bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional circuits in B cell transformation
Authors: Hu Yeguang , Yoshida Toshimi , Georgopoulos Katia
Published: April 2017

Purpose of review

Loss of IKAROS in committed B cell precursors causes a block in differentiation while at the same time augments aberrant cellular properties, such as bone marrow stromal adhesion, self-renewal and resistance to glucocorticoid-mediated cell death. B cell acute lymphoblastic leukaemias originating from these early stages of B cell differentiation and associated with IKAROS mutations share a high-risk cellular phenotype suggesting that deregulation of IKAROS-based mechanisms cause a highly malignant disease process.

Recent studies

Recent studies show that IKAROS is critical for the activity of super-enhancers at genes required for pre-B cell receptor (BCR) signalling and differentiation, working either downstream of or in parallel with B cell master regulators such as EBF1 and PAX5. IKAROS also directly represses a cryptic regulatory network of transcription factors prevalent in mesenchymal and epithelial precursors that includes YAP1, TEAD1/2, LHX2 and LMO2, and their targets, which are not normally expressed in lymphocytes. IKAROS prevents not only expression of these ‘extra-lineage’ transcription factors but also their cooperation with endogenous B cell master regulators, such as EBF1 and PAX5, leading to the formation of a de novo for lymphocytes super-enhancer network. IKAROS coordinates with the Polycomb repression complex (PRC2) to provide stable repression of associated genes during B cell development. However, induction of regulatory factors normally repressed by IKAROS starts a feed-forward loop that activates de-novo enhancers and elevates them to super-enhancer status, thereby diminishing PRC2 repression and awakening aberrant epithelial-like cell properties in B cell precursors.

Insight into IKAROS-based transcriptional circuits not only sets new paradigms for cell differentiation but also provides new approaches for classifying and treating high-risk human B-ALL that originates from these early stages of B cell differentiation.
Adiponectin, lipids and atherosclerosis
Authors: Katsiki Niki , Mantzoros Christos , Mikhailidis Dimitri P.
Published: April 2017

Purpose of review

Adiponectin is an adipokine with anti-inflammatory, antioxidant, antiatherogenic, pro-angiogenic, vasoprotective and insulin-sensitizing properties. Several factors may influence adiponectin levels, such as genetic polymorphisms, obesity / body fat distribution, diet and exercise as well as cardiovascular risk factors such as sleep deprivation and smoking as well as medications. Adiponectin has been proposed as a potential prognostic biomarker and a therapeutic target in patients with cardiometabolic diseases.

Recent findings

This narrative review discusses the associations of adiponectin with obesity-related metabolic disorders (metabolic syndrome, nonalcoholic fatty liver disease, hyperuricaemia and type 2 diabetes mellitus). We also focus on the links between adiponectin and lipid disorders and with coronary heart disease and noncardiac vascular diseases (i.e. stroke, peripheral artery disease, carotid artery disease, atherosclerotic renal artery stenosis, abdominal aortic aneurysms and chronic kidney disease). Further, the effects of lifestyle interventions and drug therapy on adiponectin levels are briefly reviewed.

Based on available data, adiponectin represents a multifaceted biomarker that may beneficially affect atherosclerosis, inflammation and insulin resistance pathways. However, there are conflicting results with regard to the associations between adiponectin levels and the prevalence and outcomes of cardiometabolic diseases. Further research on the potential clinical implications of adiponectin in the diagnosis and treatment of such diseases is needed.
Emergence and Spread of Neisseria gonorrhoeae Isolates With Decreased Susceptibility to Extended-Spectrum Cephalosporins in Argentina, 2009 to 2013
Authors: Gianecini Ricardo , Romero Maria de las Mercedes , Oviedo Claudia , Vacchino Martin , Galarza Patricia
Published: April 2017

Background

The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins represents a major concern globally. The aim of this study was to examine the phenotypic and molecular characteristics of N. gonorrhoeae isolates with decreased susceptibility to ceftriaxone and cefixime in Argentina.

Methods

A total of 1987 isolates were collected during 2009 and 2013. The susceptibility to penicillin G, tetracycline, ciprofloxacin, cefixime, ceftriaxone, and azithromycin was determined using the agar dilution method. The major extended-spectrum cephalosporin resistance determinants (penA, mtrR, and porB1b) were sequenced in 42 N. gonorrhoeae isolates that showed decreased susceptibility to ceftriaxone (minimum inhibitory concentration [MIC], 0.06–0.125 mg/L) and cefixime (MIC, 0.125–0.25 mg/L). Genotyping by N. gonorrhoeae multiantigen sequence typing (NG-MAST) was performed.

