bluuebunny/crossref_metadata_2025 huggingface dataset:
The liver and muscle secreted HFE2-protein maintains central nervous system blood vessel integrity
Authors: Wang Xue Fan , Vigouroux Robin , Syonov Michal , Baglaenko Yuriy , Nikolakopoulou Angeliki M. , Ringuette Dene , Rus Horea , DiStefano Peter V. , Dufour Suzie , Shabanzadeh Alireza P. , Lee Seunggi , Mueller Bernhard K. , Charish Jason , Harada Hidekiyo , Fish Jason E. , Wither Joan , Wälchli Thomas , Cloutier Jean-François , Zlokovic Berislav V. , Carlen Peter L. , Monnier Philippe P.
Published: February 2024

Liver failure causes breakdown of the Blood CNS Barrier (BCB) leading to damages of the Central-Nervous-System (CNS), however the mechanisms whereby the liver influences BCB-integrity remain elusive. One possibility is that the liver secretes an as-yet to be identified molecule(s) that circulate in the serum to directly promote BCB-integrity. To study BCB-integrity, we developed light-sheet imaging for three-dimensional analysis. We show that liver- or muscle-specific knockout of Hfe2/Rgmc induces BCB-breakdown, leading to accumulation of toxic-blood-derived fibrinogen in the brain, lower cortical neuron numbers, and behavioral deficits in mice. Soluble HFE2 competes with its homologue RGMa for binding to Neogenin, thereby blocking RGMa-induced downregulation of PDGF-B and Claudin-5 in endothelial cells, triggering BCB-disruption. HFE2 administration in female mice with experimental autoimmune encephalomyelitis, a model for multiple sclerosis, prevented paralysis and immune cell infiltration by inhibiting RGMa-mediated BCB alteration. This study has implications for the pathogenesis and potential treatment of diseases associated with BCB-dysfunction.
ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation
Authors: Mazzeo Luigi , Ghosh Soumitra , Di Cicco Emery , Isma Jovan , Tavernari Daniele , Samarkina Anastasia , Ostano Paola , Youssef Markus K. , Simon Christian , Dotto G. Paolo
Published: February 2024

There are significant commonalities among several pathologies involving fibroblasts, ranging from auto-immune diseases to fibrosis and cancer. Early steps in cancer development and progression are closely linked to fibroblast senescence and transformation into tumor-promoting cancer-associated fibroblasts (CAFs), suppressed by the androgen receptor (AR). Here, we identify ANKRD1 as a mesenchymal-specific transcriptional coregulator under direct AR negative control in human dermal fibroblasts (HDFs) and a key driver of CAF conversion, independent of cellular senescence. ANKRD1 expression in CAFs is associated with poor survival in HNSCC, lung, and cervical SCC patients, and controls a specific gene expression program of myofibroblast CAFs (my-CAFs). ANKRD1 binds to the regulatory region of my-CAF effector genes in concert with AP-1 transcription factors, and promotes c-JUN and FOS association. Targeting ANKRD1 disrupts AP-1 complex formation, reverses CAF activation, and blocks the pro-tumorigenic properties of CAFs in an orthotopic skin cancer model. ANKRD1 thus represents a target for fibroblast-directed therapy in cancer and potentially beyond.
A prefrontal-thalamic circuit encodes social information for social recognition
Authors: Chen Zihao , Han Yechao , Ma Zheng , Wang Xinnian , Xu Surui , Tang Yong , Vyssotski Alexei L. , Si Bailu , Zhan Yang
Published: February 2024

Social recognition encompasses encoding social information and distinguishing unfamiliar from familiar individuals to form social relationships. Although the medial prefrontal cortex (mPFC) is known to play a role in social behavior, how identity information is processed and by which route it is communicated in the brain remains unclear. Here we report that a ventral midline thalamic area, nucleus reuniens (Re) that has reciprocal connections with the mPFC, is critical for social recognition in male mice. In vivo single-unit recordings and decoding analysis reveal that neural populations in both mPFC and Re represent different social stimuli, however, mPFC coding capacity is stronger. We demonstrate that chemogenetic inhibitions of Re impair the mPFC-Re neural synchronization and the mPFC social coding. Projection pathway-specific inhibitions by optogenetics reveal that the reciprocal connectivity between the mPFC and the Re is necessary for social recognition. These results reveal an mPFC-thalamic circuit for social information processing.
Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications
Authors: Matzinger Manuel , Schmücker Anna , Yelagandula Ramesh , Stejskal Karel , Krššáková Gabriela , Berger Frédéric , Mechtler Karl , Mayer Rupert L.
Published: February 2024

Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4–12 with the CHIMERYS search engine identified +51–74% and +59–150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
Detection of senescence using machine learning algorithms based on nuclear features
Authors: Duran Imanol , Pombo Joaquim , Sun Bin , Gallage Suchira , Kudo Hiromi , McHugh Domhnall , Bousset Laura , Barragan Avila Jose Efren , Forlano Roberta , Manousou Pinelopi , Heikenwalder Mathias , Withers Dominic J. , Vernia Santiago , Goldin Robert D. , Gil Jesús
Published: February 2024

