bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved genomic island predictions with IslandPath-DIMOB
Authors: Bertelli Claire , Brinkman Fiona S L
Published: February 2018

Motivation

Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase.

Results

IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest.

Availability and implementation

IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3.

Supplementary information

Supplementary data are available at Bioinformatics online.
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms
Authors: Zhou Zilu , Wang Weixin , Wang Li-San , Zhang Nancy Ruonan
Published: February 2018

Motivation

Copy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large-scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous single-nucleotide polymorphism (SNP)-array data are available. An integrated cross-platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele-specific reads.

Results

We propose a statistical framework, integrated CNV (iCNV) detection algorithm, which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform-specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a hidden Markov model. We compare integrated two-platform CNV detection using iCNV to naïve intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only and show that the utilization of allele-specific reads improve CNV detection accuracy compared to existing methods.

Availability and implementation

https://github.com/zhouzilu/iCNV

Supplementary information

Supplementary data are available at Bioinformatics online.
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts
Authors: Swainston Neil , Dunstan Mark , Jervis Adrian J , Robinson Christopher J , Carbonell Pablo , Williams Alan R , Faulon Jean-Loup , Scrutton Nigel S , Kell Douglas B
Published: February 2018

Motivation

Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. PartsGenie is introduced to facilitate the computational design of such synthetic biology parts, bridging the gap between optimization tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language, and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimization algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimization and dissemination of reusable synthetic biology parts through an integrated application.

Availability and implementation

PartsGenie is freely available at https://parts.synbiochem.co.uk.
The Sophists
Authors: McKirahan Richard D.
Published: February 2018

Sophistês (from sophos, “wise”) originally designated epic poets, prophets, sages, Presocratic philosophers and others with wisdom beneficial to society. Sometime after c. 450 bce it was applied to a new kind of wise people. These men were professional showmen and teachers, the first to provide education beyond the traditional basic subjects—music, poetry, physical training, and arithmetic. They were entrepreneurs, rivals, and competitors who expected to be paid. They traveled from city to city, charging fees for teaching and for their public performances. Each Sophist taught whatever subjects he wished, subjects ranging from mathematics and astronomy to grammar and literary criticism. Many Sophists had interests in language and taught techniques of reasoning, argument, and public speaking that could be useful in public and private life. They came from different cities in the Greek world. They were regarded as attractive and fascinating, but suspicious and dangerous, attitudes reflected in literature, most prominently in Plato’s writings. Plato contrasts individual Sophists with Socrates and sophistry with philosophy. The negative connotations of “sophistry,” “sophism,” and “sophist” are due ultimately to Plato’s influence and should not lead us to suppose that the Sophists engaged in and taught nothing but how to reason badly and construct misleading arguments. They were important in many areas. To them is due the beginnings of the study of language and speech, which stands at the origins of grammar and rhetoric. Others puzzled about the gods and the origins of religion. Some contributed to mathematics. Most importantly, they stand at the origins of moral, political and social philosophy, anthropology, and political theory. Plato’s negative portrayal dominated until the 20th century and the few exceptions interpreted the Sophists uncritically as forerunners of their own philosophical views. Study of the Sophists requires access to information about them, not just to the interpretations of others. This information falls into three sorts: (1) Actual words of the Sophists—complete works and excerpts from works that do not survive in their entirety; (2) summaries and paraphrases of their works; (3) reports in ancient authors of their views and other information about them; and (4) interpretations by ancient and modern authors. The first three sorts form the basis of valid research. They were collected for the first time in 1903 by Diels—Die Fragmente der Vorsokratiker, 6th ed. (1952)—which remains the basic reference point. The Sophists have been viewed from many angles which cannot all be represented adequately in this bibliography, which is intended as a guide to books and articles useful for understanding who the Sophists were, their methods, aims, and achievements, how they were viewed in antiquity, and their contributions to philosophical thought.
Xenophanes
Authors: Bryan Jenny
Published: February 2018

