bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Effectiveness of Integrase Strand Transfer Inhibitor–Based Antiretroviral Regimens Among Adults With Human Immunodeficiency Virus: A Collaboration of Cohort Studies in the United States and Canada
Authors: Lu Haidong , Cole Stephen R , Westreich Daniel , Hudgens Michael G , Adimora Adaora A , Althoff Keri N , Silverberg Michael J , Buchacz Kate , Li Jun , Edwards Jessie K , Rebeiro Peter F , Lima Viviane D , Marconi Vincent C , Sterling Timothy R , Horberg Michael A , Gill M John , Kitahata Mari M , Eron Joseph J , Moore Richard D 
Published: July 2020

Abstract

Background
Integrase strand transfer inhibitor (InSTI)–based regimens are now recommended as first-line antiretroviral therapy (ART) for adults with human immunodeficiency virus, but evidence on long-term clinical effectiveness of InSTI-based regimens remains limited. We examined whether InSTI-based regimens improved longer-term clinical outcomes.

Methods
We included participants from clinical cohorts in the North American AIDS Cohort Collaboration on Research and Design who initiated their first ART regimen, containing either InSTI (ie, raltegravir, dolutegravir, and elvitegravir-cobicistat) or efavirenz (EFV) as an active comparator, between 2009 and 2016. We estimated observational analogs of 6-year intention-to-treat and per-protocol risks, risk differences (RDs), and hazard ratios (HRs) for the composite outcome of AIDS, acute myocardial infarction, stroke, end-stage renal disease, end-stage liver disease, or death.

Results
Of 15 993 participants, 5824 (36%) initiated an InSTI-based and 10 169 (64%) initiated an EFV-based regimen. During the 6-year follow-up, 440 in the InSTI group and 1097 in the EFV group incurred the composite outcome. The estimated 6-year intention-to-treat risks were 14.6% and 14.3% for the InSTI and EFV groups, respectively, corresponding to a RD of 0.3% (95% confidence interval, −2.7% to 3.3%) and a HR of 1.08 (.97–1.19); the estimated 6-year per-protocol risks were 12.2% for the InSTI group and 11.9% for the EFV group, corresponding to a RD of 0.3% (−3.0% to 3.7%) and a HR of 1.09 (.96–1.25).

Conclusions
InSTI- and EFV-based initial ART regimens had similar 6-year composite clinical outcomes. The risk of adverse clinical outcomes remains substantial even when initiating modern ART.
Prevalence-Value-Accuracy Plots: A New Method for Comparing Diagnostic Tests Based on Misclassification Costs
Authors: Remaley Alan T , Sampson Maureen L , DeLeo James M , Remaley Nancy A , Farsi Beriuse D , Zweig Mark H 
Published: July 2020

Abstract
The clinical accuracy of diagnostic tests commonly is assessed by ROC analysis. ROC plots, however, do not directly incorporate the effect of prevalence or the value of the possible test outcomes on test performance, which are two important factors in the practical utility of a diagnostic test. We describe a new graphical method, referred to as a prevalence-value-accuracy (PVA) plot analysis, which includes, in addition to accuracy, the effect of prevalence and the cost of misclassifications (false positives and false negatives) in the comparison of diagnostic test performance. PVA plots are contour plots that display the minimum cost attributable to misclassifications (z-axis) at various optimum decision thresholds over a range of possible values for prevalence (x-axis) and the unit cost ratio (UCR; y-axis), which is an index of the cost of a false-positive vs a false-negative test result. Another index based on the cost of misclassifications can be derived from PVA plots for the quantitative comparison of test performance. Depending on the region of the PVA plot that is used to calculate the misclassification cost index, it can potentially lead to a different interpretation than the ROC area index on the relative value of different tests. A PVA-threshold plot, which is a variation of a PVA plot, is also described for readily identifying the optimum decision threshold at any given prevalence and UCR. In summary, the advantages of PVA plot analysis are the following: (a) it directly incorporates the effect of prevalence and misclassification costs in the analysis of test performance; (b) it yields a quantitative index based on the costs of misclassifications for comparing diagnostic tests; (c) it provides a way to restrict the comparison of diagnostic test performance to a clinically relevant range of prevalence and UCR; and (d) it can be used to directly identify an optimum decision threshold based on prevalence and misclassification costs.
Clinical Utility of Biochemical Markers of Bone Remodeling
Authors: Watts Nelson B 
Published: July 2020

