bluuebunny/crossref_metadata_2025 huggingface dataset:
Why Lumbar Artificial Disk Replacements (LADRs) Fail
Authors: Pettine Kenneth , Ryu Robert , Techy Fernando
Published: July 2015

Study Design:

A retrospective review of prospectively collected data.

Objective:

To determine why artificial disk replacements (ADRs) fail by examining results of 91 patients in FDA studies performed at a single investigational device exemption (IDE) site with minimum 2-year follow-up.

Summary of Background Data:

Patients following lumbar ADR generally achieve their 24-month follow-up results at 3 months postoperatively.

Materials and Methods:

Every patient undergoing ADR at 1 IDE site by 2 surgeons was evaluated for clinical success. Failure was defined as <50% improvement in ODI and VAS or any additional surgery at index or adjacent spine motion segment. Three ADRs were evaluated: Maverick, 25 patients; Charité, 31 patients; and Kineflex, 35 patients. All procedures were 1-level operations performed at L4–L5 or L5–S1. Demographics and inclusion/exclusion criteria were similar and will be discussed.

Results:

Overall clinical failure occurred in 26% (24 of 91 patients) at 2-year follow-up. Clinical failure occurred in: 28% (Maverick) (7 of 25 patients), 39% (Charité) (12 of 31 patients), and 14% (Kineflex) (5 of 35 patients). Causes of failure included facet pathology, 50% of failure patients (12 of 24). Implant complications occurred in 5% of total patients and 21% of failure patients (5 of 24). Only 5 patients went from a success to failure after 3 months. Only 1 patient went from a failure to success after a facet rhizotomy 1 year after ADR.

Conclusions:

Seventy-four percent of patients after ADR met strict clinical success after 2-year follow-up. The clinical success versus failure rate did not change from their 3-month follow-up in 85 of the 91 patients (93%). Overall clinical success may be improved most by patient selection and implant type.
Radiation Therapy for Aneurysmal Bone Cysts
Authors: Zhu Simeng , Hitchcock Kathryn E. , Mendenhall William M.
Published: July 2015

Purpose:

To evaluate the long-term effectiveness of radiation therapy (RT) as an adjuvant or alternative treatment for patients with aneurysmal bone cyst (ABC).

Patients and Methods:

The medical records of 12 patients who received RT at the University of Florida for ABC between 1964 and 2011 were reviewed and patients were contacted, when possible, for follow-up. Follow-up duration ranged from 3 to 36 years (median, 20.5 y). Patient age at the time of RT ranged from 3 to 23 years (mean, 12.75 y), with 7 females and 5 males. Four patients were treated for recurrent ABCs. Three patients were treated with surgical interventions (intralesional curettage, subtotal resection, or selective arterial embolization) before RT, and the rest received open biopsy only. The prescribed doses ranged from 20 to 60 Gy (mean, 30.15 Gy). Ten (83.3%) patients received between 1.5 and 2.0 Gy per fraction.

Results:

All patients were doing well and free of any adverse reaction to RT as of the latest follow-up, including 1 who passed away from cardiac problems 34 years since completing RT and 3 who were lost to follow-up (at 16, 16, and 19 y) but were doing well at the last follow-up.

Conclusions:

RT continues to result in an excellent prognosis for patients with ABC who receive either RT alone or adjuvant RT after surgery.
Chylothorax and Recurrent Laryngeal Nerve Injury Associated with Robotic Video-Assisted Mediastinal Lymph Node Dissection
Authors: Sarkaria Inderpal S. , Finley David J. , Bains Manjit S. , Adusumilli Prasad S. , Rizk Nabil P. , Huang James , Downey Robert J. , Rusch Valerie W. , Jones David R.
Published: July 2015

Objective

Although the technical aspects of robotic video-assisted thoracic surgery (RVATS) for lung resections may be advantageous, compared with standard thoracoscopy, complications of chylothorax and recurrent laryngeal nerve injury (RLNI) associated with mediastinal lymph node dissection (MLND) may be significant.

Methods

Consecutive patients who underwent RVATS anatomic lung resection for suspected or confirmed cancer and experienced RLNI or chylothorax were identified and reviewed from a prospectively maintained database. Complications were graded according to the Common Terminology Criteria for Adverse Events version 3.0.

