bluuebunny/crossref_metadata_2025 huggingface dataset:
The energy budget of stellar magnetic fields: comparing non-potential simulations and observations
Authors: Lehmann L. T. , Jardine M. M. , Vidotto A. A. , Mackay D. H. , See V. , Donati  J.-F. , Folsom C. P. , Jeffers S. V. , Marsden S. C. , Morin J. , Petit P.
Published: October 2016

The magnetic geometry of the surface magnetic fields of more than 55 cool stars have now been mapped using spectropolarimetry. In order to better understand these observations, we compare the magnetic field topology at different surface scale sizes of observed and simulated cool stars. For ease of comparison between the high-resolution non-potential magnetofrictional simulations and the relatively low-resolution observations, we filter out the small-scale field in the simulations using a spherical harmonics decomposition. We show that the large-scale field topologies of the solar-based simulations produce values of poloidal/toroidal fields and fractions of energy in axisymmetric modes which are similar to the observations. These global non-potential evolution model simulations capture key magnetic features of the observed solar-like stars through the processes of surface flux transport and magnetic flux emergence. They do not, however, reproduce the magnetic field of M-dwarfs or stars with dominantly toroidal field. Furthermore, we analyse the magnetic field topologies of individual spherical harmonics for the simulations and discover that the dipole is predominately poloidal, while the quadrupole shows the highest fraction of toroidal fields. Magnetic field structures smaller than a quadrupole display a fixed ratio between the poloidal and toroidal magnetic energies.
Superoutburst of WZ Sge-type dwarf nova below the period minimum: ASASSN-15po
Authors: Namekata Kosuke , Isogai Keisuke , Kato Taichi , Littlefield Colin , Matsumoto Katsura , Kojiguchi Naoto , Sugiura Yuki , Uto Yusuke , Fukushima Daiki , Tatsumi Taiki , Yamada Eiji , Kamibetsunawa Taku , de Miguel Enrique , Stein William L. , Sabo Richard , Andreev Maksim V. , Morelle Etienne , Pavlenko E. P. , Babina Julia V. , Baklanov Alex V. , Antonyuk Kirill A. , Antonyuk Okasana I. , Sosnovskij Aleksei A. , Shugarov Sergey Yu. , Golysheva Polina Yu. , Gladilina Natalia G. , Miller Ian , Neustroev Vitaly V. , Chavushyan Vahram , Valdés José R. , Sjoberg George , Maeda Yutaka , Itoh Hiroshi , Masi Gianluca , Michel Raúl , Dubovsky Pavol A. , Kiyota Seiichiro , Tordai Tamás , Oksanen Arto , Ruiz Javier , Nogami Daisaku
Published: October 2016

We report on a superoutburst of a WZ Sge-type dwarf nova (DN), ASASSN-15po. The light curve showed the main superoutburst and multiple rebrightenings. In this outburst, we observed early superhumps and growing (stage A) superhumps with periods of 0.050454(2) and 0.051809(13) d, respectively. We estimated that the mass ratio of secondary to primary (q) is 0.0699(8) by using Porb and a superhump period PSH of stage A. ASASSN-15po [Porb ∼ 72.6 min] is the first DN with an orbital period between 67–76 min. Although the theoretical predicted period minimum Pmin of hydrogen-rich cataclysmic variables (CVs) is about 65–70 min, the observational cut-off of the orbital period distribution at 80 min implies that the period minimum is about 82 min, and the value is widely accepted. We suggest the following four possibilities: the object is (1) a theoretical period minimum object, (2) a binary with a evolved secondary, (3) a binary with a metal-poor (Popullation II) seconday, or (4) a binary which was born with a brown-dwarf donor below the period minimum.
A rare cause of abdominal pain and hypotension in pregnancy
Authors: Monti Jonathan D.
Published: October 2016

Splenic artery aneurysm rupture is rare. Pregnancy is a significant risk factor and the mortality for mother and fetus is very high if the rupture is undiagnosed or diagnosis is delayed. Patients typically present with abdominal pain and hemodynamic instability. This article describes a woman and fetus who survived a ruptured splenic artery aneurysm.
What is the effect of pill burden on adherence to HIV antiretroviral therapy?
Authors: Sutton S. Scott , Ahuja Divya , Magagnoli Joseph
Published: October 2016

Antiretroviral therapy (ART) is a combination treatment involving three or more antiretroviral agents for patients with HIV. ART has reduced HIV-related morbidity and mortality via single-tablet or multiple-tablet regimens. Single-tablet regimens, with their lower pill burdens, have demonstrated higher adherence rates, improved viral suppression, and reduced resource use compared with multiple-tablet regimens. In addition, select newer ARTs do not require the high levels of adherence for viral load suppression required by older ART formulations.
The mindful nurse leader
Authors: Doucette Jeffrey N. , Cotton Amy , Arnow Debra , Pipe Teri , FitzPatrick Kate
Published: October 2016

