bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of a Liquid Filled Poroelastic Cylinder Exposed to a Time Varying Pressure Load
Authors: Ceste Tyler L. , Santhanam Sridhar , Jones Gerard F. 
Published: January 2018

Porous materials are of interest for a number of applications one of them being energy absorption. These materials offer the ability to absorb more energy than a typical metallic solid and thus provide an opportunity to improve the performance of structures that endure blast loads. These structures undergo very large loads in very short periods of time and therefore maximizing energy absorption is paramount. This study seeks to improve the understanding of the response of porous materials by developing both analytical and finite element models for a liquid filled porous cylinder exposed to a dynamic compression loading.
The poroelastic cylinder consists of a porous metallic solid phase and a viscous liquid phase. These two phases provide for two mechanisms of energy dissipation which are that of the deformation of the solid and the viscous flow of the liquid. The theories of elasticity and porous media were used to formulate the governing equations for the liquid filled porous cylinder. These equations describe the coupling between the displacements of the solid cylinder and the pressure distribution of the liquid. Analytical and finite element models were developed to predict the cylinders response in order to determine the amount of energy absorbed when the cylinder is exposed to a dynamic compression load. Analytical models were developed to validate the finite element results. As more complexity is added to this problem an analytical approach becomes unviable and a finite element approach must be used. One such complexity that can be considered is the effect of utilizing a non-constant liquid viscosity, which requires developing a non-linear finite element model to account for the viscositys dependence on strain rate. This added non-linear effect should allow for additional viscous energy to be absorbed and thus can further enhance the performance of the system.
Electrokinetic Driven Micro-Mixing of Fluids in a Circular Electrode Pattern
Authors: Guduru Rakesh , Islam Nazmul 
Published: January 2018

Manipulation of fluids in a small volume is often a challenge in the field of Microfluidics. While many research groups have addressed this issue with robust methodologies, manipulation of fluids remains a scope of study due to the ever-changing technology (Processing Tools) and increase in the demand for “Lab-On-a-Chip” devices. This research peruses the flow pattern and fluid mixing behavior in a metallic circular electrode, charged with AC voltage.
In this study, micromixing in a circular electrode pattern device is demonstrated with numerical and experimental values. Experiments were performed using two buffer solutions with conductivities 1.62 S/m and 0.0732 S/m. The efficiency of mixing was found to be three to five times faster than the normal diffusion process. It was found that the increase in the conductivity of fluid increases the efficiency of mixing in the proposed device.
The Plant Kingdom in Engineering Design: Learning to Design From Trees
Authors: Jawaharlal Mariappan , Vargas Gustavo , Gutierrez Lorenzo 
Published: January 2018

A tree may be the earliest multifunctional structure, and wood is the oldest known engineering material. Yet, trees have no place in engineering education. If we view a tree from merely a mechanical or civil engineering perspective, engineering mechanics can be learned from the tree’s example.
Trees have survived by adapting to the most difficult circumstances: heavy winds, rains, floods, droughts, earthquakes, mammal damage, human intervention, etc. The root system must be strong and flexible enough to support the tree’s entire structure from varying load conditions and to provide food storage and nutrient transfer. The stem system provides structural support for the tree’s above-the-ground parts and transfers water and nutrients from the roots through the network of thick-walled cells to other parts of the tree. Leaves produce food and form the surface area surrounding the tree. Leaves come in a variety of shapes and sizes. The tree’s crown, comprising branches, leaves, and reproductive elements, help the tree to catch more sunlight. It moves upward and outward to expose more of its leaves to direct sunlight for photosynthesis while maintaining physical balance on the earth.
A tree’s lifecycle can span hundreds of years, despite its vulnerability to constantly changing loads throughout the day and throughout its life. In monsoon and windy seasons, trees endure extremely difficult fatigue-loading. Various parts of the tree and its stem are subjected to combined loading conditions: tension, compression, shear, bending, and torsion. Trees develop and adapt stress management strategies by adjusting their shapes to the type or level of stress they endure: they add more mass where more strength is needed, allows material to easily break off (or physiologically inactive) from locations where it is not necessary, design optimum shapes, and create variable notch radii for reducing stress concentration. But a tree is much more than a structural member. It provides food and shelter for wildlife. It absorbs atmospheric carbon dioxide and produces oxygen. It lowers air temperature and facilitates the water cycle.
Structural analysis of a tree can benefit engineering students and practicing engineers alike. Furthermore, a deeper understanding of trees can help us to create multifunctional designs that are in a symbiotic relationship with other members in the system. In short, studying tree mechanics can help us to become better engineers.
This paper presents our efforts to integrate trees into engineering curricula to teach mechanics ranging from equilibrium study to stress analysis. Students of statics, dynamics, the strength of materials, stress analysis, material science, design, etc., can benefit from learning about trees. This approach enables students to understand the complexities of real-world living systems, appreciate the genius of nature’s design, and develop methods for creating sustainable designs.
A Novel Corynebacterium glutamicum
l
-Glutamate Exporter
Authors: Wang Yu , Cao Guoqiang , Xu Deyu , Fan Liwen , Wu Xinyang , Ni Xiaomeng , Zhao Shuxin , Zheng Ping , Sun Jibin , Ma Yanhe 
Published: January 2018

