bluuebunny/crossref_metadata_2025 huggingface dataset:
Closer Look at the Nutritional Outcomes of Patients After Primary Repair of Congenital Diaphragmatic Hernia
Authors: Vu Lan T. , McFarland Carrie , Bratton Barbara , Lee Hanmin
Published: May 2017

Objectives:

We hypothesize that the patients after primary repair of congenital diaphragmatic hernia (CDH) can have poor nutritional outcomes and plan to identify risk factors to further stratify these patients.

Methods:

Retrospective cohort of patients who had primary repair of CDH between 2000 and 2014 and had follow‐up at our institution. Z scores (weight for age and weight for length) were calculated using the World Health Organization and Centers for Disease Control and Prevention growth standards.

Results:

For the 67 patients in the cohort, the median age at the time of repair was 3 days (interquartile range 2–5) and at the time of discharge was 20.5 days (interquartile range 16–30). Fifteen percent of the patients required supplemental tube feeding for inadequate oral intake and 69% required fortified feedings for inadequate growth at discharge (4 patients subsequently needed gastrostomy tube placement). The median z scores at discharge were −1.0 (−2.1 to −0.3) and −1.2 (−2.3 to −0.5) in weight for age and weight for length, respectively. The risk factors for low z scores included open repair and longer periods of postoperative intubation or hospitalization. The z scores were similar at 6 months of age compared to discharge, but then statistically improved at 12 months of age.

Conclusions:

Patients with primary repair of CDH are at risk for poor nutritional outcomes at the time of hospital discharge and require follow‐up to ensure adequate growth. Patients at highest risk are those who had an open repair and had prolonged intubation or hospitalization.
Assessing National Cancer Control Plan Knowledge, Prioritization, and Engagement Through a Pediatric Oncology Cancer Control Workshop
Authors: Weaver Meaghann S. , Howard Scott C. , Renner Lorna , Harif Mhamed , Lam Catherine G.
Published: May 2017

This study represents findings from a questionnaire completed before a cancer control workshop by 47 pediatric cancer control stakeholder participants from 27 countries. Respondents reported their knowledge of their country’s cancer control plan, their understanding of childhood cancer control priorities in their local setting, and barriers to high-quality pediatric cancer care. Findings reveal a knowledge gap in pediatric oncology professionals’ awareness of national cancer control plan existence, with under-recognition of existing plans, and uncertainty regarding whether pediatric cancer was included in the plans. This study supports the potential of a preworkshop needs assessment to inform cancer control planning objectives and a cancer control training agenda.
Demodicosis in Pediatric Cancer
Authors: van Atteveld Jenneke E. , Graaf Marlies de , Grotel Martine van , van den Heuvel-Eibrink Marry M.
Published: May 2017

Demodicosis is a rare condition that most often occurs in immunocompromised patients. We here describe a boy with T-cell non–Hodgkin lymphoma who developed a facial papulopustular eruption just before finalizing T-cell non–Hodgkin lymphoma treatment. He was treated for several infectious diseases without improvement. Demodicosis was considered and complete resolution was finally reached with topical metronidazole. We conducted a systematic search of all previously described cases of this condition in children with cancer, which showed that almost all demodicosis cases occurred in patients with lymphoreticular malignancies during maintenance chemotherapy. Hence, demodicosis may be seriously considered in antibiotic-resistant facial papulopustular eruptions in this group of patients to prevent delay of adequate treatment.
Human Papillomavirus (HPV) Genotypes in Condylomas, Intraepithelial Neoplasia, and Invasive Carcinoma of the Penis Using Laser Capture Microdissection (LCM)-PCR
Authors: Fernández-Nestosa María J. , Guimerà Nuria , Sanchez Diego F. , Cañete-Portillo Sofía , Velazquez Elsa F. , Jenkins David , Quint Wim , Cubilla Antonio L.
Published: May 2017

