bluuebunny/crossref_metadata_2025 huggingface dataset:
Improvement in Scoliosis Research Society-22R Pain Scores After Surgery for Adolescent Idiopathic Scoliosis
Authors: Djurasovic Mladen , Glassman Steven D. , Sucato Daniel J. , Lenke Lawrence G. , Crawford Charles H. , Carreon Leah Y.
Published: November 2016

Study Design.

Longitudinal cohort.

Objective.

To investigate whether patients with painful adolescent idiopathic scoliosis experience pain relief with surgical treatment.

Summary of Background Data.

Adolescent idiopathic scoliosis (AIS) was previously thought to be a painless condition, but recent studies have shown that a significant proportion of patients have pain. Little information is available regarding pain relief with surgical treatment for AIS.

Methods.

Patients enrolled in a prospective database of surgically treated AIS were divided into two groups based on their preoperative Scoliosis Research Society (SRS)-22R pain domain score. Patients with a preoperative pain domain score of 4 or more (N = 1005) were classified as nonpainful. If the preoperative pain domain score was less than 4 (N = 505), they were classified as painful. Demographics, SRS total and domain scores, and changes with treatment were compared for the two groups.

Results.

The two groups had similar demographics and preoperative coronal curve magnitude. Patients with painful scoliosis experienced significant improvement in SRS-22R pain scores, from 3.29 preoperatively to 4.03 postoperatively (P < 0.000). Eighty-one percent of these patients reached the minimum clinically important difference threshold (0.20) for improvement in pain score. Painful scoliosis patients also had greater 2-year improvement in total and all domain scores than the nonpainful scoliosis patients (P < 0.000). Absolute values of SRS-22R total and domain scores were all greater at 2 years in the nonpainful group than the painful group.

Conclusion.

Patients with AIS with substantial back pain can be cautiously counseled to expect significant improvement in pain level with surgical correction of their deformity, even if curve progression is the primary indication for surgery. Although these patients achieve greater improvements in health-related quality of life compared with patients with mild or no pain, 2-year SRS-22R scores were still better in patients with mild or no pain preoperatively.

Level of Evidence: 2
Brincidofovir Is Not a Substrate for the Human Organic Anion Transporter 1: A Mechanistic Explanation for the Lack of Nephrotoxicity Observed in Clinical Studies
Authors: Tippin Timothy K. , Morrison Marion E. , Brundage Thomas M. , Momméja-Marin Hervé
Published: November 2016

Background:

Brincidofovir (BCV) is an orally bioavailable lipid conjugate of cidofovir (CDV) with increased in vitro potency relative to CDV against all 5 families of double-stranded DNA viruses that cause human disease. After intravenous (IV) administration of CDV, the organic anion transporter 1 (OAT1) transports CDV from the blood into the renal proximal tubule epithelial cells with resulting dose-limiting nephrotoxicity.

Objective:

To study whether OAT1 transports BCV and to evaluate the pharmacokinetic and renal safety profile of oral BCV compared with IV CDV.

Methods:

The cellular uptake of BCV and its major metabolites was assessed in vitro. Renal function at baseline and during and after treatment in subjects in BCV clinical studies was examined.

Results:

In OAT1-expressing cells, uptake of BCV and its 2 major metabolites (CMX103 and CMX064) was the same as in mock-transfected control cells and was not inhibited by the OAT inhibitor probenecid. In human pharmacokinetic studies, BCV administration at therapeutic doses resulted in detection of CDV as a circulating metabolite; peak CDV plasma concentrations after oral BCV administration in humans were <1% of those observed after IV CDV administration at therapeutic doses. Analysis of renal function and adverse events from 3 BCV clinical studies in immunocompromised adult and pediatric subjects indicated little to no evidence of associated nephrotoxicity. Over 80% of subjects who switched from CDV or foscarnet to BCV experienced an improvement in renal function as measured by maximum on-treatment estimated glomerular filtration rate.

Conclusions:

The lack of BCV uptake through OAT1, together with lower CDV concentrations after oral BCV compared with IV CDV administration, likely explains the superior renal safety profile observed in immunocompromised subjects receiving BCV compared with CDV.
Efficacy of Autologous Platelet-rich Plasma Glue in Weight Loss Sequelae Surgery and Breast Reduction: A Prospective Study
Authors: Hersant Barbara , SidAhmed-Mezi Mounia , Lapadula Simone , Niddam Jeremy , Bouhassira Jonathan , Meningaud Jean Paul
Published: November 2016

Background:

Seroma and hematoma formations are the most common complications after plastic surgery. The aim of this study was to assess the efficacy of autologous platelet-rich plasma (A-PRP) glue to reduce postoperative wound complications and improve surgical outcomes.

