bluuebunny/crossref_metadata_2025 huggingface dataset:
The PP2A regulator IER5L supports prostate cancer progression
Authors: Crespo Jana R. , Martín-Martín Natalia , Garcia-Longarte Saioa , Corres-Mendizabal Jon , Carlevaris Onintza , Astobiza Ianire , Zabala-Letona Amaia , Guiu Marc , Azkargorta Mikel , Gonzalez-Lopez Monika , Macías-Cámara Nuria , Doan Phuong , Elortza Félix , Mendizabal Isabel , Westermack Jukka , Gomis Roger R. , Ercilla Amaia , Carracedo Arkaitz
Published: July 2024

Prostate cancer exhibits high prevalence and accounts for a high number of cancer-related deaths. The discovery and characterization of molecular determinants of aggressive prostate cancer represents an active area of research. The Immediate Early Response (IER) family of genes, which regulate Protein Phosphatase 2A (PP2A) activity, has emerged among the factors that influence cancer biology. Here, we show that the less studied member of this family, Immediate Early Response 5 like (IER5L), is upregulated in aggressive prostate cancer. Interestingly, the upregulation of IER5L expression exhibits a robust association with metastatic disease in prostate and is recapitulated in other cancer types. In line with this observation, IER5L silencing reduces foci formation, migration and invasion ability in a variety of human and murine prostate cancer cell lines. In vivo, using zebrafish and immunocompromised mouse models, we demonstrate that IER5L-silencing reduces prostate cancer tumor growth, dissemination, and metastasis. Mechanistically, we characterize the transcriptomic and proteomic landscapes of IER5L-silenced cells. This approach allowed us to identify DNA replication and monomeric G protein regulators as downstream programs of IER5L through a pathway that is consistent with the regulation of PP2A. In sum, we report the alteration of IER5L in prostate cancer and beyond and provide biological and molecular evidence of its contribution to tumor aggressiveness.
Experimental evidence of climate change extinction risk in Neotropical montane epiphytes
Authors: Hollenbeck Emily C. , Sax Dov F.
Published: July 2024

Climate change is conjectured to endanger tropical species, particularly in biodiverse montane regions, but accurate estimates of extinction risk are limited by a lack of empirical data demonstrating tropical species’ sensitivity to climate. To fill this gap, studies could match high-quality distribution data with multi-year transplant experiments. Here, we conduct field surveys of epiphyte distributions on three mountains in Central America and perform reciprocal transplant experiments on one mountain across sites that varied in elevation, temperature and aridity. We find that most species are unable to survive outside of their narrow elevational distributions. Additionally, our findings suggest starkly different outcomes from temperature conditions expected by 2100 under different climate change scenarios. Under temperatures associated with low-emission scenarios, most tropical montane epiphyte species will survive, but under emission scenarios that are moderately high, 5-36% of our study species may go extinct and 10-55% of populations may be lost. Using a test of tropical species’ climate tolerances from a large field experiment, paired with detailed species distribution data across multiple mountains, our work strengthens earlier conjecture about risks of wide-spread extinctions from climate change in tropical montane ecosystems.
An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins
Authors: Yagi Sota , Tagami Shunsuke
Published: July 2024

Abstract

Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.
Large-scale photonic network with squeezed vacuum states for molecular vibronic spectroscopy
Authors: Zhu Hui Hui , Sen Chen Hao , Chen Tian , Li Yuan , Luo Shao Bo , Karim Muhammad Faeyz , Luo Xian Shu , Gao Feng , Li Qiang , Cai Hong , Chin Lip Ket , Kwek Leong Chuan , Nordén Bengt , Zhang Xiang Dong , Liu Ai Qun
Published: July 2024

Although molecular vibronic spectra generation is pivotal for chemical analysis, tackling such exponentially complex tasks on classical computers remains inefficient. Quantum simulation, though theoretically promising, faces technological challenges in experimentally extracting vibronic spectra for molecules with multiple modes. Here, we propose a nontrivial algorithm to generate the vibronic spectra using states with zero displacements (squeezed vacuum states) coupled to a linear optical network, offering ease of experimental implementation. We also fabricate an integrated quantum photonic microprocessor chip as a versatile simulation platform containing 16 modes of single-mode squeezed vacuum states and a fully programmable interferometer network. Molecular vibronic spectra of formic acid and thymine under the Condon approximation are simulated using the quantum microprocessor chip with high reconstructed fidelity ( > 92%). Furthermore, vibronic spectra of naphthalene, phenanthrene, and benzene under the non-Condon approximation are also experimentally simulated. Such demonstrations could pave the way for solving complicated quantum chemistry problems involving vibronic spectra and computational tasks beyond the reach of classical computers.
An intranasal nanoparticle STING agonist protects against respiratory viruses in animal models
Authors: Leekha Ankita , Saeedi Arash , Kumar Monish , Sefat K. M. Samiur Rahman , Martinez-Paniagua Melisa , Meng Hui , Fathi Mohsen , Kulkarni Rohan , Reichel Kate , Biswas Sujit , Tsitoura Daphne , Liu Xinli , Cooper Laurence J. N. , Sands Courtney M. , Das Vallabh E. , Sebastian Manu , Hurst Brett L. , Varadarajan Navin
Published: July 2024