Results

Between 2009 and 2013, there was a shift in the modal MICs for ceftriaxone. Among the 42 isolates exhibiting decreased susceptibility to ceftriaxone and cefixime, 95.2% were resistant to penicillin G, 95.2% to tetracycline, 97.6% to ciprofloxacin, and 33.3% to azithromycin. Thirty-five (83.3%) of the 42 isolates had a mosaic penA allele XXXIV, which has been previously associated with resistance to ceftriaxone and cefixime as well as treatment failures. The isolates that contained the mosaic penicillin-binding protein 2 (PBP2) XXXIV were associated with NG-MAST ST1407 or closely related genotypes.

Conclusions

In Argentina, N. gonorrhoeae isolates with decreased susceptibility to cefixime and ceftriaxone have now emerged, mostly due to the introduction of the internationally spread multidrug-resistant NG-MAST ST1407.
Impact of Number of Human Papillomavirus Vaccine Doses on Genital Warts Diagnoses Among a National Cohort of U.S. Adolescents
Authors: Perkins Rebecca B. , Lin Mengyun , Wallington Sherrie F. , Hanchate Amresh
Published: April 2017

Background

The impact of fewer than 3 doses of human papillomavirus (HPV) vaccine on genital warts is uncertain.

Methods

Using the Truven Health Analytics Marketscan administrative database, we compared rates of genital warts among women receiving 0, 1, 2, or 3 doses of HPV vaccine. Females aged 9 to 18 years on January 1, 2007, who were continuously enrolled in the database through December 31, 2013, were included. Patients were assigned an HPV dose state (0, 1, 2, or 3) based on the last recorded dose. The exposure period began on January 1, 2007, or the date of the final HPV dose, and lasted until the first diagnosis of genital warts or December 31, 2013. Multivariable Poisson regression was performed to determine the risk of genital warts associated with vaccine doses.

Results

Among 387,906 subjects, mean age and exposure period were 14.73 and 5.64 years, respectively. The proportions of doses received were: 52.1%, 7.8%, 9.4%, and 30.7% for 0, 1, 2, and 3 doses, respectively. The rate of genital warts was 1.97/1000 person-years. Receipt of 0 or 1 dose was associated with more genital warts than 3 doses. The effectiveness of 2 doses following current Centers for Disease Control and Prevention guidelines was similar to 3 doses. The risk of genital warts rose with age.

Conclusions

Prevention of genital warts is higher with completion of 3 vaccine doses than with 1 dose, though 2-dose recommendations appear to provide similar protection. Prospective effectiveness studies of recommended 2-dose schedules against clinical endpoints including persistent infection, genital warts, and cervical dysplasia are necessary to ensure long-term protection of vaccinated cohorts.
Synchronous Bilateral Tubal Serous Carcinomas in a Patient With Exon 13 Duplication and Loss of Function of BRCA1
Authors: Gurda Grzegorz T. , Serdy Kate M. , Yatsenko Svetlana A. , Rajkovic Aleksandar , Carter Natalie J. , Ahmed Rafay , Olawaiye Alexander B. , Bhargava Rohit , Elishaev Esther
Published: April 2017

We report the first case of distinct, synchronous serous carcinomas of the adnexa arising in a patient with a family history of breast and ovarian cancer and a germline loss of function mutation in BRCA1. Illustrating an exceedingly rare phenomenon of synchronous high-grade carcinomas with distinct histomorphologic, immunohistochemical and cytogenetic features, the case serves as a point of departure for the discussion of phenotypic patterns of carcinomas arising in BRCA1 mutation carriers. We also review patient management, including the importance of risk-reducing salpingo-oophorectomy in women with deleterious BRCA1 mutations, as well as the potential need for an intraoperative pathologic assessment to find occult, high-grade carcinomas in this setting.
Diffusely Metastasized Adenocarcinoma Arising in a Mucinous Carcinoid of the Ovary: A Case Report
Authors: Van Rompuy Anne-Sophie , Vanderstichele Adriaan , Vergote Ignace , Moerman Philippe
Published: April 2017

Mucinous (goblet cell) carcinoids are a rare type of ovarian carcinoid tumors. Only a limited number of primary mucinous carcinoids of the ovary have been reported in the literature. We describe the case of a 55-year-old woman with a diffusely metastasized adenocarcinoma arising in a primary ovarian mucinous carcinoid. The differential diagnosis with a metastatic goblet cell carcinoid from the appendix or elsewhere can be very challenging. In our case, especially the immunohistochemical profile of the tumor with diffuse positivity for cytokeratin 7 and PAX8, and no expression of cytokeratin 20 and CDX2, directed us toward a primary ovarian origin. Expression of PAX8 in ovarian mucinous carcinoid has never been reported before.
Fibroadenoma-like Lesion of the Vagina: A Description of 2 Cases of a Previously Unreported Entity
Authors: Moore Michelle , McKenna Michael , Mandavilli Srinivas , McCluggage W. Glenn
Published: April 2017

