bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetics of SARS-CoV-2 infection biomarkers in a household transmission study
Authors: Groh Ana M. , Vehreschild Maria J. G. T. , Diaz Damian , Kuchta Alison L. , Dodoo Christopher , Alvarado Luis A. , Parkin Neil T. , Robbins Elissa M. , Moonsamy Priscilla , Toptan Tuna , Ciesek Sandra , Berger Annemarie
Published: May 2024

SARS-CoV-2 is the causative agent of COVID-19. Timely and accurate diagnostic testing is vital to contain the spread of infection, reduce delays in treatment and care, and inform patient management. Optimal specimen type (e.g. nasal swabs or saliva), timing of sampling, viral marker assayed (RNA or antigen), and correlation with viral infectivity and COVID-19 symptoms severity remain incompletely defined. We conducted a field study to evaluate SARS-CoV-2 viral marker kinetics starting from very early times after infection. We measured RNA and antigen levels in nasal swabs and saliva, virus outgrowth in cell culture from nasal swabs, and antibody levels in blood in a cohort of 30 households. Nine household contacts (HHC) became infected with SARS-CoV-2 during the study. Viral RNA was detected in saliva specimens approximately 1–2 days before nasal swabs in six HHC. Detection of RNA was more sensitive than of antigen, but antigen detection was better correlated with culture positivity, a proxy for contagiousness. Anti-nucleocapsid antibodies peaked one to three weeks post-infection. Viral RNA and antigen levels were higher in specimens yielding replication competent virus in cell culture. This study provides important data that can inform how to optimally interpret SARS-CoV-2 diagnostic test results.
Evolution and virulence of porcine epidemic diarrhea virus following in vitro and in vivo propagation
Authors: Jermsutjarit Patumporn , Mebumroong Sunit , Watcharavongtip Parin , Lin Hongyao , Tantituvanont Angkana , Kaeoket Kampon , Piñeyro Pablo , Nilubol Dachrit
Published: May 2024

Practice of inoculating porcine epidemic diarrhea virus (PEDV) in piglets generating feedback material might influence the genetic evolution and attenuation of PEDV. The study was conducted to evaluate evolutionary rate and attenuation following serial in vitro and in vivo propagation. In the study, PED-JPFP0-PJ, Passage 0 (P0), was isolated from infected pigs and serially passaged in Vero cells for 5 consecutive times, P1-P5. P0, P2 and P5 were then subjected to orally inoculate 3-day-old piglets. At 24 h post inoculation, intestines of each passage (F1), were collected, and subsequently sub-passaged in piglets for 2 additional passages (F2-F3). Virus titration, PEDV genomic copies number, VH:CD ratios, and immunohistochemistry were evaluated. S and ORF3 genes were characterized. The results of the study demonstrated that virus titer and virulence were negatively correlated with increased passages, both in vitro and in vivo. Increased substitution rate was observed in higher passages. The evolutionary rate of S gene was higher than that of ORF3. Seven aa changes at positions 223, 291, 317, 607, 694, 1114 and 1199, with reduced N-linked glycan were observed in P5F3. In conclusion, serial passage of PEDV, both in vitro and in vivo, influence the genetic development and the attenuation of PEDV.
Endovascular treatment of stroke in the late time window with large vessel occlusion using the ASPECTS as an imaging screening criterion
Authors: Liu Jiahui , Zhuo Na , Wei Jianqi , Fan Yu , Jiang Changchun
Published: May 2024

To assess the Alberta Stroke Program Early CT Score (ASPECTS) screening tool for effectiveness in endovascular treatment of late time window stroke with large vessel occlusion. A retrospective analysis was performed of individuals administered endovascular treatment in our neurology department between 2016 and 2020 for ischemic stroke induced by acute large vessel occlusion in the anterior circulation and ASPECTS ≥ 6. Detailed baseline and endovascular treatment data were collected. Patients were assigned to 2 groups based on stroke onset time, including the 0–6 h (treated within 6 h of stroke onset) and 6–24 h (earlier/unknown time of onset, up to 24 h from the last time of appearing normal) groups. Both groups were compared for baseline information, revascularization rates, symptomatic intracranial hemorrhage, and 90-day functional independence. Totally 221 individuals were enrolled. The 0–6 h and 6–24 h groups had 129 and 92 patients, respectively, whose median ages were 64 and 63 years, respectively. Both groups were similar in previous medical history, NIHSS score at onset, lesion location and surgical complications. The 6–24 h group had elevated intracranial atherosclerotic stenosis (48.9 vs. 33.3%, P = 0.020) and revascularization (96.7 vs. 86.8%, P = 0.011) rates versus the 6–24 h group. Upon adjustment for age, sex, National Institutes of Health Stroke Scale, ASPECTS, Intracranial atherosclerosis, intraoperative tirofiban, stent detachment, successful recanalization, and symptomatic intracranial hemorrhage, the 0-6 h group had a higher rate of individuals achieving functional independence (mRS score of 0–2; 52.7 vs. 47.8%, OR = 0.242 [0.070–0.833], P = 0.024). However, the rates of individuals with a favorable outcome (mRS scores of 0–3) were similar in both groups (66.7 vs. 69.6%; OR = 0.564 [0.140–2.266], P = 0.419) as well as 90-d mortality (OR = 0.889 [0.170–4.660], P = 0.889). The ASPECTS is effective for screening individuals for endovascular treatment of stroke in the late time window with large vessel occlusion. The ASPECTS should be considered a simple and practical patient screening strategy for stroke centers without multimodal imaging evaluation.
Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance
Authors: Billows Nina , Phelan Jody , Xia Dong , Peng Yonghong , Clark Taane G. , Chang Yu-Mei
Published: May 2024

