bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis
Authors: Djeghloul Dounia , Dimond Andrew , Cheriyamkunnel Sherry , Kramer Holger , Patel Bhavik , Brown Karen , Montoya Alex , Whilding Chad , Wang Yi-Fang , Futschik Matthias E. , Veland Nicolas , Montavon Thomas , Jenuwein Thomas , Merkenschlager Matthias , Fisher Amanda G. 
Published: March 2023

AbstractRecent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
Comprehensive exploration of graphically defined reaction spaces
Authors: Zhao Qiyuan , Vaddadi Sai Mahit , Woulfe Michael , Ogunfowora Lawal A. , Garimella Sanjay S. , Isayev Olexandr , Savoie Brett M. 
Published: March 2023

AbstractExisting reaction transition state (TS) databases are comparatively small and lack chemical diversity. Here, this data gap has been addressed using the concept of a graphically-defined model reaction to comprehensively characterize a reaction space associated with C, H, O, and N containing molecules with up to 10 heavy (non-hydrogen) atoms. The resulting dataset is composed of 176,992 organic reactions possessing at least one validated TS, activation energy, heat of reaction, reactant and product geometries, frequencies, and atom-mapping. For 33,032 reactions, more than one TS was discovered by conformational sampling, allowing conformational errors in TS prediction to be assessed. Data is supplied at the GFN2-xTB and B3LYP-D3/TZVP levels of theory. A subset of reactions were recalculated at the CCSD(T)-F12/cc-pVDZ-F12 and ωB97X-D2/def2-TZVP levels to establish relative errors. The resulting collection of reactions and properties are called the Reaction Graph Depth 1 (RGD1) dataset. RGD1 represents the largest and most chemically diverse TS dataset published to date and should find immediate use in developing novel machine learning models for predicting reaction properties.
A dataset of rodent cerebrovasculature from in vivo multiphoton fluorescence microscopy imaging
Authors: Poon Charissa , Teikari Petteri , Rachmadi Muhammad Febrian , Skibbe Henrik , Hynynen Kullervo 
Published: March 2023

AbstractWe present MiniVess, the first annotated dataset of rodent cerebrovasculature, acquired using two-photon fluorescence microscopy. MiniVess consists of 70 3D image volumes with segmented ground truths. Segmentations were created using traditional image processing operations, a U-Net, and manual proofreading. Code for image preprocessing steps and the U-Net are provided. Supervised machine learning methods have been widely used for automated image processing of biomedical images. While much emphasis has been placed on the development of new network architectures and loss functions, there has been an increased emphasis on the need for publicly available annotated, or segmented, datasets. Annotated datasets are necessary during model training and validation. In particular, datasets that are collected from different labs are necessary to test the generalizability of models. We hope this dataset will be helpful in testing the reliability of machine learning tools for analyzing biomedical images.
Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper
Authors: Han Wentao , Wu Shaoxuan , Ding Hui , Wang Mingyi , Wang Mengya , Bao Zhenmin , Wang Bo , Hu Jingjie 
Published: March 2023

AbstractPlectropomus leopardus, as known as leopard coral grouper, is a valuable marine fish that has gradually been bred artificially. To promote future conservation, molecular breeding, and comparative studies, we generated an improved high-quality chromosomal-level genome assembly of leopard coral grouper using Nanopore long-reads, Illumina short reads, and the Hi-C sequencing data. The draft genome is 849.74 Mb with 45 contigs and N50 of 35.59 Mb. Finally, a total of 846.49 Mb corresponding to 99.6% of the contig sequences was anchored to 24 pseudo-chromosomes using Hi-C technology. A final set of 25,965 genes is annotated after manual curation of the predicted gene models, and BUSCO analysis yielded a completeness score of 99.5%. This study significantly improves the utility of the grouper genome and provided a reference for the study of molecular breeding, genomics and biology in this species.
Individualized precision targeting of dorsal attention and default mode networks with rTMS in traumatic brain injury-associated depression
Authors: Siddiqi Shan H. , Kandala Sridhar , Hacker Carl D. , Trapp Nicholas T. , Leuthardt Eric C. , Carter Alexandre R. , Brody David L. 
Published: March 2023

