bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary clinical experience applying donor-derived cell-free DNA to discern rejection in pediatric liver transplant recipients
Authors: Zhao Dong , Zhou Tao , Luo Yi , Wu Cheng , Xu Dongwei , Zhong Chengpeng , Cong Wenming , Liu Qiang , Zhang Jianjun , Xia Qiang 
Published: January 2021

AbstractDonor-derived cell-free DNA (dd-cfDNA) has been of major interest recently as a non-invasive marker of graft injury, but has not yet been extensively tested in children. From May to September in 2019, a total of 76 pediatric patients receiving a liver graft were enrolled and there were 27 patients excluded. Ultimately plasma samples and matched liver specimens from 49 patients were successfully collected whenever rejection was suspected clinically. Dd-cfDNA were analyzed and then compared to biopsy. Of these, 11 (22.4%) patients were found to have rejection by biopsy. Dd-cfDNA levels were higher among patients with rejection compared to those with no rejection. In subgroup analysis, dd-cfDNA% among patients with rejection differed from those with EBV/CMV infection and DILI patients. Similarly, observations were available concerning dd-cfDNA (cp/mL). The AUC for dd-cfDNA% and dd-cfDNA (cp/mL) were 0.878, 0.841, respectively, both of which were higher than conventional LFTs. For rejection, dd-cfDNA% ≥ 28.7% yielded a sensitivity of 72.7%, specificity 94.7% and dd-cfDNA (cp/mL) ≥ 2076 cp/mL, yielded a sensitivity of 81.8%, specificity 81.9%. Of note, the dd-cfDNA distribution was significantly different between whole liver and LLS transplantation. In the setting of pediatric LTx, dd-cfDNA appears to be a sensitive biomarker indicating the presence of rejection.International Clinical Trails Registry Platform: ChiCTR1900022406.
Transcriptome-wide high-throughput mapping of protein–RNA occupancy profiles using POP-seq
Authors: Srivastava Mansi , Srivastava Rajneesh , Janga Sarath Chandra 
Published: January 2021

AbstractInteraction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
CRISPR-based transcriptional activation tool for silent genes in filamentous fungi
Authors: Mózsik László , Hoekzema Mirthe , de Kok Niels A. W. , Bovenberg Roel A. L. , Nygård Yvonne , Driessen Arnold J. M. 
Published: January 2021

AbstractFilamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.
Visual fixations rather than saccades dominate the developmental eye movement test
Authors: Tanke Nouk , Barsingerhorn Annemiek D. , Boonstra F. Nienke , Goossens Jeroen 
Published: January 2021

AbstractWhen children have visual and/or oculomotor deficits, early diagnosis is critical for rehabilitation. The developmental eye movement (DEM) test is a visual-verbal number naming test that aims to measure oculomotor dysfunction in children by comparing scores on a horizontal and vertical subtest. However, empirical comparison of oculomotor behavior during the two subtests is missing. Here, we measured eye movements of healthy children while they performed a digital version of the DEM. In addition, we measured visual processing speed using the Speed Acuity test. We found that parameters of saccade behavior, such as the number, amplitude, and direction of saccades, correlated with performance on the horizontal, but not the vertical subtest. However, the time spent on making saccades was very short compared to the time spent on number fixations and the total time needed for either subtest. Fixation durations correlated positively with performance on both subtests and co-varied tightly with visual processing speed. Accordingly, horizontal and vertical DEM scores showed a strong positive correlation with visual processing speed. We therefore conclude that the DEM is not suitable to measure saccade behavior, but can be a useful indicator of visual-verbal naming skills, visual processing speed, and other cognitive factors of clinical relevance.
Identification of VOCs in essential oils extracted using ultrasound- and microwave-assisted methods from sweet cherry flower
Authors: Zhang Huimin , Yan Hongguang , Li Quan , Lin Hui , Wen Xiaopeng 
Published: January 2021

