bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain
Authors: Zhang Yanxiao , Amaral Maria Luisa , Zhu Chenxu , Grieco Steven Francis , Hou Xiaomeng , Lin Lin , Buchanan Justin , Tong Liqi , Preissl Sebastian , Xu Xiangmin , Ren Bing 
Published: October 2022

AbstractLoss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidatecis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.
TumorMet: A repository of tumor metabolic networks derived from context-specific Genome-Scale Metabolic Models
Authors: Granata Ilaria , Manipur Ichcha , Giordano Maurizio , Maddalena Lucia , Guarracino Mario Rosario 
Published: October 2022

AbstractStudies about the metabolic alterations during tumorigenesis have increased our knowledge of the underlying mechanisms and consequences, which are important for diagnostic and therapeutic investigations. In this scenario and in the era of systems biology, metabolic networks have become a powerful tool to unravel the complexity of the cancer metabolic machinery and the heterogeneity of this disease. Here, we present TumorMet, a repository of tumor metabolic networks extracted from context-specific Genome-Scale Metabolic Models, as a benchmark for graph machine learning algorithms and network analyses. This repository has an extended scope for use in graph classification, clustering, community detection, and graph embedding studies. Along with the data, we developed and provided Met2Graph, an R package for creating three different types of metabolic graphs, depending on the desired nodes and edges: Metabolites-, Enzymes-, and Reactions-based graphs. This package allows the easy generation of datasets for downstream analysis.
A multi-omics longitudinal study of the murine retinal response to chronic low-dose irradiation and simulated microgravity
Authors: Kothiyal Prachi , Eley Greg , Ilangovan Hari , Hoadley Katherine A. , Elgart S. Robin , Mao Xiao W. , Eslami Parastou 
Published: October 2022

AbstractThe space environment includes unique hazards like radiation and microgravity which can adversely affect biological systems. We assessed a multi-omics NASA GeneLab dataset where mice were hindlimb unloaded and/or gamma irradiated for 21 days followed by retinal analysis at 7 days, 1 month or 4 months post-exposure. We compared time-matched epigenomic and transcriptomic retinal profiles resulting in a total of 4178 differentially methylated loci or regions, and 457 differentially expressed genes. Highest correlation in methylation difference was seen across different conditions at the same time point. Nucleotide metabolism biological processes were enriched in all groups with activation at 1 month and suppression at 7 days and 4 months. Genes and processes related to Notch and Wnt signaling showed alterations 4 months post-exposure. A total of 23 genes showed significant changes in methylation and expression compared to unexposed controls, including genes involved in retinal function and inflammatory response. This multi-omics analysis interrogates the epigenomic and transcriptomic impacts of radiation and hindlimb unloading on the retina in isolation and in combination and highlights important molecular mechanisms at different post-exposure stages.
Experimental considerations of acute heat stress assays to quantify coral thermal tolerance
Authors: Nielsen J. J. V. , Matthews G. , Frith K. R. , Harrison H. B. , Marzonie M. R. , Slaughter K. L. , Suggett D. J. , Bay L. K. 
Published: October 2022

AbstractUnderstanding the distribution and abundance of heat tolerant corals across seascapes is imperative for predicting responses to climate change and to support novel management actions. Thermal tolerance is variable in corals and intrinsic and extrinsic drivers of tolerance are not well understood. Traditional experimental evaluations of coral heat and bleaching tolerance typically involve ramp-and-hold experiments run across days to weeks within aquarium facilities with limits to colony replication. Field-based acute heat stress assays have emerged as an alternative experimental approach to rapidly quantify heat tolerance in many samples yet the role of key methodological considerations on the stress response measured remains unresolved. Here, we quantify the effects of coral fragment size, sampling time point, and physiological measures on the acute heat stress response in adult corals. The effect of fragment size differed between species (Acropora tenuis and Pocillopora damicornis). Most physiological parameters measured here declined over time (tissue colour, chlorophyll-a and protein content) from the onset of heating, with the exception of maximum photosynthetic efficiency (Fv/Fm) which was surprisingly stable over this time scale. Based on our experiments, we identified photosynthetic efficiency, tissue colour change, and host-specific assays such as catalase activity as key physiological measures for rapid quantification of thermal tolerance. We recommend that future applications of acute heat stress assays include larger fragments (> 9 cm2) where possible and sample between 10 and 24 h after the end of heat stress. A validated high-throughput experimental approach combined with cost-effective genomic and physiological measurements underpins the development of markers and maps of heat tolerance across seascapes and ocean warming scenarios.
Partially coherent conical refraction promises new counter-intuitive phenomena
Authors: Mylnikov V. Yu. , Dudelev V. V. , Rafailov E. U. , Sokolovskii G. S. 
Published: October 2022