Cellular senescence is a stress response with broad pathophysiological implications. Senotherapies can induce senescence to treat cancer or eliminate senescent cells to ameliorate ageing and age-related pathologies. However, the success of senotherapies is limited by the lack of reliable ways to identify senescence. Here, we use nuclear morphology features of senescent cells to devise machine-learning classifiers that accurately predict senescence induced by diverse stressors in different cell types and tissues. As a proof-of-principle, we use these senescence classifiers to characterise senolytics and to screen for drugs that selectively induce senescence in cancer cells but not normal cells. Moreover, a tissue senescence score served to assess the efficacy of senolytic drugs and identified senescence in mouse models of liver cancer initiation, ageing, and fibrosis, and in patients with fatty liver disease. Thus, senescence classifiers can help to detect pathophysiological senescence and to discover and validate potential senotherapies.
Local structural preferences in shaping tau amyloid polymorphism
Authors: Louros Nikolaos , Wilkinson Martin , Tsaka Grigoria , Ramakers Meine , Morelli Chiara , Garcia Teresa , Gallardo Rodrigo , D’Haeyer Sam , Goossens Vera , Audenaert Dominique , Thal Dietmar Rudolf , Mackenzie Ian R. , Rademakers Rosa , Ranson Neil A. , Radford Sheena E. , Rousseau Frederic , Schymkowitz Joost
Published: February 2024

Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each disease. However, the extent to which intrinsic structural tendencies of tau amyloid cores contribute to fibril polymorphism remains uncertain. Using a combination of experimental approaches, we here identify a new amyloidogenic motif, PAM4 (Polymorphic Amyloid Motif of Repeat 4), as a significant contributor to tau polymorphism. Calculation of per-residue contributions to the stability of the fibril cores of different pathologic tau structures suggests that PAM4 plays a central role in preserving structural integrity across amyloid polymorphs. Consistent with this, cryo-EM structural analysis of fibrils formed from a synthetic PAM4 peptide shows that the sequence adopts alternative structures that closely correspond to distinct disease-associated tau strains. Furthermore, in-cell experiments revealed that PAM4 deletion hampers the cellular seeding efficiency of tau aggregates extracted from Alzheimer’s disease, corticobasal degeneration, and progressive supranuclear palsy patients, underscoring PAM4’s pivotal role in these tauopathies. Together, our results highlight the importance of the intrinsic structural propensity of amyloid core segments to determine the structure of tau in cells, and in propagating amyloid structures in disease.
Geometric transformation adaptive optics (GTAO) for volumetric deep brain imaging through gradient-index lenses
Authors: Li Yuting , Cheng Zongyue , Wang Chenmao , Lin Jianian , Jiang Hehai , Cui Meng
Published: February 2024

The advance of genetic function indicators has enabled the observation of neuronal activities at single-cell resolutions. A major challenge for the applications on mammalian brains is the limited optical access depth. Currently, the method of choice to access deep brain structures is to insert miniature optical components. Among these validated miniature optics, the gradient-index (GRIN) lens has been widely employed for its compactness and simplicity. However, due to strong fourth-order astigmatism, GRIN lenses suffer from a small imaging field of view, which severely limits the measurement throughput and success rate. To overcome these challenges, we developed geometric transformation adaptive optics (GTAO), which enables adaptable achromatic large-volume correction through GRIN lenses. We demonstrate its major advances through in vivo structural and functional imaging of mouse brains. The results suggest that GTAO can serve as a versatile solution to enable large-volume recording of deep brain structures and activities through GRIN lenses.
Secretin-dependent signals in the ventromedial hypothalamus regulate energy metabolism and bone homeostasis in mice
Authors: Zhang Fengwei , Qiao Wei , Wei Ji-an , Tao Zhengyi , Chen Congjia , Wu Yefeng , Lin Minghui , Ng Ka Man Carmen , Zhang Li , Yeung Kelvin Wai-Kwok , Chow Billy Kwok Chong
Published: February 2024

Secretin, though originally discovered as a gut-derived hormone, is recently found to be abundantly expressed in the ventromedial hypothalamus, from which the central neural system controls satiety, energy metabolism, and bone homeostasis. However, the functional significance of secretin in the ventromedial hypothalamus remains unclear. Here we show that the loss of ventromedial hypothalamus-derived secretin leads to osteopenia in male and female mice, which is primarily induced by diminished cAMP response element-binding protein phosphorylation and upregulation in peripheral sympathetic activity. Moreover, the ventromedial hypothalamus-secretin inhibition also contributes to hyperphagia, dysregulated lipogenesis, and impaired thermogenesis, resulting in obesity in male and female mice. Conversely, overexpression of secretin in the ventromedial hypothalamus promotes bone mass accrual in mice of both sexes. Collectively, our findings identify an unappreciated secretin signaling in the central neural system for the regulation of energy and bone metabolism, which may serve as a new target for the clinical management of obesity and osteoporosis.
Phosphoglycerate kinase 1 acts as a cargo adaptor to promote EGFR transport to the lysosome
Authors: Chu Shao-Ling , Huang Jia-Rong , Chang Yu-Tzu , Yao Shu-Yun , Yang Jia-Shu , Hsu Victor W. , Hsu Jia-Wei
Published: February 2024

