bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forensic Human Identification Using Skin Microbiomes
Authors: Schmedes Sarah E. , Woerner August E. , Budowle Bruce 
Published: September 2017

ABSTRACTThe human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications; however, a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described here to classify skin microbiomes to their donors by comparing two feature types:Propionibacterium acnespangenome presence/absence features and nucleotide diversities of stable clade-specific markers. Supervised learning was used to attribute skin microbiomes from 14 skin body sites from 12 healthy individuals sampled at three time points over a >2.5-year period with accuracies of up to 100% for three body sites. Feature selection identified a reduced subset of markers from each body site that are highly individualizing, identifying 187 markers from 12 clades. Classification accuracies were compared in a formal model testing framework, and the results of this analysis indicate that learners trained on nucleotide diversity perform significantly better than those trained on presence/absence encodings. This study used supervised learning to identify individuals with high accuracy and associated stable features from skin microbiomes over a period of up to almost 3 years. These selected features provide a preliminary marker panel for future development of a robust and reproducible method for skin microbiome profiling for forensic human identification.IMPORTANCEA novel approach is described to attribute skin microbiomes, collected over a period of >2.5 years, to their individual hosts with a high degree of accuracy. Nucleotide diversities of stable clade-specific markers with supervised learning were used to classify skin microbiomes from a particular individual with up to 100% classification accuracy for three body sites. Attribute selection was used to identify 187 genetic markers from 12 clades which provide the greatest differentiation of individual skin microbiomes from 14 skin sites. This study performs skin microbiome profiling from a supervised learning approach and obtains high classification accuracy for samples collected from individuals over a relatively long time period for potential application to forensic human identification.
Antigen Localization Influences the Magnitude and Kinetics of Endogenous Adaptive Immune Response to Recombinant Salmonella Vaccines
Authors: Sevastsyanovich Yanina R. , Withers David R. , Marriott Claire L. , Morris Faye C. , Wells Timothy J. , Browning Douglas F. , Beriotto Irene , Ross Ewan , Ali Hossam Omar , Wardius Catherine A. , Cunningham Adam F. , Henderson Ian R. , Rossiter Amanda E. 
Published: September 2017

ABSTRACT

The use of recombinant attenuated
Salmonella
vaccine (RASV) strains is a promising strategy for presenting heterologous antigens to the mammalian immune system to induce both cellular and humoral immune responses. However, studies on RASV development differ on where heterologous antigens are expressed and localized within the bacterium, and it is unclear how antigen localization modulates the immune response. Previously, we exploited the plasmid-encoded toxin (Pet) autotransporter system for accumulation of heterologous antigens in cell culture supernatant. In the present study, this Pet system was used to express early secretory antigen 6 (ESAT-6), an immunodominant and diagnostic antigen from
Mycobacterium tuberculosis
, in
Salmonella enterica
serovar Typhimurium strain SL3261. Three strains were generated, whereby ESAT-6 was expressed as a cytoplasmic (SL3261/cyto), surface-bound (SL3261/surf), or secreted (SL3261/sec) antigen. Using these RASVs, the relationship between antigen localization and immunogenicity in infected C57BL/6 mice was systematically examined. Using purified antigen and specific tetramers, we showed that mice infected with the SL3261/surf or SL3261/sec strain generated large numbers of Th1 CD4
+
ESAT-6
+
splenic T cells compared to those of mice infected with SL3261/cyto. While all mice showed ESAT-6-specific antibody responses when infected with SL3261/surf or SL3261/sec, peak total serum IgG antibody titers were reached more rapidly in mice that received SL3261/sec. Thus, how antigen is localized after production within bacteria has a more marked effect on the antibody response than on the CD4
+
T cell response, which might influence the chosen strategy to localize recombinant antigen in RASVs.
Cretaceous geological evolution of the Pontides
Authors: Tüysüz Okan 
Published: September 2017

