bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum dot-enabled infrared hyperspectral imaging with single-pixel detection
Authors: Meng Heyan , Gao Yuan , Wang Xuhong , Li Xianye , Wang Lili , Zhao Xian , Sun Baoqing
Published: May 2024

Near-infrared (NIR) hyperspectral imaging is a powerful technique that enables the capture of three-dimensional (3D) spectra-spatial information within the NIR spectral range, offering a wide array of applications. However, the high cost associated with InGaAs focal plane array (FPA) has impeded the widespread adoption of NIR hyperspectral imaging. Addressing this challenge, in this study, we adopt an alternative approach—single-pixel detection for NIR hyperspectral imaging. Our investigation reveals that single-pixel detection outperforms conventional FPA, delivering a superior signal-to-noise ratio (SNR) for both spectral and imaging reconstruction. To implement this strategy, we leverage self-assembled colloidal quantum dots (CQDs) and a digital micromirror device (DMD) for NIR spectral and spatial information multiplexing, complemented by single-pixel detection for simultaneous spectral and image reconstruction. Our experimental results demonstrate successful NIR hyperspectral imaging with a detection window about 600 nm and an average spectral resolution of 8.6 nm with a pixel resolution of 128 × 128. The resulting spectral and spatial data align well with reference instruments, which validates the effectiveness of our approach. By circumventing the need for expensive and bulky FPA and wavelength selection components, our solution shows promise in advancing affordable and accessible NIR hyperspectral imaging technologies, thereby expanding the range of potential applications.
Bidirectional two-sample Mendelian randomization analyses support causal relationships between structural and diffusion imaging-derived phenotypes and the risk of major neurodegenerative diseases
Authors: Wang Zirui , Yang Xuan , Li Haonan , Wang Siqi , Liu Zhixuan , Wang Yaoyi , Zhang Xingyu , Chen Yayuan , Xu Qiang , Xu Jiayuan , Wang Zengguang , Wang Junping
Published: May 2024

Previous observational investigations suggest that structural and diffusion imaging-derived phenotypes (IDPs) are associated with major neurodegenerative diseases; however, whether these associations are causal remains largely uncertain. Herein we conducted bidirectional two-sample Mendelian randomization analyses to infer the causal relationships between structural and diffusion IDPs and major neurodegenerative diseases using common genetic variants-single nucleotide polymorphism (SNPs) as instrumental variables. Summary statistics of genome-wide association study (GWAS) for structural and diffusion IDPs were obtained from 33,224 individuals in the UK Biobank cohort. Summary statistics of GWAS for seven major neurodegenerative diseases were obtained from the largest GWAS for each disease to date. The forward MR analyses identified significant or suggestively statistical causal effects of genetically predicted three structural IDPs on Alzheimer’s disease (AD), frontotemporal dementia (FTD), and multiple sclerosis. For example, the reduction in the surface area of the left superior temporal gyrus was associated with a higher risk of AD. The reverse MR analyses identified significantly or suggestively statistical causal effects of genetically predicted AD, Lewy body dementia (LBD), and FTD on nine structural and diffusion IDPs. For example, LBD was associated with increased mean diffusivity in the right superior longitudinal fasciculus and AD was associated with decreased gray matter volume in the right ventral striatum. Our findings might contribute to shedding light on the prediction and therapeutic intervention for the major neurodegenerative diseases at the neuroimaging level.
Leisure activities as reserve mediators of the relationship between loneliness and cognition in aging
Authors: Du Chao , Li Xin , Li Jingyi , Wang Wenxu , Dang Mingxi , Cheng Jiayin , Xu Kai , Wang Jun , Chen Chuansheng , Chen Yaojing , Zhang Zhanjun
Published: May 2024

Previous studies have found that loneliness affects cognitive functions in older persons. However, the influence of loneliness on different cognitive fields and the internal mechanism of the relationship are unclear. A total of 4772 older persons aged above 50 years (Mean = 65.31, SD = 6.96, 57.7% female) were included in this study. All the participants completed the characteristics scale, as well as the loneliness scale, leisure activity scale, and cognitive function tests in six domains. The results showed that 17.6% of participants had high loneliness, while 16.7% of participants had low loneliness. Associations were observed between higher levels of loneliness and lower scores in general cognitive ability, memory, and executive functions. Mediation analysis suggested that leisure activities, encompassing mental, physical, and social activities, were associated with cognitive functions in the context of loneliness. These results indicate that leisure activities may play a significant role in the relationship between loneliness and cognitive functions in older adults. The study highlights the importance of considering leisure activities in this demographic to potentially mitigate the adverse cognitive effects associated with loneliness.
Targeting ARNT attenuates chemoresistance through destabilizing p38α-MAPK signaling in glioblastoma
Authors: Alafate Wahafu , Lv Gen , Zheng Jiantao , Cai Haiping , Wu Wei , Yang Yong , Du Shichao , Zhou Dong , Wang Peng
Published: May 2024