Respiratory viral infections cause morbidity and mortality worldwide. Despite the success of vaccines, vaccination efficacy is weakened by the rapid emergence of viral variants with immunoevasive properties. The development of an off-the-shelf, effective, and safe therapy against respiratory viral infections is thus desirable. Here, we develop NanoSTING, a nanoparticle formulation of the endogenous STING agonist, 2′−3′ cGAMP, to function as an immune activator and demonstrate its safety in mice and rats. A single intranasal dose of NanoSTING protects against pathogenic strains of SARS-CoV-2 (alpha and delta VOC) in hamsters. In transmission experiments, NanoSTING reduces the transmission of SARS-CoV-2 Omicron VOC to naïve hamsters. NanoSTING also protects against oseltamivir-sensitive and oseltamivir-resistant strains of influenza in mice. Mechanistically, NanoSTING upregulates locoregional interferon-dependent and interferon-independent pathways in mice, hamsters, as well as non-human primates. Our results thus implicate NanoSTING as a broad-spectrum immune activator for controlling respiratory virus infection.
Regioselective hydroamination of unactivated olefins with diazirines as a diversifiable nitrogen source
Authors: Xing Qingyu , Chandrachud Preeti P. , Tillett Khalilia , Lopchuk Justin M.
Published: July 2024

Nitrogen-containing compounds, such as amines, hydrazines, and heterocycles, play an indispensable role in medicine, agriculture, and materials. Alkylated derivatives of these compounds, especially in sterically congested environments, remain a challenge to prepare. Here we report a versatile method for the regioselective hydroamination of readily available unactivated olefins with diazirines. Over fifty examples are reported, including the protecting group-free amination of fourteen different natural products. A broad functional group tolerance includes alcohols, ketones, aldehydes, and epoxides. The proximate products of these reactions are diaziridines, which, under mild conditions, are converted to primary amines, hydrazines, and heterocycles. Five target- and diversity-oriented syntheses of pharmaceutical compounds are shown, along with the preparation of a bis-15N diazirine validated in the late-stage isotopic labeling of an RNA splicing modulator candidate. In this work, we report using diazirine (1) as an electrophilic nitrogen source in a regioselective hydroamination reaction, and the diversification of the resulting diaziridines.
Wide-energy programmable microwave plasma-ionization for high-coverage mass spectrometry analysis
Authors: Chu Fengjian , Zhao Gaosheng , Wei Wei , Shuaibu Nazifi Sani , Feng Hongru , Pan Yuanjiang , Wang Xiaozhi
Published: July 2024

Although numerous ambient ionization mass spectroscopy technologies have been developed over the past 20 years to address diverse analytical circumstances, a single-ion source technique that can handle all analyte types is still lacking. Here, a wide-energy programmable microwave plasma-ionization mass spectrometry (WPMPI-MS) system is presented, through which MS analysis can achieve high coverage of substances with various characteristics by digitally regulating the microwave energy. In addition, ionization energy can be rapidly scanned using programmable waveforms, enabling the simultaneous detection of biomolecules, heavy metals, non-polar molecules, etc., in seconds. WPMPI-MS performs well in analyzing real samples, rapidly analyzing nine toxicological standards in one drop of serum, and demonstrating good quantification and liquid chromatography coupling capability. The WPMPI-MS has also been used to detect soil extracts, solid pharmaceuticals, and landfill leachate, further demonstrating its robust analytical capabilities for real samples. The prospective uses of the technology in biological and chemical analysis are extensive, and it is anticipated to emerge as a viable alternative to commercially available ion sources.
Upland Yedoma taliks are an unpredicted source of atmospheric methane
Authors: Walter Anthony K. M. , Anthony P. , Hasson N. , Edgar C. , Sivan O. , Eliani-Russak E. , Bergman O. , Minsley B. J. , James S. R. , Pastick N. J. , Kholodov A. , Zimov S. , Euskirchen E. , Bret-Harte M. S. , Grosse G. , Langer M. , Nitzbon J.
Published: July 2024

Landscape drying associated with permafrost thaw is expected to enhance microbial methane oxidation in arctic soils. Here we show that ice-rich, Yedoma permafrost deposits, comprising a disproportionately large fraction of pan-arctic soil carbon, present an alternate trajectory. Field and laboratory observations indicate that talik (perennially thawed soils in permafrost) development in unsaturated Yedoma uplands leads to unexpectedly large methane emissions (35–78 mg m−2 d−1 summer, 150–180 mg m−2 d−1 winter). Upland Yedoma talik emissions were nearly three times higher annually than northern-wetland emissions on an areal basis. Approximately 70% emissions occurred in winter, when surface-soil freezing abated methanotrophy, enhancing methane escape from the talik. Remote sensing and numerical modeling indicate the potential for widespread upland talik formation across the pan-arctic Yedoma domain during the 21st and 22nd centuries. Contrary to current climate model predictions, these findings imply a positive and much larger permafrost-methane-climate feedback for upland Yedoma.
Total syntheses of (–)-macrocalyxoformins A and B and (–)-ludongnin C
Authors: Cao Zichen , Sun Wenxuan , Zhang Jingfu , Zhuo Junming , Yang Shaoqiang , Song Xiaocui , Ma Yan , Lu Panrui , Han Ting , Li Chao
Published: July 2024

The complex and diverse molecular architectures along with broad biological activities of ent-kauranoids natural products make them an excellent testing ground for the invention of synthetic methods and strategies. Recent efforts notwithstanding, synthetic access to the highly oxidized enmein-type ent-kauranoids still presents considerable challenges to synthetic chemists. Here, we report the enantioselective total syntheses of C-19 oxygenated enmein-type ent-kauranoids, including (–)-macrocalyxoformins A and B and (–)-ludongnin C, along with discussion and study of synthetic strategies. The enabling feature in our synthesis is a devised Ni-catalyzed decarboxylative cyclization/radical-polar crossover/C-acylation cascade that forges a THF ring concomitantly with the β-keto ester group. Mechanistic studies reveal that the C-acylation process in this cascade reaction is achieved through a carboxylation followed by an in situ esterification. Biological evaluation of these synthetic natural products reveals the indispensable role of the ketone on the D ring in their anti-tumor efficacy.
Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen
Authors: Sanderlin Allen G. , Kurka Margolis Hannah , Meyer Abigail F. , Lamason Rebecca L.
Published: July 2024

