bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentiation of thyroid nodules on US using features learned and extracted from various convolutional neural networks
Authors: Lee Eunjung , Ha Heonkyu , Kim Hye Jung , Moon Hee Jung , Byon Jung Hee , Huh Sun , Son Jinwoo , Yoon Jiyoung , Han Kyunghwa , Kwak Jin Young 
Published: December 2019

AbstractThyroid nodules are a common clinical problem. Ultrasonography (US) is the main tool used to sensitively diagnose thyroid cancer. Although US is non-invasive and can accurately differentiate benign and malignant thyroid nodules, it is subjective and its results inevitably lack reproducibility. Therefore, to provide objective and reliable information for US assessment, we developed a CADx system that utilizes convolutional neural networks and the machine learning technique. The diagnostic performances of 6 radiologists and 3 representative results obtained from the proposed CADx system were compared and analyzed.
The host generalist phytopathogenic fungus Sclerotinia sclerotiorum differentially expresses multiple metabolic enzymes on two different plant hosts
Authors: Allan Jefferson , Regmi Roshan , Denton-Giles Matthew , Kamphuis Lars G. , Derbyshire Mark C. 
Published: December 2019

AbstractSclerotinia sclerotiorum is a necrotrophic fungal pathogen that infects upwards of 400 plant species, including several economically important crops. The molecular processes that underpin broad host range necrotrophy are not fully understood. This study used RNA sequencing to assess whether S. sclerotiorum genes are differentially expressed in response to infection of the two different host crops canola (Brassica napus) and lupin (Lupinus angustifolius). A total of 10,864 of the 11,130 genes in the S. sclerotiorum genome were expressed. Of these, 628 were upregulated in planta relative to in vitro on at least one host, suggesting involvement in the broader infection process. Among these genes were predicted carbohydrate-active enzymes (CAZYmes) and secondary metabolites. A considerably smaller group of 53 genes were differentially expressed between the two plant hosts. Of these host-specific genes, only six were either CAZymes, secondary metabolites or putative effectors. The remaining genes represented a diverse range of functional categories, including several associated with the metabolism and efflux of xenobiotic compounds, such as cytochrome P450s, metal-beta-lactamases, tannases and major facilitator superfamily transporters. These results suggest that S. sclerotiorum may regulate the expression of detoxification-related genes in response to phytotoxins produced by the different host species. To date, this is the first comparative whole transcriptome analysis of S. sclerotiorum during infection of different hosts.
New statistical method identifies cytokines that distinguish stool microbiomes
Authors: Yang Dake , Johnson Jethro , Zhou Xin , Deych Elena , Shands Berkley , Hanson Blake , Sodergren Erica , Weinstock George , Shannon William D. 
Published: December 2019

AbstractRegressing an outcome or dependent variable onto a set of input or independent variables allows the analyst to measure associations between the two so that changes in the outcome can be described by and predicted by changes in the inputs. While there are many ways of doing this in classical statistics, where the dependent variable has certain properties (e.g., a scalar, survival time, count), little progress on regression where the dependent variable are microbiome taxa counts has been made that do not impose extremely strict conditions on the data. In this paper, we propose and apply a new regression model combining the Dirichlet-multinomial distribution with recursive partitioning providing a fully non-parametric regression model. This model, called DM-RPart, is applied to cytokine data and microbiome taxa count data and is applicable to any microbiome taxa count/metadata, is automatically fit, and intuitively interpretable. This is a model which can be applied to any microbiome or other compositional data and software (R package HMP) available through the R CRAN website.
Multimodal alterations of directed connectivity profiles in patients with attention-deficit/hyperactivity disorders
Authors: Muthuraman Muthuraman , Moliadze Vera , Boecher Lena , Siemann Julia , Freitag Christine M. , Groppa Sergiu , Siniatchkin Michael 
Published: December 2019