Methods:

Fifty-four patients were included in this study. They underwent breast reduction surgery, abdominoplasty, or limb lifting with A-PRP glue application on the entire surface of the subcutaneous tissue at the time of suture. Retrospective data were used for the control group. The primary endpoint was the incidence of postoperative seroma or hematoma. The secondary endpoint was the Patient and Observer Scar Assessment Scale score.

Results:

Demographics and clinical characteristics were not statistically different between the A-PRP glue group and the control group regarding age, sex ratio, and body mass index. After abdominoplasty, 37.5% of patients (3/8) in the control group experienced seroma and hematoma complications versus 12.5% of patients (2/16) in the A-PRP glue group (P = 0.55 and P = 0.25, respectively). After limb lifting, 50% of patients experienced postoperative complications in the control group versus no patient in the A-PRP glue group (P = 0.03*; * indicates that the P value is significant). After breast reduction, no patient experienced complication in the A-PRP glue group versus 25% of patients in the control group who experienced hematoma (P = 0.04*). The scar quality assessed 12 months after surgery showed no statistical differences between the groups.

Conclusions:

A-PRP glue seems effective to prevent seroma formation after limb lifting and hematoma formation after breast reduction. Wound-healing quality did not seem to be improved.
Hybrid practices as a means to implement quality improvement: A comparative qualitative study in a Dutch and Swedish hospital
Authors: Quartz-Topp Julia , Sanne Johan M. , Pöstges Heide
Published: November 2016

Background:

Managers and scholars commonly perceive resistance from professionals as hampering the implementation of quality improvement (QI) and refer to the incompatibility of clinical and managerial approaches to QI as a reason. Yet a growing body of research indicates that, in practice, these two approaches rather blend into hybrid practices that embody different types of QI-related knowledge and values. This opens up a new perspective on implementation challenges that moves attention away from resistance against managerial QI toward difficulties for clinicians to draw together different types of knowledge and values within their clinical work. So far, little is known about how managers can support clinicians to generate hybrid QI practices.

Purpose:

The aim of this study was to deepen our understanding of how managers can support the generation of hybrid practices that help clinicians to integrate QI into their everyday work.

Methodology/Approach:

We draw on comparative qualitative research including 21 semistructured interviews, documentary analysis, and participant observation that we conducted in one Dutch and one Swedish hospital over a period of 8 months in 2011/2012.

Results:

Hospital managers designed hybrid forums, tools, and professional roles in order to facilitate the integration of different QI practices, knowledge, and values. This integration generated new hybrid practices and an infrastructure for QI that has potential to support clinicians in their efforts to align different demands.

Practice Implications:

New opportunities to implement QI emerge when we change the implementation problem from clinical resistance to the need of support for clinicians to develop hybrid QI practices. Hospital managers then have to intentionally organize for the generation of hybrid practices by designing, for example, hybrid forums, tools, and professional roles that integrate different knowledge and values in a nonhierarchical way.
Team-based primary care: The medical assistant perspective
Authors: Sheridan Bethany , Chien Alyna T. , Peters Antoinette S. , Rosenthal Meredith B. , Brooks Joanna Veazey , Singer Sara J.
Published: November 2016

Background:

Team-based care has the potential to improve primary care quality and efficiency. In this model, medical assistants (MAs) take a more central role in patient care and population health management. MAs’ traditionally low status may give them a unique view on changing organizational dynamics and teamwork. However, little empirical work exists on how team-based organizational designs affect the experiences of low-status health care workers like MAs.

Purposes:

The aim of this study was to describe how team-based primary care affects the experiences of MAs. A secondary aim was to explore variation in these experiences.

Methodology/Approach:

In late 2014, the authors interviewed 30 MAs from nine primary care practices transitioning to team-based care. Interviews addressed job responsibilities, teamwork, implementation, job satisfaction, and learning. Data were analyzed using a thematic networks approach. Interviews also included closed-ended questions about workload and job satisfaction.

Results:

Most MAs reported both a higher workload (73%) and a greater job satisfaction (86%) under team-based primary care. Interview data surfaced four mechanisms for these results, which suggested more fulfilling work and greater respect for the MA role: (a) relationships with colleagues, (b) involvement with patients, (c) sense of control, and (d) sense of efficacy. Facilitators and barriers to these positive changes also emerged.

Conclusion:

Team-based care can provide low-status health care workers with more fulfilling work and strengthen relationships across status lines. The extent of this positive impact may depend on supporting factors at the organization, team, and individual worker levels.

