bluuebunny/crossref_metadata_2025 huggingface dataset:
Device Sales Representatives in the Operating Room: Do We Really Need or Want Them? A Survey of Orthopaedic Trauma Surgeons
Authors: Moed Berton R. , Israel Heidi A.
Published: May 2017

Introduction:

The purposes of this study were to determine the current attitude of orthopaedic trauma surgeons toward device sales representatives (DSRs), especially regarding their presence in the operating room (OR), and to establish the existence of any surgeon generational differences.

Methods:

A survey was created using a 5-point Likert response scale, related to conflict of interest (COI) and attitudes toward DSRs. Participants were solicited from the Orthopaedic Trauma Association database of 384 active members and 127 (33%) completed the survey. Respondents were divided into 2 subcategories (Generation X vs. Baby Boomers).

Results:

Overall, respondents viewed their DSRs favorably without any perception of COI. However, they perceived their peers as being at risk for COI (P ≤ 0.004). Generation X responders feel that DSRs should be in the OR for all cases, whereas Baby Boomers do not (P < 0.01).

Conclusions:

With one striking generational difference, most orthopaedic trauma surgeons feel that they need DSRs in the OR. Similar to other physician groups, they also feel that they are not subject to COI from salesman contact that affects their peers. Reasons for this perceived need and any related COI risk, and the opportunities to address both, require further study.
Challenging Authority During an Emergency—the Effect of a Teaching Intervention
Authors: Friedman Zeev , Perelman Vsovolod , McLuckie Duncan , Andrews Meghan , Noble Laura M. K. , Malavade Archana , Bould M. Dylan
Published: May 2017

Objectives:

Previous research has shown that residents were unable to effectively challenge a superior’s wrong decision during a crisis situation, a problem that can contribute to preventable mortality. We aimed to assess whether a teaching intervention enabled residents to effectively challenge clearly wrong clinical decisions made by their staff.

Subjects and Intervention:

Following ethics board approval, second year residents were randomized to a teaching intervention targeting cognitive skills needed to challenge a superior’s decision, or a control group receiving general crisis management instruction. Two weeks later, subjects participated in a simulated crisis that presented them with opportunities to challenge clearly wrong decisions in a can’t-intubate-can’t-ventilate scenario. It was only disclosed that the staff was a confederate during the debriefing. Performances were video recorded and assessed by two raters blinded to group allocation using the modified Advocacy-Inquiry Score.

Measurements and Main Results:

Fifty residents completed the study. The interrater reliability of the modified Advocacy-Inquiry Scores (intraclass correlation coefficient = 0.87) was excellent. The median (interquartile range) best modified Advocacy-Inquiry Score was significantly better in the intervention group 5.0 (4.50–5.62 [4–6]) than in the control group 3.5 (3.0–4.75 [3–6]) (p < 0.001).

Conclusions:

A short targeted teaching intervention was effective in significantly improving residents’ ability to challenge a wrong decision by a superior. This suggests that residents are not given the proper tools to challenge authority during a life-threatening crisis situation. This educational gap can have significant implications for patients’ safety.
Does Admission to the ICU Prevent African American Disparities in Withdrawal of Life-Sustaining Treatment?
Authors: Chertoff Jason , Olson Angela , Alnuaimat Hassan
Published: May 2017

Objective:

We sought to determine whether black patients admitted to an ICU were less likely than white patients to withdraw life-sustaining treatments.

Design:

We performed a retrospective cohort study of hospital discharges from October 20, 2015, to October 19, 2016, for inpatients 18 years old or older and recorded those patients, along with their respective races, who had an “Adult Comfort Care” order set placed prior to discharge. A two-sample test for equality of two proportions with continuity correction was performed to compare the proportions between blacks and whites.

Setting:

University of Florida Health.

Patients:

The study cohort included 29,590 inpatient discharges, with 21,212 Caucasians (71.69%), 5,825 African Americans (19.69%), and 2,546 non-Caucasians/non–African Americans (8.62%).

Interventions:

Withdrawal of life-sustaining treatments.

Measurements and Main Results:

Of the total discharges (n = 29,590), 525 (1.77%) had the Adult Comfort Care order set placed. Seventy-eight of 5,825 African American patients (1.34%) had the Adult Comfort Care order set placed, whereas 413 of 21,212 Caucasian patients (1.95%) had this order set placed (p = 0.00251; 95% CI, 0.00248–0.00968). Of the 29,590 patients evaluated, 6,324 patients (21.37%) spent at least one night in an ICU. Of these 6,324 patients, 4,821 (76.24%) were white and 1,056 (16.70%) were black. Three hundred fifty of 6,324 (5.53%) were discharged with an Adult Comfort Care order set. Two hundred seventy-one White patients (5.62%) with one night in an ICU were discharged with an Adult Comfort Care order set, whereas 54 Black patients (5.11%) with one night in an ICU had the order set (p = 0.516).

Conclusions:

This study suggests that Black patients may be less likely to withdraw life-supportive measures than whites, but that this disparity may be absent in patients who spend time in the ICU during their hospitalization.
OPTICAL COHERENCE TOMOGRAPHY BASELINE PREDICTORS FOR INITIAL BEST-CORRECTED VISUAL ACUITY RESPONSE TO INTRAVITREAL ANTI-VASCULAR ENDOTHELIAL GROWTH FACTOR TREATMENT IN EYES WITH DIABETIC MACULAR EDEMA
Authors: Santos Ana R. , Costa Miguel Â. , Schwartz Christian , Alves Dalila , Figueira João , Silva Rufino , Cunha-Vaz Jose G.
Published: May 2017

Purpose:

To identify baseline optical coherence tomography morphologic characteristics predicting the visual response to anti-vascular endothelial growth factor therapy in diabetic macular edema.

