bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of MicroRNAs Targeting mTOR Gene Transcripts in Skin, Lung, Kidney, Uterus and Breast Cancer
Authors: Hadi Wibowo Stefanus Satrio , Agustriawan David , Parikesit Arli Aditya , Nurdiansyah Rizky 
Published: June 2019

Abstract
mTOR constitutively activated during tumorigenesis to stimulates mRNA translation through regulating cell energy metabolism. Using in silico approach based on miTS method, correlation analysis, and meta-analysis method, miRNA biomarker related to five cancer were researched. The input of the pipeline was THCA patients from GDC Data Porta ID and was processed using TCGA2STAT, dplyr, and metacor package in R studio, Excel, and MirTarBase. This study aims to discover the significance level of mTOR in five cancer: HNSC (Head and Neck Squamous Cell), lung adenocarcinoma (LUAD), Kidney Renal Clear Cell Carcinoma (KIRC), Uterine Corpus Endometrial Carcinoma (UCEC), and Breast Invasive Carcinoma (BRCA). Our study shows that in the cancer patient, mTOR tends to support cancer growth despite miRNA targeting it has low correlation rho value. The numerous microRNAs targeting mTOR have a specific role in each tissue, meaning it can be targeted as a precise medicine.
Catalytic synthesis of diethyl carbonate via one-pot reaction from carbon dioxide, ethanol, and epoxide
Authors: Anggerta L A , Kurniawansyah Firman , Wibawa Gede 
Published: June 2019

Abstract
Carbon dioxide is one of the responsible substances of the global warming effect. Gasoline consumption had increased significantly each year, it leads to the intense elevation of particulate matter and carbon dioxide compound in the atmosphere, which are the products of combustion of fuel. Carbon dioxide is possibly converted to high valued compound, diethyl carbonate (DEC) is one of the alternative compounds that is being employed as an additive for fuel to diminish the emission with increasing octane number of the fuel. The objective of this study was to research and develop a technology of direct synthesis of DEC from Carbon dioxide, ethanol, epoxide as dehydrating agent and KI/Sodium Ethoxide and KI/Zeolite catalysts. Operation condition in this experiment had an initial pressure of 35 bar and temperature of 170°C. Further, the effects of KI/Sodium Ethoxide and KI/Zeolite catalysts were examined to the performance of DEC synthesis. In addition, the influence of the type of dehydrating agent (epoxide), which was propylene oxide and butylene oxide was investigated as well. Subsequently, the products were analyzed using gas chromatography-mass spectrometry for qualitative analysis and gas chromatography for quantitative analysis. The results showed that DEC was successfully synthesis from carbon dioxide, and the optimum yield was obtained from the use of KI/Zeolite catalyst, propylene oxide as a dehydrating agent.
Integrated of Sequences Seismic Stratigraphy, Accoustic Impedance Invertion, and Petrophysical for Resources Exploration in Offshore Southern Ardjuna Northwest Java Basin, Indonesia
Authors: Indah M S , Haris Abdul , Natsir M 
Published: June 2019

Abstract
This thesis discusses the uses of the integration of the Stratigraphic Seismic Sequence method, AI Inversion, Petrophysical Evaluation for Exploration Resource Analysis in more detail and more accurately which will produce information on contingent structures ranging from Play concepts, petroleum systems, and properties from reservoir characteristics, to prospect mapping. and evaluation of the risk of exploration findings. Understanding of seismic internal characteristics helps draw stratigraphic sequential seismic markers in seismic cross sections. The Seismic AI invasion will help in the determination of the spread of lithofasies, porosity, fluid in seismic sections. Distribution Map of AI Inversion of Structure Overlays The depth of the interval TST 2 provides trap area parameters for Sand DST 4 located on the Tidal System. Petrophysics will help provide porosity properties, netpay thickness, formation water saturation. The use of this integration method will prove if the evaluation of subsurface data is assessed by Integration of Seismic and Geophysical Methods (Seismic Inversion, Seismic Attribute Analysis, Seismic Stratigraphy Analysis) and Wells Data (DST test data, Fossil Index Catalog, and mud log well) very helpful for evaluating the Half Graben Exploration Resources in an integrated manner.
Application of Particle Swarm Optimization BP Algorithm in Air Humidity of Greenhouse Crops
Authors: Li-Li Guo , Yong Liu , Zi-Wei Liu , Hua-Wei Sun 
Published: June 2019