Glioblastoma (GBM) is the most aggressive and lethal brain tumor in adults. This study aimed to investigate the functional significance of aryl hydrocarbon receptor nuclear translocator (ARNT) in the pathogenesis of GBM. Analysis of public datasets revealed ARNT is upregulated in GBM tissues compared to lower grade gliomas or normal brain tissues. Higher ARNT expression correlated with the mesenchymal subtype and poorer survival in GBM patients. Silencing ARNT using lentiviral shRNAs attenuated the proliferative, invasive, and stem-like capabilities of GBM cell lines, while ARNT overexpression enhanced these malignant phenotypes. Single-cell RNA sequencing uncovered that ARNT is highly expressed in a stem-like subpopulation and is involved in regulating glycolysis, hypoxia response, and stress pathways. Mechanistic studies found ARNT activates p38 mitogen-activated protein kinase (MAPK) signaling to promote chemoresistance in GBM cells. Disrupting the ARNT/p38α protein interaction via the ARNT PAS-A domain restored temozolomide sensitivity. Overall, this study demonstrates ARNT functions as an oncogenic driver in GBM pathogenesis and represents a promising therapeutic target.
ROBIN: a randomised, double-masked, placebo-controlled Phase IIa study of the AOC3 inhibitor BI 1467335 in diabetic retinopathy
Authors: Dong Nguyen Quan , Ehlers Justis P. , Boyer David S. , Jin Xidong , Giani Andrea , Ehrlich Michael S. ,   On behalf of the ROBIN study investigators, Brucker Alexander , Hu Allen , Fawzi Amani , Antoszyk Andrew , Berger Brian , Jhaveri Chirag , Bailey Claire , Brown David , Kunimoto Derek , Ghanchi Faruque , Bandello Francesco , Menon Geeta , Sen Harsha , Talks James , Figueira João , Barranco Jose Juan Escobar , Donate Lopez Juan , Habib Maged , Erke Maja Gran , Weger Martin , Cunningham Matthew , Varano Monica , Manjunatha Nonavinakere , Hahn Paul , Calvo Pilar , Dugel Pravin , Maturi Raj , Rosen Richard , Silva Rufino , Pagliarini Sergio , Sivaprasad Sobha , Androudi Sofia , Patel Sunil ,   Vall d’Hebron University Hospital,   CHLC - Hospital Santo António dos Capuchos
Published: May 2024

Objective

To evaluate the safety and efficacy of BI 1467335 in patients with non-proliferative diabetic retinopathy (NPDR).

Methods

ROBIN is a Phase IIa, double-masked, randomised, placebo-controlled study (NCT03238963). Patients with NPDR and without centre-involved diabetic macular oedema were included; all had a best corrected visual acuity letter score of ≥70 Early Treatment Diabetic Retinopathy Study letters in the study eye at screening. Patients received oral BI 1467335 10 mg or placebo once daily for 12 weeks. Post-treatment follow-up was 12 weeks. The primary endpoint was the proportion of patients over the 24 weeks with ocular adverse events (AEs). Secondary endpoints were the proportion of patients with ≥2-step improvement from baseline in DRSS severity level at Week 12 and the proportion of patients with non-ocular AEs at 24 weeks.

Results

Seventy-nine patients entered the study (BI 1467335, n = 40; placebo, n = 39). The proportion of patients with ocular AEs over 24 weeks was greater in the BI 1467335 versus the placebo group (35.0% vs 23.1%, respectively). Treatment-related AEs were reported for similar numbers of patients in the placebo and BI 1467335 group (7.7% vs 7.5%, respectively). At Week 12, 5.7% (n = 2) of patients in the BI 1467335 group had a 2-step improvement in DRSS severity level from baseline, compared with 0% in the placebo group.

Conclusions

BI 1467335 was well tolerated by patients with NPDR. There was a high variability in DRSS levels for individual patients over time, with no clear efficacy signal.
Pretreatment-free SERS sensing of microplastics using a self-attention-based neural network on hierarchically porous Ag foams
Authors: Guselnikova Olga , Trelin Andrii , Kang Yunqing , Postnikov Pavel , Kobashi Makoto , Suzuki Asuka , Shrestha Lok Kumar , Henzie Joel , Yamauchi Yusuke
Published: May 2024

Low-cost detection systems are needed for the identification of microplastics (MPs) in environmental samples. However, their rapid identification is hindered by the need for complex isolation and pre-treatment methods. This study describes a comprehensive sensing platform to identify MPs in environmental samples without requiring independent separation or pre-treatment protocols. It leverages the physicochemical properties of macroporous-mesoporous silver (Ag) substrates templated with self-assembled polymeric micelles to concurrently separate and analyze multiple MP targets using surface-enhanced Raman spectroscopy (SERS). The hydrophobic layer on Ag aids in stabilizing the nanostructures in the environment and mitigates biofouling. To monitor complex samples with multiple MPs and to demultiplex numerous overlapping patterns, we develop a neural network (NN) algorithm called SpecATNet that employs a self-attention mechanism to resolve the complex dependencies and patterns in SERS data to identify six common types of MPs: polystyrene, polyethylene, polymethylmethacrylate, polytetrafluoroethylene, nylon, and polyethylene terephthalate. SpecATNet uses multi-label classification to analyze multi-component mixtures even in the presence of various interference agents. The combination of macroporous-mesoporous Ag substrates and self-attention-based NN technology holds potential to enable field monitoring of MPs by generating rich datasets that machines can interpret and analyze.
Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction
Authors: Mohr Alex E. , Sweazea Karen L. , Bowes Devin A. , Jasbi Paniz , Whisner Corrie M. , Sears Dorothy D. , Krajmalnik-Brown Rosa , Jin Yan , Gu Haiwei , Klein-Seetharaman Judith , Arciero Karen M. , Gumpricht Eric , Arciero Paul J.
Published: May 2024