Methods:

Sixty-seven patients with diabetic macular edema completed a prospective, observational study (NCT01947881-CHARTRES). All patients received monthly intravitreal injections of Lucentis for 3 months followed by PRN treatment and underwent best-corrected visual acuity measurements and spectral domain optical coherence tomography at Baseline, Months 1, 2, 3, and 6. Visual treatment response was characterized as good (≥10 letters), moderate (5–10 letters), and poor (<5 or letters loss). Spectral domain optical coherence tomography images were graded before and after treatment by a certified Reading Center.

Results:

One month after loading dose, 26 patients (38.80%) were identified as good responders, 19 (28.35%) as Moderate and 22 (32.83%) as poor responders. There were no significant best-corrected visual acuity and central retinal thickness differences at baseline (P = 0.176; P = 0.573, respectively). Ellipsoid zone disruption and disorganization of retinal inner layers were good predictors for treatment response, representing a significant risk for poor visual recovery to anti-vascular endothelial growth factor therapy (odds ratio = 10.96; P < 0.001 for ellipsoid zone disruption and odds ratio = 7.05; P = 0.034 for disorganization of retinal inner layers).

Conclusion:

Damage of ellipsoid zone, higher values of disorganization of retinal inner layers, and central retinal thickness decrease are good predictors of best-corrected visual acuity response to anti-vascular endothelial growth factor therapy.
Genetic predictors of recovery in low back and lumbar radicular pain
Authors: Bjorland Siri , Røe Cecilie , Moen Aurora , Schistad Elina , Mahmood Aqsa , Gjerstad Johannes
Published: May 2017

Previous data suggest that persistent back pain may be associated with genetic variability. In this study, we assessed the correlation between 8 genetic polymorphisms (VDR, COL11, MMP1, MMP9, IL-1α, IL-1RN, OPRM1, COMT) and pain recovery in patients with low back pain (LBP) and lumbar radicular pain (LRP). In total, 296 patients with LBP or LRP were followed for 5 years. The patients underwent standardized clinical examination and completed pain and function questionnaires. Univariate linear regression associations with P values <0.1 were included in the multivariable analysis, adjusting for pain intensity at baseline, age, sex, smoking, body mass index, and LBP or LRP. Pain intensity at 5-year follow-up was associated with VDR rs731236 (B = −0.5, 95% confidence interval [CI] −0.9 to −0.1, P = 0.017), MMP9 rs17576 (B = 0.5, 95% CI 0.1-0.9, P = 0.022), and OPRM1 rs1799971 (B = −0.8, 95% CI −1.4 to −0.2, P = 0.006) in the univariate analyses. MMP9 rs17576 and OPRM1 rs1799971 remained significant (B = 0.4, 95% CI 0.05-0.8, P = 0.026 and B = −0.8, 95% CI −1.3 to −0.2, P = 0.007) in the multivariable model. Thus, the data demonstrated that the rare allele of MMP9 rs17576 was associated with poor pain recovery, whereas the rare allele of OPRM1 rs1799971 was associated with better pain recovery at 5-year follow-up in the LBP and LRP patients. In particular, the present study suggested that the OPRM1 rs179971 A>G in men was associated with better long-term pain recovery. In men, the OPRM1 rs1799971 explained 4.7% of the variance of pain intensity. We conclude that the MMP9 rs17576 and OPRM1 rs1799971 genotypes may affect 5-year recovery in patients with LBP and LRP.
Coexistence of Colorectal Adenomas and Coronary Calcification in Asymptomatic Men and Women
Authors: Yun Kyung Eun , Chang Yoosoo , Rampal Sanjay , Zhang Yiyi , Cho Juhee , Jung Hyun-Suk , Kim Chan-Won , Jeong Chul , Cainzos-Achirica Miguel , Zhao Di , Pastor-Barriuso Roberto , Shin Hocheol , Guallar Eliseo , Ryu Seungho
Published: May 2017

Goals:

Because of shared risk factors between clinically manifest cardiovascular disease and colorectal cancer, we hypothesized the coexistence of subclinical atherosclerosis measured by coronary artery calcium (CAC) and colorectal adenoma (CRA) and that these 2 processes would also share common risk factors.

Background:

No study has directly compared the risk factors associated with subclinical coronary atherosclerosis and CRA.

Study:

This was a cross-sectional study using multinomial logistic regression analysis of 4859 adults who participated in a health screening examination (2010 to 2011; analysis 2014 to 2015). CAC scores were categorized as 0, 1 to 100, or >100. Colonoscopy results were categorized as absent, low-risk, or high-risk CRA.

Results:

The prevalence of CAC>0, CAC 1 to 100 and >100 was 13.0%, 11.0%, and 2.0%, respectively. The prevalence of any CRA, low-risk CRA, and high-risk CRA was 15.1%, 13.0%, and 2.1%, respectively. The adjusted odds ratios (95% confidence interval) for CAC>0 comparing participants with low-risk and high-risk CRA with those without any CRA were 1.35 (1.06-1.71) and 2.09 (1.29-3.39), respectively. Similarly, the adjusted odds ratios (95% confidence interval) for any CRA comparing participants with CAC 1 to 100 and CAC>100 with those with no CAC were 1.26 (1.00-1.6) and 2.07 (1.31-3.26), respectively. Age, smoking, diabetes, and family history of CRC were significantly associated with both conditions.

