bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Productive HPV16 Infection on Global Gene Expression of Cervical Epithelium
Authors: Kang Sa Do , Chatterjee Sreejata , Alam Samina , Salzberg Anna C. , Milici Janice , Burg Sjoerd H. van der , Meyers Craig 
Published: April 2018

AbstractHuman papillomavirus (HPV) infection is the world’s most common sexually transmitted infection, and is responsible for most cases of cervical cancer. Previous studies of global gene expression changes induced by HPV infection have focused on the cancerous stages of infection, and therefore, not much is known about global gene expression changes at early pre-neoplastic stages of infection. We show for the first time, global gene expression changes of early stage HPV16 infection in cervical tissue using 3-dimensional organotypic raft cultures that produce high levels of progeny virions.cDNA microarray analysis showed that a total of 594 genes were upregulated and 651 genes were downregulated at least 1.5-fold with HPV16 infection. Gene ontology analysis showed that biological processes including cell cycle progression and DNA metabolism were upregulated, while skin development, immune response, and cell death were downregulated with HPV16 infection in cervical keratinocytes. Individual genes were selected for validation at the transcriptional and translational levels including UBC, which was central to the protein association network of immune response genes, and top downregulated genes RPTN, SERPINB4, KRT23, and KLK8. In particular, KLK8 and SERPINB4 have shown to be upregulated in cancer, which contrasts our results.Organotypic raft cultures that allow full progression of the HPV life-cycle have allowed us to identify novel gene modulations and potential therapeutic targets of early stage HPV infection in cervical tissue. Additionally, our results suggest that early stage productive infection and cancerous stages of infection are distinct disease states expressing different transcriptomes.ImportancePersistent HPV infection is responsible for most cases of cervical cancer. Transition from precancerous to cancerous stages of HPV infection is marked by a significant reduction in virus production. Most global gene expression studies of HPV infection have focused on the cancerous stages. Therefore, little is known about global gene expression changes at precancerous stages. For the first time, we measured global gene expression changes at precancerous stages of HPV16 infection in human cervical tissue producing high levels of virus. We identified a group of genes that are typically overexpressed in cancerous stages to be significantly downregulated at the precancerous stage. Moreover, we identified significantly modulated genes that have not yet been studied in the context of HPV infection. Studying the role of these genes in HPV infection will help us understand what drives the transition from precancerous to cancerous stages, and may lead to development of new therapeutic targets.
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
Authors: Bush Stephen J. , Freem Lucy , MacCallum Amanda J. , O’Dell Jenny , Wu Chunlei , Afrasiabi Cyrus , Psifidi Androniki , Stevens Mark P. , Smith Jacqueline , Summers Kim M. , Hume David A. 
Published: April 2018

ABSTRACTBackgroundThe domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.ResultsRandomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Miru was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.ConclusionExpression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.
The cholinergic pesticide imidacloprid impairs contrast and direction sensitivity in motion detecting neurons of an insect pollinator
Authors: Rigosi Elisa , O’Carroll David C. 
Published: April 2018

AbstractCholinergic pesticides such as the neonicotinoid imidacloprid are the most important insecticides used for plant protection worldwide. In recent decades concerns have been raised about side effects on non-target insect species, including altered foraging behaviour and navigation. Although pollinators rely on visual cues to forage and navigate their environment, the effect of neonicotinoids on visual processing have been largely overlooked. Here we describe a modified electrophysiological setup that allowed recordings of visually evoked responses while perfusing the brainin vivo. Long-lasting recordings from wide-field motion sensitive neurons of the hoverfly pollinator,Eristalis tenax, revealed that sub-lethal exposure to imidacloprid alters their physiological response to motion stimuli. We observed substantially increased spontaneous firing rate, reduced contrast sensitivity and weaker directional tuning to wide-field moving stimuli. This approach reveals sub-lethal effects of imidacloprid in the visual motion detecting system of an important pollinator with likely implications for flight control, hovering and routing.
Polygenic risk scores for major depressive disorder and neuroticism as predictors of antidepressant response: meta-analysis of three treatment cohorts
Authors: Ward Joey , Graham Nicholas , Strawbridge Rona , Ferguson Amy , Jenkins Gregory , Chen Wenan , Frye Mark , Weinshilboum Richard , Uher Rudolf , Lewis Cathryn M. , Biernacka Joanna , Smith Daniel J. 
Published: April 2018