AbstractFunctional and effective connectivity measures for tracking brain region interactions that have been investigated using both electroencephalography (EEG) and magnetoencephalography (MEG) bringing up new insights into clinical research. However, the differences between these connectivity methods, especially at the source level, have not yet been systematically studied. The dynamic characterization of coherent sources and temporal partial directed coherence, as measures of functional and effective connectivity, were applied to multimodal resting EEG and MEG data obtained from 11 young patients (mean age 13.2 ± 1.5 years) with attention-deficit/hyperactivity disorder (ADHD) and age-matched healthy subjects. Additionally, machine-learning algorithms were applied to the extracted connectivity features to identify biomarkers differentiating the two groups. An altered thalamo-cortical connectivity profile was attested in patients with ADHD who showed solely information outflow from cortical regions in comparison to healthy controls who exhibited bidirectional interregional connectivity in alpha, beta, and gamma frequency bands. We achieved an accuracy of 98% by combining features from all five studied frequency bands. Our findings suggest that both types of connectivity as extracted from EEG or MEG are sensitive methods to investigate neuronal network features in neuropsychiatric disorders. The connectivity features investigated here can be further tested as biomarkers of ADHD.
A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina
Authors: Schroeder Mercedes M. , Lai Yan , Shirai Miwa , Alsalek Natalie , Tsuchiya Tokuji , Roberts Philip , Eulgem Thomas 
Published: December 2019

AbstractDubbed as a “global destroyer of crops”, the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.
Distribution of the parasitic isopod Tachaea chinensis in China
Authors: Xu Weibin , Han Zhibin , Xing Yuenan , Li Xin , Zhao Yingying , Chen Qijun , Li Yingdong 
Published: December 2019

AbstractTachaea chinensis Thielemann, 1910 (Isopoda: Corallanidae) is a branchial ectoparasite that attaches onto shrimps and prawns. However, the distribution of T. chinensis in China, especially its epidemiology, remains unclear. We determined the prevalence of T. chinensis on the ridgetail white prawn (Exopalaemon carinicauda Holthuis, 1950) in Jiangsu Province. Fifty ponds in 10 shrimp farms were assessed. Isopod species were identified by morphological features and mitochondrial 16S rRNA gene analysis. A literature review was performed to determine the geographical distribution of T. chinensis in China. Published data revealed that T. chinensis was geographically distributed throughout five provinces in China, including Liaoning, Tianjin, Henan, Hubei, and Guangxi. A total of 998 T. chinensis were collected from 50 ridgetail white prawn ponds in Yancheng City and Rudong County. Tachaea chinensis prevalence ranged from 0.98% to 4.42% in Yancheng City and 0.62% to 0.92% in Rudong County. This is the first study to investigate the geographical distribution of T. chinensis in China and determine the prevalence of T. chinensis on the ridgetail white prawn in Jiangsu Province. Overall, we provide available data that fill gaps in the epidemiology of T. chinensis.
Experimental evaluation of a self-propelling bio-inspired needle in single- and multi-layered phantoms
Authors: Scali M. , Breedveld P. , Dodou D. 
Published: December 2019

AbstractIn percutaneous interventions, reaching targets located deep inside the body with minimal tissue damage and patient pain requires the use of long and thin needles. However, when pushed through a solid substrate, a structure with a high aspect ratio is prone to buckle. We developed a series of multi-element needles with a diameter smaller than 1 mm and a length larger than 200 mm, and we experimentally evaluated the performance of a bio-inspired insertion mechanism that prevents needle buckling of such slender structures. The needles consisted of Nitinol wires and advance into a substrate by pushing the wires forward one after the other, followed by pulling all the wires simultaneously backward. The resulting net push force is low, allowing the needles to self-propel through the substrate. We investigated the effect of the needle design parameters (number of wires and their diameter) and substrate characteristics (stiffness and number of layers) on the needle motion. Three needle prototypes (consisting of six 0.25-mm wires, six 0.125-mm wires, and three 0.25-mm wires, respectively) were inserted into single- and multi-layered tissue-mimicking phantoms. The prototypes were able to move forward in all phantoms without buckling. The amount of needle slip with respect to the phantom was used to assess the performance of the prototypes. The six-wire 0.25-mm prototype exhibited the least slip among the three prototypes. Summarizing, we showed that a bio-inspired motion mechanism prevents buckling in very thin (diameter <1 mm), long (length >200 mm) needles, allowing deep insertion into tissue-mimicking phantoms.
Forecasting of landslide displacements using a chaos theory based wavelet analysis-Volterra filter model
Authors: Li Yuanyao , Sun Ronglin , Yin Kunlong , Xu Yong , Chai Bo , Xiao Lili 
Published: December 2019

