bluuebunny/crossref_metadata_2025 huggingface dataset:
The Directory of Open Access Journals covers more biomedical open access journals than other databases
Authors: Liljekvist Mads S , Andresen Kristoffer , Pommergaard Hans-Christian , Rosenberg Jacob
Published: January 2018

Background: Open access (OA) journals disseminate research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfil such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database searchable at article level, focusing exclusively on OA journals.

The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases.

Methods: Information on all journals listed in five conventional biomedical databases (MEDLINE, National Library of Medicine, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were 1) actively publishing, 2) full OA, 3) prospectively indexed in one or more database, and 4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined.

Results: In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7 % in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. Of journals exclusively listed in DOAJ, only one had received an impact factor. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively.

Conclusions: DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general.
Body image, visual working memory and visual mental imagery
Authors: Darling Stephen , Uytman Clare , Allen Richard J , Havelka Jelena , Pearson David G
Published: January 2018

Body dissatisfaction (BD) is a highly prevalent feature amongst females in society, with the majority of individuals regarding themselves to be overweight compared to their personal ideal, and very few self-describing as underweight. To date, explanations of this dramatic pattern have centred on extrinsic social and media factors, or intrinsic factors connected to individuals’ knowledge and belief structures regarding eating and body shape, with little research examining links between BD and basic cognitive mechanisms. This paper reports a correlational study in which visual and executive cognitive processes that could potentially impact on BD were assessed. Visual memory span and self-rated visual imagery were found to be predictive of BD, alongside a measure of inhibition derived from the Stroop task. In contrast, spatial memory and global precedence were not related to BD. Results are interpreted with reference to the influential multi-component model of working memory.
A specimen of Paralycoptera Chang & Chou 1977 (Teleostei: Osteoglossoidei) from Hong Kong (China) with a potential Late Jurassic age that extends the temporal and geographical range of the genus
Authors: Tse Tze-Kei , Pittman Michael , Chang Meemann
Published: January 2018

We identify an osteoglossoid teleost fish - Paralycoptera - from Late Jurassic volcaniclastic mudstones from the Lai Chi Chong Formation of Hong Kong, China. This partially preserved postcranial skeleton represents the first Mesozoic fish from Hong Kong and the most southerly Paralycoptera to date. A radiometric date for the Lai Chi Chong Formation of ~146 Ma implies a temporal range expansion for Paralycoptera of approximately 40 million years back from the Early Cretaceous (~110Ma). However, spores found in the Formation suggest an Early Cretaceous age that is consistent with the existing age assignment to Paralycoptera. We argue that the proposed temporal range extension is genuine because it is based on recent precise and accurate radiometric data, but given the discrepancies with the biostratigraphic ages further investigation is needed to confirm this. This study provides an important step towards revealing Hong Kong’s Mesozoic vertebrate fauna and understanding its relationship to well-studied mainland Chinese ones.
Estimating relative risk of within-lake aquatic plant invasion using combined measures of recreational boater movement and habitat suitability
Authors: Wittmann Marion E , Kendall Bruce E , Jerde Christopher L , Anderson Lars W. J.
Published: January 2018

Effective monitoring, prevention and impact mitigation of nonindigenous aquatic species (NAS) relies upon the ability to predict dispersal pathways and receiving habitats with the greatest risk of establishment. To examine mechanisms affecting species establishment within a large lake, we combined observations of recreational boater movements with empirical measurements of habitat suitability represented by nearshore wave energy to assess the relative risk (RR) of Eurasian watermilfoil (Myriophyllum spicatum) establishment. The model was evaluated using information from a 17 year (1995-2012) sequence of M. spicatum presence and absence monitoring. M. spicatum presence was not specifically correlated with recreational boater movements; however its establishment appears to be limited by wave action in Lake Tahoe. Of the sites in the "High" risk category (n=37), 54% had current or historical infestations, which included 8 of the 10 sites with the highest RR. Of the 11 sites in the "Medium" risk category, 5 had current or historical M. spicatum populations. Most (76%) of the sites in the "Low" risk category were observed in locations with higher wave action. Four sites that received zero boater visits from infested locations were occupied by M. spicatum. This suggests that the boater survey either represents incomplete coverage of boater movement, or other processes, such as the movement of propagules by surface currents or introductions from external sources are important to the establishment of this species. This study showed the combination of habitat specific and dispersal data in a relative risk framework can potentially reduce uncertainty in estimates of invasion risk.
Beliefs in being unlucky and deficits in executive functioning: An ERP study
Authors: Martin del Campo Jaime , Maltby John , Fuggetta Giorgio
Published: January 2018

