bluuebunny/crossref_metadata_2025 huggingface dataset:
MRI-only based material mass density and relative stopping power estimation via deep learning for proton therapy: a preliminary study
Authors: Gao Yuan , Chang Chih-Wei , Mandava Sagar , Marants Raanan , Scholey Jessica E. , Goette Matthew , Lei Yang , Mao Hui , Bradley Jeffrey D. , Liu Tian , Zhou Jun , Sudhyadhom Atchar , Yang Xiaofeng
Published: May 2024

Magnetic Resonance Imaging (MRI) is increasingly being used in treatment planning due to its superior soft tissue contrast, which is useful for tumor and soft tissue delineation compared to computed tomography (CT). However, MRI cannot directly provide mass density or relative stopping power (RSP) maps, which are required for calculating proton radiotherapy doses. Therefore, the integration of artificial intelligence (AI) into MRI-based treatment planning to estimate mass density and RSP directly from MRI has generated significant interest. A deep learning (DL) based framework was developed to establish a voxel-wise correlation between MR images and mass density as well as RSP. To facilitate the study, five tissue substitute phantoms were created, representing different tissues such as skin, muscle, adipose tissue, 45% hydroxyapatite (HA), and spongiosa bone. The composition of these phantoms was based on information from ICRP reports. Additionally, two animal tissue phantoms, simulating pig brain and liver, were prepared for DL training purposes. The phantom study involved the development of two DL models. The first model utilized clinical T1 and T2 MRI scans as input, while the second model incorporated zero echo time (ZTE) MRI scans. In the patient application study, two more DL models were trained: one using T1 and T2 MRI scans as input, and another model incorporating synthetic dual-energy computed tomography (sDECT) images to provide accurate bone tissue information. The DECT empirical model was used as a reference to evaluate the proposed models in both phantom and patient application studies. The DECT empirical model was selected as the reference for evaluating the proposed models in both phantom and patient application studies. In the phantom study, the DL model based on T1, and T2 MRI scans demonstrated higher accuracy in estimating mass density and RSP for skin, muscle, adipose tissue, brain, and liver. The mean absolute percentage errors (MAPE) were 0.42%, 0.14%, 0.19%, 0.78%, and 0.26% for mass density, and 0.30%, 0.11%, 0.16%, 0.61%, and 0.23% for RSP, respectively. The DL model incorporating ZTE MRI further improved the accuracy of mass density and RSP estimation for 45% HA and spongiosa bone, with MAPE values of 0.23% and 0.09% for mass density, and 0.19% and 0.07% for RSP, respectively. These results demonstrate the feasibility of using an MRI-only approach combined with DL methods for mass density and RSP estimation in proton therapy treatment planning. By employing this approach, it is possible to obtain the necessary information for proton radiotherapy directly from MRI scans, eliminating the need for additional imaging modalities.
Effects of phytosterol supplementation on lipoprotein subfractions and LDL particle quality
Authors: Machado Valeria Arruda , Santisteban Angela Rocio Niño , Martins Celma Muniz , Damasceno Nagila Raquel Teixeira , Fonseca Francisco A. , Neto Antonio M. Figueiredo , Izar Maria Cristina
Published: May 2024

Phytosterols are natural components of plant-based foods used as supplements because of their known cholesterol-lowering effect. However, their effects on lipoprotein subfractions and the quality of the LDL particle have not been studied in greater detail. We aimed to evaluate the effects of phytosterols supplements on lipids, lipoproteins subfractions, and on the quality of LDL. A prospective, pilot-type, open label, cross-over study, randomized 23 males in primary prevention of hypercholesterolemia to receive diet or diet plus phytosterol (2.6 g in 2 doses, with meals) for 12 weeks, when treatments were switched for another 12 weeks. Lipoprotein subfractions were analyzed by electrophoresis in polyacrylamide gel (Lipoprint System®). The Sampson equation estimated the small and dense (sd) and large and buoyant (lb) LDL subfractions from the lipid profile. Quality of LDL particle was analyzed by Z-scan and UV–vis spectroscopy. Primary outcome was the comparison of diet vs. diet plus phytosterols. Secondary outcomes assessed differences between baseline, diet and diet plus phytosterol. Non-parametric statistics were performed with p < 0.05. There was a trend to reduction on HDL-7 (p = 0.05) in diet plus phytosterol arm, with no effects on the quality of LDL particles. Heatmap showed strong correlations (ρ > 0.7) between particle size by different methods with both interventions. Diet plus phytosterol reduced TC, increased HDL-c, and reduced IDL-B, whereas diet increased HDL7, and reduced IDL-B vs. baseline (p < 0.05, for all). Phytosterol supplementation demonstrated small beneficial effects on HDL-7 subfraction, compared with diet alone, without effects on the quality of LDL particles.

