bluuebunny/crossref_metadata_2025 huggingface dataset:
On some lesser known sea cucumbers in the Natural History Museum, UK (Echinodermata: Holothuroidea)
Authors: THANDAR AHMED S.
Published: October 2019

A mixed batch of sea cucumbers tentatively labelled as ?Thyone or ?Havelockia species was obtained on loan from the Natural History Museum, United Kingdom (NHMUK) for identifications and records. The material dates back to 1850 and originates from shallow waters from various parts of the world. The material includes two new species and one new subspecies which have already been described in an earlier paper (see Thandar, 2017). The remaining specimens comprise a few known or poorly known nominal species and several indeterminate forms. This paper describes the known species while adding some useful information about them. Of the indeterminate species included are several specimens most belonging to the genus Thyone or Havelockia which, because of their incompleteness and absence of ossicles, are not identified beyond their suspected genus or species.
Two new species of deep-sea sponges (Porifera, Demospongiae) from submarine canyons of the Sardinian continental margin (western Mediterranean Sea)
Authors: CARDONE FRINE , PANSINI MAURIZIO , CORRIERO GIUSEPPE , BERTOLINO MARCO
Published: October 2019

Here we describe two new species of deep-sea sponges collected during the exploration of Cold-Water Coral (CWC) banks discovered in the Nora and Coda Cavallo canyons (north-eastern and south coast of Sardinia respectively). Poecillastra tavianii n. sp. differs from the other congeneric species mainly for the dicho- and mesodichotriaenes, never observed in the genus, and the abundance and variety of spirasters. Hymedesmia (Hymedesmia) quadridentata n. sp. is characterized by the presence of two types of chelae. In particular, the unguiferate chelae (round shaft and four teeth at both extremities) represent a peculiar character of the species. Our contribution increases the number of sponge fauna associated to the best known Central Mediterranean CWC habitats to 98 improving the still scant knowledge on the biodiversity of the Mediterranean CWC habitats.
Description of Titanoeca deltshevi sp. n. from Bulgaria with faunistic notes on related species in the Balkans (Araneae, Titanoecidae)
Authors: NAUMOVA MARIA
Published: October 2019

Titanoeca deltshevi sp. n. is described and illustrated from Bulgaria. It appears closely related to T. praefica (Simon, 1870), T. spominima (Taczanowski, 1866) and partially (males only) to T. flavicoma L. Koch, 1872. A faunistic synopsis of the genus Titanoeca Thorell, 1870 in Bulgaria is also presented that is based on new field data and a review of the published literature. Titanoeca flavicoma is newly recorded for Bulgaria and T. turkmenia Wunderlich, 1995 is new for Bulgaria and Albania. Titanoeca incerta (Nosek, 1905) is removed from the Bulgarian, and therefore from the European spider checklists. The possible division of the European members of Titanoeca into three groups based on differences in copulatory and somatic traits is discussed.
A new species of rock-dwelling gecko (Gekkonidae: Gehyra) from the Mt Surprise region of northern Queensland, Australia
Authors: ZOZAYA STEPHEN M. , FENKER JÉSSICA , MACDONALD STEWART L.
Published: October 2019

We describe a new species of rock-dwelling Gehyra Gray, 1834 (Gekkonidae) from the Einasleigh Uplands of inland north Queensland, Australia. Morphological, ecological, and molecular data clearly support the new species as distinct and place it within the ‘australis group’. Gehyra electrum sp. nov. is distinguished from congeners by a combination of medium adult size (SVL 46–50 mm), an orange-brown to pinkish-orange background colouration with a pattern of distinct whitish spots and irregular black to purple-brown blotches or bars, possessing 7–8 undivided subdigital lamellae on the expanded portion of the fourth toe, and a wedge-shaped mental scale that separates the inner-postmental scales along 40% or more of their length. Gehyra electrum sp. nov. is a rock specialist currently known only from granite outcrops of the Mt Surprise region, Queensland. This is the second recently described Gehyra from the Einasleigh Uplands and adds to the growing number of endemic reptiles recognised in the region.
Use of Parameter Extraction Techniques for the Evaluation of the Performance of CdTe Based Solar Array
Authors: Roy D. , Mal I. , Samajdar D. P.
Published: October 2019

