bluuebunny/crossref_metadata_2025 huggingface dataset:
RECURRENCE IN PATIENTS WITH TYPE 3 NEOVASCULARIZATION (RETINAL ANGIOMATOUS PROLIFERATION) AFTER INTRAVITREAL RANIBIZUMAB
Authors: Kim Jae Hui , Chang Young Suk , Kim Jong Woo , Kim Chul Gu , Lee Dong Won
Published: October 2016

Purpose:

To evaluate the incidence, timing, and characteristics of recurrence in patients with Type 3 neovascularization who were initially treated with ranibizumab.

Methods:

This retrospective study included 42 patients (42 eyes) who were diagnosed with Type 3 neovascularization and treated with 3 monthly injections of ranibizumab. The 12-month follow-up data of these patients were analyzed. The time of recurrence after the initial treatment was recorded. In eyes with recurrence, the association of the duration until the first recurrence and the incidence of multiple recurrences was analyzed.

Results:

During the 12 months, recurrence was noted in 32 patients (76.2%), with 20 experiencing multiple recurrences. The first recurrence occurred (mean ± SD) 5.3 ± 1.8 months (range, 2–9 months) after the third ranibizumab injection. The first recurrence was noted in 20 eyes (62.5%) at 4 months to 6 months after the third injection. A significantly higher incidence of multiple recurrences was noted in patients who experienced their first recurrence less than 6 months after the third injection (13 of 16 eyes, 83.3%) compared with patients who had their first recurrence 6 or more months after the third injection (5 of 14 eyes, 35.7%) (P = 0.011).

Conclusion:

Recurrence did not occur in 23.8% of the patients with Type 3 neovascularization who were initially treated with 3 monthly ranibizumab injections. Close follow-up examination may be needed 4 months to 6 months after the third ranibizumab injection. The close follow-up or continuous injection may also be required for patients with early first recurrences.
Autoimmune Pancreatitis and Inflammatory Bowel Disease
Authors: Tsen Adrianne , Alishahi Yasmin , Rosenkranz Laura
Published: October 2016

Autoimmune pancreatitis (AIP) occurring in association with inflammatory bowel disease (IBD) is rather rare and carries a worse prognosis and greater disease severity compared with IBD alone. Although it is an infrequently documented association, progress over the last 20 years has led to better understanding of the association between AIP and IBD. IBD has a stronger association with type 2 than with type 1 AIP. Clinical and histologic features of AIP-IBD more often reveal features of type 2 AIP. Imaging is not helpful in facilitating the diagnosis of AIP and IBD. Similarly, attempts to identify a serological marker have not yielded better result. A proposed lymphocyte homing mechanism provides some insight into the mechanism of pathogenesis. This review represents an update of our current knowledge of the association between AIP and IBD.
Role of cannabis in digestive disorders
Authors: Goyal Hemant , Singla Umesh , Gupta Urvashi , May Elizabeth
Published: October 2016

Cannabis sativa, a subspecies of the Cannabis plant, contains aromatic hydrocarbon compounds called cannabinoids. ∆9-Tetrahydrocannabinol is the most abundant cannabinoid and is the main psychotropic constituent. Cannabinoids activate two types of G-protein-coupled cannabinoid receptors: cannabinoid type 1 receptor and cannabinoid type 2 receptor. There has been ongoing interest and development in research to explore the therapeutic potential of cannabis. ∆9-Tetrahydrocannabinol exerts biological functions on the gastrointestinal (GI) tract. Cannabis has been used for the treatment of GI disorders such as abdominal pain and diarrhea. The endocannabinoid system (i.e. endogenous circulating cannabinoids) performs protective activities in the GI tract and presents a promising therapeutic target against various GI conditions such as inflammatory bowel disease (especially Crohn’s disease), irritable bowel syndrome, and secretion and motility-related disorders. The present review sheds light on the role of cannabis in the gut, liver, and pancreas and also on other GI symptoms, such as nausea and vomiting, cannabinoid hyperemesis syndrome, anorexia, weight loss, and chronic abdominal pain. Although the current literature supports the use of marijuana for the treatment of digestive disorders, the clinical efficacy of cannabis and its constituents for various GI disorders remains unclear.
Utilization of Positive and Negative Controls to Examine Comorbid Associations in Observational Database Studies
Authors: Desai Jigar R. , Hyde Craig L. , Kabadi Shaum , St Louis Matthew , Bonato Vinicius , Katrina Loomis A. , Galaznik Aaron , Berger Marc L.
Published: October 2016

Background:

Opportunities to leverage observational data for precision medicine research are hampered by underlying sources of bias and paucity of methods to handle resulting uncertainty. We outline an approach to account for bias in identifying comorbid associations between 2 rare genetic disorders and type 2 diabetes (T2D) by applying a positive and negative control disease paradigm.

