bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic resistance is lower in Staphylococcus aureus isolated from antibiotic-free raw meat as compared to conventional raw meat
Authors: Kyler J. Haskell , Samuel R. Schriever , Kenisi D. Fonoimoana , Benjamin Haws , Bryan B. Hair , Trevor M. Wienclaw , Joseph G. Holmstead , Andrew B. Barboza , Erik T. Berges , Matthew J. Heaton , Berges Bradford K. 
Published: October 2018

AbstractThe frequent use of antibiotics contributes to antibiotic resistance in bacteria, resulting in an increase in infections that are difficult to treat. Livestock are commonly administered antibiotics in their feed, but there is current interest in raising animals that are only administered antibiotics during active infections. Staphylococcus aureus (SA) is a common pathogen of both humans and livestock raised for human consumption. SA has achieved high levels of antibiotic resistance, but the origins and locations of resistance selection are poorly understood. We determined the prevalence of SA and MRSA in conventional and antibiotic-free (AF) meat products, and also measured rates of antibiotic resistance in these isolates. We isolated SA from raw conventional turkey, chicken, beef, and pork samples and also from AF chicken and turkey samples. We found that SA contamination was common, with an overall prevalence of 22.64% (range of 2.78-30.77%) in conventional meats and 13.0% (range of 12.5-13.2%) in AF poultry meats. MRSA was isolated from 15.72% of conventional raw meats (range of 2.78-20.41%) but not from AF-free meats. The degree of antibiotic resistance in conventional poultry products was significantly higher vs AF poultry products for a number of different antibiotics, and while multi-drug resistant strains were relatively common in conventional meats none were detected in AF meats. The use of antibiotics in livestock contributes to high levels of antibiotic resistance in SA found in meat products. Our results support the use of AF conditions for livestock in order to prevent antibiotic resistance development in SA.
The outer membrane proteins OmpA, FhuA, OmpF, EstA, BtuB and OmpX have unique lipopolysaccharide fingerprints
Authors: Shearer Jonathan , Jefferies Damien , Khalid Syma 
Published: October 2018

AbstractThe outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and in the outer leaflet they contain almost exclusively lipopolysaccharide (LPS) molecules. In E. coli, the outer membrane contains a wide range proteins with a beta barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of twenty-two strands. Here we report coarse-grain molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF and EstA in a range of membrane environments, which are representative of the in vivo for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 microseconds of simulation for each protein.Author summaryWe present data from over 200 microseconds of coarse-grain simulations that show the complexities of protein-lipid interactions within the outer membranes of Gram-negative bacteria. We show that the slow movement of lipolysaccharide molecules necessitate simulations of over 30 microsecond duration to achieve converged properties such as protein tilt angle. Each of the six proteins studied here shows a unique pattern of interactions with the outer membrane and thus constitute a ‘fingerprint’ or ‘signature’.
Interplay between consensus and divergent RNA polymerase II C-terminal domain repeats in viability and targeting
Authors: Lu Feiyue , Portz Bede , Gilmour David S. 
Published: October 2018

SummaryThe carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) is composed of repeats of the consensus YSPTSPS, and is an essential binding scaffold for transcription-associated factors. Metazoan CTDs have well-conserved lengths and sequence compositions arising from the evolution of divergent motifs, features thought to be essential for development. To the contrary, we show that a truncated CTD composed solely of YSPTSPS repeats fully supportsDrosophilaviability, but a CTD with enough YSPTSPS repeats to match the length of the wild-typeDrosophilaCTD is defective. Furthermore, a fluorescently-tagged CTD lacking the rest of Pol II dynamically enters transcription compartments, indicating that the CTD functions as a signal sequence. However, CTDs with too many YSPTSPS repeats are more prone to localize to static nuclear foci independent of the chromosomes. We propose that the sequence complexity of the CTD offsets aberrant behavior caused by excessive repetitive sequences without compromising its targeting function.
Mutational meltdown in asexual populations doomed to extinction
Authors: Olofsson Peter , Chipkin Logan , Daileda Ryan C. , Azevedo Ricardo B. R. 
Published: October 2018

AbstractAsexual populations are expected to accumulate deleterious mutations through a process known as Muller’s ratchet. Lynch and colleagues proposed that the ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze mutational meltdown using a multi-type branching process model where, in the presence of mutation, populations are doomed to extinction. We analyse the change in size and composition of the population and the time of extinction under this model.
Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known
Authors: Schelkunov Mikhail I. , Nuraliev Maxim S. , Logacheva Maria D. 
Published: October 2018

