bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcription factor Foxd3 induces spinal cord ischemia-reperfusion injury by potentiating microRNA-214-dependent inhibition of Kcnk2
Authors: Li Ran , Zhao Kunchi , Ruan Qing , Meng Chunyang , Yin Fei 
Published: January 2020

AbstractSpinal cord injury after surgical repair of the thoracic or thoracoabdominal aorta is a devastating complication that is associated with pathological changes, including inflammation, edema, and nerve cell damage. Recently, microRNA (miRNA)-modulated control of spinal cord injury has been actively investigated. This study aims to clarify the regulatory effect of miR-214-mediated inhibition of Kcnk2 following spinal cord ischemia-reperfusion injury (SCII) and the possible underlying mechanisms. SCII was induced in rats by occluding the aortic arch followed by reperfusion. Gain-of-function and loss-of-function experiments were conducted to explore the modulatory effects of Foxd3, miR-214 and Kcnk2 on PC12 cells under hypoxia/reoxygenation (H/R) conditions. MiR-214 and Kcnk2 were poorly expressed, while Foxd3 was highly expressed in the rat spinal cord tissues and H/R-treated PC12 cells. Kcnk2 overexpression enhanced the viability and inhibited the apoptosis of the H/R-treated PC12 cells. Notably, Foxd3 activated miR-214, and miR-214 targeted Kcnk2. In addition, upregulation of Kcnk2 or knockdown of Foxd3 promoted the cell viability and reduced the apoptosis of the H/R-treated PC12 cells. Overall, our study identified a novel mechanism of Foxd3/miR-214/Kcnk2 involving SCII, suggesting that either Foxd3 or miR-214 may be a novel target for the treatment of SCII.
Development of a protein-based system for transient epigenetic repression of immune checkpoint molecule and enhancement of antitumour activity of natural killer cells
Authors: Teratake Yoichi , Takashina Tomoki , Iijima Kenta , Sakuma Tetsushi , Yamamoto Takashi , Ishizaka Yukihito 
Published: January 2020

Abstract
Background
Immune checkpoint blockade (ICB) therapy improved the prognosis of cancer patients, but general administration of ICBs occasionally induces side effects that include immune-related adverse events and tumour hyper-progression. Here, we established a protein-based system, by which endogenous expression of IC molecule in natural killer (NK) cells was transiently repressed on enhancement of their antitumour activity.

Methods
A protein-based genome modulator (GM) system is composed of a transcription activator-like effector (TALE), DNA methyltransferase and a newly identified potent cell-penetrating peptide with nuclear-trafficking property named NTP. TALE was designed to target the promoter region of the programmed cell death-1 (PD-1) gene. After culturing human NK cells in the presence of NTP-GM protein, we examined endogenous PD-1 expression and antitumour activity of the treated cells.

Results
NTP-GM protein efficiently downregulated PD-1 expression in NK cells with increased CpG DNA methylation in the promoter region. The antitumour activity of the treated NK cells was enhanced, and repeated intraperitoneal administrations of the treated NK cells attenuated tumour growth of programmed death-ligand 1-positive tumour cells in vivo.

Conclusions
Because the incorporated NTP-GM protein was quickly degraded and negligible in the administered NK cells, the NTP-GM system could be an alternative option of an ICB without side effects.
Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1
Authors: Minderjahn Julia , Schmidt Andreas , Fuchs Andreas , Schill Rudolf , Raithel Johanna , Babina Magda , Schmidl Christian , Gebhard Claudia , Schmidhofer Sandra , Mendes Karina , Ratermann Anna , Glatz Dagmar , Nützel Margit , Edinger Matthias , Hoffmann Petra , Spang Rainer , Längst Gernot , Imhof Axel , Rehli Michael 
Published: January 2020