Two mathematical models are used for parameter extraction of a CdTe based Photovoltaic (PV) array that delivers a maximum output power of 50 kW. The two sets of extracted parameters are used to design the array and the non-linear coupled equations representing the I–V
and P–V equations of the equivalent array structure have been solved using Bisection method and Newton Raphson methods respectively. The performance of the designed array using the extracted parameters under Standard Test Condition (STC) as well as varying temperature and
irradiance levels is observed. A detailed comparative analysis of the designed array using both the models is done to monitor the change in Fill Factor (FF), efficiency (η) and Maximum Power Point (MPP) under STC and variable temperature and irradiance conditions by including the
loss resistances RS and RP in the equivalent circuit of the designed PV array module.
Spondias tuberosa Extract for Silver Nanoparticles Assisted Synthesis Against Multiresistant Bacteria
Authors: Silva José Reinaldo Oliveira , Ramos Anne Caroline Santos , Lima Zenon Machado , Lima Bruno Dos Santos , Souza Araújo Adriano Antunes de , Mendonça Marcelo da Costa , Padilha Francine Ferreira , Costa Luiz Pereira da , López Jorge Alberto , Hernández-Macedo Maria Lucila
Published: October 2019

Multiresistant bacteria represent a global health problem, encouraging the development of effective antimicrobial treatments. In this context, metallic nanoparticles like silver nanoparticles (AgNPs) can serve as an alternative to the pathogenic bacterial growth control since AgNPs
have minimal risk of promoting bacterial resistance. The chemical methods to synthesize AgNPs involves toxic agents however, an alternative way to obtain them would be employing plant extract due to its redox ability. In the current study, Spondias tuberosa hydroethanolic leaf extract
(StHE) was used to assist silver nanoparticle synthesis (AgNP) and to evaluate the antimicrobial effect of both StHE and AgNP against antibiotic-resistant bacterias Pseudomonas aeruginosa and Staphylococcus aureus. The StHE phytochemical analysis displayed
significant polyphenol and flavonoids contents, identified by HPLC. Synthesized AgNPs were spherical with an average size of 3.44–19.46 nm, characterized by UV-Vis and transmission electron microscopy (TEM). The AgNPs antimicrobial activity displayed higher capacity than the crude StHE,
mainly against Gram-negative bacteria. Therefore, StHE is an effective source of reducing agents for the AgNPs synthesis, which exhibit high antibacterial potential against multidrug-resistant bacteria.
Evaluate Mechanical Behaviour of Alumina Coated Steel Alloy Using Slow Strain Rates Test
Authors: Singh Dalip , Yadav Dharmesh , Saini Ajay , Dhayal Veena , Agarwal D. C.
Published: October 2019

This investigation is concerned with the mechanical property enhancement of the steel alloy by deposition of alumina coating using dip coating method. Alumina coatings were deposited using oxime-modified aluminum(III) isopropoxide as a sol–gel precursor. The Scanning electron
microscopy (SEM) images of the coated samples suggest deposition of uniform alumina coatings and alumina composition over steel alloy. The mechanical property of the bare, dip coated steel alloy samples were investigated by the slow strain rate test (SSRT). The SSRT indicates that dip coated
steel alloy shows higher ultimate tensile strength as compare to the bare samples.
Development and Evaluation of Ursolic Acid Co-Delivered Tamoxifen Loaded Dammar Gum Nanoparticles to Combat Cancer
Authors: Sethi Neeraj , Bhardwaj Prashant , Kumar Sandeep , Dilbaghi Neeraj
Published: October 2019

Therapeutic approaches used to manage cancer, are often associated with drug tolerance or multidrug resistance. The anticancer activity exhibited by plant secondary metabolites can be effectively enhanced by formulating them at nanometric scale. Ursolic acid (UA) is a pentacyclic triterpenoid
that reduces cancer proliferation by interfering cell growth regulation. Tamoxifen (TAM) is an adjuvant molecule employed for hormonal therapy of cancer especially breast cancer. To improve the bioavailability and synergism, UA and TAM loaded Dammar gum nanoparticles (UTDNPs) were prepared
in current study by employing oil in oil (O/O) emulsion solvent evaporation method. Zeta potential value of UTDNPs was found to be +23 mV demonstrating relative stability of nanoformulation. The percentage encapsulation efficiency value was found to be 72.5% for UA and 76.6% for TAM. The UTDNPs
posses particle size in the range of 45–55 nm as revealed by transmission electron microscopy. The UTDNPs showed sustained release and their anti-oxidant and anti-cancer potential was much more pronounced than free UA and TAM particles alone. The in vitro studies demonstrated
that UA and TAM encapsulated in dammar gum inhibited growth of A-549, MCF-7, and Hela cell lines more effectively than UA and TAM alone which proved their robust anticancer potential.
Understanding the Atmospheric Temperature Adjustment to CO2 Perturbation at the Process Level
Authors: Wang Yuwei , Huang Yi
Published: October 2019

