bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRF2 maintains the stemness of colonic stem cells by limiting physiological stress from interferon
Authors: Minamide Kana , Sato Taku , Nakanishi Yusuke , Ohno Hiroshi , Kato Tamotsu , Asano Jumpei , Ohteki Toshiaki 
Published: September 2020

AbstractThe physiological stresses that diminish tissue stem-cell characteristics remain largely unknown. We previously reported that type I interferon (IFN), which is essential for host antiviral responses, is a physiological stressor for hematopoietic stem cells (HSCs) and small intestinal stem cells (ISCs) and that interferon regulatory factor-2 (IRF2), which attenuates IFN signaling, maintains their stemness. Here, using a dextran sodium sulfate (DSS)-induced colitis model, we explore the role of IRF2 in maintaining colonic epithelial stem cells (CoSCs). In mice with a conditional Irf2 deletion in the intestinal epithelium (hereafter Irf2ΔIEC mice), both the number and the organoid-forming potential of CoSCs were markedly reduced. Consistent with this finding, the ability of Irf2ΔIEC mice to regenerate colon epithelium after inducing colitis was severely impaired, independently of microbial dysbiosis. Mechanistically, CoSCs differentiated prematurely into transit-amplifying (TA) cells in Irf2ΔIEC mice, which might explain their low CoSC counts. A similar phenotype was induced in wild-type mice by repeated injections of low doses of poly(I:C), which induces type I IFN. Collectively, we demonstrated that chronic IFN signaling physiologically stresses CoSCs. This study provides new insight into the development of colitis and molecular mechanisms that maintain functional CoSCs throughout life.
Transcriptional analysis of cleft palate in TGFβ3 mutant mice
Authors: Liu J. , Chanumolu S. K. , White K. M. , Albahrani M. , Otu H. H. , Nawshad A. 
Published: September 2020

AbstractCleft palate (CP) is one of the most common craniofacial birth defects, impacting about 1 in 800 births in the USA. Tgf-β3 plays a critical role in regulating murine palate development, andTgf-β3null mutants develop cleft palate with 100% penetrance. In this study, we compared global palatal transcriptomes of wild type (WT) andTgf-β3−/− homozygous (HM) mouse embryos at the crucial palatogenesis stages of E14.5, and E16.5, using RNA-seq data. We found 1,809 and 2,127 differentially expressed genes at E16.5 vs. E14.5 in the WT and HM groups, respectively (adjustedp < 0.05; |fold change|> 2.0). We focused on the genes that were uniquely up/downregulated in WT or HM at E16.5 vs. E14.5 to identify genes associated with CP. Systems biology analysis relating to cell behaviors and function of WT and HM specific genes identified functional non-Smad pathways and preference of apoptosis to epithelial-mesenchymal transition. We identified 24 HM specific and 11 WT specific genes that are CP-related and/or involved in Tgf-β3 signaling. We validated the expression of 29 of the 35 genes using qRT-PCR and the trend of mRNA expression is similar to that of RNA-seq data . Our results enrich our understanding of genes associated with CP that are directly or indirectly regulated via TGF-β.
Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits
Authors: Leontidou Kleopatra , Genitsaris Savvas , Papadopoulou Anastasia , Kamou Nathalie , Bosmali Irene , Matsi Theodora , Madesis Panagiotis , Vokou Despoina , Karamanoli Katerina , Mellidou Ifigeneia 
Published: September 2020

AbstractPlant growth promoting rhizobacteria (PGPR) are able to provide cross-protection against multiple stress factors and facilitate growth of their plant symbionts in many ways. The aim of this study was to isolate and characterize rhizobacterial strains under natural conditions, associated with naturally occurring representatives of wild plant species and a local tomato cultivar, growing in differently stressed Mediterranean ecosystems. A total of 85 morphologically different rhizospheric strains were isolated; twenty-five exhibited multiple in vitro PGP-associated traits, including phosphate solubilization, indole-3-acetic acid production, and 1-aminocyclopropane-1-carboxylate deaminase activity. Whole genome analysis was applied to eight selected strains for their PGP potential and assigned seven strains to Gammaproteobacteria, and one to Bacteroidetes. The genomes harboured numerous genes involved in plant growth promotion and stress regulation. They also support the notion that the presence of gene clusters with potential PGP functions is affirmative but not necessary for a strain to promote plant growth under abiotic stress conditions. The selected strains were further tested for their ability to stimulate growth under stress. This initial screening led to the identification of some strains as potential PGPR for increasing crop production in a sustainable manner.
Caffeine as a promotor of sexual development in sterile Queensland fruit fly males
Authors: Adnan Saleh Mohammad , Farhana Iffat , Park Soo Jean , Rempoulakis Polychronis , Taylor Phillip W. 
Published: September 2020