Laser capture microdissection-polymerase chain reaction (LCM-PCR) supported by p16INK4a was used for the first time to demonstrate human papillomavirus (HPV) DNA in histologically specific penile lesions, which were as follows: squamous hyperplasia (12 lesions, 10 patients), flat lesions (12 lesions, 5 patients), condylomas (26 lesions, 7 patients), penile intraepithelial neoplasia (PeIN) (115 lesions, 43 patients), and invasive squamous cell carcinomas (26 lesions, 26 patients). HPV was detected by whole-tissue section and LCM-PCR. LCM proved to be more precise than whole-tissue section in assigning individual genotypes to specific lesions. HPV was negative or very infrequent in squamous hyperplasia, differentiated PeIN, and low-grade keratinizing variants of carcinomas. HPV was strongly associated with condylomas, warty/basaloid PeIN, adjacent flat lesions, and warty/basaloid carcinomas. A single HPV genotype was found in each lesion. Some condylomas and flat lesions, especially those with atypia, were preferentially associated with high-risk HPV. Unlike invasive carcinoma, in which few genotypes of HPV were involved, there were 18 HPV genotypes in PeIN, usually HPV 16 in basaloid PeIN but marked HPV heterogeneity in warty PeIN (11 different genotypes). Variable and multiple HPV genotypes were found in multicentric PeIN, whereas unicentric PeIN was usually related to a single genotype. There was a correspondence among HPV genotypes in invasive and associated PeIN. p16INK4a was positive in the majority of HPV-positive lesions except condylomas containing LR-HPV. p16INK4a was usually negative in squamous hyperplasia, differentiated PeIN, and low-grade keratinizing variants of squamous cell carcinomas. In summary, we demonstrated that LCM-PCR was a superior research technique for investigating HPV genotypes in intraepithelial lesions. A significant finding was the heterogeneity of HPV genotypes in PeIN and the differential association of HPV genotypes with subtypes of PeIN. The presence of atypia and high-risk HPV in condylomas and adjacent flat lesions suggests a precursor role, and the correspondence of HPV genotypes in invasive carcinomas and associated PeIN indicates a causal relation. Data presented support the bimodal hypothesis of penile cancer carcinogenesis in HPV-driven and non-HPV-driven carcinomas and justify the current WHO pathologic classification of PeIN in special subtypes.
Fluid Overload and Cumulative Thoracostomy Output Are Associated With Surgical Site Infection After Pediatric Cardiothoracic Surgery
Authors: Sochet Anthony A. , Nyhan Aoibhinn , Spaeder Michael C. , Cartron Alexander M. , Song Xiaoyan , Klugman Darren , Brown Anna T.
Published: May 2017

Objectives:

To determine the impact of cumulative, postoperative thoracostomy output, amount of bolus IV fluids and peak fluid overload on the incidence and odds of developing a deep surgical site infection following pediatric cardiothoracic surgery.

Design:

A single-center, nested, retrospective, matched case-control study.

Setting:

A 26-bed cardiac ICU in a 303-bed tertiary care pediatric hospital.

Patients:

Cases with deep surgical site infection following cardiothoracic surgery were identified retrospectively from January 2010 through December 2013 and individually matched to controls at a ratio of 1:2 by age, gender, Risk Adjustment for Congenital Heart Surgery score, Society of Thoracic Surgeons—European Association for Cardiothoracic Surgery category, primary cardiac diagnosis, and procedure.

Interventions:

None.

Measurements and Main Results:

Twelve cases with deep surgical site infection were identified and matched to 24 controls without detectable differences in perioperative clinical characteristics. Deep surgical site infection cases had larger thoracostomy output and bolus IV fluid volumes at 6, 24, and 48 hours postoperatively compared with controls. For every 1 mL/kg of thoracostomy output, the odds of developing a deep surgical site infection increase by 13%. By receiver operative characteristic curve analysis, a cutoff of 49 mL/kg of thoracostomy output at 48 hours best discriminates the development of deep surgical site infection (sensitivity 83%, specificity 83%). Peak fluid overload was greater in cases than matched controls (12.5% vs 6%; p < 0.01). On receiver operative characteristic curve analysis, a threshold value of 10% peak fluid overload was observed to identify deep surgical site infection (sensitivity 67%, specificity 79%). Conditional logistic regression of peak fluid overload greater than 10% on the development of deep surgical site infection yielded an odds ratio of 9.4 (95% CI, 2–46.2).

Conclusions:

Increased postoperative peak fluid overload and cumulative thoracostomy output were associated with deep surgical site infection after pediatric cardiothoracic surgery. We suspect the observed increased thoracostomy output, fluid overload, and IV fluid boluses may have altered antimicrobial prophylaxis. Although analysis of additional pharmacokinetic data is warranted, providers may consider modification of antimicrobial prophylaxis dosing or alterations in fluid management and diuresis in response to assessment of peak fluid overload and fluid volume shifts in the immediate postoperative period.
Effect of Family Presence on Advanced Trauma Life Support Task Performance During Pediatric Trauma Team Evaluation
Authors: O'Connell Karen J. , Carter Elizabeth A. , Fritzeen Jennifer L. , Waterhouse Lauren J. , Burd Randall S.
Published: May 2017

Importance

In many hospitals, family members are separated from their children during the early phases of trauma care. Including family members during this phase of trauma care varies by institution and is limited by concerns for adverse effects on clinical care.

Objective

The aim of this study is to evaluate the effect of family presence (FP) on advanced trauma life support primary and secondary survey task performance by pediatric trauma teams. We hypothesized that trauma care with FP would be noninferior to care when families were absent.

Design

We performed a retrospective video review of consecutive pediatric trauma evaluations. Family presence status was determined by availability of the family.

