bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Solus One Salmonella Assay in Select Foods: Collaborative Study: First Action 2020.03
Authors: Bastin Benjamin , Benzinger M Joseph , Crowley Erin S , Agin James , Wakefield Raymond 
Published: June 2020

Abstract

Background
The Solus One Salmonella immunoassay utilizes Salmonella specific selective media and automated liquid handling, for the rapid and specific detection of Salmonella species in select food types.

Objective
The candidate method was evaluated using 375 g test portions in an unpaired study design for a single matrix, instant non-fat dry milk (NFDM) powder.

Method
The matrix was compared to the United States Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) Chapter 5 Salmonella reference method. Eleven participants from 10 laboratories within academia and industry, located within the United States, Mexico, South Africa, Germany, and the United Kingdom, contributed data for the collaborative study. Three levels of contamination were evaluated for each matrix: an uninoculated control level [0 colony forming units (CFU)/test portion], a low inoculum level (0.2–2 CFU/test portion) and a high inoculum level (2–5 CFU/test portion). Statistical analysis was conducted according to the Probability of Detection (POD) statistical model.

Results
Results obtained for the low inoculum level test portions produced a dLPOD value with a 95% confidence interval between the candidate method confirmed (both alternative and conventional confirmation procedures) and the reference method of 0.07 (−0.02, 0.15).

Conclusions
The dLPOD results indicate equivalence between the candidate method and the reference method for the matrix evaluated and the method demonstrated acceptable inter-laboratory reproducibility as determined in the collaborative evaluation. False positive and false negative rates were determined for the matrix and produce values of &lt;2%.

Highlights
Based on the data generated, the method demonstrated acceptable inter-laboratory reproducibility data and statistical analysis.
Drought-mediated changes in black-tailed prairie dog colonies in the Northern Great Plains
Authors: Bruggeman Jason E , Licht Daniel S 
Published: June 2020

Abstract
Populations of many mammal species living in grassland ecosystems across North America have been reduced greatly over the past 200 years due to conversion of native prairie to human-related uses. Foremost among these species is the black-tailed prairie dog (Cynomys ludovicianus), populations of which have declined an estimated 98% during that time. In addition to anthropogenic factors including plague, black-tailed prairie dog populations can vary in size in response to grazing by native ungulates, fire, and precipitation. Colonies in the Northern Great Plains have expanded and contracted during dry and wet periods, respectively. Drought reduces vegetation height; tall vegetation is known to limit colony expansion, possibly due to increased predation risk. We used mixed-effects models to analyze data sets of colony areas of black-tailed prairie dogs spanning 16–22 years and 983 total colony counts, from 142 unique colonies at Badlands National Park and Wind Cave National Park, South Dakota, United States, and Scotts Bluff National Monument, Nebraska, United States, to relate areal dynamics of colonies over time to total annual precipitation, drought stress, and plague. We also analyzed the relationship between active-burrow densities and precipitation and drought stress using 7 years of data from 271 colony counts at Badlands National Park. Black-tailed prairie dog colonies expanded in response to drought conditions in all three national parks, with colonies in Wind Cave National Park exhibiting a time-delayed response. In addition, colony area was negatively related to total accumulated precipitation for the preceding 12 months for Scotts Bluff National Monument. Active-burrow density at Badlands National Park decreased in response to drought stress with a time lag of 24–36 months. Plague first was reported at Badlands National Park in 2008 and colony areas decreased dramatically and rapidly during plague epizootic events. Our results support observations that black-tailed prairie dog colonies in the Northern Great Plains expand and contract in response to drought stress and wet weather. Furthermore, our findings provide new insights into the role of climate on a keystone species of conservation importance and demonstrate the value of collecting long-term ecological data.
Long-term Persistence of Oral HPV Over 7 Years of Follow-up
Authors: D’Souza Gypsyamber , Clemens Gwendolyn , Strickler Howard D , Wiley Dorothy J , Troy Tanya , Struijk Linda , Gillison Maura , Fakhry Carole 
Published: June 2020

Abstract

Background
Human papillomavirus–related oropharyngeal cancer (HPV-OPC) incidence is increasing, but the natural history of the precursor—oral HPV—has not been well described.