Research Design:

Association between 10 common and 2 rare genetic disorders [Hereditary Fructose Intolerance (HFI) and α-1 antitrypsin deficiency] and T2D was compared with the association between T2D and 7 negative control diseases with no established relationship with T2D in 4 observational databases. Negative controls were used to estimate how much bias and variance existed in datasets when no effect should be observed.

Results:

Unadjusted association for common and rare genetic disorders and T2D was positive and variable in magnitude and distribution in all 4 databases. However, association between negative controls and T2D was 200% greater than expected indicating the magnitude and confidence intervals for comorbid associations are sensitive to systematic bias. A meta-analysis using this method demonstrated a significant association between HFI and T2D but not for α-1 antitrypsin deficiency.

Conclusions:

For observational studies, when covariate data are limited or ambiguous, positive and negative controls provide a method to account for the broadest level of systematic bias, heterogeneity, and uncertainty. This provides greater confidence in assessing associations between diseases and comorbidities. Using this approach we were able to demonstrate an association between HFI and T2D. Leveraging real-world databases is a promising approach to identify and corroborate potential targets for precision medicine therapies.
Using the Objective Structured Clinical Examination to Assess ACGME Competencies in Pediatric Gastroenterology Fellows
Authors: Solomon Aliza B. , Reed Rachel , Benkov Keith , Kingsbery Joseph , Lusman Sarah S. , Malter Lisa B. , Levine Jeremiah , Rabinowitz Simon S. , Wolff Martin , Zabar Sondra , Weinshel Elizabeth
Published: October 2016

Background:

The Accreditation Council for Graduate Medical Education has described 6 core competencies with which trainees should demonstrate proficiency. Using the Objective Structured Clinical Examination (OSCE), we aimed to assess 4 of these competencies among Pediatric Gastrointestinal (GI) fellows (PGs).

Methods:

Eight first‐year PGs from 6 medical centers in the New York area participated in a 4‐station OSCE with trained standardized patient (SP) actors. The cases included an emergency department (ED) consult, or “ED Consult” for lower gastrointestinal bleeding; “Breaking Bad News” focusing on CF nutritional complications; “Second Opinion” for abdominal pain; “Transition of Care” for inflammatory bowel disease. At each station, attending faculty observed the encounters behind a 1‐way mirror. SPs and faculties provided immediate feedback to the examined fellows. Previously validated OSCE checklists were used to assess performance. On completion, fellows attended debriefing sessions and completed surveys about the educational value.

Results:

Median overall milestone competency scores were 6.9 (PC1), 4.8 (PC2), 5.9 (MK1), 5.7 (MK2), 6.4 (ICS1), 6.9 (Prof1), and 6.7 (Prof3). Overall, fellows score highest (7/9) on the inflammatory bowel disease “Transition of Care” case, found the “Breaking Bad News” Cystic Fibrosis OSCE to be the most challenging, and were most comfortable with the “ED Consult” OSCE, as a commonly encountered scenario. Overall, the fellows rated the educational value of the program highly.

Conclusions:

To our knowledge, although the OSCE has been validated in other medical fields, this is the first OSCE program developed for PGs fellows. These OSCEs have included Accreditation Council for Graduate Medical Education competencies, serving to assess fellows’ skills in these areas while exposing them to challenging medical and psychosocial cases that they may not frequently encounter.
Multimodal Imaging of Serpiginous Choroiditis
Authors: Khan Hashim Ali , Shahzad Muhammad Aamir
Published: October 2016

Purpose

To report a case of atypical serpiginous choroiditis with previously unreported findings on optical coherence tomographic angiography.

Case Report

A 35-year-old otherwise healthy man had a 1-week history of vision loss in his right eye. The visual acuity in right eye was counting fingers at 1 meter. Fundoscopy showed a classic peripapillary serpiginous lesion and a solitary macular lesion. Fundus fluorescein angiography revealed early hypofluorescence of active lesions with gradual increase in fluorescence across the phase of angiogram. Optical coherence tomography showed hyperreflectivity in outer retinal layers and loss of ellipsoid zone band. The patient was treated with oral prednisone and visual acuity returned to near normal. The inflammation recurred once the patient discontinued corticosteroid therapy. The flare-up was treated with intravenous methylprednisolone followed by oral steroids. Oral azathioprine was added as a steroid-sparing agent and oral prednisone was tapered slowly and discontinued. The visual acuity returned to normal with settlement of all lesions after initiating azathioprine. Optical coherence tomography showed reintegration of retinal anatomy. No recurrence was seen after discontinuation of corticosteroids. Optical coherence tomographic angiography in resolved serpiginous choroiditis was consistent with loss of choriocapillaris homogeneity.