Setting

The study was conducted at an American College of Surgeons–designated level I pediatric trauma center that serves the Washington, DC, metropolitan area.

Participants

Participants included patients younger than 16 years of age who met trauma activation criteria and were evaluated by the trauma team in our emergency department.

Outcome Measures

We compared task performance between patients with and without FP.

Results

Video recordings of 135 trauma evaluations were reviewed. Family was present for 88 (65%) evaluations. Patients with FP were younger (mean age, 6.4 years [SD = 4.1] vs 9.0 years [SD = 4.9]; P < 0.001) and more likely to have sustained blunt injuries (95% vs 85%, P = 0.03). Noninferiority of frequency and timeliness of completion of all primary survey tasks were confirmed for evaluations with FP. Noninferiority of frequencies of secondary survey task completion was confirmed for most tasks except for examination of the neck, pelvis, and upper extremities. Family members did not directly interfere with patient care in any case.

Conclusions

Performance of most advanced trauma life support tasks during pediatric trauma evaluation was not worsened by FP. Our data provide additional evidence supporting FP during the acute management of injured children.
Pediatric Drowning
Authors: Best Rebecca R. , Harris Benjamin H.L. , Walsh Jason L. , Manfield Timothy
Published: May 2017

Objectives

Drowning is one of the leading causes of death in children. Resuscitating a child following submersion is a high-pressure situation, and standard operating procedures can reduce error. Currently, the Resuscitation Council UK guidance does not include a standard operating procedure on pediatric drowning. The objective of this project was to design a standard operating procedure to improve outcomes of drowned children.

Methods

A literature review on the management of pediatric drowning was conducted. Relevant publications were used to develop a standard operating procedure for management of pediatric drowning.

Results

A concise standard operating procedure was developed for resuscitation following pediatric submersion. Specific recommendations include the following: the Heimlich maneuver should not be used in this context; however, prolonged resuscitation and therapeutic hypothermia are recommended.

Conclusions

This standard operating procedure is a potentially useful adjunct to the Resuscitation Council UK guidance and should be considered for incorporation into its next iteration.
Evaluation of Patients With Febrile Seizure: Risk Factors, Reccurence, Treatment and Prognosis
Authors: Renda Rahime , Yüksel Deniz , Gürer Y.K. Yavuz
Published: May 2017

Introduction

Febrile convulsion (FC) is the most common neurological disorder in childhood. The aim of this study was to determine the risk factors for recurrence and the development of epilepsy from the demographic data of these patients.

Methods

A retrospective study was made of 680 patients with FC who presented to our hospital. Patients with only FC were defined as group 1 and those who developed epilepsy after FC as group 2. Comparisons were made between the 2 groups of the demographic parameters, parental consanguinity, familial history of FCs or epilepsy, criteria for starting prophylactic treatment, response to treatment, risk factors for recurrence, and results of electroencephalogram.

Results

The study included a total of 680 patients comprising 399 males (59%) and 281 females (41%). A diagnosis of FC was made in 652 cases (95.8%, group 1), and epilepsy was diagnosed in 28 (4.2%, group 2). A positive familial history of FCs was determined statistically significantly higher in group 1. On the other hand, a history of pathological birth and parental consanguinity was found higher in group 2. Prophylactic treatment was administered to 89.3% of group 2 and 40.3% of group 1.

Conclusions

Febrile convulsions create fear and panic in the family and are a significant health problem in Turkey. The conclusion that has been reached is that the unnecessary administration of prophylactic treatment could be prevented with education of the families on the subject of fever and correct identification of patients at risk of developing epilepsy.
The ART Advantage: Health Care Utilization for Diabetes and Hypertension in Rural South Africa
Authors: Manne-Goehler Jennifer , Montana Livia , Gómez-Olivé Francesc Xavier , Rohr Julia , Harling Guy , Wagner Ryan G. , Wade Alisha , Kabudula Chodziwadziwa W. , Geldsetzer Pascal , Kahn Kathleen , Tollman Stephen , Berkman Lisa F. , Bärnighausen Till W. , Gaziano Thomas A.
Published: May 2017

Background:

The prevalence of diabetes and hypertension has increased in HIV-positive populations, but there is limited understanding of the role that antiretroviral therapy (ART) programs play in the delivery of services for these conditions. The aim of this study is to assess the relationship between ART use and utilization of health care services for diabetes and hypertension.

Methods:

Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa is a cohort of 5059 adults. The baseline study collects biomarker-based data on HIV, ART, diabetes, and hypertension and self-reported data on health care utilization. We calculated differences in care utilization for diabetes and hypertension by HIV and ART status and used multivariable logistic regressions to estimate the relationship between ART use and utilization of services for these conditions, controlling for age, sex, body mass index, education, and household wealth quintile.

