bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic regulation of ethanol-type fermentation of anaerobic acidogenesis at different pH based on transcriptome analysis of Ethanoligenens harbinense
Authors: Li Zhen , Lou Yu , Ding Jie , Liu Bing-Feng , Xie Guo-Jun , Ren Nan-Qi , Xing Defeng 
Published: June 2020

Abstract
Background
Ethanol-type fermentation, one of the fermentation types in mixed cultures of acidogenesis with obvious advantages such as low pH tolerance and high efficiency of H2 production, has attracted widespread attentions. pH level greatly influences the establishment of the fermentation of carbohydrate acidogenesis by shaping community assembly and the metabolic activity of keystone populations. To explore the adaptation mechanisms of ethanol-type fermentation to low pH, we report the effects of initial pH on the physiological metabolism and transcriptomes of Ethanoligenens harbinense—a representative species of ethanol-type fermentation.

Results
Different initial pH levels significantly changed the cell growth and fermentation products of E. harbinense. Using transcriptomic analysis, we identified and functionally categorized 1753 differentially expressed genes (DEGs). By mining information on metabolic pathways, we probed the transcriptional regulation of ethanol–H2 metabolism relating to pH responses. Multiple pathways of E. harbinense were co-regulated by changing gene expression patterns. Low initial pH down-regulated the expression of cell growth- and acidogenesis-related genes but did not affect the expression of H2 evolution-related hydrogenase and ferredoxin genes. High pH down-regulated the expression of H2 evolution- and acidogenesis-related genes. Multiple resistance mechanisms, including chemotaxis, the phosphotransferase system (PTS), and the antioxidant system, were regulated at the transcriptional level under pH stress.

Conclusions
Ethanoligenens adapted to low pH by regulating the gene expression networks of cell growth, basic metabolism, chemotaxis and resistance but not H2 evolution-related genes. Regulation based on pH shifts can represent an important approach to establish and enhance ethanol-type fermentation. The complete gene expression network of ethanol fermentative bacteria for pH response provides valuable insights into the acidogenic fermentation, and offers an effective regulation strategy for the sustainable energy recovery from wastewater and solid waste.
Interleukin-32 in systemic sclerosis, a potential new biomarker for pulmonary arterial hypertension
Authors: Di Benedetto Paola , Guggino Giuliana , Manzi Giovanna , Ruscitti Piero , Berardicurti Onorina , Panzera Noemi , Grazia Nicolò , Badagliacca Roberto , Riccieri Valeria , Vizza Carmine Dario , Radchenko Ganna , Liakouli Vasiliki , Ciccia Francesco , Cipriani Paola , Giacomelli Roberto 
Published: June 2020

Abstract
Background
Pulmonary arterial hypertension (PAH) is a severe complication of systemic sclerosis (SSc), associated with a progressive elevation in pulmonary vascular resistance and subsequent right heart failure and death. Due to unspecific symptoms, the diagnosis of PAH is often delayed. On this basis, it is of great value to improve current diagnostic methods and develop new strategies for evaluating patients with suspected PAH. Interleukin-32 (IL-32) is a proinflammatory cytokine expressed in damaged vascular cells, and the present study aimed to assess if this cytokine could be a new biomarker of PAH during SSc.

Methods
The IL-32 expression was evaluated in the sera and skin samples of 18 SSc-PAH patients, 21 SSc patients without PAH, 15 patients with idiopathic PAH (iPAH) and 14 healthy controls (HCs), by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry (IHC). Receiver-operating characteristic (ROC) curves were performed to evaluate the cut-off of IL-32 in identifying patients with PAH. Furthermore, in SSc patients, correlation analyses were performed between IL-32 sera levels and mean pulmonary artery pressure (mPAP) evaluated by right heart catheterization (RHC) and systolic pulmonary artery pressure (sPAP), obtained by echocardiography. Additionally, the number of skin IL-32+ cells was correlated with modified Rodnan skin score (mRSS).

Results
In SSc-PAH patients, IL-32 sera levels were significantly higher when compared with SSc patients without PAH and patients affected by iPAH. The analysis of ROC curve showed that IL-32 sera levels above 11.12 pg/ml were able to predict patients with PAH (sensitivity = 90%, specificity = 100%). Furthermore, the IL-32 sera levels of patients with SSc correlated with both mPAP and sPAP. In the skin derived from SSc-PAH patients, the number of IL-32+ cells was significantly increased when compared with the skin derived from SSc patients without PAH, correlating with the mRSS.