Tuberculosis (TB), caused by Mycobacterium tuberculosis, has a significant impact on global health worldwide. The development of multi-drug resistant strains that are resistant to the first-line drugs isoniazid and rifampicin threatens public health security. Rifampicin and isoniazid resistance are largely underpinned by mutations in rpoB and katG respectively and are associated with fitness costs. Compensatory mutations are considered to alleviate these fitness costs and have been observed in rpoC/rpoA (rifampicin) and oxyR’-ahpC (isoniazid). We developed a framework (CompMut-TB) to detect compensatory mutations from whole genome sequences from a large dataset comprised of 18,396 M. tuberculosis samples. We performed association analysis (Fisher’s exact tests) to identify pairs of mutations that are associated with drug-resistance, followed by mediation analysis to identify complementary or full mediators of drug-resistance. The analyses revealed several potential mutations in rpoC (N = 47), rpoA (N = 4), and oxyR’-ahpC (N = 7) that were considered either ‘highly likely’ or ‘likely’ to confer compensatory effects on drug-resistance, including mutations that have previously been reported and validated. Overall, we have developed the CompMut-TB framework which can assist with identifying compensatory mutations which is important for more precise genome-based profiling of drug-resistant TB strains and to further understanding of the evolutionary mechanisms that underpin drug-resistance.
Smokers with higher positive or negative urgency have lower rates of smoking cessation success 12 months after a quit attempt
Authors: Brunault Paul , Ingrand Isabelle , Solinas Marcello , Dugast Emilie , Pérault-Pochat Marie-Christine , Ingrand Pierre , Vanderkam Paul , Lafay-Chebassier Claire
Published: May 2024

Impulsivity dimensions have been shown to be associated with smoking status and tobacco use disorder severity. However, it is important to determine the specific impulsivity traits associated with smoking relapse. This study aimed at investigating the associations between impulsivity traits and smoking cessation success among adult smokers at 12 months after a quit attempt. Participants were 68 adult smokers enrolled in a 3-month course of simvastatine or placebo associated with behavioral cessation support, with a 9-month follow-up (ADDICSTATINE study). They were classified in 3 groups according to smoking status: abstinent, reduction ≥ 50%baseline or reduction < 50%baseline at 3 and 12 months. Impulsivity traits were assessed using the UPPS-P-scale. At 12 months, abstainers and participants who reduced smoking by 50% or more had significantly lower scores in negative and positive urgency compared to participants who reduced smoking by less than 50% (p = 0.011 and 0.0059). These urgency traits scores at 12 months were significantly and negatively correlated with smoking reduction at 12 months (p = 0.017 and 0.0012). These impulsivity traits were also associated with the smoking cessation success at 3 months. Patients who were abstinent at 3 months had also lower negative and positive urgency (p = 0.017 and 0.0039). Smoking cessation success at 3 and 12 months were not associated with the other impulsivity traits, sensation seeking, lack of premeditation or perseverance. Our findings suggest that positive and negative urgency are associated with smoking cessation success. Proposing better tailored-based-treatment targeting these impulsivity traits in combination with conventional treatment may help improving smoking treatment success.
A targeted fluorescent nanosensor for ratiometric pH sensing at the cell surface
Authors: Kromer Charlotte , Katz Aaron , Feldmann Ines , Laux Peter , Luch Andreas , Tschiche Harald R.
Published: May 2024

The correlation between altered extracellular pH and various pathological conditions, including cancer, inflammation and metabolic disorders, is well known. Bulk pH measurements cannot report the extracellular pH value at the cell surface. However, there is a limited number of suitable tools for measuring the extracellular pH of cells with high spatial resolution, and none of them are commonly used in laboratories around the world. In this study, a versatile ratiometric nanosensor for the measurement of extracellular pH was developed. The nanosensor consists of biocompatible polystyrene nanoparticles loaded with the pH-inert reference dye Nile red and is surface functionalized with a pH-responsive fluorescein dye. Equipped with a targeting moiety, the nanosensor can adhere to cell membranes, allowing direct measurement of extracellular pH at the cell surface. The nanosensor exhibits a sensitive ratiometric pH response within the range of 5.5–9.0, with a calculated pKa of 7.47. This range optimally covers the extracellular pH (pHe) of most healthy cells and cells in which the pHe is abnormal, such as cancer cells. In combination with the nanosensors ability to target cell membranes, its high robustness, reversibility and its biocompatibility, the pHe nanosensor proves to be well suited for in-situ measurement of extracellular pH, even over extended time periods. This pH nanosensor has the potential to advance biomedical research by improving our understanding of cellular microenvironments, where extracellular pH plays an important role.
The temporal variation of CH4 emissions embodied in Chinese supply chains, 2000–2020
Authors: Wu Jiaxi , Chen Mengxin , Sun Xialing , Meng Zheng
Published: May 2024