The first and second articles in this three-part series on mindfulness described the production of the video “In the Moment: Stories of Mindfulness in Nursing” as part of the authors' Robert Wood Johnson Foundation Executive Nurse Fellowship program.1 In this final installment, we discuss our leadership approaches and lessons learned, both as a team and individuals.
Does Dexmedetomidine Have a Perineural Mechanism of Action When Used as an Adjuvant to Ropivacaine?
Authors: Andersen Jakob H. , Grevstad Ulrik , Siegel Hanna , Dahl Jørgen B. , Mathiesen Ole , Jæger Pia
Published: October 2016

Background

Dexmedetomidine used as an adjuvant to local anesthetics may prolong the duration of peripheral nerve blocks. Whether this is mediated by a perineural or systemic mechanism remains unknown. The authors hypothesized that dexmedetomidine has a peripheral mechanism of action.

Methods

The authors conducted a randomized, paired, triple-blind trial in healthy volunteers. All received bilateral saphenous nerve blocks with 20 ml ropivacaine, 0.5%, plus 1 ml dexmedetomidine, 100 µg/ml, in one thigh and 20 ml ropivacaine 0.5% plus 1 ml saline in the other thigh. The primary outcome measure was the duration of block assessed by temperature sensation (alcohol swab). The secondary outcome measure was the duration of block assessed by pinprick, pain during tonic heat stimulation, warmth detection threshold, and heat pain detection threshold.

Results

All 21 enrolled volunteers completed the trial. The mean duration of block assessed by temperature sensation in the leg receiving ropivacaine plus dexmedetomidine was 22 h (95% CI, 21 to 24) compared to 20 h (95% CI, 19 to 21) in the leg receiving ropivacaine plus placebo with a mean difference of 2 h (95% CI, 1 to 3; P = 0.001). The duration of block was also significantly longer in the leg receiving dexmedetomidine when assessed by pinprick, pain during tonic heat stimulation, and warmth detection threshold but not heat pain detection threshold. One participant experienced numbness in an area in the leg receiving dexmedetomidine.

Conclusions

Dexmedetomidine prolongs the duration of a saphenous nerve block by a peripheral mechanism when controlling for systemic effects but not necessarily to a clinically relevant extent.
Relationship between Intraoperative Hypotension, Defined by Either Reduction from Baseline or Absolute Thresholds, and Acute Kidney and Myocardial Injury after Noncardiac Surgery
Authors: Salmasi Vafi , Maheshwari Kamal , Yang Dongsheng , Mascha Edward J. , Singh Asha , Sessler Daniel I. , Kurz Andrea
Published: October 2016

Background

How best to characterize intraoperative hypotension remains unclear. Thus, the authors assessed the relationship between myocardial and kidney injury and intraoperative absolute (mean arterial pressure [MAP]) and relative (reduction from preoperative pressure) MAP thresholds.

Methods

The authors characterized hypotension by the lowest MAP below various absolute and relative thresholds for cumulative 1, 3, 5, or 10 min and also time-weighted average below various absolute or relative MAP thresholds. The authors modeled each relationship using logistic regression. The authors further evaluated whether the relationships between intraoperative hypotension and either myocardial or kidney injury depended on baseline MAP. Finally, the authors compared the strength of associations between absolute and relative thresholds on myocardial and kidney injury using C statistics.

Results

MAP below absolute thresholds of 65 mmHg or relative thresholds of 20% were progressively related to both myocardial and kidney injury. At any given threshold, prolonged exposure was associated with increased odds. There were no clinically important interactions between preoperative blood pressures and the relationship between hypotension and myocardial or kidney injury at intraoperative mean arterial blood pressures less than 65 mmHg. Absolute and relative thresholds had comparable ability to discriminate patients with myocardial or kidney injury from those without.

Conclusions

The associations based on relative thresholds were no stronger than those based on absolute thresholds. Furthermore, there was no clinically important interaction with preoperative pressure. Anesthetic management can thus be based on intraoperative pressures without regard to preoperative pressure.
The future of n-3 polyunsaturated fatty acid therapy
Authors: Davidson Michael H. , Benes Lane B.
Published: October 2016

Purpose of review

This article focuses on the potential role by which a complex mixture of omega-3 fatty acids (OM3-FAs) may beneficially modify cardiovascular risk by modifying the cholesterol composition of atherogenic lipoproteins. This hypothesis is being tested in the STRENGTH trial, which is enrolling 13 000 patients on statins at high cardiovascular risk with hypertriglyceridemia and low HDL cholesterol (HDL-C) treated with an OM3-carboxylic acid.

Recent findings

Complex mixtures of OM3-FAs containing predominately eicosapentanoic acid and docosahexanoic acid in combination with statins lowers non-HDL by reducing triglyceride-rich lipoprotein cholesterol (TRL-C) while shifting small LDL cholesterol (LDL-C) to large LDL-C. Recent genomic and epidemiological studies have implicated TRL-C and small LDL-C as causal for cardiovascular disease. Therefore OM3-FAs containing both eicosapentanoic acid and docosahexanoic acid in combination with statins may beneficially modify the high residual risk for patients with hypertriglyceridemia and low HDL-C.