AbstractEstablishing gene regulatory networks during differentiation or reprogramming requires master or pioneer transcription factors (TFs) such as PU.1, a prototype master TF of hematopoietic lineage differentiation. To systematically determine molecular features that control its activity, here we analyze DNA-binding in vitro and genome-wide in vivo across different cell types with native or ectopic PU.1 expression. Although PU.1, in contrast to classical pioneer factors, is unable to access nucleosomal target sites in vitro, ectopic induction of PU.1 leads to the extensive remodeling of chromatin and redistribution of partner TFs. De novo chromatin access, stable binding, and redistribution of partner TFs both require PU.1’s N-terminal acidic activation domain and its ability to recruit SWI/SNF remodeling complexes, suggesting that the latter may collect and distribute co-associated TFs in conjunction with the non-classical pioneer TF PU.1.
Insulated conjugated bimetallopolymer with sigmoidal response by dual self-controlling system as a biomimetic material
Authors: Masai Hiroshi , Yokoyama Takuya , Miyagishi Hiromichi V. , Liu Maning , Tachibana Yasuhiro , Fujihara Tetsuaki , Tsuji Yasushi , Terao Jun 
Published: January 2020

AbstractBiological systems are known to spontaneously adjust the functioning of neurotransmitters, ion channels, and the immune system, being promoted or regulated through allosteric effects or inhibitors, affording non-linear responses to external stimuli. Here we report that an insulated conjugated bimetallopolymer, in which Ru(II) and Pt(II) complexes are mutually connected with insulated conjugations, exhibits phosphorescence in response to CO gas. The net profile corresponds to a sigmoidal response with a dual self-controlling system, where drastic changes were exhibited at two threshold concentrations. The first threshold for activation of the system is triggered by the depolymerization of the non-radiative conjugated polymer to luminescent monomers, while the second one for regulation is triggered by the switch in the rate-determining step of the Ru complex. Such a molecular design with cooperative multiple transition metals would provide routes for the development of higher-ordered artificial molecular systems bearing bioinspired responses with autonomous modulation.
Atomically dispersed Pt–N4 sites as efficient and selective electrocatalysts for the chlorine evolution reaction
Authors: Lim Taejung , Jung Gwan Yeong , Kim Jae Hyung , Park Sung O , Park Jaehyun , Kim Yong-Tae , Kang Seok Ju , Jeong Hu Young , Kwak Sang Kyu , Joo Sang Hoon 
Published: January 2020

AbstractChlorine evolution reaction (CER) is a critical anode reaction in chlor-alkali electrolysis. Although precious metal-based mixed metal oxides (MMOs) have been widely used as CER catalysts, they suffer from the concomitant generation of oxygen during the CER. Herein, we demonstrate that atomically dispersed Pt−N4sites doped on a carbon nanotube (Pt1/CNT) can catalyse the CER with excellent activity and selectivity. The Pt1/CNT catalyst shows superior CER activity to a Pt nanoparticle-based catalyst and a commercial Ru/Ir-based MMO catalyst. Notably, Pt1/CNT exhibits near 100% CER selectivity even in acidic media, with low Cl−concentrations (0.1 M), as well as in neutral media, whereas the MMO catalyst shows substantially lower CER selectivity. In situ electrochemical X-ray absorption spectroscopy reveals the direct adsorption of Cl−on Pt−N4sites during the CER. Density functional theory calculations suggest the PtN4C12site as the most plausible active site structure for the CER.
Glycosyl ortho-(1-phenylvinyl)benzoates versatile glycosyl donors for highly efficient synthesis of both O-glycosides and nucleosides
Authors: Li Penghua , He Haiqing , Zhang Yunqin , Yang Rui , Xu Lili , Chen Zixi , Huang Yingying , Bao Limei , Xiao Guozhi 
Published: January 2020

AbstractBoth of O-glycosides and nucleosides are important biomolecules with crucial rules in numerous biological processes. Chemical synthesis is an efficient and scalable method to produce well-defined and pure carbohydrate-containing molecules for deciphering their functions and developing therapeutic agents. However, the development of glycosylation methods for efficient synthesis of both O-glycosides and nucleosides is one of the long-standing challenges in chemistry. Here, we report a highly efficient and versatile glycosylation method for efficient synthesis of both O-glycosides and nucleosides, which uses glycosyl ortho-(1-phenylvinyl)benzoates as donors. This glycosylation protocol enjoys the various features, including readily prepared and stable donors, cheap and readily available promoters, mild reaction conditions, good to excellent yields, and broad substrate scopes. In particular, the applications of the current glycosylation protocol are demonstrated by one-pot synthesis of several bioactive oligosaccharides and highly efficient synthesis of nucleosides drugs capecitabine, galocitabine and doxifluridine.
Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau
Authors: Zhou Chaowei , Xiao Shijun , Liu Yanchao , Mou Zhenbo , Zhou Jianshe , Pan Yingzi , Zhang Chi , Wang Jiu , Deng Xingxing , Zou Ming , Liu Haiping 
Published: January 2020

