bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel, Versatile Speculum-free Callascope for Clinical Examination and Self-Visualization of the Cervix
Authors: Asiedu Mercy N. , Agudogo Júlia S. , Dotson Mary Elizabeth , Krieger Marlee S. , Schmitt John W. , Huchko Megan , Suneja Gita , Proeschold-Bell Rae Jean , Smith Jennifer S. , Jenson Deborah , Hogan Wesley , Ramanujam Nirmala 
Published: April 2019

AbstractBackgroundInvasive cervical cancer is preventable, yet affects 500,000 women worldwide each year, and over half these women die. Barriers to cervical cancer screening include lack of awareness of cervical cancer and the cervix, fear of the speculum, and lack of women-centric technologies. We developed a low-cost (∼$50), cervix-imaging device called the Callascope, which comprises an imaging component, camera and inserter that eliminates the need for a speculum and enables self-insertion. We sought to assess the quality of physicians’ images of the cervix using the Callascope versus the speculum in live patients and study women’s willingness to independently use the Callascope to image their cervix.MethodsWe conducted two main studies: (1) a clinical study in which a physician imaged the cervix of patients using both the speculum and Callascope in a 2×2 crossover design; and (2) home-based self-cervix imaging with the Callascope.ResultsParticipants of the clinical study (n=28) and home study (n=12) all indicated greater comfort and an overall preference for the Callascope over the speculum. The clinical study data indicated that the Callascope enabled similar visualization compared to the speculum while significantly improving patient experience. With physician insertion and manipulation, the Callascope enabled cervix visualization for 82% of participants. In the home-study, 83% of participants were able to visualize their cervix with the Callascope on the first try and 100% after multiple attempts.ConclusionThe Callascope is more comfortable and provides similar visualization to the speculum. The Callascope can be used by medical providers for clinical exams while also enabling home self-screening for cervical cancer and promoting a better understanding of one’s cervix to increase awareness of cervical screening needs. The Callascope may increase cervical cancer screening rates through reducing barriers including cost, discomfort, lack of awareness and stigma.
A broad-host-range CRISPRi toolkit for silencing gene expression in Burkholderia
Authors: Hogan Andrew M. , Rahman A. S. M. Zisanur , Lightly Tasia J. , Cardona Silvia T. 
Published: April 2019

AbstractGenetic tools are critical to dissecting the mechanisms governing cellular processes, from fundamental physiology to pathogenesis. Members of the genus Burkholderia have potential for biotechnological applications but can also cause disease in humans with a debilitated immune system. The lack of suitable genetic tools to edit Burkholderia GC-rich genomes has hampered the exploration of useful capacities and the understanding of pathogenic features. To address this, we have developed CRISPR interference (CRISPRi) technology for gene silencing in Burkholderia, testing it in B. cenocepacia, B. multivorans and B. thailandensis. Tunable expression was provided by placing a codon-optimized dcas9 from Streptococcus pyogenes under control of a rhamnose-inducible promoter. As a proof of concept, the paaABCDE operon controlling genes necessary for phenylacetic acid degradation was targeted by plasmid-borne sgRNAs, resulting in near complete inhibition of growth on phenylacetic acid as the sole carbon source. This was supported by reductions in paaA mRNA expression. The utility of CRISPRi to probe other functions at the single cell level was demonstrated by knocking down phbC and fliF, which dramatically reduces polyhydroxybutyrate granule accumulation and motility, respectively. As a hallmark of the mini-CTX system is the broad host-range of integration, we putatively identified 67 genera of Proteobacteria that might be amenable to modification with our CRISPRi toolkit. Our CRISPRi tool kit provides a simple and rapid way to silence gene expression to produce an observable phenotype. Linking genes to functions with CRISPRi will facilitate genome editing with the goal of enhancing biotechnological capabilities while reducing Burkholderia’s pathogenic arsenal.Author contributionsSTC conceived the idea and design of the research; AMH designed and cloned the dCas9 constructs; AMH and ASMZ designed the sgRNAs, assessed knockdown phenotypes, processed data, and wrote and edited the manuscript; TJL performed RT-qPCR analysis and edited the manuscript; STC supervised the work and provided financial support.Graphical Abstract
supFunSim: spatial filtering toolbox for EEG
Authors: Rykaczewski Krzysztof , Nikadon Jan , Duch Włodzisław , Piotrowski Tomasz 
Published: April 2019