This trial is registered in Clinical Trials (NCT06127732) and can be accessed at https://clinicaltrials.gov.
Nutraceutical blends predict enhanced health via microbiota reshaping improving cytokines and life quality: a Brazilian double-blind randomized trial
Authors: Santamarina Aline Boveto , de Freitas Jéssica Alves , Franco Lucas Augusto Moyses , Nehmi-Filho Victor , Fonseca Joyce Vanessa , Martins Roberta Cristina , Turri José Antônio , da Silva Bruna Fernanda Rio Branco , Fugi Beatriz Emi Itikawa , da Fonseca Sumaia Sobral , Gusmão Arianne Fagotti , Olivieri Eloísa Helena Ribeiro , de Souza Erica , Costa Silvia , Sabino Ester Cerdeira , Otoch José Pinhata , Pessoa Ana Flávia Marçal
Published: May 2024

Nutraceutical interventions supporting microbiota and eliciting clinical improvements in metabolic diseases have grown significantly. Chronic stress, gut dysbiosis, and metainflammation have emerged as key factors intertwined with sleep disorders, consequently exacerbating the decline in quality of life. This study aimed to assess the effects of two nutraceutical formulations containing prebiotics (fructooligosaccharides (FOS), galactooligosaccharides (GOS), yeast β-glucans), minerals (Mg, Se, Zn), and the herbal medicine Silybum marianum L. Gaertn., Asteraceae (Milk thistle or Silymarin). These formulations, namely NSupple (without silymarin) and NSupple_Silybum (with silymarin) were tested over 180 days in overweight/obese volunteers from Brazil's southeastern region. We accessed fecal gut microbiota by partial 16S rRNA sequences; cytokines expression by CBA; anthropometrics, quality of life and sleep, as well as metabolic and hormonal parameters, at baseline (T0) and 180 days (T180) post-supplementation. Results demonstrated gut microbiota reshaping at phyla, genera, and species level post-supplementation. The Bacteroidetes phylum, Bacteroides, and Prevotella genera were positively modulated especially in the NSupple_Silybum group. Gut microbiota modulation was associated with improved sleep patterns, quality-of-life perception, cytokines expression, and anthropometric parameters post-supplementation. Our findings suggest that the nutraceutical blends positively enhance cardiometabolic and inflammatory markers. Particularly, NSupple_Silybum modulated microbiota composition, underscoring its potential significance in ameliorating metabolic dysregulation. Clinical trial registry number: NCT04810572. 23/03/2021.
Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia
Authors: Norenhag Johanna , Edfeldt Gabriella , Stålberg Karin , Garcia Fabricio , Hugerth Luisa Warchavchik , Engstrand Lars , Fransson Emma , Du Juan , Schuppe-Koistinen Ina , Olovsson Matts
Published: May 2024

Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.
Dysregulation of platelet serotonin, 14–3–3, and GPIX in sudden infant death syndrome
Authors: Frelinger Andrew L. , Haynes Robin L. , Goldstein Richard D. , Berny-Lang Michelle A. , Gerrits Anja J. , Riehs Molly , Haas Elisabeth A. , Paunovic Brankica , Mena Othon J. , Campman Steven C. , Milne Ginger L. , Sleeper Lynn A. , Kinney Hannah C. , Michelson Alan D.
Published: May 2024

Sudden infant death syndrome (SIDS) is the leading cause of post-neonatal infant mortality, but the underlying cause(s) are unclear. A subset of SIDS infants has abnormalities in the neurotransmitter, serotonin (5-hydroxytryptamine [5-HT]) and the adaptor molecule, 14–3–3 pathways in regions of the brain involved in gasping, response to hypoxia, and arousal. To evaluate our hypothesis that SIDS is, at least in part, a multi-organ dysregulation of 5-HT, we examined whether blood platelets, which have 5-HT and 14–3–3 signaling pathways similar to brain neurons, are abnormal in SIDS. We also studied platelet surface glycoprotein IX (GPIX), a cell adhesion receptor which is physically linked to 14–3–3. In infants dying of SIDS compared to infants dying of known causes, we found significantly higher intra-platelet 5-HT and 14–3–3 and lower platelet surface GPIX. Serum and plasma 5-HT were also elevated in SIDS compared to controls. The presence in SIDS of both platelet and brainstem 5-HT and 14–3–3 abnormalities suggests a global dysregulation of these pathways and the potential for platelets to be used as a model system to study 5-HT and 14–3–3 interactions in SIDS. Platelet and serum biomarkers may aid in the forensic determination of SIDS and have the potential to be predictive of SIDS risk in living infants.
Mapping livestock density distribution in the Selenge River Basin of Mongolia using random forest
Authors: Liu Yaping , Wang Juanle , Yang Keming , Ochir Altansukh
Published: May 2024

Mapping dynamically distributed livestock in the vast steppe area based on statistical data collected by administrative units is very difficult as it is limited by the quality of statistical data and local geographical environment factors. While, spatial mapping of livestock gridded data is critical and necessary for animal husbandry management, which can be easily integrated and analyzed with other natural environment data. Facing this challenge, this study introduces a spatialization method using random forest (RF) in the Selenge River Basin, which is the main animal husbandry region in Mongolia. A spatialized model was constructed based on the RF to obtain high-resolution gridded distribution data of total livestock, sheep & goats, cattle, and horses. The contribution of factors influencing the spatial distribution of livestock was quantitatively analyzed. The predicted results showed that (1) it has high livestock densities in the southwestern regions and low in the northern regions of the Selenge River Basin; (2) the sheep & goats density was mainly concentrated in 0–125 sheep/km2, and the high-density area was mainly distributed in Khuvsgul, Arkhangai, Bulgan and part soums of Orkhon; (3) horses and cattle density were concentrated in 0–25 head/km2, mainly distributed in the southwest and central parts of the basin, with few high-density areas. This indicates that the RF simulation results effectively depict the characteristics of Selenge River Basin. Further study supported by Geodetector showed human activity was the main driver of livestock distribution in the basin. This study is expected to provide fundamental support for the precise regulation of animal husbandry in the Mongolian Plateau or other large steppe regions worldwide.
Comparative efficacy and safety of alpha-blockers as monotherapy for benign prostatic hyperplasia: a systematic review and network meta-analysis
Authors: Yoosuf Beema T , Panda Abhilash Kumar , KT Muhammed Favas , Bharti Saroj Kundan , Devana Sudheer Kumar , Bansal Dipika
Published: May 2024

