bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALKBH5 suppresses malignancy of hepatocellular carcinoma via m6A-guided epigenetic inhibition of LYPD1
Authors: Chen Yunhao , Zhao Yanchun , Chen Junru , Peng Chuanhui , Zhang Yanpeng , Tong Rongliang , Cheng Qiyang , Yang Beng , Feng Xiaode , Lu Yuejie , Xie Haiyang , Zhou Lin , Wu Jian , Zheng Shusen 
Published: August 2020

Abstract
Background
N6-methyladenosine (m6A) modification is an emerging layer of epigenetic regulation which is widely implicated in the tumorigenicity of hepatocellular carcinoma (HCC), offering a novel perspective for investigating molecular pathogenesis of this disease. The role of AlkB homolog 5 (ALKBH5), one of the m6A demethylases, has not been fully explored in HCC. Here we clarify the biological profile and potential mechanisms of ALKBH5 in HCC.

Methods
Expression of ALKBH5 and its correlation with clinicopathological characteristics of HCC were evaluated using tissue microarrays and online datasets. And biological effects of ALKBH5 in HCC were determined in vitro and in vivo. Subsequently, methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA sequencing (RNA-seq), and following m6A dot blot, MeRIP-qPCR, RIP-qPCR or dual luciferase reporter assays were employed to screen and validate the candidate targets of ALKBH5.

Results
We demonstrated that ALKBH5 was down-regulated in HCC, and decreased ALKBH5 expression was an independent prognostic factor of worse survival in HCC patients. Functionally, ALKBH5 suppressed the proliferation and invasion capabilities of HCC cells in vitro and in vivo. Mechanistically, ALKBH5-mediated m6A demethylation led to a post-transcriptional inhibition of LY6/PLAUR Domain Containing 1 (LYPD1), which could be recognized and stabilized by the m6A effector IGF2BP1. In addition, we identified that LYPD1 induced oncogenic behaviors of tumors in contrast to ALKBH5. Dysregulation of ALKBH5/LYPD1 axis impelled the progression of HCC.

Conclusion
Our study reveals that ALKBH5, characterized as a tumor suppressor, attenuates the expression of LYPD1 via an m6A-dependent manner in HCC cells. Our findings enrich the landscape of m6A-modulated tumor malignancy, and provide new insights into potential biomarkers and therapeutic targets of HCC treatment.
Impact of HIV-1 Vpr manipulation of the DNA repair enzyme UNG2 on B lymphocyte class switch recombination
Authors: Eldin Patrick , Péron Sophie , Galashevskaya Anastasia , Denis-Lagache Nicolas , Cogné Michel , Slupphaug Geir , Briant Laurence 
Published: August 2020

Abstract
Background
HIV-1 Vpr encodes a 14 kDa protein that has been implicated in viral pathogenesis through modulation of several host cell functions. In addition to pro-apoptotic and cytostatic properties, Vpr can redirect cellular E3 ubiquitin ligases (such as DCAF1-Cul4A E3 ligase complex) to target many host proteins and interfere with their functions. Among them, Vpr binds the uracil DNA glycosylase UNG2, which controls genome uracilation, and induces its specific degradation leading to loss of uracil removal activity in infected cells. Considering the essential role of UNG2 in antibody diversification in B-cells, we evaluated the impact of Vpr on UNG2 fate in B lymphocytes and examined the functional consequences of UNG2 modulations on class switch recombination (CSR).

Methods
The impact of Vpr-induced UNG2 deregulation on CSR proficiency was evaluated by using virus-like particles able to deliver Vpr protein to target cells including the murine model CSR B cell line CH12F3 and mouse primary B-cells. Co-culture experiments were used to re-examine the ability of Vpr to be released by HIV-1 infected cells and to effectively accumulate in bystander B-cells. Vpr-mediated UNG2 modulations were monitored by following UNG2 protein abundance and uracil removal enzymatic activity.

Results
In this study we report the ability of Vpr to reduce immunoglobulin class switch recombination (CSR) in immortalized and primary mouse B-cells through the degradation of UNG2. We also emphasize that Vpr is released by producing cells and penetrates bystander B lymphocytes.