Results:

Mean age, body mass index, hypertension, and diabetes prevalence were lower in the HIV-positive population (all P < 0.001). Multivariable logistic regression showed that ART use was significantly associated with greater odds of blood pressure measurement [adjusted odds ratio (aOR) 1.27, 95% confidence interval (CI): 1.04 to 1.55] and blood sugar measurement (aOR 1.26, 95% CI: 1.05 to 1.51), counseling regarding exercise (aOR 1.57, 95% CI: 1.11 to 2.22), awareness of hypertension diagnosis (aOR 1.52, 95% CI: 1.12 to 2.05), and treatment for hypertension (aOR 1.63, 95% CI: 1.21 to 2.19).

Conclusions:

HIV-positive patients who use ART are more likely to have received health care services for diabetes and hypertension. This apparent ART advantage suggests that ART programs may be a vehicle for strengthening health systems for chronic care.
Increasing Levels of Positive End-expiratory Pressure Improve the Left Ventricular Strain
Authors: Ruiz-Bailén Manuel , Cobo-Molinos Jesús , Castillo-Rivera Ana M. , Iniesta-Carricondo María C. , Pola Gallego de Guzmán María D. , Cárdenas-Cruz Antonio
Published: May 2017

Purpose:

The goal of this study was to evaluate possible changes in the left myocardial performance of patients with cardiogenic shock (CS) during ascending levels of positive end-expiratory pressure (PEEP) using speckle-tracking echocardiography.

Materials and Methods:

This was an interventional clinical study performed on CS patients under mechanical ventilation. These patients underwent echocardiography after 15 to 30 minutes of progressive increases in PEEP zero end-expiratory pressure (ZEEP) (PEEP 5, PEEP 10, PEEP 15 cm H2O). We evaluated the changes caused by these increasing levels of PEEP on the E/E′ ratio and the parameters of left ventricular systolic and diastolic functions, including longitudinal strain (S) and strain rate (SR). Analyses of mean values were carried out using analysis of variance.

Results:

A total of 65 CS patients were included. Their mean age was 68.58±14.61 years. Progressive increases in PEEP induced a significant decrease in the E/E′ ratio (ZEEP=12.87±1.81; PEEP=5, 8.39±3.61; PEEP=10, 6.34±1.73; and PEEP=15, 7.10±0.37; P<0.0001). Although we did not find significant changes in left ventricular ejection fraction, a clear increase in left ventricular S and SR occurred (ZEEP=−13, 15±1.27; PEEP=5, −16.97±4.01; PEEP=10, −16.89±0.46; PEEP=15, −15.39±4.21; and ZEEP=−1.02±0.02; PEEP=5, −1.49±0.13; PEEP=10, −1.57±0.21; PEEP=15, −1.24±0.29, respectively; all values were significant).

Conclusions:

Increasing levels of PEEP improve the left ventricular S and SR. PEEP levels could modify the performance of left ventricular fibers.
Effect of Beta Blockers on Mortality After Open Repair of Abdominal Aortic Aneurysm
Authors: Alshaikh Husain N. , Canner Joseph K. , Malas Mahmoud
Published: May 2017

Objective:

To assess the effect of perioperative beta blocker (BB) use on postoperative in-hospital mortality after open repair of abdominal aortic aneurysm (OAR).

Background:

Postoperative mortality after OAR ranges from 3.0% to 4.5%. Insight about the effect of BBs on postoperative mortality after OAR is currently lacking.

Methods:

This is a retrospective study of patients undergoing OAR from 2009-Q3 to 2015-Q1 in the Premier Healthcare Database. The Premier Healthcare Database includes data representing 20% of all inpatient US discharges annually. Patients under 45 years, admitted after a trauma or who underwent multiple aortic repair procedures, were excluded. Multivariable logistic regression models were created to assess the relationship between perioperative BB use and postoperative in-hospital mortality.

Results:

Of 6515 patients admitted for OAR, 5423 (83.2%) received perioperative BBs. Patients who received BBs were more likely to develop major adverse events compared with those who did not (45.6% vs 35.2%; P < 0.001); however, failure to rescue was lower among BB users (7.6% vs 19.5%; P < 0.001). In a multivariable logistic regression model, BB use was associated with 57% [odds ratio 0.43, 95% confidence interval (CI) 0.31–0.56, P = 0.001) and 81% (odds ratio 0.19, 95% CI 0.11–0.31, P < 0.001) lower odds of mortality among patients without and with a history of coronary artery disease, respectively. The predicted mortality (95% CI) for patients who did not receive BBs, or received low, intermediate, or high-intensity BBs was 11.6% (8.0%–15.2%), 5.4% (4.4%–6.5%), 2.5% (1.9%–3.0%), and 3.3% (2.3%–4.3%), respectively.