Conclusion
Our study suggested that sera determination of IL-32 may be a promising approach to evaluate the presence of PAH in SSc patients and together with longitudinal future studies could help to increase the understanding how these biomarkers mirror the vascular changes and the inflammatory process during SSc.
Genome-wide analysis of DNA methylation identifies S100A13 as an epigenetic biomarker in individuals with chronic (≥ 30 years) type 2 diabetes without diabetic retinopathy
Authors: Li Tao , Xu Yi , Shi Yongyong , Chen Jianhua , Lin Senlin , Zhu Jianfeng , Xu Xian , Lu Lina , Zou Haidong 
Published: June 2020

Abstract
Background
This study aimed to determine the epigenetic biomarkers of diabetic retinopathy (DR) in subjects with type 2 diabetes mellitus (T2DM). This retrospective study is based on the Shanghai Xinjing community prevention and treatment administrative system of chronic diseases. The subjects enrolled herein were T2DM patients who had undergone long-term follow-up evaluation in the system. Two consecutive studies were conducted. In the discovery cohort, among 19 subjects who had developed DR with a DM duration < 3 years and 21 subjects without DR > 30 years after being diagnosed with DM, an Infinium Human Methylation 850 Beadchip was used to identify differential methylation regions (DMRs) and differential methylation sites (DMSs). The function of the genes was assessed through KEGG enrichment analysis, Gene Ontology (GO) analysis, and pathway network analysis. In the replication cohort, 87 DR patients with a short DM duration and 89 patients without DR over a DM duration > 20 years were compared to assess the association between DMSs and DR upon pyrosequencing.

Results
A total of 34 DMRs were identified. Genes containing DMSs with the top 5 highest beta value differences between DR and non-DR participants were located on chromosome 1 and were present in the S100A13 gene, which was associated with 71 GO terms. Two S100A13 gene sites, i.e., cg02873163 and cg11343894, displayed a good correlation with DR on pyrosequencing.

Conclusions
DMSs in the S100A13 gene may be potential biomarkers of DR.
Decreased nuclear Pten in neural stem cells contributes to deficits in neuronal maturation
Authors: Kang Shin Chung , Jaini Ritika , Hitomi Masahiro , Lee Hyunpil , Sarn Nick , Thacker Stetson , Eng Charis 
Published: June 2020

Abstract
Background
PTEN, a syndromic autism spectrum disorder (ASD) risk gene, is mutated in approximately 10% of macrocephalic ASD cases. Despite the described genetic association between PTEN and ASD and ensuing studies, we continue to have a limited understanding of how PTEN disruption drives ASD pathogenesis and maintenance.

Methods
We derived neural stem cells (NSCs) from the dentate gyrus (DG) of Ptenm3m4 mice, a model that recapitulates PTEN-ASD phenotypes. We subsequently characterized the expression of stemness factors, proliferation, and differentiation of neurons and glia in Ptenm3m4 NSCs using immunofluorescent and immunoblotting approaches. We also measured Creb phosphorylation by Western blot analysis and expression of Creb-regulated genes with qRT-PCR.

Results
The m3m4 mutation decreases Pten localization to the nucleus and its global expression over time. Ptenm3m4 NSCs exhibit persistent stemness characteristics associated with increased proliferation and a resistance to neuronal maturation during differentiation. Given the increased proliferation of Ptenm3m4 NSCs, a significant increase in the population of immature neurons relative to mature neurons occurs, an approximately tenfold decrease in the ratio between the homozygous mutant and wildtype. There is an opposite pattern of differentiation in some Ptenm3m4 glia, specifically an increase in astrocytes. These aberrant differentiation patterns associate with changes in Creb activation in Ptenm3m4/m3m4 NSCs. We specifically observed loss of Creb phosphorylation at S133 in Ptenm3m4/m3m4 NSCs and a subsequent decrease in expression of Creb-regulated genes important to neuronal function (i.e., Bdnf). Interestingly, Bdnf treatment is able to partially rescue the stunted neuronal maturation phenotype in Ptenm3m4/m3m4 NSCs.