The gut microbiome (GM) modulates body weight/composition and gastrointestinal functioning; therefore, approaches targeting resident gut microbes have attracted considerable interest. Intermittent fasting (IF) and protein pacing (P) regimens are effective in facilitating weight loss (WL) and enhancing body composition. However, the interrelationships between IF- and P-induced WL and the GM are unknown. The current randomized controlled study describes distinct fecal microbial and plasma metabolomic signatures between combined IF-P (n = 21) versus a heart-healthy, calorie-restricted (CR, n = 20) diet matched for overall energy intake in free-living human participants (women = 27; men = 14) with overweight/obesity for 8 weeks. Gut symptomatology improves and abundance of Christensenellaceae microbes and circulating cytokines and amino acid metabolites favoring fat oxidation increase with IF-P (p < 0.05), whereas metabolites associated with a longevity-related metabolic pathway increase with CR (p < 0.05). Differences indicate GM and metabolomic factors play a role in WL maintenance and body composition. This novel work provides insight into the GM and metabolomic profile of participants following an IF-P or CR diet and highlights important differences in microbial assembly associated with WL and body composition responsiveness. These data may inform future GM-focused precision nutrition recommendations using larger sample sizes of longer duration. Trial registration, March 6, 2020 (ClinicalTrials.gov as NCT04327141), based on a previous randomized intervention trial.
Human movement and environmental barriers shape the emergence of dengue
Authors: Harish Vinyas , Colón-González Felipe J. , Moreira Filipe R. R. , Gibb Rory , Kraemer Moritz U. G. , Davis Megan , Reiner Robert C. , Pigott David M. , Perkins T. Alex , Weiss Daniel J. , Bogoch Isaac I. , Vazquez-Prokopec Gonzalo , Saide Pablo Manrique , Barbosa Gerson L. , Sabino Ester C. , Khan Kamran , Faria Nuno R. , Hay Simon I. , Correa-Morales Fabián , Chiaravalloti-Neto Francisco , Brady Oliver J.
Published: May 2024

Understanding how emerging infectious diseases spread within and between countries is essential to contain future pandemics. Spread to new areas requires connectivity between one or more sources and a suitable local environment, but how these two factors interact at different stages of disease emergence remains largely unknown. Further, no analytical framework exists to examine their roles. Here we develop a dynamic modelling approach for infectious diseases that explicitly models both connectivity via human movement and environmental suitability interactions. We apply it to better understand recently observed (1995-2019) patterns as well as predict past unobserved (1983-2000) and future (2020-2039) spread of dengue in Mexico and Brazil. We find that these models can accurately reconstruct long-term spread pathways, determine historical origins, and identify specific routes of invasion. We find early dengue invasion is more heavily influenced by environmental factors, resulting in patchy non-contiguous spread, while short and long-distance connectivity becomes more important in later stages. Our results have immediate practical applications for forecasting and containing the spread of dengue and emergence of new serotypes. Given current and future trends in human mobility, climate, and zoonotic spillover, understanding the interplay between connectivity and environmental suitability will be increasingly necessary to contain emerging and re-emerging pathogens.
TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene
Authors: Kabirova Evelyn , Ryzhkova Anastasiya , Lukyanchikova Varvara , Khabarova Anna , Korablev Alexey , Shnaider Tatyana , Nuriddinov Miroslav , Belokopytova Polina , Smirnov Alexander , Khotskin Nikita V. , Kontsevaya Galina , Serova Irina , Battulin Nariman
Published: May 2024

Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors: Kit, Kdr, Pdgfra. We used genome editing in mice to delete the TADs boundaries at the Kit locus and characterized chromatin folding and gene expression in pure cultures of fibroblasts, mast cells, and melanocytes. We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic activation only in melanocytes. Thus, the epigenetic landscape, namely the mutual arrangement of enhancers and actively transcribing genes, is important for predicting the consequences of the TAD boundaries removal. We also found that mice without a TAD border between the Kit and Kdr genes have a phenotypic manifestation of the mutation — a lighter coloration. Thus, the data obtained shed light on the principles of interaction between the 3D chromatin organization and epigenetic marks in the regulation of gene activity.
Regiodivergent biosynthesis of bridged bicyclononanes
Authors: Ernst Lukas , Lyu Hui , Liu Pi , Paetz Christian , Sayed Hesham M. B. , Meents Tomke , Ma Hongwu , Beerhues Ludger , El-Awaad Islam , Liu Benye
Published: May 2024

