bluuebunny/crossref_metadata_2025 huggingface dataset:
Socio-economic correlates of childhood obesity in urban and rural England
Authors: Titis Elzbieta , Di Salvatore Jessica , Procter Rob
Published: June 2023

Objective:

Physical access to food may affect diet and thus obesity rates. We build upon existing work to better understand how socio-economic characteristics of locations are associated with childhood overweight.

Design:

Using cross-sectional design and publicly available data, the study specifically compares rural and urban areas, including interactions of distance from supermarkets with income and population density.

Setting:

We examine cross-sectional associations with obesity prevalence both in the national scale and across urban and rural areas differing in household wealth.

Participants:

Children in reception class (aged 4–5) from all state-maintained schools in England taking part in the National Child Measurement Programme (n 6772).

Results:

Income was the main predictor of childhood obesity (adj. R-sq=.316, p<.001), whereas distance played only a marginal role (adj. R-sq=.01, p<.001). In urban areas, distance and density correlate with obesity directly and conditionally. Urban children were slightly more obese, but the opposite was true for children in affluent areas. Association between income poverty and obesity rates was stronger in urban areas (7·59 %) than rural areas (4·95 %), the former which also showed stronger association between distance and obesity.

Conclusions:

Obesogenic environments present heightened risks in deprived urban and affluent rural areas. The results have potential value for policy making as for planning and targeting of services for vulnerable groups.
Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions
Authors: Johansson Josefin , Lidéus Sarah , Frykholm Carina , Gunnarsson Cecilia , Mihalic Filip , Gudmundsson Sanna , Ekvall Sara , Molin Anna-Maja , Pham Mai , Vihinen Mauno , Lagerstedt-Robinson Kristina , Nordgren Ann , Jemth Per , Ameur Adam , Annerén Göran , Wilbe Maria , Bondeson Marie-Louise
Published: June 2023

RNA binding motif protein X‐linked (RBMX) encodes the heterogeneous nuclear ribonucleoprotein G (hnRNP G) that regulates splicing, sister chromatid cohesion and genome stability. RBMX knock down experiments in various model organisms highlight the gene’s importance for brain development. Deletion of the RGG/RG motif in hnRNP G has previously been associated with Shashi syndrome, however involvement of other hnRNP G domains in intellectual disability remain unknown. In the current study, we present the underlying genetic and molecular cause of Gustavson syndrome. Gustavson syndrome was first reported in 1993 in a large Swedish five-generation family presented with profound X-linked intellectual disability and an early death. Extensive genomic analyses of the family revealed hemizygosity for a novel in-frame deletion in RBMX in affected individuals (NM_002139.4; c.484_486del, p.(Pro162del)). Carrier females were asymptomatic and presented with skewed X-chromosome inactivation, indicating silencing of the pathogenic allele. Affected individuals presented minor phenotypic overlap with Shashi syndrome, indicating a different disease-causing mechanism. Investigation of the variant effect in a neuronal cell line (SH-SY5Y) revealed differentially expressed genes enriched for transcription factors involved in RNA polymerase II transcription. Prediction tools and a fluorescence polarization assay imply a novel SH3-binding motif of hnRNP G, and potentially a reduced affinity to SH3 domains caused by the deletion. In conclusion, we present a novel in-frame deletion in RBMX segregating with Gustavson syndrome, leading to disturbed RNA polymerase II transcription, and potentially reduced SH3 binding. The results indicate that disruption of different protein domains affects the severity of RBMX-associated intellectual disabilities.
Lava dome cycles reveal rise and fall of magma column at Popocatépetl volcano
Authors: Valade Sébastien , Coppola Diego , Campion Robin , Ley Andreas , Boulesteix Thomas , Taquet Noémie , Legrand Denis , Laiolo Marco , Walter Thomas R. , De la Cruz-Reyna Servando
Published: June 2023

Lava domes exhibit highly unpredictable and hazardous behavior, which is why imaging their morphological evolution to decipher the underlying governing mechanisms remains a major challenge. Using high-resolution satellite radar imagery enhanced with deep-learning, we image the repetitive dome construction-subsidence cycles at Popocatépetl volcano (Mexico) with very high temporal and spatial resolution. We show that these cycles resemble gas-driven rise and fall of the upper magma column, where buoyant bubble-rich magma is extruded from the conduit (in ~hours-days), and successively drained back (in ~days-months) as magma degasses and crystallizes. These cycles are superimposed on a progressive decadal crater deepening, accompanied by heat and gas flux decrease, which could be partially explained by gas depletion within the magma plumbing system. Results reinforce the idea that gas retention and escape from the magma column play a key role in the short- and long-term morphological evolution of low-viscosity lava domes and their associated hazards.
Neutrophil-derived catecholamines mediate negative stress effects on bone
Authors: Tschaffon-Müller Miriam E. A. , Kempter Elena , Steppe Lena , Kupfer Sandra , Kuhn Melanie R. , Gebhard Florian , Pankratz Carlos , Kalbitz Miriam , Schütze Konrad , Gündel Harald , Kaleck Nele , Strauß Gudrun , Vacher Jean , Ichinose Hiroshi , Weimer Katja , Ignatius Anita , Haffner-Luntzer Melanie , Reber Stefan O.
Published: June 2023