ABSTRACT

Besides metabolic pathways and regulatory networks, transport systems are also pivotal for cellular metabolism and hyperproduction of biochemicals using microbial cell factories. The identification and characterization of transporters are therefore of great significance for the understanding and engineering of transport reactions. Herein, a novel
l
-glutamate exporter, MscCG2, which exists extensively in
Corynebacterium glutamicum
strains but is distinct from the only known
l
-glutamate exporter, MscCG, was discovered in an industrial
l
-glutamate-producing
C. glutamicum
strain. MscCG2 was predicted to possess three transmembrane helices in the N-terminal region and located in the cytoplasmic membrane, which are typical structural characteristics of the mechanosensitive channel of small conductance. MscCG2 has a low amino acid sequence identity (23%) to MscCG and evolved separately from MscCG with four transmembrane helices. Despite the considerable differences between MscCG2 and MscCG in sequence and structure, gene deletion and complementation confirmed that MscCG2 also functioned as an
l
-glutamate exporter and an osmotic safety valve in
C. glutamicum
. Besides, transcriptional analysis showed that MscCG2 and MscCG genes were transcribed in similar patterns and not induced by
l
-glutamate-producing conditions. It was also demonstrated that MscCG2-mediated
l
-glutamate excretion was activated by biotin limitation or penicillin treatment and that constitutive
l
-glutamate excretion was triggered by a gain-of-function mutation of MscCG2 (A151V). Discovery of MscCG2 will enrich the understanding of bacterial amino acid transport and provide additional targets for exporter engineering.

IMPORTANCE
The exchange of matter, energy, and information with surroundings is fundamental for cellular metabolism. Therefore, studying transport systems that are essential for these processes is of great significance. Besides, transport systems of bacterial cells are usually related to product excretion as well as product reuptake, making transporter engineering a useful strategy for strain improvement. The significance of our research is in identifying and characterizing a novel
l
-glutamate exporter from the industrial workhorse
Corynebacterium glutamicum
, which will enrich the understanding of
l
-glutamate excretion and provide a new target for studying bacterial amino acid transport and engineering transport reactions.
Effect of Plasmid Design and Type of Integration Event on Recombinant Protein Expression in Pichia pastoris
Authors: Vogl Thomas , Gebbie Leigh , Palfreyman Robin W. , Speight Robert 
Published: January 2018