AbstractRecognition and interpretation of brain activity patterns from EEG or MEG signals is one of the most important tasks in cognitive neuroscience, requiring sophisticated methods of signal processing. The supFunSim library is a new Matlab toolbox which generates accurate EEG forward models and implements a collection of spatial filters for EEG source reconstruction, including linearly constrained minimum-variance (LCMV), eigenspace LCMV, nulling (NL), and minimum-variance pseudo-unbiased reduced-rank (MV-PURE) filters in various versions. It also enables source-level directed connectivity analysis using partial directed coherence (PDC) and directed transfer function (DTF) measures. The supFunSim library is based on the well-known Field-Trip toolbox for EEG and MEG analysis and is written using object-oriented programming paradigm. The resulting modularity of the toolbox enables its simple extensibility. This paper gives a complete overview of the toolbox from both developer and end-user perspectives, including description of the installation process and some use cases.
A convolutional neural network for predicting transcriptional regulators of genes in Arabidopsis transcriptome data reveals classification based on positive regulatory interactions
Authors: MacLean Dan 
Published: April 2019

AbstractGene Regulatory networks that control gene expression are widely studied yet the interactions that make them up are difficult to predict from high throughput data. Deep Learning methods such as convolutional neural networks can perform surprisingly good classifications on a variety of data types and the matrix-like gene expression profiles would seem to be ideal input data for deep learning approaches. In this short study I compiled training sets of expression data using the Arabidopsis AtGenExpress global stress expression data set and known transcription factor-target interactions from the Arabidopsis PLACE database. I built and optimised convolutional neural networks with a best model providing 95 % accuracy of classification on a held-out validation set. Investigation of the activations within this model revealed that classification was based on positive correlation of expression profiles in short sections. This result shows that a convolutional neural network can be used to make classifications and reveal the basis of those calssifications for gene expression data sets, indicating that a convolutional neural network is a useful and interpretable tool for exploratory classification of biological data. The final model is available for download and as a web application.
Angiosperm speciation speeds up near the poles
Authors: Igea J. , Tanentzap A. J. 
Published: April 2019

AbstractRecent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results from higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. These results were consistently retrieved using two other methods to test the association between occupancy of tropical habitats and speciation rates. Our speciation rate estimates were robust to the effects of both undescribed species and missing taxa. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness. Greater ecological opportunity in the temperate zones, stemming from less saturated communities, higher species turnover or greater environmental change, may ultimately explain these results.
Male competition and the evolution of mating and life history traits in experimental populations ofAedes aegypti
Authors: Qureshi Alima , Aldersley Andrew , Hollis Brian , Ponlawat Alongkot , Cator Lauren J. 
Published: April 2019

AbstractAedes aegyptiis an important disease vector and a major target of reproductive control efforts. We manipulated the opportunity for sexual selection in populations ofAe. aegyptiby controlling the number of males competing for a single female. Populations exposed to higher levels of male competition rapidly evolved higher male competitive mating success relative to populations evolved in the absence of competition, with an evolutionary response visible after only five generations. We also detected correlated evolution in other important mating and life history traits, such as acoustic signalling, fecundity and body size. Our results indicate that there is ample segregating variation for determinants of male mating competitiveness in wild populations and that increased male mating success trades-off with other important life history traits. The mating conditions imposed on laboratory-reared mosquitoes are likely a significant determinant of male mating success in populations destined for release.
Isotropic expansion of external environment induces tissue elongation and collective cell alignment
Authors: Koyama H. , Fujimori T. 
Published: April 2019

