bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting Alpha Toxin and ClfA with a Multimechanistic Monoclonal-Antibody-Based Approach for Prophylaxis of Serious Staphylococcus aureus Disease
Authors: Tkaczyk C. , Hamilton M. M. , Sadowska A. , Shi Y. , Chang C.S. , Chowdhury P. , Buonapane R. , Xiao X. , Warrener P. , Mediavilla J. , Kreiswirth B. , Suzich J. , Stover C. K. , Sellman B. R.
Published: June 2016

Staphylococcus aureusproduces numerous virulence factors, each contributing different mechanisms to bacterial pathogenesis in a spectrum of diseases. Alpha toxin (AT), a cytolytic pore-forming toxin, plays a key role in skin and soft tissue infections and pneumonia, and a human anti-AT monoclonal antibody (MAb), MEDI4893*, has been shown to reduce disease severity in dermonecrosis and pneumonia infection models. However, interstrain diversity and the complex pathogenesis ofS. aureusbloodstream infections suggests that MEDI4893* alone may not provide adequate protection againstS. aureussepsis. Clumping factor A (ClfA), a fibrinogen binding protein, is an important virulence factor facilitatingS. aureusbloodstream infections. Herein, we report on the identification of a high-affinity anti-ClfA MAb, 11H10, that inhibits ClfA binding to fibrinogen, prevents bacterial agglutination in human plasma, and promotes opsonophagocytic bacterial killing (OPK). 11H10 prophylaxis reduced disease severity in a mouse bacteremia model and was dependent on Fc effector function and OPK. Additionally, prophylaxis with 11H10 in combination with MEDI4893* provided enhanced strain coverage in this model and increased survival compared to that obtained with the individual MAbs. The MAb combination also reduced disease severity in murine dermonecrosis and pneumonia models, with activity similar to that of MEDI4893* alone. These results indicate that an MAb combination targeting multiple virulence factors provides benefit over a single MAb neutralizing one virulence mechanism by providing improved efficacy, broader strain coverage, and protection against multiple infection pathologies.

IMPORTANCEAlternative strategies to broad-spectrum antibiotics are required to combat the antibiotic resistance epidemic. Previous attempts at active or passive immunization againstStaphylococcus aureustargeting single antigens have failed in clinical trials despite positive preclinical data. To provide broad disease and isolate coverage, an effective immunization strategy likely must target multiple virulence mechanisms of the pathogen. Herein, we tested a multimechanistic MAb combination targeting alpha toxin (AT) and clumping factor A (ClfA) that neutralizes AT-mediated cytotoxicity, blocks fibrinogen binding by ClfA, prevents bacterial agglutination, targets the bacteria for opsonophagocytic killing, and provides broad isolate coverage in a lethal-bacteremia model. Although each MAb alone was effective in bacteremia against some individual isolates, the MAb combination provided improved protection against other isolates. These results illustrate the importance of targeting multiple virulence mechanisms and highlight the potential for an MAb combination targeting AT and ClfA to effectively preventS. aureusdisease.
In the Limelight: Photoreceptors in Cyanobacteria
Authors: Bhaya Devaki
Published: June 2016

Certain cyanobacteria look green if grown in red light and vice versa. This dramatic color change, called complementary chromatic adaptation (CCA), is caused by alterations of the major colored light-harvesting proteins. A major controller of CCA is the cyanobacteriochrome (CBCR) RcaE, a red-green reversible photoreceptor that triggers a complex signal transduction pathway. Now, a new study demonstrates that CCA is also modulated by DpxA, a CBCR that senses yellow and teal (greenish blue) light. DpxA acts to expand the range of wavelengths that can impact CCA, by fine-tuning the process. This dual control of CCA might positively impact the fitness of cells growing in the shade of competing algae or in a water column where light levels and spectral quality change gradually with depth. This discovery adds to the growing number of light-responsive phenomena controlled by multiple CBCRs. Furthermore, the diverse CBCRs which are exclusively found in cyanobacteria have significant biotechnological potential.
Dengue Virus Genome Uncoating Requires Ubiquitination
Authors: Byk Laura A. , Iglesias Néstor G. , De Maio Federico A. , Gebhard Leopoldo G. , Rossi Mario , Gamarnik Andrea V.
Published: June 2016

The process of genome release or uncoating after viral entry is one of the least-studied steps in the flavivirus life cycle. Flaviviruses are mainly arthropod-borne viruses, including emerging and reemerging pathogens such as dengue, Zika, and West Nile viruses. Currently, dengue virus is one of the most significant human viral pathogens transmitted by mosquitoes and is responsible for about 390 million infections every year around the world. Here, we examined for the first time molecular aspects of dengue virus genome uncoating. We followed the fate of the capsid protein and RNA genome early during infection and found that capsid is degraded after viral internalization by the host ubiquitin-proteasome system. However, proteasome activity and capsid degradation were not necessary to free the genome for initial viral translation. Unexpectedly, genome uncoating was blocked by inhibiting ubiquitination. Using different assays to bypass entry and evaluate the first rounds of viral translation, a narrow window of time during infection that requires ubiquitination but not proteasome activity was identified. In this regard, ubiquitin E1-activating enzyme inhibition was sufficient to stabilize the incoming viral genome in the cytoplasm of infected cells, causing its retention in either endosomes or nucleocapsids. Our data support a model in which dengue virus genome uncoating requires a nondegradative ubiquitination step, providing new insights into this crucial but understudied viral process.