Pathogenic bacteria secrete protein effectors to hijack host machinery and remodel their infectious niche. Rickettsia spp. are obligate intracellular bacteria that can cause life-threatening disease, but their absolute dependence on the host cell has impeded discovery of rickettsial effectors and their host targets. We implemented bioorthogonal non-canonical amino acid tagging (BONCAT) during R. parkeri infection to selectively label, isolate, and identify effectors delivered into the host cell. As the first use of BONCAT in an obligate intracellular bacterium, our screen more than doubles the number of experimentally validated effectors for the genus. The seven novel secreted rickettsial factors (Srfs) we identified include Rickettsia-specific proteins of unknown function that localize to the host cytoplasm, mitochondria, and ER. We further show that one such effector, SrfD, interacts with the host Sec61 translocon. Altogether, our work uncovers a diverse set of previously uncharacterized rickettsial effectors and lays the foundation for a deeper exploration of the host-pathogen interface.
Rejuvenation of leukocyte trafficking in aged mice through PEPITEM intervention
Authors: Hopkin Sophie J. , Nathan Poppy , Pezhman Laleh , Begum Jenefa , Manning Julia E. , Quinn Lauren M. , Rainger G. Ed , McGettrick Helen M. , Iqbal Asif J. , Chimen Myriam
Published: July 2024

Inflammageing leads to uncontrolled leukocyte trafficking in response to inflammatory insults. Here, we used a zymosan-induced peritonitis mouse model on inflammation to investigate the role of the PEPITEM pathway on leukocyte migration in ageing. We then analysed whether PEPITEM could modulate leukocyte migration in older adults. We observed a loss of functionality in the PEPITEM pathway, which normally controls leukocyte trafficking in response to inflammation, in older adults and aged mice and show that this can be rescued by supplementation with PEPITEM. Thus, leading to the exciting possibility that PEPITEM supplementation may represent a potential pre-habilitation geroprotective agent to rejuvenate immune functions.
Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects
Authors: Rosier Bob T. , Mira Alex
Published: July 2024

In our opinion, the ‘hang-time’ of nitrate-containing products discussed in the letter by Green and Green is an interesting variable that should be considered when nitrate-based treatment or prevention strategies are designed. However, due to direct nitrate recycling after nitrate intake, products with a long ‘hang-time’ (e.g., chewing gum) may not always have an advantage compared to products with a short ‘hang-time’ (e.g., vegetable juices). We argue that extending the ‘hang-time’ is especially relevant and potentially beneficial for different applications, such as using a low nitrate dose to stimulate the oral effects, reaching oral tissues that may otherwise not be exposed to dietary nitrate (e.g., periodontal pockets), and providing a longer nitrate exposure in individuals with an impaired salivary flow. Apart from the ‘hang-time’, other important variables are the nitrate dose and source (e.g., different salts and vegetable extracts), as well as the desired effect (e.g., an oral effect versus systemic effects). Finally, we believe that the alterations in salivary microbiota observed before and after chewing three nitrate-rich gums over a period of ~5 h, as reported by Green and Green, could be considered beneficial. However, the oral microbiota composition is affected by the circadian rhythm and the effect of gum mastication should be evaluated. These results should thus be confirmed by a placebo-controlled study, where these confounding factors can be accounted for.
Targeted materials discovery using Bayesian algorithm execution
Authors: Chitturi Sathya R. , Ramdas Akash , Wu Yue , Rohr Brian , Ermon Stefano , Dionne Jennifer , Jornada Felipe H. da , Dunne Mike , Tassone Christopher , Neiswanger Willie , Ratner Daniel
Published: July 2024

Rapid discovery and synthesis of future materials requires intelligent data acquisition strategies to navigate large design spaces. A popular strategy is Bayesian optimization, which aims to find candidates that maximize material properties; however, materials design often requires finding specific subsets of the design space which meet more complex or specialized goals. We present a framework that captures experimental goals through straightforward user-defined filtering algorithms. These algorithms are automatically translated into one of three intelligent, parameter-free, sequential data collection strategies (SwitchBAX, InfoBAX, and MeanBAX), bypassing the time-consuming and difficult process of task-specific acquisition function design. Our framework is tailored for typical discrete search spaces involving multiple measured physical properties and short time-horizon decision making. We demonstrate this approach on datasets for TiO2 nanoparticle synthesis and magnetic materials characterization, and show that our methods are significantly more efficient than state-of-the-art approaches. Overall, our framework provides a practical solution for navigating the complexities of materials design, and helps lay groundwork for the accelerated development of advanced materials.
Mineralogical and geochemical composition of a cementitious grout and its evolution during interaction with water
Authors: Grangeon Sylvain , Debure Mathieu , Montouillout Valerie , Elkaim Erik , Lerouge Catherine , Maubec Nicolas , Michau Nicolas , Bourbon Xavier , Martin Christelle , Cochepin Benoit , Marty Nicolas
Published: July 2024