Climate model comparisons show that there is considerable uncertainty in the atmospheric temperature response to CO2 perturbation. The uncertainty results from both the rapid adjustment that occurs before SST changes and the slow feedbacks that occur after SST changes. The analysis in this paper focuses on the rapid adjustment. We use a novel method to decompose the temperature change in AMIP-type climate simulation in order to understand the adjustment at the process level. We isolate the effects of different processes, including radiation, convection, and large-scale circulation in the temperature adjustment, through a set of numerical experiments using a hierarchy of climate models. We find that radiative adjustment triggers and largely controls the zonal mean atmospheric temperature response pattern. This pattern is characterized by stratospheric cooling, lower-tropospheric warming, and a warming center near the tropical tropopause. In contrast to conventional views, the warming center near the tropopause is found to be critically dependent on the shortwave absorption of CO2. The dynamical processes largely counteract the effect of the radiative process that increases the vertical temperature gradient in the free troposphere. The effect of local convection is to move atmospheric energy vertically, which cools the lower troposphere and warms the upper troposphere. The adjustment due to large-scale circulation further redistributes energy along the isentropic surfaces across the latitudes, which cools the low-latitude lower troposphere and warms the midlatitude upper troposphere and stratosphere. Our results highlight the importance of the radiative adjustment in the overall adjustment and provide a potential method to understand the spread in the models.
South American Climate during the Early Eocene: Impact of a Narrower Atlantic and Higher Atmospheric CO2
Authors: Liu Xiaojuan , Battisti David S. , White Rachel H. , Baker Paul A.
Published: October 2019

The Cenozoic climate of tropical South America was fundamental to the development of its biota, the most biodiverse on Earth. No previous studies have explicitly addressed how the very different atmospheric composition and Atlantic geometry during the early Eocene (approximately 55 million years ago) may have affected South American climate. At that time, the Atlantic Ocean was approximately half of its current width and the CO2 concentration of Earth’s atmosphere ranged from ~550 to ~1500 ppm or even higher. Climate model simulations were performed to examine the effects of these major state changes on the climate of tropical South America. Reducing the width of the Atlantic by approximately half produces significant drying relative to modern climate. Drying is only partly offset by an enhancement of precipitation due to the higher CO2 of the early Eocene. The main mechanism for drier conditions is simple. Low-level air crosses the tropical Atlantic from North Africa in much less time for a narrower Atlantic (2 days) than for the modern Atlantic (~6 days); as a result, much less water is evaporated into the air and thus there is far lower moisture imported to the continent in the Eocene simulation than in the modern control. The progressive wetting (during the mid- to late Cenozoic) of the Amazon due to the widening Atlantic and the rising Andes, only partly offset by decreasing CO2 values, may have been partly responsible for the accumulating biodiversity of this region.
Analysis of the shear failure of surface methane capture boreholes for improving the drainage period efficiency: A lithological perspective
Authors: Xu Hongjie , Fang Zezhong , Sang Shuxun , Liu Huihu , Ding Hai , Dou Xinzhao , Liu Qinjie
Published: October 2019

The shear failure of surface methane capture boreholes (SMCBs) is the main reason for the life cycle shortening of surface methane capture boreholes but lacks a comprehensive lithological analysis. To improve the surface methane capture borehole stability and drainage period efficiency, it is of great importance to investigate the influence of lithology on the shear failure of surface methane capture boreholes. The results of direct shear tests and geological investigations show that the shear displacement increases as the grain size decreases. A jump in mechanical properties occurs at the lithological boundaries and is mainly controlled by the composition of the rock specimens. The change in cohesion is the main possible reason for the step change of the shear strength. High quartz and low clay contents may effectively improve the shear strength and failure resistance of rock. Boreholes may potentially experience preferential casing failure in the section of the weaker mudstone and siltstone due to larger shear displacements and lower shear strengths of those rock types. Protective measures at these sections may improve the stability of the borehole casing. The detection results at the close of the borehole verify the prediction.
Preoperative imaging differences of patients with cervical spondylosis with cervical vertigo indicate the prognosis after cervical total disc replacement
Authors: Zheng Shan , Muheremu Aikeremujiang , Sun Yuqing , Tian Wei , Wu Cheng-ai
Published: October 2019

Objective

To evaluate the relationship between the preoperative imaging differences and prognosis in patients with cervical spondylosis with cervical vertigo who underwent total disc replacement (TDR).

