bluuebunny/crossref_metadata_2025_split huggingface dataset:
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
Authors: Sharan Malvika , Förstner Konrad U. , Eulalio Ana , Vogel Jörg 
Published: May 2016

ABSTRACTRNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs), and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches.We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using Position Specific Scoring Matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome ofEscherichia coli.APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available athttps://pypi.python.org/pypi/bio-apricot
Talin-KANK1 interaction controls the recruitment of cortical microtubule stabilizing complexes to focal adhesions
Authors: Bouchet Benjamin P. , Gough Rosemarie E. , van de Willige Dieudonnée , Ammon York-Christoph , Post Harm , Jacquemet Guillaume , Altelaar A.F. Maarten , Heck Albert J.R. , Goult Benjamin T. , Akhmanova Anna 
Published: May 2016

AbstractThe cross-talk between dynamic microtubules and integrin-based adhesions to the extracellular matrix plays a crucial role in cell polarity and migration. Microtubules regulate the turnover of adhesion sites, and, in turn, focal adhesions promote cortical microtubule capture and stabilization in their vicinity, but the underlying mechanism is unknown. Here, we show that cortical microtubule stabilization sites containing CLASPs, KIF21A, LL5P and liprins are recruited to focal adhesions by the adaptor protein KANK1, which directly interacts with the major adhesion component, talin. Structural studies showed that the conserved KN domain in KANK1 binds to the talin rod domain R7. Perturbation of this interaction, including a single point mutation in talin, which disrupts KANK1 binding but not the talin function in adhesion, abrogates the association of microtubule-stabilizing complexes with focal adhesions. We propose that the talin-KANK1 interaction links the two macromolecular assemblies that control cortical attachment of actin fibers and microtubules.
A scalable strategy for high-throughput GFP tagging of endogenous human proteins
Authors: Leonetti Manuel D. , Sekine Sayaka , Kamiyama Daichi , Weissman Jonathan S. , Huang Bo 
Published: May 2016

AbstractA central challenge of the post-genomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9/sgRNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.SIGNIFICANCE STATEMENTThe function of a large fraction of the human proteome still remains poorly characterized. Tagging proteins with a functional sequence is a powerful way to access function, and inserting tags at endogenous genomic loci allows the preservation of a near-native cellular background. To characterize the cellular role of human proteins in a systematic manner and in a native context, we developed a method for tagging endogenous human proteins with GFP that is both rapid and readily applicable at a genome-wide scale. Our approach allows studying both localization and interaction partners of the protein target. Our results pave the way for the large-scale generation of endogenously tagged human cell lines for a systematic functional interrogation of the human proteome.
Experimental Granulomatous Pulmonary Nocardiosis in Balb/c Mice
Authors: Mifuji Lira Roque M. , Limón Flores Alberto Yairh , Salinas Carmona Mario César , Ortiz Stern Alejandro 
Published: May 2016

AbstractPulmonary nocardiosis is a granulomatous disease with high mortality that affects both immunosuppressed and immunocompetent patients. The mechanisms leading to the establishment and progression of the infection are currently unknown. An animal model to study these mechanisms is sorely needed. We report the first in vivo model of granulomatous pulmonary nocardiosis that closely resembles human pathology. BALB/c mice infected intranasally with two different doses of GFP-expressingNocardia brasiliensisATCC700358 (NbGFP), develop weight loss and pulmonary granulomas. Mice infected with 109CFUs progressed towards death within a week while mice infected with 108CFUs died after five to six months. Histological examination of the lungs revealed that both the higher and lower doses of NbGFP induced granulomas with NbGFP clearly identifiable at the center of the lesions. Mice exposed to 108CFUs and subsequently to 109CFUs were not protected against disease severity but had less granulomas suggesting some degree of protection. Attempts to identify a cellular target for the infection were unsuccessful but we found that bacterial microcolonies in the suspension used to infect mice were responsible for the establishment of the disease. Small microcolonies of NbGFP, incompatible with nocardial doubling times starting from unicellular organisms, were identified in the lung as early as six hours after infection. Mice infected with highly purified unicellular preparations of NbGFP did not develop granulomas despite showing weight loss. Finally, intranasal delivery of nocardial microcolonies was enough for mice to develop granulomas with minimal weight loss. Taken together these results show that Nocardia brasiliensis microcolonies are both necessary and sufficient for the development of granulomatous pulmonary nocardiosis in mice.
Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator
Authors: Westbrook Alexandra M. , Lucks Julius B. 
Published: May 2016

