bluuebunny/crossref_metadata_2025_split huggingface dataset:
MITRE: predicting host status from microbiota time-series data
Authors: Bogart Elijah , Creswell Richard , Gerber Georg K. 
Published: October 2018

AbstractLongitudinal studies are crucial for discovering casual relationships between the microbiome and human disease. We present Microbiome Interpretable Temporal Rule Engine (MITRE), the first machine learning method specifically designed for predicting host status from microbiome time-series data. Our method maintains interpretability by learning predictive rules over automatically inferred time-periods and phylogenetically related microbes. We validate MITRE’s performance on semi-synthetic data, and five real datasets measuring microbiome composition over time in infant and adult cohorts. Our results demonstrate that MITRE performs on par or outperforms “black box” machine learning approaches, providing a powerful new tool enabling discovery of biologically interpretable relationships between microbiome and human host.
Tactile enrichment drives emergence of functional columns and improves sensory coding in L2/3 of mouse S1
Authors: LeMessurier Amy M. , Feldman Daniel E. 
Published: October 2018

SUMMARYSensory maps in layer (L) 2/3 of rodent cortex lack precise functional column boundaries, and instead exhibit locally heterogeneous tuning superimposed on smooth global topography. Could this organization be a byproduct of impoverished experience in laboratory housing? We compared whisker map somatotopy in L2/3 and L4 excitatory cells of somatosensory (S1) cortex in normally housed vs. tactile-enriched mice, using GCaMP6s imaging. Normally housed mice had a dispersed, salt-and-pepper whisker map in L2/3, but L4 was more topographically precise. Enrichment (P21 to P46-71) sharpened whisker tuning and decreased, but did not abolish, local tuning heterogeneity. In L2/3, enrichment strengthened and sharpened whisker point representations, and created functional boundaries of tuning similarity and noise correlations at column edges. Thus, tactile experience drives emergence of functional columnar topography in S1, and reduces salt-and-pepper tuning heterogeneity. These changes predict improved single-trial population coding of whisker deflections within each column.
Reward prediction error does not explain movement selectivity in DMS-projecting dopamine neurons
Authors: Lee Rachel S. , Mattar Marcelo G. , Parker Nathan F. , Witten Ilana B. , Daw Nathaniel D. 
Published: October 2018

AbstractAlthough midbrain dopamine (DA) neurons have been thought to primarily encode reward prediction error (RPE), recent studies have also found movement-related DAergic signals. For example, we recently reported that DA neurons in mice projecting to dorsomedial striatum are modulated by choices contralateral to the recording side. Here, we introduce, and ultimately reject, a candidate resolution for the puzzling RPE vs movement dichotomy, by showing how seemingly movement-related activity might be explained by an action-specific RPE. By considering both choice and RPE on a trial-by-trial basis, we find that DA signals are modulated by contralateral choice in a manner that is distinct from RPE, implying that choice encoding is better explained by movement direction. This fundamental separation between RPE and movement encoding may help shed light on the diversity of functions and dysfunctions of the DA system.
Computational Analysis of Single Nucleotide polymorphisms (SNPs) in Human TCell Acute Lymphocytic Leukemia Protein 1 (TAL1) Gene/Comprehensive Study
Authors: Shantier Shaza W. , Elmansi Hashim E. , Elnnewery Mihad E. , Osman Hind K. , Alhassan Isam-Aldin A. , Abdelrhman Fatima A. , Yagaub Ahmed A. , Yousif Einas M. , Abdalla Alaa I. , Elamin Rawan A. , Fadol Howina S. , Fadl Alla Afra A. , Hassan Mohamed A. 
Published: October 2018

AbstractBackgroundTAL1is a proto-oncogene whose distorted modifications in committed T-cell Precursors is related with the development of T-ALL, it also found to be related to many other human hematological diseases such as lymphoblastic lymphoma, immunodeficiency 18, acute myeloid leukemia and diamond-blackfan Anemia.ObjectivesThis study aims to predict the effect of nsSNPs onTAL1protein structure functionMethodsRetrieved nSNPs in the coding and3’UTRregions were analyzed using different in silico tools. Interactions ofTAL1with functionally similar genes were investigated using Genemania. Post-translational modifications in several sites of the protein were also investigated.ResultsOut of ninety nsSNPs identified, only eight were found damaging to protein function of which one is located in the basis helix-loop-helix domain (bHLH). Two SNPs were anticipated by PolymiRTs to prompt disturbance or creation of miR binding sites.ConclusionThe present study is the first ever computational analysis ofTAL1’s nsSNPs hence this effort might be of help in the near future for inventing early diagnostic and therapeutic measures for T-ALL
Setting Starting Level for a Trial of an Biofilm-Disrupting Adjuvant
Authors: Adams Braden , Lodder Robert A. 
Published: October 2018

