bluuebunny/crossref_metadata_2025 huggingface dataset:
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations
Authors: Cario Clinton L , Witte John S
Published: October 2017

Motivation

As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments and machine learning algorithms, there is also a need for the integration of functionality across frameworks.

Results

We present orchid, a python based software package for the management, annotation and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier.

Availability and implementation

Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid. Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution.

Supplementary information

Supplementary data are available at Bioinformatics online.
Vancomycin Plus Piperacillin-Tazobactam and Acute Kidney Injury in Adults: A Systematic Review and Meta-Analysis
Authors: Luther Megan K. , Timbrook Tristan T. , Caffrey Aisling R. , Dosa David , Lodise Thomas P. , LaPlante Kerry L.
Published: October 2017

Objectives:

The objective of this systematic review and meta-analysis was to assess acute kidney injury with combination therapy of vancomycin plus piperacillin-tazobactam, in general, adult patients and in critically ill adults. Rates of acute kidney injury, time to acute kidney injury, and odds of acute kidney injury were compared with vancomycin monotherapy, vancomycin plus cefepime or carbapenem, or piperacillin-tazobactam monotherapy.

Data Sources:

Studies were identified by searching Pubmed, Embase, Web of Science, and Cochrane from inception to April 2017. Abstracts from selected conference proceedings were manually searched.

Study Selection:

Articles not in English, pediatric studies, and case reports were excluded.

Data Extraction:

Two authors independently extracted data on study methods, rates of acute kidney injury, and time to acute kidney injury. Effect estimates and 95% CIs were calculated using the random effects model in RevMan 5.3.

Data Synthesis:

Literature search identified 15 published studies and 17 conference abstracts with at least 24,799 patients. The overall occurrence rate of acute kidney injury was 16.7%, with 22.2% for vancomycin plus piperacillin-tazobactam and 12.9% for comparators. This yielded an overall number needed to harm of 11. Time to acute kidney injury was faster for vancomycin plus piperacillin-tazobactam than vancomycin plus cefepime or carbapenem, but not significantly (mean difference, –1.30; 95% CI, –3.00 to 0.41 d). The odds of acute kidney injury with vancomycin plus piperacillin-tazobactam were increased versus vancomycin monotherapy (odds ratio, 3.40; 95% CI, 2.57–4.50), versus vancomycin plus cefepime or carbapenem (odds ratio, 2.68; 95% CI, 1.83–3.91), and versus piperacillin-tazobactam monotherapy (odds ratio, 2.70; 95% CI, 1.97–3.69). In a small subanalysis of 968 critically ill patients, the odds of acute kidney injury were increased versus vancomycin monotherapy (odds ratio, 9.62; 95% CI, 4.48–20.68), but not significantly different for vancomycin plus cefepime or carbapenem (odds ratio, 1.43; 95% CI, 0.83–2.47) or piperacillin-tazobactam monotherapy (odds ratio, 1.35; 95% CI, 0.86–2.11).

Conclusions:

The combination of vancomycin plus piperacillin-tazobactam increased the odds of acute kidney injury over vancomycin monotherapy, vancomycin plus cefepime or carbapenem, and piperacillin-tazobactam monotherapy. Limited data in critically ill patients suggest the odds of acute kidney injury are increased versus vancomycin monotherapy, and mitigated versus the other comparators. Further research in the critically ill population is needed.
Pilot Study Assessing the Use of High-density Polyethylene (Su-Por) for Tube Shunt Patch Grafts
Authors: Abramowitz Benjamin , Moster Marlene R. , Pro Michael , Schmidt Courtland , Dale Elizabeth , Yung Edward , Williams Alice
Published: October 2017

Purpose:

To assess the viability of a manufactured high-density polyethylene patch graft material (Su-Por) for prevention of tube shunt exposure.

Materials and Methods:

Retrospective review of the first 11 patients from the Wills Eye Hospital Glaucoma Service to receive the high-density polyethylene patch graft during tube shunt surgery.

Results:

Four patients (36.3%) experienced an extrusion of the Su-Por patch without a leak within 2.5 months of postoperative follow-up. All 4 patients developed either symptomatic or progressive extrusion. Operative repair was completed with Su-Por removal and replacement with a new human donor patch graft. No patient developed any sign of infection despite the extrusions. The remaining 7 patients had an uneventful postoperative course and continue to have no complications from the Su-Por patch with 9 months of follow-up.

