bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vastus intermedius vs vastus lateralis fascicle behaviors during maximal concentric and eccentric contractions
Authors: Ando R. , Nosaka K. , Tomita A. , Watanabe K. , Blazevich A. J. , Akima H. 
Published: November 2017

Vastus intermedius (VI) plays a major role in knee extension, but its fascicle behaviors during dynamic contractions are not well understood. This study aimed to compare VI and vastus lateralis (VL) fascicle behaviors during singular maximal concentric and eccentric contractions. Thirteen men (27.1 ± 3.4 years) performed maximal isokinetic concentric contractions through knee joint angles of 105° to 35° (0° = full extension) and eccentric contractions from 35° to 105° at an angular velocity of 30°/s. Longitudinal VI and VL sonographic images were simultaneously recorded at 30 Hz, and muscle fascicle lengths at the knee joint angles of 40° and 100° were measured to compare the magnitudes of fascicle length change between the muscles. During concentric contractions, VI and VL fascicle lengths at 100° were 108 ± 12 mm and 104 ± 12 mm, respectively, and shortened by 36 ± 12 mm for VI and 28 ± 13 mm for VL (not statistically different; P = .13) at 40°. During eccentric contractions, VI and VL fascicle lengths at 40° were 72 ± 7 mm and 75 ± 8 mm, respectively, but lengthened by 35 ± 9 mm for VI and 24 ± 5 mm for VL at 100°, with a significant difference between the muscles (P = .01). These results indicate that VI fascicles are lengthened 1.4 times more than VL fascicles during eccentric contractions, whereas VI and VL fascicles shorten similarly during concentric contractions. This suggests a possibility that a greater mechanical strain is imposed to VI than VL during eccentric contractions.
Contamination of small watercourses with heavy metals depending on distance from emission sources: Lesser Poland case study
Authors: Miśkowiec Paweł 
Published: November 2017

AbstractDespite the size of small watercourses, their contamination is a major environmental problem. The Małopolska Upland and the adjacent Silesian‐Cracow Upland, situated in the Lesser Poland region, are two good examples of an area with many small rivers and creeks, which are highly susceptible to contamination. The study reports the condition of small watercourses in terms of their contamination with zinc, lead and cadmium. Both water and sediments were studied. The atomic absorption spectrometry (AAS) method was used to determine the concentrations of metallic elements. The analytical results showed that despite the decreasing impact of the local industry, levels of concentration of all the studied metals in sediments are significantly elevated in the distance range approximately up to 20 km from the emitters. However, analysing the changes of metallic contaminants content with increasing distance one can state that watercourses located further than 30 km from the emitters are safe for aquatic organisms.
Verification of Ceftazidime-Avibactam and Ceftolozane-Tazobactam Susceptibility Testing Methods against Carbapenem-Resistant Enterobacteriaceae and Pseudomonas aeruginosa
Authors: Shields Ryan K. , Clancy Cornelius J. , Pasculle A. William , Press Ellen G. , Haidar Ghady , Hao Binghua , Chen Liang , Kreiswirth Barry N. , Nguyen M. Hong 
Published: November 2017

ABSTRACT

Ceftazidime-avibactam and ceftolozane-tazobactam are newly approved agents for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. Resistance to both agents has been described clinically. Susceptibility testing on automated systems is unavailable for either agent. Our objective was to compare the disk diffusion and Etest methods to standard broth microdilution (BMD) methods for testing ceftazidime-avibactam and ceftolozane-tazobactam against a diverse collection of carbapenem-resistant
Enterobacteriaceae
(CRE) and carbapenem-resistant
Pseudomonas aeruginosa
(CRP) isolates, respectively. Among 74 ceftazidime-avibactam-susceptible and -resistant CRE isolates, BMD categorical agreement was higher with Etest (96%) than with disk diffusion (72%;
P
= 0.0003). Twenty-eight percent of ceftazidime-avibactam-susceptible CRE isolates were classified as resistant by disk diffusion. Results were comparable to those obtained with resistance defined genotypically. Among 72 ceftolozane-tazobactam-susceptible and -resistant CRP isolates, the levels of BMD categorical agreement with disk diffusion and Etest were 94% and 96%, respectively; the only errors identified were minor. Our findings demonstrate that Etest measurements of ceftazidime-avibactam and ceftolozane-tazobactam susceptibility correlate closely with standard BMD methods, suggesting a useful role clinically. On the other hand, disk diffusion measurements overcalled CRE resistance to ceftazidime-avibactam. A better understanding of ceftazidime-avibactam interpretive breakpoints is needed before disk diffusion is used routinely in the clinic. Until clinicians and microbiologists understand Etest and disk diffusion performance at their centers, test results should be interpreted cautiously.
Evaluation of the Copan ESwab Transport System for Viability of Pathogenic Fungi by Use of a Modification of Clinical and Laboratory Standards Institute Document M40-A2
Authors: Gandhi Bharat , Summerbell Richard , Mazzulli Tony 
Published: November 2017

