bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy
Authors: Luo Ting , Srinivasan Usha , Ramadugu Kirtana , Shedden Kerby A. , Neiswanger Katherine , Trumble Erika , Li Jiean J. , McNeil Daniel W. , Crout Richard J. , Weyant Robert J. , Marazita Mary L. , Foxman Betsy 
Published: July 2016

ABSTRACT
Community profiling of the oral microbiome requires the recovery of quality sequences in order to accurately describe microbial community structure and composition. Our objective was to assess the effects of specimen collection method, storage medium, and storage conditions on the relative abundance of taxa in saliva and plaque identified using 16S rRNA genes. We also assessed short-term changes in taxon composition and relative abundance and compared the salivary and dental plaque communities in children and adults. Over a 2-week period, four successive saliva and dental plaque specimens were collected from four adults with no dental decay (108 samples), and two successive specimens were collected from six children with four or more erupted teeth (48 samples). There were minimal differences in community composition at the phylum and operational taxonomic unit levels between dental plaque collection using a scaler and collection using a CytoSoft brush. Plaque samples stored in OMNIgene medium showed higher within-sample Shannon diversity, were compositionally different, and were more similar to each other than plaque stored in liquid dental transport medium. Saliva samples stored in OMNIgene recovered similar communities for at least a week following storage at room temperature. However, the microbial communities recovered from plaque and saliva stored in OMNIgene were significantly different in composition from their counterparts stored in liquid dental transport medium. Dental plaque communities collected from the same tooth type over four successive visits from the same adult did not significantly differ in structure or composition.

IMPORTANCE
Large-scale epidemiologic studies require collection over time and space, often with multiple teams collecting, storing, and processing data. Therefore, it is essential to understand how sensitive study results are to modest changes in collection and storage protocols that may occur with variation in personnel, resources available at a study site, and shipping requirements. The research presented in this paper measures the effects of multiple storage parameters and collection methodologies on the measured ecology of the oral microbiome from healthy adults and children. These results will potentially enable investigators to conduct oral microbiome studies at maximal efficiency by guiding informed administrative decisions pertaining to the necessary field or clinical work.
A Small Number of Phylogenetically Distinct Clonal Complexes Dominate a Coastal Vibrio cholerae Population
Authors: Kirchberger Paul C. , Orata Fabini D. , Barlow E. Jed , Kauffman Kathryn M. , Case Rebecca J. , Polz Martin F. , Boucher Yan 
Published: July 2016

ABSTRACT

Vibrio cholerae
is a ubiquitous aquatic microbe in temperate and tropical coastal areas. It is a diverse species, with many isolates that are harmless to humans, while others are highly pathogenic. Most notable among them are strains belonging to the pandemic O1/O139 serogroup lineage, which contains the causative agents of cholera. The environmental selective regimes that led to this diversity are key to understanding how pathogens evolve in environmental reservoirs. A local population of
V. cholerae
and its close relative
Vibrio metoecus
from a coastal pond and lagoon system was extensively sampled during two consecutive months across four size fractions (480 isolates). In stark contrast to previous studies, the observed population was highly clonal, with 60% of
V. cholerae
isolates falling into one of five clonal complexes, which varied in abundance in the short temporal scale sampled.
V. cholerae
clonal complexes had significantly different distributions across size fractions and the two environments sampled, the pond and the lagoon. Sequencing the genomes of 20 isolates representing these five
V. cholerae
clonal complexes revealed different evolutionary trajectories, with considerable variations in gene content with potential ecological significance. Showing genotypic differentiation and differential spatial distribution, the dominant clonal complexes are likely ecologically divergent. Temporal variation in the relative abundance of these complexes suggests that transient blooms of specific clones could dominate local diversity.