Mental traumatization is associated with long-bone growth retardation, osteoporosis and increased fracture risk. We revealed earlier that mental trauma disturbs cartilage-to-bone transition during bone growth and repair in mice. Trauma increased tyrosine hydroxylase-expressing neutrophils in bone marrow and fracture callus. Here we show that tyrosine hydroxylase expression in the fracture hematoma of patients correlates positively with acknowledged stress, depression, and pain scores as well as individual ratings of healing-impairment and pain-perception post-fracture. Moreover, mice lacking tyrosine hydroxylase in myeloid cells are protected from chronic psychosocial stress-induced disturbance of bone growth and healing. Chondrocyte-specific β2-adrenoceptor-deficient mice are also protected from stress-induced bone growth retardation. In summary, our preclinical data identify locally secreted catecholamines in concert with β2-adrenoceptor signalling in chondrocytes as mediators of negative stress effects on bone growth and repair. Given our clinical data, these mechanistic insights seem to be of strong translational relevance.
A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest
Authors: Kessler Sandra , Minoux Maryline , Joshi Onkar , Ben Zouari Yousra , Ducret Sebastien , Ross Fiona , Vilain Nathalie , Salvi Adwait , Wolff Joachim , Kohler Hubertus , Stadler Michael B. , Rijli Filippo M.
Published: June 2023

Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data
Authors: Maity Alok K. , Teschendorff Andrew E.
Published: June 2023

Variations of cell-type proportions within tissues could be informative of biological aging and disease risk. Single-cell RNA-sequencing offers the opportunity to detect such differential abundance patterns, yet this task can be statistically challenging due to the noise in single-cell data, inter-sample variability and because such patterns are often of small effect size. Here we present a differential abundance testing paradigm called ELVAR that uses cell attribute aware clustering when inferring differentially enriched communities within the single-cell manifold. Using simulated and real single-cell and single-nucleus RNA-Seq datasets, we benchmark ELVAR against an analogous algorithm that uses Louvain for clustering, as well as local neighborhood-based methods, demonstrating that ELVAR improves the sensitivity to detect cell-type composition shifts in relation to aging, precancerous states and Covid-19 phenotypes. In effect, leveraging cell attribute information when inferring cell communities can denoise single-cell data, avoid the need for batch correction and help retrieve more robust cell states for subsequent differential abundance testing. ELVAR is available as an open-source R-package.
Quantum simulation of Hawking radiation and curved spacetime with a superconducting on-chip black hole
Authors: Shi Yun-Hao , Yang Run-Qiu , Xiang Zhongcheng , Ge Zi-Yong , Li Hao , Wang Yong-Yi , Huang Kaixuan , Tian Ye , Song Xiaohui , Zheng Dongning , Xu Kai , Cai Rong-Gen , Fan Heng
Published: June 2023

Hawking radiation is one of the quantum features of a black hole that can be understood as a quantum tunneling across the event horizon of the black hole, but it is quite difficult to directly observe the Hawking radiation of an astrophysical black hole. Here, we report a fermionic lattice-model-type realization of an analogue black hole by using a chain of 10 superconducting transmon qubits with interactions mediated by 9 transmon-type tunable couplers. The quantum walks of quasi-particle in the curved spacetime reflect the gravitational effect near the black hole, resulting in the behaviour of stimulated Hawking radiation, which is verified by the state tomography measurement of all 7 qubits outside the horizon. In addition, the dynamics of entanglement in the curved spacetime is directly measured. Our results would stimulate more interests to explore the related features of black holes using the programmable superconducting processor with tunable couplers.
Parallel interrogation of the chalcogenide-based micro-ring sensor array for photoacoustic tomography
Authors: Pan Jingshun , Li Qiang , Feng Yaoming , Zhong Ruifeng , Fu Zhihao , Yang Shuixian , Sun Weiyuan , Zhang Bin , Sui Qi , Chen Jun , Shen Yuecheng , Li Zhaohui
Published: June 2023

Photoacoustic tomography (PAT), also known as optoacoustic tomography, is an attractive imaging modality that provides optical contrast with acoustic resolutions. Recent progress in the applications of PAT largely relies on the development and employment of ultrasound sensor arrays with many elements. Although on-chip optical ultrasound sensors have been demonstrated with high sensitivity, large bandwidth, and small size, PAT with on-chip optical ultrasound sensor arrays is rarely reported. In this work, we demonstrate PAT with a chalcogenide-based micro-ring sensor array containing 15 elements, while each element supports a bandwidth of 175 MHz (−6 dB) and a noise-equivalent pressure of 2.2 mPaHz−1/2. Moreover, by synthesizing a digital optical frequency comb (DOFC), we further develop an effective means of parallel interrogation to this sensor array. As a proof of concept, parallel interrogation with only one light source and one photoreceiver is demonstrated for PAT with this sensor array, providing images of fast-moving objects, leaf veins, and live zebrafish. The superior performance of the chalcogenide-based micro-ring sensor array and the effectiveness of the DOFC-enabled parallel interrogation offer great prospects for advancing applications in PAT.
Biodiversity time series are biased towards increasing species richness in changing environments
Authors: Kuczynski Lucie , Ontiveros Vicente J. , Hillebrand Helmut
Published: June 2023