Although outcome trials are underway, subgroup analyses of data from previous randomized controlled trials are suggestive of a reduction in coronary artery disease and atherosclerotic cardiovascular disease event rates with triglyceride and TRL-C lowering therapies, particularly if accompanied by low HDL-C. Although the limitations of such data are acknowledged, clinicians must make treatment decisions while awaiting more definitive results from well-designed large-scale randomized controlled trials.
Ocular Focusing Behavior of the One-Eyed Child
Authors: Sravani N. Geetha , Bharadwaj Shrikant R.
Published: October 2016

Purpose

To compare the accommodative gain and pupil miosis of children with only one functional eye with the binocular and monocular accommodative and pupil responses of typically developing age-matched controls.

Methods

Forty-one uniocular cases and 43 controls (3–14 years for both cohorts) watched a cartoon movie on an LCD screen that ramped between 90 and 30 cm, with a stable period of 4 seconds at both viewing distances. Cases performed the task with their only functional eye whereas controls performed the task binocularly and monocularly. A subset of subjects also repeated the task while reading 20/40-sized letters on the LCD screen. Accommodative and pupil responses were recorded using the Plusoptix PowerRef3 photorefractor.

Results

Accommodative gain of cases [median (25th–75th IQR): 0.73 (0.60–0.85)] was larger than the monocular gain of controls [0.56 (0.47–0.79)] (P = .03). Both responses were lower than the binocular gain of controls [0.95 (0.81–1.11)] (P < .001). Uniocular pupil miosis of cases [0.14 mm (0.06–0.24 mm)] were similar to monocular [0.12 mm (0.05–0.29 mm)] (P = .69) and smaller than binocular [0.23 mm (0.14–0.34 mm)] (P < .001) responses of controls. The increase in accommodative gain from movie watching to reading was significant only for controls (P = .02) but not for cases (P = .15). Age and time of visual deficit were poorly correlated with accommodative gain and pupil miosis of cases (r ≤ 0.25; P ≥ .1 for all). Age was also poorly correlated with the binocular and monocular accommodative and pupil performance of controls (r ≤ −0.3; P = .33).

Conclusions

The accommodative gain of children with permanent loss of binocularity is in between the binocular and monocular gains of typically developing children. Their accommodative gains do not show any significant increase with a cognitively demanding task even while such a behavior is observed in controls. Pupil responses of uniocular children are similar to the monocular responses of age-matched controls.
Acute Kidney Injury in Patients Undergoing the Extracardiac Fontan Operation With and Without the Use of Cardiopulmonary Bypass
Authors: Algaze Claudia A. , Koth Andrew M. , Faberowski Lisa W. , Hanley Frank L. , Krawczeski Catherine D. , Axelrod David M.
Published: October 2016

Objectives:

To describe the prevalence and risk factors for acute kidney injury in patients undergoing the extracardiac Fontan operation with and without cardiopulmonary bypass, and to determine whether acute kidney injury is associated with duration of mechanical ventilation, cardiovascular ICU and hospital postoperative length of stay, and early mortality.

Design:

Single-center retrospective cohort study.

Setting:

Pediatric cardiovascular ICU, university-affiliated children’s hospital.

Patients:

Patients with a preoperative creatinine before undergoing first-time extracardiac Fontan between January 1, 2004, and April 30, 2012.

Interventions:

None.

Measurements and Main Results:

Acute kidney injury occurred in 55 of 138 patients (39.9%), including 41 (29.7%) with stage 1, six (4.4%) with stage 2, and eight (5.8%) with stage 3 acute kidney injury. Cardiopulmonary bypass was strongly associated with a higher risk of any acute kidney injury (adjusted odds ratio, 4.8 [95% CI, 1.4–16.0]; p = 0.01) but not stage 2/3 acute kidney injury. Lower renal perfusion pressure on the day of surgery (postoperative day, 0) was associated with a higher risk of stage 2/3 acute kidney injury (adjusted odds ratio, 1.2 [95% CI, 1.0–1.5]; p = 0.03). Higher vasoactive-inotropic score on postoperative day 0 was associated with a higher risk for stage 2/3 acute kidney injury (adjusted odds ratio, 1.9 [95% CI, 1.0–3.4]; p = 0.04). Stage 2/3 acute kidney injury was associated with longer cardiovascular ICU length of stay (mean, 7.3 greater d [95% CI, 3.4–11.3]; p < 0.001) and hospital postoperative length of stay (mean, 6.4 greater d [95% CI, 0.06–12.5]; p = 0.04).