Conclusions:

In-hospital use of BBs was associated with a significant reduction in postoperative mortality after OAR. This is the first study to demonstrate a dose–response relationship between BBs and postoperative mortality after OAR.
Effect of Surgeon Age on Bariatric Surgery Outcomes
Authors: Stevens Haley , Carlin Arthur M. , Ross Rachel , Stricklen Amanda , Wood Michael H. , Ghaferi Amir A.
Published: May 2017

Objective:

This study sought to explore the relationship of bariatric surgeon age and patient outcomes.

Background:

Regulators, policy makers, and patient advocacy groups have recently been pushing to establish clear guidelines for physician retirement in the United States. Although it is often assumed that increasing physician age leads to worse patient outcomes, the relationship is lacking robust evidence, and is still unclear.

Methods:

We conducted a study analyzing all bariatric surgeons in Michigan who participated in a statewide collaborative quality improvement program (n = 71) who performed primary laparoscopic Roux-en-Y Gastric Bypass, or sleeve gastrectomy operations, and data on their patients (n = 60430) over the past 10 years. Our primary outcomes were 30-day postoperative complications. Odds ratios for overall complications and serious complications were calculated for each age group, and surgery type.

Results:

Late career surgeons had more bariatric surgery experience and had a higher average annual case volume than early career surgeons. Considering all cases in the past 10 years, older surgeons performed more Roux-en-Y Gastric Bypass (40%) and less sleeve gastrectomy (38.8%) than younger surgeons (34.7% and 51.5%). When adjusting for patient and surgeon characteristics, there were no statistically significant differences in overall or serious complication rates for either procedure among surgeon age groups.

Conclusions:

When evaluating bariatric surgeons in the State of Michigan, we found no statistically significant association between surgeon age and patient outcomes. Our findings do not provide evidence for age-specific retirement cut-offs, but support the development of guidelines which are holistic, and focus on evaluating and improving physician outcomes at all career levels.
Pain, Neuropsychiatric Symptoms, and Quality of Life of Nursing Home Residents With Advanced Dementia in The Netherlands
Authors: van Kooten Janine , van der Wouden Johannes C. , Sikkes Sietske A.M. , Smalbrugge Martin , Hertogh Cees M.P.M. , Stek Max L.
Published: May 2017

Background:

Many studies have investigated factors associated with quality of life (QoL) in nursing home residents with dementia. Both pain and neuropsychiatric symptoms (NPS) are clinically relevant and individually associated with a lower QoL; however, there are no studies that investigated pain and NPS together in relation to QoL.

Purpose:

In this study, we explored the relationship of pain and NPS with QoL in nursing home residents with dementia by investigating the association between pain concurrently with NPS, and QoL.

Methods and Patients:

Secondary data analyses of cross-sectional data from 199 residents were collected by observations at dementia special care units of 10 nursing homes. QoL was measured with Qualidem, pain with the Mobilization Observation Behavior Intensity Dementia (MOBID-2) Pain Scale and NPS with the Neuropsychiatric Symptoms Inventory. The relation of pain and NPS to QoL was studied using multiple linear regression analyses. Analyses were adjusted for age, sex, activities of daily living, comorbidity, medication use, and dementia severity.

Results:

Regression models with pain and NPS, showed no independent relationship between pain and QoL subdomains, but NPS, in particular agitation and depressive symptoms, were significantly associated with lower QoL subdomain scores. Agitation was related to lower scores on the subdomains “relationship” [95% confidence interval (CI), −0.083 to −0.059], “positive affect” (95% CI, −0.037 to −0.013), “restless tense behavior” (95% CI, −0.003 to −0.004), and “social relations” (95% CI, −0.033 to −0.009), whereas depression was related to lower scores on the subdomains “positive affect” (95% CI, −0.054 to −0.014), “negative affect” (95% CI, −0.114 to −0.074), “restless tense behavior” (95% CI, −0.075 to −0.025), and “social relations” (95% CI, −0.046 to −0.002).

Conclusions:

Only NPS were significantly associated with QoL in nursing home residents with dementia. Further longitudinal research is needed to estimate the nature of the relationship between pain, NPS, and QoL.
Dependence Stage and Pharmacoeconomic Outcomes in Patients With Alzheimer Disease
Authors: Michaud Tzeyu L. , High Robin , Charlton Mary E. , Murman Daniel L.
Published: May 2017