AbstractLandslide displacement time series can directly reflects landslide deformation and stability characteristics. Hence, forecasting of the non-linear and non-stationary displacement time series is necessary and significant for early warning of landslide failure. Traditionally, conventional machine learning methods are adopted as forecasting models, these forecasting models mainly determine the input and output variables experientially and does not address the non-stationary characteristics of displacement time series. However, it is difficult for these conventional machine learning methods to obtain appropriate input-output variables, to determine appropriate model parameters and to acquire satisfied prediction performance. To deal with these drawbacks, this study proposes the wavelet analysis (WA) to decompose the displacement time series into low- and high-frequency components to address the non-stationary characteristics; then proposes thee chaos theory to obtain appropriate input-output variables of forecasting models, and finally proposes Volterra filter model to construct the forecasting model. The GPS monitoring cumulative displacement time series, recorded on the Shuping and Baijiabao landslides, distance measuring equipment monitoring displacements on the Xintan landslide in Three Gorges Reservoir area of China, are used as test data of the proposed chaotic WA-Volterra model. The chaotic WA-support vector machine (SVM) model and single chaotic Volterra model without WA method, are used as comparisons. The results show that there are chaos characteristics in the GPS monitoring displacement time series, the non-stationary characteristics of landslide displacements are captured well by the WA method, and the model input-output variables are selected suitably using chaos theory. Furthermore, the chaotic WA-Volterra model has higher prediction accuracy than the chaotic WA-SVM and single chaotic Volterra models.
Crebl2 regulates cell metabolism in muscle and liver cells
Authors: Tiebe Marcel , Lutz Marilena , Senyilmaz Tiebe Deniz , Teleman Aurelio A. 
Published: December 2019

AbstractWe previously identified Drosophila REPTOR and REPTOR-BP as transcription factors downstream of mTORC1 that play an important role in regulating organismal metabolism. We study here the mammalian ortholog of REPTOR-BP, Crebl2. We find that Crebl2 mediates part of the transcriptional induction caused by mTORC1 inhibition. In C2C12 myoblasts, Crebl2 knockdown leads to elevated glucose uptake, elevated glycolysis as observed by lactate secretion, and elevated triglyceride biosynthesis. In Hepa1-6 hepatoma cells, Crebl2 knockdown also leads to elevated triglyceride levels. In sum, this works identifies Crebl2 as a regulator of cellular metabolism that can link nutrient sensing via mTORC1 to the metabolic response of cells.
ezTrack: An open-source video analysis pipeline for the investigation of animal behavior
Authors: Pennington Zachary T. , Dong Zhe , Feng Yu , Vetere Lauren M. , Page-Harley Lucia , Shuman Tristan , Cai Denise J. 
Published: December 2019

AbstractTracking animal behavior by video is one of the most common tasks in the life sciences. Although commercial software exists for executing this task, they often present enormous cost to the researcher and can entail purchasing hardware that is expensive and lacks adaptability. Additionally, the underlying code is often proprietary. Alternatively, available open-source options frequently require model training and can be challenging for those inexperienced with programming. Here we present an open-source and platform independent set of behavior analysis pipelines using interactive Python that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual animal, amenable to a wide range of behavioral tasks. A second module is described for the analysis of freezing behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce the anticipated results. Moreover, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes alignment with biological recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time, and defining regions of interest, are readily implemented.
Differential IL-17A response to S. pneumoniae in adenoid tissue of children with sleep disordered breathing and otitis media with effusion
Authors: Huang Chien-Chia , Wu Pei-Wen , Lee Ta-Jen , Chen Chyi-Liang , Wang Chun-Hua , Tsai Chi-Neu , Chiu Cheng-Hsun 
Published: December 2019

