bluuebunny/crossref_metadata_2025_split huggingface dataset:
A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization
Authors: Barth Zachary K , Netter Zoe , Angermeyer Angus , Bhardwaj Pooja , Seed Kimberley D 
Published: March 2020

AbstractMany viruses possess temporally unfolding gene expression patterns aimed at subverting host defenses, commandeering host metabolism, and ultimately producing a large number of progeny virions. High throughput -omics tools, such as RNA-seq, have dramatically enhanced resolution of expression patterns during infection. Less studied have been viral satellites, mobile genomes that parasitize viruses and have far reaching effects on host-cell fitness. By performing RNA-seq on infection time courses, we have obtained the first time-resolved transcriptomes for bacteriophage satellites during lytic infection. Specifically, we have acquired transcriptomes for the lyticVibrio choleraephage ICP1 and all five known variants of ICP1’s parasite, thePhage Inducible Chromosomal Island-LikeElements (PLEs). PLEs rely on ICP1 for both DNA replication and mobilization, and abolish production of ICP1 progeny in infected cells. We investigated PLEs impact on ICP1 gene expression and found that PLEs did not broadly restrict or reduce ICP1 gene expression. A major exception occurred in ICP1’s capsid morphogenesis operon, which was downregulated by each of the PLE variants. This transcriptional manipulation, conserved among PLEs, has also evolved independently in at least one other phage satellite, suggesting that viral satellites may be under strong selective pressure to reduce the capsid expression of their larger host viruses. Surprisingly, PLEs were also found to alter the gene expression of CTXϕ, the integrative phage that encodes cholera toxin and is necessary for virulence of toxigenicV. cholerae. One PLE, PLE1, upregulated CTXϕ genes involved in replication and integration, and boosted CTXϕ mobility following induction of the SOS response. Our data show that PLEs exhibit conserved manipulation of their host-phage’s gene expression, but divergent effects on CTXϕ, revealing that PLEs can influence both their hosts’ resistance to phage and the mobility of virulence encoding elements.
A Piezo1 Open State Reveals a Multi-fenestrated Ion Permeation Pathway
Authors: Jiang Wenjuan , Del Rosario John Smith , Botello-Smith Wesley , Zhao Siyuan , Lin Yi-chun , Zhang Han , Lacroix Jérôme , Rohacs Tibor , Luo Yun Lyna 
Published: March 2020

ABSTRACTForce-sensing Piezo channels are essential to many aspects of vertebrate physiology. Activation of Piezo1 is facilitated by the presence of negative membrane lipids in the inner leaflet, such as phosphatidylinositol-4,5-bisphosphate (PIP2). Here, to study how Piezo1 opens, we performed molecular dynamics simulations of Piezo1 in membranes flattened by the periodic boundary effect and with or without PIP2 lipids. The Piezo1 pore spontaneously opens in the asymmetrical bilayer but not in the symmetric membrane or when PIP2 lipids are neutralized. Electrophysiological characterization of putative PIP2-interacting Piezo1 residues suggests the contribution of multiple PIP2 binding sites. Our Piezo1 open state recapitulates ionic selectivity, unitary conductance and mutant phenotypes obtained from numerous experimental studies. Tracking ion diffusion through the open pore reveals the presence of intracellular and extracellular fenestrations, delineating a multi-fenestrated permeation pathway. This open state sheds light on the mechanisms of lipid modulation, permeation, and selectivity in a Piezo channel.
Translational accuracy of a tethered ribosome
Authors: Fabret Celine , Namy Olivier 
Published: March 2020