We report 2 cases of a previously undescribed vaginal lesion, which we term “fibroadenoma-like lesion of the vagina” because of the close morphologic resemblance to breast fibroadenoma. Both lesions arose in the upper vagina and exhibited a biphasic appearance with benign epithelial and stromal elements. The glandular epithelium comprised a double layer of luminal and basal cells with focal squamous differentiation in 1 case. The stromal component was fibroblastic and morphologically bland for the most part, although occasional atypical symplastic-like cells were present in 1 case. Both lesions exhibited a similar immunophenotype with the luminal and basal glandular epithelium expressing PAX8 and GATA3 while estrogen receptor and progesterone receptor were largely negative. The basal cell layer was p63 and CK5/6 positive. We discuss the possible origin and histogenesis of this rare lesion which we believe to be benign based on the morphologic features and uneventful 5 years follow-up in 1 case.
Advanced MRI of the Optic Nerve
Authors: Hoch Michael J. , Bruno Mary T. , Shepherd Timothy M.
Published: April 2017

Background:

Clinical orbital MRI protocols are routinely used to study the optic nerves and exclude compressive lesions, infarctions, or inflammation. However, the small caliber and divergent oblique orientations of the optic nerves make it challenging to characterize them well with conventional MRI, especially since adjacent air-filled bony structures distort the MRI signal and motion is a problem even in cooperative, healthy volunteers.

Evidence Acquisition:

Over the past 3 years we have experimented with multiple novel MRI approaches and sequences to better characterize the optic nerves. The perfect MRI protocol would be quantitative and sensitive to subtle optic nerve pathologic changes, provide high spatial resolution, be rapidly acquired, and resistant to motion degradation.

Results:

This review provides an update of recent MRI sequence innovations for the optic nerves being currently translated into clinical practice. Methods discussed include rapid MRI with compressed sensing or simultaneous multislice approaches, postprocessing techniques for quantitative T2 mapping or track density imaging, and multiple MRI sequences for measuring diffusion in the optic nerves.

Conclusions:

Recently-developed orbit-specific MRI coils, quantitative sequences, and rapid acquisition techniques can improve our future ability to study optic nerve pathologies noninvasively. As advanced MRI becomes more proficient at characterizing the optic nerves, its role in the clinical management of patients should increase.
Encoding and Decoding Dynamic Sensory Signals with Recurrent Neural Networks: An Application of Conceptors to Birdsongs
Authors: Gast Richard , Faion Patrick , Standvoss Kai , Suckro Andrea , Lewis Brian , Pipa Gordon
Published: April 2017

In a constantly changing environment the brain has to make sense of dynamic patterns of sensory input. These patterns can refer to stimuli with a complex and hierarchical structure which has to be inferred from the neural activity of sensory areas in the brain. Such areas were found to be locally recurrently structured as well as hierarchically organized within a given sensory domain. While there is a great body of work identifying neural representations of various sensory stimuli at different hierarchical levels, less is known about the nature of these representations. In this work, we propose a model that describes a way to encode and decode sensory stimuli based on the activity patterns of multiple, recurrently connected neural populations with different receptive fields. We demonstrate the ability of our model to learn and recognize complex, dynamic stimuli using birdsongs as exemplary data. These birdsongs can be described by a 2-level hierarchical structure, i.e. as sequences of syllables. Our model matches this hierarchy by learning single syllables on a first level and sequences of these syllables on a top level. Model performance on recognition tasks is investigated for an increasing number of syllables or songs to recognize and compared to state-of-the-art machine learning approaches. Finally, we discuss the implications of our model for the understanding of sensory pattern processing in the brain. We conclude that the employed encoding and decoding mechanisms might capture general computational principles of how the brain extracts relevant information from the activity of recurrently connected neural populations.
An experimental approach to understanding elevation limits in a montane terrestrial salamander,plethodon montanus
Authors: Caruso Nicholas M. , Jacobs Jeremy F. , Rissler Leslie J.
Published: April 2017

Understanding the abiotic and biotic factors that determine the limits to species’ range is an essential goal in ecology, biogeography, evolutionary biology, and conservation biology. Moreover, predictions of shifts in species’ distributions under future changes in climate can be improved through understanding the spatial variation in survival, growth, and reproduction. A long-standing hypothesis postulates that, for Northern Hemisphere species, abiotic factors like temperature limit northern and/or higher elevation extents, while biotic factors like competition limit the southern and/or lower elevation range edges; though amphibians may not follow this general trend. Therefore, we combined environmental suitability models and a reciprocal transplant experiment across an elevational gradient to explore the role of the abiotic environment on the range limits of a montane salamander (Plethodon montanus). We first determined suitability of the abiotic environment forP. montanus, under current (1960 – 2000) and future (2050) climate scenarios. Second, we collected juveniles from each of three elevations and transplanted them within mesocosms such that each origin population was represented within each transplant location and vice-versa. We found that environmental suitability in 2050 decreased throughout the range compared to current predictions, especially at lower elevations. Additionally, we found that individuals’ starting body condition and transplant location were important predictors of survival, growth, and reproduction condition; importantly, individuals transplanted to low elevation had lower survival and growth rates compared to those moved to mid or high elevations. Our study provides experimental support that the abiotic environment limits the lower elevation distribution ofP. montanusand, unfortunately, our results also paint a possible bleak future for this species and likely other montane terrestrial plethodontids. The abiotic environment, which will become increasingly limited under future changes in climate, was found to have more influence on survival and growth than population identity.
TGFβ mediated structural remodeling facilitates optic fissure fusion and the necessity of BMP antagonism in this process
Authors: Knickmeyer Max D. , Mateo Juan L. , Eckert Priska , Roussa Eleni , Rahhal Belal , Zuniga Aimee , Krieglstein Kerstin , Wittbrodt Joachim , Heermann Stephan
Published: April 2017