AbstractThe floral fragrance of plants is an important indicator in their evaluation. The aroma of sweet cherry flowers is mainly derived from their essential oil. In this study, based on the results of a single-factor experiment, a Box–Behnken design was adopted for ultrasound- and microwave-assisted extraction of essential oil from sweet cherry flowers of the Brooks cultivar. With the objective of extracting the maximum essential oil yield (w/w), the optimal extraction process conditions were a liquid–solid ratio of 52 mL g−1, an extraction time of 27 min, and a microwave power of 435 W. The essential oil yield was 1.23%, which was close to the theoretical prediction. The volatile organic compounds (VOCs) of the sweet cherry flowers of four cultivars (Brooks, Black Pearl, Tieton and Summit) were identified via headspace solid phase microextraction (SPME) and gas chromatography–mass spectrometry (GC–MS). The results showed that a total of 155 VOCs were identified and classified in the essential oil from sweet cherry flowers of four cultivars, 65 of which were shared among the cultivars. The highest contents of VOCs were aldehydes, alcohols, ketones and esters. Ethanol, linalool, lilac alcohol, acetaldehyde, (E)-2-hexenal, benzaldehyde and dimethyl sulfide were the major volatiles, which were mainly responsible for the characteristic aroma of sweet cherry flowers. It was concluded that the VOCs of sweet cherry flowers were qualitatively similar; however, relative content differences were observed in the four cultivars. This study provides a theoretical basis for the metabolism and regulation of the VOCs of sweet cherry flowers.
In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology
Authors: Bibi Shaheen , Ullah Inayat , Zhu Bingdong , Adnan Muhammad , Liaqat Romana , Kong Wei-Bao , Niu Shiquan 
Published: January 2021

AbstractTuberculosis (TB) kills more individuals in the world than any other disease, and a threat made direr by the coverage of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Bacillus Calmette–Guérin (BCG) is the single TB vaccine licensed for use in human beings and effectively protects infants and children against severe military and meningeal TB. We applied advanced computational techniques to develop a universal TB vaccine. In the current study, we select the very conserved, experimentally confirmed Mtb antigens, including Rv2608, Rv2684, Rv3804c (Ag85A), and Rv0125 (Mtb32A) to design a novel multi-epitope subunit vaccine. By using the Immune Epitopes Database (IEDB), we predicted different B-cell and T-cell epitopes. An adjuvant (Griselimycin) was also added to vaccine construct to improve its immunogenicity. Bioinformatics tools were used to predict, refined, and validate the 3D structure and then docked with toll-like-receptor (TLR-3) using different servers. The constructed vaccine was used for further processing based on allergenicity, antigenicity, solubility, different physiochemical properties, and molecular docking scores. The in silico immune simulation results showed significant response for immune cells. For successful expression of the vaccine in E. coli, in-silico cloning and codon optimization were performed. This research also sets out a good signal for the design of a peptide-based tuberculosis vaccine. In conclusion, our findings show that the known multi-epitope vaccine may activate humoral and cellular immune responses and maybe a possible tuberculosis vaccine candidate. Therefore, more experimental validations should be exposed to it.
Quantitative evaluation and comparison of coronary artery characteristics by 3D coronary volume reconstruction
Authors: Kim Yongcheol , Bray Jonathan James Hyett , Waterhouse Benjamin , Gall Alexander , Connolly Georgia May , Sammut Eva , Bruno Vito Domenico , Tulloh Robert , Adlam David , Johnson Thomas W. 
Published: January 2021