ABSTRACT
The Copan ESwab system was evaluated for its ability to maintain the viability of pathogenic fungi. Tests followed the Clinical and Laboratory Standards Institute (CLSI) document M40-A2 roll-plate method at room and refrigerator temperatures. A system was devised for standardizing homogeneous inoculum suspensions of variously sized conidia and sporangiospores of filamentous fungi. A total of 19 clinical and reference strains were standardized to a 0.5 McFarland turbidity standard with a simple photometer. Corresponding optical densities were measured with a spectrophotometer. Colony counts equal to or greater than those seen at time zero were obtained for the entire test panel. Results indicate that the Copan ESwab system effectively maintains prevalent opportunistic fungal organisms for at least 48 h.
Perioperative Antibiotic Prophylaxis Has No Effect on Time to Positivity and Proportion of Positive Samples: a Cohort Study of 64 Cutibacterium acnes Bone and Joint Infections
Authors: Anagnostopoulos Alexia , Bossard Daniel A. , Ledergerber Bruno , Zingg Patrick O. , Zinkernagel Annelies S. , Gerber Christian , Achermann Yvonne 
Published: November 2017

ABSTRACT

If a bone or joint infection is suspected, perioperative antibiotic prophylaxis is frequently withheld until intraoperative microbiological sampling has been performed. This practice builds upon the hypothesis that perioperative antibiotics could render culture results negative and thus impede tailored antibiotic treatment of infections. We aimed to assess the influence of antibiotic prophylaxis within 30 to 60 min before surgery on time to positivity of microbiological samples and on proportion of positive samples in
Cutibacterium acnes
bone and joint infections. Patients with at least one sample positive for
C. acnes
between January 2005 and December 2015 were included and classified as having an “infection” if at least 2 samples were positive; otherwise they were considered to have a sample “contamination.” Kaplan-Meier curves were used to illustrate time to culture positivity. We found 64 cases with a
C. acnes
infection and 46 classified as having a
C. acnes
contamination. Application of perioperative prophylaxis significantly differed between the infection and contamination groups (72.8% versus 55.8%;
P
< 0.001). Within the infection group, we found no difference in time to positivity between those who had or had not received a perioperative prophylaxis (7.07 days; 95% confidence interval [CI], 6.4 to 7.7, versus 7.11 days; 95% CI, 6.8 to 7.5;
P
= 0.3). Also, there was no association between the proportion of sample positivity and the application of perioperative prophylaxis (71.6% versus 65.9%;
P
= 0.39). Since perioperative prophylaxis did not negatively influence the microbiological yield in
C. acnes
infections, antibiotic prophylaxis can be routinely given to avoid surgical site infections.
Antibodies Directed toward Neuraminidase N1 Control Disease in a Mouse Model of Influenza
Authors: Job E. R. , Schotsaert M. , Ibañez L. I. , Smet A. , Ysenbaert T. , Roose K. , Dai M. , de Haan C. A. M. , Kleanthous H. , Vogel T. U. , Saelens X. 
Published: November 2017