AbstractRibosomes are evolutionary conserved ribonucleoprotein complexes that function as two separate subunits in all kingdoms. During translation initiation, the two subunits assemble to form the mature ribosome, which is responsible for translating the messenger RNA. When the ribosome reaches a stop codon, release factors promote translation termination and peptide release, and recycling factors then dissociate the two subunits, ready for use in a new round of translation. A tethered ribosome, called Ribo-T, in which the two subunits are covalently linked to form a single entity, was recently described inEscherichia coli1. A hybrid ribosomal RNA (rRNA) consisting of both the small and large subunit rRNA sequences was engineered. The ribosome with inseparable subunits generated in this way was shown to be functional and to sustain cell growth. Here, we investigated the translational properties of Ribo-T. We analyzed its behavior in −1 or +1 frameshifting, stop codon readthrough, and internal translation initiation. Our data indicate that covalent attachment of the two subunits modifies the properties of the ribosome, altering its ability to initiate and terminate translation correctly.
Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh
Authors: Yulandi Adi , Waturangi Diana Elizabeth , Wahyudi Aris Tri , Suwanto Antonius 
Published: March 2020

AbstractObjectiveAmplicon sequencing targeted 16S ribosomal RNA (rRNA) has been widely used for the analysis profile of the microbial community from fermented food samples. Previous results of 16S rRNA analysis metagenome showed thatFirmicuteswas the dominantphylumin tempeh. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in the estimation of microbial community composition. An alternative approach known as shotgun metagenomic might be able to avoid this limitation. In this study, we employed total metagenomic DNA fragments sequenced directly for taxonomic dan functional profiling analysis.ResultTaxonomic profiling showed thatProteobacteria,Firmicutes, andBacteroideteswere the dominantphylafrom direct shotgun metagenomic analysis in all tempeh samples. In terms of composition, the shotgun metagenomic study revealed thatProteobacteriawas the most relatively abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed genes based on metagenome from tempeh samples.
The Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurement with Biomolecular Simulations
Authors: Fuchigami Sotaro , Niina Toru , Takada Shoji 
Published: March 2020

ABSTRACTThe high-speed atomic force microscopy (HS-AFM) can observe structural dynamics of biomolecules at single-molecule level in real time near physiological condition, but its spatiotemporal resolution is limited. Complementarily, molecular dynamics (MD) simulations have higher spatiotemporal resolutions albeit with some artifact. Here, in order to integrate the HS-AFM data and coarse-grained (CG)-MD simulations, we develop a particle filter method, one of the sequential Bayesian data assimilation approaches. We tested the method in a twin experiment. We first made a reference HS-AFM movie from a CG-MD trajectory of a test molecule, a nucleosome, which serves as an “experimental measurement”. Then, we performed the particle filter simulation with 512 particles that captured large-scale nucleosome structural dynamics compatible with the AFM movie. Comparing the particle filter simulations with 8 - 8192 particles, we found that the use of more particles consistently results in larger likelihood for the whole AFM movie. By comparing the likelihoods from different ionic concentrations and from different timescales, we found that the “true” concentration and timescale can be inferred as the largest likelihood of the whole AFM movie, but not that of each AFM image. The particle filter method provides a general approach to integrate the HS-AFM data with MD simulations.
Uncovering new drug properties in target-based drug-drug similarity networks
Authors: Udrescu Lucreţia , Bogdan Paul , Chiş Aimée , Sîrbu Ioan Ovidiu , Topîrceanu Alexandru , Văruţ Renata-Maria , Udrescu Mihai 
Published: March 2020

ABSTRACTDespite recent advances in bioinformatics, systems biology, and machine learning, the accurate prediction of drug properties remains an open problem. Indeed, because the biological environment is a complex system, the traditional approach – based on knowledge about the chemical structures – cannot fully explain the nature of interactions between drugs and biological targets. Consequently, in this paper, we propose an unsupervised machine learning approach that uses the information we know about drug-target interactions to infer drug properties. To this end, we define drug similarity based on drug-target interactions and build a weighted Drug-Drug Similarity Network according to the drug-drug similarity relationships. Using an energy-model network layout, we generate drug communities that are associated with specific, dominant drug properties. DrugBank confirms the properties of 59.52% of the drugs in these communities, and 26.98% are existing drug repositioning hints we reconstruct with our DDSN approach. The remaining 13.49% of the drugs seem not to match the dominant pharmacologic property; thus, we consider them as drug repurposing hints. The resources required to test all these repurposing hints are considerable. Therefore we introduce a mechanism of prioritization based on the betweenness/degree node centrality. By using betweenness/degree as an indicator of drug repurposing potential, we select Azelaic acid and Meprobamate as a possible antineoplastic and antifungal, respectively. Finally, we use a test procedure, based on molecular docking, to further analyze the repurposing of Azelaic acid and Meprobamate.
Development of transient expression assay forCannabis sativawhich revealed differentialAgrobacteriumsusceptibility among cannabis cultivars
Authors: Sorokin Alexei , Yadav Narendra Singh , Gaudet Daniel , Kovalchuk Igor 
Published: March 2020

