bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated nomogram combining lncRNAs classifier and clinicopathologic factors to predict the recurrence of head and neck squamous cell carcinoma
Authors: Cui Jie , Wen Qingquan , Tan Xiaojun , Piao Jinsong , Zhang Qiong , Wang Qian , He Lizhen , Wang Yan , Chen Zhen , Liu Genglong 
Published: November 2019

AbstractLong non-coding RNAs (lncRNAs) which have little or no protein-coding capacity, due to their potential roles in the cancer disease, caught a particular interest. Our study aims to develop an lncRNAs-based classifier and a nomogram incorporating the lncRNAs classifier and clinicopathologic factors to help to improve the accuracy of recurrence prediction for head and neck squamous cell carcinoma (HNSCC) patients. The HNSCC lncRNAs profiling data and the corresponding clinicopathologic information were downloaded from TANRIC database and cBioPortal. Using univariable Cox regression and Least absolute shrinkage and selection operator (LASSO) analysis, we developed 15-lncRNAs-based classifier related to recurrence. On the basis of multivariable Cox regression analysis results, a nomogram integrating the genomic and clinicopathologic predictors was built. The predictive accuracy and discriminative ability of the inclusive nomogram were confirmed by calibration curve and a concordance index (C-index), and compared with TNM stage system by C-index, receiver operating characteristic (ROC) analysis. Decision curve analysis (DCA) was conducted to evaluate clinical value of our nomogram. Consequently, fifteen recurrence-free survival (RFS) -related lncRNAs were identified, and the classifier consisting of the established 15 lncRNAs could effectively divide patients into high-risk and low-risk subgroup. The prediction ability of the 15-lncRNAs-based classifier for predicting 3- year and 5-year RFS were 0.833 and 0.771. Independent factors derived from multivariable analysis to predict recurrence were number of positive LNs, margin status, mutation count and lncRNAs classifier, which were all embedded into the nomogram. The calibration curve for the recurrence probability showed that the predictions based on the nomogram were in good coincide with practical observations. The C-index of the nomogram was 0.76 (0.72–0.79), and the area under curve (AUC) of nomogram in predicting RFS was 0.809, which were significantly higher than traditional TNM stage and 15-lncRNAs-based classifier. Decision curve analysis further demonstrated that our nomogram had larger net benefit than TNM stage and 15-lncRNAs-based classifier. The results were confirmed externally. In summary, a visually inclusive nomogram for patients with HNSCC, comprising genomic and clinicopathologic variables, generates more accurate prediction of the recurrence probability when compared TNM stage alone, but more additional data remains needed before being used in clinical practice.
Spatio-temporal analysis of association between incidence of malaria and environmental predictors of malaria transmission in Nigeria
Authors: Okunlola Oluyemi A. , Oyeyemi Oyetunde T. 
Published: November 2019

AbstractMalaria still poses a significant threat in Nigeria despite the various efforts to abate its transmission. Certain environmental factors have been implicated to increase the risk of malaria in Nigeria and other affected countries. The study aimed to evaluate the spatial and temporal association between the incidence of malaria and some environmental risk factors in Nigeria. The study used malaria incidence and environmental risk factors data emanating from 2015 Nigeria Malaria Indicator Survey accessed from the Demographic and Health Survey database. A total of 333 and 326 clusters throughout the country were used for malaria incidence study and environmental variables respectively. The spatial autocorrelation of malaria incidence and hotspot analysis was determined by the Moran’s diagram and local Moran’s I index, respectively. The relationships between the malaria incidence and the ecological predictors of transmission were analysed in all the six geopolitical zones of Nigeria from 2000–2015 using ordinary least square (OLS), spatial lag model (SLM), and spatial error model (SEM). Annual rainfall, precipitation and proximity to water showed significant positive relationship with the incidence rate of malaria in the OLS model (P < 0.01), whereas aridity was negatively related to malaria incidence (P < 0.001) in the same model. The rate of incidence of malaria increased significantly with increase in temperature, aridity, rainfall and proximity to water in the SEM whereas only temperature and proximity to water have significant positive effect on malaria incidence in the SLM. The modelling of the ecological predictors of malaria transmission and spatial maps provided in this study could aid in developing framework to mitigate malaria and identify its hotspots for urgent intervention in the endemic regions.
Evaluation of longitudinal time-lapsed in vivo micro-CT for monitoring fracture healing in mouse femur defect models
Authors: Wehrle Esther , Tourolle né Betts Duncan C. , Kuhn Gisela A. , Scheuren Ariane C. , Hofmann Sandra , Müller Ralph 
Published: November 2019

