bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms
Authors: Nam Bo-Hye , Yoo DongAhn , Kim Young-Ok , Park Jung Youn , Shin Younhee , Shin Ga-hee , Park Chan-Il , Kim Heebal , Kwak Woori 
Published: April 2019

AbstractRed sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. It is hypothesized that the genomes of red sea bream are influenced by decades of artificial selection. This study investigates the impact of artificial selection on genomes of red sea bream. Whole genome sequencing was conducted for 40 samples of red sea bream either from Ehime, Nagasaki and Tongyeong fish farms or from the wild. Population stratification based on whole genome data was investigated and the genomic regions of fish farm populations under selection were identified using XP-EHH and relative nucleotide diversity. Gene ontology analysis revealed that different functions were enriched in different fish farms. In conclusion, this study highlights the difference between independently cultured red sea bream populations by showing that influence of artificial selection acted upon completely different genes related to different functions including metabolic and developmental processes.
In vivo synaptic activity-independent co-uptakes of amyloid β1–42 and Zn2+ into dentate granule cells in the normal brain
Authors: Tamano Haruna , Oneta Naoya , Shioya Aoi , Adlard Paul A. , Bush Ashley I. , Takeda Atsushi 
Published: April 2019

AbstractNeuronal amyloid β1–42(Aβ1–42) accumulation is considered an upstream event in Alzheimer’s disease pathogenesis. Here we report the mechanism on synaptic activity-independent Aβ1–42uptakein vivo. When Aβ1–42uptake was compared in hippocampal slices after incubating with Aβ1–42,In vitroAβ1–42uptake was preferentially high in the dentate granule cell layer in the hippocampus. Because the rapid uptake of Aβ1–42with extracellular Zn2+is essential for Aβ1–42-induced cognitive declinein vivo, the uptake mechanism was tested in dentate granule cells in association with synaptic activity.In vivorapid uptake of Aβ1–42was not modified in the dentate granule cell layer after co-injection of Aβ1–42and tetrodotoxin, a Na+channel blocker, into the dentate gyrus. Both the rapid uptake of Aβ1–42and Zn2+into the dentate granule cell layer was not modified after co-injection of CNQX, an AMPA receptor antagonist, which blocks extracellular Zn2+influx, Both the rapid uptake of Aβ1–42and Zn2+into the dentate granule cell layer was not also modified after either co-injection of chlorpromazine or genistein, an endocytic repressor. The present study suggests that Aβ1–42and Zn2+are synaptic activity-independently co-taken up into dentate granule cells in the normal brain and the co-uptake is preferential in dentate granule cells in the hippocampus. We propose a hypothesis that Zn-Aβ1–42oligomers formed in the extracellular compartment are directly incorporated into neuronal plasma membranes and form Zn2+-permeable ion channels.
Effect of topography and protecting barriers on revegetation of sandy land, Southern Tibetan Plateau
Authors: Liao Chengrui , Liu Beichen , Xu Yannan , Li Yingkui , Li Haidong 
Published: April 2019

AbstractRevegetation on sandy land has attracted worldwide attention, especially on the extremely fragile alpine eco-region of the Tibetan Plateau. However, the effectiveness of revegetation and its controlling factors have rarely been reported. We collected plant growths and species composition from seven field sites in 2011 and conducted a follow-up random investigation in 2016. The indicators, including richness and diversity, were used to compare the differences among these sites based on redundancy and cluster analyses. The results indicated that plant growth has different characteristics in different land types. The distribution and growth of Artemisia sphaerocephala, Artemisia younghusbandii and Heteropappus gouldii varied with topography, and the crown widths of A. sphaerocephala were 100.6 cm × 87.2 cm on barchan dune and 26.0 cm × 25.4 cm on moving sandy land at valley slopes. These species are likely the pioneer plants for revegetation on sandy land. It seems that sand-protecting barriers play an important role in revegetation. The stone and plastic checkerboard barriers increase plant diversity, while straw barrier promotes the plant growth. These findings provide useful guidance to the ongoing vegetation recovery on sandy land, an important component of the Project on Construction and Protection of Ecological Security Barriers on the Tibetan Plateau.
Accurate early prediction of tumour response to PDT using optical coherence angiography
Authors: Sirotkina M. A. , Moiseev A. A. , Matveev L. A. , Zaitsev V. Y. , Elagin V. V. , Kuznetsov S. S. , Gelikonov G. V. , Ksenofontov S. Y. , Zagaynova E. V. , Feldchtein F. I. , Gladkova N. D. , Vitkin A. 
Published: April 2019

