as well as newly recommended, advanced statistical approaches: the Glejser test of heteroscedasticity and nonlinear quadratic regression. We found that the results indeed depended on the employed statistical method: While classical analyses supported the Dunning–Kruger effect across all conditions, it was not consistently supported by the more advanced statistical methods. These findings are in line with recent work challenging certain assumptions of the Dunning–Kruger effect and we discuss factors that undermine accurate self-assessments, especially in the context of creative performance.
Improving the antinutritional profiles of common beans (Phaseolus vulgaris L.) moderately impacts carotenoid bioaccessibility but not mineral solubility
Authors: Alvarado-Ramos Katherine , Bravo-Nunez Ángela , Halimi Charlotte , Maillot Matthieu , Icard-Vernière Christèle , Forti Chiara , Preite Chiara , Ferrari Luisa , Sala Tea , Losa Alessia , Cominelli Eleonora , Sparvoli Francesca , Camilli Emanuela , Lisciani Silvia , Marconi Stefania , Georgé Stephane , Mouquet-Rivier Claire , Kunert Karl , Reboul Emmanuelle
Published: May 2024

Common beans are a common staple food with valuable nutritional qualities, but their high contents in antinutritional factors (ANFs) can decrease the bioavailability of (i) fat-soluble micronutrients including carotenoids and (ii) minerals. Our objective was to select ANF-poor bean lines that would not interfere with carotenoid and mineral bioavailability. To achieve this objective, seeds of commercial and experimental Phaseolus vulgaris L. bean lines were produced for 2 years and the bean’s content in ANFs (saponins, phytates, tannins, total polyphenols) was assessed. We then measured carotenoid bioaccessibility and mineral solubility (i.e. the fraction of carotenoid and mineral that transfer into the aqueous phase of the digesta and is therefore absorbable) from prepared beans using in vitro digestion. All beans contained at least 200 mg/100 g of saponins and 2.44 mg/100 g tannins. The low phytic acid (lpa) lines, lpa1 and lpa12 exhibited lower phytate levels (≈ − 80%, p = 0.007 and p = 0.02) than their control BAT-93. However, this decrease had no significant impact on mineral solubility. HP5/1 (lpa + phaseolin and lectin PHA-E free) bean line, induced an improvement in carotenoid bioaccessibility (i.e., + 38%, p = 0.02, and + 32%, p = 0.005, for phytofluene bioaccessibility in 2021 and 2022, respectively). We conclude that decrease in the phytate bean content should thus likely be associated to decreases in other ANFs such as tannins or polyphenols to lead to significant improvement of micronutrient bioaccessibility.
Unraveling the role of natriuretic peptide clearance receptor (NPR3) in glomerular diseases
Authors: Dabaghie Dina , Charrin Emmanuelle , Tonelius Pernilla , Rosengren Birgitta , Korkut Gizem , Granqvist Anna B. , Lal Mark , Patrakka Jaakko
Published: May 2024

Natriuretic peptides (NPs) are cardio-derived hormones that have a crucial role in maintaining cardiovascular homeostasis. Physiological effects of NPs are mediated by binding to natriuretic peptide receptors 1 and 2 (NPR1/2), whereas natriuretic peptide receptor 3 (NPR3) acts as a clearance receptor that removes NPs from the circulation. Mouse studies have shown that local NP-signaling in the kidney glomerulus is important for the maintenance of renal homeostasis. In this study we examined the expression of NPR3 in kidney tissue and explored its involvement in renal physiology and disease by generating podocyte-specific knockout mice (NPR3podKO) as well as by using an NPR3 inhibitor (NPR3i) in rodent models of kidney disease. NPR3 was highly expressed by podocytes. NPR3podKO animals showed no renal abnormalities under healthy conditions and responded similarly to nephrotoxic serum (NTS) induced glomerular injury. However, NPR3i showed reno-protective effects in the NTS-induced model evidenced by decreased glomerulosclerosis and reduced podocyte loss. In a ZSF1 rat model of diabetic kidney injury, therapy alone with NPR3i did not have beneficial effects on renal function/histology, but when combined with losartan (angiotensin receptor blocker), NPR3i potentiated its ameliorative effects on albuminuria. In conclusion, these results suggest that NPR3 may contribute to kidney disease progression.
The speed of news in Twitter (X) versus radio
Authors: Brannon William , Roy Deb
Published: May 2024

