bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unzipped genome assemblies of polyploid root-knot nematodes reveal new kinds of unilateral composite telomeric repeats
Authors: Danchin Etienne , Mota Ana Paula Zotta , Koutsovoulos Georgios , Perfus-Barbeoch Laetitia , Despot-Slade Evelin , Labadie Karine , Aury Jean Marc , Robbe-Sermesant Karine , Bailly-Bechet Marc , Belser Caroline , Pere Arthur , Rancurel Corinne , Kozlowski Djampa , Hassanaly-Goulamhoussen Rahim , Rocha Martine Da , Noel Benjamin , Meštrović Nevenka , Wincker Patrick 
Published: May 2023

Abstract
Using long read sequencing we have assembled and unzipped the genomes of Meloidogyne incognita, M. javanica and M. arenaria, the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats enriched at one extremity of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using fluorescent in situ hybridization, we confirmed these repeats had telomeric location at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles in senescence, aging and chromosome integrity and opens new perspectives towards the development of more specific control methods against these pests.
Acute mania in Fanconi Bickel syndrome, a case report
Authors: Chen Allen , Russell Geoffrey , Ashour Amnie , Yacoub Adeeb 
Published: May 2023

Abstract
Fanconi-Bickel syndrome is a rare metabolic disorder caused by decreased glucose transporter 2 (GLUT2) function due to several known mutations in the SLC2A2 gene. As of 2020, 144 cases of FBS had been described in the literature. Metabolic and somatic sequelae include dysglycemia and accumulation of glycogen in the kidney and liver. However, there are no descriptions in the literature of possible neuropsychiatric manifestations of FBS. This case report is to our knowledge the first in this regard, describing a patient with Fanconi Bickel syndrome who was admitted to our psychiatric inpatient unit while experiencing acute mania. We conceptualize the case as a novel psychiatric presentation of acute mania in Fanconi Bickel syndrome, which may inform our understanding of bipolar disorder pathophysiology because of the hypothesized functional changes in neural pathways involving the paraventricular thalamus induced by decreased GLUT2 activity in FBS.
From Mindfulness to Flow in the Coronavirus Pandemic: Investigating the mediating role of psychological capital and coping competence. (a cross-sectional study of pre-Hospital Emergency staff)
Authors: Rahnama Nargess , zadeh Gholamreza Malek , Moshtari Mohammad 
Published: May 2023

Abstract
Background
The present study aims to investigate whether and how mindfulness leads to the flow experience in high-pressure situations during the coronavirus pandemic peak, especially in high-risk, challenging contexts such as emergencies. So, the authors aim to expand existing knowledge about experiencing flow at work, specifically in the crisis context of the COVID-19 period, when challenges convert to hindrance demands. Before examining the possible processes and mechanisms in this relationship, we examined the mediating role of two variables: psychological capital and coping competence.
Method
The statistical population of this study consists of all employees of emergency centers in Mashhad, Iran; there were 550 at the time of the study. Using a simple random sampling method and the Morgan table, a sample of 220 people was considered. A structural equation model, AMOS, and SPSS software were used to analyze the collected data.
Result
The results emphasize that among employees who experienced mindfulness, an optimal experience did not necessarily occur, specifically in those situations in which challenge stressors become hindrance stressors. Although the association of mindfulness and coping competence was verified, its association with flow through coping competence was rejected. It is verified that mindfulness would be associated with flow through psychological capital.
Conclusion
The study extends our understanding of occurring flow at high-risk work environments in which challenges are not motivational. The authors studied the experience of flow in a work context with challenges that appear in the form of hindrance demands, different from the previous ones that have studied flow experience in challenging and motivating contexts such as sports contexts, including mountain climbing, surfing, and similar cases. In addition, there was no consensus in different past studies about associating mindfulness with flow experience. Therefore, in this case, further study had been left to future studies. Moreover, the process of this relationship through the mediating role of psychological capital and coping competence has not been investigated in previous studies.
Comprehensive Genomic Analysis of the Prognostic and Immunological Characteristics of Tertiary Lymphoid structures and CD8+ T-cells in Pancreatic Ductal Adenocarcinoma
Authors: Hu Hao , Xu Yang , Ai Xiangnan , Wang Tengfei , Li Huixing , Jin Changguo , Ouyang Caiguo , Wu Zhenyu 
Published: May 2023