AbstractThe Schizothoracinae fishes, endemic species in the Tibetan Plateau, are considered as ideal models for highland adaptation and speciation investigation. Despite several transcriptome studies for highland fishes have been reported before, the transcriptome information of Schizothoracinae is still lacking. To obtain comprehensive transcriptome data for Schizothoracinae, the transcriptome of a total of 183 samples from 14 representative Schizothoracinae species, were sequenced and de novo assembled. As a result, about 1,363 Gb transcriptome clean data was obtained. After the assembly, we obtain 76,602–154,860 unigenes for each species with sequence N50 length of 1,564–2,143 bp. More than half of the unigenes were functionally annotated by public databases. The Schizothoracinae fishes in this work exhibited diversified ecological distributions, phenotype characters and feeding habits; therefore, the comprehensive transcriptome data of those species provided valuable information for the environmental adaptation and speciation of Schizothoracinae in the Tibetan Plateau.
Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis
Authors: Hackl Thomas , Martin Roman , Barenhoff Karina , Duponchel Sarah , Heider Dominik , Fischer Matthias G. 
Published: January 2020

AbstractThe heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99–282 × coverage per strain) and 5.09 Gb of PacBio RSII data (13–45 × coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34–36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857–8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a bicosoecid fill an important gap in sequenced stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists.
High-throughput identification of protein functional similarities using a gene-expression-based siRNA screen
Authors: Neilsen Beth K. , Kelly David L. , Chakraborty Binita , Kim Hyun Seok , White Michael A. , Lewis Robert E. , Fisher Kurt W. 
Published: January 2020

AbstractA gene expression-based siRNA screen was used to evaluate functional similarity between genetic perturbations to identify functionally similar proteins. A siRNA library (siGenome library, Dharmacon) consisting of multiple siRNAs per gene that have been pooled in to one well per gene was arrayed in a 384-well format and used to individually target 14,335 proteins for depletion in HCT116 colon cancer cells. For each protein depletion, the gene expression of eight genes was quantified using the multiplexed Affymetrix Quantigene 2.0 assay in technical triplicate. As a proof of concept, six genes (BNIP3, NDRG1, ALDOC, LOXL2, ACSL5, BNIP3L) whose expression pattern reliably reflect the disruption of the molecular scaffold KSR1 were measured upon each protein depletion. The remaining two genes (PPIB and HPRT) are housekeeping genes used for normalization. The gene expression signatures from this screen can be used to estimate the functional similarity between any two proteins and successfully identified functional relationships for specific proteins such as KSR1 and more generalized processes, such as autophagy.
Reference values for resting and post exercise hemodynamic parameters in a 6–18 year old population
Authors: Havasi Katalin , Maróti Zoltán , Jakab Andrea , Raskó István , Kalmár Tibor , Bereczki Csaba 
Published: January 2020

AbstractThis database is the first large dataset of haemodynamic changes of normal-weight pupils during a field exercise test. Here, we present a dataset for anthropometric and hemodynamic parameters measured both during relaxation and after exercise containing 1,173,342 data segments from 65,345 acquisition points of 10,894 normal weight subjects, covering an age range of 6–18 years collected in a course of 12 years. Data acquisition was carried out under standardised measuring conditions and specifications. Hemodynamic parameters were measured in the normal-weight population with a new and simple Fit-Test which could facilitate new projects worldwide to study and compare cardiovascular fitness.
Modelling regional futures at decadal scale: application to the Kimberley region
Authors: Boschetti Fabio , Lozano-Montes Hector , Stelfox Brad 
Published: January 2020

