bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long noncoding RNA TRPM2-AS acts as a microRNA sponge of miR-612 to promote gastric cancer progression and radioresistance
Authors: Xiao Jian , Lin Linling , Luo Dakui , Shi Liang , Chen Wangwang , Fan Hao , Li Zengliang , Ma Xiang , Ni Peidong , Yang Li , Xu Zekuan 
Published: March 2020

AbstractLong noncoding RNAs (lncRNAs) are emerging as important regulators of tumorigenesis and are frequently dysregulated in cancers. Here, we identify a critical lncRNA TRPM2-AS which is aberrantly expressed in gastric cancer (GC) tissues by screening The Cancer Genome Atlas Program(TCGA) database of GC cohort, and its upregulation is clinically associated with advanced pathologic stages and poor prognosis in GC patients. Silencing TRPM2-AS inhibits the proliferation, metastasis and radioresistance of GC cell whereas ectopic expression of TRPM2-AS significantly improves the progression of GC cell in multiple experiments. Mechanistically, TRPM2-AS serves as a microRNA sponge or a competitive endogenous RNA (ceRNA) for tumor suppressive microRNA miR-612 and consequently modulates the derepression of IGF2BP1 and FOXM1. Moreover, induced upregulation of IGF2BP1 subsequently increases the expression of c-Myc and promotes GC cell progression. Meanwhile, TRPM2-AS promotes the radioreistance of GC cell through enhancing the expression of FOXM1 as well. Thus, our findings support a new regulatory axis between TRPM2-AS, miR-612, IGF2BP1, or FOXM1 which serve as crucial effectors in GC tumorigenesis and malignant development, suggesting a promising therapeutic and diagnostic direction for GC.
Dual metabolic reprogramming by ONC201/TIC10 and 2-Deoxyglucose induces energy depletion and synergistic anti-cancer activity in glioblastoma
Authors: Pruss Maximilian , Dwucet Annika , Tanriover Mine , Hlavac Michal , Kast Richard Eric , Debatin Klaus-Michael , Wirtz Christian Rainer , Halatsch Marc-Eric , Siegelin Markus David , Westhoff Mike-Andrew , Karpel-Massler Georg 
Published: March 2020

Abstract
Background
Dysregulation of the metabolome is a hallmark of primary brain malignancies. In this work we examined whether metabolic reprogramming through a multi-targeting approach causes enhanced anti-cancer activity in glioblastoma.

Methods
Preclinical testing of a combined treatment with ONC201/TIC10 and 2-Deoxyglucose was performed in established and primary-cultured glioblastoma cells. Extracellular flux analysis was used to determine real-time effects on OXPHOS and glycolysis. Respiratory chain complexes were analysed by western blotting. Biological effects on tumour formation were tested on the chorioallantoic membrane (CAM).

Results
ONC201/TIC10 impairs mitochondrial respiration accompanied by an increase of glycolysis. When combined with 2-Deoxyglucose, ONC201/TIC10 induces a state of energy depletion as outlined by a significant decrease in ATP levels and a hypo-phosphorylative state. As a result, synergistic anti-proliferative and anti-migratory effects were observed among a broad panel of different glioblastoma cells. In addition, this combinatorial approach significantly impaired tumour formation on the CAM.

Conclusion
Treatment with ONC201/TIC10 and 2-Deoxyglucose results in a dual metabolic reprogramming of glioblastoma cells resulting in a synergistic anti-neoplastic activity. Given, that both agents penetrate the blood–brain barrier and have been used in clinical trials with a good safety profile warrants further clinical evaluation of this therapeutic strategy.
Mutations in the coat complex II component SEC23B promote colorectal cancer metastasis
Authors: Yang Chunyuan , Chen Nan , Li Xiang , Lu Dan , Hou Zhiyuan , Li Yuhua , Jin Yan , Gu Jin , Yin Yuxin 
Published: March 2020