Conclusions
This work therefore opens up new perspectives to study alterations of the B-cell response by using Vpr as a specific CSR blocking tool. Moreover, our results raise the question of whether extracellular HIV-1 Vpr detected in some patients may manipulate the antibody diversification process that engineers an adapted response against pathogenic intruders and thereby contribute to the intrinsic B-cell humoral defect reported in infected patients.
Passive, yet not inactive: robotic exoskeleton walking increases cortical activation dependent on task
Authors: Peters Sue , Lim Shannon B. , Louie Dennis R. , Yang Chieh-ling , Eng Janice J. 
Published: August 2020

Abstract
Background
Experimental designs using surrogate gait-like movements, such as in functional magnetic resonance imaging (MRI), cannot fully capture the cortical activation associated with overground gait. Overground gait in a robotic exoskeleton may be an ideal tool to generate controlled sensorimotor stimulation of gait conditions like ‘active’ (i.e. user moves with the device) and ‘passive’ (i.e. user is moved by the device) gait. To truly understand these neural mechanisms, functional near-infrared spectroscopy (fNIRS) would yield greater ecological validity. Thus, the aim of this experiment was to use fNIRS to delineate brain activation differences between ‘Active’ and ‘Passive’ overground gait in a robotic exoskeleton.

Methods
Fourteen healthy adults performed 10 walking trials in a robotic exoskeleton for Passive and Active conditions, with fNIRS over bilateral frontal and parietal lobes, and electromyography (EMG) over bilateral thigh muscles. Digitization of optode locations and individual T1 MRI scans were used to demarcate the brain regions fNIRS recorded from.

Results
Increased oxyhemoglobin in the right frontal cortex was found for Passive compared with Active conditions. For deoxyhemoglobin, increased activation during Passive was found in the left frontal cortex and bilateral parietal cortices compared with Active; one channel in the left parietal cortex decreased during Active when compared with Passive. Normalized EMG mean amplitude was higher in the Active compared with Passive conditions for all four muscles (p ≤ 0.044), confirming participants produced the conditions asked of them.

Conclusions
The parietal cortex is active during passive robotic exoskeleton gait, a novel finding as research to date has not recorded posterior to the primary somatosensory cortex. Increased activation of the parietal cortex may be related to the planning of limb coordination while maintaining postural control. Future neurorehabilitation research could use fNIRS to examine whether exoskeletal gait training can increase gait-related brain activation with individuals unable to walk independently.
Feasibility and potential effects of using the electro-dress Mollii on spasticity and functioning in chronic stroke
Authors: Palmcrantz Susanne , Pennati Gaia Valentina , Bergling Hanna , Borg Jörgen 
Published: August 2020

AbstractBackgroundSpasticity after lesions of central motor pathways may be disabling and there is a need for new, cost-effective treatment methods. One novel approach is offered by the electro-dress Mollii®, primarily designed to enhance reciprocal inhibition of spastic muscles by multifocal, transcutaneous antagonist stimulation.MethodsThe Mollii® suit was set individually for 20 participants living with spasticity and hemiplegia after stroke and used in the home setting for 6 weeks. Usability and perceived effects were monitored by weekly telephone interviews. Outcome was assessed by use of the NeuroFlexor™ method for quantification of the neural component (NC) of resistance to passive stretch (spasticity), and the modified Ashworth scale (MAS) for total resistance, Fugl-Meyer Assessment of motor recovery for sensorimotor function in upper (FM-UE) and lower extremities (FM-LE), activity performance with the Action Research Arm Test (ARAT), Berg balance scale, 10 m and 6 min walk tests, and perceived functioning with the Stroke Impact Scale.ResultsCompliance was high (mean 19.25 of 21 sessions). Perceived positive effects were reported by 60% and most commonly related to decreased muscle tone (n = 9), improved gait pattern function (n = 7) and voluntary movement in the upper extremity (n = 6). On a group level, the NC decreased significantly in the wrist flexors of the affected hand (p = 0.023) and significant improvements according to FM-UE (p = 0.000) and FM-LE (p = 0.003) were seen after the intervention. No significant difference was detected with MAS or assessed activity performance, except for the ARAT (p = 0.000). FM-UE score change correlated significantly and fairly with the perceived effect in the upper extremity (r0.498p = 0.025) and in the corresponding analysis for the FM-LE and perceived effect in the lower extremity (r = 0.469p = 0.037).ConclusionThis study indicates that the Mollii® method is feasible when used in the home setting to decrease spasticity and improve sensorimotor function. The results may guide a larger controlled study combined with rehabilitation interventions to enhance effects on activity and participation domains.Trial registrationNCT04076878. Registered 2 September 2019 - Retrospectively registered
Crystalline silica particles cause rapid NLRP3-dependent mitochondrial depolarization and DNA damage in airway epithelial cells
Authors: Wu Rongrong , Högberg Johan , Adner Mikael , Ramos-Ramírez Patricia , Stenius Ulla , Zheng Huiyuan 
Published: August 2020

Abstract
Background
Respirable crystalline silica causes lung carcinomas and many thousand future cancer cases are expected in e.g. Europe. Critical questions are how silica causes genotoxicity in the respiratory epithelium and if new cases can be avoided by lowered permissible exposure levels. In this study we investigate early DNA damaging effects of low doses of silica particles in respiratory epithelial cells in vitro and in vivo in an effort to understand low-dose carcinogenic effects of silica particles.