AbstractWe address the question of how to provide meaningful scientific information to support environmental decision making at the regional scale and at the temporal scale of several decades in a network of marine parks in the Kimberley region of Western Australia. Where environmental sustainability is affected by slow-dynamics climate change processes and one-off investments in large infrastructure which can affect a region for decades to come, both strategic and reactive planning is necessary and prediction becomes as urgent as standard adaptive management. At the interface between future studies, socio-economic modelling and environmental modelling, we define 18 scenarios of economic development and climate change impacts and five management strategies. We explore these potential futures using coupled models of terrestrial and marine ecosystem dynamics. We obtain a projection of the Kimberley marine system to the year 2050, conditional on the chosen scenarios and management strategies. Our results suggest that climate change, not economic development, is the largest factor affecting the future of marine ecosystems in the Kimberley region, with site-attached species such as reef fish at greatest risk. These same species also benefit most from more stringent management strategies, especially expansion of sanctuary zones and Marine Protected Areas.
Kidney transplant monitoring by urinary flow cytometry: Biomarker combination of T cells, renal tubular epithelial cells, and podocalyxin-positive cells detects rejection
Authors: Goerlich Nina , Brand Hannah Antonia , Langhans Valerie , Tesch Sebastian , Schachtner Thomas , Koch Benjamin , Paliege Alexander , Schneider Wolfgang , Grützkau Andreas , Reinke Petra , Enghard Philipp 
Published: January 2020

AbstractCreatinine and proteinuria are used to monitor kidney transplant patients. However, renal biopsies are needed to diagnose renal graft rejection. Here, we assessed whether the quantification of different urinary cells would allow non-invasive detection of rejection. Urinary cell numbers of CD4+ and CD8+ T cells, monocytes/macrophages, tubular epithelial cells (TEC), and podocalyxin(PDX)-positive cells were determined using flow cytometry and were compared to biopsy results. Urine samples of 63 renal transplant patients were analyzed. Patients with transplant rejection had higher amounts of urinary T cells than controls; however, patients who showed worsening graft function without rejection had similar numbers of T cells. T cells correlated with histological findings (interstitial inflammation p = 0.0005, r = 0.70; tubulitis p = 0.006, r = 0.58). Combining the amount of urinary T cells and TEC, or T cells and PDX+ cells, yielded a significant segregation of patients with rejection from patients without rejection (all p < 0.01, area under the curve 0.89–0.91). Urinary cell populations analyzed by flow cytometry have the potential to introduce new monitoring methods for kidney transplant patients. The combination of urinary T cells, TEC, and PDX-positive cells may allow non-invasive detection of transplant rejection.
Initial report of γ-aminobutyric acidergic locomotion regulatory system and its 3-mercaptopropionic acid-sensitivity in metamorphic juvenile of sea urchin, Hemicentrotus pulcherrimus
Authors: Katow Hideki , Yoshida Hiromi , Kiyomoto Masato 
Published: January 2020

AbstractThe γ-aminobutyric acid (GABA) signal transmission system (GSTS) contributes to larval swimming through the regulation of ciliary beating. However, whether this system also contributes to the primary podia (PP)-generated motility of juveniles remained unclear. The present study aimed to elucidate the involvement of the GSTS in the motility of metamorphic juveniles (juveniles) (1) by immunohistochemically elucidating the location of molecular constituents of the PP, and (2) by inhibiting the activity of GΑΒΑ decarboxylase (GAD) with 3-mercaptopropionic acid (3-MPA). During metamorphosis, the echinus rudiment protrudes its PP out of the body surface in 8-arm plutei. The PP expresses immunopositive signal (-IS) of GAD, GABA, GABAA receptor and tropomyosin, and is constituted with the GABA-IS negative distal tip and the GABA/GAD-IS gaiter region. The latter radiates distal projections to the disc that contains a GAD-IS cellular network. The juvenile body cavity houses a GABA/βIII-tubulin-IS Penta-radial ring (PrR) that extends branches into each PP and several bridges to the GAD/GABA-IS Penta-radial plate (PrP) on the oral side but does not reach to the gaiter region. 3-MPA reversibly inhibits the juvenile motility and GABA-IS expression in the PrR/PrP complex. This indicates that the complex is the major contributor to the GABAergic motility in juveniles.
Prevalence and predictors of proton pump inhibitor partial response in gastroesophageal reflux disease in systemic sclerosis: a prospective study
Authors: Foocharoen Chingching , Chunlertrith Kitti , Mairiang Pisaln , Mahakkanukrauh Ajanee , Suwannaroj Siraphop , Namvijit Suwassa , Wantha Orathai , Nanagara Ratanavadee 
Published: January 2020

