bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA-210 downregulates TET2 and contributes to inflammatory response in neonatal hypoxic-ischemic brain injury
Authors: Ma Qingyi , Dasgupta Chiranjib , Shen Guofang , Li Yong , Zhang Lubo 
Published: January 2021

Abstract
Background
Neonatal hypoxic-ischemic (HI) brain injury is a leading cause of acute mortality and chronic disability in newborns. Our previous studies demonstrated that HI insult significantly increased microRNA-210 (miR-210) in the brain of rat pups and inhibition of brain endogenous miR-210 by its inhibitor (LNA) provided neuroprotective effect in HI-induced brain injury. However, the molecular mechanisms underpinning this neuroprotection remain unclear.

Methods
We made a neonatal HI brain injury model in mouse pups of postnatal day 7 to uncover the mechanism of miR-210 in targeting the ten eleven translocation (TET) methylcytosine dioxygenase 2 that is a transcriptional suppressor of pro-inflammatory cytokine genes in the neonatal brain. TET2 silencing RNA was used to evaluate the role of TET2 in the neonatal HI-induced pro-inflammatory response and brain injury. MiR-210 mimic and inhibitor (LNA) were delivered into the brain of mouse pups to study the regulation of miR-210 on the expression of TET2. Luciferase reporter gene assay was performed to validate the direct binding of miR-210 to the 3′ untranslated region of the TET2 transcript. Furthermore, BV2 mouse microglia cell line was employed to confirm the role of miR-210-TET2 axis in regulating pro-inflammatory response in microglia. Post-assays included chromatin immunoprecipitation (ChIP) assay, co-immunoprecipitation, RT-PCR, brain infarct assay, and neurobehavioral test. Student’s t test or one-way ANOVA was used for statistical analysis.

Results
HI insult significantly upregulated miR-210, downregulated TET2 protein abundance, and increased NF-κB subunit p65 acetylation level and its DNA binding capacity to the interleukin 1 beta (IL-1β) promoter in the brain of mouse pups. Inhibition of miR-210 rescued TET2 protein level from HI insult and miR-210 mimic decreased TET2 protein level in the brain of mouse pups, suggesting that TET2 is a functional target of miR-210. The co-immunoprecipitation was performed to reveal the role of TET2 in HI-induced inflammatory response in the neonatal brain. The result showed that TET2 interacted with NF-κB subunit p65 and histone deacetylase 3 (HDAC3), a co-repressor of gene transcription. Furthermore, TET2 knockdown increased transcriptional activity of acetyl-p65 on IL-1β gene in the neonatal brain and enhanced HI-induced upregulation of acetyl-p65 level and pro-inflammatory cytokine expression. Of importance, TET2 knockdown exacerbated brain infarct size and neurological deficits and counteracted the neuroprotective effect of miR-210 inhibition. Finally, the in vitro results demonstrated that the miR-210-TET2 axis regulated pro-inflammatory response in BV2 mouse microglia cell line.

Conclusions
The miR-210-TET2 axis regulates pro-inflammatory cytokine expression in microglia, contributing to neonatal HI brain injury.
Measuring body condition of lizards: a comparison between non-invasive dual-energy X-ray absorptiometry, chemical fat extraction and calculated indices
Authors: Sion Guy , Watson Maggie J. , Bouskila Amos 
Published: January 2021

Abstract
Background
Condition indices (CIs) are used in ecological studies as a way of measuring an individual animal’s health and fitness. Noninvasive CIs are estimations of a relative score of fat content or rely on a ratio of body mass compared to some measure of size, usually a linear dimension such as tarsus or snout-vent length. CIs are generally validated invasively by lethal fat extraction as in a seasonal sample of individuals in a population. Many alternatives to lethal fat extraction are costly or time consuming. As an alternative, dual-energy X-ray absorptiometry (DXA) allows for non-destructive analysis of body composition and enables multiple measurements during an animal’s life time. DXA has never been used for ecological studies in a small, free-ranging lizard before, therefore we calibrated this method against a chemical extraction of fat from a sample of 6 geckos (Israeli fan toed gecko Ptyodactylus guttatus) ranging in body mass between 4.2–11.5 g. We then used this calibrated DXA measurements to determine the best linear measurement calculated CI for this species.