The epidermal growth factor receptor (EGFR) plays important roles in multiple cellular events, including growth, differentiation, and motility. A major mechanism of downregulating EGFR function involves its endocytic transport to the lysosome. Sorting of proteins into intracellular pathways involves cargo adaptors recognizing sorting signals on cargo proteins. A dileucine-based sorting signal has been identified previously for the sorting of endosomal EGFR to the lysosome, but a cargo adaptor that recognizes this signal remains unknown. Here, we find that phosphoglycerate kinase 1 (PGK1) is recruited to endosomal membrane upon its phosphorylation, where it binds to the dileucine sorting signal in EGFR to promote the lysosomal transport of this receptor. We also elucidate two mechanisms that act in concert to promote PGK1 recruitment to endosomal membrane, a lipid-based mechanism that involves phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and a protein-based mechanism that involves hepatocyte growth factor receptor substrate (Hrs). These findings reveal an unexpected function for a metabolic enzyme and advance the mechanistic understanding of how EGFR is transported to the lysosome.
Artesunate treats obesity in male mice and non-human primates through GDF15/GFRAL signalling axis
Authors: Guo Xuanming , Asthana Pallavi , Zhai Lixiang , Cheng Ka Wing , Gurung Susma , Huang Jiangang , Wu Jiayan , Zhang Yijing , Mahato Arun Kumar , Saarma Mart , Ustav Mart , Kwan Hiu Yee , Lyu Aiping , Chan Kui Ming , Xu Pingyi , Bian Zhao-Xiang , Wong Hoi Leong Xavier
Published: February 2024

Obesity, a global health challenge, is a major risk factor for multiple life-threatening diseases, including diabetes, fatty liver, and cancer. There is an ongoing need to identify safe and tolerable therapeutics for obesity management. Herein, we show that treatment with artesunate, an artemisinin derivative approved by the FDA for the treatment of severe malaria, effectively reduces body weight and improves metabolic profiles in preclinical models of obesity, including male mice with overnutrition-induced obesity and male cynomolgus macaques with spontaneous obesity, without inducing nausea and malaise. Artesunate promotes weight loss and reduces food intake in obese mice and cynomolgus macaques by increasing circulating levels of Growth Differentiation Factor 15 (GDF15), an appetite-regulating hormone with a brainstem-restricted receptor, the GDNF family receptor α-like (GFRAL). Mechanistically, artesunate induces the expression of GDF15 in multiple organs, especially the liver, in mice through a C/EBP homologous protein (CHOP)-directed integrated stress response. Inhibition of GDF15/GFRAL signalling by genetic ablation of GFRAL or tissue-specific knockdown of GDF15 abrogates the anti-obesity effect of artesunate in mice with diet-induced obesity, suggesting that artesunate controls bodyweight and appetite in a GDF15/GFRAL signalling-dependent manner. These data highlight the therapeutic benefits of artesunate in the treatment of obesity and related comorbidities.
East Antarctic warming forced by ice loss during the Last Interglacial
Authors: Hutchinson David K. , Menviel Laurie , Meissner Katrin J. , Hogg Andrew McC.
Published: February 2024

During the Last Interglacial (LIG; 129-116 thousand years before present), the Antarctic ice sheet (AIS) was 1 to 7 m sea level equivalent smaller than at pre-industrial. Here, we assess the climatic impact of partial AIS melting at the LIG by forcing a coupled climate model with a smaller AIS and the equivalent meltwater input around the Antarctic coast. We find that changes in surface elevation induce surface warming over East Antarctica of 2 to 4 °C, and sea surface temperature (SST) increases in the Weddell and Ross Seas by up to 2 °C. Meltwater forcing causes a high latitude SST decrease and a subsurface (100–500 m) ocean temperature increase by up to 2 °C in the Ross Sea. Our results suggest that the combination of a smaller AIS and enhanced meltwater input leads to a larger sub-surface warming than meltwater alone and induces further Antarctic warming than each perturbation separately.
Possible chiral spin liquid state in the S = 1/2 kagome Heisenberg model
Authors: Sun Rong-Yang , Jin Hui-Ke , Tu Hong-Hao , Zhou Yi
Published: February 2024

The nature of the ground state for the S = 1/2 Kagome Heisenberg antiferromagnet (KHAF) has been elusive. We revisit this challenging problem and provide numerical evidence that its ground state is a chiral spin liquid. Combining the density matrix renormalization group method with analytical analyses, we demonstrate that the previously observed chiral spin liquid phase in the KHAF with longer-range couplings is stable in a broader region of the phase diagram. We characterize the nature of the ground state by computing energy derivatives, revealing the ground-state degeneracy arising from the spontaneous breaking of the time-reversal symmetry, and targeting the semion sector. We further investigate the phase diagram in the vicinity of the KHAF and observe a $$\sqrt{3}\times \sqrt{3}$$