Abstract
The advancement of artificial intelligence, the synonym of precision agriculture has approached the public’s vision, and the different requirements for air humidity in different growth periods of crops are proposed. The BP neural network optimized by particle swarm optimization algorithm is proposed to predict the air humidity of crops. Algorithm, this paper chooses BP algorithm network topology structure is 2-5-1, improves the inertia weight of PSO algorithm, proposes nonlinear inertia weight reduction strategy

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, trains BP algorithm with improved PSO algorithm, has no gradient information, jumps out local pole Value, reduce the number of iterations of the algorithm, and speed up the training speed of the neural network. According to the experimental results of MATLAB simulation, the air humidity prediction model of particle swarm optimization neural network is constructed, which proves the effectiveness of the improved particle swarm neural network prediction system. It can be shown that the proposed algorithm has a relative error of at least 0.0134 compared with other algorithms.
Design of Secure Enhanced Privacy Protection Electronic Hotel-card Based on QR Code
Authors: Chen Eryang , Ye Ansheng , Miao Fang , Fan Wenjie , Jiang Yi 
Published: June 2019

Abstract
The development of the Internet and economy urges researchers to look for a safe and more economical way to secure online hotel-users’ private information. This study is rooted in online-hotel user personal privacy and some information protection. The traditional RFID hotel-room card was replaced by the proposed QR e-ID, which combines cryptography, verification code, passwords and multi-directional identity authentication module. All of the privacy information should be registered in the data register center (DRC) with encrypted mode. In order to ensure safety in case if the QR e-ID is used by unknown person it needs a password. The main goal of this study is to investigate how the co-use of computers and mobile devices protect online hotel-users’ private information, in addition, reduce the hotel operating costs effectively. The results of the study also provide guidelines to IT developers for future directions in virtual assets protection.
Approximate Yield Estimation of Correlated Failure Events for Near-threshold SRAM
Authors: Sun Zhongmao , Huang Shuaibo , Yan Hao 
Published: June 2019

Abstract
In advanced manufacturing technology, SRAM yield estimation with correlation is a significant challenge due to process variations and structures especially at low voltage. In this paper, Double Asymptotic Probability Approximation (DAPA) method with Subset Analytical Model (SAM) is proposed to effectively estimate the probability of correlated failure event. SAM models SRAM failure events based on simulation of subsets of the equivalent circuit. DAPA obtains the recursive function of partial failure rate. The key idea is to approximate the failure rate of the entire system based on a linear combination of partial failure rates by decoupling failure correlation. Under TSMC 28 nm process, (M=N=8) SRAM failure rate is estimated at 500 mV with an error of less than 5% by the proposed method. Besides 2.5 hours of modeling consumption, the calculation can be completed in 7 seconds, which greatly reduces SRAM failure estimation time, compared with Monte Carlo method.
The Generalized Modular Design Method of Emergency Rescue Equipment Vehicle
Authors: Anhu Li , Qiao Li , Fei Gao , Yihe Zhou , Guangjun Liu , Mengru Li 
Published: June 2019