Results
We found that fat mass measured with DXA was significantly correlated with the mass of chemically extracted fat for specimens more than 4.8 g (N = 5, R2 = 0.995, P < 0.001). Fat percentage regressed with body mass significantly predicted the DXA fat percentage (N = 29, R2adj. = 0.862, p < 0.001). Live wet mass was significantly correlated with predicted fat mass (N = 30, R2 = 0.984, P < 0.001) for specimens more than 4.8 g. Among the five calculated non-invasive CIs that we tested, the best was mass/SVL.

Conclusions
We recommend that in situations where DXA cannot be used, that the most accurate of the body condition estimators for this species is mass/SVL (snout-vent length) for both sexes.
Conditional knock out of transcription factor CTCF in excitatory neurons induces cognitive deficiency
Authors: Choi Dong Il , Kim Myeongwon , Kim Somi , Yu Nam-Kyung , Kwak Chuljung , Seo Hyunhyo , Lee Kyungmin , Kaang Bong-Kiun 
Published: January 2021

AbstractCCCTC-binding factor (CTCF) is a transcription factor that is involved in organizing chromatin structure. A reduction of CTCF expression is known to develop distinct clinical features. Furthermore, conditional knock out (cKO) study revealed reactive gliosis of astrocytes and microglia followed by age-dependent cell death in the excitatory neurons of CTCF cKO mice. To assess the cognitive ability in CTCF cKO mice of over 20 weeks of age, we examined pairwise discrimination (PD), PD reversal learning (PDr), and different paired-associate learning (dPAL) tasks using a touch screen apparatus. We found cognitive impairment in dPAL touch screen tests, suggesting that prolonged Ctcf gene deficiency results in cognitive deficits.
Preclinical models of pancreatic ductal adenocarcinoma: challenges and opportunities in the era of precision medicine
Authors: Yu Yiqi , Yang Gang , Huang Hua , Fu Ziyao , Cao Zhe , Zheng Lianfang , You Lei , Zhang Taiping 
Published: January 2021

AbstractPancreatic ductal adenocarcinoma (PDAC) is an extremely lethal malignancy, with an average 5-year survival rate of 9% (Siegel RL, Miller KD, Jemal A. Ca Cancer J Clin. 2019;69(1):7-34). The steady increase in mortality rate indicates limited efficacy of the conventional regimen. The heterogeneity of PDAC calls for personalized treatment in clinical practice, which requires the construction of a preclinical system for generating patient-derived models. Currently, the lack of high-quality preclinical models results in ineffective translation of novel targeted therapeutics. This review summarizes applications of commonly used models, discusses major difficulties in PDAC model construction and provides recommendations for integrating workflows for precision medicine.
Circular RNA circLMO7 acts as a microRNA-30a-3p sponge to promote gastric cancer progression via the WNT2/β-catenin pathway
Authors: Cao Jiacheng , Zhang Xing , Xu Penghui , Wang Haixiao , Wang Sen , Zhang Lu , Li Zheng , Xie Li , Sun Guangli , Xia Yiwen , Lv Jialun , Yang Jing , Xu Zekuan 
Published: January 2021

Abstract
Background
Gastric cancer (GC) is one of the most common malignant tumors worldwide. Currently, the overall survival rate of GC is still unsatisfactory despite progress in diagnosis and treatment. Therefore, studying the molecular mechanisms involved in GC is vital for diagnosis and treatment. CircRNAs, a type of noncoding RNA, have been proven to act as miRNA sponges that can widely regulate various cancers. By this mechanism, circRNA can regulate tumors at the genetic level by releasing miRNA from inhibiting its target genes. The WNT2/β-Catenin regulatory pathway is one of the canonical signaling pathways in tumors. It can not only promote the development of tumors but also provide energy for tumor growth through cell metabolism (such as glutamine metabolism).