Conclusions:

We observed a graded association between CAC and CRA in apparently healthy individuals. The coexistence of both conditions further emphasizes the need for more evidence of comprehensive approaches to screening and the need to consider the impact of the high risk of coexisting disease in individuals with CAC or CRA, instead of piecemeal approaches restricted to the detection of each disease independently.
Literature review: impacts of socioeconomic status on the risk of inflammatory bowel disease and its outcomes
Authors: Wardle Richard A. , Wardle Andrew J. , Charadva Creana , Ghosh Subrata , Moran Gordon W.
Published: May 2017

The relationship between socioeconomic status (SES) and inflammatory bowel disease (IBD) is controversial. To date, research has focused on effects on incidence and prevalence, disease management and clinical outcomes; however, conclusions remain uncertain. This review examines current evidence, identifies what remains to be understood and explores the practical implications this has for today. A structured literature search in Ovid, Medline, the Cochrane library, Google Scholar and clinicaltrials.gov was performed using defined key words, including all articles up until 5 October 2016 assessing SES as a primary or secondary outcome measure. Twenty-one studies were identified, investigating incidence and prevalence (n=13), disease outcomes (n=5) and mortality (n=3). Data linking SES with IBD incidence are conflicting, with studies citing both positive and negative trends. Patients with low SES, particularly those with Crohn’s disease, show higher rates of hospitalization, service usage and IBD-associated mortality. On the basis of the available study data, it is difficult to relate SES with the risk of IBD. For Crohn’s disease, in particular, the link between deprivation and increased hospitalization and mortality observed from world-wide studies is alarming. It seems most likely that the cause links to well-documented behavioural, materialistic, psychosocial and life-course models used to explain social class inequalities in other diseases.
Early detection of sporadic pancreatic cancer: time for change
Authors: Frič Přemysl , Šedo Aleksi , Škrha Jan , Bušek Petr , Laclav Martin , Škrha Pavel , Zavoral Miroslav
Published: May 2017

Sporadic pancreatic cancer amounts to ∼90% of all pancreatic cancers. It is a gloomy depressive disease and the most recalcitrant malignancy, with a very low 5-year survival (3–6%). At present, diagnostic methods are commonly applied, as used half a century ago, after the appearance of local and systemic symptoms (abdominal and back pain, cholestasis, painless jaundice, fatigue, anorexia, weight loss, anemia, peripheral phlebitis, and cachexia). Unfortunately, these symptoms are harbingers of an advanced disease. The subsequent imaging methods may offer additional information on the location, size, and morphology of the lesion, but they do not influence the prognosis. Radical surgery may be offered to 15–20% of patients. The relapses after surgery are frequent and chemotherapy may be palliative. Preventive programs represent the only possibility of improvement. We propose the first multistep and multidisciplinary preventive program for early detection of sporadic pancreatic cancer for the differential identification of average-risk patients who probably have the disease from those who do not.
Age and Sex Normalization of Intestinal Permeability Measures for the Improved Assessment of Enteropathy in Infancy and Early Childhood
Authors: Kosek Margaret N. , Lee Gwenyth O. , Guerrant Richard L. , Haque Rashidul , Kang Gagandeep , Ahmed Tahmeed , Bessong Pascal , Ali Asad , Mduma Estomih , Peñataro Yori Pablo , Faubion William A. , Lima Aldo A.M. , Paredes Olortegui Maribel , Mason Carl , Babji Sudhir , Singh Ravinder , Qureshi Shahida , Kosek Peter S. , Samie Amidou , Pascal John , Shrestha Sanjaya , McCormick Benjamin J.J. , Seidman Jessica C. , Lang Dennis R. , Zaidi Anita , Caulfield Laura E. , Gottlieb Michael ,   MAL‐ED Network
Published: May 2017

Objectives:

The aim of the study was to describe changes in intestinal permeability in early childhood in diverse epidemiologic settings.

Methods:

In a birth cohort study, the lactulose:mannitol (L:M) test was administered to 1980 children at 4 time points in the first 24 months of life in 8 countries. Data from the Brazil site with an incidence of diarrhea similar to that seen in the United States and no growth faltering was used as an internal study reference to derive age‐ and sex‐specific z scores for mannitol and lactulose recoveries and the L:M ratio.

Results:

A total of 6602 tests demonstrated mannitol recovery, lactulose recovery, and the L:M ratio were associated with country, sex, and age. There was heterogeneity in the recovery of both probes between sites with mean mannitol recovery ranging for 1.34% to 5.88%, lactulose recovery of 0.19% to 0.58%, and L:M ratios 0.10 to 0.17 in boys of 3 months of age across different sites. We observed strong sex‐specific differences in both mannitol and lactulose recovery, with boys having higher recovery of both probes. Alterations in intestinal barrier function increased in most sites from 3 to 9 months of age and plateaued or diminished from 9 to 15 months of age.