AbstractAt the group level, antidepressant efficacy of rTMS targets is inversely related to their normative connectivity with subgenual anterior cingulate cortex (sgACC). Individualized connectivity may yield better targets, particularly in patients with neuropsychiatric disorders who may have aberrant connectivity. However, sgACC connectivity shows poor test–retest reliability at the individual level. Individualized resting-state network mapping (RSNM) can reliably map inter-individual variability in brain network organization. Thus, we sought to identify individualized RSNM-based rTMS targets that reliably target the sgACC connectivity profile. We used RSNM to identify network-based rTMS targets in 10 healthy controls and 13 individuals with traumatic brain injury-associated depression (TBI-D). These “RSNM targets” were compared with consensus structural targets and targets based on individualized anti-correlation with a group-mean-derived sgACC region (“sgACC-derived targets”). The TBI-D cohort was also randomized to receive active (n = 9) or sham (n = 4) rTMS to RSNM targets with 20 daily sessions of sequential high-frequency left-sided stimulation and low-frequency right-sided stimulation. We found that the group-mean sgACC connectivity profile was reliably estimated by individualized correlation with default mode network (DMN) and anti-correlation with dorsal attention network (DAN). Individualized RSNM targets were thus identified based on DAN anti-correlation and DMN correlation. These RSNM targets showed greater test–retest reliability than sgACC-derived targets. Counterintuitively, anti-correlation with the group-mean sgACC connectivity profile was also stronger and more reliable for RSNM-derived targets than for sgACC-derived targets. Improvement in depression after RSNM-targeted rTMS was predicted by target anti-correlation with the portions of sgACC. Active treatment also led to increased connectivity within and between the stimulation sites, the sgACC, and the DMN. Overall, these results suggest that RSNM may enable reliable individualized rTMS targeting, although further research is needed to determine whether this personalized approach can improve clinical outcomes.
Effects of UV-B radiation on epiphytic bacterial communities on male and female Sargassum thunbergii
Authors: Wang Jing , Yang Zhibo , Lu Peiyao , Sun Yan , Xue Song , Tang Xuexi , Xiao Hui 
Published: March 2023

AbstractThe effects of increased UV-B radiation on macroalgae have been widely studied, but knowledge concerning the response of communities of algal epiphytic bacteria to increased UV-B radiation and differences between male and female algae is still lacking. Via 16S rDNA high-throughput sequencing technology, changes in the epiphytic bacterial communities on male and female S. thunbergii under increased UV-B radiation were studied in the lab. Under different UV-B radiation intensities, although the α diversity and community composition of epiphytic bacteria changed little, the β diversity indicated that the community structure of bacteria on S. thunbergii was obviously clustered, and the relative abundance of dominant bacteria and indicator species changed considerably. There were unique bacteria in each experimental group, and the bacteria whose abundance obviously changed were members of groups related to environmental resistance or adaptability. The variation in the abundance of epiphytic bacteria was different in male and female S. thunbergii, and the bacteria whose abundance greatly changed were mainly related to algal growth and metabolism. The abundance of genes with predicted functions related to metabolism, genetic information processing, environmental adaptation and infectious diseases changed with increased UV-B radiation, and those variations differed between epiphytic bacteria on male and female S. thunbergii. This study found that the algal epiphytic bacteria were influenced by the increase in UV-B radiation and underwent certain adaptations through adjustments to community structure and function, and this response was also affected by the sex of the macroalgae. These results are expected to serve as experimental basis and provide reference for further understanding of the response of algae epiphytic bacteria to enhanced UV-B radiation caused by the thinning of the ozone layer and the resulting changes in the relationship between algae and bacteria, which may change the community of the marine ecosystem and affect important marine ecological process.
The effect of intravenous unit-dose tranexamic acid on visible and hidden blood loss in posterior lumbar interbody fusion: a randomized clinical trial
Authors: Hao Shenshen , Li Hongke , Liu Shuai , Meng Saike , Zhang Xiaopeng , Wang Linfei , Yang Hongjie , Zhang Liyan , Dong Shengli 
Published: March 2023