Methods
Through RNA sequencing, we found that hsa_circ_0008259 (circLMO7) was highly expressed in GC tissues. After verifying the circular characteristics of circLMO7, we determined the downstream miRNA (miR-30a-3p) of circLMO7 by RNA pull-down and luciferase reporter assays. We verified the effect of circLMO7 and miR-30a-3p on GC cells through a series of functional experiments, including colony formation, 5-ethynyl-2′-deoxyuridine and Transwell assays. Through Western blot and immunofluorescence analyses, we found that WNT2 was the downstream target gene of miR-30a-3p and further confirmed that the circLMO7-miR-30a-3p-WNT2 axis could promote the development of GC. In addition, measurement of related metabolites confirmed that this axis could also provide energy for the growth of GC cells through glutamine metabolism. We found that circLMO7 could promote the growth and metastasis of GC in vivo by the establishment of nude mouse models. Finally, we also demonstrated that HNRNPL could bind to the flanking introns of the circLMO7 exons to promote circLMO7 cyclization.

Results
CircLMO7 acted as a miR-30a-3p sponge affecting the WNT2/β-Catenin pathway to promote the proliferation, migration and invasion of GC cells. Moreover, animal results also showed that circLMO7 could promote GC growth and metastasis in vivo. CircLMO7 could also affect the glutamine metabolism of GC cells through the WNT2/β-Catenin pathway to promote its malignant biological function. In addition, we proved that HNRNPL could promote the self-cyclization of circLMO7.

Conclusions
CircLMO7 promotes the development of GC by releasing the inhibitory effect of miR-30a-3p on its target gene WNT2.
Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity
Authors: Planterose Jiménez Benjamin , Liu Fan , Caliebe Amke , Montiel González Diego , Bell Jordana T. , Kayser Manfred , Vidaki Athina 
Published: January 2021

AbstractBackgroundAlthough the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring post-twinning during embryonic development and early life. However, to what extent such stochastic mechanisms can systematically provide a stable source of inter-individual epigenetic variation remains uncertain until now.ResultsWe enriched for inter-individual stochastic variation by using an equivalence testing-based statistical approach on whole blood methylation microarray data from healthy adolescent monozygotic twins. As a result, we identified 333 CpGs displaying similarly large methylation variation between monozygotic co-twins and unrelated individuals. Although their methylation variation surpasses measurement error and is stable in a short timescale, susceptibility to aging is apparent in the long term. Additionally, 46% of these CpGs were replicated in adipose tissue. The identified sites are significantly enriched at the clustered protocadherin loci, known for stochastic methylation in developing neurons. We also confirmed an enrichment in monozygotic twin DNA methylation discordance at these loci in whole genome bisulfite sequencing data from blood and adipose tissue.ConclusionsWe have isolated a component of stochastic methylation variation, distinct from genetic influence, measurement error, and epigenetic drift. Biomarkers enriched in this component may serve in the future as the basis for universal epigenetic fingerprinting, relevant for instance in the discrimination of monozygotic twin individuals in forensic applications, currently impossible with standard DNA profiling.
Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape
Authors: Guan Jiantao , Xu Yaoguang , Yu Yang , Fu Jun , Ren Fei , Guo Jiying , Zhao Jianbo , Jiang Quan , Wei Jianhua , Xie Hua 
Published: January 2021

AbstractBackgroundStructural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.ResultsHere, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of thePpOFP2gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes thatPpOFP2is causal for flat-fruit shape.ConclusionsThus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.
Enzymatic degradation of maize shoots: monitoring of chemical and physical changes reveals different saccharification behaviors
Authors: Barron Cécile , Devaux Marie-Françoise , Foucat Loïc , Falourd Xavier , Looten Rachelle , Joseph-Aime Maud , Durand Sylvie , Bonnin Estelle , Lapierre Catherine , Saulnier Luc , Rouau Xavier , Guillon Fabienne 
Published: January 2021