The optic fissure is a transient gap in the developing vertebrate eye, which must be closed as development proceeds. A persisting optic fissure, coloboma, is a major cause for blindness in children. Multiple factors are genetically linked to coloboma formation. However, especially the process of optic fissure fusion is still largely elusive on a cellular and molecular basis.

We found a coloboma phenotype in mice with a targeted inactivation of the transforming growth factor 2 (TGFβ2). Here the optic fissure margins got in touch, however, failed to fuse. Transcriptomic analyses indicated TGFβ mediated ECM remodeling during optic fissure fusion. For functional analyses, we switched model systems and made use of zebrafish. We found TGFβ ligands expressed in the developing zebrafish eye, and the ligand binding receptor in the optic fissure. Using a new in vivo TGFβ signaling reporter, we also found active TGFβ signaling in the margins of the optic fissure. We addressed the function of Cadherin 6 (cdh6), one of the TGFβ regulated genes, by knock down experiments in zebrafish and found a prominent coloboma phenotype.Cdh6was often found involved in processes of epithelial to mesenchymal transition (EMT), strengthening our hypothesis that an EMT-like process is also necessary for optic fissure fusion. Furthermore, we found Gremlin 2b (grem2b) and Follistatin a (fsta), homologs of TGFβ regulated bone morphogenetic protein (BMP) antagonists, expressed in the optic fissure margins, indicating the necessity of a localized inhibition of BMP signaling. Finally, we show that induced BMP expression is sufficient to inhibit optic fissure fusion. Together with our previous findings this indicates a dual role of BMP signaling during optic fissure closure.

Summary statement

TGFβ is crucial for optic fissure fusion, involvingcdh6. TGFβ mediated optic fissure fusion is potentially hampered by BMP signaling, which is blocked by TGFβ induced BMP antagonists within the optic fissure margins.
GTC: a novel attempt to maintenance of huge genome collections compressed
Authors: Danek Agnieszka , Deorowicz Sebastian
Published: April 2017

Motivation

Results

We present GTC, a novel compressed data structure for representation of huge collections of genetic variation data. GTC significantly outperforms existing solutions in terms of compression ratio and time of answering various types of queries. We show that the largest of publicly available database of about 60 thousand haplotypes at about 40 million SNPs can be stored in less than 4 Gbytes, while the queries related to variants are answered in a fraction of a second.

Availability

GTC can be downloaded fromhttps://github.com/refresh-bio/GTCorhttp://sun.aei.polsl.pl/REFRESH/GTC.

Contact

sebastian.deorowicz@polsl.pl
Genome-scale detection of positive selection in 9 primates predicts human-virus evolutionary conflicts
Authors: der Lee Robin van , Wiel Laurens , van Dam Teunis J.P. , Huynen Martijn A.
Published: April 2017

Hotspots of rapid genome evolution hold clues about human adaptation. Here, we present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection acting on 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our stringent procedure and quality control of alignments and evolutionary inferences reveal substantial artefacts (20% of initial predictions) that have inflated previous estimates of positive selection, the large majority relating to transcript definitions (61%) or gene models (38%). Our final set of 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immune functions, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokine pathways, defensins, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction, chromosome segregation and meiosis (e.g. centromere-associatedCENPO, CENPT), apolipoproteins, smell/taste receptors, and proteins interacting with mitochondrial-encoded molecules. Focusing on the virus-host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g.TRIM5,MAVS,SAMHD1, tetherin) and predict 70 novel cases through integration with virus-host interaction data (virus-human PPIs, immune cell expression, infection screens). Protein structure analysis identifies positive selection in the interaction interfaces between viruses and their human cellular receptors (CD4– HIV;CD46[MCP] – measles, adenoviruses;CD55[DAF] – picornaviruses). Finally, the primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positively selected genes and positions, available athttp://www.cmbi.umcn.nl/∼rvdlee/positive_selection/, is a rich source for studying the genetics underlying human (antiviral) phenotypes.
Altering expression of a vacuolar iron transporter doubles iron content in white wheat flour
Authors: Connorton James M. , Jones Eleanor R. , Rodríguez-Ramiro Ildefonso , Fairweather-Tait Susan , Uauy Cristobal , Balk Janneke
Published: April 2017