Results
We find DNA damage accumulation already after 5–10 min exposure to low doses (5 μg/cm2) of silica particles (Min-U-Sil 5) in vitro. DNA damage was documented as increased levels of γH2AX, pCHK2, by Comet assay, AIM2 induction, and by increased DNA repair (non-homologous end joining) signaling. The DNA damage response (DDR) was not related to increased ROS levels, but to a NLRP3-dependent mitochondrial depolarization. Particles in contact with the plasma membrane elicited a Ser198 phosphorylation of NLRP3, co-localization of NLRP3 to mitochondria and depolarization. FCCP, a mitochondrial uncoupler, as well as overexpressed NLRP3 mimicked the silica-induced depolarization and the DNA damage response. A single inhalation of 25 μg silica particles gave a similar rapid DDR in mouse lung. Biomarkers (CC10 and GPRC5A) indicated an involvement of respiratory epithelial cells.

Conclusions
Our findings demonstrate a novel mode of action (MOA) for silica-induced DNA damage and mutagenic double strand breaks in airway epithelial cells. This MOA seems independent of particle uptake and of an involvement of macrophages. Our study might help defining models for estimating exposure levels without DNA damaging effects.
SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species
Authors: Vilanova Santiago , Alonso David , Gramazio Pietro , Plazas Mariola , García-Fortea Edgar , Ferrante Paola , Schmidt Maximilian , Díez María José , Usadel Björn , Giuliano Giovanni , Prohens Jaime 
Published: August 2020

AbstractBackgroundThe use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues.ResultsSILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted fromSolanum elaeagnifoliumusing this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio.ConclusionsA high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.
Preoperative anterior coverage of the medial acetabulum can predict postoperative anterior coverage and range of motion after periacetabular osteotomy: a cohort study
Authors: Hayashi Shinya , Hashimoto Shingo , Matsumoto Tomoyuki , Takayama Koji , Kamenaga Tomoyuki , Niikura Takahiro , Kuroda Ryosuke 
Published: August 2020

AbstractBackgroundWe hypothesized that preoperative pelvic morphology may affect postoperative anterior coverage and postoperative clinical range of motion (ROM) leading to postoperative pincer type femoroacetabular impingement (FAI). The aim of this study was to evaluate the relationships between preoperative bone morphology and postoperative ROMs to prevent postoperative FAI after periacetabular osteotomy.MethodsSixty-eight patients (71 hips) with hip dysplasia participated in this study and underwent curved PAO. The acetabular fragment was usually moved only by lateral rotation of the acetabulum, without intraoperative anterior or posterior rotation. The pre- and postoperative three-dimensional center-edge (CE) angles were measured and compared to the postoperative ROM.ResultsPreoperative medial anterior CE angle was significantly associated with postoperative anterior CE angle, and the correlation coefficient of medial anterior CE and postoperative anterior CE was higher than the coefficient of preoperative anterior CE and postoperative anterior CE (preoperative anterior CE, rr = 0.27,p= 0.020; preoperative medial anterior CE, rr = 0.54,p< 0.001). Femoral anteversion correlated with postoperative internal rotation angle at 90° flexion (r= 0.32,p= 0.021). In multiple linear regressions, postoperative internal rotation angle at 90° flexion angle was significantly affected by both medial CE angle through the medial one fourth of femoral head and femoral anteversion.ConclusionsPreoperative medial anterior acetabular coverage was associated with postoperative anterior acetabular coverage. Further, the combination with preoperative medial anterior acetabular coverage and femoral anteversion can predict postoperative internal rotation at 90° flexion. Therefore, the direction of acetabular reorientation should be carefully considered when the patients have high preoperative medial anterior CE angle and small femoral anteversion.
Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields
Authors: Li Mengzhi , Chen Zhongjian , Qian Jun , Wei Fugang , Zhang Guozhuang , Wang Yong , Wei Guangfei , Hu Zhigang , Dong Linlin , Chen Shilin 
Published: August 2020

Abstract
Background
Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction.

Methods
This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields.

Results
At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields.

Conclusions
This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.
Using the GHQ-12 to screen for mental health problems among primary care patients: psychometrics and practical considerations
Authors: Anjara S. G. , Bonetto C. , Van Bortel T. , Brayne C. 
Published: August 2020

Abstract
Background
This study explores the factor structure of the Indonesian version of the GHQ-12 based on several theoretical perspectives and determines the threshold for optimum sensitivity and specificity. Through a focus group discussion, we evaluate the practicality of the GHQ-12 as a screening tool for mental health problems among adult primary care patients in Indonesia.