AbstractCell movement is crucial for morphogenesis in multicellular organisms. Growing embryos or tissues often expand isotropically, i.e., uniformly, in all dimensions. On the surfaces of these expanding environments, which we call “fields,” cells are subjected to frictional forces and move passively in response. However, the potential roles of isotropically expanding fields in morphogenetic events have not been investigated well. In this study, we mathematically analyzed the effect of isotropically expanding fields using a vertex model, a standard type of multi-cellular model. We found that cells located on fields were elongated along a similar direction each other. Simultaneously, the cell clusters were also elongated, even though field expansion was absolutely isotropic. We then investigated the mechanism underlying these counterintuitive phenomena. In particular, we asked whether elongation was caused by the properties of the field, the cell cluster, or both. Theoretical analyses involving simplification of the model revealed that cell clusters have an intrinsic ability to asymmetrically deform, leading to their elongation. Importantly, this ability is effective only under the non-equilibrium conditions provided by field expansion. This may explain the elongation of the notochord, located on the surface of the growing mouse embryo. We established that passive cell movement induced by isotropically expanding external environments can contribute to both cell and tissue elongation, as well as collective cell alignment, providing key insight into morphogenesis involving multiple adjacent tissues.Statement of SignificanceIt is a central question of developmental biology how the symmetric shapes of eggs can develop the asymmetric structures of embryos. Embryos expand through their growth. Simultaneously, elongation of tissues such as the notochord occurs, which is fundamental phenomena of morphogenesis. However, possible relationships between tissue elongation and the expansion of embryos have not been investigated well. Here we mathematically present that, even if the expansion is isotropic, tissues located on the embryos are asymmetrically deformed by the expansion, resulting in elongation. We generalize the effect of expanding environments on tissue elongation through model reduction and uncover the mechanism underlying elongation. This process can be a novel key piece for symmetry breaking of embryos, together with previously established morphogenetic processes.
Telomere dysfunction represses HNF4α leading to impaired hepatocyte development and function
Authors: Niero Evandro L. , Fok Wilson C. , Vessoni Alexandre T. , Brenner Kirsten A. , Batista Luis F.Z. 
Published: April 2019

ABSTRACTTelomere attrition is a risk factor for end-stage liver disease. Due to a lack of adequate models and intrinsic difficulties in studying telomerase in physiologically relevant cells, the molecular mechanisms responsible for liver disease in patients with telomere syndromes remain elusive. To circumvent that, we used genome editing to generate isogenic human embryonic stem cell lines (hESCs) harboring a clinically relevant mutation in telomerase (DKC1_A353V) and subjected them to an in vitro, stage-specific hepatocyte differentiation protocol, that resembles hepatocyte development in vivo. Our results show that while telomerase is highly expressed in hESCs, it is quickly silenced, due to TERT down-regulation, after endoderm differentiation, and completely absent in in vitro derived hepatocytes, similarly to what is observed in primary hepatocytes. While endoderm derivation is not impacted by telomere shortening, progressive telomere dysfunction impaired hepatic endoderm formation. Consequently, hepatocyte-derivation, as measured by expression of specific markers, as well by albumin expression and secretion, is severely compromised in telomerase mutant cells with short telomeres. Interestingly, this phenotype was not caused by cell death induction or senescence. Rather, telomere shortening induces down regulation of the human hepatocyte nuclear factor 4α (HNF4α), in a p53 dependent manner. Telomerase reactivation, as well as p53 silencing, rescued hepatocyte formation in telomerase mutants. Likewise, conditional expression of HNF4α, even in cells that retained short telomeres, accrued DNA damage, and p53 stabilization, successfully restored hepatocyte formation from hESCS.ConclusionsCombined, our data shows that telomere dysfunction acts a major regulator of HNF4α during hepatocyte development and function, pointing to a potential novel target for the clinical management of liver disease in telomere-syndrome patients.
Preparation of anti-HER-2 antibody PLGA polymer nano- ultrasound contrast agent In vitro targeting experiment
Authors: Lin Ji , Stevens Molly , Smith John 
Published: April 2019

