bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-throughput test enables specific detection of hepatocellular carcinoma
Authors: Cheishvili David , Wong Chifat , Karim Mohammad Mahbubul , Kibria Mohammad Golam , Jahan Nusrat , Das Pappu Chandra , Yousuf Md. Abul Khair , Islam Md. Atikul , Das Dulal Chandra , Noor-E-Alam Sheikh Mohammad , Szyf Moshe , Alam Sarwar , Khan Wasif A. , Al Mahtab Mamun
Published: June 2023

High-throughput tests for early cancer detection can revolutionize public health and reduce cancer morbidity and mortality. Here we show a DNA methylation signature for hepatocellular carcinoma (HCC) detection in liquid biopsies, distinct from normal tissues and blood profiles. We developed a classifier using four CpG sites, validated in TCGA HCC data. A single F12 gene CpG site effectively differentiates HCC samples from other blood samples, normal tissues, and non-HCC tumors in TCGA and GEO data repositories. The markers were validated in a separate plasma sample dataset from HCC patients and controls. We designed a high-throughput assay using next-generation sequencing and multiplexing techniques, analyzing plasma samples from 554 clinical study participants, including HCC patients, non-HCC cancers, chronic hepatitis B, and healthy controls. HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC. Implementing this assay for high-risk individuals could significantly decrease HCC morbidity and mortality.
The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells
Authors: Quendera Ana Patrícia , Pinto Sandra Nunes , Pobre Vânia , Antunes Wilson , Bonifácio Vasco D. B. , Arraiano Cecília Maria , Andrade José Marques
Published: June 2023

Biofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. Here we show that the RNA-binding protein and ribonuclease polynucleotide phosphorylase (PNPase) is a positive regulator of biofilm formation in the human pathogen Listeria monocytogenes, a major responsible for food contamination in food-processing environments. The PNPase mutant strain produces less biofilm biomass and exhibits an altered biofilm morphology that is more susceptible to antibiotic treatment. Through biochemical assays and microscopical analysis, we demonstrate that PNPase is a previously unrecognized regulator of the composition of the biofilm extracellular matrix, greatly affecting the levels of proteins, extracellular DNA, and sugars. Noteworthy, we have adapted the use of the fluorescent complex ruthenium red-phenanthroline for the detection of polysaccharides in Listeria biofilms. Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. Overall, this work demonstrates that PNPase is an important post-transcriptional regulator for virulence and adaptation to the biofilm lifestyle of Gram-positive bacteria and highlights the expanding role of ribonucleases as critical players in pathogenicity.
Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage
Authors: Leung Howell , Xiong Ling , Ni Yueqiong , Busch Anne , Bauer Michael , Press Adrian T. , Panagiotou Gianni
Published: June 2023

Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.
Interchange reconnection as the source of the fast solar wind within coronal holes
Authors: Bale S. D. , Drake J. F. , McManus M. D. , Desai M. I. , Badman S. T. , Larson D. E. , Swisdak M. , Horbury T. S. , Raouafi N. E. , Phan T. , Velli M. , McComas D. J. , Cohen C. M. S. , Mitchell D. , Panasenco O. , Kasper J. C.
Published: June 2023

The fast solar wind that fills the heliosphere originates from deep within regions of open magnetic field on the Sun called ‘coronal holes’. The energy source responsible for accelerating the plasma is widely debated; however, there is evidence that it is ultimately magnetic in nature, with candidate mechanisms including wave heating1,2 and interchange reconnection3–5. The coronal magnetic field near the solar surface is structured on scales associated with ‘supergranulation’ convection cells, whereby descending flows create intense fields. The energy density in these ‘network’ magnetic field bundles is a candidate energy source for the wind. Here we report measurements of fast solar wind streams from the Parker Solar Probe (PSP) spacecraft6 that provide strong evidence for the interchange reconnection mechanism. We show that the supergranulation structure at the coronal base remains imprinted in the near-Sun solar wind, resulting in asymmetric patches of magnetic ‘switchbacks’7,8 and bursty wind streams with power-law-like energetic ion spectra to beyond 100 keV. Computer simulations of interchange reconnection support key features of the observations, including the ion spectra. Important characteristics of interchange reconnection in the low corona are inferred from the data, including that the reconnection is collisionless and that the energy release rate is sufficient to power the fast wind. In this scenario, magnetic reconnection is continuous and the wind is driven by both the resulting plasma pressure and the radial Alfvénic flow bursts.
Structural basis for FGF hormone signalling
Authors: Chen Lingfeng , Fu Lili , Sun Jingchuan , Huang Zhiqiang , Fang Mingzhen , Zinkle Allen , Liu Xin , Lu Junliang , Pan Zixiang , Wang Yang , Liang Guang , Li Xiaokun , Chen Gaozhi , Mohammadi Moosa
Published: June 2023