AbstractMetastasis is the leading cause of death for colorectal cancer (CRC). However, the protein transport process involved in CRC metastasis remains unclear. In this report, we use whole-exome sequencing and bioinformatics analysis to identify somatic mutations in CRC samples and found mutations of the protein transport gene Sec23 homolog B (SEC23B) in patients with metachronous liver metastasis. We show that deletion of SEC23B suppresses the membrane localization of adhesion proteins and augments cell mobility. SEC23B mutations either cause a premature stop (C649T) or impair its protein transport activity (C1467G and T488C + G791A + G2153A). Furthermore, SEC23B mutations inhibit the transport of epithelial cell adhesion molecule (EPCAM) and CD9 molecule, thereby attenuating cell adhesion and promoting invasiveness both in vitro and in vivo. Taken together, these data demonstrate the important impact of SEC23B mutations on metastasis, and we propose that SEC23B is a potential suppressor of CRC metastasis.
Reference values of body composition parameters and visceral adipose tissue (VAT) by DXA in adults aged 18–81 years—results from the LEAD cohort
Authors: Ofenheimer Alina , Breyer-Kohansal Robab , Hartl Sylvia , Burghuber Otto C. , Krach Florian , Schrott Andrea , Wouters Emiel F. M. , Franssen Frits M. E. , Breyer Marie-Kathrin 
Published: March 2020

Abstract
Background
Increasing attention has been drawn on the assessment of body composition phenotypes, since the distribution of soft tissue influences cardio-metabolic risk. Dual-energy X-ray absorptiometry (DXA) is a validated technique to assess body composition. European reference values from population-based cohorts are rare.

Aims
To provide age- and sex-related reference values of body composition parameters and visceral adipose tissue (VAT) mass, and for lean mass index (LMI) with regard to fat mass index (FMI) quantities and BMI categories.

Methods
GE-Lunar Prodigy DXA scans of 10.894 participants, aged 18–81 years, recruited from 2011 to 2019 by the Austrian LEAD study, a population-based cohort study, have been used to construct reference curves using the LMS method. Parameters assessed are FMI, LMI, appendicular LMI, fat mass ratios android/gynoid and trunk/limbs, and VAT.

Results
All lean mass and fat mass parameters indicating central fat accumulation were higher in men, whereas other fat mass indices were higher in women. LMI differed between each FMI subgroup (low vs. normal, low vs. high, normal vs. high), and BMI category in all ages and LMI increased with FMI and BMI classes. VAT mass was higher in men compared with women and increased across all age groups within both sexes.

Conclusion
The present study provides age- and sex-related reference values for European adults aged 18–81 years for body composition parameters and VAT mass for Lunar Prodigy DXA. In addition, this study reports LMI reference values with regard to fat mass quantities, showing a positive association with increasing FMI percentiles and BMI categories.
Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing
Authors: Hall David , Zhao Wei , Wennström Ulfstand , Andersson Gull Bengt , Wang Xiao-Ru 
Published: March 2020

AbstractEstimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestrisL.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.
Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade
Authors: Alvarez José M. , Schinke Anna-Lena , Brooks Matthew D. , Pasquino Angelo , Leonelli Lauriebeth , Varala Kranthi , Safi Alaeddine , Krouk Gabriel , Krapp Anne , Coruzzi Gloria M. 
Published: March 2020

AbstractDynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genome-wide can be applied to validate dynamic GRN models for any pathway or organism of interest.
Post-translational protein modifications in schizophrenia
Authors: Mueller Toni M. , Meador-Woodruff James H. 
Published: March 2020