In the present study, the chemical composition, mineralogy, and mechanisms of alteration of a cementitious grout based on a CEM III/C with addition of smectite, hydrotalcite, and silica fume, are studied using a combination of chemical and physical methods. This material was designed in the context of geological repository of radioactive wastes, with a twofold aim: first, to fill the technical voids left by drilling operations at the interface between the geological formation and the disposal galleries. Second, to neutralize a potential acidic transient due to pyrite oxidation, and to create an environment that favors low corrosion rates of carbon steels. The grout is mainly composed of calcium silicate hydrates having a Ca/Si ratio of ~0.8, incorporating Al in the bridging site of the Si chains (C-A-S-H), and accounting for 29–36 wt.% of the sample. It also contains silica fume (38–48 wt.%), smectite with interlayer Na (11–17 wt.%), hydrotalcite with interlayer CO32− (3–4 wt.%), and lower amounts of portlandite, calcite, and possibly gibbsite and gypsum. Upon alteration by water in a flow-through reactor, the main modifications affecting the sample are calcite and gypsum dissolution, hence releasing aqueous Ca2+ that is adsorbed in smectite interlayer by replacing Na+, and stoichiometric C-A-S-H dissolution. The evolution of solution chemistry and of the solid phase composition are reproduced successfully using a thermokinetic model.
Parental education and children’s depression, anxiety, and ADHD traits, a within-family study in MoBa
Authors: Hughes Amanda M. , Torvik Fartein Ask , van Bergen Elsje , Hannigan Laurie J. , Corfield Elizabeth C. , Andreassen Ole A. , Ystrom Eivind , Ask Helga , Smith George Davey , Davies Neil M. , Havdahl Alexandra
Published: July 2024

Children born to parents with fewer years of education are more likely to have depression, anxiety, and attention-deficit hyperactivity disorder (ADHD), but it is unclear to what extent these associations are causal. We estimated the effect of parents’ educational attainment on children’s depressive, anxiety, and ADHD traits at age 8 years, in a sample of 40,879 Norwegian children born in 1998–2009 and their parents. We used within-family Mendelian randomization, which employs genetic variants as instrumental variables, and controlled for direct genetic effects by adjusting for children’s polygenic indexes. We found little evidence that mothers’ or fathers’ educational attainment independently affected children’s depressive, anxiety, or ADHD traits. However, children’s own polygenic scores for educational attainment were independently and negatively associated with these traits. Results suggest that differences in these traits according to parents’ education may reflect direct genetic effects more than genetic nurture. Consequences of social disadvantage for children’s mental health may however be more visible in samples with more socioeconomic variation, or contexts with larger socioeconomic disparities than present-day Norway. Further research is required in populations with more educational and economic inequality and in other age groups.
Profiling protein–protein interactions to predict the efficacy of B-cell-lymphoma-2-homology-3 mimetics for acute myeloid leukaemia
Authors: Chun Changju , Byun Ja Min , Cha Minkwon , Lee Hongwon , Choi Byungsan , Kim Hyunwoo , Hong Saem , Lee Yunseo , Park Hayoung , Koh Youngil , Yoon Tae-Young
Published: July 2024

B-cell-lymphoma-2 (BCL2) homology-3 (BH3) mimetics are inhibitors of protein–protein interactions (PPIs) that saturate anti-apoptotic proteins in the BCL2 family to induce apoptosis in cancer cells. Despite the success of the BH3-mimetic ABT-199 for the treatment of haematological malignancies, only a fraction of patients respond to the drug and most patients eventually develop resistance to it. Here we show that the efficacy of ABT-199 can be predicted by profiling the rewired status of the PPI network of the BCL2 family via single-molecule pull-down and co-immunoprecipitation to quantify more than 20 types of PPI from a total of only 1.2 × 106 cells per sample. By comparing the obtained multidimensional data with BH3-mimetic efficacies determined ex vivo, we constructed a model for predicting the efficacy of ABT-199 that designates two complexes of the BCL2 protein family as the primary mediators of drug effectiveness and resistance, and applied it to prospectively assist therapeutic decision-making for patients with acute myeloid leukaemia. The characterization of PPI complexes in clinical specimens opens up opportunities for individualized protein-complex-targeting therapies.
Quadrupling the depairing current density in the iron-based superconductor SmFeAsO1–xHx
Authors: Miura Masashi , Eley Serena , Iida Kazumasa , Hanzawa Kota , Matsumoto Jumpei , Hiramatsu Hidenori , Ogimoto Yuki , Suzuki Takumi , Kobayashi Tomoki , Ozaki Toshinori , Kurokawa Hodaka , Sekiya Naoto , Yoshida Ryuji , Kato Takeharu , Okada Tatsunori , Okazaki Hiroyuki , Yamaki Tetsuya , Hänisch Jens , Awaji Satoshi , Maeda Atsutaka , Maiorov Boris , Hosono Hideo
Published: July 2024

Iron-based 1111-type superconductors display high critical temperatures and relatively high critical current densities Jc. The typical approach to increasing Jc is to introduce defects to control dissipative vortex motion. However, when optimized, this approach is theoretically predicted to be limited to achieving a maximum Jc of only ∼30% of the depairing current density Jd, which depends on the coherence length and the penetration depth. Here we dramatically boost Jc in SmFeAsO1–xHx films using a thermodynamic approach aimed at increasing Jd and incorporating vortex pinning centres. Specifically, we reduce the penetration depth, coherence length and critical field anisotropy by increasing the carrier density through high electron doping using H substitution. Remarkably, the quadrupled Jd reaches 415 MA cm–2, a value comparable to cuprates. Finally, by introducing defects using proton irradiation, we obtain high Jc values in fields up to 25 T. We apply this method to other iron-based superconductors and achieve a similar enhancement of current densities.
Efficacy of stem cells versus microvesicles in ameliorating chronic renal injury in rats (histological and biochemical study)
Authors: Mohammed Maha Z. , Abdelrahman Shaimaa A. , El-Shal Amal S. , Abdelrahman Abeer A. , Hamdy Marwa , Sarhan Walaa M.
Published: July 2024