AbstractLongitudinal in vivo micro-computed tomography (micro-CT) is of interest to non-invasively capture the healing process of individual animals in preclinical fracture healing studies. However, it is not known whether longitudinal imaging itself has an impact on callus formation and remodeling. In this study, a scan group received weekly micro-CT measurements (week 0–6), whereas controls were only scanned post-operatively and at week 5 and 6. Registration of consecutive scans using a branching scheme (bridged vs. unbridged defect) combined with a two-threshold approach enabled assessment of localized bone turnover and mineralization kinetics relevant for monitoring callus remodeling. Weekly micro-CT application did not significantly change any of the assessed callus parameters in the defect and periosteal volumes. This was supported by histomorphometry showing only small amounts of cartilage residuals in both groups, indicating progression towards the end of the healing period. Also, immunohistochemical staining of Sclerostin, previously associated with mediating adverse radiation effects on bone, did not reveal differences between groups. The established longitudinal in vivo micro-CT-based approach allows monitoring of healing phases in mouse femur defect models without significant effects of anesthesia, handling and radiation on callus properties. Therefore, this study supports application of longitudinal in vivo micro-CT for healing-phase-specific monitoring of fracture repair in mice.
Ultrasensitive and label-free biosensor for the detection of Plasmodium falciparum histidine-rich protein II in saliva
Authors: Soraya Gita V. , Abeyrathne Chathurika D. , Buffet Christelle , Huynh Duc H. , Uddin Shah Mukim , Chan Jianxiong , Skafidas Efstratios , Kwan Patrick , Rogerson Stephen J. 
Published: November 2019

AbstractMalaria elimination is a global public health priority. To fulfil the demands of elimination diagnostics, we have developed an interdigitated electrode sensor platform targeting the Plasmodium falciparum Histidine Rich Protein 2 (PfHRP2) protein in saliva samples. A protocol for frequency-specific PfHRP2 detection in phosphate buffered saline was developed, yielding a sensitivity of 2.5 pg/mL based on change in impedance magnitude of the sensor. This protocol was adapted and optimized for use in saliva with a sensitivity of 25 pg/mL based on change in resistance. Further validation demonstrated detection in saliva spiked with PfHRP2 from clinical isolates in 8 of 11 samples. With a turnaround time of ~2 hours, the label-free platform based on impedance sensors has the potential for miniaturization into a point-of-care diagnostic device for malaria elimination.
Blood transcriptome analysis in a buck-ewe hybrid and its parents
Authors: Falker-Gieske Clemens , Knorr Christoph , Tetens Jens 
Published: November 2019