AbstractSterile insect technique (SIT) is an environmentally benign pest management technique that involves releasing millions of sterile insects to suppress reproduction of pest populations. Many fruit flies, including Queensland fruit fly (Bactrocera tryoni Froggatt, ‘Q-fly’), have long adult maturation periods such that pre-maturation mortality can greatly reduce abundance of sexually active sterile males and impede SIT efficacy. Q-fly is the most difficult and costly challenge to market access for Australia’s horticulture industries, and has been targeted for intensive use of SIT program. We here demonstrate potential of pre-release caffeine supplements as a novel means to accelerate sexual maturation in male Q-fly. In mating trials, analytical caffeine was very effective at accelerating sexual maturation, while no positive effects of caffeine-containing instant coffee or guarana supplements were detected. In parallel, development of testes and ejaculatory apodemes was accelerated in males provided analytical caffeine but not instant coffee or guarana. High doses of guarana and instant coffee reduced longevity while even the highest doses of analytical caffeine did not affect longevity. Pre-release caffeine supplements promote sexual maturation in Q-flies, and similar benefits are expected in other fruit flies having long adult maturation periods.
The potential of gypsum speleothems for paleoclimatology: application to the Iberian Roman Humid Period
Authors: Gázquez Fernando , Bauska Thomas K. , Comas-Bru Laia , Ghaleb Bassam , Calaforra José-María , Hodell David A. 
Published: September 2020

AbstractCarbonate cave deposits (speleothems) have been used widely for paleoclimate reconstructions; however, few studies have examined the utility of other speleothem-forming minerals for this purpose. Here we demonstrate for the first time that stable isotopes (δ17O, δ18O and δD) of structurally-bound gypsum (CaSO4·2H2O) hydration water (GHW) can be used to infer paleoclimate. Specifically, we used a 63 cm-long gypsum stalactite from Sima Blanca Cave to reconstruct the climate history of SE Spain from ~ 800 BCE to ~ 800 CE. The gypsum stalactite indicates wet conditions in the cave and humid climate from ~ 200 BCE to 100 CE, at the time of the Roman Empire apogee in Hispania. From ~ 100 CE to ~ 600 CE, evaporation in the cave increased in response to regional aridification that peaked at ~ 500–600 CE, roughly coinciding with the transition between the Iberian Roman Humid Period and the Migration Period. Our record agrees with most Mediterranean and Iberian paleoclimate archives, demonstrating that stable isotopes of GHW in subaerial gypsum speleothems are a useful tool for paleoclimate reconstructions.
Behavioral effects of SGK1 knockout in VTA and dopamine neurons
Authors: Doyle Marie A. , Stark Ali R. , Fejes-Tóth Geza , Náray-Fejes-Tóth Aniko , Mazei-Robison Michelle S. 
Published: September 2020

AbstractDrugs of abuse cause significant neuroadaptations within the ventral tegmental area (VTA), with alterations in gene expression tied to changes in reward behavior. Serum- and glucocorticoid-inducible kinase 1 (SGK1) transcription, catalytic activity, and phosphorylation are upregulated in the VTA by chronic cocaine or morphine treatment, positioning SGK1 as a critical mediator of reward behavior. Using transgenic mouse models, we investigated the effect of SGK1 knockout in the VTA and in dopamine (DA) neurons to evaluate the necessity of protein expression for natural and drug reward behaviors. SGK1 knockdown in the VTA did not impact reward behaviors. Given VTA cellular heterogeneity, we also investigated a DA neuron-specific SGK1 knockout (KO). DA SGK1 KO significantly decreased body weight of adult mice as well as increased general locomotor activity; however, reward behaviors were similarly unaltered. Given that SGK1 mutants virally overexpressed in the VTA are capable of altering drug-associated behavior, our current results suggest that changes in SGK1 protein signaling may be distinct from expression. This work yields novel information on the impact of SGK1 deletion, critical for understanding the role of SGK1 signaling in the central nervous system and evaluating SGK1 as a potential therapeutic target for treatment of substance use disorders.
Parallel assessment of albuminuria and plasma sTNFR1 in people with type 2 diabetes and advanced chronic kidney disease provides accurate prognostication of the risks of renal decline and death
Authors: Martin William P. , Tuohy Colm , Doody Alison , Jackson Sabrina , Canavan Ronan J. , Slattery David , Twomey Patrick J. , McKenna Malachi J. , le Roux Carel W. , Docherty Neil G. 
Published: September 2020