AbstractCombination therapy is beneficial treatment modality for multiple diseases. Cinnamon oil may be an advantageous agent in a number of combination therapies as cinnamon oil has antibacterial activity. Cinnamon oil has also been shown to be effective against biofilm cultures of Streptococcus mutans and Lactobacillus plantarum. Cinnamomum osmophloeum inhibits planktonic cultures of many gram-positive and gram-negative bacteria, including MRSA (methicillin-resistant Staphylococcus aureus). Subjecting S. epidermidis to cinnamon oil eliminates planktonic cells or staphylococci in biofilms. Cinnamon oil is an essential oil used throughout the food industry because of its pleasant and distinctive aroma. The purpose of this study is to estimate the amount of exposure to cinnamon through selected foods in the United States in order to propose an initial target level for pharmacokinetic studies of a novel combination drug.
Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth
Authors: Pizzinga Mariavittoria , Bates Christian , Lui Jennifer , Forte Gabriella , Morales-Polanco Fabián , Linney Emma , Knotkova Barbora , Wilson Beverley , Solari Clara A. , Berchowitz Luke E. , Portela Paula , Ashe Mark P. 
Published: October 2018

AbstractmRNA localization serves key functions in localized protein production making it critical that the translation machinery itself is present at these locations. Here we show that translation factor mRNAs are localized to distinct granules within yeast cells. In contrast to many mRNP granules, such as P-bodies and stress granules, which contain translationally repressed mRNAs, these granules harbor translated mRNAs under active growth conditions. The granules require Pablp for their integrity and are inherited by developing daughter cells in a She2p/ She3p dependent manner. These results point to a model where roughly half the mRNA for certain translation factors are specifically directed in granules toward the tip of the developing daughter cell where protein synthesis is most heavily required, which has particular implications for filamentous forms of growth. Such a feedforward mechanism would ensure adequate provision of the translation machinery where it is to be needed most over the coming growth cycle.SummaryThis study shows that mRNAs encoding a range of translation factors are localized to granules that get transported into the yeast daughter cell using the She2p/She3p machinery. This likely supports an intensification of protein synthetic activity to facilitate apical polarized growth.
Jackknife model averaging prediction methods for complex phenotypes with gene expression levels by integrating external pathway information
Authors: Yu Xinghao , Xiao Lishun , Zeng Ping , Huang Shuiping 
Published: October 2018

AbstractMotivationIn the past few years many novel prediction approaches have been proposed and widely employed in high dimensional genetic data for disease risk evaluation. However, those approaches typically ignore in model fitting the important group structures or functional classifications that naturally exists in genetic data.MethodsIn the present study, we applied a novel model averaging approach, called Jackknife Model Averaging Prediction (JMAP), for high dimensional genetic risk prediction while incorporating KEGG pathway information into the model specification. JMAP selects the optimal weights across candidate models by minimizing a cross-validation criterion in a jackknife way. Compared with previous approaches, one of the primary features of JMAP is to allow model weights to vary from 0 to 1 but without the limitation that the summation of weights is equal to one. We evaluated the performance of JMAP using extensive simulation studies and compared it with existing methods. We finally applied JMAP to five real cancer datasets that are publicly available from TCGA.ResultsThe simulations showed that, compared with other existing approaches, JMAP performed best or are among the best methods across a range of scenarios. For example, among 14 out of 16 simulation settings with PVE=0.3, JMAP has an average of 0.075 higher prediction accuracy compared with gsslasso. We further found that in the simulation the model weights for the true candidate models have much smaller chances to be zero compared with those for the null candidate models and are substantially greater in magnitude. In the real data application, JMAP also behaves comparably or better compared with the other methods for both continuous and binary phenotypes. For example, for the COAD, CRC and PAAD data sets, the average gains of predictive accuracy of JMAP are 0.019, 0.064 and 0.052 compared with gsslasso.ConclusionThe proposed method JMAP is a novel method that can provide more accurate phenotypic prediction while incorporating external useful group information.
Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway
Authors: Resa-Infante Patricia , Bonet Jaume , Thiele Swantje , Alawi Malik , Oliva Baldo , Gabriel Gülsah 
Published: October 2018