AbstractExamples of living sheep-goat hybrids are rare, mainly due to incorrect chromosome pairing, which is thought to be the main cause for species incompatibility. This case represents the first report of a buck-ewe hybrid and the first mammalian hybrid to be analyzed with next generation sequencing. The buck-ewe hybrid had an intermediate karyotype to the parental species, with 57 chromosomes. Analysis of the blood transcriptomes of the hybrid and both parents revealed that gene expression levels differed between the hybrid and its parents. This could be explained in part by age-dependent differences in gene expression. Contribution to the geep transcriptome was larger from the paternal, compared to the maternal, genome. Furthermore, imprinting patterns deviated considerably from what is known from other mammals. Potentially deleterious variants appeared to be compensated for by monoallelic expression of transcripts. Hence, the data imply that the buck-ewe hybrid compensated for the phylogenetic distance between the parental species by several mechanisms: adjustment of gene expression levels, adaptation to imprinting incompatibilities, and selective monoallelic expression of advantageous transcripts. This study offers a unique opportunity to gain insights into the transcriptome biology and regulation of a hybrid mammal.
Towards Quantification of Inflammation in Atherosclerotic Plaque in the Clinic – Characterization and Optimization of Fluorine-19 MRI in Mice at 3 T
Authors: Darçot Emeline , Colotti Roberto , Pellegrin Maxime , Wilson Anne , Siegert Stefanie , Bouzourene Karima , Yerly Jérôme , Mazzolai Lucia , Stuber Matthias , van Heeswijk Ruud B. 
Published: November 2019

AbstractFluorine-19 (19F) magnetic resonance imaging (MRI) of injected perfluorocarbons (PFCs) can be used for the quantification and monitoring of inflammation in diseases such as atherosclerosis. To advance the translation of this technique to the clinical setting, we aimed to 1) demonstrate the feasibility of quantitative 19F MRI in small inflammation foci on a clinical scanner, and 2) to characterize the PFC-incorporating leukocyte populations and plaques. To this end, thirteen atherosclerotic apolipoprotein-E-knockout mice received 2 × 200 µL PFC, and were scanned on a 3 T clinical MR system. 19F MR signal was detected in the aortic arch and its branches in all mice, with a signal-to-noise ratio of 11.1 (interquartile range IQR = 9.5–13.1) and a PFC concentration of 1.15 mM (IQR = 0.79–1.28). Imaging flow cytometry was used on another ten animals and indicated that PFC-labeled leukocytes in the aortic arch and it branches were mainly dendritic cells, macrophages and neutrophils (ratio 9:1:1). Finally, immunohistochemistry analysis confirmed the presence of those cells in the plaques. We thus successfully used 19F MRI for the noninvasive quantification of PFC in atherosclerotic plaque in mice on a clinical scanner, demonstrating the feasibility of detecting very small inflammation foci at 3 T, and advancing the translation of 19F MRI to the human setting.
Multivariate nonparametric chart for influenza epidemic monitoring
Authors: Liu Liu , Yue Jin , Lai Xin , Huang Jianping , Zhang Jian 
Published: November 2019

AbstractControl chart methods have been received much attentions in biosurvillance studies. The correlation between charting statistics or regions could be considerably important in monitoring the states of multiple outcomes or regions. In addition, the process variable distribution is unknown in most situations. In this paper, we propose a new nonparametric strategy for multivariate process monitoring when the distribution of a process variable is unknown. We discuss the EWMA control chart based on rank methods for a multivariate process, and the approach is completely nonparametric. A simulation study demonstrates that the proposed method is efficient in detecting shifts for multivariate processes. A real Japanese influenza data example is given to illustrate the performance of the proposed method.
Realtime optimization of multidimensional NMR spectroscopy on embedded sensing devices
Authors: Tang Yiqiao , Song Yi-Qiao 
Published: November 2019

AbstractThe increasingly ubiquitous use of embedded devices calls for autonomous optimizations of sensor performance with meager computing resources. Due to the heavy computing needs, such optimization is rarely performed, and almost never carried out on-the-fly, resulting in a vast underutilization of deployed assets. Aiming at improving the measurement efficiency, we show an OED (Optimal Experimental Design) routine where quantities of interest of probable samples are partitioned into distinctive classes, with the corresponding sensor signals learned by supervised learning models. The trained models, digesting the compressed live data, are subsequently executed at the constrained device for continuous classification and optimization of measurements. We demonstrate the closed-loop method with multidimensional NMR (Nuclear Magnetic Resonance) relaxometry, an analytical technique seeing a substantial growth of field applications in recent years, on a wide range of complex fluids. The realtime portion of the procedure demands minimal computing load, and is ideally suited for instruments that are widely used in remote sensing and IoT networks.
Mass Spectrometry Imaging of Lipids in Human Skin Disease Model Hidradenitis Suppurativa by Laser Desorption Ionization from Silicon Nanopost Arrays
Authors: Fincher Jarod A. , Jones Derek R. , Korte Andrew R. , Dyer Jacqueline E. , Parlanti Paola , Popratiloff Anastas , Brantner Christine A. , Morris Nicholas J. , Pirlo Russell K. , Shanmugam Victoria K. , Vertes Akos 
Published: November 2019