Medicinal compounds from plants include bicyclo[3.3.1]nonane derivatives, the majority of which are polycyclic polyprenylated acylphloroglucinols (PPAPs). Prototype molecules are hyperforin, the antidepressant constituent of St. John’s wort, and garcinol, a potential anticancer compound. Their complex structures have inspired innovative chemical syntheses, however, their biosynthesis in plants is still enigmatic. PPAPs are divided into two subclasses, named type A and B. Here we identify both types in Hypericum sampsonii plants and isolate two enzymes that regiodivergently convert a common precursor to pivotal type A and B products. Molecular modelling and substrate docking studies reveal inverted substrate binding modes in the two active site cavities. We identify amino acids that stabilize these alternative binding scenarios and use reciprocal mutagenesis to interconvert the enzymatic activities. Our studies elucidate the unique biochemistry that yields type A and B bicyclo[3.3.1]nonane cores in plants, thereby providing key building blocks for biotechnological efforts to sustainably produce these complex compounds for preclinical development.
SARS-CoV-2-specific immune responses converge in kidney disease patients and controls with hybrid immunity
Authors: Aguilar-Bretones Muriel , den Hartog Yvette , van Dijk Laura L. A. , Malahe S. Reshwan K. , Dieterich Marjolein , Mora Héctor Tejeda , Mueller Yvonne M. , Koopmans Marion P. G. , Reinders Marlies E. J. , Baan Carla C. , van Nierop Gijsbert P. , de Vries Rory D. ,   RECOVAC Consortium, Abrahams Alferso C. , Baas Marije C. , Hemmelder Marc H. , Bouwmans Pim , ten Dam Marc A. G. J. , Gommers Lennert , de Vries Aiko P. J.
Published: May 2024

Healthy individuals with hybrid immunity, due to a SARS-CoV-2 infection prior to first vaccination, have stronger immune responses compared to those who were exclusively vaccinated. However, little is known about the characteristics of antibody, B- and T-cell responses in kidney disease patients with hybrid immunity. Here, we explored differences between kidney disease patients and controls with hybrid immunity after asymptomatic or mild coronavirus disease-2019 (COVID-19). We studied the kinetics, magnitude, breadth and phenotype of SARS-CoV-2-specific immune responses against primary mRNA-1273 vaccination in patients with chronic kidney disease or on dialysis, kidney transplant recipients, and controls with hybrid immunity. Although vaccination alone is less immunogenic in kidney disease patients, mRNA-1273 induced a robust immune response in patients with prior SARS-CoV-2 infection. In contrast, kidney disease patients with hybrid immunity develop SARS-CoV-2 antibody, B- and T-cell responses that are equally strong or stronger than controls. Phenotypic analysis showed that Spike (S)-specific B-cells varied between groups in lymph node-homing and memory phenotypes, yet S-specific T-cell responses were phenotypically consistent across groups. The heterogeneity amongst immune responses in hybrid immune kidney patients warrants further studies in larger cohorts to unravel markers of long-term protection that can be used for the design of targeted vaccine regimens.
Mycobacterium tuberculosis produces d-serine under hypoxia to limit CD8+ T cell-dependent immunity in mice
Authors: Cheng Hongyu , Ji Zhe , Wang Yang , Li Shenzhi , Tang Tianqi , Wang Fei , Peng Cheng , Wu Xiangyang , Cheng Yuanna , Liu Zhonghua , Ma Mingtong , Wang Jie , Huang Xiaochen , Wang Lin , Qin Lianhua , Liu Haipeng , Chen Jianxia , Zheng Ruijuan , Feng Carl G. , Cai Xia , Qu Di , Ye Lilin , Yang Hua , Ge Baoxue
Published: May 2024

Adaptation to hypoxia is a major challenge for the survival of Mycobacterium tuberculosis (Mtb) in vivo. Interferon (IFN)-γ-producing CD8+ T cells contribute to control of Mtb infection, in part by promoting antimicrobial activities of macrophages. Whether Mtb counters these responses, particularly during hypoxic conditions, remains unknown. Using metabolomic, proteomic and genetic approaches, here we show that Mtb induced Rv0884c (SerC), an Mtb phosphoserine aminotransferase, to produce d-serine. This activity increased Mtb pathogenesis in mice but did not directly affect intramacrophage Mtb survival. Instead, d-serine inhibited IFN-γ production by CD8+ T cells, which indirectly reduced the ability of macrophages to restrict Mtb upon co-culture. Mechanistically, d-serine interacted with WDR24 and inhibited mTORC1 activation in CD8+ T cells. This decreased T-bet expression and reduced IFN-γ production by CD8+ T cells. Our findings suggest an Mtb evasion mechanism where pathogen metabolic adaptation to hypoxia leads to amino acid-dependent suppression of adaptive anti-TB immunity.
Long non-coding RNAs expression and regulation across different brain regions in primates
Authors: Navandar Mohit , Vennin Constance , Lutz Beat , Gerber Susanne
Published: May 2024

Human and non-human primates have strikingly similar genomes, but they strongly differ in many brain-based processes (e.g., behaviour and cognition). While the functions of protein-coding genes have been extensively studied, rather little is known about the role of non-coding RNAs such as long non-coding RNAs (lncRNAs). Here, we predicted lncRNAs and analysed their expression pattern across different brain regions of human and non-human primates (chimpanzee, gorilla, and gibbon). Our analysis identified shared orthologous and non-orthologous lncRNAs, showing striking differences in the genomic features. Differential expression analysis of the shared orthologous lncRNAs from humans and chimpanzees revealed distinct expression patterns in subcortical regions (striatum, hippocampus) and neocortical areas while retaining a homogeneous expression in the cerebellum. Co-expression analysis of lncRNAs and protein-coding genes revealed massive proportions of co-expressed pairs in neocortical regions of humans compared to chimpanzees. Network analysis of co-expressed pairs revealed the distinctive role of the hub-acting orthologous lncRNAs in a region- and species-specific manner. Overall, our study provides novel insight into lncRNA driven gene regulatory landscape, neural regulation, brain evolution, and constitutes a resource for primate’s brain lncRNAs.
EpCAM-CD24+ circulating cells associated with poor prognosis in breast cancer patients
Authors: Perelmuter V. M. , Grigoryeva E. S. , Savelieva O. E. , Alifanov V. V. , Andruhova E. S. , Zavyalova M. V. , Bragina O. D. , Garbukov E. Yu. , Menyailo M. E. , Khozyainova A. A. , Denisov E. V. , Cherdyntseva N. V. , Tashireva L. A.
Published: May 2024