Iron deficiency anaemia is a major global health issue, which has prompted mandatory fortification of cereal products with iron salts or elemental iron in many countries around the world. Rather than post-harvest fortification, biofortification - increasing the intrinsic nutritional quality of crops - is a more sustainable way of alleviating nutrient deficiencies. To identify target genes for biofortification of wheat (Triticum aestivum), we functionally characterized homologues of theVacuolar Iron Transporter(VIT). The wheat genome contains twoVITparalogues,TaVIT1andTaVIT2, which have different expression patterns, but are both low in the endosperm. TaVIT2, but not TaVIT1, was able to transport iron in a yeast complementation assay. TaVIT2 also transported manganese but not zinc. By over-expressingTaVIT2under the control of an endosperm-specific promoter, we achieved a 2-fold increase in iron in white flour fractions, exceeding minimum UK legal fortification levels. The highiron trait was consistent across independent lines and was stable in the next generation and in two different growth conditions. The single-gene approach impacted minimally on plant growth and was also effective in barley. The anti-nutrient phytate was not increased in white flour from the cisgenic wheat lines, suggesting that food products made from it could contribute to improved iron nutrition.
Variation in the modality of a yeast signaling pathway is mediated by a single regulator
Authors: Palme Julius , Wang Jue , Springer Michael
Published: April 2017

Bimodal gene expression by genetically identical cells is a pervasive feature of signaling networks. In the galactose-utilization (GAL) pathway ofSaccharomyces cerevisiae, induction can be unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation of modality is regulated by an interplay between two features of the pathway response, the fraction of cells that are in the induced subpopulation and their expression level. Combined, the variations in these features are sufficient to explain the observed effects of natural variation and pre-induction conditions on the modality of induction in both mechanistic and phenomenological models. Both natural variation and pre-induction conditions act by modulating the expression and function of the galactose sensorGAL3. The ability to alter modality may allow organisms to adapt their level of “bet hedging” to the conditions they experience, and thus help optimize fitness in complex, fluctuating natural environments.
NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma
Authors: Xiao Zhi-Jie , Liu Jing , Wang Si-Qi , Zhu Yun , Gao Xu-Yuan , Tin Vicky Pui-Chi , Qin Jing , Wang Jun-Wen , Wong Maria Pik
Published: April 2017

Cancers display intratumoral genetic and molecular heterogeneity with tumor initiating cells (TIC) showing enhanced tumor phenotypes. In this study, we show the calcium pathway transcription factor NFATc2 is a novel regulator of lung TIC through the NFATc2/SOX2/ALDH1A1 regulatory axis.In vitroandin vivocancer cell modeling demonstrated supportive evidences including cell renewal, tumorigenicity at limiting dose, cell motility, resistance to cytotoxic chemotherapy and EGFR targeted therapy. In human lung cancers, high NFATc2 expression predicts poor tumor differentiation, adverse recurrence-free and overall patient survivals. Mechanistic investigations identified NFATc2 response elements in the SOX2 3’ enhancer region, and NFATc2/SOX2 coupling upregulates ALDH1A1 by binding to its 5’ enhancer. Through this axis, oxidative stresses and reactive oxygen species induced by cancer drug treatment are attenuated, accounting for a mutation-independent mechanism of drug resistance. Targeting this axis provides a novel approach for the long term treatment of lung cancer through TIC elimination.
Comprehensive characterization of the complexlolalocus reveals a novel role in the octopaminergic pathway via Tyramine beta-hydroxylase activation
Authors: Dinges Nadja , Morin Violeta , Kreim Nastasja , Southall Tony D. , Roignant Jean-Yves
Published: April 2017

longitudinals lacking (lola)is among the most complex genes inDrosophila melanogaster, encoding up to twenty protein isoforms and acting as a key transcription factor in axonal pathfinding and neural reprogramming. Most of previous studies employed loss-of-function alleles disrupting common exons oflola, making it difficult to delineate its functions. To address this issue we have generated specific mutations in each isoform using the CRISPR/Cas9 system. Our targeted screen allows us to revisit the previously demonstrated roles for few isoforms and to demonstrate a specific function for one variant in axon guidance via activation of the microtubule-associated factor Futsch. Importantly, we also reveal a critical role for a second variant in preventing neurodegeneration via the control of the octopaminergic pathway. This variant is expressed almost exclusively in the octopaminergic cells and is involved in the transcriptional activation of a key enzyme of the pathway. Thus, our comprehensive study greatly expands the functional repertoire of Lola functions, and adds novel insights into the transcriptional regulatory control of neurotransmitter expressionin vivo.
Exploring the Diversity ofBacilluswhole genome sequencing projects using Peasant, the Prokaryotic Assembly and Annotation Tool
Authors: Brenner Jonathon , Kalesinskas Laurynas , Putonti Catherine
Published: April 2017

Background

The persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects.