Practice Implications:

To maximize the benefits of team-based care, primary care leaders should recognize the larger role that MAs play under this model and support them as increasingly valuable team members. Contingent on organizational conditions, practices may find MAs who are willing to manage the increased workload that often accompanies team-based care.
Telavancin for MRSA Endocarditis
Authors: Majumdar Rohit , Crum-Cianflone Nancy F.
Published: November 2016

Methicillin-resistant Staphylococcus aureus (MRSA) endocarditis refractory to standard therapies is an increasingly prevalent clinical entity. Telavancin is a newly developed lipoglycopeptide with potent activity against MRSA, but few data exist regarding its potential role for MRSA endocarditis. We report a case of MRSA persistent bacteremia and endocarditis successfully treated with telavancin after failing standard agents due to multiple adverse effects. Additionally, we summarize the patient characteristics, clinical courses, and outcomes of all 15 published cases of MRSA endocarditis treated with telavancin in the peer-reviewed literature. These cases demonstrate telavancin's potential role in the treatment of MRSA invasive endovascular infections in the setting of refractory disease.
History of the Endolymphatic Sac: From Anatomy to Surgery
Authors: Corrales C. Eduardo , Mudry Albert
Published: November 2016

Objectives:

To evaluate the historical descriptive origins of the anatomy of endolymphatic sac (ELS), its initial dilation description, its association with tumors, and lastly its surgical implication.

Methods:

A collection of historical and contemporary references, and selected textbooks were compiled spanning the 18th century to present day with specific focus on the description of the ELS, ELS dilation, and ELS tumors (ELSTs).

Results:

Domenico Cotugno describes the ELS in 1760. Carl Hasse introduces the term endolymphatic sac (saccus endolymphaticus) in 1873, which has remained in use till today. Carlo Mondini, in 1791, describes ELS dilation. Georges Portmann proposes opening the ELS for the treatment of Ménière's disease (MD) in 1926. In 1984, the first reported case of an ELST is described with pathology consisting of an adenoma. Four years later, in 1988, the first report is published suggesting ELSTs in direct association to von Hippel-Lindau disease.

Conclusion:

Domenico Cotugno is precise in describing the ELS in 1760. A timeline of important events relating to the ELS is presented. These include ELS dilation, surgical opening of the ELS for Meniere's, and ELSTs relating to von Hippel-Lindau disease.
Cochlear Implantation in Ménière's Disease With and Without Labyrinthectomy
Authors: Mukherjee Payal , Eykamp Kate , Brown Daniel , Curthoys Ian , Flanagan Sean , Biggs Nigel , McNeill Celene , Gibson William
Published: November 2016

Objective:

To investigate outcomes of cochlear implantation (CI) in patients with Ménière's disease (MD) with and without surgical labyrinthectomy.

Study Design:

Retrospective study.

Setting:

Multiple tertiary referral centers.

Subjects:

Thirty one ears from 27 patients (17 men, 10 women, aged 42–84) with CI in ipsilateral MD ear.

Intervention:

CI in ears with intact labyrinths (Group 1), CI with simultaneous surgical labyrinthectomy (Group 2), and CI sequential to surgical labyrinthectomy (Group 3).

Main Outcome Measure:

Within-subject improvement on Bamford Kowal Bench test or City University of New York open set sentence tests.

Results:

Majority of ears achieved excellent open-set speech recognition by 12 months post-CI, irrespective of intervention group. Preoperative details including patient age and sex, implant, MD and previous intervention, and audiological test results did not significantly affect outcomes. Patients with MD undergoing CI only may experience vestibular dysfunction which may cause long-term concerns. Incidental finding was noted of eight ears with fluctuating symptoms in ipsilateral ear during 12-month period post-CI, with five of eight ears showing objective fluctuating impedances and mapping.

Conclusion:

CI in MD can yield good hearing outcomes in all three groups and this is possible even after a long delay after labyrinthectomy. Bilateral MD patients are complex and prospective quality of life (QoL) measures would be beneficial in being better able to manage the vestibular outcomes as well as the audiological ones.
The Use of Nesiritide in Children With Congenital Heart Disease
Authors: Bronicki Ronald A. , Domico Michele , Checchia Paul A. , Kennedy Curtis E. , Akcan-Arikan Ayse
Published: November 2016

Objective:

We evaluated the use of nesiritide in children with critical congenital heart disease, pulmonary congestion, and inadequate urine output despite conventional diuretic therapy.

Design:

We conducted a retrospective analysis of 26 consecutive patients, comprising 37 infusions occurring during separate hospitalizations. Hemodynamic variables, urine output, and serum creatinine levels were monitored prior to and throughout the duration of therapy with nesiritide. In addition, the stage of acute kidney injury was determined prior to and throughout the duration of the therapy using a standardized definition of acute kidney injury—The Kidney Disease: Improving Global Outcomes criteria.

Setting:

Cardiac ICU.

Patients:

Pediatric patients with critical congenital heart disease, pulmonary congestion, and inadequate urinary output despite diuretic therapy.

Intervention:

Nesiritide infusion.

Measurements and Main Results:

The use of nesiritide was associated with a significant decrease in the central venous pressure and heart rate with a trend toward a significant increase in urine output. During the course of therapy with nesiritide, the serum creatinine and stage of acute kidney injury decreased significantly. The decrease in stage of acute kidney injury became significant by day 4 (p = 0.006) and became more significant with time (last day of therapy compared with baseline; p < 0.001). During 12 of the 37 infusions, the stage of acute kidney injury decreased by two or more (p < 0.001).

