bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence that an internal schema adapts swallowing to upper airway requirements
Authors: Wong Seng Mun , Domangue Rickie J. , Fels Sidney , Ludlow Christy L. 
Published: November 2016

Key points
To swallow food and liquid safely, airway protection is essential.
Upward and forward movements of the hyoid and larynx in the neck during swallowing vary in magnitude between individuals.
In healthy human adults, hyoid and laryngeal movements during swallowing were scaled by differences in initial upper airway area before swallowing.
Individuals increased laryngeal elevation during swallowing in response to increased airway opening before swallowing.
We show that when upper airway protection requirements change, individuals use an internal sensorimotor scaling system to adapt movements to maintain swallow safety.
AbstractHyoid and laryngeal movements contribute to laryngeal vestibule closure and upper oesophageal sphincter opening during swallowing. Evidence of an internal sensorimotor scaling system allowing individuals to achieve these functional goals is lacking. In speech, speakers adjust their articulatory movement magnitude according to the movement distance required to reach an articulatory target for intelligible speech. We investigated if swallowing is similar in that movement amplitude may be scaled by the functional goal for airway protection during swallowing, rather than by head and neck size. We hypothesized that healthy individuals adapt to their own anatomy by adjusting hyo‐laryngeal movements to achieve closure of the upper airway. We also investigated if individuals would automatically compensate for changes in their initial hyo‐laryngeal positions and area when head position was changed prior to swallowing. Videofluoroscopy was performed in 31 healthy adults. Using frame‐by‐frame motion analysis, anterior and superior hyoid and laryngeal displacement, and hyo‐laryngeal area were measured prior to and during swallowing. Kinematic measurements during swallowing were examined for relationships with pharyngeal neck length, and initial hyo‐laryngeal positions, length and area before swallowing. During swallowing, individuals altered laryngeal elevation magnitude to exceed hyoid elevation based on hyo‐laryngeal length before swallowing. Anterior laryngeal displacement was related to initial larynx distance from the spine, while hyoid elevation was predicted by pharyngeal neck length and initial hyoid distance from the mandible prior to the swallow. In conclusion, individuals automatically adapt hyo‐laryngeal movement during swallowing based on targets required for closing the hyo‐laryngeal area for safe swallowing.
A new algorithm for estimating the rod volume fraction and the trabecular thickness from in vivo computed tomography
Authors: Thomsen Felix Sebastian Leo , Peña Jaime Andrés , Lu Yongtao , Huber Gerd , Morlock Michael , Glüer Claus‐Christian , Delrieux Claudio Augusto 
Published: November 2016

Purpose:Existing microstructure parameters are able to predict vertebral in vitro failure load, but for noisy in vivo data more complex algorithms are needed for a robust assessment.Methods:A new algorithm is proposed for the microstructural analysis of trabecular bone under in vivo quantitative computed tomography (QCT). Five fractal parameters are computed: (1) the average local fractal dimension FD, (2) its standard deviation FD.SD, (3) the fractal rod volume ratio fRV/BV, (4) the average fractal trabecular thickness fTb.Th, and (5) its coefficient of variation fTb.Th.CV. The algorithm requires neither an explicit skeletonization of the trabecular bone, nor a well‐defined transition between bone and marrow phases. Two experiments were conducted to compare the fractal with established microstructural parameters. In the first, 20 volumes‐of‐interest of embedded vertebrae phantoms were scanned five times under QCT and high‐resolution (HR‐)QCT and once under peripheral HRQCT (HRpQCT), to derive accuracy and precision. In the second experiment, correlations between in vitro HRQCT structural parameters were obtained from 76 human T11, T12, or L1 vertebrae. In vitro fracture data were available for a subset of 17 human T12 vertebrae so that linear regression models between failure load and microstructural HRQCT parameters could be analyzed.Results:The results showed correlations of fTb.Th and fRV/BV with their nonfractal pendants trabecular thickness (Tb.Th) and respective structure model index (SMI) while higher precision and accuracy was observed on the fractal measures. Linear models of bone mineral density with two and three fractal microstructural HRQCT parameters explained 86% and 90% (adjusted R2) of the failure load and significantly improved the linear models based only on BMD and established standard microstructural parameters (68%–77% adjusted R2).Conclusions:The application of fractal methods may grant further insight into the study of bone quality in vivo when image resolution and quality are less than optimal for current standard methods.
Defining and assessing an anisotropic delineation margin for modern radiotherapy
Authors: Bell L. R. , Pogson E. M. , Metcalfe P. E. , Holloway L. C. 
Published: November 2016