Abstract
Background Pancreatic ductal adenocarcinoma (PDAC), the most common subtype of pancreatic cancer, is associated with poor prognosis. Previous publications have indicated tertiary lymphoid structure (TLSs) and CD8 + T-cells as prognostic indicators for PDAC, and a positive correlation between CD8 + T-cell infiltration and TLSs was also observed in PDAC. However, different states of TLSs infiltration occurs, and not all stages of TLSs maturation are correlated with a high abundance of CD8 + T-cells in the tumor microenvironment (TME), also CD8 + T-cell infiltration could be influenced by other factors, thus an integrative characterization of the TLSs and CD8 + T-cells is urgently needed. Herein, we aimed to establish a novel scoring system for evaluating the risk for PDAC based on TLSs- and CD8 + T-cells-related genes.Methods In this study, we analyzed single-cell sequence (scRNA-seq) data from PDAC patients in GSA: CRA001160 cohort, which indicated the positive relationship between TLSs presence and CD8 + T-cell infiltration. TCGA-PAAD was used as the training cohort. ICGC-CA, E-MTAB-6134, and the joint cohort of GSE71729 and GSE85916 were used for validation. Using bioinformatics and machine algorithms, we established and validated a scoring method (T-C score) based on survival related genes highly expressed in TLSs and CD8 + T-cells in PDAC, which was then used to stratify patients into the low- and high- T-C score groups. Following that, we analyzed the differences in survival, pathway enrichment, mutation status, immune cell infiltration, expression of immune checkpoint associated genes, tumor stemness, and response to anti-tumor therapy between the two groups.Results The overall survival differed significantly between the low- and high- T-C score groups throughout the training and validation cohort. Good accuracy of the T-C score in predicting 1-, 2-, 3-, 4-, and 5-year survival was further confirmed in the training and validation cohort, respectively. Furthermore, the low T-C score group was correlated with lower tumor mutation burden (TMB), and lower levels of tumor stemness, compared to the high T-C score group, Besides, analysis using the TIDE web tool has verified that patients with lower T-C score exhibited advantages in immunotherapeutic responses. Patients with lower T-C scores might be more sensitive to the chemotherapeutic regimen and multi-kinase inhibitors. Collectively, the T-C score based on the TLSs- and CD8 + T-cells-related gene signature could serve as an effective model for predicting the survival and therapeutic responses of PDAC patients.
Ovarian leptin signalling regulates NLRP3 inflammasome activation and macrophage infiltration in a cell specific manner
Authors: Adamowski Marek , Sharma Yashaswi , Molcan Tomasz , Wołodko Karolina , Kelsey Gavin , Galvão António M. 
Published: May 2023

Abstract
Background: Obesity is associated with increased ovarian inflammation and the establishment of local leptin resistance. We presently investigated the role of leptin signalling on Nod-Like Receptor Protein 3 (NLPR3) inflammasome and macrophage prevalence in the pathophysiology of ovarian failure of obese mice.
Methods: We collected ovaries from: (i) diet-induced obese (DIO) mice fed chow diet (CD) or high-fat diet (HFD) for 4 or 16 weeks (wk); (ii) mice lacking the long-isoform of leptin receptor (ObRb; db/db); (iii) mice lacking leptin (ob/ob); and (iv) pharmacologically hyperleptinemic (LEPT) mice for protein and mRNA expression analysis. Next, granulosa cells (GCs) from antral follicles isolated from db/db and ob/ob mice were subjected to transcriptome analysis.
Results: We observed no changes in the mRNA and protein levels of NLRP3 inflammasome components in the ovaries of db/db mice, as well as in markers of M1 and M2 macrophage infiltration. This contrasted with the downregulation of NLRP3 inflammasome components and M1 markers in ob/ob -/- and 16 wk HFD mice. Transcriptional analysis revealed opposing profiles between genetic models, with genes associated with steroid metabolism and prostaglandin action in db/db mice and genes controlling extracellular matrix in ob/ob mice being downregulated, despite both processes being crucial for follicular development and ovulation.
Conclusions: Leptin signalling regulated NLRP3 inflammasome activation and expression of M1 markers in ovaries of obese mice, in an ObRb-dependent and -independent manner. Absence of changes in the expression of leptin signalling and proinflammatory mediators in GCs from db/db and ob/ob mice was associated with impaired folliculogenesis.
Determination of Natural Radioactivity Concentrations and Radiation Hazards in Rolled Oat Brands Available in the Iraqi Market
Authors: Al-Khazzar Akram , Al-Dulaimi Rand 
Published: May 2023