IMPORTANCE
Dengue is the most significant arthropod-borne viral infection in humans. Although the number of cases increases every year, there are no approved therapeutics available for the treatment of dengue infection, and many basic aspects of the viral biology remain elusive. After entry, the viral membrane must fuse with the endosomal membrane to deliver the viral genome into the cytoplasm for translation and replication. A great deal of information has been obtained in the last decade regarding molecular aspects of the fusion step, but little is known about the events that follow this process, which leads to viral RNA release from the nucleocapsid. Here, we investigated the fate of nucleocapsid components (capsid protein and viral genome) during the infection process and found that capsid is degraded by the ubiquitin-proteasome system. However, in contrast to that observed for other RNA and DNA viruses, dengue virus capsid degradation was not responsible for genome uncoating. Interestingly, we found that dengue virus genome release requires a nondegradative ubiquitination step. These results provide the first insights into dengue virus uncoating and present new opportunities for antiviral intervention.
Urachal adenocarcinoma incidentally discovered in a young woman at elective caesarean section
Authors: Goldman Hariette , Sowter Steven
Published: June 2016

Urachal adenocarcinoma is a rare non-urothelial malignancy that represents only 0.5% of all vesical cancers. Urachal adenocarcinoma most commonly occurs in the 5th to 7th decade. We describe a case of a 35-year-old woman (G3P1) who presented at 20 weeks pregnancy with two episodes of post-coital bleeding. Ultrasound demonstrated a uterine mass measuring 59×43×56 mm, presumed to be a leiomyoma. The decision was made to proceed to caesarean section at 38 weeks, given the progression of the presumed leiomyoma. A 2 cm bladder dome mass was incidentally discovered at the time of the caesarean section and an urgent intraoperative urology consult was sought. Resultantly, the bladder mass was dissected to the dome, and pathology returned urachal adenocarcinoma. This case report considers the treatment decisions involved when faced with urachal adenocarcinoma and reviews the literature surrounding this rare malignancy.
Type 1 Brugada pattern ECG due to supra-therapeutic phenytoin level
Authors: Swe Thein , Bhattarai Bikash , Dufresne Alix
Published: June 2016

Brugada syndrome is an inherited arrhythmogenic disease, characterised by a coved-type ST segment elevation in right precordial leads and an increased risk of sudden cardiac death due to ventricular arrhythmia. To unmask or exacerbate a Brugada ECG pattern, class IA or IC antiarrhythmic agents are used, and clinicians can predict sudden cardiac death in a high-risk patient. However, phenytoin, one of the class IB agents, may induce a Brugada pattern ECG at a supra-therapeutic level and this association has rarely been reported. We describe a case of a patient with a phenytoin level about twice as high as the therapeutic level, which led to the emergence of a type 1 Brugada pattern ECG. Awareness should be made between this important association of supra-therapeutic phenytoin level and type 1 Brugada pattern ECG because symptomatic Brugada syndrome can lead to sudden cardiac death.
Fungus ball in the nasal cavity mimicking a rhinolith
Authors: Bhandarkar Ajay M , Kudva Ranjini , Damry Keshwar , Radhakrishnan Balaji
Published: June 2016

A 63-year-old man presented to the outpatient department of our tertiary care hospital, with unilateral left nasal obstruction, foul smelling nasal discharge and occasional mild epistaxis. On examination, a hard greyish black mass was noted in the anteroinferior portion of the inferior turbinate, with extension posteriorly into the inferior meatus with surrounding unhealthy granulation tissue. Provisional diagnosis of rhinolith was surprisingly reversed by histopathology, which suggested the presence of anAspergillusfungus ball withActinomycescolonisation.
Multiple brown tumours from parathyroid carcinoma
Authors: Dagang Daryl Jade Tardo , Gutierrez Jerico Baliton , Sandoval Mark Anthony Santiago , Lantion-Ang Frances Lina
Published: June 2016

We report a case of a 29-year-old woman who suffered from severe bilateral inguinal pain and left mandibular mass. CT scan showed innumerable expansile osteolytic bone masses on the iliac wings, femur, ribs and vertebral bodies, diffuse skeletal osteopaenia, calyceal lithiasis on the right kidney and a left thyroid mass. Ionised calcium and intact parathyroid hormone (PTH) were elevated. Parathyroid sestamibi scan showed a hyperfunctioning left inferior parathyroid gland. Biopsy of the left mandibular mass was consistent with brown tumour. The patient underwent parathyroidectomy of the enlarged parathyroid gland. Final histopathology, however, revealed parathyroid carcinoma, 4.7 cm in widest dimension, with capsular and vascular space invasion. The patient underwent repeat surgery, specifically, left thyroid lobectomy, isthmectomy and central node dissection. Intact PTH decreased from 681.3 to 74 pg/mL (normal range: 10–65) 24 hours postoperatively. Follow-up at 6 months showed normal serum calcium levels, size reduction of bone lesions and improvement of quality of life.
Evaluating the accessibility and utility of HIV-related point-of-care diagnostics for maternal health in rural South Africa: a study protocol
Authors: Mashamba-Thompson T P , Drain P K , Sartorius B
Published: June 2016

Introduction

Poor healthcare access is a major barrier to receiving antenatal care and a cause of high maternal mortality in South Africa (SA). ‘Point-of-care’ (POC) diagnostics is a powerful emerging healthcare approach to improve healthcare access. This study focuses on evaluating the accessibility and utility of POC diagnostics for maternal health in rural SA primary healthcare (PHC) clinics in order to generate a model framework of implementation of POC diagnostics in rural South African clinics.