Conclusions:

Nesiritide had a favorable impact on hemodynamics and urine output in children with critical congenital heart disease and pulmonary congestion, and there was no worsening of renal function.
Differences in Risk Behavior and Demographic Factors Between Men Who Have Sex With Men With Acute and Nonacute Human Immunodeficiency Virus Infection in a Community-Based Testing Program in Los Angeles
Authors: Joseph Davey Dvora , Beymer Matthew , Roberts Chelsea P. , Bolan Robert K. , Klausner Jeffrey D.
Published: November 2016

Introduction:

High viremia combined with HIV-infection status unawareness and increased sexual risk behavior contributes to a disproportionate amount of new HIV infections.

Methods:

From August 2011 to July 2015, the Los Angeles Lesbian, Gay, Bisexual, and Transgender Center conducted 66,546 HIV tests. We compared factors, including the presence of concomitant sexually transmitted infections, number of recent sex partners and reported condomless anal intercourse between men who have sex with men (MSM) diagnosed with an acute HIV infection and a nonacute HIV infection using multivariable logistic regression.

Results:

Of 1082 unique MSM who tested HIV-infected for the first time, 165 (15%) had an acute infection and 917 had a nonacute infection. HIV rapid antibody testing was 84.8% sensitive for detecting HIV infection (95% confidence interval (CI): 82.9% to 87.1%). Median HIV viral load among acutely infected MSM was 842,000 copies per milliliter (interquartile range = 98,200–4,897,318). MSM with acute infection had twice the number of sex partners in the prior 30 days (median = 2) and prior 3 months (median = 4) before diagnosis compared with those diagnosed with nonacute infection (P ≤ 0.0001). The odds of acute HIV infection were increased with the numbers of recent sex partners after controlling for age and race/ethnicity (adjusted odds ratio (aOR) >5 partners in past 30 days = 2.74; 95% CI: 1.46 to 5.14; aOR >10 partners in past 3 months = 2.41; 95% CI: 1.36 to 4.25). Non-African American MSM had almost double the odds of being diagnosed with an acute HIV infection compared with African American MSM (aOR = 1.97; 95% CI: 1.10 to 3.52).

Conclusions:

MSM with acute HIV infection had nearly twice as many sex partners in the past 30 days and 3 months compared with MSM with newly diagnosed nonacute HIV infection. Those diagnosed with acute HIV infection had decreased odds of being African American MSM.
Higher Cystatin C Levels Are Associated With Neurocognitive Impairment in Older HIV+ Adults
Authors: Sakoda Marissa E. , Fazeli Pariya L. , Ellis Ronald J. , Jeste Dilip V. , Grant Igor , Letendre Scott L. , Moore David J.
Published: November 2016

Objective:

The study aims to determine whether cystatin C is associated with HIV disease and HIV-associated neurocognitive impairment (NCI).

Methods:

Participants included 124 (HIV+ n = 77; HIV− n = 47) older adults (age ≥ 50 years) examined at the University of California, San Diego HIV Neurobehavioral Research Program. Cystatin C, a biomarker of kidney functioning that has been linked to poor health outcomes, was measured in blood. Participants completed a comprehensive neurocognitive assessment that was used to define both global and domain NCI.

Results:

The HIV+ group had significantly higher cystatin C concentrations than the HIV− group (d = 0.79 P < 0.001). Among HIV+ participants, those with NCI had higher cystatin C concentrations than those without NCI (d = 0.42, P = 0.055), particularly among participants taking tenofovir (d = 0.78, P = 0.004). A receiver–operator characteristic curve identified that cystatin C levels ≥0.75 mg/L were associated with NCI in the HIV+ group. Using this binary variable and including relevant covariates, multivariate modeling confirmed that NCI was associated with higher cystatin C levels (OR = 3.0; P = 0.03).

Conclusions:

Our results confirm that HIV+ older adults have higher cystatin C than HIV− older adults and further identify that cystatin C may be associated with NCI in this population, particularly if they use tenofovir. This blood biomarker may be a useful clinical tool to identify older HIV+ persons at greater risk for cognitive decline.
Semen Bacterial Concentrations and HIV-1 RNA Shedding Among HIV-1–Seropositive Kenyan Men
Authors: Korhonen Christine J. , Srinivasan Sujatha , Huang Dandi , Ko Daisy L. , Sanders Eduard J. , Peshu Norbert M. , Krieger John N. , Muller Charles H. , Coombs Robert W. , Fredricks David N. , Graham Susan M.
Published: November 2016

Introduction:

HIV-1 is transmitted through semen from men to their sexual partners. Genital infections can increase HIV-1 RNA shedding in semen, but shedding also occurs in the absence of typical pathogens. We hypothesized that higher bacterial concentrations in semen would be associated with higher HIV-1 RNA levels.