Abstract
The aim of this study is to measure the natural radioactivity of potassium-40, uranium-238 and thorium-232 in rolled oat brands that widely consumed in Iraq. Based on these results, the radiological hazard parameters were evaluated. Five types of oat brands retailed Baghdad markets were tested. High purity germanium detector (HPGE) was used for the radiometric analysis. The mean activity concentration values of 238U, 232Th and 40K ranged from 6.88–10.61, 3.92–6.68 and 210.44–484.2 Bq/kg, respectively. The annual effective dose was the highest for a Ukrainian brand with 36.02 µSv/yr, while the radium equivalent activity values range from 31.43–56.1 Bq/kg. The results show that, regular consumption of these kinds of oats is radiologically safe for human health.
Comparative Effectiveness of Tocilizumab vs Standard Care in Patients with severe COVID-19–related Pneumonia: A retrospective cohort study utilizing registry data as a synthetic control
Authors: Uemura Yukari , Ozaki Ryoto , Shinozaki Tomohiro , Ohtsu Hiroshi , Shimizu Yousuke , Izumi Kazuo , Saito Sho , Matsunaga Nobuaki , Ohmagari Norio 
Published: May 2023

Abstract
Background The severity of coronavirus disease 2019 (COVID-19) infections has led to the development of several therapeutic agents, with tocilizumab becoming increasingly used to treat patients with COVID-19-related pneumonia. Therefore, this study compared the use of tocilizumab treatment with the standard of care (SOC) to determine its efficacy against severe COVID-19-related pneumonia in Japan.Methods This retrospective cohort study was designed to evaluate the efficacy of tocilizumab in two different databases: the JA42434 single-arm study and COVID-19 Registry Japan (COVIREGI-JP) data, with a synthetic control group from the COVIREGI-JP cohort as a benchmark for the tocilizumab group. The study’s primary objective was to evaluate the efficacy of tocilizumab in treating severe COVID-19-related pneumonia compared to the SOC among patients included in the above two databases. The SOC group was extracted as the synthetic control group using exact matching and a propensity score matching in sequence per subject. As a secondary objective, the efficacy of tocilizumab compared to SOC was evaluated exclusively among patients included in the COVIREGI-JP database. In each objective, the primary endpoint was defined as the time to discharge or the status of awaiting discharge.Results For the primary endpoint, the hazard ratio (HR) of the tocilizumab group against the SOC group was 1.070 (95% CI: 0.565 to 2.028). The median time from Study Day 1 to discharge or the state of awaiting discharge was 15 days in the tocilizumab group and 16 days in the SOC group. The HRs for the secondary endpoints, namely, time to improvement in the clinical state, time to clinical failure, and time to recovery, were 1.112 (95% CI: 0.596 to 2.075), 0.628 (95% CI: 0.202 to 1.953), and 1.019 (95% CI: 0.555 to 1.871), respectively. Similarly, the HR of the primary endpoint for the secondary objective was 0.846 (95% CI: 0.582 to 1.230).Conclusions Tocilizumab did not demonstrate a positive effect on time to discharge or the state of awaiting discharge. Furthermore, no statistical differences, such as time to improvement in the clinical state, time to clinical failure, and time to recovery, were observed among the groups in other clinical outcomes.
Exploring the potential mechanism of Kaixinsan powder for the same pathogenesis of PTSD and anxiety based on network pharmacology and molecular docking
Authors: Li Wen-Wei , Wang Jia , Wu Han-Biao , Qiu Zhi-Kun 
Published: May 2023