The discrepancy between global loss and local constant species richness has led to debates over data quality, systematic biases in monitoring programmes and the adequacy of species richness to capture changes in biodiversity. We show that, more fundamentally, null expectations of stable richness can be wrong, despite independent yet equal colonization and extinction. We analysed fish and bird time series and found an overall richness increase. This increase reflects a systematic bias towards an earlier detection of colonizations than extinctions. To understand how much this bias influences richness trends, we simulated time series using a neutral model controlling for equilibrium richness and temporal autocorrelation (that is, no trend expected). These simulated time series showed significant changes in richness, highlighting the effect of temporal autocorrelation on the expected baseline for species richness changes. The finite nature of time series, the long persistence of declining populations and the potential strong dispersal limitation probably lead to richness changes when changing conditions promote compositional turnover. Temporal analyses of richness should incorporate this bias by considering appropriate neutral baselines for richness changes. Absence of richness trends over time, as previously reported, can actually reflect a negative deviation from the positive biodiversity trend expected by default.
Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus
Authors: Jespersen Marion , Wagner Tristan
Published: June 2023

Methanothermococcus thermolithotrophicus is the only known methanogen that grows on sulfate as its sole sulfur source, uniquely uniting methanogenesis and sulfate reduction. Here we use physiological, biochemical and structural analyses to provide a snapshot of the complete sulfate reduction pathway of this methanogenic archaeon. We find that later steps in this pathway are catalysed by atypical enzymes. PAPS (3′-phosphoadenosine 5′-phosphosulfate) released by APS kinase is converted into sulfite and 3′-phosphoadenosine 5′-phosphate (PAP) by a PAPS reductase that is similar to the APS reductases of dissimilatory sulfate reduction. A non-canonical PAP phosphatase then hydrolyses PAP. Finally, the F420-dependent sulfite reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that the sulfate reduction pathway is present in several methanogens, the sulfate assimilation pathway in M. thermolithotrophicus is distinct. We propose that this pathway was ‘mix-and-matched’ through the acquisition of assimilatory and dissimilatory enzymes from other microorganisms and then repurposed to fill a unique metabolic role.
Psychedelics promote plasticity by directly binding to BDNF receptor TrkB
Authors: Moliner Rafael , Girych Mykhailo , Brunello Cecilia A. , Kovaleva Vera , Biojone Caroline , Enkavi Giray , Antenucci Lina , Kot Erik F. , Goncharuk Sergey A. , Kaurinkoski Katja , Kuutti Mirjami , Fred Senem M. , Elsilä Lauri V. , Sakson Sven , Cannarozzo Cecilia , Diniz Cassiano R. A. F. , Seiffert Nina , Rubiolo Anna , Haapaniemi Hele , Meshi Elsa , Nagaeva Elina , Öhman Tiina , Róg Tomasz , Kankuri Esko , Vilar Marçal , Varjosalo Markku , Korpi Esa R. , Permi Perttu , Mineev Konstantin S. , Saarma Mart , Vattulainen Ilpo , Casarotto Plinio C. , Castrén Eero
Published: June 2023

Psychedelics produce fast and persistent antidepressant effects and induce neuroplasticity resembling the effects of clinically approved antidepressants. We recently reported that pharmacologically diverse antidepressants, including fluoxetine and ketamine, act by binding to TrkB, the receptor for BDNF. Here we show that lysergic acid diethylamide (LSD) and psilocin directly bind to TrkB with affinities 1,000-fold higher than those for other antidepressants, and that psychedelics and antidepressants bind to distinct but partially overlapping sites within the transmembrane domain of TrkB dimers. The effects of psychedelics on neurotrophic signaling, plasticity and antidepressant-like behavior in mice depend on TrkB binding and promotion of endogenous BDNF signaling but are independent of serotonin 2A receptor (5-HT2A) activation, whereas LSD-induced head twitching is dependent on 5-HT2A and independent of TrkB binding. Our data confirm TrkB as a common primary target for antidepressants and suggest that high-affinity TrkB positive allosteric modulators lacking 5-HT2A activity may retain the antidepressant potential of psychedelics without hallucinogenic effects.
A revised landslide inventory of the Campania region (Italy)
Authors: Fusco Francesco , Tufano Rita , De Vita Pantaleone , Di Martire Diego , Di Napoli Mariano , Guerriero Luigi , Mileti Florindo Antonio , Terribile Fabio , Calcaterra Domenico
Published: June 2023

Landslides represent a severe geohazard in many countries. The availability of inventories depicting the spatial and temporal distribution of landslides is crucial for assessing landslide susceptibility and risk for territorial planning or investigating landscape evolution. Nevertheless, these inventories are usually affected by limitations due to their nonpublic availability and inhomogeneities in characterization and mapping. Such problems are fully recognizable by the analysis of the multiple landslide inventories of the Campania region, which is one of the Italian regions with the highest exposure to landslide hazard and risk. On this basis, a revised Landslide Inventory of the Campania region (LaICa), resulting from the processing of multiple existing landslide inventories, has been reconstructed. It aims to (i) provide a new geodatabase that is able to overcome issues derived from the coexistence of multiple inventories and (ii) provide a methodological paradigm able to support the reorganization of existing official inventories. The implication of LaICa, with its 83,284 records, will possibly improve the assessment of landslide susceptibility and then reassess the related risk.
Probing the structural, mechanical, phonon, thermal, and transport properties of magnetic halide perovskites XTiBr3 (X = Rb, Cs) through ab-initio results
Authors: Shivhare Vishal , Khandy Saveer Ahmad , Gupta Dinesh C.
Published: June 2023