Methods
This observational cohort study of people living with HIV and at-risk HIV uninfected people evaluated participants semiannually using 30-second oral rinse and gargle specimens over 7 years. Initially, 447 participants were followed for 4 years as part of the Persistent Oral Papillomavirus Study, and a subset of 128 who showed persistent infections at the last Persistent Oral Papillomavirus Study visit had an additional visit, as part of the Men and Women Understanding Throat HPV Study, on average 2.5 years later. Extracted DNA from oral rinse and gargle specimens was amplified using polymerase chain reaction and type specification of 13 oncogenic HPV types. Risk factors for oncogenic oral HPV clearance were evaluated using Cox models.

Results
The majority of oncogenic oral HPV infections cleared quickly, with a median time to clearance of 1.4 years (interquartile range = 0.5-3.9 years). After 7 years of follow-up, 97% of incident and 71% of prevalent infections had cleared. Lower HPV-16 viral load was statistically significantly associated with clearance (per 10-fold decrease in copy number: adjusted hazard ratio [aHR] = 2.51, 95% confidence interval [CI] = 1.20 to 5.26; P = .01). Adjusted analyses showed that oncogenic oral HPV clearance was lower among prevalent than incident-detected infections (aHR = 0.44, 95% CI = 0.35 to 0.55), among men than women (aHR = 0.74, 95% CI = 0.60 to 0.91), for older participants (aHR per 10 years increasing age = 0.81, 95% CI = 0.74 to 0.89), and among people living with HIV (aHR = 0.76, 95% CI = 0.60 to 0.95). One participant who had oral HPV-16 consistently detected at 10 study visits over 4.5 years was subsequently diagnosed with HPV-OPC.

Conclusions
This prospective study of oncogenic oral HPV infection is the longest and largest quantification of oral HPV-16 infections to date.
Impact of endoplasmic reticulum stress on oocyte aging mechanisms
Authors: Takehara Isao , Igarashi Hideki , Kawagoe Jun , Matsuo Koki , Takahashi Kyoko , Nishi Michi , Nagase Satoru 
Published: June 2020

Abstract
Endoplasmic reticulum (ER) stress is associated with several aging-related diseases; however, the mechanism underlying age-related deterioration of oocyte quality is unclear. Here, we used post-ovulatory, in vivo aged mouse oocytes as a model. Super-ovulated oocytes harvested from the oviduct at 14 h and 20 h post-hCG injection were designated as ‘fresh’ and ‘aged’, respectively. Embryo development following IVF was compared between fresh, aged and ER stress-induced oocytes. Expression of the ER stress marker GRP78 was examined at each stage. To evaluate the effect of salubrinal, an ER stress suppressor, on embryo development following IVF, expression levels of GRP78 and phospho-eukaryotic initiation factor 2 alpha were compared between aged and salubrinal-treated aged oocytes. Embryo transfer of salubrinal-treated aged oocytes was performed to examine the safety of salubrinal. Similar to aged oocytes, ER stress-induced oocytes showed lower fertilization rates and poor embryo development. Following IVF, expression of GRP78 decreased with embryo development. GRP78 expression was significantly higher in aged oocytes than in fresh oocytes. Salubrinal lowered GRP78 levels and improved embryo development. No adverse effect of salubrinal treatment was found on the birth weight of pups or on organogenesis in mice. The limitation of this study was that protein kinase-like ER kinase was the only ER stress pathway examined; the role of IRE1 and ATF6 pathways was not considered. Nevertheless, salubrinal can significantly improve embryo development in in vivo aged oocytes undergoing ER stress. Hence, regulation of ER stress might represent a promising therapeutic strategy to overcome poor oocyte quality.
qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide
Authors: Crossley Magdalena P , Bocek Michael J , Hamperl Stephan , Swigut Tomek , Cimprich Karlene A 
Published: June 2020