IMPORTANCE
Vibrio cholerae
is commonly found in coastal areas worldwide, with only a single group of this bacterium capable of causing severe cholera outbreaks. However, the potential to evolve the ability to cause disease exists in many strains of this species in its aquatic reservoir. Understanding how pathogenic bacteria evolve requires the study of their natural environments. By extensive sampling in a geographically restricted location in the United States, we found that most cells of a
V. cholerae
population belong to only a small number of strains. Analysis of their genome composition and spatial distribution indicates differential environmental adaptations between these strains. Other strains exist in smaller numbers, and the population was found to be temporally varied. This suggests frequent bloom and collapse cycles on a time scale of weeks. These population dynamics make it possible that more virulent strains could stochastically rise to large numbers, allowing for infection to occur.
A Rapid Method for Quantifying Viable Mycobacterium avium subsp. paratuberculosis in Cellular Infection Assays
Authors: Pooley Hannah B. , de Silva Kumudika , Purdie Auriol C. , Begg Douglas J. , Whittington Richard J. , Plain Karren M. 
Published: July 2016

ABSTRACT

Determining the viability of bacteria is a key outcome of
in vitro
cellular infection assays. Currently, this is done by culture, which is problematic for fastidious slow-growing bacteria such as
Mycobacterium avium
subsp.
paratuberculosis
, where it can take up to 4 months to confirm growth. This study aimed to identify an assay that can rapidly quantify the number of viable
M. avium
subsp.
paratuberculosis
cells in a cellular sample. Three commercially available bacterial viability assays along with a modified liquid culture method coupled with high-throughput quantitative PCR growth detection were assessed. Criteria for assessment included the ability of each assay to differentiate live and dead
M. avium
subsp.
paratuberculosis
organisms and their accuracy at low bacterial concentrations. Using the culture-based method,
M. avium
subsp.
paratuberculosis
growth was reliably detected and quantified within 2 weeks. There was a strong linear association between the 2-week growth rate and the initial inoculum concentration. The number of viable
M. avium
subsp.
paratuberculosis
cells in an unknown sample was quantified based on the growth rate, by using growth standards. In contrast, none of the commercially available viability assays were suitable for use with samples from
in vitro
cellular infection assays.

IMPORTANCE
Rapid quantification of the viability of
Mycobacterium avium
subsp.
paratuberculosis
in samples from
in vitro
cellular infection assays is important, as it allows these assays to be carried out on a large scale.
In vitro
cellular infection assays can function as a preliminary screening tool, for vaccine development or antimicrobial screening, and also to extend findings derived from experimental animal trials. Currently, by using culture, it takes up to 4 months to obtain quantifiable results regarding
M. avium
subsp.
paratuberculosis
viability after an
in vitro
infection assay; however, with the quantitative PCR and liquid culture method developed, reliable results can be obtained at 2 weeks. This method will be important for vaccine and antimicrobial screening work, as it will allow a greater number of candidates to be screened in the same amount of time, which will increase the likelihood that a favorable candidate will be found to be subjected to further testing.
Socioeconomic status inequalities in low-grade inflammation during childhood
Authors: Schmeer Kammi K , Yoon Aimee 
Published: July 2016

BackgroundFamily socioeconomic status (SES) is an important source of child health disparities in the USA. Chronic stress is one way SES may impact children's physiology with implications for later health inequalities. These processes may work differently across childhood due to differences in exposure and susceptibility to stressors at different ages. We assess associations between family SES and one biomarker of chronic stress exposure—low-grade inflammation detected by elevated C reactive protein (CRP)—and evaluate differences in the associations by child age.MethodsWe used nationally representative data from the National Health and Nutrition Examination Survey and Tobit regression models to estimate SES associations with CRP and the moderating effects of age for children age 2–18 years. Our sample was limited to CRP ≤10 mg/l to focus on low-grade inflammation (N=13 165).ResultsChildren whose parent had less than a high school degree had 35% higher CRP than those with a college graduate parent; and, poor children had 24% higher CRP than those with high family income, net of controls. When children's body mass index was accounted for, low education and poverty associations were reduced to 19% and 15%, respectively. Child age interactions were negative and significant for both parental education and family income.ConclusionsThis study provides new evidence that SES is associated with low-grade inflammation in children, and that these associations may be particularly strong during early and mid-childhood. Future research should further our understanding of stressors related to low family SES that may lead to immune system dysregulation during childhood.
Population attributable risk estimates for factors associated with non-use of postnatal care services among women in Nigeria
Authors: Agho K E , Ezeh O K , Issaka A I , Enoma A I , Baines S , Renzaho A M N 
Published: July 2016