3

×

3

magnetically ordered phase and two valence-bond crystal phases.
The neutrophil-to-Lymphocyte ratio is associated with clinical symptoms in first-episode medication-naïve patients with schizophrenia
Authors: Wang Xuan , Chen Xiaofang , Guan Xiaoni , Li Zezhi
Published: February 2024

Innate immunity has been shown to be associated with schizophrenia (Sch). This study explored the relationship between symptoms and neutrophil-to-lymphocyte ratio (NLR) (a marker of innate immunity) in patients with Sch. Ninety-seven first-episode medication-naïve (FEMN) patients with Sch and 65 healthy controls were recruited in this study. We measured the complete blood count and assessed the clinical symptoms using the PANSS scales. We found higher NEU counts and NLR in patients with Sch compared with control subjects. Male patients showed a higher NEU count than female patients. In addition, FEMN patients with higher NLR and NEU values showed higher PANSS-p, PANSS-g, and PANSS-total scores (all p < 0.05). Regression analysis revealed that NLR was a predictor for PANSS total scores in patients with Sch. Higher NLR value was observed in patients with Sch and the significant associations between NLR and psychotic symptoms indicate that an imbalance in inflammation and innate immune system may be involved in the pathophysiology of Sch.
Effects of gelatin type and concentration on the preparation and properties of freeze-dried fish oil powders
Authors: Yang Mengyang , Peng Jiawei , Shi Cuiping , Zi Ye , Zheng Yulu , Wang Xichang , Zhong Jian
Published: February 2024

The effects of gelatin type (porcine skin gelatin, PSG; bovine skin gelatin, BSG; fish gelatin, FG; or cold-water fish skin gelatin, CFG) and concentration on the preparation and properties of fish oil powders were investigated in this work. The oil powders were prepared using the combination method of gelatin-sodium hexametaphosphate complex coacervation with starch sodium octenyl succinate (SSOS)-aided freeze-drying. Compared with the other gelatins, CFG—with an unobvious isoelectric point, a lower molecular weight, more hydrogen bonds, and longer gel formation time—could not form complex coacervates, which are necessary to prepare oil powders. For oil powders obtained from the other gelatins, gelatin type and concentration did not have obvious effects on microscale morphologies; they did, however, have significant effects on physicochemical properties. The highest peroxide values of the oil powders were mainly dependent on the gelatins, expressed in the following manner: PSG (153 ± 5 – 168 ± 3 meq/Kg oil) < BSG (176 ± 5 – 188 ± 1 meq/Kg oil) < FG (196 ± 11 – 201 ± 22 meq/Kg oil). Acidic and neutral pH could not dissolve the complex coacervates. However, the oil powders could be quickly dissolved to form emulsion droplets in the gastric phase, and that SSOS increased coacervate stability and promoted oil digestion during the in vitro gastrointestinal process. In sum, this study contributes fundamental information to understanding the development of fish oil solid encapsulation preparations.
A therapeutic hepatitis B mRNA vaccine with strong immunogenicity and persistent virological suppression
Authors: Zhao Huajun , Shao Xianyu , Yu Yating , Huang Lulu , Amor Narh Philip , Guo Kun , Weng Changzhen , Zhao Weijun , Yang Ailu , Hu Jiesen , Yang Hongbao , Liu Zhenguang , Han Qiuju , Shi Leilei , Sun Shiyu , Zhang Jian , Lin Ang , Yang Yong
Published: February 2024

Here we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.
Phytoplankton optical fingerprint libraries for development of phytoplankton ocean color satellite products
Authors: Lomas Michael W. , Neeley Aimee R. , Vandermeulen Ryan , Mannino Antonio , Thomas Crystal , Novak Michael G. , Freeman Scott A.
Published: February 2024

Phytoplankton respond to physical and hydrographic forcing on time and space scales up to and including those relevant to climate change. Quantifying changes in phytoplankton communities over these scales is essential for predicting ocean food resources, occurrences of harmful algal blooms, and carbon and other elemental cycles, among other predictions. However, one of the best tools for quantifying phytoplankton communities across relevant time and space scales, ocean color sensors, is constrained by its own spectral capabilities and availability of adequately vetted and relevant optical models. To address this later shortcoming, greater than fifty strains of phytoplankton, from a range of taxonomic lineages, geographic locations, and time in culture, alone and in mixtures, were grown to exponential and/or stationary phase for determination of hyperspectral UV-VIS absorption coefficients, multi-angle and multi-spectral backscatter coefficients, volume scattering functions, particle size distributions, pigment content, and fluorescence. The aim of this publication is to share these measurements to expedite their utilization in the development of new optical models for the next generation of ocean color satellites.
Two chromosome-level genomes of Smittia aterrima and Smittia pratorum (Diptera, Chironomidae)
Authors: Fu Yue , Fang Xiangliang , Xiao Yunli , Mao Bin , Xu Zigang , Shen Mi , Wang Xinhua
Published: February 2024