Herein, we have first reported the intrinsic properties, including structural, mechanical, electronic, magnetic, thermal, and transport properties of XTiBr3 (X = Rb, Cs) halide perovskites within the simulation scheme of density functional theory as integrated into Wien2k. First and foremost, the structural stability in terms of their ground state energies has been keenly evaluated from their corresponding structural optimizations, which advocate that XTiBr3 (X = Rb, Cs) has a stable ferromagnetic rather than the competing non-magnetic phase. Later on, the electronic properties have been computed within the mix of two applied potential schemes like Generalized Gradient Approximation (GGA) along with Trans-Bhala modified Becke Johnson (TB-mBJ), which thoroughly addresses the half-metallic behaviour with spin-up as metallic and in contrast to opposite spin-down channel signatures the semiconducting behaviour. Furthermore, the spin-splitting seen from their corresponding spin-polarised band structures offers a net magnetism of 2 µB which lends their opportunities to unlock the application branch of spintronics. In addition, these alloys have been characterised to show their mechanical stability describing the ductile feature. Moreover, phonon dispersions decisively certify the dynamical stability within the density functional perturbation theory (DFPT) context. Finally, the transport and thermal properties predicted within their specified packages have also been forwarded in this report.
A generalised deep learning-based surrogate model for homogenisation utilising material property encoding and physics-based bounds
Authors: Nakka Rajesh , Harursampath Dineshkumar , Ponnusami Sathiskumar A
Published: June 2023

The use of surrogate models based on Convolutional Neural Networks (CNN) is increasing significantly in microstructure analysis and property predictions. One of the shortcomings of the existing models is their limitation in feeding the material information. In this context, a simple method is developed for encoding material properties into the microstructure image so that the model learns material information in addition to the structure-property relationship. These ideas are demonstrated by developing a CNN model that can be used for fibre-reinforced composite materials with a ratio of elastic moduli of the fibre to the matrix between 5 and 250 and fibre volume fractions between 25 and 75%, which span end-to-end practical range. The learning convergence curves, with mean absolute percentage error as the metric of interest, are used to find the optimal number of training samples and demonstrate the model performance. The generality of the trained model is showcased through its predictions on completely unseen microstructures whose samples are drawn from the extrapolated domain of the fibre volume fractions and elastic moduli contrasts. Also, in order to make the predictions physically admissible, models are trained by enforcing Hashin–Shtrikman bounds which led to enhanced model performance in the extrapolated domain.
The impact of vitamin D3 supplementation on the faecal and oral microbiome of dairy calves indoors or at pasture
Authors: Vigors S. , Flores-Villalva S. , Meade K. G.
Published: June 2023

Vitamin D (VitD) is emerging as an immune regulator in addition to its established role in metabolism and mineral homeostasis. This study sought to determine if in vivo VitD modulated the oral and faecal microbiome in Holstein–Friesian dairy calves. The experimental model consisted of two control groups (Ctl-In, Ctl-Out) which were fed with a diet containing 6000 IU/Kg of VitD3 in milk replacer and 2000 IU/Kg in feed, and two treatment groups (VitD-In, VitD-Out) with 10,000 IU/Kg of VitD3 in milk replacer and 4000 IU/Kg in feed. One control and one treatment group were moved outdoors post-weaning at approximately 10 weeks of age. Saliva and faecal samples were collected after 7 months of supplementation and analysis of the microbiome was performed using 16S rRNA sequencing. Bray–Curtis dissimilarity analysis identified that both sampling site (oral vs. faecal) and housing (indoor vs. outdoor) had significant influences on the composition of the microbiome. The calves housed outdoors had greater microbial diversity in the faecal samples based on Observed, Chao1, Shannon, Simpson and Fisher measures in comparison to calves housed indoors (P < 0.05). A significant interaction between housing and treatment was observed for the genera Oscillospira, Ruminococcus, CF231 and Paludibacter in faecal samples. The genera Oscillospira and Dorea were increased while Clostridium and Blautia were decreased following VitD supplementation in the faecal samples (P < 0.05). An interaction between VitD supplementation and housing was detected in the abundance of the genera Actinobacillus and Streptococcus in the oral samples. VitD supplementation increased the genera Oscillospira, Helcococcus and reduced the genera Actinobacillus, Ruminococcus, Moraxella, Clostridium, Prevotella, Succinivibrio and Parvimonas. These preliminary data suggest that VitD supplementation alters both the oral and faecal microbiome. Further research will now be conducted to establish the significance of microbial alterations for animal health and performance.
Chemical pancreatectomy in non-human primates ablates the acini and ducts and enhances beta-cell function
Authors: Kalsi Ranjeet S. , Kreger Alexander M. , Saleh Mohamed , Yoshida Shiho , Sharma Kartikeya , Fusco Joseph , Saloman Jami L. , Zhang Ting , Thomas Madison , Sehrawat Anuradha , Wang Yan , Reif Jason , Mills Juliana , Raad Sarah , Zengin Bugra , Gomez Ana , Singhi Aatur , Tadros Sameh , Slivka Adam , Esni Farzad , Prasadan Krishna , Gittes George
Published: June 2023