The poet-philosopher Xenophanes of Colophon (in Ionia, now western Turkey) was active in the 6th to 5th centuries bce. While his precise dates are uncertain, it is plausible that he was born toward the beginning of the 6th century (perhaps around 570–560 bce), and he himself claimed to have lived into his nineties. The biographical tradition suggests that he traveled widely, and he is often associated with Elea, in southern Italy. On some accounts, he is named as the founder of the Eleatic school of philosophy, and even as the teacher of its most prominent figure, Parmenides of Elea, but neither claim is certain. Xenophanes composed verse in both hexameter and elegiac meter, but only some forty-five fragments of his work survive. These fragments are preserved as quotations in the works of various later authors, and our understanding of Xenophanes relies on reading these in combination with the ancient testimonia (accounts given by other authors) on his life and thought. The elegiac fragments indicate a concern with proper behavior within the civic and sympotic contexts. Some of his hexameter fragments are critical, particularly of contemporary theology, and these came to be labelled Silloi (Satires). Xenophanes is often classed as part of the tradition of Ionian natural philosophy, and some of the fragments indicate an interest in providing rationalizing explanations of natural phenomena as well as a commitment to earth, water, and cloud as basic physical principles. Xenophanes is perhaps best known as a critic of contemporary anthropomorphic religion, which he appears to have rejected in favor of some sort of rational monotheism. His rejection of anthropomorphic religion is tied to criticism of Homer and Hesiod as its most prominent representatives. In addition to his interests in morality, theology, and natural philosophy, Xenophanes offers a couple of intriguing epistemological fragments, and there is a long-running debate over the nature and extent of his skepticism. Scholars have noted a possible connection between Xenophanes’ concerns with civic propriety and critique of the gods in poetry on ethical grounds and similar ideas found in Plato’s Republic. Xenophanes’ fragments do not present philosophical argument as such, tending instead toward assertion and critique. Scholarship on Xenophanes’ thought tends to rely on attempts to build up implications and connections within and between the fragments.
Contemporary Hylomorphism
Authors: Bailey Andrew , Wilkins Shane Maxwell
Published: February 2018

Aristotle famously held that objects are comprised of matter and form. That is the central doctrine of hylomorphism (sometimes rendered “hylemorphism”—hyle, matter; morphe, form), and the view has become a live topic of inquiry today. Contemporary proponents of the doctrine include Jeffrey Brower, Kit Fine, David Hershenov, Mark Johnston, Kathrin Koslicki, Anna Marmodoro, Michael Rea, and Patrick Toner, among others. In the wake of these contemporary hylomorphic theories the doctrine has seen application to various topics within mainstream analytic metaphysics. Here, appeals to form and matter are used to shed light on problems about ontology, personal identity, philosophy of mind, and philosophy of religion. The current entry documents this resurgence of interest in hylomorphism, the ways it has been applied, and its reception.
Climate Change and Conflict in Northern Africa
Authors: Schilling Janpeter , Krause Lisa
Published: February 2018

Climate change is one of the key challenges the world is facing in the 21st century. Concerns are increasingly raised that climate change might not only undermine the livelihoods of millions of people across the globe but that it might actually act as a multiplier of risks and threats that could result in violent conflict. In 2014 the Intergovernmental Panel on Climate Change (IPCC) for the first time included a chapter on human security in one of its assessment reports (cited under General Overviews). The security and conflict implications of climate change have made it to the international policy agenda. The pathways from climate change to conflict are, however, indirect and highly complex. Global climate change has local effects in the form of changing temperatures and rainfall patterns, extreme events such as drought and flooding, and sea-level rise. Conflicts related to climate change may be violent or non-violent and occur on subnational, national, or regional scales. Intermediate variables between climate change and conflict may include altered availability of resources such as land and water, migration, displacement, decline or loss of livelihoods, and food insecurity. To have an overview of these linkages in northern Africa is particularly important as the region is characterized by both strong vulnerability to climate change and conflicts of varying intensities. This article first gives a general introduction to the topic of climate change and conflict (see General Overviews and Special Issues and Edited Volumes) before Fundamental Theories and Concepts and Critical Perspectives are addressed and Quantitative Studies and Qualitative Case Studies are described. Thereafter the focus is placed on linkages between climate change and conflict in the following countries: Algeria, Chad, Egypt, Libya, Mali, Morocco, Niger, South Sudan and Sudan, and Tunisia. The final section of the article gives an overview of relevant Reports by Nongovernmental Organizations.
Postcolonial Theory in Film
Authors: Ponzanesi Sandra
Published: February 2018