α/βKlotho coreceptors simultaneously engage fibroblast growth factor (FGF) hormones (FGF19, FGF21 and FGF23)1,2 and their cognate cell-surface FGF receptors (FGFR1–4) thereby stabilizing the endocrine FGF–FGFR complex3–6. However, these hormones still require heparan sulfate (HS) proteoglycan as an additional coreceptor to induce FGFR dimerization/activation and hence elicit their essential metabolic activities6. To reveal the molecular mechanism underpinning the coreceptor role of HS, we solved cryo-electron microscopy structures of three distinct 1:2:1:1 FGF23–FGFR–αKlotho–HS quaternary complexes featuring the ‘c’ splice isoforms of FGFR1 (FGFR1c), FGFR3 (FGFR3c) or FGFR4 as the receptor component. These structures, supported by cell-based receptor complementation and heterodimerization experiments, reveal that a single HS chain enables FGF23 and its primary FGFR within a 1:1:1 FGF23–FGFR–αKlotho ternary complex to jointly recruit a lone secondary FGFR molecule leading to asymmetric receptor dimerization and activation. However, αKlotho does not directly participate in recruiting the secondary receptor/dimerization. We also show that the asymmetric mode of receptor dimerization is applicable to paracrine FGFs that signal solely in an HS-dependent fashion. Our structural and biochemical data overturn the current symmetric FGFR dimerization paradigm and provide blueprints for rational discovery of modulators of FGF signalling2 as therapeutics for human metabolic diseases and cancer.
Unveiling the transition from niche to dispersal assembly in ecology
Authors: Loke Lynette H. L. , Chisholm Ryan A.
Published: June 2023

A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a ‘niche detector’ and a tool for assessing when communities are niche versus dispersal assembled.
Full scale, microscopically resolved tomographies of sandstone and carbonate rocks augmented by experimental porosity and permeability values
Authors: Esteves Ferreira Matheus , Rodrigues Del Grande Mariana , Neumann Barros Ferreira Rodrigo , Ferreira da Silva Ademir , Nogueira Pereira da Silva Márcio , Tirapu-Azpiroz Jaione , Lucas-Oliveira Everton , de Araújo Ferreira Arthur Gustavo , Soares Renato , B. Eckardt Christian , J. Bonagamba Tito , Steiner Mathias
Published: June 2023

We report a dataset containing full-scale, 3D images of rock plugs augmented by petrophysical lab characterization data for application in digital rock and capillary network analysis. Specifically, we have acquired microscopically resolved tomography datasets of 18 cylindrical sandstone and carbonate rock samples having lengths of 25.4 mm and diameters of 9.5 mm. Based on the micro-tomography data, we have computed porosity-values for each imaged rock sample. For validating the computed porosity values with a complementary lab method, we have measured porosity for each rock sample by using standard petrophysical characterization techniques. Overall, the tomography-based porosity values agree with the measurement results obtained from the lab, with values ranging from 8% to 30%. In addition, we provide for each rock sample the experimental permeabilities, with values ranging from 0.4 mD to above 5D. This dataset will be essential for establishing, benchmarking, and referencing the relation between porosity and permeability of reservoir rock at pore scale.
Unified real-time environmental-epidemiological data for multiscale modeling of the COVID-19 pandemic
Authors: Badr Hamada S. , Zaitchik Benjamin F. , Kerr Gaige H. , Nguyen Nhat-Lan H. , Chen Yen-Ting , Hinson Patrick , Colston Josh M. , Kosek Margaret N. , Dong Ensheng , Du Hongru , Marshall Maximilian , Nixon Kristen , Mohegh Arash , Goldberg Daniel L. , Anenberg Susan C. , Gardner Lauren M.
Published: June 2023

An impressive number of COVID-19 data catalogs exist. However, none are fully optimized for data science applications. Inconsistent naming and data conventions, uneven quality control, and lack of alignment between disease data and potential predictors pose barriers to robust modeling and analysis. To address this gap, we generated a unified dataset that integrates and implements quality checks of the data from numerous leading sources of COVID-19 epidemiological and environmental data. We use a globally consistent hierarchy of administrative units to facilitate analysis within and across countries. The dataset applies this unified hierarchy to align COVID-19 epidemiological data with a number of other data types relevant to understanding and predicting COVID-19 risk, including hydrometeorological data, air quality, information on COVID-19 control policies, vaccine data, and key demographic characteristics.
LDLR gene’s promoter region hypermethylation in patients with familial hypercholesterolemia
Authors: Zorzo R. A. , Suen V. M. M. , Santos J. E. , Silva-Jr W. A. , Suazo V. K. , Honorato A. L. S. C. , Santos R. D. , Jannes C. E. , Pereira A. , Krieger J. E. , Liberatore-Jr R. D. R.
Published: June 2023