ABSTRACTInfluenza A viruses are able to adapt to restrictive conditions due to their high mutation rates. Here, we addressed the question by which mechanisms influenza A viruses may escape restriction by the cellular importin-α7 protein, a component of the nuclear import machinery required for avian-mammalian adaptation and replicative fitness in human cells. Therefore, we assessed viral evolution in mice lacking the importin-α7 gene. Here, we show that particularly three mutations occur with high frequency in the viral NP protein (G102R, M105K and D375N) in a specific structural area uponin vivoadaptation. Moreover, our findings suggest that the adaptive NP mutations mediate viral escape from importin-α7 requirement likely due to the utilization of alternative interaction sites in NP beyond the classical nuclear localization signal and importin-α isoforms. However, viral escape from importin-α7 is, at least in part, associated with reduced replicative fitness in human cells.
Collective radioresistance of T47D breast carcinoma cells is mediated by a Syncytin-1 homologous protein
Authors: Chignola Roberto , Sega Michela , Molesini Barbara , Baruzzi Anna , Stella Sabrina , Milotti Edoardo 
Published: October 2018

AbstractIt is generally accepted that radiotherapy must target clonogenic cells, i.e., those cells in a tumour that have self-renewing potential. Focussing on isolated clonogenic cells, however, may lead to an underestimate or even to an outright neglect of the importance of biological mechanisms that regulate tumour cell sensitivity to radiation. We develop a new statistical and experimental approach to quantify the effects of radiation on cell populations as a whole. In our experiments, we change the proximity relationships of the cells by culturing them in wells with different shapes, and we find that the radiosensitivity of T47D human breast carcinoma cells in tight clusters is different from that of isolated cells. Molecular analyses show that T47D cells express a Syncytin-1 homologous protein (SyHP). We observe that SyHP translocates to the external surface of the plasma membrane of cells killed by radiation treatment. The data support the fundamental role of SyHP in the formation of intercellular cytoplasmic bridges and in the enhanced radioresistance of surviving cells. We conclude that complex and unexpected biological mechanisms of tumour radioresistance take place at the cell population level. These mechanisms may significantly bias our estimates of the radiosensitivity of breast carcinomasin vivoand thereby affect treatment plans, and they call for further investigations.
Analysis of an HIV model with post-treatment control
Authors: Wang Shaoli , Xu Fei 
Published: October 2018

AbstractRecent investigation indicated that latent reservoir and immune impairment are responsible for the post-treatment control of HIV infection. In this paper, we simplify the disease model with latent reservoir and immune impairment and perform a series of mathematical analysis. We obtain the basic infection reproductive number R0 to characterize the viral dynamics. We prove that when R0 < 1, the uninfected equilibrium of the proposed model is globally asymptotically stable. When R0 > 1, we obtain two thresholds, the post-treatment immune control threshold and the elite control threshold. The model has bistable behaviors in the interval between the two thresholds. If the proliferation rate of CTLs is less than the post-treatment immune control threshold, the model does not have positive equilibria. In this case, the immune free equilibrium is stable and the system will have virus rebound. On the other hand, when the proliferation rate of CTLs is greater than the elite control threshold, the system has stable positive immune equilibrium and unstable immune free equilibrium. Thus, the system is under elite control.Author summaryIn this article, we use mathematical model to investigate the combined effect of latent reservoir and immune impairment on the post-treatment control of HIV infection. By simplifying an HIV model with latent reservoir and immune impairment, and performing mathematical analysis, we obtain the post-treatment immune control threshold and the elite control threshold for the HIV dynamics when R0 > 1. The HIV model displays bistable behaviors in the interval between the two thresholds. We illustrate our results using both mathematical analysis and numerical simulation. Our result is consistent with recent medical experiment. We show that patient with low proliferation rate of CTLs may undergo virus rebound, and patient with high proliferation rate of CTLs may obtain elite control of HIV infection. We perform bifurcation analysis to illustrate the infection status of patient with the variation of proliferation rate of CTLs, which potentially explain the reason behind different outcomes among HIV patients.
Wolbachia endosymbionts subvert the endoplasmic reticulum to acquire host membranes without triggering ER stress
Authors: Fattouh Nour , Cazevieille Chantal , Landmann Frédéric 
Published: October 2018