AbstractIn this paper, we extend the paraxial conical refraction model to the case of the partially coherent light using the unified optical coherence theory. We demonstrate the decomposition of conical refraction correlation functions into well-known conical refraction coherent modes for a Gaussian Schell-model source. Assuming randomness of the electrical field phase of the input beam, we reformulated and significantly simplified the rigorous conical refraction theory. This approach allows us to consider the propagation of light through a conical refraction crystal in exactly the same way as in the classical case of coherent radiation. Having this in hand, we derive analytically the conical refraction intensity both in the focal plane and in the far field, which allows us to explain and rigorously justify earlier experimental findings and predict new phenomena. The last include the counterintuitive effect of narrowing of the conical refraction ring width, disappearance of the dark Poggendorff’s ring in the Lloyd’s plane, and shift of Raman spots for the low-coherent conical refraction light. We also demonstrate a universal power-law dependence of conical refraction cones coherence degree on the input correlation length and diffraction-free propagation of the low-coherent conical refraction light in the far field.
Assessing the consequences of prolonged usage of disposable face masks
Authors: Buzzin Alessio , Domènech-Gil Guillem , Fraschetti Elena , Giovine Ennio , Puglisi Donatella , Caputo Domenico 
Published: October 2022

AbstractDue to the SARS-CoV-2 outbreak, wearing a disposable face mask has become a worldwide daily routine, not only for medical operators or specialized personnel, but also for common people. Notwithstanding the undeniable positive effect in reducing the risk of virus transmission, it is important to understand if a prolonged usage of the same face mask can have effectiveness on filtering capability and potential health consequences. To this aim, we present three investigations. A survey, carried out in central Italy, offers an overview of the distorted public awareness of face mask usage. A functional study shows how prolonged wearing leads to substantial drops in humid air filtration efficiency. Finally, a morphological analysis reports the proliferation of fungal or bacteria colonies inside an improperly used mask. Our study highlights therefore that wearing a face mask is really beneficial only if it is used correctly.
Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level
Authors: He Chengcheng , Liang Jinghui , Wu Zhaoqun , Zhuge Xianglin , Xu Nan , Yang Hailing 
Published: October 2022

AbstractCyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1–D7) and 7 (CDKA–CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.
M1 macrophages evoke an increase in polymeric immunoglobulin receptor (PIGR) expression in MDA-MB468 breast cancer cells through secretion of interleukin-1β
Authors: Asanprakit Wichitra , Lobo Dileep N. , Eremin Oleg , Bennett Andrew J. 
Published: October 2022

AbstractHigh expression of polymeric immunoglobulin receptor (PIGR) in breast cancer is associated with increased 5-year survival rate. However, the factors influencing PIGR expression in breast cancer have not been elucidated. The aim of this study was to determine the role of macrophages and cytokines affecting expression of PIGR in two breast cancer cell lines. M1, M2 macrophage conditioned media (CM) and recombinant human cytokines were used to determine factors which increased PIGR expression in MCF7 (HTB-22) and MDA-MB468 (HTB-132) breast cancer cell lines. The level of PIGR expression in the cells and PIGR secretory component were evaluated by real-time quantitative polymerase chain reaction and Western blotting. M1 macrophage CM induced a dose-dependent increase in PIGR mRNA expression in MDA-MB468 cells, up to 20-fold. The level of PIGR expression in MCF7 cells was very low and not affected by M1 and M2 CM. Interferon gamma (IFN-γ) and interleukin (IL)-1β also increased PIGR expression in MDA-MB468 and MCF7 cells. However, IL-1β was demonstrated to increase in M1 macrophages, while IFN-γ was not. The role of IL-1β secreted from M1 macrophages in increasing expression of PIGR was confirmed by IL-1 receptor blockade, indicating that IL-1β was the major M1 macrophage-derived cytokine that enhanced PIGR expression. Elevated PIGR expression in breast cancer in vivo may reflect the polarization state of tumor-associated immune cells.
Possibilities of reducing the number of welds on rail vehicle doors
Authors: Sigmund Marian , Spichal Jan 
Published: October 2022