Conclusions:

Alterations in recovery of the probes differ markedly in different epidemiologic contexts in children living in the developing world. The rate of change in the L:M‐z ratio was most rapid and consistently disparate from the reference standard in the period between 6 and 9 months of age, suggesting that this is a critical period of physiologic impact of enteropathy in these populations.
Using the Rothman Index and Length of Stay as a Trigger for Palliative Care in the Medical Intensive Care Unit and Step-Down Units
Authors: Henderson Rebecca Gagne , McCloskey Barbara , Walter Ellen , Rimar Joan , Bai Mei , Moritz Ernest D.
Published: May 2017

Despite the increased number of palliative care teams in the United States, access to palliative care in the hospital continues to be inadequate. The availability of a simple method to identify appropriate patients for palliative care may increase access. A pilot study was conducted using an observational prospective approach to analyze the effects of palliative interventions for those with a Rothman Index score of less than 40 and a length of stay of greater than 5 days for patients in the medical intensive care and step-down units in an urban teaching hospital, which provides tertiary palliative care. The Rothman Index is a validated formula providing a real-time measure of patient condition based on existing data in the electronic medical record. Patients receiving the palliative intervention had a decrease in the mean length of stay from 26.3 days for all other groups to 13.9 days. The odds ratio of a 30-day readmission for those patients without a palliative visit was 4.4. Costs were lowered by 54% for the palliative intervention group. The Rothman/length of stay trigger for palliative care intervention may have the potential to bend the cost curve for the health care system.
Simulation: A Tool to Assist Nursing Professional Development Practitioners to Help Nurses to Better Recognize Early Signs of Clinical Deterioration of Patients
Authors: Elder Loretta
Published: May 2017

The need to enhance the knowledge and skills of nurses caring for patients exhibiting signs of clinical deterioration has been documented. The literature has further supported the registered nurse as the key individual expected to recognize signs of clinical deterioration in the patient. The use of simulation as an effective teaching strategy has been well documented. The purpose of this project was to use simulation as an educational intervention to increase nurse knowledge, self-confidence, and competency when caring for patients exhibiting signs of clinical deterioration. A significant improvement in nurse knowledge and self-confidence was shown after a simulation-based educational intervention. Competency evaluation during the simulation-based intervention provided information to help nurses when caring for deteriorating patients. Nursing professional development practitioners can use the information from this project in planning educational interventions for staff nurses.
Promoting the Utilization of Science in Healthcare (PUSH) Project
Authors: Cline Genieveve J. , Burger Kristina J. , Amankwah Ernest K. , Goldenberg Neil A. , Ghazarian Sharon R.
Published: May 2017

The purpose of this descriptive study was to identify the perceived barriers and facilitators to research utilization and evidence-based practice among nurses employed in a tertiary care children's hospital. Results revealed seven facilitator and six barrier themes that contribute to the understanding of the problem. The themes can be utilized by nursing professional development specialists to customize organizational infrastructure and educational programs.
Low-Energy Virtual Monochromatic Dual-Energy Computed Tomography Images for the Evaluation of Head and Neck Squamous Cell Carcinoma: A Study of Tumor Visibility Compared With Single-Energy Computed Tomography and User Acceptance
Authors: Forghani Reza , Kelly Hillary , Yu Eugene , Belair Manon , Létourneau-Guillon Laurent , Le Huy , Proulx Francesca , Ong Thomas , Tan Xianming , Curtin Hugh D. , Levental Mark
Published: May 2017

Objective

Dual-energy computed tomography (CT) 40-keV virtual monochromatic images (VMIs) have been reported to improve visualization of head and neck squamous cell carcinoma, but a direct comparison to single-energy CT (SECT) is lacking, and there is debate regarding subjective user preference. We compared 40-keV VMIs with SECT and performed a subjective evaluation of their utility and acceptability for clinical use.

Methods

A total of 60 dual-energy CT and 60 SECT scans from 2 different institutions were evaluated. Tumor conspicuity was evaluated objectively using absolute and relative attenuation and subjectively by 3 head and neck specialists and 3 general radiologists.

Results

Tumors had significantly higher absolute and relative attenuation on 40-keV VMIs (P< 0.0001). Subjectively, the 40-keV VMIs improved visualization, with substantial (κ, 0.61–0.80) to almost perfect (κ, 0.81–1) interrater agreements.

Conclusions

The 40-keV VMIs improve tumor visibility objectively and subjectively both by head and neck specialists and general radiologists.
Reoxygenation with 100% Oxygen Following Hypoxia in Mice Causes Apoptosis
Authors: Nishimura Yoshiro , Ueki Masaaki , Imanishi Masaki , Tomita Shuhei , Ueno Masaki , Morishita Jun , Nishiyama Takashi
Published: May 2017

After hypoxia, reoxygenation with air is the consensus treatment for full-term neonates; however, the effect of hyperoxic reoxygenation of adults is unknown. The present study was designed to investigate the effects of reoxygenation with 100% oxygen after hypoxia on inflammation and apoptosis in mice. Eight-week-old mice were either subjected to hypoxia in 8% oxygen for 30 min or air served as controls. Following hypoxia, mice underwent reoxygenation for 30 min with 21% or 100% oxygen. Tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), caspase-3 and brain derived neurotrophic factor (BDNF) mRNA study and histopathological study were performed. Reoxygenation with 100% oxygen significantly increased TNF-α (2.5 h after hypoxia), IL-1β (5 h after hypoxia), caspase-3 (8 h after hypoxia) mRNA levels in the whole brain compared with 21% oxygen, and significantly decreased erythropoietin mRNA expression compared with 21% oxygen 9 h after reoxygenation. However, reoxygenation with 100% oxygen and 21% oxygen significantly decreased BDNF mRNA levels compared with control air group. There were no clear abnormal findings showing neuronal death among the three groups. Reoxygenation with 100% oxygen after hypoxia induced inflammation and apoptosis in adult mice. Therefore, these results suggest that the reoxygenation with 100% oxygen after hypoxia has harmful effects on adult brain as well as on neonatal brain.
Pharmacological Stimulation of Neuronal Plasticity in Acquired Brain Injury
Authors: Carrillo-Mora Paul , Alcantar-Shramm Juan Manuel , Almaguer-Benavides Kievka M. , Macías-Gallardo Julio José , Fuentes-Bello Alim , Rodríguez-Barragán Marlene A.
Published: May 2017