Chronic exposure to heavy metals as aluminum chloride (AlCl3) could result in severe health hazards such as chronic renal injury. The present study aimed to evaluate the therapeutic potential of adipose tissue-derived stem cells (ASCs) in comparison to their microvesicles (MV) in AlCl3-induced chronic renal injury. Forty-eight adult male Wistar rats were divided into four groups: Control group, AlCl3-treated group, AlCl3/ASC-treated group, and AlCl3/MV-treated group. Biochemical studies included estimation of serum urea and creatinine levels, oxidative biomarkers assay, antioxidant biomarkers, serum cytokines (IL-1β, IL-8, IL-10, and IL-33), real time-PCR analysis of renal tissue MALT1, TNF-α, IL-6, and serum miR-150-5p expression levels. Histopathological studies included light and electron microscopes examination of renal tissue, Mallory trichrome stain for fibrosis, Periodic acid Schiff (PAS) stain for histochemical detection of carbohydrates, and immunohistochemical detection of Caspase-3 as apoptosis marker, IL-1B as a proinflammatory cytokine and CD40 as a marker of MVs. AlCl3 significantly deteriorated kidney function, enhanced renal MDA and TOS, and serum cytokines concentrations while decreased the antioxidant parameters (SOD, GSH, and TAC). Moreover, serum IL-10, TNF-α, miR-150-5p, and renal MALT1 expression values were significantly higher than other groups. Kidney sections showed marked histopathological damage in both renal cortex and medulla in addition to enhanced apoptosis and increased inflammatory cytokines immunoexpression than other groups. Both ASCs and MVs administration ameliorated the previous parameters levels with more improvement was detected in MVs-treated group. In conclusion: ASCs-derived MVs have a promising ameliorating effect on chronic kidney disease.
Surface-energy ratchet motor with geometrical symmetry driven by biased random walk
Authors: Hatatani Miku , Yamamoto Daigo , Shioi Akihisa
Published: July 2024

A geometrically symmetric gear with asymmetric surface wettability exhibits one-way spin on a vibrating water bed. On the side face of the gear, a parafilm was coated to create asymmetry in the surface energy. The gear shows fluctuations in both directions within a shorter timescale; however, for a longer timescale, the gear exhibits a one-way spin. This unique motion is generated by a stochastic process with a biased driving force produced by the interaction between the vibrating water surface and the side face of the gear. This new model resembles an active Brownian ratchet. Until now, most ratchet motors, which obtain regular motion from nonthermal fluctuations, utilize a geometrical ratchet structure. However, in this study, the surface energy forms a ratchet that rectifies the noisy motion.
Systematic study on date palm seeds (Phoenix dactylifera L.) extraction optimisation using natural deep eutectic solvents and ultrasound technique
Authors: Alfaleh Alanood A. , Sindi Heba A.
Published: July 2024

Natural deep eutectic solvents (NADES) are emerging, environment-friendly solvents that have garnered attention for their application in extracting phenolic compounds. This study investigated the effects of four synthetic NADES on polyphenols extracted from date seeds (DS) using choline chloride (ChCl) as a hydrogen-bond acceptor and lactic acid (La), citric acid (Citri), glycerol (Gly), and fructose (Fruc) as hydrogen-bond donors, in comparison with DS extracts extracted by conventional solvents (water, 70% methanol, and 70% ethanol). The antioxidant activity (DPPH), total phenolic content (TPC) and 6 phenolic compounds were determined using HPLC. The results showed that the ChCl–La and ChCl–Citri systems exhibited a high extraction efficiency regarding TPC, and DPPH in the DS extracts extracted by NADES compare to those DS extracts extracted with conventional solvents (p ˂ 0.001). HPLC results demonstrated that DS extracted by ChCl–La contained all measured phenolic compounds. Also gallic acid and catechin were the major compounds identified in the DS extracts. In addition DS extracted by ChCl–Citri and ChCl–Gly had the highest concentration of catechin. In conclusion, combining NADES is a promising and environment-friendly alternative to the conventional solvent extraction of phenolic compounds from DS.
Identifying subtypes and developing prognostic models based on N6-methyladenosine and immune microenvironment related genes in breast cancer
Authors: Wang Lizhao , Li Jianpeng , Mei Nan , Chen Heyan , Niu Ligang , He Jianjun , Wang Ru
Published: July 2024