Abstract
Kaixinsan powder(KXS), a commonly used prescription in traditional Chinese medicine, has been widely used to treat psychiatric disorders such as Alzheimer’s disease, anxiety, and post-traumatic stress disorder(PTSD), but its mechanism is still unclear. There are many similarities and psychopathological overlap between PTSD and anxiety. Herein, we use the methods of network pharmacology study and molecular docking to explore the potential mechanism of KXS for the same pathogenesis of PTSD and anxiety. The bioactive components and relevant target genes of KXS were obtained and analyzed from TCMSP, BATMAN-TCM, and Swiss-ADME databases. The key genes of PTSD and anxiety were derived from disease databases. The network of protein-protein interaction(PPI) and a network of “drug-components-disease-targets” was constructed. Gene ontology(GO) enrichment and signaling pathway enrichment(KEGG) were analyzed by using R language and components-targets associated were validated by molecular docking. 64 bioactive components and 270 relevant targets were obtained from KXS. 3474 disease genes of PTSD and 4910 disease genes of anxiety were obtained. The results of KEGG have shown that neuroactive ligand-receptor interaction, calcium signaling pathway, and cAMP signaling pathway may play crucial roles in the effect of KXS on treating PTSD and anxiety. The results of PPI analysis and molecular docking indicated that AKT1 and IL-6 were crucial targets. Beta-sitosterol, Tenulin, Fumarine, and Stigmasterol might be crucial components via analyzing the network of “drug-components-disease-targets”. The network pharmacology study and molecular docking indicated that KXS treated anxiety and PTSD by multiple components, targets, and signaling pathways.
Quantum-chemical modeling of NO ligand activity in cationic nitrosyl iron complex [Fe(SC (NH2)2)2(NO)2]+ occurring in aerobic aqueous conditions
Authors: Gutsev Lavrenty G. , Emel’yanova Nina S. , Pokidova Olesya V. , Shestakov Alexandr F. , Sanina Nataliya A. , Aldoshin Sergei M. 
Published: May 2023

Abstract
The chemical reaction of a cationic ironnitrosyl complex with thiourea ligands of the composition [Fe(SC(NH2)2)2(NO)2]+ in aerobic aqueous conditions was studied via kinetic and quantum chemical modeling. An implicit expression is found for the kinetic curve which describes this process. The mechanism of interaction of the complex with molecular oxygen in the presence of water molecules was studied with density functional method. An optimized geometry of the initial, final, intermediate and transition states were obtained and the, energy profiles of the reactions were constructed. It was shown that the explicit inclusion of the water molecules in the reaction of the interaction of the complex with oxygen and the further transformation of the resulting products demonstrated not only the mechanism of the NO release, but also the intramolecular transformation of NO into NO2, NO2−, NO3−, ONOO−. A mechanism was proposed for the formation of a OH radical in the system and its release, along with the previously mentioned products, into solution.
A Paradigm Shifting View of Intellectual Disability: A Near Normal Distribution of IQ in Fragile X Syndrome
Authors: Schmitt Lauren M. , Will Meredith , Shaffer Rebecca , Erickson Craig 
Published: May 2023

Abstract

Fragile X Syndrome (FXS) is an X-linked disorder leading to the loss of expression of FMR1-protein product, FMRP. The absence or deficiency of FMRP is thought to result in the characteristic FXS phenotypes, including intellectual disability. Identifying the relationship between FMRP levels and IQ may be critical to better understand underlying mechanisms and advance treatment development and planning. A sample of 80 individuals with FXS (67% male), aged 8–45 years, completed IQ testing and blood draw via venipuncture to determine the relationship between IQ scores and FMRP levels as well as the normalcy of IQ distributions. In females with FXS only, higher FMRP levels were associated with higher IQ. In contrast, males with FXS showed a downward shifted but otherwise normal distribution of IQ scores. Our findings offer a paradigm-shifting views of FXS—males with FXS have normally distributed IQ that is downshifted 5 standard deviations. Our novel work provides evidence of a “FXS standard curve”, and is a critical step towards establishing molecular markers of disease severity in FXS. There is much future work to better understand the mechanism by which FMRP loss leads to intellectual disability and what biological/genetic and socio-environmental factors contribute to variation in IQ.
The effect of Cordia myxa mouthwash on the incidence and severity of stomatitis in leukemia patients undergoing chemotherapy: A protocol study
Authors: Molavynejad Shahram , Saberipour Bayan , Deilami Ahmad Ahmadzadeh , Siahpoush Amir , Mousavi Seyed Ali , Kambo Masoumeh Salehi , Javadi Mostafa 
Published: May 2023

