bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiphoton imaging of neural structure and activity in Drosophila through the intact cuticle
Authors: Aragon Max Jameson , Wang Mengran , Mok Aaron T. , Shea Jamien , Kim Haein , Barkdull Nathan , Xu Chris , Yapici Nilay 
Published: October 2019

AbstractWe developed a multiphoton imaging method to capture neural structure and activity in behaving flies through the intact cuticles. Our measurements show that the fly head cuticle has surprisingly high transmission at wavelengths > 900 nm, and the difficulty of through-cuticle imaging is due to the air sacs and/or fat tissue underneath the head cuticle. By compressing the air sacs, we performed deep multiphoton imaging of fly brains through the intact cuticle. Our anatomical and functional imaging results show that 2- and 3-photon imaging are comparable in superficial regions such as the mushroom body, but 3-photon imaging is superior in deeper regions such as the central complex and beyond. We further demonstrated 2-photon through-cuticle functional imaging of odor-evoked calcium responses from the mushroom body γ-lobes in behaving flies short-term and long-term (12 consecutive hours). The through-cuticle imaging method developed here extends the time limits of in vivo imaging in flies, and opens up new ways to capture neural structure and activity from the intact fly brain.
Whole brain delivery of an instability-proneMecp2transgene improves behavioral and molecular pathological defects in mouse models of Rett syndrome
Authors: Luoni Mirko , Giannelli Serena , Indrigo Marzia , Niro Antonio , Massimino Luca , Iannielli Angelo , Passeri Laura , Russo Fabio , Morabito Giuseppe , Calamita Piera , Gregori Silvia , Deverman Benjamin , Broccoli Vania 
Published: October 2019

AbstractRett syndrome (RTT) is an incurable neurodevelopmental disorder caused by mutations in the gene encoding for methyl-CpG binding-protein 2 (MeCP2). Gene therapy for this disease presents inherent hurdles sinceMECP2is expressed throughout the brain and its duplication leads to severe neurological conditions as well. However, the recent introduction of AAV-PHP.eB, an engineered capsid with an unprecedented efficiency in crossing the blood-brain barrier upon intravenous injection, has provided an invaluable vehicle for gene transfer in the mouse nervous system. Herein, we use AAV-PHP.eB to deliver an instability-proneMecp2(iMecp2) transgene cassette which, increasing RNA destabilization and inefficient protein translation of the viralMecp2transgene, limits supraphysiological Mecp2 protein levels in transduced neural tissues. Intravenous injections of the PHP.eB-iMecp2virus in symptomatic male and femaleMecp2mutant mice significantly ameliorated the disease progression with improved locomotor activity, coordination, lifespan and normalization of altered gene expression and mTOR signaling. Remarkably, PHP.eB-iMecp2administration did not result in severe toxicity effects either in femaleMecp2mutant or in wild-type animals. In contrast, we observed a strong immune response to the transgene in treated maleMecp2mutant mice that was overcome by immunosuppression. Overall, PHP.eB-mediated delivery of theiMecp2cassette provided widespread and efficient gene transfer maintaining physiological Mecp2 protein levels in the brain. This combination defines a novel viral system with significant therapeutic efficacy and increased safety which can contribute to overcome the hurdles that are delaying clinical applications of gene therapy for RTT.One Sentence SummaryGlobal brain transduction of the instability-proneMecp2transgene by systemic AAV-PHP.eB administration is both safe and effective in protecting male and femaleMecp2mutant mice from the RTT disease phenotype.
Apparent Propagator Anisotropy from reduced Diffusion MRI acquisitions
Authors: Aja-Fernández Santiago , Tristán-Vega Antonio , Jones Derek 
Published: October 2019

AbstractThe Propagator Anisotropy (PA) is a measurement of the orientational variability inside a tissue estimated from diffusion MRI using the Ensemble Average diffusion Propagator (EAP). It is based on the quantification of the angular difference between the propagator in a specific voxel and its isotropic counterpart. The PA has shown the ability to reveal microstructural information of interest and meaningful descriptive maps inside the white matter. However, the use of PA is not generalized among the clinical community, due to the great amount of data needed for its calculation, together with the associated long processing times. In order to calculate the PA, the EAP must also be properly estimated. This task would require a dense sampling of the Cartesian q-space. Alternatively, more efficient techniques have been proposed in the last decade. Even so, all of them imply acquiring a large number of diffusion gradients with different b-values and long processing times.In this work, we propose an alternative implementation to drastically reduce the number of samples needed, as well as boosting the estimation procedure. We avoid the calculation of the whole EAP by assuming that the diffusion anisotropy is roughly independent from the radial direction. With such an assumption, we achieve a closed-form expression for a measure similar to the PA but using information from one single shell: the Apparent Propagator Anisotropy (APA). The new measure remains compatible with standard acquisition protocols commonly used for HARDI (based on just one b-value). The intention of the APA is not to exactly replicate the PA but inferring microstructural information with comparable discrimination power as the PA but using a reduced amount of data.We report extensive results showing that the proposed measures present a robust behavior in clinical studies and they are computationally efficient and robust when compared with PA and other anisotropy measures.
Impact of small RNAs in retrograde signalling pathways inArabidopsis thaliana
Authors: Habermann Kristin , Tiwari Bhavika , Krantz Maria , Adler Stephan O. , Klipp Edda , Arif M. Asif , Frank Wolfgang 
Published: October 2019