Breast cancer (BC) is the most prevalent cancer in women globally. The tumor microenvironment (TME), comprising epithelial tumor cells and stromal elements, is vital for breast tumor development. N6-methyladenosine (m6A) modification plays a key role in RNA metabolism, influencing its various aspects such as stability and translation. There is a notable link between m6A methylation and immune cells in the TME, although this relationship is complex and not fully deciphered. In this research, BC expression and clinicopathological data from TCGA were scrutinized to assess expression profiles, mutations, and CNVs of 31 m6A genes and immune microenvironment-related genes, examining their correlations, functions, and prognostic impacts. Lasso and Cox regression identified prognostic genes for constructing a nomogram. Single-cell analyses mapped the distribution and patterns of these genes in BC cell development. We investigated associations between gene-derived risk scores and factors like immune infiltration, TME, checkpoints, TMB, CSC indices, and drug response. As a complement to computational analyses, in vitro experiments were conducted to confirm these expression patterns. We included 31 m6A regulatory genes and discovered a correlation between these genes and the extent of immune cell infiltration. Subsequently, a 7-gene risk score was generated, encompassing HSPA2, TAP1, ULBP2, CXCL1, RBP1, STC2, and FLT3. It was observed that the low-risk group exhibited better overall survival (OS) in BC, with higher immune scores but lower tumor mutational burden (TMB) and cancer stem cell (CSC) indices, as well as lower IC50 values for commonly used drugs. To enhance clinical applicability, age and stage were incorporated into the risk score, and a more comprehensive nomogram was constructed to predict OS. This nomogram was validated and demonstrated good predictive performance, with area under the curve (AUC) values for 1-year, 3-year, and 5-year OS being 0.848, 0.807, and 0.759, respectively. Our findings highlight the profound impact of prognostic-related genes on BC immune response and prognostic outcomes, suggesting that modulation of the m6A-immune pathway could offer new avenues for personalized BC treatment and potentially improve clinical outcomes.
Oligoclonal CD4+CXCR5+ T cells with a cytotoxic phenotype appear in tonsils and blood
Authors: Liang Chunguang , Spoerl Silvia , Xiao Yin , Habenicht Katharina M. , Haeusl Sigrun S. , Sandner Isabel , Winkler Julia , Strieder Nicholas , Eder Rüdiger , Stanewsky Hanna , Alexiou Christoph , Dudziak Diana , Rosenwald Andreas , Edinger Matthias , Rehli Michael , Hoffmann Petra , Winkler Thomas H. , Berberich-Siebelt Friederike
Published: July 2024

In clinical situations, peripheral blood accessible CD3+CD4+CXCR5+ T-follicular helper (TFH) cells may have to serve as a surrogate indicator for dysregulated germinal center responses in tissues. To determine the heterogeneity of TFH cells in peripheral blood versus tonsils, CD3+CD4+CD45RA–CXCR5+ cells of both origins were sorted. Transcriptomes, TCR repertoires and cell-surface protein expression were analysed by single-cell RNA sequencing, flow cytometry and immunohistochemistry. Reassuringly, all blood-circulating CD3+CD4+CXCR5+ T-cell subpopulations also appear in tonsils, there with some supplementary TFH characteristics, while peripheral blood-derived TFH cells display markers of proliferation and migration. Three further subsets of TFH cells, however, with bona fide T-follicular gene expression patterns, are exclusively found in tonsils. One additional, distinct and oligoclonal CD4+CXCR5+ subpopulation presents pronounced cytotoxic properties. Those ‘killer TFH (TFK) cells’ can be discovered in peripheral blood as well as among tonsillar cells but are located predominantly outside of germinal centers. They appear terminally differentiated and can be distinguished from all other TFH subsets by expression of NKG7 (TIA-1), granzymes, perforin, CCL5, CCR5, EOMES, CRTAM and CX3CR1. All in all, this study provides data for detailed CD4+CXCR5+ T-cell assessment of clinically available blood samples and extrapolation possibilities to their tonsil counterparts.
Multi-decadal groundwater observations reveal surprisingly stable levels in southwestern Europe
Authors: Chávez García Silva Rafael , Reinecke Robert , Copty Nadim K. , Barry David A. , Heggy Essam , Labat David , Roggero Pier Paolo , Borchardt Dietrich , Rode Michael , Gómez-Hernández J. Jaime , Jomaa Seifeddine
Published: July 2024

Climate change and human activity are leading to water scarcity in southwestern Europe. Groundwater use is thought to be unsustainable in the region, yet regional assessments using measured data are missing. Here, we evaluate long-term trends and drivers of groundwater levels and found a more complex situation. Historical data (1960–2020) from 12,398 wells in Portugal, Spain, France, and Italy showed 20% with rising groundwater levels, 68% were stable, and only 12% were declining. Rising wells in temperate climates were due to increased precipitation. Recovering wells in semi-arid regions were attributed to improved groundwater management. Stable wells are concentrated in temperate climates with year-round high precipitation. Declining wells in semi-arid regions are primarily located near agricultural areas and experience prolonged summer soil moisture loss, whereas in temperate regions, the decline is associated with large urban areas. Systematic groundwater monitoring and data sharing are essential for sustainable and science-based water resources management.
A framework for neurophysiological experiments on flow states
Authors: Durcan Oliver , Holland Peter , Bhattacharya Joydeep
Published: July 2024

Csikszentmihalyi’s concept of the “flow state” was initially discovered in experts deeply engaged in self-rewarding activities. However, recent neurophysiology research often measures flow in constrained and unfamiliar activities. In this perspective article, we address the challenging yet necessary considerations for studying flow state’s neurophysiology. We aggregate an activity-autonomy framework with several testable hypotheses to induce flow, expanding the traditional “challenge skill balance” paradigm. Further, we review and synthesise the best methodological practices from neurophysiological flow studies into a practical 24-item checklist. This checklist offers detailed guidelines for ensuring consistent reporting, personalising and testing isolated challenge types, factoring in participant skills, motivation, and individual differences, and processing self-report data. We argue for a cohesive approach in neurophysiological studies to capture a consistent representation of flow states.
Analysis of therapeutic monoclonal antibodies by imaged capillary isoelectric focusing (icIEF)
Authors: Sutton Haley , Hong Feng , Han Xuemei , Rauniyar Navin
Published: July 2024