Method and analyses

We will use several research methods, including a systematic review, quasi-experiments, survey, key informant interviews and audits. We will conduct a systematic review and experimental study to determine the impact of POC diagnostics on maternal health. We will perform a cross-sectional case study of 100 randomly selected rural primary healthcare clinics in KwaZulu-Natal to measure the context and patterns of POC diagnostics access and usage by maternal health providers and patients. We will conduct interviews with relevant key stakeholders to determine the reasons for POC deficiencies regarding accessibility and utility of HIV-related POC diagnostics for maternal health. We will also conduct a vertical audit to investigate all the quality aspects of POC diagnostic services including diagnostic accuracy in a select number of clinics. On the basis of information gathered, we will propose a model framework for improved implementation of POC diagnostics in rural South African public healthcare clinics. Statistical (Stata-13) and thematic (NVIVO) data analysis will be used in this study.

Ethics and dissemination

The study protocol was approved by the Ethics Committee of the University of KwaZulu-Natal (BE 484/14) and the KwaZulu-Natal Department of Health based on the Helsinki Declaration (HRKM 40/15). Findings of this study will be disseminated electronically and in print. They will be presented to conferences related to HIV/AIDS, diagnostics, maternal health and strengthening of health systems.
Prevalence of clinically significant decisional conflict: an analysis of five studies on decision-making in primary care
Authors: Thompson-Leduc Philippe , Turcotte Stéphane , Labrecque Michel , Légaré France
Published: June 2016

Objectives

Unresolved clinically significant decisional conflict (CSDC) in patients following a consultation with health professionals is often the result of inadequate patient involvement in decision-making and may result in poor outcomes. We sought to identify the prevalence of CSDC in studies on decision-making in primary care and to explore its risk factors.

Setting

We performed a secondary analysis of existing data sets from studies conducted in Primary Care Practice-Based Research Networks in Québec and Ontario, Canada.

Participants

Eligible studies included a patient-reported measure on the 16-item Decisional Conflict Scale (DCS) following a decision made with a healthcare professional with no study design restriction.

Primary and secondary outcome measures

CSDC was defined as a score ≥25/100 on the DCS. The prevalence of CSDC was stratified by sex; and patient-level logistic regression analysis was performed to explore its potential risk factors. Data sets of studies were analysed individually and qualitatively compared.

Results

5 projects conducted between 2003 and 2010 were included. They covered a range of decisions: prenatal genetic screening, antibiotics for acute respiratory infections and miscellaneous. Altogether, the 5 projects gathered data from encounters with a total of 1338 primary care patients (69% female; range of age 15–83). The prevalence of CSDC in patients varied across studies and ranged from 10.3% (95% CI 7.2% to 13.4%) to 31.1% (95% CI 26.6% to 35.6%). Across the 5 studies, risk factors of CSDC included being male, living alone and being 45 or older.

Conclusions

Prevalence of CSDC in patients who had enrolled in studies conducted in primary care contexts was substantial and appeared to vary according to the type of decision as well as to patient characteristics such as sex, living arrangement and age. Patients presenting risk factors of CSDC should be offered tools to increase their involvement in decision-making.
Lumbar intervertebral disc degeneration and related factors in Korean firefighters
Authors: Jang Tae-Won , Ahn Yeon-Soon , Byun Junsu , Lee Jong-In , Kim Kun-Hyung , Kim Youngki , Song Han-Soo , Lee Chul-Gab , Kwon Young-Jun , Yoon Jin-Ha , Jeong Kyoungsook
Published: June 2016

Objectives

The job of firefighting can cause lumbar burden and low back pain. This study aimed to identify the association between age and lumbar intervertebral disc degeneration and whether the association differs between field and administrative (non-field) firefighters.

Methods

Subjects were selected using a stratified random sampling method. Firefighters were stratified by geographic area, gender, age and type of job. First, 25 fire stations were randomly sampled considering regional distribution. Then firefighters were stratified by gender, age and their job and randomly selected among the strata. A questionnaire survey and MRI scans were performed, and then four radiologists used Pfirrmann classification methods to determine the grade of lumbar intervertebral disc degeneration.

Results

Pfirrmann grade increased with lumbar intervertebral disc level. Analysis of covariance showed that age was significantly associated with lumbar intervertebral disc degeneration (p<0.05). The value of β (parameter estimate) was positive at all lumbar intervertebral disc levels and was higher in the field group than in the administrative group at each level. In logistic regression analysis, type of job was statistically significant only with regard to the L4–5 intervertebral disc (OR 3.498, 95% CI 1.241 to 9.860).