Despite the availability of various drugs for benign prostatic hyperplasia (BPH), alpha(α)-blockers are the preferred first-line treatment. However, there remains a scarcity of direct comparisons among various α-blockers. Therefore, this network meta-analysis (NMA) of randomized controlled trials (RCTs) aimed to evaluate the efficacy and safety of α-blockers in the management of BPH. A comprehensive electronic search covered PubMed, Embase, Ovid MEDLINE, and Cochrane Library until August 2023. The primary endpoints comprised international prostate symptom score (IPSS), maximum flow rate (Qmax), quality of life (QoL), and post-void residual volume (PVR), while treatment-emergent adverse events (TEAEs) were considered as secondary endpoints. This NMA synthesized evidence from 22 studies covering 3371 patients with six kinds of α-blockers with 12 dose categories. IPSS has been considerably improved by tamsulosin 0.4 mg, naftopidil 50 mg and silodosin 8 mg as compared to the placebo. Based on the p-score, tamsulosin 0.4 mg had the highest probability of ranking for IPSS, PVR, and Qmax, whereas doxazosin 8 mg had the highest probability of improving QoL. A total of 297 adverse events were reported among all the α-blockers, silodosin has reported a notable number of TEAEs. Current evidence supports α-blockers are effective in IPSS reduction and are considered safer. Larger sample size with long-term studies are needed to refine estimates of IPSS, QoL, PVR, and Qmax outcomes in α-blocker users.
Expression analyses of CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS in the one-leaf plant Monophyllaea glabra reveal neoteny evolution of shoot meristem
Authors: Nakamura Shunji , Kinoshita Ayaka , Koga Hiroyuki , Tsukaya Hirokazu
Published: May 2024

The one-leaf plant Monophyllaea glabra exhibits a unique developmental manner in which only one cotyledon continues growing without producing new vegetative organs. This morphology is formed by specific meristems, the groove meristem (GM) and the basal meristem (BM), which are thought to be modified shoot apical meristem (SAM) and leaf meristem. In this study, we analysed the expression of the organ boundary gene CUP-SHAPED COTYLEDON (CUC) and the SAM maintenance gene SHOOT MERISTEMLESS (STM) orthologs by whole-mount in situ hybridisation. We found that CUCs did not show clear border patterns around GM and BM during the vegetative phase. Furthermore, double-colour detection analysis at the cellular level revealed that CUC and STM expression overlapped in the GM region during the vegetative phase. We also found that this overlap is dissolved in the reproductive phase when normal shoot organogenesis is observed. Since co-expression of these genes occurs during SAM initiation under embryogenesis in Arabidopsis, our results demonstrate that GM is a prolonged stage of pre-mature SAM. Therefore, we propose that neotenic meristems could be a novel plant trait acquired by one-leaf plants.
A method for delivering the required neutron fluence in an accelerator-based boron neutron capture therapy system employing a lithium target
Authors: Nakamura Satoshi , Takemori Mihiro , Nakaichi Tetsu , Shuto Yasunori , Kashihara Tairo , Iijima Kotaro , Chiba Takahito , Nakayama Hiroki , Urago Yuka , Nishina Shuka , Kobayashi Yuta , Kishida Hironori , Imamichi Shoji , Takahashi Kana , Masutani Mitsuko , Okamoto Hiroyuki , Nishio Teiji , Itami Jun , Igaki Hiroshi
Published: May 2024

Accelerator-based boron neutron capture therapy (BNCT) systems employing a solid-state lithium target indicated the reduction of neutron flux over the lifetime of a target, and its reduction could represent the neutron flux model. This study proposes a novel compensatory approach for delivering the required neutron fluence and validates its clinical applicability. The proposed approach relies on the neutron flux model and the cumulative sum of real-time measurements of proton charges. The accuracy of delivering the required neutron fluence for BNCT using the proposed approach was examined in five Li targets. With the proposed approach, the required neutron fluence could be delivered within 3.0%, and within 1.0% in most cases. However, those without using the proposed approach exceeded 3.0% in some cases. The proposed approach can consider the neutron flux reduction adequately and decrease the effect of uncertainty in neutron measurements. Therefore, the proposed approach can improve the accuracy of delivering the required fluence for BNCT even if a neutron flux reduction is expected during treatment and over the lifetime of the Li target. Additionally, by adequately revising the approach, it may apply to other type of BNCT systems employing a Li target, furthering research in this direction.
Assessment of smell disturbances 6 months after COVID-19 in Polish population
Authors: Okrzeja Jakub , Sołomacha Sebastian , Alimowski Maciej , Sowa Paweł , Dubatówka Marlena , Łapińska Magda , Kiszkiel Łukasz , Szczerbiński Łukasz , Laskowski Piotr Paweł , Czupryna Piotr , Kubas Bożena , Garkowski Adam , Kamiński Karol Adam , Moniuszko-Malinowska Anna
Published: May 2024