Conclusions

Serpiginous choroiditis may manifest with multifocal lesions and may be confused with relentless placoid chorioretinitis. However, it ends up in a typical geographic scar. Optical coherence tomography can be used to monitor the changes in retinal structure. Choriocapillaris changes as seen on optical coherence tomographic angiography may be a possible mechanism behind the development of choroidal neovascularization in later stages of the disease.
Separation of Thoraco-Omphalo-Ischiopagus Conjoined Twins: Surgical Planning, Management, and Outcomes
Authors: Trost Jeffrey G. , Lin Lawrence O. , Clark Sarah Jane , Khechoyan David Y. , Hollier Larry H. , Buchanan Edward P.
Published: October 2016

Background:

Conjoined twins are a rare medical phenomenon that offers a unique challenge for medical professionals. The complex anatomy of conjoined twins dictates their survival and amenability to separation, making each case different in terms of medical management, surgical planning, and patient outcomes. Thoraco-omphalo-ischiopagus twins, joined from the thorax to the pelvis, are one of the rarest orientations recorded in the medical literature, and successful separation of this subset of conjoined twins has not been documented. This report presents a novel case of thoraco-omphalo-ischiopagus tetrapus twins who were successfully separated at 10 months of age. The preoperative planning, operative details, and postoperative course are discussed as they relate to the reconstructive effort.

Methods:

Three-dimensional medical modeling was pursued early in the planning process and was used to estimate the soft-tissue requirements for reconstruction and to design custom tissue expanders.

Results:

The reconstructive effort required postponement until respiratory status was optimized. Even with elaborate preoperative planning, primary closure of the abdomen was limited because of tissue edema and other less predictable patient factors. Delayed closure of the abdominal wall was made possible with negative-pressure wound therapy and secondary flap advancements.

Conclusion:

Preoperative coordination with necessary vendors, a multidisciplinary surgical effort, and optimal timing of the surgical intervention all contribute to the successful separation and long-term survival of thoraco-omphalo-ischiopagus conjoined twins.

Clinical Question/Level of Evidence:

Therapeutic, V.
The “Air in the CT X-ray Tube Oil” Artifact—Examples of the Quality Control Images and the Evaluation of Four Potential Clinical Patients' Head Computed Tomography Cases
Authors: Törmänen Juhani , Rautiainen Jari , Tahvonen Pirita , Leinonen Kimmo , Nieminen Miika T. , Tervonen Osmo
Published: October 2016

We present a newly reposted scanner-based artifact—with 4 potential patients' head computed tomography (CT) cases—the “Air in the CT X-ray Tube Oil” artifact with a 64-slice multidetector CT. This artifact mimics diseases, which cause hypodense findings in CT images. It can be difficult to notice in the clinical patient imaging but can be also very difficult to verify in quality control tests.
Antibiotic Treatment of Small Intestinal Bacterial Overgrowth
Authors: Schwartz Emily , Brunetti Luigi , Ziegler Jane
Published: October 2016

Small intestinal bacterial overgrowth (SIBO) is characterized by an abnormally high concentration of bacteria in the small bowel, and is often associated with abdominal pain, bloating, and/or stool changes. Antibiotics, prebiotics, and probiotics have been considered as treatment options for individuals with SIBO. The aim of this literature review was to evaluate the evidence supporting antibiotic therapy for SIBO treatment. A systematic search of PubMed, Cochrane Library, and Web of Science databases was performed, and 13 studies were included for analysis. The analysis of the available data suggests that antibiotics, particularly rifaximin, may be effective in normalizing breath tests and improving gastrointestinal symptoms in patients with SIBO.
Drivers of variation in species impacts for a multi-host fungal disease of bats
Authors: Langwig Kate E. , Frick Winifred F. , Hoyt Joseph R. , Parise Katy L. , Drees Kevin P. , Kunz Thomas H. , Foster Jeffrey T. , Kilpatrick A. Marm
Published: October 2016

Disease can play an important role in structuring species communities because the effects of disease vary among hosts; some species are driven towards extinction, while others suffer relatively little impact. Why disease impacts vary among host species remains poorly understood for most multi-host pathogens, and factors allowing less-susceptible species to persist could be useful in conserving highly affected species. White-nose syndrome (WNS), an emerging fungal disease of bats, has decimated some species while sympatric and closely related species have experienced little effect. We analysed data on infection prevalence, fungal loads and environmental factors to determine how variation in infection among sympatric host species influenced the severity of WNS population impacts. Intense transmission resulted in almost uniformly high prevalence in all species. By contrast, fungal loads varied over 3 orders of magnitude among species, and explained 98% of the variation among species in disease impacts. Fungal loads increased with hibernating roosting temperatures, with bats roosting at warmer temperatures having higher fungal loads and suffering greater WNS impacts. We also found evidence of a threshold fungal load, above which the probability of mortality may increase sharply, and this threshold was similar for multiple species. This study demonstrates how differences in behavioural traits among species—in this case microclimate preferences—that may have been previously adaptive can be deleterious after the introduction of a new pathogen. Management to reduce pathogen loads rather than exposure may be an effective way of reducing disease impact and preventing species extinctions.

