bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute theDrosophilaMushroom Bodies
Authors: Shih Meng-Fu Maxwell , Davis Fred Pejman , Henry Gilbert Lee , Dubnau Josh 
Published: November 2018

AbstractThe insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α′/β′ and α/β) and 7 cell subtypes (γd, γm, α′/β′ap, α′/β′m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker Fas2 and the α′/β′ class marker trio. Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.
Detecting Adaptation with Genome-Scale Molecular Evolutionary Analysis: An Educational Primer for Use with “RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates”
Authors: Lazzaro Brian P 
Published: November 2018

Abstract
Hosts and pathogens impose coevolutionary pressure on each other as pathogens strive to establish themselves and hosts seek to suppress infection. RNA interference (RNAi) is a mechanism by which cells repress viruses and transposable elements, thereby serving as a form of immune defense. Previous studies have shown that antiviral RNAi genes evolve extraordinarily quickly in the fruit fly Drosophila melanogaster, suggesting that they may adaptively coevolve with viruses and transposable elements. An article by Palmer and colleagues extends this observation to nematodes and multiple insects. Their article can be combined with this Primer to demonstrate the use of comparative genomics and molecular evolutionary analyses in the measurement of natural selection.
Related article in GENETICS: Palmer, W. H., J. D. Hadfield, and D. J. Obbard, 2018 RNA-Interference pathways display high rates of adaptive protein evolution in multiple invertebrates. Genetics 208: 1585–1599.
Genotyping Polyploids from Messy Sequencing Data
Authors: Gerard David , Ferrão Luis Felipe Ventorim , Garcia Antonio Augusto Franco , Stephens Matthew 
Published: November 2018

AbstractGerard et al. highlight several issues encountered when genotyping polyploid organisms from next-generation sequencing data, including allelic bias, overdispersion, and outlying observations. They present modeling solutions and software to account for these issues...Detecting and quantifying the differences in individual genomes (i.e., genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use reduced representation next-generation sequencing (NGS) approaches for genotyping. Genotyping diploid individuals using NGS is a well-studied field, and similar methods for polyploid individuals are just emerging. However, there are many aspects of NGS data, particularly in polyploids, that remain unexplored by most methods. Our contributions in this paper are fourfold: (i) We draw attention to, and then model, common aspects of NGS data: sequencing error, allelic bias, overdispersion, and outlying observations. (ii) Many datasets feature related individuals, and so we use the structure of Mendelian segregation to build an empirical Bayes approach for genotyping polyploid individuals. (iii) We develop novel models to account for preferential pairing of chromosomes, and harness these for genotyping. (iv) We derive oracle genotyping error rates that may be used for read depth suggestions. We assess the accuracy of our method in simulations, and apply it to a dataset of hexaploid sweet potato (Ipomoea batatas). An R package implementing our method is available at https://cran.r-project.org/package=updog.
Scaling of G1 Duration with Population Doubling Time by a Cyclin in Saccharomyces cerevisiae
Authors: Blank Heidi M , Callahan Michelle , Pistikopoulos Ioannis P E , Polymenis Aggeliki O , Polymenis Michael 
Published: November 2018

Abstract
The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells, the length of the G1 phase (TG1) regressed on Td with a slope of ≈0.75, while in the yeast Saccharomyces cerevisiae, the slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Td or TG1 in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short upstream ORF (uORF) in the CLN3 transcript. Cln3p was also necessary for the proper scaling between TG1 and Td. In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1 and Td. These data reveal fundamental scaling relationships between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relationships in yeast, and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.
Effects of Transmission Bottlenecks on the Diversity of Influenza A Virus
Authors: Sigal Daniel , Reid Jennifer N S , Wahl Lindi M 
Published: November 2018

AbstractWe investigate the fate of de novo mutations that occur during the in-host replication of a pathogenic virus, predicting the probability that such mutations are passed on during disease transmission to a new host. Using influenza A virus as a model organism, we develop a life-history model of the within-host dynamics of the infection, deriving a multitype branching process with a coupled deterministic model to capture the population of available target cells. We quantify the fate of neutral mutations and mutations affecting five life-history traits: clearance, attachment, budding, cell death, and eclipse phase timing. Despite the severity of disease transmission bottlenecks, our results suggest that in a single transmission event, several mutations that appeared de novo in the donor are likely to be transmitted to the recipient. Even in the absence of a selective advantage for these mutations, the sustained growth phase inherent in each disease transmission cycle generates genetic diversity that is not eliminated during the transmission bottleneck.
A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids
Authors: Boatwright J Lucas , McIntyre Lauren M , Morse Alison M , Chen Sixue , Yoo Mi-Jeong , Koh Jin , Soltis Pamela S , Soltis Douglas E , Barbazuk W Brad 
Published: November 2018

AbstractPolyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood. We describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogon mirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome.
Patterns of Transmission Ratio Distortion in Interspecific Lettuce Hybrids Reveal a Sex-Independent Gametophytic Barrier
Authors: Giesbers Anne K J , den Boer Erik , Ulen Jacqueline J W E H , van Kaauwen Martijn P W , Visser Richard G F , Niks Rients E , Jeuken Marieke J W 
Published: November 2018

Abstract
Interspecific crosses can result in progeny with reduced vitality or fertility due to genetic incompatibilities between species, a phenomenon known as hybrid incompatibility (HI). HI is often caused by a bias against deleterious allele combinations, which results in transmission ratio distortion (TRD). Here, we determined the genome-wide distribution of HI between wild lettuce, Lactuca saligna, and cultivated lettuce, L. sativa, in a set of backcross inbred lines (BILs) with single introgression segments from L. saligna introgressed into a L. sativa genetic background. Almost all BILs contained an introgression segment in a homozygous state except a few BILs, for which we were able to obtain only a single heterozygous introgression. Their inbred progenies displayed severe TRD with a bias toward the L. sativa allele and complete nontransmission of the homozygous L. saligna introgression, i.e., absolute HI. These HI might be caused by deleterious heterospecific allele combinations at two loci. We used an multilocus segregating interspecific F2 population to identify candidate conspecific loci that can nullify the HI in BILs. Segregation analysis of developed double-introgression progenies showed nullification of three HI and proved that these HI are explained by nuclear pairwise incompatibilities. One of these digenic HI showed 29% reduced seed set and its pattern of TRD pointed to a sex-independent gametophytic barrier. Namely, this HI was caused by complete nontransmission of one heterospecific allele combination at the haploid stage, surprisingly in both male and female gametophytes. Our study shows that two-locus incompatibility systems contribute to reproductive barriers among Lactuca species.
Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating
Authors: Ruby J Graham , Wright Kevin M , Rand Kristin A , Kermany Amir , Noto Keith , Curtis Don , Varner Neal , Garrigan Daniel , Slinkov Dmitri , Dorfman Ilya , Granka Julie M , Byrnes Jake , Myres Natalie , Ball Catherine 
Published: November 2018

AbstractHere, Ruby et al. analyze an unprecedented amount of public family tree data from Ancestry and determine that the heritability of human longevity was well below 10%, lower than the widely-held belief that lifespan...Human life span is a phenotype that integrates many aspects of health and environment into a single ultimate quantity: the elapsed time between birth and death. Though it is widely believed that long life runs in families for genetic reasons, estimates of life span “heritability” are consistently low (∼15–30%). Here, we used pedigree data from Ancestry public trees, including hundreds of millions of historical persons, to estimate the heritability of human longevity. Although “nominal heritability” estimates based on correlations among genetic relatives agreed with prior literature, the majority of that correlation was also captured by correlations among nongenetic (in-law) relatives, suggestive of highly assortative mating around life span-influencing factors (genetic and/or environmental). We used structural equation modeling to account for assortative mating, and concluded that the true heritability of human longevity for birth cohorts across the 1800s and early 1900s was well below 10%, and that it has been generally overestimated due to the effect of assortative mating.
Maternal Intellectual or Developmental Disability and Newborn Discharge to Protective Services
Authors: Brown Hilary K. , Potvin Lynne A. , Lunsky Yona , Vigod Simone N. 
Published: November 2018

BACKGROUND:
Approximately half of women with intellectual and developmental disabilities (IDDs) lose custody of their children at some point in their child’s development, but their rates of and risk factors for newborn discharge to child protective services from the birth hospitalization are relatively unknown.

METHODS:
We conducted a population-based study of newborns of 3845 women with IDDs and 379 834 women without IDDs in Ontario, Canada (2002–2012). We used modified Poisson regression to estimate adjusted relative risks (aRRs) and 95% confidence intervals (CIs) for discharge to child protective services directly from the birth hospitalization (1) comparing newborns of women with and without IDDs and (2) among newborns of women with IDDs according to sociodemographic, health, service, and perinatal characteristics.

