bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating gene delivery and gene-editing technologies by adenoviral vector transfer of optimized CRISPR-Cas9 components
Authors: Maggio Ignazio , Zittersteijn Hidde A. , Wang Qian , Liu Jin , Janssen Josephine M. , Ojeda Ivan Toral , van der Maarel Silvère M. , Lankester Arjan C. , Hoeben Rob C. , Gonçalves Manuel A. F. V. 
Published: January 2020

AbstractEnhancing the intracellular delivery and performance of RNA-guided CRISPR-Cas9 nucleases (RGNs) remains in demand. Here, we show that nuclear translocation of commonly used Streptococcus pyogenes Cas9 (SpCas9) proteins is suboptimal. Hence, we generated eCas9.4NLS by endowing the high-specificity eSpCas9(1.1) nuclease (eCas9.2NLS) with additional nuclear localization signals (NLSs). We demonstrate that eCas9.4NLS coupled to prototypic or optimized guide RNAs achieves efficient targeted DNA cleavage and probe the performance of SpCas9 proteins with different NLS compositions at target sequences embedded in heterochromatin versus euchromatin. Moreover, after adenoviral vector (AdV)-mediated transfer of SpCas9 expression units, unbiased quantitative immunofluorescence microscopy revealed 2.3-fold higher eCas9.4NLS nuclear enrichment levels than those observed for high-specificity eCas9.2NLS. This improved nuclear translocation yielded in turn robust gene editing after nonhomologous end joining repair of targeted double-stranded DNA breaks. In particular, AdV delivery of eCas9.4NLS into muscle progenitor cells resulted in significantly higher editing frequencies at defective DMD alleles causing Duchenne muscular dystrophy (DMD) than those achieved by AdVs encoding the parental, eCas9.2NLS, protein. In conclusion, this work provides a strong rationale for integrating viral vector and optimized gene-editing technologies to bring about enhanced RGN delivery and performance.
Stacked nanocarbon photosensitizer for efficient blue light excited Eu(III) emission
Authors: Kitagawa Yuichi , Suzue Fumiya , Nakanishi Takayuki , Fushimi Koji , Seki Tomohiro , Ito Hajime , Hasegawa Yasuchika 
Published: January 2020

AbstractPhotosensitizer design to allow effective use of low-energy light is important for developing photofunctional materials. Herein, we describe a rational photosensitizer design for effective use of low-energy light. The developed photosensitizer is a stacked nanocarbon based on a rigid polyaromatic framework, which allows efficient energy transfer from the low-energy T1 level to the energy acceptor. We prepared an Eu(III) complex consisting of a luminescent center (Eu(III)) and stacked-coronene photosensitizer. The brightness of photosensitized Eu(III) excited using low-energy light (450 nm) is more than five times higher than the maximum brightness of previously reported Eu(III) complexes.
Live-cell monitoring of protein localization to membrane rafts using protein-fragment complementation
Authors: Merezhko Maria , Pakarinen Emmi , Uronen Riikka-Liisa , Huttunen Henri J. 
Published: January 2020

Abstract
The plasma membrane consists of a variety of discrete domains differing from the surrounding membrane in composition and properties. Selective partitioning of protein to these microdomains is essential for membrane functioning and integrity. Studying the nanoscale size and dynamic nature of the membrane microdomains requires advanced imaging approaches with a high spatiotemporal resolution and, consequently, expensive and specialized equipment, unavailable for most researchers and unsuited for large-scale studies. Thus, understanding of protein partitioning to the membrane microdomains in health and disease is still hampered by the lack of inexpensive live-cell approaches with an appropriate spatial resolution. Here, we have developed a novel approach based on Gaussia princeps luciferase protein-fragment complementation assay to quantitively investigate protein partitioning to cholesterol and sphingomyelin-rich domains, sometimes called ‘lipid rafts’, in intact living cells with a high-spatial resolution. In the assay, the reporter construct, carrying one half of the luciferase protein, is targeted to lipid microdomains through the fused acetylation motif from Src-family kinase Fyn. A protein of interest carries the second half of the luciferase protein. Together, this serves as a reversible real-time sensor of raft recruitment for the studied protein. We demonstrated that the assay can efficiently detect the dynamic alterations in raft localization of two disease-associated proteins: Akt and APP. Importantly, this method can be used in high-throughput screenings and other large-scale studies in living cells. This inexpensive, and easy to implement raft localization assay will benefit all researchers interested in protein partitioning in rafts.
Going video: Understanding interpreter-mediated clinical
communication through the video lens
Authors: Krystallidou Demi 
Published: January 2020