Conclusions:

Given the high rate of extrusion of the Su-Por graft, this material seems to be an inadequate alternative for covering tube shunts. Harvested human tissue or other more flexible, manufactured grafts remain the standard of care for covering tube shunts.
Familial Exudative Vitreoretinopathy and Glaucoma: Observations, Insights, and Management Strategies
Authors: Selvan Harathy , Swamy Deepa R. , Temkar Shreyas , Venkatesh Pradeep , Gupta Shikha
Published: October 2017

We report two cases of bilateral severe familial exudative vitreoretinopathy (FEVR) presenting with bilateral angle closure glaucoma, with evidence of neovascularization in one eye of each case. Both cases displayed bilateral disc dragging with evidence of avascular retinae on fundus fluorescein angiography. Retinal laser photocoagulation and antivascular endothelial growth factor injections provided satisfactory regression of the neovascularization. Medical management of glaucoma was administered to both patients. Lens aspiration with posterior chamber intraocular lens implantation was performed for one eye of each patient. It helped in clearing media as well as in increasing anterior chamber depth, helping in indirect control of intraocular pressure. Although the primary pathology of FEVR lies in the retina, a comprehensive glaucoma screening is essential. We conclude that neovascular glaucoma albeit uncommon in FEVR, may be the presenting feature in advanced unlasered cases, and should be specifically looked for.
Magnetic Resonance Imaging and Arthroscopic Correlation in Shoulder Instability
Authors: Knapik Derrick M. , Voos James E.
Published: October 2017

The shoulder is the most inherently unstable joint in the body, prone to high rates of anterior dislocations with subsequent injuries to soft tissue and bony stabilizing structures, resulting in recurrent shoulder instability. Advanced imaging utilizing magnetic resonance (MR) imaging and MR arthrography allows for thorough evaluation of lesions present in the unstable shoulder and is critical for preoperative planning. Arthroscopic shoulder stabilization in the appropriately selected patient can help restore stability and function. This review highlights correlations between MR imaging and arthroscopy of the most commonly reported soft tissue and bony injuries present in patients with shoulder instability.
Roles of High-resolution Manometry in Predicting Incomplete Bolus Transit in Patients With Dysphagia
Authors: Shi Zhaohong , Guo Jie , Clarke John , Jin Haifeng , Wang Xinjun , Zhang Nina , Stein Ellen , Dhalla Sameer , Pasricha Pankaj J. , Chen Jiande D.Z.
Published: October 2017

Background:

High-resolution manometry (HRM) is used to assess esophageal motility diseases. Abnormalities in a number of HRM parameters have been reported in patients with dysphagia. However, it is unclear whether some of abnormal HRM parameters are predictive of dysphagia. The aim of this retrospective study was to investigate the roles of HRM parameters in predicting incomplete bolus clearance (IBC) in patients with dysphagia using high-resolution impedance manometry.

Methods:

A total of 644 wet swallows were reviewed and analyzed in 63 patients with symptoms of dysphagia or reflux who underwent a clinical high-resolution impedance manometry test. IBC was defined based on impedance measurement. The relationship of each of abnormal HRM parameters with IBC was analyzed and their roles in predicting IBC were determined.

Results:

Patients with symptoms of both dysphagia and reflux showed the highest IBC rate, and patients with symptoms of reflux had the lowest IBC rate. The IBC was more prevalent in the distal esophagus. Premature contractions and peristalsis with large breaks were associated with a higher IBC rate in the proximal esophagus (P<0.05); large breaks, ineffective peristalsis, and abnormalities of the esophageal gastric junction functions were associate with higher IBC rates in the distal esophagus (P<0.05). Abnormalities in a number of motility parameters were able to predict IBC with high specificities and/or high sensitivity, such as pan esophageal pressurization, ineffective peristalsis, and large breaks. Abnormal integrative relaxation pressure of the lower esophageal sphincter with concurrent pan esophageal pressurization, ineffective peristalsis, or large breaks is predictive of IBC with nearly 100% of specificity.

Conclusions:

Abnormalities in a number of HRM parameters are not only useful in diagnosing esophageal motility diseases, but also valuable in predicting IBC during swallowing.
Rates of Duodenal Biopsy During Upper Endoscopy Differ Widely Between Providers
Authors: Pitman Max , Sanders David S. , Green Peter H.R. , Lebwohl Benjamin
Published: October 2017

Goal:

The goal of this study is to determine factors associated with performance of duodenal biopsy during upper endoscopy.

Background:

Celiac disease (CD) prevalence approaches 1% in the United States and Europe, yet CD remains underdiagnosed, in part because of low rates of duodenal biopsy during upper endoscopy. We aimed to identify patient and provider factors associated with performance of duodenal biopsy during upper endoscopy.

Study:

In our hospital-based endoscopy suite, we identified all patients not previously diagnosed with CD who underwent upper endoscopy during a 5-year period for one of the following indications: abdominal pain/dyspepsia, gastroesophageal reflux (GERD), anemia/iron deficiency, diarrhea, and weight loss. We employed univariate and multivariate analysis to determine the association between clinical factors and the performance of duodenal biopsy.

Results:

Of 8572 patients included in the study, 4863 (57%) underwent duodenal biopsy. Of those who underwent duodenal biopsy, 24 (0.49%) were found to have CD. On multivariate analysis, age, gender, indication, gross endoscopic appearance, physician affiliation with a celiac disease center, and absence of a participating trainee were all significantly associated with the performance of duodenal biopsy. There was wide variability among providers, with duodenal biopsy rates ranging from 27% to 91% during these procedures.