AbstractIn this report, we demonstrated a novel method to prepare a hollow nano-targeted ultrasound contrast agent carrying anti-HER-2 antibody with high molecular weight polylactic acid-glycolic acid (PLGA) as a film-forming material, and to investigate in vitro targeting and imaging effects. We utilized the camphor as porogen, PLGA nano-ultrasound contrast agent was prepared by modified double emulsion solvent evaporation method. The general characteristics were characterized by scanning electron microscope, transmission electron microscope and laser particle size analyzer. The angiography was performed by carbodiimide method. The anti-HER-2 antibody was used to prepare the PLGA-targeted nano-ultrasound contrast agent with anti-HER-2 antibody. The in-situ imaging ability was evaluated by laser confocal scanning microscopy. Results indicate that the average particle size of PLGA nano-ultrasound contrast agent was (152.00± 58.08) nm. The particles were regular spherical, uniform in size and good in dispersion. In vitro targeting experiments showed that PLGA-targeted contrast agents with anti-HER-2 antibodies were more strongly aggregated on the surface of breast cancer cells. In vitro imaging experiments showed that the PLGA-targeted nano-ultrasound contrast imaging showed a fine and uniform point-like hyperechoic echo, and no significant attenuation of the posterior echo. This study successfully produced a PLGA-targeted nano-ultrasound contrast agent with anti-HER-2 antibody, which can specifically bind to breast cancer cells with high expression of HER-2 receptor in vitro, and the imaging effect in vitro is better.
Workshops increase invasive species records to EDDMapS in the Mid-Atlantic United States
Authors: Wallace Rebekah D. , Bargeron Charles T. , Swearingen Jil , LaForest Joseph H. , Moorhead David J. , Luo Xuelin 
Published: April 2019

AbstractAs the prevalence of smartphones and smartphone applications has penetrated the cellular phone market, and the capabilities of features within smartphones allowed for the replacement of commonly used mapping and identification tools, Bugwood developers began to release smartphone applications for reporting invasive species. To encourage and demonstrate reporting, workshops have been held to walk users through these apps’ features and overall EDDMapS capabilities. To ascertain the effectiveness of workshops in encouraging reporting via smartphone apps and the EDDMapS MAEDN website, a General Linear Model was used to evaluate the number of records received across the 2012-2017 time frame and evaluate if there was a difference in the number of records in the years MAEDN workshops were held at the Mid-Atlantic Invasive Plant Council conferences and workshops and years no MAEDN workshop was held. The model indicated that the workshops and time were significant factors in the number of records submitted. Being able to confidently demonstrate the effect that workshops can positively impact data recruitment can aid in funding for outreach and educational events.
Increased Dynamics of α-Synuclein Fibrils by β-Synuclein Leads to Reduced Seeding and Cytotoxicity
Authors: Yang Xue , Williams Jonathan K. , Yan Run , Mouradian M. Maral , Baum Jean 
Published: April 2019

AbstractAlpha-synuclein (αS) fibrils are toxic to cells and contribute to the pathogenesis and progression of Parkinson’s disease and other synucleinopathies. β-Synuclein (βS), which co-localizes with αS, has been shown to provide a neuroprotective effect, but the molecular mechanism by which this occurs remains elusive. Here we show that αS fibrils formed in the presence of βS are less cytotoxic, exhibit reduced cell seeding capacity and are more resistant to fibril shedding compared to αS fibrils alone. Using solid-state NMR, we found that the overall structure of the core of αS fibrils when co-incubated with βS is minimally perturbed, however, the dynamics of Lys and Thr residues, located primarily in the imperfect KTKEGV repeats of the αS N-terminus, are increased. Our results suggest that amyloid fibril dynamics may play a key role in modulating toxicity and seeding. Thus, enhancing the dynamics of amyloid fibrils may be a strategy for future therapeutic targeting of neurodegenerative diseases.
The influence of snippet length on user behavior in mobile web search
Authors: Sachse Jacqueline 
Published: April 2019

Purpose
Web search is more and more moving into mobile contexts. However, screen size of mobile devices is limited and search engine result pages face a trade-off between offering informative snippets and optimal use of space. One factor clearly influencing this trade-off is snippet length. The purpose of this paper is to find out what snippet size to use in mobile web search.