Methods

This was a retrospective study of patients with cervical spondylosis with cervical vertigo treated with single-segment TDR. The severity of pre- and postoperative cervical vertigo was evaluated separately. Paired samples t-tests were used to compare the severity of the symptoms before and after surgery. Characteristics of plain films, computed tomography myelography and magnetic resonance imaging were compared between patients with different outcomes by analysis of variance and Fisher’s exact tests.

Results

The severity of cervical vertigo was significantly different after single-segment TDR. Three groups with different treatment outcomes were not significantly different with regard to gender, age, type of the cervical spondylosis, follow-up time, segment of surgery, cervical curve, range of motion, T2WI high signal in the spinal cord, and location of compression. The type of compression was significantly different between the three groups.

Conclusions

Cervical vertigo was improved in patients with cervical spondylosis through the TDR procedure. Those in whom a herniated disc was the main source of compression may have a better prognosis following TDR.
Soft-computing-based false alarm reduction for hierarchical data of intrusion detection system
Authors: Singh Parminder , Krishnamoorthy Sujatha , Nayyar Anand , Luhach Ashish Kr , Kaur Avinash
Published: October 2019

A false alarm rate of online anomaly-based intrusion detection system is a crucial concern. It is challenging to implement in the real-world scenarios when these anomalies occur sporadically. The existing intrusion detection system has been developed to limit or decrease the false alarm rate. However, the state-of-the-art approaches are attack or algorithm specific, which is not generic. In this article, a soft-computing-based approach has been designed to reduce the false-positive rate for hierarchical data of anomaly-based intrusion detection system. The recurrent neural network model is applied to classify the data set of intrusion detection system and normal instances for various subclasses. The designed approach is more practical, reason being, it does not require any assumption or knowledge of the data set structure. Experimental evaluation is conducted on various attacks on KDDCup’99 and NSL-KDD data sets. The proposed method enhances the intrusion detection systems that can work with data with dependent and independent features. Furthermore, this approach is also beneficial for real-life scenarios with a low occurrence of attacks.
Integrated Design of D.D.I., Filament Winding and Curing Processes for Manufacturing the High Pressure Vessel (Type II)
Authors: Kwak Hyoseo , Park Gunyoung , Seong Hansaem , Kim Chul
Published: October 2019

As energy crisis and environment pollution all around the world threaten the widespread use of fossil fuels, compressed natural gas (CNG) vehicles are explored as an alternative to the conventional gasoline powered vehicles. Because of the limited space available for the car, the composite pressure vessel (Type II) has been applied to the CNG vehicles to reach large capacity and weight lightening vehicles. High pressure vessel (Type II) is composed of a composite layer and a metal liner. The metal liner is formed by the deep drawing and ironing (D.D.I.) process, which is a complex process of deep drawing and ironing. The cylinder part is reinforced by composite layer wrapped through the filament winding process and is bonded to the liner by the curing process. In this study, an integrated design method was presented by establishing the techniques for FE analysis of entire processes (D.D.I., filament winding and curing processes) to manufacture the CNG composite pressure vessel (Type II). Dimensions of the dies and the punches of the 1st (cup drawing), 2nd (redrawing-ironing 1-ironing 2) and 3rd (redrawing-ironing) stages were calculated theoretically, and shape of tractrix die to be satisfied with the minimum forming load was suggested for life improvement and manufacturing costs in the D.D.I. process. Thickness of the composite material was determined in the filament winding process, finally, conditions of the curing process (number of heating stage, curing temperature, heating rate and time) were proposed to reinforce adhesive strength between the composite layers.
Cuttlebone morphometrics and sex identification of Sepia bertheloti (d’Orbigny, 1835) from the central-east Atlantic
Authors: Guerra-Marrero Airam , Jiménez-Alvarado David , Hernández-García Vicente , Curbelo-Muñoz Leticia , Castro-Hernández José Juan
Published: October 2019