Introduction

Brain injuries are one of the leading causes of disability worldwide. It is estimated that nearly half of patients who develop severe sequelae will continue with a chronic severe disability despite having received an appropriate rehabilitation program. For more than 3 decades, there has been a worldwide effort to investigate the possibility of pharmacologically stimulating the neuroplasticity process for enhancing the recovery of these patients.

Objective

The objective of this article is to make a critical and updated review of the available evidence that supports the positive effect of different drugs on the recovery from brain injury.

Method

To date, there have been several clinical trials that tested different drugs that act on different neurotransmitter systems: catecholaminergic, cholinergic, serotonergic, and glutamatergic. There is both basic and clinical evidence that may support some positive effect of these drugs on motor, cognitive, and language skills; however, only few of the available studies are of sufficient methodological quality (placebo controlled, randomized, blinded, multicenter, etc) to make solid conclusions about their beneficial effects.

Conclusions

Currently, the pharmacological stimulation of neuroplasticity still does not have enough scientific evidence to make a systematic therapeutic recommendation for all patients, but it certainly is a feasible and very promising field for future research.
Elementary exact calculations of degree growth and entropy for discrete equations
Authors: Halburd R. G.
Published: May 2017

Second-order discrete equations are studied over the field of rational functions

C

(
z
)

, where
z
is a variable not appearing in the equation. The exact degree of each iterate as a function of
z
can be calculated easily using the standard calculations that arise in singularity confinement analysis, even when the singularities are not confined. This produces elementary yet rigorous entropy calculations.
Biological imaging using light-addressable potentiometric sensors and scanning photo-induced impedance microscopy
Authors: Wu Fan , Campos Inmaculada , Zhang De-Wen , Krause Steffi
Published: May 2017

Light-addressable potentiometric sensors (LAPS) and scanning photo-induced impedance microscopy (SPIM) use photocurrent measurements at electrolyte–insulator–semiconductor substrates for spatio-temporal imaging of electrical potentials and impedance. The techniques have been used for the interrogation of sensor arrays and the imaging of biological systems. Sensor applications range from the detection of different types of ions and the label-free detection of charged molecules such as DNA and proteins to enzyme-based biosensors. Imaging applications include the temporal imaging of extracellular potentials and dynamic concentration changes in microfluidic channels and the lateral imaging of cell surface charges and cell metabolism. This paper will investigate the current state of the art of the measurement technology with a focus on spatial and temporal resolution and review the biological applications, these techniques have been used for. An outlook on future developments in the field will be given.
Are flowers vulnerable to xylem cavitation during drought?
Authors: Zhang Feng-Ping , Brodribb Timothy J.
Published: May 2017

Water stress is known to cause xylem cavitation in the leaves, roots and stems of plants, but little is known about the vulnerability of flowers to xylem damage during drought. This is an important gap in our understanding of how and when plants become damaged by water stress. Here we address fundamental questions about if and when flowers suffer cavitation damage, using a new technique of cavitation imaging to resolve the timing of cavitation in water-stressed flower petals compared with neighbouring leaves. Leaves and flowers from a sample of two herbaceous and two woody eudicots were exposed to a severe water stress while the spatial and temporal propagation of embolism through veins was recorded. Although in most cases water potentials inducing 50% embolism of herbaceous flower veins were more negative than neighbouring leaves, there was no significant difference between the average vulnerability of leaves and petals of herbaceous species. In both woody species, petals were more vulnerable to cavitation than leaves, in one case by more than 3 MPa. Early cavitation and subsequent damage of flowers in the two woody species would thus be expected to precede leaf damage during drought. Similar cavitation thresholds of flowers and leaves in the herb sample suggest that cavitation during water shortage in these species will occur simultaneously among aerial tissues. Species-specific differences in the cavitation thresholds of petals provide a new axis of variation that may explain contrasting flowering ecology among plant species.
Sex chromosome evolution: historical insights and future perspectives
Authors: Abbott Jessica K. , Nordén Anna K. , Hansson Bengt
Published: May 2017

Many separate-sexed organisms have sex chromosomes controlling sex determination. Sex chromosomes often have reduced recombination, specialized (frequently sex-specific) gene content, dosage compensation and heteromorphic size. Research on sex determination and sex chromosome evolution has increased over the past decade and is today a very active field. However, some areas within the field have not received as much attention as others. We therefore believe that a historic overview of key findings and empirical discoveries will put current thinking into context and help us better understand where to go next. Here, we present a timeline of important conceptual and analytical models, as well as empirical studies that have advanced the field and changed our understanding of the evolution of sex chromosomes. Finally, we highlight gaps in our knowledge so far and propose some specific areas within the field that we recommend a greater focus on in the future, including the role of ecology in sex chromosome evolution and new multilocus models of sex chromosome divergence.
Fathers matter: male body mass affects life-history traits in a size-dimorphic seabird
Authors: Cornioley Tina , Jenouvrier Stéphanie , Börger Luca , Weimerskirch Henri , Ozgul Arpat
Published: May 2017