Abstract
The Pontides forming the southern continental margin of the Black Sea consist of the Strandja, İstanbul and Sakarya zones. The Zonguldak-Ulus Basin, located in the NE part of the İstanbul Zone, has traditionally been viewed as opening during the Barremian and deepening until the Albian under the control of normal faults. New outcrop data indicate that the southern and eastern parts of this basin facing towards the Intra-Pontide Ocean in the south were already open during the Berriasian or earlier. Uplift and erosion of the Zonguldak-Ulus Basin during the Cenomanian is attributed to collision of the İstanbul and the Sakarya zones along the Intra-Pontide Suture. The Sinop Basin in the Sakarya Zone opened during Hauterivian–Barremian time. Sedimentation in this basin continued in a deepening environment until the development of the Pontide Magmatic Belt during the Turonian. The contact between the İstanbul and the Sakarya zones is represented by a shear zone that consists of siliciclastic distal turbidites, debris-flow deposits and radiolarian cherts imbricated with Middle Jurassic–Lower Cretaceous magmatic arc fragments. This shear zone is interpreted as being the eastern continuation of the Intra-Pontide Suture, separating the İstanbul and the Sakarya zones.
The Western Black Sea Basin to the north of the Pontides possibly opened in two stages. In the first stage, coeval with the opening of the Zonguldak-Ulus Basin, the rifting was a wide-rift style and caused thinning of the continental crust. During the Turonian–Santonian, the Pontide Magmatic Belt started to develop as an extensional arc, and caused break-up of the already thinned crust and the start of oceanic spreading in the Western Black Sea Basin.
Age- and strain-related aberrant Ca2+release is associated with sudden cardiac death in theACTCE99K mouse model of hypertrophic cardiomyopathy
Authors: Rowlands Christina T. , Owen Thomas , Lawal Saheed , Cao Shuangyi , Pandey Samata S. , Yang Hsiang-Yu , Song Weihua , Wilkinson Ross , Alvarez-Laviada Anita , Gehmlich Katja , Marston Steven B. , MacLeod Kenneth T. 
Published: September 2017

Patients with hypertrophic cardiomyopathy, particularly young adults, can die from arrhythmia, but the mechanism underlying abnormal rhythm formation remains unknown. C57Bl6 × CBA/Ca mice carrying a cardiac actin ( ACTC) E99K (Glu99Lys) mutation reproduce many aspects of human hypertrophic cardiomyopathy, including increased myofilament Ca2+sensitivity and sudden death in a proportion (up to 40%) of young (28−40 day old) animals. We studied the hearts of transgenic (TG; ACTC E99K) mice and their non-TG (NTG) littermates when they were in their vulnerable period (28–40 days old) and when they were adult (8–12 wk old). Ventricular myocytes were isolated from the hearts of TG and NTG mice at these two time points. We also examined the hearts of mice that died suddenly (SCD). SCD animals had approximately four times more collagen compared with age-matched NTG mice, yet myocyte cell size was normal. Young TG mice had double the collagen content of NTG mice. Contraction and Ca2+transients were greater in cells from young TG mice compared with their NTG littermates but not in cells from adult mice (TG or NTG). Cells from young TG mice had a greater propensity for Ca2+waves than NTG littermates, and, despite similar sarcoplasmic reticulum Ca2+content, a proportion of these cells had larger Ca2+spark mass. We found that the probability of SCD in young TG mice was increased when the mutation was expressed in animals with a CBA/Ca2+background and almost eliminated in mice bred on a C57Bl6 background. The latter TG mice had normal cellular Ca2+homeostasis.NEW & NOTEWORTHY Mice with the actin Glu99Lys hypertrophic cardiomyopathy mutation ( ACTC E99K) are prone to sudden cardiac death around 40 days, associated with increased Ca2+transients, spark mass, and fibrosis. However, adult survivors have normal Ca2+transients and spark density accompanied by hypertrophy. Penetrance of the sudden cardiac death phenotype depends on the genetic background of the mouse.Listen to this article’s corresponding podcast at http://ajpheart.podbean.com/e/calcium-regulation-in-e99k-mouse-heart/ .
An Exploration of Changes in the Measurement of Mammography in the National Health Interview Survey
Authors: Gonzales Felisa A. , Willis Gordon B. , Breen Nancy , Yan Ting , Cronin Kathy A. , Taplin Stephen H. , Yu Mandi 
Published: September 2017