AbstractNon-atherosclerotic abnormalities of vessel calibre, aneurysm and ectasia, are challenging to quantify and are often overlooked in qualitative reporting. Utilising a novel 3-dimensional (3D) quantitative coronary angiography (QCA) application, we have evaluated the characteristics of normal, diabetic and aneurysmal or ectatic coronary arteries. We selected 131 individuals under 50 years-of-age, who had undergone coronary angiography for suspected myocardial ischaemia between 1st January 2011 and 31st December 2015, at the Bristol Heart Institute, Bristol, UK. This included 42 patients with angiographically normal coronary arteries, 36 diabetic patients with unobstructed coronaries, and 53 patients with abnormal coronary dilatation (aneurysm and ectasia). A total of 1105 coronary segments were analysed using QAngio XA 3D (Research Edition, Medis medical imaging systems, Leiden, The Netherlands). The combined volume of the major coronary arteries was significantly different between each group (1240 ± 476 mm3 diabetic group, 1646 ± 391 mm3 normal group, and 2072 ± 687 mm3 abnormal group). Moreover, the combined coronary artery volumes correlated with patient body surface area (r = 0.483, p < 0.01). Inter-observer variability was assessed and intraclass correlation coefficient of the total coronary artery volume demonstrated a low variability of 3D QCA (r = 0.996, p < 0.001). Dedicated 3D QCA facilitates reproducible coronary artery volume estimation and allows discrimination of normal and diseased vessels.
Increased infiltration of regulatory T cells in hepatocellular carcinoma of patients with hepatitis B virus pre-S2 mutant
Authors: Teng Chiao-Fang , Li Tsai-Chung , Wang Ting , Liao Da-Ching , Wen Yi-Hsuan , Wu Tzu-Hua , Wang John , Wu Han-Chieh , Shyu Woei-Cherng , Su Ih-Jen , Jeng Long-Bin 
Published: January 2021

AbstractHepatocellular carcinoma (HCC) is a frequent and deadly human cancer worldwide that is intimately associated with chronic hepatitis B virus (HBV) infection. Pre-S2 mutant is a HBV oncoprotein that plays important roles in HCC development and is linked to poor prognosis in HCC patients. However, the profiles of tumor-infiltrating lymphocytes in HCC tissues of pre-S2 mutant-positive patients remain unknown. In this study, we performed fluorescent immunohistochemistry staining to detect the infiltration of ‘anti-tumor’ cytotoxic T lymphocytes (CTLs) and ‘pro-tumor’ regulatory T cells (Tregs) in pre-S2 mutant-positive and -negative HCC patients. We showed that pre-S2 mutant-positive patients had a significantly higher infiltration of CD4+CD25+ cells and forkhead box P3 (Foxp3)-expressing cells but similar CTLs and lower granzyme B-expressing cells in HCC tissues compared with pre-S2 mutant-negative patients. Moreover, the percentage of pre-S2 plus pre-S1 + pre-S2 deletion (pre-S2 mutant) was positively correlated with the density of CD4+CD25+ cells and Foxp3-expressing cells but negatively with granzyme B-expressing cells in HCC tissues. Considering that increased intratumoral Tregs have been shown to promote tumor immune evasion, our data may provide new insights into the pathogenesis of HBV pre-S2 mutant-induced HCC and suggest that therapeutics targeting Tregs may be a promising strategy for treating pre-S2 mutant-positive high-risk patient population.
Aberrant serum parathyroid hormone, calcium, and phosphorus as risk factors for peritonitis in peritoneal dialysis patients
Authors: Liao Chia-Te , Zheng Cai-Mei , Lin Yen-Chung , Wu Mei-Yi , Lin Yuh-Feng , Hsu Yung-Ho , Hsu Chih-Cheng , Wu Mai-Szu 
Published: January 2021