Although the issue of embodied pollutants in China’s supply chains has garnered increasing attention, the dynamic changes occurring within them are unclear. Several existing studies analyze one-year or short-term data in supply chain. China’s overall CH4 emissions have risen from 41.1 Tg in 2000 to 60 Tg in 2020, so conducting long-term analyses can yield a deeper understanding of the dynamic changes across the entire supply chain from production to consumption. This study uses the environmentally extended input–output analysis (EEIOA) and structural path analysis (SPA) methods to investigate the dynamic variation of China’s embodied CH4 emissions in 20 industry sectors from 2000 to 2020, aiming to determine the key supply chain and key sectors. The results reveal that from the final demand perspective, consumption, investment and export drove 52.1%, 32%, and 15.9% of embodied CH4 emissions in 2020. The sector with the highest embodied CH4 emissions has changed from “Agriculture” in 2000 to “Construction” in 2010 to “Other service and activities” in 2020. The top listed supply chain path of embodied CH4 emissions has also evolved (starting from production to consumption) from “Agriculture → Rural consumption” in 2000 to “Agriculture → Food and tobacco → Urban consumption” in 2010 to “Agriculture → Urban consumption” in 2020. Notably, the high-ranked path, “Agriculture → Food and tobacco → Rural consumption”, shows that the embodied CH4 emission flowing between agriculture and the food industry cannot be ignored. The supply chain path “Coal Mining → Nonmetal Mineral Products → Construction → Capital Formation” has risen from 17th in 2000 to 3rd in 2020. Thus, it is necessary to control CH4 emissions from sectors upstream, which are predominantly influenced by the construction industry, and a coordinated effort between sectors is also required to effectively reduce emissions. By 2020, the CH4 emissions driven by urban consumption were 3.1 times that of rural consumption. This study provides a comprehensive analysis of China's supply chain over the past two decades. In particular, it suggests policy interventions by controlling critical supply chain paths and key sectors associated with embodied CH4 emission, thereby facilitating the coordinated reduction of anthropogenic CH4 emissions.
Polyurethane-based three-dimensional printing for biological mesh carriers
Authors: Wang Feng , Hou Lin , Shan Yan-Hui , Li Zhen-Su , Yang Xiao-Feng
Published: May 2024

Repair and reconstruction of the myopectineal orifice area using meshes is the mainstay of surgical treatment of inguinal hernias. However, the limitations of existing meshes are becoming increasingly evident in clinical applications; thus, the idea of using three-dimensionally (3D)-printed biological meshes was put forward. According to the current level of the 3D printing technology and the inherent characteristics of biological materials, the direct use of the 3D printing technology for making biological materials into finished products suitable for clinical applications is not yet supported, but synthetic materials can be first printed into 3D form carriers, compounded with biological materials, and finally made into finished products. The purpose of this study was to develop a technical protocol for making 3D-printed biomesh carriers using polyurethane as a raw material. In our study: raw material, polyurethane; weight, 20–30 g/m2; weaving method, hexagonal mesh; elastic tension aspect ratio, 2:1; diameters of pores, 0.1–1 mm; surface area, 8 × 12 cm2; the optimal printing layer height, temperature and velocity were 0.1 mm, 210–220 °C and 60 mm/s. Its clinical significance lies in: (1) applied to preoperative planning and design a detailed surgical plan; (2) applied to special types of surgery including patients in puberty, recurrent and compound inguinal hernias; (3) significantly improve the efficiency of doctor-patient communication; (4) it can shorten the operation and recovery period by about 1/3 and can save about 1/4 of the cost for patients; (5) the learning curve is significantly shortened, which is conducive to the cultivation of reserve talents.
On the advantages of using AI-generated images of filler faces for creating fair lineups
Authors: Bell Raoul , Menne Nicola Marie , Mayer Carolin , Buchner Axel
Published: May 2024

Recent advances in artificial intelligence (AI) enable the generation of realistic facial images that can be used in police lineups. The use of AI image generation offers pragmatic advantages in that it allows practitioners to generate filler images directly from the description of the culprit using text-to-image generation, avoids the violation of identity rights of natural persons who are not suspects and eliminates the constraints of being bound to a database with a limited set of photographs. However, the risk exists that using AI-generated filler images provokes more biased selection of the suspect if eyewitnesses are able to distinguish AI-generated filler images from the photograph of the suspect’s face. Using a model-based analysis, we compared biased suspect selection directly between lineups with AI-generated filler images and lineups with database-derived filler photographs. The results show that the lineups with AI-generated filler images were perfectly fair and, in fact, led to less biased suspect selection than the lineups with database-derived filler photographs used in previous experiments. These results are encouraging with regard to the potential of AI image generation for constructing fair lineups which should inspire more systematic research on the feasibility of adopting AI technology in forensic settings.
Murine bone-derived mesenchymal stem cells undergo molecular changes after a single passage in culture
Authors: Hughes Anastasia M. , Kuek Vincent , Oommen Joyce , Kotecha Rishi S. , Cheung Laurence C.
Published: May 2024

The rarity of the mesenchymal stem cell (MSC) population poses a significant challenge for MSC research. Therefore, these cells are often expanded in vitro, prior to use. However, long-term culture has been shown to alter primary MSC properties. Additionally, early passage primary MSCs in culture are often assumed to represent the primary MSC population in situ, however, little research has been done to support this. Here, we compared the transcriptomic profiles of murine MSCs freshly isolated from the bone marrow to those that had been expanded in culture for 10 days. We identified that a single passage in culture extensively altered MSC molecular signatures associated with cell cycling, differentiation and immune response. These findings indicate the critical importance of the MSC source, highlighting the need for optimization of culture conditions to minimize the impact on MSC biology and a transition towards in vivo methodologies for the study of MSC function.
Research on underwater robot ranging technology based on semantic segmentation and binocular vision
Authors: Hu Qing , Wang Kekuan , Ren Fushen , Wang Zhongyang
Published: May 2024

