bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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

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

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.
Hereditarily normal manifolds of dimension greater than one may all be metrizable
Authors: Dow Alan , Tall Franklin
Published: June 2019

P. J. Nyikos has asked whether it is consistent that every hereditarily normal manifold of dimension greater than one is metrizable, and he proved that it is if one assumes the consistency of a supercompact cardinal, and, in addition, that the manifolds are hereditarily collectionwise Hausdorff. We are able to omit these extra assumptions.
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

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

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

Marked 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

Voluntary 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

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

Acacia 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

The 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

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.
A Web-Based HIV/STD Prevention Intervention for Divorced or Separated Older Women
Authors: Weitzman Patricia Flynn , Zhou Yi , Kogelman Laura , Mack Sarah , Sharir Jie Yang , Vicente Sara Romero , Levkoff Sue E
Published: June 2019

Background and Objective

Sexually transmitted diseases (STDs) are increasing among older adults concomitant with a rise in divorce after the age of 50 years. The objective of this study was to examine the effectiveness of a web-based human immunodeficiency virus (HIV)/STD risk reduction intervention for divorced and separated women aged more than 50 years.

Research Design and Methods

Two hundred nineteen divorced or separated women, aged 50 years and older, participated in 60-day randomized pre–post control group study. Recruitment occurred via health agencies in Boston and Columbia, SC, and Craigslist advertisements placed in Boston, Columbia, Charleston, New York City, Washington DC, Baltimore, Chicago, Atlanta, Orlando, and Miami.

Results

Intervention group reported greater intention to practice safe sex compared to the control group (B = .55, p = .03). Intention to practice safe sex differed by perceived stress (B = .15, p = .005), with no difference between control and intervention groups for those with low levels of stress. For high levels of stress, intervention group reported greater intention to practice safe sex compared to controls. Sexual risk was reduced by 6.10 points (SD: 1.10), and self-efficacy for sexual discussion was increased by 2.65 points (SD: 0.56) in the intervention group.

Discussion and Implications

A web-based intervention represents a promising tool to reduce HIV/STD risk among older women. Offering HIV/STD education in the context of other topics of interest to at-risk older women, such as divorce, may solve the problem of at-risk older women not seeking out prevention information due to lack of awareness of their heightened risk.
G-quadruplex-mediated reduction of a pathogenic mitochondrial heteroplasmy
Authors: Naeem Mansur M , Maheshan Rathena , Costford Sheila R , Wahedi Azizia , Trajkovski Marko , Plavec Janez , Yatsunyk Liliya A , Ciesielski Grzegorz L , Kaufman Brett A , Sondheimer Neal
Published: June 2019

Disease-associated variants in mitochondrial DNA (mtDNA) are frequently heteroplasmic, a state of co-existence with the wild-type genome. Because heteroplasmy correlates with the severity and penetrance of disease, improvement in the ratio between these genomes in favor of the wild-type, known as heteroplasmy shifting, is potentially therapeutic. We evaluated known pathogenic mtDNA variants and identified those with the potential for allele-specific differences in the formation of non-Watson-Crick G-quadruplex (GQ) structures. We found that the Leigh syndrome (LS)-associated m.10191C variant promotes GQ formation within local sequence in vitro. Interaction of this sequence with a small molecule GQ-binding agent, berberine hydrochloride, further increased GQ stability. The GQ formed at m.10191C differentially impeded the processivity of the mitochondrial DNA polymerase gamma (Pol γ) in vitro, providing a potential means to favor replication of the wild-type allele. We tested the potential for shifting heteroplasmy through the cyclical application of two different mitochondria-targeted GQ binding compounds in primary fibroblasts from patients with m.10191T>C heteroplasmy. Treatment induced alternating mtDNA depletion and repopulation and was effective in shifting heteroplasmy towards the non-pathogenic allele. Similar treatment of pathogenic heteroplasmies that do not affect GQ formation did not induce heteroplasmy shift. Following treatment, heteroplasmic m.10191T>C cells had persistent improvements and heteroplasmy and a corresponding increase in maximal mitochondrial oxygen consumption. This study demonstrates the potential for using small-molecule GQ-binding agents to induce genetic and functional improvements in m.10191T>C heteroplasmy.
Microfluidic platform enables live-cell imaging of signaling and transcription combined with multiplexed secretion measurements in the same single cells
Authors: Ramji Ramesh , Alexander Amanda F , Muñoz-Rojas Andrés R , Kellman Laura N , Miller-Jensen Kathryn
Published: June 2019