Abstract
Most of the research on dialogue interpreting has been conducted
by taking only verbal interaction into account. Although the existing
research has managed to shed some light on the complexity of
interpreter-mediated interaction, there is still a lot to be unravelled by
adopting a multimodal stance and including non-verbal cues in the analysis
of verbal interaction. This study builds on the findings of recent research
by Davitti (2013); Davitti & Pasquandrea (2017);
Krystallidou (2013, 2014, 2016); Pasquandrea (2011, 2012). In this study, I draw on data taken from a corpus of
authentic video-recorded interpreter-mediated consultations at a large urban
hospital in Belgium. By applying multimodal analysis to data and comparing
it to analysis based on transcripts alone, I highlight a set of
interactional dynamics that touch upon new aspects of the complexity of
interpreter-mediated interaction and which a transcript-based analysis alone
would have failed to capture. It will be shown that participants’ gaze,
gestures and body orientation, along with verbal interaction, are used by
the interpreter as semiotic resources that do affect the doctor’s and the
patient’s participation in interaction. However, the weight the interpreter
seems to attach to the primary participants’ semiotic resources seems to be
subject to the participation status of each participant.
I ~ You > I ~ Me
Authors: Lantolf James P. 
Published: January 2020

Abstract
An often-unquestioned
assumption regarding psychological and linguistic
development is that the interesting and relevant
processes occur inside the head of the individual.
It is a position that “fetishizes” the fact that
development necessarily entails social relations
as a component. Vygotsky, on the other hand,
proposes that uniquely human forms of mental
behavior, including language development, arise as
a result of social relations: “I relate to myself
as others relate to me” (1997). In other words, “I ~
You” interactions become, over time, “I ~ Me”
interactions in which the voices of others are
appropriated and transformed into my voice. This
paper fleshes out the theoretical argument
underlying the hidden or “fetishized” social other
and considers the implications of this stance for
second language development.
Examining the role of instructor first
language in classroom-based oral input
Authors: Long Avizia Y. , Geeslin Kimberly L. 
Published: January 2020

Abstract
In instructed second
language (L2) settings, instructor-provided input
is essential for learners’ interlanguage
development. While some input is consciously
modified by instructors to assist learners, much
of instructors’ speech contains inherent
linguistic variability mediated by linguistic,
social, and situational factors. Variable,
learner-directed input may also be influenced by
instructors’ individual characteristics (e.g.,
Gurzynski-Weiss, Geeslin, Long, & Daidone,
2017; Gurzynski-Weiss et al., 2018). The present
study extends this work by examining instructor
first language (L1) in relation to patterns of
variable subject expression in Spanish in
learner-directed classroom speech. Twelve
instructors of second year, university-level L2
Spanish – half with L1 Spanish and half with L1
English – were recorded teaching one
vocabulary-focused lesson. Analyses of subject
forms produced in finite clauses in relation to
independent variables known to constrain subject
expression in Spanish revealed that some constraints on
subject form use in instructor speech were
influenced by the instructors’ L1.
Single-step, acid-based fabrication of homogeneous gelatin-polycaprolactone fibrillar scaffolds intended for skin tissue engineering
Authors: Prado-Prone Gina , Bazzar Masoomeh , Letizia Focarete Maria , García-Macedo Jorge A , Perez-Orive Javier , Ibarra Clemente , Velasquillo Cristina , Silva-Bermudez Phaedra 
Published: January 2020