This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
Clinical implications of globally emerging azole resistance in
Aspergillus fumigatus
Authors: Meis Jacques F. , Chowdhary Anuradha , Rhodes Johanna L. , Fisher Matthew C. , Verweij Paul E.
Published: October 2016

Aspergillus
fungi are the cause of an array of diseases affecting humans, animals and plants. The triazole antifungal agents itraconazole, voriconazole, isavuconazole and posaconazole are treatment options against diseases caused by
Aspergillus
. However, resistance to azoles has recently emerged as a new therapeutic challenge in six continents. Although de novo azole resistance occurs occasionally in patients during azole therapy, the main burden is the aquisition of resistance through the environment. In this setting, the evolution of resistance is attributed to the widespread use of azole-based fungicides. Although ubiquitously distributed,
A. fumigatus
is not a phytopathogen. However, agricultural fungicides deployed against plant pathogenic moulds such as
Fusarium
,
Mycospaerella
and
A. flavus
also show activity against
A. fumigatus
in the environment and exposure of non-target fungi is inevitable. Further, similarity in molecule structure between azole fungicides and antifungal drugs results in cross-resistance of
A. fumigatus
to medical azoles. Clinical studies have shown that two-thirds of patients with azole-resistant infections had no previous history of azole therapy and high mortality rates between 50% and 100% are reported in azole-resistant invasive aspergillosis. The resistance phenotype is associated with key mutations in the
cyp51A
gene, including TR
34
/L98H, TR
53
and TR
46
/Y121F/T289A resistance mechanisms. Early detection of resistance is of paramount importance and if demonstrated, either with susceptibility testing or through molecular analysis, azole monotherapy should be avoided. Liposomal amphotericin B or a combination of voriconazole and an echinocandin are recomended for azole-resistant aspergillosis.

This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
An agent-based model of dengue virus transmission shows how multiple uncertainties about vaccine efficacy influence public health impact projections
Authors: Perkins T. Alex , Reiner Robert C. , España Guido , ten Bosch Quirine A. , Verma Amit , Liebman Kelly A. , Paz-Soldan Valerie A. , Elder John P. , Morrison Amy C. , Stoddard Steven T. , Kitron Uriel , Vazquez-Prokopec Gonzalo M. , Scott Thomas W. , Smith David L.
Published: October 2016

Given the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia®from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) “statistical uncertainty” about the numerical value of the vaccine’s efficacy against disease, and (2) “biological uncertainty” about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia®took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccine’s public health impact.
GSKB: A gene set database for pathway analysis in mouse
Authors: Lai Liming , Hennessey Jason , Bares Valerie , Son Eun Woo , Ban Yuguang , Wang Wei , Qi Jianli , Jiang Gaixin , Liberzon Arthur , Xijin Ge Steven
Published: October 2016

Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. In this study, we created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes,etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). Using our knowledgebase, we were able to detect the correct microRNA (miR-29) pathway that was suppressed using antisense oligonucleotides and confirmed its role in inhibiting fibrogenesis, which might involve upregulation of transcription factor SMAD3. The knowledgebase can be queried as a source of published gene lists for further meta-analysis. Through meta-analysis of 56 published gene lists related to retina cells, we revealed two fundamentally different types of gene expression changes. One is related to stress and inflammatory response blamed for causing blindness in many diseases; the other associated with visual perception by normal retina cells. GSKB is available online athttp://ge-lab.org/gs/, and also as a Bioconductor package (gskb,https://bioconductor.org/packages/gskb/). This database enables in-depth interpretation of mouse genomics data both in terms of known pathways and the context of thousands of published expression signatures.
LR-DNase: Predicting TF binding from DNase-seq data
Authors: van der Velde Arjan , Purcaro Michael , Noble William Stafford , Weng Zhiping
Published: October 2016