AbstractIdentification of people with diabetes and chronic kidney disease at high-risk of early mortality is a priority to guide intensification of therapy. We aimed to investigate the complementary prognostic value of baseline urine albumin-to-creatinine ratio (uACR) and plasma soluble tumour necrosis factor receptor-1 (sTNFR1) with respect to early mortality and renal functional decline in a population with type 2 diabetes and advanced chronic kidney disease. We measured plasma sTNFR1 in people with type 2 diabetes (HbA1c ≥ 48 mmol/mol) at 2 hospital sites in Dublin between October 15th, 2014 and July 17th, 2015. In a subgroup of patients with advanced chronic kidney disease at baseline (estimated glomerular filtration rate (eGFR) ≤ 60 mL/min/BSA) (n = 118), we collected clinical and longitudinal laboratory data to investigate relationships between sTNFR1 and renal and mortality endpoints by multivariable linear mixed-effects models and Cox proportional hazards regression models. The cohort was 64% male and 97% Caucasian. Mean age was 74 years, with a median type 2 diabetes duration of 16 years. Mean CKD-EPI eGFR was 42 mL/min/BSA and median [IQR] uACR was 3 [11] mg/mmol. Twenty-three (39%) people in quartiles 3 and 4 for plasma sTNFR1 died over 4-year follow-up. After adjustment for clinical variables, annual CKD-EPI eGFR decreased by − 0.56 mL/min/BSA/year for each logarithm unit increase in baseline uACR, corresponding to an annual loss of renal function of 3% per year. Furthermore, elevated uACR, but not sTNFR1, increased the risk of ≥ 40% decline in CKD-EPI eGFR (HR 1.5, p = 0.001) and doubling of serum creatinine (HR 2.0, p < 0.001). Plasma sTNFR1 did not predict a more negative trajectory in eGFR slope. However, for those people in quartiles 3 and 4 for plasma sTNFR1, an increased risk of incident mortality was detected (HR 4.9, p = 0.02). No such association was detected for uACR. In this elderly cohort of patients with type 2 diabetes and chronic kidney disease, sTNFR1 predicted short-to-medium term mortality risk but not risk of progressive renal functional decline. In contrast, parallel assessment of uACR predicted renal functional decline but not mortality, highlighting the complementary prognostic information provided by both parameters.
Tyrosine kinase inhibitor neratinib attenuates liver fibrosis by targeting activated hepatic stellate cells
Authors: Park Yong Joo , An Hyoung-Tae , Park Jong-Sung , Park Ogyi , Duh Alexander J. , Kim Kwangmeyung , Chung Kyu Hyuck , Lee Kang Choon , Oh Yumin , Lee Seulki 
Published: September 2020

AbstractLiver fibrosis, a common outcome of chronic liver disease characterized by excessive accumulation of extracellular matrix (ECM), is a leading cause of mortality worldwide. The tyrosine kinase inhibitor neratinib is a human epidermal growth factor receptor 2 (HER2) inhibitor approved by the FDA for HER2-positive breast cancer treatment; however, it has not yet been evaluated for liver fibrosis treatment. We elucidated the anti-fibrotic effects of neratinib in hepatic stellate cells (HSCs) and in vivo models of CCl4-induced liver fibrosis. HSC activation is a key step in liver fibrogenesis and has a crucial role in collagen deposition, as it is primarily responsible for excessive ECM production. The effect of neratinib on HSC was evaluated in transforming growth factor (TGF-β)-incubated LX-2 cells and culture-activated primary human HSCs. In vivo study results indicated that neratinib inhibited the inflammatory response, HSC differentiation, and collagen accumulation induced by CCl4. Moreover, the anti-fibrotic effects of neratinib were not associated with the HER2 signaling pathways. Neratinib inhibited FGF2 expression in activated HSCs and serum FGF2 level in the model, suggesting that neratinib possessed therapeutic potency against liver fibrosis and the potential for application against other fibrotic diseases.
Differentiation of Cyanthillium cinereum, a smoking cessation herb, from its adulterant Emilia sonchifolia using macroscopic and microscopic examination, HPTLC profiles and DNA barcodes
Authors: Thongkhao Kannika , Pongkittiphan Veerachai , Phadungcharoen Thatree , Tungphatthong Chayapol , Urumarudappa Santhosh Kumar J. , Pengsuparp Thitima , Sutanthavibul Narueporn , Wiwatcharakornkul Worakorn , Kengtong Surapong , Sukrong Suchada 
Published: September 2020