Considering the frequency and severity of olfactory disorders associated with SARS-CoV-2 infection, attention to the olfactory loss has expanded. The aim of our study was to assess of smell disturbances 6 months after COVID-19. The study population consisted of 2 groups: 196 Post-COVID-19 patients who were hospitalized because of COVID-19, control sample–130 patients without reported smell disorders from general population-Bialystok PLUS study. People from both groups were asked to participate in the Sniffin Sticks Test (half year after the disease). Sniffin Sticks Test consisted of 12 standardized smell samples. The participant's test score was counted based on correct scent recognition. Middle/older age was related with lower likelihood of olfaction recovery. The biggest differences in recognition of particular fragrances were observed for: orange and lemon, lemon and coffee (p.adj < 0.001). Patients had the greatest problem in assessing smell of lemon. The comparison of scores between Delta, Omicron, Wild Type, Wild Type Alpha waves showed statistically significant difference between Delta and Wild Type waves (p = 0.006). Duration of the disease (r = 0.218), age (r = -0.253), IL-6 (r = -0.281) showed significant negative correlations with the score. Statistically significant variables in the case of smell disorders were Omicron wave (CI = 0.045–0.902; P = 0.046) and Wild Type wave (CI = 0.135–0.716; P = 0.007) compared to Delta wave reference. Moreover, patients with PLT count below 150 000/μl had greater olfactory disorders than those with PLT count over 150 000/μl. There are: smell differences between post-COVID-19 patients and healthy population; statistically significant difference between Delta and Wild Type waves in Post-COVID-19 group in score of the Sniffin Sticks Test. Smell disturbances depend on the age, cognitive impairments, clinical characteristics of the COVID-19 disease and sex of the patient.
A study of the relationship between serum asprosin levels and MAFLD in a population undergoing physical examination
Authors: Lv Dan , Wang Zepu , Meng Cuiqiao , Li Yan , Ji Shuai
Published: May 2024

Asprosin, an adipokine, was recently discovered in 2016. Here, the correlation between asprosin and metabolic-associated fatty liver disease (MAFLD) was examined by quantitatively assessing hepatic steatosis using transient elastography and controlled attenuation parameter (CAP). According to body mass index (BMI), 1276 adult participants were enrolled and categorized into three groups: normal, overweight, and obese. The study collected and evaluated serum asprosin levels, general biochemical indices, liver stiffness measure, and CAP via statistical analysis. In both overweight and obese groups, serum asprosin and CAP were greater than in the normal group (p < 0.01). Each group showed a positive correlation of CAP with asprosin (p < 0.01). The normal group demonstrated a significant and independent positive relationship of CAP with BMI, low-density lipoprotein cholesterol (LDL-C), asprosin, waist circumference (WC), and triglycerides (TG;p < 0.05). CAP showed an independent positive association (p < 0.05) with BMI, WC, asprosin, fasting blood glucose (FBG), and TG in the overweight group, and with high-density lipoprotein cholesterol (HDL-C) showed an independent negative link (p < 0.01). CAP showed an independent positive relationship (p < 0.05) with BMI, WC, asprosin, TG, LDL-C, FBG, glycated hemoglobin A1c (HbA1c), and alanine transferase in the obese group. CAP also showed an independent positive link (p < 0.01) with BMI, WC, asprosin, TG, LDL-C, and FBG in all participants while independently and negatively correlated (p < 0.01) with HDL-C. Since asprosin and MAFLD are closely related and asprosin is an independent CAP effector, it may offer a novel treatment option for metabolic diseases and MAFLD.
Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing
Authors: Engvall Kristina , Uvdal Hanna , Björn Niclas , Åvall-Lundqvist Elisabeth , Gréen Henrik
Published: May 2024

Persistent taxane-induced peripheral neuropathy (TIPN) is highly prevalent among early-stage breast cancer survivors (ESBCS) and has detrimental effect on quality of life. We leveraged logistic regression models to develop and validate polygenic prediction models to estimate the risk of persistent PN symptoms in a training cohort and validation cohort taking clinical risk factors into account. Based on 337 whole-exome sequenced ESBCS two of five prediction models for individual PN symptoms obtained AUC results above 60% when validated. Using the model for numbness in feet (35 SNVs) in the test cohort, 73% survivors were correctly predicted. For tingling in feet (55 SNVs) 70% were correctly predicted. Both models included SNVs from the ADAMTS20, APT6V0A2, CCDC88C, CYP2C8, EPHA5, NR1H3, PSKH2/APTV0D2, and SCN10A genes. For cramps in feet, difficulty climbing stairs and difficulty opening a jar the validation was unsuccessful. Polygenic prediction models including clinical risk factors can estimate the risk of persistent taxane-induced numbness in feet and tingling in feet in ESBCS.
Vocal convergence and social proximity shape the calls of the most basal Passeriformes, New Zealand Wrens
Authors: Moran Ines G. , Loo Yen Yi , Louca Stilianos , Young Nick B. A. , Whibley Annabel , Withers Sarah J. , Salloum Priscila M. , Hall Michelle L. , Stanley Margaret C. , Cain Kristal E.
Published: May 2024

Despite extensive research on avian vocal learning, we still lack a general understanding of how and when this ability evolved in birds. As the closest living relatives of the earliest Passeriformes, the New Zealand wrens (Acanthisitti) hold a key phylogenetic position for furthering our understanding of the evolution of vocal learning because they share a common ancestor with two vocal learners: oscines and parrots. However, the vocal learning abilities of New Zealand wrens remain unexplored. Here, we test for the presence of prerequisite behaviors for vocal learning in one of the two extant species of New Zealand wrens, the rifleman (Acanthisitta chloris). We detect the presence of unique individual vocal signatures and show how these signatures are shaped by social proximity, as demonstrated by group vocal signatures and strong acoustic similarities among distantly related individuals in close social proximity. Further, we reveal that rifleman calls share similar phenotypic variance ratios to those previously reported in the learned vocalizations of the zebra finch, Taeniopygia guttata. Together these findings provide strong evidence that riflemen vocally converge, and though the mechanism still remains to be determined, they may also suggest that this vocal convergence is the result of rudimentary vocal learning abilities.
Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality
Authors: Wang Yangzi , Duchen Pablo , Chávez Alexandra , Sree K. Sowjanya , Appenroth Klaus J. , Zhao Hai , Höfer Martin , Huber Meret , Xu Shuqing
Published: May 2024

Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that genes associated with stress adaptations, flowering and embryogenesis were under positive selection. These data are consistent with the hypothesize that natural selection can shape the evolution of asexuality during habitat expansions, which alters genomic and epigenomic diversity levels.
Vesicle and reaction-diffusion hybrid modeling with STEPS
Authors: Hepburn Iain , Lallouette Jules , Chen Weiliang , Gallimore Andrew R. , Nagasawa-Soeda Sarah Y. , De Schutter Erik
Published: May 2024

Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling, restricting the realism of computational models. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our software STochastic Engine for Pathway Simulation (STEPS), a stochastic reaction-diffusion simulator that supports realistic reconstructions of cell tissue in tetrahedral meshes. The implementation is validated in an extensive test suite, parallel performance is demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.
Preservation of Bacillus subtilis’ cellular liquid state at deep sub-zero temperatures in perchlorate brines
Authors: Gault Stewart , Fonseca Fernanda , Cockell Charles S.
Published: May 2024

Although a low temperature limit for life has not been established, it is thought that there exists a physical limit imposed by the onset of intracellular vitrification, typically occurring at ~−20 °C for unicellular organisms. Here, we show, through differential scanning calorimetry, that molar concentrations of magnesium perchlorate can depress the intracellular vitrification point of Bacillus subtilis cells to temperatures much lower than those previously reported. At 2.5 M Mg(ClO4)2, the peak vitrification temperature was lowered to −83 °C. Our results show that inorganic eutectic salts can in principle maintain liquid water in cells at much lower temperatures than those previously claimed as a lower limit to life, raising the prospects of active biochemical processes in low temperature natural settings. Our results may have implications for the habitability of Mars, where perchlorate salts are pervasive and potentially other terrestrial and extraterrestrial, cryosphere environments.
B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles
Authors: Krause Robert , Ogongo Paul , Tezera Liku , Ahmed Mohammed , Mbano Ian , Chambers Mark , Ngoepe Abigail , Magnoumba Magalli , Muema Daniel , Karim Farina , Khan Khadija , Lumamba Kapongo , Nargan Kievershen , Madansein Rajhmun , Steyn Adrie , Shalek Alex K. , Elkington Paul , Leslie Al
Published: May 2024

B cells are important in tuberculosis (TB) immunity, but their role in the human lung is understudied. Here, we characterize B cells from lung tissue and matched blood of patients with TB and found they are decreased in the blood and increased in the lungs, consistent with recruitment to infected tissue, where they are located in granuloma associated lymphoid tissue. Flow cytometry and transcriptomics identify multiple B cell populations in the lung, including those associated with tissue resident memory, germinal centers, antibody secretion, proinflammatory atypical B cells, and regulatory B cells, some of which are expanded in TB disease. Additionally, TB lungs contain high levels of Mtb-reactive antibodies, specifically IgM, which promotes Mtb phagocytosis. Overall, these data reveal the presence of functionally diverse B cell subsets in the lungs of patients with TB and suggest several potential localized roles that may represent a target for interventions to promote immunity or mitigate immunopathology.
An at-leg pellet and associated Penicillium sp. provide multiple protections to mealybugs
Authors: Li Zicheng , Tong Haojie , Ni Meihong , Zheng Yiran , Yang Xinyi , Tan Yumei , Li Zihao , Jiang Mingxing
Published: May 2024

Beneficial fungi are well known for their contribution to insects’ adaptation to diverse habitats. However, where insect-associated fungi reside and the underlying mechanisms of insect-fungi interaction are not well understood. Here, we show a pellet-like structure on the legs of mealybugs, a group of economically important insect pests. This at-leg pellet, formed by mealybugs feeding on tomato but not by those on cotton, potato, or eggplant, originates jointly from host secretions and mealybug waxy filaments. A fungal strain, Penicillium citrinum, is present in the pellets and it colonizes honeydew. P. citrinum can inhibit mealybug fungal pathogens and is highly competitive in honeydew. Compounds within the pellets also have inhibitory activity against mealybug pathogens. Further bioassays suggest that at-leg pellets can improve the survival rate of Phenacoccus solenopsis under pathogen pressure, increase their sucking frequency, and decrease the defense response of host plants. Our study presents evidences on how a fungi-associated at-leg pellet provides multiple protections for mealybugs through suppressing pathogens and host defense, providing new insights into complex insect × fungi × plant interactions and their coevolution.
Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
Authors: Ehle Charlotte , Iyer-Bierhoff Aishwarya , Wu Yunchen , Xing Shaojun , Kiehntopf Michael , Mosig Alexander S. , Godmann Maren , Heinzel Thorsten
Published: May 2024