Based on the principle of light refraction and binocular ranging, the underwater imaging model is obtained. It provides a theoretical basis for underwater camera calibration. In order to meet the requirement of underwater vehicle to identify and distance underwater target, a new underwater vehicle distance measurement system based on semantic segmentation and binocular vision is proposed. The system uses Deeplabv3 + to identify the underwater target captured by the binocular camera and generate the target map, which is then used for binocular ranging. Compared with the binocular ranging using the original drawing, the measurement accuracy of the proposed method has not changed, the measurement speed is increased by 30%, and the error rate is controlled within 5%, which meets the needs of underwater robot operations.
Inhibiting HSD17B8 suppresses the cell proliferation caused by PTEN failure
Authors: Zhao Wei , Huang Ruiting , Ran Dongyang , Zhang Yutong , Qu Zhi , Zheng Shanqing
Published: May 2024

Loss of the tumor suppressor PTEN homolog daf-18 in Caenorhabditis elegans (C. elegans) triggers diapause cell division during L1 arrest. While prior studies have delved into established pathways, our investigation takes an innovative route. Through forward genetic screening in C. elegans, we pinpoint a new player, F12E12.11, regulated by daf-18, impacting cell proliferation independently of PTEN's typical phosphatase activity. F12E12.11 is an ortholog of human estradiol 17-beta-dehydrogenase 8 (HSD17B8), which converts estradiol to estrone through its NAD-dependent 17-beta-hydroxysteroid dehydrogenase activity. We found that PTEN engages in a physical interplay with HSD17B8, introducing a distinctive suppression mechanism. The reduction in estrone levels and accumulation of estradiol may arrest tumor cells in the G2/M phase of the cell cycle through MAPK/ERK. Our study illuminates an unconventional protein interplay, providing insights into how PTEN modulates tumor suppression by restraining cell division through intricate molecular interactions.
Phase-separating resins for light-based three-dimensional printing of oxide glasses
Authors: Barbera Lorenzo , Korhonen Henry , Masania Kunal , Studart André R.
Published: May 2024

Silica-based glasses can be shaped into complex geometries using a variety of additive manufacturing technologies. While the three-dimensional printing of glasses opens unprecedented design opportunities, the development of up-scaled, reliable manufacturing processes is crucial for the broader dissemination of this technology. Here, we design and study phase-separating resins that enable light-based 3D printing of oxide glasses with high-aspect-ratio features and enhanced manufacturing yields. The effect of the resin composition on the microstructure, mechanical properties and delamination resistance of parts printed by digital light processing is investigated with the help of printing experiments, compression tests and electron microscopy analysis. The chemical composition and microstructure of the cured resins were found to strongly affect the stiffness, delamination resistance, and calcination behavior of printed parts. These findings provide useful guidelines to enhance the reliability and yield of the DLP printing process of multicomponent silica-based glasses.
Impaired autonomic function and somatosensory disturbance in patients with treated autoimmune thyroiditis
Authors: Bazika-Gerasch Bojana , Kumowski Nina , Enax-Krumova Elena , Kaisler Miriam , Eitner Lynn Bernadette , Maier Christoph , Dietrich Johannes W.
Published: May 2024

Despite treatment with levothyroxine, hypothyroidism and autoimmune thyroiditis (AIT) may be associated with reduced quality of life (QoL), an enigmatic condition referred to as "syndrome T". Peripheral neuropathy, described in untreated thyroid disease, could be a contributing mechanism. We analysed autonomic and somatosensory function in 29 patients with AIT and treated hypothyroidism and 27 healthy volunteers. They underwent heart rate variability (HRV) analysis and quantitative sensory testing (n = 28), comprising 13 parameters of small and large nerve fibre function and pain thresholds. Autonomic cardiovascular function was assessed in rest, deep respiration and orthostasis. Additionally, biomarkers for autoimmunity and thyroid function were measured. Anxiety, depression and QoL were assessed using validated questionnaires. 36% of the patients showed at least one sign of somatosensory small or large fibre dysfunction. 57% presented with mild hyperalgesia to at least one stimulus. Several markers of autonomic function and some detection thresholds were related to the antibody titres. Anxiety, depression scores and QoL correlated to antibody titres and HRV measures. Autonomic and somatosensory dysfunction indicate that in treated hypothyroidism and AIT a subgroup of patients suffers from neuropathic symptoms leading to impaired QoL. Additionally, mild hyperalgesia as a possible sensitisation phenomenon should be considered a target for symptomatic treatment.
Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities
Authors: Eliette Ascensio-Schultz , Elodie Barbier , Arnaud Mounier , Tiffany Raynaud , Aymé Spor , Pascal Piveteau
Published: May 2024

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze–thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.
Chromatin modifier Hmga2 promotes adult hematopoietic stem cell function and blood regeneration in stress conditions
Authors: Kubota Sho , Sun Yuqi , Morii Mariko , Bai Jie , Ideue Takako , Hirayama Mayumi , Sorin Supannika , Eerdunduleng  , Yokomizo-Nakano Takako , Osato Motomi , Hamashima Ai , Iimori Mihoko , Araki Kimi , Umemoto Terumasa , Sashida Goro
Published: May 2024