The rapid evolution of the Internet is reshaping the media landscape, with frequent claims of an accelerated and increasingly outraged news cycle. We test these claims empirically, investigating the dynamics of news spread, decay, and sentiment on Twitter (now known as X) compared to talk radio. Analyzing 2019–2021 data including 517,000 hour of radio content and 26.6 million tweets by elite journalists, politicians, and general users, we identified 1694 news events. We find that news on Twitter circulates faster, fades faster, and is more negative and outraged compared to radio, with Twitter outrage also more short-lived. These patterns are consistent across various user types and robustness checks. Our results illustrate an important way social media may influence traditional media: framing and agenda-setting simply by speaking first. As journalism evolves with these media, news audiences may encounter faster shifts in focus, less attention to each news event, and much more negativity and outrage.
Learning the mechanisms of network growth
Authors: Touwen Lourens , Bucur Doina , van der Hofstad Remco , Garavaglia Alessandro , Litvak Nelly
Published: May 2024

We propose a novel model-selection method for dynamic networks. Our approach involves training a classifier on a large body of synthetic network data. The data is generated by simulating nine state-of-the-art random graph models for dynamic networks, with parameter range chosen to ensure exponential growth of the network size in time. We design a conceptually novel type of dynamic features that count new links received by a group of vertices in a particular time interval. The proposed features are easy to compute, analytically tractable, and interpretable. Our approach achieves a near-perfect classification of synthetic networks, exceeding the state-of-the-art by a large margin. Applying our classification method to real-world citation networks gives credibility to the claims in the literature that models with preferential attachment, fitness and aging fit real-world citation networks best, although sometimes, the predicted model does not involve vertex fitness.
Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space
Authors: Nastasi Nicholas , Haines Sarah R. , Bope Ashleigh , Meyer Marit E. , Horack John M. , Dannemiller Karen C.
Published: May 2024

Human occupied built environments are no longer confined to Earth. In fact, there have been humans living and working in low-Earth orbit on the International Space Station (ISS) since November 2000. With NASA’s Artemis missions and the age of commercial space stations set to begin, more human-occupied spacecraft than ever will be in Earth’s orbit and beyond. On Earth and in the ISS, microbes, especially fungi, can be found in dust and grow when unexpected, elevated moisture conditions occur. However, we do not yet know how indoor microbiomes in Earth-based homes and in the ISS differ due to their unique set of environmental conditions. Here we show that bacterial and fungal communities are different in dust collected from vacuum bags on Earth and the ISS, with Earth-based homes being more diverse (465 fungal OTUs and 237 bacterial ASVs) compared to the ISS (102 fungal OTUs and 102 bacterial ASVs). When dust from these locations were exposed to varying equilibrium relative humidity conditions (ERH), there were also significant fungal community composition changes as ERH and time elevated increased (Bray Curtis: R2 = 0.35, P = 0.001). These findings can inform future spacecraft design to promote healthy indoor microbiomes that support crew health, spacecraft integrity, and planetary protection.
Label-free electrochemical biosensor based on green-synthesized reduced graphene oxide/Fe3O4/nafion/polyaniline for ultrasensitive detection of SKBR3 cell line of HER2 breast cancer biomarker
Authors: Hosseine Mojtaba , Naghib Seyed Morteza , Khodadadi Abbasali
Published: May 2024