Chronic pancreatitis is a debilitating disease affecting millions worldwide. These patients suffer from bouts of severe pain that are minimally relieved by pain medications and may necessitate major surgeries with high morbidity and mortality. Previously, we demonstrated that “chemical pancreatectomy,” a pancreatic intraductal infusion of dilute acetic acid solution, ablated the exocrine pancreas while preserving the endocrine pancreas. Notably, chemical pancreatectomy resolved chronic inflammation, alleviated allodynia in the cerulein pancreatitis model, and improved glucose homeostasis. Herein, we extensively tested the feasibility of a chemical pancreatectomy in NHPs and validated our previously published pilot study. We did serial computed tomography (CT) scans of the abdomen and pelvis, analyzed dorsal root ganglia, measured serum enzymes, and performed histological and ultrastructural assessments and pancreatic endocrine function assays. Based on serial CT scans, chemical pancreatectomy led to the loss of pancreatic volume. Immunohistochemistry and transmission electron microscopy demonstrated exocrine pancreatic ablation with endocrine islet preservation. Importantly, chemical pancreatectomy did not increase pro-nociceptive markers in harvested dorsal root ganglia. Also, chemical pancreatectomy improved insulin secretion to supranormal levels in vivo and in vitro. Thus, this study may provide a foundation for translating this procedure to patients with chronic pancreatitis or other conditions requiring a pancreatectomy.
The dynamics of telomere length in primary and metastatic colorectal cancer lesions
Authors: Kroupa Michal , Kubecek Ondrej , Tomasova Kristyna , Hanak Petr , Krupova Marketa , Cervena Klara , Siskova Anna , Rosendorf Jachym , Hosek Petr , Vodickova Ludmila , Vodicka Pavel , Liska Vaclav , John Stanislav , Vymetalkova Veronika , Petera Jiri
Published: June 2023

Telomeric sequences, the structures comprised of hexanucleotide repeats and associated proteins, play a pivotal role in chromosome end protection and preservation of genomic stability. Herein we address telomere length (TL) dynamics in primary colorectal cancer (CRC) tumour tissues and corresponding liver metastases. TL was measured by multiplex monochrome real-time qPCR in paired samples of primary tumours and liver metastases along with non-cancerous reference tissues obtained from 51 patients diagnosed with metastatic CRC. Telomere shortening was observed in the majority of primary tumour tissues compared to non-cancerous mucosa (84.1%, p < 0.0001). Tumours located within the proximal colon had shorter TL than those in the rectum (p < 0.05). TL in liver metastases was not significantly different from that in primary tumours (p = 0.41). TL in metastatic tissue was shorter in the patients diagnosed with metachronous liver metastases than in those diagnosed with synchronous liver metastases (p = 0.03). The metastatic liver lesions size correlated with the TL in metastases (p < 0.05). Following the neoadjuvant treatment, the patients with rectal cancer had shortened telomeres in tumour tissue than prior to the therapy (p = 0.01). Patients with a TL ratio between tumour tissue and the adjacent non-cancerous mucosa of ≥ 0.387 were associated with increased overall survival (p = 0.01). This study provides insights into TL dynamics during progression of the disease. The results show TL differences in metastatic lesions and may help in clinical practice to predict the patient’s prognosis.
Radiocesium mobility in different parts of the two major tree species in Fukushima
Authors: Manaka Takuya , Araki Masatake G. , Ohashi Shinta , Imamura Naohiro , Sakashita Wataru , Ogo Sumika , Komatsu Masabumi , Sakata Tadashi , Shinomiya Yoshiki
Published: June 2023

Radiocesium (137Cs) released in the Fukushima Dai-ichi Nuclear Power Plant accident is still cycling in the forest ecosystem. We examined the mobility of 137Cs in the external parts—leaves/needles, branches, and bark—of the two major tree species in Fukushima, Japanese cedar (Cryptomeria japonica) and konara oak (Quercus serrata). This variable mobility will likely lead to spatial heterogeneity of 137Cs and difficulty in predicting its dynamics for decades. We conducted leaching experiments on these samples by using ultrapure water and ammonium acetate. In Japanese cedar, the 137Cs percentage leached from current-year needles was 26–45% (ultrapure water) and 27–60% (ammonium acetate)—similar to those from old needles and branches. In konara oak, the 137Cs percentage leached from leaves was 47–72% (ultrapure water) and 70–100% (ammonium acetate)—comparable to those from current-year and old branches. Relatively poor 137Cs mobility was observed in the outer bark of Japanese cedar and in organic layer samples from both species. Comparison of the results from corresponding parts revealed greater 137Cs mobility in konara oak than in Japanese cedar. We suggest that more active cycling of 137Cs occurs in konara oak.
Multiple visual objects are represented differently in the human brain and convolutional neural networks
Authors: Mocz Viola , Jeong Su Keun , Chun Marvin , Xu Yaoda
Published: June 2023