The present study tested the Dysexecutive Luck hypothesis by examining whether deficits in the early stage of top down attentional control led to an increase of neural activity in later stages of response related selection process among those who thought themselves to be unlucky. Individuals with these beliefs were compared to a control group using an Event-Related Potential (ERP) measure assessing underlying neural activity of semantic inhibition while completing a Stroop test. Results showed stronger main interference effects in the former group, via greater reaction times and a more negative distributed scalp late ERP component during incongruent trials in the time window of 450 – 780 ms post stimulus onset. Further, less efficient maintenance of task set among the former group was associated with greater late ERP response-related activation to compensate for the lack of top-down attentional control. These findings provide electrophysiological evidence to support the Dysexecutive Luck hypothesis.
Visual search contributes to subjective judgment of visual efficiency in older adults
Authors: Setti Annalisa , Loughman James , Savva George M , Kenny RoseAnne
Published: January 2018

Introduction: The determinant factors that influence self-reported quality of vision have yet to be fully elucidated. This study evaluated a range of contextual information, established psychophysical tests, and in particular, a series of cognitive tests as potentially determinant factors. Materials & Methods: Community dwelling adults (aged 50+) recruited to Wave 1 of The Irish Longitudinal Study on Ageing, excluding those registered blind, participated in this study (N=5021). Self-reports of vision were analysed in relation to visual acuity and contrast sensitivity, ocular pathology, visual (Choice Response Time task; Trail Making Test) and global cognition. Contextual factors such as having visited an optometrist and wearing glasses were also considered. Ordinal logistic regression was used to determine univariate and multivariate associations. Results and Discussion: Visual acuity (Odds ratio (OR) =1.71), ocular pathology (cataract, OR=1.78; glaucoma, OR=2.43; ARMD, OR=3.48; other pathologies, OR=2.83), lack of correction (glasses, OR=1.34), poor visual cognition (Trail Making Test, OR= 1.35) were determinant factors for poor versus excellent vision in self-reports. Education, wealth, age, depressive symptoms and general cognitive fitness also contributed to determining self-reported vision. Conclusions: Ocular pathology underlies the presence of visual deficits that are not fully captured by the acuity test. Poor visual search and visual attention skills capture the functional use of vision linked to higher level visual processing. Age, education and wealth, as well as mental health also bias responses. A careful examination of the respective contribution of such factors should be considered when using self-reports to asses vision and its role in cognitive and functional health.
A new method to analyze species abundances in space using generalized dimensions
Authors: Saravia Leonardo A
Published: January 2018

Species-area relationships (SAR) and species abundance distributions (SAD) are among the most studied patterns in ecology, due to their application to both theoretical and conservation issues. One problem with these general patterns is that different theories can generate the same predictions, and for this reason they cannot be used to detect different mechanisms of community assembly. A solution is to search for more sensitive patterns, for example by extending the SAR to the whole species abundance distribution. A generalized dimension ($D_q$) approach has been proposed to study the scaling of SAD, but to date there has been no evaluation of the ability of this pattern to detect different mechanisms. An equivalent way to express SAD is the rank abundance distribution (RAD). Here I introduce a new way to study SAD scaling using a spatial version of RAD: the species-rank surface (SRS), which can be analyzed using $D_q$. Thus there is an old $D_q$ based on SAR ($D_q^{SAD}$), and a new one based on SRS ($D_q^{SRS}$). I perform spatial simulations to examine the relationship of $D_q$ with SAD, spatial patterns and number of species. Finally I compare the power of both $D_q$, SAD, SAR exponent, and the fractal information dimension to detect different community patterns using a continuum of hierarchical and neutral spatially explicit models. The SAD, $D_q^{SAD}$ and $D_q^{SRS}$ all had good performance in detecting models with contrasting mechanisms. $D_q^{SRS}$, however, had a better fit to data and allowed comparisons between hierarchical communities where the other methods failed. The SAR exponent and information dimension had low power and should not be used. SRS and $D_q^{SRS}$ could be interesting methods to study community or macroecological patterns.
Enterococci levels in the Bronx River during dry and wet weather conditions
Authors: Enecio Maria Leanna , Krakauer Nir Y.
Published: January 2018

The purpose of this project was to understand fecal microorganism contamination in the Bronx River within New York City and how it is affected by combined sewer overflow (CSO) events. Nine sites along the Bronx River were sampled throughout the summer of 2014 during wet and dry weather conditions. The samples were analyzed for enterococcus fecal indicator bacteria (FIB) concentration. The data revealed that wet weather enterococci concentrations are as 3 to 28 times greater than dry weather concentrations. The highest enterococci concentrations were found where the river enters Bronx County from Westchester County and near a storm water outfall. The positive correlation shown between the amount of rainfall and the FIB concentrations verifies that CSO and storm water discharges are a major source of FIB contamination in the river.
The effect of the spatial repellent metofluthrin on landing rates of outdoor biting anophelines in Cambodia, S.E. Asia
Authors: Charlwood Jacques Derek D , Nenhep Nep , Protopopoff Natacha , Siv Sovannaroth , Morgan John C , Hemingway Janet
Published: January 2018