The level of assistance patients with Alzheimer disease (AD) require in their care may be an important predictor of resource use, costs of care, and quality of life. The Dependence Scale (DS), a measure of care-assistance required, was used to estimate costs of care and quality of life of patients with AD categorized into 6 dependence stages based upon the summated item scores of the DS. Data were derived from a 3-year, noninterventional study of 132 patients with probable AD (ages, 50 to 85 y) and caregiver dyads. We investigated the association between DS scores and health care costs, health-related quality of life (HRQoL), caregiver burden and estimated annual costs and HRQoL for 6 dependence stages in adjusted models. DS scores were significant predictors of health care costs, HRQoL, and caregiver burden. The estimated annual health care costs and a measure of HRQoL (EuroQoL-5D) ranged from $11,418 and 1.00 for those at very mild dependence stage to $101,715 and 0.26 for those at very severe dependence stage. DS scores classified into 6 dependence stages provides a useful method to estimate unique levels of care-associated costs and health utilities for pharmacoeconomic evaluations of new treatments for AD.
Extreme weather and climate events with ecological relevance: a review
Authors: Ummenhofer Caroline C. , Meehl Gerald A.
Published: May 2017

Robust evidence exists that certain extreme weather and climate events, especially daily temperature and precipitation extremes, have changed in regard to intensity and frequency over recent decades. These changes have been linked to human-induced climate change, while the degree to which climate change impacts an individual extreme climate event (ECE) is more difficult to quantify. Rapid progress in event attribution has recently been made through improved understanding of observed and simulated climate variability, methods for event attribution and advances in numerical modelling. Attribution for extreme temperature events is stronger compared with other event types, notably those related to the hydrological cycle. Recent advances in the understanding of ECEs, both in observations and their representation in state-of-the-art climate models, open new opportunities for assessing their effect on human and natural systems. Improved spatial resolution in global climate models and advances in statistical and dynamical downscaling now provide climatic information at appropriate spatial and temporal scales. Together with the continued development of Earth System Models that simulate biogeochemical cycles and interactions with the biosphere at increasing complexity, these make it possible to develop a mechanistic understanding of how ECEs affect biological processes, ecosystem functioning and adaptation capabilities. Limitations in the observational network, both for physical climate system parameters and even more so for long-term ecological monitoring, have hampered progress in understanding bio-physical interactions across a range of scales. New opportunities for assessing how ECEs modulate ecosystem structure and functioning arise from better scientific understanding of ECEs coupled with technological advances in observing systems and instrumentation.

This article is part of the themed issue ‘Behavioural, ecological and evolutionary responses to extreme climatic events’.
How birds cope physiologically and behaviourally with extreme climatic events
Authors: Wingfield John C. , Pérez Jonathan H. , Krause Jesse S. , Word Karen R. , González-Gómez Paulina L. , Lisovski Simeon , Chmura Helen E.
Published: May 2017

As global climate change progresses, the occurrence of potentially disruptive climatic events such as storms are increasing in frequency, duration and intensity resulting in higher mortality and reduced reproductive success. What constitutes an extreme climatic event? First we point out that extreme climatic events in biological contexts can occur in any environment. Focusing on field and laboratory data on wild birds we propose a mechanistic approach to defining and investigating what extreme climatic events are and how animals cope with them at physiological and behavioural levels. The life cycle of birds is made up of life-history stages such as migration, breeding and moult that evolved to match a range of environmental conditions an individual might expect during the year. When environmental conditions deteriorate and deviate from the expected range then the individual must trigger coping mechanisms (emergency life-history stage) that will disrupt the temporal progression of life-history stages, but enhance survival. Using the framework of allostasis, we argue that an extreme climatic event in biological contexts can be defined as when the cumulative resources available to an individual are exceeded by the sum of its energetic costs—a state called allostatic overload. This allostatic overload triggers the emergency life-history stage that temporarily allows the individual to cease regular activities in an attempt to survive extreme conditions. We propose that glucocorticoid hormones play a major role in orchestrating coping mechanisms and are critical for enduring extreme climatic events.

This article is part of the themed issue ‘Behavioural, ecological and evolutionary responses to extreme climatic events’.
Micropatterned substrates to promote and dissect reprogramming of human somatic cells
Authors: Carlson-Stevermer Jared , Harkness Ty , Prestil Ryan , Seymour Stephanie , Knight Gavin , Ashton Randolph , Saha Krishanu
Published: May 2017

Reprogramming of human somatic cells to induce pluripotent stem cells (iPSCs) generates valuable precursors for disease modeling and regenerative medicine. However, the reprogramming process can be inefficient and noisy, creating many partially reprogrammed cells in addition to fully reprogrammed iPSCs. To address these shortcomings, we developed a micropatterned substrate that allows for dynamic live-cell microscopy of thousands of cell subpopulations undergoing reprogramming. Micropatterning facilitated a change in shape, size and clustering of nuclei to promote somatic identity erasure. Increased proliferation, cell density and decreased intercellular YAP signaling accompanied these nuclear changes. A combination of eight nuclear characteristics could be used to track reprogramming progression and distinguish partially reprogrammed cells from those that were fully reprogrammed.