Objects in the real world usually appear with other objects. To form object representations independent of whether or not other objects are encoded concurrently, in the primate brain, responses to an object pair are well approximated by the average responses to each constituent object shown alone. This is found at the single unit level in the slope of response amplitudes of macaque IT neurons to paired and single objects, and at the population level in fMRI voxel response patterns in human ventral object processing regions (e.g., LO). Here, we compare how the human brain and convolutional neural networks (CNNs) represent paired objects. In human LO, we show that averaging exists in both single fMRI voxels and voxel population responses. However, in the higher layers of five CNNs pretrained for object classification varying in architecture, depth and recurrent processing, slope distribution across units and, consequently, averaging at the population level both deviated significantly from the brain data. Object representations thus interact with each other in CNNs when objects are shown together and differ from when objects are shown individually. Such distortions could significantly limit CNNs’ ability to generalize object representations formed in different contexts.
Effect of signal timing on vehicles’ near misses at intersections
Authors: Islam Zubayer , Abdel-Aty Mohamed , Goswamy Amrita , Abdelraouf Amr , Zheng Ou
Published: June 2023

Driving characteristics often vary between the different states of the signal. During red and yellow phase, drivers tend to speed up and reduce the following distance which in turn increases the possibility of rear end crashes. Intersection safety, therefore, relies on the correct modelling of signal phasing and timing parameters, and how drivers respond to its changes. This paper aims to identify the relationship between surrogate safety measures and signal phasing. Unmanned aerial vehicle (UAV) video data has been used to study a major intersection. Post encroachment time (PET) between vehicles was calculated from the video data as well as speed, heading and relevant signal timing parameters such as all red time, red clearance time, yellow time, etc. Random parameter ordered logit model was used to model the relationship between PET and signal timing parameters. Overall, the results showed that yellow time and red clearance time is positively related to PETs. The model was also able to identify certain signal phases that could be a potential safety hazard and would need to be retimed by considering the PETs. The odds ratios from the models also indicate that increasing the mean yellow and red clearance times by one second can improve the PET levels by 10% and 3%, respectively.
Physics-assisted machine learning methods for predicting the splitting tensile strength of recycled aggregate concrete
Authors: Liu Jianguo , Han Xiangyu , Pan Yin , Cui Kai , Xiao Qinghua
Published: June 2023

Recycled aggregate concrete (RAC) has become a popular building material due to its eco-friendly features, but the difficulty in predicting the crack resistance of RAC is increasingly impeding its application. In this study, splitting tensile strength is adopted to describe the crack resistance ability of RAC, and physics-assisted machine learning (ML) methods are used to construct the predictive models for the splitting tensile strength of RAC. The results show that the AdaBoost model has excellent predictive performance with the help of the Firefly algorithm, and physical assistance plays a remarkable role in selecting features and verifying the ML models. Due to the limit in data size and the generalizability of the model, the dataset should be supplemented with more representative data, and an algorithm for small sample sizes could be studied in the future.
Simulation study of oxytetracycline contamination remediation in groundwater circulation wells enhanced by nano-calcium peroxide and ozone
Authors: Wang Xinyi , Zhang Lei , Han Chunmei , Zhang Yanyan , Zhuo Jiaxin
Published: June 2023

The widespread use of antibiotics in recent years has led to increasing antibiotic contamination of shallow groundwater. As the most widely used tetracycline antibiotic, oxytetracycline has received a lot of attention from researchers due to its stable molecular structure and difficulty in degradation. Aiming at remediation of oxytetracycline pollution in shallow groundwater, nano-calcium peroxide (nCaO2) and ozone (O3) are used to enhance the degradation of oxytetracycline in groundwater circulation well (GCW). A three-dimensional sand box test device for circulation wells is designed to explore the repair efficiency of circulation wells strengthened by different oxidants. The results show that after nCaO2 and O3 enhancing circulation wells operate for 10 h, the average removal rate of OTC reaches 83%, and the highest removal rate is 88.13%, which is 79.23% and 13.96% respectively higher than that of nCaO2 and O3 enhanced circulation wells alone, and there is no rebound phenomenon after aeration stops. The in-situ treatment of enhanced GCW by nCaO2 and O3 has potential applications for the removal of OTC in groundwater environments.
SSMD-UNet: semi-supervised multi-task decoders network for diabetic retinopathy segmentation
Authors: Ullah Zahid , Usman Muhammad , Latif Siddique , Khan Asifullah , Gwak Jeonghwan
Published: June 2023