Analysis of 322 cuttlebones of Sepia bertheloti caught in the waters of the Northwest Africa showed significant differences in growth between males and females. Morphometric analysis revealed a relatively different cuttlebone growth pattern between sexes, with males presenting faster growth in length to reach larger sizes and females displaying greater growth in width. This difference in cuttlebone growth is related to female gonadal development and the subsequent increase of the paleal cavity, providing more support and space to accommodate a higher number of oocytes.
Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data
Authors: Kim Kipoong , Sun Hokeun
Published: October 2019

Background

In human genetic association studies with high-dimensional gene expression data, it has been well known that statistical selection methods utilizing prior biological network knowledge such as genetic pathways and signaling pathways can outperform other methods that ignore genetic network structures in terms of true positive selection. In recent epigenetic research on case-control association studies, relatively many statistical methods have been proposed to identify cancer-related CpG sites and their corresponding genes from high-dimensional DNA methylation array data. However, most of existing methods are not designed to utilize genetic network information although methylation levels between linked genes in the genetic networks tend to be highly correlated with each other.

Results

We propose new approach that combines data dimension reduction techniques with network-based regularization to identify outcome-related genes for analysis of high-dimensional DNA methylation data. In simulation studies, we demonstrated that the proposed approach overwhelms other statistical methods that do not utilize genetic network information in terms of true positive selection. We also applied it to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project.

Conclusions

The proposed variable selection approach can utilize prior biological network information for analysis of high-dimensional DNA methylation array data. It first captures gene level signals from multiple CpG sites using data a dimension reduction technique and then performs network-based regularization based on biological network graph information. It can select potentially cancer-related genes and genetic pathways that were missed by the existing methods.
Construction of strains to identify novel factors for regulation of centromeric cohesion protection (CCP) and sister kinetochore mono-orientation (SKM)
Authors: Bharati Akhilendra Pratap , Ghosh Santanu Kumar
Published: October 2019

Background

Meiosis-I is a unique type of chromosome segregation where each chromosome aligns and segregates from its homolog. The mechanism of meiosis I homolog separation in different eukaryotes depends on their centromere and kinetochore architecture which in turn relies mainly on two processes, first on a specialized four protein complex known as monopolin and second, the centromeric cohesion protection (CCP). However, in mammals the complex has not been identified. Furthermore, in budding yeast, there could be additional factors in this process which includes some meiosis specific and some non meiosis specific factors.

Result

We constructed two strains. In the first strain we expressed Mam1 and Cdc5 which leads to sister kinetochore monoorientation (SKM) and in the second case we expressed Rec8 and Spo13 which enhanced CCP even in mitosis. The expression of these proteins in mitotically dividing cells caused co-orientation of the chromosomes, which lead to the cell death followed by miss-segregation of chromosomes. Then we utilized these strains to screen the cDNA libraries from yeast and mammals to identify the novel factors which participate in CCP and SKM. Finally, SGY4119 strain expressing Spo13 and Rec8 was transformed with pRS316 gal cDNA library and transformants were screened for lethality on galactose. We screened ~ 105transformants colonies. Out of these ~ 3000 colonies were able to survive on galactose plate which was narrow down to 6 on the basis of desired phenotype.

Conclusion

So far, meiosis specific kinetochore proteins have been identified only in two yeasts. Recently, in mammals a meiosis specific kinetochore protein (MEIKIN) has been identified with similar function. Till now a single protein in mammals and four proteins monopolin complex in budding yeast has been identified to coorient the centromere. Many more novel factors have to be identified yet. That is why we wished to device genetic screen using a functional genomics approach. Since the list of proteins already identified in yeast is not exhaustive as the circumstantial evidence suggests, we wish to use the same yeast strains to identify additional novel yeast proteins that may be involved in the execution of meiosis.
A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression
Authors: Burgess Stewart T. G. , Marr Edward J. , Bartley Kathryn , Nunn Francesca G. , Down Rachel E. , Weaver Robert J. , Prickett Jessica C. , Dunn Jackie , Rombauts Stephane , Van Leeuwen Thomas , Van de Peer Yves , Nisbet Alasdair J.
Published: October 2019

Background

Psoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources.

Results

Building on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression.