Abstract
R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA–DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA–RNA immunoprecipitation (qDRIP), a method combining synthetic RNA–DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. We also use these quantitative comparisons to make the first estimates of the absolute count of RNA–DNA hybrids per cell and their half-lives genome-wide. Finally, we identify a subset of RNA–DNA hybrids with high GC skew which are partially resistant to RNase H. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.
Sodium zirconium cyclosilicate increases serum bicarbonate concentrations among patients with hyperkalaemia: exploratory analyses from three randomized, multi-dose, placebo-controlled trials
Authors: Roger Simon D , Spinowitz Bruce S , Lerma Edgar V , Fishbane Steven , Ash Stephen R , Martins Julian G , Quinn Carol Moreno , Packham David K 
Published: June 2020

AbstractBackgroundSodium zirconium cyclosilicate (SZC) binds potassium and ammonium in the gastrointestinal tract. In addition to serum potassium reduction, Phase 2 trial data have shown increased serum bicarbonate with SZC, which may be clinically beneficial because maintaining serum bicarbonate ≥22 mmol/L preserves kidney function. This exploratory analysis examined serum bicarbonate and urea, and urine pH data from three SZC randomized, placebo-controlled Phase 3 studies among patients with hyperkalaemia [ZS-003 (n = 753), HARMONIZE (n = 258) and HARMONIZE-Global (n = 267)].MethodsIn all studies, patients received ≤10 g SZC 3 times daily (TID) for 48 h to correct hyperkalaemia, followed by randomization to maintenance therapy with SZC once daily (QD) versus placebo for ≤29 days among those achieving normokalaemia.ResultsSignificant dose-dependent mean serum bicarbonate increases from baseline of 0.3 to 1.5 mmol/L occurred within 48 h of SZC TID in ZS-003 (all P &lt; 0.05), which occurred regardless of chronic kidney disease (CKD) stage. Similar acute increases in HARMONIZE and HARMONIZE-Global were maintained over 29 days. With highest SZC maintenance doses, patient proportions with serum bicarbonate &lt;22 mmol/L fell from 39.4% at baseline to 4.9% at 29 days (P = 0.005) in HARMONIZE and from 87.9% to 70.1%, (P = 0.006) in HARMONIZE-Global. Path analyses demonstrated that serum urea decreases (but not serum potassium or urine pH changes) were associated with SZC effects on serum bicarbonate.ConclusionsSZC increased serum bicarbonate concentrations and reduced patient proportions with serum bicarbonate &lt;22 mmol/L, likely due to SZC-binding of gastrointestinal ammonium. These SZC-induced serum bicarbonate increases occurred regardless of CKD stage and were sustained during ongoing maintenance therapy.
Geochemistry and Petrogenesis of Mafic and Ultramafic Inclusions in Sublayer and Offset Dikes, Sudbury Igneous Complex, Canada
Authors: Wang Yujian , Lesher C Michael , Lightfoot Peter C , Pattison Edward F , Golightly J Paul 
Published: June 2020