Conclusions

Lumbar intervertebral disc degeneration is associated with age, and field work such as firefighting, emergency and rescue may accelerate degeneration in the L4–5 intervertebral disc. The effects of field work on lumbar intervertebral disc degeneration were not clear in discs other than at the level L4–5.
Protocol for the ‘Virtual Traveller’ cluster-randomised controlled trial: a behaviour change intervention to increase physical activity in primary-school Maths and English lessons
Authors: Norris E , Dunsmuir S , Duke-Williams O , Stamatakis E , Shelton N
Published: June 2016

Introduction

Physical activity (PA) has been shown to be an important factor for health and educational outcomes in children. However, a large proportion of children's school day is spent in sedentary lesson-time. There is emerging evidence about the effectiveness of physically active lessons: integrating physical movements and educational content in the classroom. ‘Virtual Traveller’ is a novel 6-week intervention of 10-min sessions performed 3 days per week, using classroom interactive whiteboards to integrate movement into primary-school Maths and English teaching. The primary aim of this project is to evaluate the effect of the Virtual Traveller intervention on children's PA, on-task behaviour and student engagement.

Methods and analysis

This study will be a cluster-randomised controlled trial with a waiting-list control group. Ten year 4 (aged 8–9 years) classes across 10 primary schools will be randomised by class to either the 6-week Virtual Traveller intervention or the waiting-list control group. Data will be collected 5 times: at baseline, at weeks 2 and 4 of the intervention, and 1 week and 3 months postintervention. At baseline, anthropometric measures, 4-day objective PA monitoring (including 2 weekend days; Actigraph accelerometer), PA and on-task behaviour observations and student engagement questionnaires will be performed. All but anthropometric measures will be repeated at all other data collection points. Changes in overall PA levels and levels during different time-periods (eg, lesson-time) will be examined. Changes in on-task behaviour and student engagement between intervention groups will also be examined. Multilevel regression modelling will be used to analyse the data. Process evaluation will be carried out during the intervention period.

Ethics and dissemination

The results of this study will be disseminated through peer-review publications and conference presentations. Ethical approval was obtained through the University College London Research Ethics Committee (reference number: 3500-004).
Collaborative healthcare remodelling through sequential simulation: a patient and front-line staff perspective
Authors: Weldon Sharon-Marie , Kneebone Roger , Bello Fernando
Published: June 2016

Background

The Department of health funded an initiative to pioneer new approaches that would create a more integrated form of care.

Local problem

In order to receive funding, local Clinical Commissioning Groups were required to engage a range of stakeholders in a practical approach that generated the development of an integrated model of care.

Intervention

Two sequential simulation (SqS) workshops comprising 65 and 93 participants, respectively, were designed using real patient scenarios from the locality, covering areas of general practice, community health and adult social care. Workshops were attended by a diverse group of stakeholders. The first workshop addressed current care pathways and the second modelled ideal care pathways generated from the data obtained at the first workshop.

Methods

Discussions were captured through video recording, field-notes and pre and post questionnaires. Data was collated, transcribed and analysed through a combination of descriptive statistics and thematic analysis.

Results

The questionnaires revealed that attendees strongly agreed that they had had an opportunity to contribute to all discussions and raise questions, concerns and ideas (100%). Pre and post knowledge of current and new models of care was vastly improved. The opportunity to share information and to network was valued, with the SqS approach seen as breaking professional barriers (100%).

Conclusions

Simulation can be used as a tool to engage stakeholders in designing integrated models of care. The systematic data collection from the diverse ideas generated also allows for a much-needed ‘ear’ to those providing the solutions, as well as a legitimate and balanced perspective.
TheCalreticulingene and myeloproliferative neoplasms
Authors: Clinton Aoibhinn , McMullin Mary Frances
Published: June 2016

The Philadelphia negative myeloproliferative neoplasms include polycythaemia vera (PV), essential thrombocytopenia (ET) and primary myelofibrosis (PMF). Patients with these conditions were mainly thought to harbourJAK2V617Fmutations or anMyeloproliferative leukaemia(MPL) substitution. In 2013, two revolutionary studies identified recurrent mutations in a gene that encodes the protein calreticulin (CALR). This mutation was detected in patients with PMF and ET with non-mutatedJAK2orMPLbut was absent in patients with PV. TheCALRgene encodes the calreticulin protein, which is a multifactorial protein, mainly located in the endoplasmic reticulum in chromosome 19 and regulates calcium homeostasis, chaperones and has also been implicated in multiple cellular processes including cell signalling, regulation of gene expression, cell adhesion, autoimmunity and apoptosis. Somatic 52 bp deletions and recurrent 52 bp insertion mutations inCALRwere detected and all resulted in frameshift and clusters in exon 9 of the gene. This review will summarise the current knowledge on theCALRgene and mutation of the gene in pathological conditions and patient phenotypes.
Resolution of Abnormal Cardiac Mri T2 Signal following Immune Suppression for Cardiac Sarcoidosis
Authors: Crouser Elliott D , Ruden Emily , Julian Mark W , Raman Subha V
Published: June 2016