ABSTRACTRNA transcriptional regulators are emerging as versatile components for genetic circuit construction. However, RNA transcriptional regulators suffer from incomplete repression, making their dynamic range less than that of their protein counterparts. This incomplete repression can cause expression leak, which impedes the construction of larger RNA synthetic regulatory networks. Here we demonstrate how naturally derived antisense RNA-mediated transcriptional regulators can be configured to regulate both transcription and translation in a single compact RNA mechanism that functions in Escherichia coli. Using in vivo gene expression assays, we show that a combination of transcriptional termination and RBS sequestration increases repression from 85% to 98% and activation from 10 fold to over 900 fold in response to cognate antisense RNAs. We also show that orthogonal versions of this mechanism can be created through engineering minimal antisense RNAs. Finally, to demonstrate the utility of this dual control mechanism, we use it to reduce circuit leak in an RNA-only transcriptional cascade that activates gene expression as a function of a small molecule input. We anticipate these regulators will find broad use as synthetic biology moves beyond parts engineering to the design and construction of larger and more sophisticated circuits.
Relationships among attachment theory, social capital perspective, personality characteristics, and Facebook self-disclosure
Authors: Aharony Noa 
Published: May 2016

Purpose– Due to the growth of Facebook use, the question arises regarding which factors may influence individuals’ self-disclosure while using the site. The purpose of this paper is to examine: first, to what extent does attachment theory explain users’ self-disclosure on Facebook; second, to what extent does the social capital paradigm explain users’ self-disclosure on Facebook; third, to what extent do personality characteristics explain users’ self-disclosure on Facebook; and fourth, to what extent do demographic details explain users’ self-disclosure on Facebook.Design/methodology/approach– Research was conducted in Israel and included 183 library and information science students. Participants were asked to complete the following questionnaires: personal details, Facebook use, importance of Facebook use, demographic disclosure, picture disclosure, disclosure, social capital, attachment, and personality.Findings– The current study extends research about Facebook self-disclosure and confirms that attachment theory, as well as social capital, personality traits, and age significantly predict Facebook self-disclosure.Originality/value– We should bear in mind that there are certain people who may benefit from disclosing information on Facebook, while there are others who may be at risk, because they reveal more personal information than they intended and the line between the two is fuzzy. Individuals should bear in mind that if they disclose too much information, they might become easy targets for abuse, internet predators, sexual solicitation, sexting, cyberbullying, and online harassment.
Determinants of effective SoLoMo advertising from the perspective of social capital
Authors: Lee Ya-Ching 
Published: May 2016

Purpose
– The purpose of this paper is to investigate factors affecting attitudes toward social-local-mobile (SoLoMo) advertising from the perspective of social capital.

Design/methodology/approach
– There were 422 respondents filling out the survey instrument. The research model in this study is tested using SPSS 20 software.

Findings
– The results show that structural, relational, and cognitive dimensions of social capital have impacts on consumer attitudes toward SoLoMo advertising.

Originality/value
– It contributes to the literature by advancing our knowledge about determinants of effective SoLoMo advertising from the perspective of social capital. It also provides constructs that constitute the three dimensions in advertising. The author expands the understanding of the social relations under the context of business to consumer by adding substantial nuances to the understanding of the role of social capital in advertising. Finally, this study provides practical suggestions.
Product advertising and viral stealth marketing in online videos
Authors: Wendt Lars Michael , Griesbaum Joachim , Kölle Ralph 
Published: May 2016

Purpose– In the context of social media marketing, so called viral stealth videos (VSVs) often attract as much or even more attention than videos that directly advertise products (product advertising video (PAV)). However, beyond this, the product or brand-related impact of such videos is not so clear. In this context, the purpose of this paper is to investigate brand perception of PAVs and VSVs in YouTube.Design/methodology/approach– The research design is based on an examination of comments of six VSVs and six PAVs on YouTube. Therefore, the content of 1,080 posts was analyzed to capture the topic, the attitude toward the video and the pragmatic intent of posts.Findings– Results indicate that there are strong differences with regard to users ' perception of the two analyzed video type segments. The content of VSVs is clearly recognized as positive more often than the content of PAVs. In contrast, only PAVs evoke substantial brand awareness but receive rather mixed results with regards to brand assessment.Research limitations/implications– As a whole, the study is widely descriptive and of explorative value. Nevertheless, the research design can be estimated as a first step to measure the brand-related impact of online videos. Ideally, the data generated in the investigation should be combined with traffic and conversion data of the brands’ websites to get an encompassing picture of the marketing related impact of the investigated online videos.Practical implications– Seen from a marketers’ perspective, one can recommend PAVs over VSVs as there are hardly any brand-related impacts of VSVs visible in online communication. PAVs are perceived less positively but they are able to evoke brand awareness at least.Originality/value– According to the authors’ knowledge this investigation is one of only a few studies that analyzes real online communication in the context of video-based online marketing.
A toolkit for optimizing fish passage barrier mitigation actions
Authors: King Steven , O'Hanley Jesse R. , Newbold Lynda R. , Kemp Paul S. , Diebel Matthew W. 
Published: May 2016