AbstractCyanthillium cinereum (L.) H.Rob. is one of the most popular herbal smoking cessation aids currently used in Thailand, and its adulteration with Emilia sonchifolia (L.) DC. is often found in the herbal market. Therefore, the quality of the raw material must be considered. This work aimed to integrate macro- and microscopic, chemical and genetic authentication strategies to differentiate C. cinereum raw material from its adulterant. Different morphological features between C. cinereum and E. sonchifolia were simply recognized at the leaf base. For microscopic characteristics, trichome and pappus features were different between the two plants. HPTLC profiles showed a distinct band that could be used to unambiguously differentiate C. cinereum from E. sonchifolia. Four triterpenoid compounds, β-amyrin, taraxasterol, lupeol, and betulin, were identified from the distinct HPTLC band of C. cinereum. The use of core DNA barcode regions; rbcL, matK, ITS and psbA-trnH provided species-level resolution to differentiate the two plants. Taken together, the integration of macroscopic and microscopic characterization, phytochemical analysis by HPTLC and DNA barcoding distinguished C. cinereum from E. sonchifolia. The signatures of C. cinereum obtained here can help manufacturers to increase the quality control of C. cinereum raw material in commercialized smoking cessation products.
Characterization of capacitive electromyography biomedical sensor insulated with porous medical bandages
Authors: Ng Charn Loong , Reaz Mamun Bin Ibne , Crespo Maria Liz , Cicuttin Andres , Chowdhury Muhammad Enamul Hoque 
Published: September 2020

AbstractA capacitive electromyography (cEMG) biomedical sensor measures the EMG signal from human body through capacitive coupling methodology. It has the flexibility to be insulated by different types of materials. Each type of insulator will yield a unique skin–electrode capacitance which determine the performance of a cEMG biomedical sensor. Most of the insulator being explored are solid and non-breathable which cause perspiration in a long-term EMG measurement process. This research aims to explore the porous medical bandages such as micropore, gauze, and crepe bandage to be used as an insulator of a cEMG biomedical sensor. These materials are breathable and hypoallergenic. Their unique properties and characteristics have been reviewed respectively. A 50 Hz digital notch filter was developed and implemented in the EMG measurement system design to further enhance the performance of these porous medical bandage insulated cEMG biomedical sensors. A series of experimental verifications such as noise floor characterization, EMG signals measurement, and performance correlation were done on all these sensors. The micropore insulated cEMG biomedical sensor yielded the lowest noise floor amplitude of 2.44 mV and achieved the highest correlation coefficient result in comparison with the EMG signals captured by the conventional wet contact electrode.
Analysis of tear film spatial instability for pediatric myopia under treatment
Authors: Cho Wan-Hua , Fang Po-Chiung , Yu Hun-Ju , Lin Pei-Wen , Huang Hsiu-Mei , Kuo Ming-Tse 
Published: September 2020

AbstractIn Taiwan, the prevalence of myopia in children between 6 and 18 years old is over 80%, and high myopia accounts for over 20%, which turned out to be in the leading place worldwide. Orthokeratology and low-dose atropine are proven treatments to reduce myopia progression, though the potential corneal disturbances remain an issue in young populations. The alteration of the tear film is widely discussed but there is no consensus to date, so we aim to investigate the tear film spatial instability in children with myopia control using atropine or orthokeratology. Thirty-eight treatment-naïve participants and 126 myopic children under treatments were enrolled. The ocular surface homeostasis, spatial distribution of tear break-up, and high-order aberrations (HOAs) of the corneal surface were assessed. We found out that myopic children treated with either atropine or orthokeratology showed ocular surface homeostasis similar to that in treatment-naïve children. Nevertheless, children treated with orthokeratology presented higher HOAs (p < 0.00001) and a tendency of the first tear break-up zone at the inner half of the cornea (p = 0.04). This unique spatial instability of the tear film associated with myopia treatment might provide a more focused way of monitoring the pediatric tear film instability.
ODiNPred: comprehensive prediction of protein order and disorder
Authors: Dass Rupashree , Mulder Frans A. A. , Nielsen Jakob Toudahl 
Published: September 2020