ABSTRACTPichia pastoris(syn.Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast toSaccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient inP. pastorisand ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high-throughput screening of >700 transformants and whole-genome sequencing of 27 transformants. Different vector designs and linearization approaches were used to mimic the most common integration events targeted inP. pastoris. Fluorescence of an enhanced green fluorescent protein (eGFP) reporter protein was highly uniform among transformants when the expression cassettes were correctly integrated in the targeted locus. Surprisingly, most nonspecifically integrated transformants showed highly uniform expression that was comparable to specific integration, suggesting that nonspecific integration does not necessarily influence expression. However, a few clones (<10%) harboring ectopically integrated cassettes showed a greater variation spanning a 25-fold range, surpassing specifically integrated reference strains up to 6-fold. High-expression strains showed a correlation between increased gene copy numbers and high reporter protein fluorescence levels. Our results suggest that for comparing expression levels between strains, the integration locus can be neglected as long as a sufficient numbers of transformed strains are compared. For expression optimization of highly expressible proteins, increasing copy number appears to be the dominant positive influence rather than the integration locus, genomic rearrangements, deletions, or single-nucleotide polymorphisms (SNPs).IMPORTANCEYeasts are commonly used as biotechnological production hosts for proteins and metabolites. In the yeastSaccharomyces cerevisiae, expression cassettes carrying foreign genes integrate highly specifically at the targeted sites in the genome. In contrast, cassettes often integrate at random genomic positions in nonconventional yeasts, such asPichia pastoris(syn.Komagataella phaffii). Hence, cells from the same transformation event often behave differently, with significant clonal variation necessitating the screening of large numbers of strains. The importance of this study is that we systematically investigated the influence of integration events in more than 700 strains. Our findings provide novel insight into clonal variation inP. pastorisand, thus, how to avoid pitfalls and obtain reliable results. The underlying mechanisms may also play a role in other yeasts and hence could be generally relevant for recombinant yeast protein production strains.
Genome Sequence of
Galleria mellonella
(Greater Wax Moth)
Authors: Lange Anna , Beier Sina , Huson Daniel H. , Parusel Raphael , Iglauer Franz , Frick Julia-Stefanie 
Published: January 2018

ABSTRACT

The larvae of the greater wax moth,
Galleria mellonella
, are pests of active beehives. In infection biology, these larvae are playing a more and more attractive role as an invertebrate host model. Here, we report on the first genome sequence of
Galleria mellonella
.
Complete Genome Sequence of Bacteriophage St11Ph5, Which Infects Uropathogenic
Escherichia coli
Strain up11
Authors: Golomidova Alla K. , Kulikov Eugene E. , Babenko Vladislav V. , Kostryukova Elena S. , Letarov Andrey V. 
Published: January 2018

ABSTRACT

Bacteriophage St11Ph5 was isolated from a sewage sample on a particularly phage-resistant uropathogenic
Escherichia coli
(UPEC) up11 host strain. It appeared to be closely related to bacteriophage G7C, isolated from horse feces; however, it carries a highly divergent host recognition module.
Draft Genome Sequence of
Talaromyces adpressus
Authors: Cerullo Gabriella , Houbraken Jos , Granchi Zoraide , Pepe Olimpia , Varriale Simona , Ventorino Valeria , Chin-A-Woeng Thomas , Meijer Martin , de Vries Ronald P. , Faraco Vincenza 
Published: January 2018

ABSTRACT

Here we present the draft genome sequence of the fungus
Talaromyces adpressus
A-T1C-84X (=CBS 142503). This strain was isolated from lignocellulosic biomass of
Arundo donax
during biodegradation under natural conditions in the Gussone Park of the Royal Palace of Portici, Naples, Italy.
Draft Genome Sequence of
Saccharomycopsis fermentans
CBS 7830, a Predacious Yeast Belonging to the
Saccharomycetales
Authors: Hesselbart Ana , Junker Klara , Wendland Jürgen 
Published: January 2018

ABSTRACT

Saccharomycopsis fermentans
is an ascomycetous necrotrophic fungal pathogen that penetrates and kills fungal prey cells via targeted penetration pegs. Here, we report the draft genome sequence and scaffold assembly of this mycoparasite.
Genome Sequence of a Lethal Strain of Xylem-Invading
Verticillium nonalfalfae
Authors: Jakše Jernej , Jelen Vid , Radišek Sebastjan , de Jonge Ronnie , Mandelc Stanislav , Majer Aljaž , Curk Tomaž , Zupan Blaž , Thomma Bart P. H. J. , Javornik Branka 
Published: January 2018

ABSTRACT

Verticillium nonalfalfae
, a soilborne vascular phytopathogenic fungus, causes wilt disease in several crop species. Of great concern are outbreaks of highly aggressive
V. nonalfalfae
strains, which cause a devastating wilt disease in European hops. We report here the genome sequence and annotation of
V. nonalfalfae
strain T2, providing genomic information that will allow better understanding of the molecular mechanisms underlying the development of highly aggressive strains.
Draft Genome Sequence of
Megamonas funiformis
Strain Marseille-P3344, Isolated from a Human Fecal Microbiota
Authors: Maaloum Mossaab , Diop Awa , Ndongo Sokhna , Nguyen Thi-Tien , Cadoret Frederic , Raoult Didier , Fournier Pierre-Edouard 
Published: January 2018