ObjectivesTo determine population attributable risks (PARs) estimates for factors associated with non-use of postnatal care (PNC) in Nigeria.Design, setting and participantsThe most recent Nigeria Demographic and Health Survey (NDHS, 2013) was examined. The study consisted of 20 467 mothers aged 15–49 years. Non-use of PNC services was examined against a set of demographic, health knowledge and social structure factors, using multilevel regression analysis. PARs estimates were obtained for each factor associated with non-use of PNC in the final multivariate logistic regression model.Main outcomePNC services.ResultsNon-use of PNC services was attributed to 68% (95% CI 56% to 76%) of mothers who delivered at home, 61% (95% CI 55% to 75%) of those who delivered with the help of non-health professionals and 37% (95% CI 31% to 45%) of those who lacked knowledge of delivery complications in the study population. Multiple variable analyses revealed that non-use of PNC services among mothers was significantly associated with rural residence, household poverty, no or low levels of mothers' formal education, small perceived size of neonate, poor knowledge of delivery-related complications, and limited or no access to the mass media.ConclusionsPAR estimates for factors associated with non-use of PNC in Nigeria highlight the need for community-based interventions regarding maternal education and services that focus on mothers who delivered their babies at home. Our study also recommends financial support from the Nigerian government for mothers from low socioeconomic settings, so as to minimise the inequitable access to pregnancy and delivery healthcare services with trained healthcare personnel.
Differing expression profiles ofNotch/enterocyte andWnt/secretory lineage signallings are associated with morphological diversity of appendiceal tumours
Authors: Gui Xianyong , Meng Ziran , McConnell Yarrow J , Liu Shuhong , Falck Vincent G , Mack Lloyd A , Temple Walley J 
Published: July 2016

BackgroundTumours of appendix, including classic carcinoid tumour (CCT), goblet cell carcinoid (GCC), low-grade appendiceal mucinous neoplasm, high-grade appendiceal mucinous neoplasm/mucinous carcinoma (MCA) and non-mucinous adenocarcinoma (NMA), show different and sometimes mixed morphological features. It was hypothesised that these tumours originate from common tumour stem cell(s) with potential of various cell lineage differentiation. In normal intestinal epithelium, absorptive lineage (enterocytes) differentiation is driven byNotch-Hes1pathway, while secretory lineage is driven byWnt-Math1pathway and further separated by different downstream signallings into three sublineages (Gfi1-Klf4/Elf3for goblet cells,Gfi1-Sox9for Paneth cells andNgn3-Pdx1/Beta2/Pax4for enteroendocrine cells).MethodsThe expressions of various signalling proteins in different appendiceal tumours were detected by immunohistochemistry on tumour tissue microarray.ResultsCCT showed reducedHes1/Elf3andSox9/Klf4coupled with elevatedMath1, in keeping with endocrine phenotype. As compared with CCT, GCC showed higherKlf4and similarNgn3/Pax4, indicative of a shift of differentiation towards goblet cells as well as endocrine cells. GCC displayed aNotchsignalling similar to adenocarcinoma. Mucinous tumours showed lowerElf3than normal appendiceal epithelium and higherMath1/Gfi1/Klf4, suggestive of a differentiation towards less enterocytes but more goblet cells. NMA showedNotchsignalling similar to other glandular tumours, but lowerKlf4. However, some seemingly paradoxical changes were also observed, probably suggesting gene mutations and/or our incomplete understanding of the intestinal cell differentiation.ConclusionsWnt/secretory lineage protein andNotch/absorptive lineage protein expression profiles are generally associated with the tumour cell differentiation and morphological diversity of common appendiceal tumours.
Single best answer question-writing tips for clinicians
Authors: Walsh J L , Harris B H L , Smith P E 
Published: July 2016