One of the predicted consequences of climate change is a shift in body mass distributions within animal populations. Yet body mass, an important component of the physiological state of an organism, can affect key life-history traits and consequently population dynamics. Over the past decades, the wandering albatross—a pelagic seabird providing bi-parental care with marked sexual size dimorphism—has exhibited an increase in average body mass and breeding success in parallel with experiencing increasing wind speeds. To assess the impact of these changes, we examined how body mass affects five key life-history traits at the individual level: adult survival, breeding probability, breeding success, chick mass and juvenile survival. We found that male mass impacted all traits examined except breeding probability, whereas female mass affected none. Adult male survival increased with increasing mass. Increasing adult male mass increased breeding success and mass of sons but not of daughters. Juvenile male survival increased with their chick mass. These results suggest that a higher investment in sons by fathers can increase their inclusive fitness, which is not the case for daughters. Our study highlights sex-specific differences in the effect of body mass on the life history of a monogamous species with bi-parental care.
A unified internal model theory to resolve the paradox of active versus passive self-motion sensation
Authors: Laurens Jean , Angelaki Dora
Published: May 2017

Brainstem and cerebellar neurons implement an internal model to accurately estimate self-motion during externally-generated (‘passive’) movements. However, these neurons show reduced responses during self-generated (‘active’) movements, indicating that the brain computes the predicted sensory consequences of motor commands in order to cancel sensory signals. Remarkably, the computational processes underlying sensory prediction during active motion and their relationship to internal model computations established during passive movements remain unknown. Here we construct a Kalman filter that incorporates motor commands into a previously-established model of optimal passive self-motion estimation. We find that the simulated sensory error and feedback signals match experimentally measured neuronal response during active and passive head and trunk rotations and translations. We conclude that a single internal model of head motion can process motor commands and sensory afferent signals optimally, and we describe how previously identified neural responses in the brainstem and cerebellum may represent distinct nodes in these computations.
Metagenomic binning through low density hashing
Authors: Luo Yunan , William Yu Y. , Zeng Jianyang , Berger Bonnie , Peng Jian
Published: May 2017

Bacterial microbiomes of incredible complexity are found throughout the world, from exotic marine locations to the soil in our yards to within our very guts. With recent advances in Next-Generation Sequencing (NGS) technologies, we have vastly greater quantities of microbial genome data, but the nature of environmental samples is such that DNA from different species are mixed together. Here, we present Opal for metagenomic binning, the task of identifying the origin species of DNA sequencing reads. Our Opal method introduces low-density, even-coverage hashing to bioinformatics applications, enabling quick and accurate metagenomic binning. Our tool is up to two orders of magnitude faster than leading alignment-based methods at similar or improved accuracy, allowing computational tractability on large metagenomic datasets. Moreover, on public benchmarks, Opal is substantially more accurate than both alignment-based and alignment-free methods (e.g. on SimHC20.500, Opal achieves 95% F1-score while Kraken and CLARK achieve just 91% and 88%, respectively); this improvement is likely due to the fact that the latter methods cannot handle computationally-costly long-range dependencies, which our even-coverage, low-density fingerprints resolve. Notably, capturing these long-range dependencies drastically improves Opal’s ability to detect unknown species that share a genus or phylum with known bacteria. Additionally, the family of hash functions Opal uses can be generalized to other sequence analysis tasks that rely on k-mer based methods to encode long-range dependencies.
NMDA receptor blockade causes selective prefrontal disinhibition in a roving auditory oddball paradigm
Authors: Rosch Richard E , Auksztulewicz Ryszard , Leung Pui Duen , Friston Karl J , Baldeweg Torsten
Published: May 2017

N-methyl-D-aspartate receptors (NMDARs) are expressed widely throughout the human cortex. Yet disturbances in NMDAR transmission - as implicated in patients with schizophrenia or pharmacologically induced - can cause a regionally specific set of electrophysiological effects. Here, we present a double-blind placebo-controlled study of the effects of the NMDAR blocker ketamine in human volunteers. We employ a marker of auditory learning and putative synaptic plasticity - the mismatch negativity - in a roving auditory oddball paradigm. Using recent advances in Bayesian modelling of group effects in dynamic causal modelling, we fit biophysically plausible network models of the auditory processing hierarchy to whole-scalp evoked response potential recordings. This allowed us to identify the regionally specific effects of ketamine in a distributed network of interacting cortical sources. Under placebo, our analysis replicated previous findings regarding the effects of stimulus repetition and deviance on connectivity within the auditory hierarchy. Crucially, we show that the effect of ketamine is best explained as a selective change in intrinsic inhibition, with a pronounced ketamine-induced reduction of inhibitory interneuron connectivity in frontal sources. These results are consistent with findings from invasive recordings in animal models exposed to NMDAR blockers, and provide evidence that inhibitory-interneuron specific NMDAR dysfunction may be sufficient to explain electrophysiological abnormalities of sensory learning induced by ketamine in human subjects.
Deep Sequencing: Intra-terrestrial metagenomics illustrates the potential of off-grid Nanopore DNA sequencing
Authors: Edwards Arwyn , Soares André , Rassner Sara M.E. , Green Paul , Félix João , Mitchell Andrew C.
Published: May 2017