Results

From July 28, 2010, to December 20, 2013, 251 patients underwent RVATS segmentectomy, lobectomy, or bilobectomy with MLND. Eleven patients (4.4%) experienced MLND-related complications and composed the study group; 81.8% were right-sided resections, and the median lymph node counts in right station IV and station VII were 9 (range, 1–23) and 5.5 (range, 1–10); 72.7% of the cases were performed for early-stage I and II lung cancers. Chylothorax [6/251 (2.4%)] and RLNI [6/251 (2.4%)] were significantly more common in the RVATS group than in the open thoracotomy and standard VATS groups. Complications requiring procedural intervention (Grade 3) are as follows: 4 cases of RLNI in patients undergoing percutaneous vocal cord medialization and 3 cases of chylothorax in patients undergoing image-guided thoracic duct embolization or maceration. No operative interventions were required.

Conclusions

RVATS MLND may be associated with increased rates of chylothorax and RLNI. Attention must be paid to identifying potential technical pitfalls with RVATS lung resections, adjusting surgical techniques accordingly, and minimizing patient morbidity.
Outpatient Medication Use in Chinese Geriatric Patients Admitted for Falls: A Case–Control Study at an Acute Hospital in Hong Kong
Authors: Lee Vivian W. Y. , Leung Teresa P. Y. , Lee Vincent W. H.
Published: July 2015

The study objective was to investigate the association of polypharmacy and medications with patient falls resulting in hip fractures among community-living geriatric patients. A case–control study was conducted at an acute public hospital in Hong Kong. The study population was community-living Chinese patients aged 65 years and above who were admitted for falls resulting in hip fractures during an 18-month study period. Each of these patients was matched to a control patient with the same age and sex, but without falls and fractures. Data were collected from electronic patient record. Data of 170 cases and 170 controls were eventually collected. The following variables associated with increased risk of falls resulting in hip fractures remained statistically significant after multivariate logistic regression, including benign prostatic hyperplasia [odds ratio (OR) = 2.654; 95% confidence interval (CI), 1.105–6.378; P = 0.029], first-generation antihistamines (OR = 3.176; 95% CI, 1.044–9.664; P = 0.042), antiparkinson medications (OR = 3.754; 95% CI, 1.158–12.169; P = 0.027), osteoporosis (OR = 3.159; 95% CI, 1.167–8.552; P = 0.024), and use of walking aids (OR = 2.543; 95% CI, 1.544–4.188; P < 0.001). In conclusion, this study identified various medications and comorbidities, rather than polypharmacy based on the number of medications, as predictors associated with increased risk of falls resulting in hip fractures for local geriatric patients. The findings provided insights into the potential medication-related fall prevention strategies, including clinical medication review, adverse drug event monitoring, and drug optimization.
Impact of Dobutamine in Patients With Septic Shock: A Meta-Regression Analysis
Authors: Nadeem Rashid , Sockanathan Shivani , Singh Mukesh , Hussain Tamseela , Kent Patrick , AbuAlreesh Sarah
Published: July 2015

Septic shock frequently requires vasopressor agents. Conflicting evidence exists for use of inotropes in patients with septic shock. Data from English studies on human adult septic shock patients were collected. A total of 83 studies were reviewed, while 11 studies with 21 data sets including 239 patients were pooled for meta-regression analysis. For VO2, pooled difference in means (PDM) was 0.274. For cardiac index (CI), PDM was 0.783. For delivery of oxygen, PDM was −0.890. For heart rate, PDM was −0.714. For left ventricle stroke work index, PDM was 0.375. For mean arterial pressure, PDM was −0.204. For mean pulmonary artery pressure, PDM was 0.085. For O2 extraction, PDM was 0.647. For PaCO2, PDM was −0.053. For PaO2, PDM was 0.282. For pulmonary artery occlusive pressure, PDM was 0.270. For pulmonary capillary wedge pressure, PDM was 0.300. For PVO2, PDM was −0.492. For right atrial pressure, PDM was 0.246. For SaO2, PDM was 0.604. For stroke volume index, PDM was 0.446. For SvO2, PDM was −0.816. For systemic vascular resistance, PDM was −0.600. For systemic vascular resistance index, PDM was 0.319. Meta-regression analysis was performed for VO2, DO2, CI, and O2 extraction. Age was found to be significant confounding factor for CI, DO2, and O2 extraction. APACHE score was not found to be a significant confounding factor for any of the parameters. Dobutamine seems to have a positive effect on cardiovascular parameters in patients with septic shock. Prospective studies with larger samples are required to further validate this observation.
Treatment of Femoral Head Necrosis With Bone Marrow Mesenchymal Stem Cells Expressing Inducible Hepatocyte Growth Factor
Authors: Pan Zhi-Min , Zhang Yu , Cheng Xi-Gao , Gao Gui-Cheng , Wang Xiang-Rui , Cao Kai
Published: July 2015