AbstractIn plant biology, transient expression analysis plays a vital role to provide a fast method to study the gene of interest and subsequently leads the path to develop an improved crop variety with better agronomic traits. In this study, we have reported a rapid and efficient method for transient expression inCannabis sativaseedlings usingAgrobacterium tumefaciens-mediated transformation.A. tumefaciensstrain EHA105 carrying the pCAMBIA1301 construct withuidA gene was used to transform cannabis seedlings and the GUS assay was used to detect theuidA expression. A 1% hydrogen peroxide (H2O2) solution was used for both seed sterilization and rapid germination steps. Transient transformation revealed that both cotyledons and young true leaves are amenable to transformation. Comparison toNicotiana tabacum(tobacco) showed that cannabis seedlings were less susceptible to transformation withAgrobacterium tumefaciens. The susceptibility toAgrobacteriuminfection also varied with the different cannabis cultivars. The method established in this study has potential to be an important tool for gene-function studies and genetic improvement in cannabis.
Establishing Prokaryotic Expression System of Angiotensin-Converting Enzyme 2 (ACE2) gene in pigs
Authors: Xiao Hang , Nie Xin-Tian , Ji Xiao-Xia , Yan Shu-ping , Zhu Bin , Zhang Yuan-Shu 
Published: March 2020

AbstractIn this paper, ACE2 gene of pigs was cloned and the purified protein was obtained via the prokaryotic expression system. Polyclonal antibody of high titer and sensitivity was obtained using Wastar rats immunization method and is then used to determine of the expression of ACE2 using immunohistochemistry. The sequence of ACE2 in pigs covered 2418 nucleotides and coded 805 amino acid (aa) residues. Sequence homology analysis showed that the ACE2 sequence in pigs is highly conserved among species at the nucleotide and amino acid levels. Genetic evolution analysis revealed that ACE2 gene in pigs has the shortest genetic distance with that in goats while residing in a totally different branch from that in zebra fishes. Analysis of protein structure predicted that ACE2 protein is a transmembrane secreted protein with high hydrophilicity, containing a signal peptide sequences locating between 1aa to 17aa. The ACE2 fusion protein expressed (under the induction with 1.0 mmol/L IPTG for 10 h) was of approximately 100 kDa and mainly existed in inclusion body. Wastar rats immunization showed that the titer of the anti-ACE2 antiserum in rats was 1: 3200. Western blot showed that the antibody binds specifically. Immunohistochemistry showed that the ACE2 protein was expressed in all major tissues of pigs. It is the first time that polyclonal antibody of ACE2 in pigs was obtained and the expression of ACE2 was confirmed. These results will provide a basis for investigating on ACE2’s biological activity in pigs.
Characterizing the Human Heart Rate Circadian Pacemaker through Widely Available Wearable Devices
Authors: Bowman Clark , Huang Yitong , Walch Olivia J , Fang Yu , Frank Elena , Goldstein Cathy , Sen Srijan , Forger Daniel B. 
Published: March 2020