Familial hypercholesterolemia (FH) is characterized by high low-density lipoprotein cholesterol (LDL-C) levels and a high risk of early coronary heart disease. Structural alterations in theLDLR,APOB, andPCSK9genes were not found in 20–40% of patients diagnosed using the Dutch Lipid Clinic Network (DCLN) criteria. We hypothesized that methylation in canonical genes could explain the origin of the phenotype in these patients. This study included 62 DNA samples from patients with a clinical diagnosis of FH according to the DCLN criteria, who previously tested negative for structural alterations in the canonical genes, and 47 DNA samples from patients with normal blood lipids (control group). All DNA samples were tested for methylation in the CpG islands of the three genes. The prevalence of FH relative to each gene was determined in both groups and the respective prevalence ratios (PRs) were calculated. The methylation analysis ofAPOBandPCSK9was negative in both groups, showing no relationship between methylation in these genes and the FH phenotype. Asthe LDLRgene has two CpG islands, we analyzed each island separately. The analysis ofLDLR-island1 showed PR = 0.982 (CI 0.33–2.95; χ2 = 0.001; p = 0.973), also suggesting no relationship between methylation and the FH phenotype. Analysis ofLDLR-island2 showed a PR of 4.12 (CI 1.43–11.88; χ2 = 13,921; p = 0.00019), indicating a possible association between methylation on this island and the FH phenotype.
Decomposing solar and geomagnetic activity and seasonal dependencies to examine the relationship between GPS loss of lock and ionospheric turbulence
Authors: Lovati Giulia , De Michelis Paola , Consolini Giuseppe , Pezzopane Michael , Pignalberi Alessio , Berrilli Francesco
Published: June 2023

Ionospheric irregularities are plasma density variations that occur at various altitudes and latitudes and whose size ranges from a few meters to a few hundred kilometers. They can have a negative impact on the Global Navigation Satellite Systems (GNSS), on their positioning accuracy and even cause a signal loss of lock (LoL), a phenomenon for which GNSS receivers can no longer track the satellites’ signal. Nowadays, the study of plasma density irregularities is important because many of the crucial infrastructures of our society rely on the efficient operation of these positioning systems. It was recently discovered that, of all possible ionospheric plasma density fluctuations, those in a turbulent state and characterized by extremely high values of the Rate Of change of the electron Density Index appear to be associated with the occurrence of LoL events. The spatial distributions of this class of fluctuations at mid and high latitudes are reconstructed for the first time using data collected on Swarm satellites between July 15th, 2014 and December 31st, 2021, emphasizing their dependence on solar activity, geomagnetic conditions, and season. The results unequivocally show that the identified class of plasma fluctuations exhibits spatio-temporal behaviours similar to those of LoL events.
How transform fault shear influences where detachment faults form near mid-ocean ridges
Authors: Schierjott Jana C. , Ito Garrett , Behn Mark D. , Tian Xiaochuan , Morrow Thomas , Kaus Boris J. P. , Escartín Javier
Published: June 2023

Oceanic detachment faults represent an end-member form of seafloor creation, associated with relatively weak magmatism at slow-spreading mid-ocean ridges. We use 3-D numerical models to investigate the underlying mechanisms for why detachment faults predominantly form on the transform side (inside corner) of a ridge-transform intersection as opposed to the fracture zone side (outside corner). One hypothesis for this behavior is that the slipping, and hence weaker, transform fault allows for the detachment fault to form on the inside corner, and a stronger fracture zone prevents the detachment fault from forming on the outside corner. However, the results of our numerical models, which simulate different frictional strengths in the transform and fracture zone, do not support the first hypothesis. Instead, the model results, combined with evidence from rock physics experiments, suggest that shear-stress on transform fault generates excess lithospheric tension that promotes detachment faulting on the inside corner.
Dengue virus infection during window period of consecutive outbreaks in Nepal and assessment of clinical parameters
Authors: Rauniyar Ramanuj , Prajapati Sabita , Manandhar Binod , Bastola Anup , Chalise Bimal Sharma , Shrestha Srijan , Khanal Chetana , Thapa Machchhendra , Napit Rajindra , Bajracharya Anup Muni , Shrestha Shova , Adhikari Anurag , Das Manandhar Krishna
Published: June 2023

Nepal is an endemic country for dengue infection with rolling of every 3 year’s clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017–2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal.
Comprehensive RNA-Seq-based study and metabolite profiling to identify genes involved in podophyllotoxin biosynthesis in Linum album Kotschy ex Boiss. (Linaceae)
Authors: Danaeipour Zahra , Garoosi Ghasemali , Tohidfar Masoud , Bakhtiarizadeh Mohammad Reza , Mirjalili Mohammad Hossein
Published: June 2023