Results

The Prokaryotic Assembly and Annotation Tool, Peasant, automates the processes of read quality control, genome assembly, and annotation for microbial sequencing projects. High-quality assemblies and annotations can be generated by Peasant without the need of programming expertise or high-performance computing resources. Furthermore, statistics are calculated so that users can evaluate their sequencing project. To illustrate the computational speed and accuracy of Peasant, the SRA records of 322 Illumina platform whole genome sequencing assays forBacillusspecies were retrieved from NCBI, assembled and annotated on a single desktop computer. From the assemblies and annotations produced, a comprehensive analysis of the diversity of over 200 high-quality samples was conducted, looking at both the 16S rRNA phylogenetic marker as well as theBacilluscore genome.

Conclusions

Peasant provides an intuitive solution for high-quality whole genome sequence assembly and annotation for users with limited programing experience and/or computational resources. The analysis of theBacilluswhole genome sequencing projects exemplifies the utility of this tool. Furthermore, the study conducted here provides insight into the diversity of the species, the largest such comparison conducted to date.
Mode of sucrose delivery alters reward-related phasic dopamine signals in nucleus accumbens
Authors: McCutcheon James E , Roitman Mitchell F
Published: April 2017

In studies of appetitive Pavlovian conditioning, rewards are often delivered to subjects in a manner that confounds several processes. For example, delivery of a sugar pellet to a rodent requires movement to collect the pellet and is associated with sensory stimuli such as the sight and sound of the pellet arrival. Thus, any neurochemical events occurring in proximity to the reward may be related to multiple coincident phenomena. We used fast-scan cyclic voltammetry in rats to compare nucleus accumbens dopamine responses to two different modes of delivery: sucrose pellets, which require goal-directed action for their collection and are associated with sensory stimuli, and intraoral infusions of sucrose, which are passively received and not associated with external stimuli. We found that when rewards were unpredicted both pellets and infusions evoked similar dopamine release. However, when rewards were predicted by distinct cues, greater dopamine release was evoked by pellet cues than infusion cues. Thus, dopamine responses to pellets, infusions as well as predictive cues suggest a nuanced role for dopamine in both reward seeking and reward evaluation.
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
Authors: Ramazzotti Daniele , Graudenzi Alex , De Sano Luca , Antoniotti Marco , Caravagna Giulio
Published: April 2017

Background

A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types.

Results

We introduceTRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools,TRaITsupports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena.TRaITimproves accuracy, robustness to data-specific errors and computational complexity compared to competing methods.

Conclusions

We show that the application ofTRaITto single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses.
A theoretical model of jump diffusion-mean reversion
Authors: Chakrabarty Anindya , Luo Zongwei , Dubey Rameshwar , Jiang Shan
Published: April 2017

Purpose

The purpose of this paper is to develop a theoretical model of a jump diffusion-mean reversion constant proportion portfolio insurance strategy under the presence of transaction cost and stochastic floor as opposed to the deterministic floor used in the previous literatures.

Design/methodology/approach

The paper adopts Merton’s jump diffusion (JD) model to simulate the price path followed by risky assets and the CIR mean reversion model to simulate the path followed by the short-term interest rate. The floor of the CPPI strategy is linked to the stochastic process driving the value of a fixed income instrument whose yield follows the CIR mean reversion model. The developed model is benchmarked against CNX-NIFTY 50 and is back tested during the extreme regimes in the Indian market using the scenario-based Monte Carlo simulation technique.

Findings

Back testing the algorithm using Monte Carlo simulation across the crisis and recovery phases of the 2008 recession regime revealed that the portfolio performs better than the risky markets during the crisis by hedging the downside risk effectively and performs better than the fixed income instruments during the growth phase by leveraging on the upside potential. This makes it a value-enhancing proposition for the risk-averse investors.

Originality/value

The study modifies the CPPI algorithm by re-defining the floor of the algorithm to be a stochastic mean reverting process which is guided by the movement of the short-term interest rate in the economy. This development is more relevant for two reasons: first, the short-term interest rate changes with time, and hence the constant yield during each rebalancing steps is not practically feasible; second, the historical literatures have revealed that the short-term interest rate tends to move opposite to that of the equity market. Thereby, during the bear run the floor will increase at a higher rate, whereas the growth of the floor will stagnate during the bull phase which aids the model to capitalize on the upward potential during the growth phase and to cut down on the exposure during the crisis phase.
A bibliographic study on big data: concepts, trends and challenges
Authors: Mishra Deepa , Luo Zongwei , Jiang Shan , Papadopoulos Thanos , Dubey Rameshwar
Published: April 2017

Purpose

The purpose of paper is twofold. First, it provides a consolidated overview of the existing literature on “big data” and second, it presents the current trends and opens up various future directions for researchers who wish to explore and contribute in this rapidly evolving field.