Conclusions:

A duodenal biopsy is more likely to be performed in younger patients, females, and for key indications such as weight loss, diarrhea, and anemia. Providers varied widely in the performance of duodenal biopsy. Further study is warranted to better understand the decision to perform duodenal biopsy and to determine the optimal scenarios for its performance.
C9ORF72 Intermediate Repeat Expansion in a Patient With Psychiatric Disorders and Progressive Cerebellar Ataxia
Authors: Meloni Mario , Farris Rita , Solla Paolo , Mascia Marcello M. , Marrosu Francesco , Cannas Antonino
Published: October 2017

Introduction:

Large expansions of the noncoding GGGGCC repeat (more than 30) in the first intron of the C9ORF72 gene have been demonstrated to cause amyotrophic lateral sclerosis and frontotemporal dementia. Recent papers have investigated the possible pathogenic role and associated clinical phenotypes of hexanucleotide expansions with intermediate repeat lengths ranging between 20 and 29 repeats.

Case Report:

We report a case of a 71-year-old Sardinian female patient with a long history of psychiatric disorders such as mixed anxiety-depressive disorder associated with somatization disorder and histrionic personality who developed a slowly progressive cerebellar syndrome, mild cognitive impairment, pyramidal signs, and rapid eye movement sleep behavior disorder with imaging abnormalities on the DaTSCAN single-photon emission computed tomography indicating an alteration in the presynaptic dopaminergic system. The patient was found to have intermediate C9ORF72 repeat expansions.

Conclusions:

Early psychiatric presentations are a recurrent phenotypic manifestation of C9ORF72 expansions. In our patient, the intermediate C9ORF72 repeat expansion may have a pathogenic role in the cooccurrence of psychiatric and sleep disorders, cognitive dysfunctions, pyramidal system involvement, and late-onset cerebellar ataxia. This observation widens the spectrum of neurodegenerative conditions linked to C9ORF72 mutations.
Novel GFAP Variant in Adult-onset Alexander Disease With Progressive Ataxia and Palatal Tremor
Authors: Gass Jennifer M. , Cheema Anvir , Jackson Jessica , Blackburn Patrick R. , Van Gerpen Jay , Atwal Paldeep S.
Published: October 2017

Introduction:

Alexander disease is a rare neurodegenerative disease caused by variants in the glial fibrillary acidic protein gene (GFAP). This disorder can develop as an infantile, juvenile or adult-onset form and is characterized by several clinical features, including macrocephaly, seizures, ataxia, and bulbar/pseudobulbar signs. While the majority of these patients have the more progressive infantile form which causes severe leukodystrophy and early death; the less common adult form is more variable (ie, onset age, symptoms), with bulbar dysfunction as the primary feature.

Case Report:

In our investigation, we describe a patient with progressive neuromuscular issues including dyspnea, dysphagia, dysarthria and progressive ataxia with palatal tremor.

Conclusions:

Through genetic testing, we determined that our patient has a novel variant in GFAP typical of Alexander disease.
ALKALs arein vivoligands for ALK family Receptor Tyrosine Kinases in the neural crest and derived cells
Authors: Fadeev Andrey , Garcia Patricia Mendoza , Irion Uwe , Guan Jikui , Pfeifer Kathrin , Wiessner Stephanie , Serluca Fabrizio , Singh Ajeet Pratap , Nüsslein-Volhard Christiane , Palmer Ruth H.
Published: October 2017

Mutations in Anaplastic Lymphoma Kinase (ALK) are implicated in somatic and familial neuroblastoma, a paediatric tumour of neural crest-derived tissues. Recently, biochemical analyses have identified secreted small ALKAL proteins (FAM150, AUG) as potential ligands for human ALK and the related Leukocyte Tyrosine Kinase (LTK). In the zebrafishDanio rerio, DrLtk, which is similar to human ALK in sequence and domain structure, controls the development of iridophores, neural crest-derived pigment cells. Hence, the zebrafish system allows studying Alk/Ltk and Alkals involvement in neural crest regulationin vivo. Using zebrafish pigment pattern formation,Drosophilaeye patterning, and cell culture-based assays, we show that zebrafish Alkals potently activate zebrafish Ltk and human ALK driving downstream signalling events. Overexpression of the three Dr Alkals cause ectopic iridophore development whereas loss of function alleles lead to spatially distinct patterns of iridophore loss in zebrafish larvae and adults.alkalloss of function triple mutants completely lack iridophores and are larval lethal as is the case forltknull mutants. Our results provide the firstin vivoevidence of (i) activation of ALK/LTK family receptors by ALKALs and (ii) an involvement of these ligand-receptor complexes in neural crest development.
Analysis of the Genomic Basis of Functional Diversity in Dinoflagellates using a Transcriptome-Based Sequence Similarity Network
Authors: Meng Arnaud , Corre Erwan , Probert Ian , Gutierrez-Rodriguez Andres , Siano Raffaele , Annamale Anita , Alberti Adriana , Da Silva Corinne , Wincker Patrick , Le Crom Stéphane , Not Fabrice , Bittner Lucie
Published: October 2017