AbstractIdentifying modifiable risk factors of peritoneal dialysis (PD)-related peritonitis is of clinical importance in patient care. Mineral bone disease (MBD) has been associated with mortality and morbidity in end-stage kidney disease (ESKD) patients. However, its influence on PD related peritonitis due to altered host immunity remains elusive. This study investigated whether abnormal biomarkers of MBD are associated with the development of peritonitis in patients undergoing maintenance PD. We conducted a retrospective observational cohort study, analysing data derived from a nationwide dialysis registry database in Taiwan, from 2005 to 2012. A total of 5750 ESKD patients commencing PD therapy during this period were enrolled and followed up to 60 months or by the end of the study period. The patients were stratified based on their baseline serum parathyroid hormone (PTH) levels, calcium (Ca) levels or phosphorus (P) levels, respectively or in combinations. The primary outcome was the occurrence of first episode of peritonitis, and patient outcomes such as deaths, transfer to haemodialysis or receiving renal transplantation were censored. Peritonitis-free survival and the influence of PTH, Ca, P (individual or in combination) on the peritonitis occurrence were analysed. A total of 5750 PD patients was enrolled. Of them, 1611 patients experienced their first episode of peritonitis during the study period. Patients with low PTH, high Ca or low P levels, respectively or in combination, had the lowest peritonitis-free survival. After adjusting for age, sex and serum albumin levels, we found that the combinations of low PTH levels with either high Ca levels or low/normal P levels were significant risk factors of developing peritonitis. Abnormal mineral bone metabolism in maintenance PD patients with low serum PTH levels, in combination with either high Ca levels or low/normal P levels, could be novel risk factors of PD-related peritonitis.
Hyperpolarized 13C pyruvate magnetic resonance spectroscopy for in vivo metabolic phenotyping of rat HCC
Authors: Bliemsrieder Elisabeth , Kaissis Georgios , Grashei Martin , Topping Geoffrey , Altomonte Jennifer , Hundshammer Christian , Lohöfer Fabian , Heid Irina , Keim Dominik , Gebrekidan Selamawit , Trajkovic-Arsic Marija , Winkelkotte AM , Steiger Katja , Nawroth Roman , Siveke Jens , Schwaiger Markus , Makowski Marcus , Schilling Franz , Braren Rickmer 
Published: January 2021

AbstractThe in vivo assessment of tissue metabolism represents a novel strategy for the evaluation of oncologic disease. Hepatocellular carcinoma (HCC) is a high-prevalence, high-mortality tumor entity often discovered at a late stage. Recent evidence indicates that survival differences depend on metabolic alterations in tumor tissue, with particular focus on glucose metabolism and lactate production. Here, we present an in vivo imaging technique for metabolic tumor phenotyping in rat models of HCC. Endogenous HCC was induced in Wistar rats by oral diethyl-nitrosamine administration. Peak lactate-to-alanine signal ratios (L/A) were assessed with hyperpolarized magnetic resonance spectroscopic imaging (HPMRSI) after [1-13C]pyruvate injection. Cell lines were derived from a subset of primary tumors, re-implanted in nude rats, and assessed in vivo with dynamic hyperpolarized magnetic resonance spectroscopy (HPMRS) after [1-13C]pyruvate injection and kinetic modelling of pyruvate metabolism, taking into account systemic lactate production and recirculation. For ex vivo validation, enzyme activity and metabolite concentrations were spectroscopically quantified in cell and tumor tissue extracts. Mean peak L/A was higher in endogenous HCC compared to non-tumorous tissue. Dynamic HPMRS revealed higher pyruvate-to-lactate conversion rates (kpl) and lactate signal in subcutaneous tumors derived from high L/A tumor cells, consistent with ex vivo measurements of higher lactate dehydrogenase (LDH) levels in these cells. In conclusion, HPMRS and HPMRSI reveal distinct tumor phenotypes corresponding to differences in glycolytic metabolism in HCC tumor tissue.
Age affects procedural paired-associates learning in the grey mouse lemur (Microcebus murinus)
Authors: Schmidtke Daniel 
Published: January 2021