Transcription factors play a key role in the regulation of gene expression. Hypersensitivity to DNase I cleavage has long been used to gauge the accessibility of genomic DNA for transcription factor binding and as an indicator of regulatory genomic locations. An increasing amount of ChIP-seq data on a large number of TFs is being generated, mostly in a small number of cell types. DNase-seq data are being produced for hundreds of cell types. We aimed to develop a computational method that could combine ChIP-seq and DNase-seq data to predict TF binding sites in a wide variety of cell types. We trained and tested a logistic regression model, called LR-DNase, to predict binding sites for a specific TF using seven features derived from DNase-seq and genomic sequence. We calculated the area under the precision-recall curve at a false discovery rate cutoff of 0.5 for the LR-DNase model, a number of logistic regression models with fewer features, and several existing state-of-the-art TF binding prediction methods. The LR-DNase model outperformed existing unsupervised and supervised methods. Additionally, for many TFs, a model that uses only two features, DNase-seq reads and motif score, was sufficient to match the performance of the best existing methods.
Structure and origin of theWhite Caplocus and its role in evolution of grain color in maize
Authors: Tan Bao-Cai , Guan Jiahn-Chou , Ding Shuo , Wu Shan , Saunders Jonathan W. , Koch Karen E. , McCarty Donald R.
Published: October 2016

Selection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to theYellow1(Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factorWhite Cap(Wc). We show that theWclocus contains multiple, tandem copies of aCarotenoid cleavage dioxygenase 1(Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 21 teosinte accessions reveals thatWcis exclusive to maize, where it is prevalent in white-grain (y1) varieties. Moreover,Ccd1copy number varies extensively amongWcalleles (from 1 to 23 copies), and confers a proportional range ofCcd1expression in diverse organs. We propose that this dynamic source of quantitative variation inCcd1expression was created in maize shortly after domestication by a two-step,Tam3Ltransposon-mediated process. First, a chromosome segment containingCcd1and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitorCcd1rlocus on chromosome 9. Second, a subsequent interaction ofTam3Ltransposons at the new locus created a 28-kb tandem duplication, setting up expansion ofCcd1copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at theWclocus created phenotypic variation that provided a foundation for breeding and selection of white grain color in maize.
CASTOR: A machine learning platform for reproducible viral genome classification
Authors: Remita Mohamed Amine , Halioui Ahmed , Diouara Abou Abdallah Malick , Daigle Bruno , Kiani Golrokh , Diallo Abdoulaye Baniré
Published: October 2016

Motivation

Advances in cloning and sequencing technology yielded a massive number of genome of virus strains. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for a well-studied virus. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families.

Results

Here, we introduce a fast, accurate and generic virus classification platform, CASTOR, based on a machine learning approach. CASTOR is inspired by a well-known technique in molecular biology: Restriction Fragment Length Polymorphism (RFLP). It simulates the restriction digestion of genomic material by different enzymes into fragments in-silico. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of Human Papillomaviruses (HPV), Hepatitis B Viruses (HBV) and Human Immunodeficiency viruses (HIV). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV M group subtyping respectively. Furthermore, CASTOR shows a competitive performance compare to well-known HIV-specific classifier REGA and COMET on whole genome andpolfragments. With such prediction rates, genericity and robustness, as well as rapidity, such approach could constitute a reference in large-scale virus studies. Finally, we developed the CASTOR web platform for open access and reproducible viral machine learning classifiers.

Availability

http://castor.bioinfo.uqam.ca

Contact

diallo.abdoulaye@uqam.ca
Towards an ontology-based recommender system for relevant bioinformatics workflows
Authors: Halioui Ahmed , Valtchev Petko , Diallo Abdoulaye Baniré
Published: October 2016

Background

With the large and diverse type of biological data, bioinformatic solutions are being more complex and computationally intensive. New specialized data skills need to be acquired by researchers in order to follow this development. Workflow Management Systems rise as an efficient way to automate tasks through abstract models in order to assist users during their problem solving tasks. However, current solutions could have several problems in reusing the developed models for given tasks. The large amount of heterogenous data and the lack of knowledge in using bioinformatics tools could mislead the users during their analyses. To tackle this issue, we propose an ontology-based workflow-mining framework generating semantic models of bioinformatic best practices in order to assist scientists. To this end, concrete workflows are extracted from scientific articles and then mined using a rich domain ontology.

Results

In this study, we explore the specific topics of phylogenetic analyses. We annotated more than 300 recent articles using different ontological concepts and relations. Relative supports (frequencies) of discovered workflow components in texts show interesting results of relevant resources currently used in the different phylogenetic analysis steps. Mining concrete workflows from texts lead us to discover abstract but relevant patterns of the best combinations of tools, parameters and input data for specific phylogenetic problems.