Postcolonial theory has hardly been a defining paradigm in the field of film studies. Postcolonial theory originally emerged from comparative literature departments and film from film and media studies departments, and despite the many intersections postcolonial theory has not been explicitly foregrounded. However, there are more similarities and natural points of intersections between the two areas than it would at first appear. For example, both postcolonial theory and film studies emerged at the end of the 1970s with the development of semiotic theory and poststructuralist thought. Both areas engage intensively with the field of representation, implying the ways in which a language, be it cinematic or otherwise, manages to convey reality as “mediated” and “discursive,” and therefore influenced by power relations. An example could be the notion of the gendered gaze by Laura Mulvey and her concept of looked-at-ness and how it also applies to the screening and representation of black and colonized bodies in films, which bell hooks later theorized as black looks, to which she proposed the response of an oppositional gaze. Despite their different genealogies, it is therefore not only very natural but also necessary to combine postcolonial theory and film in order to unearth how the visual field is inherently hegemonizing and hierarchical and therefore in need of critical appraisal and a deconstructive take, such as postcolonial theory. Postcolonial theory has critically contributed to revisiting the representation of the Other, addressing long-standing tropes and stereotypes about cultural difference and racial otherness. This implies new interventions on how visual representations are implicated in the policing of boundaries between East and West, between Europe and the Rest, the self and the other, undoing or rethinking the ways in which the visual field conveys operation of a mastery that needs to be undone and decoded. For example, empire cinema contributed to specific ways of seeing, making films that legitimated the domination of colonies by the colonial powers. Colonial images of gender, race, and class carried ideological connotations that confirmed imperial epistemologies and racial taxonomies, depicting natives, in documentary or fictional films, as savages, primitive, and outside modernity. More recent cinema genres such as border cinema, transnational cinema, accented cinema, haptic cinema, migrant cinema, diasporic cinema, and world cinema can be considered affiliated with the postcolonial paradigm as they all embrace ethnic, immigrant, hyphenated counter-narratives. Yet the field of postcolonial cinema studies, which relates postcolonial theory to film, is a false friend to all these categories as it connects with but also departs from the projects they name in order to pursue the tense power asymmetries generated by the legacies of conquest and colonialism.
HEMORRHAGIC OCCLUSIVE RETINAL VASCULITIS AFTER INTRACAMERAL VANCOMYCIN USE IN CATARACT SURGERY AFTER INTRAVENOUS EXPOSURE
Authors: Alasil Tarek , Wong James J.Y. , Adelman Ron A. , Tom David , Coady Patrick A.
Published: February 2018

Purpose:

To report a case of hemorrhagic occlusive retinal vasculitis after cataract surgery.

Methods:

A 74-year-old woman presented with blurry vision and distorted vision, which started 2 days after an uncomplicated cataract surgery in the left eye. Intracameral vancomycin was injected during the case. The patient reported being treated with systemic vancomycin in the past.

Results:

The visual acuity was 20/80 in the left eye. She had trace cells in the anterior chamber with no hypopyon and intraocular lens implant within the capsular bag in the left eye. Dilated fundus examination revealed no vitritis, There were large patches of peripheral retinal hemorrhages and retinal ischemia. The patient was diagnosed with hemorrhagic occlusive retinal vasculitis likely secondary to hypersensitivity reaction to intracameral vancomycin. The patient was started on oral prednisone, and the topical difluprednate course was escalated. Within 3 weeks, vision improved to 20/30 in the left eye. She underwent pan retinal photocoagulation targeting the ischemic areas in the periphery.

Conclusion:

The patient had previous exposure to systemic vancomycin, which may have sensitized her immune system. Later on, the hypersensitivity reaction took place after exposure to intracameral vancomycin during cataract surgery. Our hemorrhagic occlusive retinal vasculitis case had a favorable visual outcome, and recognition of this entity will ensure that vancomycin will not be used for infection prophylaxis in the fellow eye at the time of cataract surgery.
PROFOUND VISUAL RECOVERY AT 16 MONTHS AFTER RESOLUTION OF SEROUS RETINAL DETACHMENTS SECONDARY TO THROMBOTIC THROMBOCYTOPENIC PURPURA: CASE REPORT AND LITERATURE REVIEW
Authors: Williams Parker J. , Pearce William A. , Smith Jesse M. , Robinson Joshua
Published: February 2018

Purpose:

To report a unique case of dramatic improvement in objective visual function during the recovery phase, after resolution of thrombotic thrombocytopenic purpura–related serous retinal detachments and to review prognostic trends in reported cases involving the macula.

Methods:

Observational case report and literature review.

Results:

A 36-year-old white woman with thrombotic thrombocytopenic purpura developed vision loss from serous retinal detachments in both eyes. Over a 16-month period, after both retinae remained attached, best-corrected visual acuity improved from 20/400 to 20/50 in both eyes with dramatic improvement on optical coherence tomography and autofluorescence imaging.

Conclusion:

Although thrombotic thrombocytopenic purpura is a life-threatening illness, visual prognosis in patients with macula off serous retinal detachments appears excellent. Most cases reviewed in literature improved to baseline visual acuity, but recovery periods ranged from days to many months. Hyperautofluorescent granularity on autofluorescence photography may be an indicator of chronic retinal detachment and a more delayed visual recovery.
INVERTED INTERNAL LIMITING MEMBRANE–FLAP TECHNIQUE FOR OPTIC DISK PIT MACULOPATHY: MORPHOLOGIC AND FUNCTIONAL ANALYSIS
Authors: Sborgia Giancarlo , Recchimurzo Nicola , Sborgia Luigi , Niro Alfredo , Sborgia Alessandra , Piepoli Marina , Alessio Giovanni
Published: February 2018

Purpose:

To analyze morphologic and functional changes after inverted internal limiting membrane–flap technique for optic disk pit maculopathy using optical coherence tomography, multifocal electroretinography, and microperimetry.