Following the discovery of circulating tumor cells (CTCs) in the peripheral blood of cancer patients, CTCs were initially postulated to hold promise as a valuable prognostic tool through liquid biopsy. However, a decade and a half of accumulated data have revealed significant complexities in the investigation of CTCs. A challenging aspect lies in the reduced expression or complete loss of key epithelial markers during the epithelial-mesenchymal transition (EMT). This likely hampers the identification of a pathogenetically significant subset of CTCs. Nevertheless, there is a growing body of evidence regarding the prognostic value of such molecules as CD24 expressing in the primary breast tumor. Herewith, the exact relevance of CD24 expression on CTCs remains unclear. We used two epithelial markers (EpCAM and cytokeratin 7/8) to assess the count of CTCs in 57 breast cancer patients, both with (M0mts) and without metastasis (M0) during the follow-up period, as well as in M1 breast cancer patients. However, the investigation of these epithelial markers proved ineffective in identifying cell population expressing different combinations of EpCAM and cytokeratin 7/8 with prognostic significance for breast cancer metastases. Surprisingly, we found CD24+ circulating cells (CCs) in peripheral blood of breast cancer patients which have no epithelial markers (EpCAM and cytokeratin 7/8) but was strongly associated with distant metastasis. Namely, the count of CD45-EpCAM-CK7/8-CD24+ N-cadherin—CCs was elevated in both groups of patients, those with existing metastasis and those who developed metastases during the follow-up period. Simultaneously, an elevation in these cell counts beyond the established threshold of 218.3 cells per 1 mL of blood in patients prior to any treatment predicted a 12-fold risk of metastases, along with a threefold decrease in distant metastasis-free survival over a 90-month follow-up period. The origin of CD45-EpCAM-CK7/8-CD24+ N-cadherin—CCs remains unclear. In our opinion their existence can be explained by two most probable hypotheses. These cells could exhibit a terminal EMT phenotype, or it might be immature cells originating from the bone marrow. Nonetheless, if this hypothesis holds true, it's worth noting that the mentioned CCs do not align with any of the recognized stages of monocyte or neutrophil maturation, primarily due to the presence of CD45 expression in the myeloid cells. The results suggest the presence in the peripheral blood of patients with metastasis (both during the follow-up period and prior to inclusion in the study) of a cell population with a currently unspecified origin, possibly arising from both myeloid and tumor sources, as confirmed by the presence of aneuploidy.
A forensic genetic investigation reveals a captive origin for a wild alien population of raccoons in Italy
Authors: Garofalo Luisa , Cappai Nadia , Mencucci Marco , Mori Emiliano , Attili Lorenzo , Lorenzini Rita
Published: May 2024

Invasive alien species have extensively impacted the ecosystems, where they may affect the native biodiversity. The North American raccoon Procyon lotor is one of the most successful invaders in Europe since its introduction in the early twentieth century. In Italy, a wild population was first established in the North at the beginning of the 2000s following a local introduction event. A further self-sustaining population was reported ten years later in Central Italy. To support an official investigation by the authorities, who suspected a captive origin of the free-ranging raccoons in Central Italy, we used nuclear and mitochondrial DNA markers, combined with different statistical approaches, to characterise their gene pool and trace the source of the founders. Results revealed that founders came from a private zoo-park from which they had inadvertently escaped, soon establishing a reproductive population in the wild. Additionally, our mitochondrial DNA data were used to supplement the haplotype variability known to date in captive and wild raccoons from Europe, Asia and their native range. The comparisons allowed us to update previous networks based on the control region with a new mitochondrial lineage, which had not been detected so far.
Extracellular vesicles from GABAergic but not glutamatergic neurons protect against neurological dysfunction following cranial irradiation
Authors: Smith Sarah M. , Ranjan Kashvi , Hoover Brianna M. , Drayson Olivia G. G. , Acharya Munjal M. , Kramár Eniko A. , Baulch Janet E. , Limoli Charles L.
Published: May 2024

Cranial irradiation used to control brain malignancies invariably leads to progressive and debilitating declines in cognition. Clinical efforts implementing hippocampal avoidance and NMDAR antagonism, have sought to minimize dose to radiosensitive neurogenic regions while normalizing excitatory/inhibitory (E/I) tone. Results of these trials have yielded only marginal benefits to cognition, prompting current studies to evaluate the potential of systemic extracellular vesicle (EV) therapy to restore neurocognitive functionality in the irradiated brain. Here we tested the hypothesis that EVs derived from inhibitory but not excitatory neuronal cultures would prove beneficial to cognition and associated pathology. Rats subjected to a clinically relevant, fractionated cranial irradiation paradigm were given multiple injections of either GABAergic- or glutamatergic-derived EV and subjected to behavioral testing. Rats treated with GABAergic but not glutamatergic EVs showed significant improvements on hippocampal- and cortical-dependent behavioral tasks. While each treatment enhanced levels of the neurotrophic factors BDNF and GDNF, only GABAergic EVs preserved granule cell neuron dendritic spine density. Additional studies conducted with GABAergic EVs, confirmed significant benefits on amygdala-dependent behavior and modest changes in synaptic plasticity as measured by long-term potentiation. These data point to a potentially more efficacious approach for resolving radiation-induced neurological deficits, possibly through a mechanism able to restore homeostatic E/I balance.
A python based algorithmic approach to optimize sulfonamide drugs via mathematical modeling
Authors: Ahmed Wakeel , Ali Kashif , Zaman Shahid , Agama Fekadu Tesgera
Published: May 2024