Conclusions:

Postoperative acute kidney injury in patients undergoing the extracardiac Fontan operation is common and is associated with lower postoperative renal perfusion pressure and higher vasoactive-inotropic score. Cardiopulmonary bypass was strongly associated with any acute kidney injury, although not stage 2/3 acute kidney injury. Stage 2/3 acute kidney injury is a compelling risk factor for longer cardiovascular ICU and hospital postoperative length of stay. Increased attention to and management of renal perfusion pressure may reduce postoperative acute kidney injury and improve outcomes.
Brief Report: Assessing and Interpreting the Association Between Continuous Covariates and Outcomes in Observational Studies of HIV Using Splines
Authors: Shepherd Bryan E. , Rebeiro Peter F. ,   the Caribbean, Central and South America network for HIV epidemiology
Published: October 2016

The HIV epidemiology literature is replete with studies that categorize continuous predictors, such as age and CD4+ cell count. It is well known that such an approach is suboptimal, but it persists in part because results are easy to interpret after categorization. Splines may be used to incorporate continuous predictors with smoothed curves into regression models without categorization or linearity assumptions. Properly presenting and interpreting results from analyses with splines is critical for their widespread use. With data from 13,706 antiretroviral initiators in Latin America, we demonstrate how to interpret results from a Cox regression model using restricted cubic splines.
How recent findings on the pharmacokinetics and pharmacodynamics of integrase inhibitors can inform clinical use
Authors: Elliot Emilie , Chirwa Mimie , Boffito Marta
Published: October 2016

Purpose of review

This review of recent published literature and data presented at scientific meetings on integrase stand transfer inhibitors (InSTIs) examines how these findings may impact on their future clinical use.

Recent findings

Elvitegravir (EVG), raltegravir (RAL) and dolutegravir (DTG) are InSTIs recommended as first-line options for treatment naive patients by the European AIDS Clinical Society, British HIV Association, International AIDS Society-USA and DHHS. InSTIs have gained a leading role in the management of HIV-1 because of increased viral suppression and maintaining undetectability with fewer side-effects.

RAL 1200 mg once-daily (QD) has been shown to be noninferior to 400 mg BD, and the European Medicines Agency has approved QD RAL for review. RAL and DTG are not metabolized via cytochrome P450 (CYP) resulting in fewer drug interactions and less toxicity risk in patients receiving direct-acting antivirals and other coadministered medications.

EVG is currently available as a single tablet regimen and requires cobisistat, a pharmacokinetic booster and CYP3A inhibitor to allow QD dosing. EVG will soon be available in combination with tenofovir alfenamide, which is as efficacious as tenofovir disoproxil fumarate, but offers better renal and bone outcomes.

DTG has a high genetic barrier to resistance and has been the subject of a number of simplification and treatment failure trials and shown promise. There are some emerging reports of neuropsychiatric and gastrointestinal side-effects associated with DTG, which were not reported in clinical trials emphasizing the importance of real-life data.

Carbotegravir, a long-acting InSTI, is currently in the pipeline of development.

All three InSTIs have impressive data on efficacy, tolerability and safety. The unique differences of each InSTI's pharmacokinetics and pharmacodynamics lend themselves to various clinical scenarios, enabling us as clinicians to provide better patient-centred care.
HIV-associated neurocognitive disorder
Authors: Clifford David B.
Published: October 2016

Purpose of review

HIV-associated neurocognitive disease is the most active topic for neuroAIDS investigations at present. Although impairment is mild in patients successfully treated with modern antiviral regimens, it remains an ongoing problem for HIV patients. It is important to update the emerging research concerning HIV-associated neurocognitive disease.

Recent findings

The virus enters the brain during acute infection, with evidence for abnormal functioning that may occur early and often persists. Direct relationships with ongoing viral infection continue to be monitored, but chronic inflammation often associated with monocytes and macrophages appears to be the most likely driver of cognitive dysfunction. Appreciation for cerebrovascular disease as a significant comorbidity that is associated with cognitive deficits is increasing. Neuroimaging is actively being developed to address detection and measurement of changes in the brain. Optimal combined antiretroviral treatment therapy has vastly improved neurologic outcomes, but so far has not been demonstrated to reverse the remaining mild impairment. Inflammatory and vascular mechanisms of cerebral dysfunction may need to be addressed to achieve better outcomes.