Micropatterned substrates constitute a new tool for facile iPSC production and can be used in high-throughput to probe and understand the subcellular changes that accompany human cell fate transitions.
Assessment of the Potential Role ofStreptomycesin Cave Moonmilk Formation
Authors: Maciejewska Marta , Adam Delphine , Naômé Aymeric , Martinet Loïc , Tenconi Elodie , Całusińska Magdalena , Delfosse Philippe , Hanikenne Marc , Baurain Denis , Compère Philippe , Carnol Monique , Barton Hazel , Rigali Sébastien
Published: May 2017

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real bacterial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic versus abiotic) involved. In this work we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originatingStreptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3deposition. The metabolic activities involved in CaCO3transformation were furthermore assessedin vitroamong the collection of moonmilkStreptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally,in silicosearch for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2allowed to identify genetic predispositions for carbonate precipitation inStreptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.
6S RNA supports recovery from nitrogen depletion inSynechocystissp. PCC 6803
Authors: Heilmann Beate , Hakkila Kaisa , Georg Jens , Tyystjärvi Taina , Hess Wolfgang R. , Axmann Ilka M. , Dienst Dennis
Published: May 2017

Background

The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles.

Results

Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type.

Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA.In vivopull-down studies of the RNA polymerase complex indicated a promoting effect of 6S RNA on the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation.

Conclusions

This study reveals 6S RNA as an integral part of the cellular response ofSynechocystissp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by regulating the switch from group 2 σ factors SigB, SigC and SigE to SigA- dependent transcription.
Interacting Learning Processes during Skill Acquisition: Learning to control with gradually changing system dynamics
Authors: Ludolph Nicolas , Giese Martin A. , Ilg Winfried
Published: May 2017

There is increasing evidence that sensorimotor learning under real-life conditions relies on a composition of several learning processes. Nevertheless, most studies examine learning behaviour in relation to one specific learning mechanism. In this study, we examined the interaction between reward-based skill acquisition and motor adaptation to changes of object dynamics. Thirty healthy subjects, split into two groups, acquired the skill of balancing a pole on a cart in virtual reality. In one group, we gradually increased the gravity, making the task easier in the beginning and more difficult towards the end. In the second group, subjects had to acquire the skill on the maximum, most difficult gravity level. We hypothesized that the gradual increase in gravity during skill acquisition supports learning despite the necessary adjustments to changes in cart-pole dynamics. We found that the gradual group benefits from the slow increment, although overall improvement was interrupted by the changes in gravity and resulting system dynamics, which caused short-term degradations in performance and timing of actions. In conclusion, our results deliver evidence for an interaction of reward-based skill acquisition and motor adaptation processes, which indicates the importance of both processes for the development of optimized skill acquisition schedules.
Frequent non-allelic gene conversion on the human lineage and its effect on the divergence of gene duplicates
Authors: Harpak Arbel , Lan Xun , Gao Ziyue , Pritchard Jonathan K.
Published: May 2017

Gene conversion is the copying of genetic sequence from a “donor” region to an “acceptor”. In non-allelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well-characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC-bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250bp and a probability of 2.5×10−7per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.
Positive sexual imprinting for human eye color
Authors: DeBruine Lisa M. , Jones Benedict C. , Little Anthony C.
Published: May 2017

Human romantic partners tend to have similar physical traits1, but the mechanisms causing this homogamy are controversial. One potential explanation is direct matching to own characteristics2,3. Alternatively, studies showing similarity between parent and partner4,5 support positive sexual imprinting6,7, where individuals are more likely to choose mates with the physical characteristics of their other-sex parent. This interpretation has been strongly criticized because the same pattern could also be caused by sex-linked heritable preferences3, where similarity in appearance between an individual’s partner and their other-sex parent is caused by similarity in preferences between the individual and their same-sex parent. The relationships among own, parents’ and same-sex partner’s eye color provide an elegant test of these hypotheses, which each postulate a different best predictor of partner’s eye color. While the matching hypothesis predicts this will be own eye color, the sex-linked heritable preference hypothesis predicts this will be the other-sex parent’s eye color and the positive sexual imprinting hypothesis predicts this will be the partner-sex parent’s eye color. Here we show that partner eye color was best predicted by the partner-sex parent’s eye color. Our results provide clear evidence against matching and sex-linked heritable preference hypotheses, and support the positive sexual imprinting hypothesis of the relationship between own and partner’s eye color.
Insight into the mechanism of protein thermostability based on the residue interaction degrees
Authors: Ge Huihua , Chu Yunmeng , Zhang Guangya
Published: May 2017