Summary

The presence of dams, stream–road crossings and other infrastructure often compromises the connectivity of rivers, leading to reduced fish abundance and diversity. The assessment and mitigation of river barriers is critical to the success of restoration efforts aimed at restoring river integrity.

In this study, we present a combined modelling approach involving statistical regression methods and mixed integer linear programming to maximize resident fish species richness within a catchment through targeted barrier mitigation. Compared to existing approaches, our proposed method provides enhanced biological realism while avoiding the use of complex and computationally intensive population/ecosystem models.

To estimate barrier passability quickly and at low cost, we further outline a rapid barrier assessment methodology. The methodology is used to characterize potential passage barriers for various fish species common to the UK but can be readily adapted to different planning areas and other species of interest.

We demonstrate the applicability of our barrier assessment and prioritization approach based on a case study of the River Wey, located in south‐east England. We find that significant increases in species richness can be achieved for modest investment in barrier mitigation. In particular, dams and weirs with low passability located on mid‐ to high‐order streams are identified as top priorities for mitigation.

Synthesis and applications. Our study shows the benefits of combining a coarse resolution barrier assessment methodology with state‐of‐the‐art optimization modelling to cost‐effectively plan fish passage barrier mitigation actions. The modelling approach can help inform on‐the‐ground river restoration decision‐making by providing a recommended course of action that best allocates limited resources in order to restore longitudinal connectivity and maximize ecological gains.
Exon capture optimization in amphibians with large genomes
Authors: McCartney‐Melstad Evan , Mount Genevieve G. , Shaffer H. Bradley 
Published: May 2016

AbstractGathering genomic‐scale data efficiently is challenging for nonmodel species with large, complex genomes. Transcriptome sequencing is accessible for organisms with large genomes, and sequence capture probes can be designed from such mRNA sequences to enrich and sequence exonic regions. Maximizing enrichment efficiency is important to reduce sequencing costs, but relatively few data exist for exon capture experiments in nonmodel organisms with large genomes. Here, we conducted a replicated factorial experiment to explore the effects of several modifications to standard protocols that might increase sequence capture efficiency for amphibians and other taxa with large, complex genomes. Increasing the amounts of c0t‐1 repetitive sequence blocker and individual input DNA used in target enrichment reactions reduced the rates of PCR duplication. This reduction led to an increase in the percentage of unique reads mapping to target sequences, essentially doubling overall efficiency of the target capture from 10.4% to nearly 19.9% and rendering target capture experiments more efficient and affordable. Our results indicate that target capture protocols can be modified to efficiently screen vertebrates with large genomes, including amphibians.
Deficits in axon‐associated proteins in prefrontal white matter in bipolar disorder but not schizophrenia
Authors: Shao Li , Golbaz Khashayar , Honer William G , Beasley Clare L 
Published: May 2016

ObjectivesBrain imaging studies have implicated white matter dysfunction in the pathophysiology of both bipolar disorder (BD) and schizophrenia (SCZ). However, the contribution of axons to white matter pathology in these disorders is not yet understood. Maintenance of neuronal function is dependent on the active transport of biological material, including synaptic proteins, along the axon. In this study, the expression of six proteins associated with axonal transport of synaptic cargoes was quantified in postmortem samples of prefrontal white matter in subjects with BD, those with SCZ, and matched controls, as a measure of axonal dysfunction in these disorders.MethodsLevels of the microtubule‐associated proteins β‐tubulin and microtubule‐associated protein 6 (MAP6), the motor and accessory proteins kinesin‐1 and disrupted‐in‐schizophrenia 1 (DISC1), and the synaptic cargoes synaptotagmin and synaptosomal‐associated protein‐25 (SNAP‐25) were quantified in white matter adjacent to the dorsolateral prefrontal cortex in subjects with BD (n = 34), subjects with SCZ (n = 35), and non‐psychiatric controls (n = 35) using immunoblotting and an enzyme‐linked immunosorbent assay (ELISA).ResultsProtein expression of β‐tubulin, kinesin‐1, DISC1, synaptotagmin, and SNAP‐25 was significantly lower in subjects with BD compared to controls. Levels of axon‐associated proteins were also lower in subjects with SCZ, but failed to reach statistical significance.ConclusionsThese data provide evidence for deficits in axon‐associated proteins in prefrontal white matter in BD. Findings are suggestive of decreased axonal density or dysregulation of axonal function in this disorder.
New mouse model of acute adult T‐cell leukemia generated by transplantation of AKT, BCLxL, and HBZ‐transduced T cells
Authors: Kasugai Yumiko , Yoshida Noriaki , Ohshima Koichi , Matsuo Keitaro , Seto Masao , Tsuzuki Shinobu 
Published: May 2016