Our study assessed the effect of bone marrow mesenchymal stem cells (BMSCs) expressing inducible hepatocyte growth factor (HGF) on the recovery of femoral head necrosis (FHN). BMSCs were isolated by density gradient centrifugation. A recombinant AdTRE-HGF was constructed as the response plasmid and Adeno-X Tet-on as the regulator vector. The regulator and the response vectors were coinfected into BMSCs and induced at 0, 200, 500, 1000, and 1200 ng/mL doxycycline (Dox). After 3 days, the concentration of HGF was determined using enzyme-linked immunosorbent assay. Forty rabbits were selected to establish the FHN model and divided into 4 experimental groups. After the rabbits were killed by ketamine overdose, the restoration of FHN was assessed. The distribution of HGF-positive cells was observed by immunohistochemical method. Enzyme-linked immunosorbent assay results showed that 1000 ng/mL Dox induced the highest HGF expression level, even higher than the 1200 ng/mL Dox induction. The highest osteonecrosis incidence and empty lacunae percentage were found in group A compared with all the other groups (all P < 0.05). Furthermore, dramatically lower osteonecrosis incidence and empty lacunae percentage were found in group C compared with those of groups B and D (all P < 0.05). A significantly higher level of HGF protein was detected in group C compared with the other groups (all P < 0.05). Our study successfully developed the AdTRE-HGF, a recombinant adenovirus carrying HGF gene, for high expression of HGF in BMSCs. Importantly, introduction of BMSCs expressing HGF successfully produced the desired therapeutic effect in reversing FHN, in a Dox-dependent manner.
Outcomes of Vitamin D Supplementation in Adults Who are Deficient and Critically Ill: A Review of the Literature
Authors: Williams Sarah , Heuberger Roschelle
Published: July 2015

Vitamin D deficiency is known to be common in the general population and has been linked to all-cause mortality. The classically recognized role of vitamin D is its involvement in calcium and phosphorous homeostasis and bone health. Recent evidence suggests that vitamin D may also play a role in other nonskeletal processes, such as anti-proliferation, immunity, regulation of hormone section, and muscle strength. An extensive literature review of vitamin D and critical illness from 2000 to 2015 (PubMed and CINAL) produced multiple observational studies revealing a high prevalence of vitamin D deficiency in intensive care patients. Many of these studies have indicated that there is an association between vitamin D deficiency and clinical outcomes such as mortality, sepsis, duration of mechanical ventilation, and length of stay. This review article provides an overview of vitamin D physiology in adults, a summary of observational studies on vitamin D deficiency in critical illness, and an examination of the few clinical trials on vitamin D supplementation in intensive care patients.
Ciprofloxacin as a Trigger for Bullous Pemphigoid: The Second Case in the Literature
Authors: Cozzani Emanuele , Chinazzo Chiara , Burlando Martina , Romagnoli Marina , Parodi Aurora
Published: July 2015

Drug-induced bullous pemphigoid (DIBP) has been reported to be an autoimmune bullous disease induced or precipitated by several drugs, immunopathologically similar to classic bullous pemphigoid. Several medications may not only cause DIBP, including diuretics, antiarrythmics–antihypertensives, and recently antitumor necrosis factor agents, other drugs as chloroquine, but also rarely by antibiotics as amoxicillin and penicillin. The authors present the third case of DIBP induced by quinolones and the second case of localized DIBP triggered by oral ciprofloxacin. A DIBP can be suspected in old patients when they add or change some drugs in their normal medication regimen.
Neurocognitive Predictors of Academic Outcomes Among Childhood Leukemia Survivors
Authors: Moore Ida M. (Ki) , Lupo Philip J. , Insel Kathleen , Harris Lynnette L. , Pasvogel Alice , Koerner Kari M. , Adkins Kristin B. , Taylor Olga A. , Hockenberry Marilyn J.
Published: July 2015

Background:

Acute lymphoblastic leukemia is the most common pediatric cancer, and survival approaches 90%. Acute lymphoblastic leukemia survivors are more likely than healthy peers or siblings to experience academic underachievement, yet little is known about neurocognitive predictors of academic outcomes.

Objectives:

Objectives were to compare neurocognitive abilities to age-adjusted standardized norms, examine change over time in neurocognitive abilities, and establish neurocognitive predictors of academic outcomes.