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
Targeting the Untargetable: Predicting Pramlintide Resistance Using a Neural Network Based Cellular Automata
Authors: Kim Eunjung , Schenck Ryan , West Jeffrey , Cross William , Harris Valerie , McKenna Joseph , Cho Heyrim , Coker Elizabeth , Tsai Steven Lee-Kramer Kenneth Y. , Flores Elsa R. , Gatenbee Chandler
Published: October 2017

De novo resistance is a major issue for the use of targeted anticancer drugs in the clinic. By integrating experimental data we have created a hybrid neural network/agent-based model to simulate the evolution and spread of resistance to the drug Pramlintide in cutaneous squamous cell carcinoma. Our model can eventually be used to predict patient responses to the drug and thus enable clinicians to make decisions regarding personalized, precision treatment regimes for patients.
Extracting active modules from multilayer PPI network: a continuous optimization approach
Authors: Li Dong , Zhu Zexuan , Pan Zhisong , Hu Guyu , He Shan
Published: October 2017

Active modules identification has received much attention due to its ability to reveal regulatory and signaling mechanisms of a given cellular response. Most existing algorithms identify active modules by extracting connected nodes with high activity scores from a graph. These algorithms do not consider other topological properties such as community structure, which may correspond to functional units. In this paper, we propose an active module identification algorithm based on a novel objective function, which considers both and network topology and nodes activity. This objective is formulated as a constrained quadratic programming problem, which is convex and can be solved by iterative methods. Furthermore, the framework is extended to the multilayer dynamic PPI networks. Empirical results on the single layer and multilayer PPI networks show the effectiveness of proposed algorithms.

Availability: The package and code for reproducing all results and figures are available at https://github.com/fairmiracle/ModuleExtraction.
Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making
Authors: Dezfouli Amir , Balleine Bernard W.
Published: October 2017

State-space and action representations form the building blocks of decision-making processes in the brain; states map external cues to the current situation of the agent whereas actions provide the set of motor commands from which the agent can choose to achieve specific goals. Although these factors differ across environments, it is not currently known whether or how accurately state and action representations are acquired by the agent because previous experiments have typically provided this information a priori through instruction or pre-training. Here we show that, in the absence of such a priori knowledge, state and action representations adapt to reflect the structure of the world. We used a sequential decision-making task in rats in which they were required to pass through multiple states before reaching the goal, and for which the number of states and how they map onto external cues were not known a priori. We found that, early in training, animals selected actions as if the task was not sequential and outcomes were the immediate consequence of the most proximal action. During the course of training, however, rats recovered the true structure of the environment and made decisions based on the expanded state-space, reflecting the multiple stages of the task. We found a similar pattern with actions; early in training animals only considered the execution of single actions whereas, after training, they created useful action sequences that expanded the set of available actions. We conclude that the profile of choices shows a gradual shift from simple representations of actions and states to more complex structures compatible with the structure of the world.
Genomic imprinting of Xist by maternal H3K27me3
Authors: Inoue Azusa , Jiang Lan , Lu Falong , Zhang Yi
Published: October 2017

Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X-chromosome inactivation (XCI) in female mammals. However, the mechanism underlying Xist imprinting is unclear. Here we show that the Xist locus is coated with a broad H3K27me3 domain that is established during oocyte growth and persists through preimplantation development in mice. Loss of maternal H3K27me3 induces maternal Xist expression and maternal XCI in preimplantation embryos. Our study thus identifies maternal H3K27me3 as the imprinting mark of Xist.
The role of employee autonomy for open innovation performance
Authors: Burcharth Ana , Præst Knudsen Mette , Søndergaard Helle Alsted
Published: October 2017

Purpose

The purpose of this paper is to examine how organisational activities that formally provide employees with work autonomy explain the performance of open innovation (OI).

Design/methodology/approach

The study reports the results of mediation analyses conducted on the basis of survey data from 307 firms.

Findings

The economic benefits of both inbound and outbound OI are fully captured only if firms provide employees with time, freedom and independence. The results show that employee autonomy fully mediates the relationship between openness and innovation sales, while the adoption of inbound OI is positively associated with the introduction of new products.

Practical implications

The opening of innovation induces managers to provide employees with discretion, as OI requires high levels of flexibility and experimentation.

Originality/value

The paper addresses theoretically and empirically the role of job design in the implementation of OI, while also distinguishing between the effects of inbound and outbound practices on innovation performance.
Fatigue design of a twin internal combustion engine for a light helicopter by a CAE-based approach
Authors: Gilioli Andrea , Braconi Dario , Guagliano Mario
Published: October 2017

Purpose

The purpose of this paper is to apply a computer-aided engineering approach in order to improve the performance and the reliability of an innovative internal combustion engine. The engine is called twin engine packs system and it consists into the presence of two independent piston engines working in the same crankcase, thus allowing the helicopter to meet the safety standards of the fail-safe design approach, as happens with the twin-turbine helicopters, but with reduced operative costs. The goal is to propose to the designers modifications aimed to improve the performance of the components.