Abstract
Blends of natural and synthetic polymers have recently attracted great attention as scaffolds for tissue engineering applications due to their favorable biological and mechanical properties. Nevertheless, phase-separation of blend components is an important challenge facing the development of electrospun homogeneous fibrillar natural-synthetic polymers scaffolds; phase-separation can produce significant detrimental effects for scaffolds fabricated by electrospinning. In the present study, blends of gelatin (Gel; natural polymer) and polycaprolactone (PCL; synthetic polymer), containing 30 and 45 wt% Gel, were prepared using acetic acid as a ‘green’ sole solvent to straightforwardly produce appropriate single-step Gel-PCL solutions for electrospinning. Miscibility of Gel and PCL in the scaffolds was assessed and the morphology, chemical composition and structural and solid-state properties of the scaffolds were thoroughly investigated. Results showed that the two polymers proved miscible under the single-step solution process used and that the electrospun scaffolds presented suitable properties for potential skin tissue engineering applications. Viability, metabolic activity and protein expression of human fibroblasts cultured on the Gel-PCL scaffolds were evaluated using LIVE/DEAD (calcein/ethidium homodimer), MTT-Formazan and immunocytochemistry assays, respectively. In vitro results showed that the electrospun Gel-PCL scaffolds enhanced cell viability and proliferation in comparison to PCL scaffolds. Furthermore, scaffolds allowed fibroblasts expression of extracellular matrix proteins, tropoelastin and collagen Type I, in a similar way to positive controls. Results indicated the feasibility of the single-step solution process used herein to obtain homogeneous electrospun Gel-PCL scaffolds with Gel content ≥30 wt% and potential properties to be used as scaffolds for skin tissue engineering applications for wound healing.
Wastewater management strategies for sustained shale gas production
Authors: Menefee Anne H , Ellis Brian R 
Published: January 2020

Abstract
Recent advances in shale gas development have largely outpaced efforts to manage associated waste streams that pose significant environmental risks. Wastewater management presents significant challenges in the Marcellus shale, where increasing fluid volumes concomitant with expanding development will threaten to overwhelm existing infrastructure over the next decade. In this work, we forecast growth in drilling, flowback, and produced fluid volumes through 2025 based on historic data and consider conventional and alternative disposal options to meet future demands. The results indicate that nearly 12 million m3 (74 MMbbl) of wastewater will be generated annually by 2025. Even assuming wastewater recycling rates in the region rebound, meeting increased demands for wastewater that cannot be reused due to poor quality or logistics would require significant capital investment to expand existing disposal pathways, namely treatment and discharge at centralized facilities or dedicated brine injection in Ohio. Here, we demonstrate the logistical and environmental advantages of an alternative strategy: repurposing depleted oil and gas wells for dedicated injection of wastewater that cannot otherwise be reused or recycled. Hubs of depleted wells could accommodate projected increases in wastewater volumes more efficiently than existing disposal options, primarily because the proximity of depleted wells to active production sites would substantially reduce wastewater transport distances and associated costs. This study highlights the need to reevaluate regional-scale shale wastewater management practices in the context of evolving wastewater qualities and quantities, as strategic planning will result in more socially and economically favorable options while avoiding adverse environmental impacts that have overshadowed the environmental benefits of natural gas expansion in the energy sector.
Noncrop Habitat Use by Wild Bees (Hymenoptera: Apoidea) in a Mixed-Use Agricultural Landscape
Authors: Du Clos Brianne , Drummond Francis A , Loftin Cynthia S 
Published: January 2020