Cardiac MR (CMR) with late gadolinium enhancement is commonly used to detect cardiac damage in the setting of cardiac sarcoidosis. The addition of T2 mapping to CMR was recently shown to enhance cardiac sarcoidosis detection and correlates with increased cardiac arrhythmia risk. This study was conducted to determine if CMR T2 abnormalities and related arrhythmias are reversible following immune suppression therapy. A retrospective study of subjects with cardiac sarcoidosis with abnormal T2 signal on baseline CMR and a follow-up CMR study at least 4 months later was conducted at The Ohio State University from 2011 to 2015. Immune suppression treated participants had a significant reduction in peak myocardial T2 value (70.0±5.5 vs 59.2±6.1 ms, pretreatment vs post-treatment; p=0.017), and 83% of immune suppression treated subjects had objective improvement in cardiac arrhythmias. Two subjects who had received inadequate immune suppression treatment experienced progression of cardiac sarcoidosis. This report indicates that abnormal CMR T2 signal represents an acute inflammatory manifestation of cardiac sarcoidosis that is potentially reversible with adequate immune suppression therapy.
H9N2 low pathogenic avian influenza in Pakistan (2012–2015)
Authors: Lee Dong‐Hun , Swayne David E. , Sharma Poonam , Rehmani Shafqat Fatima , Wajid Abdul , Suarez David L. , Afonso Claudio L.
Published: June 2016

Significant economic losses from deaths and decreased egg production have resulted from H9N2 low pathogenic avian influenza virus (LPAIV) infections in poultry across North Africa, the Middle East and Asia. The H9N2 LPAIVs have been endemic in Pakistani poultry since 1996, but no new viruses have been reported since 2010. Because novel genotypes of Pakistani H9N2 contain mammalian host‐specific markers, recent surveillance is essential to better understand any continuing public health risk. Here the authors report on four new H9N2 LPAIVs, three from 2015 and one from 2012. All of the viruses tested in this study belonged to Middle East B genetic group of G1 lineage and had PAKSSR/G motif at the haemagglutinin cleavage site. The mammalian host‐specific markers at position 226 in the haemagglutinin receptor‐binding site and internal genes suggest that Pakistan H9N2 viruses are still potentially infectious for mammals. Continued active surveillance in poultry and mammals is needed to monitor the spread and understand the potential for zoonotic infection by these H9N2 LPAIVs.
Cumulative incidence and risk factors for limber tail in the Dogslife labrador retriever cohort
Authors: Pugh C. A. , de C. Bronsvoort B. M. , Handel I. G. , Querry D. , Rose E. , Summers K. , Clements D. N.
Published: June 2016

Limber tail is a condition that typically affects larger working breeds causing tail limpness and pain, resolving without veterinary intervention. It is poorly understood and the disease burden has not been well characterised. Data collected from owners of the Dogslife cohort of Labrador Retrievers have been used to describe incidents and a case–control study was undertaken to elucidate risk factors with 38 cases and 86 controls. The cumulative incidence of unexplained tail limpness was 9.7 per cent. Swimming is not a necessary precursor for limber tail, but it is a risk factor (OR=4.7) and working dogs were more susceptible than non‐working dogs (OR=5.1). Higher latitudes were shown to be a risk factor for developing the condition and the case dogs were more related to each other than might be expected by chance. This suggests that dogs may have an underlying genetic predisposition to developing the condition. This study is the first, large‐scale investigation of limber tail and the findings reveal an unexpectedly high illness burden. Anecdotally, accepted risk factors have been confirmed and the extent of their impact has been quantified. Identifying latitude and a potential underlying genetic predisposition suggests avenues for future work on this painful and distressing condition.
Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair
Authors: Scott Daniel D. , Oeffinger Marlene
Published: June 2016

The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
Genetic resistance to white pine blister rust in limber pine (Pinus flexilis): major gene resistance in a northern population
Authors: Sniezko Richard A. , Danchok Robert , Savin Douglas P. , Liu Jun-Jun , Kegley Angelia
Published: June 2016

Limber pine, Pinus flexilis E. James, a wide-ranging tree species in western North America, is highly susceptible to white pine blister rust (WPBR), caused by the non-native fungal pathogen Cronartium ribicola J.C. Fisch. The Canadian populations in particular have been heavily impacted, and in 2014, limber pine was designated endangered in Canada by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). Little is known about genetic resistance to WPBR in limber pine, but major gene resistance (MGR) has been characterized in some populations in the United States. This study examines resistance in seedling families from 13 parent trees from British Columbia, Alberta, and Oregon, representing the northern- and northwestern-most populations. Most families were susceptible, with 100% of the seedlings cankered, but one family from Alberta segregated 1:1 for cankered and canker free. This is the first report of (a) MGR in Canada of any of the four species of five-needle pines native to Canada and (b) any resistance in limber pine in Canadian populations and is the northernmost known incidence of putative R-gene resistance in a natural stand of any five-needle pine species. Many of the Canadian selections were from stands with high incidence of WPBR infection, and their high susceptibility in this trial suggests that further infection and mortality is likely in the Canadian populations.
Effects of petroleum hydrocarbon concentration and bulk density on the hydraulic properties of lean oil sand overburden
Authors: Pernitsky Trent , Hu Wei , Si Bing Cheng , Barbour Lee
Published: June 2016