Design/methodology/approach

The crankshaft, connecting rod and the piston of the engine have been investigated by means of numerical FE models. Numerical fatigue assessments have been performed along with vibrational modes and buckling analysis in order to verify the structural integrity of the system.

Findings

On the basis of the numerical results, some modifications have been proposed to the designers and the originally proposed geometry has been modified. Eventually, the mass of the engine has been reduced keeping a high reliability level.

Practical implications

The prototype of the engine has been built following the modifications proposed in this paper. This paper represents a comprehensive application of a CAE methodology to a real industrial application.

Originality/value

This paper shows a complete CAE procedure applied to a real working engine whose performances and reliability have been improved by following the findings of this paper.
National Registration of Health Practitioners: A Comparative Study of the Complaints and Notification System Under the National System and in New South Wales – Decision Makers who Handle Complaints/Notifications About Regulated Health Practitioners in Australia
Authors: Chiarella Mary , Nagy Marie , Satchell Claudette S. , Walton Merrilyn , Carney Terry , Bennett Belinda , Pierce Suzanne M. , Kelly Patrick J.
Published: October 2017

When the National Registration and Accreditation Scheme (NRAS) for health practitioners commenced in Australia in 2010, all jurisdictions joined the scheme for the registration and accreditation of health practitioners, but NSW retained its existing co‐regulatory complaint‐handling system. We sought to compare the new National notifications and the NSW complaints handling processes, as NSW has an independent investigative and prosecutory body to manage serious complaints. Decision makers from both the National and NSW schemes, who handled notifications/complaints at assessment, were invited to participate in a survey consisting of case studies. A qualitative thematic approach was used to determine and compare contributing factors to decision makers’ priorities when assessing a notification/complaint for the National and NSW schemes. The 123 completed surveys comprised 50 NSW respondents and 73 National respondents from the other jurisdictions. No consistent differences in contributory factors when assessing a complaint/notification were observed between the two schemes. This evidence points towards national consistency in decisions about assessment of complaints and notifications in Australia.
Epstein‐Barr virus positive diffuse large B‐cell lymphoma presenting with vaginal sloughing and ulcerated skin nodule
Authors: Lee Lynette Y. , Namuduri Rama , Chan Michelle M. F. , Quek Jeffrey K. S. , Koh Mark J.‐A.
Published: October 2017

Malignant lymphomas presenting in the female genital tract are extremely rare. We report a case of Epstein‐Barr virus associated diffuse large B‐cell lymphoma of the genital tract and skin in a 60‐year‐old woman on long‐term azathioprine.
Entomopathogenic nematodes as potential biological control agents of Popillia japonica (Coleoptera, Scarabaeidae) in Piedmont Region (Italy)
Authors: Marianelli L. , Paoli F. , Torrini G. , Mazza G. , Benvenuti C. , Binazzi F. , Sabbatini Peverieri G. , Bosio G. , Venanzio D. , Giacometto E. , Priori S. , Koppenhöfer A. M. , Roversi P. F.
Published: October 2017

In 2014, the Japanese beetle Popillia japonica (Coleoptera: Scarabaeidae) was first spotted in northern Italy in the Nature Park of the Ticino Valley, its first detection in continental Europe. This polyphagous invasive species has the potential to cause serious losses to horticulture and agriculture. Particularly for its management in a Nature Park, environmentally friendly strategies are necessary. To develop baseline data for a biological control approach to the Italian outbreak of P. japonica, we conducted laboratory and field experiments testing several indigenous and commercial strains of the entomopathogenic nematode (EPN) species Heterorhabditis bacteriophora and Steinernema carpocapsae against P. japonica larvae. In the laboratory, strains of H. bacteriophora caused greater mortality (ranging from 57% to 100%) than those of S. carpocapsae (3% to 77%). In micro‐plot field tests carried out at three different times, the most virulent indigenous EPN strain, H. bacteriophora ItH‐LU1, showed again the best results ranging from 44% to 93% against young larvae. Finally, in a large‐plot field trial, the commercial H. bacteriophora product provided 46% larval mortality. This study shows that H. bacteriophora strains have good potential as biological control agents of larvae of the invasive P. japonica in northern Italy.
Effectiveness of aromatic plant species for repelling and preventing oviposition of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae)
Authors: Wagan T. A. , He Y. P. , Long M. , Chakira H. , Zhao J. , Hua H. X.
Published: October 2017