AbstractStreptococcus pneumonia, one of the major colonizers in nasopharyngeal adenoids, has been the predominant pathogen causing acute otitis media (AOM) in children. Recent evidence suggests an association between IL-17A-mediated immune response and the clearance of pneumococcal colonization in nasopharyngeal adenoids. Here, we evaluated the expressions of IL-17A and associated genes in hypertrophic adenoid tissues of children with sleep-disordered breathing (SDB) and otitis media with effusion (OME) and their association with pneumococcal carriage. Sixty-six pediatric patients with adenoid hypertrophy were enrolled. During adenoidectomy, nasopharyngeal swab and adenoid tissues were used to determine pneumococcal carriage and IL-17A expression. Our results revealed significantly higher levels of IL-17A and IL-17A:IL-10 mRNA in the SDB patients positive for nasopharyngeal pneumococcal carriage than those negative. However, these differences were not significant in the OME group. These results suggested, in OME patients, prolonged or chronic pneumococcal carriage may occur because of insufficient IL-17A-mediated mucosal clearance, and could further lead to AOM and OME development.
Heavy metal contents and enzymatic activity in soils exposed to the impact of road traffic
Authors: Jaworska Hanna , Lemanowicz Joanna 
Published: December 2019

AbstractThe aim of the research was to evaluate the influence of car traffic on the content of selected heavy metals in soil from a park area, and to define the dependency between their content and enzyme activity. Soil samples were collected from 13 points located along a communication route, each 100 m from the next and 50 m from the border of the road. Soil material was obtained from two depths (0–20 cm and 20–40 cm) and analysed for: pH in H2O and in KCl, OC, and texture by laser method. Total content of heavy metals (Pb, Cd, Zn, Cu, Ni), available phosphorus and the activity of selected enzymes: catalase, dehydrogenase, acidic and alkaline phosphatase were all determined. The examined soils have the texture of loamy sands or sands (USDA 2012), slightly acidic or neutral pH, Organic Carbon (OC) content in the range from 3.50 to 13.80 g kg−1. The total contents of elements in surface horizons were, in order of decreasing concentrations: Pb>Zn>Cu>Ni>Cd, although in subsurface horizons it was Zn>Pb>Cu>Ni>Cd. Contamination Factor (CF) determined for Ni, Pb, Cd, Zn, Cu reaches higher values in samples from subsurface horizons, which confirms the influence of car traffic on the content of heavy metals in the surrounding soils. The calculated CF shows contamination is moderate for Ni, Cd, Zn and Cu and high for Pb and Cu. The investigated soils may be classified as class IV (low) in terms of available phosphorus. The activity of the examined enzymes was higher in soil samples collected from the 0–20 cm layer than from 20–40 cm. The correlation analysis indicates a significant positive dependency between OC content in soils and enzymatic activity. Principal Component Analysis (PCA) was also performed. Two principal components PC1 and PC2 account for 66.57% of the variability.
ADAR1 function affects HPV replication and is associated to recurrent human papillomavirus-induced dysplasia in HIV coinfected individuals
Authors: Pujantell Maria , Badia Roger , Galván-Femenía Iván , Garcia-Vidal Edurne , de Cid Rafael , Alcalde Carmen , Tarrats Antonio , Piñol Marta , Garcia Francesc , Chamorro Ana M. , Revollo Boris , Videla Sebastian , Parés David , Corral Javier , Tural Cristina , Sirera Guillem , Esté José A. , Ballana Ester , Riveira-Muñoz Eva 
Published: December 2019