Purpose:Uncertainty in target volume delineation for modern radiotherapy impacts dosimetry and patient outcomes. Delineation uncertainty is generally overlooked in practice as a source of error, potentially since historically, other uncertainties have been the main focus. This work defined and assessed an anisotropic delineation margin in both polar and spherical coordinate systems in order to account for the spatially varying nature of this uncertainty using a whole breast radiotherapy cohort as a proof of concept.Methods:A cohort of 21 whole breast radiotherapy patient datasets with clinical target volumes delineated by eight independent observers was utilized. Patients were divided into categories based on target volume and laterality. An anisotropic delineation margin for each category was determined by multiplying the average standard deviation in observer contours in each category by a factor of two. Standard deviation was determined in both polar and spherical coordinates at angular increments. This anisotropic approach was compared to a conventional clinical approach, where the delineation margin was applied in the cardinal directions only. The assessment of the delineation margin was undertaken by comparing the encompassment of the observer volumes by the target volume with added margin. The extra, presumed healthy tissue included in the margin and the malignant tissue missed by the margin were determined.Results:The proposed delineation margin is effective at accounting for inter‐observer variation, producing >95% coverage of all CTVs for polar, spherical, and Cartesian margins in 82%, 79%, and 92% of cases, respectively. Additionally, <1% malignant tissue was missed for 65%, 70%, and 91% of cases and <37% healthy tissue was included in 95%, 89%, and 97% of cases. A conventional delineation margin approach is most appropriate for small and gold standard target volumes. However, for large target volumes, an anisotropic margin is necessary, producing significantly greater coverage of CTVs, including significantly less presumed healthy tissue and missing significantly less malignant tissue.Conclusions:All delineation margin methods that account for target volume and laterality proved to be adequate, with appropriate encompassment of interobserver variation and minimal inclusion of extra excess healthy tissue and exclusion of possible malignant tissue. The anisotropic approach was found to be superior to a conventional approach for target volumes >1400 cm3 only with significantly greater encompassment of interobserver variation, less missed malignant tissue and less included healthy tissue. This methodology has been validated for a whole breast radiotherapy cohort as a proof of concept, however could be applied to other anatomical sites.
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
Authors: Huang Andrew D. , Luo Chengwei , Pena-Gonzalez Angela , Weigand Michael R. , Tarr Cheryl L. , Konstantinidis Konstantinos T. 
Published: November 2016

ABSTRACT

Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified by culture-dependent methods as distinct strains of
Salmonella enterica
subsp.
enterica
serovar Heidelberg. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the
in situ
abundance and level of intrapopulation diversity of the pathogen, the possibility of coinfections with
Staphylococcus aureus
, overgrowth of commensal
Escherichia coli
, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with the analysis of clinical samples, such as the high frequency of coeluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several, but not all, cases of diarrheal outbreaks, the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics.

IMPORTANCE
Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques, but a total of 38.4 million cases of foodborne illness per year cannot be attributed to specific causes. This study describes new culture-independent metagenomic approaches and the associated bioinformatics pipeline to detect and type the causative agents of microbial disease with unprecedented accuracy, opening new possibilities for the future development of health technologies and diagnostics. Our tools and approaches should be applicable to other microbial diseases in addition to foodborne diarrhea.
Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection
Authors: Challacombe Jean F. , Petersen Jeannine M. , Gallegos-Graves La Verne , Hodge David , Pillai Segaran , Kuske Cheryl R. 
Published: November 2016

ABSTRACT

Francisella tularensis
is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of
F. tularensis
may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental
Francisella
isolates have been obtained in recent years. Here we present 7 new
Francisella
genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and
sdhA
genes from over 90
Francisella
strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within
Francisella
varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA,
sdhA
), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus;
Francisella opportunistica
sp. nov. (MA06-7296),
Francisella salina
sp. nov. (TX07-7308),
Francisella uliginis
sp. nov. (TX07-7310), and
Francisella frigiditurris
sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected
Francisella
bacteria.

IMPORTANCE
DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new
Francisella
isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate
F. tularensis
from clinical and environmental
Francisella
isolates and provide a knowledge base for future comparison of
Francisella
organisms identified in clinical samples or environmental surveys.
Enhanced Glucose Consumption and Organic Acid Production by Engineered Corynebacterium glutamicum Based on Analysis of a
pfkB1
Deletion Mutant
Authors: Hasegawa Satoshi , Tanaka Yuya , Suda Masako , Jojima Toru , Inui Masayuki 
Published: November 2016

ABSTRACT

In the analysis of a carbohydrate metabolite pathway, we found interesting phenotypes in a mutant strain of
Corynebacterium glutamicum
deficient in
pfkB1
, which encodes fructose-1-phosphate kinase. After being aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced organic acid, predominantly
l
-lactate, at a level more than 2-fold higher than that of the wild-type grown with glucose under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of
pfkB1
deletion and cultivation with fructose. In the metabolome and transcriptome analyses of this strain, marked intracellular accumulation of fructose-1-phosphate and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis were identified. We then examined strains overexpressing several of the identified genes and demonstrated enhanced glucose consumption and organic acid production by these engineered strains, whose values were found to be comparable to those of the model
pfkB1
deletion mutant grown with fructose.
l
-Lactate production by the
ppc
deletion mutant of the engineered strain was 2,390 mM (i.e., 215 g/liter) after 48 h under oxygen deprivation, which was a 2.7-fold increase over that of the wild-type strain with a deletion of
ppc
.