Chironomids are one of the most abundant aquatic insects and are widely distributed in various biological communities. However, the lack of high-quality genomes has hindered our ability to study the evolution and ecology of this group. Here, we used Nanopore long reads and Hi-C data to produce two chromosome-level genomes from mixed genomic data. The genomes of Smittia aterrima (SateA) and Smittia pratorum (SateB) were assembled into three chromosomes, with sizes of 78.45 Mb and 71.56 Mb, scaffold N50 lengths of 25.73 and 23.53 Mb, and BUSCO completeness of 98.5% and 97.8% (n = 1,367), 5.68 Mb (7.24%) and 1.94 Mb (2.72%) of repetitive elements, and predicted 12,330 (97.70% BUSCO completeness) and 11,250 (97.40%) protein-coding genes, respectively. These high-quality genomes will serve as valuable resources for comprehending the evolution and environmental adaptation of chironomids.
Prevalence of radiographic appendicular osteoarthritis and associated clinical signs in young dogs
Authors: Enomoto Masataka , de Castro Nicholas , Hash Jonathan , Thomson Andrea , Nakanishi-Hester Aoi , Perry Erin , Aker Savannah , Haupt Emily , Opperman Logan , Roe Simon , Cole Tracey , Thompson Nichola Archer , Innes J. F. , Lascelles B. Duncan X.
Published: February 2024

This study aimed to determine the prevalence of osteoarthritis (OA) and associated clinical signs in young dogs. Owners of dogs aged 8 months–4 years from a single practice, were contacted in random order, to participate in a general health screen. Clinical and orthopedic examinations were performed. Each joint was scored for pain reactions (0–4). Orthogonal radiographs of all joints were made under sedation. Each joint was scored for radiographic OA (rOA) severity on an 11-point scale. Clinical OA (cOA) was defined as an overlap of rOA and joint pain in ≥ 1 joint. Owners completed OA questionnaires. The owners of 123 dogs agreed to participate. Overall, 39.8% (49/123) of dogs had rOA in ≥ 1 joint, and 16.3% (20/123) or 23.6% (29/123) dogs had cOA, depending on the cut-off value of joint pain; moderate (2), or mild (1), respectively. Owners of dogs with cOA observed signs of impairment in approximately 30% of cases. Only 2 dogs with cOA were receiving OA pain management. The most commonly affected joints in descending order of frequency were elbow, hip, tarsus, and stifle. Radiographically visible OA is common in young dogs, and 40–60% of dogs with rOA had cOA. However, OA-pain appears underdiagnosed and undertreated in young dogs.
Uncovering floral composition of paper wasp nests (Hymenoptera: Vespidae: Polistes) through DNA metabarcoding
Authors: Mohamadzade Namin Saeed , Son Minwoong , Jung Chuleui
Published: February 2024

As the social organism, Polistes wasps build a communal nest using woody fibers with saliva for sustaining brood and adult population throughout the season. Limited information exists regarding the identification specific plant materials employed in wasp nest building. Thus, we firstly tested if the DNA metabarcoding approach utilizing rbcL and trnL molecular markers could identify the plant species quantitatively and qualitatively inform the mixed-origin woody samples. A threshold of 0.01 proportion of reads was applied for rbcL and trnL molecular markers, while this threshold for median proportion was 0.0025. In assessing taxa richness, the median proportion demonstrated superior performance, exhibiting higher taxa detection power, however, rbcL marker outperformed in quantitative analysis. Subsequently, we applied DNA metabarcoding to identify the plant materials from the nests of two Polistes species, P. mandarinus and P. rothneyi. The results showed that higher preference of Quercus and Robinia as the major nest building materials regardless of the surrounding plant communities, by two wasp species. Material diversity was higher for P. rothneyi than P. mandarinus, which may explain the abundance of this species possibly with heightened adaptive capacities in their nesting behavior. This study demonstrated that DNA metabarcoding could identify the complex nest-building plant materials of paper wasps and provide insights into their ecological interactions in the natural ecosystem.
Vibrations and energy distribution in inhomogeneous rods with elastic and viscous boundary conditions
Authors: Lelkes János , Bak Bendegúz Dezső , Kalmár-Nagy Tamás
Published: February 2024

Functionally graded materials have broad engineering applications including mechanical engineering, electronics, chemistry, and biomedical engineering. One notable advantage of such materials is that their stiffness distribution can be optimized to avoid stress concentration. A novel approach for solving the equations describing the longitudinal vibration of functionally graded rods with viscous and elastic boundary conditions is proposed. The characteristic equation of the system is derived for the solution of the undamped case for the constant stiffness rod. Then, a homotopy method is applied to compute the eigenvalues and mode shapes of graded rods for viscoelastic boundary conditions. The changes of the eigenvalues and mode shapes as function of the damping parameters are investigated. The optimal damping of the system is computed. It is shown that the qualitative behavior depends on the relation between the actual damping and the optimal damping of the system. The energy density distribution of graded rods is also discussed. An energy measure, the mean scaled energy density distribution is introduced to characterize the energy distribution along the rod in the asymptotic time limit. The significance of such a measure is that it reveals how the energy tends to distribute along the rod. It is shown that the energy distribution can be manipulated by changing the damping parameters. Qualitative changes depending on the relation between the actual damping and the optimal damping are highlighted.
Particle flow numerical simulation model for coal and gas outburst and its microscopic outburst mechanism description
Authors: Jiao Huice , Song Weihua
Published: February 2024