AbstractRemodeling is essential for bone health. It begins with resorption of old bone by osteoclasts, followed by the formation of new bone by osteoblasts. Remodeling is coupled (formation is linked to resorption). After middle age or perhaps beginning earlier, bone loss occurs because resorption exceeds formation. This imbalance is accentuated by estrogen deficiency as well as by many diseases and conditions. Biochemical markers that reflect remodeling and can be measured in blood or urine include resorption markers (e.g., collagen cross-links) and formation markers (e.g., alkaline phosphatase).Bone markers exhibit substantial short-term and long-term fluctuations related to time of day, phase of the menstrual cycle, and season of the year, as well as diet, exercise, and anything else that alters bone remodeling. These biological factors, in addition to assay imprecision, produce significant intra- and interindividual variability in markers.Bone marker measurements are noninvasive, inexpensive, and can be repeated often. Unfortunately, most of the studies that provided insight on clinical situations did not focus on markers as a primary endpoint. Bone markers have been useful in clinical practice and have been helpful in understanding the pathogenesis of osteoporosis and the mechanism of action of therapies. In clinical trials, markers aid in selecting optimal dose and in understanding the time course of onset and resolution of treatment effect. Clinical questions that might be answered by bone markers include diagnosing osteoporosis, identifying “fast bone losers” and patients at high risk of fracture, selecting the best treatment for osteoporosis, and providing an early indication of the response to treatment. Additional information is needed to define specific situations and cut points to allow marker results to be used with confidence in making decisions about individual patients.
Objective Criteria for Partitioning Gaussian-distributed Reference Values into Subgroups
Authors: Lahti Ari , Hyltoft Petersen Per , Boyd James C , Fraser Callum G , Jørgensen Nils 
Published: July 2020

AbstractBackground: The aim of this study was to develop new and useful criteria for partitioning reference values into subgroups applicable to gaussian distributions and to distributions that can be transformed to gaussian distributions.Methods: The proposed criteria relate to percentages of the subgroups outside each of the reference limits of the combined distribution. Critical values suggested as partitioning criteria for these percentages were derived from analytical bias quality specifications for using common reference intervals throughout a geographic area. As alternative partitioning criteria to the actual percentages, these were transformed mathematically to critical distances between the reference limits of the subgroup distributions, to be applied to each pair of reference limits, the upper and the lower, at a time. The new criteria were tested using data on various plasma proteins collected from ∼500 reference individuals, and the outcomes were compared with those given by the currently widely applied and recommended partitioning model of Harris and Boyd, the “Harris-Boyd model”.Results: We suggest 4.1% as the critical minimum percentage outside that would justify partitioning into subgroups, and 3.2% as the critical maximum percentage outside that would justify combining them. Percentages between these two values should be classified as marginal, implying that nonstatistical considerations are required to make the final decision on partitioning. The correlation between the critical percentages and the critical distances was mathematically precise in the new model, whereas this correlation is rather approximate in the Harris-Boyd model because focus on the difference between means in this model makes high precision hard to achieve. The application examples suggested that the new model is more radical than the Harris-Boyd model.Conclusions: New percentage and distance criteria, to be used for partitioning gaussian-distributed data, have been developed. The distance criteria, applied separately to both reference limit pairs of the subgroup distributions, seemed more reliable and correlated more accurately with the critical percentages than the distance criteria of the Harris-Boyd model. As opposed to the Harris-Boyd model, the new model is easily adjustable to new critical values of the percentages, should they need to be changed in the future.
Differential Migration in Western Sandpipers with Respect to Body Size and Wing Length
Authors: O'Hara Patrick D. , Fernández Guillermo , Haase Ben , de la Cueva Horacio , Lank David B. 
Published: July 2020