Abstract
Background: Using the National Health Interview Survey (NHIS), we examined the effect of question wording on estimates of past-year mammography among racially/ethnically diverse women ages 40–49 and 50–74 without a history of breast cancer.
Methods: Data from one-part (“Have you had a mammogram during the past 12 months?”) and two-part (“Have you ever had a mammogram”; “When did you have your most recent mammogram?”) mammography history questions administered in the 2008, 2011, and 2013 NHIS were analyzed. χ2 tests provided estimates of changes in mammography when question wording was either the same (two-part question) or differed (two-part question followed by one-part question) in the two survey years compared. Crosstabulations and regression models assessed the type, extent, and correlates of inconsistent responses to the two questions in 2013.
Results: Reports of past-year mammography were slightly higher in years when the one-part question was asked than when the two-part question was asked. Nearly 10% of women provided inconsistent responses to the two questions asked in 2013. Black women ages 50 to 74 [adjusted OR (aOR), 1.50; 95% confidence interval (CI), 1.16–1.93] and women ages 40–49 in poor health (aOR, 2.22; 95% CI, 1.09–4.52) had higher odds of inconsistent responses; women without a usual source of care had lower odds (40–49: aOR, 0.42; 95% CI, 0.21–0.85; 50–74: aOR, 0.42; 95% CI, 0.24–0.74).
Conclusions: Self-reports of mammography are sensitive to question wording. Researchers should use equivalent questions that have been designed to minimize response biases such as telescoping and social desirability.
Impact: Trend analyses relying on differently worded questions may be misleading and conceal disparities. Cancer Epidemiol Biomarkers Prev; 26(11); 1611–8. ©2017 AACR.
Biomarker-Stratified Phase III Clinical Trials: Enhancement with a Subgroup-Focused Sequential Design
Authors: Matsui Shigeyuki , Crowley John 
Published: September 2017

Abstract
Among various design approaches to phase III clinical trials with a predictive biomarker, the marker-stratified all-comers design is advantageous because it allows for establishing the utility of both treatment and biomarker, but it is often criticized for requiring large sample sizes, as the design includes both marker-positive and marker-negative patients. In this article, we propose a simple but flexible subgroup-focused design for marker-stratified trials that allow both sequential assessment across marker-defined subgroups and adaptive subgroup selection while retaining an assessment using the entire patient cohort at the final analysis stage, possibly using established marker-based multiple testing procedures. Numerical evaluations indicate that the proposed marker-stratified design has a robustness property in preserving statistical power for detecting various profiles of treatment effects across the subgroups while effectively reducing the number of randomized patients in the marker-negative subgroup with presumably limited treatment efficacy. In contrast, the traditional all-comers and sequential enrichment designs could suffer from low statistical power for some possible profiles of treatment effects. The latter also needs long study durations and a large number of marker-screened patients. We also provide an application to SWOG S0819, a trial to assess the role of cetuximab in treating non–small cell lung cancers. These evaluations indicate that the proposed subgroup-focused approach can enhance the efficiency of the marker-stratified design for definitive evaluation of treatment and biomarker in phase III clinical trials. Clin Cancer Res; 24(5); 994–1001. ©2017 AACR.
Technical Considerations on Phase Mapping for Identification of Atrial Reentrant Activity in Direct- and Inverse-Computed Electrograms
Authors: Rodrigo Miguel , Climent Andreu M. , Liberos Alejandro , Fernández-Avilés Francisco , Berenfeld Omer , Atienza Felipe , Guillem Maria S. 
Published: September 2017

Background:
Phase mapping has become a broadly used technique to identify atrial reentrant circuits for ablative therapy guidance. This work studies the phase mapping process and how the signal nature and its filtering affect the reentrant pattern characterization in electrogram (EGM), body surface potential mapping, and electrocardiographic imaging signals.

Methods and Results:
EGM, body surface potential mapping, and electrocardiographic imaging phase maps were obtained from 17 simulations of atrial fibrillation, atrial flutter, and focal atrial tachycardia. Reentrant activity was identified by singularity point recognition in raw signals and in signals after narrow band-pass filtering at the highest dominant frequency (HDF). Reentrant activity was dominantly present in the EGM recordings only for atrial fibrillation and some atrial flutter propagations patterns, and HDF filtering allowed increasing the reentrant activity detection from 60% to 70% of time in atrial fibrillation in unipolar recordings and from 0% to 62% in bipolar. In body surface potential mapping maps, HDF filtering increased from 10% to 90% the sensitivity, although provoked a residual false reentrant activity ≈30% of time. In electrocardiographic imaging, HDF filtering allowed to increase ≤100% the time with detected rotors, although provoked the apparition of false rotors during 100% of time. Nevertheless, raw electrocardiographic imaging phase maps presented reentrant activity just in atrial fibrillation recordings accounting for ≈80% of time.