In the Alberta oil sands, sand containing less than 8% petroleum hydrocarbon (PHC) is referred to as lean oil sand (LOS) and is used as subsoil in reclamation. The objective of this study was to determine how bulk density and PHC concentration affect the hydraulic properties of LOS. The LOS was packed in soil cores at varying bulk densities and PHC concentrations, representing the range in these parameters that occur in the reclamation setting. The cores were placed on a tension table and pressure plates to measure water retention. The constant head method was used to measure the saturated hydraulic conductivity (Ks) of the LOS. Results show that increasing PHC concentration reduced the water retention of LOS due to the presence of PHCs in soil micropores. PHC concentration also had a significant effect on the van Genuchten curve fitting parameters for the water retention curve, although the shape of the curves remained similar regardless of PHC content. Furthermore, there is a significant reduction in Ks at the high bulk density and high PHC concentrations (3.25%–7.48%), compared with low PHC concentrations (0%–1.63%). Due to the reduced Ks with increased PHCs and bulk density, LOS used as the base material in reclamation will reduce percolation and increase water storage in the reclamation soil cover.
Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea)
Authors: Shi Ainong , Mou Beiquan
Published: June 2016

Leafminer (Liriomyza langei) is a major insect pest of many important agricultural crops, including spinach (Spinacia oleracea). Use of genetic resistance is an efficient, economic, and environment-friendly method to control this pest. The objective of this research was to conduct association analysis and identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance in spinach germplasm. A total of 300 USDA spinach germplasm accessions were used for the association analysis of leafminer resistance. Genotyping by sequencing (GBS) was used for genotyping and 783 SNPs from GBS were used for association analysis. The leafminer resistance showed a near normal distribution with a wide range from 1.1 to 11.7 stings per square centimeter leaf area, suggesting that the leafminer resistance in spinach is a complex trait controlled by multiple genes with minor effect in this spinach panel. Association analysis indicated that five SNP markers, AYZV02040968_7171, AYZV02076752_412, AYZV02098618_4615, AYZV02147304_383, and AYZV02271373_398, were associated with the leafminer resistance with LOD 2.5 or higher. The SNP markers may be useful for breeders to select plants and lines for leafminer resistance in spinach breeding programs through marker-assisted selection.
Modification of superconducting and resistive properties of HoBa2Cu3O7−δ single crystals under application-removal of high hydrostatic pressure
Authors: Vovk R. V. , Khadzhai G. Ya. , Dobrovolskiy O. V. , Kamchatna S. N. , Chroneos A.
Published: June 2016

The influence of a high hydrostatic pressure on the basal-plane electrical resistance along the twin boundaries in underdoped HoBa2Cu3O[Formula: see text] single crystals is investigated. An enhancement of the phase segregation caused by the high-pressure-induced redistribution of the labile oxygen has been revealed. The temperature dependences of the electrical resistance above [Formula: see text] can be approximated well within the framework of the model of [Formula: see text] electron–phonon scattering.
Simulating the frontal instability of lock-exchange density currents with dissipative particle dynamics
Authors: Li Yanggui , Geng Xingguo , Wang Heping , Zhuang Xin , Ouyang Jie
Published: June 2016

The frontal instability of lock-exchange density currents is numerically investigated using dissipative particle dynamics (DPD) at the mesoscopic particle level. For modeling two-phase flow, the “color” repulsion model is adopted to describe binary fluids according to Rothman–Keller method. The present DPD simulation can reproduce the flow phenomena of lock-exchange density currents, including the lobe-and-cleft instability that appears at the head, as well as the formation of coherent billow structures at the interface behind the head due to the growth of Kelvin–Helmholtz instability. Furthermore, through the DPD simulation, some small-scale characteristics can be observed, which are difficult to be captured in macroscopic simulation and experiment.
The effect of CH4/H2 ratio on the surface properties of HDPE treated by CHx ion beam bombardment
Authors: Ding Wanyu , Guo Yuanyuan , Ju Dongying , Sato Susumu , Tsunoda Teruo
Published: June 2016

The surface of high density polyethylene (HDPE) substrate was bombarded by the CH[Formula: see text] group ion beam, which was generated by the mixture of CH4/H2. Varying the CH4/H2 ratio, HDPE surfaces with different chemical bond structures and properties were obtained. Raman and XPS results show that [Formula: see text] and [Formula: see text] bond structures are formed at HDPE surface bombarded by CH[Formula: see text] group ions. The [Formula: see text] bond fraction at bombarded HDPE surface depends on the H2 ratio in CH4/H2 mixture, because the H ion/atom/molecule can improve the growth of [Formula: see text] bond structure. For HDPE surface bombarded by CH4/H2 = 50/50, [Formula: see text] bond fraction reaches the maximum of 30.5%, the surface roughness decreases to 17.04 nm, and the static contact angle of polar H2O molecule increased to 140.2[Formula: see text].
A Simple Chaotic Flow with a Plane of Equilibria
Authors: Jafari Sajad , Sprott J. C. , Molaie Malihe
Published: June 2016