AbstractHomogeneous, agriculturally intense landscapes have abundant records of pollinator community research, though similar studies in the forest-dominated, heterogeneous mixed-use landscape that dominates the northeastern United States are sparse. Trends of landscape effects on wild bees are consistent across homogeneous agricultural landscapes, whereas reported studies in the northeastern United States have not found this consistency. Additionally, the role of noncrop habitat in mixed-use landscapes is understudied. We assessed wild bee communities in the mixed-use lowbush blueberry (Vaccinium angustifolium Ait.) production landscape of Maine, United States at 56 sites in eight land cover types across two regional landscapes and analyzed effects of floral resources, landscape pattern, and spatial scale on bee abundance and species richness. Within survey sites, cover types with abundant floral resources, including lowbush blueberry fields and urban areas, promoted wild bee abundance and diversity. Cover types with few floral resources such as coniferous and deciduous/mixed forest reduced bee abundance and species richness. In the surrounding landscape, lowbush blueberry promoted bee abundance and diversity, while emergent wetland and forested land cover strongly decreased these measures. Our analysis of landscape configuration revealed that patch mixing can promote wild bee abundance and diversity; however, this was influenced by strong variation across our study landscape. More surveys at intra-regional scales may lead to better understanding of the influence of mixed-use landscapes on bee communities.
Photoperiod Effect on Megachile rotundata (Hymenoptera: Megachilidae) Female Regarding Diapause Status of Progeny: The Importance of Data Scrutiny
Authors: Pitts-Singer Theresa L 
Published: January 2020

AbstractMegachile rotundata F. populations are managed to pollinate alfalfa, Medicago sativa L. (Fabaceae), for seed production in western North America. Some progeny produced in summer by overwintered M. rotundata females enter diapause as prepupae to overwinter and become adults the following year. Other offspring avert diapause to undergo adult emergence in summer. The regulatory mechanism(s) of diapause induction or aversion is unknown; the process apparently involves multiple and integrated factors. This 4-yr study sought to determine effects of the exposure of mother bees to short, long, very long, and natural photoperiods on their production of non-diapausing and diapausing progeny. Just-emerged adult bees from both Utah and Canada sources were exposed to different photoperiods for 3 d in incubators and then released into field enclosures placed over blooming alfalfa. Control bees were those exposed to only outdoor conditions. Reproduction was monitored for each female bee, and offspring diapause outcome was recorded. Progeny outcome data were informative for only two of the four study years. Generally, progeny of Utah mothers exposed to long and very long photoperiods were more likely to be non-diapausers compared to progeny of mothers exposed to short and control photoperiods. Short and long (but not very long) photoperiod maternal exposures increased the likelihood of diapause aversion in Canada progeny. Performing multiyear field studies on geographically distinct populations is imperative for revealing environmental challenges and inconsistent bee performance that can impair analyses and interpretation. Future similar studies are needed to more fully evaluate photoperiod effects on diapause.
Aortic valve repair with a newly approved geometric annuloplasty ring in patients undergoing proximal aortic repair: early results from a single-centre experience
Authors: Jawitz Oliver K , Raman Vignesh , Anand Jatin , Bishawi Muath , Voigt Soraya L , Doberne Julie , Vekstein Andrew M , Weissler E Hope , Turek Joseph W , Hughes G Chad 
Published: January 2020