Without controlling outdoor transmission, the goal of elimination of malaria is unlikely to be reached. This is particularly the case in places like Cambodia where people spend considerable amounts of time away from houses at night. Metofluthrin is a synthetic pyrethroid insecticide with a high vapor action at ambient temperatures and has been developed as a long lasting insect repellent device that works without the need to apply heat. Emanators of 10% of metofluthrin were therefore tested in landing collections against potential malaria vectors from three areas of the country (Pailin, Pursat and Koh Kong). One to four emanators were hung on wire 1m off the ground on one or four sides of a square 1.5m from collectors. Collections were also undertaken with Furvela tent-traps. 2086 hrs of landing collection were undertaken in Pailin, 528hrs in Veal Veng and 320 in Kroh Salau. Rate ratios were used to determine the significance of the difference between collections. The principal anophelines collected varied between locations. Anopheles minimus s.l. was the most common mosquito in Pailin, An. maculatus s.l in Veal Veng and An. sinensis in Kroh Salau. Among all species collected in Pailin landing rates were reduced by 50% (95% CI 55-44%) when a single emanator was used and by 58% (95% CI 63- 52%) when four were used. The effect was greater in An.minimus s.l 51% ( 95% CI 54-47%) and 70% (72%-66%) respectively. A similar result was obtained in Pursat, where 67% (95% CI 66- 42%) reductions were observed when four emanators were in use, but no significant reduction was observed in Koh Kong. Although the results show promise it is argued that the product needs further development.
Codon optimization of Col H gene encoding Clostridium histolyticum collagenase to express in Escherichia coli
Authors: Alipour Hamzeh , Raz Abbasali , Dinparast Djadid Navid , Rami Abbas , Mahdian Seyed Mohammad Amin
Published: January 2018

A given amino acid sequence can be encoded by a huge number of different nucleic acid sequences. These sequences, however, prove not to be equally useful. The choice of sequence can significantly impact the expression of an encoded protein. As regards the importance of protein-coding sequence and promising industrial and medicinal applications of Clostridium histolyticum collagenase, this study examined the codon optimization of the Col H gene so as to enhance collagenase expression in Escherichia coli (E. coli). The coding region of mature Col H gene was optimized according to the codon usage of E. coli using Gene Designer software (DNA 2.0). The results revealed that relative frequency of codon usage in Col H gene was adapted to the most preferred triplets in E. coli in such a way that codon usage bias in E. coli was enhanced after codon optimization. Similarly, the higher level of collagenase expression was more likely the result of substituting rare codons with optimal codons. As has been reported elsewhere, the findings from this study suggest that codon optimization provides a theoretical improvement in Col H gene expression in E. coli. In spite of that, experimental research is needed to confirm the improvement.
Ambient air pollution and depressive symptoms
Authors: Szyszkowicz Mieczyslaw , Rowe Brian H
Published: January 2018

Background. Depression is among the most common mental health problems. Depression interferes with daily functioning and quality of life. Many factors can contribute to depression and air pollution can initiate or intensify symptoms of depression.

Methods. Case-crossover method was used to study associations between emergency department (ED) visits for depression and ambient air pollution. The statistical analysis was applied for patients of different ages.

Results. Positive and statistically significant results, (communicated as odds ratios), were obtained for exposure to ambient carbon monoxide and ED visits for depression.

Discussion. The presented results support the hypothesis that recent exposures to ambient levels of air pollutants can contribute clinically significant worsening in depression symptoms leading to ED visits. As the results suggest the associations are age dependent.
Health status of veterans with spinal cord injury during screening program in Tehran 2013: Investigating the pulmonary function - a preliminary report
Authors: Azimi Ghasem , Divanbeigi Arash , Doroudi Taher , Emami Amir , Yarandi Alireza
Published: January 2018

Respiratory problems are a major cause of mortality in people with spinal cord injury. More than 2000 veterans with spinal cord injury live in Iran. This study aimed to evaluate the pulmonary function of veterans with spinal cord injury participating in the health-screening program in Tehran-2013. This retrospective descriptive study was conducted by reviewing participants’ medical records. All veterans (368) were male with the mean age of 49.62 ± 6.45 years. The mean time since injury was 27.17 ± 5.03 years; 32 veterans (8.7%) suffered from tetraplegia and 336 (91.3%) were paraplegic; 120 veterans (32.6%) had complete spinal cord injury and 248 had incomplete spinal cord injury (67.4%). Among them, 159 veterans had difficulty coughing; 198 complained of dyspnea and 119 had a history of hospitalization for pneumonia during the last year. It seems that veterans’ pulmonary status in the screening was appropriate indicating the suitability of periodic visits to veterans in the home care program. It is suggested that future studies be conducted simultaneously with health screening programs.
Cryopreservation of lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt
Authors: Norðberg Gunnvør , Johannesen Asa , Arge Regin
Published: January 2018