AbstractWe examined differential migration in the Western Sandpiper (Calidris mauri) with respect to body size and wing chord allometry within sex and age categories. Culmen and wing chord data were collected as indices of structural body size at three sites that vary latitudinally: Ecuador, Panama, and Mexico. Within all sex and age categories, larger individuals (i.e., those with longer culmens and wing chords) and those with a disproportionately longer wing chord relative to the culmen migrated farther south. Our results, coupled with known molting schedules, indicate that i) immature sandpipers that grow disproportionately longer primary feathers on breeding grounds migrate farther during their first southward migration, and ii) adults that fly farther grow disproportionately longer primary feathers on the nonbreeding grounds. Although no single-factor hypothesis accounts for all aspects of age, sex, and size of Western Sandpiper distributions, costs associated with flight during migration play a significant role in determining differential nonbreeding latitudinal distributions.
P787Long-term prognostic value of the combination of fibrosis-4 index and acute kidney injury in patients with admitted for acute decompensated heart failure
Authors: Yamada T , Morita T , Furukawa Y , Tamaki S , Kawasaki M , Kikuchi A , Kawai T , Seo M , Nakamura J , Abe M , Yamamoto K , Kayama K , Kawahira M , Tanabe K , Fukunami M 
Published: July 2020

Abstract

Background
Liver dysfunction in patients with heart failure (HF) is caused by liver congestion, which is related to liver stiffness. It was reported that liver stiffness assessed by non-invasive fibrosis marker such as Fibrosis-4 (FIB4) index (based on age, aspartate aminotransferase [AST] and alanine aminotransferase [ALT] levels, and platelet counts) predicts mortality in HF pts. Acute kidney injury (AKI) during HF treatment is associated with poor outcome in pts admitted for acute decompensated heart failure (ADHF). However, there is no information available on the long-term prognostic significance of the combination of FIB4 index and AKI in ADHF pts.

Methods and results
We studied 299 ADHF pts with survival discharge. FIB4 index was calculated by the formula: age (yrs) × AST[U/L]/(platelets [103/μL] × (ALT[U/L])1/2). AKI during ADHF treatment was defined according to AKI Network criteria (stage 1: mild, stage 2: moderate, stage 3: severe). During a follow-up period of 4.3±3.3 yrs, 94 pts died. At multivariate Cox analysis, FIB4 index and stage2/3 AKI, but not stage1 AKI, significantly associated with total mortality, independently of prior HF hospitalization and serum sodium and blood urea nitrogen levels after adjustment with BMI, systolic blood pressure, hemoglobin, serum creatinine and albumin levels, left ventricular end-diastolic and left atrial dimension indexes. Pts with both greater FIB4 index (&gt;2.674: median) and stage 2/3 AKI had a significantly higher risk of total mortality than those with none of them. Adjusted hazard ratio in pts with both greater FIB4 index and stage 2/3 AKI was 3.5 (95% CI 1.6–7.7), which was two-fold of that in pts with either of them (1.7 [95% CI 1.1–2.7]).

Conclusion
The combination of FIB4 index and moderate to severe AKI might identify higher risk subset for total mortality in ADHF pts.
P964Relationships between extent of ischemic burden and changes in absolute myocardial perfusion after chronic total occlusion percutaneous coronary intervention
Authors: Schumacher S P , Kockx M , Stuijfzand W J , Driessen R S , Van Diemen P A , Bom M J , Everaars H , Raijmakers P G , Boellaard R , Van Rossum A C , Opolski M P , Nap A , Knaapen P 
Published: July 2020

Abstract

Background
The patient benefits after chronic coronary total occlusion (CTO) percutaneous coronary intervention (PCI) are being questioned.

Purpose
The present study explored the relationships between baseline ischemic burden findings and subsequent changes in absolute myocardial perfusion after CTO PCI.

Methods
Consecutive patients underwent serial [15O]H2O positron emission tomography perfusion imaging prior and 3 months after successful CTO PCI. Change in perfusion defect size (in myocardial segments), quantitative (hyperemic) myocardial blood flow (MBF) and coronary flow reserve (CFR) in the CTO area were compared between patients with a limited (0–1 segment), moderate (2–3 segments) and large perfusion defect (≥4 segments).

