bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficiency and hospital effectiveness in improving Hospital Consumer Assessment of Healthcare Providers and Systems ratings
Authors: Al-Amin Mona , Makarem Suzanne C. , Rosko Michael
Published: June 2015

Background:

Efficiency has emerged as a central goal to the operations of health care organizations. There are two competing perspectives on the relationship between efficiency and organizational performance. Some argue that organizational slack is a waste and that efficiency contributes to organizational performance, whereas others maintain that slack acts as a buffer, allowing organizations to adapt to environmental demands and contributing to organizational performance.

Purposes:

As value-based purchasing becomes more prevalent, health care organizations are incented to become more efficient and, at the same time, improve their patients’ experiences and outcomes. Unused slack resources might facilitate the timely implementation of these improvements. Building on previous research on organizational slack and inertia, we test whether efficiency and other organizational factors predict organizational effectiveness in improving Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) ratings.

Methodology:

We rely on data from the American Hospital Association and HCAHPS. We estimate hospital cost-efficiency by Stochastic Frontier Analysis and use regression analysis to determine whether efficiency, competition, hospital size, and other organizational factors are significant predictors of hospital effectiveness.

Findings:

Our findings indicate that efficiency and hospital size have a significant negative association with organizational ability to improve HCAHPS ratings.

Practice Implications:

Although achieving organizational efficiency is necessary for health care organizations, given the changes that are currently occurring in the U.S. health care system, it is important for health care managers to maintain a certain level of slack to respond to environmental demands and have the resources needed to improve their performance.
Design Concepts and Preclinical Results of a Miniaturized HeartWare Platform: The MVAD System
Authors: Cheung Anson , Chorpenning Katherine , Tamez Daniel , Shambaugh Charles , Dierlam Anne E. , Taskin M. Ertan , Ashenuga Michael , Reyes Carlos , LaRose Jeffrey A.
Published: June 2015

Objective

Ventricular assist device (VAD) miniaturization is one design trend that may result in less-invasive implantation techniques and more versatility with patient selection. The MVAD System is a miniature, continuous-flow device implanted in the ventricle. The pump is capable of delivering between 0 and 7 L/min of flow at a mean arterial pressure of 75 mm Hg. The impeller was optimized from its original design to improve hydraulic performance, minimize shear regions, and enhance the impeller's radial stiffness. These studies evaluated the MVAD System with modified impeller in the preclinical setting.

Methods

This modified pump design was tested through chronic studies (n = 6) in a healthy ovine model where 4 animals were implanted for a duration of 30 ± 5 days and 2 animals were implanted for a duration of 90 ± 5 days. The pump was placed in the left ventricular apex with the outflow graft anastomosed to the descending aorta. Postoperatively, no anticoagulant or antiplatelet therapies were administered throughout the study duration.

Results

All 6 animals reached their elective date of kill, demonstrating no evidence of organ compromise or device-related complications. Average pump parameters did not deviate significantly, and average rotational speed, pump flow, and power consumption were 14095 ± 139 RPM, 4.1 ± 0.4 L/min, and 4.3 ± 0.1 W, respectively. Examination of pump components postexplant demonstrated no mechanical wear or thrombus formation.

Conclusions

Hemocompatibility and biocompatibility of the modified MVAD System were demonstrated through pump parameters, blood chemistry panels, and histopathology analysis.
Managing One’s Symptoms
Authors: Yeager Katherine A. , Sterk Claire E. , Quest Tammie E. , DiIorio Colleen , Vena Catherine , Bauer-Wu Susan
Published: June 2015

Background:

African Americans endure disproportionately high advanced cancer rates and also are disproportionately represented in the lower socioeconomic strata. These individuals work to manage symptoms in order to function and have a satisfactory quality of life.

Objective:

The purpose of this study was to discover what low-income African American adults with advanced cancer do on a day-to-day basis to relieve and manage symptoms. This study viewed the individuals as experts and asked them not what they are told to do, but rather what they actually do.

Methods:

A purposive sample of 27 individuals participated in semistructured interviews conducted by 2 research interviewers. This qualitative descriptive approach used content analysis to develop themes to describe symptom self-management.

Results:

Participants described 2 approaches: making continual adjustments and finding stability through spirituality. In seeking comfort from the distress of their symptoms, they were constantly altering their activities and fine-tuning strategies. They adjusted medical regimens and changed the speed and selection of daily activities, including comfort measures and diet modifications. In contrast, their spirituality was a consistent presence in their lives that provided balance to their unstable symptom experience.

Conclusions:

This study illustrates that people with advanced cancer actively engage in multiple complex self-management strategies in response to symptoms.

