bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population structure and minimum core genome typing of Legionella pneumophila
Authors: Qin Tian , Zhang Wen , Liu Wenbin , Zhou Haijian , Ren Hongyu , Shao Zhujun , Lan Ruiting , Xu Jianguo 
Published: February 2016

AbstractLegionella pneumophila is an important human pathogen causing Legionnaires’ disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila.
Hydrate-based heavy metal separation from aqueous solution
Authors: Song Yongchen , Dong Hongsheng , Yang Lei , Yang Mingjun , Li Yanghui , Ling Zheng , Zhao Jiafei 
Published: February 2016

AbstractA novel hydrate-based method is proposed for separating heavy metal ions from aqueous solution. We report the first batch of experiments and removal characteristics in this paper, the effectiveness and feasibility of which are verified by Raman spectroscopy analysis and cross-experiment. 88.01–90.82% of removal efficiencies for Cr3+, Cu2+, Ni2+, and Zn2+ were obtained. Further study showed that higher R141b–effluent volume ratio contributed to higher enrichment factor and yield of dissociated water, while lower R141b–effluent volume ratio resulted in higher removal efficiency. This study provides insights into low-energy, intensive treatment of wastewater.
A Radio-genomics Approach for Identifying High Risk Estrogen Receptor-positive Breast Cancers on DCE-MRI: Preliminary Results in Predicting OncotypeDX Risk Scores
Authors: Wan Tao , Bloch B. Nicolas , Plecha Donna , Thompson CheryI L. , Gilmore Hannah , Jaffe Carl , Harris Lyndsay , Madabhushi Anant 
Published: February 2016

AbstractTo identify computer extracted imaging features for estrogen receptor (ER)-positive breast cancers on dynamic contrast en-hanced (DCE)-MRI that are correlated with the low and high OncotypeDX risk categories. We collected 96 ER-positivebreast lesions with low (<18, N = 55) and high (>30, N = 41) OncotypeDX recurrence scores. Each lesion was quantitatively charac-terize via 6 shape features, 3 pharmacokinetics, 4 enhancement kinetics, 4 intensity kinetics, 148 textural kinetics, 5 dynamic histogram of oriented gradient (DHoG), and 6 dynamic local binary pattern (DLBP) features. The extracted features were evaluated by a linear discriminant analysis (LDA) classifier in terms of their ability to distinguish low and high OncotypeDX risk categories. Classification performance was evaluated by area under the receiver operator characteristic curve (Az). The DHoG and DLBP achieved Az values of 0.84 and 0.80, respectively. The 6 top features identified via feature selection were subsequently combined with the LDA classifier to yield an Az of 0.87. The correlation analysis showed that DHoG (ρ = 0.85, P < 0.001) and DLBP (ρ = 0.83, P < 0.01) were significantly associated with the low and high risk classifications from the OncotypeDX assay. Our results indicated that computer extracted texture features of DCE-MRI were highly correlated with the high and low OncotypeDX risk categories for ER-positive cancers.
Cell surface localization of importin α1/KPNA2 affects cancer cell proliferation by regulating FGF1 signalling
Authors: Yamada Kohji , Miyamoto Yoichi , Tsujii Akira , Moriyama Tetsuji , Ikuno Yudai , Shiromizu Takashi , Serada Satoshi , Fujimoto Minoru , Tomonaga Takeshi , Naka Tetsuji , Yoneda Yoshihiro , Oka Masahiro 
Published: February 2016

AbstractImportin α1 is involved in nuclear import as a receptor for proteins with a classical nuclear localization signal (cNLS). Here, we report that importin α1 is localized to the cell surface in several cancer cell lines and detected in their cultured medium. We also found that exogenously added importin α1 is associated with the cell membrane via interaction with heparan sulfate. Furthermore, we revealed that the cell surface importin α1 recognizes cNLS-containing substrates. More particularly, importin α1 bound directly to FGF1 and FGF2, secreted cNLS-containing growth factors and addition of exogenous importin α1 enhanced the activation of ERK1/2, downstream targets of FGF1 signalling, in FGF1-stimulated cancer cells. Additionally, anti-importin α1 antibody treatment suppressed the importin α1−FGF1 complex formation and ERK1/2 activation, resulting in decreased cell growth. This study provides novel evidence that functional importin α1 is located at the cell surface, where it accelerates the proliferation of cancer cells.
Transdermal Delivery of siRNA through Microneedle Array
Authors: Deng Yan , Chen Jiao , Zhao Yi , Yan Xiaohui , Zhang Li , Choy Kwongwai , Hu Jun , Sant Himanshu J. , Gale Bruce K. , Tang Tao 
Published: February 2016