Cancer stands as one of the most impactful illnesses in the modern world, primarily owing to its lethal consequences. The fundamental concern in this context likely stems from delayed diagnoses in patients. Hence, detecting various forms of cancer is imperative. A formidable challenge in cancer research has been the diagnosis and treatment of this disease. Early cancer diagnosis is crucial, as it significantly influences subsequent therapeutic steps. Despite substantial scientific efforts, accurately and swiftly diagnosing cancer remains a formidable challenge. It is well known that the field of cancer diagnosis has effectively included electrochemical approaches. Combining the remarkable selectivity of biosensing components—such as aptamers, antibodies, or nucleic acids—with electrochemical sensor systems has shown positive outcomes. In this study, we adapt a novel electrochemical biosensor for cancer detection. This biosensor, based on a glassy carbon electrode, incorporates a nanocomposite of reduced graphene oxide/Fe3O4/Nafion/polyaniline. We elucidated the modification process using SEM, TEM, FTIR, RAMAN, VSM, and electrochemical methods. To optimize the experimental conditions and monitor the immobilization processes, electrochemical techniques such as CV, EIS, and SWV were employed. The calibration graph has a linear range of 102–106 cells mL−1, with a detection limit of 5 cells mL−1.
Maximum information measurement for qubit states
Authors: Varga Árpád , Adam Peter , Bergou János A.
Published: May 2024

We determine the optimal measurement that maximizes the average information gain about the state of a qubit system. The qubit is prepared in one of two known states with known prior probabilities. To treat the problem analytically we employ the formalism developed for the maximum confidence quantum state discrimination strategy and obtain the POVM which optimizes the information gain for the entire parameter space of the system. We show that the optimal measurement coincides exactly with the minimum-error quantum measurement only for two pure states, or when the two states have the same Bloch radius or they are on the same diagonal of the Bloch disk.
A novel transcranial MR Guided focused ultrasound method based on the ultrashort echo time skull acoustic model and phase retrieval techniques
Authors: Kong Dechen , Liu Gaojie , Cheng Bochao , Qi Xu , Zhu Jiayu , He Qiang , Xing Haoyang , Gong Qiyong
Published: May 2024

Transcranial ultrasound stimulation (TUS) has been clinically applied as a neuromodulation tool. Particularly, the phase array ultrasound can be applied in TUS to non-invasively focus on the cortex or deep brain. However, the vital phase distortion of the ultrasound induced by the skull limits its clinical application. In the current study, we aimed to develop a hybrid method that combines the ultrashort echo time (UTE) magnetic resonance imaging (MRI) sequences with the prDeep technique to achieve focusing ventral intermediate thalamic nucleus (VIM). The time-reversal (TR) approach of the UTE numerical acoustic model of the skull combined with the prDeep algorithm was used to reduce the number of iterations. The skull acoustic model simulation therapy process was establish to valid this method’s prediction and focus performance, and the classical TR method were considered as the gold standard (GS). Our approach could restore 75% of the GS intensity in 25 iteration steps, with a superior the noise immunity. Our findings demonstrate that the phase aberration caused by the skull can be estimated using phase retrieval techniques to achieve a fast and accurate transcranial focus. The method has excellent adaptability and anti-noise capacity for satisfying complex and changeable scenarios.
The E3 ubiquitin-protein ligase UHRF1 promotes adipogenesis and limits fibrosis by suppressing GPNMB-mediated TGF-β signaling
Authors: Vakayil Muneera , Madani Aisha Y. , Agha Maha V. , Majeed Yasser , Hayat Shahina , Yonuskunju Shameem , Mohamoud Yasmin Ali , Malek Joel , Suhre Karsten , Mazloum Nayef A.
Published: May 2024

The E3 ubiquitin-ligase UHRF1 is an epigenetic regulator coordinating DNA methylation and histone modifications. However, little is known about how it regulates adipogenesis or metabolism. In this study, we discovered that UHRF1 is a key regulatory factor for adipogenesis, and we identified the altered molecular pathways that UHRF1 targets. Using CRISPR/Cas9-based knockout strategies, we discovered the whole transcriptomic changes upon UHRF1 deletion. Bioinformatics analyses revealed that key adipogenesis regulators such PPAR-γ and C/EBP-α were suppressed, whereas TGF-β signaling and fibrosis markers were upregulated in UHRF1-depleted differentiating adipocytes. Furthermore, UHRF1-depleted cells showed upregulated expression and secretion of TGF-β1, as well as the glycoprotein GPNMB. Treating differentiating preadipocytes with recombinant GPNMB led to an increase in TGF-β protein and secretion levels, which was accompanied by an increase in secretion of fibrosis markers such as MMP13 and a reduction in adipogenic conversion potential. Conversely, UHRF1 overexpression studies in human cells demonstrated downregulated levels of GPNMB and TGF-β, and enhanced adipogenic potential. In conclusion, our data show that UHRF1 positively regulates 3T3-L1 adipogenesis and limits fibrosis by suppressing GPNMB and TGF-β signaling cascade, highlighting the potential relevance of UHRF1 and its targets to the clinical management of obesity and linked metabolic disorders.
Autolyzed yeast and sodium butyrate supplemented alone to diets promoted improvements in performance, intestinal health and nutrient transporter in weaned piglets
Authors: Correia Amanda Medeiros , Genova Jansller Luiz , Kim Sung Woo , Abranches Fernanda Fialho , Rocha Gabriel Cipriano
Published: May 2024