AbstractNeutral lipids have been implicated in a host of potentially debilitating human diseases, such as heart disease, type-2 diabetes, and metabolic syndrome. Matrix-assisted laser desorption ionization (MALDI), the method-of-choice for mass spectrometry imaging (MSI), has led to remarkable success in imaging several lipid classes from biological tissue sections. However, due to ion suppression by phospholipids, MALDI has limited ability to efficiently ionize and image neutral lipids, such as triglycerides (TGs). To help overcome this obstacle, we have utilized silicon nanopost arrays (NAPA), a matrix-free laser desorption ionization (LDI) platform. Hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory skin disease of the apocrine sweat glands. The ability of NAPA to efficiently ionize lipids is exploited in the analysis of human skin samples from sufferers of HS. Ionization by LDI from NAPA allows for the detection and imaging of a number of neutral lipid species, including TGs comprised of shorter, odd-chain fatty acids, which strongly suggests an increased bacterial load within the host tissue, as well as hexosylceramides (HexCers) and galabiosyl-/lactosylceramides that appear to be correlated with the presence of HS. Our results demonstrate that NAPA-LDI-MSI is capable of imaging and potentially differentiating healthy and diseased human skin tissues based on changes in detected neutral lipid composition.
Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics
Authors: Chen Cheng , Li Qiang , Fu Rongtao , Wang Jian , Xiong Chuan , Fan Zhonghan , Hu Rongping , Zhang Hong , Lu Daihua 
Published: November 2019

AbstractScytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
A Necropsy Study of Disease and Comorbidity Trends in Morbidity and Mortality in the Koala (Phascolarctos cinereus) in South-East Queensland, Australia
Authors: Gonzalez-Astudillo V. , Henning J. , Valenza L. , Knott L. , McKinnon A. , Larkin R. , Allavena R. 
Published: November 2019

AbstractKoalas are an iconic Australian marsupial undergoing precipitous population reduction in South-East Queensland from complex interacting threats. To investigate the causes of death and the interaction of comorbidities with demography in South-East Queensland koalas, a large scale, high-throughput prospective necropsy survey was conducted spanning 2013–2016. During this period, 519 necropsies were conducted in 155 young/subadult koalas, 235 mature, 119 old koalas and 10 of unknown age. Similar numbers of males and females were assessed. Trauma and infectious disease at were the most common single diagnoses. However, comorbidity was frequent, including multicentric infection or infectious disease in combination with trauma or senescence. Female koalas had proportionally more reproductive chlamydiosis compared to males in which the ocular and urinary systems were more commonly affected. Comorbidity and disease were strongly associated with poor body condition, and trauma was associated with good body condition. Animals affected by motor vehicle trauma were often in better body condition than those affected by animal attack, tree fall or other causes of trauma. This study identified a higher frequency of infections and comorbidity then previously reported, confirming the complex nature of interacting threats to the koala population.
Whole-body exposures to radiofrequency-electromagnetic energy can cause DNA damage in mouse spermatozoa via an oxidative mechanism
Authors: Houston Brendan J. , Nixon Brett , McEwan Kristen E. , Martin Jacinta H. , King Bruce V. , Aitken R. John , De Iuliis Geoffry N. 
Published: November 2019