AbstractThere are currently no reliable approaches for correctly identifying which patients with major depressive disorder (MDD) will respond well to antidepressant therapy. However, recent genetic advances suggest that Polygenic Risk Scores (PRS) could allow MDD patients to be stratified for antidepressant response. We used PRS for MDD and PRS for neuroticism as putative predictors of antidepressant response within three treatment cohorts: The Genome-based Therapeutic Drugs for Depression (GENDEP) cohort, and 2 sub-cohorts from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study PRGN-AMPS (total patient number = 783). Results across cohorts were combined via meta-analysis within a random effects model. Overall, PRS for MDD and neuroticism did not significantly predict antidepressant response but there was a consistent direction of effect, whereby greater genetic loading for both MDD (best MDD result, p < 5*10-5 MDD-PRS at 4 weeks, β = -0.019, S.E = 0.008, p = 0.01) and neuroticism (best neuroticism result, p < 0.1 neuroticism-PRS at 8 weeks, β = -0.017, S.E = 0.008, p = 0.03) were associated with less favourable response. We conclude that the PRS approach may offer some promise for treatment stratification in MDD and should now be assessed within larger clinical cohorts.
Training enhances the ability of listeners to exploit visual information for auditory scene analysis
Authors: Atilgan Huriye , Bizley Jennifer K. 
Published: April 2018

AbstractThe ability to use temporal relationships between cross-modal cues facilitates perception and behavior. Previously we observed that temporally correlated changes in the size of a visual stimulus and the intensity in an auditory stimulus influenced the ability of listeners to perform an auditory selective attention task (Maddox et al., 2015). In this task participants detected timbral changes in a target sound while ignoring those in a simultaneously presented masker. When the visual stimulus was temporally coherent with the target sound, performance was significantly better than when it was temporally coherent with the masker sound, despite the visual stimulus conveying no task-relevant information. Here, we trained observers to detect audiovisual temporal coherence and asked whether this improved their ability to benefit from visual cues during the auditory selective attention task. We observed these listeners improved performance in the auditory selective attention task and changed the way in which they benefited from a visual stimulus: after training performance was better when the visual stimulus was temporally coherent with either the target or the masker stream, relative to the condition in which the visual stimulus was coherent with neither auditory stream. A second group which trained to discriminate modulation rate differences between temporally coherent audiovisual streams improved task performance, but did not change the way in which they used visual information. A control group did not change their performance between pretest and post-test. These results provide insights into how crossmodal experience may optimize multisensory integration.
Phospholipid membranes promote the early stage assembly of α-synuclein aggregates
Authors: Lv Zhengjian , Hashemi Mohtadin , Banerjee Siddhartha , Zagorski Karen , Rochet Jean-Christophe , Lyubchenko Yuri L. 
Published: April 2018

AbstractDevelopment of Parkinson’s disease is associated with spontaneous self-assembly of α-synuclein (α-syn). Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive. We report a novel effect of phospholipid bilayers on the catalysis of α-syn aggregation from monomers. We directly visualized α-syn aggregation on supported lipid bilayers using time-lapse atomic force microscopy. We discovered that α-syn assemble in aggregates on bilayer surfaces even at the nanomolar concentration of monomers in solution. The efficiency of the aggregation process depends on the membrane composition, being highest for a negatively charged bilayer. Furthermore, assembled aggregates can dissociate from the surface, suggesting that on-surface aggregation can be a mechanism by which pathological aggregates are produced. Computational modeling revealed that interaction of α-syn with bilayer surface changes the protein conformation and its affinity to assemble into dimers, and these properties depend on the bilayer composition. A model of the membrane-mediated aggregation triggering the assembly of neurotoxic aggregates is proposed.
Molecular basis for voltage sensitivity in membrane proteins
Authors: Kasimova Marina A. , Lindahl Erik , Delemotte Lucie 
Published: April 2018