Imaged capillary isoelectric focusing (icIEF) is a preferred analytical method for determining isoelectric points (pIs) and charge heterogeneity profiles in biotherapeutic proteins.
Synthesis of triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers and bis-Re(i) triphyrin dimer complex
Authors: Kaur Gurpreet , Ravikanth Mangalampalli
Published: July 2024

First examples of covalently linked triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers and bis-Re(i) homo dimer complex were synthesized from 2-bromo triphyrin(2.1.1), which adopted anti-conformations and exhibited unique physicochemical properties.
Continuous-flow synthesis of CsPbI3/TiO2 nanocomposites with enhanced water and thermal stability
Authors: Hou Jingshan , Hu Jiafeng , Wu Jianghua , Zhang Qing , Liu Zhifu , Dong Langping , Jiang Guangxiang , Liu Yufeng , Gao Wei , Fang Yongzheng
Published: July 2024

CsPbI3/TiO2 nanocomposites with high water and thermal stability were continuously prepared by a microfluidic method.
Effects of polystyrene nanoplastics on hormonal regulation and glucose metabolism of Pacific whiteleg shrimp (Litopenaeus vannamei)
Authors: Li Yiming , Zhu Bihong , Zhu Xiaoyi , Ye Yucong , Liu Xingguo , Wang Xiaodong , Che Xuan , Zhao Yunlong
Published: July 2024

High concentration of nanoplastics inhibited serum hormone levels, glucose metabolism related enzyme activity and gene expression. Nanoplastic exposure may have a negative effect on glucose metabolites via inhibition of the pentose phosphate pathway.
Formation of chlorinated disinfection by-products and fate of their precursors in individual processes of a conventional water treatment plant assessed using high-resolution mass spectrometry
Authors: Yuthawong Vitharuch , Thongnueaha Chatyapha , Phungsai Phanwatt
Published: July 2024

Capability of water treatment processes to remove DBP precursors.
Ovomucin and its hydrolysates differentially influenced colitis severity in Citrobacter rodentium-infected mice
Authors: Bao Xiaoyu , Ju Tingting , Tollenaar Stephanie , Sergi Consolato , Willing Benjamin P. , Wu Jianping
Published: July 2024

Ovomucin (OVM) and ovomucin-Protex 26L hydrolysate (OP) alleviated Citrobacter rodentium-induced colitis in mice through different protective mechanisms, whereas its pepsin–pancreatin hydrolysate (OPP) exacerbated colitis severity.
Hydrogen storage capacity of freeze cast microporous monolithic composites
Authors: Butler Catherine , Mays Timothy J. , Sahadevan Vijay , O’Malley Rachel , Graham Daniel P. , Bowen Christopher R.
Published: July 2024

3D adsorptive monoliths, with potential for incorporation into ullage of liquid storage tanks, providing reduced boil-off, increasing safety and efficiency.
Self-formation of compositionally complex surface oxides on high entropy alloys observed by accelerated atom probe tomography: a route to sustainable catalysts
Authors: Strotkötter Valerie , Li Yujiao , Kostka Aleksander , Lourens Florian , Löffler Tobias , Schuhmann Wolfgang , Ludwig Alfred
Published: July 2024

Accelerated approach for analysis of electrochemical states with atom probe tomography reveals modification of oxygen-containing surface layers of high entropy catalysts.
Correction: Synthesis of template-free magnetite nanospheres grown on Sb2WO6 hierarchical structures for sunlight-driven photo-Fenton catalysis of organic pollutants
Authors: AlObaid Abeer A. , Shrotriya Vipin Bihari , Sharma Girraj , Nazir Ghazanfar , Ul Haq Zia
Published: July 2024

Correction for ‘Synthesis of template-free magnetite nanospheres grown on Sb2WO6 hierarchical structures for sunlight-driven photo-Fenton catalysis of organic pollutants’ by Abeer A. AlObaid et al., New J. Chem., 2024, 48, 10616–10627, https://doi.org/10.1039/D4NJ01160K.
Supracluster assembly of an Al4 precursor toward the study of enhanced optical properties
Authors: Yang Fan , Chen Rui-Yan , Wang San-Tai , He Yan-Ping , Fang Wei-Hui , Zhang Jian
Published: July 2024

Presented herein is a designed synthesis toward the enhancement of intended optical properties through a supracluster assembly strategy based on a pre-designed Al4 precursor.
Chelation-assisted α and β C–H functionalization of aryl alkenes with alkynes and alkenes
Authors: Zhang Cheng , Lin Yu , Zhu Yuhang , Peng Chengxing , Lv Binbin , Zhao Li , Zhong Guofu , Wei Jinfeng , Zhang Jian
Published: July 2024

α C–H alkenylation of aryl alkenes by six-membered exo-palladacycles was demonstrated to afford aryl dienes, which underwent β C–H alkenylation through seven-membered endo-palladacycles to produce aryl trienes with excellent E/Z ratio selectivity.
Surface pre-treatment of aluminum alloy for mechanical improvement of adhesive bonding by maple-assisted pulsed laser evaporation technique
Authors: Rusen Edina , Brîncoveanu Oana , Dincă Valentina , Toader Gabriela , Diacon Aurel , Dinescu Miron Adrian , Mocanu Alexandra
Published: July 2024