Using a systematic computer search, a simple four-dimensional chaotic flow was found that has the unusual feature of having a plane of equilibria. Such a system belongs to a newly introduced category of chaotic systems with hidden attractors that are important and potentially problematic in engineering applications.
Dynamic Analysis of a Reaction–Diffusion Rumor Propagation Model
Authors: Zhao Hongyong , Zhu Linhe
Published: June 2016

The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.
Big Bang Bifurcation Analysis and Allee Effect in Generic Growth Functions
Authors: Leonel Rocha J. , Taha Abdel-Kaddous , Fournier-Prunaret D.
Published: June 2016

The main purpose of this work is to study the dynamics and bifurcation properties of generic growth functions, which are defined by the population size functions of the generic growth equation. This family of unimodal maps naturally incorporates a principal focus of ecological and biological research: the Allee effect. The analysis of this kind of extinction phenomenon allows to identify a class of Allee’s functions and characterize the corresponding Allee’s effect region and Allee’s bifurcation curve. The bifurcation analysis is founded on the performance of fold and flip bifurcations. The dynamical behavior is rich with abundant complex bifurcation structures, the big bang bifurcations of the so-called “box-within-a-box” fractal type being the most outstanding. Moreover, these bifurcation cascades converge to different big bang bifurcation curves with distinct kinds of boxes, where for the corresponding parameter values several attractors are associated. To the best of our knowledge, these results represent an original contribution to clarify the big bang bifurcation analysis of continuous 1D maps.
Experimental gravitation
Authors: Lämmerzahl Claus , Di Virgilio Angela
Published: June 2016

100 years after the invention of General Relativity (GR) and 110 years after the development of Special Relativity (SR) we have to state that until now no single experiment or observation allows any doubt about the validity of these theories within the accuracy of the available data. Tests of GR can be divided into three categories: (i) test of the foundations of GR, (ii) tests of the consequences of GR, and (iii) test of the interplay between GR and quantum mechanics. In the first category, we have tests of the Einstein Equivalence Principle and the structure of the Newton axioms, in the second category we have effects like the gravitational redshift, light defection, gravitational time delay, the perihelion shift, the gravitomagnetic effects as the Lense–Thirring and Schiff effect, and gravitational waves. Tests of the effects of gravity on quantum systems are a first step towards experiments searching for a quantum gravity theory. In this paper, we also highlight practical applications in positioning, geodesy, and the International Atomic Time. After 100 years, GR can now definitely be regarded also as practical and applied science.
Shadows of Kerr black holes with and without scalar hair
Authors: Cunha Pedro V. P. , Herdeiro Carlos A. R. , Radu Eugen , Rúnarsson Helgi F.
Published: June 2016

For an observer, the Black Hole (BH) shadow is the BHs apparent image in the sky due to the gravitational lensing of nearby radiation, emitted by an external source. A recent class of solutions dubbed Kerr BHs with scalar hair possess smaller shadows than the corresponding Kerr BHs and, under some conditions, novel exotic shadow shapes can arise. Thus, these hairy BHs could potentially provide new shadow templates for future experiments such as the Event Horizon Telescope. In order to obtain the shadows, the backward ray-tracing algorithm is briefly introduced, followed by numerical examples of shadows of Kerr BHs with scalar hair contrasting with the Kerr analogues. Additionally, an analytical solution for the Kerr shadow is derived in closed form for a ZAMO observer at an arbitrary position.
Synthesis and characterization of chlorophyllaenol derivatives: Chlorophyllatert-butyldimethylsilyl-enol ether and 131-deoxo-131, 132-didehydro-chlorophylla
Authors: Hynninen Paavo H. , Mesilaakso Markku
Published: June 2016

Using the sterically hindered base, 1,8-diazabicyclo[5.4.0]undec-7-ene, for enolization and tert-butyldimethylsilyl-trifluoromethanesulfonate for silylation, chlorophyll (Chl) [Formula: see text] produced after 15 min at 0 [Formula: see text]C in deaerated pyridine solution under argon, after work-up and chromatographic purification on a sucrose column, tert-butyldimethylsilyl-enol ether of Chl [Formula: see text] in a yield of 77%. The 131-deoxo-131,132-didehydro-chlorophyll [Formula: see text], was obtained in a yield of 23% through a reaction sequence, where Chl [Formula: see text] was first reduced with sodium borohydride to 13[Formula: see text]-hydroxy-Chl [Formula: see text], which via demetalation yielded 13[Formula: see text]-hydroxypheophytin [Formula: see text]. In the presence of the sterically hindered base, 1,8-bis(dimethylamino)naphthalene, trifluoroacetylimidazole dehydrated 13[Formula: see text]-hydroxypheophytin [Formula: see text] to 131-deoxo-131,132-didehydro-pheophytin [Formula: see text], which after metalation yielded 131-deoxo-131,132-didehydro-Chl [Formula: see text]. Using 1,8-bis(dimethylamino)naphthalene and trifluoroacetylimidazole, the straight conversion of 13[Formula: see text]-hydroxy-Chl [Formula: see text] to 131-deoxo-131,132-didehydro-Chl [Formula: see text] was found unsuccessful. The major products were characterized by electronic absorption spectra (UV-vis) and practically completely assigned1H and [Formula: see text]C NMR spectra. Some intermediates of the syntheses were also characterized by ESI-TOF mass spectra. Compared with Chl [Formula: see text], the macrocyclic ring-current in the synthesized Chl [Formula: see text] enol derivatives was found weakened by the expansion of the [Formula: see text]-system to include the isocyclic ring E. Nevertheless, these enol derivatives were still considered to be diamagnetic and aromatic. The possibility of the functional role of the enol derivatives of chlorophyll in photosynthesis is discussed.
Improving PCM Endurance with a Constant-Cost Wear Leveling Design
Authors: Chang Yu-Ming , Hsiu Pi-Cheng , Chang Yuan-Hao , Chen Chi-Hao , Kuo Tei-Wei , Wang Cheng-Yuan Michael
Published: June 2016