ABSTRACTThere is increasing evidence to suggest that antibodies directed toward influenza A virus (IAV) neuraminidase (NA) are an important correlate of protection against influenza in humans. Moreover, the potential of NA-specific antibodies to provide broader protection than conventional hemagglutinin (HA) antibodies has been recognized. Here, we describe the isolation of two monoclonal antibodies, N1-7D3 and N1-C4, directed toward the N1 NA. N1-7D3 binds to a conserved linear epitope in the membrane-distal, carboxy-terminal part of the NA and reacted with the NA of seasonal H1N1 isolates ranging from 1977 to 2007 and the 2009 H1N1pdm virus, as well as A/Vietnam/1194/04 (H5N1). However, N1-7D3 lacked NA inhibition (NI) activity and the ability to protect BALB/c mice against a lethal challenge with a range of H1N1 viruses. Conversely, N1-C4 bound to a conformational epitope that is conserved between two influenza virus subtypes, 2009 H1N1pdm and H5N1 IAV, and displayed potentin vitroantiviral activity mediating both NI and plaque size reduction. Moreover, N1-C4 could provide heterosubtypic protection in BALB/c mice against a lethal challenge with 2009 H1N1pdm or H5N1 virus. Glutamic acid residue 311 in the NA was found to be critical for the NA binding and antiviral activity of monoclonal antibody N1-C4. Our data provide further evidence for cross-protective epitopes within the N1 subtype and highlight the potential of NA as an important target for vaccine and therapeutic approaches.IMPORTANCEInfluenza remains a worldwide burden on public health. As such, the development of novel vaccines and therapeutics against influenza virus is crucial. Human challenge studies have recently highlighted the importance of antibodies directed toward the viral neuraminidase (NA) as an important correlate of reduced influenza-associated disease severity. Furthermore, there is evidence that anti-NA antibodies can provide broader protection than antibodies toward the viral hemagglutinin. Here, we describe the isolation and detailed characterization of two N1 NA-specific monoclonal antibodies. One of these monoclonal antibodies broadly binds N1-type NAs, and the second displays NA inhibition andin vitroandin vivoantiviral activity against 2009 H1N1pdm and H5N1 influenza viruses. These two new anti-NA antibodies contribute to our understanding of the antigenic properties and protective potential of the influenza virus NA antigen.
Identification and Functional Characterization of Phosphorylation Sites of the Human Papillomavirus 31 E8^E2 Protein
Authors: van de Poel Saskia , Dreer Marcel , Velic Ana , Macek Boris , Baskaran Praveen , Iftner Thomas , Stubenrauch Frank 
Published: November 2017

ABSTRACT
The papillomavirus E2 protein regulates transcription, replication, and nuclear retention of viral genomes. Phosphorylation of E2 in the hinge region has been suggested to modulate protein stability, DNA-binding activity, and chromosomal attachment. The papillomavirus E8^E2 protein shares the hinge domain with E2 and acts as a repressor of viral replication. Mass spectrometry analyses of human papillomavirus 31 (HPV31) E8^E2 and E2 proteins identify phosphorylated S78, S81, and S100 in E8^E2 and S266 and S269 in E2 in their hinge regions. Phos-tag analyses of wild-type and mutant proteins indicate that S78 is a major phosphorylation site in E8^E2, but the corresponding S266 in E2 is not. Phosphorylation at S78 regulates E8^E2's repression activity of reporter constructs, whereas the corresponding E2 mutants do not display a phenotype. Phosphorylation at S78 does not alter E8^E2's protein stability, nuclear localization, or binding to DNA or to cellular NCoR/SMRT complexes. Surprisingly, in the context of HPV31 genomes, mutation of E8^E2 S78 does not modulate viral replication or transcription in undifferentiated or differentiated cells. However, comparative transcriptome analyses of differentiated HPV31 E8^E2 S78A and S78E cell lines reveal that the expression of a small number of cellular genes is changed. Validation experiments suggest that the transcription of the cellular LYPD2 gene is altered in a phospho-S78 E8^E2-dependent manner. In summary, our data suggest that phosphorylation of S78 in E8^E2 regulates its repression activity by a novel mechanism, and this seems to be important for the modulation of host cell gene expression but not viral replication.