Conclusions

The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.
Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity
Authors: Yin Zhiqiu , Yuan Chao , Du Yuhui , Yang Pan , Qian Chengqian , Wei Yi , Zhang Si , Huang Di , Liu Bin
Published: October 2019

Background

The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

Results

One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

Conclusions

Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.
Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research
Authors: Król Jarosław E. , Hall Donald C. , Balashov Sergey , Pastor Steven , Sibert Justin , McCaffrey Jennifer , Lang Steven , Ehrlich Rachel L. , Earl Joshua , Mell Joshua C. , Xiao Ming , Ehrlich Garth D.
Published: October 2019

Background

Escherichia coliC forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced.

Results

Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor lipopolysaccharide (LPS) synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene. And finally,E. coliC encodes an additional sigma70subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway inE. coli.

Conclusions

Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.
Cohabitation is associated with a greater resemblance in gut microbiota which can impact cardiometabolic and inflammatory risk
Authors: Finnicum Casey T. , Beck Jeffrey J. , Dolan Conor V. , Davis Christel , Willemsen Gonneke , Ehli Erik A. , Boomsma Dorret I. , Davies Gareth E. , de Geus Eco J. C.
Published: October 2019

Background

The gut microbiota composition is known to be influenced by a myriad of factors including the host genetic profile and a number of environmental influences. Here, we focus on the environmental influence of cohabitation on the gut microbiota as well as whether these environmentally influenced microorganisms are associated with cardiometabolic and inflammatory burden. We perform this by investigating the gut microbiota composition of various groups of related individuals including cohabitating monozygotic (MZ) twin pairs, non-cohabitating MZ twin pairs and spouse pairs.

Results

A stronger correlation between alpha diversity was found in cohabitating MZ twins (45 pairs, r = 0.64, p = 2.21 × 10− 06) than in non-cohabitating MZ twin pairs (121 pairs, r = 0.42, p = 1.35 × 10− 06). Although the correlation of alpha diversity did not attain significance between spouse pairs (42 pairs, r = 0.23, p = 0.15), the correlation was still higher than those in the 209 unrelated pairs (r = − 0.015, p = 0.832). Bray-Curtis (BC) dissimilarity metrics showed cohabitating MZ twin pairs had the most similar gut microbiota communities which were more similar than the BC values of non-cohabitating MZ twins (empirical p-value = 0.0103), cohabitating spouses (empirical p-value = 0.0194), and pairs of unrelated non-cohabitating individuals (empirical p-value< 0.00001). There was also a significant difference between the BC measures from the spouse pairs and those from the unrelated non-cohabitating individuals (empirical p-value< 0.00001). Intraclass correlation coefficients were calculated between the various groups of interest and the results indicate the presence of OTUs with an environmental influence and one OTU that appeared to demonstrate genetic influences. One of the OTUs (Otu0190) was observed to have a significant association with both the cardiometabolic and inflammatory burden scores (p’s < 0.05).

Conclusions

Through the comparison of the microbiota contents of MZ twins with varying cohabitation status and spousal pairs, we showed evidence of environmentally influenced OTUs, one of which had a significant association with cardiometabolic and inflammatory burden scores.
Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production
Authors: Rubio Julia , Sánchez Evelyn , Tricon David , Montes Christian , Eyquard Jean-Philippe , Chague Aurélie , Aguirre Carlos , Prieto Humberto , Decroocq Véronique
Published: October 2019

Background

In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. ManySgenes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due toPlum pox virus(PPV).

Results

For this purpose, hairpin-inducing silencing constructs based onPrunus persicaorthologs were used to generatePrunus salicina(Japanese plum) 4E and 4G silenced plants byAgrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulatedeIFiso4Etransgenic Japanese plums were not regenerated in our conditions,eIFiso4G11-, but not theeIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka.

Conclusions

Our results indicate thatSgene function of the translation initiation complex isoform is conserved inPrunusspecies. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.
Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm
Authors: Pipan Barbara , Meglič Vladimir
Published: October 2019

Background

Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.

Results

We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).

Conclusions

This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.
Accepting new patients who require opioids into family practice: results from the MAAP-NS census survey study
Authors: Marshall Emily Gard , Burge Frederick , Gibson Richard J. , Lawson Beverley , O’Connell Colleen
Published: October 2019

Background

Acceptance to a family practice is key to access and continuity of care. While Canadian patients increasingly report not being able to acquire acceptance to a family practice, little is known about the association between requiring opioids and acceptance. We aim to determine the proportion of family physicians who would accept new patients who require opioids and describe physician and practice characteristics associated with willingness to accept these patients.