AbstractThe reproductive parasite Wolbachia are the most common endosymbionts on earth, present in a plethora of arthropod species. They have been introduced into mosquitos to successfully prevent the spread of vector-borne diseases, yet the strategies of host cell subversion underlying their obligate intracellular lifestyle remain to be explored in depth in order to gain insights into the mechanisms of pathogen-blocking. Like some other intracellular bacteria, Wolbachia reside in a host-derived vacuole in order to replicate and escape the immune surveillance. Using here the pathogen-blocking Wolbachia strain from Drosophila melanogaster, introduced into two different Drosophila cell lines, we show that Wolbachia subvert the endoplasmic reticulum to acquire their vacuolar membrane and colonize the host cell at high density. Wolbachia redistribute the endoplasmic reticulum to increase contact sites, and time lapse experiments reveal tight coupled dynamics suggesting important signalling events or nutrient uptake. They however do not affect the tubular or cisternal morphologies. A fraction of endoplasmic reticulum becomes clustered, allowing the endosymbionts to reside in between the endoplasmic reticulum and the Golgi apparatus, possibly modulating the traffic between these two organelles. Gene expression analyses and immunostaining studies suggest that Wolbachia achieve persistent infections at very high titers without triggering endoplasmic reticulum stress or enhanced ERAD-driven proteolysis, suggesting that amino acid salvage is achieved through modulation of other signalling pathways.Author summaryWolbachia are a genus of intracellular bacteria living in symbiosis with millions of arthropod species. They have the ability to block the transmission of arboviruses when introduced into mosquito vectors, by interfering with the cellular resources exploited by these viruses. Despite the biomedical interest of this symbiosis, little is known about the mechanisms by which Wolbachia survive and replicate in the host cell. We show here that the membrane composing the Wolbachia vacuole is acquired from the endoplasmic reticulum, a central organelle required for protein and lipid synthesis, and from which originates a vesicular trafficking toward the Golgi apparatus and the secretory pathway. Wolbachia modify the distribution of this organelle to increase their interactions with this source of membrane and likely of nutrients as well. In contrast to some intracellular pathogenic bacteria, the effect of Wolbachia on the cell homeostasis does not induce a stress on the endoplasmic reticulum. One of the consequences of such a stress would be an increased proteolysis used to relieve the cell from an excess of misfolded proteins. Incidentally, this shows that Wolbachia do not acquire amino acids from the host cell through this strategy.
Major Domestication-Related Phenotypes inIndicaRice Are Due to Loss of miRNA-Mediated Laccase Silencing
Authors: Swetha Chenna , Basu Debjani , Pachamuthu Kannan , Tirumalai Varsha , Nair Ashwin , Prasad Melvin , Shivaprasad P. V. 
Published: October 2018

AbstractDomestication of rice (Oryza sativa) included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key proteins such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA-mediated regulation. Analysis of small (s) RNA data sets from cultivated indica rice lines, a few landraces, and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 was expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs encoding laccases that decayed and induced robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, overexpression of miR397 induced de-domestication phenotypes. At least 26 uncharacterized QTLs previously implicated in rice yield overlapped with laccases and miR397 genes. These results suggest that miRNAs contribute to rice domestication-associated phenotypes.
Hybridization of training aircraft with real world flight profiles
Authors: Donateo Teresa , Totaro Roberto 
Published: October 2018

Purpose
The purpose of this paper is to analyze real-world flight data of a piston engine training aircraft collected from an internet-based radar service, along with wind data provided by a weather forecast model, and to use such data to design a hybrid electric power system.

Design/methodology/approach
The modeling strategy starts from the power demand imposed by a real-world wind-corrected flight profile, where speed and altitude are provided as functions of time, and goes through the calculation of the efficiency of the powertrain components when they meet such demand. Each component of the power system and, in particular, the engine and the propeller, is simulated as a black box with an efficiency depending on the actual working conditions. In the case of hybrid electric power system, the battery charging and discharging processes are simulated with the Shepherd model.

Findings
The variability of power demand and fuel consumption for a training aircraft is analyzed by applying the proposed methodology to the Piper PA-28-180 Cherokee, a very popular aircraft used for flight training, air taxi and personal use. The potentiality of hybridization is assessed by analyzing the usage of the engine over more than 90 flights. A tentative sizing of a hybrid electric power system is also proposed. It guarantees a fuel saving of about 5%.

Originality/value
The scientific contribution and the novelty of the investigation are related to the modeling methodology, which takes into account real-world flight conditions, and the application of hybridization to a training aircraft.
Satellite angular motion classification for active on-orbit debris removal using robots
Authors: Seweryn Karol , Sasiadek Jurek Z. 
Published: October 2018

PurposeThis paper aims to present a novel method for identification and classification of rotational motion for uncontrolled satellites. These processes are shown in context of close proximity orbital operations. In particular, it includes a manipulator arm mounted on chaser satellite and used to capture target satellites. In such situations, a precise extrapolation of the target’s docking port position is needed to determine the manipulator arm motion. The outcome of this analysis might be used in future debris removal or servicing space missions.Design/methodology/approachNonlinear, and in some special cases, chaotic nature of satellite rotational motion was considered. Four parameters were defined: range of motion toward docking port, dominant frequencies, fractal dimension of the motion and its time dependencies.FindingsThe qualitative analysis was performed for presented cases of spacecraft rotational motion and for each case the respective parameters were calculated. The analysis shows that it is possible to detect the type of rotational motion.Originality/valueA novel procedure allowing to estimate the type of satellite rotational motion based on fractal approach was proposed.