Methods:

We analyzed semen samples from 42 HIV-1–seropositive Kenyan men using quantitative polymerase chain reaction (PCR) to assess bacterial concentrations and real-time PCR to measure HIV-1 RNA levels. Generalized estimation equations were used to evaluate associations between these 2 measures. Broad-range 16S rRNA gene PCR with pyrosequencing was performed on a subset of 13 samples to assess bacterial community composition.

Results:

Bacteria were detected in 96.6% of 88 samples by quantitative PCR. Semen bacterial concentration and HIV-1 RNA levels were correlated 0.30 (P = 0.01). The association between bacterial concentration and HIV-1 RNA detection was not significant after adjustment for antiretroviral therapy (ART) (adjusted odds ratio: 1.27, 95% CI: 0.84 to 1.91). Factors associated with semen bacterial concentration included insertive anal sex (adjusted beta 0.92, 95% CI: 0.12 to 1.73) and ART use (adjusted beta: −0.77, 95% CI: −1.50 to 0.04). Among 13 samples with pyrosequencing data, Corynebacterium spp., Staphylococcus spp., and Streptococcus spp. were most frequently detected.

Conclusion:

Most of these HIV-1–infected men had bacteria in their semen. ART use was associated with undetectable semen HIV-1 RNA and lower semen bacterial concentrations, whereas insertive anal sex was associated with higher bacterial concentrations. Additional studies evaluating the relationship between semen bacteria, inflammation, mucosal immunity, and HIV-1 shedding are needed to understand implications for HIV-1 transmission.
Rapidly Progressive Dementia: Prevalence and Causes in a Neurologic Unit of a Tertiary Hospital in Brazil
Authors: Studart Neto Adalberto , Soares Neto Herval R. , Simabukuro Mateus M. , Solla Davi J.F. , Gonçalves Márcia R.R. , Fortini Ida , Castro Luiz H.M. , Nitrini Ricardo
Published: November 2016

Background:

Rapidly progressive dementia (RPD) is usually associated with Creutzfeldt-Jakob disease, a fatal condition. Current advances in the understanding of immune-mediated diseases allow the diagnosis of previously unrecognized treatable RPDs.

Objective of the Study:

The objective of the study was to describe the prevalence and causes of RPD in a neurology service, identifying potentially reversible causes.

Methods:

We carried out a cross-sectional evaluation of all patients admitted to the neurology unit of a tertiary hospital in Brazil between March 2012 and February 2015. We included patients who had progressed to moderate or severe dementia within a few months or up to 2 years at the time of hospitalization, and used multivariable logistic regression analysis to identify factors associated with a favorable outcome.

Results:

We identified 61 RPD (3.7%) cases among 1648 inpatients. Mean RPD patients’ age was 48 years, and median time to progression was 6.4 months. Immune-mediated diseases represented the most commonly observed disease group in this series (45.9% of cases). Creutzfeldt-Jakob disease (11.5%) and nonprion neurodegenerative diseases (8.2%) were less common in this series. Outcome was favorable in 36/61 (59.0%) RPD cases and in 28/31 (89.3%) of immune-mediated cases. Favorable outcome was associated with shorter time from symptom onset to diagnosis and abnormal cerebrospinal fluid findings.

Conclusions:

Immune-mediated diseases were the most common cause of RPD in this series. Timely evaluation and diagnosis along with institution of appropriate therapy are required in RPD, especially in view of potentially reversible causes.
Mood and personality interact to determine cognitive biases in pigs
Authors: Asher Lucy , Friel Mary , Griffin Kym , Collins Lisa M.
Published: November 2016

Cognitive bias has become a popular way to access non-human animal mood, though inconsistent results have been found. In humans, mood and personality interact to determine cognitive bias, but to date, this has not been investigated in non-human animals. Here, we demonstrate for the first time, to the best of our knowledge, in a non-human animal, the domestic pig (
Sus scrofa domesticus
), that mood and personality interact, impacting on judgement. Pigs with a more proactive personality were more likely to respond optimistically to unrewarded ambiguous probes (spatially positioned between locations that were previously rewarded and unrewarded) independent of their housing (or enrichment) conditions. However, optimism/pessimism of reactive pigs in this task was affected by their housing conditions, which are likely to have influenced their mood state. Reactive pigs in the less enriched environment were more pessimistic and those in the more enriched environment, more optimistic. These results suggest that judgement in non-human animals is similar to humans, incorporating aspects of stable personality traits and more transient mood states.
Co-adjustment of yolk antioxidants and androgens in birds
Authors: Giraudeau Mathieu , Ducatez Simon
Published: November 2016