IMPORTANCE
Posttranslational modification of viral proteins is a common feature to modulate their activities. Phosphorylation of serine residues S298 and S301 in the hinge region of the bovine papillomavirus type 1 E2 protein has been shown to restrict viral replication. The papillomavirus E8^E2 protein shares the hinge domain with E2 and acts as a repressor of viral replication. A large fraction of HPV31 E8^E2 is phosphorylated at S78 in the hinge region, and this is important for E8^E2's repression activity. Surprisingly, phosphorylation at S78 in E8^E2 has no impact on viral replication in tissue culture but rather seems to modulate the expression of a small number of cellular genes. This may indicate that phosphorylation of viral transcription factors serves to broaden their target gene specificity.
Glycine Zipper Motifs in Hepatitis C Virus Nonstructural Protein 4B Are Required for the Establishment of Viral Replication Organelles
Authors: Paul David , Madan Vanesa , Ramirez Omar , Bencun Maja , Stoeck Ina Karen , Jirasko Vlastimil , Bartenschlager Ralf 
Published: November 2017

ABSTRACT
Hepatitis C virus (HCV) RNA replication occurs in tight association with remodeled host cell membranes, presenting as cytoplasmic accumulations of single-, double-, and multimembrane vesicles in infected cells. Formation of these so-called replication organelles is mediated by a complex interplay of host cell factors and viral replicase proteins. Of these, nonstructural protein 4B (NS4B), an integral transmembrane protein, appears to play a key role, but little is known about the molecular mechanisms of how this protein contributes to organelle biogenesis. Using forward and reverse genetics, we identified glycine zipper motifs within transmembrane helices 2 and 3 of NS4B that are critically involved in viral RNA replication. Foerster resonance energy transfer analysis revealed the importance of the glycine zippers in NS4B homo- and heterotypic self-interactions. Additionally, ultrastructural analysis using electron microscopy unraveled a prominent role of glycine zipper residues for the subcellular distribution and the morphology of HCV-induced double-membrane vesicles. Notably, loss-of-function NS4B glycine zipper mutants prominently induced single-membrane vesicles with secondary invaginations that might represent an arrested intermediate state in double-membrane vesicle formation. These findings highlight a so-far-unknown role of glycine residues within the membrane integral core domain for NS4B self-interaction and functional as well as structural integrity of HCV replication organelles.

IMPORTANCE
Remodeling of the cellular endomembrane system leading to the establishment of replication organelles is a hallmark of positive-strand RNA viruses. In the case of HCV, expression of the nonstructural proteins induces the accumulation of double-membrane vesicles that likely arise from a concerted action of viral and coopted cellular factors. However, the underlying molecular mechanisms are incompletely understood. Here, we identify glycine zipper motifs within HCV NS4B transmembrane segments 2 and 3 that are crucial for the protein's self-interaction. Moreover, glycine residues within NS4B transmembrane helices critically contribute to the biogenesis of functional replication organelles and, thus, efficient viral RNA replication. These results reveal how glycine zipper motifs in NS4B contribute to structural and functional integrity of the HCV replication organelles and, thus, viral RNA replication.
Novel Synthesis and Phenotypic Analysis of Mutant Clouds for Hepatitis E Virus Genotype 1
Authors: Agarwal Shubhra , Baccam Prasith , Aggarwal Rakesh , Veerapu Naga Suresh 
Published: November 2017

ABSTRACT

Many RNA viruses exist as an ensemble of genetically diverse, replicating populations known as a mutant cloud. The genetic diversity (cloud size) and composition of this mutant cloud may influence several important phenotypic features of the virus, including its replication capacity. We applied a straightforward, bacterium-free approach using error-prone PCR coupled with reverse genetics to generate infectious mutant RNA clouds with various levels of genetic diversity from a genotype 1 strain of hepatitis E virus (HEV). Cloning and sequencing of a genomic fragment encompassing 70% of open reading frame 1 (
ORF1
) or of the full genome from variants in the resultant clouds showed the occurrence of nucleotide mutations at a frequency on the order of 10
−3
per nucleotide copied and the existence of marked genetic diversity, with a high normalized Shannon entropy value. The mutant clouds showed transient replication in cell culture, while wild-type HEV did not. Cross-sectional data from these cell cultures supported the existence of differential effects of clouds of various sizes and compositions on phenotypic characteristics, such as the replication level of (+)-RNA progeny, the amounts of double-stranded RNA (a surrogate for the rate of viral replication) and ORF1 protein, and the expression of interferon-stimulated genes. Since mutant cloud size and composition influenced the viral phenotypic properties, a better understanding of this relationship may help to provide further insights into virus evolution and prediction of emerging viral diseases.