AbstractThere are few reports of intravenous unit-dose tranexamic acid (TXA) on the relationship between visible blood loss (VBL) and hidden blood loss (HBL) in posterior lumbar interbody fusion (PLIF). Therefore, the objective of this randomized, prospective, double-blind, single center study was to investigate the effect of intravenous unit-dose TXA on VBL and HBL in patients who underwent PLIF. Among 100 patients, 11 were excluded due to failue to comply with the study, 1 was excluded due to non-conpliance with the study, and 88 were eligible for inclusion in the study. 46 patients who treated with PLIF received unit-dose of TXA (1 g/100 mL) intravenously 15 min before skin incision after general anesthesia (observation group) and 42 patients were given 100 mL of normal saline (control group). The operation time, intraoperative blood loss, postoperative drainage, VBL, HBL, blood transfusion rate, and adverse events were recorded in the two groups. Besides, activated partial prothrombin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen (FIB), platelets (PLT), red blood cells (RBC), hemoglobin (HB), hematocrit (HCT), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) on the 1st postoperative day; and RBC, HB, HCT, CRP, ESR on the 4th postoperative day were recorded. All 88 patients successfully completed the operation, the incision healed well, and there was no deep vein thrombosis of the lower extremity after operation. The intraoperative blood loss, postoperative drainage, VBL, HBL, and blood transfusion rate in the observation group were lower than those in the control group, and the differences were statistically significant (p < 0.05). There was no significant difference in operation time between the two groups (p > 0.05). There was no significant difference in postoperative APTT, PT, TT, FIB, PLT, RBC, HB, HCT, CRP and ESR between the two groups (p > 0.05). Intravenous unit-dose TXA is safe and feasible in PLIF, and it can effectively reduce perioperative VBL and HBL.
Research on SPDTRS-PNN based intelligent assistant diagnosis for breast cancer
Authors: Kong Xixi , Zhou Mengran , Bian Kai , Lai Wenhao , Hu Feng , Dai Rongying , Yan Jingjing 
Published: March 2023

AbstractBreast cancer is the second dangerous cancer in the world. Breast cancer data often contains more redundant information. Redundant information makes the breast cancer auxiliary diagnosis less accurate and time consuming. Dimension reduction algorithm combined with machine learning can solve these problems well. This paper proposes the single parameter decision theoretic rough set (SPDTRS) combined with the probability neural network (PNN) model for breast cancer diagnosis. We find that when the parameter value of SPDTRS is 2.5 and the SPREAD value is 0.75, the number of 30 attributes of the original breast cancer data dropped to 12, the accuracy of the SPDTRS-PNN model training set is 99.25%, the accuracy of the test set is 97.04%, and the test time is 0.093 s. The experimental results show that the SPDTRS-PNN model can improve the ac-curacy of breast cancer recognition, reduce the time required for diagnosis.
Physical and mental health impact of the COVID-19 pandemic at first year in a Spanish adult cohort
Authors: Castellvi Obiols Pere , Miranda-Mendizabal Andrea , Recoder Silvia , Calbo Sebastian Ester , Casajuana-Closas Marc , Leiva David , Manolov Rumen , Matilla-Santander Nuria , Lloveras-Bernat Isaac , Forero Carlos G. 
Published: March 2023