The hepatic acute-phase response is characterized by a massive upregulation of serum proteins, such as haptoglobin and serum amyloid A, at the expense of liver homeostatic functions. Although the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has a well-established role in safeguarding liver function and its cistrome spans around 50% of liver-specific genes, its role in the acute-phase response has received little attention so far. We demonstrate that HNF4A binds to and represses acute-phase genes under basal conditions. The reprogramming of hepatic transcription during inflammation necessitates loss of HNF4A function to allow expression of acute-phase genes while liver homeostatic genes are repressed. In a pre-clinical liver organoid model overexpression of HNF4A maintained liver functionality in spite of inflammation-induced cell damage. Conversely, HNF4A overexpression potently impaired the acute-phase response by retaining chromatin at regulatory regions of acute-phase genes inaccessible to transcription. Taken together, our data extend the understanding of dual HNF4A action as transcriptional activator and repressor, establishing HNF4A as gatekeeper for the hepatic acute-phase response.
Synthesis of ultra-high molecular weight homo- and copolymers via an ultrasonic emulsion process with a fast rate
Authors: Kalita Uddhab , Jafari Vianna F. , Ashokkumar Muthupandian , Singha Nikhil K. , Qiao Greg G.
Published: May 2024

In the forefront of advanced materials, ultra-high molecular weight (UHMW) polymers, renowned for their outstanding mechanical properties, have found extensive applications across various domains. However, their production has encountered a significant challenge: the attainment of UHMW polymers with a low dispersity (Ɖ). Herein, we introduce the pioneering technique of ultrasound (US) initiated polymerization, which has garnered attention for its capability to successfully polymerize a multitude of monomers. This study showcases the synthesis of UHMW polymers with a comparatively low Ɖ ( ≤ 1.1) within a remarkably short duration ( ~ 15 min) through the amalgamation of emulsion polymerization and high-frequency ultrasound-initiated polymerization. Particularly noteworthy is the successful copolymerization of diverse monomers, surpassing the molecular weight and further narrowing the Ɖ compared to their respective homopolymers. Notably, this includes monomers like vinyl acetate, traditionally deemed unsuitable for controlled polymerization. The consistent production and uniform dispersion of radicals during ultrasonication have been identified as key factors facilitating the swift fabrication of UHMW polymers with exceptionally low Ɖ.
The choice of land-based climate change mitigation measures influences future global biodiversity loss
Authors: Hirata Akiko , Ohashi Haruka , Hasegawa Tomoko , Fujimori Shinichiro , Takahashi Kiyoshi , Tsuchiya Kazuaki , Matsui Tetsuya
Published: May 2024

Climate mitigation is reported to benefit biodiversity globally. However, the impacts of mitigation measures based on large-scale land-use modifications can be concentrated in the regions where they are introduced, resulting in regional mismatches between mitigation efforts and biodiversity benefits. Here, we evaluated the impacts of large-scale deployment of bioenergy with carbon capture and storage and afforestation to attain the climate stabilization target stated by the Paris Agreement on global and regional biodiversity by using an integrated model framework. Our results highlight that climate mitigation efforts can benefit global biodiversity regardless of large-scale implementation of land-based mitigation measures. However, the negative impacts of mitigation measures on biodiversity are concentrated in regions with a higher contribution to land-use change and carbon sequestration. The results imply the need to consider the unequal regional distribution of benefits from climate mitigation, as well as mitigation options that avoid regional biodiversity loss by minimizing land-use change.
Ex vivo validation of magnetically actuated intravascular untethered robots in a clinical setting
Authors: Ligtenberg Leendert-Jan W. , Rabou Nicole C. A. , Goulas Constantinos , Duinmeijer Wytze C. , Halfwerk Frank R. , Arens Jutta , Lomme Roger , Magdanz Veronika , Klingner Anke , Klein Rot Emily A. M. , Nijland Colin H. E. , Wasserberg Dorothee , Liefers H. Remco , Jonkheijm Pascal , Susarrey-Arce Arturo , Warlé Michiel , Khalil Islam S. M.
Published: May 2024

Intravascular surgical instruments require precise navigation within narrow vessels, necessitating maximum flexibility, minimal diameter, and high degrees of freedom. Existing tools often lack control during insertion due to undesirable bending, limiting vessel accessibility and risking tissue damage. Next-generation instruments aim to develop hemocompatible untethered devices controlled by external magnetic forces. Achieving this goal remains complex due to testing and implementation challenges in clinical environments. Here we assess the operational effectiveness of hemocompatible untethered magnetic robots using an ex vivo porcine aorta model. The results demonstrate a linear decrease in the swimming speed of untethered magnetic robots as arterial blood flow increases, with the capability to navigate against a maximum arterial flow rate of 67 mL/min. The untethered magnetic robots effectively demonstrate locomotion in a difficult-to-access target site, navigating through the abdominal aorta and reaching the distal end of the renal artery.
A red-fleshed apple rich in anthocyanins improves endothelial function, reduces inflammation, and modulates the immune system in hypercholesterolemic subjects: the AppleCOR study
Authors: Pedret Anna , Companys Judit , Calderón-Pérez Lorena , Llauradó Elisabet , Pla-Pagà Laura , Salamanca Patricia , Sandoval-Ramírez Berner-Andree , Catalán Úrsula , Fernández-Castillejo Sara , Yuste Silvia , Macià Alba , Gutiérrez-Tordera Laia , Bulló Mónica , Camps Jordi , Canela Núria , Valls Rosa Maria , Rubió-Piqué Laura , Motilva Maria José , Solà Rosa
Published: May 2024