This article explores the structural properties of eleven distinct chemical graphs that represent sulfonamide drugs using topological indices by developing python algorithm. To find significant relationships between the topological characteristics of these networks and the characteristics of the associated sulfonamide drugs. We use quantitative structure-property relationship (QSPR) approaches. In order to model and forecast these correlations and provide insights into the structure-activity relationships that are essential for drug design and optimization, linear regression is a vital tool. A thorough framework for comprehending the molecular characteristics and behavior of sulfonamide drugs is provided by the combination of topological indices, graph theory and statistical models which advances the field of pharmaceutical research and development.
Quantum computing for several AGV scheduling models
Authors: Tang Liang , Yang Chao , Wen Kai , Wu Wei , Guo Yiyun
Published: May 2024

Due to the high degree of automation, automated guided vehicles (AGVs) have been widely used in many scenarios for transportation, and traditional computing power is stretched in large-scale AGV scheduling. In recent years, quantum computing has shown incomparable performance advantages in solving specific problems, especially Combinatorial optimization problem. In this paper, quantum computing technology is introduced into the study of the AGV scheduling problem. Additionally two types of quadratic unconstrained binary optimisation (QUBO) models suitable for different scheduling objectives are constructed, and the scheduling scheme is coded into the ground state of Hamiltonian operator, and the problem is solved by using optical coherent Ising machine (CIM). The experimental results show that compared with the traditional calculation method, the optical quantum computer can save 92% computation time on average. It has great application potential.
Bile promotes Lactobacillus johnsonii N6.2 extracellular vesicle production with conserved immunomodulatory properties
Authors: Beliakoff Reagan E. , Gonzalez Claudio F. , Lorca Graciela L.
Published: May 2024

Recently, Lactobacillus johnsonii N6.2-derived extracellular vesicles (EVs) were shown to reduce apoptosis in human beta cell lines and stimulate insulin secretion in human islets. Our goal was to identify a physiologically relevant environmental condition that induces a hypervesiculation phenotype in L. johnsonii N6.2 and to evaluate if transcriptional changes are involved in this process. Culturing this strain in the presence of 0.2% bovine bile, which mimics a stressor encountered by the bacterium in the small intestine, resulted in approximately a 100-fold increase in EVs relative to cells grown in media without bile. Whole transcriptome analysis of cells grown with bile revealed upregulation of several peptidoglycan hydrolases as well as several genes involved in fatty acid utilization. These results suggest that the hypervesiculation phenotype may be the result of increased cell wall turnover combined with increased accumulation of phospholipids, in agreement with our previous proteomic and lipidomics results. Additionally, EVs isolated from L. johnsonii N6.2 grown in presence of bile maintained their immunomodulatory properties in host-derived βlox5 pancreatic and THP-1 macrophage cell lines. Our findings suggest that in L. johnsonii N6.2 vesiculogenesis is significantly impacted by the expression of cell wall modifying enzymes and proteins utilized for exogenous fatty acid uptake that are regulated at the transcriptional level. Furthermore, this data suggests that vesiculogenesis could be stimulated in vivo using small molecules thereby maximizing the beneficial interactions between bacteria and their hosts.
Mathematical modeling of rare earth element separation in electrodialysis with adjacent anion exchange membranes and ethylenediaminetetraacetic acid as chelating agent
Authors: Ding Lingyang , Azimi Gisele
Published: May 2024

This research delves into the effective use of electrodialysis for the separation of rare earth elements (REEs), specifically separating dysprosium (Dy) from praseodymium (Pr) and neodymium (Nd). A robust mathematical model based on the extended Nernst-Planck equation is introduced, simulating the process within a configuration that includes two adjacent anion exchange membranes. The model integrates aspects such as feed equilibrium, ion exchange within the membrane, and overall ion flux. Validation of the model's predictability was conducted through Chi-squared tests and root mean square error (RMSE) calculations, affirming its capability to accurately predict ion concentrations across different compartments. The study examines essential parameters such as applied voltage, rinse solution concentration, and feed concentration, assessing their impacts on separation performance and energy efficiency. Results indicate that higher voltages above 8 V, while speeding up separation, detrimentally impact energy use. It also highlights a critical balance in rinse solution concentration; lower concentrations below 0.05 mol/L enhance energy efficiency but may undercut separation efficacy due to early depletion. A linear correlation between the necessary rinse concentration and feed concentration was established, with higher feed concentrations demonstrating reduced specific energy consumption, thus enhancing overall efficiency. However, challenges remain in current efficiency due to the independent migration of SO42− ions in this specific setup. The findings advocate exploring alternative configurations, like alternating cation and anion exchange membranes, to optimize both environmental and economic aspects of REE separation. This study provides valuable insights and recommendations for refining electrodialysis systems in REE processing, contributing to sustainable and cost-effective electrodialysis systems.
Strong influence of magnetic field and non-uniform stress on elastic modulus and transition temperatures of twinned Ni–Fe(Co)–Ga alloy
Authors: Kosogor Anna , Soprunyuk Viktor , Koraltan Sabri , Golub Vladimir , Velyhotskyi Dmytro , Chernenko Volodymyr , Hosoda Hideki , Suess Dieter , Schranz Wilfried , L’vov Victor A.
Published: May 2024