Innate immune cells, including macrophages and dendritic cells, protect the host from pathogenic assaults in part through secretion of a program of cytokines and chemokines (C/Cs). Cell-to-cell variability in C/C secretion appears to contribute to the regulation of the immune response, but the sources of secretion variability are largely unknown. To begin to track the biological sources that control secretion variability, we developed and validated a microfluidic device to integrate live-cell imaging of fluorescent reporter proteins with a single-cell assay of protein secretion. We used this device to image NF-κB RelA nuclear translocation dynamics and Tnf transcription dynamics in macrophages in response to stimulation with the bacterial component lipopolysaccharide (LPS), followed by quantification of secretion of TNF, CCL2, CCL3, and CCL5. We found that the timing of the initial peak of RelA signaling in part determined the relative level of TNF and CCL3 secretion, but not CCL2 and CCL5 secretion. Our results support evidence that differences in timing across cell processes partly account for cell-to-cell variability in downstream responses, but that other factors introduce variability at each biological step.
Characterization of MRSA in Canada from 2007 to 2016
Authors: Nichol Kimberly A , Adam Heather J , Golding George R , Lagacé-Wiens Philippe R S , Karlowsky James A , Hoban Daryl J , Zhanel George G ,   Canadian Antimicrobial Resistance Alliance (CARA) and CANWARD, Zhanel George G , Hoban Daryl J , Adam Heather J , Baxter Melanie R , Nichol Kimberly A , Lagacé-Wiens Philippe R S , Walkty Andrew , Karlowsky James A , Blondeau J , Slinger R , Davidson R , Zhanel G , Hoban D , Delport J , Ellis C , Laverdière M , Loo V , Poutanen S , Fuller J , Roscoe D , Desjardins M , Matukas L , Goyette M , Lee C , Carignan A , Bergevin M , Pelletier R
Published: June 2019

Objectives

This study assessed the demographic and molecular characteristics of community-associated (CA) and healthcare-associated (HA) MRSA genotypes in Canadian hospitals between 2007 and 2016.

Methods

A total of 1963 MRSA were identified among 9103 Staphylococcus aureus isolates collected from inpatients and outpatients presenting to tertiary-care medical centres across Canada. Antimicrobial susceptibility testing was performed by broth microdilution in accordance with CLSI standards (M7 11th edition, 2018). PCR was performed to detect the Panton–Valentine leucocidin (PVL) genes and molecular analysis was performed by spa typing.

Results

Between 2007 and 2016, the annual proportion of S. aureus that were MRSA decreased from 26.1% to 16.9% (P < 0.0001). The proportion of CA-MRSA genotypes increased significantly from 20.8% in 2007 to 56.3% in 2016 (P < 0.0001) while HA-MRSA genotypes decreased from 79.2% to 43.8% throughout the study period (P < 0.0001). Predominant genotypes included HA genotype CMRSA2 (USA100/800) (53.6%) and CA genotype CMRSA10 (USA300) (24.9%). PVL was present in 30.1% of all MRSA isolates, including 78.4% of CA-MRSA and 1.7% of HA-MRSA genotypes. Resistance to clarithromycin, clindamycin, trimethoprim/sulfamethoxazole and fluoroquinolones decreased significantly over time (P < 0.0001).

Conclusions

The proportion of MRSA in Canada declined between 2007 and 2016. In contrast, the proportion of CA-MRSA strain types, particularly CMRSA10 (USA300), continues to increase. In 2016, CA-MRSA genotypes surpassed HA-MRSA as the most common cause of MRSA infections in Canadian hospitals.
Oral Pain in the Cancer Patient
Authors: Epstein Joel B , Miaskowski Christine
Published: June 2019

Oral pain due to cancer and associated treatments is common. The prevalence and severity of oral cancer is high. Painful oral mucositis develops in head and neck cancer patients following surgery and associated radiation therapy and/or chemotherapy. In addition, oral pain, including pain from mucositis, occurs in patients receiving chemotherapy for cancers of the hematopoietic system and cancers at other anatomic sites. Despite pain management practices that include high-dose opioid analgesics, patients rarely obtain relief from either head and neck cancer pain or mucositis pain. Because oral pain in cancer patients is likely due to both nociceptive and neuropathic mechanisms, effective management of pain requires treatments for both processes. As knowledge of the pathophysiology of oral pain in cancer patients increases, new approaches for the prevention and management are anticipated. This article focuses on the emerging evidence that supports the molecular mechanisms and the unique oral micro-neuroanatomy that in combination produce the severe oral pain experienced by cancer patients. In addition, this article summarizes the current state of clinical management of oral mucositis pain.
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion
Authors: Karnkowska Anna , Treitli Sebastian C , Brzoň Ondřej , Novák Lukáš , Vacek Vojtěch , Soukal Petr , Barlow Lael D , Herman Emily K , Pipaliya Shweta V , Pánek Tomáš , Žihala David , Petrželková Romana , Butenko Anzhelika , Eme Laura , Stairs Courtney W , Roger Andrew J , Eliáš Marek , Dacks Joel B , Hampl Vladimír
Published: June 2019