Implications for Practice:

As providers assess how individuals manage their symptoms, they must find ways to support those efforts. Providers then will recognize the challenges faced by advanced cancer patients in obtaining the best quality of life while managing multiple symptoms, activities, and family responsibilities.
Effectiveness and Safety of Selective Neck Dissection in Lymph Node-Positive Squamous Cell Carcinoma of the Head and Neck
Authors: Polat Mustafa , Celenk Fatih , Baysal Elif , Durucu Cengiz , Kul Seval , Mumbuc Semih , Kanlikama Muzaffer
Published: June 2015

The aim of this study was to investigate the effectiveness and safety of selective neck dissection in patients with lymph node-positive head and neck squamous cell carcinoma to determine regional control and survival rates. Eighty patients with lymph node-positive head and neck squamous cell carcinoma who underwent selective dissection were included in the study. Regional control, survival rates, and factors affecting survival were analyzed. Regional control was 90%, disease-specific survival was 93.4%, and the overall survival rate was 87.25%. T stage, N stage, age, and extracapsular spread were included in hazard regression models. None of the factors were statistically significant. Selective neck dissection is an effective and oncologically safe treatment option in selected cases. T stage, N stage, and extracapsular spread had no significant impact on disease-specific survival.
Frontal Sinolith
Authors: Lee Dong Hoon , Yoon Tae Mi , Lee Joon Kyoo , Lim Sang Chul
Published: June 2015

Sinolith in the paranasal sinus is still a rare entity. A sinolith in the frontal sinus is extremely rare, and only 2 patients have been reported in the English literature. Herein, the authors present an additional patient of frontal sinolith in a 78-year-old woman. The patient was preoperatively diagnosed with fungus ball of the frontal sinus, based on radio-opaque densities on computed tomography. Endoscopic surgery was performed and surgical biopsy was interpreted as sinolith. Clinical manifestations of frontal sinolith, including imaging study findings, are discussed with a review of the literature pertaining to this condition. Despite its rarity, frontal sinolith should be considered in the differential diagnosis of radio-densities in the frontal sinus.
Giant Solitary Fibrous Tumor of Orbit
Authors: Tenekeci Goktekin , Sari Alper , Vayisoglu Yusuf , Serin Onur
Published: June 2015

Solitary fibrous tumors (SFTs) have been reported in various locations in the body. Solitary fibrous tumors are extremely rare tumors, especially when located in the orbit. Diagnosis of SFT cannot be made based on histopathology only because it exhibits a variable microscopic appearance, and necessitates immunohistochemistry to confirm the diagnosis.

A 51-year-old man was admitted to our clinic for the evaluation of a mass bulging in his left eye. Clinical examination revealed a painless mass extruding out of the orbital cavity with dimensions of 8 × 7 cm. Exenteration of the left eye including the upper and lower eyelid and reconstruction of the orbital cavity using a temporoparietal fascia flap and a temporal muscle flap was performed.

SFT of orbital region is known as a slow growing and painless tumor. Based on previous studies, increased mitotic rate of the tumor gives the impression that the tumor has a malignant nature. Until now a small number or orbital SFTs were reported and none of them presented with a giant mass protruding out of the orbital cavity. We present a unique case of orbital SFT filling the whole orbital cavity and protruding outward as a giant mass. This case has been reported to expand our knowledge in this debated entity.
Surgical Management of Giant Scalp Neurofibroma After Ultra-Selective Embolization of Nutrient Artery
Authors: Yuan Si-Ming , Guo Yao , Cui Lei , Wang Jun , Hu Xin-Bao , Zhou Ji-Hong , Jiang Hui-Qing , Hong Zhi-Jian
Published: June 2015

Objectives:

Neurofibroma, a common benign tumor in soft tissue, continues to grow, so it often appears to be giant. Surgical management of giant neurofibroma is a challenge due to the risk of excessive bleeding. Embolization of tumor's nutrient artery may reduce the blood loss in operation. This study introduces the surgical management of giant scalp neurofibroma with preoperative ultra-selective embolization of nutrient artery.

Methods:

From January 2006 to December 2013, 9 patients with giant scalp neurofibroma were enrolled into the study. Digital subtraction angiography (DSA) showed tumor's nutrient artery. Ultra-catheter was inserted into the nutrient artery and its branches as close as possible to the tumor. Then ultra-selective embolization was performed with gelatin sponge particles. Surgical removal of tumor was performed in 3 days after embolization. The wound was repaired by skin graft.