Methods:

One case report.

Results:

A 30-year-old woman presented us with decreased visual acuity (20/63) in the left eye because of retinoschisis and serous macular detachment associated with optic disk pit. Optical coherence tomography did not localize the source of intraretinal and subretinal fluid. A partial flattening of serous detachment after vitrectomy with internal limiting membrane peeling, inverted internal limiting membrane–flap technique, and gas tamponade was reported. Visual acuity and multifocal electroretinography improved while retinal sensitivity decreased at microperimetry during 3 months of follow-up.

Conclusion:

Optical coherence tomography is helpful to assess the effectiveness of surgical maneuvers to treat optic disk pit maculopathy. Multifocal electroretinography and microperimetry might offer additional tools for follow-up analysis of retinal function after surgery.
Impact of 3D virtual planning on reconstruction of mandibular and maxillary surgical defects in head and neck oncology
Authors: Witjes Max J.H. , Schepers Rutger H. , Kraeima Joep
Published: February 2018

Purpose of review

This review describes the advances in 3D virtual planning for mandibular and maxillary reconstruction surgical defects with full prosthetic rehabilitation. The primary purpose is to provide an overview of various techniques that apply 3D technology safely in primary and secondary reconstructive cases of patients suffering from head and neck cancer.

Recent findings

Methods have been developed to overcome the problem of control over the margin during surgery while the crucial decision with regard to resection margin and planning of osteotomies were predetermined by virtual planning. The unlimited possibilities of designing patient-specific implants can result in creative uniquely applied solutions for single cases but should be applied wisely with knowledge of biomechanical engineering principles.

The high surgical accuracy of an executed 3D virtual plan provides tumor margin control during ablative surgery and the possibility of planned combined use of osseus free flaps and dental implants in the reconstruction in one surgical procedure. A thorough understanding of the effects of radiotherapy on the reconstruction, soft tissue management, and prosthetic rehabilitation is imperative in individual cases when deciding to use dental implants in patients who received radiotherapy.
Magnetization Transfer Ratio in Peripheral Nerve Tissue
Authors: Kollmer Jennifer , Kästel Thorsten , Jende Johann M.E. , Bendszus Martin , Heiland Sabine
Published: February 2018

Background and Purpose

Magnetization transfer contrast imaging provides indirect information on the concentration of “bound” water protons and their interactions with “free” water molecules. The purpose of this study is to analyze location- and age-dependent changes in the magnetization transfer ratio (MTR) of lower extremity nerves.

Materials and Methods

Ten younger (20–32 years) and 5 older (50–63 years) healthy volunteers underwent magnetization transfer contrast imaging at 3 Tesla Two 3-dimensional gradient echo sequences with and without an off-resonance saturation pulse (repetition time: 58 milliseconds; echo time: 2.46 milliseconds; band width: 530 Hz/Px; flip angle: α = 7°) were acquired at 3 different locations covering the proximal thigh to the distal lower leg in the group of younger volunteers and at 2 different locations covering the proximal to distal thigh in the group of older volunteers. Sciatic and tibial nerve regions of interest (ROIs) were manually drawn and additional ROIs were placed in predetermined muscles. Magnetization transfer ratios were extracted from respective ROIs and calculated for each individual and location.

Results

In young volunteers, mean values of nerve and muscle MTR were not different between the proximal thigh (nerve: 20.34 ± 0.91; muscle: 31.71 ± 0.29), distal thigh (nerve: 19.90 ± 0.98; P = 0.76; muscle: 31.53 ± 0.69; P = 0.87), and lower leg (nerve: 20.82 ± 1.07; P = 0.73; muscle: 32.44 ± 1.11; P = 0.51). An age-dependent decrease of sciatic nerve MTR was observed in the group of older volunteers (16.95 ± 1.2) compared with the group of younger volunteers (20.12 ± 0.65; P = 0.019). Differences in muscle MTR were not significant between older (31.01 ± 0.49) and younger (31.62 ± 0.37; P = 0.20) volunteers.