Design/methodology/approach

To achieve the objective of this study, the bibliographic and network techniques of citation and co-citation analysis was adopted. This analysis involved an assessment of 57 articles published over a period of five years (2011-2015) in ten selected journals.

Findings

The findings reveal that the number of articles devoted to the study of “big data” has increased rapidly in recent years. Moreover, the study identifies some of the most influential articles of this area. Finally, the paper highlights the new trends and discusses the challenges associated with big data.

Research limitations/implications

This study focusses only on big data concepts, trends, and challenges and excludes research on its analytics. Thus, researchers may explore and extend this area of research.

Originality/value

To the knowledge of the authors, this is the first study to review the literature on big data by using citation and co-citation analysis.
Fabric defect detection based on sparse representation of main local binary pattern
Authors: Liu Zhoufeng , Yan Lei , Li Chunlei , Dong Yan , Gao Guangshuai
Published: April 2017

Purpose

The purpose of this paper is to find an efficient fabric defect detection algorithm by means of exploring the sparsity characteristics of main local binary pattern (MLBP) extracted from the original fabric texture.

Design/methodology/approach

In the proposed algorithm, original LBP features are extracted from the fabric texture to be detected, and MLBP are selected by occurrence probability. Second, a dictionary is established with MLBP atoms which can sparsely represent all the LBP. Then, the value of the gray-scale difference between gray level of neighborhood pixels and the central pixel, and the mean of the difference which has the same MLBP feature are calculated. And then, the defect-contained image is reconstructed as normal texture image. Finally, the residual is calculated between reconstructed and original images, and a simple threshold segmentation method can divide the residual image, and the defective region is detected.

Findings

The experiment result shows that the fabric texture can be more efficiently reconstructed, and the proposed method achieves better defect detection performance. Moreover, it offers empirical insights about how to exploit the sparsity of one certain feature, e.g. LBP.

Research limitations/implications

Because of the selected research approach, the results may lack generalizability in chambray. Therefore, researchers are encouraged to test the proposed propositions further.

Originality/value

In this paper, a novel fabric defect detection method which extracts the sparsity of MLBP features is proposed.
Experimental study on cutting flexible sheet materials using an oscillating knife
Authors: Cosson-Coche Quentin , Cahuc Olivier , Darnis Philippe , Laheurte Raynald , Teissandier Denis , Chabirand Didier
Published: April 2017

Purpose

The purpose of this paper is to understand the impact of the cutting forces on the quality of pieces in industrial cutting of multi-ply textile material. It also tries to establish a cutting model that can simulate the cutting forces in order to understand the behaviour of the blade.

Design/methodology/approach

Working on an industrial machine, a cutting head with an oscillating knife is instrumented with different sensors. Using this equipment, cutting forces can be analysed experimentally while the fabric is being cut along a straight line.

Findings

A model of the physical phenomena of the cutting forces is proposed, taking different parameters into account such as the geometry of the blade, the properties of the material being cut and the parameters of the cut. The simulated forces and the monitored forces are compared and parameters for minimising the cutting forces of fabrics are deduced.

Research limitations/implications

Due to the wide diversity of fabrics, all with different mechanical characteristics, this research only began with the study of denim in a straight cut.

Originality/value

This paper describes an instrumentation of automatic cutting head for textile. It manages to simulate the action of the fabrics on the blade through effort monitoring and help in the understanding of the multi-ply cutting process.
Assessment of the non-woven, goose down and duck down as thermally insulating materials for the clothing protecting against cold
Authors: Dabrowska Anna Katarzyna , Bartkowiak Grazyna , Karcz Jagna , Frydrych Iwona
Published: April 2017

Purpose

The purpose of this paper is to compare morphological and physical features of three kinds of materials intended for the insulating layer in the clothing protecting against cold – high-bulk non-woven, goose down (GD) and duck down (DD).

Design/methodology/approach

Comparison of thermal performance of developed textile systems with the non-woven, GD and DD content was based on basic biophysical properties related to comfort sensations of the user such as thermal resistance, water vapor resistance and air permeability. In this study, light microscopy and scanning electron microscopy methods were employed to visualize the surface and internal structure of non-woven, GD and DD samples.

Findings

The paper indicates the advantages and disadvantages of each of selected insulating material. For the down samples, significantly higher thermal resistance in a dry state than for the non-woven samples can be achieved. Meanwhile, textile systems with the non-woven provide lower value of water vapor resistance. The selected textile systems for the research were characterized by a comparable air permeability.

Originality/value

This paper allows for an evaluation of high-bulk non-woven, DD and GD samples in terms of providing optimal thermal performance in clothing protecting against cold.
The migration and institutional sheltering of children and adolescents in the Federal District, Brazil
Authors: Penso Maria Aparecida , Fukuda Cláudia Cristina , Costa Liana Fortunato , Villela Luisa
Published: April 2017

Purpose

The purpose of this paper is to relate the phenomenon of migration to the Federal District (DF, Brazil), with the figures for institutional shelter of children and adolescents.