AbstractThe COVID-19 pandemic and the political and health measures have profoundly affected the health of our populations. However, very few studies have been published assessing its impact using a prospective cohort. The aim of this study is to describe the impact on physical and mental health due to the COVID-19 pandemic in the general population in Spain, and according to COVID-19 clinical status, during the first year of the pandemic. A longitudinal cohort study with two online surveys were performed on a representative sample of the adult Spanish population before (N = 2005, October/November 2019) and during the pandemic (N = 1357, November/December 2020). We assessed disability using the World Health Organisation Disability Assessment Schedule (WHODAS), major depressive episode (MDE) and suicidal thoughts and behaviours (STB), using an adapted version of the Composite International Diagnostic Interview (CIDI 3.0); generalised anxiety disorder (GAD) using the GAD-7 scale; post-traumatic stress disorder (PTSD) symptoms using the PTSD checklist for DSM-5 (PCL-5). For physical health, there was a statistically significant loss of weight (mean/SD) (T0, 73.22/15.56 vs. T1, 71.21/11.94), less use of tobacco (T0, 11.4% vs. T1, 9.0%) and decreased disability (mean/SD) (T0, 21.52/9.22 vs. T1, 19.03/7.32). For mental health, there was a significant increase in MDE (T0, 6.5% vs. T1, 8.8%) and in the prevalence of GAD (T0, 13.7% vs. T1, 17.7%). The prevalence of STB (T0, 15.1% vs. T1, 7.1%) significantly decreased. Individuals who declared they had been diagnosed with COVID-19 (3.6%) showed a worsening in physical health and an increase in mental health problems and PTSD symptoms. Although suicide risk during the first year of the pandemic was significantly less, many suicide risk factors increased: such as the incidence and persistence of MDE and GAD, the presence of PTSD symptoms in those diagnosed with COVID-19, and a worsening in self-assessed health status. We expect an increase in STB in the population in the long-term. Future research should gather information about the long-term impact of the pandemic.
High temperature performance of wire-arc additive manufactured Inconel 718
Authors: James William Sean , Ganguly Supriyo , Pardal Goncalo 
Published: March 2023

AbstractIn developing a wire-arc directed energy deposition process for superalloys used in high-speed flight environments, Inconel 718 was deposited using a plasma arc process and tested for its high temperature performance. The deposited material was tested in both the as deposited condition and after an age-hardening industry standard heat-treatment for this alloy. Results showed a reduced performance in both deposited conditions, with heat-treated material significantly outperforming as deposited material up to 538 °C. The difference in performance was less significant from 760 to 1000 °C, owing to an in-test aging process which increased the performance of the as deposited material. The microstructure of deposited material showed significant cracking throughout the alloy and formation of secondary phases throughout the matrix, with significantly more precipitation after heat-treating.
A simplified model to estimate nonlinear turbulent transport by linear dynamics in plasma turbulence
Authors: Nakayama Tomonari , Nakata Motoki , Honda Mitsuru , Narita Emi , Nunami Masanori , Matsuoka Seikichi 
Published: March 2023

AbstractA simplified model to estimate nonlinear turbulent transport only by linear calculations is proposed, where the turbulent heat diffusivity in tokamak ion temperature gradient(ITG) driven turbulence is reproduced for a wide parameter range including near- and far-marginal ITG stability. The optimal nonlinear functional relation(NFR) between the turbulent diffusivity, the turbulence intensity $$\mathcal{T}$$
T
, and the zonal-flow intensity $$\mathcal{Z}$$
Z
is determined by means of mathematical optimization methods. Then, an extended modeling for $$\mathcal{T}$$
T
and $$\mathcal{Z}$$
Z
to incorporate the turbulence suppression effects and the temperature gradient dependence is carried out. The simplified transport model is expressed as a modified nonlinear function composed of the linear growth rate and the linear zonal-flow decay time. Good accuracy and wide applicability of the model are demonstrated, where the regression error of $$\sigma _{\textrm{model}} = 0.157$$

σ
model

=
0.157

indicates improvement by a factor of about 1/4 in comparison to that in the previous works.
Based on network pharmacology and bioinformatics to analyze the mechanism of action of Astragalus membranaceus in the treatment of vitiligo and COVID-19
Authors: Wang Yaojun , Ding Ming , Chi Jiaoni , Wang Tao , Zhang Yue , Li Zhimin , Li Qiang 
Published: March 2023