Methods:

Seventy-one children were followed over the course of therapy. Cognitive abilities were assessed during induction when the child was in remission (baseline) and annually for 3 years (years 1, 2, and 3). Reading and mathematics abilities were assessed at year 3.

Results:

Fine motor dexterity was significantly below age-adjusted norms at all data points but showed improvement over time. Baseline visual-motor integration was within the reference range but significantly declined by year 3, and mean scores at years 2 and 3 were significantly below age-adjusted norms. Verbal short-term memory was significantly below age-adjusted norms at all assessments. Visual-motor integration predicted reading and mathematics abilities. Verbal short-term memory predicted reading abilities, and visual short-term memory predicted mathematics abilities.

Conclusions:

Central nervous system–directed therapy is associated with specific neurocognitive problems. Visual-spatial skills and verbal and visual short-term memory predict academic outcomes.

Implications for Practice:

Early assessment of visual-spatial perception and short-term memory can identify children at risk of academic problems. Children who are at risk of academic problems could benefit from a school-based individual educational program and/or educational intervention.
Pericarditis as the Presenting Feature of Graves Disease in a Pediatric Patient
Authors: Cullen Danielle , Munjal Neil , Chalal Hannah , Ramgopal Sriram , Tas Emir , Witchel Selma
Published: July 2015

Pericarditis is a rare presentation of thyrotoxicosis associated with Graves disease. This association has not been previously described in the pediatric literature. We report a 17-year-old male patient who presented with chest pain, dyspnea, and tachycardia. He was found to have diffuse ST-segment elevation consistent with pericarditis. At presentation, he was noted to have bilateral proptosis. Abnormal thyroid function studies and an elevated thyroid-stimulating hormone receptor antibody level confirmed the diagnosis of Graves thyrotoxicosis. The patient was treated with anti-inflammatory and antithyroid agents and improved in time. We discuss previously reported cases of Graves disease–associated pericarditis in adults, potential etiologies, and management strategies.
Visual Acuity in Orbital Floor Fractures
Authors: Richards Nikisha Q. , Brown Ninita H. , Kidwell Earl D.R.
Published: July 2015

Purpose:

At the time of this writing, there is no consensus regarding orbital floor fracture (OFFx) management. Proper management of OFFxs is imperative to help prevent well known complications and the possibility of decreased visual acuity (VA). The VA outcomes have been largely underreported in the literature. The current study identifies the complications of the different subspecialty management including VA outcome.

Methods:

A retrospective chart review study was performed to identify patients who suffered an OFFx and were managed by ophthalmology alone or in conjunction with either ENT or oral maxillofacial surgery at a single hospital. The primary outcome included VA at injury and subsequent visits. Secondary outcomes included epiphora, diplopia, enophthalmos, infraorbital dysesthesia, and decreased motility. Data were analyzed using Microsoft Office Excel 2007 using the Student t-test to find a P value < 0.05.

Results:

There were 54 patients with OFFx. The majority were Black (83.3%) and men (77.8%) with their average age at time of injury being 37.6 (SE = 17.02) years. The majority of OFFxs were secondary to assault (65%). The average follow-up was 2.84 (SE = 5.38) months. The 34 patients who did not undergo surgical correction had statistically significant improvement of their VA by 1 week after injury (P = 0.02). There was no statistically significant improvement in VA outcomes for surgical patients of ophthalmology (P = 0.45) or oral maxillofacial surgery (P = 0.12).

Conclusions:

Patients undergoing OFFx repair did not have improved VA. The VA of nonsurgical patients was statistically significantly improved by 1 week after injury (P 
= 0.02).
Immediate Single-Stage Cranioplasty Following Calvarial Resection for Benign and Malignant Skull Neoplasms Using Customized Craniofacial Implants
Authors: Berli Jens U. , Thomaier Lauren , Zhong Shuting , Huang Judy , Quinones Alfredo , Lim Michael , Weingart Jon , Brem Henry , Gordon Chad R.
Published: July 2015

Craniectomy defects following resection of calvarial lesions are most often reconstructed using on-table manufacturing. With the advent of computer-aided design/manufacturing and customized craniofacial implants (CCIs), there seems to be more suited alternatives. In this study, the authors report their institutional experience and outcome using immediate, single-stage, CCI-based reconstruction for benign and malignant skull neoplasm defects.