Conclusions

Extracted patterns would make workflows more intuitive and easy to be reused in similar situations. This could provide a stepping-stone into the identification of best practices and pave the road to a recommender system.
Inferability of transcriptional networks from large scale gene deletion studies
Authors: Blum Christopher Frederik , Heramvand Nadia , Khonsari Armin S. , Kollmann Markus
Published: October 2016

Generating a comprehensive map of molecular interactions in living cells is difficult and great efforts are undertaken to infer molecular interactions from large scale perturbation experiments. Here, we develop the analytical and numerical tools to quantify the fundamental limits for inferring transcriptional networks from gene knockout screens and introduce a network inference method that is unbiased and scalable to large network sizes. We show that it is possible to infer gene regulatory interactions with high statistical significance, even if prior knowledge about potential regulators is absent.
Concerted action of neuroepithelial basal shrinkage and active epithelial migration ensures efficient optic cup morphogenesis
Authors: Sidhaye Jaydeep , Norden Caren
Published: October 2016

Organ formation is a multi-scale event that involves changes at the intracellular, cellular and tissue level. Organogenesis often starts with the formation of characteristically shaped organ precursors. However, the cellular mechanisms driving organ precursor formation are often not clear. Here, using zebrafish, we investigate the epithelial rearrangements responsible for the development of the hemispherical retinal neuroepithelium (RNE), a part of the optic cup. We show that in addition to basal shrinkage of RNE cells, active migration of connected epithelial cells into the RNE is a crucial player in its formation. This cellular movement is driven by progressive cell-matrix contacts and actively translocates prospective RNE cells to their correct location before they adopt neuroepithelial fate. Failure of this migration during neuroepithelium formation leads to ectopic determination of RNE cells and consequently impairs optic cup formation. Overall, this study illustrates how spatiotemporal coordination between morphogenic movements and fate determination critically influences organogenesis.
Compromised External Validity: Federally ProducedCannabisDoes Not Reflect Legal Markets
Authors: Vergara Daniela , Bidwell L. Cinnamon , Gaudino Reggie , Torres Anthony , Du Gary , Ruthenburg Travis C. , deCesare Kymron , Land Donald P. , Hutchison Kent E. , Kane Nolan C.
Published: October 2016

As the most widely used illicit drug, the basis of the fastest growing major industry in the US, and as a source of numerous under-studied psychoactive compounds, understanding the psychological and physiological effects ofCannabisis essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer ofCannabisfor use in US research studies. We sought to compare the chemical profiles ofCannabisvarieties that are available to consumers in states that have state-legalized useversuswhat is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally producedCannabishas significantly less variety and lower concentrations of cannabinoids. Current research, which has focused on material that is far less diverse and less potent than that used by the public, limits our understanding of the plant’s chemical, biological, psychological, medical, and pharmacological properties. Investigation is urgently needed on the diverse forms ofCannabisused by the public in state-legal markets.
Fractal Features of Proto-Plant’s Origin and their Possible Consequences
Authors: Galitskii V.V.
Published: October 2016

The extension of the sectional model of the spruce crown’s dynamics into diapason (0, 1) of the fractal parameter μ has demonstrated the existence of green biomass on branches of three orders in form of photosynthesizing (green) points. We investigated the growth of point sets on an interval as a model of the origin of proto-plants, which are formed due to endosymbiosis of cyanobacteria and protists. The fractal properties of the sets of evenly placed points and group sets were studied using the box-counting method. For the group sets, the character of dependence μ on the growing total number of points changes radically differently depending on whether the number of the points per group or the number of groups was fixed. As the host does not have the initial infrastructure needed for an increase in cyanobacteria per group, the first path is implemented and μ decreases from 1 to 0.25 when groups consist of two points per group. If and when the host develops necessary anatomical features (infrastructure), the second pathway is realized and μ grows to 1. The combined trajectory of μ initially demonstrates a slow growth of the size of the photosynthetic system and then an exponential growth after the development of the host’s infrastructure. Similar fractal peculiarity also characterizes trees and is an innate property of plants. Assumptions on the morphological recapitulation of proto-plant in higher plants’ ontogenesis (embryogenesis and seed germination) and also a possibility to fix the number of cyanobacteria per group are discussed.
Phenotype-specific information improves prediction of functional impact for noncoding variants
Authors: Bodea Corneliu A. , Mitchell Adele A. , Bloemendal Alex , Day-Williams Aaron G. , Runz Heiko , Sunyaev Shamil R.
Published: October 2016

Functional characterization of the noncoding genome is essential for the biological understanding of gene regulation and disease. Here, we introduce the computational framework PINES (Phenotype-Informed Noncoding Element Scoring) which predicts the functional impact of noncoding variants by integrating epigenetic annotations in a phenotype-dependent manner. A unique feature of PINES is that analyses may be customized towards genomic annotations from cell types of the highest relevance given the phenotype of interest. We illustrate that PINES identifies functional noncoding variation more accurately than methods that do not use phenotype-weighted knowledge, while at the same time being flexible and easy to use via a dedicated web portal.
Metafounders are Fst fixation indices and reduce bias in single step genomic evaluations
Authors: Garcia-Baccino Carolina Andrea , Legarra Andres , Christensen Ole F , Misztal Ignacy , Pocrnic Ivan , Vitezica Zulma G , Cantet Rodolfo J.C.
Published: October 2016

BACKGROUND

Metafounders are pseudo-individuals that condense the genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses estimation and usefulness of metafounder relationships in Single Step GBLUP.