The magnetization value and electric resistivity of the single-crystalline sample of Ni50Fe19Co4Ga27 shape memory alloy were measured. The elastic modulus was determined by the Dynamic Mechanical Analysis (DMA). The characteristic temperatures of martensitic transformation (MT) of the alloy were estimated from the temperature dependences of magnetization, electric resistivity and elastic modulus. A significant disparity between MT temperatures resulting from DMA and those estimated from magnetic and resistivity measurements was discovered. It was argued that the discrepancy is caused by the non-uniform mechanical stressing of twinned single crystal by the DMA analyzer. Moreover, the DMA measurements revealed a significant decrease of the elastic modulus of twinned martensite under the applied magnetic field of 1.5 kOe. To explain this effect, the temperature-dependent Young’s modulus of twinned crystal lattice was computed. The computations showed that the experimentally observed field-induced change of the elastic modulus is caused by the stress-assisted detwinning of the crystal lattice by the applied magnetic field.
Sagittal spinal curvatures of young adults in the context of their self-reported physical activity and somatic parameters
Authors: Grabara Małgorzata , Witkowska Anna
Published: May 2024

The objective of this study was to assess the thoracic kyphosis (ThKA) and lumbar lordosis (LLA) in healthy young adults and to investigate potential relationships between spinal curvatures, self-reported physical activity (PA), and somatic parameters. The study included 380 female students and 211 male students aged 20.7 ± 1.5 years. The ThKA and LLA were measured using a Plurimeter-V gravity inclinometer. The level of PA was estimated using the International Physical Activity Questionnaire. ThKA was lower in women compared to men, while LLA was higher in women than in men (p < 0.0001). Female students reported lower PA than male students (p < 0.001). Female students with ThKA within normal values reported a significantly higher amount of low-intensity PA compared to those with ThKA below or above the norm. A correlation was found between ThKA and body mass index (BMI), body adiposity index (BAI), WC, and fat percentage (rho < 0.2), whereas LLA showed correlations with BMI, BAI, waist circumference, and fat percentage (rho < 0.2). Among male students, a correlation was found between LLA and BMI as well as WC (rho < 0.2). Maintaining a healthy body composition may be instrumental in mitigating the risk of developing spinal curvature abnormalities.
Discovery of potent antimycobacterial agents targeting lumazine synthase (RibH) of Mycobacterium tuberculosis
Authors: Singh Monica , Dhanwal Anannya , Verma Arpita , Augustin Linus , Kumari Niti , Chakraborti Soumyananda , Agarwal Nisheeth , Sriram Dharmarajan , Dey Ruchi Jain
Published: May 2024

Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, as a potential drug target against Mycobacterium tuberculosis (M. tb) using a CRISPRi-based conditional gene knockdown strategy. We employ a high-throughput molecular docking approach to screen ~ 600,000 compounds targeting RibH. Through in vitro screening of 55 shortlisted compounds, we discover 3 compounds that exhibit potent antimycobacterial activity. These compounds also reduce intracellular burden of M. tb during macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these three compounds enhance the bactericidal effect of first-line anti-TB drugs, isoniazid and rifampicin. Corroborating with the in silico predicted high docking scores along with favourable ADME and toxicity profiles, all three compounds demonstrate binding affinity towards purified lumazine synthase enzyme in vitro, in addition these compounds exhibit riboflavin displacement in an in vitro assay with purified lumazine synthase indicative of specificity of these compounds to the active site. Further, treatment of M. tb with these compounds indicate reduced production of flavin adenine dinucleotide (FAD), the ultimate end product of the riboflavin biosynthetic pathway suggesting the action of these drugs on riboflavin biosynthesis. These compounds also show acceptable safety profile in mammalian cells, with a high selective index. Hence, our study validates RibH as an important drug target against M. tb and identifies potent antimycobacterial agents.
Resistance to pyrethroids and the relationship between adult resistance and knockdown resistance (kdr) mutations in Aedes albopictus in dengue surveillance areas of Guizhou Province, China
Authors: Zhang Yan , Wang Dan , Shi Weifang , Zhou Jingzhu , Xiang Yulong , Guan Yuwei , Kong Xuexue , Liang Wenqin , Hu Yong
Published: May 2024