Red-fleshed apples (RFA), improve endothelial function and decrease inflammation. RFA induce more improvements in inflammation than aronia infusion (AI), whereas AI improves lipid profile. RFA, white-fleshed apples and AI modulate immune system.
Size-dependent plasmonic activity of AuNPs for the rational design of catalysts for organic reactions
Authors: Votkina Daria , Trelin Andrii , Semin Viktor , Lyutakov Oleksiy , Svorcik Vaclav , Petunin Pavel , Audran Gérard , Marque Sylvain R. A. , Guselnikova Olga , Postnikov Pavel
Published: May 2024

The rational design of plasmonic catalysts encompasses the manipulation of nanoparticle (NP) size: the smaller the AuNPs size is, the higher catalytic activity occurs.
Introduction to integrated approaches for methane activation
Authors: Shimizu Ken-ichi , Ueda Wataru , Song Hua
Published: May 2024

Kenichi Shimizu, Wataru Ueda & Hua Song introduce the Catalysis Science & Technology themed collection on Integrated approaches for methane activation.
A highly anisotropic family of hexagonal bipyramidal Dy(iii) unsaturated 18-crown-6 complexes exceeding the blockade barrier over 2700 K: a computational exploration
Authors: Moorthy Shruti , Tarannum Ibtesham , Kumari Kusum , Singh Saurabh Kumar
Published: May 2024

DFT and ab initio calculations were performed on Dy(III) complexes of saturated/unsaturated 18-crown-6 ligands to unravel the bonding and SIM behaviour. U18C6 ligands stabilize D5h geometry around Dy(III) ion, resulting in a giant barrier over 2700 K.
Mechanistic study of pyrazole synthesis via oxidation-induced N–N coupling of diazatitanacycles
Authors: Cheng Yukun , Huh Daniel N. , Tonks Ian A.
Published: May 2024

Metal-mediated inner-sphere N–N coupling is an uncommon route to N–N bond formation.
Inhibitory activities and mechanisms of free and bound phenolics on α-glucosidase in fresh fruits of Phyllanthus emblica Linn. using spectroscopy and molecular docking
Authors: Xing Mingxia , Xie Fan , Zeng Jingyi , Zhu Zengjin , Wang Guangqiang , Xia Yongjun , Zhang Hui , Song Zibo , Ai Lianzhong
Published: May 2024

Phyllanthus emblica Linn. (PE) fresh fruits contain high concentrations of polyphenolics, of which free and bound phenolics are rich in biological activities.
Bioactive compounds and benefits of by-products of Amazon babassu oil production: potential for dietary supplement, biomedical and food applications
Authors: Lima Rayssa Cruz , Carvalho Anna Paula Azevedo de , Almeida Antonio Eugenio Castro Cardoso de , Conte-Junior Carlos Adam
Published: May 2024

Babassu mesocarp flour is promising for application as biodegradable packaging and as an antioxidant for foods. Phytochemicals, antiparasitic and antibacterial activities and mesocarp flour were shown, but fungi and viruses can get more attention.
Tuning melanin: theoretical analysis of functional group impact on electrochemical and optical properties
Authors: Heppner Florian , Al-Shamery Noah , Lee Pooi See , Bredow Thomas
Published: May 2024

Theoretical analysis of derivatized melanin tetramer protomolecules highlights aminated melanin as a promising candidate for energy storage, given its favourable electronic and optical properties.
Mechanistic insights into the rhodium catalysed dehydrogenative cycloaddition of cyano-yne-allene substrates
Authors: Díaz-Jiménez Àlex , Roglans Anna , Solà Miquel , Pla-Quintana Anna
Published: May 2024

DFT calculations explored the Rh-catalysed dehydrogenative cycloaddition of cyano-yne-allene substrates. The reaction involves cycloaddition, hydrogen shift, 6π electrocyclization, and acceptorless H2 elimination.
Acid-assisted self-assembly of pyrene-capped tyrosine ruptures lysosomes to induce cancer cell apoptosis
Authors: Li Jing , Song Jiaqi , Shao Liang , Zhang Xianpeng , Wang Ziyi , Li Guanying , Wang Jiansheng , Zhang Jia
Published: May 2024

Acid-responsive assembly of pyrene-capped tyrosine induces lysosomal membrane permeabilization (LMP), triggering cancer apoptosis.
Influence of the hard segments content on the properties of electrospun aliphatic poly(carbonate-urethane-urea)s
Authors: Rolińska Karolina , Bakhshi Hadi , Balk Maria , Parzuchowski Paweł , Mazurek-Budzyńska Magdalena
Published: May 2024

The study investigated the impact of hard segments (HS) content on the morphology and thermomechanical properties of electrospun aliphatic poly(carbonate-urea-urethane)s (PCUUs).
Transition metal-free decarboxylative olefination of carboxylic acid salts
Authors: Joseph Ebbin , Brar Deshkanwar S. , Stuhlsatz Gaven , Tunge Jon A.
Published: May 2024

An expedient synthesis of electron-deficient styrenes is accomplished through decarboxylation and oxidation via halogen ion transfer. The resulting umpoled intermediates undergo a rebound elimination to furnish olefins.
Liquid crystalline elastomer self-oscillating fiber actuators fabricated from soft tubular molds
Authors: Sun Yuying , Men Yanli , Liu Shiyu , Wang Xiuxiu , Li Chensha
Published: May 2024

A strategy is developed for fabricating liquid crystalline elastomer self-oscillators by using soft tubes as molds. Through different soft tube configurations, the prepared oscillators perform different self-oscillation modes under light stimuli.
Ultrafast hole relaxation between dual valence bands in methylammonium lead iodide
Authors: Mou Sen , Leoncini Mauro , Macis Salvatore , Nisticò Gabriele , Tomarchio Luca , D'Arco Annalisa , Paolozzi Maria Chiara , Petrarca Massimo , Gambino Salvatore , Rizzo Aurora , Lupi Stefano
Published: May 2024