Conclusions
Constitutional disruption of Pten nuclear localization with subsequent global decrease in Pten expression generates abnormal patterns of differentiation, a stunting of neuronal maturation. The propensity of Pten disruption to restrain neurons to a more progenitor-like state may be an important feature contributing to PTEN-ASD pathogenesis.

Graphical abstract
Copy number variants (CNVs): a powerful tool for iPSC-based modelling of ASD
Authors: Drakulic Danijela , Djurovic Srdjan , Syed Yasir Ahmed , Trattaro Sebastiano , Caporale Nicolò , Falk Anna , Ofir Rivka , Heine Vivi M. , Chawner Samuel J. R. A. , Rodriguez-Moreno Antonio , van den Bree Marianne B. M. , Testa Giuseppe , Petrakis Spyros , Harwood Adrian J. 
Published: June 2020

AbstractPatients diagnosed with chromosome microdeletions or duplications, known as copy number variants (CNVs), present a unique opportunity to investigate the relationship between patient genotype and cell phenotype. CNVs have high genetic penetrance and give a good correlation between gene locus and patient clinical phenotype. This is especially effective for the study of patients with neurodevelopmental disorders (NDD), including those falling within the autism spectrum disorders (ASD). A key question is whether this correlation between genetics and clinical presentation at the level of the patient can be translated to the cell phenotypes arising from the neurodevelopment of patient induced pluripotent stem cells (iPSCs).Here, we examine how iPSCs derived from ASD patients with an associated CNV inform our understanding of the genetic and biological mechanisms underlying the aetiology of ASD. We consider selection of genetically characterised patient iPSCs; use of appropriate control lines; aspects of human neurocellular biology that can capture in vitro the patient clinical phenotype; and current limitations of patient iPSC-based studies. Finally, we consider how future research may be enhanced to maximise the utility of CNV patients for research of pathological mechanisms or therapeutic targets.
Adipose mesenchymal stem cell transplantation alleviates spinal cord injury-induced neuroinflammation partly by suppressing the Jagged1/Notch pathway
Authors: Zhou Zhilai , Tian Xiaobo , Mo Biling , Xu Huali , Zhang Li , Huang Lishan , Yao Shun , Huang Zixiang , Wang Yeyang , Xie Huan , Xu Liwei , Zhang Hui 
Published: June 2020

Abstract
Background
The therapeutic effects of adipose-derived mesenchymal stem cell (ADSC) transplantation have been demonstrated in several models of central nervous system (CNS) injury and are thought to involve the modulation of the inflammatory response. However, the exact underlying molecular mechanism is poorly understood. Activation of the Jagged1/Notch signaling pathway is thought to involve inflammatory and gliotic events in the CNS. Here, we elucidated the effect of ADSC transplantation on the inflammatory reaction after spinal cord injury (SCI) and the potential mechanism mediated by Jagged1/Notch signaling pathway suppression.

Methods
To evaluate the therapeutic effects of ADSC treatment and the potential inhibitory effects of ADSCs on Notch signaling, mice were subjected to contusion SCI, and GFP-labeled ADSCs were injected into the lesion site immediately after the injury. Locomotor function, spinal cord tissue morphology, and the levels of Notch-related proteins and proinflammatory transcripts were compared between groups. To validate the hypothesis that the therapeutic effects of ADSCs are partly due to Notch1 signaling inhibition, a Jagged1 small interfering RNA (siRNA) was injected into the spinal cord to knock down Jagged1/Notch signaling. Neuronal staining and analyses of microglia/macrophage activation and signaling pathways were performed.

Results
We demonstrated that ADSCs survived in the injured spinal cord for at least 28 days without differentiating into glial or neuronal elements. ADSC treatment resulted in significant downregulation of proinflammatory mediator expression and reduced ionized calcium-binding adapter molecule 1 (IBA1) and ED-1 staining in the injured spinal cord, eventually improving functional recovery. The augmentation of the Jagged1/Notch signaling pathway after SCI was suppressed by ADSC transplantation. The inhibition of the Jagged1/Notch signaling pathway by Jagged1 siRNA resulted in decreases in SCI-induced proinflammatory cytokines and the activation of microglia and an increase in the survival of neurons. Furthermore, Jagged1 knockdown suppressed the phosphorylation of JAK/STAT3 in astrocytes following SCI.