AbstractArtificially generated radiofrequency-electromagnetic energy (RF-EME) is now ubiquitous in our environment owing to the utilization of mobile phone and Wi-Fi based communication devices. While several studies have revealed that RF-EME is capable of eliciting biological stress, particularly in the context of the male reproductive system, the mechanistic basis of this biophysical interaction remains largely unresolved. To extend these studies, here we exposed unrestrained male mice to RF-EME generated via a dedicated waveguide (905 MHz, 2.2 W/kg) for 12 h per day for a period of 1, 3 or 5 weeks. The testes of exposed mice exhibited no evidence of gross histological change or elevated stress, irrespective of the RF-EME exposure regimen. By contrast, 5 weeks of RF-EME exposure adversely impacted the vitality and motility profiles of mature epididymal spermatozoa. These spermatozoa also experienced increased mitochondrial generation of reactive oxygen species after 1 week of exposure, with elevated DNA oxidation and fragmentation across all exposure periods. Notwithstanding these lesions, RF-EME exposure did not impair the fertilization competence of spermatozoa nor their ability to support early embryonic development. This study supports the utility of male germ cells as sensitive tools with which to assess the biological impacts of whole-body RF-EME exposure.
Co-occurrence of thelytokous and bisexual Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae) in a natural population
Authors: Liu Quan-quan , Zhou Jin-cheng , Zhang Chen , Ning Su-fang , Duan Li-jia , Dong Hui 
Published: November 2019

AbstractTrichogramma dendrolimi is one of the most successful biocontrol agents in China. However, an inundative condition is necessary to obtain acceptable parasitism effect. A good solution to this is the application of its thelytokous counterparts which unfortunately are scarce in field. We here report the first case of a natural T. dendrolimi population in China comprising both bisexual wasps and an extremely low proportion of thelytokous wasps. These two forms of T. dendrolimi are phylogenetically related based on the reconstructions of ITS-2 and COI genes. Also, the phylogenetic results suggested a potentially Wolbachia-drived ITS-2 variation. The expression of thelytoky was hardly affected by temperature, which might help control Asian corn borer and Dendrolimus punctatus. Wolbachia are responsible for current thelytoky according to phylogenetic analyses, antibiotic treatment and introgression experiment. We also present the third case of paternal sex ratio chromosome that restrains the expansion of Wolbachia. Moreover, the low frequency of thelytoky may be common in natural populations. Consequently if for biological control it is determined that a thelytokous strain is to be preferred, then large number of field collected females should be set up as isofemale lines, to detect the rare thelytoky.
Parkinson’s disease prognostic scores for progression of cognitive decline
Authors: Gramotnev Galina , Gramotnev Dmitri K. , Gramotnev Alexandra 
Published: November 2019

AbstractClinical and biochemical diversity of Parkinson’s disease (PD) presents a major challenge for accurate diagnosis and prediction of its progression. We propose, develop and optimize PD clinical scores as efficient integrated progression biomarkers for prediction of the likely rate of cognitive decline in PD patients. We considered 269 drug-naïve participants from the Parkinson’s Progression Marker Initiative database, diagnosed with idiopathic PD and observed between 4 and 6 years. Nineteen baseline clinical and pathological measures were systematically considered. Relative variable importance and logistic regressions were used to optimize combinations of significant baseline measures as integrated biomarkers. Parkinson’s disease cognitive decline scores were designed as new clinical biomarkers using optimally categorized baseline measures. Specificities and sensitivities of the biomarkers reached ~93% for prediction of severe rate of cognitive decline (with more than 5 points decline in 4 years on the Montreal Cognitive Assessment scale), and up to ~73% for mild-to-moderate decline (between 1 and 5 points decline). The developed biomarkers and clinical scores could resolve the long-standing clinical problem about reliable prediction of PD progression into cognitive deterioration. The outcomes also provide insights into the contributions of individual clinical and pathological measures to PD progression, and will assist with better-targeted treatment regiments, stratification of clinical trial and their evaluation.