RESULTS:
Approximately 5.7% of newborns of women with IDDs, compared with 0.2% of newborns of women without IDDs, were discharged to child protective services (aRR 8.10; 95% CI 6.51–10.09). Among newborns of women with IDDs, risk factors were maternal psychotic disorder (aRR 2.58; 95% CI 1.90–3.50), social assistance receipt (aRR 2.55; 95% CI 1.87–3.47), failure to receive an ultrasound by 20 weeks’ gestation (aRR 1.76; 95% CI 1.32–2.34), and receipt of &lt;4 prenatal visits by 36 weeks’ gestation (aRR 1.71; 95% CI 1.05–2.78).

CONCLUSIONS:
Although women with IDDs are at risk for custody loss immediately postdelivery, certain subgroups are at higher risk than others. Women with vulnerabilities related to comorbid psychotic disorders, poverty, and inadequate prenatal care may benefit from tailored, behavior-based parenting interventions before and during pregnancy to prevent maternal-newborn separations.
Designing interaction models that meet user expectations towards new technologies
Authors: Talug Deniz Yesim 
Published: November 2018

Currently, technology is an interesting and expanding field for social and consumer research. Conversely, standard consumer researches, academic marketing studies, economics or sociology fall short of representing theories and perspectives that ties technology and human needs. New technological opportunities not only create changes in appearance and functionalities of products but it also creates change on user expectations and behaviors, which is mainly emotionally driven. Needs and emotions lead people to make judgments about what they would prefer to keep around themselves. This characteristic of human beings forces them to choose among variants and to involve in the design process. Selecting among variants means designing of the environment. In the study of design, the idea of consumer participation offered new horizons to design.

This paper focuses on new perspectives to combine technology and human beings and aims to provide theoretical contribution and strategic information to the designers, progresses through a discussion of the conceptual framework with a review of the relevant literature. Initial attempt involves investigating user experiences created and shaped through technology and how to deliberately design those.

Keywords: Emotions and Design; User Experience; Product Experience; Technology.
Modelling and power control of grid connected wind energy system
Authors: Ben Si Ali Nadia , Benalia Nadia , Zerzouri Nora 
Published: November 2018

Wind energy generation has attracted great interests in recent years. Doubly-fed induction generator (DFIG) for wind turbines (WTs) are largely deployed, because variable-speed WTs have many advantages over fixed-speed generation such as increased energy capture, operation at maximum power point, improved efficiency and power quality. This paper presents the operation and vector control of a DFIG system, where the stator is connected directly to a stiff grid and the rotor is connected to the grid through bidirectional back-to-back ACâ€“DCâ€“AC converter. The basic operational characteristics, mathematical model of the aerodynamic system and vector control technique, which is used to obtain decoupled control of powers, are investigated using the software Matlab/Simulink.

Keywords: Wind turbine, doubly-fed induction generator, active and reactive power controller.
Comparative Analysis of Erbium Doped Fiber Amplifier (EDFA) and Raman Optical Amplifier (ROA) in Nonlinear-CWDM System
Authors: Zulherman Dodi , Utami Sri , Fahmi Fahmi 
Published: November 2018

The massive demands for high-rate application drove the telecommunication service to use large bandwidth capacity. The Coarse Wavelength Division Multiplexing (CWDM), a common use in Metro-WDM, can be a solution to provide large bandwidth in optical communications. In a communications system, there are attenuation and nonlinear effect decreasing the system performance. In order to overcome the limitation imposed by electrical regeneration to maintain system performance, a means of optical amplification was sought. In this paper presents the comparison of two competing technologies emerged: Erbium Doped Fiber Amplifier (EDFA) and Raman Optical Amplifier (ROA) to overcome the attenuation in the nonlinear system. We designed the CWDM system using 8 channels with 20 nm channel spacing and 60 km length. The result was conducted by varying the CW Laser power using -8, -6, -4, -2, 0, 2, 4, and 6 dBm. Based on the result of the research, raman amplification can maintain the BER and the Q-factor of the CWDM system better than EDFA. In addition, the received power in raman amplification larger than that received in EDFA. In conclusion,a CWDM system using ROA amplifier has better performance for the system than using EDFA amplifier.
Improved Load Balancing on Software Defined Network-based Equal Cost Multipath Routing in Data Center Network
Authors: Dewanto Ramadhika , Munadi Rendy , Negara Ridha Muldina 
Published: November 2018