AbstractResearch investigating the pathophysiology of schizophrenia has not yet precisely defined the molecular phenotype of this disorder. Many studies have investigated cellular dysfunction by examining expression levels of molecular targets in postmortem patient brain; however, inconsistencies between transcript and protein measures in schizophrenia are common in the field and represent a challenge to the identification of a unified model of schizophrenia pathogenesis. In humans, >4800 unique proteins are expressed, and the majority of these are modified by glycans and/or lipids. Estimates indicate ~70% of all eukaryotic proteins are modified by at least one type of glycosylation, while nearly 20% of all proteins are known to be lipid-modified. Protein post-translational modification (PTM) by glycosylation and lipidation rely on the spatiotemporal colocalization of enzyme, substrate, and glycan or lipid donor molecule and do not require an upstream “blueprint” or specialized processing machinery for synthesis. Glycan and lipid PTMs can thus facilitate cellular adaptation to environmental signals more rapidly than changes of gene or protein expression, and can significantly impact the localization, function, and interactions of modified substrates, though relatively few studies in schizophrenia have evaluated the PTM status of target proteins. A growing body of literature reports glycosylation and lipidation abnormalities in schizophrenia brain as well as in patient peripheral fluids. In this review, we explain the functional significance of key glycan and lipid PTMs and summarize current findings associated with abnormal glycosylation and lipidation in this illness.
Characterisation of serum progesterone and progesterone-induced blocking factor (PIBF) levels across trimesters in healthy pregnant women
Authors: Lim Mark Kit , Ku Chee Wai , Tan Thiam Chye , Lee Yin Hao Justin , Allen John Carson , Tan Nguan Soon 
Published: March 2020

AbstractProgesterone-induced blocking factor (PIBF), which plays an important role in maintaining healthy pregnancies, has shown great promise as a prognostic biomarker for threatened miscarriage. To better characterise the physiological trends of progesterone and PIBF, we analysed serum progesterone and PIBF concentrations in healthy non-pregnant and pregnant women across trimesters. We saw increasing concentrations of progesterone and PIBF in pregnant women with advancing trimesters. The serum progesterone and PIBF percentiles across gestational age in healthy pregnancies can be used as a guide for the formulation of reference ranges. We also demonstrated a significant positive correlation between progesterone and PIBF levels. This study demonstrates increasing progesterone and PIBF concentrations in later trimesters and underscores the importance of progesterone and PIBF in healthy pregnancies. Characterisation of progesterone and PIBF across gestational age in healthy pregnant women may help to prognosticate pregnancy viability and support further research into the importance of progesterone and PIBF in the maintenance of healthy pregnancies.
Nutrients, minerals, pigments, phytochemicals, and radical scavenging activity in Amaranthus blitum leafy vegetables
Authors: Sarker Umakanta , Oba Shinya 
Published: March 2020

AbstractA. blitum is good sources of abundant natural antioxidant phytopigments such as anthocyanin, betalain, betaxanthin, and betacyanin and antioxidant phytochemicals of interest in the food industry. The chances of utilizing amaranth pigments and phytochemicals had been evaluated for extracting colorful juice as drink purposes. Hence, the presence of nutrients, phytopigments, phytochemicals, and radical scavenging activity of selected A. blitum leafy vegetables were evaluated. Leaves of A. blitum have considerable fiber, moisture, protein, and carbohydrates. It has considerable magnesium, calcium, potassium (30.42, 24.74, 10.24 mg g−1), zinc, iron, copper, manganese, (878.98, 1153.83, 26.13, 207.50 µg g−1), phytopigments such as chlorophyll a, chlorophyll ab, chlorophyll b, (63.69, 90.60, 29.32 mg 100 g−1), betalain, betaxanthin, betacyanin (112.01, 58.38, 53.63 µg 100 g−1), vitamin C (1848.15 µg g−1), total carotenoids, β-carotene (1675.38, 1281.66 µg g−1), TPC, TFC (253.45 GAE and 162.97 RE µg g−1 DW), and TAC (29.46, 55.72 µg g−1 DW in Tolax equivalent DPPH and ABTS+ radical scavenging capacity) in A. blitum. The accessions DS3, DS6, DS8, and DS12 exhibited the highest TAC in Trolox equivalent DPPH and ABTS+ radical scavenging capacity, flavonoids, and considerable phytopigments. These accessions had excellent antioxidant profiles along with high yielding potentiality. Hence, A. blitum provides an excellent source of proximate, phenolics, minerals, flavonoids, vitamins, and phytopigments to address the nutritional and antioxidant deficiency in daily diet.
Identification and sequence analyses of the gliding machinery proteins from Mycoplasma mobile
Authors: Tulum Isil , Kimura Kenta , Miyata Makoto 
Published: March 2020