The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less “reduced” than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe–S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
Newly acquired N-terminal extension targets threonyl-tRNA synthetase-like protein into the multiple tRNA synthetase complex
Authors: Zhou Xiao-Long , Chen Yun , Zeng Qi-Yu , Ruan Zhi-Rong , Fang Pengfei , Wang En-Duo
Published: June 2019

A typical feature of eukaryotic aminoacyl-tRNA synthetases (aaRSs) is the evolutionary gain of domains at either the N- or C-terminus, which frequently mediating protein–protein interaction. TARSL2 (mouse Tarsl2), encoding a threonyl-tRNA synthetase-like protein (ThrRS-L), is a recently identified aaRS-duplicated gene in higher eukaryotes, with canonical functions in vitro, which exhibits a different N-terminal extension (N-extension) from TARS (encoding ThrRS). We found the first half of the N-extension of human ThrRS-L (hThrRS-L) is homologous to that of human arginyl-tRNA synthetase. Using the N-extension as a probe in a yeast two-hybrid screening, AIMP1/p43 was identified as an interactor with hThrRS-L. We showed that ThrRS-L is a novel component of the mammalian multiple tRNA synthetase complex (MSC), and is reliant on two leucine zippers in the N-extension for MSC-incorporation in humans, and mouse cell lines and muscle tissue. The N-extension was sufficient to target a foreign protein into the MSC. The results from a Tarsl2-deleted cell line showed that it does not mediate MSC integrity. The effect of phosphorylation at various sites of hThrRS-L on its MSC-targeting is also explored. In summary, we revealed that ThrRS-L is a bona fide component of the MSC, which is mediated by a newly evolved N-extension domain.
High Hepatitis E virus (HEV) Positivity Among Domestic Pigs and Risk of HEV Infection of Individuals Occupationally Exposed to Pigs and Pork Meat in Hanoi, Vietnam
Authors: Hoan Nghiem Xuan , Huy Pham Xuan , Sy Bui Tien , Meyer Christian G , Son Trinh Van , Binh Mai Thanh , Giang Dao Phuong , Tu Anh Dam , Bock C-Thomas , Wang Bo , Tong Hoang Van , Kremsner Peter G , Song Le Huu , Toan Nguyen Linh , Velavan Thirumalaisamy P
Published: June 2019

Background

Hepatitis E virus (HEV) infection can occur through consumption of undercooked pork meat or exposure to animal feces. Because there are scarce data only in developing countries, we assessed whether pigs might be a potential source of human HEV infections in Vietnam. In addition, we determined anti-HEV seroprevalences in the general population and in individuals professionally exposed to pigs and pork meat.

Methods

The study took place in Hanoi, Vietnam. Liver tissues from domestic pigs (n = 210) and serum samples obtained from individuals occupationally exposed to pigs and pork meat (n = 283) and from unexposed healthy controls (n = 168) were screened for HEV-ribonucleic acid (RNA) by reverse-transcription polymerase chain reaction. The exposed group was divided into pork meat vendors (n = 81), pig farmers (n = 96), and slaughterers (n = 106). Serum samples were subjected to HEV immunoglobulin (Ig)G and IgM enzyme-linked immunosorbent assays. The HEV genotypes were assessed by direct sequencing, followed by phylogenetic analyses.

Results

Hepatitis E virus seroprevalence was higher among persons occupationally exposed to pigs/pork meat compared with unexposed individuals (anti-HEV IgM 11% vs 6%, P = .07; anti-HEV IgG 53% vs 31%, P < .0001). Positivity of anti-HEV IgG among slaughterhouse staff was 66%, followed by 51% in pig-farmers and 38% in pork meat vendors (P = .00073). A similar trend was observed for IgM positivity. Of the pig liver tissues, 26 of 210 (12.4%) were positive for HEV-RNA and assessed to be HEV genotype 3.