The molecular mechanisms governing the response of hematopoietic stem cells (HSCs) to stress insults remain poorly defined. Here, we investigated effects of conditional knock-out or overexpression of Hmga2 (High mobility group AT-hook 2), a transcriptional activator of stem cell genes in fetal HSCs. While Hmga2 overexpression did not affect adult hematopoiesis under homeostasis, it accelerated HSC expansion in response to injection with 5-fluorouracil (5-FU) or in vitro treatment with TNF-α. In contrast, HSC and megakaryocyte progenitor cell numbers were decreased in Hmga2 KO animals. Transcription of inflammatory genes was repressed in Hmga2-overexpressing mice injected with 5-FU, and Hmga2 bound to distinct regions and chromatin accessibility was decreased in HSCs upon stress. Mechanistically, we found that casein kinase 2 (CK2) phosphorylates the Hmga2 acidic domain, promoting its access and binding to chromatin, transcription of anti-inflammatory target genes, and the expansion of HSCs under stress conditions. Notably, the identified stress-regulated Hmga2 gene signature is activated in hematopoietic stem progenitor cells of human myelodysplastic syndrome patients. In sum, these results reveal a TNF-α/CK2/phospho-Hmga2 axis controlling adult stress hematopoiesis.
Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum
Authors: Kadavá Tereza , Hevler Johannes F , Kalaidopoulou Nteak Sofia , Yin Victor C , Strasser Juergen , Preiner Johannes , Heck Albert JR
Published: May 2024

The complement is a conserved cascade that plays a central role in the innate immune system. To maintain a delicate equilibrium preventing excessive complement activation, complement inhibitors are essential. One of the major fluid-phase complement inhibitors is C4b-binding protein (C4BP). Human C4BP is a macromolecular glycoprotein composed of two distinct subunits, C4BPα and C4BPβ. These associate with vitamin K-dependent protein S (ProS) forming an ensemble of co-occurring higher-order structures. Here, we characterize these C4BP assemblies. We resolve and quantify isoforms of purified human serum C4BP using distinct single-particle detection techniques: charge detection mass spectrometry, and mass photometry accompanied by high-speed atomic force microscopy. Combining cross-linking mass spectrometry, glycoproteomics, and structural modeling, we report comprehensive glycoproteoform profiles and full-length structural models of the endogenous C4BP assemblies, expanding knowledge of this key complement inhibitor’s structure and composition. Finally, we reveal that an increased C4BPα to C4BPβ ratio coincides with elevated C-reactive protein levels in patient plasma samples. This observation highlights C4BP isoform variation and affirms a distinct role of co-occurring C4BP assemblies upon acute phase inflammation.
Building and analyzing metacells in single-cell genomics data
Authors: Bilous Mariia , Hérault Léonard , Gabriel Aurélie AG , Teleman Matei , Gfeller David
Published: May 2024

The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The scaling of computational methods to analyze and visualize such data is a constant challenge, and tools need to be regularly updated, if not redesigned, to cope with ever-growing numbers of cells. Over the last few years, metacells have been introduced to reduce the size and complexity of single-cell genomics data while preserving biologically relevant information and improving interpretability. Here, we review recent studies that capitalize on the concept of metacells—and the many variants in nomenclature that have been used. We further outline how and when metacells should (or should not) be used to analyze single-cell genomics data and what should be considered when analyzing such data at the metacell level. To facilitate the exploration of metacells, we provide a comprehensive tutorial on the construction and analysis of metacells from single-cell RNA-seq data (https://github.com/GfellerLab/MetacellAnalysisTutorial) as well as a fully integrated pipeline to rapidly build, visualize and evaluate metacells with different methods (https://github.com/GfellerLab/MetacellAnalysisToolkit).
Time-resolved EPR observation of blue-light-induced radical ion pairs in a flavin–Trp dyad
Authors: Oka Yoshimi , Inoue Katsuya
Published: May 2024

A flavin–Trp dyad was synthesized and characterized as a model system for magnetic-field sensors relevant to blue-light photoreceptor proteins.
Recent advances in rational structure design for nonlinear optical crystals: leveraging advantageous templates
Authors: Yan Ziting , Fan Jinbin , Pan Shilie , Zhang Min
Published: May 2024

An efficient strategy for designing nonlinear optical (NLO) crystals leveraging advantageous templates is proposed, and the recent advancements and prospects have been analyzed, providing valuable insights for the development of NLO materials.
Improvement in the sensitivity of LA-ICP-MS bioimaging by addition of nitrogen to the argon carrier gas
Authors: Mello Monique G. , Lockwood Thomas E. , Wanagat Jonathan , Westerhausen Mika T. , Bishop David P.
Published: May 2024

The addition of nitrogen improves signal-to-background in LA-ICP-MS bioimaging.
Environmentally responsible production of lime from recycled gypsum and weakly alkaline wastewater
Authors: Tafu Masamoto , Suzuki Asumi , Nakamura Juna , Fukumura Takuya , Tobe Tomofumi , Tobe Noboru
Published: May 2024

Benefits associated the treatment of wastewater from a returnable glass bottle-washing process as applied in this study. Our result transforms wastewater treatment into resource recovery, producing lime in an environmentally responsible manner.
Recent advances in graphene-based electroanalytical devices for healthcare applications
Authors: Kammarchedu Vinay , Asgharian Heshmat , Zhou Keren , Soltan Khamsi Pouya , Ebrahimi Aida
Published: May 2024

Recent advances in graphene-based electroanalytical biodevices: different methods for graphene synthesis, functionalization, device fabrication, and transduction mechanisms are discussed for various healthcare applications.
Heterogeneous distribution of kinesin–streptavidin complexes revealed by mass photometry
Authors: Xu Jing , Brown Nathaniel J. S. , Seol Yeonee , Neuman Keir C.
Published: May 2024

