bluuebunny/crossref_metadata_2025_split huggingface dataset:
De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense
Authors: Das Rasmita Rani , Pradhan Seema , Parida Ajay 
Published: December 2020

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.
An integrated approach to biomarker discovery reveals gene signatures highly predictive of cancer progression
Authors: Sheng Kevin L. , Kang Lin , Pridham Kevin J. , Dunkenberger Logan E. , Sheng Zhi , Varghese Robin T. 
Published: December 2020

AbstractCurrent cancer biomarkers present variability in their predictive power and demonstrate limited clinical efficacy, possibly due to the lack of functional relevance of biomarker genes to cancer progression. To address this challenge, a biomarker discovery pipeline was developed to integrate gene expression profiles from The Cancer Genome Atlas and essential survival gene datasets from The Cancer Dependency Map, the latter of which catalogs genes driving cancer progression. By applying this pipeline to lung adenocarcinoma, lung squamous cell carcinoma, and glioblastoma, genes highly associated with cancer progression were identified and designated as progression gene signatures (PGSs). Analysis of area under the receiver operating characteristics curve revealed that PGSs predicted patient survival more accurately than previously identified cancer biomarkers. Moreover, PGSs stratified patients with high risk for progressive disease indicated by worse prognostic outcomes, increased frequency of cancer progression, and poor responses to chemotherapy. The robust performance of these PGSs were recapitulated in four independent microarray datasets from Gene Expression Omnibus and were further verified in six freshly dissected tumors from glioblastoma patients. Our results demonstrate the power of an integrated approach to cancer biomarker discovery and the possibility of implementing PGSs into clinical biomarker tests.
Continuous and automatic mortality risk prediction using vital signs in the intensive care unit: a hybrid neural network approach
Authors: Baker Stephanie , Xiang Wei , Atkinson Ian 
Published: December 2020

AbstractMortality risk prediction can greatly improve the utilization of resources in intensive care units (ICUs). Existing schemes in ICUs today require laborious manual input of many complex parameters. In this work, we present a scheme that uses variations in vital signs over a 24-h period to make mortality risk assessments for 3-day, 7-day, and 14-day windows. We develop a hybrid neural network model that combines convolutional (CNN) layers with bidirectional long short-term memory (BiLSTM) to predict mortality from statistics describing the variation of heart rate, blood pressure, respiratory rate, blood oxygen levels, and temperature. Our scheme performs strongly compared to state-of-the-art schemes in the literature for mortality prediction, with our highest-performing model achieving an area under the receiver-operator curve of 0.884. We conclude that the use of a hybrid CNN-BiLSTM network is highly effective in determining mortality risk for the 3, 7, and 14 day windows from vital signs. As vital signs are routinely recorded, in many cases automatically, our scheme could be implemented such that highly accurate mortality risk could be predicted continuously and automatically, reducing the burden on healthcare providers and improving patient outcomes.
Dynamics of salivary markers of kidney functions in acute and chronic kidney diseases
Authors: Kovalčíková Alexandra Gaál , Pavlov Kristína , Lipták Róbert , Hladová Marianna , Renczés Emese , Boor Peter , Podracká Ľudmila , Šebeková Katarína , Hodosy Július , Tóthová Ľubomíra , Celec Peter 
Published: December 2020

AbstractSaliva can be used as an alternative diagnostic fluid enabling easy and non-invasive disease monitoring. Urea and creatinine can be measured in saliva and both were shown to be increased in renal failure. However, the dynamics of these markers during the development of kidney diseases is unknown. We aimed to describe the dynamics of salivary urea and creatinine in various animal models of acute kidney injury (AKI) and chronic kidney disease (CKD) and in patients with different stages AKI or CKD. Ninety Wistar rats underwent bilateral nephrectomy (BNX), ischemia–reperfusion injury (IRI) or glycerol-induced kidney injury to model AKI. CKD was modelled using 5/6 nephrectomy. In the clinical part 57 children aged 12.6 ± 4.9 years with AKI (n = 11) or CKD (n = 46) and 29 healthy controls (aged 10.2 ± 3.7 years) were enrolled. Saliva and blood samples were collected in both, animal experiments and the human study. In animal models of AKI, plasma urea and creatinine were higher than in controls. An increase of salivary urea and creatinine (twofold) was observed in BNX and IRI, but only after 12 h and 24 h, respectively. In glycerol nephropathy and 5/6 nephrectomy, salivary urea increased (by 100% and by 50%), while salivary creatinine did not change during the observation period. Salivary urea and creatinine were significantly higher in all patients compared to controls (threefold) and in both, AKI and CKD they were associated with the severity of renal failure. Plasma and salivary concentrations correlated only in children with renal failure (R = 0.72 for urea; R = 0.93 for creatinine), but not in controls (R = -0.007 for urea; R = 0.02 for creatinine). Our study indicates that during the development of renal impairment saliva could be used for non-invasive monitoring in higher stages of AKI or CKD, rather than for screening of early stages of kidney diseases.
Non-basic amino acids in the hemagglutinin proteolytic cleavage site of a European H9N2 avian influenza virus modulate virulence in turkeys
Authors: Blaurock Claudia , Scheibner David , Landmann Maria , Vallbracht Melina , Ulrich Reiner , Böttcher-Friebertshäuser Eva , Mettenleiter Thomas C. , Abdelwhab Elsayed M. 
Published: December 2020