Diabetic retinopathy (DR) is a diabetes complication that can cause vision loss among patients due to damage to blood vessels in the retina. Early retinal screening can avoid the severe consequences of DR and enable timely treatment. Nowadays, researchers are trying to develop automated deep learning-based DR segmentation tools using retinal fundus images to help Ophthalmologists with DR screening and early diagnosis. However, recent studies are unable to design accurate models due to the unavailability of larger training data with consistent and fine-grained annotations. To address this problem, we propose a semi-supervised multitask learning approach that exploits widely available unlabelled data (i.e., Kaggle-EyePACS) to improve DR segmentation performance. The proposed model consists of novel multi-decoder architecture and involves both unsupervised and supervised learning phases. The model is trained for the unsupervised auxiliary task to effectively learn from additional unlabelled data and improve the performance of the primary task of DR segmentation. The proposed technique is rigorously evaluated on two publicly available datasets (i.e., FGADR and IDRiD) and results show that the proposed technique not only outperforms existing state-of-the-art techniques but also exhibits improved generalisation and robustness for cross-data evaluation.
In vivo toxicity evaluation of a polyoxotungstate nanocluster as a promising contrast agent for computed tomography
Authors: Stojanović Marko , Lalatović Jovana , Milosavljević Aleksandra , Savić Nada , Simms Charlotte , Radosavljević Branimir , Ćetković Mila , Kravić Stevović Tamara , Mrda Davor , Čolović Mirjana B. , Parac-Vogt Tatjana N. , Krstić Danijela
Published: June 2023

In this study, we demonstrate for the first time, that a discrete metal-oxo cluster α-/β-K6P2W18O62 (WD-POM) exhibits superior performance as a computed tomography (CT) contrast agent, in comparison to the standard contrast agent iohexol. A toxicity evaluation of WD-POM was performed according to standard toxicological protocols using Wistar albino rats. The maximum tolerable dose (MTD) of 2000 mg/kg was initially determined after oral WD-POM application. The acute intravenous toxicity of single WD-POM doses (1/3, 1/5, and 1/10 MTD), which are at least fifty times higher than the typically used dose (0.015 mmol W kg−1) of tungsten-based contrast agents, was evaluated for 14 days. The results of arterial blood gas analysis, CO-oximetry status, electrolyte and lactate levels for 1/10 MTD group (80% survival rate) indicated the mixed respiratory and metabolic acidosis. The highest deposition of WD-POM (0.6 ppm tungsten) was found in the kidney, followed by liver (0.15 ppm tungsten), for which the histological analysis revealed morphological irregularities, although the renal function parameters (creatinine and BUN levels) were within the physiological range. This study is the first and important step in evaluating side effects of polyoxometalate nanoclusters, which in recent years have shown a large potential as therapeutics and contrast agents.
Membrane protease prostasin promotes insulin secretion by regulating the epidermal growth factor receptor pathway
Authors: Ishii Toshihisa , Miyasato Yoshikazu , Ichijo Masashi , Uchimura Kohei , Furuya Fumihiko
Published: June 2023

Prostasin (PRSS8) is a serine protease that metabolizes and moderates the effect of specific substrates. Epidermal growth factor receptor (EGFR), which modulates insulin secretion and pancreatic β-cell proliferation, is regulated via proteolytic shedding by PRSS8. We first detected PRSS8 expression in β-cells of pancreatic islets of mice. To better understand the molecular processes involved in PRSS8-associated insulin secretion, pancreatic β-cell-specific PRSS8 knockout (βKO) and PRSS8-overexpressing (βTG) male mice were generated. We found that glucose intolerance and reduction in glucose-stimulated insulin secretion developed in βKO mice compared with the control subjects. A higher response to glucose was noted in islets retrieved from βTG mice. Erlotinib, a specific blocker of EGFR, blocks EGF- and glucose-stimulated secretion of insulin among MIN6 cells, and glucose improves EGF release from β-cells. After silencing PRSS8 in MIN6 cells, glucose-stimulated insulin secretion decreased, and EGFR signaling was impaired. Conversely, overexpression of PRSS8 in MIN6 cells induced higher concentrations of both basal and glucose-stimulated insulin secretion and increased phospho-EGFR concentrations. Furthermore, short-term exposure to glucose improved the concentration of endogenous PRSS8 in MIN6 cells through inhibition of intracellular degradation. These findings suggest that PRSS8 is involved in glucose-dependent physiological regulation of insulin secretion via the EGF–EGFR signaling pathway in pancreatic β-cells.
Optimizing upside variability and antifragility in renewable energy system design
Authors: Coppitters Diederik , Contino Francesco
Published: June 2023

Despite the considerable uncertainty in predicting critical parameters of renewable energy systems, the uncertainty during system design is often marginally addressed and consistently underestimated. Therefore, the resulting designs are fragile, with suboptimal performances when reality deviates significantly from the predicted scenarios. To address this limitation, we propose an antifragile design optimization framework that redefines the indicator to optimize variability and introduces an antifragility indicator. The variability is optimized by favoring upside potential and providing downside protection towards a minimum acceptable performance, while the skewness indicates (anti)fragility. An antifragile design primarily enhances positive outcomes when the uncertainty of the random environment exceeds initial estimations. Hence, it circumvents the issue of underestimating the uncertainty in the operating environment. We applied the methodology to the design of a wind turbine for a community, considering the Levelized Cost Of Electricity (LCOE) as the quantity of interest. The design with optimized variability proves beneficial in 81% of the possible scenarios when compared to the conventional robust design. The antifragile design flourishes (LCOE drops by up to 120%) when the real-world uncertainty is higher than initially estimated in this paper. In conclusion, the framework provides a valid metric for optimizing the variability and detects promising antifragile design alternatives.
Preparation and characterization of different micro/nano structures on the surface of bredigite scaffolds
Authors: Qin Changcai , Che Dezhao , Liu Dongxue , Zhang Zefei , Feng Yihua
Published: June 2023