Linum albumis a well-known rich source of anticancer compounds, i.e., podophyllotoxin (PTOX) and other lignans. These compounds play an important role in the plant’s defensive system. The RNA-Seq data of flax (L. usitatissimum) were analyzed under various biotic and abiotic stresses to comprehend better the importance of lignans in plant defense responses. Then, the association between the lignan contents and some related gene expressions was experimented with HPLC and qRT-PCR, respectively. Transcriptomic profiling showed a specific expression pattern in different organs, and just the commonly regulated geneEP3was detected with a significant increase under all stresses. The in silico analysis of the PTOX biosynthesis pathway identified a list of genes, including laccase (LAC11), lactoperoxidase (POD), 4-coumarate-CoA ligase (4CL), and secoisolariciresinol dehydrogenase (SDH). These genes increased significantly under individual stresses. The HPLC analysis showed that the measured lignan contents generally increased under stress. In contrast, a quantitative expression of the genes involved in this pathway using qRT-PCR showed a different pattern that seems to contribute to regulating PTOX content in response to stress. Identified modifications of critical genes related to PTOX biosynthesis in response to multiple stresses can provide a baseline for improving PTOX content inL. album.
Three-dimensional growth and biomechanical risk progression of abdominal aortic aneurysms under serial computed tomography assessment
Authors: Siika Antti , Bogdanovic Marko , Liljeqvist Moritz Lindquist , Gasser T. Christian , Hultgren Rebecka , Roy Joy
Published: June 2023

Growth of abdominal aortic aneurysms (AAAs) is often described as erratic and discontinuous. This study aimed at describing growth patterns of AAAs with respect to maximal aneurysm diameter (Dmax) and aneurysm volume, and to characterize changes in the intraluminal thrombus (ILT) and biomechanical indices as AAAs grow. 384 computed tomography angiographies (CTAs) from 100 patients (mean age 70.0, standard deviation, SD = 8.5 years, 22 women), who had undergone at least three CTAs, were included. The mean follow-up was 5.2 (SD = 2.5) years. Growth of Dmax was 2.64 mm/year (SD = 1.18), volume 13.73 cm3/year (SD = 10.24) and PWS 7.3 kPa/year (SD = 4.95). For Dmax and volume, individual patients exhibited linear growth in 87% and 77% of cases. In the tertile of patients with the slowest Dmax-growth (< 2.1 mm/year), only 67% belonged to the slowest tertile for volume-growth, and 52% and 55% to the lowest tertile of PWS- and PWRI-increase, respectively. The ILT-ratio (ILT-volume/aneurysm volume) increased with time (2.6%/year, p < 0.001), but when adjusted for volume, the ILT-ratio was inversely associated with biomechanical stress. In contrast to the notion that AAAs grow in an erratic fashion most AAAs displayed continuous and linear growth. Considering only change in Dmax, however, fails to capture the biomechanical risk progression, and parameters such as volume and the ILT-ratio need to be considered.
Efficacy of atosiban for repeated implantation failure in frozen embryo transfer cycles
Authors: Li Xiufang , Du Yanbo , Han Xu , Wang Huidan , Sheng Yan , Lian Fang , Lian Qingfeng
Published: June 2023

Atosiban was commonly added to improve pregnancy outcomes of patients with repeated embryo implantation failure (RIF). In this study, we aimed to investigate the effect of atosiban before transferring the frozen-thawed embryo to RIF patients. This retrospective study was conducted in the Hospital for Reproductive Medicine affiliated to Shandong University from August 2017 to June 2021. A total of 1774 women with a history of RIF undergoing frozen embryo transfer (FET) were included in this study. All the participants were classified into atosiban or control group: Group A included 677 patients who were administered atosiban intravenously 30 min prior to FET with a dose of 37.5 mg; Group B included 1097 patients who received no atosiban before the transfer. There were no significant differences observed in the live birth rate (LBR) (39.73% vs. 39.02%, P = 0.928) between the two groups. Other secondary outcomes including biochemical pregnancy rate, clinical pregnancy rate, implantation rate, clinical miscarriage rate and preterm birth rate were similar between the two groups (all P > 0.05). However, subgroup analysis demonstrated significantly higher preterm birth rates in the control group compared with the atosiban group (0 versus 3.0%, P = 0.024) in the natural FET cycles. Atosiban may not improve pregnancy outcomes of RIF patients in FET cycles. However, the effects of Atosiban on pregnancy outcomes should be assessed in clinical trials with larger sample sizes.
A nomogram for predicting cancer-specific survival in patients with uterine clear cell carcinoma: a population-based study
Authors: Cheng Wen-li , Wang Rui-min , Zhao Yi , Chen Juan
Published: June 2023