Methods

Census telephone survey of family physicians’ practices in Nova Scotia, Canada. Measures: physician (i.e., age, sex, years in practice) and practice (i.e., number/type of provider in the practice, care hours/week) characteristics and practice-reported willingness to accept new patients who require opioids.

Results

The survey was completed for 587 family physicians (83.7% response rate). 354 (60.3%) were taking new patients unconditionally or with conditions; 326 provided a response to whether they would accept new patients who require opioids; 91 (27.9%) reported they would not accept a new patient who requires opioids. Compared to family physicians who would not accept patients who require opioids, in bivariate analysis, those who would, tended to work in larger practices; had fewer years in practice; are female; and provided more patient care. The relationship to number of providers in the practice, having a nurse, and experience persisted in multivariate analysis.

Conclusions

The strongest predictors of willingness to accept patients who require opioids are fewer years in practice (OR = 0.96 [95% CI 0.93, 0.99]) and variables indicating a family physician has support of a larger (OR = 1.19 [95% CI 1.00, 1.42]), interdisciplinary team (e.g., nurses, mental health professionals) (OR = 1.15 [95% CI 1.11, 5.05]). Almost three-quarters (72.1%) of surveyed family physicians would accept patients requiring opioids.
Tolerability of IM penicillin G benzathine diluted or not with local anesthetics, or different gauge needles for syphilis treatment: a randomized clinical trial
Authors: Estrada Vicente , Santiago Eva , Cabezas Inmaculada , Cotano Juan Luis , Carrió Juan Carlos , Fuentes-Ferrer Manuel , Vera Mar , Ayerdi Oskar , Rodríguez Carmen , López Laura , Cabello Noemí , Núñez María José , Puerta Teresa , Sagastagoitia Iñigo , Del Romero Jorge
Published: October 2019

Background

Penicillin G Benzathine (PGB) is the cornerstone of syphilis treatment. However, its intramuscular (IM) administration is associated with pain at the site of injection. The dilution of PGB with local anesthetics is recommended in some guidelines, but the evidence that supports it, particularly in adults and in HIV infection, is scarce. Preliminary clinical experience also suggests that the IM administration of PGB through increased needle gauges might improve its tolerability. The aim of the study to identify less painful ways of administering IM PGB in the treatment of syphilis in adults.

Methods

Multicenter, randomized, double-blinded clinical trial in patients diagnosed with primary syphilis that required a single IM injection of PGB 2400,00 IU. Patients were randomized to receive PGB diluted with 0.5 mL mepivacaine 1% (MV) or PGB alone, and both groups either with a long 19G or short 21G IM needle. The primary objective was the effect on local pain immediately after the administration through a visual scale questionnaire on pain (0 to 10).

Results

One hundred eight patients were included, 27 in each group. Ninety-four (94.4%) were male, and 41.7% were also HIV-infected. Mean age 36.6 years (SD 11). Significant differences in immediate pain intensity were observed when comparing the long 19G group with anesthesia (mean pain intensity, [MPI] 2.92 [CI 95% 1.08-4.07]) vs long 19G without anesthesia (MPI 5.56 [CI 95% 4.39-6.73), p < 0.001; and also between short 21G group with anesthesia (MPI 3.36 [CI 95% 2.22-4.50]) vs short 21G without anesthesia (MPI 5.06 [CI 95% 3.93-6.19]), p = 0.015). No significant differences in immediate pain were observed between 19G and 21G in the presence or absence of anesthesia (p = 1.0 in both cases). No differences were found between study arms after 6 and 24 h.

Conclusions

The IM administration of 1% mepivacaine-diluted PGB induces significantly less immediate local pain as compared to PGB alone. The needle gauge did not have any effect on the pain. Based on these results, we suggest anesthetic-diluted IM PGB as the standard treatment for primary syphilis.