The finite difference model and particle flow model were constructed to reproduce the process of coal and gas outburst in front of the tunnel. The reliability of the particle flow model was verified by studying the internal stress, gas pressure, and related parameters of gas and coal two-phase flow. Then the process of coal and gas outburst is described from a microscopic perspective. The results show that the particle flow numerical model of coal and gas outburst is in line with reality and can intuitively and conveniently monitor relevant parameters; The concentrated stress caused by excavation of tunnels can reach 1.2 times the in-situ stress; High stress causes the adhesion between coal particles to break down, which is the main reason for the initiation of coal and gas outbursts; The intermittent breakthrough of gas on the coal particle collection that blocks the release channel has caused pulsating characteristics of coal and gas outbursts.
Evidence of population genetic structure in Ecuadorian Andean bears
Authors: Cueva Dario F. , Zug Rebecca , Pozo María José , Molina Santiago , Cisneros Rodrigo , Bustamante Martín R. , Torres María de Lourdes
Published: February 2024

Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
Efficiency of transcription and translation of cell-free protein synthesis systems in cell-sized lipid vesicles with changing lipid composition determined by fluorescence measurements
Authors: Miwa Akari , Wakamori Masatoshi , Ariyoshi Tetsuro , Okada Yasushi , Shirouzu Mikako , Umehara Takashi , Kamiya Koki
Published: February 2024

To develop artificial cell models that mimic living cells, cell-sized lipid vesicles encapsulating cell-free protein synthesis (CFPS) systems are useful for protein expressions or artificial gene circuits for vesicle–vesicle communications. Therefore, investigating the transcriptional and translational properties of CFPS systems in lipid vesicles is important for maximizing the synthesis and functions of proteins. Although transcription and translation using CFPS systems inside lipid vesicles are more important than that outside lipid vesicles, the former processes are not investigated by changing the lipid composition of lipid vesicles. Herein, we investigated changes in transcription and translation using CFPS systems inside giant lipid vesicles (approximately 5–20 μm in diameter) caused by changing the lipid composition of lipid vesicles containing neutral, positively, and negatively charged lipids. After incubating for 30 min, 1 h, 2 h, and 4 h, the transcriptional and translational activities in these lipid vesicles were determined by detecting the fluorescence intensities of the fluorogenic RNA aptamer on the 3′-untranslated region of mRNA (transcription) and the fluorescent protein sfCherry (translation), respectively. The results revealed that transcriptional and translational activities in a lipid vesicle containing positively charged lipids were high when the protein was synthesized using the CFPS system inside the lipid vesicle. Thus, the present study provides an experimental basis for constructing complex artificial cell models using bottom-up approaches.
Multi-scale habitat modeling framework for predicting the potential distribution of sheep gastrointestinal nematodes across Iran’s three distinct climatic zones: a MaxEnt machine-learning algorithm
Authors: Meshgi Behnam , Hanafi-Bojd Ahmad Ali , Fathi Saeid , Modabbernia Galia , Meshgi Kourosh , Shadman Mohammad
Published: February 2024

Ecological niche models (ENMs) serve as valuable tools in assessing the potential species distribution, identifying crucial habitat components for species associations, and facilitating conservation efforts. The current study aimed to investigate the gastrointestinal nematodes (GINs) infection in sheep, predict and analyze their ecological niches and ranges, and identify the key bioclimatic variables influencing their distribution across three distinct climatic regions in Iran. In a cross-sectional study, a total of 2140 fecal samples were collected from semi-arid (n = 800), arid (n = 500), and humid-subtropical (n = 840) climates in East Azerbaijan, Kerman, and Guilan provinces, respectively. The flotation method was employed to assess stool samples, whereby the fecal egg count (the number of parasite eggs per gram [EPG]) was ascertained for each individual specimen. Employing a presence-only approach, the multi-scale maximum entropy (MaxEnt) method was used to model GINs' habitat suitability using 93 selected points/locations. The findings revealed that Guilan (34.2%) and East Azerbaijan (19.62%) exhibited the utmost proportion of Strongyle-type eggs. East Azerbaijan province also displayed the highest proportion of Marshallagia and Nematodirus, respectively (approximately 40% and 27%), followed by Guilan and Kerman provinces, while Kerman province had the highest proportion of Trichuris (approximately 15%). Ecological niche modeling revealed that the precipitation of the driest quarter (Bio17) exerted the most significant influence on Marshallagia, Nematodirus, Trichuris, and ُSُُُtrongyle-type eggs' presence in East Azerbaijan and Kerman provinces. For Guilan province, the most influential factor defining habitat suitability for Strongyle-type eggs, Marshallagia, and Nematodirus was increasing slope. Additionally, the distribution of Trichuris was most affected by the variable Bio2 in Guilan province. The study highlights the response of GINs to climate drivers in highly suitable regions, providing insights into ecologically favorable areas for GINs. In conclusion, this study provides a better understanding of GINs and the environmental factors influencing their transmission dynamics.
Exploration capacity versus specific enzymatic activity of ectomycorrhizas in response to primary productivity and soil phosphorus availability in Bornean tropical rainforests
Authors: Okada Kei-ichi , Yokoyama Daiki , Aiba Shin-ichiro , Kitayama Kanehiro
Published: February 2024