Mass photometry reveals the mass and the relative abundance of kinesin–streptavidin complex species. Our data indicate that complex heterogeneity arises from both the kinesin–streptavidin mixing ratio and the kinesin-biotinylation efficiency.
Integration of protein L-immobilized epoxy magnetic bead capture with LC-MS/MS for therapeutic monoclonal antibody quantification in serum
Authors: Cao Rongrong , Xu Songlin , Yu Zhirui , Xu Liang , Ge Zhiqiang , Huo Qianyu , Zhu Guoqing , Qiao Bin
Published: May 2024

Procedures for integrating protein L-immobilized magnetic bead capture with LC-MS/MS for mAb quantification in mouse serum.
Crystalline/amorphous nickel sulfide interface for high current density in alkaline HER: surface and volume confinement matters!
Authors: Sagayaraj Prince J. J. , Sekar Karthikeyan
Published: May 2024

In this report, we have developed a novel CA interface between crystalline and amorphous nickel sulfide which required a low overpotential of 15 mV for 10 mA cm−2 with the intrinsic activation for alkaline hydrogen evolution reaction.
Expedient access to polysubstituted acrylamides via strain-release-driven dual phosphine and palladium catalysis
Authors: Yao Yu-Xiang , Zhang Jing , Min Xuehong , Qin Lan , Wei Yi , Gao Yang , Hu Xiao-Qiang
Published: May 2024

A synergistic phosphine/palladium catalytic system has been developed for the three-component reaction of aromatic amines, cyclopropenones, and aryl halides, delivering polysubstituted acrylamides in satisfactory yields with (E)-selectivity.
Catalytic effect of microflow space for supramolecular block co-polymerization of water-soluble porphyrins
Authors: Takemori Haruna , Kanzaki Chisako , Nomura Shota , Maeda Takato , Numata Munenori
Published: May 2024

Microflow power plant opens up a new kinetic pathway to make new non-covalent bonds.
Selective recognition and reversible encapsulation of tetrameric alcohol clusters via hydrogen bonds using a perfluorinated dinuclear nickel(ii) complex
Authors: Habuka Yusuke , Usui Hirotomo , Okawa Mizuki , Shinohara Takanori , Yuge Hidetaka , Mao Yuchen , Gong Jin , Richards Gary J. , Hori Akiko
Published: May 2024

A perfluorinated Ni(ii) complex encapsulates MeOH, forming unique tetrameric clusters stabilized by hydrogen bonding in the crystal to achieve remarkable uptake of MeOH over EtOH and water, demonstrating potential for separation and sensing.
Study on the crystal structure and properties of a new crystal form of 3-nitro-1,2,4-triazole-5-one (NTO)
Authors: Wang Manman , Zhang Xing , Wang Zifeng , Li Dongze , Chen Shusen , Shu Qinghai
Published: May 2024

γ-NTO as an outstanding explosive compound.
Advancements in controlling COFs structure for enhanced crystallization properties and self-generated photocatalytic hydrogen peroxide
Authors: Bai Xiaojuan , Liu Rujiao , Zhu Bowen , Liu Xin , Cao Yihan , Dong Jiaqian , Yang Hua
Published: May 2024

Highly crystalline COFs can improve the photocatalytic hydrogen peroxide yield.
High-level reverse intersystem crossing of charge transfer compounds: to fluoresce or not to fluoresce?
Authors: Deng Ziqi , Huang Guanheng , Li Jiayu , Pang Junhong , He Jiaxing , Phillips David Lee , Li Ming-De
Published: May 2024

The mechanism of hRISC-TADF for p-TPA-BP: the delayed PL spectrum on the right side reveals the actual excited-state energy levels of this molecule.
Iodine capture of a two-dimensional layered uranyl–organic framework: a combined DFT and AIMD study
Authors: Shi Mingyang , Cheng Kunyang , Cheng Xiujuan , Zhou Xuying , Jiang Gang , Du Jiguang
Published: May 2024

To develop nuclear energy sustainably, it is important to effectively capture radioiodine in nuclear waste.
A cobalt molecular catalyst for hydrogen evolution reaction with remarkable activity in phosphate buffered water solution
Authors: Trotta Caterina , Dahiya Pardeep , Baldinelli Lorenzo , Menendez Rodriguez Gabriel , Chakraborty Priyanka , Bistoni Giovanni , De Angelis Filippo , Sundararaju Basker , Macchioni Alceo
Published: May 2024

Herein, we show that [Cp*Co(2-ampy)I]I (2-ampy = 2-aminomethyl-pyridine) is an extremely active catalyst for HER, exhibiting a TOF of 109 000 s−1 in phosphate buffered water solution (pH 7).
Development of ruthenium complexes with S-donor ligands for application in synthesis, catalytic acceptorless alcohol dehydrogenation and crossed-aldol condensation
Authors: Chandra Anushri , Basu Pousali , Raha Shreya , Dhibar Papu , Bhattacharya Samaresh
Published: May 2024

We synthesized a group of four [RuII(Ln)2(dmso)2] complexes (Ln = xanthate ligand), from which the dmso's could be easily displaced by bpy or phen. These complexes efficiently catalyze the AAD and, with base as co-catalyst, crossed-aldol condensation.
Reactive direct air capture of CO2 to C–C coupled products using multifunctional materials
Authors: Satter Shazia Sharmin , Saavedra Lopez Johnny , Hubbard Michael L. , Jiang Yuan , Dagle Robert A. , Kothandaraman Jotheeswari
Published: May 2024