This study assesses the effectiveness of essential oils for repelling whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), and deterring oviposition. We evaluated essential oils from four plants: Curcuma longa (Zingiberaceae), Litsea cubeba (Lauraceae), Piper nigrum (Piperaceae) and Zanthoxylum bungeanum (Rutaceae), under laboratory and glasshouse conditions. In the laboratory, ethanol‐extracted essential oils were applied uniformly on both sides of a tomato leaf in the treatment groups, and the same volume of liquid but without essential oil was used for the control. Results showed that essential oils from L. cubeba, P. nigrum, C. longa and Z. bungeanum provided some repellency of whiteflies and reduced oviposition. Oils from L. cubeba repelled adult females (69.14% and 62.49% repellency at 24 and 48 hr, respectively), and oils from C. longa deterred oviposition (68.46% and 65.94% at 24 and 48 hr exposures, respectively). In the glasshouse, potted tomato plants with eight leaves were sprayed with treatments and control material. Five‐day‐old adult female whiteflies were released in a cage between both pots. Essential oils from L. cubeba repelled females 54.77 at 24 hr and P. nigrum 44.37% at 48 hr whereas oils from P. nigrum reduced oviposition by 43.35 at 24 hr and Z. bungeanum 21.08% at 48 hr, under glasshouse conditions. Essential oils show potential to be used to reduce feeding and oviposition, and thus being important components of integrated pest management programs. However, future research is needed to investigate individual compounds of these oils against whitefly, and to enhance their effectiveness.
Diel flight pattern and size‐dependent flight speed of kudzu bug, Megacopta cribraria (Fabricius)
Authors: Merwin A. C. , Yilmaz A. R.
Published: October 2017

Kudzu bug, Megacopta cribraria (Fabricius) (Hemiptera: Plataspidae), was introduced to North America in 2009 and has since spread across the eastern and south‐eastern United States, where it poses an economic threat to leguminous crop production, especially soya bean. However, we still lack an understanding of many basic aspects of their flight‐related biology, including descriptions of their pattern of diel flight activity, their dispersal capacity and the determinants of each. Using cross‐vane bucket traps and flight mills, we found that kudzu bug exhibits a diel flight activity pattern in the field that is well characterized by temperature and a quadratic relationship with time of day. In general, the number of adults collected in the cross‐vane bucket traps rose from 07:30 and declined from 17:30 to 19:30. No kudzu bugs were collected before 07:30 or after 19:30 during any of the replicates. We also demonstrate on flight mills that females fly faster than males, and that this difference is due to differences in their size. These basic biological findings may help to inform management decisions and improve our understanding of the invasion dynamics of M. cribraria.
Identification of risk factors for sessile and traditional serrated adenomas of the colon by using big data analysis
Authors: Pyo Jeung Hui , Ha Sang Yun , Hong Sung Noh , Chang Dong Kyung , Son Hee Jung , Kim Kyoung‐Mee , Kim Hyeseung , Kim Kyunga , Kim Jee Eun , Choi Yoon‐Ho , Kim Young‐Ho
Published: October 2017

Background and Aim

Little is known about the risk factors associated with serrated polyps, because the early studies, which occurred before the new World Health Organization classification was introduced, included mixtures of serrated polyps. This study aimed to evaluate the risk factors associated with the presence of sessile serrated adenomas (SSAs) and traditional serrated adenomas (TSAs) using big data analytics.

Methods

Using a case–control design, we evaluated the risk factors associated with the presence of SSAs and TSAs. Subjects who underwent colonoscopies from 2002 to 2012 as part of the comprehensive health screening programs undertaken at the Samsung Medical Center, Korea, participated in this study.

Results

Of the 48 677 individuals who underwent colonoscopies, 183 (0.4%) had SSAs and 212 (0.4%) had TSAs. The multivariate analysis determined that being aged ≥ 50 years (odds ratio [OR] 1.91, 95% confidential interval [CI] 1.27–2.90, P = 0.002) and a history of colorectal cancer among first‐degree relatives (OR 3.14, 95% CI 1.57–6.27, P = 0.001) were significant risk factors associated with the presence of SSAs and that being aged ≥ 50 years (OR 2.61, 95% CI 1.79–3.80, P < 0.001), obesity (OR 1.63, 95% CI 1.12–2.36, P = 0.010), and a higher triglyceride level (OR 1.63, 95% CI 1.12–2.36, P = 0.010) were independent risk factors associated with the presence of TSAs.

Conclusions

We used big data analytics to determine the risk factors associated with the presence of specific polyp subgroups, and individuals who have these risk factors should be carefully scrutinized for the presence of SSAs or TSAs during screening colonoscopies.
Dermatological and environmental toxicological impact of the sunscreen ingredient oxybenzone/benzophenone‐3
Authors: DiNardo Joseph C , Downs Craig A
Published: October 2017