ABSTRACTVoltage-sensitive membrane proteins are united by the ability to transform changes in the membrane potential into mechanical work. They are responsible for a spectrum of key physiological processes in living organisms, including electric signaling and progression along the cell cycle. While the voltage-sensing mechanism has been well characterized for some membrane proteins such as voltage-gated ion channels, for others even the location of the voltage-sensing elements remains unknown. The detection of these elements using experimental techniques is complicated due to the large diversity of membrane proteins. Here, we suggest a computational approach to predict voltage-sensing elements in any membrane protein independent of structure or function. It relies on the estimation of the capacity of a protein to respond to changes in the membrane potential. We first show how this property correlates well with voltage sensitivity by applying our approach to a set of membrane proteins including voltage-sensitive and voltage-insensitive ones. We further show that it correctly identifies true voltage-sensitive residues in the voltage sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions potentially involved in the response to voltage. The suggested approach is fast and simple and allows for characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application prior to mutagenesis experiments will allow for significant reduction of the number of potential voltage-sensitive elements to be tested.
Terrorism and female teacher leadership in girls’ secondary school
Authors: Usman Lantana Martha 
Published: April 2018

PurposeThe purpose of this paper is to explore female teachers and vice principal’s leadership on girls attendance and learning, safety and security issues in rural girls’ schools experiencing Boko Haram insurgencies. The secondary purpose is to recommend innovative educational policy initiatives at the school, community and state levels, so as to ameliorate girls and teachers’ challenges, and to sustain girls in schools.Design/methodology/approachQualitative educational research orientation and an ethnographic-narrative research design were used for the study. Purposeful sampling procedure was adopted through the selection of female teachers and a vice principal. Soft qualitative oral data (SQOD) were collected from structured interviews and focus groups and participant observation data. Data analysis engaged hand data analysis (HAD) for transcription, while the coding and theming process involved qualitative computer software data analysis (CSDA) of NVivo 8.0. The measures of validity involved the qualitative process of member checking, while ethical issues of anonymity with participants were addressed in the process of data collection, and reporting.FindingsMajor findings revealed a symbiotic relationship between female teacher’s moral leadership and the application of law of tort in the girls’ school; teachers’ adopted spiritual leadership and moral decision making process on girls’ safety, and learning motivation; and improved school community collaboration for security and safety of the girls and effective communication.Practical implicationsEducational policy options are prescribed. They include the training of teachers and girls on fire safety and conflict crisis; recruitment of female school counsellors; housing incentives for female teachers; support grassroot initiatives on school security; and sustaining school-community/parents involvement.Originality/valueBoko Haram’s impact on teacher and school leadership in girls’ school(s) has not been studied so far. The paper is the first, thereby filling the gap of the literature on girls’ rural education and terrorism.
An econophysics non-monetized theory of value
Authors: Baer Wolfgang , Bounfour Ahmed , Housel Thomas J. 
Published: April 2018

Purpose
Mobile phones are radically transforming micro-finance in Sub-Saharan Africa, and Kenya, in particular. The introduction of the micro-financial transaction mobile phone application, “MPesa,” created a means to facilitate micro-transactions without the need for an intermediary, such as a banking system. The purpose of this paper is to posit an econophysics model to predict the value of Mpesa for Kenyan and South African consumers. The econophysics framework posits several fitness matrices and a distance measure that can account for the concepts of mass, distance, momentum, velocity, action, and force. The authors begin with a table of the match between the physics concepts and the economic concepts followed by the vector model that utilizes these concepts for the MPesa application case. In this paper, the authors will argue that MPesa succeeded in Sub-Saharan African countries, such as Kenya, because the fit between what this group of customers needed and the solutions Safaricom’s MPesa offered was a better fit with a smaller distance to adoption than in the South African case.

Design/methodology/approach
The research develops an econophysics approach to the assessment of micro-finance development in Sub-Saharan countries.

Findings
The research shows clearly the reasons of the success of MPesa in Kenya in comparison of its relative failure in South Africa: the distance between customers’ expectations and the system supply.

Research limitations/implications
The research is limited to two case studies and needs to be extended to other contexts, in order to demonstrate its robustness, especially with regard to the intangible dimension, e.g., the distance between a system potential and what it really offers.

Practical implications
The research shows the importance of system’s characteristics in its success.

Social implications
The social implications are very high, especially in this case, where micro-finance is a high stake for developing societies.