Conclusions

Hepatitis E virus circulates in domestic pigs in Hanoi and constitutes a permanent zoonotic disease risk. The high HEV seroprevalence among occupationally exposed individuals indicates an associated risk of HEV infection.
Sedentary behavior is more related with cardiovascular parameters in normal weight than overweight adolescents
Authors: Tebar William R , Ritti Dias Raphael M , Scarabottolo Catarina C , Gil Fernanda C S , Saraiva Bruna T C , Delfino Leandro D , Zanuto Edner F , Vanderlei Luiz Carlos M , Christofaro Diego G D
Published: June 2019

This study analyzed the relationship between sedentary behavior and cardiovascular parameters in normal weight and overweight adolescents. The sample included 449 boys and 555 girls with mean age of 13 years from public schools, which were divided into five geographical regions, with data collections performed in one selected school from each region. Sedentary behavior was assessed by screen time on TV, computer, videogame and cell phone/tablet, with good reliability in adolescents. Physical activity was assessed by Baecke’s questionnaire, validated for adolescents. Measures of body weight, height and waist circumference were collected. Adolescents were classified as overweight or normal weight by cut-off points of body mass index for age and sex. Cardiovascular parameters were evaluated by oscillometric device and heart rate by specific monitor. Computer use was positively related to systolic blood pressure (SBP) (β = 0.35; 95%CI = 0.07–0.62) and diastolic blood pressure (DBP) (β = 0.25; 95%CI = 0.05–0.44) in normal weight but not in overweight adolescents. Similar results were observed for cell phone/tablet in SBP (β = 0.46; 95%CI = 0.20–0.72) and DBP (β = 0.36; 95%CI = 0.18–0.54), only for normal weight. The cluster of screen time was related to SBP in normal weight (β = 0.44; 95%CI = 0.03–0.84) and overweight (β = 0.60; 95%CI = 0.01–1.19). Screen time in computer and cell phone/tablet was more related to cardiovascular parameters in normal weight than overweight adolescents.
Can net energy values be determined from animal performance measurements? A review of factors affecting application of the California Net Energy System1
Authors: Owens Fredric N , Hicks Robert B
Published: June 2019

The California Net Energy System (CNES) can reliably project performance of feedlot cattle based on three factors: expected dry matter intake (DMI), some index of degree of maturity of cattle linked to body composition (fat and protein content), and an estimate of the net energy (NE) content of the diet. The CNES allowed feedlot managers to monitor growth and efficiency of individual pens of cattle. Through assigning distinct values for net energy for maintenance (NEm) vs. net energy for gain (NEg) of the metabolizable energy (ME) present in feeds, the CNES enables valid economic comparisons among feedstuffs, an appraisal not feasible based on total digestible nutrients or digestible energy (DE) values. Because NEm and NEg are linked mathematically to ME, the CNES also allows performance-adjusted ME (paME) value of diets to be calculated from observed DMI and growth or carcass measurements. Compared with other productivity measures (e.g., average daily gain and gain-to-feed ratio) that are confounded with and affected by DMI, the CNES logically separates production responses by cattle into two factors—DMI and ME of the diet. This enables research scientists or cattle producers to appraise responses within these two factors independently. In feeding studies, means of paME values were related closely to ME values of diets calculated from the ME of diet ingredients. But unlike ME values projected from diet analyses, paME estimates are affected by environmental conditions (e.g., season, weather, animal interactions, stress, nutritional history and deficiencies, associative effects of feeds, imprecise feed management, and animal healthfulness and disorders). These factors typically overestimate ME intake or increase energy requirements, both of which decrease energetic efficiency. By comparing paME with ME values calculated from diet composition, logical reasons behind performance responses to and quantitative benefits from feed additives, grain processing, hormone implants, and animal management can be appraised. Considering the evolution in cattle types, management and marketing conditions, and changes in diet ingredients and processing that have occurred during the past 50 yr, updating by a skilled committee to correct certain anomalies within the CNES as currently being applied seems appropriate. Developing simplified spreadsheets could help users evaluate their own dietary and management conditions and assure that the CNES continues to be widely applied by the feedlot industry within the United States and worldwide.
Molecular Characterization of Pseudomonas syringae pv. coriandricola and Biochemical Changes Attributable to the Pathological Response on Its Hosts Carrot, Parsley, and Parsnip
Authors: Popović Tatjana , Jelušić Aleksandra , Dimkić Ivica , Stanković Slaviša , Poštić Dobrivoj , Aleksić Goran , Veljović Jovanović Sonja
Published: June 2019