Conclusions:
Rotor identification is accurate and sensitive and does not require additional signal processing in measured or noninvasively computed unipolar EGMs. Bipolar EGMs and body surface potential mapping do require HDF filtering to detect rotors at the expense of a decreased specificity.
Prognostic Value of Aortic Stiffness in Patients After ST‐Elevation Myocardial Infarction
Authors: Feistritzer Hans‐Josef , Klug Gert , Reinstadler Sebastian J. , Reindl Martin , Niess Lea , Nalbach Timo , Kremser Christian , Mayr Agnes , Metzler Bernhard 
Published: September 2017

Background

High aortic stiffness has been shown to be a strong predictor of morbidity and mortality in the general population and several patient cohorts. However, in patients after
ST
‐elevation myocardial infarction, the prognostic value of high aortic stiffness is unknown so far.

Methods and Results

This prospective observational study included 160 consecutive patients with first acute
ST
‐elevation myocardial infarction. Aortic pulse wave velocity (
PWV
) was measured 2 (interquartile range 2‐4 days) days after infarction using cardiac magnetic resonance imaging. The primary end point was defined as a composite end point of major adverse cardiac and cerebrovascular events (
MACCE
) comprising death, nonfatal myocardial reinfarction, new congestive heart failure, and stroke. During a median follow‐up of 1.2 years (interquartile range 1.0‐3.1 years), 19 (12%)
MACCE
events occurred. Kaplan‐Meier analysis showed a significantly lower
MACCE
‐free survival in patients with high
PWV
(
PWV
>7.3 m/s, log‐rank
P
=0.003). Multivariable Cox regression analysis revealed
PWV
>7.3 m/s to be an independent predictor of
MACCE
after adjustment for age, sex, mean blood pressure, N‐terminal pro–brain natriuretic peptide levels, presence of multivessel disease, and left ventricular stroke volume (hazard ratios ≥3.5; 95% confidence interval 1.4‐13.3; all
P
≤0.018). In reclassification analysis the addition of
PWV
to a risk model comprising major clinical prognostic parameters led to a net reclassification improvement of 0.11 (95% confidence interval 0.06‐0.17;
P
<0.001).

Conclusions

Increased aortic stiffness is an independent predictor of
MACCE
after acute
ST
‐elevation myocardial infarction. Moreover, the assessment of aortic stiffness in addition to classical risk factors significantly improved early risk stratification.
Influence of Penumbral Reperfusion on Clinical Outcome Depends on Baseline Ischemic Core Volume
Authors: Chen Chushuang , Parsons Mark W. , Clapham Matthew , Oldmeadow Christopher , Levi Christopher R. , Lin Longting , Cheng Xin , Lou Min , Kleinig Timothy J. , Butcher Kenneth S. , Dong Qiang , Bivard Andrew 
Published: September 2017

Background and Purpose—
In alteplase-treated patients with acute ischemic stroke, we investigated the relationship between penumbral reperfusion at 24 hours and clinical outcomes, with and without adjustment for baseline ischemic core volume.

Methods—
Data were collected from consecutive acute ischemic stroke patients with baseline and follow-up perfusion imaging presenting to hospital within 4.5 hours of symptom onset at 7 hospitals. Logistic regression models were used for predicting the effect of the reperfused penumbral volume on the dichotomized modified Rankin Scale (mRS) at 90 days and improvement of National Institutes of Health Stroke Scale at 24 hours, both adjusted for baseline ischemic core volume.

Results—

This study included 1507 patients. Reperfused penumbral volume had moderate ability to predict 90-day mRS 0 to 1 (area under the curve, 0.77;
R
2
, 0.28;
P
<0.0001). However, after adjusting for baseline ischemic core volume, the reperfused penumbral volume was a strong predictor of good functional outcome (area under the curve, 0.946;
R
2
, 0.55;
P
<0.0001). For every 1% increase in penumbral reperfusion, the odds of achieving mRS 0 to 1 at day 90 increased by 7.4%. Improvement in acute 24-hour National Institutes of Health Stroke Scale was also significantly related to the degree of reperfused penumbra (
R
2
, 0.31; P<0.0001). This association was again stronger after adjustment for baseline ischemic core volume (
R
2
, 0.41;
P
<0.0001). For each 1% of penumbra that was reperfused, the 24-hour National Institutes of Health Stroke Scale decreased by 0.069 compared with baseline.