Genetic and genomic analysis of nucleic acids from environmental samples has helped transform our perception of the Earth’s subsurface as a major reservoir of microbial novelty. Many of the microbial taxa living in the subsurface are under-represented in culture-dependent investigations. In this regard, metagenomic analyses of subsurface environments exemplify both the utility of metagenomics and its power to explore microbial life in some of the most extreme and inaccessible environments on Earth. Hitherto, the transfer of microbial samples to home laboratories for DNA sequencing and bioinformatics is the standard operating procedure for exploring microbial diversity. This approach incurs logistical challenges and delays the characterization of microbial biodiversity. For selected applications, increased portability and agility in metagenomic analysis is therefore desirable. Here, we describe the implementation of sample extraction, metagenomic library preparation, nanopore DNA sequencing and taxonomic classification using a portable, battery-powered, suite of off-the-shelf tools (the “MetageNomad”) to sequence ochreous sediment microbiota while within the South Wales Coalfield. While our analyses were frustrated by short read lengths and a limited yield of DNA, within the assignable reads, Proteobacterial (α-, β-, γ-Proteobacteria) taxa dominated, followed by members ofActinobacteria, FirmicutesandBacteroidetes, all of which have previously been identified in coals. Further to this, the fungal genusCandidawas detected, as well as a methanogenic archaeal taxon. To the best of our knowledge, this application of the MetageNomad represents an initial effort to conduct metagenomics within the subsurface, and stimulates further developments to take metagenomics off the beaten track.
Identification of hair shaft progenitors that create a niche for hair pigmentation
Authors: Liao Chung-Ping , Booker Reid C. , Morrison Sean J. , Le Lu Q.
Published: May 2017

Hair differentiates from follicle stem cells through progenitor cells in the matrix. In contrast to stem cells in the bulge, the identities of the progenitors and the mechanisms by which they regulate hair shaft components are poorly understood. Hair is also pigmented by melanocytes in the follicle. However, the niche that regulates follicular melanocytes is not well characterized. Here, we report the identification of hair shaft progenitors in the matrix that are differentiated from follicular epithelial cells expressing transcription factor KROX20. Depletion of Krox20 lineage cells results in arrest of hair growth, confirming the critical role of KROX20+ cells as antecedents of structural cells found in hair. Expression of stem cell factor (SCF) by these cells is necessary for the maintenance of differentiated melanocytes and for hair pigmentation. Our findings reveal the identities of hair matrix progenitors that regulate hair growth and pigmentation, partly by creating an SCF-dependent niche for follicular melanocytes.
IMAGE cDNA Clones, UniGene Clustering, and ACeDB: An Integrated Resource for Expressed Sequence Information
Authors: Miller Greg , Fuchs Rainer , Lai Eric
Published: May 2017

In this study we describe a new information resource that provides integrated access to information on IMAGE (integrated molecular analysis of genomes and their expression) cDNA library clones and derived expressed sequence tags (ESTs). We have developed an automated procedure that collates data from various public sources into a single ACeDB database. This database is a valuable tool for electronic cloning experiments and gene expression studies. It allows researchers to find information about cDNA libraries, plate addresses, insert sizes, and sequence data for IMAGE clones, the assignment of ESTs to UniGene clusters, and the chromosomal location of those genes in an efficient, graphically oriented manner.
Interpreting a Sequenced Genome: Toward a Cosmid Transgenic Library ofCaenorhabditis elegans
Authors: Janke Diana L. , Schein Jacqueline E. , Ha Thê , Franz Norman W. , O’Neil Nigel J. , Vatcher Greg P. , Stewart Helen I. , Kuervers Lynnette M. , Baillie David L. , Rose Ann M.
Published: May 2017

We have generated a library of transgenic Caenorhabditis elegans strains that carry sequenced cosmids from the genome of the nematode. Each strain carries an extrachromosomal array containing a single cosmid, sequenced by the C. elegans Genome Sequencing Consortium, and a dominate Rol-6 marker. More than 500 transgenic strains representing 250 cosmids have been constructed. Collectively, these strains contain approximately 8 Mb of sequence data, or ∼8% of the C. elegans genome. The transgenic strains are being used to rescue mutant phenotypes, resulting in a high-resolution map alignment of the genetic, physical, and DNA sequence maps of the nematode. We have chosen the region of chromosome III deleted bysDf127 and not covered by the duplicationsDp8(III;I) as a starting point for a systematic correlation of mutant phenotypes with nucleotide sequence. In this defined region, we have identified 10 new essential genes whose mutant phenotypes range from developmental arrest at early larva, to maternal effect lethal. To date, 8 of these 10 essential genes have been rescued. In this region, these rescues represent ∼10% of the genes predicted by GENEFINDER and considerably enhance the map alignment. Furthermore, this alignment facilitates future efforts to physically position and clone other genes in the region.