Methods:

A retrospective review of a prospectively maintained database of all implant cranioplasties performed between 2011 and 2014, by a single craniofacial surgeon at a tertiary academic medical institution was performed. Preoperative and postoperative computed tomography scans with 3D reconstruction were performed for the purpose of assessing adequate resection and reconstructive outcomes. Primary endpoints included length of surgery, predicted defect versus postoperative implant surface area, contour irregularities, and complications.

Results:

Of the 108 patients with cranioplasty identified, 7 patients were found to undergo immediate CCI-based reconstruction for calvarial neoplasms; 4 patients (4/7, 57%) presented with malignant pathology. All defects were >5 cm2. As compared with their original size, all implants were modified intraoperatively between 0.2% and 40.8%, with a mean of 13.8%. With follow-up ranging between 1 and 16 months, there were no implant-related complications identified. The immediate and long-term aesthetic results, as well as patient satisfaction, were ideal.

Conclusion:

With this preliminary experience, the authors have successfully demonstrated that immediate customized implant reconstructive techniques, by way of intraoperative modification, are both safe and feasible for benign and malignant skull neoplasms. The authors believe that with wider acceptance of this multidisciplinary approach and increased surgeon familiarity, this technique will soon become the reconstructive standard of care.
A Multivariate Analysis of Unilateral Cleft Lip and Palate Facial Skeletal Morphology
Authors: Starbuck John M. , Ghoneima Ahmed , Kula Katherine
Published: July 2015

Unilateral cleft lip and palate (UCLP) occurs when the maxillary and nasal facial prominences fail to fuse correctly during development, resulting in a palatal cleft and clefted soft and hard tissues of the dentoalveolus. The UCLP deformity may compromise an individual's ability to eat, chew, and speak. In this retrospective cross-sectional study, cone beam computed tomography (CBCT) images of 7–17-year-old individuals born with UCLP (n = 24) and age- and sex-matched controls (n = 24) were assessed. Coordinate values of three-dimensional anatomical landmarks (n = 32) were recorded from each CBCT image. Data were evaluated using principal coordinates analysis (PCOORD) and Euclidean distance matrix analysis (EDMA). Approximately 40% of morphometric variation is captured by PCOORD axes 1–3, and the negative and positive ends of each axis are associated with specific patterns of morphological differences. Approximately 36% of facial skeletal measures significantly differ by confidence interval testing (α = 0.10) between samples. Although significant form differences occur across the facial skeleton, strong patterns of morphological differences were localized to the lateral and superioinferior aspects of the nasal aperture, particularly on the clefted side of the face. The UCLP deformity strongly influences facial skeletal morphology of the midface and oronasal facial regions, and to a lesser extent the upper and lower facial skeletons. The pattern of strong morphological differences in the oronasal region combined with differences across the facial complex suggests that craniofacial bones are integrated and covary, despite influences from the congenital cleft.
Basal View Reference Photographs for Nasolabial Appearance Rating in Unilateral Cleft Lip and Palate
Authors: Rubin Marcie S. , Lowe Kristen M. , Clouston Sean , Shetye Pradip R. , Warren Stephen M. , Grayson Barry H.
Published: July 2015

The Asher-McDade system is a 5-point ordinal scale frequently used to rate the components of nasolabial appearance, including nasal form and nasal symmetry, in unilateral cleft lip and palate. Although reference photographs illustrating this scale have been identified for the frontal and right profile view, no reference photographs exist for the basal view. The aim of this study was to identify reference photographs for nasal form and nasal symmetry from the basal view to illustrate this scale and facilitate its use. Four raters assessed nasolabial appearance (form and symmetry) on basal view photographs of 50 children (average age 8 years) with a repaired cleft lip. Intraclass correlation coefficients show fair to moderate inter-rater reliability. Cronbach α indicated strong agreement between raters (0.77 nasal form; 0.78 nasal symmetry; 0.80 overall), along with low duplicate measurement error and strong internal consistency between the measures. The photographs with the highest agreement among raters were selected to illustrate each point on the 5-point scale for nasal form and for nasal symmetry, resulting in the selection of 10 reference photographs. The basal view reference photograph set developed from this study may complement existing reference photograph sets for other views and facilitate rating tasks.
A Comparison Between K-Wire Splinting and Intranasal Gauze Packing in Nasal Bone Fracture
Authors: Yu Sang Soo , Cho Pil Dong , Shin Hyun Woo , Rhee Seung Chul , Lee Soo Hyang
Published: July 2015

Background:

The aim of this study was to compare the outcomes between Kirschner wire (K-wire) splinting and intranasal packing.