This study investigated the effects of supplemental nucleotides, autolyzed yeast (Saccharomyces cerevisiae), and sodium butyrate in diets for nursery pigs on growth performance, diarrhea incidence, blood profile, intestinal morphology, mRNA expression of nutrient transporters, inflammatory markers, antioxidant profile, and tight junction proteins in the small intestine. One hundred eighty 21-day-old pigs (5.17 ± 0.57 kg) were assigned in a randomized block design to 1 of 4 dietary treatments: (1) CON: control, basal diet, (2) NUC: CON + nucleotides, (3) YSC: CON + lysed yeast S. cerevisiae, (4) ASB: CON + acidifier sodium butyrate. Pigs were fed for 24 days, phase 1 (21–32 days) and 2 (32–45 days). During phase 1, YSC and ASB improved average daily gain (ADG) and feed conversion (FC) compared with CON. At the overall period, ASB improved ADG and YSC improved FC compared with CON. The NUC diet did not affect growth performance. The ASB increased ileal villus height compared to CON. The YSC and ASB reduced the number of Peyer’s patches in the ileum compared with CON. The YSC increased mRNA expression of nutrient transporters (SMCT2, MCT1, and PepT1), tight junction proteins (OCL and ZO-1), antioxidants (GPX), and IL1-β in the jejunum compared with CON. The ASB increased mRNA expression of nutrient transporters (SGLT1 and MCT1), tight junction proteins (OCL and ZO-1), and antioxidants (GPX and SOD) compared with CON. In conclusion, autolyzed yeast and sodium butyrate promoted growth performance by improving the integrity of the intestinal barrier, the mRNA expression of nutrient transporters, and antioxidant enzymes in the jejunum of nursery pigs whereas supplementation of nucleotides did not show such effects.
Salvianolic acid A alleviates H2O2-induced endothelial oxidative injury via miR-204-5p
Authors: Qiao Xilin , Cao Shuyu , Chen Shuaiyu , Guo Yan , Chen Nipi , Zheng Ying , Jin Bo
Published: May 2024

Oxidative stress induced endothelial dysfunction plays a particularly important role in promoting the development of cardiovascular diseases (CVDs). Salvianolic acid A (SalA) is a water-soluble component of traditional Chinese medicine Salvia miltiorrhiza Bunge with anti-oxidant potency. This study aims to explore the regulatory effect of SalA on oxidative injury using an in vitro model of H2O2-induced injury in human umbilical vein endothelial cells (HUVECs). In the study, we determined cell viability, the activities of Lactate dehydrogenase (LDH) and Superoxide dismutase (SOD), cell proliferation rate and intracellular reactive oxygen species (ROS). Flow cytometry was used to detect cell apoptosis. Western-blotting was used to evaluate the expression of cell senescence, apoptosis, autophagy and pyroptosis protein factors. The expression level of miRNA was determined by qRT-PCR. Compared with H2O2-induced HUVECs, SalA promoted cell viability and cell proliferation rate; decreased LDH and ROS levels; and increased SOD activity. SalA also significantly attenuated endothelial senescence, inhibited cell apoptosis, reversed the increase of LC3 II/I ratio and NLRP3 accumulation. Furthermore, miR-204-5p was regulated by SalA. Importantly, miR-204-5p inhibitor had similar effect to that of SalA on H2O2-induced HUVECs. Our results indicated that SalA could alleviate H2O2-induced oxidative injury by downregulating miR-204-5p in HUVECs.