[Updated information about the Transgenic Library is available via the Internet at http://darwin.mbb.sfu.ca/imbb/dbaillie/cosmid.html.]
Detection of Numerous Y Chromosome Biallelic Polymorphisms by Denaturing High-Performance Liquid Chromatography
Authors: Underhill Peter A. , Jin Li , Lin Alice A. , Mehdi S. Qasim , Jenkins Trefor , Vollrath Douglas , Davis Ronald W. , Cavalli-Sforza L. Luca , Oefner Peter J.
Published: May 2017

Y chromosome haplotypes are particularly useful in deciphering human evolutionary history because they accentuate the effects of drift, migration, and range expansion. Significant acceleration of Y biallelic marker discovery and subsequent typing involving heteroduplex detection has been achieved by implementing an innovative and cost-efficient method called denaturing high-performance liquid chromatography (DHPLC). The power of the method resides in its sensitivity and ability to rapidly compare amplified sequences in an automated manner. We have determined the allelic states of 22 Y polymorphisms; 19 of which are unreported, in 718 diverse extant chromosomes; established haplotype frequencies; and deduced a phylogeny. All major geographic regions, including Eurasia, are characterized by mutations reflecting episodes of genetic drift and expansion. Most biallelic markers are localized regionally. However, some show wider dispersal and designate older, core haplotypes. One transversion defines a major haplogroup that distinguishes a previously unknown deep, apparently non-African branch. It provides evidence of an ancient bottleneck event. It is now possible to anticipate the inevitable detailed reconstruction of human Y chromosome genealogy based on several tens to even hundreds of these important polymorphisms.
Genome Mapping by Fluorescent Fingerprinting
Authors: Gregory Simon G. , Howell Gareth R. , Bentley David R.
Published: May 2017

The construction of sequence-ready maps of overlapping genomic clones is central to large-scale genome sequencing. We have implemented a method for fluorescent fingerprinting of bacterial clones to assemble contig maps. The method utilizes three spectrally distinct fluorescently tagged dideoxy ATPs to specifically label theHindIII termini in HindIII and Sau3AI restriction digests of clones that are multiplexed prior to electrophoresis and data collection. There is excellent reproducibility of raw data, improved resolution of large fragments, and concordance between the results obtained using this and the equivalent radioactive protocol. This method also allows detection of smaller overlaps between clones when compared to the analysis of restriction digests on nondenaturing agarose gels.
A Linkage Map of the Rat Genome Derived from Three F2 Crosses
Authors: Bihoreau Marie Thérèse , Gauguier Dominique , Kato Norihiro , Hyne Gina , Lindpaintner Klaus , Rapp John P. , James Michael R. , Lathrop G. Mark
Published: May 2017

We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY × S (n = 159), BN × S (n = 91), and BN × GK (n = 139) were selected and genotyped for combinations of microsatellite markers. The loci define 21 linkage groups corresponding to the 20 rat autosomal chromosomes and the X chromosome. The map spans a genetic length of 1998 cM. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of rat models characterized for complex phenotypes.
The Organization of the γ-Glutamyl Transferase Genes and Other Low Copy Repeats in Human Chromosome 22q11
Authors: Collins John E. , Mungall Andrew J. , Badcock Karen L. , Fay Joanne M. , Dunham Ian
Published: May 2017

A clone map consisting of YACs, cosmids, and fosmids has been constructed covering low copy repeat regions of human chromosome 22q11. A combination of clone restriction digest analysis, single-copy landmark content analysis, HindIII–Sau3AI fingerprinting, and sequencing of PCR products derived from clones was required to resolve the map in this region. Seven repeat-containing contigs were placed in 22q11, five containing γ-glutamyl transferase (GGT) sequences described previously. In one case, a single interval at the resolution of the YAC map was shown to contain at least three GGT sequences after higher resolution mapping. The sequence information was used to design a rapid PCR/restriction digest technique that distinguishes the GGT loci placed in the YAC map. This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11.

[The sequence data described in this paper have been submitted to EMBL under accession nos. Z93342 (gene 11; EMBL identification no. HSGGT11), Z93343 (gene 12; EMBL no. HSGGT12), Z93344(gene 1; EMBL no. HSGGT1A), Z93345 (gene 2; EMBL no. HSGGT2A), Z93346(gene 3; EMBL no. HSGGT3A), Z93347 (gene 3-like; EMBL no. HSGGT3L), andZ93348 (gene 6; EMBL no. HSGGT6).]
The Human Homolog of a Mouse-Imprinted Gene, Peg3, Maps to a Zinc Finger Gene-Rich Region of Human Chromosome 19q13.4
Authors: Kim Joomyeong , Ashworth Linda , Branscomb Elbert , Stubbs Lisa
Published: May 2017

Peg3 (paternally expressedgene 3) is the first imprinted gene detected in the proximal region of mouse chromosome 7. Because imprinting is a trait that is generally conserved among mammals, and imprinted domains generally encompass several adjacent genes, expression patterns and chromosomal environment of the human counterpart of Peg3 are of special interest. In this study we have localized human PEG3 ∼2 Mb proximal of the telomere of chromosome 19q, within a region known to carry large numbers of tandemly clustered Krüppel-type zinc finger-containing (ZNF) genes. Peg3 also encodes a Krüppel-type ZNF protein but one that is distinguished from other ZNF gene products by the fact that it carries two novel proline-rich motifs. Comparison between mousePeg3 and partial human PEG3 gene sequences revealed a high level of conservation between the two species, despite the fact that one of the two proline-rich repeats is absent from the human gene. Our data demonstrate that the human gene is expressed at highest levels in ovary and placenta; mouse Peg3, by contrast, is transcribed at highest levels in the adult brain. These comparative mapping, sequencing, and expression data provide the first clues to the potential activities of PEG3, and generate new tools to aid in the analysis of structure and function of a potentially new imprinted domain located in human chromosome 19q13.4 and mouse chromosome 7.