This study has established a successful protocol to cryopreserve lumpfish Cyclopterus lumpus (Linnaeus, 1758) milt. Three cryosolutions were tested based on Mounib’s medium; the original medium including reduced l-glutathione (L-Glu), the basic sucrose and potassium bicarbonate medium without L-Glu, or with hen’s egg yolk (EY). Dimethyl sulphoxide (DMSO) was used as the cryoprotectant along with all three diluents in a 1 to 2 dilution. Cryopreservation was performed with the mentioned cryosolutions at two freezing rates. Motility percentages of spermatozoa were evaluated using ImageJ with a computer assisted sperm analyzer (CASA) plug-in. Findings revealed that spermatozoa cryopreserved in Mounib’s medium without L-Glu had a post-thaw motility score of 8.64 percentage points (pp) higher than to that with added L-Glu, and an addition of EY to the Mounib’s medium lowered the post-thaw motility score by 15.07 pp. The difference in motility between both freezing rates was 5.23 pp, and samples cryopreserved on a 4.8 cm high tray resulted in a better post-thaw motility score. Cryopreserved milt had a 23.76 pp lower post-thaw motility score when compared with fresh milt. Cryopreservation of lumpfish milt has, to our knowledge, never been successfully carried out before. The established protocol will be a main contributing factor in a stable production of lumpfish juveniles in future.
Unusual characteristics of opaque Ishikawa endometrial cells include the envelopment of chromosomes with material containing endogenous biotin in the latter stages of cytokinesis
Authors: Fleming Honoree
Published: January 2018

We have identified a small dynamic population of opaque cells in Ishikawa endometrial cultures whose unusual characteristics include the fact that chromosomes become enveloped during the final stages of cytokinesis by material staining for endogenous biotin. Endogenous biotin, ultimately shown to be due to mitochondrial carboxylases, was detected in a membrane that wraps around aggregated nuclei in syncytia that develop as part of the differentiation of domes in Ishikawa cells. (Fleming H et al. 1998). The “wrapped chromosomes” in individual opaque Ishikawa cells stain similarly suggesting a similar origin. We were able to show that opaque cells form from transparent monolayer cells, can be polyploid, and often appear to be detaching from the colony and from the underlying substrate. We were also able to show an opaque cell fissioning asymmetrically, to give rise to a monolayer cell whose nucleus appeared to be wrapped. We believe that the cycle of differentiation of monolayer cells into opaque, polyploid cells and depolyploidization back into monolayer cells is involved in the spatial extension of cells as they develop from discrete colonies into a confluent monolayer. Wrapping of chromosomes may ensure that complete genomes are inherited by daughter cells during depolyploidization.
Fine motor deficits in reading disability and language impairment: same or different?
Authors: Bishop Dorothy V , McDonald Sarah , McDonald David , Brookman Annie
Published: January 2018

Several studies have found evidence of motor deficits in poor readers. There is no obvious reason for motor and literacy skills to go together, and it has been suggested that both deficits could be indicative of an underlying problem with cerebellar function and/or procedural learning. However, the picture is complicated by the fact that reading problems often co-occur with oral language impairments, which have also been linked with motor deficits. This raises the question of whether motor deficits characterise poor readers when language impairment has been accounted for – and vice versa. We considered these questions by assessing motor deficits associated with reading disability (RD) and language impairment (LI). A large community sample provided a subset of 9- to 10-year-olds, selected to oversample children with reading and/or language difficulties, to give 37 children with comorbid LI+RD, 67 children with RD only, 32 children with LI only, and 117 typically-developing (TD) children with neither type of difficulty. These children were given four motor tasks that taxed speed, sequence, and imitation abilities to differing extents. Different patterns of results were found for the four motor tasks. There was no effect of RD or LI on two speeded fingertip tapping tasks, one of which involved sequencing of movements. LI, but not RD, was associated with problems in imitating hand positions and slowed performance on a speeded peg-moving task that required a precision grip. Fine motor deficits in poor readers may be more a function of language impairment than literacy problems.
Do New Zealand men with prostate cancer benefit from a Mediterranean-style diet?
Authors: Erdrich Sharon , Bishop Karen S , Karunasinghe Nishi , Han Dug Yeo , Ferguson Lynnette R
Published: January 2018

Carcinoma of the prostate is the most commonly diagnosed malignancy and the third leading cause of mortality in New Zealand men, making it a significant health issue in this country. Global distribution patterns suggest that diet and lifestyle factors may be linked to the development and progression of this cancer. Twenty men with diagnosed prostate cancer adhered to a Mediterranean diet, with specific adaptations, for three months. Dietary data, prostate-specific antigen, C-reactive protein and DNA damage were evaluated at baseline after three months of following the diet. A significant reduction in DNA damage compared to baseline was apparent, with particular benefit noted for overall adherence to the diet (p = 0.013), increased intake of folate (p = 0.023), vitamin C (p = 0.007), legumes (p = 0.004) and green tea (p = 0.002). Higher intakes of red meat and dairy products were inversely associated with DNA damage (p = 0.003 and p = 0.008 respectively). This small study demonstrated that a high-antioxidant diet, modelled on Mediterranean traditions, may be of benefit for men with prostate cancer. Protection against DNA damage appears to be associated with the diet implemented, ostensibly due to reduction in reactive oxidant species. These findings warrant further exploration in a longer trial, with a larger cohort.
Chemically modified plastic tube for high volume removal and collection of circulating tumor cells
Authors: Gaitas Angelo , Kim Gwangseong
Published: January 2018