AbstractCoronavirus disease 2019 (COVID-19) is spreading rapidly around the world. However, the treatment of vitiligo combined with COVID-19 has not been reported. Astragalus membranaceus (AM) has a therapeutic effect on patients with vitiligo and COVID-19. This study aims to discover its possible therapeutic mechanisms and provide potential drug targets. Using the Chinese Medicine System Pharmacological Database (TCMSP), GEO database and Genecards websites and other databases, AM target, vitiligo disease target, and COVID-19 related gene set were established. Then find the crossover genes by taking the intersection. Then use GO, KEGG enrichment analysis, and PPI network to discover its underlying mechanism. Finally, by importing drugs, active ingredients, crossover genes, and enriched signal pathways into Cytoscape software, a “drug-active ingredient-target signal pathway-” network is constructed. TCMSP screened and obtained 33 active ingredients including baicalein (MOL002714), NEOBAICALEIN (MOL002934), Skullcapflavone II (MOL002927), and wogonin (MOL000173), which acted on 448 potential targets. 1166 differentially expressed genes for vitiligo were screened by GEO. CIVID-19 related genes were screened by Genecards. Then by taking the intersection, a total of 10 crossover genes (PTGS2, CDK1, STAT1, BCL2L1, SCARB1, HIF1A, NAE1, PLA2G4A, HSP90AA1, and HSP90B1) were obtained. KEGG analysis found that it was mainly enriched in signaling pathways such as IL-17 signaling pathway, Th17 cell differentiation, Necroptosis, NOD-like receptor signaling pathway. Five core targets (PTGS2, STAT1, BCL2L1, HIF1A, and HSP90AA1) were obtained by analyzing the PPI network. The network of "active ingredients-crossover genes" was constructed by Cytoscape, and the 5 main active ingredients acting on the 5 core crossover genes acacetin, wogonin, baicalein, bis2S)-2-ethylhexyl) benzene-1,2-dicarboxylate and 5,2′-Dihydroxy-6,7,8-trimethoxyflavone. The core crossover genes obtained by PPI and the core crossover genes obtained by the "active ingredient-crossover gene" network are intersected to obtain the three most important core genes (PTGS2, STAT1, HSP90AA1). AM may act on PTGS2, STAT1, HSP90AA1, etc. through active components such as acacetin, wogonin, baicalein, bis2S)-2-ethylhexyl) benzene-1,2-dicarboxylate and 5,2′-Dihydroxy-6,7,8-trimethoxyflavone to activate IL-17 signaling pathway, Th17 cell differentiation, Necroptosis, NOD-like receptor signaling pathway, Kaposi sarcoma-associated herpesvirus infection, and VEGF signaling pathway and other signaling pathways to achieve the effect of treating vitiligo and COVID-19.
Risk factors for Baerveldt glaucoma drainage implantation for uveitic glaucoma
Authors: Manako Kiyofumi , Takahashi Eri , Saruwatari Junji , Matsumura Tomoyo , Kojima Sachi , Inoue Toshihiro 
Published: March 2023

AbstractUveitic glaucoma (UG) is sometimes intractable, including intricate interaction between intraocular pressure (IOP) elevation associated with inflammation and side effects of steroids. Based on the Tube Versus Trabeculectomy study in refractory glaucoma results in 2012, tube shunt surgeries have been performed for UG, but few reports have focused on UG. We retrospectively examined the surgical efficacy, complications, and risk factors in 62 eyes with UG that underwent Baerveldt glaucoma drainage device (BGD) implantation at Kumamoto University. The IOPs significantly dropped, and the mean number of glaucoma medications was reduced by more than two. Kaplan‒Meier survival curves were presented under 2 conditions: an IOP reduction of 20% and 6 ≤ IOP ≤ 18 mmHg (criterion A) or 6 ≤ IOP ≤ 15 mmHg (criterion B). In criterion A, the median survival times (MST) were 124 days (complete) and 997 days (qualified). In criterion B, the MST was 129 days (complete) and 867 days (qualified). The Cox hazard proportional model found that the hazard ratio was 0.170 for a history of cataract surgery (95% CI 0.0303–0.950) and 8.669 for systemic immunosuppressive therapy (95% CI 1.810–41.51). BGD implantation is effective for treating UG, but the presence of systemic treatment and the lens status should be considered.