Uterine clear cell carcinoma (UCCC) is a relatively rare endometrial cancer. There is limited information on its prognosis. This study aimed to develop a predictive model predicting the cancer-specific survival (CSS) of UCCC patients based on data from the Surveillance, Epidemiology, and End Results (SEER) database between 2000 and 2018. A total of 2329 patients initially diagnosed with UCCC were included in this study. Patients were randomized into training and validation cohorts (7:3). Multivariate Cox regression analysis identified that age, tumor size, SEER stage, surgery, number of lymph nodes detected, lymph node metastasis, radiotherapy and chemotherapy were independent prognostic factors for CSS. Based on these factors, a nomogram for predicting the prognosis of UCCC patients was constructed. The nomogram was validated using concordance index (C-index), calibration curves, and decision curve analyses (DCA). The C-index of the nomograms in the training and validation sets are 0.778 and 0.765, respectively. Calibration curves showed good consistency of CSS between actual observations and nomogram predictions, and DCA showed that the nomogram has great clinical utility. In conclusion, a prognostic nomogram was firstly established for predicting the CSS of UCCC patients, which can help clinicians make personalized prognostic predictions and provide accurate treatment recommendations.
Knocking out alpha-synuclein in melanoma cells downregulates L1CAM and decreases motility
Authors: Gajendran Nithya , Rajasekaran Santhanasabapathy , Witt Stephan N.
Published: June 2023

The Parkinson’s disease (PD) associated protein, alpha-synuclein (α-syn/SNCA), is highly expressed in aggressive melanomas. The goal of this study was to reveal possible mechanism(s) of α-syn involvement in melanoma pathogenesis. Herein, we asked whether α-syn modulates the expression of the pro-oncogenic adhesion molecules L1CAM and N-cadherin. We used two human melanoma cell lines (SK-MEL-28, SK-MEL-29), SNCA-knockout (KO) clones, and two human SH-SY5Y neuroblastoma cell lines. In the melanoma lines, loss of α-syn expression resulted in significant decreases in the expression of L1CAM and N-cadherin and concomitant significant decreases in motility. On average, there was a 75% reduction in motility in the four SNCA-KOs tested compared to control cells. Strikingly, comparing neuroblastoma SH-SY5Y cells that have no detectable α-syn to SH-SY5Y cells that stably express α-syn (SH/+αS), we found that expressing α-syn increased L1CAM and single-cell motility by 54% and 597%, respectively. The reduction in L1CAM level in SNCA-KO clones was not due to a transcriptional effect, rather we found that L1CAM is more efficiently degraded in the lysosome in SNCA-KO clones than in control cells. We propose that α-syn is pro-survival to melanoma (and possibly neuroblastoma) because it promotes the intracellular trafficking of L1CAM to the plasma membrane.
Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson's disease
Authors: Wang Dan , Xie Daojun , Zhang Juan , Cai Biao , Yang Bo , Zhou Lei , Huang Xiaofeng
Published: June 2023

Wilson's disease (WD) is an autosomal recessive disorder with a genetic basis. The predominant non-motor symptom of WD is cognitive dysfunction, although the specific genetic regulatory mechanism remains unclear. Tx-J mice, with an 82% sequence homology of the ATP7B gene to the human gene, are considered the most suitable model for WD. This study employs deep sequencing to investigate the differences in RNA transcript profiles, both coding and non-coding, as well as the functional characteristics of the regulatory network involved in WD cognitive impairment. The cognitive function of tx-J mice was evaluated using the Water Maze Test (WMT). Long non-coding RNA (lncRNA), circular RNA (circRNA), and messenger RNA (mRNA) profiles were analyzed in the hippocampal tissue of tx-J mice to identify differentially expressed RNAs (DE-RNAs). Subsequently, the DE-RNAs were used to construct protein–protein interaction (PPI) networks, as well as DE-circRNAs and lncRNAs-associated competing endogenous RNA (ceRNA) expression networks, and coding-noncoding co-expression (CNC) networks. To elucidate their biological functions and pathways, the PPI and ceRNA networks were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 361 differentially expressed mRNAs (DE-mRNAs), comprising 193 up-regulated and 168 down-regulated mRNAs, 2627 differentially expressed long non-coding RNAs (DE-lncRNAs), consisting of 1270 up-regulated and 1357 down-regulated lncRNAs, and 99 differentially expressed circular RNAs (DE-circRNAs), consisting of 68 up-regulated and 31 down-regulated circRNAs, were observed in the tx-J mice group when compared to the control mice group. Gene Ontology (GO) and pathway analyses revealed that DE-mRNAs were enriched in cellular processes, calcium signaling pathways, and mRNA surveillance pathways. In contrast, the DE-circRNAs-associated competing endogenous RNA (ceRNA) network was enriched for covalent chromatin modification, histone modification, and axon guidance, whereas the DE-lncRNAs-associated ceRNA network was enriched for dendritic spine, regulation of cell morphogenesis involved in differentiation, and mRNA surveillance pathway. The study presented the expression profiles of lncRNA, circRNA, and mRNA in the hippocampal tissue of tx-J mice. Furthermore, the study constructed PPI, ceRNA, and CNC expression networks. The findings are significant in comprehending the function of regulatory genes in WD associated with cognitive impairment. These results also offer valuable information for the diagnosis and treatment of WD.
Simultaneous determination of 2-(3-hydroxy-5-phosphonooxymethyl-2-methyl-4-pyridyl)-1,3-thiazolidine-4-carboxylic acid and main plasma aminothiols by HPLC–UV based method
Authors: Piechocka Justyna , Wyszczelska-Rokiel Monika , Głowacki Rafał
Published: June 2023