The preparation of controllable micro/nano structures on the surface of the bredigite scaffold is expected to exhibit the same support and osteoconductive capabilities as living bone. However, the hydrophobicity of the white calciμm silicate scaffold surface restricts the adhesion and spreading of osteoblasts. Furthermore, during the degradation process of the bredigite scaffold, the release of Ca2+ results in an alkaline environment around the scaffold, which inhibits the growth of osteoblasts. In this study, the three-dimensional geometry of the Primitive surface in the three-periodic minimal surface with an average curvature of 0 was used as the basis for the scaffold unit cell, and a white hydroxyapatite scaffold was fabricated via photopolymerization-based 3D printing. Nanoparticles, microparticles, and micro-sheet structures with thicknesses of 6 μm, 24 μm, and 42 μm, respectively, were prepared on the surface of the porous scaffold through a hydrothermal reaction. The results of the study indicate that the micro/nano surface did not affect the morphology and mineralization ability of the macroporous scaffold. However, the transition from hydrophobic to hydrophilic resulted in a rougher surface and an increase in compressive strength from 45 to 59–86 MPa, while the adhesion of the micro/nano structures enhanced the scaffold's ductility. In addition, after 8 days of degradation, the pH of the degradation solution decreased from 8.6 to around 7.6, which is more suitable for cell growth in the hμman body. However, there were issues of slow degradation and high P element concentration in the degradation solution for the microscale layer group during the degradation process, so the nanoparticle and microparticle group scaffolds could provide effective support and a suitable environment for bone tissue repair.
Chemical composition of extracts from leaves, stems and roots of wasabi (Eutrema japonicum) and their anti-cancer, anti-inflammatory and anti-microbial activities
Authors: Dos Santos Szewczyk Katarzyna , Skowrońska Weronika , Kruk Aleksandra , Makuch-Kocka Anna , Bogucka-Kocka Anna , Miazga-Karska Małgorzata , Grzywa-Celińska Anna , Granica Sebastian
Published: June 2023

The purpose of our study was to evaluate the composition of the extracts obtained from the roots and leaves of Eutrema japonicum cultivated in Poland. For this purpose, LC-DAD-IT-MS and LC-Q-TOF-MS analyses were used. The results revealed the presence of forty-two constituents comprising glycosinolates, phenylpropanoid glycosides, flavone glycosides, hydroxycinnamic acids, and other compounds. Then, the resultant extracts were subjected to an assessment of the potential cytotoxic effect on human colon adenocarcinoma cells, the effect on the growth of probiotic and intestinal pathogenic strains, as well as their anti-inflammatory activity. It was demonstrated that 60% ethanol extract from the biennial roots (WR2) had the strongest anti-inflammatory, antibacterial, and cytotoxic activities compared to the other samples. Our results suggest that extracts from E. japonicum may be considered as a promising compound for the production of health-promoting supplements.
Effects of anoxic prognostic model on immune microenvironment in pancreatic cancer
Authors: Wu Yangdong , Kou Qingyan , Sun Lin , Hu Xiao
Published: June 2023

Pancreatic cancer has one of the worst prognoses in the world, which suggests that the tumor microenvironment, which is characterized by hypoxia and immunosuppression, plays a significant role in the prognosis and progression of pancreatic cancer. We identified PLAU, LDHA, and PKM as key genes involved in pancreatic cancer hypoxia through GO/KEGG enrichment related hypoxia pathways and cox regression, established prognostic models, and studied their relationship to immune invasion through bioinformatics using R and related online databases. We verified the high expression of PLAU, LDHA, and PKM in pancreatic cancer cells using qPCR in vitro, and we also discovered that the expression of PLAU, LDHA, and PKM in hypoxic pancreatic cancer cells differed from that in normal cultured pancreatic cancer cells. Finally, we discovered that our prognostic model accurately predicted postrain in pancreatic cancer patients with hypoxia and immune infiltration.
Global tropical cyclone precipitation scaling with sea surface temperature
Authors: Stansfield Alyssa M. , Reed Kevin A.
Published: June 2023

Understanding the relationship between tropical cyclone (TC) precipitation and sea surface temperature (SST) is essential for both TC hazard forecasting and projecting how these hazards will change in the future due to climate change. This work untangles how global TC precipitation is impacted by present-day SST variability (known as apparent scaling) and by long-term changes in SST caused by climate change (known as climate scaling). A variety of datasets are used including precipitation and SST observations, realistic climate model simulations, and idealized climate model simulations. The apparent scaling rates depend on precipitation metric; examples shown here have ranges of 6.1 to 9.5% per K versus 5.9 to 9.8% per K for two different metrics. The climate scaling is estimated at about 5% per K, which is slightly less than the atmospheric moisture scaling based on thermodynamic principles of about 7% per K (i.e., the Clausius–Clapeyron scaling). The apparent scaling is greater than the climate scaling, which implies that the relationship between TC precipitation and present-day SST variability should not be used to project the long-term response of TC precipitation to climate change.