Conclusion
The results of this study demonstrated that the therapeutic effects of ADSCs in SCI mice were partly due to Jagged1/Notch signaling pathway inhibition and a subsequent reduction in JAK/STAT3 phosphorylation in astrocytes.
Reversible data hiding for binary images based on adaptive overlapping pattern
Authors: Dong Keming , Kim Hyoung Joong , Yu Xiaohan , Feng Xiaoqing 
Published: June 2020

AbstractPattern substitution (PS) method (Ho et al., Comput. Stand. Interfaces 31:787–794, 2009) is a recent reversible data hiding method for binary images. It generates one pattern pair, the patterns in which are called PM and PF, and substitutes between them to embed one bit. Two types of PS have been proposed: non-overlapping PS and overlapping PS. However, Dong et al. (ETRI J. 37:990–1000, 2015) states that the overlapping PS sometimes cannot decode correctly, which is called as miscoding problem. Moreover, to the PS-based methods (Ho et al., Comput. Stand. Interfaces 31:787–794, 2009; Dong et al., ETRI J. 37:990–1000, 2015; Dong et al., Lect. Notes Comput. Sci. 6526:3516–3522, 2011), although chosen of two patterns to form the pattern pair which relates the embedding performance much, the previous methods only use a fixed pattern pair during the whole data hiding process. In order to overcome these two shortcomings, this paper proposes an adaptive overlapping PS method. Firstly, two modes of the embedding are proposed so that the miscoding problem can be solved. Secondly, one window which contains the context of current processing pixel is generated and updated when the process proceeds to the next pixel. Thus, the optimum pair of the local context for embedding can be chosen. Thirdly, in order to get a smaller location map, a three-round embedding mechanism is also proposed. With these three improvements, our method can embed larger payloads with less distortion than the previous works.
Measurement properties of smartphone approaches to assess key lifestyle behaviours: protocol of a systematic review
Authors: Thornton Louise , Osman Bridie , Wescott Annie B. , Sunderland Matthew , Champion Katrina , Green Olivia , Kay-Lambkin Frances , Slade Tim , Newton Nickie , Chapman Cath , Teesson Maree , Mills Katherine , Birrell Louise , Lubans David , Van de Ven Pepijn , Torous John , Parmenter Belinda , Gardner Lauren ,   Health4Life team
Published: June 2020

Abstract
Background
Six core behavioural risk factors (poor diet, physical activity, sedentary behaviour, alcohol misuse, smoking and unhealthy sleep patterns) have been identified as strong determinants of chronic disease, such as cardiovascular disease, diabetes and cancers. Smartphones have the potential to provide a real-time, pervasive, unobtrusive and cost-effective way to measure health behaviours and deliver instant feedback to users. Despite this, validity of using smartphones to measure these six key behaviours is largely unknown. The proposed systematic review aims to address this gap by identifying existing smartphone-based approaches to measure these health behaviours and critically appraising, comparing and summarizing the quality of their measurement properties.

Methods
A systematic search of the Ovid MEDLINE, Embase (Elsevier), Cochrane Library (Wiley), PsychINFO (EBSCOhost), CINAHL (EBSCOHost), Web of Science (Clarivate), SPORTDiscus (EBSCOhost) and IEEE Xplore Digital Library databases will be conducted from January 2007 to March 2020. Eligible studies will be those written in English that measure at least one of the six health behaviours of interest via a smartphone and report on at least one measurement property. The primary outcomes will be validity, reliability and/or responsiveness of these measurement approaches. A secondary outcome will be the feasibility (e.g. user burden, usability and cost) of identified approaches. No restrictions will be placed on the participant population or study design. Two reviewers will independently screen studies for eligibility, extract data and assess the risk of bias. The study methodological quality (or bias) will be appraised using an appropriate tool. Our results will be described in a narrative synthesis. If feasible, random effects meta-analysis will be conducted where appropriate.

Discussion
The results from this review will provide important information about the types of smartphone-based approaches currently available to measure the core behavioural risk factors for chronic disease and the quality of their measurement properties. It will allow recommendations on the most suitable and effective measures of these lifestyle behaviours using smartphones. Valid and reliable measurement of these behaviours and risk factor opens the door to targeted and real-time delivery of health behaviour interventions, providing unprecedented opportunities to offset the trajectory toward chronic disease.