Oxybenzone (Benzophenone‐3) is an emerging human and environmental contaminant used in sunscreens and personal care products to help minimize the damaging effects of ultraviolet radiation. The Center for Disease Control fourth national report on human exposure to environmental chemicals demonstrated that approximately 97% of the people tested have oxybenzone present in their urine, and independent scientists have reported various concentrations in waterways and fish worldwide. Oxybenzone can also react with chlorine, producing hazardous by‐products that can concentrate in swimming pools and wastewater treatment plants. Moreover, adverse reactions could very well be increased by the closed loop of ingesting fish contaminated with oxybenzone and/or washing the ingredient off our bodies and having it return in drinking water as treatment plants do not effectively remove the chemical as part of their processing protocols. In humans, oxybenzone has been reported to produce contact and photocontact allergy reactions, implemented as a possible endocrine disruptor and has been linked to Hirschsprung's disease. Environmentally, oxybenzone has been shown to produce a variety of toxic reactions in coral and fish ranging from reef bleaching to mortality. Lastly, with the rise in skin cancer rates and the availability of more effective sunscreen actives such as micronized zinc oxide and titanium dioxide, serious doubts about the relative prevention benefit of personal care products containing oxybenzone must be raised and compared with the potential negative health and environmental effects caused by the accumulation of this and other chemicals in the ecosystem.
Analysis of Shade Matching in Natural Dentitions Using Intraoral Digital Spectrophotometer in LED and Filtered LED Light Sources
Authors: Chitrarsu Vijai Krishnan , Chidambaranathan Ahila Singaravel , Balasubramaniam Muthukumar
Published: October 2017

Purpose

To evaluate the shade matching capabilities in natural dentitions using Vita Toothguide 3D‐Master and an intraoral digital spectrophotometer (Vita Easyshade Advance 4.0) in various light sources.

Materials and Methods

Participants between 20 and 40 years old with natural, unrestored right maxillary central incisors, no history of bleaching, orthodontic treatment, or malocclusion and no rotations were included. According to their shades, subjects were randomly selected and grouped into A1, A2, and A3. A total of 100 participants (50 male and 50 female) in each group were chosen for this study. Shade selection was made between 10 am and 2 pm for all light sources. The same examiner selected the shade of natural teeth with Vita Toothguide 3D‐Master under natural light within 2 minutes. Once the Vita Toothguide 3D‐Masterwas matched with the maxillary right central incisor, the L*, a*, and b* values, chroma, and hue were recorded with Vita Easyshade Advance 4.0 by placing it on the shade tab under the same light source. The values were statistically analyzed using one‐way ANOVA and Tukey's HSD post hoc test with SPSS v22.0 software.

Results

The mean ∆E*ab values for shades A1, A2, and A3 for groups 1, 2, and 3 were statistically significantly different from each other (p < 0.001).

Conclusion

The intraoral digital spectrophotometer showed statistically significant differences in shade matching compared to Vita Toothguide 3D‐Master. Incandescent light showed more accurate shade matching than the filtered LED, LED, and daylight.
Synergistic effect of photodynamic therapy and alendronate on alveolar bone loss in rats with ligature‐induced periodontitis
Authors: Camacho‐Alonso F. , Davia‐Peña R. S. , Vilaplana‐Vivo C. , Tudela‐Mulero M. R. , Merino J. J. , Martínez‐Beneyto Y.
Published: October 2017

Background and Objective

Photodynamic therapy (PDT) and antiresorptive drugs, such as alendronate (ALN), have been shown to reduce alveolar bone loss. The aim of this study was to evaluate the possible synergic effects of combining PDT and ALN on bone loss in periodontitis in rats.

Material and Methods

Periodontitis was induced by ligature in 60 Wistar rats randomized into the following groups: control (Group 1); PDT (Group 2); ALN 0.01 mg/kg (Group 3); ALN 0.25 mg/kg (Group 4); PDT + ALN 0.01 mg/kg (Group 5); and PDT + ALN 0.25 mg/kg (Group 6). The rats were killed on day 12 and the mandibles were processed for macroscopic morphometric analysis, micro‐computed tomography to analyze bone mineral density (BMD) and histological analysis. Gingival samples were collected to evaluate myeloperoxidase (MPO) and malonaldehyde (MDA) levels.

Results

Bone loss and inflammatory activity in histological studies, from the greatest to least was: control > ALN 0.01 mg/kg > PDT > ALN 0.25 mg/kg > PDT + ALN 0.01 mg/kg > PDT + ALN 0.25 mg/kg, while the order from least to greatest BMD was: control < ALN 0.01 mg/kg < PDT < ALN 0.25 mg/kg < PDT + ALN 0.01 mg/kg < PDT + ALN 0.25 mg/kg. The order of MPO and MDA activity from greatest to least was: control > ALN 0.01 mg/kg > PDT > ALN 0.25 mg/kg > PDT + ALN 0.01 mg/kg > PDT + ALN 0.25 mg/kg. The positive results obtained in the group treated with PDT + ALN 0.25 mg/kg showed statistically significant differences (P ≤ .05) compared with the other 5 groups for BMD, MPO and MDA.