Results:

All of the 9 patients underwent successful DSA and ultra-selective embolization. Among them, occipital artery was embolized in 3 patients (left side in 1 patient and right side in 2 patients). Both occipital artery and superficial temporal artery were embolized in 6 patients (left side in 2 patients, right side in 3 patients, and both side in 1 patient). No complications, such as ectopic embolism, occurred in the patients. All of the tumors were resected completely without blood transfusion. The skin graft survived very well on the wounds.

Conclusions:

Preoperative ultra-selective embolization of nutrient artery is a feasible, safe, and effective method to reduce the blood loss in operation and facilitate the surgical management of giant scalp neurofibroma.
The Risk of Blepharoptosis in Contact Lens Wearers
Authors: Hwang Kun , Kim Joo Ho
Published: June 2015

The aim of this systematic review was to summarize and evaluate the risk of blepharoptosis in contact lens wearers. In a PubMed search, 393 papers were found using the terms “lens and ptosis.” The abstracts were read and 16 full text articles were reviewed. Among them, 5 articles were analyzed. Five studies were subgrouped and a meta-analysis of these data suggested there is an increased risk of blepharoptosis in hard contact lens wearers over nonwearers (n = 7426, OR, 17.38, 95% CI = 3.71–81.29, P < 0.00001). One study was subgrouped and these data suggested there is also an increased risk of blepharoptosis in soft contact lens wearers over nonwearers (n = 90, OR, 8.12, 95% CI = 2.68–24.87, P < 0.0002). Patients wearing rigid contact lenses should be advised of the risk of ptosis, and a history of contact lens use should be sought in all patients who have acquired ptosis as the previous authors have recommended.
Aging as the Impact Factor on Septoplasty Success
Authors: Habesoglu Mehmet , Kilic Osman , Caypinar Basak , Onder Serap
Published: June 2015

Objective:

The aim of the study was to discuss the impact of aging on septoplasty success.

Study Design and Setting:

This prospective case control study was conducted at the Umraniye Education and Research Hospital.

Methods:

Our study group consists of 23 patients older than 60-year-old who have septal deviation and have previously been postponed for this surgery due to various reasons. Twenty-six patients under 40-year-old are randomly chosen as the control group who were running to septoplasty. Postoperative Glasgow Benefit Inventory Index, preoperative and postoperative NOSE score, and nasal mucociliary clearance time (MCCt) were noted for both the groups. All collected data were compared between the groups.

Results:

In both the groups, postoperative NOSE scores decreased significantly compared to preoperative values (P < 0.01). This decrease was not significantly different between the groups. In both the groups, a significant decrease was noted in nasal MCCt with surgery (P = 0.004). However, this difference between two groups was not statistically significant. In addition, the Glasgow Benefit Inventory (GBI) index of control group was notably higher than the study group and this was statistically significant (P = 0.027). Also, the decrease of NOSE scores was conversely related to high GBI indexes and this is statistically significant (P = 0.005).

Conclusion:

For many surgical procedures, aging is considered as one of the important prognostic factors on success. To date no study in the literature discussed this relationship between aging and the success of septoplasty. At this point, our results showed that septoplasty is a successfully performed procedure in all ages. But, satisfaction of patients is statistically decreasing with aging.
Orthoptic Sequelae Following Conservative Management of Pure Blowout Orbital Fractures
Authors: Steinegger Ken , De Haller Raoul , Courvoisier Delphine , Scolozzi Paolo
Published: June 2015

The aim of this study was to prospectively assess the prevalence of orthoptic anomalies following conservative management of pure blowout orbital fractures and to evaluate their clinical relevance. Clinical and radiologic data of patients with unilateral conservatively managed pure blowout orbital fractures with a minimum follow-up of 6 months were reviewed. Eligible patients were contacted and invited to undergo an extended ophthalmologic examination as follows: distance and near visual acuities, Hertel exophthalmometry, corneal light reflex (Hirschberg test), ductions and versions in the 6 cardinal fields of gaze, eye deviation with prisms and alternate cover test in all of the 9-gaze directions with Maddox rod, degrees of incyclo/excyclotorsion with right and left eye fixation, horizontal and vertical deviation with Hess-Weiss coordimetry, degree of horizontal/vertical and incyclo/excyclotorsion deviation with Harms wall deviometry, and vertical deviation with Bielschowsky head-tilt test. Of the 69 patients contacted, 49 declined to participate given that they were asymptomatic. Twenty patients agreed to undergo the examination. One patient complained of minimal double vision limited to the extreme downgaze. Four patients had asymptomatic ocular motility disturbances limited to the extreme gaze. Seven patients had asymptomatic horizontal heterophoria. These disturbances did not interfere with daily or professional activities in any of the patients. The current study demonstrated that conservative management of pure orbital blowout fractures can result in orthoptic anomalies. These sequelae were restricted to a very limited portion of the binocular field of the vision and were not found to be clinically relevant.
New Screw Design for Securing Buried Distractors Usefulness and Ease of Removal
Authors: Fariña Rodrigo , Hinojosa Andrés , Sánchez Martín , Olate Sergio
Published: June 2015