ABSTRACT

In this article, we present the draft genome sequence of
Megamonas funiformis
strain Marseille-P3344, isolated from a human fecal sample. The genome described here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76 RNA genes.
Genomic Insights into Biofilm-Forming
Enterococcus faecalis
SK460 Isolated from a Chronic Diabetic Ulcer Patient
Authors: Suryaletha Karthika , Narendrakumar Lekshmi , John Joby , Reghunathan Dinesh , Prasannakumar Manoj , Thomas Sabu 
Published: January 2018

ABSTRACT

Enterococcus faecalis
is recognized as one of the leading pathogens causing nosocomial infections. Here we report a draft genome sequence of
Enterococcus faecalis
SK460, isolated from a chronic diabetic foot ulcer patient. This strain exhibits various biofilm-associated genes, virulence genes, and antibiotic-resistance genes related to aminoglycoside, macrolide, and tetracycline resistance.
Draft Genome Sequence of
Chryseobacterium mucoviscidosis
sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis
Authors: Tetz George , Tetz Victor 
Published: January 2018

ABSTRACT

We report here the draft genome sequence of
Chryseobacterium mucoviscidosis
VT16-26, a novel bacterium isolated from the lungs of a patient with cystic fibrosis. The genome was composed of 4,403,956 bp and had 36.2% G+C content. We detected 4,048 genes with predicted protein-coding functions, including those associated with antibiotic resistance and virulence.
MicroRNA 130a Regulates both Hepatitis C Virus and Hepatitis B Virus Replication through a Central Metabolic Pathway
Authors: Duan Xiaoqiong , Li Shilin , Holmes Jacinta A. , Tu Zeng , Li Yujia , Cai Dachuan , Liu Xiao , Li Wenting , Yang Chunhui , Jiao Baihai , Schaefer Esperance A. , Fusco Dahlene N. , Salloum Shadi , Chen Limin , Lin Wenyu , Chung Raymond T. 
Published: January 2018

ABSTRACT
Hepatitis C virus (HCV) infection has been shown to regulate microRNA 130a (miR-130a) in patient biopsy specimens and in cultured cells. We sought to identify miR-130a target genes and to explore the mechanisms by which miR-130a regulates HCV and hepatitis B virus (HBV) replication. We used bioinformatics software, including miRanda, TargetScan, PITA, and RNAhybrid, to predict potential miR-130a target genes. miR-130a and its target genes were overexpressed or were knocked down by use of small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 guide RNA (gRNA). Selected gene mRNAs and their proteins, together with HCV replication in OR6 cells, HCV JFH1-infected Huh7.5.1 cells, and HCV JFH1-infected primary human hepatocytes (PHHs) and HBV replication in HepAD38 cells, HBV-infected NTCP-Huh7.5.1 cells, and HBV-infected PHHs, were measured by quantitative reverse transcription-PCR (qRT-PCR) and Western blotting, respectively. We selected 116 predicted target genes whose expression was related to viral pathogenesis or immunity for qPCR validation. Of these, the gene encoding pyruvate kinase in liver and red blood cell (PKLR) was confirmed to be regulated by miR-130a overexpression. miR-130a overexpression (via a mimic) knocked down PKLR mRNA and protein levels. A miR-130a inhibitor and gRNA increased PKLR expression, HCV replication, and HBV replication, while miR-130a gRNA and PKLR overexpression increased HCV and HBV replication. Supplemental pyruvate increased HCV and HBV replication and rescued the inhibition of HCV and HBV replication by the miR-130a mimic and PKLR knockdown. We concluded that miR-130a regulates HCV and HBV replication through its targeting of PKLR and subsequent pyruvate production. Our data provide novel insights into key metabolic enzymatic pathway steps regulated by miR-130a, including the steps involving PKLR and pyruvate, which are subverted by HCV and HBV replication.