Conclusion

The MTR of lower extremity nerves shows no proximal-to-distal gradient in young healthy volunteers but decreases with age. For future studies using MTR in peripheral nerve disorders, these findings suggest that referencing magnetization transfer contrast values in terms of age, but not anatomical nerve location is required.
Early Heterogenic Response of Renal Microvasculature to Hemorrhagic Shock/Resuscitation and the Influence of NF-κB Pathway Blockade
Authors: Yan Rui , van Meurs Matijs , Popa Eliane R. , Li Ranran , Zwiers Peter J. , Zijlstra Jan G. , Moser Jill , Molema Grietje
Published: February 2018

Hemorrhagic shock (HS) is associated with low blood pressure due to excessive loss of circulating blood and causes both macrocirculatory and microcirculatory dysfunction. Fluid resuscitation after HS is used in the clinic to restore tissue perfusion. The persistent microcirculatory damage caused by HS and/or resuscitation can result in multiple organ damage, with the kidney being one of the involved organs. The kidney microvasculature consists of different segments that possess a remarkable heterogeneity in functional properties. The aim of this study was to investigate the inflammatory responses of these different renal microvascular segments, i.e., arterioles, glomeruli, and postcapillary venules, to HS and resuscitation (HS/R) in mice and to explore the effects of intervention with a nuclear factor-kappa B (NF-κB) inhibitor on these responses. We found that HS/R disturbed the balance of the angiopoietin-Tie2 ligand-receptor system, especially in the glomeruli. Furthermore, endothelial adhesion molecules, proinflammatory cytokines, and chemokines were markedly upregulated by HS/R, with the strongest responses occurring in the glomerular and postcapillary venous segments. Blockade of NF-κB signaling during the resuscitation period only slightly inhibited HS/R-induced inflammatory activation, possibly because NF-κB p65 nuclear translocation already occurred during the HS period. In summary, although all three renal microvascular segments were activated upon HS/R, responses of endothelial cells in glomeruli and postcapillary venules to HS/R, as well as to NF-κB inhibition were stronger than those in arterioles. NF-κB inhibition during the resuscitation phase does not effectively counteract NF-κB p65 nuclear translocation initiating inflammatory gene transcription.
Aurora B-mediated exclusion of HP1a from latesegregating chromatin prevents formation of micronuclei
Authors: Warecki Brandt , Sullivan William
Published: February 2018

Late-segregating acentric chromosomes pose a serious risk to genomic integrity when they are excluded from dividing daughter nuclei and form damage-prone micronuclei. Insight into the cellular mechanisms that prevent the formation of micronuclei from acentrics come from studies demonstrating that acentrics reincorporate into daughter telophase nuclei by passing through Aurora B kinase-dependent channels in the nuclear envelope ofDrosophilaneuroblasts. Here, we uncover a mechanism of nuclear envelope channel formation in which localized concentrations of Aurora B preferentially phosphorylate H3(S10) on heterochromatic acentrics and their associated DNA tethers. This phosphorylation event prevents HP1a from associating with heterochromatin and results in localized inhibition of nuclear envelope reassembly on endonuclease- and X-irradiation-induced acentrics and the main daughter nuclei at the sites of acentric entry to promote the formation of channels. Finally, we find that HP1a also specifies initiation sites of nuclear envelope reassembly on undamaged chromatin. Taken together, these results demonstrate that Aurora B-mediated regulation of HP1a-chromatin interactions plays a key role maintaining genome integrity by locally preventing nuclear envelope assembly and facilitating incorporation of late-segregating acentrics into daughter nuclei.
Ubiquitous abundance distribution of non-dominant plankton across the world’s ocean
Authors: Ser-Giacomi Enrico , Zinger Lucie , Malviya Shruti , De Vargas Colomban , Karsenti Eric , Bowler Chris , De Monte Silvia
Published: February 2018

Species Abundance Distributions (SADs) bear the imprint of ecological processes that shape biological communities, and are therefore used to discriminate among different scenarios of community assembly. Even though empirical distributions appear to follow a handful of qualitative laws, it is still unclear if and how quantitative variation in SADs reflects peculiar features of the communities and their environmental context. Here, we use the extensive dataset generated by theTaraOceans expedition for marine microbial eukaryotes (protists) and an adaptive algorithm to explore how SADs vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant OTUs, comprising over 99% of local richness, is commonly governed by a power-law. The power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Our findings suggest that large-scale ubiquitous ecological processes govern the assembly of non-dominant plankton throughout the global ocean.
Light Pollution Increases West Nile Virus Competence in a Ubiquitous Passerine Reservoir Species
Authors: Kernbach M. E. , Miller J. M. , Hall R. J. , Unnasch T. R. , Burkett-Cadena N. D. , Martin L. B.
Published: February 2018

One sentence summary

Light pollution increases host infectiousness.