AbstractPrediction of tumour treatment response may play a crucial role in therapy selection and optimization of its delivery parameters. Here we use optical coherence angiography (OCA) as a minimally-invasive, label-free, real-time bioimaging method to visualize normal and pathological perfused vessels and monitor treatment response following vascular-targeted photodynamic therapy (PDT). Preclinical results are reported in a convenient experimental model (CT-26 colon tumour inoculated in murine ear), enabling controlled PDT and post-treatment OCA monitoring. To accurately predict long-term treatment outcome, a robust and simple microvascular metric is proposed. It is based on perfused vessels density (PVD) at t = 24 hours post PDT, calculated for both tumour and peri-tumour regions. Histological validation in the examined experimental cohort (n = 31 animals) enabled further insight into the excellent predictive power of the derived early-response OCA microvascular metric. The results underscore the key role of peri-tumour microvasculature in determining the long-term PDT response.
Intermolecular Reactions of Pyridyl Radicals with Olefins via Photoredox Catalysis
Authors: Seath Ciaran P. , Jui Nathan T. 
Published: April 2019

Pyridines are valuable motifs in a number of bioactive and functional molecules. The chemoselective functionalization of these structures from stable and widely available starting materials is a meaningful goal. We have demonstrated selective formation of pyridyl radicals at any position (2-, 3-, 4-pyridyl), through the action of a reducing photoredox catalyst. These radicals readily engage alkenes to deliver high-value products. Alteration of the reaction medium has enabled the use of a diverse range of alkene subtypes in a highly divergent and chemoselective manner.1	Introduction2	Minisci-Type Pyridine Alkylation3	An Alternate Approach – Reductive Radical Formation4	Conjugate Addition of Pyridyl Radicals5	Radical Hydroarylation of Neutral and Rich Olefins6	Solvent-Based Chemoselectivity7	Summary and Outlook
Platelet Activation by Antiphospholipid Antibodies Depends on Epitope Specificity and is Prevented by mTOR Inhibitors
Authors: Hollerbach Anne , Müller-Calleja Nadine , Ritter Svenja , Häuser Friederike , Canisius Antje , Orning Carolin , Jurk Kerstin , Lackner Karl J. 
Published: April 2019

AbstractAntiphospholipid antibodies (aPL) have been reported to activate platelets. This is considered to be one of the pathogenic properties of aPL. Even though aPL heterogeneity is quite well established, little is known, if the ability to activate platelets is common to all aPL or depends on antigen specificity. To further study this issue, we analyzed the ability of three human monoclonal aPL with distinctly different antigenic specificities to activate platelets in vitro. The results obtained with human monoclonal aPL were validated with immunoglobulin G (IgG) fractions obtained from patients with antiphospholipid syndrome (APS). A co-factor-independent human monoclonal anticardiolipin aPL had no discernible effect on human platelets. Two monoclonal aPL reactive against β2 glycoprotein I (β2GPI) induced platelet aggregation, integrin αIIbβ3 activation and P-selectin surface expression. These data could be confirmed with patient IgG fractions which could only induce aggregation, if they had anti-β2GPI activity. Anti-β2GPI aPL-induced platelet activation depended on interaction of aPL with the low affinity Fcγ-receptor IIa on the platelet surface. It was completely abolished by pretreatment of platelet-rich plasma with the mechanistic target of rapamycin (mTOR) inhibitors rapamycin or everolimus. This extends previous data showing that mTOR is involved in signaling of anti-β2GPI in monocytes and endothelial cells. In conclusion, anti-β2GPI aPL activate platelets while co-factor-independent anticardiolipin aPL have no effect. mTOR is involved in this signaling process which has implications beyond APS, because so far the role of mTOR signaling in platelets is incompletely explored and requires further study.
Translabyrinthine Approach for Resection of Large Cystic Acoustic Neuroma: Operative Video and Technical Nuances of Subperineural Dissection for Facial Nerve Preservation
Authors: Liu James K. , Dodson Vincent N. , Jyung Robert W. 
Published: April 2019