Abstract
Background and purpose: Stomatitis or oral inflammation is one of the common complications in patients undergoing chemotherapy, which causes pain, discomfort, infection and long-term hospitalization. The only way to prevent this condition is to use a suitable mouthwash and maintain oral hygiene. The purpose of this study is to investigate the effect of Cordia myxa mouthwash on preventing stomatitis in patients undergoing chemotherapy.
Method: This study will be a double-blind, single-center randomized controlled clinical trial focusing on 60 patients undergoing chemotherapy. The samples will be randomly divided into intervention and control groups. In addition to receiving the routine betadine mouthwash, participants in the intervention group will receive a solution of 30 drops of 5% Cordia myxa formulation in 20 cc of water, and they will be asked to put the solution in their mouth, swirl it in their mouth for a minute and then spit it out. In the control group, in addition to betadine mouthwash, sterile water placebo (having the same taste and smell) will be used. Patients will brush their mouths with a soft toothbrush and the same toothpaste 3 times a day after breakfast, lunch, and dinner followed by mouthwash use for 14 days. Data will be collected using a demographic information questionnaire and the oral stomatitis severity checklist. The data will be analyzed based on statistical tests using SPSS version 22.
Discussion: This study is expected to shed light on the effectiveness of Cordia myxa mouthwash in improving the severity of stomatitis among leukemia patients. To the best of our knowledge, no valid scientific research has so far been conducted on this very topic. If this intervention proves effective in improving access and adherence to treatment, it would be a step forward in addressing a chronic health problem that is common among leukemia patients undergoing chemotherapy. Given its natural essence and the fact that it is not associated with any complications, the Cordia myxa mouthwash can be used safely alongside the main treatment to prevent and reduce the severity of mouth ulcers caused by chemotherapy.
Graphitization of Oak tree-based White Charcoals by High Temperature Heat Treatment
Authors: Park Yongnam , Park Young-Nam , Kwac Lee-Ku , Ryu Seung-Kon , Kim Hong-Gun 
Published: May 2023

Abstract
-Oak-tree-based white charcoals were subjected to high-temperature heat treatment at up to 2400°C to analyze changes in their surface morphology and internal structure using scanning electron microscopy and transmission electron microscopy. When the treatment temperature was increased, micropores became smaller and disappeared, but macropores and mesopores remained, resulting in an increase in average pore size. At a treatment temperature of 1800°C, some pores still remained. At treatment temperatures of 2000°C or higher, however, all the pores disappeared, and the internal structure changed into a dense graphite-like structure. The X-ray diffraction patterns of charcoals heat-treated at 1800°C or higher in an argon atmosphere exhibited a sharp peak at 2θ = 26.5°, and Raman spectroscopy also showed clear D and 2D bands near 1360 and 2680 cm−1 , respectively, indicating that carbon graphite crystals were developing. The presence of the D band and the ID/IG ratio confirmed that the newly developed structure was turbostratic. The Brunauer–Emmett–Teller adsorption isotherm of the as-received charcoals exhibited peculiar characteristics in which Types I and IV were mixed. This result is due to low-pressure hysteresis, in which nitrogen is embedded in the crevices of charcoal during adsorption and is hardly desorbed during desorption. This low-pressure hysteresis disappeared as the heat-treatment temperature increased; the adsorption isotherm of charcoal treated at 2400°C was Type II, and the specific surface area was 8.45 m2 /g, indicating that the charcoal was completely transformed to nonporous graphite
The SAUR family gene OsSAUR56 regulates heading date in rice
Authors: Zhao Zhe , Chen Tengkui , Yue Jicheng , Pu Na , Liu Jinzhao , Luo Lixin , Huang Ming , Guo Tao , Xiao Wuming 
Published: May 2023

Abstract
Heading date is one of the most important agronomic traits and a fundamental factor determining crop yield. Although many genes related to heading date have been reported in rice, the molecular mechanism of heading date is still poorly understood. The Small Auxin-Up RNA (SAUR) family genes regulate many aspects of plant growth and development. However, their functions involved in heading date of rice (Oryza sativa L.) are not characterized. Here, OsSAUR56 gene was edited by the CRISPR/Cas9 technology in the japonica cultivar Zhonghua11 (ZH11). We found that loss-of-function of OsSAUR56 led to early heading phenotype regardless of day length. OsSAUR56 was mainly expressed in anther, and its protein was localized in the cytoplasm and the nucleus. Gene expression analysis with quantitative RT-PCR showed that OsSAUR56 regulated flowering time and heading date by affecting the expression of a clock gene OsGI and two repressors, HEADING DATE 7 (Ghd7) and DTH8 (Ghd8/LHD1). Moreover, evolutionary analysis showed that OsSAUR56 presents divergence between indica and japonica, showing natural selection during the domestication of cultivated rice. These results indicate that OsSAUR56 plays an important role in the regulation of heading date, and may be an important target for rice breeding programs.