Originality/value
This is one of the first works to develop an econophysics approach for the evaluation of the key characteristics of a system.
A comparative study of intangible investment in Egypt and South Africa
Authors: Chen Wen 
Published: April 2018

PurposeThe purpose of this paper is to understand the recent developments and trends of intangible investment in Egypt and South Africa.Design/methodology/approachThis paper follows the framework pioneered by Corrado, Hulten and Sichel (2005, 2009) and measures investments in scientific R&D, organizational capital, and brand equity using the expenditure-based approach.FindingsThe main findings are that South Africa invests consistently and considerably more in intangible assets than Egypt. Among the three intangible assets examined, namely, scientific R&D, organizational capital, and brand equity, South Africa seems to invest more evenly across these assets, whereas intangible investment in Egypt is predominantly driven by investment in brand equity and very little in R&D.Originality/valueThis is the first paper to formally examine intangible investment in African countries. The ballpark estimate provided in this study is a useful step forward in understanding the trends of intangible investment in Egypt and South Africa.
Does Wall Street buy your growth story? For how long?
Authors: McGrath Rita Gunther , van Putten Alexander B. , Pierantozzi Ron 
Published: April 2018

Purpose
The article introduces the authors’ “ Imagination Premium™” metric which assesses the confidence of the investing community in a business’ growth strategy.

Design/methodology/approach
The article explains how the Imagination Premium is calculated and applies it to several cases--Amazon, Tesla and Buffalo Wild Wings.

Findings
Amazon’s implied value of growth was nearly four times its value from operations, a result completely consistent with its “profits are optional” motto. Amazon is a prototypical example of a company that is built to thrive in the ‘transient advantage economy.

Practical implications
Sky-high expectations for growth can be dashed by external events over which businesses have little control as Tesla found out. Unless a business can show, as Amazon has historically done, that it can turn expectations into gold-spun reality, lofty investor expectations can become a liability.

Originality/value
By applying the Imagination Premium concept to successful and problematic cases the authors illustrate the risks and advantages of a bold growth-before-profits strategy.
How industry leaders enhance the value of ecosystems
Authors: Davidson Steven , Giesen Edward , Harmer Martin , Marshall Anthony 
Published: April 2018

Purpose
The article explains how industry leaders engage in ecosystems effectively to access new markets and new geographies, and through intensive collaboration within new partnering arrangements, ecosystems have become an essential resource for building their new capabilities.

Design/methodology/approach
Executives of the most successful organizations surveyed embrace their existing ecosystems and expect to pursue new and different partnering arrangements. Outperforming organizations credit their ecosystems with generating value and innovation. The article looks at what they did differently than under-performers.

Findings
Ecosystems can drive a broad range of strategic opportunities including new engagement and monetization models.

Practical implications
Ecosystems help organizations access critical capabilities that would have otherwise been unavailable or very difficult to obtain. 10; 10; 10;

Originality/value
3BLeaders of outperforming organizations recognize the significant opportunity to improve skills by learning alongside ecosystem partners.
China’s “New Silk Road” initiative – implications for competitors and partners, near and far
Authors: Leavy Brian 
Published: April 2018

Purpose
The author explains how the story of China geo-political vision has recently taken a new turn under the leadership of Xi Jinping, and signals a major shift towards a more expansive and outward-looking economic policy.

Design/methodology/approach
Understanding more fully what is happening in the latest phase of China’s modern resurgence is a strategic imperative for both public policy analysts and corporate leaders with global interests and ambitions.

Findings
China is now convinced that extending its ‘infrastructure and connectivity” focus outwards in this way will help ‘to dismantle investment barriers, create new trade routes, improve international logistics and deepen financial integration.’

Practical implications
Beijing is ‘adamant’ that it should not be called a ‘plan’ or a ‘strategy’ lest it ‘be interpreted as ruse to build a vast economic empire.’

Originality/value
China's BRI extends beyond ports, railways and highways to other major types of infrastructure including oil and gas pipelines, electricity power plants and telecommunications networks. So the invitation to be part of BRI presents ‘a vast economic carrot,’ and the prospect of becoming major hubs on emerging new pan-regional trade routes is enormously attractive to many of China’s underdeveloped neighbors. 10;