There are 2 types of distraction devices for mandibular distraction: buried and external. The advantage of buried devices is the stability, but the difficulty in removing the screws is the greatest disadvantage. To resolve this problem, an osteosynthesis screw (Fariña Screw) has been designed, which greatly facilitates its removal when buried distractors are used.
Cryptococcus gattii genotype AFLP6/VGII meningoencephalitis in an immunocompetent Filipino male in Kuwait: activation of a dormant infection
Authors: Alfouzan Wadha , Al-Sheridah Saud , Alenzi Laila , Hagen Ferry , Meis Jacques F. , Khan Ziauddin
Published: June 2015

Introduction

Cases of Cryptococcus gattii infections are being increasingly recognized in geographical regions that were traditionally regarded as non-endemic. Here, we describe a case of C. gattii meningoencephalitis in an immunocompetent Filipino male diagnosed in Kuwait.

Case presentation:

A 34-year-old healthy Filipino male presented with a history of progressive generalized headache, nausea and repeated episodes of vomiting. The patient had continuously lived and worked in Kuwait for three consecutive years before developing the disease. The diagnosis of meningoencephalitis was established by demonstrating capsulated budding yeast cells in cerebrospinal fluid, isolating C. gattii in culture and detecting cryptococcal polysaccharide antigen in serum and cerebrospinal fluid specimens. Molecular characterization of the isolate confirmed its identity as C. gattii, genotype AFLP6/VGII. The isolate showed reduced susceptibility to fluconazole and was treated suboptimally until flucytosine became available.

Conclusions:

A case of C. gattii meningoencephalitis in a healthy Filipino male, who apparently acquired the infection in his native country, is described. The infection remained dormant for several years before becoming clinically apparent. To the best of our knowledge, this is the first report of C. gattii meningitis diagnosed in Kuwait.
Scedosporium apiospermum: a fungal pathogen causing pneumonia in a patient with cystic fibrosis
Authors: Schwarz Carsten , Thronicke Anja , Staab Doris , Tintelnot Kathrin
Published: June 2015

Introduction:

Scedosporium apiospermum is a slow-growing pathogenic fungus that can cause pneumonia. Diagnosis of this rare filamentous fungus is challenging. To the best of our knowledge, this is the first case describing an acute pulmonary infection caused by this fungal pathogen in a patient with cystic fibrosis (CF).

Case presentation:

A 35-year-old female with CF, with a 1-month history of irritating cough, increased sputum production and dyspnoea, was admitted to hospital. A chest computed tomography scan revealed new bilateral infiltrations, mediastinal lymphadenopathy and bronchiectasis. Pseudomonas aeruginosa and S. apiospermum were detected in the bronchoalveolar lavage. The patient's clinical status was not improved by standard antibiotic therapy. Antifungal systemic therapy consisting of systemic caspofungin and oral posaconazole against the highly suspected scedosporiosis was initiated, but the clinical outcome was not significantly improved. Antibodies against the S. apiospermum complex were present in the patient's serum. Only after the addition of 50 mg once a day of inhaled liposomal amphotericin B the patient was successfully treated.

Conclusion:

The patient was cured by a combined therapy of two systemic antimycotic drugs and one local antimycotic drug.
Myopericarditis and atrial fibrillation complicating meningococcal meningitis in a human immunodeficiency virus-infected man who has sex with men: a case report
Authors: Zhu Ziqiang , Shahzad Ali , Rozin Alexander
Published: June 2015

Introduction:

Neisseria meningitidis is the leading cause of bacterial meningitis in children and young adults. Multiple complications have been reported previously, either at the time of presentation or later during the recovery phase of the illness. Cardiac arrhythmias and electrocardiogram (ECG) abnormalities have rarely been reported in N. meningitidis infection.

Case presentation:

We report a 48-year-old African-American man, with newly diagnosed human immunodeficiency virus infection, admitted with a diagnosis of meningococcal meningitis. An initial 12-lead ECG at admission showed a normal sinus rhythm with widespread concave ST elevation. The patient's troponin level was significantly elevated. A Transthoracic echocardiogram revealed left ventricle moderate anterior pericardial effusion. He was treated with antibiotics for meningitis and ibuprofen for myopericarditis. He subsequently developed atrial fibrillation, which was suppressed with metoprolol, diltiazem and amiodarone during hospitalization. To the best of our knowledge, this is the first reported case of atrial fibrillation complicating meningococcal meningitis.