Methods:

The authors performed a retrospective and comparative analysis of subjective patient discomfort and objective postoperative computed tomography (CT) imaging after closed reduction for treating type II and type III nasal bone fractures from April 2010 to April 2013 in 2 groups, 1 with K-wire splinting and 1 with intranasal packing.

Results:

Complaints of nasal obstruction, dry mouth, loss of appetite, and sleep disturbance were significantly less in K-wire group. Mean scores for concerns about aesthetics/postoperative asymmetry did not differ significantly between groups. There was no significant difference in accuracy of reduction and support provided to the reduced nasal bones between groups.

Conclusions:

The K-wire fixation can be considered a reliable and useful immobilization method for treating type II and type III nasal bone fractures.
Extensive Inflammatory Gingival Tumor in a Young Nonsmoking Woman
Authors: Hajji Farah , Beraud Guillaume , Genay Armel , Raoul Gwenaël , Faure Karine , Guery Benoit , Ferri Joël
Published: July 2015

Tuberculous lesions of the oral cavity are rare and can be a diagnostic challenge, particularly in young immunocompetent patients. Most of the cases in the literature are secondary to pulmonary disease, whereas primary form is uncommon. This paper presents a case of gingival tuberculosis in a 26-year-old Indian female patient, manifesting as a rapidly extensive ulcer. The diagnosis was confirmed by histopathology and immunological investigations. Although oral manifestations of tuberculosis are rare, clinicians should include them in the differential diagnosis of various types of oral ulcers. An early diagnosis with a prompt treatment can prevent complications and potential contaminations.
Accelerating Scientific Publication in Biology
Authors: Vale Ronald D.
Published: July 2015

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. More experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.
Allele specific expression and methylation in the bumblebee,Bombus terrestris
Authors: Lonsdale Zoë N. , Lee Kate D. , Kyriakidou Maria , Amarasinghe Harindra E. , Nathanael Despina , O’Connor Catherine J. , Mallon Eamonn B.
Published: July 2015

The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee,Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the, as yet unquantified, role of genetic cis effects in insect allele specific methylation and expression.
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks
Authors: Hansen Peter , Hecht Jochen , Ibrahim Daniel M. , Krannich Alexander , Truss Matthias , Robinson Peter N.
Published: July 2015

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein–DNA interactions based on various measures of enrichment of sequence reads. In this work, we introduce an algorithm, Q, that uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5′ ends of reads. We show that our method not only is substantially faster than several competing methods but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs. We show that Q has superior performance in the delineation of double RNAPII and H3K4me3 peaks surrounding transcription start sites related to a better ability to resolve individual peaks. The method is implemented in C+l+ and is freely available under an open source license.
Corporate social disclosures in Indonesia: stakeholders’ influence and motivation
Authors: Gunawan Juniati
Published: July 2015

Purpose

– This study aims to investigate stakeholders’ influence and motivation for Indonesian listed companies in practicing corporate social disclosures (CSDs) in their annual reports.

Design/methodology/approach

– A questionnaire was distributed to the upper level of management in the companies and attained 252 respondents.

Findings

– The findings show that “community” is the most stakeholder group that influence the practice of CSD and “creating a positive image” is the main motivation from companies in providing CSD.

Practical implications

– The research supports the majority of studies in CSD areas, especially in developing countries.

Originality/value

– Based on questionnaires, enriched by field visits and interviews, this paper provides evidence about stakeholder’s influences and company motivations in practising CSD. The study is valuable to understand the information disclosed in annual reports from both stakeholders’ and companies perspectives.
Plant phenological responses to a long‐term experimental extension of growing season and soil warming in the tussock tundra of Alaska
Authors: Khorsand Rosa Roxaneh , Oberbauer Steven F. , Starr Gregory , Parker La Puma Inga , Pop Eric , Ahlquist Lorraine , Baldwin Tracey
Published: July 2015