Ongoing research is required to improve neurological outcomes for persons living with HIV. It is likely that interventions beyond antiviral approaches will be required to control or reverse HIV-associated neurocognitive disease.
Effect of Increasing Awareness of Genital Anatomy on Pelvic Floor Muscle Strength in Postmenopausal Women
Authors: Jácomo Raquel Henriques , Alves Aline Teixeira , Bontempo Albênica Paulino dos Santos , Botelho Thamires Lopes , Teixeira Fellipe Amatuzzi , de Sousa João Batista
Published: October 2016

Pelvic floor muscles (PFMs) are those that help support the pelvic organs during rest and participate in the occlusion of the urogenital hiatus, playing an important role in maintaining urinary and fecal continence. Women's lack of knowledge or ignorance of these muscles makes awareness a mandatory step in any perineal reeducation intervention. The aim of the study was to evaluate and quantify the influence of knowledge of genital anatomy on the function of contraction of these muscles. It is a prospective, randomized, and blinded study including 43 volunteers divided into 2 groups: with an explanation (WE) group, consisting of 18 women who received an explanation of pelvic anatomy, and a no explanation (NE) group, with 19 women. Explanations were given regarding location of the genital structures and purposes of the PFM. To find out whether the patients understood the explanation, they were asked to confirm some questions. Patients who gave incorrect responses to the questions were excluded. NE measurements were carried out before and after a casual conversation who were not given any guidance. An evaluation of the PFM, using a perineometer (Peritron, Australia), was performed before and after intervention. PFM strength was analyzed for normality using the Shapiro-Wilk test, and analysis of variance for repeated measures with the Tukey post hoc was used for comparison of the pre- and postintervention means. Statistical analysis was performed using SPSS. The WE group had 12.6 (±1.3) and 15.2 (±2.01) mm Hg in pre- and postmeasurement, respectively. Providing education about genital anatomy and PFM function can immediately improve the strength of the PFM contraction by 20% (P = .005). The brief anatomical explanation produced positive effects on the function of the PFM and recommended that professionals provide these explanations during the evaluation of pelvic floor function and before starting treatment for pelvic floors dysfunction.
Recognition of Asymptomatic Hypertension in an Urban Emergency Department
Authors: Souffront Kimberly , Gestal Christina , Melkus Gail D'Eramo , Richardson Lynne
Published: October 2016

Persistently elevated blood pressure ([BP]; hypertension [HTN]) occurs at higher rates in the emergency department ([ED]; 44%) than in the general population (27%) and disproportionately affects black patients and older adults. The American College of Emergency Physicians recommends referral to primary care for HTN confirmation and management when patients are asymptomatic and their BP is persistently elevated (W. Decker, S. Godwin, E. Hess, C. Lenamond, & A. Jagoda, 2006). However, adherence to this clinical policy is suboptimal. The purpose of this study was to examine the prevalence of asymptomatic HTN, rates of BP reassessment and referral, and factors associated with it among adult patients who visit the ED and who were discharged a decade after this policy was disseminated. A retrospective chart analysis of adults with an initial BP of 140/90 mmHg or greater and who were discharged was included in the sampling frame. Appropriate bivariate analysis, followed by multivariate regression, was conducted. There were 2,367 patients who met inclusion criteria, of which 1,184 patients had asymptomatic HTN. A greater proportion of the sample was male (51.3%), Black (43.2%; p < 0.000), middle aged (μ = 50.2 ± 16), and covered by Medicaid (39.8%). Mean initial BP was 170/88 mmHg. A large proportion of patients with asymptomatic HTN (94.2%) had no previously diagnosed cardiovascular disease (CVD). The BP reassessment rate was 49% (μ = 158/88), and these patients were more likely to have no previously diagnosed CVDs (p = 0.02). Only 4.6% (n = 28) of patients with asymptomatic HTN were referred, and these patients were more likely to have no previously diagnosed CVDs (p = 0.000) and be middle-aged (p = 0.008). Adherence to follow-up was 100%.
Presentation of Testicular Torsion in the Emergency Department
Authors: Ann Kroger-Jarvis Melanie , Gillespie Gordon Lee
Published: October 2016

Testicular torsion is a urological emergency affecting 3.8 per 100,000 males younger than 18 years. Differential diagnosis of the acutely painful scrotum is crucial for the advance practice nurse to understand. Advanced practice nurses should consider the differential diagnosis of testicular torsion for any patient with testicular pain despite the patient's age, history, or physical examination findings. The standard of care for a patient with testicular pain to rule out testicular torsion is a Doppler ultrasound scan and an emergent urology consult. Immediate attention to this urological emergency will decrease risks to testicular viability.
Reducing Inappropriate Antibiotic Prescribing for Adults With Acute Bronchitis in an Urgent Care Setting
Authors: Link Tamara L. , Townsend Mary L. , Leung Eugene , Kommu Sekhar , Vega Rhonda Y. , Hendrix Cristina C.
Published: October 2016

