bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parity, Preference and Puzzlement
Authors: Gert Joshua 
Published: March 2015

AbstractRuth Chang has argued for the existence of a fourth positive value relation, distinct from betterness, worseness and equality, which she calls “parity.” In an earlier article I seemed to criticize Chang's suggestion by offering an interval model for the values of items that I claimed could accommodate all the phenomena characteristic of parity. Wlodek Rabinowicz, offering his own model of value relations, endorsed one central feature of my proposal: the need to distinguish permissible preferences from required ones. But he, along with Chang, correctly pointed out that my own model suffered from serious formal problems. The present article offers an improved interval model, but the main point is not the model itself. Rather, it is the derivation of the model from a response‐dependent account of practical rationality. This derivation helps explain why we have a concept for which Rabinowicz's model is appropriate, and therefore supplements Chang's existence arguments. My conclusion is that we can take Chang's view, Rabinowicz's and mine as providing a reinforcing set of views.
Bartonella henselae infection‐associated vasculitis and crescentic glomerulonephritis leading to renal allograft loss
Authors: Chaudhry A.R. , Chaudhry M.R. , Papadimitriou J.C. , Drachenberg C.B. 
Published: March 2015

AbstractBartonella henselae (BH) is the main cause of cat scratch disease (CSD), which more typically presents as a self‐limited localized suppurative lymphadenopathy in immunocompetent individuals. In contrast, immunocompromised patients commonly have systemic disease with life‐threatening complications. In addition to the angioproliferative lesions, such as bacillary angiomatosis, an increasing number of immune post‐infectious complications are being recognized with BH infections, including glomerulonephritis, vasculitis, hemophagocytic syndrome, and neurological problems. We report the case of a renal transplant recipient who developed CSD in the second year post transplantation. In addition to prolonged fever and generalized lymphadenopathy and splenomegaly requiring differentiation from a post‐transplant lymphoproliferative disorder, the course was complicated by the development of dermal leukocytoclastic vasculitis and pauci‐immune necrotizing and crescentic glomerulonephritis, which led to failure of the renal graft. Glomerulonephritis as a complication of CSD has never been described in a kidney allograft, to our knowledge. Awareness of the diverse clinical symptoms associated with BH, including granulomatous/suppurative lesions and other less common complications can lead to more rapid and accurate diagnosis. Also, as recommended by the current guidelines, a thorough history of pet ownership should be part of the clinical evaluation before and after transplantation for all transplant recipients.
Racial Differences in Weight Loss Among Adults in a Behavioral Weight Loss Intervention: Role of Diet and Physical Activity
Authors: Davis Kelliann K. , Tate Deborah F. , Lang Wei , Neiberg Rebecca H. , Polzien Kristen , Rickman Amy D. , Erickson Karen , Jakicic John M. 
Published: March 2015

Background:African-Americans lose less weight during a behavioral intervention compared with Whites, which may be from differences in dietary intake or physical activity.Methods:Subjects (30% African American, 70% White; n = 346; 42.4 ± 9.0 yrs.; BMI = 33.0 ± 3.7 kg/m2) in an 18-month weight loss intervention were randomized to a standard behavioral (SBWI) or a stepped-care (STEP) intervention. Weight, dietary intake, self-report and objective physical activity, and fitness were assessed at 0, 6, 12, and 18 months.Results:Weight loss at 18 months was greater in Whites (–8.74 kg with 95% CI [–10.10, –7.35]) compared with African Americans (–5.62 kg with 95% CI [–7.86, –3.37]) (P = .03) in the SBWI group and the STEP group (White: –7.48 kg with 95% CI [–8.80, –6.17] vs. African American: –4.41kg with 95% CI [–6.41, –2.42]) (P = .01). Patterns of change in dietary intake were not different between groups. Objective physical activity (PA) changed over time (P < .0001) and was higher in Whites when compared with African Americans (P = .01).Conclusions:Whites lost more weight (3.10 kg) than African American adults. Although there were no differences in dietary intake, Whites had higher levels of objective PA and fitness. Thus, the discrepancy in weight loss may be due to differences in PA rather than dietary intake. However, the precise role of these factors warrants further investigation.
Periodic Change in Sufficient Physical Activity: A 2-Year Study of a Multi-Ethnic Cohort
Authors: Dishman Rod K. , Nigg Claudio 
Published: March 2015