Results
193 patients were included, with 15, 61 and 117 patients having a limited, moderate and large perfusion defect at baseline. Hyperemic MBF and CFR were lower in a large perfusion defect compared to smaller defects (all comparisons p&lt;0.01). The median decrease in defect size was 1 [0–1] vs 2 [1–3] vs 4 [2–5] in patients with a limited, moderate and large defect (all comparisons p&lt;0.01), whereas hyperemic MBF and CFR improved significantly regardless of baseline defect size (between groups p=0.45 and p=0.55, respectively). Furthermore, when all 193 patients were divided in a low, median and high tertile based on hyperemic MBF and CFR at baseline, changes in hyperemic MBF and CFR after CTO PCI were comparable between patients in different tertiles (between groups p=0.75 and p=0.79, respectively)

Conclusions
Patients with a CTO and a larger perfusion defect have more severe hyperemic MBF and CFR levels. Major reductions in ischemic burden can be achieved by CTO PCI, with more defect size reduction in patients with a larger perfusion defect, whereas hyperemic MBF and CFR significantly improve irrespective of starting values before PCI.

Acknowledgement/Funding
None
Description of Shewanella salipaludis sp. nov., isolated from a salt marsh
Authors: Park Sooyeon , Chen Siyu , Lee Jung-Sook , Kim Wonyong , Yoon Jung-Hoon 
Published: July 2020

ABSTRACT
A Gram-stain-negative and flagellated bacterial strain, SHSM-M6T, was isolated from salt marsh from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain SHSM-M6T belongs to the genus Shewanella. 16S rRNA gene sequence similarity values between strain SHSM-M6T and the type strains of Shewanella species were &lt;98.0%. The average nucleotide identity and DNA–DNA hybridization values between genomic sequences of strain SHSM-M6T and the type strains of Shewanella species were &lt;73.3 and 20.7%, respectively. Strain SHSM-M6T contained MK-6 as predominant menaquinone and Q-7 and Q-8 as the predominant ubiquinones. The novel strain contained C16:1ω7c and/or C16:1ω6c, iso-C15:0 and C16:0 as major fatty acids. Major polar lipids of strain SHSM-M6T were phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. Differential phenotypic properties of strain SHSM-M6T, together with its phylogenetic and genetic distinctiveness, revealed that strain SHSM-M6T is separated from recognized Shewanella species. On the basis of the data presented, strain SHSM-M6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella salipaludis sp. nov. is proposed. The type strain is SHSM-M6T (=KACC 19901T = NBRC 113646T).
Archaea join the conversation: detection of AHL-like activity across a range of archaeal isolates
Authors: Charlesworth James , Kimyon Onder , Manefield Michael , Beloe Charlotte J , Burns Brendan P 
Published: July 2020

ABSTRACT
Quorum sensing is a mechanism of genetic control allowing single cell organisms to coordinate phenotypic response(s) across a local population and is often critical for ecosystem function. Although quorum sensing has been extensively studied in bacteria comparatively less is known about this mechanism in Archaea. Given the growing significance of Archaea in both natural and anthropogenic settings, it is important to delineate how widespread this phenomenon of signaling is in this domain. Employing a plasmid-based AHL biosensor in conjunction with thin-layer chromatography (TLC), the present study screened a broad range of euryarchaeota isolates for potential signaling activity. Data indicated the presence of 11 new Archaeal isolates with AHL-like activity against the LuxR-based AHL biosensor, including for the first time putative AHL activity in a thermophile. The presence of multiple signals and distinct changes between growth phases were also shown via TLC. Multiple signal molecules were detected using TLC in Haloferax mucosum, Halorubrum kocurii, Natronococcus occultus and Halobacterium salinarium. The finding of multiple novel signal producers suggests the potential for quorum sensing to play an important role not only in the regulation of complex phenotypes within Archaea but the potential for cross-talk with bacterial systems.
Association of Blood Chemistry Quantifications of Biological Aging With Disability and Mortality in Older Adults
Authors: Parker Daniel C , Bartlett Bryce N , Cohen Harvey J , Fillenbaum Gerda , Huebner Janet L , Kraus Virginia Byers , Pieper Carl , Belsky Daniel W 
Published: July 2020