Acute bronchitis is a predominantly viral illness and, according to clinical practice guidelines, should not be treated with antibiotics. Despite clear guidelines, acute bronchitis continues to be the most common acute respiratory illness for which antibiotics are incorrectly prescribed. Although the national benchmark for antibiotic prescribing for adults with acute bronchitis is 0%, a preliminary record review before implementing the intervention at the project setting showed that 96% (N = 30) of adults with acute bronchitis in this setting were prescribed an antibiotic. This quality improvement project utilized a single-group, pre-post design. The setting for this project was a large urgent care network with numerous locations in central North Carolina. The purpose was to determine whether nurse practitioners and physician assistants, after participating in a multifaceted provider education session, would reduce inappropriate antibiotic prescribing for healthy adults with acute uncomplicated bronchitis. Twenty providers attended 1 of 4 training sessions offered in October and November 2015. The face-to-face interactive training sessions focused on factors associated with inappropriate antibiotic prescribing, current clinical practice guidelines, and patient communication skills. Retrospective medical record review of 217 pretraining and 335 posttraining encounters for acute bronchitis by 19 eligible participating providers demonstrated a 61.9% reduction in immediate antibiotic prescribing from 91.7% to 29.8%. Delayed prescribing, which accounted for a small percentage of the total prescriptions given, had a small but significant increase of 9.3% after training. Overall, this multifaceted, interactive provider training resulted in significant reductions in inappropriate prescriptions.
Does Persistent Pain Following a Motor Vehicle Crash Impact Functional Status in Older Adults?
Authors: Proud Matthew E. , Howard Patricia Kunz
Published: October 2016

Review of recent evidence with translation to practice for the advanced practice nurse (APN) role is presented using a case study module for “Persistent Pain Among Older Adults Discharged Home From the Emergency Department After Motor Vehicle Crash: A Prospective Cohort Study.” This longitudinal inquiry enrolled 161 patients 65 years or older seeking care in an emergency department (ED) following a motor vehicle crash. Interviews were conducted at the initial ED visit and at 6 weeks, 6 months, and 1 year. Variables of interest were persistent pain, depressive symptoms, and interference with activities of daily living, with an end goal of impact on functionality. Study subjects with persistent pain at 6 months reported an overall decrease in their health status, and 23% needed additional assistance with their activities of daily living, resulting in a change in living arrangements compared with 8% of the subjects without persistent pain. Repeat ED visits in the 6 months following the crash were more likely to occur in those with persistent pain (30% vs. 15%). This study highlights the important role of the APN in providing quality care, communication about pain management, and related follow-up care.
Persistent homology in graph power filtrations
Authors: Parks Allen D. , Marchette David J.
Published: October 2016

The persistence of homological features in simplicial complex representations of big datasets in

R

n

resulting from Vietoris–Rips or Čech filtrations is commonly used to probe the topological structure of such datasets. In this paper, the notion of homological persistence in simplicial complexes obtained from power filtrations of graphs is introduced. Specifically, the
r
th complex,
r
 ≥ 1, in such a power filtration is the clique complex of the
r
th power
G

r

of a simple graph
G
. Because the graph distance in
G
is the relevant proximity parameter, unlike a Euclidean filtration of a dataset where regional scale differences can be an issue, persistence in power filtrations provides a scale-free insight into the topology of
G
. It is shown that for a power filtration of
G
, the girth of
G
defines an
r
range over which the homology of the complexes in the filtration are guaranteed to persist in all dimensions. The role of chordal graphs as trivial homology delimiters in power filtrations is also discussed and the related notions of ‘persistent triviality’, ‘transient noise’ and ‘persistent periodicity’ in power filtrations are introduced.
A comprehensive survey of genetic variation in 20,691 subjects from four large cohorts
Authors: Lindström Sara , Loomis Stephanie , Turman Constance , Huang Hongyan , Huang Jinyan , Aschard Hugues , Chan Andrew T. , Choi Hyon , Cornelis Marilyn , Curhan Gary , De Vivo Immaculata , Eliassen A. Heather , Fuchs Charles , Gaziano Michael , Hankinson Susan E. , Hu Frank , Jensen Majken , Kang Jae H. , Kabrhel Christopher , Liang Liming , Pasquale Louis R. , Rimm Eric , Stampfer Meir J. , Tamimi Rulla M. , Tworoger Shelley S. , Wiggs Janey L. , Hunter David J. , Kraft Peter
Published: October 2016

The Nurses’ Health Study (NHS), Nurses’ Health Study II (NHSII), Health Professionals Follow Up Study (HPFS) and the Physicians Health Study (PHS) have collected detailed longitudinal data on multiple exposures and traits for approximately 310,000 study participants over the last 35 years. Over 160,000 study participants across the cohorts have donated a DNA sample and to date, 20,691 subjects have been genotyped as part of genome-wide association studies (GWAS) of twelve primary outcomes. However, these studies utilized six different GWAS arrays making it difficult to conduct analyses of secondary phenotypes or share controls across studies. To allow for secondary analyses of these data, we have created three new datasets merged by platform family and performed imputation using a common reference panel, the 1,000 Genomes Phase I release. Here, we describe the methodology behind the data merging and imputation and present imputation quality statistics and association results from two GWAS of secondary phenotypes (body mass index (BMI) and venous thromboembolism (VTE)).