AbstractInfection by human papillomavirus (HPV) alters the microenvironment of keratinocytes as a mechanism to evade the immune system. A-to-I editing by ADAR1 has been reported to regulate innate immunity in response to viral infections. Here, we evaluated the role of ADAR1 in HPV infectionin vitroandin vivo. Innate immune activation was characterized in human keratinocyte cell lines constitutively infected or not with HPV. ADAR1 knockdown induced an innate immune response through enhanced expression of RIG-I-like receptors (RLR) signaling cascade, over-production of type-I IFNs and pro-inflammatory cytokines. ADAR1 knockdown enhanced expression of HPV proteins, a process dependent on innate immune function as no A-to-I editing could be identified in HPV transcripts. A genetic association study was performed in a cohort of HPV/HIV infected individuals followed for a median of 6 years (range 0.1–24). We identified the low frequency haplotype AACCAT significantly associated with recurrent HPV dysplasia, suggesting a role of ADAR1 in the outcome of HPV infection in HIV+ individuals. In summary, our results suggest that ADAR1-mediated innate immune activation may influence HPV disease outcome, therefore indicating that modification of innate immune effectors regulated by ADAR1 could be a therapeutic strategy against HPV infection.
Target of initial sub-movement in multi-component arm-reaching strategy
Authors: Peternel Luka , Babič Jan 
Published: December 2019

AbstractGoal-directed human reaching often involves multi-component strategy with sub-movements. In general, the initial sub-movement is fast and less precise to bring the limb’s endpoint in the vicinity of the target as soon as possible. The final sub-movement then corrects the error accumulated during the previous sub-movement in order to reach the target. We investigate properties of a temporary target of the initial sub-movement. We hypothesise that the peak spatial dispersion of movement trajectories in the axis perpendicular to the movement is in front of the final reaching target, and that it indicates the temporary target of the initial sub-movement. The reasoning is that the dispersion accumulates, due to signal-dependent noise during the initial sub-movement, until the final corrective sub-movement is initiated, which then reduces the dispersion to successfully reach the actual target. We also hypothesise that the reaching movement distance and size of the actual target affect the properties of the temporary target of the initial sub-movement. The increased reaching movement distance increases the magnitude of peak dispersion and moves its location away from the actual target. On the other hand, the increased target size increases the magnitude of peak dispersion and moves its location closer to the actual target.
Magnetic resonance microscopy and correlative histopathology of the infarcted heart
Authors: Perez-Terol Itziar , Rios-Navarro Cesar , de Dios Elena , Morales Jose M. , Gavara Jose , Perez-Sole Nerea , Diaz Ana , Minana Gema , Segura-Sabater Remedios , Bonanad Clara , Bayés-Genis Antoni , Husser Oliver , Monmeneu Jose V. , Lopez-Lereu Maria P. , Nunez Julio , Chorro Francisco J. , Ruiz-Sauri Amparo , Bodi Vicente , Monleon Daniel 
Published: December 2019

AbstractDelayed enhancement cardiovascular magnetic resonance (MR) is the gold-standard for non-invasive assessment after myocardial infarction (MI). MR microscopy (MRM) provides a level of detail comparable to the macro objective of light microscopy. We used MRM and correlative histopathology to identify infarct and remote tissue in contrast agent-free multi-sequence MRM in swine MI hearts. One control group (n = 3 swine) and two experimental MI groups were formed: 90 min of ischemia followed by 1 week (acute MI = 6 swine) or 1 month (chronic MI = 5 swine) reperfusion. Representative samples of each heart were analysed by contrast agent-free multi-sequence (T1-weighting, T2-weighting, T2*-weighting, T2-mapping, and T2*-mapping). MRM was performed in a 14-Tesla vertical axis imager (Bruker-AVANCE 600 system). Images from MRM and the corresponding histopathological stained samples revealed differences in signal intensities between infarct and remote areas in both MI groups (p-value < 0.001). The multivariable models allowed us to precisely classify regions of interest (acute MI: specificity 92% and sensitivity 80%; chronic MI: specificity 100% and sensitivity 98%). Probabilistic maps based on MRM images clearly delineated the infarcted regions. As a proof of concept, these results illustrate the potential of MRM with correlative histopathology as a platform for exploring novel contrast agent-free MR biomarkers after MI.