Improving PCM endurance is a fundamental issue when it is considered as an alternative to replace DRAM as main memory. Memory-based wear leveling (WL) is an effective way to improve PCM endurance, but its major challenge is how to efficiently determine the appropriate memory pages for allocation or swapping. In this article, we present a constant-cost WL design that is compatible with existing memory management. Two implementations, namely bucket-based and array-based WL, with constant-time (or nearly zero) search cost are proposed to be integrated into the OS layer and the hardware layer, respectively, as well as to trade between time and space complexity. The results of experiments conducted based on an implementation in Android, as well as simulations with popular benchmarks, to evaluate the effectiveness of the proposed design are very encouraging.
Report on ECIR 2016
Authors: Ferro Nicola , Crestani Fabio , Moens Marie-Francine , Mothe Josiane , Silvestri Fabrizio , Kekäläinen Jaana , Rosso Paolo , Clough Paul , Pasi Gabriella , Lioma Christina , Mizzaro Stefano , Di Nunzio Giorgio Maria , Hauff Claudia , Alonso Omar , Serdyukov Pavel , Silvello Gianmaria
Published: June 2016

The 38th European Conference on Information Retrieval took place from the 20th to the 23rd of March 2016 in Padua, Italy. This report summarizes the conference in terms of the presented keynotes, scientific and social programme, industry day, tutorials, workshops and student support.
Report on the 3rd International Workshop on Bibliometric-enhanced Information Retrieval (BIR 2016)
Authors: Mayr Philipp , Frommholz Ingo , Cabanac Guillaume
Published: June 2016

To foster collaboration and knowledge transfer between the fields of bibliometrics / scientometrics / informetrics on the one hand and information retrieval on the other hand, we successfully ran a workshop series on bibliometric-enhanced information retrieval (BIR). This workshop report presents the BIR 2016 workshop, which has been co-located with ECIR for the third time this year. We motivate our workshop and outline the papers (one keynote and seven regular papers) presented at ECIR 2016 in Padua, Italy. Finally we reflect on past BIR workshops and conclude with an outlook of future direction.
Increasing Reproducibility in IR
Authors: Ferro Nicola , Fuhr Norbert , Järvelin Kalervo , Kando Noriko , Lippold Matthias , Zobel Justin
Published: June 2016

The Dagstuhl Seminar on "Reproducibility of Data-Oriented Experiments in e-Science", held on 24-29 January 2016, focused on the core issues and approaches to reproducibility of experiments from a multidisciplinary point of view, sharing the experience coming from several fields of computer science.

In this paper, we discuss, summarize, and adapt the main findings of the seminar to the context of IR evaluation -- both system-oriented and user-oriented -- in order to raise awareness in our community and stimulate the fields towards and increased reproducibility of our experiments.
Relating normalization to neuronal populations across cortical areas
Authors: Ruff Douglas A. , Alberts Joshua J. , Cohen Marlene R.
Published: June 2016

Normalization, which divisively scales neuronal responses to multiple stimuli, is thought to underlie many sensory, motor, and cognitive processes. In every study where it has been investigated, neurons measured in the same brain area under identical conditions exhibit a range of normalization, ranging from suppression by nonpreferred stimuli (strong normalization) to additive responses to combinations of stimuli (no normalization). Normalization has been hypothesized to arise from interactions between neuronal populations, either in the same or different brain areas, but current models of normalization are not mechanistic and focus on trial-averaged responses. To gain insight into the mechanisms underlying normalization, we examined interactions between neurons that exhibit different degrees of normalization. We recorded from multiple neurons in three cortical areas while rhesus monkeys viewed superimposed drifting gratings. We found that neurons showing strong normalization shared less trial-to-trial variability with other neurons in the same cortical area and more variability with neurons in other cortical areas than did units with weak normalization. Furthermore, the cortical organization of normalization was not random: neurons recorded on nearby electrodes tended to exhibit similar amounts of normalization. Together, our results suggest that normalization reflects a neuron's role in its local network and that modulatory factors like normalization share the topographic organization typical of sensory tuning properties.