A single sorbent-catalytic (non-noble metal) material has been developed for the integrated direct air capture and catalytic conversion of captured CO2 into C-C coupled products.
Incorporation of renewable carbons via formamide reactivity for the production of novel biobased polymers
Authors: Rocha Bianca C. , Dourado Isabela L. A. , Sanabria Marialy N. , Kimura Noemi S. P. , Cordeiro Priscila H. , Catalani Luiz H. , Andrade Leandro H.
Published: May 2024

A synthetic pathway for novel biobased polymers based on the reactivity of formamide towards renewable acrylate derivatives was developed.
A mild protocol for the development of an innovative green heterogeneous catalyst for the Hilbert-Johnson reaction
Authors: Elmoussaoui Soukaina , Lachhab Saida , El Mansouri Az-eddine , Fkhar Lahcen , Mehdi Ahmad , Sanghvi Yogesh S. , Ait-Ali Mustapha , Lazrek Hassan B.
Published: May 2024

Ammonium iodide-coated g-C3N4 (NH4I@g-C3N4) is investigated as a new and sustainable heterogeneous catalyst for the selective N1-alkylation of pyrimidines.
Cooperativity between coordinative unsaturated Fe(iii) and aryl-π electrons in MIL-100(Fe) for adsorption of small molecules
Authors: Tasaki-Handa Yuiko , Shibuya Kazuki , Saito Shingo
Published: May 2024

Coordinatively unsaturated sites and aryl-π electrons coorperatively affect the adsorption of aromatics with polar groups.
Highly efficient selective oxidation of toluene to benzaldehyde over Cu–V oxides supported on amorphous SiO2
Authors: Wang Xiaozhong , Shi Xiongfei , Gao Shenyuan , Xu Gang , Yang Jianhai , Guo Jia , Dai Liyan
Published: May 2024

Selective oxidation of toluene into high-value-added benzaldehyde is meaningful and challenging.
Hydrogen bond strengths in microhydrated clusters of HNO and HONO: energetic insights via a molecular tailoring approach
Authors: Ismail Thufail M. , Patkar Deepak , Sajith Pookkottu K. , Deshmukh Milind M.
Published: May 2024

The strengths of all individual hydrogen bonds (HBs) present in microhydrated clusters of HNO and HONO, i.e., HNO(H2O)n and HONO(H2O)n (n = 1–4), were examined using a molecular tailoring approach-based (MTA-based) method.
Terpenoids of plants from Chloranthaceae family: chemistry, bioactivity, and synthesis
Authors: Zhou Bin , Yue Jian-Min
Published: May 2024

This review systematically summarizes 682 structurally characterized terpenoids of 22 Chloranthaceae plants and their key biological activities as well as the chemical synthesis of selected terpenoids.
Dehydrogenative oxidation of hydrosilanes using gold nanoparticle deposited on citric acid-modified fibrillated cellulose: unveiling the role of molecular oxygen
Authors: Suwattananuruk Butsaratip , Uetake Yuta , Ichikawa Rise , Toyoshima Ryo , Kondoh Hiroshi , Sakurai Hidehiro
Published: May 2024

We developed an efficient and environmentally friendly catalyst, Au:F-CAC, for the dehydrogenative oxidation of hydrosilanes. Detailed analyses revealed that the cationic Au sites generated via the adsorption of oxygen play an important role.
Advances in the synthesis of rearranged homoisoflavonoids
Authors: Demidoff Felipe C. , Costa Paulo R. R. , Caleffi Guilherme S.
Published: May 2024

This review examines the progress in the total syntheses of these unique complex structures, highlighting their challenges and opportunities.
Semisynthesis and antitumor activity of endertiin B and related triterpenoids from Ganoderma lucidum
Authors: Liu Yu , Wen Hong-Kai , Xu Rui-Xuan , Liu Chang , Li Xiao-Han , Qin Xiang-Dong , Zhao You-Xing , Jia Yan-Xing , Luo Dou-Qiang
Published: May 2024

Four natural products of Ganoderma lucidum triterpenoids were semi-synthesized for the first time and the active compound endertiin B was demonstrated to play an anti-breast cancer role through the PI3K-AKT pathway.
The potential of an MOF accelerator in an electrochemiluminescence system for sensitive detection of menthol enantiomers
Authors: Kuang Xuan , Ruan Yeqian , Xin Jianping , Lan Lin
Published: May 2024

The critical element of an electrochemiluminescence (ECL) chiral sensor is the chiral electrode modifier.
Recent advances in SnS2-based nanomaterials as high-performance anodes for sodium ion batteries
Authors: Xiao Mingjun , Qi Dongming , Sun Huizhen , Meng Yanshuang , Zhu Fuliang
Published: May 2024

Tin disulfide (SnS2) is a promising anode material owing to its high theoretical capacity and large interlayer spacing. In this paper, the basic properties and storage mechanism are reviewed, with emphasis on the structure design of SnS2.
One-pot molten-salt construction of channels for hole transport and mass transfer over CoS2 nanocubes for visible-light-driven CO2 reduction
Authors: Wang Fulin , Zhou Man , Huang Weiya , Lu Kangqiang , Ouyang Shaobo , Xiang Wentao , Zhou Chensheng , Yu Changlin , Yang Kai
Published: May 2024

CuSCN loaded on CoS2 can construct carriers for hole transport and enhance CO2 mass transfer to improve photocatalytic CO2 reduction activity.
Exploring the multifaceted properties: electronic, magnetic, Curie temperature, elastic, thermal, and thermoelectric characteristics of gadolinium-filled PtSb3 skutterudite
Authors: Nayak Poorva , Gupta Dinesh C.
Published: May 2024