Adhesive joints are widely used for structural bonding in various industrial sectors. Surface pre-treatment of aluminum alloys by MAPLE technique using polymers with different molecular weights.
Co-precipitation synthesis of highly pure and Mg-doped CdO nanoparticles: from rod to sphere shapes
Authors: Lims S. Cathrin , Jose M. , Aswathappa Sivakumar , Dhas S. Sahaya Jude , Kumar Raju Suresh , Pham Phuong V.
Published: July 2024

This study reports a facile approach for examining surface morphology transitions in semiconductor nanoparticles (NPs), with a focus on pristine and magnesium-doped cadmium oxide NPs.
A scalable approach using a gC3N4-covalent organic framework hybrid catalyst towards sustainable hydrogen production from seawater and wastewater
Authors: Asokan Kiran , Bhagyasree T. M. , Devasia George , Krishnamurty Sailaja , Solim Sabah , Rueda Lina , Al-Mohannadi Dhabia M. , Al-Hashimi Mohammed , Kakosimos Konstantinos , Santhosh Babu Sukumaran
Published: July 2024

Hybridization of a COF with gC3N4 resulted in remarkable H2 evolution from seawater and industrial wastewater.
An automated screening platform for improving the responsiveness of genetically encoded Ca2+ biosensors in mammalian cells
Authors: Zhao Yufeng , Shen Yi , Veres Teodor , Campbell Robert E.
Published: July 2024

We developed a novel automated platform to screen the responsiveness of fluorescent protein (FP)-based biosensors to chemical stimulation in mammalian cells and discovered improved red fluorescent Ca2+ biosensor variants using this platform.
Unraveling the mechanism of methyl acetate additive for reinforcing the solid electrolyte interface on graphite anodes
Authors: Hao Jing , Liu Wen , Tian Yao , Wu Junru , Guo Hexin , Zhang Guobin , Yi Yong , Han Cuiping , Kang Feiyu , Li Baohua
Published: July 2024

A stable ultrathin SEI with an inorganic/organic bilayer structure is in situ formed with addition of methyl acetate, the formation and evolution process are investigated by in situ scanning electrochemical microscopy and atomic force microscopy.
Heavy-atom-free π-twisted photosensitizers for fluorescence bioimaging and photodynamic therapy
Authors: Sánchez Darío Puchán , Morice Korentin , Mutovska Monika G. , Khrouz Lhoussain , Josse Pierre , Allain Magali , Gohier Frédéric , Blanchard Philippe , Monnereau Cyrille , Le Bahers Tangui , Sabouri Nasim , Zagranyarski Yulian , Cabanetos Clement , Deiana Marco
Published: July 2024

Schematic illustration of the twisted π-conjugated system strategy to achieve enhanced fluorescence emission and ROS generation efficiency.
ESIPT-active columnar liquid crystal: organic dyes and quantum dots-assisted fluorescence modulation
Authors: Agarwal Shikha , Khatavi Santosh Y. , Singh Bhupendra Pratap , Kanakala Madhu Babu , Santra Pralay Kumar , Kumar Sandeep , Huang Chi-Yen , Yelamaggad Channabasaveshwar V. , Manohar Rajiv
Published: July 2024

The fluorescent attributes of several composites realized by dispersing dyes and quantum dots in an ESIPT-active columnar liquid crystal have been reported in three condensed states, viz., solid, LC, and liquid states, and their solutions.
Carbon-based binary organic photocatalysts for rapid dye degradation under weak light: performance and mechanistic study
Authors: Huang Ciyuan , Shi Shasha , Cai Songlin , Qiao Yue , Wang Caiyun , Yang Linji , Wang Yuchen , Cheng Hao , Yang Tao , Huang Kai , Zou Bingsuo , Liu Tao
Published: July 2024

Congo red (CR), a stable benzidine diazo dye due to its azo bonds, resists natural photodegradation and poses a significant ecological threat.
Correction: Copper and iron co-doping effects on the structure, optical energy band gap, and catalytic behaviour of Co3O4 nanocrystals towards low-temperature total oxidation of toluene
Authors: Assaouka Hippolyte Todou , Nsangou Issah Ngouh , Daawe Daniel Manhouli , Mevoa Daniel Onana , Zigla Abraham Atour , Ndouka Patrick Ndouka , Kouotou Patrick Mountapmbeme
Published: July 2024

Correction for ‘Copper and iron co-doping effects on the structure, optical energy band gap, and catalytic behaviour of Co3O4 nanocrystals towards low-temperature total oxidation of toluene’ by Hippolyte Todou Assaouka et al., Energy Adv., 2023, 2, 829–842, https://doi.org/10.1039/D3YA00082F.
An adaptive gain phase‐locked loop for position sensorless control of permanent magnet synchronous motor drives
Authors: Han Pengcheng , Lou Ying , Wu Chao , Zeng Li , Wang Huimin
Published: July 2024

In view of the cost and reliability issues caused by mechanical position sensors, position sensorless control (PSC) of permanent magnet synchronous motors (PMSMs) has received widespread attention. A series of rotor position estimation (RPE) schemes have been developed, in which the phase‐locked loop (PLL) plays an important role. However, the conventional phase‐locked loops face two thorny issues, one is the degradation of RPE performance under motor acceleration and deceleration conditions, and the other is high noise sensitivity. To this end, an adaptive gain PLL (AG‐PLL) is proposed for PSC of PMSM drives. The gains of the loop filter in the proposed AG‐PLL are adaptively adjusted with the estimation error in order to find a compromise between the estimation performance under motor acceleration and deceleration conditions and the noise sensitivity. Moreover, the proposed scheme avoids increasing the order of the PLL, so its dynamic performance is also guaranteed. The proposed scheme is tested based on the hardware‐in‐the‐loop platform.