We observed the strongest BMI association for the FTO SNP rs55872725 (β=0.45, p=3.48×10−22), and using a significance level of p=0.05, we replicated 19 out of 32 known BMI SNPs. For VTE, we observed the strongest association for the rs2040445 SNP (OR=2.17, 95% CI: 1.79-2.63, p=2.70×10−15), located downstream of F5 and also observed significant associations for the known ABO and F11 regions. This pooled resource can be used to maximize power in GWAS of phenotypes collected across the cohorts and for studying gene-environment interactions as well as rare phenotypes and genotypes.
Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types
Authors: Ecker Simone , Chen Lu , Pancaldi Vera , Bagger Frederik O. , Fernandez José Maria , Carrillo de Santa Pau Enrique , Juan David , Mann Alice L. , Watt Stephen , Casale Francesco Paolo , Sidiropoulos Nikos , Rapin Nicolas , Merkel Angelika ,   BLUEPRINT Consortium, Stunnenberg Henk , Stegle Oliver , Frontini Mattia , Downes Kate , Pastinen Tomi , Kuijpers Taco W. , Rico Daniel , Valencia Alfonso , Beck Stephan , Soranzo Nicole , Paul Dirk S.
Published: October 2016

Background

A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.

Results

We applied a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16−monocytes, CD66b+CD16+neutrophils, and CD4+CD45RA+naïve T cells, from the same 125 healthy individuals. We discovered substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression were found to be implicated in key immune pathways and to associate with cellular properties and environmental exposure. We also observed increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites were enriched at dynamic chromatin regions and active enhancers.

Conclusions

Our data highlight the importance of transcriptional and epigenetic variability for the neutrophils’ key role as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from:http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability.
Rare disruptive variants in the DISC1 Interactome and Regulome: association with cognitive ability and schizophrenia
Authors: Teng Shaolei , Thomson Pippa A. , McCarthy Shane E. , Kramer Melissa , Muller Stephanie , Lihm Jayon , Morris Stewart , Soares Dinesh , Hennah William , Harris Sarah , Camargo Luiz Miguel , Malkov Vladislav , McIntosh Andrew M , Millar J. Kirsty , Blackwood Douglas , Evans Kathryn L. , Deary Ian J. , Porteous David J. , McCombie W. Richard
Published: October 2016

Schizophrenia (SCZ), bipolar disorder (BD) and recurrent major depressive disorder (rMDD) are common psychiatric illnesses. All have been associated with lower cognitive ability, and show evidence of genetic overlap and substantial evidence of pleiotropy with cognitive function and neuroticism.Disrupted in schizophrenia 1(DISC1) protein directly interacts with a large set of proteins (DISC1 Interactome) that are involved in brain development and signaling. Modulation of DISC1 expression alters the expression of a circumscribed set of genes (DISC1 Regulome) that are also implicated in brain biology and disorder. Here, we report targeted sequencing of 59 DISC1 Interactome genes and 154 Regulome genes in 654 psychiatric patients and 889 cognitively-phenotyped control subjects, on whom we previously reported evidence for trait association from complete sequencing of the DISC1 locus. Burden analyses of rare and singleton variants predicted to be damaging were performed for psychiatric disorders, cognitive variables and personality traits. The DISC1 Interactome and Regulome showed differential association across the phenotypes tested. After family-wise error correction across all traits (FWERacross), an increased burden of singleton disruptive variants in the Regulome was associated with SCZ (FWERacrossP=0.0339). The burden of singleton disruptive variants in the DISC1 Interactome was associated with low cognitive ability at age 11 (FWERacrossP=0.0043). These results suggest that variants in the DISC1 Interactome effect the risk of psychiatric illness through altered expression of schizophrenia-associated genes. The biological impact of rare variants highlighted here merit further study.
Scaffolding of long read assemblies using long range contact information
Authors: Ghurye Jay , Pop Mihai , Koren Sergey , Chin Chen-Shan
Published: October 2016

Motivation

Long read technologies have made a revolution inde novogenome assembly by generating contigs of size orders of magnitude more than that of short read assemblies. Although the assembly contiguity has increased, it still does not span a chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scalable and computationally efficient scaffolding method that can boost the contiguity of the assembly by a large extent using genome wide chromatin interaction data such as Hi-C. Particularly, we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding ofde novolong read genome assemblies.

Results

We tested our methods on two long read assemblies of different organisms. We compared our method with previously developed method and show that our approach performs better in terms of accuracy of scaffolding.