Abstract
Emergency rescue equipment vehicles (EREV), with the ability that carry a variety of rescue equipment in different rescue scenes, play an important role in emergency rescue field. However, there still exists some issues in existing EREV products, such as small types and quantity, large volume, small loading capacity, low design efficiency and so on, which can not meet the increasingly complex rescue needs. Because of its low cost, high efficiency, strong interchangeability and reliable product performance, the modular design technology is widely used in machine tool manufacturing, toy production, electronic products, aerospace, automobile manufacturing, building construction and other fields. In this paper, a process model of the generalized modular design method for EREV is designed in order to solve the above issues. All structures and functions of modules in a product genealogy are expressed in a matrix form. This generalized modular design method proposed in this paper gives theoretical references to the design issues of other similar construction machinery devices.
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons
Authors: Chagas Vinicius S , Groeneveld Clarice S , Oliveira Kelin G , Trefflich Sheyla , de Almeida Rodrigo C , Ponder Bruce A J , Meyer Kerstin B , Jones Steven J M , Robertson A Gordon , Castro Mauro A A 
Published: June 2019

Abstract

Motivation
Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analyzing pairs of regulons.

Results
RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts.

Availability and implementation
RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Isoform function prediction based on bi-random walks on a heterogeneous network
Authors: Yu Guoxian , Wang Keyao , Domeniconi Carlotta , Guo Maozu , Wang Jun 
Published: June 2019

Abstract

Motivation
Alternative splicing contributes to the functional diversity of protein species and the proteoforms translated from alternatively spliced isoforms of a gene actually execute the biological functions. Computationally predicting the functions of genes has been studied for decades. However, how to distinguish the functional annotations of isoforms, whose annotations are essential for understanding developmental abnormalities and cancers, is rarely explored. The main bottleneck is that functional annotations of isoforms are generally unavailable and functional genomic databases universally store the functional annotations at the gene level.

Results
We propose IsoFun to accomplish Isoform Function prediction based on bi-random walks on a heterogeneous network. IsoFun firstly constructs an isoform functional association network based on the expression profiles of isoforms derived from multiple RNA-seq datasets. Next, IsoFun uses the available Gene Ontology annotations of genes, gene–gene interactions and the relations between genes and isoforms to construct a heterogeneous network. After this, IsoFun performs a tailored bi-random walk on the heterogeneous network to predict the association between GO terms and isoforms, thus accomplishing the prediction of GO annotations of isoforms. Experimental results show that IsoFun significantly outperforms the state-of-the-art algorithms and improves the area under the receiver-operating curve (AUROC) and the area under the precision-recall curve (AUPRC) by 17% and 44% at the gene-level, respectively. We further validated the performance of IsoFun on the genes ADAM15 and BCL2L1. IsoFun accurately differentiates the functions of respective isoforms of these two genes.

Availability and implementation
The code of IsoFun is available at http://mlda.swu.edu.cn/codes.php? name=IsoFun.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cohesin complex-associated holoprosencephaly
Authors: Kruszka Paul , Berger Seth I , Casa Valentina , Dekker Mike R , Gaesser Jenna , Weiss Karin , Martinez Ariel F , Murdock David R , Louie Raymond J , Prijoles Eloise J , Lichty Angie W , Brouwer Oebele F , Zonneveld-Huijssoon Evelien , Stephan Mark J , Hogue Jacob , Hu Ping , Tanima-Nagai Momoko , Everson Joshua L , Prasad Chitra , Cereda Anna , Iascone Maria , Schreiber Allison , Zurcher Vickie , Corsten-Janssen Nicole , Escobar Luis , Clegg Nancy J , Delgado Mauricio R , Hajirnis Omkar , Balasubramanian Meena , Kayserili Hülya , Deardorff Matthew , Poot Raymond A , Wendt Kerstin S , Lipinski Robert J , Muenke Maximilian 
Published: June 2019