In this preliminary effort, we use a commercially available and chemically modified tube to selectively capture circulating tumor cells (CTCs) from the blood stream by immobilizing human anti-EpCAM antibodies on the tube's interior surface. We describe the steps required to modify a tube into a cancer cell capturing device. Using these simple modifications, at this proof-of-concept stage of development, we were able to capture about 85% of cancer cells from suspension and 44% of cancer cells from spiked whole blood, the capture percentage being dependent on the tube's length and the number of cancer cells present. Previous work by other researchers has focused on extracting small blood volumes and capturing CTCs with complicated micro-fluidic devices for diagnostic purposes. In addition, prior results of other researchers point to a possible reduction in metastasis achieved by removing CTCs from the bloodstream. We believe that with the utilization of appropriate tube lengths and procedures, we can ensure capture and removal of nearly the entire CTC population in whole blood. Following whole blood flow through the tube, the tube can be trypsinized to release the captured live CTCs for further analysis and testing.
The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating
Authors: Wang Xiaolong , Wang Xuxiang , Chen Gang , Zhang Jianye , Liu Yongqiang , Yang Chao
Published: January 2018

The genetic code defines the relationship between a protein and its coding DNA sequence. It was presumed that most frameshifts would yield non-functional, truncated or cytotoxic products. In this study, we report that in E. coli, a frameshift β-lactamase (bla) gene is still functional if all of the inner stop codons were readthrough or replaced by a sense codon. By analyzing a large dataset including all available protein coding genes in major model organisms, it is demonstrated that in any species, and in any protein-coding genes, the three translational products from the three different reading frames, are always similar to each other and with constant ~50% similarities and ~100% coverages, and the similarities is predefined by the genetic code rather than the sequences themselves. It is likely that a coding gene can be translated into three isoforms from each of the three reading frames, we propose a new gene expression paradigm, “one transcript, three translations”, which is an amendment to the traditional “one gene, one/multiple peptides” hypotheses. Finally, we concluded that the genetic code was optimized for frameshift tolerating in the early evolution, which endows every protein coding gene a character of shiftability, an inherent and everlasting ability to tolerate frameshift mutations, and serves as an innate mechanism for cells to deal with the frameshift problem.
Pooling morphometric estimates: a statistical equivalence approach
Authors: Pardoe Heath R , Cutter Gary , Alter Rachel A , Kucharsky Hiess Rebecca , Semmelroch Mira , Parker Donna , Farquharson Shawna , Jackson Graeme , Kuzniecky Ruben
Published: January 2018

Changes in hardware or image processing settings are a common issue for large multi-center studies. In order to pool MRI data acquired under these changed conditions, it is necessary to demonstrate that the changes do not affect MRI-based measurements. In these circumstances classical inference testing is inappropriate because it is designed to detect differences, not prove similarity. We used a method known as statistical equivalence testing to address this limitation.

Equivalence testing was carried out on three datasets: (i) cortical thickness and automated hippocampal volume estimates obtained from 16 healthy individuals imaged different multi-channel head coils; (ii) manual hippocampal volumetry obtained using two readers; and (iii) corpus callosum area estimates obtained using an automated method with manual cleanup carried out by two readers. Equivalence testing was carried out using the “two one-sided tests” approach.

Cortical thickness values were found to be equivalent over 78% of the cortex when different head coils were used (p = 0.024). Automated hippocampal volume estimates obtained using the same two coils were statistically equivalent (p = 4.28 × 10-15). Manual hippocampal volume estimates obtained using two readers were not statistically equivalent (p = 0.97). The use of different readers to carry out limited correction of automated corpus callosum segmentations yielded equivalent area estimates (1.28 × 10-14).