Bacterial leaf spot caused by the plant pathogenic bacterium Pseudomonas syringae pv. coriandricola (Psc) was observed on carrot, parsnip, and parsley grown on a vegetable farm in the Vojvodina Province of Serbia. Nonfluorescent bacterial colonies were isolated from diseased leaves and characterized using different molecular techniques. Repetitive element PCR fingerprinting with five oligonucleotide primers (BOX, ERIC, GTG5, REP, and SERE) and the randomly amplified polymorphic DNA-PCR with the M13 primer revealed identical fingerprint patterns for all tested strains. Multilocus sequence analysis of four housekeeping genes (gapA, gltA, gyrB, and rpoD) showed a high degree (99.8 to 100%) of homology with sequences of Psc strains deposited in the Plant-Associated Microbes Database and NCBI database. The tested strains caused bacterial leaf spot symptoms on all three host plants. Host-strain specificity was not found in cross-pathogenicity tests, but the plant response (peroxidase induction and chlorophyll bleaching) was more pronounced in carrot and parsley than in parsnip.
Mental Health and Functional Competence in the Cape Town Adolescent Antiretroviral Cohort
Authors: Hoare Jacqueline , Phillips Nicole , Brittain Kirsty , Myer Landon , Zar Heather J. , Stein Dan J.
Published: June 2019

Background:

The impact of HIV and antiretrovirals (ART) on long-term mental health in perinatally infected children has not been well studied in sub-Saharan Africa where HIV is most prevalent.

Setting:

Cape Town, South Africa.

Methods:

We investigated mental health measures, including depression, anxiety, attention-deficit hyperactivity disorder, motivation, disruptive behavior, and functioning in perinatally infected adolescents (PHIV+) stable on ART within the Cape Town Adolescent Antiretroviral Cohort. Two hundred four adolescents living with HIV (median age 10 years; mean CD4 953) and a sample of 44 uninfected adolescents were enrolled. The Beck Youth Inventories, Children's Motivation Scale, Conner's Parent's Rating Scale, and Child Behavior Checklist were administered. Among PHIV+, we explored independent associations between HIV-related stigma, recent life stressors, sociodemographic, clinical, and caregiver-related variables, and mental health measures.

Results:

PHIV+ had poorer functional competence, self-concept and motivation, higher levels of disruptive behavior, depression and attention-deficit hyperactivity disorder symptoms and clinically significant anger and disruptive behavior. Within the PHIV+ group, the loss of both biological parents was associated with higher levels of disruptive behavior. Within the PHIV+, factors associated with mental health symptoms and poorer functioning were mostly sociodemographic factors, HIV-related stigma, and life stressors. Age of initiation of ART was associated with self-concept, and failing first-line ART with internalizing and externalizing behavior problems.

Conclusions:

PHIV+ are likely to face future physical and psychological health consequences related to the functional competence challenges they face if mental health care is not made a priority in the fight against HIV.
Variation of carbon contents in eelgrass (
Zostera marina
) sediments implied from depth profiles
Authors: Kindeberg Theodor , Röhr Emilia , Moksnes Per-Olav , Boström Christoffer , Holmer Marianne
Published: June 2019

Seagrass meadows are able to store significant amounts of organic carbon in their underlying sediment, but global estimates are uncertain partly owing to spatio-temporal heterogeneity between and within areas and species. In order to provide robust estimates, there is a need to better understand the fate of, and mechanisms behind, organic carbon storage. In this observational study, we analyse a suite of biotic and abiotic parameters in sediment cores from 47 different eelgrass (
Zostera marina
) beds spanning the distributional range of the Northern Hemisphere. Depth profiles of particulate organic carbon (POC) revealed three patterns of vertical distribution where POC either increased, decreased or showed no pattern with sediment depth. These categories exhibited distinct profiles of δ
13
C and C:N ratios, where high POC profiles had a proportionally larger storage of eelgrass-derived material whereas low POC profiles were dominated by phytoplanktonic and macroalgal material. However, high POC did not always translate into high carbon density. Nevertheless, this large-scale dataset provides evidence that the variability in organic matter source in response to natural and anthropogenic environmental changes affects the potential role of eelgrass beds as POC sinks, particularly where eelgrass decline is observed.
Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record
Authors: Babarović Frane , Puttick Mark N. , Zaher Marta , Learmonth Elizabeth , Gallimore Emily-Jane , Smithwick Fiann M. , Mayr Gerald , Vinther Jakob
Published: June 2019