AbstractOBJECTIVESAortic insufficiency (AI) is common in patients with proximal aortic disease, but limited options exist to facilitate aortic valve repair (AVr) in this population. This study reports ‘real-world’ early results of AVr using newly FDA-approved trileaflet and bicuspid geometric annuloplasty rings for patients with AI undergoing proximal aortic repair (PAR) in a single referral centre.METHODSAll patients undergoing AVr with a rigid internal geometric annuloplasty ring (n = 47) in conjunction with PAR (ascending +/− root +/− arch) were included. Thirty-six patients underwent AVr with a trileaflet ring, and 11 patients underwent AVr with a bicuspid ring. The rings were implanted in the subannular position, and concomitant leaflet repair was performed if required for cusp prolapse identified after ring placement.RESULTSThe median age was 58 years [interquartile range (IQR) 46–70]. PAR included supracoronary ascending replacement in 26 (55%) patients and remodelling valve-sparing root replacement with selective sinus replacement in 20 (42%) patients. Arch replacement was performed in 38 (81%) patients, including hemi-arch in 34 patients and total arch in 4 patients. There was no 30-day/in-hospital mortality. Preoperative AI was 3–4+ in 37 (79%) patients. Forty-one (87%) patients had zero–trace AI on post-repair transoesophageal echocardiography, and 6 patients had 1+ AI. The median early post-repair mean gradient was 13 mmHg (IQR 5–20). Follow-up imaging was available in 32 (68%) patients at a median of 11 months (IQR 10–13) postsurgery. AI was ≤1+ in 97% of patients with 2+ AI in 1 patient. All patients were alive and free from aortic valve reintervention at last follow-up.CONCLUSIONSEarly results with geometric rigid internal ring annuloplasty for AVr in patients undergoing PAR appear promising and allow a standardized approach to repair with annular diameter reduction and cusp plication when needed. Longer-term follow-up will be required to ensure the durability of the procedure.
Radiomics-based prediction for tumour spread through air spaces in stage I lung adenocarcinoma using machine learning
Authors: Chen Donglai , She Yunlang , Wang Tingting , Xie Huikang , Li Jian , Jiang Gening , Chen Yongbing , Zhang Lei , Xie Dong , Chen Chang 
Published: January 2020

Abstract

OBJECTIVES
As evidence has proven that sublobar resection is oncologically contraindicated by tumour spread through air spaces (STAS), its preoperative recognition is vital in customizing surgical strategies. We aimed to assess the value of radiomics in predicting STAS in stage I lung adenocarcinoma.

METHODS
We retrospectively reviewed the patients with stage I lung adenocarcinoma, who accepted curative resection in our institution between January 2011 and December 2013. Using ‘PyRadiomics’ package, 88 radiomics features were extracted from computed tomography (CT) images and a prediction model was consequently constructed using Naïve Bayes machine-learning approach. The accuracy of the model was assessed through receiver operating curve analysis, and the performance of the model was validated both internally and externally.

RESULTS
A total of 233 patients were included as the training cohort with 69 (29.6%) patients being STAS (+). Patients with STAS had worse recurrence-free survival and overall survival (P &lt; 0.001). After feature extraction, 5 most contributing radiomics features were selected out to develop a Naïve Bayes model. In the internal validation, the model exhibited good performance with an area under the curve value of 0.63 (0.55–0.71). External validation was conducted on a test cohort with 112 patients and produced an area under the curve value of 0.69.

CONCLUSIONS
CT-based radiomics is valuable in preoperatively predicting STAS in stage I lung adenocarcinoma, which may aid surgeons in determining the optimal surgical approach.
Atrial fibrosis as a dominant factor for the development of atrial fibrillation: facts and gaps
Authors: Xintarakou Anastasia , Tzeis Stylianos , Psarras Stelios , Asvestas Dimitrios , Vardas Panos 
Published: January 2020

AbstractAtrial fibrillation (AF), the most commonly diagnosed arrhythmia, affects a notable percentage of the population and constitutes a major risk factor for thromboembolic events and other heart-related conditions. Fibrosis plays an important role in the onset and perpetuation of AF through structural and electrical remodelling processes. Multiple molecular pathways are involved in atrial substrate modification and the subsequent maintenance of AF. In this review, we aim to recapitulate underlying molecular pathways leading to atrial fibrosis and to indicate existing gaps in the complex interplay of atrial fibrosis and AF.
A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers
Authors: Hecker Nikolai , Hiller Michael 
Published: January 2020

Abstract

Background
Multiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment.

Results
To utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2 exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals. Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average 4.7%–15.6% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta.

Conclusion
The 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/and for download at https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/.