AbstractSuccessful development of siRNA therapies has significant potential for the treatment of skin conditions (alopecia, allergic skin diseases, hyperpigmentation, psoriasis, skin cancer, pachyonychia congenital) caused by aberrant gene expression. Although hypodermic needles can be used to effectively deliver siRNA through the stratum corneum, the major challenge is that this approach is painful and the effects are restricted to the injection site. Microneedle arrays may represent a better way to deliver siRNAs across the stratum corneum. In this study, we evaluated for the first time the ability of the solid silicon microneedle array for punching holes to deliver cholesterol-modified housekeeping gene (Gapdh) siRNA to the mouse ear skin. Treating the ear with microneedles showed permeation of siRNA in the skin and could reduce Gapdh gene expression up to 66% in the skin without accumulation in the major organs. The results showed that microneedle arrays could effectively deliver siRNA to relevant regions of the skin noninvasively.
A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei
Authors: Fleming Ian M. C. , Paris Zdeněk , Gaston Kirk W. , Balakrishnan R. , Fredrick Kurt , Rubio Mary Anne T. , Alfonzo Juan D. 
Published: February 2016

AbstractMost eukaryotic ribosomes contain 26/28S, 5S, and 5.8S large subunit ribosomal RNAs (LSU rRNAs) in addition to the 18S rRNA of the small subunit (SSU rRNA). However, in kinetoplastids, a group of organisms that include medically important members of the genus Trypanosoma and Leishmania, the 26/28S large subunit ribosomal RNA is uniquely composed of 6 rRNA fragments. In addition, recent studies have shown the presence of expansion segments in the large ribosomal subunit (60S) of Trypanosoma brucei. Given these differences in structure, processing and assembly, T. brucei ribosomes may require biogenesis factors not found in other organisms. Here, we show that one of two putative 3-methylcytidine methyltransferases, TbMTase37 (a homolog of human methyltransferase-like 6, METTL6), is important for ribosome stability in T. brucei. TbMTase37 localizes to the nucleolus and depletion of the protein results in accumulation of ribosomal particles lacking srRNA 4 and reduced levels of polysome associated ribosomes. We also find that TbMTase37 plays a role in cytokinesis, as loss of the protein leads to multi-flagellated and multi-nucleated cells.
Structural and biochemical characterization of an RNA/DNA binding motif in the N-terminal domain of RecQ4 helicases
Authors: Marino Francesca , Mojumdar Aditya , Zucchelli Chiara , Bhardwaj Amit , Buratti Emanuele , Vindigni Alessandro , Musco Giovanna , Onesti Silvia 
Published: February 2016

AbstractThe RecQ4 helicase belongs to the ubiquitous RecQ family but its exact role in the cell is not completely understood. In addition to the helicase domain, RecQ4 has a unique N-terminal part that is essential for viability and is constituted by a region homologous to the yeast Sld2 replication initiation factor, followed by a cysteine-rich region, predicted to fold as a Zn knuckle. We carried out a structural and biochemical analysis of both the human and Xenopus laevis RecQ4 cysteine-rich regions and showed by NMR spectroscopy that the Xenopus fragment indeed assumes the canonical Zn knuckle fold, whereas the human sequence remains unstructured, consistent with the mutation of one of the Zn ligands. Both the human and Xenopus Zn knuckles bind to a variety of nucleic acid substrates, with a mild preference for RNA. We also investigated the effect of a segment located upstream the Zn knuckle that is highly conserved and rich in positively charged and aromatic residues, partially overlapping with the C-terminus of the Sld2-like domain. In both the human and Xenopus proteins, the presence of this region strongly enhances binding to nucleic acids. These results reveal novel possible roles of RecQ4 in DNA replication and genome stability.
Generation of elliptically polarized nitrogen ion laser fields using two-color femtosecond laser pulses
Authors: Li Ziting , Zeng Bin , Chu Wei , Xie Hongqiang , Yao Jinping , Li Guihua , Qiao Lingling , Wang Zhanshan , Cheng Ya 
Published: February 2016