Mothers can shape the developmental trajectory of their offspring through the transmission of resources such as hormones, antioxidants or immunoglobulins. Over the last two decades, an abundant literature on maternal effects in birds has shown that several of these compounds (i.e. androgens, glucocorticoids and antioxidants) often influence the same offspring phenotypic traits (i.e. growth, immunity or oxidative stress levels), making interaction effects between egg components a likely scenario. However, the potential interactive effects of maternally transmitted compounds on offspring development and potential co-adjustment of these compounds within an egg are still poorly understood. Here, we report the results of an interspecific comparative analysis on birds' egg yolk composition (i.e. androgens and antioxidants) where we found that yolk carotenoid and vitamin E concentrations are positively associated, supporting the hypothesis that these two antioxidants act in synergy. The concentrations of vitamin E also increased with increasing concentrations of testosterone. This last result confirms the emerging idea that androgens and antioxidants are co-adjusted within eggs and that maternally transmitted antioxidants might limit the potential direct and indirect effects of prenatal exposure to high testosterone levels on oxidative stress.
Goffin's cockatoos make the same tool type from different materials
Authors: Auersperg Alice M. I. , Borasinski Stefan , Laumer Isabelle , Kacelnik Alex
Published: November 2016

Innovative tool manufacture is rare and hard to isolate in animals. We show that an Indonesian generalist parrot, the Goffin's cockatoo, can flexibly and spontaneously transfer the manufacture of stick-type tools across three different materials. Each material required different manipulation patterns, including substrates that required active sculpting for achieving a functional, elongated shape.
Minerals in the gut: scoping a Cambrian digestive system
Authors: Strang K. M. , Armstrong H. A. , Harper D. A. T.
Published: November 2016

The Sirius Passet Lagerstätte of North Greenland contains the first exceptionally preserved mat-ground community of the Cambrian, dominated, in terms of abundance, by trilobites but particularly characterized by iconic arthropods and lobopods, some also occurring in the Burgess shale. High-resolution photography, scanning electron imaging and elemental mapping have been carried out on a variety of specimens of the non-mineralized arthropod
Campanamuta mantonae
(Budd 2011
J. Syst. Palaeontol.
9
, 217–260 (
doi:10.1080/14772019.2010.492644
)) which has three-dimensional gut and muscle preservation. Results show that the guts contain a high concentration of calcium phosphate (approximating to the mineral francolite), whereas the adjacent muscles are silicified. This indicates a unique, tissue-specific taphonomy for this Cambrian taxon. We hypothesize that the precipitation of calcium phosphate in the guts occurs rapidly after death by ‘crystal seed’ processes in suboxic, slightly acidic conditions; critically, the gut wall remained intact during precipitation. We postulate that the calcium phosphate was derived from ingested cellular material. Silicification of the muscles followed as the localized water chemistry became saturated in silica, high in Fe
2+
, and low in oxygen and sulfate. We document here the unique occurrence of two distinct but mechanistically similar taphonomic pathways within a diverse suite of possibilities in an Early Cambrian Lagerstätte.
The ecological connectivity of whale shark aggregations in the Indian Ocean: a photo-identification approach
Authors: Andrzejaczek Samantha , Meeuwig Jessica , Rowat David , Pierce Simon , Davies Tim , Fisher Rebecca , Meekan Mark
Published: November 2016

Genetic and modelling studies suggest that seasonal aggregations of whale sharks (
Rhincodon typus
) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification (photo-ID) data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated program I
3
S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (hundreds to thousands of kilometres) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were resighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations.
An optimal tuning strategy for tidal turbines
Authors: Vennell Ross
Published: November 2016

Tuning wind and tidal turbines is critical to maximizing their power output. Adopting a wind turbine tuning strategy of maximizing the output at any given time is shown to be an extremely poor strategy for large arrays of tidal turbines in channels. This ‘impatient-tuning strategy’ results in far lower power output, much higher structural loads and greater environmental impacts due to flow reduction than an existing ‘patient-tuning strategy’ which maximizes the power output averaged over the tidal cycle. This paper presents a ‘smart patient tuning strategy’, which can increase array output by up to 35% over the existing strategy. This smart strategy forgoes some power generation early in the half tidal cycle in order to allow stronger flows to develop later in the cycle. It extracts enough power from these stronger flows to produce more power from the cycle as a whole than the existing strategy. Surprisingly, the smart strategy can often extract more power without increasing maximum structural loads on the turbines, while also maintaining stronger flows along the channel. This paper also shows that, counterintuitively, for some tuning strategies imposing a cap on turbine power output to limit loads can increase a turbine’s average power output.
Contact probing of stretched membranes and adhesive interactions: graphene and other two-dimensional materials
Authors: Borodich Feodor M. , Galanov Boris A.
Published: November 2016

