bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mailed Human Papillomavirus Self-Collection With Papanicolaou Test Referral for Infrequently Screened Women in the United States
Authors: Smith Jennifer S. , Des Marais Andrea C. , Deal Allison M. , Richman Alice R. , Perez-Heydrich Carolina , Yen-Lieberman Belinda , Barclay Lynn , Belinson Jerome , Rinas Allen , Brewer Noel T. 
Published: July 2017

Background
Testing for high-risk human papillomavirus (HPV) infection using mailed, self-collected samples is a promising approach to increase screening in women who do not attend clinic screening at recommended intervals.

Methods
To assess this intervention among high-risk women in the United States, 429 women without a Papanicolaou (Pap) test in 4 or more years (overdue by US guidelines) were recruited from the general population. Participants aged 30 to 65 years were mailed a kit to self-collect a cervicovaginal sample at home, return the sample by mail, and receive HPV results by telephone, with referral to follow-up cytological Pap testing at a local clinic. Cervicovaginal self-samples were collected with a Viba brush, stored in Scope mouthwash, and tested by Hybrid Capture 2. Data were collected in 2010 to 2011 and analyzed in 2017.

Results
Two-thirds (64%) of participants returned a self-collected sample, of whom 15% tested HPV DNA positive. Human papillomavirus self-test–positive women reported higher rates of follow-up Pap tests (82%) than did those with self-test negative results (51%). No demographic differences were found in self-test return rate or HPV positivity. High acceptability was reported in participant surveys: most women (81%) had “mostly positive” overall thoughts about the self-test, and most reported being comfortable receiving the kit in the mail (99%), returning their self-collected sample by mail (82%), and receiving their test results by telephone (97%).

Conclusions
Conducting HPV self-testing through population-based recruitment, mailed kit delivery and return by mail, and results delivery by telephone has the potential to reach a broad segment of US underscreened women.
Interhospital Transport of Children Undergoing Cardiopulmonary Resuscitation: A Practical and Ethical Dilemma*
Authors: Noje Corina , Fishe Jennifer N. , Costabile Philomena M. , Klein Bruce L. , Hunt Elizabeth A. , Pronovost Peter J. 
Published: July 2017

Objectives:
To discuss risks and benefits of interhospital transport of children in cardiac arrest undergoing cardiopulmonary resuscitation.

Design:
Narrative review.

Results:
Not applicable.

Conclusions:
Transporting children in cardiac arrest with ongoing cardiopulmonary resuscitation between hospitals is potentially lifesaving if it enables access to resources such as extracorporeal support, but may risk transport personnel safety. Research is needed to optimize outcomes of patients transported with ongoing cardiopulmonary resuscitation and reduce risks to the staff caring for them.
A Prospective Study of the Association Between Clinically Significant Bleeding in PICU Patients and Thrombocytopenia or Prolonged Coagulation Times*
Authors: Moorehead Paul C. , Barrowman Nicholas J. , Cyr Janelle , Ray Jamie , Klaassen Robert , Menon Kusum 
Published: July 2017

Objective:
There are no proven methods to predict the risk of clinically significant bleeding in the PICU. A retrospective study identified platelet count as a risk marker for clinically significant bleeding. We conducted a study to examine any association of platelet count, international normalized ratio, and activated partial thromboplastin time with bleeding risk in PICU patients.

Design:
Prospective observational cohort study.

Setting:
The PICU at the Children’s Hospital of Eastern Ontario, a university-affiliated tertiary care pediatric center.

Patients:
Consecutive patients admitted to the PICU. Exclusion criteria were prior inclusion, admission with bleeding, inherited bleeding disorders, weight less than 3 kg, and age less than 60 days or 18 years or more.

Interventions:
There were no interventions in this observational study.

Measurements and Main Results:
Patients were monitored in real time for clinically significant bleeding, using a broadly inclusive definition of clinically significant bleeding, for up to 72 hours after admission to the PICU, or until death or discharge. All measurements of platelet count, international normalized ratio, and activated partial thromboplastin time obtained during the study period were included as time-varying covariates in Cox proportional hazard models. Two hundred thirty-four patients were eligible, and 25 (11%) had one or more episodes of clinically significant bleeding. Platelet count was associated with increased hazard of clinically significant bleeding (hazard ratio, 0.96 per 10 × 109/L increase in platelet count; 95% CI (0.93–0.997; p = 0.03). Increasing hazard for clinically significant bleeding was seen with decreasing platelet count. Neither international normalized ratio nor activated partial thromboplastin time was significantly associated with clinically significant bleeding.