The report presents the first method for simultaneous determination of plasma 2-(3-hydroxy-5-phosphonooxymethyl-2-methyl-4-pyridyl)-1,3-thiazolidine-4-carboxylic acid (HPPTCA), an adduct of cysteine (Cys) and active form of vitamin B6 pyridoxal 5′-phosphate (PLP), as well as total low molecular-weight thiols content, including Cys, homocysteine (Hcy), cysteinyl-glycine (Cys-Gly), and glutathione (GSH). The assay is based on high performance liquid chromatography coupled with ultraviolet detection (HPLC–UV) and involves disulfides reduction with tris(2-carboxyethyl)phosphine (TCEP), derivatization with 2-chloro-1-methylquinolinium tetrafluoroborate (CMQT) followed by sample deproteinization with perchloric acid (PCA). The chromatographic separation of obtained stable UV-absorbing derivatives is achieved on ZORBAX SB-C18 (150 × 4.6 mm, 5.0 µm) column using gradient elution with eluent consisted of 0.1 mol/L trichloroacetic acid (TCA), pH 1.7 and acetonitrile (ACN), delivered at a flow rate 1 mL/min. Under these conditions, the analytes are separated within 14 min at room temperature, and quantified by monitoring at 355 nm. Regarding HPPTCA, the assay linearity was demonstrated within a 1–100 µmol/L in plasma and the lowest concentration on the calibration curve was recognized as the limit of quantification (LOQ). The accuracy ranged from 92.74 to 105.57% and 95.43 to 115.73%, while precision varied from 2.48 to 6.99% and 0.84 to 6.98% for intra- and inter-day measurements, respectively. The utility of the assay was proved by application to plasma samples delivered by apparently healthy donors (n = 18) in which the HPPTCA concentration ranged from 19.2 to 65.6 µmol/L. The HPLC–UV assay provides complementary tool for routine clinical analysis, facilitating further studies on the role of aminothiols and HPPTCA in living systems.
Synthesis of substituted pyridines with diverse functional groups via the remodeling of (Aza)indole/Benzofuran skeletons
Authors: Vaithegi Kannan , Yi Sihyeong , Lee Ji Hyae , Varun Begur Vasanthkumar , Park Seung Bum
Published: June 2023

Substituted pyridines with diverse functional groups are important structural motifs found in numerous bioactive molecules. Several methodologies for the introduction of various bio-relevant functional groups to pyridine have been reported, but there is still a need for a single robust method allowing the selective introduction of multiple functional groups. This study reports a ring cleavage methodology reaction for the synthesis of 2-alkyl/aryl 3-electron-withdrawing groups (esters, sulfones, and phosphonates) 5-aminoaryl/phenol pyridines via the remodeling of 3-formyl (aza)indoles/benzofurans. Totally ninety-three 5-aminoaryl pyridines and thirty-three 5-phenol pyridines were synthesized showing the robustness of the developed methodology. The application of this methodology further provided a privileged pyridine scaffold containing biologically relevant molecules and direct drug/natural product conjugation with ethyl 2-methyl nicotinate.
A multi-model assessment of the Global Warming Potential of hydrogen
Authors: Sand Maria , Skeie Ragnhild Bieltvedt , Sandstad Marit , Krishnan Srinath , Myhre Gunnar , Bryant Hannah , Derwent Richard , Hauglustaine Didier , Paulot Fabien , Prather Michael , Stevenson David
Published: June 2023

With increasing global interest in molecular hydrogen to replace fossil fuels, more attention is being paid to potential leakages of hydrogen into the atmosphere and its environmental consequences. Hydrogen is not directly a greenhouse gas, but its chemical reactions change the abundances of the greenhouse gases methane, ozone, and stratospheric water vapor, as well as aerosols. Here, we use a model ensemble of five global atmospheric chemistry models to estimate the 100-year time-horizon Global Warming Potential (GWP100) of hydrogen. We estimate a hydrogen GWP100 of 11.6 ± 2.8 (one standard deviation). The uncertainty range covers soil uptake, photochemical production of hydrogen, the lifetimes of hydrogen and methane, and the hydroxyl radical feedback on methane and hydrogen. The hydrogen-induced changes are robust across the different models. It will be important to keep hydrogen leakages at a minimum to accomplish the benefits of switching to a hydrogen economy.
Magnetic Soft Matter in a Rotating Field
Authors: Cēbers A.
Published: June 2023