AbstractH9N2 avian influenza virus (AIV) is the most widespread low pathogenic (LP) AIV in poultry and poses a serious zoonotic risk. Vaccination is used extensively to mitigate the economic impact of the virus. However, mutations were acquired after long-term circulation of H9N2 virus in poultry, particularly in the hemagglutinin (HA) proteolytic cleavage site (CS), a main virulence determinant of AIV. Compared to chickens, little is known about the genetic determinants for adaptation of H9N2 AIV to turkeys. Here, we describe 36 different CS motifs in Eurasian H9N2 viruses identified from 1966 to 2019. The European H9N2 viruses specify unique HACS with particular polymorphism by insertion of non-basic amino acids at position 319. Recombinant viruses carrying single HACS mutations resembling field viruses were constructed (designated G319, A319, N319, S319, D319 and K319). Several viruses replicated to significantly higher titers in turkey cells than in chicken cells. Serine proteases were more efficient than trypsin to support multicycle replication in mammalian cells. Mutations affected cell-to-cell spread and pH-dependent HA fusion activity. In contrast to chickens, mutations in the HACS modulated clinical signs in inoculated and co-housed turkeys. G319 exhibited the lowest virulence, however, it replicated to significantly higher titers in contact-turkeys and in vitro. Interestingly, H9N2 viruses, particularly G319, replicated in brain cells of turkeys and to a lesser extent in mammalian brain cells independent of trypsin. Therefore, the silent circulation of potentially zoonotic H9N2 viruses in poultry should be monitored carefully. These results are important for understanding the adaptation of H9N2 in poultry and replication in mammalian cells.
Variation in 100 relevant pharmacogenes among emiratis with insights from understudied populations
Authors: Al-Mahayri Zeina N. , Patrinos George P. , Wattanapokayakit Sukanya , Iemwimangsa Nareenart , Fukunaga Koya , Mushiroda Taisei , Chantratita Wasun , Ali Bassam R. 
Published: December 2020

AbstractGenetic variations have an established impact on the pharmacological response. Investigating this variation resulted in a compilation of variants in “pharmacogenes”. The emergence of next-generation sequencing facilitated large-scale pharmacogenomic studies and exhibited the extensive variability of pharmacogenes. Some rare and population-specific variants proved to be actionable, suggesting the significance of population pharmacogenomic research. A profound gap exists in the knowledge of pharmacogenomic variants enriched in some populations, including the United Arab Emirates (UAE). The current study aims to explore the landscape of variations in relevant pharmacogenes among healthy Emiratis. Through the resequencing of 100 pharmacogenes for 100 healthy Emiratis, we identified 1243 variants, of which 63% are rare (minor allele frequency ≤ 0.01), and 30% were unique. Filtering the variants according to Pharmacogenomics Knowledge Base (PharmGKB) annotations identified 27 diplotypes and 26 variants with an evident clinical relevance. Comparison with global data illustrated a significant deviation of allele frequencies in the UAE population. Understudied populations display a distinct allelic architecture and various rare and unique variants. We underscored pharmacogenes with the highest variation frequencies and provided investigators with a list of candidate genes for future studies. Population pharmacogenomic studies are imperative during the pursuit of global pharmacogenomics implementation.
Targeting continuity of care and polypharmacy to reduce drug–drug interaction
Authors: Weng Yi-An , Deng Chung-Yeh , Pu Christy 
Published: December 2020