AbstractProton pump inhibitor (PPI) twice daily dosing is a standard therapy for gastroesophageal reflux disease (GERD) in systemic sclerosis (SSc) but there is no data on its response rate or the predictors of PPI-partial response GERD. Aims were to determine the prevalence of PPI-partial response GERD in SSc and to define its predictors. A prospective study was conducted in SSc patients with GERD. The patients were treated with omeprazole 20 mg bid for 4 weeks. The severity of symptom-grading by visual analogue scale (VAS) and frequency of symptoms by frequency scale for symptoms of GERD (FSSG) were assessed at baseline and 4 weeks after treatment. PPI-partial response GERD was defined as less than 50% improvement in the VAS for severity of symptom as well as acid reflux score by FSSG after treatment. According to the sample size calculation, 243 SSc-GERD patients were enrolled; of whom 166 (68.3%) had the diffuse cutaneous SSc. PPI-partial response GERD was found in 131 SSc patients (prevalence 53.9%; 95%CI 47.4–60.3). The multivariate analysis revealed that esophageal dysphagia was an only predictor the PPI-partial response GERD (OR 1.82; 95%CI 1.01–3.29) while neither SSc subset nor severity of skin tightness were significantly associated with PPI-partial response GERD. Half of the SSc patients were PPI-partial response GERD. Esophageal dysphagia was the only predictor of PPI-partial response GERD in SSc patients. Screening for dysphagia before starting GERD treatment is helpful for assessment the risk of PPI refractoriness GERD in SSc patients.
Pollination Mechanisms are Driving Orchid Distribution in Space
Authors: Štípková Zuzana , Tsiftsis Spyros , Kindlmann Pavel 
Published: January 2020

AbstractUnderstanding the abundance and distribution patterns of species at large spatial scales is one of the goals of biogeography and macroecology, as it helps researchers and authorities in designing conservation measures for endangered species. Orchids, one of the most endangered groups of plants, have a complicated system of pollination mechanisms. Their survival strongly depends on pollination success, which then determines their presence and distribution in space. Here we concentrate on how pollination mechanisms (presence/absence of nectar) are associated with orchid species density and mean niche breadth along an altitudinal gradient in six different phytogeographical regions in the Czech Republic. We found differences between these regions in terms of orchid species numbers and density. The trend (hump-shaped curve) in species density of nectarless and nectariferous orchids were very similar in all phytogeographical regions, peaking between 300–900 m. The trend strongly depends on habitat cover and pollinator availability. In general, the most specialist species of orchids were found from low to middle altitudes. The association of altitude with the richness of orchid flora is much stronger than that with the biogeography. Climate change is a factor that should not be neglected, as it may affect the presence/absence of many species in the future.
Implications of C1q/TNF-related protein superfamily in patients with coronary artery disease
Authors: Zhang Yanwei , Liu Caihong , Liu Jing , Guo Rui , Yan Zheyi , Liu Wenxia , Lau Wayne Bond , Jiao Xiangying , Cao Jimin , Xu Kun , Jia Yongping , Ma Xinliang , Wang Yajing 
Published: January 2020

AbstractThe C1q complement/TNF-related protein superfamily (CTRPs) displays differential effects on the regulation of metabolic homeostasis, governing cardiovascular function. However, whether and how they may serve as predictor/pro-diagnosis factors for assessing the risks of coronary artery disease (CAD) remains controversial. Therefore, we performed a clinical study to elaborate on the implication of CTRPs (CTRP1, CTRP5, CTRP7, and CTRP15) in CAD. CTRP1 were significantly increased, whereas CTRP7 and CTRP15 levels were decreased in CAD patients compared to the non-CAD group. Significant differences in CTRP1 levels were discovered between the single- and triple-vascular-vessel lesion groups. ROC analysis revealed that CTRP7 and CTRP15 may serve as CAD markers, while CTRP1 may serve as a marker for the single-vessel lesion of CAD. CTRP1 and CTRP5 can serve as markers for the triple-vessel lesion. CTRP1 may serve as an independent risk predictor for triple-vessel lesion, whereas CTRP15 alteration may serve for a single-vessel lesion of CAD. CTRP1 may serve as a novel superior biomarker for diagnosis of severity of vessel-lesion of CAD patients. CTRP7, CTRP15 may serve as more suitable biomarker for the diagnosis of CAD patients, whereas CTRP5 may serve as an independent predictor for CAD. These findings suggest CTRPs may be the superior predictive factors for the vascular lesion of CAD and represent novel therapeutic targets against CAD.