AbstractThe paper developed methods that can be employed to reduce the number of welds on a specific rail-vehicle frame door welded from the EN AW 6060 aluminum alloy profiles thermally processed into the T66 state. The profiles were welded by the GTAW method using an S Al 5087 (AlMg4,5MnZr) wire as the filler material. Tensile tests were performed on the supplied samples after welding to check the mechanical properties required. The resulting tensile test data were subsequently used as boundary values for a new design of the door frame having fewer welds. A FEM simulation was carried out using the Virtual Performance Solution software with PAM—Crash extension. The study's biggest achievement was reducing two welds on a real frame door without changing door frame stability. In view of saving welding and producing time and finance by reducing the number of loaded welds. In conclusion, this designed variant is evaluated and tested.
Temporal variation in the prokaryotic community of a nearshore marine environment
Authors: Korlević Marino , Markovski Marsej , Herndl Gerhard J. , Najdek Mirjana 
Published: October 2022

AbstractProkaryotic communities inhabiting surface waters of temperate areas exhibit patterns of seasonal succession. Generally, studies describing these temporal changes are not performed in the proximity to the coast. In the present study, temporal variation of these communities was determined in surface waters at two stations located in the close proximity to the eastern shore of the northern Adriatic Sea. Sequencing of the V4 region of the 16S rRNA gene identified the highest community richness in December with distinct shifts in community structure between periods from April to May, June to October, and November to March. Temperature was shown to be the main environmental force explaining community temporal variation. The NS5 marine group, uncultured Cryomorphaceae, SAR86 clade, and Synechococcus were present throughout the year. Members without know relatives within Rhodobacteraceae and the NS4 marine group were more pronounced in the period from April to May, the AEGEAN-169 marine group, SAR11 subclade III, and HIMB11 in the period from June to October, and SAR11 subclade Ia and Archaea in the period from November to March. Litoricola and OM60 (NOR5) clade were characteristic for both the community sampled from April to May and November to March. Taken together, prokaryotic communities inhabiting nearshore surface waters exhibit a general pattern in community structure similar to other surface associated assemblages of temperate areas. However, the identified specific community composition and temporal patterns differ from other coastal areas.
Switchable unidirectional waves on mono- and diatomic metamaterials
Authors: Yan Jiaruo , Radkovskaya Anna , Solymar Laszlo , Stevens Chris , Shamonina Ekaterina 
Published: October 2022

AbstractWe demonstrate switchable unidirectional propagation of slow waves of coupling within a metamaterial array of strongly coupled elements. We predict theoretically and verify experimentally that the direction of propagation of magnetoinductive waves for any chosen excitation pattern is dictated by the dispersion relations, with forward and backward waves propagating in opposite directions along a chain of meta-atoms. We further prove that the same fundamental phenomenon of direction selectivity due to the forward/backward wave nature is not limited to magnetoinductive waves: we predict analytically and verify numerically the same selective unidirectional signal propagation occurring in nanostructured metamaterial arrays with purely electric coupling. Generalising our method of unidirectional waveguiding to a diatomic magnetoinductive array featuring both forward-wave and backward-wave dispersion branches, switchable unidirectional signal propagation is achieved with distinct frequency bands with opposite directions of signal propagation. Finally, by expanding our technique of selective unidirectional waveguiding to a 2D metasurface, a selective directional control of waves in two dimensions is demonstrated opening up possibilities for directional wireless signal transfer via magnetoinductive surfaces. The observed phenomenon is analogous to polarisation-controlled near-field interference for unidirectional guiding of surface plasmon-polaritons.
Multi-trait genome-wide association study of opioid addiction: OPRM1 and beyond
Authors: Gaddis Nathan , Mathur Ravi , Marks Jesse , Zhou Linran , Quach Bryan , Waldrop Alex , Levran Orna , Agrawal Arpana , Randesi Matthew , Adelson Miriam , Jeffries Paul W. , Martin Nicholas G. , Degenhardt Louisa , Montgomery Grant W. , Wetherill Leah , Lai Dongbing , Bucholz Kathleen , Foroud Tatiana , Porjesz Bernice , Runarsdottir Valgerdur , Tyrfingsson Thorarinn , Einarsson Gudmundur , Gudbjartsson Daniel F. , Webb Bradley Todd , Crist Richard C. , Kranzler Henry R. , Sherva Richard , Zhou Hang , Hulse Gary , Wildenauer Dieter , Kelty Erin , Attia John , Holliday Elizabeth G. , McEvoy Mark , Scott Rodney J. , Schwab Sibylle G. , Maher Brion S. , Gruza Richard , Kreek Mary Jeanne , Nelson Elliot C. , Thorgeirsson Thorgeir , Stefansson Kari , Berrettini Wade H. , Gelernter Joel , Edenberg Howard J. , Bierut Laura , Hancock Dana B. , Johnson Eric Otto 
Published: October 2022