ABSTRACTAssessment is essential for progression in medical careers. Thus, an important aspect of developing as a clinical teacher is the ability to produce high-quality assessments for junior colleagues. The single best answer (SBA) question format is becoming ubiquitous in the assessment of the application of knowledge in clinical medicine; writing this style of examination question can be a challenge. This concise guide highlights key SBA question-writing tips, aiming to help aspiring clinical teachers set high-quality knowledge assessments.
Right Ventricular Myocardial Stiffness in Experimental Pulmonary Arterial Hypertension
Authors: Rain Silvia , Andersen Stine , Najafi Aref , Gammelgaard Schultz Jacob , da Silva Gonçalves Bós Denielli , Handoko M. Louis , Bogaard Harm-Jan , Vonk-Noordegraaf Anton , Andersen Asger , van der Velden Jolanda , Ottenheijm Coen A.C. , de Man Frances S. 
Published: July 2016

Background—
The purpose of this study was to determine the relative contribution of fibrosis-mediated and myofibril-mediated stiffness in rats with mild and severe right ventricular (RV) dysfunction.

Methods and Results—
By performing pulmonary artery banding of different diameters for 7 weeks, mild RV dysfunction (Ø=0.6 mm) and severe RV dysfunction (Ø=0.5 mm) were induced in rats. The relative contribution of fibrosis- and myofibril-mediated RV stiffness was determined in RV trabecular strips. Total myocardial stiffness was increased in trabeculae from both mild and severe RV dysfunction in comparison to controls. In severe RV dysfunction, increased RV myocardial stiffness was explained by both increased fibrosis-mediated stiffness and increased myofibril-mediated stiffness, whereas in mild RV dysfunction, only myofibril-mediated stiffness was increased in comparison to control. Histological analyses revealed that RV fibrosis gradually increased with severity of RV dysfunction, whereas the ratio of collagen I/III expression was only elevated in severe RV dysfunction. Stiffness measurements in single membrane-permeabilized RV cardiomyocytes demonstrated a gradual increase in RV myofibril stiffness, which was partially restored by protein kinase A in both mild and severe RV dysfunction. Increased expression of compliant titin isoforms was observed only in mild RV dysfunction, whereas titin phosphorylation was reduced in both mild and severe RV dysfunction.

Conclusions—
RV myocardial stiffness is increased in rats with mild and severe RV dysfunction. In mild RV dysfunction, stiffness is mainly determined by increased myofibril stiffness. In severe RV dysfunction, both myofibril- and fibrosis-mediated stiffness contribute to increased RV myocardial stiffness.
The Right to Health in Old Age
Authors: Bershtling Orit , Doron Israel , Werner Perla , Laish-Shamir Adva 
Published: July 2016

Objectives To develop a better understanding of the right to health in old age through the personal knowledge and experience of older persons and professionals in Israel. Methods A qualitative research method was adopted based on focus groups. Information was collected through four focus groups with 33 participants. Results Three main themes emerged: The first focused on the older persons’ self-positioning vis-à-vis the health-care system. The second illustrated the verbal means chosen by the participants to situate the health-care system itself. The third elaborated on the institutional and cultural processes involved in upholding health rights in old age. Discussion Future discussions regarding conceptualization of the right to health in old age should relate to its human aspects, that is, communication and interaction, and the older person’s knowledge, participation, and involvement in shaping the medical services that they receive.
Risperidone long-acting injectable in the treatment of treatment-resistant schizophrenia with dopamine supersensitivity psychosis: Results of a 2-year prospective study, including an additional 1-year follow-up
Authors: Kimura Hiroshi , Kanahara Nobuhisa , Sasaki Tsuyoshi , Komatsu Naoya , Ishige Minoru , Muneoka Katsumasa , Ino Hidetoshi , Yoshimura Kazuyuki , Yamanaka Hiroshi , Suzuki Tomotaka , Komatsu Hideki , Watanabe Hiroyuki , Shimizu Eiji , Iyo Masaomi 
Published: July 2016