AbstractWe experimentally investigate generation of nitrogen molecular ion ("Equation missing") lasers with two femtosecond laser pulses at different wavelengths. The first pulse serves as the pump which ionizes the nitrogen molecules and excites the molecular ions to excited electronic states. The second pulse serves as the probe which leads to stimulated emission from the excited molecular ions. We observe that changing the angle between the polarization directions of the two pulses gives rise to elliptically polarized "Equation missing" laser fields, which is interpreted as a result of strong birefringence of the gain medium near the wavelengths of the "Equation missing" laser.
The cannabinoid quinol VCE-004.8 alleviates bleomycin-induced scleroderma and exerts potent antifibrotic effects through peroxisome proliferator-activated receptor-γ and CB2 pathways
Authors: del Río Carmen , Navarrete Carmen , Collado Juan A. , Bellido M. Luz , Gómez-Cañas María , Pazos M. Ruth , Fernández-Ruiz Javier , Pollastro Federica , Appendino Giovanni , Calzado Marco A. , Cantarero Irene , Muñoz Eduardo 
Published: February 2016

AbstractScleroderma is a group of rare diseases associated with early and transient inflammation and vascular injury, followed by fibrosis affecting the skin and multiple internal organs. Fibroblast activation is the hallmark of scleroderma and disrupting the intracellular TGFβ signaling may provide a novel approach to controlling fibrosis. Because of its potential role in modulating inflammatory and fibrotic responses, both PPARγ and CB2 receptors represent attractive targets for the development of cannabinoid-based therapies. We have developed a non-thiophilic and chemically stable derivative of the CBD quinol (VCE-004.8) that behaves as a dual agonist of PPARγ and CB2 receptors, VCE-004.8 inhibited TGFβ-induced Col1A2 gene transcription and collagen synthesis. Moreover, VCE-004.8 inhibited TGFβ–mediated myofibroblast differentiation and impaired wound-healing activity. The anti-fibrotic efficacy in vivo was investigated in a murine model of dermal fibrosis induced by bleomycin. VCE-004.8 reduced dermal thickness, blood vessels collagen accumulation and prevented mast cell degranulation and macrophage infiltration in the skin. These effects were impaired by the PPARγ antagonist T0070907 and the CB2 antagonist AM630. In addition, VCE-004.8 downregulated the expression of several key genes associated with fibrosis, qualifying this semi-synthetic cannabinoid as a novel compound for the management of scleroderma and, potentially, other fibrotic diseases.
TRPV-1-mediated elimination of residual iPS cells in bioengineered cardiac cell sheet tissues
Authors: Matsuura Katsuhisa , Seta Hiroyoshi , Haraguchi Yuji , Alsayegh Khaled , Sekine Hidekazu , Shimizu Tatsuya , Hagiwara Nobuhisa , Yamazaki Kenji , Okano Teruo 
Published: February 2016

AbstractThe development of a suitable strategy for eliminating remaining undifferentiated cells is indispensable for the use of human-induced pluripotent stem (iPS) cell-derived cells in regenerative medicine. Here, we show for the first time that TRPV-1 activation through transient culture at 42 °C in combination with agonists is a simple and useful strategy to eliminate iPS cells from bioengineered cardiac cell sheet tissues. When human iPS cells were cultured at 42 °C, almost all cells disappeared by 48 hours through apoptosis. However, iPS cell-derived cardiomyocytes and fibroblasts maintained transcriptional and protein expression levels and cardiac cell sheets were fabricated after reducing the temperature. TRPV-1 expression in iPS cells was upregulated at 42 °C and iPS cell death at 42 °C was TRPV-1-dependent. Furthermore, TRPV-1 activation through thermal or agonist treatment eliminated iPS cells in cardiac tissues for a final concentration of 0.4% iPS cell contamination. These findings suggest that the difference in tolerance to TRPV-1 activation between iPS cells and iPS cell-derived cardiac cells could be exploited to eliminate remaining iPS cells in bioengineered cell sheet tissues, which will further reduce the risk of tumour formation.
Image processing methods to elucidate spatial characteristics of retinal microglia after optic nerve transection
Authors: Zhang Yudong , Peng Bo , Wang Shuihua , Liang Yu-Xiang , Yang Jiquan , So Kwok-Fai , Yuan Ti-Fei 
Published: February 2016