The translabyrinthine approach is advantageous for the resection of large acoustic neuromas compressing the brainstem when hearing loss is nonserviceable. This approach provides wide access through the presigmoid corridor without prolonged cerebellar retraction. Early identification of the facial nerve at the fundus is also achieved. In this operative video atlas manuscript, the authors demonstrate a step-by-step technique for microsurgical resection of a large cystic acoustic neuroma via a translabyrinthine approach. The nuances of microsurgical and skull base technique are illustrated including performing extracapsular dissection of the tumor while maintaining a subperineural plane of dissection to preserve the facial nerve. This strategy maximizes the extent of removal while preserving facial nerve function. A microscopic remnant of tumor was left adherent to the perineurium. A near-total resection of the tumor was achieved and the facial nerve stimulated briskly at low thresholds. Other than preexisting hearing loss, the patient was neurologically intact with normal facial nerve function postoperatively. In summary, the translabyrinthine approach and the use of subperineural dissection are important strategies in the armamentarium for surgical management of large acoustic neuromas while preserving facial nerve function.The link to the video can be found at: https://youtu.be/zld2cSP8fb8.
Nanoscale imaging reveals miRNA-mediated control of functional states of dendritic spines
Authors: Park Ikbum , Kim Hyun Jin , Kim Youngkyu , Hwang Hye Sung , Kasai Haruo , Kim Joung-Hun , Park Joon Won 
Published: April 2019

Significance
Although synaptic plasticity is intimately controlled by synthesis of transmitter receptors and regulatory proteins, it remains largely unknown how synthesis and distribution of synaptic proteins could be modulated at the specific synapses. microRNAs (miRNAs) such as miR-134 could adjust synapse development and plasticity due to their regulatory functions for a distinct set of proteins. We developed an imaging method for in situ microRNAs mediated by atomic force microscopy (AFM), which revealed that miR-134s are enriched at nearby dendritic shafts and necks of spines. Notably, the abundance of miR-134s varied among distinct spine types, and their amounts were inversely correlated with maturity and functional states of individual spines. The functional impact of miR-134s would represent a molecular means of miRNAs, dynamically tuning synaptic connectivity and plasticity.
Genome-wide CRISPR screen for Zika virus resistance in human neural cells
Authors: Li Yun , Muffat Julien , Omer Javed Attya , Keys Heather R. , Lungjangwa Tenzin , Bosch Irene , Khan Mehreen , Virgilio Maria C. , Gehrke Lee , Sabatini David M. , Jaenisch Rudolf 
Published: April 2019

Significance
Zika virus (ZIKV) is a neurotropic and neurovirulent arbovirus that has severe detrimental impact on the developing human fetal brain. We used a genome-wide CRISPR-Cas9 knockout screen to identify ZIKV host genes in human neural progenitors. The screen identified host factors involved in heparan sulfation, endocytosis, endoplasmic reticulum processing, Golgi function, and interferon activity. Our findings provide insights into host-dependent mechanisms for ZIKV infection in the highly vulnerable human neural progenitor cells and identify molecular targets for potential therapeutic intervention.
Overlooked roles of DNA damage and maternal age in generating human germline mutations
Authors: Gao Ziyue , Moorjani Priya , Sasani Thomas A. , Pedersen Brent S. , Quinlan Aaron R. , Jorde Lynn B. , Amster Guy , Przeworski Molly 
Published: April 2019

Significance
More than three-fourths of human germline mutations are paternal in origin and their total number increases with the father’s age at conception. These observations are thought to support the textbook view that germline point mutations stem mostly from DNA replication errors. Analyzing large germline mutation datasets for humans, we find that this understanding cannot explain the observed patterns of new mutations. Instead, we show that the male mutation bias is not driven by spermatogenesis. We further find evidence that a substantial fraction of mutations are not replicative in origin and uncover a potential effect of a mother’s age on the number of mutations that happen early in the development of the embryo.
Coulomb anti-blockade in a Rydberg gas
Authors: Bounds A D , Jackson N C , Hanley R K , Bridge E M , Huillery P , Jones M P A 
Published: April 2019