We have presented a statistical method for determining if morphometric measures obtained under variable conditions can be pooled. The equivalence testing technique is applicable for analyses in which experimental conditions vary over the course of the study.
spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Authors: Vitting-Seerup Kristoffer , Porse Bo T , Sandelin Albin , Waage Johannes E
Published: January 2018

With the advent of increasing depth and decreasing costs in digital gene expression technologies exemplified by RNA-sequencing, researchers are now able to profile the transcriptome with unprecedented detail. These advances not only allow for precise approximation of gene expression levels, but also for characterization of alternative isoform usage/switching between samples. Recent software improvements in full transcript deconvolution prompted us to develop spliceR , an R package for classification of alternative splicing. spliceR labels isoforms based on fully assembled transcripts, detecting single- and multiple exon skipping, alternative donor or acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. Alongside, event spliced-in/out values are calculated for effective post-filtering, and genomic coordinates of differentially spliced elements are annotated for downstream sequence analysis. Furthermore, spliceR has the option to predict the coding potential and thereby the nonsense mediated decay (NMD) sensitivity of transcripts based on stop codon position.
Morphological diversity in tenrecs (Afrosoricida, Tenrecidae): comparing tenrec skull diversity to their closest relatives
Authors: Finlay Sive , Cooper Natalie
Published: January 2018

It is important to quantify patterns of morphological diversity to enhance our understanding of variation in ecological and evolutionary traits. Here, we present a quantitative analysis of morphological diversity in a family of small mammals, the tenrecs (Afrosoricida, Tenrecidae). Tenrecs are often cited as an example of an exceptionally morphologically diverse group. However, this assumption has not been tested quantitatively. We use geometric morphometric analyses of skull shape to test whether tenrecs are more morphologically diverse than their closest relatives, the golden moles (Afrosoricida, Chrysochloridae). Tenrecs occupy a wider range of ecological niches than golden moles so we predict that they will be more morphologically diverse. Contrary to our expectations, we find that tenrec skulls are only more morphologically diverse than golden moles when measured in lateral view. Furthermore, similarities among the species-rich Microgale tenrec genus appear to mask higher morphological diversity in the rest of the family. These results reveal new insights into the morphological diversity of tenrecs and highlight the importance of using quantitative methods to test qualitative assumptions about patterns of morphological diversity.
Hypothesis for changing models: current pharmaceutical paradigms, trends and approaches in drug discovery
Authors: Fuoco Domenico
Published: January 2018

Despite the increasing availability of chemicals, the number of New Drug Approvals (NDA) from the Food and Drug Administration (FDA) remains unchanged. The number of chemical structures available online via web-based open source applications will reach the symbolic 1 billion in the 10 next years. However, for no apparent reasons, the number of NDA accepted yearly has not changed in the past 25 years. One of the emerging paradigms of Big Pharma is that the more we know about molecular mechanisms and cell signaling pathways, the less we understand how to use this knowledge to make New Chemical Entities (NCE). Moreover, the annual number of pharmaceutical patents collected in the OCSE database has virtually not increased. Unexpectedly, the number of patents originating in the USA is decreasing significantly, while Asia is doing very well. The comparison between the number of NCEs and the American investment in Research and Development (R&D) in the last 35 years shows that to obtain a new drug blockbuster, the total investment is quasi 4 USD billion. One of the peculiarities is the inverse relationship between the investment in R&D and the continued shortfall in productivity. A main reason for this decline is that the quality of scientific reasoning done by experienced chemists is too often replaced by Big Data . It is time to change the role of chemistry in Big Pharma and to re-position it as the central science to progress and to lead to much needed innovation.
An examination of disparities in cancer incidence in Texas using Bayesian random coefficient models
Authors: Sparks Corey
Published: January 2018

Disparities in cancer risk exist between ethnic groups in the United States. These disparities often result from differential access to healthcare, differences in socioeconomic status and differential exposure to carcinogens. This study uses cancer incidence data from the population based Texas Cancer Registry to investigate the disparities in digestive and respiratory cancers from 2000 to 2008. A Bayesian hierarchical regression approach is used. Specifically, a spatially varying coefficient model of the disparity between Hispanic and Non-Hispanic incidence is used. Results suggest that a spatio-temporal heterogeneity model best accounts for the observed Hispanic disparity in cancer risk. Overall, there is a significant disadvantage for the Hispanic population of Texas with respect to both of these cancers, and this disparity varies significantly over space. The greatest disparities between Hispanics and Non-Hispanics in digestive and respiratory cancers occur in eastern Texas, with patterns emerging as early as 2000 and continuing until 2008.
CRISPR-Cas9 in gene therapy: much control on breaking, little control on repairing
Authors: Daneshvar Kaveh
Published: January 2018

Recent advances in CRISPR-Cas9 genome editing tool have made great promises to basic and biomedical research as well as gene therapy. Efforts to make the CRISPR-Cas9 system applicable in gene therapy are largely focused on two aspects: 1) increasing the specificity of this system by eliminating off-target effects, and 2) optimizing in vivo delivery of the CRISPR-Cas9 DNA constructs to target cells and limiting the expression of Cas9 and gRNA to prevent immune responses. However, there is an unnoted but crucial consideration about the mode of DNA repair at the lesion caused by CRISPR-Cas9. In this commentary, I briefly highlight recent publications on in vivo use of the CRISPR-Cas9 system in gene therapy. I then discuss the undesired on-target DNA repair events that can occur as a result of the activity of CRISPR-Cas9. Overall, this commentary underscores the need for more study on controlled DNA repair in systems targeted with CRISPR-Cas9 genome editing tools.
The European and Japanese outbreaks of H5N8 derive from a single source population that has most likely been dispersed along the long distance bird migratory flyways
Authors: Dalby Andrew , Iqbal Munir
Published: January 2018