AbstractDrug–drug interaction (DDI) is common among the elderly, and it can have detrimental effects on patients. However, how DDI can be targeted has been under-researched. This study investigates whether DDI can be reduced by targeting continuity of care (COC) through reducing polypharmacy. Population claims data of Taiwan National Health Insurance were used to conduct a 7-year-long longitudinal study on patients aged ≥ 65 years (n = 2,318,766). Mediation analysis with counterfactual method and a 4-way decomposition of the effect of COC on DDI was conducted. Mediation effect through excessive polypharmacy differed from that through lower-level polypharmacy. Compared with the low COC group, the high COC group demonstrated reduced excess relative risk of DDI by 26% (excess relative risk =  − 0.263; 95% Confidence Interval (CI) =  − 0.263 to − 0.259) to 30% (excess relative risk =  − 0.297; 95% CI =  − 0.300 to − 0.295) with excessive polypharmacy as the mediator. The risk only reduced by 8% (excess relative risk =  − 0.079; 95% CI, − 0.08 to − 0.078) to 10% (excess relative risk =  − 0.096; 95% CI, − 0.097 to − 0.095) when the mediator was changed to lower-level polypharmacy. The effect of COC on DDI was mediated by polypharmacy, and the mediation effect was higher with excessive polypharmacy. Therefore, to reduce DDI in the elderly population, different policy interventions should be designed by considering polypharmacy levels to maximize the positive effect of COC on DDI.
Probing stacking configurations in a few layered MoS2 by low frequency Raman spectroscopy
Authors: Sam Rhea Thankam , Umakoshi Takayuki , Verma Prabhat 
Published: December 2020

AbstractNovel two-dimensional (2D) layered materials, such as MoS2, have recently gained a significant traction, chiefly due to their tunable electronic and optical properties. A major attribute that affects the tunability is the number of layers in the system. Another important, but often overlooked aspect is the stacking configuration between the layers, which can modify their electro-optic properties through changes in internal symmetries and interlayer interactions. This demands a thorough understanding of interlayer stacking configurations of these materials before they can be used in devices. Here, we investigate the spatial distribution of various stacking configurations and variations in interlayer interactions in few-layered MoS2 flakes probed through the low-frequency Raman spectroscopy, which we establish as a versatile imaging tool for this purpose. Some interesting anomalies in MoS2 layer stacking, which we propose to be caused by defects, wrinkles or twist between the layers, are also reported here. These types of anomalies, which can severely affect the properties of these materials can be detected through low-frequency Raman imaging. Our findings provide useful insights for understanding various structure-dependent properties of 2D materials that could be of great importance for the development of future electro-optic devices, quantum devices and energy harvesting systems.
Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress
Authors: Subudhi Prasanta K. , Shankar Rama , Jain Mukesh 
Published: December 2020

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.
A sensitive colorimetric probe for detection of the phosphate ion
Authors: Chen Yin-Chien , Lo Kuang-Min , Wang Yu-Xian , Chiu Tai-Chia , Hu Cho-Chun 
Published: December 2020

AbstractIn the present article, we report a novel colorimetric probe (TNT@MB) for the detection of the phosphate ion, which is based on the strong binding affinity between the phosphate ion and titanium dioxide nanotubes (TNTs). TNTs were synthesized from TiO2 nanoparticles by hydrothermal treatment. The obtained TNTs had an average length of 200 ± 50 nm and an average width of 12 ± 5 nm. TNT@MB was prepared by adsorbing methyl blue onto TNTs in acidic condition. The optimal synthesis conditions for TNT@MB consisted in having 0.05 g of TNTs react with 1 μmole of methyl blue at pH 2 for 90 min. TNTs and TNT@MB were characterized by UV–vis diffuse reflection spectroscopy, TEM, FTIR, and XPS. The phosphate-ion sensing behavior of TNT@MB was investigated by UV–visible spectroscopy. The phosphate-ion concentration linear range and detection limit of this method based on TNT@MB were 1–40 μM and 0.59 μM, respectively. A sample of lake water was used as a real sample, and analyte recovery rates were measured in the 102.5–103.6% range, with relative standard deviations below 5.6% (n = 3). We also found that this probe could be reused after regeneration in alkaline solution. These results indicate that as a colorimetric probe, TNT@MB has the advantages of being environmentally friendly, inexpensive, and simple to use, as well as giving rise to an easily observable color change.
Longitudinal analysis of total serum IgE levels with allergen sensitization and atopic diseases in early childhood
Authors: Wong Chun-Ying , Yeh Kuo-Wei , Huang Jing-Long , Su Kuan-Wen , Tsai Ming-Han , Hua Man-Chin , Liao Sui-Ling , Lai Shen-Hao , Chen Li-Chen , Chiu Chih-Yung 
Published: December 2020