Light pollution is a growing problem, but its impacts on infectious disease risk have not been considered. Previous research has revealed that dim light at night (dLAN) dysregulates various immune functions and biorhythms, which hints that dLAN could change the risk of disease epidemics. Here, we demonstrate that dLAN enhances infectiousness of the house sparrow (Passer domesticus), an urban-dwelling avian host of West Nile virus (WNV). Sparrows exposed to dLAN maintained viral titers above the transmission threshold to a biting vector (105 plaque-forming units) for two days longer than controls but did not die at higher rates. A mathematical model revealed that such effects could increase WNV outbreak potential by ~41%. dLAN likely affects other host and vector traits relevant to transmission, so additional research is needed to advise management of zoonotic diseases in light polluted areas.
Bead Enhancement of EV Analysis
Authors: Lin Hsing-Ying , Yang Katherine S. , Curley Caleigh , Lee Hakho , Welch Marisa W. , Wolpin Brian M. , Weissleder Ralph , Im Hyungsoon , Castro Cesar
Published: February 2018

Extracellular vesicles (EVs) are recognized cancer biomarkers, however, clinical analysis has been difficult due to a lack of simple and sensitive assays. Here, we describe a bead-enhanced flow cytometry method, BEAD flow, using biotinylated EVs captured on streptavidin particles. With this method, we show analysis of patient-derived EVs using a panel of pancreatic cancer biomarkers. BEAD flow is easily translatable to any biomarker or cancer type and can be run with conventional flow cytometers, making it highly flexible and adaptable to diverse research and clinical needs.
Vps74 connects the Golgi apparatus and telomeres in Saccharomyces cerevisiae
Authors: Rodrigues Joana , Banks Peter , Lydall David
Published: February 2018

In mammalian cell culture, the Golgi apparatus fragment upon DNA damage. GOLPH3, a Golgi component, is a phosphorylation target of DNA-PK after DNA damage and contributes to Golgi fragmentation. The function of the yeast (Saccharomyces cerevisiae) ortholog of GOLPH3, Vps74, in the DNA damage response has been little studied, although genome-wide screens suggested a role at telomeres. In this study we investigated the role of Vps74 at telomeres and in the DNA damage response. We show that Vps74 decreases the fitness of telomere defective cdc13-1 cells and contributes to the fitness of yku70Δ cells. Importantly, loss of Vps74 in yku70Δ cells exacerbates the temperature dependent growth defects of these cells in a Chk1 and Mec1-dependent manner. Furthermore, Exo1 reduces fitness of vps74Δ yku70Δ cells suggesting that ssDNA contributes to the fitness defects of vps74Δ yku70Δ cells. Systematic genetic interaction analysis of vps74Δ, yku70Δ and yku70Δ vps74Δ cells suggests that vps74Δ causes a milder but similar defect to that seen in yku70Δ cells. vps74Δ cells have slightly shorter telomeres and loss of VPS74 in yku70Δ or mre11Δ cells further shortens the telomeres of these cells. Interestingly, loss of Vps74 leads to increased levels of Stn1, a partner of Cdc13 in the CST telomere capping complex. Overexpression of Stn1 was previously shown to cause telomere shortening, suppression of cdc13-1 and enhancement of yku70Δ growth defects, suggesting that increased levels of Stn1 may be the route by which Vps74 affects telomere function. These results establish Vps74 as a novel regulator of telomere biology.
Extracellular Pax6 regulates tangential Cajal-Retzius cell migration in the developing mouse neocortex
Authors: Kaddour H. , Coppola E. , Di Nardo A. A. , Wizenmann A. , Volovitch M. , Prochiantz A. , Pierani A.
Published: February 2018

The embryonic mouse cortex displays a striking low caudo-medial and high rostro-lateral graded expression of the homeoprotein transcription factor Pax6, which presents both cell autonomous and direct non-cell autonomous activities. Through the genetic induction of anti-Pax6 single-chain antibody secretion, we have analyzed Pax6 non-cell autonomous activity on the migration of cortical hem- and septum-derived Cajal-Retzius (CR) neurons by live imaging of flat mount developing cerebral cortices. We observed that blocking extracellular Pax6 disrupts tangential CR cell migration patterns. We found a decrease in the distance travelled and changes both in directionality and in the depth at which CR cells migrate. Tracking of single CR cells in mutant cortices revealed that extracellular Pax6 neutralization enhances or reduces contact repulsion in medial and lateral regions, respectively. This study demonstrates that secreted Pax6 controls neuronal migration thus acting as a bona fide morphogen at an early stage of cerebral cortex development.

Summary statement

Cajal-Retzius cell distribution in the embryonic cortex participates in determining the size and positioning of cortical areas. Here, Kaddour et al. establish that the direct non-cell autonomous activity of the Pax6 transcription factor regulates Cajal-Retzius cell migration.
Does monetary policy affect economic growth: evidence from Malaysia
Authors: Akalpler Ergin , Duhok Dilgash
Published: February 2018

Purpose

The purpose of this paper is to investigate the relationship between monetary policy and economic growth in the light of a developing economy, with the main focus on Malaysia. Primarily, the research will concentrate on the interactions between interest rates, inflation, money supply and growth in GDP, which will serve as the instrument for measuring economic growth.