Non-iridescent structural colour in avian feathers is produced by coherent light scattering through quasi-ordered nanocavities in the keratin cortex of the barbs. To absorb unscattered light, melanosomes form a basal layer underneath the nanocavities. It has been shown that throughout Aves, melanosome morphology reflects broad categories of melanin-based coloration, as well as iridescence, allowing identification of palaeocolours in exceptionally preserved fossils. However, no studies have yet investigated the morphology of melanosomes in non-iridescent structural colour. Here, we analyse a wide sample of melanosomes from feathers that express non-iridescent structural colour from a phylogenetically broad range of extant avians to describe their morphology and compare them with other avian melanosome categories. We find that investigated melanosomes are typically wide (approx. 300 nm) and long (approx. 1400 nm), distinct from melanosomes found in black, brown and iridescent feathers, but overlapping significantly with melanosomes from grey feathers. This may suggest a developmental, and perhaps evolutionary, relationship between grey coloration and non-iridescent structural colours. We show that through analyses of fossil melanosomes, melanosomes indicative of non-iridescent structural colour can be predicted in an Eocene stem group roller (
Eocoracias
: Coraciiformes) and with phylogenetic comparative methods the likely hue can be surmised. The overlap between melanosomes from grey and non-iridescent structurally coloured feathers complicates their distinction in fossil samples where keratin does not preserve. However, the abundance of grey coloration relative to non-iridescent structural coloration makes the former a more likely occurrence except in phylogenetically bracketed specimens like the specimen of
Eocoracias
studied here.
Adult
Drosophila
muscle morphometry through microCT reveals dynamics during ageing
Authors: Chaturvedi Dhananjay , Prabhakar Sunil , Aggarwal Aman , Atreya Krishan B. , VijayRaghavan K.
Published: June 2019

Indirect flight muscles (IFMs) in adult
Drosophila
provide the key power stroke for wing beating. They also serve as a valuable model for studying muscle development. An age-dependent decline in
Drosophila
free flight has been documented, but its relation to gross muscle structure has not yet been explored satisfactorily. Such analyses are impeded by conventional histological preparations and imaging techniques that limit exact morphometry of flight muscles. In this study, we employ microCT scanning on a tissue preparation that retains muscle morphology under homeostatic conditions. Focusing on a subset of IFMs called the dorsal longitudinal muscles (DLMs), we find that DLM volumes increase with age, partially due to the increased separation between myofibrillar fascicles, in a sex-dependent manner. We have uncovered and quantified asymmetry in the size of these muscles on either side of the longitudinal midline. Measurements of this resolution and scale make substantive studies that test the connection between form and function possible. We also demonstrate the application of this method to other insect species making it a valuable tool for histological analysis of insect biodiversity.
Dendropanax morbiferus
leaf extract facilitates oligodendrocyte development
Authors: Kim Ji-Young , Yoon Ju-Young , Sugiura Yuki , Lee Soo-Kyoung , Park Jae-Don , Song Gyun-Jee , Yang Hyun-Jeong
Published: June 2019

Treatment of multiple sclerosis is effective when anti-inflammatory, neuroprotective and regenerative strategies are combined.
Dendropanax morbiferus
(
DM
) has anti-inflammatory, anti-oxidative properties, which may be beneficial for multiple sclerosis. However, there have been no reports on the effects of
DM
on myelination, which is critical for regenerative processes. To know whether
DM
benefits myelination, we checked differentiation and myelination of oligodendrocytes (OLs) in various primary culture systems treated with
DM
leaf EtOH extracts or control.
DM
extracts increased the OL membrane size in the mixed glial and pure OL precursor cell (OPC) cultures and changed OL-lineage gene expression patterns in the OPC cultures. Western blot analysis of
DM
-treated OPC cultures showed upregulation of MBP and phosphorylation of ERK1/2. In myelinating cocultures,
DM
extracts enhanced OL differentiation, followed by increased axonal contacts and myelin gene upregulations such as Myrf, CNP and PLP. Phytochemical analysis by LC-MS/MS identified multiple components from
DM
extracts, containing bioactive molecules such as quercetin, cannabidiol, etc. Our results suggest
DM
extracts enhance OL differentiation, followed by an increase in membrane size and axonal contacts, thereby indicating enhanced myelination. In addition, we found that
DM
extracts contain multiple bioactive components, warranting further studies in relation to finding effective components for enhancing myelination.