AbstractThere are few studies addressing the longitudinal analysis of serum IgE levels and its impact to the development of atopic diseases in early childhood. We investigated 170 children who regularly followed up at our clinic for 4 years in a birth cohort study with at least 3 time-points of serum samples. The pattern of total serum IgE levels from 6 months to 4 years of age was clustered using K-means method in R software. Specific immunoglobulin E antibodies against food (egg white and milk) and inhalant allergens (D. pteronyssinus and D. farinae) were measured at 0.5, 1, 1.5, 2, 3 and 4 years of age. By using K-means clustering, the dynamic changes in serum IgE levels was significantly stratified into 3 clusters (cluster A, < 100 kU/L, n = 106; cluster B, 100–200 kU/L, n = 35; cluster C, ≥ 200 kU/L, n = 29). A persistent total IgE levels higher than 100 kU/L appeared to be associated with higher prevalence of sensitization to food but not mite. However, a persistent IgE levels higher than 200 kU/L was not only remarkably related to increased prevalence of mite sensitization, but also risk of eczema at age 1 and allergic rhinitis and asthma at age 2, 3 and 4. In conclusion, a persistent total serum IgE level ≥ 200 kU/L since infancy is strongly associated with the presence of food and mite sensitization, as well as the development of eczema in infants, and rhinitis and asthma later in early childhood.
Saturation transfer properties of tumour xenografts derived from prostate cancer cell lines 22Rv1 and DU145
Authors: Tan Ziyu , Lam Wilfred W. , Oakden Wendy , Murray Leedan , Koletar Margaret M. , Liu Stanley K. , Stanisz Greg J. 
Published: December 2020

AbstractHistopathology is currently the most reliable tool in assessing the aggressiveness and prognosis of solid tumours. However, developing non-invasive modalities for tumour evaluation remains crucial due to the side effects and complications caused by biopsy procedures. In this study, saturation transfer MRI was used to investigate the microstructural and metabolic properties of tumour xenografts in mice derived from the prostate cancer cell lines 22Rv1 and DU145, which express different aggressiveness. The magnetization transfer (MT) and chemical exchange saturation transfer (CEST) effects, which are associated with the microstructural and metabolic properties in biological tissue, respectively, were analyzed quantitatively and compared amongst different tumour types and regions. Histopathological staining was performed as a reference. Higher cellular density and metabolism expressed in more aggressive tumours (22Rv1) were associated with larger MT and CEST effects. High collagen content in the necrotic regions might explain their higher MT effects compared to tumour regions.
Changes in serum fibronectin levels predict tumor recurrence in patients with early hepatocellular carcinoma after curative treatment
Authors: Kim Sun Ah , Cho Eun Ju , Lee Sungyoung , Cho Young Youn , Kim Boram , Yoon Jung-Hwan , Park Taesung 
Published: December 2020

AbstractFibronectin, a matrix glycoprotein aberrantly expressed in various tumor cells, is a known candidate biomarker for the early diagnosis of hepatocellular carcinoma (HCC). In this study, we investigated whether serum fibronectin levels could predict tumor recurrence in patients with early-stage HCC after curative treatment. A total of 83 patients who showed complete response after initial curative treatment were included. The levels of serum fibronectin at baseline and 4–6 weeks after initial treatment were analyzed with regard to their associations with recurrence. Multivariate logistic regression analyses were performed to construct a prognostic nomogram. Baseline fibronectin levels were not significantly correlated with tumor size, number, stage, and serum α-fetoprotein levels. However, decrease in serum fibronectin levels after treatment was significantly associated with reduced HCC recurrence in multivariate logistic regression (odds ratio, 0.009; p < 0.001). Furthermore, a nomogram consisting of gender and changes in serum fibronectin showed a good discriminatory capability for the prediction of HCC recurrence with an area under the receiver-operating curve of 0.87. In conclusion, changes in serum fibronectin levels may be a surrogate indicator for assessment of treatment response in patients with early HCC after curative treatment.
Synthesis of 14C-labelled polystyrene nanoplastics for environmental studies
Authors: Al-Sid-Cheikh Maya , Rowland Steven J. , Kaegi Ralf , Henry Theodore B. , Cormier Marc-André , Thompson Richard C. 
Published: December 2020

AbstractAvailable analytical methods cannot detect nanoplastics at environmentally realistic concentrations in complex matrices such as biological tissues. Here, we describe a one-step polymerization method, allowing direct radiolabeling of a sulfonate end-capped nano-sized polystyrene (nPS; proposed as a model nanoplastic particle representing negatively charged nanoplastics). The method, which produces nanoplastics trackable in simulated environmental settings which have already been used to investigate the behavior of a nanoplastic in vivo in a bivalve mollusc, was developed, optimized and successfully applied to synthesis of 14C-labeled nPS of different sizes. In addition to a description of the method of synthesis, we describe the details for quantification, mass balance and recovery of the labelled particles from complex matrices offered by the radiolabelling approach. The radiolabeling approach described here, coupled to use of a highly sensitive autoradiographic method for monitoring nanoplastic body burden and distributions, may provide a valuable procedure for investigating the environmental pathways followed by negatively charged nanoplastics at low predicted environmental concentrations. Whether the behaviour of the synthetic nPS manufactured here, synthesised using a very common inititator, represents that of manufactured nPS found in the environment, remains to be seen.