AbstractThe ability to associate memorized objects with their location in space gradually declines during normal aging and can drastically be affected by neurodegenerative diseases. This study investigates object-location paired-associates learning (PAL) in the grey mouse lemur (Microcebus murinus), a nonhuman primate model of brain aging. Touchscreen-based testing of 6 young adults (1–5 years) and 6 old adults (> 7 years) in the procedural rodent dPAL-task revealed significant age-related performance decline, evident in group differences in the percentage of correct decision during learning and the number of sessions needed to reach a predefined criterion. Response pattern analyses suggest decreased susceptibility to relative stimulus-position biases in young animals, facilitating PAL. Additional data from a subset of “overtrained” individuals (n = 7) and challenge sessions using a modified protocol (sPAL) further suggest that learning criteria routinely used in animal studies on PAL can underestimate the endpoint at which a stable performance is reached and that more conservative criteria are needed to improve construct validity of the task. To conclude, this is the first report of an age effect on dPAL and corroborates the role of mouse lemurs as valuable natural nonhuman primate models in aging research.
Fenofibrate attenuates doxorubicin-induced cardiac dysfunction in mice via activating the eNOS/EPC pathway
Authors: Huang Wen-Pin , Yin Wei-Hsian , Chen Jia-Shiong , Huang Po-Hsun , Chen Jaw-Wen , Lin Shing-Jong 
Published: January 2021

AbstractEndothelial progenitor cells (EPCs) improve endothelial impairment, which in turn restores endothelial function in patients with heart failure (HF). In the present study, we tested whether fenofibrate, with its anti-inflammatory and vasoprotective effects, could improve myocardial function by activating EPCs through the eNOS pathway in a doxorubicin (DOX)-induced cardiomyopathy mouse model. Wild-type mice were divided into 4 groups and treated with vehicle, DOX + saline, DOX + fenofibrate, and DOX + fenofibrate + L-NAME (N(ω)-nitro-L-arginine methyl ester). DOX-induced cardiac atrophy, myocardial dysfunction, the number of circulating EPCs and tissue inflammation were analyzed. Mice in the DOX + fenofibrate group had more circulating EPCs than those in the DOX + saline group (2% versus 0.5% of total events, respectively) after 4 weeks of treatment with fenofibrate. In addition, the inhibition of eNOS by L-NAME in vivo further abolished the fenofibrate-induced suppression of DOX-induced cardiotoxic effects. Protein assays revealed that, after DOX treatment, the differential expression of MMP-2 (matrix metalloproteinase-2), MMP-9 (matrix metalloproteinase-9), TNF-α (tumor necrosis factor-α), and NT-pro-BNP (N-terminal pro-B-type natriuretic peptide) between saline- and DOX-treated mice was involved in the progression of HF. Mechanistically, fenofibrate promotes Akt/eNOS and VEGF (vascular endothelial growth factor), which results in the activation of EPC pathways, thereby ameliorating DOX-induced cardiac toxicity.
Disturbance type determines how connectivity shapes ecosystem resilience
Authors: Pearson Ryan M. , Schlacher Thomas A. , Jinks Kristin I. , Olds Andrew D. , Brown Christopher J. , Connolly Rod M. 
Published: January 2021

AbstractConnectivity is fundamentally important for shaping the resilience of complex human and natural networks when systems are disturbed. Ecosystem resilience is, in part, shaped by the spatial arrangement of habitats, the permeability and fluxes between them, the stabilising functions performed by organisms, their dispersal traits, and the interactions between functions and stressor types. Controlled investigations of the relationships between these phenomena under multiple stressors are sparse, possibly due to logistic and ethical difficulties associated with applying and controlling stressors at landscape scales. Here we show that grazing performance, a key ecosystem function, is linked to connectivity by manipulating the spatial configuration of habitats in microcosms impacted by multiple stressors. Greater connectivity enhanced ecosystem function and reduced variability in grazing performance in unperturbed systems. Improved functional performance was observed in better connected systems stressed by harvesting pressure and temperature rise, but this effect was notably reversed by the spread of disease. Connectivity has complex effects on ecological functions and resilience, and the nuances should be recognised more fully in ecosystem conservation.