Background:Measuring the way people vary across time in meeting recommended levels of physical activity is a prerequisite to quantifying exposure in outcome studies or identifying determinants of sufficient physical activity. The study determined whether distinct patterns of change in sufficient physical activity could be identified in a population.Methods:A cohort (N = 497) from a random, multiethnic sample of adults living in Hawaii was assessed every 6 months for 2 years beginning spring 2004. Latent transition analysis classified people as sufficiently or insufficiently active each time.Results:In the total cohort, odds that people would move from insufficient to sufficient activity (45% to 59%) at each 6-month transition were higher than odds they would move from sufficient to insufficient activity (8% to 13%). However, those odds, as well as types and amounts of physical activity, differed widely among and within 3 of 4 transition classes that represented 21% of the cohort.Conclusions:Point-prevalence of sufficient physical activity in the total cohort was similar to contemporary U.S. estimates. However, physical activity varied between and within subgroups of the cohort. Further research is needed using self-report and objective measures to determine patterns of change in sufficient physical activity in other representative cohorts.
Intensity- and Domain-Specific Levels of Physical Activity and Sedentary Behavior in 10- to 14-Year-Old Children
Authors: De Baere Stijn , Seghers Jan , Philippaerts Renaat , De Martelaer Kristine , Lefevre Johan 
Published: March 2015

Background:to investigate levels of physical activity (PA) and sedentary behavior (SB) in 10- to 14-year-olds and to determine PA differences between week-weekend days, genders and school stages.Methods:241 children were recruited from 15 primary and 15 secondary schools. PA was assessed for 7 days using the SenseWear Mini Armband and an electronic diary. Week-weekend and gender differences were determined using 2-way repeated-measures ANOVA. Combined intensity- and domain-specific PA differences between genders and school stages were examined using 2-way ANOVA.Results:Weekdays were more active compared with weekend days. Physical activity level (PAL) of boys was higher compared with girls. Boys showed more moderate (+15 min/day) and vigorous PA (+9 min/day), no differences were found for SB and light PA. Secondary school children showed more SB (+111 min/day), moderate (+8 min/day) and vigorous (+9 min/day) PA and less light PA (-66 min/day) compared with primary school children. No difference was found for PAL. The results of the combined intensity- and domain-specific parameters revealed more nuanced differences between genders and school stages.Conclusions:Our results demonstrate the complexity of PA and SB behavior of children, indicating the need for a multidimensional and differentiated approach in PA promotion.
Effect of a Comprehensive School Physical Activity Program on School Day Step Counts in Children
Authors: Burns Ryan D. , Brusseau Timothy A. , Hannon James C. 
Published: March 2015

Background:Comprehensive School Physical Activity Programming (CSPAP) has the potential to increase physical activity (PA) in children over time. The purpose of this study was to examine the effect of CSPAP on school day step counts in children.Methods:Participants were 327 fourth and fifth grade children recruited from 4 elementary schools. The study was conducted within an Interrupted Time-Series Design framework. School day step counts were collected for 5 days across preintervention and postintervention time-points (10 days total) using NL-1000 piezoelectric pedometers. Robust piecewise regression examined pre- and postintervention intercepts and slopes, and the change in these parameters using postestimation statistics.Results:The slope coefficient was statistically significant across preintervention (β = –105.23, P < .001) but not postintervention time-points (β = –63.23, P = .347), suggesting decreases in steps counts across preintervention and stability of step counts across postintervention school days. Postestimation statistics yielded increases in school day step counts from the end of preintervention (day 5) to the start of postintervention (day 6; t(319) = –4.72, P < .001, Cohen’s d = 4.72).Conclusions:The CSPAP intervention increased average school day step counts and attenuated decreases in step counts throughout the school week in children.
Evolutionary changes in promoter and enhancer activity during human corticogenesis
Authors: Reilly Steven K. , Yin Jun , Ayoub Albert E. , Emera Deena , Leng Jing , Cotney Justin , Sarro Richard , Rakic Pasko , Noonan James P. 
Published: March 2015