SummaryChloroplast perturbations activate retrograde signalling pathways causing dynamic changes of gene expression. Besides transcriptional control of gene expression different classes of small non-coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling is lacking. We performed sRNA profiling in response to norflurazon (NF) that provokes retrograde signals inA. thalianawild type and the two retrograde signalling mutantsgun1andgun5. The RNA samples were also used for mRNA and long non-coding RNA (lncRNA) profiling to link altered sRNA levels to changes of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in wild type. Strikingly, 140 and 213 sRNAs were found to be differentially regulated in both mutants indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression we detected about 1500 differentially expressed mRNAs in the NF treated wild type and around 900 and 1400 mRNAs that were differentially regulated in thegun1andgun5mutant with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid localised proteins. The analyses of sRNA-target pairs identified pairs with an anticorrelated expression as well pairs showing other expressional relations pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression we assume a considerable impact of sRNAs in retrograde-dependent transcriptional changes to adjust plastidic and nuclear gene expression.Significance statementPerturbations of plastid functions trigger retrograde signalling to adjust plastidic and nuclear gene expression, however, the role of small non-coding RNAs acting as regulators in these pathways is not well understood. We analysed small non-coding RNA expression in response to retrograde signals inA. thalianawild type and two retrograde signalling mutants and identified members of all known small non-coding RNA classes pointing to a functional role of these RNA classes in retrograde pathways.
Substrate-mediated regulation of the arginine transporter ofToxoplasma gondii
Authors: Rajendran Esther , Clark Morgan , Goulart Cibelly , Steinhöfel Birte , Tjhin Erick T. , Smith Nicholas C. , Kirk Kiaran , van Dooren Giel G. 
Published: October 2019

ABSTRACTIntracellular parasites, such as the apicomplexanToxoplasma gondii, are adept at scavenging nutrients from their host. However, there is little understanding of how parasites sense and respond to the changing nutrient environments they encounter during an infection.TgApiAT1, a member of the apicomplexan ApiAT family of amino acid transporters, is the major uptake route for the essential amino acid L-arginine (Arg) inT. gondii. Here, we show that the abundance ofTgApiAT1, and hence the rate of uptake of Arg, is regulated by the availability of Arg in the parasite’s external environment, increasing in response to decreased [Arg]. Using a luciferase-based ‘biosensor’ strain ofT. gondii, we demonstrate that parasites vary the expression ofTgApiAT1 in different organs within their host, indicating that parasites are able to modulateTgApiAT1-dependent uptake of Arg as they encounter different nutrient environmentsin vivo. Finally, we show that Arg-dependent regulation ofTgApiAT1 expression is post-transcriptional, mediated by an upstream open reading frame (uORF) in theTgApiAT1 transcript, and we provide evidence that the peptide encoded by this uORF is critical for mediating regulation. Together, our data reveal the mechanism by which an apicomplexan parasite responds to changes in the availability of a key nutrient.
Trade-offs between host tolerances to different pathogens in plant-virus interactions
Authors: Montes Nuria , Vijayan Viji , Pagán Israel 
Published: October 2019

AbstractAlthough accumulating evidence indicates that tolerance is a plant defence strategy against pathogens as widespread as resistance, how plants evolve tolerance is poorly understood. Theory predicts that hosts will evolve to maximize tolerance or resistance, but not both. Remarkably, most experimental works failed in finding this trade-off. We tested the hypothesis that the evolution of tolerance to one virus is traded-off against tolerance to others, rather than against resistance, and identified the associated mechanisms. To do so, we challenged eighteen Arabidopsis thaliana genotypes with Turnip mosaic virus (TuMV) and Cucumber mosaic virus (CMV). We characterized plant life-history trait modifications associated with reduced effects of TuMV and CMV on plant seed production (fecundity tolerance) and life period (mortality tolerance), both measured as a norm of reaction across viral loads (range tolerance). Also, we analysed resistance-tolerance and tolerance-tolerance trade-offs. Results indicate that tolerance to TuMV is associated with changes in the length of the pre-reproductive and reproductive periods, and tolerance to CMV with resource reallocation from growth to reproduction; and that tolerance to TuMV is traded-off against tolerance to CMV in a virulence-dependent manner. Thus, this work provides novel insights on the mechanisms of plant tolerance and highlights the importance of considering the combined effect of different pathogens to understand how plant defences evolve.
StoatyDive: Evaluation and Classification of Peak Profiles for Sequencing Data
Authors: Heyl Florian , Backofen Rolf 
Published: October 2019