AbstractMycoplasma mobile, a fish pathogen, exhibits its own specialized gliding motility on host cells based on ATP hydrolysis. The special protein machinery enabling this motility is composed of surface and internal protein complexes. Four proteins, MMOBs 1630, 1660, 1670, and 4860 constitute the internal complex, including paralogs of F-type ATPase/synthase α and β subunits. In the present study, the cellular localisation for the candidate gliding machinery proteins, MMOBs 1620, 1640, 1650, and 5430 was investigated by using a total internal reflection fluorescence microscopy system after tagging these proteins with the enhanced yellow fluorescent protein (EYFP). The M. mobile strain expressing a fusion protein MMOB1620-EYFP exhibited reduced cell-binding activity and a strain expressing MMOB1640 fused with EYFP exhibited increased gliding speed, showing the involvement of these proteins in the gliding mechanism. Based on the genomic sequences, we analysed the sequence conservativity in the proteins of the internal and the surface complexes from four gliding mycoplasma species. The proteins in the internal complex were more conserved compared to the surface complex, suggesting that the surface complex undergoes modifications depending on the host. The analyses suggested that the internal gliding complex was highly conserved probably due to its role in the motility mechanism.
Drone Surveys Do Not Increase Colony-wide Flight Behaviour at Waterbird Nesting Sites, But Sensitivity Varies Among Species
Authors: Barr Jared R. , Green M. Clay , DeMaso Stephen J. , Hardy Thomas B. 
Published: March 2020

AbstractThe popularity of using unmanned aerial vehicles (UAVs) to survey colonial waterbirds has increased in the past decade, but disturbance associated with this bourgeoning technology requires further study. Disturbance was investigated by conducting aerial surveys with a consumer-grade quadcopter (DJI Phantom 3), while concurrently recording behavioural reactions on video. Surveys of mixed-species waterbird colonies (1-6 species per colony) were flown in horizontal transects at heights of 122, 91, 61, and 46 m, which is a typical range for collecting aerial imagery and producing high-resolution mosaicked orthophotos of nesting bird sites. An upper limit of 122 m was used due to local regulations prohibiting higher-altitude flights without federal authorization. Behavioural reactions were tallied every minute and a disturbance score was calculated for each sampling period. When compared to control periods, we found no evidence that colony-wide escape (i.e., flight) behaviour increased during drone flights, at any altitude flown. However, disturbance score increased significantly by 53% for surveys at 46 m. Some species were more sensitive to surveys than others. Laughing Gulls, in particular, exhibited a significant (125%) increase in escape behaviour for surveys at 91 m. Our results indicate when used in a capacity to gather high-resolution imagery for estimating breeding pairs, UAV surveys affected some species more than others, but severe reactions did not appear to increase for mixed-species colonies as a whole. Further study on safe operating thresholds is essential, especially at local and regional scales.
CVD-Grown Carbon Nanotube Branches on Black Silicon Stems for Ultrahigh Absorbance in Wide Wavelength Range
Authors: Phan Thanh Luan , Yu Woo Jong 
Published: March 2020