Abstract
We perform a comprehensive investigation of the coupling between a Rydberg-dressed atomic gas and an ultra-cold plasma (UCP). Using simultaneous time-resolved measurements of both neutral atoms and ions, we show that plasma formation occurs via a Coulomb anti-blockade mechanism, in which background ions DC Stark shift nearby atoms into resonance at specific distances. The result is a highly correlated growth of the Rydberg population that shares some similarities with that previously observed for van der Waals interactions. We show that a rate equation model that couples the laser-driven Rydberg gas to the UCP via a Coulomb anti-blockade mechanism accurately reproduces both the plasma formation and its subsequent decay. Using long-lived high angular momentum states as a probe, we also find evidence of a crossover from Coulomb anti-blockade to Coulomb blockade at high density. As well as shedding light on loss mechanisms in Rydberg-dressed gases, our results open new ways to create low-entropy states in UCPs.
Quantification of solute deuterium in titanium deuteride by atom probe tomography with both laser pulsing and high-voltage pulsing: influence of the surface electric field
Authors: Chang Y H , Mouton I , Stephenson L , Ashton M , Zhang G K , Szczpaniak A , Lu W J , Ponge D , Raabe D , Gault B 
Published: April 2019

Abstract
Atom probe tomography (APT) has been increasingly used to investigate hydrogen embrittlement in metals due to its unique capacity for direct imaging of H atoms interacting with microstructural features. The quantitativeness of hydrogen measurements by APT is yet to be established in views of erroneous compositional measurements of bulk hydrides and the influence of spurious hydrogen, e.g. residual gas inside the analysis chamber. Here, we analyzed titanium deuteride (approx. 65.0 at%–66.6 at% D) in lieu of hydride to minimize the overlap with residual gas, both with laser pulsing and high-voltage (HV) pulsing. Strategies were deployed to prevent H pick-up during specimen fabrication, including preparing specimens at cryogenic temperature. The measured composition of deuterium by APT with laser pulsing decreases significantly with the applied laser pulse energy, which is interpreted with regards to the strength of the corresponding surface electrostatic field, as assessed by the evolution of charge-state ratio. In contrast, compositional analyses with HV pulsing are roughly independent of the applied experimental parameters, although approx. 15 at%–20 at% off the nominal composition. Aided by plotting paired mass-to-charge correlations, the mechanisms of composition bias in both pulsing modes are discussed. A special emphasis is placed on the local variations of the measured composition as a function of the local electric field across the specimen’s surface, which is not uniform due to asymmetric heat distribution related to the localized laser absorption and the faceted nature of surface caused by the crystallographic structure. Our investigations demonstrate the challenges of quantitative analysis of solute deuterium by APT but nevertheless provide insight to achieving the best possible experimental protocol.
Weighted estimates for one-sided martingale transforms
Authors: Chen Wei , Han Rui , Lacey Michael 
Published: April 2019

Let

T
f
=

∑

I

ε
I

⟨
f
,

h

I
+

⟩

h

I
−

Tf =\sum _{I} \varepsilon _I \langle f,h_{I^+}\rangle h_{I^-}

. Here,

|

ε
I

|
=
1

\lvert \varepsilon _I\rvert =1

, and

h
J

h_J

is the Haar function defined on dyadic interval

J
J

. We show that, for instance,

‖
T

‖

L

2

(
w
)
→

L

2

(
w
)

≲
[
w

]

A
2

+

.

\begin{equation*} \lVert T \rVert _{L ^{2} (w) \to L ^{2} (w)} \lesssim [w] _{A_2 ^{+}} . \end{equation*}

Above, we use the one-sided

A
2

A_2

characteristic for the weight

w
w

. This is an instance of a one-sided

A
2

A_2

conjecture. Our proof of this fact is difficult, as the very quick known proofs of the

A
2

A_2

theorem do not seem to apply in the one-sided setting.
Graphical data mining of cancer mechanisms with SEMA
Authors: Solmaz Mustafa , Lane Adam , Gonen Bilal , Akmamedova Ogulsheker , Gunes Mehmet H , Komurov Kakajan 
Published: April 2019

Abstract

Motivation
An important goal of cancer genomics initiatives is to provide the research community with the resources for the unbiased query of cancer mechanisms. Several excellent web platforms have been developed to enable the visual analyses of molecular alterations in cancers from these datasets. However, there are few tools to allow the researchers to mine these resources for mechanisms of cancer processes and their functional interactions in an intuitive unbiased manner.