The Ae. albopictus mosquito has gained global attention due to its ability to transmit viruses, including the dengue and zika. Mosquito control is the only effective way to manage dengue fever, as no effective treatments or vaccines are available. Insecticides are highly effective in controlling mosquito densities, which reduces the chances of virus transmission. However, Ae. albopictus has developed resistance to pyrethroids in several provinces in China. Pyrethroids target the voltage-gated sodium channel gene (VGSC), and mutations in this gene may result in knockdown resistance (kdr). Correlation studies between resistance and mutations can assist viruses in managing Ae. albopictus, which has not been studied in Guizhou province. Nine field populations of Ae. albopictus at the larval stage were collected from Guizhou Province in 2022 and reared to F1 to F2 generations. Resistance bioassays were conducted against permethrin, beta-cypermethrin, and deltamethrin for both larvae and adults of Ae. albopictus. Kdr mutations were characterized by PCR and sequencing. Additionally, the correlation between the kdr allele and pyrethroid resistance was analyzed. All nine populations of Ae. albopictus larvae and adults were found to be resistant to three pyrethroid insecticides. One kdr mutant allele at codon 1016, one at 1532 and three at 1534 were identified with frequencies of 13.86% (V1016G), 0.53% (I1532T), 58.02% (F1534S), 11.69% (F1534C), 0.06% (F1534L) and 0.99% (F1534P), respectively. Both V1016G and F1534S mutation mosquitoes were found in all populations. The kdr mutation F1534S was positively correlated with three pyrethroid resistance phenotypes (OR > 1, P < 0.05), V1016G with deltamethrin and beta-cypermethrin resistance (OR > 1, P < 0.05) and F1534C only with beta-cypermethrin resistance (OR > 1, P < 0.05). Current susceptibility status of wild populations of Ae. albopictus to insecticides and a higher frequency of kdr mutations from dengue-monitored areas in Guizhou Province are reported in this paper. Outcomes of this study can serve as data support for further research and development of effective insecticidal interventions against Ae. albopictus populations in Guizhou Province.
Deep learning algorithm-enabled sediment characterization techniques to determination of water saturation for tight gas carbonate reservoirs in Bohai Bay Basin, China
Authors: Hu Xiao , Meng Qingchun , Guo Fajun , Xie Jun , Hasi Eerdun , Wang Hongmei , Zhao Yuzhi , Wang Li , Li Ping , Zhu Lin , Pu Qiongyao , Feng Xuguang
Published: May 2024

Understanding water saturation levels in tight gas carbonate reservoirs is vital for optimizing hydrocarbon production and mitigating challenges such as reduced permeability due to water saturation (Sw) and pore throat blockages, given its critical role in managing capillary pressure in water drive mechanisms reservoirs. Traditional sediment characterization methods such as core analysis, are often costly, invasive, and lack comprehensive spatial information. In recent years, several classical machine learning models have been developed to address these shortcomings. Traditional machine learning methods utilized in reservoir characterization encounter various challenges, including the ability to capture intricate relationships, potential overfitting, and handling extensive, multi-dimensional datasets. Moreover, these methods often face difficulties in dealing with temporal dependencies and subtle patterns within geological formations, particularly evident in heterogeneous carbonate reservoirs. Consequently, despite technological advancements, enhancing the reliability, interpretability, and applicability of predictive models remains imperative for effectively characterizing tight gas carbonate reservoirs. This study employs a novel data-driven strategy to prediction of water saturation in tight gas reservoir powered by three recurrent neural network type deep/shallow learning algorithms—Gated Recurrent Unit (GRU), Recurrent Neural Networks (RNN), Long Short-Term Memory (LSTM), Support Vector Machine (SVM), K-nearest neighbor (KNN) and Decision tree (DT)—customized to accurately forecast sequential sedimentary structure data. These models, optimized using Adam's optimizer algorithm, demonstrated impressive performance in predicting water saturation levels using conventional petrophysical data. Particularly, the GRU model stood out, achieving remarkable accuracy (an R-squared value of 0.9973) with minimal errors (RMSE of 0.0198) compared to LSTM, RNN, SVM, KNN and, DT algorithms, thus showcasing its proficiency in processing extensive datasets and effectively identifying patterns. By achieving unprecedented accuracy levels, this study not only enhances the understanding of sediment properties and fluid saturation dynamics but also offers practical implications for reservoir management and hydrocarbon exploration in complex geological settings. These insights pave the way for more reliable and efficient decision-making processes, thereby advancing the forefront of reservoir engineering and petroleum geoscience.
Genetic landscape of interval and screen detected breast cancer
Authors: Mills Charlie , Sud Amit , Everall Andrew , Chubb Daniel , Lawrence Samuel E. D. , Kinnersley Ben , Cornish Alex J. , Bentham Robert , Houlston Richard S.
Published: May 2024

Interval breast cancers (IBCs) are cancers diagnosed between screening episodes. Understanding the biological differences between IBCs and screen-detected breast-cancers (SDBCs) has the potential to improve mammographic screening and patient management. We analysed and compared the genomic landscape of 288 IBCs and 473 SDBCs by whole genome sequencing of paired tumour-normal patient samples collected as part of the UK 100,000 Genomes Project. Compared to SDBCs, IBCs were more likely to be lobular, higher grade, and triple negative. A more aggressive clinical phenotype was reflected in IBCs displaying features of genomic instability including a higher mutation rate and number of chromosomal structural abnormalities, defective homologous recombination and TP53 mutations. We did not however, find evidence to indicate that IBCs are associated with a significantly different immune response. While IBCs do not represent a unique molecular class of invasive breast cancer they exhibit a more aggressive phenotype, which is likely to be a consequence of the timing of tumour initiation. This information is relevant both with respect to treatment as well as informing the screening interval for mammography.