AbstractStructural disorder is widespread in eukaryotic proteins and is vital for their function in diverse biological processes. It is therefore highly desirable to be able to predict the degree of order and disorder from amino acid sequence. It is, however, notoriously difficult to predict the degree of local flexibility within structured domains and the presence and nuances of localized rigidity within intrinsically disordered regions. To identify such instances, we used the CheZOD database, which encompasses accurate, balanced, and continuous-valued quantification of protein (dis)order at amino acid resolution based on NMR chemical shifts. To computationally forecast the spectrum of protein disorder in the most comprehensive manner possible, we constructed the sequence-based protein order/disorder predictor ODiNPred, trained on an expanded version of CheZOD. ODiNPred applies a deep neural network comprising 157 unique sequence features to 1325 protein sequences together with the experimental NMR chemical shift data. Cross-validation for 117 protein sequences shows that ODiNPred better predicts the continuous variation in order along the protein sequence, suggesting that contemporary predictors are limited by the quality of training data. The inclusion of evolutionary features reduces the performance gap between ODiNPred and its peers, but analysis shows that it retains greater accuracy for the more challenging prediction of intermediate disorder.
Effects of finish rolling temperature and yield ratio on variations in yield strength after pipe-forming of API-X65 line-pipe steels
Authors: Kim Dae Woong , Kim Wan-Keun , Bae Jin-ho , Choi Won-Doo , Sohn Seok Su , Lee Sunghak 
Published: September 2020

AbstractFlattened plates often show the lower or higher yield strength than initial leveled plates because tensile and compressive strains are repeatedly experienced at outer and inner walls during the pipe-forming and flattening, but reasons for the yield-strength variation after the pipe-forming are not sufficiently verified yet. In this study, ten line-pipe steels were fabricated by controlling alloying elements and finish rolling temperatures (FRTs), and the yield strength of pipe-flattened steel plates was predicted by using cyclic simulation tests, based on competing contributions of Bauschinger effect (BE) and strain hardening (SH) effect quantified from yield drop (YD) and yield rise (YR) parameters, respectively. High-FRT-treated steels (H steels) showed the lower BE and the higher SH than low-FRT-treated steels (L steels), thereby resulting in the smaller yield-strength reduction. This lower BE in the H steels was caused by the lower total boundary density, while the higher SH was caused by the higher fraction of granular bainite. According to the SH analyses between the YR parameters obtained from cyclic simulation tests and the yield ratios obtained from ordinary tensile tests, the decrease in yield-strength reduction with decreasing yield ratio was not attributed to the increase in ordinary tensile SH but to the increase in YR parameter.
Temperature sensitivity differs between heart and red muscle mitochondria in mahi-mahi (Coryphaena hippurus)
Authors: Lau Gigi Y. , Cox Georgina K. , Stieglitz John D. , Benetti Daniel D. , Grosell Martin 
Published: September 2020

AbstractMaintaining energy balance over a wide range of temperatures is critical for an active pelagic fish species such as the mahi-mahi (Coryphaena hippurus), which can experience rapid changes in temperature during vertical migrations. Due to the profound effect of temperature on mitochondrial function, this study was designed to investigate the effects of temperature on mitochondrial respiration in permeabilized heart and red skeletal muscle (RM) fibres isolated from mahi-mahi. As RM is thought to be more anatomically isolated from rapid ambient temperature changes compared to the myocardium, it was hypothesized that heart mitochondria would be more tolerant of temperature changes through a greater ability to match respiratory capacity to an increase in temperature and to maintain coupling, when compared to RM mitochondria. Results show that heart fibres were more temperature sensitive and increased respiration rate with temperature increases to a greater degree than RM. Respiratory coupling ratios at the three assay temperatures (20, 26, and 30 °C), revealed that heart mitochondria were less coupled at a lower temperature (26 °C) compared to RM mitochondria (30 °C). In response to an in vitro acute temperature challenge, both tissues showed irreversible effects, where both heart and RM increased uncoupling whether the assay temperature was acutely changed from 20 to 30 °C or 30 to 20 °C. The findings from this study indicate that mahi-mahi heart mitochondria were more temperature sensitive compared to those from RM.