Results
To address this need, we developed SEMA, a web platform for building and testing of models of cancer mechanisms from large multidimensional cancer genomics datasets. Unlike the existing tools for the analyses and query of these resources, SEMA is explicitly designed to enable exploratory and confirmatory analyses of complex cancer mechanisms through a suite of intuitive visual and statistical functionalities. Here, we present a case study of the functional mechanisms of TP53-mediated tumor suppression in various cancers, using SEMA, and identify its role in the regulation of cell cycle progression, DNA repair and signal transduction in different cancers.
SEMA is a first-in-its-class web application designed to allow visual data mining and hypothesis testing from the multidimensional cancer datasets. The web application, an extensive tutorial and several video screencasts with case studies are freely available for academic use at https://sema.research.cchmc.org/.

Availability and implementation
SEMA is freely available at https://sema.research.cchmc.org. The web site also contains a detailed Tutorial (also in Supplementary Information), and a link to the YouTube channel for video screencasts of analyses, including the analyses presented here. The Shiny and JavaScript source codes have been deposited to GitHub: https://github.com/msolmazm/sema.

Supplementary information
Supplementary data are available at Bioinformatics online.
Habitat Type Influences Danaus plexippus (Lepidoptera: Nymphalidae) Oviposition and Egg Survival on Asclepias syriaca (Gentianales: Apocynaceae)
Authors: Myers Andrew , Bahlai Christie A , Landis Douglas A 
Published: April 2019

AbstractAs agricultural practices intensify, species once common in agricultural landscapes are declining in abundance. One such species is the monarch butterfly (Danaus plexippus L.), whose eastern North American population has decreased approximately 80% during the past 20 yr. One hypothesis explaining the monarch’s decline is reduced breeding habitat via loss of common milkweed (Asclepias syriaca L.) from agricultural landscapes in the north central United States due to the adoption of herbicide-tolerant row crops. Current efforts to enhance monarch breeding habitat primarily involve restoring milkweed in perennial grasslands. However, prior surveys found fewer monarch eggs on common milkweed in grassland versus crop habitats, indicating potential preference for oviposition in row crop habitats, or alternatively, greater egg loss to predation in grasslands. We tested these alternative mechanisms by measuring oviposition and egg predation on potted A. syriaca host plants. Our study revealed that habitat context influences both monarch oviposition preference and egg predation rates and that these patterns vary by year. We found higher monarch egg predation rates during the first 24 h after exposure and that much of the predation occurs at night. Overall, we documented up to 90% egg mortality over 72 h in perennial grasslands, while predation rates in corn were lower (10–30% mortality) and more consistent between years. These findings demonstrate that weekly monarch egg surveys are too infrequent to distinguish oviposition habitat preferences from losses due to egg predation and suggest that monarch restoration efforts need to provide both attractive and safe habitats for monarch reproduction.
Guidance for the Evaluation of Tuberculosis Diagnostics That Meet the World Health Organization (WHO) Target Product Profiles: An Introduction to WHO Process and Study Design Principles
Authors: Denkinger Claudia M , Schumacher Samuel G , Gilpin Christopher , Korobitsyn Alexei , Wells William A , Pai Madhukar , Leeflang Mariska , Steingart Karen R , Bulterys Michelle , Schünemann Holger , Glaziou Philippe , Weyer Karin 
Published: April 2019

Abstract
Existing high-priority target product profiles (TPPs) of the World Health Organization (WHO) establish important needs for tuberculosis (TB) diagnostic development. Building on this earlier work, this guidance series aims to provide study guidance for performing accuracy studies of novel diagnostic products that may meet the 4 high-priority WHO TPPs and thus enable adequate evidence generation to inform a WHO evidence review process. Diagnostic accuracy studies represent a fundamental step in the validation of all tests. Unfortunately, such studies often have limitations in design, execution, and reporting, leading to low certainty of the evidence about true test performance, which can delay or impede policy and scale-up decisions.
This introductory paper outlines the following: (1) the purpose of this series of papers on study guidance; (2) WHO evidence needs and process for the development of policy guidelines for new TB diagnostic tests; and (3) study design considerations, ie, general diagnostic study considerations, intended use of test and role in the clinical pathway, choice of population and setting, index-test specific issues, suitable reference standard and comparators, study flow and specimen issues, and finally key issues beyond accuracy that should be considered. The other 4 papers in this series will provide more detailed guidance for each of the 4 WHO high-priority TPPs.
By increasing the clarity around the clinical evaluation needs for tests that have the potential to meet the TPP specifications, we hope to support harmonized evidence generation and enable the WHO review process towards meeting the WHO End TB Strategy targets for reducing the incidence and mortality associated with TB.