Conclusions:
There is a statistically significant association in PICU patients between decrease in platelet count and clinically significant bleeding, and this association is stronger with lower platelet counts. Further study is required to determine whether platelet transfusion can reduce bleeding risk. International normalized ratio and activated partial thromboplastin time do not predict clinically significant bleeding, and these tests should not be used for this purpose in a general PICU patient population.
Intravoxel Incoherent Motion
Authors: Ciritsis Alexander , Rossi Cristina , Wurnig Moritz C. , Phi Van Valerie , Boss Andreas 
Published: July 2017

Purpose
For diffusion data sets including low and high b-values, the intravoxel incoherent motion model is commonly applied to characterize tissue. The aim of the present study was to show that machine learning allows a model-free approach to determine tissue type without a priori assumptions on the underlying physiology.

Materials and Methods
In 8 healthy volunteers, diffusion data sets were acquired using an echo-planar imaging sequence with 16 b-values in the range between 0 and 1000 s/mm2. Using the k-nearest neighbors technique, the machine learning algorithm was trained to distinguish abdominal organs (liver, kidney, spleen, muscle) using the signal intensities at different b-values as training features. For systematic variation of model complexity (number of neighbors), performance was assessed by calculation of the accuracy and the kappa coefficient (κ). Most important b-values for tissue discrimination were determined by principal component analysis.

Results
The optimal trade-off between model complexity and overfitting was found in the range between K = 11 to 13. On “real-world” data not previously applied to optimize the algorithm, the k-nearest neighbors algorithm was capable to accurately distinguish tissue types with best accuracy of 94.5% and κ = 0.92 reached for intermediate model complexity (K = 11). The principal component analysis showed that most important b-values are (with decreasing importance): b = 1000 s/mm2, b = 970 s/mm2, b = 750 s/mm2, b = 20 s/mm2, b = 620 s/mm2, and b = 40 s/mm2. Applying a reduced set of 6 most important b-values, still a similar accuracy was achieved on the real-world data set with an average accuracy of 93.7% and a κ coefficient of 0.91.

Conclusions
Machine learning allows for a model-free determination of tissue type using intra voxel incoherent motion signal decay curves as features. The technique may be useful for segmentation of abdominal organs or distinction between healthy and pathological tissues.
Kidney Transplantation in Patients With Active Multiple Myeloma: Case Reports
Authors: Lum Erik Lawrence , Kogut Neil , Pham Thu , Danovitch Gabriel M. , Bunnapradist Suphamai 
Published: July 2017

Abstract
Kidney disease is a common complication in patients with multiple myeloma. Traditionally, patients with active multiple myeloma and end-stage renal disease have been excluded from kidney transplantation due to the risk of malignancy progression. The introduction of bortezomib-based therapy for patients with multiple myeloma and renal impairment has significantly improved survival in this population. In this report, we present 2 cases of patients with active and controlled multiple myeloma who underwent successful kidney transplantation without progression of their underlying malignancy. In patients with active multiple myeloma controlled with bortezomib, kidney transplantation should be considered a valid option for patients with end-stage kidney disease.
Autistic traits and suicidal thoughts, plans and self-harm in late adolescence: population based cohort study
Authors: Culpin Iryna , Mars Becky , Pearson Rebecca M. , Golding Jean , Heron Jon , Bubak Isidora , Carpenter Peter , Magnusson Cecilia , Gunnell David , Rai Dheeraj 
Published: July 2017

AbstractImportanceThere have been recent concerns about a higher incidence of mortality by suicide in people withautism spectrum disorder (ASD). To our knowledge, no large cohort studies have examined which features of autism may lead to suicidal ideation and behaviour, and whether there are any potential modifiable mechanisms.ObjectiveTo examine the hypothesis that ASD diagnosis and traits in childhood are associated with suicidal thoughts, plans and self-harm at 16 years, and that any of the observed associations are explained by depression in adolescence at 12 years.Design, setting and participantsProspective investigation of associations between ASD diagnosis and autistic traits with suicidal ideation and behaviour and a potential risk pathway via depression in early adolescence in 5,031 members of the Avon Longitudinal Study of Parents and Children.Main outcomes and measuresHistory of self-harm with and without suicidal intent, suicidal thoughts and plans at 16 years assessed using a detailed self-report questionnaire. Exposures were ASD diagnosis and four measures (the coherence subscale of the Children’s Communication Checklist, the Social and Communication Disorders Checklist, a repetitive behaviour measure, and the sociability temperament subscale of the Emotionality, Activity and Sociability scale) dichotomised to represent the autism trait groups. Depressive symptoms in early adolescence were measured by the Short Moods and Feelings Questionnaire at 12 years.ResultsChildren with impaired social communication had a higher risk of self-harm with suicidal intent (RR 2.10, 95% CI 1.28, 3.34), suicidal thoughts (1.42 times (95% CI 1.06, 1.91) and suicidal plans (RR 1.95, 95% CI 1.09, 3.47) by the age of 16 years as compared to those without. There was no evidence for an association between ASD diagnosis and the outcomes although these analyses were imprecise due to small numbers. There was also no evidence of an association between other autism trait measures and the outcomes. Approximately 32% of the total estimated association between social communication impairment and self-harm was explained by depressive symptoms at age 12 years.ConclusionsImpairments in social communication are important in relation to suicidality. Early identification and management of depression may be a preventative mechanism and future research identifying other modifiable mechanisms may lead to preventative action or interventions against suicidal behaviour in this high-risk group.
Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms
Authors: Matz Mikhail V. 
Published: July 2017