SummaryThe effects of real-world stimuli and how they vary across individuals remains largely unknown for lack of a continuous real-world circadian marker. Here, we show how an underlying circadian rhythm in heart rate (CRHR) can be extracted from several widely used wearables. Analysis of over 130,000 days of data from medical interns on rotating shifts shows how CRHR dynamics are distinct from those of sleep-wake timing and vary greatly among individuals. Analysis of circadian timekeeping in travelers in 5 continents shows how the circadian timekeeping more carefully controls wake time rather than sleep time. We determine a personalized phase response curve (PRC) of CRHR to activity for each individual, representing the first passive and personalized determination of how human circadian timekeeping continuously changes due to real-world stimuli. These results collectively establish CRHR as a practical method to study circadian rhythms in the real world.eTOC BlurbWe show how the circadian rhythm in heart rate can be extracted from real world data collected by wearables. Studying data from a large cohort of medical interns working on shifts, we find very interesting dynamics of this circadian rhythm that are independent of the acute effects of activity or sleep-wake timing. These techniques can also determine personalized parameters of circadian timekeeping.
The CDK inhibitor SIAMESE targets both CDKA;1 and CDKB1 complexes to establish endoreplication in trichomes
Authors: Wang Kai , Ndathe Ruth , Kumar Narender , Zeringue Elizabeth A. , Kato Naohiro , Larkin John C. 
Published: March 2020

AbstractEndoreplication, also known as endoreduplication, is a modified cell cycle in which DNA is replicated without subsequent cell division. Endoreplication plays important roles in both normal plant development and in stress responses. TheSIAMESE(SIM) gene of Arabidopsis (Arabidopsis thaliana) encodes a cyclin-dependent kinase inhibitor that plays an central role in establishing endoreplication, and is the founding member of theSIAMESE-RELATED(SMR) family of plant-specific cyclin-dependent kinase inhibitors genes. However, there has been conflicting evidence regarding which specific cyclin/CDK complexes are inhibited by SIM in vivo. In this work, we use genetic evidence to show that SIM likely inhibits both CDKA;1- and CDKB1-containing CDK complexes in vivo to promote endoreplication in developing Arabidopsis trichomes. We also show that SIM interacts with CYCA2;3, a binding partner of CDKB1;1, via SIM Motif A, which we previously identified as a CDK-binding motif. In contrast, SIM Motif C, which has been indicated as a cyclin binding motif in other contexts, appears to be relatively unimportant for interaction between SIM and CYCA2;3. Together with earlier results, our work suggests that SIM and other SMRs likely have a multivalent interaction with CYC/CDK complexes.One sentence summaryThe cyclin-dependent kinase inhibitor SIAMESE (SIM) targets both CDKA;1 and CDKB1 complexes to establish endoreplication, and that SIM interacts with the cyclin CYCA2;3 via SIM Motif A.
Clues on an intraspecific communication system in early plant establishment: The seed-seedling transition from the point of view of a crosstalk between information theory and gene expression
Authors: Ribeiro-Oliveira João Paulo , Silveira Lilian E. D. , Pinto Lilian V. A. , Silva Edvaldo A. A. , Hilhorst Henk W. M. 
Published: March 2020

AbstractHow much interactivity is there in a seed-seedling transition system? The answer for this question can reveal a key aspect for early plant establishment. Thus, we hypothesize that information entropy is correlated with early plant development because it is directly related to interactions between seed-seed, seed-seedling, and seedling-seedling. To test this hypothesis, we perform an overlapping of classical physiological measurements (embryo protrusion), gene expression in germinationsensu stricto, water dynamics in germinating seeds and information theory. For a biological model, we usedSolanum lycocarpumA. St.◻Hil. seeds. This is a Neotropical species with high intra-specific variability in the seed sample. Our finds demonstrate that the dynamic and transient seed-seedling transition system is influenced by the number of individuals (seed or seedling) in the sample, especially at a same physiological stage. In addition, we also discuss that: (i) information entropy enables the quantification of system disturbance relative to individuals in the same physiological stage (seed-seed or seedling-seedling), which may be determinant for embryo growth during germination. (ii) there is possible intraspecific communication in seed-seedling transition systems formed by germinating seeds with the potential to alter the pattern of embryonic development of the sample. In view of this, we suggest the use of information entropy as a tool for studies of biological systems to clarify the phenomenon of mutual stimulation in the germination process.
Predicting corporate credit rating based on qualitative information of MD&A transformed using document vectorization techniques
Authors: Choi Jinwook , Suh Yongmoo , Jung Namchul 
Published: March 2020