Methylammonium lead iodide exhibits dual valence bands. A pump at 400 nm excites the transition between VB2 and CB1, creating holes in VB2 (lighter and more conductive) that relax to VB1 rather than directly recombine with the electrons in CB1.
High performance of regenerated LiFePO4 from spent cathodes via an in situ coating and heteroatom-doping strategy using amino acids
Authors: Wang Junwei , Ji Shuaijing , Han Qigao , Wang Fengqian , Sha Wuxin , Cheng Danpeng , Zhang Weixin , Tang Shun , Cao Yuan-Cheng , Cheng Shijie
Published: May 2024

Schematic of the regeneration mechanism of spent LiFePO4via a redox process induced by sucrose and amino acids. High-temperature oxidation process transforms structure, eliminates additives, and facilitates nitrogen-doped carbon layer regeneration.
Photocatalyzed dimethylacrylamide polymerization in an aqueous solution using 4-nitrophenylacetylene-modified Cu2O crystals
Authors: Chen Yu-Chien , Huang Xing-Fu , Hsu Huei-Ting , Wu Er-Ting , Peng Chi-How , Huang Michael H.
Published: May 2024

4-Nitrophenylacetylene-functionalized Cu2O polyhedra can readily photocatalyze dimethylacrylamide polymerization in water. The orange gel becomes transparent after particle removal.
Visible-light-responsive S-vacancy ZnIn2S4/N-doped TiO2 nanoarray heterojunctions for high-performance photoelectrochemical water splitting
Authors: Bao Zhiyong , Jiang Yu , Zhang Zhihong , Lv Jun , Shen Wangqiang , Dai Jiyan , Wang Jiaheng , Cai Jing , Wu Yucheng
Published: May 2024

Sv-ZIS/N–TiO2 nanoarrays produced a photocurrent density of 4.9 mA cm−2 at an external potential of 1.23 V vs. RHE, and achieved PEC H2 evolution rate of 49.59 mmol g−1 h−1. The IPCE of the photoanode device is ∼57.9% at 350 nm and ∼7.3% at 400 nm.
Tough and single lithium-ion conductive nanocomposite electrolytes based on PAES-g-PEG and POSS–PEG for lithium–sulfur batteries
Authors: Shin Yunho , Le Mong Anh , Nguyen Thi Linh Chi , Kim Dukjoon
Published: May 2024

Tough nanocomposite solid electrolytes exhibit facile single Li-ion transport using POSS–PEG and simultaneously achieve both superior conductivity and excellent thermal/mechanical stability via self-assembled PAES-g-PEG for long-term safe LSBs.
Insights into electrolyte flooding in flexible gas diffusion electrodes for CO2 electrolysis: from mechanisms to effective mitigation strategies
Authors: Wu Yuming , Rabiee Hesamoddin , Zhao Xiu Song , Wang Geoff , Jiang Yijiao
Published: May 2024

This review aims to offer insights into the fundamental mechanisms of triggering electrolyte flooding in GDEs for CO2 electrolysis approaches for characterizing flooding, and potential strategies for mitigating electrolyte flooding.
Multistep synergistic modified NaNbO3-based ceramics for high-performance electrostatic capacitors
Authors: Lv Ling , Pan Zhongbin , Hu Jiawen , Zhou Zhixin , Li Huanhuan , Chen Xiqi , Liu Jinjun , Li Peng , Zhai Jiwei
Published: May 2024

NaNbO3-based lead-free energy storage ceramics are highlighted as essential components for the next-generation pulsed power capacitors, especially in the context of eco-friendly renewable energy sources.
A ratiometric fluorescent probe revealing the abnormality of acetylated tau by visualizing polarity in Alzheimer's disease
Authors: Sun Panpan , Chen Hai-Chao , Guo Wenting , Zhang Zefan , Sun Shihao , Gao Ningshuang , Jing Yu-Hong , Wang Baodui
Published: May 2024

A ratiometric fluorescent probe with high fluorescence efficiency in hydrophilic environment was developed. The probe not only tracked changes in cell polarity, but also found abnormal brain polarity in APP/PS1 mice compared to wild-type mice.
Natural gambogic acid-tuned self-assembly of nanodrugs towards synergistic chemophototherapy against breast cancer
Authors: Lin Baohang , Peng Xun , Cheng Jianjun , Wang Jiacheng
Published: May 2024

Self-assembled gambogic acid as a single-component active carrier for highly efficient synergistic and safe drug delivery against breast cancer.
Food-borne bacteria analysis using a diatomite bioinspired SERS platform
Authors: Chen Yikai , Ye Binggang , Ning Mengling , Li Meng , Pu Yixuan , Liu Zhiming , Zhong Huiqing , Hu Chaofan , Guo Zhouyi
Published: May 2024

Composites based on diatomaceous earth (Dia), a metal-phenolic network (MPN) and gold nanoparticles display outstanding SERS activity that can be used to distinguish species of food-borne bacteria.
Comparative effectiveness of myocardial patches and intramyocardial injections in treating myocardial infarction with a MitoQ/hydrogel system
Authors: Tan Ying , Nie Yali , ZhengWen Lei , Zheng Zhi
Published: May 2024

Schematic illustration of the comparative effectiveness of myocardial patches and intramyocardial injections in the treatment of myocardial infarction using a MitoQ/hydrogel system.