Climate warming is strongly altering the timing of season initiation and season length in the Arctic. Phenological activities are among the most sensitive plant responses to climate change and have important effects at all levels within the ecosystem. We tested the effects of two experimental treatments, extended growing season via snow removal and extended growing season combined with soil warming, on plant phenology in tussock tundra in Alaska from 1995 through 2003. We specifically monitored the responses of eight species, representing four growth forms: (i) graminoids (Carex bigellowii and Eriophorum vaginatum); (ii) evergreen shrubs (Ledum palustre, Cassiope tetragona, and Vaccinium vitis‐idaea); (iii) deciduous shrubs (Betula nana and Salix pulchra); and (iv) forbs (Polygonum bistorta). Our study answered three questions: (i) Do experimental treatments affect the timing of leaf bud break, flowering, and leaf senescence? (ii) Are responses to treatments species‐specific and growth form‐specific? and (iii) Which environmental factors best predict timing of phenophases? Treatment significantly affected the timing of all three phenophases, although the two experimental treatments did not differ from each other. While phenological events began earlier in the experimental plots relative to the controls, duration of phenophases did not increase. The evergreen shrub, Cassiope tetragona, did not respond to either experimental treatment. While the other species did respond to experimental treatments, the total active period for these species did not increase relative to the control. Air temperature was consistently the best predictor of phenology. Our results imply that some evergreen shrubs (i.e., C. tetragona) will not capitalize on earlier favorable growing conditions, putting them at a competitive disadvantage relative to phenotypically plastic deciduous shrubs. Our findings also suggest that an early onset of the growing season as a result of decreased snow cover will not necessarily result in greater tundra productivity.
Quantitative analysis of breast echotexture patterns in automated breast ultrasound images
Authors: Chang Ruey‐Feng , Hou Yu‐Ling , Lo Chung‐Ming , Huang Chiun‐Sheng , Chen Jeon‐Hor , Kim Won Hwa , Chang Jung Min , Bae Min Sun , Moon Woo Kyung
Published: July 2015

Purpose:

Breast tissue composition is considered to be associated with breast cancer risk. This study aimed to develop a computer‐aided classification (CAC) system to automatically classify echotexture patterns as heterogeneous or homogeneous using automated breast ultrasound (ABUS) images.

Methods:

A CAC system was proposed that can recognize breast echotexture patterns in ABUS images. For each case, the echotexture pattern was assessed by two expert radiologists and classified as heterogeneous or homogeneous. After neutrosophic image transformation and fuzzy c‐mean clusterings, the lower and upper boundaries of the fibroglandular tissues were defined. Then, the number of hypoechoic regions and histogram features were extracted from the fibroglandular tissues, and the support vector machine model with the leave‐one‐out cross‐validation method was utilized as the classifier. The authors’ database included a total of 208 ABUS images of the breasts of 104 females.

Results:

The accuracies of the proposed system for the classification of heterogeneous and homogeneous echotexture patterns were 93.48% (43/46) and 92.59% (150/162), respectively, with an overall Az (area under the receiver operating characteristic curve) of 0.9786. The agreement between the radiologists and the proposed system was almost perfect, with a kappa value of 0.814.

Conclusions:

The use of ABUS and the proposed method can provide quantitative information on the echotexture patterns of the breast and can be used to evaluate whether breast echotexture patterns are associated with breast cancer risk in the future.
Image‐based reconstruction of three‐dimensional myocardial infarct geometry for patient‐specific modeling of cardiac electrophysiology
Authors: Ukwatta Eranga , Arevalo Hermenegild , Rajchl Martin , White James , Pashakhanloo Farhad , Prakosa Adityo , Herzka Daniel A. , McVeigh Elliot , Lardo Albert C. , Trayanova Natalia A. , Vadakkumpadan Fijoy
Published: July 2015

Purpose:

Accurate three‐dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient‐specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two‐dimensional (2D) late‐gadolinium enhanced cardiac magnetic resonance (LGE‐CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE‐CMR images has been lacking. The purpose of this study was to address this need.

Methods:

The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low‐resolution (Lo‐res) clinical LGE‐CMR images. Their methodology employed the so‐called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high‐resolution (Hi‐res) LGE‐CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi‐res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method.

Results:

The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo‐ECGs.

Conclusions:

The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo‐res clinical 2D LGE‐CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.
High geothermal heat flux measured below the West Antarctic Ice Sheet
Authors: Fisher Andrew T. , Mankoff Kenneth D. , Tulaczyk Slawek M. , Tyler Scott W. , Foley Neil ,   and the WISSARD Science Team
Published: July 2015

First direct measurements of heat flux from Lake Whillans may explain abundance of subglacial lakes and ice streams in region.
Passion is just the start
Authors: McNutt Marcia
Published: July 2015

Last month, 65 Nobel laureates gathered in Lindau, Germany, for an annual exchange of knowledge between these most honored scientists and a group of selected young researchers from around the globe. To extend the reach of the conference,
Science
hosted a webinar to address a common concern of young scientists everywhere: persevering in science. Some advice on this topic may have been unexpected.
Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater
Authors: Montazeri Naim , Goettert Dorothee , Achberger Eric C. , Johnson Crystal N. , Prinyawiwatkul Witoon , Janes Marlene E.
Published: July 2015