Design/methodology/approach

The method chosen was the documental analysis of special folders that were processed in the Defense Office for Children and Adolescents of the DF from January 2007 to August 2009. The sample consisted of 545 special folders, referring to a total of 1,007 children and adolescents.

Findings

The results indicate that most children and adolescents received at the shelters were from families living in the satellite cities of the DF (53.4 percent) and surroundings (8.3 percent), and were mainly from rural areas of the Northeast region of the country and also from the deprived areas of the states of Goiás and Minas Gerais, near the DF. Among the main reasons for institutional shelter, is violence, abandonment by family, poverty and living on the streets.

Research limitations/implications

It can be inferred that the policies of “population clusters” in the DF were responsible for this migratory process and population growth of satellite cities and surrounding areas. It is understood in this way that the migration processes resulted in the rupture of the bond with the family of origin and an insertion into a reality, which again challenge these families in a situation of poverty and violence.

Social implications

The reality of vulnerability and social exclusion of migrant families who leave their support networks in their home states need urgent attention of local public policies, especially with regard to encouraging the construction of other support networks and creating contexts of cultural identification in the communities, especially the neediest. The support and presence of quality public services in these communities and the preventive action of social policies are also considered essential to ensure quality of life and adequate subsistence to the people who migrate to the DF.

Originality/value

Brasília became the symbol of hope for unemployed people or for those suffering from their income being below the poverty level. Faced with this migratory reality, this paper discusses the situation of families of children and adolescents institutionally sheltered in the DF, given their social situation regarding poverty, unemployment, lack of support from their family of origin and lack of access of distribution of public policies and income generation.
The journey from first inspection to quality standards (1857-2016): are we there yet?
Authors: Campbell Martin
Published: April 2017

Purpose

The purpose of this paper is to qualitatively analyse the inspection and regulation of care for people with learning disabilities and mental health problems in Scotland, in two time periods.

Design/methodology/approach

The paper uses comparative historical research drawing on primary sources from 1857 to 1862 in the form of Annual Reports of the General Board of Commissioners in Lunacy for Scotland and associated papers, to compare inspection methods, quality standards and to identify persistent challenges to effective inspection.

Findings

Political, clinical and public awareness led initially to criticisms of existing care and eventually to the development of the “The Lunacy Act” of 1857. This Act resulted in the first attempts to set minimum standards of care for individuals at risk, with enforceable regulation. Some factors recur as challenges to effective practice in the inspection and regulation of care today.

Practical implications

There are problems of definition, reliable monitoring of quality standards and adequate, independent inspection of services that respond to unacceptable standards of care. There is a growing evidence base about best methods of inspection of services for people in care who are most at risk. These methods attempt to strike a balance between evidence- and value-based judgments. Perspectives from history may help focus resources.

Originality/value

This paper compares common and common challenges in two time periods to investigate what can be learned about the development of policy and practice in inspection and regulation of care.
Restatements and accounting quality: a comparison between IFRS and US-GAAP
Authors: El-Gazzar Samir M. , Finn Philip M.
Published: April 2017

Purpose

This paper aims to examine whether sanctioning adoption of IFRS for US firms would produce accounting information of the same quality as those produced under US Generally Accepted Accounting Principles (GAAP). This is a timely research since the Securities and Exchange Commission (SEC; 2014) has asked for further review.

Design/methodology/approach

This study uses restatements of financial statements made by a sample of foreign firms listed on US stock exchanges using International Financial Reporting Standards (IFRS) in comparison to a control sample of US firms using US GAAP during the period of 2001to 2010. Statistical analysis of the frequency, sources and magnitude of the restatements and market revaluations to the announcement of the restatements are examined. Cross-country differences are also examined.

Findings

The results indicate that IFRS firms have a lower rate of restatements than US GAAP firms but with no significant differences in terms of sources of restatements and the impact on net income or shareholders’ equity. The market revaluations to restatement announcements show no significant differences between the two accounting regimes. Cross-sectional analyses indicate IFRS firms are on average from countries characterized by weak rule of law, ineffective corruption controls and lower efforts to promote private sector advancement.

Research limitations/implications

The sample size in the paper is relatively small. To increase validity of the inferences from the Results, this issue should be readdressed with larger sample.

Practical implications

Results are important to accounting practitioners and policymakers.

Social implications

Results are contributing in clarifying the SEC’s concerns of adopting the IFRS by US-based firms; thus, saving the investors the additional efforts and costs in comparing financial statements prepared under different accounting regimes.

Originality/value

This research is the first to use restatements as accounting quality criteria. The results suggest that adoption of IFRS by US-based firms would not produce accounting information that is significantly different in quality from those generated under US GAAP. This result should be of interest to the SEC in clarifying its concerns.