The origin of recent parallel outbreaks of the high pathogenicity H5N8 avian flu virus in Europe and in Japan can be traced to a single source population, which has most likely been spread by migratory birds. By using Bayesian coalescence methods to analyze the DNA sequences of the virus to find the times for divergence and combining bird migration data we can show the most likely locations and migratory pathways involved in the origin of the current outbreak. This population was most likely located in the Siberian summer breeding grounds of long-range migratory birds. These breeding grounds provide a connection between different migratory flyways and explain the current outbreaks in remote locations. By combining genetic methods and epidemiological data we can rapidly identify the sources and the dispersion pathways for novel avian influenza outbreaks.
New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies
Authors: Foth Christian , Evers Serjoscha , Pabst Ben , Mateus Octávio , Flisch Alexander , Patthey Mike , Rauhut Oliver W. M.
Published: January 2018

Adult large-bodied theropods are often found with numerous pathologies. A large, almost complete, probably adult Allosaurus specimen from the Howe Stephens Quarry, Morrison Formation (Late Kimmeridgian–Early Tithonian), Wyoming, shows multiple pathologies. Pathologic bones include the left dentary, two cervical vertebrae, one cervical and several dorsal ribs, the left scapula, the left humerus, right ischium, and two left pedal phalanges. These pathologies can be classified as follows: the fifth cervical vertebra, the scapula, several ribs and the ischium are traumatic, and a callus on the shaft of the left pedal phalanx II-2 is traumatic-infectious. Traumatically fractured elements exposed to frequent movement (e.g. the scapula and the ribs) show a tendency to develop pseudarthroses instead of callus healing. The pathologies in the lower jaw and a reduced flexor tubercle of the left pedal phalanx II-2 are most likely traumatic or developmental in origin. The pathologies on the fourth cervical are most likely developmental in origin or idiopathic, that on the left humerus is infectious or idiopathic, whereas left pedal phalanx IV-1 is classified as idiopathic. With exception of the ischium, all traumatic / traumatic-infectious pathologic elements show unambiguous evidences of healing, indicating that the respective pathologies did not cause the death of this individual. Alignment of the scapula and rib pathologies from the left side suggests that all may have been caused by a single traumatic event. The ischial fracture may have been fatal. The occurrence of multiple traumatic pathologies again underlines that large-bodied theropods experienced frequent injuries during life, indicating an active predatory lifestyle, and their survival perhaps supports a gregarious behavior for Allosaurus. Signs of infections are scarce and locally restricted, indicating a successful prevention of the spread of pathogens, as it is the case in extant reptiles (including birds).
An empirical study of goto in C code
Authors: Nagappan Meiyappan , Robbes Romain , Kamei Yasutaka , Tanter Éric , McIntosh Shane , Mockus Audris , Hassan Ahmed E.
Published: January 2018

It is nearly 50 years since Dijkstra argued that goto obscures the flow of control in program execution and urged programmers to abandon the goto statement. While past research has shown that goto is still in use, little is known about whether goto is used in the unrestricted manner that Dijkstra feared, and if it is ‘harmful’ enough to be a part of a post-release bug. We, therefore, conduct a two part empirical study - (1) qualitatively analyze a statistically representative sample of 384 files from a population of almost 2 million C programming language files collected from over 11K Github repositories and find that developers use goto in C files for error handling (80.21 ± 5%) and cleaning up resources at the end of a procedure (40.36 ± 5%); and (2) quantitatively analyze the commit history from the release branches of six OSS projects and find that no goto statement was removed/modified in the post-release phase of four of the six projects. We conclude that developers limit themselves to using goto appropriately in most cases, and not in an unrestricted manner like Dijkstra feared, thus suggesting that goto does not appear to be harmful in practice.
The influence of weed management on the growth and yield of direct seeded rice (Oryza sativa L.)
Authors: Saqib Muhammad , Ali Sajid , Ijaz Muhammad , Latif Muhammad , Ahmad Maqshoof , Akbar Nadeem , Ghaffar Abdul
Published: January 2018

Weed management is a primary concern in direct seeded rice (DSR) cropping because weed growth becomes a major constraint on crop yield. A two year field study was set up to evaluate the effect of various weed control measures on crop growth, grain yield and grain quality of DSR. The dry seeded non flooded rice experiment involved five different weed control measures: hand weeding, hoeing, inter-row tine cultivation, inter-row spike hoeing and herbicide treatment (Nominee 100 SC). The extent of weed control (compared to a non-weeded control) ranged from 50-95%. The highest crop yield was obtained using hand weeding. Hand weeding, tine cultivation and herbicide treatment raised the number of fertile rice tillers formed per unit area and the thousand grain weight. Tine cultivation provided an effective and economical level of weed control in the DSR crop.
The Bioinformatics Open Source Conference (BOSC) 2013
Authors: Harris Nomi L , Cock Peter J A , Chapman Brad A , Goecks Jeremy , Hotz Hans-Rudolf , Lapp Hilmar
Published: January 2018