Pathogenic enteric viruses are responsible for a wide range of infections in humans, with diverse symptoms. Raw and partially treated wastewaters are major sources of environmental contamination with enteric viruses. We monitored a municipal secondary wastewater treatment plant (New Orleans, LA) on a monthly basis for norovirus (NoV) GI and GII and enterovirus serotypes using multiplex reverse transcription-quantitative PCR (RT-qPCR) and microbial indicators of fecal contamination using standard plating methods. Densities of indicator bacteria (enterococci, fecal coliforms, and
Escherichia coli
) did not show monthly or seasonal patterns. Norovirus GII was more abundant than GI and, along with enterovirus serotypes, increased in influent during fall and spring. The highest NoV GI density in influent was in the fall, reaching an average of 4.0 log
10
genomic copies/100 ml. Norovirus GI removal (0.95 log
10
) was lower than that for GII, enterovirus serotypes, and male-specific coliphages (1.48 log
10
) or for indicator bacteria (4.36 log
10
), suggesting higher resistance of viruses to treatment. Male-specific coliphages correlated with NoV GII densities in influent and effluent (
r
= 0.48 and 0.76, respectively) and monthly removal, indicating that male-specific coliphages can be more reliable than indicator bacteria to monitor norovirus GII load and microbial removal. Dominant norovirus genotypes were classified into three GI genotypes (GI.1, GI.3, and GI.4) and four GII genotypes (GII.3, GII.4, GII.13, and GII.21), dominated by GI.1 and GII.4 strains. Some of the seasonal and temporal patterns we observed in the pathogenic enteric viruses were different from those of epidemiological observations.
Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems
Authors: Shaw Jennifer L. A. , Monis Paul , Weyrich Laura S. , Sawade Emma , Drikas Mary , Cooper Alan J.
Published: July 2015

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as
Nitrospira
, were detected.
Burkholderiales
were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.
Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured
Authors: Walke Jenifer B. , Becker Matthew H. , Hughey Myra C. , Swartwout Meredith C. , Jensen Roderick V. , Belden Lisa K.
Published: July 2015

Currently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogen
Batrachochytrium dendrobatidis
, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened by
B. dendrobatidis
. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (
Lithobates catesbeianus
), eastern newts (
Notophthalmus viridescens
), spring peepers (
Pseudacris crucifer
), and American toads (
Anaxyrus americanus
). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health.
The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family
Authors: Poudel Nirmal , Pfannstiel Jens , Simon Oliver , Walter Nadine , Papageorgiou Anastassios C. , Jendrossek Dieter
Published: July 2015

Pseudomonas aeruginosa
is one of only a few
Pseudomonas
species that are able to use acyclic monoterpenoids, such as citronellol and citronellate, as carbon and energy sources. This is achieved by the acyclic terpene utilization pathway (Atu), which includes at least six enzymes (AtuA, AtuB, AtuCF, AtuD, AtuE, AtuG) and is coupled to a functional leucine-isovalerate utilization (Liu) pathway. Here, quantitative proteome analysis was performed to elucidate the terpene metabolism of
P. aeruginosa
. The proteomics survey identified 187 proteins, including AtuA to AtuG and LiuA to LiuE, which were increased in abundance in the presence of citronellate. In particular, two hydratases, AtuE and the PA4330 gene product, out of more than a dozen predicted in the
P. aeruginosa
proteome showed an increased abundance in the presence of citronellate. AtuE (isohexenyl-glutaconyl coenzyme A [CoA] hydratase; EC 4.2.1.57) most likely catalyzes the hydration of the unsaturated distal double bond in the isohexenyl-glutaconyl-CoA thioester to yield 3-hydroxy-3-isohexenyl-glutaryl-CoA. Determination of the crystal structure of AtuE at a 2.13-Å resolution revealed a fold similar to that found in the hydratase (crotonase) superfamily and provided insights into the nature of the active site. The AtuE active-site architecture showed a significantly broader cavity than other crotonase superfamily members, in agreement with the need to accommodate the branched isoprenoid unit of terpenes. Glu139 was identified to be a potential catalytic residue, while the backbone NH groups of Gly116 and Gly68 likely form an oxyanion hole. The present work deepens the understanding of terpene metabolism in
Pseudomonas
and may serve as a basis to develop new strategies for the biotechnological production of terpenoids.