Abstract
Quantification of biological aging has been proposed for population surveillance of age-related decline in system integrity and evaluation of geroprotective therapies. However, methods of quantifying biological aging have been little studied in geriatric populations. We analyzed three clinical-biomarker-algorithm methods to quantify biological aging. Klemera–Doubal method Biological Age and homeostatic dysregulation algorithms were parameterized from analysis of U.S. National Health and Nutrition Examination Surveys (NHANES) data (N = 36,207) based on published methods. Levine method Biological Age was adapted from published analysis of NHANES data. Algorithms were applied to biomarker data from the Duke Established Populations for Epidemiologic Studies of the Elderly (Duke-EPESE) cohort of older adults (N = 1,374, aged 71–102 years, 35% male, 52% African American). We tested associations of biological aging measures with participant reported Activities of daily living (ADL), instrumental activities of daily living (IADL) dependencies, and mortality. We evaluated the sensitivity of results to the demographic composition of reference samples and biomarker sets used to develop biological aging algorithms. African American and white Duke-EPESE participants with more advanced biological aging reported dependence in more ADLs and IADLs and were at increased risk of death over follow-up through 2017. Effect sizes were similar across algorithms, but were strongest for Levine method Biological Age (per-quintile increase in ADL incidence rate ratio = 1.25, 95% confidence interval [1.17–1.37], IADL incidence rate ratio = 1.23 [1.15–1.32], mortality hazard ratio = 1.12 [1.08–1.16]). Results were insensitive to demographic composition of reference samples, but modestly sensitive to the biomarker sets used to develop biological aging algorithms. Blood-chemistry-based quantifications of biological aging show promise for evaluating the effectiveness of interventions to extend healthy life span in older adults.
More Than Selection Effects: Volunteering Is Associated With Benefits in Cognitive Functioning
Authors: Kail Ben Lennox , Carr Dawn C 
Published: July 2020

Abstract

Objectives
Volunteering is a lifestyle behavior that bolsters cognitive resilience. However, previous studies have not assessed the degree to which cognitive functioning is predictive of becoming a volunteer (i.e., selection into volunteering), and how this might contribute to the superior cognitive performance observed among volunteers. The purpose of this brief report is to address the role of cognition-related selection into becoming a volunteer in the association between formal volunteering and two cognitive measures: (a) overall cognitive function and (b) self-rated memory.

Method
The Health and Retirement Study was used to assess whether, net of cognitive selection into volunteering, formal volunteering is associated with cognitive function.

Results
Selection explained between 4.9% and 29% of the effect of volunteering on cognitive function (depending on the cognitive outcome and the level of volunteering). However, net of cognitive selection into volunteering, among all cognitive measures there are beneficial effects of formal volunteering on cognitive function.

Discussion
These findings suggest a proportion of the positive association between volunteering and cognitive function is explained by selection. However, net of selection, formal volunteering is associated with benefits to cognitive function. These findings offer promise for the development of volunteer-based interventions designed to bolster cognitive functioning.
Thrust Into the Spotlight: COVID-19 Focuses Media Attention on Nursing Homes
Authors: Miller Edward Alan , Simpson Elizabeth , Nadash Pamela , Gusmano Michael 
Published: July 2020

AbstractObjectiveThis study sheds light on the agenda-setting role of the media during the COVID-19 crisis by examining trends in nursing home (NH) coverage in 4 leading national newspapers—The New York Times, Washington Post, USA Today, and Los Angeles Times.MethodKeyword searches of the Nexis Uni database identified 2,039 NH-related articles published from September 2018 to June 2020. Trends in the frequency of NH coverage and its tone (negative) and prominence (average words, daily article count, opinion piece) were examined.ResultsFindings indicate a dramatic rise in the number of NH articles published in the months following the first COVID-19 case, far exceeding previous levels. NH coverage became considerably more prominent, as the average number of words and daily articles on NHs increased. The proportion of negative articles largely remained consistent, though volume rose dramatically. Weekly analysis revealed acceleration in observed trends within the post-COVID-19 period itself. These trends, visible in all papers, were especially dramatic in The New York Times.DiscussionOverall, findings reveal marked growth in the frequency and number of prominent and negative NH articles during the COVID-19 crisis. The increased volume of coverage has implications for the relative saliency of NHs to other issues during the pandemic. The increased prominence of coverage has implications for the perceived importance of addressing pre-existing deficits and the devastating consequences of the pandemic for NHs.