SummaryApplication of genomic approaches to “obscure model organisms” (OMOs), meaning species with little or no genomic resources, enables increasingly sophisticated studies of genomic basis of evolution, acclimatization and adaptation in real ecological contexts. Here, I highlight sequencing solutions and data handling techniques most suited for genomic analysis of OMOs.Glossary-Allele Frequency Spectrum, AFS(same as Site Frequency Spectrum, SFS): histogram of the number of segregating variants depending on their frequency in one or more populations.-Restriction site-Associated DNA (RAD) sequencing: family of diverse genotyping methods that sequence short fragments of the genome adjacent to recognition site(s) for specific restriction endonuclease(s).-Linkage Disequilibrium (LD): in this review, correlation of genotypes at a pair of markers across individuals.-LD block: typical distance between markers in the genome across which their genotypes remain correlated.-Genome scan:profiling of genotypes along the genome looking for unusual patterns. Often used to look for signatures of natural selection or introgression.-“Denser-than-LD” genotyping: genotyping of several polymorphic markers per LD block.-Highly contiguous reference: genome or transcriptome reference sequence containing the least amount of fragmentation.-Phased data: data showing which SNP alleles belong to the same homologous chromosome copy.-Cross-tissue gene expression analysis: looking for individual-specific shifts in gene expression detectable across multiple tissues. Such shifts are predominantly genetic in nature.
Multinucleotide mutations cause false inferences of lineage-specific positive selection
Authors: Venkat Aarti , Hahn Matthew W. , Thornton Joseph W. 
Published: July 2017

ABSTRACTPhylogenetic tests of adaptive evolution, which infer positive selection from an excess of nonsynonymous changes, assume that nucleotide substitutions occur singly and independently. But recent research has shown that multiple errors at adjacent sites often occur in single events during DNA replication. These multinucleotide mutations (MNMs) are overwhelmingly likely to be nonsynonymous. We therefore evaluated whether phylogenetic tests of adaptive evolution, such as the widely used branch-site test, might misinterpret sequence patterns produced by MNMs as false support for positive selection. We explored two genome-wide datasets comprising thousands of coding alignments – one from mammals and one from flies – and found that codons with multiple differences (CMDs) account for virtually all the support for lineage-specific positive selection inferred by the branch-site test. Simulations under genome-wide, empirically derived conditions without positive selection show that realistic rates of MNMs cause a strong and systematic bias in the branch-site and related tests; the bias is sufficient to produce false positive inferences approximately as often as the branch-site test infers positive selection from the empirical data. Our analysis indicates that genes may often be inferred to be under positive selection simply because they stochastically accumulated one or a few MNMs. Because these tests do not reliably distinguish sequence patterns produced by authentic positive selection from those caused by neutral fixation of MNMs, many published inferences of adaptive evolution using these techniques may therefore be artifacts of model violation caused by unincorporated neutral mutational processes. We develop an alternative model that incorporates MNMs and may be helpful in reducing this bias.
Context-dependent Requirements for FimH and Other Canonical Virulence Factors in Gut Colonization by Extraintestinal PathogenicEscherichia coli
Authors: Russell Colin W. , Fleming Brittany A. , Stenquist Alan T. , Wambaugh Morgan A. , Bronner Mary P. , Mulvey Matthew A. 
Published: July 2017