AbstractMarked by incomplete division of the embryonic forebrain, holoprosencephaly is one of the most common human developmental disorders. Despite decades of phenotype-driven research, 80–90% of aneuploidy-negative holoprosencephaly individuals with a probable genetic aetiology do not have a genetic diagnosis. Here we report holoprosencephaly associated with variants in the two X-linked cohesin complex genes, STAG2 and SMC1A, with loss-of-function variants in 10 individuals and a missense variant in one. Additionally, we report four individuals with variants in the cohesin complex genes that are not X-linked, SMC3 and RAD21. Using whole mount in situ hybridization, we show that STAG2 and SMC1A are expressed in the prosencephalic neural folds during primary neurulation in the mouse, consistent with forebrain morphogenesis and holoprosencephaly pathogenesis. Finally, we found that shRNA knockdown of STAG2 and SMC1A causes aberrant expression of HPE-associated genes ZIC2, GLI2, SMAD3 and FGFR1 in human neural stem cells. These findings show the cohesin complex as an important regulator of median forebrain development and X-linked inheritance patterns in holoprosencephaly.
Decoding Changes of Mind in Voluntary Action—Dynamics of Intentional Choice Representations
Authors: Löffler Anne , Haggard Patrick , Bode Stefan 
Published: June 2019

AbstractVoluntary actions rely on appropriate flexibility of intentions. Usually, we should pursue our goals, but sometimes we should change goals if they become too costly to achieve. Using functional magnetic resonance imaging, we investigated the neural dynamics underlying the capacity to change one’s mind based on new information after action onset. Multivariate pattern analyses revealed that in visual areas, neural representations of intentional choice between 2 visual stimuli were unchanged by additional decision-relevant information. However, in fronto-parietal cortex, representations changed dynamically as decisions evolved. Precuneus, angular gyrus, and dorsolateral prefrontal cortex encoded new externally cued rewards/costs that guided subsequent changes of mind. Activity in medial frontal cortex predicted changes of mind when participants detached from externally cued evidence, suggesting a role in endogenous decision updates. Finally, trials with changes of mind were associated with an increase in functional connectivity between fronto-parietal areas, allowing for integration of various endogenous and exogenous decision components to generate a distributed consensus about whether to pursue or abandon an initial intention. In conclusion, local and global dynamics of choice representations in fronto-parietal cortex allow agents to maintain the balance between adapting to changing environments versus pursuing internal goals.
Impact of apical foreshortening on deformation measurements: a report from the EACVI-ASE Strain Standardization Task Force
Authors: Ünlü Serkan , Duchenne Jürgen , Mirea Oana , Pagourelias Efstathios D , Bézy Stéphanie , Cvijic Marta , Beela Ahmed Salem , Thomas James D , Badano Luigi P , Voigt Jens-Uwe ,   EACVI-ASE Industry Standardization Task Force, Badano Luigi P , Thomas James D , Hamilton Jamie , Pedri Stefano , Lysyansky Peter , Hansen Gunnar , Ito Yasuhiro , Chono Tomoaki , Vogel Jane , Prater David , Song Joo Hyun , Lee Jin Yong , Houle Helene , Georgescu Bogdan , Baumann Rolf , Mumm Bernhard , Abe Yashuhiko , Gorissen Willem 
Published: June 2019

Abstract

Aims
Foreshortening of apical views is a common problem in echocardiography. It results in an abnormally thick false apex and a shortened left ventricular (LV) long axis. We sought to evaluate the impact of foreshortened (FS) on LV ejection fraction (LVEF) and layer-specific 2D speckle tracking based segmental (S) and global (G) longitudinal strain (LS) measurements.

Methods and results
We examined 72 participants using a GE Vivid E9 system. FS apical views were collected from an imaging window one rib-space higher than the optimal images. Ejection fraction as well as layer-specific GLS and SLS measurements were analysed by GE EchoPAC v201 and TomTec Image Arena 4.6 and compared between optimal and FS images. On average, LV long axis was 10% shorter in FS images than in optimal images. FS induced a relative change in LVEF of 3.3% and 6.9% for GE and TomTec, respectively (both, P < 0.001). Endocardial GLS was 9.0% higher with GE and 23.2% with TomTec (P < 0.001). Midwall GLS measurements were less affected (7.8% for GE and 14.1% for TomTec, respectively, both P < 0.001). Segmental strain analysis revealed that the mid-ventricular and apical segments were more affected by foreshortening, and endocardial measurements were more affected than midwall.