AbstractAlthough most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their genomes, especially plastid genomes, markedly differ from the genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing on other plants. The genome is highly reduced (18 622 base pairs versus approximately 150 kilobase pairs in autotrophic plants) and possesses an outstanding AT content, 86.8%, the highest of all sequenced plant plastid genomes. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologues from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.
A relative comparison between Hidden Markov- and Log-Linear-based models for differential expression analysis in a real time course RNA sequencing data
Authors: Gholizadeh Fatemeh , Salehi Zahra , banaei-Moghaddam Ali Mohammad , Rahimi Foroushani Abbas , kavousi Kaveh 
Published: October 2018

AbstractWith the advent of the Next Generation Sequencing technologies, RNA-seq has become known as an optimal approach for studying gene expression profiling. Particularly, time course RNA-seq differential expression analysis has been used in many studies to identify candidate genes. However, applying a statistical method to efficiently identify differentially expressed genes (DEGs) in time course studies is challenging due to inherent characteristics of such data including correlation and dependencies over time. Here we aim to relatively compare EBSeq-HMM, a Hidden Markov-based model, with multiDE, a Log-Linear-based model, in a real time course RNA sequencing data. In order to conduct the comparison, common DEGs detected by edgeR, DESeq2 and Voom (referred to as Benchmark DEGs) were utilized as a measure. Each of the two models were compared using different normalization methods. The findings revealed that multiDE identified more Benchmark DEGs and showed a higher agreement with them than EBSeq-HMM. Furthermore, multiDE and EBSeq-HMM displayed their best performance using TMM and Upper-Quartile normalization methods, respectively.
The jellyfish genome sheds light on the early evolution of active predation
Authors: Kim Hak-Min , Weber Jessica A. , Lee Nayoung , Park Seung Gu , Sung Cho Yun , Bhak Youngjune , Lee Nayun , Jeon Yeonsu , Jeon Sungwon , Luria Victor , Karger Amir , Kirschner Marc W. , Jo Ye Jin , Woo Seonock , Shin Kyoungsoon , Chung Oksung , Ryu Jae-Chun , Yim Hyung-Soon , Lee Jung-Hyun , Edwards Jeremy S. , Manica Andrea , Bhak Jong , Yum Seungshic 
Published: October 2018

AbstractBackgroundUnique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column. One of the first animals to become free-swimming, jellyfish employ pulsed jet propulsion and venomous tentacles to capture prey.ResultsTo understand these key innovations, we sequenced the genome of the giant Nomura’s jellyfish (Nemopilema nomurai), the transcriptomes of its bell and tentacles, and transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains; possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes, and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation).ConclusionsTaken together, the jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits that have combined to make these animals one of the world’s earliest and most successful multi-cellular predators.
Heart Rate n-Variability (HRnV): A Novel Representation of Beat-to-Beat Variation in Electrocardiogram
Authors: Liu Nan , Guo Dagang , Koh Zhi Xiong , Wah Ho Andrew Fu , Hock Ong Marcus Eng 
Published: October 2018

AbstractHeart rate variability (HRV) is a widely adopted tool for evaluating changes in cardiac autonomic regulation. The majority of efforts have focused on developing methods to assess HRV by deriving sophisticated parameters with linear and nonlinear techniques and adopting advanced signal processing tools for efficient noise removal and accurate QRS detection. In this paper, we propose a novel representation of beat-to-beat variation in an electrocardiogram (ECG), called heart rate n-variability (HRnV), as an alternative to conventional HRV measures. We derived two novel HRnV measures based on non-overlapped and overlapped RR intervals. We also conducted a simulation study by using an ECG record from the MIT-BIH Normal Sinus Rhythm Database to demonstrate the feasibility of calculating HRnV parameters. Among the time domain parameters, we observed that the values were generally incremental with the increase in n. We observed the same trend of changes for the frequency domain parameters. In the nonlinear analysis, the differences between HRV and HRnV from Poincare plot measures were obvious, while those from entropy and detrended fluctuation analysis metrics were not. HRnV measures enable us to augment conventional HRV measures with additional parameters. Although issues remain to be addressed regarding HRnV, we hope to stimulate a new stream of research on this new representation of HRV. HRnV is an important addition to HRV and will contribute to extending the landscape of current studies on HRV.
DNA-mediated self-assembly of gold nanoparticles on protein superhelix
Authors: Zhang Tao , André Ingemar 
Published: October 2018