AbstractBackgroundThe recalcitrance of lignocellulosics to enzymatic saccharification has been related to many factors, including the tissue and molecular heterogeneity of the plant particles. The role of tissue heterogeneity generally assessed from plant sections is not easy to study on a large scale. In the present work, dry fractionation of ground maize shoot was performed to obtain particle fractions enriched in a specific tissue. The degradation profiles of the fractions were compared considering physical changes in addition to chemical conversion.ResultsCoarse, medium and fine fractions were produced using a dry process followed by an electrostatic separation. The physical and chemical characteristics of the fractions varied, suggesting enrichment in tissue from leaves, pith or rind. The fractions were subjected to enzymatic hydrolysis in a torus reactor designed for real-time monitoring of the number and size of the particles. Saccharification efficiency was monitored by analyzing the sugar release at different times. The lowest and highest saccharification yields were measured in the coarse and fine fractions, respectively, and these yields paralleled the reduction in the size and number of particles. The behavior of the positively- and negatively-charged particles of medium-size fractions was contrasted. Although the amount of sugar release was similar, the changes in particle size and number differed during enzymatic degradation. The reduction in the number of particles proceeded faster than that of particle size, suggesting that degradable particles were degraded to the point of disappearance with no significant erosion or fragmentation. Considering all fractions, the saccharification yield was positively correlated with the amount of water associated with [5–15 nm] pore size range at 67% moisture content while the reduction in the number of particles was inversely correlated with the amount of lignin.ConclusionReal-time monitoring of sugar release and changes in the number and size of the particles clearly evidenced different degradation patterns for fractions of maize shoot that could be related to tissue heterogeneity in the plant. The biorefinery process could benefit from the addition of a sorting stage to optimise the flow of biomass materials and take better advantage of the heterogeneity of the biomass.
A new high-performance liquid chromatographic method for the quality control of bioconverted Mori Folium extracts with appropriate marker compounds related to antidiabetes
Authors: Kim Jin Hyeok , Kim Tae Jung , Kim Hyun June , Cho Chong Woon , Kim Seok Jin , Cho Hyun So , Kim Kyung Tae , Kang Jong Seong 
Published: January 2021

AbstractA HPLC method was developed to assess the enhanced bioactivity of bioconverted Mori Folium (MF) extract and to apply a quality-control system. Liquid-liquid extraction was applied to observe changes in chemical composition through enzymatic bioconversion. The ethyl acetate layer was used for quality control of the anti-diabetic functional MF product. A high-performance liquid chromatography method was developed to analyze five marker compounds (syringaldehyde, trans-caffeic acid, morin 3-O-β-D-glucopyranoside, astragalin, and moracin M 3′-O-β-glucopyranoside) within 60 min. Optimized sample preparation was sonication for 44 min and a water-to-material ratio of 102.5 mL/g by response surface methodology. Comparing MF water extract, trans-caffeic acid and syringaldehyde contents were increased 1.89 times and 2.70 times at Viscozyme-bioconverted material by applying the developed method. This HPLC method can be used to control the quality of bioconverted MF based on suitable bioactive markers and also applied to develop anti-diabetic functional foods containing Mori Folium.
Proctalgia secondary to rectal arteriovenous malformation and inferior mesenteric vein stenosis in a patient post liver transplant
Authors: Healy GM , Gondal F , Rutledge N , Houlihan DD , McCann JW 
Published: January 2021

Abstract
Background
Chronic proctalgia can have a major impact upon quality of life. There are many potential aetiologies however, in some patients no cause can be identified.

Case presentation
We present a patient post liver transplant with intractable proctalgia, despite multidisciplinary management including opioids, nerve blocks and surgical intervention. An underlying rectal arteriovenous malformation (AVM) was subsequently identified and successfully treated with embolotherapy. The onset of symptoms coincided with the development of inferior mesenteric vein stenosis, likely leading to engorgement of the malformation due to impaired venous outflow. Neovascularisation secondary to the liver transplant procedure may also have contributed to growth of the lesion.