Conclusion
Optimal image geometry is crucial for accurate LV function assessment. Foreshorhening of apical views has a substantial impact on longitudinal strain measurements, predominantly in the apex and in the endocardial layer. Our data suggest that measuring midwall strain might therefore be the more robust approach for clinical routine use.
A leguminous species exploiting alpha- and beta-rhizobia for adaptation to ultramafic and volcano-sedimentary soils: an endemic Acacia spirorbis model from New Caledonia
Authors: Vincent Bryan , Juillot Farid , Fritsch Emmanuel , Klonowska Agnieszka , Gerbert Noëmie , Acherar Sarah , Grangeteau Cedric , Hannibal Laure , Galiana Antoine , Ducousso Marc , Jourand Philippe 
Published: June 2019

ABSTRACTAcacia spirorbis subsp. spirorbis Labill. is a widespread tree legume endemic to New Caledonia that grows in ultramafic (UF) and volcano-sedimentary (VS) soils. The aim of this study was to assess the symbiotic promiscuity of A. spirorbis with nodulating and nitrogen-fixing rhizobia in harsh edaphic conditions. Forty bacterial strains were isolated from root nodules and characterized through (i) multilocus sequence analyses, (ii) symbiotic efficiency and (iii) tolerance to metals. Notably, 32.5% of the rhizobia belonged to the Paraburkholderia genus and were only found in UF soils. The remaining 67.5%, isolated from both UF and VS soils, belonged to the Bradyrhizobium genus. Strains of the Paraburkholderia genus showed significantly higher nitrogen-fixing capacities than those of Bradyrhizobium genus. Strains of the two genera isolated from UF soils showed high metal tolerance and the respective genes occurred in 50% of strains. This is the first report of both alpha- and beta-rhizobia strains associated to an Acacia species adapted to UF and VS soils. Our findings suggest that A. spirorbis is an adaptive plant that establishes symbioses with whatever rhizobia is present in the soil, thus enabling the colonization of contrasted ecosystems.
Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack
Authors: Venneman Jolien , De Tender Caroline , Debode Jane , Audenaert Kris , Baert Geert , Vermeir Pieter , Cremelie Pieter , Bekaert Boris , Landschoot Sofie , Thienpondt Bert , Djailo Benoît Dhed'a , Vereecke Danny , Haesaert Geert 
Published: June 2019

ABSTRACTThe unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant–fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) spa type t127, Sequence Type (ST)1, quickly spreads and persists among young pigs
Authors: Merialdi Giuseppe , Feltrin Fabiola , Gaetarelli Barbara , Lombardi Guerino , Iurescia Manuela , Alba Patricia , Luppi Andrea , Martinelli Nicola , Ramini Mattia , Carfora Virginia , Franco Alessia , Battisti Antonio 
Published: June 2019

ABSTRACT
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clones other than Clonal Complex (CC)398, as CC1, have been isolated in pigs in some countries, and appeared to be prevalent in Italy. The aim of this study was to evaluate the capability of Sequence Type (ST)1, CC1, LA-MRSA clone to colonize and to be transmitted among piglets. Eighteen caesarean-derived/colostrum-deprived piglets of 35 days of age were assigned randomly to three groups: four seeder piglets were contaminated with a spa type t127, ST1, SCCmec V, MRSA (Group A), 10 MRSA-negative piglets were exposed to Group A after 2 days post-contamination, dpc (Group B) and 4 piglets were used as control group (Group C). Piglets were evaluated until 44 dpc (Group A) or at 42 days post-exposure, dpe (Group B) and then euthanized and necropsied. All nasal and skin cultures of Group A resulted MRSA-positive throughout the experiment starting from two dpc, while Group C tested always MRSA-negative. At first sampling, all Group B piglets became positive and remained positive throughout the experiment. This is the first colonization/transmission study with a CC1 LA-MRSA in pigs. The results add further knowledge on the ability of CC1 LA-MRSA to colonize pigs, and on colonization/transmission patterns, both suggesting good host adaptation.