ABSTRACTExtraintestinal pathogenicEscherichia coli(ExPEC) act as commensals within the mammalian gut, but can induce pathology upon dissemination to other host environments such as the urinary tract and bloodstream. It is thought that ExPEC genomes are shaped in large part by evolutionary forces encountered within the gut where the bacteria spend much of their time, provoking the question of how their extraintestinal virulence traits arose. The principle of coincidental evolution, in which a gene that evolved in one niche happens to be advantageous in another, has been used to argue that ExPEC virulence factors originated in response to selective pressures within the gut ecosystem. As a test of this hypothesis, the fitness of ExPEC mutants lacking canonical virulence factors was assessed within the intact murine gut in the absence of any antibiotic treatment. We found that most of the tested factors—including CNF1, Usp, colibactin, flagella, and the plasmid pUTI89—were dispensable for gut colonization. Deletion of genes encoding the adhesin PapG or the toxin HlyA caused transient defects, but did not affect longer-term persistence. In contrast, a mutant missing the type 1 pilus-associated adhesin FimH displayed reduced persistence within the gut. However, this phenotype was variable, being dependent on the presence of specific competing strains and partially attributable to aberrant flagellin expression by thefimHmutant. These data indicate that FimH and other key ExPEC-associated factors are not strictly required for gut colonization, suggesting that selective pressures within the gut do not drive the development of all extraintestinal virulence traits.
Whole genome optical mapping reveals multiple fusion events chained by large novel sequences in cancer
Authors: Chan Eva K.F. , Petersen Desiree C. , Lyons Ruth J. , Baldi Benedetta F. , Papenfuss Anthony T. , Thomas David M. , Hayes Vanessa M. 
Published: July 2017

AbstractGenomic rearrangements are common in cancer, with demonstrated links to disease progression and treatment response. These rearrangements can be complex, resulting in fusions of multiple chromosomal fragments and generation of derivative chromosomes. While methods exist for detecting individual fusions, they are generally unable to reconstruct complex chained events. To overcome these limitations, we adopted a new optical mapping approach, allowing for megabase length DNA to be captured, and in turn rearranged genomes to be visualized without loss of integrity. Whole genome mapping (Bionano Genomics) of a well-studied highly rearranged liposarcoma cell line, resulted in 3,338 assembled haploid genome maps, including 101 fusion maps. These fusion maps represent 175 Mb of highly rearranged genomic regions, illuminating the complex architecture of chained fusions, including content, order, orientation, and size. Spanning the junction of 151 chromosomal translocations, we found a total of 32 Mb of novel interspersed sequences that were not detected from short-read sequencing. We demonstrate that optical mapping provides a powerful new approach for capturing a higher level of complex genomic architecture, creating a scaffold for renewed interpretation of sequencing data of particular relevance to human cancer.
Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control
Authors: Carroni Marta , Franke Kamila B. , Maurer Michael , Jäger Jasmin , Hantke Ingo , Gloge Felix , Linder Daniela , Gremer Sebastian , Turgay Kürşad , Bukau Bernd , Mogk Axel 
Published: July 2017

AbstractRing-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA. ClpC forms large two-helical assemblies that associate via head-to-head contacts between coiled-coil middle domains (MDs). MecA converts this resting state to an active planar ring structure by binding to MD interaction sites. Loss of ClpC repression in MD mutants causes constitutive activation and severe cellular toxicity. These findings unravel an unexpected regulatory concept executed by coiled-coil MDs to tightly control AAA+ chaperone activity.
The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary
Authors: Otten Timothy G. , Paerl Hans W. , Dreher Theo W. , Kimmerer Wim J. , Parker Alexander E. 
Published: July 2017

SummaryHarmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High‐throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin‐producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H′ = 0.61) relative to periods preceding (H′ = 2.32) or following (H′ = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis.
Mycotoxin Contamination of Maize in China
Authors: Sun Xiang Dong , Su Ping , Shan Hong 
Published: July 2017

AbstractChina is a major cereal‐producing country and almost one third of the annual cereal yield is maize. The maize plant and kernel are prone to infection by fungal attack and are most likely to be contaminated with mycotoxins under suitable temperature and humidity conditions, during both the growing and storage period. A number of investigations conducted in China have demonstrated that maize had been infected by fungi and contaminated with mycotoxins to varying degrees. Although most of the maize produced in China is used as feed and raw materials for the chemistry industry, a small amount of maize is consumed directly by humans and the hazards of mycotoxin to humans cannot be ignored. The state of mycotoxin contamination of maize in China is analyzed in this review. Due to unfavorable weather and poor storage conditions, the high incidences of mycotoxin contamination of maize are of great concern to the Chinese. It is imperative for the national and local governments to increase investments on building large‐scale modern warehouses and instructing farmers to grow, harvest, and store maize safely. Meanwhile, due to accumulative toxic effects of mycotoxins, quality control should be enforced to guarantee that animal products are safe for human consumption.