The 14th annual Bioinformatics Open Source Conference (BOSC) was held in Berlin in July 2013, bringing together over 100 bioinformatics researchers, developers and users of open source software. Since its inception in 2000, BOSC has been organised as a Special Interest Group (SIG) satellite meeting preceding the large International Conference on Intelligent Systems for Molecular Biology (ISMB), which is the annual meeting of the International Society for Computational Biology (ISCB). BOSC provides bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community, and a focused environment for developers and users to interact and share ideas about standards, software development practices, and practical techniques for solving bioinformatics problems. As in previous years, BOSC 2013 was preceded by a Codefest, a two day hackathon that brings together bioinformatics open source project developers and members of the community and allows them to work collaboratively and achieve greater interoperability between tools developed by different groups.

The session topics at BOSC 2013 included several that have been popular in previous years, including Cloud and Parallel Computing, Visualization, Software Interoperability, Genome-scale Data Management, and a session for updates on ongoing open source projects, as well as two new sessions: Translational Bioinformatics, recognizing the growing use of computational biology in medical applications, and Open Science and Reproducible Research. Open Science, a movement dedicated to making all aspects of scientific knowledge production freely available for reuse and extension, not only validates published results by allowing others to reproduce them, but also accelerates the pace of scientific discovery by enabling researchers to more efficiently build on previous work, rather than having to reinvent tools and reassemble data sets.

BOSC typically features two keynote talks by researchers who are influential in some aspect of open source bioinformatics. Our first keynote talk this year was by Cameron Neylon, the Advocacy Director for the Public Library of Science (PLOS), who is a prominent advocate for open science. He discussed the cultural issues that are hindering open science, and how openness in scientific collaborations can generate impact. Our second keynote speaker, Sean Eddy, who is perhaps best known as the author of the HMMER software suite, began his keynote talk with an inspiring history of how he got involved in bioinformatics and proceeded to argue that dedicating effort to thorough engineering in tool development, which is often shunned as incremental, can become the key to creating a lasting impact.

With the increasing reliance of more and more fields of biology on computational tools to manage and analyze their data, BOSC is well positioned to stay relevant to life science, and thus life scientists, for many years to come.
To beat or not to beat a tick: Comparison of DNA extraction methods from ticks (Ixodes scapularis)
Authors: Ammazzalorso Alyssa D , Zolnik Christine P , Daniels Thomas J , Kolokotronis Sergios-Orestis
Published: January 2018

Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens to humans, including bacteria, protozoa, and viruses. Their importance as a disease vector necessitates reliable and comparable methods for extracting microbial DNA from ticks. Furthermore, to explore the population genetics or genomics of this tick, appropriate DNA extraction techniques are needed for both the vector and its microbes. Although a few studies have investigated different methods of DNA isolation from ticks, they are limited in the number and types of DNA extraction and lack species-specific quantification of DNA yield. Methods. Here we determined the most efficient and consistent method of DNA extraction from two different developmental stages of I. scapularis – nymph and adult - that are the most important for disease transmission. We used various methods of physical disruption of the hard, chitinous exoskeleton, as well as commercial and non-commercial DNA isolation kits. To gauge the effectiveness of these methods we quantified the DNA yield and confirmed the DNA quality via PCR of both tick and microbial genetic material. Results. DNA extraction using the Thermo GeneJET Genomic DNA Purification kit resulted in the highest DNA yields and the strongest, most consistent PCR amplification. We also found that physical disruption of the tick exoskeleton was most effective using cross-sectional cutting compared to any type of bead-beating matrices used. Storing ticks at -80°C resulted in considerably higher DNA yields than those from ticks stored in ethanol. Discussion. We contrasted a variety of readily available methods of DNA extraction from single individual blacklegged ticks and presented the results through a quantitative and qualitative assessment.
Matrix compression methods
Authors: Paixão Crysttian A. , Coelho Flávio Codeço
Published: January 2018

The biggest cost of computing with large matrices in any modern computer is related to memory latency and bandwidth. The average latency of modern RAM reads is 150 times greater than a clock step of the processor (Alted, 2010). Throughput is a little better but still 25 times slower than the CPU can consume. The application of bitstring compression allows for larger matrices to be moved entirely to the cache memory of the computer, which has much better latency and bandwidth (average latency of L1 cache is 3 to 4 clock steps). This allows for massive performance gains as well as the ability to simulate much larger models efficiently. In this work, we propose a methodology to compress matrices in such a way that they retain their mathematical properties. Considerable compression of the data is also achieved in the process. Thus allowing for the computation of much larger linear problems within the same memory constraints when compared with the traditional representation of matrices.