AbstractWe report a black silicon-carbon nanotube (bSi-CNT) hybrid structure for ultrahigh absorbance at wide spectral range of wavelength (300–1200 nm). CNTs are densely grown on entire bSi stems by chemical vapor deposition (CVD) through uniformly coating Fe catalyst. The bSi-CNT not only increases the surface roughness for enhancing the light suppression, but also allows the absorption of light in a wide wavelength range over the Si band gap (>1000 nm owing to 1.1 eV) due to the small band gap of CNT (0.6 eV). At short wavelength below Si band gap (<1000 nm), the absorbance of bSi-CNT shows average of 98.1%, while bSi shows 89.4%, which is because of high surface roughness of bSi-CNT that enhancing the light trapping. At long wavelength over Si band gap, the absorbance of bSi-CNT was maintained to 96.3% because of the absorption in CNT, while absorbance of bSi abruptly reduces with increase wavelength. Especially, the absorbance of bSi-CNT was showed 93.5% at 1200 nm, which is about 30~90% higher than previously reported bSi. Simple growth of CNTs on bSi can dramatically enhances the absorbance without using any antireflection coating layer. Thus, this study can be employed for realizing high efficiency photovoltaic, photocatalytic applications.
Hepatic stellate cell hypertrophy is associated with metabolic liver fibrosis
Authors: Hoffmann Céline , Djerir Nour El Houda , Danckaert Anne , Fernandes Julien , Roux Pascal , Charrueau Christine , Lachagès Anne-Marie , Charlotte Frédéric , Brocheriou Isabelle , Clément Karine , Aron-Wisnewsky Judith , Foufelle Fabienne , Ratziu Vlad , Hainque Bernard , Bonnefont-Rousselot Dominique , Bigey Pascal , Escriou Virginie 
Published: March 2020

AbstractHepatic fibrosis is a major consequence of chronic liver disease such as non-alcoholic steatohepatitis which is undergoing a dramatic evolution given the obesity progression worldwide, and has no treatment to date. Hepatic stellate cells (HSCs) play a key role in the fibrosis process, because in chronic liver damage, they transdifferentiate from a “quiescent” to an “activated” phenotype responsible for most the collagen deposition in liver tissue. Here, using a diet-induced liver fibrosis murine model (choline-deficient amino acid-defined, high fat diet), we characterized a specific population of HSCs organized as clusters presenting simultaneously hypertrophy of retinoid droplets, quiescent and activated HSC markers. We showed that hypertrophied HSCs co-localized with fibrosis areas in space and time. Importantly, we reported the existence of this phenotype and its association with collagen deposition in three other mouse fibrosis models, including CCl4-induced fibrosis model. Moreover, we have also shown its relevance in human liver fibrosis associated with different etiologies (obesity, non-alcoholic steatohepatitis, viral hepatitis C and alcoholism). In particular, we have demonstrated a significant positive correlation between the stage of liver fibrosis and HSC hypertrophy in a cohort of obese patients with hepatic fibrosis. These results lead us to conclude that hypertrophied HSCs are closely associated with hepatic fibrosis in a metabolic disease context and may represent a new marker of metabolic liver disease progression.
National Institutes of Health Stroke Scale (NIHSS) on admission predicts acute symptomatic seizure risk in ischemic stroke: a population-based study involving 135,117 cases
Authors: Zöllner Johann Philipp , Misselwitz Björn , Kaps Manfred , Stein Marco , Konczalla Jürgen , Roth Christian , Krakow Karsten , Steinmetz Helmuth , Rosenow Felix , Strzelczyk Adam 
Published: March 2020

AbstractThe National Institutes of Health Stroke Scale (NIHSS) score is the most frequently used score worldwide for assessing the clinical severity of a stroke. Prior research suggested an association between acute symptomatic seizures after stroke and poorer outcome. We determined the frequency of acute seizures after ischemic stroke in a large population-based registry in a central European region between 2004 and 2016 and identified risk factors for acute seizures in univariate and multivariate analyses. Additionally, we determined the influence of seizures on morbidity and mortality in a matched case–control design. Our analysis of 135,117 cases demonstrated a seizure frequency of 1.3%. Seizure risk was 0.6% with an NIHSS score at admission <3 points and increased up to 7.0% with >31 score points. Seizure risk was significantly higher in the presence of acute non-neurological infections (odds ratio: 3.4; 95% confidence interval: 2.8–4.1). A lower premorbid functional level also significantly increased seizure risk (OR: 1.7; 95%CI: 1.4–2.0). Mortality in patients with acute symptomatic seizures was almost doubled when compared to controls matched for age, gender, and stroke severity. Acute symptomatic seizures increase morbidity and mortality in ischemic stroke. Their odds increase with a higher NIHSS score at admission.