Ectomycorrhizal (ECM) fungi are functionally important in biogeochemical cycles in tropical ecosystems. Extracellular enzymatic activity of ECM on a ground-area basis is the product of two attributes; exploration capacity (ECM surface-area) and specific enzymatic activity. Here, we elucidated which attribute better explained the ECM enzymatic activity in response to different levels of soil phosphorus (P) and Nitrogen (N) availability in five Bornean tropical rainforests. We determined the surface area of ECM root tips as well as the enzymatic activities per ECM surface area for carbon (C), N and P degrading enzymes in each site. We evaluated the relationship of ECM enzyme activities with the resource availabilities of C (Above-ground net primary production; ANPP), N, and P of ECM by a generalized linear mixed model. The ECM enzymatic activities on a ground-area basis were more significantly determined by specific enzymatic activity than by the exploration capacity. Specific enzymatic activities were generally negatively affected by C (ANPP) and soil P availability. ECM fungi enhance the specific enzyme activity rather than the exploration capacity to maintain the capacity of nutrient acquisition. The less dependence of ECM fungi on the exploration capacity in these forests may be related to the limitation of C supply from host trees. We highlighted the adaptive mechanisms of ECM fungi on nutrient acquisition in tropical ecosystems through the response of enzymatic activity to nutrient availability across the elements.
Nutrient patterns in relation to insulin resistance and endothelial dysfunction in Iranian women
Authors: Dehghani Farimah , Hajhashemy Zahra , Keshteli Ammar Hassanzadeh , Yazdannik Ahmadreza , Falahi Ebrahim , Saneei Parvane , Esmaillzadeh Ahmad
Published: February 2024

Prior studies have mainly focused on the association of one specific nutrient with insulin resistance (IR) and endothelial dysfunction and limited studies have assessed the association with different nutrient patterns (NPs). We examined the association between various NPs and IR and endothelial dysfunction among Iranian women. This cross-sectional study was carried out on a sample of 368 female nurses. A 106-items food frequency questionnaire (FFQ) was applied for dietary assessments. Using factor analysis, the relationships between NPs and markers of insulin resistance (HOMA-IR, HOMA-β, and QUICKY), and endothelial dysfunction (E-selectin, sICAM-1, and sVCAM-1) were assessed. Mean age and body mass index of participants were respectively 35.21 years and 24.04 kg/m2. Three major NPs were identified. NP1, named as “dairy, fruits, and vegetables” had high values of potassium, folate, vitamins A and C, magnesium, and beta carotene. No significant association was observed between this NP and insulin resistance or endothelial dysfunction indices. The second NP was full of chromium, selenium, copper, vitamin B6, monounsaturated fatty acid (MUFA), thiamin, vitamin D, and iron. Adherence to NP2 (named “legumes, nuts, and protein foods”) was associated with lower values of insulin (6.8 ± 1.1 versus 8.4 ± 1.1, P = 0.01), homeostasis model assessment-Insulin resistance (HOMA-IR) (1.3 ± 0.2 versus 1.7 ± 0.2, P = 0.02), and vascular adhesion molecule 1 (VCAM-1) (444.2 ± 27.9 versus 475.8 ± 28.4, P = 0.03). However, adherence to the third NP, rich in saturated fatty acid (SFA), cholesterol, sodium, zinc, vitamin E, and B12, described as “animal fat and meat + vitamin E”, was associated with higher amounts of homeostasis model assessment-β (HOMA-β) (531.3 ± 176.2 versus 48.7 ± 179.8, P = 0.03). In conclusion, following the NP2, correlated with higher intakes of chromium, selenium, copper, vitamin B6, MUFA and thiamin was associated with lower values of insulin, HOMA-IR, and sVCAM-1. Adherence to NP3, rich in SFA, cholesterol, vitamin E, vitamin B12, and zinc was associated with higher levels of HOMA-β.
Rapid prototyping of PMMA-based microfluidic spheroid-on-a-chip models using micromilling and vapour-assisted thermal bonding
Authors: Ahmed Monieb A. M. , Jurczak Klaudia M. , Lynn N. Scott , Mulder Jean-Paul S. H. , Verpoorte Elisabeth M. J. , Nagelkerke Anika
Published: February 2024