AbstractOpioid addiction (OA) is moderately heritable, yet only rs1799971, the A118G variant in OPRM1, has been identified as a genome-wide significant association with OA and independently replicated. We applied genomic structural equation modeling to conduct a GWAS of the new Genetics of Opioid Addiction Consortium (GENOA) data together with published studies (Psychiatric Genomics Consortium, Million Veteran Program, and Partners Health), comprising 23,367 cases and effective sample size of 88,114 individuals of European ancestry. Genetic correlations among the various OA phenotypes were uniformly high (rg > 0.9). We observed the strongest evidence to date for OPRM1: lead SNP rs9478500 (p = 2.56 × 10–9). Gene-based analyses identified novel genome-wide significant associations with PPP6C and FURIN. Variants within these loci appear to be pleiotropic for addiction and related traits.
Missed Monteggia fractures in children treated by open reduction of the radial head and corrective osteotomy of the ulna
Authors: Cao Shu , Dong Zhong-Gen , Liu Li-Hong , Wei Jian-Wei , Luo Zhao-Biao , Peng Ping 
Published: October 2022

AbstractMissed Monteggia fractures in children may cause pain, deformity, decreased range of motion, neurological symptoms, and late arthritis of the elbow. Numerous surgical techniques have been advocated to reconstruct missed Monteggia lesions. The purpose of the present study were first to evaluate the clinical and radiographic outcomes after open reduction of the radial head and corrective osteotomy of the ulna, second to identify the factors associated with the preoperative radial notch/head appearance and the postoperative radiographic results. This study investigated the preoperative MRI presentation and the treatment of 29 patients who were diagnosed missed Monteggia fracture. Radiologic and clinical results of these patients were evaluated retrospectively, and the patient’s and surgical factors related to preoperative radial notch/head appearance and the postoperative radiographic results were analyzed. Of the 29 patients, the average Kim elbow performance score at the last follow-up was 93.6, with 25 excellent, three good, one fair, and no poor results. 19 children had reduced radial heads, 8 had a subluxated radial head and 2 had dislocated radial heads at the last follow-up. The patient’s gender and age had no significant influence on the appearance of radial notch/head and final radiographic results. However, the appearance of radial notch/head can significantly affect the final radiographic result (P < 0.001). The interval time was an important factor which related with the appearance of radial notch/head and final radiographic results (P < 0.001). Treating a missed Monteggia fracture by open reduction of the radial head and corrective osteotomy of the ulna is generally successful and preoperative MRI is meaningful for evaluation of the condition of the radial head and the radial notch which is related with the final radiographic result. The interval time from injury to operation exceeds 6 months, the risk of radial notch/head abnormality and radial head subluxation/re-dislocation after operation significantly increase.
Universal ingredients to parenting teens: parental warmth and autonomy support promote adolescent well-being in most families
Authors: Bülow Anne , Neubauer Andreas B. , Soenens Bart , Boele Savannah , Denissen Jaap J. A. , Keijsers Loes 
Published: October 2022

AbstractEven though each adolescent is unique, some ingredients for development may still be universal. According to Self-Determination Theory, every adolescent’s well-being should benefit when parents provide warmth and autonomy. To rigorously test this idea that each family has similar mechanisms, we followed 159 Dutch parent-adolescent dyads (parent: Mage = 45.34, 79% mothers; adolescent: Mage = 13.31, 62% female) for more than three months, and collected 100 consecutive daily reports of parental warmth, autonomy support, positive and negative affect. Positive effects of parental warmth and autonomy support upon well-being were found in 91–98% of the families. Preregistered analysis of 14,546 daily reports confirmed that effects of parenting differed in strength (i.e., some adolescents benefited more than others), but were universal in their direction (i.e., in fewer than 1% of families effects were in an unexpected direction). Albeit stronger with child-reported parenting, similar patterns were found with parent-reports. Adolescents who benefited most from need-supportive parenting in daily life were characterized by higher overall sensitivity to environmental influences. Whereas recent work suggests that each child and each family have unique developmental mechanisms, this study suggests that need-supportive parenting promotes adolescent well-being in most families.