An overview of soft matter behavior in a rotating magnetic field is given and the basic phenomena of single ferromagnetic and paramagnetic particles are described: synchronous and asynchronous regimes, structural instability leading to the precessional regime and others. Their applications in microrheology are discussed. As a particular example of an active magnetic system, magnetotactic bacteria are considered and several important phenomena, such as complex trajectories, synchronization, diffusion due to the internal noise are described. As an important application of these descriptions, hydrodynamics with spin is considered and the conditions for the transformation from microscopic rotational motion of the particles to the macroscopic motion of their suspension are described. Finally, exciting perspectives for further development of the field, such as hydrodynamics of systems with odd viscosity, are briefly discussed.
Maleic anhydride from bio-based 1-butanol and furfural: a life cycle assessment at the pilot scale
Authors: Cucciniello Raffaele , Cespi Daniele , Riccardi Matteo , Neri Elena , Passarini Fabrizio , Pulselli Federico Maria
Published: June 2023

The necessity to feed the chemical industry with bio-based platform chemicals encourages the usage of a life cycle perspective in order to evaluate potentialities and drawbacks, before launching them at the industrial scale.
A homogeneous hybridization magnetic biosensor based on electric field assistance for ultrafast nucleic acid detection
Authors: Cui Jinling , Sun Ritong , Zhao Xiaoli , Zhao Mingyuan , Zhang Xiaojun , Li Yong , Wang Lei , Shi Chao , Ma Cuiping
Published: June 2023

A homogeneous-hybridization-based DNA biosensor was constructed with electric field assistance, which quickly detects the target DNA within 400 s with superior sensitivity and specificity.
Calcium-triggered DNA-mediated membrane fusion in synthetic cells
Authors: Hsu Yen-Yu , Chen Samuel J. , Bernal-Chanchavac Julio , Sharma Bineet , Moghimianavval Hossein , Stephanopoulos Nicholas , Liu Allen P.
Published: June 2023

We develop a novel calcium-triggered membrane fusion strategy for synthetic cells by regulating DNA-mediated membrane fusion with membrane-bound polyethylene glycol polymeric chains that are cleavable by the calcium-activated protease calpain-1.
The role of covalency in enhancing stability of Eu and Am complexes: a DFT comparison of BTP and BTPhen
Authors: Fryer-Kanssen Izaak , Malcomson Thomas , Austin Jonathan , Kerridge Andrew
Published: June 2023

BTP and BTPhen complexes of americium are shown to exhibit greater covalent bond stabilisation than their europium analogues.
Correction: An insight into the optical properties of a sub nanosize glutathione stabilized gold cluster
Authors: Nair Lakshmi V. , Nair Resmi V. , Jayasree Ramapurath S.
Published: June 2023

Correction for ‘An insight into the optical properties of a sub nanosize glutathione stabilized gold cluster’ by Lakshmi V. Nair et al., Dalton Trans., 2016, 45, 11286–11291, https://doi.org/10.1039/C6DT01753C.
Nonviable carbon neutrality with plastic waste-to-energy
Authors: Kwon Serang , Kang Jieun , Lee Beomhui , Hong Soonwook , Jeon Yongseok , Bak Moonsoo , Im Seong-kyun
Published: June 2023

Energy recovery of plastic waste without carbon capture resulted in higher CO2 emissions than from fossil fuels. Potential electricity generation in 2050 from plastic waste-to-energy could be significantly increased.
Highly selective CO2 sensing response of lanthanum oxide nanoparticle electrodes at ambient temperature
Authors: Eswaran Amutha , Thirumalainambi Madhumitha , Subramaniam Rajaduraipandian , Annadurai Gurusamy
Published: June 2023

La2O3 nanoparticles were synthesized using a simple hydrothermal method and then used in a gas sensor which displayed high sensitivity towards CO2.
Spatially resolved photoactivation of dynamic exchange reactions in 3D-printed thiol–ene vitrimers
Authors: Reisinger David , Hellmayr Alexander , Paris Matthias , Haas Michael , Griesser Thomas , Schlögl Sandra
Published: June 2023

On-demand photoactivation of dynamic transesterification in cross-linked thiol–ene polymers manufactured by digital light processing 3D printing.
Modular and stereoselective access to cis-diphosphinoalkenes
Authors: Dong Bingbing , Liu Min , Li Yunpu , Zhu Wenjuan , Li Siyuan , Wang Tongtong , Liu Ying-Guo , Wu Junliang
Published: June 2023

Diphosphine ligands are highly popular but costly toolkit in organic chemistry.
Selection of a compatible electron transport layer and hole transport layer for the mixed perovskite FA0.85Cs0.15Pb (I0.85Br0.15)3, towards achieving novel structure and high-efficiency perovskite solar cells: a detailed numerical study by SCAPS-1D
Authors: Rahman Md. Bulu , Noor-E-Ashrafi  , Miah Md. Helal , Khandaker Mayeen Uddin , Islam Mohammad Aminul
Published: June 2023