Understanding the basis of protein thermostability raises a general question: which residue with specific interaction degrees is more important to the protein thermostability? A strictly selected dataset of 131 pairs of thermophilic (TPs) and mesophilic proteins (MPs) was constructed. There were 6.4% and 8.4% of the total residues in sequences did not interact with others in TPs and MPs. The amino acid contents in sequences are closest to those with the interaction degrees of 3 according to the Chi-squared distances. Only Glu, Gln and the amide residues showed significant differences in sequences, which was the same as identified at low residue interaction degrees. However, we observed significant Phe, Lys, Leu, Gln and the charged, aliphatic, aromatic, positive charged and small residues at high interaction degree. Among them, Phe was rarely reported previously although aromatic residues were well-known contributor to protein thermostability. Finally, we took aspartate transcarbamylases as an example to explain how a residue with various interaction degrees contributed differently to their thermostability. Our results clearly demonstrated the differences of amino acids in sequence between TPs and MPs could only represent those involved in low interaction degrees. Much more residues with significant differences existed at high interaction degrees even if they had few significant amino acids in sequences. The interaction degree-based method should be an alternative tool in extracting valuable eigenvalues for predicting proteins attributes in bioinformatics. It could also provide a new perspective for studying the thermostability of proteins and engineering novel thermostable proteins.

List of abbreviations

TPs

thermophilic proteins

MPs

mesophilic proteins

OGT

optimal growth temperature

ASA

absolute surface areas
Heat shock protein 70 (Hsp70) is involved in the Zika virus cellular infection process
Authors: Pujhari Sujit , Macias Vanessa M. , Nissly Ruth H. , Nomura Masashi , Kuchipudi Suresh V. , Rasgon Jason L.
Published: May 2017

Zika virus (ZIKV) is a historically neglected flavivirus that has recently caused epidemics in the western hemisphere. ZIKV has been associated with severe symptoms including infant microcephaly and Guillain Barré syndrome, stimulating interest in understanding factors governing ZIKV infection. Heat shock protein 70 (Hsp70) has been shown to be an infection factor for multiple viruses. We investigated the role of Hsp70 in the ZIKV infection process. We localized Hsp70 protein to the Vero cell membrane surface by confocal microscopy and demonstrated that, inside the cell, there is significant co-localization between Hsp70 and ZIKV E protein. Inducing and suppressing Hsp70 expression increased and decreased ZIKV production, respectively. Antibody blocking cell surface-localized Hsp70 decreased ZIKV cell infection rates and production of infectious virus particles, as did competition with recombinant Hsp70 protein. Our data suggest that Hsp70 is an important factor in the ZIKV infection process. Understanding the interactions between Hsp70 and ZIKV may lead to novel therapeutics for ZIKV infection, particularly for pregnant women and fetuses.
Arousal dependent modulation of thalamo-cortical functional interaction
Authors: Stitt Iain , Zhou Zhe Charles , Radtke-Schuller Susanne , Fröhlich Flavio
Published: May 2017

Summary paragraph

Cognition and behavior emerge from the dynamic interaction of widely distributed, but functionally specialized brain networks. However, it remains unclear how network-level interactions dynamically reorganize to support ever-shifting cognitive and behavioral demands. Here, we investigate how the interaction between posterior parietal cortex (PPC) and lateral posterior (LP) / Pulvinar is shaped by ongoing fluctuations in pupil-linked arousal, which is a non-invasive measure related to neuromodulatory tone in the brain. We found that fluctuations in pupil-linked arousal tracked the dynamic interaction between PPC and LP/Pulvinar characterized by changes in the direction and carrier frequency of oscillatory interaction. Active visual exploration by saccadic eye movements elicited similar transitions in thalamo-cortical interaction. These findings suggest a common network substrate of both spontaneous activity and active vision. Thus, neuromodulators may play a role in dynamically sculpting the patterns of thalamo-cortical functional interaction that underlie visual processing.
Ultra-accurate Genome Sequencing and Haplotyping of Single Human Cells
Authors: Chu Wai Keung , Edge Peter , Lee Ho Suk , Bansal Vikas , Bafna Vineet , Huang Xiaohua , Zhang Kun
Published: May 2017

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensivein vitroamplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (Single-Stranded Sequencing using micrOfluidic Reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10−8and average 500kb long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.
Coordinated Changes In The Accumulation Of Metal Ions In Maize (Zea mays ssp. mays L.) In Response To Inoculation With The Arbuscular Mycorrhizal FungusFunneliformis mosseae
Authors: Ramirez-Flores M. Rosario , Rellan-Alvarez Ruben , Wozniak Barbara , Gebreselassie Mesfin-Nigussie , Jakobsen Iver , Olalde-Portugal Victor , Baxter Ivan , Paszkowski Uta , Sawers Ruairidh J.H.
Published: May 2017

Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of nineteen elements was determined in the roots and leaves of a panel of thirty maize varieties, grown under phosphorus limiting conditions, with, or without, inoculation with the fungusFunneliformis mosseae.Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a coordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants.

Abbreviations

NC

non-colonized

M

mycorrhizal

SDW

shoot dry weight

ICP-MS

inductively coupled plasma mass spectrometry

PC

principal component