Trial registration

EudraCT 2014-003969-24 (Date of registration 18/09/2014).
The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo
Authors: Deutsch-Feldman Molly , Aydemir Ozkan , Carrel Margaret , Brazeau Nicholas F. , Bhatt Samir , Bailey Jeffrey A. , Kashamuka Melchior , Tshefu Antoinette K. , Taylor Steve M. , Juliano Jonathan J. , Meshnick Steven R. , Verity Robert
Published: October 2019

Background

Drug resistant malaria is a growing concern in the Democratic Republic of the Congo (DRC), where previous studies indicate that parasites resistant to sulfadoxine/pyrimethamine or chloroquine are spatially clustered. This study explores longitudinal changes in spatial patterns to understand how resistant malaria may be spreading within the DRC, using samples from nation-wide population-representative surveys.

Methods

We selected 552 children with PCR-detectablePlasmodium falciparuminfection and identified known variants in thepfdhpsandpfcrtgenes associated with resistance. We compared the proportion of mutant parasites in 2013 to those previously reported from adults in 2007, and identified risk factors for carrying a resistant allele using multivariate mixed-effects modeling. Finally, we fit a spatial-temporal model to the observed data, providing smooth allele frequency estimates over space and time.

Results

The proportion of co-occurringpfdhpsK540E/A581G mutations increased by 16% between 2007 and 2013. The spatial-temporal model suggests that the spatial range of thepfdhpsdouble mutants expanded over time, while the prevalence and range ofpfcrtmutations remained steady.

Conclusions

This study uses population-representative samples to describe the changing landscape of SP resistance within the DRC, and the persistence of chloroquine resistance. Vigilant molecular surveillance is critical for controlling the spread of resistance.
Broad spectrum resistance in Helicobacter pylori isolated from gastric biopsies of patients with dyspepsia in Cameroon and efflux-mediated multiresistance detection in MDR isolates
Authors: Kouitcheu Mabeku Laure Brigitte , Eyoum Bille Bertrand , Tepap Zemnou Cromwell , Tali Nguefack Lionel Danny , Leundji Hubert
Published: October 2019

Background

Antibiotic resistance is a leading cause of treatment failure in Helicobacter pylori infection. In Africa, there are very little data concerning the susceptibility of Helicobacter pylori isolates to antibiotics. The purpose of this study was to evaluate the resistance prevalence of Helicobacter pylori strains circulating in Cameroon, and to assess overexpression of efflux pump as a possible multi-drug resistance mechanisms.

Methods

A total of 140 H. pylori isolates were recovered from gastric biopsies of dyspeptic patients in two reference hospitals in Cameroon and analyzed for their antimicrobial susceptibility to amoxicillin, co-amoxiclav, ampicillin, penicillin, imipenem, metronidazole, rifabutin, erythromycin, clarithromycin, azithromycin, levofloxacin, ciprofloxacin, norfloxacin, tetracycline, doxycycline and minocycline. Antibiotic sensitivity was tested by disk diffusion method. Phe-Arg-naphthylamide (PAßN) was used as efflux pump inhibitor. INT broth microdilution method in supplemented Brain Heart Infusion broth was used to determine the MIC of ampicillin, amoxicillin, metronidazole, erythromycin, clarithromycin and doxycycline in the absence and the presence of PAßN against 32 selected MDR isolates.

Results

Overall H. pylori resistance rate was 100% to ampicillin, penicillin and co-amoxiclav; 97.14% to amoxicillin, 97.85% to metronidazole, 47.85% to erythromycin, 13.57% to clarithromycin; 5, 2.86 and 0.71% to doxycycline, tetracycline and minocycline respectively. No resistance to azithromycin, rifabutin, imipenem, ciprofloxacin, norfloxacin and levofloxacin was detected among H. pylori isolates. Seventy percent (70%) of the tested isolates elicited a multiple drugs resistance pattern; 42.57% double, 15.71% triple and 5.71% quadruple drugs resistance. Metronidazole and amoxicillin were more concerned with double resistance pattern (86.76%). The spectrum of activity recorded with metronidazole, doxycycline, clarithromycin and erythromycin ranged from 0 to 100% in the absence to the presence of PAßN against the tested MDR isolates. An 8 to 128-fold increase in potency was also noticed with these antibiotics in the presence of PAßN.

Conclusion

With regard to the high resistance rate to both amoxicillin and metronidazole, these drugs should be avoided as components of triple therapy in our milieu. In contrast, ciprofloxacin, norfloxacin, levofloxacin and tetracyclines could be used to achieve a better eradication rate and to reduce the risk of selection of H. pylori resistant strains.