IMPORTANCE
Several biological or practical limitations currently prevent the study of phenotypic behavior of a mutant cloud
in vitro
. We developed a simple and rapid method for synthesizing mutant clouds of hepatitis E virus (HEV), a single-stranded (+)-RNA [ss(+) RNA] virus, with various and controllable levels of genetic diversity, which could then be used in a cell culture system to study the effects of cloud size and composition on viral phenotype. In a cross-sectional analysis, we demonstrated that a particular mutant cloud which had an extremely high genetic diversity had a replication rate exceeding that of wild-type HEV. This method should thus provide a useful model for understanding the phenotypic behavior of ss(+) RNA viruses.
Lactobacillus acidophilus
Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals
Authors: Theilmann Mia C. , Goh Yong Jun , Nielsen Kristian Fog , Klaenhammer Todd R. , Barrangou Rodolphe , Abou Hachem Maher 
Published: November 2017

ABSTRACT

Therapeutically active glycosylated phytochemicals are ubiquitous in the human diet. The human gut microbiota (HGM) modulates the bioactivities of these compounds, which consequently affect host physiology and microbiota composition. Despite a significant impact on human health, the key players and the underpinning mechanisms of this interplay remain uncharacterized. Here, we demonstrate the growth of
Lactobacillus acidophilus
on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones. Transcriptional analysis revealed the upregulation of host interaction genes and identified two loci that encode phosphotransferase system (PTS) transporters and phospho-β-glucosidases, which mediate the uptake and deglucosylation of these compounds, respectively. Inactivating these transport and hydrolysis genes abolished or severely reduced growth on PG, establishing the specificity of the loci to distinct groups of PGs. Following intracellular deglucosylation, the aglycones of PGs are externalized, rendering them available for absorption by the host or for further modification by other microbiota taxa. The PG utilization loci are conserved in
L. acidophilus
and closely related lactobacilli, in correlation with versatile growth on these compounds. Growth on the tested PG appeared more common among human gut lactobacilli than among counterparts from other ecologic niches. The PGs that supported the growth of
L. acidophilus
were utilized poorly or not at all by other common HGM strains, underscoring the metabolic specialization of
L. acidophilus
. These findings highlight the role of human gut
L. acidophilus
and select lactobacilli in the bioconversion of glycoconjugated phytochemicals, which is likely to have an important impact on the HGM and human host.

IMPORTANCE
Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by
Lactobacillus acidophilus
and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota.
Synthesis of limnological data from lakes and ponds across Arctic and Boreal Canada
Authors: Dranga Stefana Aurora , Hayles Simon , Gajewski Konrad 
Published: November 2017

A compilation of published and new limnological data from 1489 shallow lakes and ponds in northern Canada, sampled between 1979 and 2009, revealed significant patterns that correlated with landscape features and climate. Lakes and ponds underlain by Archean or Proterozoic bedrock had lower specific conductivity and pH. Vegetation cover had a lesser influence on these parameters. Forested landscapes tended to have higher phosphorus and nitrogen, as did younger rock types. Dissolved organic carbon was higher, but dissolved inorganic carbon was lower in forested regions. Phytoplankton biomass of the surface waters, as estimated by chlorophyll a concentrations, was positively correlated with July air temperature and nutrients, and was higher in forested relative to polar desert regions. There were no significant differences in the measured limnological variables between shallow (<2 m depth) and deep lakes (>2 m); however, all water chemistry parameters were negatively correlated with depth. Despite large variability within and among regions, spatial trends in water chemistry were associated with geology, vegetation, and climate at a continental scale.