Of mice, men, and macaque brainsThe human brain represents a unique evolutionary trajectory. To better understand how the human brain came to be, Reillyet al.sought to identify changes in gene expression between mice, macaques, and humans. They compared epigenetic marks in the embryonic cortex, which revealed changes in gene regulation in biological pathways associated with cortical development.Science, this issue p.1155
High-Level Association of Bovine Digital Dermatitis Treponema spp. with Contagious Ovine Digital Dermatitis Lesions and Presence of Fusobacterium necrophorum and Dichelobacter nodosus
Authors: Sullivan L. E. , Clegg S. R. , Angell J. W. , Newbrook K. , Blowey R. W. , Carter S. D. , Bell J. , Duncan J. S. , Grove-White D. H. , Murray R. D. , Evans N. J. 
Published: March 2015

ABSTRACT

Contagious ovine digital dermatitis (CODD) is an important foot disease in sheep, with significant animal welfare and economic implications. It is thought that CODD emerged from bovine digital dermatitis (BDD) via treponemal bacteria. With wildlife species such as elk now suffering a CODD-like disease, it is imperative to clarify these disease etiologies. A large investigation into treponemal association with CODD is warranted. CODD lesions (
n
= 58) and healthy sheep foot tissues (
n
= 56) were analyzed by PCR for the three BDD-associated
Treponema
phylogroups and two other lameness-associated bacteria,
Dichelobacter nodosus
and
Fusobacterium necrophorum
. Spirochete culture was also attempted on CODD lesions. “
Treponema medium
/
Treponema vincentii
-like,” “
Treponema phagedenis
-like,” and
Treponema pedis
spirochetes were identified in 39/58 (67%), 49/58 (85%), and 41/58 (71%) of CODD lesions, respectively. One or more BDD-associated
Treponema
phylogroups were detected in 100% of CODD lesions. Healthy foot tissues did not amplify BDD-associated
Treponema
phylogroup DNA.
D. nodosus
and
F. necrophorum
were present in 34/58 (59%) and 41/58 (71%) of CODD lesions and 22/56 (39%) and 5/56 (9%) of healthy foot tissues, respectively. Thirty-two spirochetes were isolated from CODD lesions, with representatives clustering with, and indistinguishable from, each of the three BDD-associated
Treponema
phylogroups based on 16S rRNA gene comparisons. This study for the first time demonstrates a high-level association for BDD treponeme phylogroups in CODD and their absence from healthy tissues, supporting the hypothesis that BDD treponemes play a primary causative role in CODD and confirming that the specific PCR assays are an effective differential diagnostic tool for CODD.
Impact of Introduction of the BD Kiestra InoqulA on Urine Culture Results in a Hospital Clinical Microbiology Laboratory
Authors: Strauss Sharon , Bourbeau Paul P. 
Published: March 2015

ABSTRACTThis study compared results from plating urine specimens with the BD InoqulA instrument using a 10-μl inoculum with results from cultures plated manually with a 1-μl loop for comparable 2-month periods. The positivity rates, turnaround times for positive cultures, and BD Phoenix identification and antimicrobial susceptibility test results were comparable for both time periods. We experienced no problems with culture interpretation as the result of moving to the 10-μl inoculum.
Laboratory Evaluation of the Liat HIV Quant (IQuum) Whole-Blood and Plasma HIV-1 Viral Load Assays for Point-of-Care Testing in South Africa
Authors: Scott Lesley , Gous Natasha , Carmona Sergio , Stevens Wendy 
Published: March 2015

ABSTRACT

Point-of-care (POC) HIV viral load (VL) testing offers the potential to reduce turnaround times for antiretroviral therapy monitoring, offer near-patient acute HIV diagnosis in adults, extend existing centralized VL services, screen women in labor, and prompt pediatrics to early treatment. The Liat HIV Quant plasma and whole-blood assays, prerelease version, were evaluated in South Africa. The precision, accuracy, linearity, and agreement of the Liat HIV Quant whole-blood and plasma assays were compared to those of reference technologies (Roche CAP CTMv2.0 and Abbott RealTime HIV-1) on an HIV verification plasma panel (
n
= 42) and HIV clinical specimens (
n
= 163). HIV Quant plasma assay showed good performance, with a 2.7% similarity coefficient of variation (CV) compared to the Abbott assay and a 1.8% similarity CV compared to the Roche test on the verification panel, and 100% specificity. HIV Quant plasma had substantial agreement (

p
c

[concordance correlation] = 0.96) with Roche on clinical specimens and increased variability (