The prediction of binding sites (peak calling) is a common task in the data analysis of methods such as crosslinking or chromatin immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq, ChIP-Seq). The predicted binding sites are often further analyzed to predict sequence motifs or structure patterns as an example. However, the obtained peak set can vary in their profile shapes because of the used peakcaller method, different binding domains of the protein, protocol biases, or other factors. Thus, a tool is missing that evaluates and classifies the predicted peaks based on their shapes. We hereby present StoatyDive, a tool that can be used to filter for specific peak profile shapes of sequencing data such as CLIP and ChIP. StoatyDive therefore fine tunes downstream analysis steps such as structure or sequence motif predictions and acts as a quality control.With StoatyDive we were able to classify distinct peak profile shapes from CLIP-seq data of the histone stem-loop-binding protein (SLBP). We show the potential of StoatyDive, as a quality control tool and as a filter to pick different shapes based on biological or methodical questions.StoatyDive is open source and freely available under GLP-3 athttps://github.com/BackofenLab/StoatyDiveand at biocondahttps://anaconda.org/bioconda/stoatydive.
Imprecise neural computations as source of human adaptive behavior in volatile environments
Authors: Findling Charles , Chopin Nicolas , Koechlin Etienne 
Published: October 2019

AbstractEveryday life features uncertain and ever-changing situations. In such environments, optimal adaptive behavior requires higher-order inferential capabilities to grasp the volatility of external contingencies. These capabilities however involve complex and rapidly intractable computations, so that we poorly understand how humans develop efficient adaptive behaviors in such environments. Here we demonstrate this counterintuitive result: simple, low-level inferential processes involving imprecise computations conforming to the psychophysical Weber Law actually lead to near-optimal adaptive behavior, regardless of the environment volatility. Using volatile experimental settings, we further show that such imprecise, low-level inferential processes accounted for observed human adaptive performances, unlike optimal adaptive models involving higher-order inferential capabilities, their biologically more plausible, algorithmic approximations and non-inferential adaptive models like reinforcement learning. Thus, minimal inferential capabilities may have evolved along with imprecise neural computations as contributing to near-optimal adaptive behavior in real-life environments, while leading humans to make suboptimal choices in canonical decision-making tasks.
An assessment of digital literacy skills and knowledge-based competencies among librarians working in university libraries in Africa
Authors: Baro Ebikabowei Emmanuel , Obaro Onyedikachi G. , Aduba Emetarom Doris 
Published: October 2019

PurposeThe purpose of this paper is to assess digital literacy skills possessed by library and information professionals working in university libraries in Africa.Design/methodology/approachOnline questionnaire was developed to collect data from 214 librarians working in various university libraries in English-speaking countries in Africa.FindingsThe study found that librarians working in university libraries in Africa rated their database search skills, uploading documents to online platforms, skills in using different social media, sending and receiving e-mails skill, digital library development skills, skills in applying new technologies into library services, ability to create different file formats and ability to use open source software as very high. While, metadata development skills, and library website development skills were rated to be moderate and low. Overall, the librarians rated their level of digital literacy skills possessed to be moderate, and differences emerged between librarians in Nigeria and South Africa with regard to digital literacy skills possessed.Practical implicationsThis study attempts to identify skills that are central to librarians working in university libraries. The study will be useful for trainers who want to arrange training for academic librarians in Africa and other developing countries. For some library schools, it may help them to review their curriculum in accordance with the required skills and competencies for academic librarians in the market.Originality/valueFindings will be helpful to explore the skills and competencies needed by information professionals and to act as a guideline for competency development and curriculum update in library schools in developing countries.
Physical and cognitive demands of work in building construction
Authors: Rodriguez Franciscsa S. , Spilski Jan , Hekele Felix , Beese Nils Ove , Lachmann Thomas 
Published: October 2019