IMPORTANCE
Enhancement of glycolytic flux is important for improving microbiological production of chemicals, but overexpression of glycolytic enzymes has often resulted in little positive effect. That is presumably because the central carbon metabolism is under the complex and strict regulation not only transcriptionally but also posttranscriptionally, for example, by the ATP/ADP ratio. In contrast, we studied a mutant strain of
Corynebacterium glutamicum
that showed markedly enhanced glucose consumption and organic acid production and, based on the findings, identified several genes whose overexpression was effective in enhancing glycolytic flux under conditions of oxygen deprivation. These results will further understanding of the regulatory mechanisms of glycolytic flux and can be widely applied to the improvement of the microbial production of useful chemicals.
Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa
Authors: Chatterjee Payel , Davis Elizabeth , Yu Fengan , James Sarah , Wildschutte Julia H. , Wiegmann Daniel D. , Sherman David H. , McKay Robert M. , LiPuma John J. , Wildschutte Hans 
Published: November 2016

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic
P. aeruginosa
in cystic fibrosis (CF) patients, less is known of its ecological properties.
P. aeruginosa
dominates the lungs during chronic infection in CF patients, yet its abundance in some environments is less than that of other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of
P. aeruginosa
are vulnerable to environmental pseudomonads that dominate soil and water habitats in one-to-one competitions which may provide a source of inhibitory factors. We isolated a total of 330 pseudomonads from diverse habitats of soil and freshwater ecosystems and competed these strains against one another to determine their capacity for antagonistic activity. Over 900 individual inhibitory events were observed. Extending the analysis to
P. aeruginosa
isolates revealed that clinical isolates, including ones with increased alginate production, were susceptible to competition by multiple environmental strains. We performed transposon mutagenesis on one isolate and identified an ∼14.8-kb locus involved in antagonistic activity. Only two other environmental isolates were observed to carry the locus, suggesting the presence of additional unique compounds or interactions among other isolates involved in outcompeting
P. aeruginosa
. This collection of strains represents a source of compounds that are active against multiple pathogenic strains. With the evolution of resistance of
P. aeruginosa
to currently used antibiotics, these environmental strains provide opportunities for novel compound discovery against drug-resistant clinical strains.

IMPORTANCE
We demonstrate that clinical CF-derived isolates of
P. aeruginosa
are susceptible to competition in the presence of environmental pseudomonads. We observed that many diverse environmental strains exhibited varied antagonistic profiles against a panel of clinical
P. aeruginosa
isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for
P. aeruginosa
infections.
Complete Genome Sequence of Mycobacterium chimaera Strain AH16
Authors: Hasan Nabeeh A. , Honda Jennifer R. , Davidson Rebecca M. , Epperson L. Elaine , Bankowski Matthew J. , Chan Edward D. , Strong Michael 
Published: November 2016

ABSTRACT

Mycobacterium chimaera
is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of
M. chimaera
. This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes.
Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long-Term at Elevated Copper Levels
Authors: Cusick Kathleen D. , Dale Jason R. , Little Brenda J. , Biffinger Justin C. 
Published: November 2016

ABSTRACT

Alteromonas macleodii
is a marine bacterium involved in the early stages of biofouling on ship hulls treated with copper as an antifouling agent. We report here the draft genome sequences of an
A. macleodii
strain isolated from copper coupons and three laboratory mutants grown long-term at elevated copper levels.
Performance Characteristics of a New Consensus Commercial Kit for Hepatitis D Virus RNA Viral Load Quantification
Authors: Le Gal Frédéric , Dziri Samira , Gerber Athenaïs , Alloui Chakib , Ben Abdesselam Zahia , Roulot Dominique , Brichler Ségolène , Gordien Emmanuel 
Published: November 2016

ABSTRACTHepatitis D virus (HDV) is responsible for fulminant hepatitis and liver failure and accelerates evolution toward cirrhosis and hepatocellular carcinoma in hepatitis B virus (HBV)-infected patients. To date, treatment relies upon long-term administration of pegylated alpha-interferon with a sustained virological response in 30% of the patients. Very recently, new, promising anti-HDV therapies have been developed and are already being used in clinical trials. HDV RNA viral load (HDVL) monitoring must be an integral part of the management of the infected patients. However, HDV genus is characterized by a high genetic variability into eight genotypes (HDV-1 to -8), and most available in-house or commercial assays are useful for only a limited subset of genotypes. Results of a comparison of the performance of a new kit for HDVL quantification with the consensus in-house assay of the French National Reference Laboratory for HDV developed in 2005 are reported here. A total of 611 clinical samples of all HDV genotypes with various HDVL values, including several consecutive samples over several years from 36 patients, were studied. A specificity, sensitivity, and reproducibility evaluation was conducted using HDV-positive clinical samples, hepatitis A, B, C and E (HAV, HBV, HCV, and HEV, respectively) and HIV mono-infected samples, and the WHO HDV RNA international standard. Overall results were strictly comparable between the two assays (median difference, 0.07 log IU/ml), with high diagnosis precision and capacity. In summary, this new kit showed high performance in detection/quantification of HDVL, regardless of the genotype of the infecting strain used, and seems to be a suitable tool for patient management.