Design/methodology/approach
For this purpose, an eye-tracking experiment was conducted showing participants search interfaces with snippets of one, three or five lines on a mobile device to analyze 17 dependent variables. In total, 31 participants took part in the study. Each of the participants solved informational and navigational tasks.

Findings
Results indicate a strong influence of page fold on scrolling behavior and attention distribution across search results. Regardless of query type, short snippets seem to provide too little information about the result, so that search performance and subjective measures are negatively affected. Long snippets of five lines lead to better performance than medium snippets for navigational queries, but to worse performance for informational queries.

Originality/value
Although space in mobile search is limited, this study shows that longer snippets improve usability and user experience. It further emphasizes that page fold plays a stronger role in mobile than in desktop search for attention distribution.
When benchmark rates change: the case of Islamic banks
Authors: Archer Simon , Abdel Karim Rifaat Ahmed 
Published: April 2019

Purpose
This paper aims to examine the issue that arises in the context of benchmark rate (or interest rate) changes made for reasons of monetary policy in a jurisdiction with a significant presence of Islamic banks. Changes, especially increases, in the prevailing interest rate made by central banks raise issues of asset-liability management for banks, which typically have longer maturities on the asset side than on the liabilities side, resulting in exposure to interest rate risk for conventional banks, and what is known as rate of return (RoR) risk for Islamic banks, which for reasons of compliance with Islamic religious law (Shari’ah) do not use interest in their operations. Islamic banks use various financial instruments which reflect the cost of funds by means of contracts of sale on credit or of leasing or forms of partnership, which allow them to earn returns on their funds and to pay returns to customers who deposit funds with them.

Design/methodology/approach
The methodology of this study consisted of a descriptive analysis of the relevant characteristics of Islamic banks and their economic and regulatory environments, illustrated by a case study approach applied to two jurisdictions, namely, Sudan and Malaysia.

Findings
In jurisdictions where Islamic banks represent a significant share of the market for financial services, if the contracts used in Islamic financing allow for periodic adjustments of the profit rate or lease rental, this could result in a significant impediment to the full implementation of monetary policy and hence to the maintenance of financial stability.

Originality/value
This study is (to the best of authors’ knowledge) the first thorough analysis in the literature of the issues arising from the exposure of Islamic banks to RoR risk and has clear implications for regulatory and central bank policy.
A system dynamics investigation of project portfolio management evolution in the energy sector
Authors: Hosseini Seyed Hossein , Shakouri G. Hamed , Kazemi Aliyeh , Zareayan Rahman , Mousavian H. Milad 
Published: April 2019

Purpose
Project portfolio management (PPM) is a commonly used technique to align projects with strategy and to ensure adequate resourcing for projects. In this paper, to gain a better understanding of PPM dynamics, a system dynamics (SD) model was developed. To do so, an Iranian independent power producer was used as a case study in the energy sector; moreover, policy options were derived and generalized for such a developer company.

Design/methodology/approach
To cope with the complexity of business processes in a power producer company and to formulate an optimum policy, causal relations and loops were derived first and then state-flow diagrams were designed to simulate the problem in the system, as it is usual in the SD methodology.

Findings
The proposed model was applied to a real-world case study to rectify managers’ viewpoint about their business dynamics and to formulate new project portfolio strategies to improve the viability of the company. The model proved how a static portfolio analysis can misguide managers in planning their project portfolio strategies, and how effective feedback can improve PPM in developing companies in the energy sector.

Originality/value
Systems approach, especially SD methodology, has been rarely used to analyze PPM problems in the energy sector. This study highlights the implications of feedback and dynamics in PPM and tries to derive optimal value of portfolios.