Adult T‐cell leukemia/lymphoma (ATL) develops in human T‐cell leukemia virus type 1 (HTLV‐1) carriers. Although the HTLV‐1‐encoded HBZ gene is critically involved, HBZ alone is insufficient and additional, cooperative “hits” are required for the development of ATL. Candidate cooperative hits are being defined, but methods to rapidly explore their roles in ATL development in collaboration with HBZ are lacking. Here, we present a new mouse model of acute type ATL that can be generated rapidly by transplanting in vitro‐induced T cells that have been retrovirally transduced with HBZ and two cooperative genes, BCLxL and AKT, into mice. Co‐transduction of HBZ and BCLxL/AKT allowed these T cells to grow in vitro in the absence of cytokines (Flt3‐ligand and interleukin‐7), which did not occur with any two‐gene combination. Although transplanted T cells were a mixture of cells transduced with different combinations of the genes, tumors that developed in mice were composed of HBZ/BCLxL/AKT triply transduced T cells, showing the synergistic effect of the three genes. The genetic/epigenetic landscape of ATL has only recently been elucidated, and the roles of additional “hits” in ATL pathogenesis remain to be explored. Our model provides a versatile tool to examine the roles of these hits, in collaboration with HBZ, in the development of acute ATL.
Parent Discrimination Predicts Mexican‐American Adolescent Psychological Adjustment 1 Year Later
Authors: Espinoza Guadalupe , Gonzales Nancy A. , Fuligni Andrew J. 
Published: May 2016

This study examined whether Mexican‐American parents' experiences with discrimination are related to adolescent psychological adjustment over time. The extent to which associations between parent discrimination and adolescent adjustment vary as a function of parents' ethnic socialization of their children was also examined. Participants included 344 high school students from Mexican or Mexican‐American backgrounds (primarily second generation; ages 14–16 at Wave 1) and their primary caregivers who completed surveys in a 2‐year longitudinal study. Results revealed that parent discrimination predicted internalizing symptoms and self‐esteem among adolescents 1 year later. Additionally, adolescents were more likely to report low self‐esteem in relation to parents' increased experiences of discrimination when parents conveyed ethnic socialization messages to them.
Imaging and identification of brown adipose tissue on CT scan
Authors: Prodhomme Hugo , Ognard Julien , Robin Philippe , Alavi Zarrin , Salaun Pierre‐Yves , Ben Salem Douraied 
Published: May 2016

SummaryTwo types of adipose tissue (AT) have been described in the field of physiology: white (W) and brown (B) AT. Although WAT is well identified on human imaging, BAT imaging aspect remains to be further explored. The aim of this study was to investigate imaging aspect of BAT and its identification on CT (computed tomography) with iodine‐based contrast media injection. We retrospectively reviewed 464 positron emission tomography (PET)/CT, performed during 21 months on adults younger than 37 years. In 39 cases only, the PET revealed the presence of activated BAT. ROI was placed on both white and brown adipose tissue simultaneously on both PET and CT. Several patients’ characteristics (blood sugar level, gender, age, body mass index) as well as BAT and WAT parameters were assessed. Mean CT densities for WAT and BAT were −99·5 HU versus −32·6, mean SUV were 1·38 versus 13·2 and SUVmax were 1·79 versus 16·57, respectively. We found a statistically significant inverse relation between BMI and BAT density. BAT has a higher density than WAT. In this manner, BAT can be misinterpreted as an infiltration of adipose tissue in neoplasic and inflammatory context. Contrast‐enhanced CT scan allows visualization and identification of BAT.