PurposeThe purpose of this study is to investigate the effectiveness of qualitative information extracted from firm’s annual report in predicting corporate credit rating. Qualitative information represented by published reports or management interview has been known as an important source in addition to quantitative information represented by financial values in assigning corporate credit rating in practice. Nevertheless, prior studies have room for further research in that they rarely employed qualitative information in developing prediction model of corporate credit rating.Design/methodology/approachThis study adopted three document vectorization methods, Bag-Of-Words (BOW), Word to Vector (Word2Vec) and Document to Vector (Doc2Vec), to transform an unstructured textual data into a numeric vector, so that Machine Learning (ML) algorithms accept it as an input. For the experiments, we used the corpus of Management’s Discussion and Analysis (MD&A) section in 10-K financial reports as well as financial variables and corporate credit rating data.FindingsExperimental results from a series of multi-class classification experiments show the predictive models trained by both financial variables and vectors extracted from MD&A data outperform the benchmark models trained only by traditional financial variables.Originality/valueThis study proposed a new approach for corporate credit rating prediction by using qualitative information extracted from MD&A documents as an input to ML-based prediction models. Also, this research adopted and compared three textual vectorization methods in the domain of corporate credit rating prediction and showed that BOW mostly outperformed Word2Vec and Doc2Vec.
Development of a modular garment assembly line simulator
Authors: Kim Eung Tae , Kim Sungmin 
Published: March 2020

PurposeThe purpose of this study is to develop a modular garment assembly line simulator that can be used for various production methods such as traditional mass production or modern small quantity batch production.Design/methodology/approachFor realistic simulation, the actual shape and sewing information of the garment patterns were used. The assembly line consists of process units including the cutter, preprocessor, module assembly, final assembly, finish, and stack units. Any number of units can be arranged and connected to form various layouts. The simulation can be run at an arbitrary speed.FindingsThis system can be used to estimate the time required to process the given order for a specific layout. Therefore, it can be utilized as the basis for optimum production line design.Originality/valueThis system is expected to be utilized by garment manufacturers for obtaining the productivity improvement, production cost reduction, and increased competitiveness.
Building a destination image: images of exclusiveness and refuge
Authors: de Castro Mendes Bruna , Jose Cavenaghi Airton 
Published: March 2020

Purpose
This paper aims to highlight the political influences that account for the destination image of a tourist city: Campos do Jordão, São Paulo State, Brazil. The study took into consideration the collective imagination and its influence on the formation of touristic destinations.

Design/methodology/approach
Descriptive study based on literature and document review, accompanied by an analysis of texts and photos available on non-official websites – about Campos do Jordão – from November to December 2018 and by visits to selected location.

Findings
“Charm”, “refinement” and “sophistication” are the most frequently used words to describe Campos do Jordão, which remains a symbol of exclusiveness and refuge for the highest social classes. These images are shaped by political and economic influences.

Research limitations/implications
The investigation focussed on a single city. Also, as it is an analytical study aimed at showing the permanence of preconceived values used to build the image of a destination it is not possible to talk about extrapolating the present study to other cities. In addition, the research was done by using the reproduction of physical and cultural aspects in addition to the use of European landscapes structures and values in a locality with an exceptional environmental context.

Social implications
Many of the images connected to Campos do Jordão are replicated by local citizens, a fact that evidences the importance of associative memory, which concerns memories citizens have of their living space. The social implications presented herein seek to recover the formative memories of the assessed city, although it is not the focus of the current study. Assumingly, becoming an active segment of the tourism sector is the only way for local citizens to appropriate the city.

Originality/value
The influence of local government and public actions in tourism construction and in the image linked to the city is used as a case study. Building a touristic imagination demands a wide range of businesses, but this process takes time and effort, as highlighted by the applied documental review; it would not happen without the straight interference of the public sector through the local government.