Conclusion

Combined approach therapy of PDT + ALN 0.25 mg/kg demonstrated a protective effect on alveolar bone loss.
The Emergence of the Allophonic Perception of Unfamiliar Speech Sounds: The Effects of Contextual Distribution and Phonetic Naturalness
Authors: Noguchi Masaki , Kam Carla L. Hudson
Published: October 2017

In human languages, different speech sounds can be contextual variants of a single phoneme, called allophones. Learning which sounds are allophones is an integral part of the acquisition of phonemes. Whether given sounds are separate phonemes or allophones in a listener's language affects speech perception. Listeners tend to be less sensitive to acoustic differences between sounds that are allophones. This study investigated the mechanisms behind the learning of allophones by looking at adults’ sensitivity to acoustic differences between two unfamiliar sounds when they were exposed to input in which the sounds behave like separate phonemes versus allophones in terms of their contextual distribution. The results of two experiments showed that adults became less sensitive to acoustic differences between two unfamiliar sounds after being exposed to input in which the sounds were in complementary distribution and that the emergence of allophonic perception was constrained by the phonetic naturalness of complementary distribution.
Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char
Authors: Moore Jean‐Sébastien , Harris Les N. , Le Luyer Jérémy , Sutherland Ben J.G. , Rougemont Quentin , Tallman Ross F. , Fisk Aaron T. , Bernatchez Louis
Published: October 2017

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of nonmodel organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise FST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in nonbreeding years. Genome scans and genetic–environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in nonmodel organisms in logistically challenging environments such as the Arctic.
Rhizosphere‐associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens
Authors: Haney Cara H. , Wiesmann Christina L. , Shapiro Lori R. , Melnyk Ryan A. , O'Sullivan Lucy R. , Khorasani Sophie , Xiao Li , Han Jiatong , Bush Jenifer , Carrillo Juli , Pierce Naomi E. , Ausubel Frederick M.
Published: October 2017

Plant‐associated soil microbes are important mediators of plant defence responses to diverse above‐ground pathogen and insect challengers. For example, closely related strains of beneficial rhizosphere Pseudomonas spp. can induce systemic resistance (ISR), systemic susceptibility (ISS) or neither against the bacterial foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Using a model system composed of root‐associated Pseudomonas spp. strains, the foliar pathogen Pto DC3000 and the herbivore Trichoplusia ni (cabbage looper), we found that rhizosphere‐associated Pseudomonas spp. that induce either ISS and ISR against Pto DC3000 all increased resistance to herbivory by T. ni. We found that resistance to T. ni and resistance to Pto DC3000 are quantitative metrics of the jasmonic acid (JA)/salicylic acid (SA) trade‐off and distinct strains of rhizosphere‐associated Pseudomonas spp. have distinct effects on the JA/SA trade‐off. Using genetic analysis and transcriptional profiling, we provide evidence that treatment of Arabidopsis with Pseudomonas sp. CH267, which induces ISS against bacterial pathogens, tips the JA/SA trade‐off towards JA‐dependent defences against herbivores at the cost of a subset of SA‐mediated defences against bacterial pathogens. In contrast, treatment of Arabidopsis with the ISR strain Pseudomonas sp. WCS417 disrupts JA/SA antagonism and simultaneously primes plants for both JA‐ and SA‐mediated defences. Our findings show that ISS against the bacterial foliar pathogens triggered by Pseudomonas sp. CH267, which is a seemingly deleterious phenotype, may in fact be an adaptive consequence of increased resistance to herbivory. Our work shows that pleiotropic effects of microbiome modulation of plant defences are important to consider when using microbes to modify plant traits in agriculture.
A fast, low‐cost and efficient method for the diagnosis of sperm DNA fragmentation in several species
Authors: Rui BR , Angrimani DSR , Bicudo LC , Losano JDA , Nichi M , Pereira RJG
Published: October 2017

Contents

Sperm DNA fragmentation is a condition that interferes directly in the reproductive efficiency. Currently, there are several methods for assessing the sperm DNA integrity, such as Alkaline Comet, TUNEL and Sperm Chromatin Structure Assay. However, many of these techniques are laborious and require high‐precision equipment. Thus, the development of new techniques can optimize the evaluation of sperm DNA damage. Therefore, the aim of this study was to standardize the toluidine blue (TB) stain technique for the analysis of DNA fragmentation of dog, cat, bull, stallion and ram spermatozoa. For this purpose, we used six animals of each specie (n = 30), in reproductive age. Sperm was collected by different methods according to the particularities of each species, and such samples were divided into two aliquots: a sperm sample was kept at 5°C (considered as intact sperm DNA), and the remaining samples were submitted to the induction of DNA fragmentation by exposure to ultraviolet light for 4 hr. Samples were then mixed with the intact sample to obtain known and progressive proportions of sperm with fragmented DNA (0%, 25%, 50%, 75% and 100%). Semen smears were performed and subjected to staining with TB. Blue‐stained spermatozoa were considered to have DNA fragmentation. We observed high linear regression coefficients between the expected proportion of damaged DNA and the results of TB for dog, cat, ram, bull and stallion samples. In conclusion, TB stain was considered a fast and effective technique for the study of spermatozoa DNA in several species.