Contact probing is the preferable method for studying mechanical properties of thin two-dimensional (2D) materials. These studies are based on analysis of experimental force–displacement curves obtained by loading of a stretched membrane by a probe of an atomic force microscope or a nanoindenter. Both non-adhesive and adhesive contact interactions between such a probe and a 2D membrane are studied. As an example of the 2D materials, we consider a graphene crystal monolayer whose discrete structure is modelled as a 2D isotropic elastic membrane. Initially, for contact between a punch and the stretched circular membrane, we formulate and solve problems that are analogies to the Hertz-type and Boussinesq frictionless contact problems. A general statement for the slope of the force–displacement curve is formulated and proved. Then analogies to the JKR (Johnson, Kendall and Roberts) and the Boussinesq–Kendall contact problems in the presence of adhesive interactions are formulated. General nonlinear relations among the actual force, displacements and contact radius between a sticky membrane and an arbitrary axisymmetric indenter are derived. The dimensionless form of the equations for power-law shaped indenters has been analysed, and the explicit expressions are derived for the values of the pull-off force and corresponding critical contact radius.
Thermal convection in a magnetized conducting fluid with the Cattaneo–Christov heat-flow model
Authors: Bissell J. J.
Published: November 2016

By substituting the Cattaneo–Christov heat-flow model for the more usual parabolic Fourier law, we consider the impact of hyperbolic heat-flow effects on thermal convection in the classic problem of a magnetized conducting fluid layer heated from below. For stationary convection, the system is equivalent to that studied by Chandrasekhar (
Hydrodynamic and Hydromagnetic Stability,
1961), and with free boundary conditions we recover the classical critical Rayleigh number

R

c

(

c

)

(
Q
)

which exhibits inhibition of convection by the field according to

R

c

(

c

)

→

π
2

Q

as

Q
→
∞

, where
Q
is the Chandrasekhar number. However, for oscillatory convection we find that the critical Rayleigh number

R

c

(

o

)

(
Q
,

P

1

,

P

2

,
C
)

is given by a more complicated function of the thermal Prandtl number

P

1

, magnetic Prandtl number

P

2

and Cattaneo number
C
. To elucidate features of this dependence, we neglect

P

2

(in which case overstability would be classically forbidden), and thereby obtain an expression for the Rayleigh number that is far less strongly inhibited by the field, with limiting behaviour

R

c

(

o

)

→
π

Q

/

C

, as

Q
→
∞

. One consequence of this weaker dependence is that onset of instability occurs as overstability provided
C
exceeds a threshold value
C
T
(
Q
); indeed, crucially we show that when
Q
is large,

C

T

∝
1

/

Q

, meaning that oscillatory modes are preferred even when
C
itself is small. Similar behaviour is demonstrated in the case of fixed boundaries by means of a novel numerical solution.
Actuarial senescence in a long-lived orchid challenges our current understanding of ageing
Authors: Dahlgren Johan Petter , Colchero Fernando , Jones Owen R. , Øien Dag-Inge , Moen Asbjørn , Sletvold Nina
Published: November 2016

The dominant evolutionary theory of actuarial senescence—an increase in death rate with advancing age—is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study ofDactylorhiza lapponicathat replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival–reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics.
Attention-like processes in insects
Authors: Nityananda Vivek
Published: November 2016

Attention is fundamentally important for sensory systems to focus on behaviourally relevant stimuli. It has therefore been an important field of study in human psychology and neuroscience. Primates, however, are not the only animals that might benefit from attention-like processes. Other animals, including insects, also have to use their senses and select one among many stimuli to forage, avoid predators and find mates. They have evolved different mechanisms to reduce the information processed by their brains to focus on only relevant stimuli. What are the mechanisms used by insects to selectively attend to visual and auditory stimuli? Do these attention-like mechanisms achieve the same functions as they do in primates? To investigate these questions, I use an established framework for investigating attention in non-human animals that proposes four fundamental components of attention: salience filters, competitive selection, top-down sensitivity control and working memory. I discuss evidence for each of these component processes in insects and compare the characteristics of these processes in insects to what we know from primates. Finally, I highlight important outstanding questions about insect attention that need to be addressed for us to understand the differences and similarities between vertebrate and insect attention.
MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs
Authors: Kibet Caleb Kipkurui , Machanick Philip
Published: November 2016

We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that ‘correct motifs’ are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 – this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif discovery. It can be accessed athttp://www.bioinf.ict.ru.ac.za/.
Trace metal imaging of sulfate-reducing bacteria and methanogenic archaea at single-cell resolution by synchrotron X-ray fluorescence imaging
Authors: Glass Jennifer B. , Chen Si , Dawson Katherine S. , Horton Damian R. , Vogt Stefan , Ingall Ellery D. , Twining Benjamin S. , Orphan Victoria J.
Published: November 2016