PurposeInvestigating demands within an occupational context has always been an essential endeavor to guarantee worker well-being and performance efficiency. In blue-collar occupations, the physical demands of manual labor have always been the major focus, but recent technological changes may come with higher demands on the intellectual capacities of workers. For this reason, the purpose of this paper is to assess physical and cognitive demands that construction workers face.Design/methodology/approachThe authors conducted a quantitative study using standardized research instruments. Construction workers of three German construction companies were asked to volunteer to participate in interviews (n=35) and a survey (n=30) that assessed the extent of physical demands and a variety of cognitive demands experienced by construction workers.FindingsThe results suggest that construction work is demanding in physical terms as well as in perceptual, psychomotor, social and cognitive terms. Using and updating specialized knowledge, giving advice and providing consultation, friendliness, assertiveness and reliability are important demands among construction workers.Research limitations/implicationsConstruction workers face an undervalued level of demands in their everyday work environment. As high demands can affect well-being and mental health, construction companies would greatly benefit from investing efforts into evaluating the multi-component demands profile of their workers and the impact on their health, in particular through the strongly increasing cognitive demands due to the ongoing digitization of the sector.Originality/valueThe study identified essential demands in construction work that are relevant for the workers’ productivity and well-being.
Do academia-industry R&D collaborations necessarily facilitate industrial innovation in China?
Authors: Hou Bojun , Hong Jin , Chen Qiong , Shi Xing , Zhou Yu 
Published: October 2019

Purpose
It is widely accepted that enterprises obtaining academic discoveries through R&D collaboration improve their innovation performance. However, it is not necessarily true in emerging economies, such as China and post-socialist countries in Europe. The purpose of this paper is to fill the gap by investigating how R&D collaboration between industry and academia (i.e. universities and research institutes) affects the industrial innovation performance; and whether and how intermediaries moderate their relationships.

Design/methodology/approach
This paper constructs the research model according to the knowledge production function, and the pooled ordinary least square regression is used to verify our hypotheses.

Findings
Evidence from a sample of Chinese industrial enterprises in thirty provinces spanning from 2009 to 2014 suggests that R&D collaboration with research institutes (CWR) is positively related to innovation output, while R&D collaboration with universities (CWU) exerts negative effect on innovation output measured by sales revenue of new product (NPSR). The significant moderating role of technology transfer institutions is confirmed in the negative relationship between CWU and NPSR.

Originality/value
This paper empirically examines the moderating role of intermediary organisations in academia–industry cooperation and industrial innovation, and has practical implications for the government to formulate policies to improve the quality and effectiveness of cooperation between academic and industrial sectors. These results vary in inland and coastal areas, which suggest the policy makers to formulate policies according to local conditions not only in China but also in other countries, like European countries.
Making secret sharing based cloud storage usable
Authors: Framner Erik , Fischer-Hübner Simone , Lorünser Thomas , Alaqra Ala Sarah , Pettersson John Sören 
Published: October 2019

Purpose
The purpose of this paper is to develop a usable configuration management for Archistar, which utilizes secret sharing for redundantly storing data over multiple independent storage clouds in a secure and privacy-friendly manner. Selecting the optimal secret sharing parameters, cloud storage servers and other settings for securely storing the secret data shares, while meeting all of end user’s requirements and other restrictions, is a complex task. In particular, complex trade-offs between different protection goals and legal privacy requirements need to be made.

Design/methodology/approach
A human-centered design approach with structured interviews and cognitive walkthroughs of user interface mockups with system administrators and other technically skilled users was used.

Findings
Even technically skilled users have difficulties to adequately select secret sharing parameters and other configuration settings for adequately securing the data to be outsourced.

Practical implications
Through these automatic settings, not only system administrators but also non-technical users will be able to easily derive suitable configurations.

Originality/value
The authors present novel human computer interaction (HCI) guidelines for a usable configuration management, which propose to automatically set configuration parameters and to solve trade-offs based on the type of data to be stored in the cloud. Through these automatic settings, not only system administrators but also non-technical users will be able to easily derive suitable configurations.
Lawyers and the “new extraction” in Africa
Authors: Dezalay Sara 
Published: October 2019

Purpose
The purpose of this paper is to examine the ongoing “new extraction” on the African continent. Contrary to mainstream scholarship and policies that see in law an external variable to remedy the “resource curse,” this paper channels attention toward the role of law as an institution of extraction in the longue durée. Unpacking the close association of law with the conversion of economic surpluses and power into enduring social relationships can help trace the mechanisms by which the uneven and unequal connection between Africa and the world is being negotiated, justified and challenged over time.

Design/methodology/approach
To this end, this paper deploys an approach anchored in political sociology of law and focuses on the roles played specifically by lawyers to trace the “interconnectedness” between European colonialism on the continent and the consolidation of the contemporary international economic and legal political order. It illustrates this approach with the case study of the “Africa” Bar in Paris as a key site in which extractive deals between multinational corporations and Francophone African states are negotiated.

Findings
This micro focus helps to explain the dual position of the “Africa” Bar in Paris, as offshore yet connected as it is shaped by both imperial legacies and ongoing waves of globalization into the African continent.

Originality/value
This approach traces a more nuanced explanation of Africa’s unequal and uneven relationship with the global economy as one shaped by the path of imperial legacies and successive and interconnected waves of globalization across Africa.