Systematic review registration
PROSPERO: CRD42019122242
Some Hermite–Jensen–Mercer type inequalities for k-Caputo-fractional derivatives and related results
Authors: Zhao Shupeng , Butt Saad Ihsan , Nazeer Waqas , Nasir Jamshed , Umar Muhammad , Liu Ya 
Published: June 2020

AbstractIn this paper, certain Hermite–Hadamard–Mercer type inequalities are proved via k-Caputo fractional derivatives. We established some new k-Caputo fractional derivatives inequalities with Hermite–Hadamard–Mercer type inequalities for differentiable mapping $\psi^{(n)}$ψ(n) whose derivatives in the absolute values are convex.
Generation of new fractional inequalities via n polynomials s-type convexity with applications
Authors: Rashid Saima , İşcan İmdat , Baleanu Dumitru , Chu Yu-Ming 
Published: June 2020

AbstractThe celebrated Hermite–Hadamard and Ostrowski type inequalities have been studied extensively since they have been established. We find novel versions of the Hermite–Hadamard and Ostrowski type inequalities for the n-polynomial s-type convex functions in the frame of fractional calculus. Taking into account the new concept, we derive some generalizations that capture novel results under investigation. We present two different general techniques, for the functions whose first and second derivatives in absolute value at certain powers are n-polynomial s-type convex functions by employing $\mathcal{K}$
K
-fractional integral operators have yielded intriguing results. Applications and motivations of presented results are briefly discussed that generate novel variants related to quadrature rules that will be helpful for in-depth investigation in fractal theory, optimization and machine learning.
A scenario generation pipeline for autonomous vehicle simulators
Authors: Wen Mingyun , Park Jisun , Cho Kyungeun 
Published: June 2020

Abstract
To develop a realistic simulator for autonomous vehicle testing, the simulation of various scenarios that may occur near vehicles in the real world is necessary. In this paper, we propose a new scenario generation pipeline focused on generating scenarios in a specific area near an autonomous vehicle. In this method, a scenario map is generated to define the scenario simulation area. A convolutional neural network (CNN)-based scenario agent selector is introduced to evaluate whether the selected agents can generate a realistic scenario, and a collision event detector handles the collision message to trigger an accident event. The proposed event-centric action dispatcher in the pipeline enables agents near events to perform related actions when the events occur near the autonomous vehicle. The proposed scenario generation pipeline can generate scenarios containing pedestrians, animals, and vehicles, and, advantageously, no user intervention is required during the simulation. In addition, a virtual environment for autonomous driving is also implemented to test the proposed scenario generation pipeline. The results show that the CNN-based scenario agent selector chose agents that provided realistic scenarios with 92.67% accuracy, and the event-centric action dispatcher generated a visually realistic scenario by letting the agents surrounding the event generate related actions.
The Belgian health examination survey: objectives, design and methods
Authors: Nguyen Diem , Hautekiet Pauline , Berete Finaba , Braekman Elise , Charafeddine Rana , Demarest Stefaan , Drieskens Sabine , Gisle Lydia , Hermans Lize , Tafforeau Jean , Van der Heyden Johan 
Published: June 2020

AbstractBackgroundIn 2018 the first Belgian Health Examination Survey (BELHES) took place. The target group included all Belgian residents aged 18 years and older. The BELHES was organized as a second stage of the sixth Belgian Health Interview Survey (BHIS). This paper describes the study design, recruitment method and the methodological choices that were made in the BELHES.MethodsAfter a pilot period during the first quarter of the BHIS fieldwork, eligible BHIS participants were invited to participate in the BELHES until a predefined number (n = 1100) was reached. To obtain the required sample size, 4918 eligible BHIS participants had to be contacted. Data were collected at the participant’s home by trained nurses. The data collection included: 1) a short set of questions through a face-to-face interview, 2) a clinical examination consisting of the measurement of height, weight, waist circumference, blood pressure and for people aged 50 years and older handgrip strength and 3) a collection of blood and urine samples. The BELHES followed as much as possible the guidelines provided in the framework of the European Health Examination Survey (EHES) initiative. Finally 1184 individuals participated in the BELHES, resulting in a participation rate of 24.1%. Results for all the core BELHES measurements were obtained for more than 90% of the participants.ConclusionIt is feasible to organize a health examination survey as a second stage of the BHIS. The first successfully organized BELHES provides useful information to support Belgian health decision-makers and health professionals. As the BELHES followed EHES recommendations to a large extent, the results can be compared with those from similar surveys in other EU (European Union) member states.