IMPORTANCE
We identified that miR-130a regulates the target gene
PKLR
and its subsequent effect on pyruvate production. Pyruvate is a key intermediate in several metabolic pathways, and we identified that pyruvate plays a key role in regulation of HCV and HBV replication. This previously unrecognized, miRNA-regulated antiviral mechanism has implications for the development of host-directed strategies to interrupt the viral life cycle and prevent establishment of persistent infection for HCV, HBV, and potentially other viral infections.
Two-year neurodevelopmental outcomes of extremely preterm infants treated with early hydrocortisone: treatment effect according to gestational age at birth
Authors: Baud Olivier , Trousson Clémence , Biran Valérie , Leroy Emilie , Mohamed Damir , Alberti Corinne 
Published: January 2018

ObjectiveTo determine whether early hydrocortisone treatment in extremely preterm infants affects neurodevelopmental outcomes at 2 years of age according to gestational age at birth.Patients and methodsThis is an exploratory analysis of neurodevelopmental outcomes by gestational age strata from the PREMILOC trial, in which patients were randomly assigned to receive either placebo or low-dose hydrocortisone and randomisation was stratified by gestational age groups (24–25 and 26–27 weeks of gestation). Neurodevelopmental impairment (NDI) was assessed using a standardised neurological examination and the revised Brunet-Lézine scale at 22 months of corrected age.ResultsA total of 379 of 406 survivors were evaluated, 96/98 in the gestational age group of 24–25 weeks and 283/308 in the gestational age group of 26–27 weeks. Among surviving infants born at 24–25 weeks, significant improvement in global neurological assessment was observed in the hydrocortisone group compared with the placebo group (P=0.02) with a risk of moderate-to-severe NDI of 2% and 18%, respectively (risk difference 16 (95% CI −28% to −5%)). In contrast, no statistically significant difference between treatment groups was observed in infants born at 26–27 weeks (P=0.95) with a similar risk of moderate-to-severe NDI of 9% in both groups. The incidence of cerebral palsy or other major neurological impairments were found similar between treatment groups in each gestational group.ConclusionsIn an exploratory analysis of neurodevelopmental outcomes from the PREMILOC trial, early low-dose hydrocortisone was associated with a statistically significant improvement in neurodevelopmental outcomes in infants born at 24 and 25 weeks of gestation.
Cerebrospinal fluid Alzheimer biomarkers can be useful for discriminating dementia with Lewy bodies from Alzheimer’s disease at the prodromal stage
Authors: Bousiges Olivier , Bombois Stephanie , Schraen Susanna , Wallon David , Quillard Muriel Muraine , Gabelle Audrey , Lehmann Sylvain , Paquet Claire , Amar-Bouaziz Elodie , Magnin Eloi , Miguet-Alfonsi Carole , Delbeuck Xavier , Lavaux Thomas , Anthony Pierre , Philippi Nathalie , Blanc Frederic 
Published: January 2018

BackgroundDifferential diagnosis between dementia with Lewy bodies (DLB) and Alzheimer’s disease (AD) is not straightforward, especially in the early stages of disease. We compared AD biomarkers (phospho-Tau181, total-Tau, Aβ42 and Aβ40) in cerebrospinal fluid (CSF) of patients with DLB and AD, focusing especially on the prodromal stage.MethodsA total of 1221 CSF were collected in different memory centres (ePLM network) in France and analysed retrospectively. Samples were obtained from patients with prodromal DLB (pro-DLB; n=57), DLB dementia (DLB-d; n=154), prodromal AD (pro-AD; n=132) and AD dementia (n=783), and control subjects (CS; n=95). These centres use the same diagnostic procedure and criteria to evaluate the patients.ResultsIn patients with pro-DLB, CSF Aβ42 levels appeared much less disrupted than in patients at the demented stage (DLB-d) (P<0.05 CS>pro-DLB; P<0.001 CS>DLB-d). On average, Aβ40 levels in patients with DLB (pro-DLB and DLB-d) were much below those in patients with pro-AD (P<0.001 DLB groups<pro-AD). The Aβ42/Aβ40 ratio in patients with pro-DLB remained close to that of CS. t-Tau and phospho-Tau181 levels were unaltered in patients with DLB (pro-DLB and DLB-d).ConclusionsReduced levels of CSF Aβ42 were found in patients with DLB but rather at a later stage, reaching those of patients with AD, in whom Aβ42 levels were decreased even at the prodromal stage. At the prodromal stage of DLB, the majority of patients presented a normal CSF profile. CSF t-Tau and phospho-Tau181 were the best biomarkers to discriminate between AD and DLB, whatever the stage of disease.