RESULTS

We show that the ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, like Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals, and pedigree. Simple methods for estimation include naïve computation of allele frequencies from marker genotypes or a method of moments equating average pedigree-based and marker-based relationships. Complex methods include generalized least squares or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fstcoefficients and Fstdifferentiation have not been developed for related populations.

A compatible genomic relationship matrix constructed as a crossproduct of {−1,0,1} codes, and equivalent (up to scale factors) to an identity by state relationship matrix at the markers, is derived. Using a simulation with a single population under selection, in which only males and youngest animals were genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the other two (naïve and method of moments) were biased (estimates of 0.43 and 0.35). We also observed that genomic evaluation by Single Step GBLUP using metafounders was less biased in terms of accurate genetic trend (0.01 instead of 0.12 bias), slightly overdispersed (0.94 instead of 0.99) and as accurate (0.74) than the regular Single Step GBLUP. Single Step GBLUP using metafounders also provided consistent estimates of heritability.

CONCLUSIONS

Estimation of metafounder relationship can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships improves bias of genomic predictions with no loss in accuracy.
Touching on transparency in city local law making
Authors: Leshinsky Rebecca
Published: October 2016

Purpose

The purpose for this paper is to share jurisdictional knowledge on local law-making theory and praxis, an area of law not well represented in the literature despite its involvement in day-to-day life.

Design/methodology/approach

The paper not only shares knowledge about the local law-making process in Melbourne, Australia, but also explores attitudes to local law-making gathered through semi-structured interviews from a sample of relevant stakeholders.

Findings

The paper reports on findings from a study undertaken in Melbourne, Australia. Stakeholder perceptions and attitudes were canvassed regarding local law-making in the areas of land use planning and waste management. Overall, stakeholders were satisfied that Melbourne is a robust jurisdiction offering a fair and transparent local law-making system, but they see scope for more public participation.

Research limitations/implications

The findings suggest that even though the state of Victoria offers a fair and transparent system of local law-making, there is still significant scope for more meaningful involvement from the community, as well as space for more effective enforcement of local laws. The stage is set for greater cross-jurisdictional reciprocal learning about local law-making between cities.

Originality/value

This paper offers meaningful and utilitarian insight for policy and law makers, academics and built environment professionals from relevant stakeholders on the operation and transparency of local law-making.
Open supply? On the future of document supply in the world of open science
Authors: Schöpfel Joachim
Published: October 2016

Purpose

The purpose of this paper is to propose a personal viewpoint on the development of document supply in the context of the recent European Union (EU) decisions on open science.

Design/methodology/approach

The paper provides some elements to the usual questions of service development, about business, customers, added value, environment and objectives.

Findings

The EU goal for open science is 100 per cent available research results in 2020. To meet the challenge, document supply must change, include more and other content, serve different targets groups, apply innovative technology and provide knowledge. If not, document supply will become a marginalized library service.

Originality/value

Basically, open science is not library-friendly, and it does not offer a solution for the actual problems of document supply. But it may provide an opportunity for document supply to become a modern service able to deal with new forms of unequal access and digital divide.
An analysis of business’ acceptance of internet banking: an integration of e-trust to the TAM
Authors: Ben Mansour Kaouther
Published: October 2016

Purpose

The purpose of this research is to provide insights into the determinants of businesses’ internet banking acceptance. It attempts to address a research need for extending the technology acceptance model (TAM) by adding contextual variables. As trust has never failed to be a significant predictor in e-commerce research, this study proposes to integrate trust into the TAM to get a better understanding of business e-banking adoption.

Design/methodology/approach

A research model reflecting the effect of e-trust dimensions on TAM constructs is proposed. Based on relevant literature, a questionnaire was designed and administrated to 102 business managers through a Web survey. A structural modelling analysis was applied.

Findings

The results confirm the dimensions and relations of the TAM. Moreover, two main trust dimensions – integrity and credibility – positively influence perceived usefulness and exert both a direct and an indirect positive effect on attitude towards business’ internet banking adoption and behavioural intention.