AbstractMicroglia are the mononuclear phagocytes with various functions in the central nervous system and the morphologies of microglia imply the different stages and functions. In optical nerve transection model of the retina, the retrograde degeneration of retinal ganglion cells induces microglial activations to a unique morphology termed rod microglia. A few studies described the rod microglia in the cortex and retina; however, the spatial characteristic of rod microglia is not fully understood. In this study, we built a mathematical model to characterize the spatial trait of rod microglia. In addition, we developed a Matlab-based image processing pipeline that consists of log enhancement, image segmentation, mathematical morphology based cell detection, area calculation and angle analysis. This computer program provides researchers a powerful tool to quickly analyze the spatial trait of rod microglia.
Synthesis of mono‐dispersed ceria hollow nanospheres by a hydrothermal method
Authors: Jiang Xueliang , Zhang Jiao , Yu Lu , Chen Ruiqi , Xu Xiong 
Published: February 2016

Mono‐dispersed ceria (CeO2) hollow nanospheres about 400 nm have been prepared via a facile one‐step hydrothermal method, wherein cerium nitrate hexahydrate (Ce(NO3)3 ·6H2O) was used as cerium sources with the assistance of polyvinylpyrrolidone (PVP) in the ethylene glycol aqueous solution. X‐ray diffraction, X‐ray photoelectron spectra, scanning electron microscope, transmission electron microscope, nitrogen adsorption–desorption and Fourier transform infrared results indicate that PVP can improve the dispersion and control the morphology and sizes of CeO2 hollow nanospheres as a surfactant, and the internal diameter of CeO2 hollow nanosphere gradually increases with reaction time. Based on the time‐dependent experiment, the formation mechanism was proposed and discussed. These CeO2 hollow nanospheres show an excellent adsorption rate of heavy metal ions for Cr(VI) and the adsorption rate is about 70%. The CeO2 hollow nanospheres also had exhibited superior performance in the degradation of methyl orange dye.
Risk and Benefits of Statins in Glucose Control Management of Type II Diabetes
Authors: Sunjaya Angela , Halim Samuel , Ferdinal Frans , Sunjaya Anthony 
Published: February 2016

AbstractWorldwide statins are considered to be the first-line pharmacological treatment for dyslipidemia and reducing the risk of coronary heart disease. However, recently various studies have shown its adverse effect on glucose control among diabetic patients and the U.S. Food and Drug Administration have revised statin drug labels to include information that increases in fasting serum glucose and glycated hemoglobin levels have been reported. This systematic review objective is to evaluate the risks and benefits of statins in glucose control management of type 2 diabetes patients based on the 44 published journal articles included and obtained through MEDLINE full text, PubMed, Science Direct, Pro Quest, SAGE, Taylor and Francis Online, Google Scholar, High Wire, and Elsevier Clinical Key. Statins were found to affect glucose control through several ways, namely, by affecting insulin production and secretion by β-pancreatic cells, insulin resistance, insulin uptake by the muscles and adipocytes and production of adipokines. Current evidence available shows that most of the statins give unfavorable side effects with regards to glucose control among diabetic patients. A dose-dependent and time-dependent effect was also observed in some statins which may be present among other statins as well.
ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling
Authors: Karampelias Michael , Neyt Pia , De Groeve Steven , Aesaert Stijn , Coussens Griet , Rolčík Jakub , Bruno Leonardo , De Winne Nancy , Van Minnebruggen Annemie , Van Montagu Marc , Ponce María Rosa , Micol José Luis , Friml Jiří , De Jaeger Geert , Van Lijsebettens Mieke 
Published: February 2016