Dopamine supersensitivity psychosis (DSP) resulting from antipsychotic treatment is related to treatment-resistant schizophrenia (TRS), and its treatment has not been established to date. Maintaining thoroughly stable occupancy of the dopamine D2 receptor by risperidone long-acting injectable (RLAI) is one strategy for treatment. In this study, RLAI was given as an adjunctive medication to oral antipsychotic(s), which were switched partially and gradually to RLAI in 108 treatment-resistant patients for an additional 1-year follow-up in a 2-year study, and to compare the effects in 72 patients with a DSP history (DSP group) and 36 patients without this history (NonDSP group). Although both groups showed significant improvements in the total Brief Psychotic Rating Scale (BPRS) score during the follow-up period, greater improvement was observed for the DSP group than the NonDSP group. High doses (> 850 mg chlorpromazine-dose combined of oral antipsychotics and RLAI) did not significantly change in both groups throughout the study period; however, extrapyramidal symptoms, including tardive dyskinesia, were significantly improved only in the patients with DSP. This study strongly suggested that the RLAI treatment, even with only partial switching, provides relief from refractory symptoms, particularly for patients with a history of DSP. Clinical trial registration: http://www.umin.ac.jp/:UMIN000008487
Faecal haemoglobin concentration is related to detection of advanced colorectal neoplasia in the next screening round
Authors: Digby Jayne , Fraser Callum G , Carey Francis A , Diament Robert H , Balsitis Margaret , Steele Robert JC 
Published: July 2016

Objective To examine associations between faecal haemoglobin concentrations below the cut-off used in colorectal cancer screening and outcomes in the next screening round. Methods In the Scottish Bowel Screening Programme, faecal haemoglobin concentrations and diagnostic outcomes were investigated for participants with a negative result (faecal haemoglobin concentrations < 80.0 µg Hb/g faeces), followed by a positive result within two years. Results Of 37,780 participants with negative results, at the next screening round, 556 (1.5%) screened positive and 30,293 (80.2%) negative. Initial median faecal haemoglobin concentrations (2.1 µg Hb/g faeces, IQR: 0.0–13.2) were higher in those with subsequent positive results than those with subsequent negative results (0.0 µg Hb/g faeces, IQR: 0.0–1.4; p < 0.0001). Using faecal haemoglobin concentrations 0.0–19.9 µg Hb/g faeces as reference, logistic regression analysis showed high adjusted odds ratios for advanced neoplasia (advanced neoplasia: colorectal cancer or higher risk adenoma) detection at the next round of 14.3 (95% CI: 8.9–23.1) in those with initial faecal haemoglobin concentrations 20.0–39.9 µg Hb/g faeces, and 38.0 (95% CI: 20.2–71.2) with 60.0–79.9 µg Hb/g faeces. Conclusions A higher proportion of participants with faecal haemoglobin concentrations of ≥ 20 µg Hb/g faeces had advanced neoplasia detected at the next round than participants with lower faecal haemoglobin concentrations. Although most relevant when using high faecal haemoglobin concentrations cut-offs, studies of faecal haemoglobin concentrations and outcomes over screening rounds may provide strategies to direct available colonoscopy towards those at highest risk.
Effects of a Training Intervention for Enhancing Recovery after Ivor-Lewis Esophagus Surgery: A Randomized Controlled Trial
Authors: Fagevik Olsén M. , Kjellby Wendt G. , Hammerlid E. , Smedh U. 
Published: July 2016

Background and Aims: There is a risk of decreased physical function, quality of life and persistent pain after open surgery for esophageal cancer. There are currently no studies that evaluate the effect of any postoperative intervention, including physical exercises, after this type of surgery. The aim of the study was therefore to evaluate the effect of a training intervention after Ivor-Lewis resection of the esophagus. Material and Methods: Patients scheduled for esophagus resection according to Ivor-Lewis were randomized to an intervention group or a control group. The training intervention started at discharge and lasted three months. Before discharge, patients were given three leaflets with exercises to increase range of motion in the affected area and exercises aiming to restore lung function and physical function. All exercises were described in detail and the patients carried out the ones in the first program under supervision. Before surgery and three months after discharge, the patients estimated their level of physical function, level of physical activity, and quality of life. They also underwent spirometry, measurements of range of motion in the rib cage, spine, and shoulders, and three functional tests. Comparisons of differences within and between the groups were made. Results: A total of 43 of 64 randomized patients participated in the follow-up. Postoperatively, the patients in the intervention group had a significantly higher degree of physical function and less deteriorated range of motion in right shoulder flexion and thoracic left lateral flexion. There were no significant differences between the groups in lung function, pain, or quality of life. Conclusion: The results of the three-month intervention indicate that specific training can positively affect physical function and range of motion to preoperative values. The intervention was well tolerated, and no side effects were registered.