Conclusion:

Myopericarditis complicates the course of meningococcal meningitis. Various forms of cardiac arrhythmias can occur during the course of meningococcal infection. Therefore, telemetry and serial ECG monitoring are recommended throughout the course of meningococcal infection.
Hi-Cpipe: a pipeline for high-throughput chromosome capture
Authors: Castellano Giancarlo , Le Dily François , Hermoso Pulido Antonio , Beato Miguel , Roma Guglielmo
Published: June 2015

Hi-Cpipe is a bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome alignment, quality control and filtering, identification of genome-wide chromatin interactions, visualization and statistics. An interactive browser enables visual inspection of interaction data and results.
Decoding the Population Activity of Grid Cells for Spatial Localization and Goal-Directed Navigation
Authors: Stemmler Martin , Mathis Alexander , Herz Andreas VM
Published: June 2015

Mammalian grid cells fire whenever an animal crosses the points of an imaginary, hexagonal grid tessellating the environment. Here, we show how animals can localize themselves and navigate by reading-out a simple population vector of grid cell activity across multiple scales, even though this activity is intrinsically stochastic. This theory of dead reckoning explains why grid cells are organized into modules with equal lattice scale and orientation. Computing the homing vector is least error-prone when the ratio of successive grid scales is around 3/2. Silencing intermediate-scale modules should cause systematic errors in navigation, while knocking out the module at the smallest scale will only affect navigational precision. Read-out neurons should behave like goal-vector cells subject to nonlinear gain fields.
Variation-preserving normalization unveils blind spots in gene expression profiling
Authors: Roca Carlos P. , Gomes Susana I. L. , Amorim Mónica J. B. , Scott-Fordsmand Janeck J.
Published: June 2015

RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following an implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much greater than currently believed, and that it can be measured with available technologies. Our results also explain, at least partially, the problems encountered in transcriptomics studies. We expect this improvement in detection to help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
Metacommunity in dynamic landscapes
Authors: de Santana Charles Novaes , Klecka Jan , Palamara Gian M. , Melián Carlos J.
Published: June 2015

Predictions from theory, field data, and experiments have shown that high landscape connectivity promotes higher species richness than low connectivity. However, examples demonstrating high diversity in low connected landscapes also exist. Here we describe the many factors that drive landscape connectivity at different spatiotemporal scales by varying the amplitude and frequency of changes in the dispersal radius of spatial networks. We found that the fluctuations of landscape connectivity support metacommunities with higher species richness than static landscapes. Our results also show a dispersal radius threshold below which species richness drops dramatically in static landscapes. Such a threshold is not observed in dynamic landscapes for a broad range of amplitude and frequency values determining landscape connectivity. We conclude that merging amplitude and frequency as drivers of landscape connectivity together with patch dynamics into metacommunity theory can provide new testable predictions about species diversity in rapidly changing landscapes.
TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R
Authors: Höhna Sebastian , May Michael R. , Moore Brian R.
Published: June 2015

Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation – extinction). We develop a flexible Bayesian framework for specifying an effectively infinite array of diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. Additionally we provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.

Availability and implementation

the source code for TESS is freely available athttp://cran.r-project.org/web/packages/TESS/.

Contact

Sebastian.Hoehna@gmail.com
A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing
Authors: Uribe-Convers Simon , Settles Matthew L. , Tank David C.
Published: June 2015

Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses a Fluidigm microfluidic PCR array and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per microfluidic array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our subgenomic method and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genusBartsiaL. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ∼25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ∼13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ∼40,500bp for 349 samples.
Exon capture optimization in large-genome amphibians
Authors: McCartney-Melstad Evan , Mount Genevieve G. , Shaffer H. Bradley
Published: June 2015