Metal cofactors are required for many enzymes in anaerobic microbial respiration. This study examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron x-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. For both species, zinc and iron were consistently the most abundant cellular metals.M. acetivoranscontained higher nickel and cobalt content thanD. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper-sulfides.
Accelerated simulation of evolutionary trajectories in origin–fixation models
Authors: Teufel Ashley I. , Wilke Claus O.
Published: November 2016

We present an accelerated algorithm to forward-simulate origin--fixation models. Our algorithm requires on average only about two fitness evaluations per fixed mutation, whereas traditional algorithms require, per one fixed mutation, a number of fitness evaluations on the order of the effective population size Ne. Our accelerated algorithm yields the exact same steady state as the original algorithm but produces a different order of fixed mutations. By comparing several relevant evolutionary metrics, such as the distribution of fixed selection coefficients and the probability of reversion, we find that the two algorithms behave equivalently in many respects. However, the accelerated algorithm yields less variance in fixed selection coefficients. Notably, we are able to recover the expected amount of variance by rescaling population size, and we find a linear relationship between the rescaled population size and the population size used by the original algorithm. Considering the widespread usage of origin--fixation simulations across many areas of evolutionary biology, we introduce our accelerated algorithm as a useful tool for increasing the computational complexity of fitness functions without sacrificing much in terms of accuracy of the evolutionary simulation.
Computational model of a positive BDNF feedback loop in hippocampal neurons following inhibitory avoidance training
Authors: Zhang Yili , Smolen Paul , Alberini Cristina M. , Baxter Douglas A. , Byrne John H.
Published: November 2016

Inhibitory avoidance (IA) training in rodents initiates a molecular cascade within hippocampal neurons. This cascade contributes to the transition of short- to long-term memory (i.e., consolidation). Here, a differential equation-based model was developed to describe a positive feedback loop within this molecular cascade. The feedback loop begins with an IA-induced release of brain-derived neurotrophic factor (BDNF), which in turn leads to rapid phosphorylation of the cAMP response element-binding protein (pCREB), and a subsequent increase in the level of the β isoform of the CCAAT/enhancer binding protein (C/EBPβ). Increased levels of C/EBPβ lead to increased bdnf expression. Simulations predicted that an empirically observed delay in the BDNF-pCREB-C/EBPβ feedback loop has a profound effect on the dynamics of consolidation. The model also predicted that at least two independent self-sustaining signaling pathways downstream from the BDNF-pCREB-C/EBPβ feedback loop contribute to consolidation. Currently, the nature of these downstream pathways is unknown.
Rats can acquire conditional fear of faint light leaking through the acrylic resin used to mount fiber optic cannulas
Authors: Eckmier Adam , Daney de Marcillac Willy , Maître Agnès , Jay Thérèse M. , Sanders Matthew J. , Godsil Bill P.
Published: November 2016

Rodents are exquisitely sensitive to light and optogenetic behavioral experiments routinely introduce light-delivery materials into experimental situations, which raises the possibility that light could leak and influence behavioral performance. We examined whether rats respond to a faint diffusion of light, termedcaplight, which emanated through the translucent dental acrylic resin used to affix deep-brain optical cannulas in place. Although rats did not display significant changes in locomotion or rearing to caplight in a darkened open field, they did acquire conditional fear via caplight-footshock pairings. These findings highlight the potential confounding influence of extraneous light emanating from light-delivery materials during optogenetic analyses.
Neural circuits via which single prolonged stress exposure leads to fear extinction retention deficits
Authors: Knox Dayan , Stanfield Briana R. , Staib Jennifer M. , David Nina P. , Keller Samantha M. , DePietro Thomas
Published: November 2016

Single prolonged stress (SPS) has been used to examine mechanisms via which stress exposure leads to post-traumatic stress disorder symptoms. SPS induces fear extinction retention deficits, but neural circuits critical for mediating these deficits are unknown. To address this gap, we examined the effect of SPS on neural activity in brain regions critical for extinction retention (i.e., fear extinction circuit). These were the ventral hippocampus (vHipp), dorsal hippocampus (dHipp), basolateral amygdala (BLA), prelimbic cortex (PL), and infralimbic cortex (IL). SPS or control rats were fear conditioned then subjected to extinction training and testing. Subsets of rats were euthanized after extinction training, extinction testing, or immediate removal from the housing colony (baseline condition) to assay c-Fos levels (measure of neural activity) in respective brain region. SPS induced extinction retention deficits. During extinction training SPS disrupted enhanced IL neural activity and inhibited BLA neural activity. SPS also disrupted inhibited BLA and vHipp neural activity during extinction testing. Statistical analyses suggested that SPS disrupted functional connectivity within the dHipp during extinction training and increased functional connectivity between the BLA and vHipp during extinction testing. Our findings suggest that SPS induces extinction retention deficits by disrupting both excitatory and inhibitory changes in neural activity within the fear extinction circuit and inducing changes in functional connectivity within the Hipp and BLA.