The application of microfluidic devices as next-generation cell and tissue culture systems has increased impressively in the last decades. With that, a plethora of materials as well as fabrication methods for these devices have emerged. Here, we describe the rapid prototyping of microfluidic devices, using micromilling and vapour-assisted thermal bonding of polymethyl methacrylate (PMMA), to create a spheroid-on-a-chip culture system. Surface roughness of the micromilled structures was assessed using scanning electron microscopy (SEM) and atomic force microscopy (AFM), showing that the fabrication procedure can impact the surface quality of micromilled substrates with milling tracks that can be readily observed in micromilled channels. A roughness of approximately 153 nm was created. Chloroform vapour-assisted bonding was used for simultaneous surface smoothing and bonding. A 30-s treatment with chloroform-vapour was able to reduce the surface roughness and smooth it to approximately 39 nm roughness. Subsequent bonding of multilayer PMMA-based microfluidic chips created a durable assembly, as shown by tensile testing. MDA-MB-231 breast cancer cells were cultured as multicellular tumour spheroids in the device and their characteristics evaluated using immunofluorescence staining. Spheroids could be successfully maintained for at least three weeks. They consisted of a characteristic hypoxic core, along with expression of the quiescence marker, p27kip1. This core was surrounded by a ring of Ki67-positive, proliferative cells. Overall, the method described represents a versatile approach to generate microfluidic devices compatible with biological applications.
Changes in RDW according to prognostic predictors in newly diagnosed multiple myeloma
Authors: Carlisi Melania , Presti R. Lo , Plano F. , Mancuso S. , Siragusa S. , Caimi G.
Published: February 2024

RDW is an erythrocyte index that increase in multiple myeloma, in which it appears to have an important role in predicting outcome. For this reason, we performed a retrospective analysis to evaluate the relationships of RDW with some important prognostic predictors. Specifically, in a cohort of 190 newly diagnosed multiple myeloma patients, we have examined the behaviour of RDW and its trend in relation to the ISS stage and other prognostic factors, such as albumin, beta-2 microglobulin, LDH and bone marrow plasma cell infiltration. We performed the analysis in the entire cohort of patients and in the three different disease isotypes (Light chain, IgA, and IgG multiple myeloma). The evaluation of RDW in the different isotypes was made with the Kruskal–Wallis test, integrated by the Dunn test. The comparison between the subgroups allocated above and below the median value of each prognostic factor, was made with the Mann–Whitney test. From our analysis, we observed that RDW is higher in the IgA multiple myeloma, and it increases significantly from ISS I to III. Moreover, RDW increases in the presence of lower albumin values, higher levels of beta2-microglobulin and LDH and in the presence of a greater bone marrow plasma cell infiltrate.
Giant enhancement of third harmonic generation in an array of graphene ribbons using amplification of surface plasmon polaritons by optical gain
Authors: Sedaghat Nejad Marzieh , Ghasempour Ardakani Abbas
Published: February 2024

In this paper, we theoretically study the enhancement of third-harmonic generation in a plasmonic structure composed of an array of trilayer graphene ribbons sandwiched between two $$CaF_{2}$$

C
a

F
2

layers. In fact, we suggest a new method for more enhancement of nonlinearity in plasmonic structures using incorporation of optical gain into graphene ribbons. As the pump intensity increases, the maximum output intensity of third harmonic generated (THG) wave versus fundamental frequency is blue-shifted while its value enhances. Our analysis indicates that the enhancement factor of THG in our proposed structure is 1.1 × 107 without occurring an electric breakdown compared to case at which an optically pumped trilayer graphene sheet sandwiched between two CaF2 layers. Therefore, only presence of optical gain is not sufficient for significant enhancement of output intensity of THG wave and excitation of SPPs through the structure is also essential. On the other hand, our results demonstrate that the output intensity of THG wave from the proposed structure under optical pumping enhances by $$10^{5}$$

10
5

times compared to the plasmonic structure without optical gain which confirms the role of optical gain for THG enhancement in the plasmonic structure. This is because the gain in graphene ribbons amplifies the SPPs waves leading to the more field enhancement along the graphene ribbons which results in significant enhancement of THG wave in the plasmonic structure in comparison with one without gain. Therefore, we reveal that both SPPs and optical gain contribute to the strong output intensity of THG in our proposed structure compared to the trilayer graphene sheet inserted between two CaF2 layers.
YOLOX target detection model can identify and classify several types of tea buds with similar characteristics
Authors: Yang Mengdao , Yuan Weihao , Xu Gaojian
Published: February 2024

Currently, the accuracy of tea bud identification is crucial in the intelligent development of the tea industry, and this is due to the fact that identifying tea buds is a key step in determining the quality of tea and distinguishing the categories. In this experiment, 3728 tea shoots with similar characteristics in four categories (Anji White Tea, Huangshan Seed, Longjing 43, and NongKang Early) were photographed to establish the dataset TBD (Tea Bud Dataset). In this experiment, we constructed a tea shoot recognition model. We used seven mainstream algorithms (YOLOv4, YOLOv5, YOLOX, YOLOv7, EfficientDet, Faster R-CNN and CenterNet) to conduct shoot recognition comparison experiments and found that the YOLOX algorithm performs the best with its Precision, Recall, F1 score, mAP 89.34%, 93.56%, 0.91, and 95.47%, respectively. Then the YOLOX algorithm combined with the dataset to construct the shoot recognition model, the shoots of four kinds of tea to establish a tea shoot classification model, the model to identify the Anji white tea shoots of Precision 76.19%, the yellow mountain species of Precision 90.54%, Longjing 43 Precision 80%, NongKang early to the morning of the Precision was 77.78%. The results of this experiment show that the established tea shoot classification model has achieved a better classification of the above four types of tea shoots, which can also understand the feasibility of mechanical intelligent tea picking and provide some theoretical support for the application of mechanical intelligent tea picking in practice.