Background Gathering genomic-scale data efficiently is challenging for non-model species with large, complex genomes. Transcriptome sequencing is accessible for even large-genome organisms, and sequence capture probes can be designed from such mRNA sequences to enrich and sequence exonic regions. Maximizing enrichment efficiency is important to reduce sequencing costs, but, relatively little data exist for exon capture experiments in large-genome non-model organisms. Here, we conducted a replicated factorial experiment to explore the effects of several modifications to standard protocols that might increase sequence capture efficiency for large-genome amphibians. Methods We enriched 53 genomic libraries from salamanders for a custom set of 8,706 exons under differing conditions. Libraries were prepared using pools of DNA from 3 different salamanders with approximately 30 gigabase genomes: California tiger salamander (Ambystoma californiense), barred tiger salamander (Ambystoma mavortium), and an F1 hybrid between the two. We enriched libraries using different amounts of c0t-1 blocker, individual input DNA, and total reaction DNA. Enriched libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq 2500, and the efficiency of target enrichment was quantified using unique read mapping rates and average depth across targets. The different enrichment treatments were evaluated to determine if c0t-1 and input DNA significantly impact enrichment efficiency in large-genome amphibians. Results Increasing the amounts of c0t-1 and individual input DNA both reduce the rates of PCR duplication. This reduction led to an increase in the percentage of unique reads mapping to target sequences, essentially doubling overall efficiency of the target capture from 10.4% to nearly 19.9%. We also found that post-enrichment DNA concentrations and qPCR enrichment verification were useful for predicting the success of enrichment. Conclusions Increasing the amount of individual sample input DNA and the amount of c0t-1 blocker both increased the efficiency of target capture in large-genome salamanders. By reducing PCR duplication rates, the number of unique reads mapping to targets increased, making target capture experiments more efficient and affordable. Our results indicate that target capture protocols can be modified to efficiently screen large-genome vertebrate taxa including amphibians.
Inference under a Wright-Fisher model using an accurate beta approximation
Authors: Tataru Paula , Bataillon Thomas , Hobolth Asger
Published: June 2015

The large amount and high quality of genomic data available today enables, in principle, accurate inference of evolutionary history of observed populations. The Wright-Fisher model is one of the most widely used models for this purpose. It describes the stochastic behavior in time of allele frequencies and the influence of evolutionary pressures, such as mutation and selection. Despite its simple mathematical formulation, exact results for the distribution of allele frequency (DAF) as a function of time are not available in closed analytic form. Existing approximations build on the computationally intensive diffusion limit, or rely on matching moments of the DAF. One of the moment-based approximations relies on the beta distribution, which can accurately describe the DAF when the allele frequency is not close to the boundaries (zero and one). Nonetheless, under a Wright-Fisher model, the probability of being on the boundary can be positive, corresponding to the allele being either lost or fixed. Here, we introduce the beta with spikes, an extension of the beta approximation, which explicitly models the loss and fixation probabilities as two spikes at the boundaries. We show that the addition of spikes greatly improves the quality of the approximation. We additionally illustrate, using both simulated and real data, how the beta with spikes can be used for inference of divergence times between populations, with comparable performance to existing state-of-the-art method.
A seasonal copepod ‘lipid pump’ promotes carbon sequestration in the deep North Atlantic
Authors: Jónasdóttir Sigrún H. , Visser André W. , Richardson Katherine , Heath Michael R.
Published: June 2015

Estimates of carbon flux to the deep oceans are essential for our understanding for global carbon budgets. We identify an important mechanism, the lipid pump, that has been unrecorded in previous estimates. The seasonal lipid pump is highly efficient in sequestering carbon in the deep ocean. It involves the vertical transport and respiration of carbon rich compounds (lipids) by hibernating zooplankton. Estimates for one species, the copepodCalanus finmarchicusoverwintering in the North Atlantic, sequester around the same amount of carbon as does the flux of detrital material that is usually thought of as the main component of the biological pump. The efficiency of the lipid pump derives from a near complete decoupling between nutrient and carbon cycling and directly transports carbon through the meso-pelagic with very little attenuation to below the permanent thermocline. Consequently the seasonal transport of lipids by migrating zooplankton is overlooked in estimates of deep ocean carbon sequestration by the biological pump.
GAP Activity, but Not Subcellular Targeting, Is Required for Arabidopsis RanGAP Cellular and Developmental Functions
Authors: Boruc Joanna , Griffis Anna H.N. , Rodrigo-Peiris Thushani , Zhou Xiao , Tilford Bailey , Van Damme Daniël , Meier Iris
Published: June 2015