Design/methodology/approach

The research will apply quantitative analysis to determine the relationship between GDP growth and monetary policy instruments, particularly interest rate, money supply and level of inflation. Given the advancement and achievement in econometric analysis and computer software creation, the least-squares estimates analysis will be used to investigate the relationship and significance between these variables.

Findings

It is observed that relationship between economic growth and inflation is positive. This entails that a 1 percent change in inflation will result in a 77 percent increase in the level of economic growth in this economy. The linkage between economic growth and interest rates has also been observed to be positive. A positive nexus can be observed between economic growth and money supply. The coefficient value of 0.02 for money supply growth shows that it has the smallest effect on economic growth amongst the variables tested in the model.

Research limitations/implications

Based on the findings of this study, the following recommendations can be made, which could serve as policies instruments for Malaysian economic development. This does not mean that the findings can be generalized for other developing economies.

Practical implications

Observations from the test for economic application significance are based on the signs of the parameters. It was observed that inflation, interest rates and money supply all have a positive relationship with economic growth, which is in line with the a priori expectations. This means that monetary policy has positively affected the economic growth.

Social implications

The results of the OLS analysis reveal that the monetary policy instruments used for the model demonstrated that monetary policy has a positive relationship with economic growth in Malaysia. A breakdown of the individual monetary policy instruments shows that the interest rate, inflation and money supply all have individual positive relationships with economic growth.

Originality/value

A positive relationship exists between economic growth in Malaysia and all selected monetary instruments, namely, inflation, money supply and interest rate. The results show that the results show that inflation, interest rate and money supply will cause the economy to grow but their contribution to the developments is affected from other policy instruments which are used by the governments.
Human papillomavirus (HPV) vaccination and factors related to intention to obtain the vaccine among young college women in Thailand
Authors: Ratanasiripong Nop T. , Sri-Umporn Sirinat , Kathalae Duangrat , Hanklang Suda , Ratanasiripong Paul
Published: February 2018

Purpose

Most cervical cancers are caused by genital human papillomavirus (HPV). However, it can be prevented if females receive an HPV vaccine. Nevertheless, there is limited evidence of HPV vaccination and predictors of intention to obtain the vaccine among young women in Thailand. The paper aims to discuss this issue.

Design/methodology/approach

This cross-sectional study examined HPV vaccination and factors influencing intention to vaccinate among a convenient sample of college women in Thailand. The data collection was conducted via a self-administered “HPV and HPV vaccine-related knowledge, attitudes, and behaviors” questionnaire.

Findings

Out of 1,030 participants, 309 (30.0 percent) were aware of HPV and the HPV vaccine. Out of these, 257 participants reported that they had not obtained the vaccine and 18 participants were unsure if they had already obtained the vaccine or not. Only 34 participants confirmed that they had received the vaccine. Among those who were aware of HPV and the HPV vaccine, 56.4 percent of them did not know that most HPV-infected persons do not show any signs or symptoms, and 53.3 percent thought that the vaccine provided protection against other sexually transmitted infections as well. Most had positive attitudes toward vaccination and subjective norms. Among the participants who had not received the vaccine, the intention to obtain the vaccine was predicted by age, knowledge, attitudes toward vaccination, and subjective norms. The reasons for not being vaccinated included the cost of the vaccine, lack of knowledge, and perception of themselves being at low risk.

Originality/value

This study found low HPV vaccination among college women. However, those who had not received the vaccine intended to obtain the vaccine at some point in the future. An HPV vaccination campaign may be well tailored in order to increase the intention to obtain the vaccine which, in turn, may increase the HPV vaccination. Vaccination cost sharing should be discussed among Thai policy makers in order to alleviate the financial burden for women.
Linking managerial competence to small enterprise performance within the dynamic capability logic
Authors: Zacca Robert , Dayan Mumin
Published: February 2018

Purpose

The purpose of this paper is to link management competence to small enterprise performance and assess the role of entrepreneurial orientation (EO) and willingness to change on this relationship.

Design/methodology/approach

The authors use structural equation modeling to test a theoretical model based on a data set from two survey instruments: one instrument was administered to the owners of 125 small enterprises within the United Arab Emirates and the second was administered to managers within the same enterprises.

Findings

Results show that within the small enterprise setting, managerial competence indirectly influences performance by influencing EO and willingness to change plays a partial mediating role through which EO benefits performance.

Research limitations/implications

The case for linking managerial competence to performance is supported by the dynamic capability logic, which maintains that an enterprise’s advantage lies in its ability to reconfigure its resources, capabilities and routines appropriately in the pursuit of new opportunities and performance benefits. The study suggests that EO plays a pre-eminent role in developing dynamic capability.