Nomination of compatible ETL and HTL for the absorber layer FA0.85Cs0.15Pb (I0.85Br0.15)3via numerical analysis.
Kinetic analysis of silicon–lithium alloying reaction in silicon single crystal using soft X-ray absorption spectroscopy
Authors: Chamidah Nur , Suzuki Akito , Shimizu Takeshi , Zhong Chengchao , Shimoda Keiji , Okazaki Ken-ichi , Yaji Toyonari , Nakanishi Koji , Nishijima Motoaki , Kinoshita Hajime , Orikasa Yuki
Published: June 2023

The anisotropy of the silicon–lithium alloying reaction is governed by the surface reaction of silicon.
Iron(ii) carboxylates and simple carboxamides: an inexpensive and modular catalyst system for the synthesis of PLLA and PLLA-PCL block copolymers
Authors: Kirchhecker Sarah , Nguyen Ngoc , Reichert Stefan , Lützow Karola , Eselem Bungu Paul S. , Jacobi von Wangelin Axel , Sandl Sebastian , Neffe Axel T.
Published: June 2023

The combination of inexpensive Fe(ii) acetate with low molecular weight aliphatic carboxamides in situ generates an effective catalyst system for the ring opening polymerisation of lactones.
Structural inhomogeneity: a potential strategy to improve the hydrogen storage performance of metal hydrides
Authors: Zhao Yingyan , Zhu Yunfeng , Shi Rui , Jia Zhen , Zhang Jiguang , Liu Yana , Cheng Honghui , Tang Qinke , Ba Zhixin , Hu Xiaohui , Li Liquan
Published: June 2023

Nano-micro MNH with structural inhomogeneity was prepared through hydriding chemical vapor deposition. It started to release H2 at ∼175 °C with a saturated capacity of 3.55 wt% and exhibited excellent dehydrogenation kinetics and cycling stability.
Tuning the aggregation-induced emission behavior of novel luminescence probes for DNP and Fe3+sensing by molecular stacking
Authors: Song Yaru , Dong Jie , Yuan Jiangyan , Zhang Xinyu , Wu Guoling , Zhang Enbing , Feng Guangyuan , Wu Lingli , Lei Shengbin , Hu Wenping
Published: June 2023

The effect of molecular stacking on AIE behavior was explored by synthesizing a series of biscarbazole-type molecules with different substituents. The non-compact packed TPAK molecules have AIE behavior and can be used to detect DNP and Fe3+.
Na7(SeO4)3(IO3) and K2(SeO4)[IO2(OH)]: two new iodate-selenates with short-wave UV cutoff edge and large birefringence
Authors: Song Wen , Ren Jinxuan , Tan Jinwen , Cao Liling , Dong Xuehua , Huang Ling , Gao Daojiang , Zou Guohong
Published: June 2023

By combining non-π-conjugated [SeO4] tetrahedra with highly polar [IO3]/[IO2(OH)] groups, large optical band gaps and large birefringence in two novel iodate-selenates Na7(SeO4)3(IO3) and K2(SeO4)[IO2(OH)] have been successfully achieved.
Structures and coordination chemistry of transporters involved in manganese and iron homeostasis
Authors: Ray Shamayeeta , Gaudet Rachelle
Published: June 2023

A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion–protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
Legal Issues and Opportunities Associated With Serving Children With Pediatric Feeding Disorders in Schools
Authors: Power-deFur Lissa A.
Published: June 2023

Purpose:

This review of federal statutes, regulations, administrative directions, and case law related to special education, disabilities, and school nutrition is designed to provide speech-language pathologists (SLPs) with information essential for determining eligibility children with pediatric feeding disorder (PFD). Despite the absence of mention of dysphagia or PFD in federal statutes and regulations, special education, disability, and school food service requirements provide direction for serving children with health care needs, which include children with dysphagia. The federal requirements, court cases, and policy interpretations are detailed to provide guidance to SLPs and their school teams when working with children with PFDs.

Method:

Federal statutes and regulations, administrative directions, and case law were reviewed. This review details the application of federal statutes and regulations for children with PFDs. Furthermore, administrative direction and case law identify the importance of attending to the safety of children with dysphagia.

Results:

As a result of this review, sections of the various federal statutes and regulations that support provision of services to children with PFD are identified. In addition, information from case law and administrative reviews further highlights the importance of attending to the rights and needs of children with PFD.

Conclusions:

The rights of all children with disabilities are established through statutes, regulations, and case law, and children with PFDs benefit from these rights. These requirements can guide SLPs in working with school teams, so that children with dysphagia can be found eligible for and receive school-based services for dysphagia.