Abstract
The c. 1·85 Ga Sudbury Igneous Complex (SIC) is the igneous remnant of one of the oldest, largest and best-preserved impact structures on Earth and contains some of the world’s largest magmatic Ni–Cu–PGE sulfide deposits. Most of the mineralization occurs in Sublayer, Footwall Breccia and inclusion-bearing quartz diorite (IQD), all of which contain significant (Sublayer and IQD) to minor (Footwall Breccia) amounts of olivine-bearing mafic–ultramafic inclusions. These inclusions have only rare equivalents in the country rocks and are closely associated with the Ni–Cu–PGE sulfide mineralization. They can be divided into three groups on the basis of petrography and geochemical characteristics. Group I (n = 47) includes igneous-textured olivine melanorite and olivine melagabbronorite inclusions in the Whistle and Levack embayments on the North Range with Zr/Y, Zr/Nb, Nb/U and Zr/Hf similar to igneous-textured Sublayer matrix. Group I inclusions are interpreted to be anteliths that crystallized from a mixture of SIC impact melt and a more mafic melt, probably derived by melting of ultramafic footwall rocks. Group II includes Group IIA (n = 17) shock metamorphosed wehrlite and olivine clinopyroxenite inclusions in the Levack embayment and Group IIB (n = 2) shock metamorphosed olivine melanorite inclusions in the Foy Offset on the North Range. Group II inclusions have similar trace element patterns [e.g. negative Th–U, Nb–Ta–(Ti), Sr and Zr–Hf anomalies] and overlapping Nb/U to a layered mafic–ultramafic intrusion in the footwall of the Levack and Fraser deposits, which together with their limited distribution suggests that Group II inclusions are locally-derived xenoliths. Group III (n = 21) includes phlogopite lherzolite and feldspar lherzolite inclusions with igneous, recrystallized and shock-metamorphic textures in the Trill, Levack and Bowell embayments, and the Foy Offset dike on the North Range. They have no equivalents in the exposed country rocks. The calculated parental magma is similar to continental arc basalt formed by approximately 5% partial melting of garnet peridotite. Ol–Cpx–Pl thermobarometry of several Group III inclusions indicate equilibration at 900–1120 ºC and 210 ± 166 MPa to 300 ± 178 MPa, suggesting crystallization in the upper-middle crust (7·7 ± 6·6 to 10·9 ± 6·5 km), prior to being incorporated into the lower parts of the impact melt sheet during impact excavation. The exotic xenoliths provide information about the depth of impact and composition of upper-middle crust in the Sudbury region at 1850 Ma, the local xenoliths provide information about the thermomechanical erosion process that followed generation of the impact melt, the anteliths provide information about the early crystallization history of the SIC, and all of the inclusions provide constraints on the genesis of Sublayer, IQD, footwall breccia, and associated Ni–Cu–PGE mineralization.
Predictors of persistent inflammation in familial Mediterranean fever and association with damage
Authors: Babaoglu Hakan , Armagan Berkan , Bodakci Erdal , Satis Hasan , Atas Nuh , Sari Alper , Yasar Bilge Nazife Sule , Bilici Salman Reyhan , Yardımcı Gozde Kubra , Avanoglu Guler Aslihan , Karadeniz Hazan , Kilic Levent , Ozturk Mehmet Akif , Goker Berna , Haznedaroglu Seminur , Kalyoncu Umut , Kasifoglu Timucin , Tufan Abdurrahman 
Published: June 2020

Abstract

Objective
Persistent inflammation is an insidious and less studied feature of FMF. We investigated clinical determinants of persistent inflammation and its associations with individual damage items.

Methods
This is a cross-sectional analysis of 917 FMF patients, who fulfilled the Tel Hashomer criteria and had at least 6 months’ follow-up. Patients were stratified based on whether they had persistent inflammation. We used logistic regression analysis to investigate independent predictors of persistent inflammation and the associated individual damage items.

Results
One hundred and forty-two (15%) patients had persistent inflammation. Active FMF (54%) was the most prominent reason for the persistent inflammation. Spondylarthritis (16%), other inflammatory arthritis (8%) and IBD (2%) were other frequent reasons. Male gender, history of exertional leg pain, inflammatory comorbidities, M694V homozygosity, colchicine resistance, lower education levels and musculoskeletal attack dominance were found to be the independent predictors of persistent inflammation. Earlier disease onset led to a tendency towards persistent inflammation. Patients with persistent inflammation were more likely to suffer damage. There is an increased risk of developing proteinuria, amyloidosis and renal insufficiency.

Conclusion
We identified, for the first time, the predictors of persistent inflammation in adult FMF patients and related individual damage items of the Autoinflammatory Disease Damage Index. Persistent inflammation is insidious and one of the chief causes of damage; therefore, especially patients with these predictors should be followed up more closely. If detected, underlying inflammatory comorbidities should be assessed meticulously as early detection and proper treatment strategies may favourably impact the natural history of the disease.
Heterogeneity of Outcomes and Network Connectivity in Early-Stage Psychosis: A Longitudinal Study
Authors: Chan Shi Yu , Brady Roscoe , Hwang Melissa , Higgins Amy , Nielsen Kathryn , Öngür Dost , Hall Mei-Hua 
Published: June 2020