The Ran GTPase activating protein (RanGAP) is important to Ran signaling involved in nucleocytoplasmic transport, spindle organization, and postmitotic nuclear assembly. Unlike vertebrate and yeast RanGAP, plant RanGAP has an N-terminal WPP domain, required for nuclear envelope association and several mitotic locations of Arabidopsis thaliana RanGAP1. A double null mutant of the two Arabidopsis RanGAP homologs is gametophyte lethal. Here, we created a series of mutants with various reductions in RanGAP levels by combining a RanGAP1 null allele with different RanGAP2 alleles. As RanGAP level decreases, the severity of developmental phenotypes increases, but nuclear import is unaffected. To dissect whether the GAP activity and/or the subcellular localization of RanGAP are responsible for the observed phenotypes, this series of rangap mutants were transformed with RanGAP1 variants carrying point mutations abolishing the GAP activity and/or the WPP-dependent subcellular localization. The data show that plant development is differentially affected by RanGAP mutant allele combinations of increasing severity and requires the GAP activity of RanGAP, while the subcellular positioning of RanGAP is dispensable. In addition, our results indicate that nucleocytoplasmic trafficking can tolerate both partial depletion of RanGAP and delocalization of RanGAP from the nuclear envelope.
Do tutorials on application method enhance adapalene–benzoyl peroxide combination gel tolerability in the treatment of acne?
Authors: Kwon Hyuck Hoon , Park Seon Yong , Yoon Ji Young , Min Seonguk , Suh Dae Hun
Published: June 2015

Fixed‐dose combination adapalene 0.1% and benzoyl peroxide 2.5% gel (A‐BPO) has rarely been studied for Asian acne patients, while they have complained of local irritations more often when applying individual components. In this study, we compared A‐BPO gel with benzoyl peroxide (BPO) in terms of efficacy and tolerability in Korean patients first, and assessed the clinical benefit of a dermatological tutorial on application technique in reducing irritations for A‐BPO. This study was conducted as a single‐blind controlled split‐face trial for a 12‐week period. Each half facial side of 85 patients was randomly assigned to either A‐BPO or BPO. Success rate, lesion counts and safety profiles were evaluated (analysis I). During initial assignment, all patients were further randomized to either dermatological tutorial (DT) or non‐tutorial (NT) subgroups depending on the presence of dermatologists' tutorials for application methods to their A‐BPO sides. Clinical data of the A‐BPO side was compared between two subgroups (analysis II). As a result, A‐BPO gel outperformed BPO, demonstrating better efficacy in success rates and lesion counts as early as 1 week. However, A‐BPO proved significantly less tolerable compared with both BPO and previous A‐BPO data from Caucasians. Bioengineering measurements further confirmed clinical data (analysis I). The DT subgroup achieved much better tolerability with comparable therapeutic efficacies compared with the NT subgroup (analysis II). In conclusion, A‐BPO demonstrated higher efficacies in acne compared with BPO in Korean patients, while skin irritation levels were notable concurrently. Dermatologists' education for application methods would significantly decrease these side‐effects, maintaining superior efficacy levels.
Improvement in T helper 1‐related immune responses in BALB/c mice immunized with an HIV‐1 gag plasmid combined with a chimeric plasmid encoding interleukin‐18 and flagellin
Authors: Chen Ya‐Lei , Chen Yao‐Shen , Hung Yi‐Chien , Liu Pei‐Ju , Tasi Hsi‐Ying , Ni Wei‐Feng , Hseuh Pei‐Tan , Lin Hsi‐Hsun
Published: June 2015

Both flagellin (fliC) and IL‐18 (INF‐γ‐inducing factor) have been developed as adjuvants for improving immunogenicity in DNA‐vaccinated hosts. An HIV‐1 gag plasmid encodes a protein harboring broad epitopes for cytotoxic T‐lymphocytes. In this study, the immunogenicity of BALB/c mice immunized with an HIV‐1 gag plasmid (pVAX/gag) combined with a chimeric plasmid encoding IL‐18 fused to flagellin (pcDNA3/IL‐18_fliC) or a single plasmid encoding IL‐18 (pcDNA3/IL‐18) and/or flagellin (pcDNA3/fliC) was assessed. Through in vitro transcription and translation, it was demonstrated that both mRNA and protein were appropriately expressed by each construct. The IL‐18 and flagellin fusion protein, which could be detected in supernatants from transfected cells, was effective in inducing IFN‐γ by lymphocytes. Following i.m. immunization, expressions of flagellin or IL‐18 were detected in muscle cells by immunohistochemistry analysis from 72 hr. At 12 weeks post‐immunization, both gag‐specific IgG in sera and spleen cell proliferation were high in all murine groups. However, the IgG2a/IgG1 ratio, Th1 cytokine (IL‐2 and IFN‐γ) production and proportion of gag‐specific CD3+CD8+ IFN‐γ‐secreting cells were significantly higher in the murine group co‐immunized with pVAX/gag plasmid and pcDNA3/IL‐18_fliC than in the mice immunized with pVAX/gag plasmid combined with either pcDNA3/fliC or pcDNA3/IL‐18 plasmid or both. These findings suggest that a chimeric plasmid encoding IL‐18 fused to flagellin can be used as an adjuvant‐like plasmid to improve the Th1 immune response, particularly for induction of CD3+CD8+ IFN‐γ‐secreting cells in gag plasmid‐vaccinated mice.
Orientation to the sun by animals and its interaction with crypsis
Authors: Penacchio Olivier , Cuthill Innes C. , Lovell P. George , Ruxton Graeme D. , Harris Julie M.
Published: June 2015

Orientation with respect to the sun has been observed in a wide range of species and has generally been interpreted in terms of thermoregulation and/or ultraviolet (UV) protection. For countershaded animals, orientation with respect to the sun may also result from the pressure to exploit the gradient of coloration optimally to enhance crypsis.