Conclusions—
In patients treated with alteplase, the extent of the penumbra that is reperfused is a powerful predictor of early and late clinical outcomes, particularly when baseline ischemic core is taken into account.
ʻHow Bourgeois Were the Bourgeois Revolutions?ʼ
Authors: Gerstenberger Heide 
Published: September 2017

AbstractWhile the overview concerning debates on bourgeois revolutions is impressive, it cannot elucidate the theoretical concept of bourgeois revolutions. Neil Davidson’s own suggestion centres on the removal of hindrances to the breakthrough of capitalism, especially the pre-capitalist state. This formalistic definition is based on the assumption that revolutions occurred when the superstructure became a hindrance to the further development of productive forces. It deprives the theoretical concept of bourgeois revolutions of any concrete historical content. This paper suggests restricting the use of the theoretical concept ‘bourgeois revolution’ to those revolutionary changes of domination and appropriation which occurred in European societies of theancien régime.
Effectiveness of Cognitive Processing Therapy and Prolonged Exposure in the Department of Veterans Affairs
Authors: Rutt Benjamin T. , Oehlert Mary E. , Krieshok Thomas S. , Lichtenberg James W. 
Published: September 2017

Objective This study evaluated the effectiveness of cognitive processing therapy and prolonged exposure in conditions reflective of current clinical practice within the Veterans Health Administration. Method This study involved a retrospective review of 2030 charts. A total of 750 veterans from 10 U.S. states who received cognitive processing therapy or prolonged exposure in individual psychotherapy were included in the study (participants in cognitive processing therapy, N = 376; participants in prolonged exposure, N = 374). The main dependent variable was self-reported posttraumatic stress disorder symptoms as measured by total scores on the Posttraumatic Stress Disorder Checklist. The study used multilevel modeling to evaluate the absolute and relative effectiveness of both treatments and determine the relationship between patient-level variables and total Posttraumatic Stress Disorder Checklist scores during treatment. Results Cognitive processing therapy and prolonged exposure were equally effective at reducing total Posttraumatic Stress Disorder Checklist scores. Veterans who completed therapy reported significantly larger reductions in the Posttraumatic Stress Disorder Checklist than patients who did not complete therapy. There were no significant differences in the improvement of posttraumatic stress disorder symptoms with respect to age and three racial/ethnic groups (Caucasian, African American, and Hispanic). Conclusions Cognitive processing therapy and prolonged exposure were shown to be effective in conditions highly reflective of clinical practice and with a highly diverse sample of veterans. Challenges related to dropout from trauma focused therapy should continue to be researched.
Cross‐sectional Analysis of the Relationship between Paranasal Sinus Balloon Catheter Dilations and Industry Payments among Otolaryngologists
Authors: Fujiwara Rance J. T. , Shih Allen F. , Mehra Saral 
Published: September 2017

ObjectiveTo characterize the relationship between industry payments and use of paranasal sinus balloon catheter dilations (BCDs) for chronic rhinosinusitis.Study DesignCross‐sectional analysis of Medicare B Public Use Files and Open Payments data.SettingTwo national databases, 2013 to 2014.Subjects and MethodsPhysicians with Medicare claims with Current Procedural Terminology codes 31295 to 31297 were identified and cross‐referenced with industry payments. Multivariate linear regression controlling for age, race, sex, and comorbidity in a physician’s Medicare population was performed to identify associations between use of BCDs and industry payments. The final analysis included 334 physicians performing 31,506 procedures, each of whom performed at least 11 balloon dilation procedures.ResultsOf 334 physicians, 280 (83.8%) received 4392 industry payments in total. Wide variation in payments to physicians was noted (range, $43.29‐$111,685.10). The median payment for food and beverage was $19.26 and that for speaker or consulting fees was $409.45. One payment was associated with an additional 3.05 BCDs (confidence interval [95% CI],1.65‐4.45; P <. 001). One payment for food and beverages was associated with 3.81 additional BCDs (95% CI, 2.13‐5.49; P <. 001), and 1 payment for speaker or consulting fees was associated with 5.49 additional BCDs (95% CI, 0.32‐10.63; P =. 04).ConclusionPayments by manufacturers of BCD devices were associated with increased use of BCD for chronic rhinosinusitis. On separate analyses, the number of payments for food and beverages as well as that for speaker and consulting fees was associated with increased BCD use. This study was cross‐sectional and cannot prove causality, and several factors likely exist for the uptrend in BCD use.