This guide covers skutterudite compounds' structural, physical, electronic, and magnetic properties, offering insights into their metallic behavior through detailed density of states analysis.
Biodegradable polyester copolymers: synthesis based on the Biginelli reaction, characterization, and evaluation of their application properties
Authors: Lu Kai , Shen Xinyi , Shi Yunhai , He Zejian , Zhang Dahong , Zhou Mi
Published: May 2024

Utilizing the Biginelli reaction, we synthesized four biodegradable polyester copolymers. These DHPMs exhibit diverse traits, including enhanced hydrophilicity and enabling self-assembled micelles; notably, DHPM–PPDO accelerates cell growth.
Degradation of different wastewater by a biological sponge iron system: microbial growth and influencing factors
Authors: Xie Huina , Zhao Wei , Li Jing , Li Jie
Published: May 2024

Strains isolated from the SFe-M system exhibit characteristics conducive to degrading organic pollutants and participating in nitrogen removal. SFe-acclimated microorganisms are capable of resisting the poison of excessive iron.
Expression of concern: Antibacterial and antibiofilm activities of silver-decorated zinc ferrite nanoparticles synthesized by a gamma irradiation-coupled sol–gel method against some pathogenic bacteria from medical operating room surfaces
Authors: Abdel Maksoud M. I. A. , El-Sayyad Gharieb S. , El-Bastawisy Hanan S. , Fathy Rasha M.
Published: May 2024

Expression of concern for ‘Antibacterial and antibiofilm activities of silver-decorated zinc ferrite nanoparticles synthesized by a gamma irradiation-coupled sol–gel method against some pathogenic bacteria from medical operating room surfaces’ by M. I. A. Abdel Maksoud et al., RSC Adv., 2021, 11, 28361–28374, https://doi.org/10.1039/D1RA04785J.
Calibration-free reaction yield quantification by HPLC with a machine-learning model of extinction coefficients
Authors: McDonald Matthew A. , Koscher Brent A. , Canty Richard B. , Jensen Klavs F.
Published: May 2024

Reaction optimization and characterization depend on reliable measures of reaction yield, often measured by high-performance liquid chromatography (HPLC).
A strategy for the controllable generation of organic superbases from benchtop-stable salts
Authors: Sujansky Stephen J. , Hoteling Garrett A. , Bandar Jeffrey S.
Published: May 2024

Benchtop-stable organic superbase (SB) carboxylate salts, when paired with an epoxide in situ, controllably generate netural superbases for reaction applications.
Implications of intracrystalline OC17 on the protection of lattice incorporated proteins
Authors: Caliskan Huseyin Burak , Ustok Fatma Isik
Published: May 2024

Incorporation of OC17 into crystal lattice protects the protein against high temperature denaturation. In-lattice protection may be utilized for stabilization of temperature-sensitive proteins in resource-limited settings.
A low Pt-loaded electrode electrochemically synthesized from bulk metal for electrocatalytic applications
Authors: Lu Xiaofeng , Wu Shizhao , Zheng Shitao , Sun Xinying , Wang Enjie , Chu Youqun , Gao Jing , Li Guohua
Published: May 2024

A Pt/WC1−x/WO3 self-supported electrode is fabricated from bulk metals by a electrochemical method. The interfacial effect of Pt and WC1−x/WO3 regulates the adsorption/desorption and transfer of Hads, thus optimizing the electrocatalytic performance.
Enhanced electrostatic shielding effect through incorporation of trace amounts of highly chelating anions for establishing a more stable electric double layer
Authors: Wang Minghui , Yin Junyi , Feng Xiang , Li Fuxiang , Li Zhuo , Zhang Wen , Cheng Yonghong , Xu Xin
Published: May 2024

IDHA anions with strong chelating capabilities participate in the solvation shell of Zn2+ and Na+. This interaction between IDHA anions and Na+ serves to stabilize the solvated sheath, thereby enhancing the electrostatic shielding effect of Na+.
Densely accessible Fe/Co–Nx dual-atom site coupled core–shell Co3Fe7@C as an efficient bifunctional oxygen electrocatalyst for rechargeable zinc–air batteries
Authors: Srinivas Katam , Yu Hesheng , Chen Zhuo , Chen Anran , Zhu Ming-qiang , Chen Yuanfu , Yang Chengtao
Published: May 2024

The symmetric electronic structure of an Fe single-atom site catalyst was effectively regulated by incorporating Co–Nx sites and core–shell Co3Fe7@C nanoparticles, resulting in high performance towards the ORR and Zn–air batteries.
Roles of G proteins and their GTPase-activating proteins in platelets
Authors: O'Donoghue Lorna , Smolenski Albert
Published: May 2024

Platelets are small anucleate blood cells supporting vascular function. They circulate in a quiescent state monitoring the vasculature for injuries. Platelets adhere to injury sites and can be rapidly activated to secrete granules and to form platelet/platelet aggregates. These responses are controlled by signalling networks that include G proteins and their regulatory guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Recent proteomics studies have revealed the complete spectrum of G proteins, GEFs, and GAPs present in platelets. Some of these proteins are specific for platelets and very few have been characterised in detail. GEFs and GAPs play a major role in setting local levels of active GTP-bound G proteins in response to activating and inhibitory signals encountered by platelets. Thus, GEFs and GAPs are highly regulated themselves and appear to integrate G protein regulation with other cellular processes. This review focuses on GAPs of small G proteins of the Arf, Rab, Ras, and Rho families, as well as of heterotrimeric G proteins found in platelets.