Methods
This is a prospective study exploring the construct validity, criterion validity and reliability of the GHQ-12, conducted with 676 primary care patients attending 28 primary care clinics randomised for participation in the study. Participants’ GHQ-12 scores were compared with their psychiatric diagnosis based on face-to-face clinical interviews with GPs using the CIS-R. Exploratory and Confirmatory Factor Analyses determined the construct validity of the GHQ-12 in this population. The appropriate threshold score of the GHQ-12 as a screening tool in primary care was determined using the receiver operating curve. Prior to data collection, a focus group discussion was held with research assistants who piloted the screening procedure, GPs, and a psychiatrist, to evaluate the practicality of embedding screening within the routine clinic procedures.

Results
Of all primary care patients attending the clinics during the recruitment period, 26.7% agreed to participate (676/2532 consecutive patients approached). Their median age was 46 (range 18–82 years); 67% were women. The median GHQ-12 score for our primary care sample was 2, with an interquartile range of 4. The internal consistency of the GHQ-12 was good (Cronbach’s α = 0.76). Four factor structures were fitted on the data. The GHQ-12 was found to best fit a one-dimensional model, when response bias is taken into consideration. Results from the ROC curve indicated that the GHQ-12 is ‘fairly accurate’ when discriminating primary care patients with indication of mental disorders from those without, with average AUC of 0.78. The optimal threshold of the GHQ-12 was either 1/2 or 2/3 point depending on the intended utility, with a Positive Predictive Value of 0.68 to 0.73 respectively. The screening procedure was successfully embedded into routine patient flow in the 28 clinics.

Conclusions
The Indonesian version of the GHQ-12 could be used to screen primary care patients at high risk of mental disorders although with significant false positives if reasonable sensitivity is to be achieved. While it involves additional administrative burden, screening may help identify future users of mental health services in primary care that the country is currently expanding.
The IL1β-IL1R signaling is involved in the stimulatory effects triggered by hypoxia in breast cancer cells and cancer-associated fibroblasts (CAFs)
Authors: Lappano Rosamaria , Talia Marianna , Cirillo Francesca , Rigiracciolo Damiano Cosimo , Scordamaglia Domenica , Guzzi Rita , Miglietta Anna Maria , De Francesco Ernestina Marianna , Belfiore Antonino , Sims Andrew H. , Maggiolini Marcello 
Published: August 2020

Abstract
Background
Hypoxia plays a relevant role in tumor-related inflammation toward the metastatic spread and cancer aggressiveness. The pro-inflammatory cytokine interleukin-1β (IL-β) and its cognate receptor IL1R1 contribute to the initiation and progression of breast cancer determining pro-tumorigenic inflammatory responses. The transcriptional target of the hypoxia inducible factor-1α (HIF-1α) namely the G protein estrogen receptor (GPER) mediates a feedforward loop coupling IL-1β induction by breast cancer-associated fibroblasts (CAFs) to IL1R1 expression by breast cancer cells toward the regulation of target genes and relevant biological responses.

Methods
In order to ascertain the correlation of IL-β with HIF-1α and further hypoxia-related genes in triple-negative breast cancer (TNBC) patients, a bioinformatics analysis was performed using the information provided by The Invasive Breast Cancer Cohort of The Cancer Genome Atlas (TCGA) project and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) datasets. Gene expression correlation, statistical analysis and gene set enrichment analysis (GSEA) were carried out with R studio packages. Pathway enrichment analysis was evaluated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. TNBC cells and primary CAFs were used as model system. The molecular mechanisms implicated in the regulation of IL-1β by hypoxia toward a metastatic gene expression profile and invasive properties were assessed performing gene and protein expression studies, PCR arrays, gene silencing and immunofluorescence analysis, co-immunoprecipitation and ChiP assays, ELISA, cell spreading, invasion and spheroid formation.

Results
We first determined that IL-1β expression correlates with the levels of HIF-1α as well as with a hypoxia-related gene signature in TNBC patients. Next, we demonstrated that hypoxia triggers a functional liaison among HIF-1α, GPER and the IL-1β/IL1R1 signaling toward a metastatic gene signature and a feed-forward loop of IL-1β that leads to proliferative and invasive responses in TNBC cells. Furthermore, we found that the IL-1β released in the conditioned medium of TNBC cells exposed to hypoxic conditions promotes an invasive phenotype of CAFs.

Conclusions
Our data shed new light on the role of hypoxia in the activation of the IL-1β/IL1R1 signaling, which in turn triggers aggressive features in both TNBC cells and CAFs. Hence, our findings provide novel evidence regarding the mechanisms through which the hypoxic tumor microenvironment may contribute to breast cancer progression and suggest further targets useful in more comprehensive therapeutic strategies.