Availability

The software is available for free use and can be downloaded from here:https://github.com/machinegun/hi-c-scaffold

Contact

jchin@pacificbiosciences.com
An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization
Authors: Szałaj Przemysław , Tang Zhonghui , Michalski Paul , Pietal Michal J. , Luo Oscar J. , Sadowski Michał , Li Xingwang , Radew Kamen , Ruan Yijun , Plewczynski Dariusz
Published: October 2016

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures.
A privacy-preserving solution for compressed storage and selective retrieval of genomic data
Authors: Huang Zhicong , Ayday Erman , Lin Huang , Aiyar Raeka S. , Molyneaux Adam , Xu Zhenyu , Fellay Jacques , Steinmetz Lars M. , Hubaux Jean-Pierre
Published: October 2016

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients’ complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data.
Calcium Deficiency Triggers Phloem Remobilization of Cadmium in a Hyperaccumulating Species
Authors: Tian Shengke , Xie Ruohan , Wang Haixin , Hu Yan , Ge Jun , Liao Xingcheng , Gao Xiaoyu , Brown Patrick , Lin Xianyong , Lu Lingli
Published: October 2016

Understanding cadmium (Cd) accumulation in plants is critical for the development of plant-based strategies for soil remediation and crop safety. Sedum alfredii is a nonbrassica plant species known to hyperaccumulate Cd. The characteristics of Cd uptake, distribution, and retranslocation affected by the Ca status were investigated at cellular levels in S. alfredii. Low Ca supply significantly increased Cd contents in shoots of S. alfredii, particularly in the young leaves. Micro x-ray fluorescence images confirmed that sequestration of Cd was greatly enhanced in the young leaves under Ca deficiency stress, with a significant amount of Cd localized in mesophyll cells, compared to the young leaves supplied with high Ca levels. Cd influx into protoplasts isolated from young leaves was significantly inhibited by the addition of Ca channel inhibitors, but not by pre-exposure to Ca deficiency. In stems, the Cd signal in vascular systems under low Ca levels was 10-fold higher than in those treated with higher Ca levels. A detailed investigation of vascular bundles revealed that an extremely high Cd signal induced by low Ca supply occurred in the phloem tissues, but not in the xylem tissues. Transfer of Cd pretreated plants to nutrient solutions at different Ca levels confirmed that a much higher amount of Cd was reallocated to the new growth tissues under low Ca stress compared to plants supplied with sufficient Ca. These results suggest that Ca deficiency triggered a highly efficient phloem remobilization of Cd in S. alfredii and subsequently enhanced Cd accumulation in its young leaves.
Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) fromClostridium thermocellum
Authors: Freire Filipe , Verma Anil , Bule Pedro , Alves Victor D. , Fontes Carlos M. G. A. , Goyal Arun , Najmudin Shabir
Published: October 2016

Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) fromClostridium thermocellumis reported.CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates.CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure ofCtXyn30A displays a (β/α)8TIM-barrel core with a side-associated β-sheet domain. Structural analysis of theCtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites −3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the −1 subsite ofCtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes.CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.
5-Methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl)]sulfinyl}-1-(prop-2-yn-1-yl)-1H-benzimidazole
Authors: El Bakri Youness , Ramli Youssef , Harmaoui Abdallah , Elhafi Mohamed , Essassi El Mokhtar , Mague Joel T.
Published: October 2016

In the title omeprazole derivative, C20H21N3O3S, the benzimidazole ring is inclined to the pyridine ring by 21.21 (8)°. In the crystal, neighbouring molecules are linked by C—H...O hydrogen bonds, forming chains along the a-axis direction. Within the chains, there are offset π–π interactions [intercentroid distance = 3.880 (2) Å] involving neighbouring benzimidazole rings. There are no other significant intermolecular interactions present.
1-(2′-Ethoxy-4′-fluoro-[1,1′-biphenyl]-4-yl)-4-phenyl-1H-1,2,3-triazole
Authors: Gilandoust Maryam , Naveen S. , Harsha K. B. , Lokanath N. K. , Rangappa K. S.
Published: October 2016

In the title compound, C22H18FN3O, the triazole ring is planar. The plane of the triazole ring makes dihedral angles of 19.31 (10), 20.52 (10) and 39.82 (9)° with the planes of the benzene rings, indicating the overall nonplanarity of the molecule. No classical hydrogen bonds were observed in the structure.
A conceptual safety-oriented job demands and resources model for the fire service
Authors: Smith Todd D. , Dyal Mari-Amanda
Published: October 2016

Purpose

The purpose of this paper is to develop and present a safety-oriented job demands-resources (JD-R) model that supports the notion that excessive job demands in the fire service, when not controlled or countered, may increase firefighter burnout and diminish firefighter safety.

Design/methodology/approach

The approach for the present project includes a review of the JD-R literature and the presentation of a conceptual model specific to fire service organizations.

Findings

A conceptual model, relevant to fire service organizations was derived. The model argues that excessive job demands associated with workload, physical demands, emotional demands, and complexity can result in burnout if not controlled or countered. Safety-specific resources, including recovery, support, safety-specific transformational leadership and safety climate are theorized to buffer these effects and are suggested to enhance firefighter engagement. These effects are argued then to improve firefighter safety. Ultimately, the findings will help guide future research, intervention projects and workplace safety and health management programs and initiatives.

Originality/value

This paper and conceptual model extends the application of the JD-R model to fire service organizations. Further, the conceptual model supports the application of safety-specific job resources vs more traditional job resources as a means to enhance firefighter safety.