Here, we use computational modelling to predict the optimal countershading pattern for an oriented body. We assess how camouflage performance declines as orientation varies using a computational model that incorporates realistic lighting environments.

Once an optimal countershading pattern for crypsis has been chosen, we determine separately how UV protection/irradiation and solar thermal inflow fluctuate with orientation.

We show that body orientations that could optimally use countershading to enhance crypsis are very similar to those that allow optimal solar heat inflow and UV protection.

Our findings suggest that crypsis has been overlooked as a selective pressure on orientation and that new experiments should be designed to tease apart the respective roles of these different selective pressures. We propose potential experiments that could achieve this.
The downside of eDNA as a survey tool in water bodies
Authors: Roussel Jean‐Marc , Paillisson Jean‐Marc , Tréguier Anne , Petit Eric
Published: June 2015

There is a growing literature on the detection of species‐specific DNA fragments in water to reveal animals' presence in aquatic environments.

Analysis of Rees et al. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down.

Non‐detection of species‐specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.

Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.
Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals
Authors: Rees Helen C. , Gough Kevin C. , Middleditch David J. , Patmore James R. M. , Maddison Ben C.
Published: June 2015

In Rees et al. (2014b), we reviewed the current status of environmental DNA (eDNA) to monitor aquatic populations. Our aim was to focus on discussion of methodologies used, application of eDNA analysis as a survey tool in ecology, and to include some innovative ideas for using eDNA in conservation and management.

Roussel et al. (2015) claim that analysis of Rees et al. (2014b) and other publications highlights the downsides of the method, and they suggest that some conclusions should be toned down. Many of their arguments were covered in our original paper (Rees et al., 2014b); however, they make the point that modelling approaches should be encouraged, and we fully agree with this suggestion.

Roussel et al. (2015) also claim that we neglected to recognize that there are two sources of imperfect detection (at the field level and at the laboratory level). We feel that our review paper implies this point.

Synthesis and applications. Roussel et al. (2015) reiterate many of the points made in the original paper but do cover some additional areas that improve the debate on the use of environmental DNA (eDNA). Both the comment (Roussel et al., 2015) and our rebuttal clearly highlight that detailed laboratory protocols and rigorous field sampling design are crucial factors which require sufficient reporting in the literature to allow for experimental comparison and replication. Any development of a new method for eDNA detection should be compared directly with established ‘gold standard’ methods for the detection of the species or habitat under investigation. None of the issues raised in Roussel et al. (2015) would alter our main conclusions.
Avoiding the crowds: the evolution of plastic responses to seasonal cues in a density‐dependent world
Authors: Metcalf C. Jessica E. , Burghardt Liana T. , Koons David N.
Published: June 2015

Across a range of organisms, life‐history transitions can be triggered by specific levels of seasonal cues, such as day length or temperature. This acts to regulate the life cycle relative to seasonal fluctuations, so that, for example, reproduction occurs when resources are most abundant.

At an environmentally optimal cue level, individuals might be selected to respond in a similar way, and consequently abruptly increase population density through, for example, the production of offspring. However, if density dependence is operating, crowding will reduce individual fitness, and selection will then favour life‐history transitions at different cue levels.

We explore the eco‐evolutionary dynamics that result from the interaction between density dependence and phenology using a life‐history model of an annual plant and focus on the timing of seed germination within the year. We characterize the adaptive dynamics of the mean and variance across the year of germination timing.

Our results indicate that, even in predictably varying environments, mean timing of germination is not evolutionarily stable, but may experience evolutionary branching if variance in germination timing is sufficiently constrained. Unpredictably varying environments extend contexts where this is the case.

Synthesis. Even if there is a restricted time period in the year during which environmental conditions are most appropriate for germination, observed timing of germination might be very diverse. Density dependence selects for persistence of traits conferring variance in timing across the year and additionally can lead to evolutionary branching of mean germination timing, resulting in multiple coexisting genotypes corresponding to different mean germination timings.