p
c

= 0.73) in the range of <3.0 log copies/ml range with the HIV Quant whole-blood assay. HIV Quant plasma assay had good linearity (2.0 to 5.0 log copies/ml;
R
2
= 0.99). Clinical sensitivity at a viral load of 1,000 copies/ml of the HIV Quant plasma and whole-blood assays compared to that of the Roche assay (
n
= 94) was 100% (confidence interval [CI], 95.3% to 100%). The specificity of HIV Quant plasma was 88.2% (CI, 63.6% to 98.5%), and that for whole blood was 41.2% (CI, 18.4% to 67.1%). No virological failure (downward misclassification) was missed. Liat HIV Quant plasma assay can be interchanged with existing VL technology in South Africa. Liat HIV Quant whole-blood assay would be advantageous for POC early infant diagnosis at birth and adult adherence monitoring and needs to be evaluated further in this clinical context. LIAT cartridges currently require cold storage, but the technology is user-friendly and robust. Clinical cost and implementation modeling is required.
DNA Sequencing for Confirmation of Rifampin Resistance Detected by Cepheid Xpert MTB/RIF Assay
Authors: McAlister Allison J. , Driscoll Jeffrey , Metchock Beverly 
Published: March 2015

ABSTRACT

DNA sequencing of
rpoB
and culture-based drug susceptibility results were evaluated for samples referred for confirmation of rifampin resistance detected by the Cepheid Xpert MTB/RIF assay. Silent mutations and mutations associated with low-level resistance were found in the study population. These data support CDC recommendations to confirm Xpert rifampin resistance results.
Multicenter Evaluation of the BD Max Enteric Bacterial Panel PCR Assay for Rapid Detection of Salmonella spp., Shigella spp., Campylobacter spp. (C. jejuni and C. coli), and Shiga Toxin 1 and 2 Genes
Authors: Harrington S. M. , Buchan B. W. , Doern C. , Fader R. , Ferraro M. J. , Pillai D. R. , Rychert J. , Doyle L. , Lainesse A. , Karchmer T. , Mortensen J. E. 
Published: March 2015

ABSTRACT

Diarrhea due to enteric bacterial pathogens causes significant morbidity and mortality in the United States and worldwide. However, bacterial pathogens may be infrequently identified. Currently, culture and enzyme immunoassays (EIAs) are the primary methods used by clinical laboratories to detect enteric bacterial pathogens. We conducted a multicenter evaluation of the BD Max enteric bacterial panel (EBP) PCR assay in comparison to culture for the detection of
Salmonella
spp.,
Shigella
spp.,
Campylobacter jejuni
, and
Campylobacter coli
and an EIA for Shiga toxins 1 and 2. A total of 4,242 preserved or unpreserved stool specimens, including 3,457 specimens collected prospectively and 785 frozen, retrospective samples, were evaluated. Compared to culture or EIA, the positive percent agreement (PPA) and negative percent agreement (NPA) values for the BD Max EBP assay for all specimens combined were as follows: 97.1% and 99.2% for
Salmonella
spp., 99.1% and 99.7% for
Shigella
spp., 97.2% and 98.4% for
C. jejuni
and
C. coli
, and 97.4% and 99.3% for Shiga toxins, respectively. Discrepant results for prospective samples were resolved with alternate PCR assays and bidirectional sequencing of amplicons. Following discrepant analysis, PPA and NPA values were as follows: 97.3% and 99.8% for
Salmonella
spp., 99.2% and 100% for
Shigella
spp., 97.5% and 99.0% for
C. jejuni
and
C. coli
, and 100% and 99.7% for Shiga toxins, respectively. No differences in detection were observed for samples preserved in Cary-Blair medium and unpreserved samples. In this large, multicenter study, the BD Max EBP assay showed superior sensitivity compared to conventional methods and excellent specificity for the detection of enteric bacterial pathogens in stool specimens.
Culture-Independent Genome Sequencing of Clinical Samples Reveals an Unexpected Heterogeneity of Infections by Chlamydia pecorum
Authors: Bachmann Nathan L. , Sullivan Mitchell J. , Jelocnik Martina , Myers Garry S. A. , Timms Peter , Polkinghorne Adam 
Published: March 2015

ABSTRACT

Chlamydia pecorum
is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence
C. pecorum
genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate
C. pecorum
strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct
C. pecorum
isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala
C. pecorum
strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strains.
Comparison of Abbott RealTime HCV Genotype II with Versant Line Probe Assay 2.0 for Hepatitis C Virus Genotyping
Authors: Liu Chen-Hua , Liang Cheng-Chao , Liu Chun-Jen , Lin Chih-Lin , Su Tung-Hung , Yang Hung-Chih , Chen Pei-Jer , Chen Ding-Shinn , Kao Jia-Horng 
Published: March 2015