AbstractRecent advances in protein engineering have enabled methods to control the self-assembly of protein on various length-scales. One attractive application for designed proteins is to direct the spatial arrangement of nanomaterials of interest. Until now, however, a reliable conjugation method is missing to facilitate site-specific positioning. In particular, bare inorganic nanoparticles tend to aggregate in the presence of buffer conditions that are often required for the formation of stable proteins. Here, we demonstrated a DNA mediated conjugation method to link gold nanoparticles with protein structures. To achieve this, we constructed de novo designed protein fibers based on previously published uniform alpha-helical units. DNA modification rendered gold nanoparticles with increased stability against ionic solutions and the use of complementary strands hybridization guaranteed the site-specific binding to the protein. The combination of high resolution placement of anchor points in designed protein assemblies with the increased control of covalent attachment through DNA binding can enable investigations of multilevel physical coupling events of nanocomponents on protein templates and expand the application of protein structures to material sciences.
Striking reduction in neurons and glial cells in anterior thalamic nuclei of older patients with Down’s syndrome
Authors: Perry James C. , Pakkenberg Bente , Vann Seralynne D. 
Published: October 2018

AbstractThe anterior thalamic nuclei are important for spatial and episodic memory; however, there is surprisingly little information about how these nuclei are affected in many conditions that present with memory impairments, including Down’s syndrome. To assess the status of the anterior thalamic nuclei in Down’s syndrome we quantified neurons and glial cells in the brains from four older patients with this condition. There was a striking reduction in the volume of the anterior thalamic nuclei and this appeared to reflect the loss of approximately 70% of neurons. The number of glial cells was also reduced but to a lesser degree than neurons. The anterior thalamic nuclei appear to be particularly sensitive to effects of aging in Down’s syndrome and the pathology in this region likely contributes to the memory impairments observed. These findings re-affirm the importance of assessing the status of the anterior thalamic nuclei in conditions where memory impairments have been principally assigned to pathology in the medial temporal lobe.
Adding function to the genome of AfricanSalmonellaST313
Authors: Canals Rocío , Hammarlöf Disa L. , Kröger Carsten , Owen Siân V. , Fong Wai Yee , Lacharme-Lora Lizeth , Zhu Xiaojun , Wenner Nicolas , Carden Sarah E. , Honeycutt Jared , Monack Denise M. , Kingsley Robert A. , Brownridge Philip , Chaudhuri Roy R. , Rowe Will P. M. , Predeus Alexander V. , Hokamp Karsten , Gordon Melita A. , Hinton Jay C. D. 
Published: October 2018

AbstractSalmonellaTyphimurium ST313 causes invasive nontyphoidalSalmonella(iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered theS.Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of theSalmonellaexpression compendium SalComD23580:bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.
Parallel comparison of pre-conditioning and post-conditioning effects in human cancers and keratinocytes upon acute gamma irradiation
Authors: Cohen Jason , Vo Nguyen T. K. , Seymour Colin B. , Mothersill Carmel E. 
Published: October 2018

AbstractPURPOSETo determine and compare the effects of pre-conditioning and post-conditioning towards gamma radiation responses in human cancer cells and keratinocytesMATERIALS AND METHODSThe clonogenic survival of glioblastoma cells (T98G), keratinocytes (HaCaT), and colorectal carcinoma cells (HCT116 p53+/+and p53-/-) was assessed following gamma ray exposure from a Cs-137 source. The priming dose preceded the challenge dose in pre-conditioning whereas the priming dose followed the challenge dose in post-conditioning. The priming dose was either 5 mGy or 0.1 Gy. The challenge dose was 0.5 – 5 Gy.RESULTSIn both pre- and post-conditioning where the priming dose was 0.1 Gy and the challenge dose was 4 Gy, RAR developed in T98G but not in HaCaT cells. In HCT116 p53+/+, pre-conditioning had either no effect or a radiosensitizing effect and whereas post-conditioning induced either radiosensitizing or radioadaptive effect. The different observed outcomes were dependent on dose, the time interval between the priming and challenge dose, and the time before the first irradiation. Post-conditioning effects could occur with a priming dose as low as 5 mGy in HCT116 p53+/+cells. When HCT116 cells had no p53 protein expression, the radiosensitizing or radioadaptive response by the conditioning effect was abolished.CONCLUSIONSThe results suggest that radiation conditioning responses are complex and depend on at least the following factors: the magnitude of priming/challenge dose, the time interval between priming and challenge dose, p53 status, cell seeding time prior to the first radiation treatment. This work is the first parallel comparison demonstrating the potential outcomes of pre- and post-conditioning in different human cell types using environmentally and medically relevant radiation doses.
Widespread alteration of protein autoinhibition in human cancers
Authors: Jha Ashwani , Bui Jennifer M. , Na Dokyun , Gsponer Jörg 
Published: October 2018

ABSTRACTAutoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins as it prevents spurious pathway activation and primes for signal propagation only under appropriate inputs. Altered functioning of inhibitory allosteric switches underlies the tumorigenic potential of numerous cancer drivers. However, whether protein autoinhibition is altered generically in cancer cells remains elusive. Here, we reveal that cancer-associated missense mutations and fusion breakpoints are found with significant enrichment within inhibitory allosteric switches across all cancer types, which in the case of the fusion breakpoints is specific to cancer and not present in other diseases. Recurrently disrupted or mutated allosteric switches identify established and new cancer drivers. Cancer-specific mutations in allosteric switches are associated with distinct changes in signaling, and suggest molecular mechanisms for altered protein regulation, which in the case of ASK1, DAPK2 and EIF4G1 were supported by biophysical simulations. Our results demonstrate that autoinhibition-modulating genetic alterations are positively selected for by cancer cells, and that their study provides valuable insights into molecular mechanisms of cancer misregulation.
The use of open government data to citizen empowerment: an empirical validation of a proposed model
Authors: Hossain Md Nahin , Talukder Md Shamim , Hoque Md Rakibul , Bao Yukun 
Published: October 2018

Purpose
The purpose of this paper is to measure the impact of open government data (OGD) on citizen empowerment.

Design/methodology/approach
This study advances the body of knowledge on OGD by proposing an integrated research model based on transparency, accountability, participation and collaboration dimensions. The research model was empirically tested using 275 responses using the on-paper survey from the university students and professionals in Bangladesh. Data were analyzed using the structured equation modeling technique.

Findings
Findings revealed that transparency and participation have a positive and significant direct and indirect influence on citizen empowerment through accountability and collaboration. Overall, the four basic pillars of OGD such as transparency, participation, accountability and collaboration interrelated with each other and have the impact on citizen empowerment.

Research limitations/implications
This study has proposed an instrument that sums the dimensions of open government, which avoids tautology and redundancy among OGD dimensions. More research should be done to validate the proposed model and the instruments used in this study.

Practical implications
For the researchers, this study provides a basis for further refinement of individual models of empowerment. For practitioners, understanding the key constructs is crucial to design, refine and implement OGD systems and applications that empower citizens, create public values and strengthen the democratic process.

Originality/value
This research is the first step that empirically investigates the impact of OGD on citizen empowerment which is the ultimate goals of any democratic government.
The effect of accounting methods on financial reporting quality
Authors: Hadiyanto Andrain , Puspitasari Evita , Ghani Erlane K. 
Published: October 2018

PurposeThis study aims to examine the relationship between accounting measurement method of biological asset and financial reporting quality. Specifically, this study examines whether using fair value method or the historical cost method on biological asset provides different financial reporting quality.Design/methodology/approachThis study uses data from 38 agricultural companies that are members of the Roundtable on Sustainable Palm Oil. The annual reports of 38 companies from the Palm Oil Growers over a five-year period starting from 2011 to 2014 are analysed.FindingsThis study shows that companies using historical cost measurement produce less reliable and less relevant information compared to the companies that are using fair value measurement.Research limitations/implicationsThe results in this study imply that the use of fair value measurement improves the quality of financial information.Practical implicationsThis study supports IASB’s justification of developing IAS 41 as the principle-based standard that better represents the financial information related to biological asset and subsequently lead to good accountability and harmonisation practices.Originality/valueThis study provides evidence on the best measurement to be used in agriculture activities using a larger sample size of few countries. In addition, this study contributes to the existing literature on the effect of accounting methods on financial reporting quality.