Significance
PIN-FORMED (PIN) proteins actively transport the plant hormone auxin, of which the directionality, referred to as polarity, steers developmental processes throughout the plant’s lifecycle. The polarity of the PIN localization at the cell membrane is regulated by protein complexes, implying temporary internalization in the cell through vesicles and changes in the activity state. We identified the ROTUNDA3 protein as a regulator of the protein phosphatase 2A-driven PIN recycling and revealed its importance in auxin transport-related plant developmental programs.
How bad can a good enough parent be?
Authors: Shields Liam 
Published: February 2016

AbstractAlmost everyone accepts that parents must provide a good enough upbringing in order to retain custodial rights over children, but little has been said about how that level should be set. In this paper, I examine ways of specifying a good enough upbringing. I argue that the two dominant ways of setting this level, the Best Interests and Abuse and Neglect Views, are mistaken. I defend the Dual Comparative View, which holds that an upbringing is good enough when shortfalls from the best alternative upbringing in terms of the child's interests are no more significant than the parents' interest.
On nodal domains in Euclidean balls
Authors: Helffer Bernard , Sundqvist Mikael 
Published: February 2016

Å. Pleijel (1956) has proved that in the case of the Laplacian with Dirichlet condition, the equality in the Courant nodal theorem (Courant sharp situation) can only be true for a finite number of eigenvalues when the dimension is

≥
2

\geq 2

. Recently Polterovich extended the result to the Neumann problem in two dimensions in the case when the boundary is piecewise analytic. A question coming from the theory of spectral minimal partitions has motivated the analysis of the cases when one has equality in Courant’s theorem.

We identify the Courant sharp eigenvalues for the Dirichlet and the Neumann Laplacians in balls in

R

d

\mathbb R^d

,

d
≥
2

d\geq 2

. It is the first result of this type holding in any dimension. The corresponding result for the Dirichlet Laplacian in the disc in

R

2

\mathbb R^2

was obtained by B. Helffer, T. Hoffmann-Ostenhof and S. Terracini.
A note on 𝐿^{𝑝}-bounded point evaluations for polynomials
Authors: Yang Liming 
Published: February 2016

We construct a compact nowhere dense subset

K
K

of the closed unit disk

D

¯

\bar {\mathbb D}

in the complex plane

C

\mathbb C

such that

R
(
K
)
=
C
(
K
)

R(K) = C(K)

and bounded point evaluations for

P
t

(
d
A

|

K

)
,

1
≤
t
>
∞
,

P^t(dA | _K), ~ 1 \le t > \infty ,

is the open unit disk

D

.

\mathbb D.

In fact, there exists

C
=
C
(
t
)
>
0

C=C(t) > 0

such that
\[

∫

D

|

p

|

t

d
A
≤
C

∫
K

|

p

|

t

d
A
,

\ \int _{\mathbb D} |p|^t dA \le C \int _K |p|^t dA,

\]
for

1
≤
t
>
∞

1 \le t > \infty

and all polynomials

p
.

p.
On the dimension of self-affine sets and measures with overlaps
Authors: Bárány Balázs , MichałRams  , Simon Károly 
Published: February 2016

In this paper we consider diagonally affine, planar IFS

Φ
=

\Phi =

{

S
i

(
x
,
y
)

=

(

α
i

x
+

t

i
,
1

,

β
i

y
+

t

i
,
2

)

}

i
=
1

m

\{S_i(x,y)\!=\!(\alpha _ix+t_{i,1},\beta _iy+t_{i,2})\}_{i=1}^m

. Combining the techniques of Hochman and Feng and Hu, we compute the Hausdorff dimension of the self-affine attractor and measures and we give an upper bound for the dimension of the exceptional set of parameters.
Interpreting Weak König’s Lemma using the Arithmetized Completeness Theorem
Authors: Wong Tin Lok 
Published: February 2016

We present a previously unpublished proof of the conservativity of

W
K
L

0

\mathrm {WKL}_0

over

I

Σ
1

\mathrm I\Sigma _1

using the Arithmetized Completeness Theorem, which, in particular, constitutes an

ω
\omega

-interpretation of

W
K
L

0

\mathrm {WKL}_0

in

I

Σ
1

\mathrm I\Sigma _1

. We also show that

W
K
L

0
∗

\mathrm {WKL}_0^*

is interpretable in

I

Δ
0

+

e
x
p

\mathrm I\Delta _0+\mathrm {exp}

.