ABSTRACT
Genotyping and subtyping of 225 samples with hepatitis C virus (HCV) genotype 1, 2, 3, or 6 infection were done with Versant LiPA 2.0 and Abbott RealTime HCV Genotype (GT) II by using direct sequencing of the NS5B and 5′ untranslated regions as the reference standards. The concordance rates were >99.2% for genotypes and 96.1% for subtypes 1a and 1b. Both the Abbott RealTime and Versant LiPA assays can accurately determine hepatitis C virus genotypes. (This study has been registered at ClinicalTrials.gov under registration no. NCT00979979.)
Molecular Identification of Mycobacterium avium subsp. silvaticum by Duplex High-Resolution Melt Analysis and Subspecies-Specific Real-Time PCR
Authors: Rónai Zsuzsanna , Csivincsik Ágnes , Dán Ádám 
Published: March 2015

ABSTRACT

Accurate identification of mycobacterial species and subspecies is essential to evaluate their significance and to perform epidemiological studies. The subspecies of
Mycobacterium avium
have different attributes but coincide in their zoonotic potential. Our knowledge about
M. avium
subsp.
silvaticum
is limited, since its identification is uncertain.
Mycobacterium avium
subsp.
avium
and
M. avium
subsp.
silvaticum
can be discriminated from each other based only on phenotypic characteristics, as they have almost identical genome sequences. Here we describe the development of a diagnostic method which enables the molecular identification of
M. avium
subsp.
silvaticum
and discrimination from
M. avium
subsp.
avium
based on genomic differences in a duplex high-resolution melt and
M. avium
subsp.
silvaticum
-specific mismatch real-time PCR. The developed assay was tested on reference strains and 199 field isolates, which were analyzed by phenotypic methods previously. This assay not only identified all 63
M. avium
subsp.
silvaticum
and 138
M. avium
subsp.
avium
strains correctly but also enabled the detection of mixed
M. avium
subsp.
avium
-
M. avium
subsp.
silvaticum
cultures. This is the first time that such a large panel of strains has been analyzed, and we also report the first isolation of
M. avium
subsp.
silvaticum
from red fox, red deer, wild boar, cattle, and badger. This assay is reliable, rapid, simple, inexpensive, and robust. It eliminates the long-existing problem of ambiguous phenotypic identification and opens up the possibility for detailed and comprehensive strain studies.
Serologic Cross-Reactions between Nucleocapsid Proteins of Human Respiratory Syncytial Virus and Human Metapneumovirus
Authors: Zhang Yange , Pohl Jan , Brooks W. Abdullah , Erdman Dean D. 
Published: March 2015

ABSTRACTHuman respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) share virologic and epidemiologic features and cause clinically similar respiratory illness predominantly in young children. In a previous study of acute febrile respiratory illness in Bangladesh, we tested paired serum specimens from 852 children presenting fever and cough for diagnostic increases in titers of antibody to hRSV and hMPV by enzyme immunoassay (EIA). Unexpectedly, of 93 serum pairs that showed a ≥4-fold increase in titers of antibody to hRSV, 24 (25.8%) showed a concurrent increase in titers of antibody to hMPV; of 91 pairs showing an increase to hMPV, 13 (14.3%) showed a concurrent increase to hRSV. We speculated that common antigens shared by these viruses explain this finding. Since the nucleocapsid (N) proteins of these viruses show the greatest sequence homology, we tested hyperimmune antisera prepared for each virus against baculovirus-expressed recombinant N (recN) proteins for potential cross-reactivity. The antisera were reciprocally reactive with both proteins. To localize common antigenic regions, we first expressed the carboxy domain of the hMPV N protein that was the most highly conserved region within the hRSV N protein. Although reciprocally reactive with antisera by Western blotting, this truncated protein did not react with hMPV IgG-positive human sera by EIA. Using 5 synthetic peptides that spanned the amino-terminal portion of the hMPV N protein, we identified a single peptide that was cross-reactive with human sera positive for either virus. Antiserum prepared for this peptide was reactive with recN proteins of both viruses, indicating that a common immunoreactive site exists in this region.