Abstract
Imaging studies in psychotic disorders typically examine cross-sectional relationships between magnetic resonance imaging (MRI) signals and diagnosis or symptoms. We sought to examine changes in network connectivity identified using resting-state functional MRI (fMRI) corresponding to divergent functional recovery trajectories and relapse in early-stage psychosis (ESP). Prior studies have linked schizophrenia to hyperconnectivity in the default mode network (DMN). Given the correlations between the DMN and behavioral impairments in psychosis, we hypothesized that dynamic changes in DMN connectivity reflect the heterogeneity of outcomes in ESP. Longitudinal data were collected from 66 ESP patients and 20 healthy controls. Longitudinal cluster analysis identified subgroups of patients with similar trajectories in terms of symptom severity and functional outcomes. DMN connectivity was measured in a subset of patients (n = 36) longitudinally over 2 scans separated by a mean of 12 months. We then compared connectivity between patients and controls, and among the different outcome trajectory subgroups. Among ESP participants, 4 subgroups were empirically identified corresponding to: “Poor,” “Middle,” “Catch-up,” and “Good” trajectory outcomes in the complete dataset (n = 36), and an independent replication (n = 30). DMN connectivity changes differed significantly between functional subgroups (F3,32 = 6.06, P-FDR corrected = .01); DMN connectivity increased over time in the “Poor” outcome cluster (β = +0.145) but decreased over time in the “Catch-up” cluster (β = −0.212). DMN connectivity is dynamic and correlates with a change in functional status over time in ESP. This approach identifies a brain-based marker that reflects important neurobiological processes required to sustain functional recovery.
Development and Validation of an Individualized Nomogram for Predicting Overall Survival in Patients With Typical Lung Carcinoid Tumors
Authors: Dong Shenghua , Liang Jun , Zhai Wenxin , Yu Zhuang 
Published: June 2020

Objective:We aim to develop and validate an effective nomogram prognostic model for patients with typical lung carcinoid tumors using a large patient cohort from the Surveillance, Epidemiology, and End Results (SEER) database.Materials and Methods:Data from patients with typical lung carcinoid tumors between 2010 and 2015 were selected from the SEER database for retrospective analysis. Univariate and multivariate Cox analysis was performed to clarify independent prognostic factors. Next, a nomogram was formulated to predict the probability of 3- and 5-year overall survival (OS). Concordance indexes (c-index), receiver operating characteristic analysis and calibration curves were used to evaluate the model.Results:The selected patients were randomly divided into a training and a validation cohort. A nomogram was established based on the training cohort. Cox analysis results indicated that age, sex, T stage, N stage, surgery, and bone metastasis were independent variables for OS. All these factors, except surgery, were included in the nomogram model for predicting 3- and 5-year OS. The internally and externally validatedc-indexes were 0.787 and 0.817, respectively. For the 3-year survival prediction, receiver operating characteristic analysis showed that the areas under the curve in the training and validation cohorts were 0.824 and 0.795, respectively. For the 5-year survival prediction, the area under the curve in the training and validation cohorts were 0.812 and 0.787, respectively. The calibration plots for probability of survival were in good agreement.Conclusion:The nomogram brings us closer to personalized medicine and the maximization of predictive accuracy in the prediction of OS in patients with typical lung carcinoid tumors.
A comparison between perpendicular and parallel plating methods for distal humerus fractures
Authors: Wang Xiaohan , Liu Guoyan 
Published: June 2020

Abstract

Objective:
To compare the clinical outcomes of perpendicular and parallel plating for the treatment of distal humerus fractures.

Methods:
Two investigators independently searched PubMed, OVID, and ScienceDirect databases prior to April 2019, without any limitations on language or publication status. The outcomes were union time, range of motion of elbow, Mayo Elbow Performance Score, and postoperative complications. Two authors independently performed a methodological quality and risk of bias assessment using Cochrane collaboration's tool. Data analysis was performed with STATA version 13.0.

Results:
Six randomized controlled trials with 305 participants were included. The present meta-analysis indicated that orthogonal plating was associated with a longer union time compared with parallel plating. There were no significant differences between the 2 groups regarding Elbow function, Mayo Elbow Performance Score, operation time, reduction quality, or postoperative complications.

Conclusion:
Both parallel plating and orthogonal plating are considered to be effective methods when treating distal humerus fractures. The results of this study found that parallel plating is superior to orthogonal plating in humerus fracture healing.