Practical implications

Understanding the link between managerial competence and small enterprise performance has important implications for enterprise owners, investors, educators, researchers and policy makers.

Originality/value

The model is a valuable contributor to understanding the dynamic capability perspective within a small enterprise and adds to the growing body of research examining the ability of small enterprises to continuously recognize and exploit new opportunities for sustainable competitive advantage.
Incorrect Inferences When Using Residuals as Dependent Variables
Authors: CHEN WEI , HRIBAR PAUL , MELESSA SAMUEL
Published: February 2018

We analyze a procedure common in empirical accounting and finance research where researchers use ordinary least squares to decompose a dependent variable into its predicted and residual components and use the residuals as the dependent variable in a second regression. This two‐step procedure is used to examine determinants of constructs such as discretionary accruals, real activities management, discretionary book‐tax differences, and abnormal investment. We show that the typical implementation of this procedure generates biased coefficients and standard errors that can lead to incorrect inferences, with both Type I and Type II errors. We further show that the magnitude of the bias in coefficients and standard errors is a function of the correlations between model regressors. We illustrate the potential magnitude of the bias in accounting research in four commonly used settings. Our results indicate significant bias in many of these settings. We offer three solutions to avoid the bias.
Identification and characterisation of RNA editing sites in chloroplast transcripts of einkorn wheat (Triticum monococcum)
Authors: Kumbhar F. , Nie X. , Xing G. , Zhao X. , Lin Y. , Wang S. , Weining S.
Published: February 2018

RNA editing is a biological process that the RNA molecule occurred base change or modification to result in the change of genetic information at the post‐transcription level, which played the vital roles in plant growth and development as well as in response to diverse stresses. To understand the composition and characteristic of chloroplast RNA editing patterns in einkorn wheat, the progenitor of wheat A subgenome, we systematically predicted and identified the RNA editing sites in plastome of three einkorn wheat species using bioinformatics analysis combined with RT‐PCR method. A total of 33 sites distributed in 15 genes, 34 in 15 genes and 33 in 14 genes were predicted in Triticum urartu, Triticum boeoticum and Triticum monococcum, respectively, all of which were C to U conversion and most of them could be validated by RNA‐seq data. Furthermore, all of the predicted editing sites were validated experimentally in T. urartu. Totally, 24 sites were found to be consistent with the prediction. The secondary structure and transmembrane domains of these five transcripts with the most abundant editing sites were further investigated. The results showed that the secondary structures of all five genes were changed, together with the transmembrane domains of ndhB were also altered as the result of editing, suggesting that RNA editing could have impact on the biological function of target genes. Finally, comparative analysis of the RNA editing patterns among Triticum species was performed to identify the conserved and species‐specific editing sites. This study reported the chloroplast RNA editing in einkorn wheat, which laid the foundation for further study on the biological function of chloroplast RNA editing in wheat, and also provided the important information to reveal the origin and evolution of wheat from the perspective of RNA editing.
Biochemical response between insects and plants: an investigation of enzyme activity in the digestive system of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and leaves of Coffea arabica (Rubiaceae) after herbivory
Authors: Meriño‐Cabrera Y. , Zanuncio J.C. , da Silva R.S. , Solis‐Vargas M. , Cordeiro G. , Rainha F.R. , Campos W.G. , Picanço M.C. , de Almeida Oliveira M.G.
Published: February 2018

Plant defence mechanisms can reduce the digestive enzyme activity of insect pests. The aim of this study was to determine the relationship between the production of proteinase inhibitors, lipoxygenase and polyphenol oxidase activity in Coffea arabica (Catuai IAC 15) plants, and the digestive enzyme activity in the pest Leucoptera coffeella (Lepidoptera: Lyonetiidae) after feeding on the plant. The production of proteinase inhibitors was evaluated with L‐BApNA as a substrate. We studied lipoxygenase activity with linoleic acid and polyphenol oxidase activity with catechol substrates, in coffee plants damaged (T1) and not damaged (T2) by L. coffeella. L. coffeella digestive enzyme activity was verified by trypsin‐like (substrate l‐BApNA and l‐TAME), chymotrypsin‐like (BTpNA and ATEE), cysteine proteases (l‐BApNA) and total protease (azocasein). Proteinase inhibitor production and lipoxygenase and polyphenol oxidase activity in C. arabica increases (P ≤ 0.05) with L. coffeella damage. Our results provide important information that these enzymatic activities may play a role in plant defence processes in C. arabica. Trypsin‐like activity increases, whereas chymotrypsin‐like and cysteine protease activity decrease in the midgut of L. coffeella, which acts as a defence mechanism.