Practical implications

The managerial implications of the study are that Tunisian banks should consider influencing internet banking behaviour not only by developing ease of use and usefulness beliefs, but also by promoting professional credibility and integrity. They should, also, try to attract business users by focusing on and communicating the integrity and the credibility of the bank and highlight the ways in which these concerns have been ensured.

Originality/value

This study supplies the valuable integration of trust to the TAM. It reveals that extended TAM could be used to provide a solid theoretical foundation of business’ acceptance of internet banking. In this study, trust construct is measured through a multidimensional scale including four dimensions (benevolence, credibility, integrity and orientation to resolve problems). Moreover, this study focused on an emergent country, Tunisia, whereas most studies in the literature concentrate on research cases of developed countries.
Using response to intervention/multi-tiered systems of supports to promote social justice in schools
Authors: Avant Deneca Winfrey
Published: October 2016

Purpose

The purpose of this study was to explore the use of response to intervention/multi-tiered systems of supports (RtI/MTSS) in promoting social justice in schools.

Design/methodology/approach

This study used survey research, using a 32-item questionnaire, and presented results of approximately 200 school social workers (SSWs).

Findings

Findings suggest that RtI/MTSS encourages a sense of fairness for students by providing a greater understanding of culturally diverse approaches although some room for improvement does exist.

Practical implications

Implications for addressing educational interventions with explicit cultural responsiveness are discussed.

Originality/value

As more diverse students are entering the school system, different backgrounds and learning styles must be taken into consideration. Unfortunately, many schools today continue a legacy of deficit thinking and marginalization (Shields et al., 2005). An expansion of school programs and services are needed to better serve changing student demographics. SSWs lead the way in this paradigm shift by intervening in the educational process at multiple levels. In fact, social workers’ commitment to change is evident from how they promote social and economic equality among people who are marginalized and excluded from social and economic processes.
Urban icons and city branding development
Authors: Castillo-Villar Fernando Rey
Published: October 2016

Purpose

The purpose of this paper is to understand how future urban icons can effectively contribute to the development of an authentic city brand linked to local identity. Urban icons have been one of the main tools of city branding to promote a unique and distinctive image of the city. However, the rising of the globalization reflects a series of strong dilemmas regarding the contemporary urban icons because these have been reproduced in a standardized way around the world without any connection to the local context.

Design/methodology/approach

This exploratory study consisted of 30 in-depth interviews with visual aids of urban icons conducted with local residents of the city of Monterrey, Mexico.

Findings

The results demonstrate that the acceptance of a contemporary urban icon by local residents depends on their relationship with the most representative aspects of the local identity and their ability to generate positive experiences. The outcomes of the research suggest that future urban icons should favor the local identity and the free coexistence between local residents over the attractive visual design and the private space.

Originality/value

The article discusses the dynamics between urban icons and the city brand from a new theoretical approach supported by empirical evidence. The novelty of this approach consists of the vision of the urban icon as an element capable of linking the city brand with the values and ideals of local residents.
Shopping districts and centres, markets, neighbourhoods, public squares, and urban gardens
Authors: Kalandides Ares , Millington Steve , Parker Cathy , Quin Simon
Published: October 2016

Purpose

This paper aims to reflect upon a recent study trip to Berlin to offer some conclusions about similarities and differences in approaches to place management.

Design/methodology/approach

The authors start with a short overview of the visits made to City West (a shopping district), Bikini Berlin (a shopping centre), Visit Berlin (a destination management organisation), Leopoldplatz (a public square), Brunnenstrasse and Bayerischer Platz Quartier (both neighbourhoods), Markthalle IX (a covered market) and Prinzessinnengarten (an urban garden) before identifying some key lessons learnt.

Findings

The eight visits made as part of the study trip offered a brief but diverse insight into how different areas and functions of the city were managed, maintained, developed and promoted. Key lessons learnt and identified in the paper are as follows. Place management, as a practice, consists of people with passion working in partnership within the context of a place “patch”. Place management is practiced somewhere, and that somewhere has its own political, legal, economic, technological and social environment. People learn more about places in places. Place management is more akin to gardening than architecture.

Research limitations/implications

The conclusions drawn in this paper are based, predominantly, upon the observations of the study trip facilitators, along with some comments and feedback from the delegates.

Practical implications

Place managers can and should learn from each other. Other places and people can be a source of inspiration – not necessarily providing a readily transferable solution (as the legal or political environments may not be conducive to carbon-copy interventions) – but offering alternative perspectives and approaches which can then be contextualised and adapted locally.

Social implications

Enlarging the pool of information and evidence from which practitioners can draw from when solving place problems can ultimately lead to places that are more successful, liveable and equitable.

Originality/value

Many place managers are volunteers or may not have access to a professional development budget. The authors hope that this paper can help to share the reflections of one study tour with a much wider audience.