Conclusion
This is a rare presentation of rectal AVM. These lesions can be treated with minimally invasive embolisation/sclerotherapy and should be considered in cases of unexplained proctalgia.
A fungus-eat-fungus world: Digitopodium, with particular reference to mycoparasites of the coffee leaf rust, Hemileia vastatrix
Authors: Colmán Adans A. , Evans Harry C. , Salcedo-Sarmiento Sara S. , Braun Uwe , Belachew-Bekele Kifle , Barreto Robert W. 
Published: January 2021

AbstractDigitopodium hemileiae was described originally in 1930 as Cladosporium hemileiae; growing as a mycoparasite of the coffee leaf rust (CLR), Hemileia vastatrix, in a sample of diseased leaves of Coffea canephora collected in the Democratic Republic of Congo. No cultures from this material exist. More recently, the type material was re-examined and, based on morphological features, considered to be incorrectly placed in Cladosporium. The new genus Digitopodium was erected to accommodate this species. Interest in fungal antagonists of H. vastarix, as potential biocontrol agents of CLR, led to comprehensive surveys for mycoparasites, both in the African centre of origin of the rust, as well as in its South American exotic range. Among the rust specimens from Ethiopia, one was found to be colonized by a fungus congeneric with, and similar to, D. hemileiae. Pure cultures obtained from the Ethiopian material enabled a molecular study and for its phylogenetic position to be elucidated, based on DNA sequence data from the ITS and LSU regions. Molecular data showed that two members of the recently erected genus Hyalocladosporiella (Herpotrichiellaceae: Chaetothyriales) are congeneric with Digitopodium from Ethiopia and morphologically similar to both D. hemileiae and the two Ethiopian isolates. These isolates were found to be morphologically and genetically identical to H. tectonae, described previously from Brazil. Thus, species of Hyalocladosporiella are re-allocated to Digitopodium here; including D. tectonae, and a novel species, D. canescens, recently found in Brazil growing as a mycoparasite of Puccinia thaliae. The potential use of D. hemileiae and D. tectonae for classical biological control of CLR is discussed.
Square-well potential in quaternionic quantum mechanics
Authors: Sergio Giardino 
Published: January 2021

Abstract
The one-dimensional infinite square well is the simplest solution of quantum mechanics, and consequently one of the most important. In this paper, we provide this solution using the real Hilbert space approach to quaternionic quantum mechanics (

). We further provide the one-dimensional finite as well and a method to generate quaternionic solutions from non-degenerate complex solutions.
Computed tomography features of cor triatriatum: an institutional review
Authors: Goel Archita , Viswamitra Sanjaya , Reddy Bhavana Nagabhushana , Gaduputi Jahnavi 
Published: January 2021

Objectives:
Cor Triatriatum is a rare anomaly that can either involves the left atrium (Cor Triatriatum Sinister-CTS) or the right atrium (Cor Triatriatum Dexter- CTD). Preoperative identification of this anomaly is important in determining patient treatment course. The objective of this paper is to understand imaging findings, classification and to familiarise the reader with other associated congenital cardiac anomalies that influence patient management.

Methods:
From the hospital electronic health records (EHR) database, we identified 10 patients of Cor Triatriatum out of 974 patients who underwent cardiac CT between 15 July 2014 and 20 March 2020 for congenital heart disease. Medical records and imaging findings were reviewed retrospectively.

Results:
Out of 10 patients, nine patients had CTS (90%) and only one patient had CTD (10%). Five out of nine patients (55.5%) had CTS type II and four (44.4%) had CTS type III. The mean of the membrane orifices in CTS type III was 18.5 mm and was 5.78 mm in CTS type II. Pulmonary veins were dilated in all patients of CTS type II (62.5%), two patient of CTS type III (25%) and in only patient with CTD (12.5%). Ostium secundum atrial septal defect was the most common (66%) associated cardiac anomaly, followed by ventricular septal defect (44%).

Conclusions:
CT allows excellent pre-operative evaluation of Cor Triatriatum and associated cardiac anomalies.

Advances in knowledge:
CT is excellent in making a diagnosis and classifying Cor Triatriatum and for identification of cardiac anomalies and complications associated with it.