Equal Cost Multipath Routing (ECMP) is a routing application where all available paths between two nodes is utilized by statically mapping each path to possible traffics between source and destination hosts in a network. This configuration can lead to congestion if there are two or more traffics being transmitted into paths with overlapping links, despite the availability of less busy paths. Software Defined Networking (SDN) has the ability to increase the dynamicity of ECMP by allowing controller to monitor available bandwidths of all links in the network in real-time. The measured bandwidth is then implemented as the basis of the calculation to determine which path a traffic will take. In this research, a SDN-based ECMP application that can prevent network congestion is made by measuring available bandwidth of each available paths beforehand, thus making different traffics transmitted on non-overlapped paths as much as possible. The proposed scheme increased the throughput by 14.21% and decreased the delay by 99% in comparison to standard ECMP when congestion occurs and has 75.2% lower load standard deviation in comparison to round robin load balancer.
Performance Analysis of Reactive Routing Protocol on VANET with Wormhole Attack Schemeaper
Authors: Ratnasih Ratnasih , Perdana Doan , Wulandari Triani , Pratama M. Irfan 
Published: November 2018

Entering the information era, the current needs of global community is increasing very rapidly. Vehicular Ad-hoc Networks (VANET) has drawn significant attentions from both industry and academia as an important developmnt of vehicular communication technology. VANET is one of open network and communication media without security mechanism. There are many kinds of security threat that can interrupt data communication in VANET. Wormhole attacks as one of security threat can be a good challenge in VANET security research. In this paper, we evaluate performance of reactive routing protocol on VANET with wormhole attack scheme. The project is simulated using NS-3 in Ubuntu platform with performance analysis of routing protocol by changing of initial power and node density. We conclude that throughput values are increasing along with the changing of initial power while the delay values are decreasing rapidly. By the changing of node density, the highest delay value is 0.122 ns on 10 nodes condition and 0.215 Mbps for throughput value on 8 nodes condition.
Synthesis, Antioxidant and Anti-inflammatory Activities of 5-((styrylsulfonyl) methyl)-1,3,4-Oxadiazol / Thiadiazol-2-amine Derivatives
Authors: Sravya Gundala , Nagarjuna Ummadi , Padmavathi Venkatapuram , Rajitha Galla , priya Sakuri Chandi , Padmaja Adivireddy 
Published: November 2018

Background:
A new class of 5-(styrylsulfonylmethyl)-1,3,4-oxadiazol-2-amine and 5-
(styrylsulfonylmethyl)-1,3,4-thiadiazol-2-amine derivatives were prepared by derivatization of amino
function.

Methods:
All the synthesized compounds were tested for antioxidant and anti-inflammatory activities.

Results:
The 2-amino-3-chloro-N-(5-(4-methylstyrylsulfonylmethyl)-1,3,4-oxadiazol-2-yl)-propanamide
(12b) and 3-chloro-N-(5-(4-methylstyrylsulfonylmethyl)-1,3,4-oxadiazol-2-yl)-butanamide
(14b) displayed significant antioxidant activity, greater than the standard Ascorbic acid.

Conclusion:
Moreover, 12b and 14b also exhibited promising anti-inflammatory activity
Design and Synthesis of Novel Sulfonamide-Derived Triazoles and Bioactivity Exploration
Authors: He Shi-Chao , Zhang Hui-Zhen , Zhang Hai-Juan , Sun Qing , Zhou Cheng-He 
Published: November 2018

Objective:
Due to the incidence of resistance, a series of sulfonamide-derived 1,2,4-
triazoles were synthesized and evaluated.

Method:
The novel sulfonamide-derived 1,2,4-triazoles were prepared starting from commercial
acetaniline and chlorosulfonic acid by sulfonylation, aminolysis, N-alkylation and so on. The antimicrobial
activity of the synthesized compounds were evaluated in vitro by two-fold serial dilution
technique.

Results:
In vitro antimicrobial evaluation found that 2-chlorobenzyl sulfonamide 1,2,4-triazole 7c
exhibited excellent antibacterial activities against MRSA, B. subtilis, B. typhi and E. coli with MIC
values of 0.02−0.16 μmol/mL, which were comparable or even better than Chloromycin. The preliminary
mechanism suggested that compound 7c could effectively bind with DNA, and also it
could bind with human microsomal heme through hydrogen bonds in molecular docking. Computational
chemical studies were performed on compound 7c to understand the structural features
that are essential for activity. Additionally, compound 7c could generate a small amount of reactive
oxygen species (ROS).

Conclusion:
Compound 7c could serve as a potential clinical antimicrobial candidate.