bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diffusion of /l/-vocalization in Swiss German
Authors: Leemann Adrian , Kolly Marie-José , Werlen Iwar , Britain David , Studer-Joho Dieter 
Published: June 2014

AbstractSeveral western Swiss German dialects roughly grouped around the nation's capital Bern show /l/ > [u] vocalization in various contexts. The spatial boundaries of /l/-vocalization in Swiss German are suspected to have been expanding since being described in theLinguistic Atlas of German-Speaking Switzerlandin the middle of the 20th century. The present study assesses the overall expansion of /l/-vocalization by means of a rapid anonymous survey in 20 urban regional centers situated just beyond the traditional boundaries of /l/-vocalization highlighted by theAtlas. Results show that the expansion of /l/-vocalization mainly progresses in southeasterly, southerly, and westerly directions, but with much less success to the north and northwest, where the equally influential dialectal areas of Basel and Zürich seem to exert opposing influences. Further analysis of the data indicates that somewhat differing constraint hierarchies are at work in the different places to which vocalization has diffused.
Childhood adversities and adolescent depression: A matter of both risk and resilience
Authors: Oldehinkel Albertine J. , Ormel Johan , Verhulst Frank C. , Nederhof Esther 
Published: June 2014

AbstractChildhood adversities have been proposed to modify later stress sensitivity and risk of depressive disorder in several ways: by stress sensitization, stress amplification, and stress inoculation. Combining these models, we hypothesized that childhood adversities would increase risk of early, but not later, onsets of depression (Hypothesis 1). In those without an early onset, childhood adversities were hypothesized to predict a relatively low risk of depression in high-stress conditions (Hypothesis 2a) and a relatively high risk of depression in low-stress conditions (Hypothesis 2b), compared to no childhood adversities. These hypotheses were tested in 1,584 participants of the Tracking Adolescents' Individual Lives Survey, a prospective cohort study of adolescents. Childhood adversities were assessed retrospectively at ages 11 and 13.5, using self-reports and parent reports. Lifetime DSM-IV major depressive episodes were assessed at age 19, by means of the Composite International Diagnostic Interview. Stressful life events during adolescence were established using interview-based contextual ratings of personal and network events. The results provided support for all hypotheses, regardless of the informant and timeframe used to assess childhood adversities and regardless of the nature (personal vs. network, dependent vs. independent) of recent stressful events. These findings suggest that age at first onset of depression may be an effective marker to distinguish between various types of reaction patterns.
FROM SEPARABLE POLYNOMIALS TO NONEXISTENCE OF RATIONAL POINTS ON CERTAIN HYPERELLIPTIC CURVES
Authors: DONG QUAN NGUYEN NGOC 
Published: June 2014

AbstractWe give a separability criterion for the polynomials of the form$$\begin{equation*} ax^{2n + 2} + (bx^{2m} + c)(d x^{2k} + e). \end{equation*}$$Using this separability criterion, we prove a sufficient condition using the Brauer–Manin obstruction under which curves of the form$$\begin{equation*} z^2 = ax^{2n + 2} + (bx^{2m} + c)(d x^{2k} + e) \end{equation*}$$have no rational points. As an illustration, using the sufficient condition, we study the arithmetic of hyperelliptic curves of the above form and show that there are infinitely many curves of the above form that are counterexamples to the Hasse principle explained by the Brauer–Manin obstruction.
CAYLEY SUM GRAPHS OF IDEALS OF A COMMUTATIVE RING
Authors: AFKHAMI M. , BARATI Z. , KHASHYARMANESH K. , PAKNEJAD N. 
Published: June 2014

AbstractLet $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}R$ be a commutative ring, $I(R)$ be the set of all ideals of $R$ and $S$ be a subset of $I^*(R)=I(R)\setminus \{0\}$. We define a Cayley sum digraph of ideals of $R$, denoted by $\overrightarrow{\mathrm{Cay}}^+ (I(R),S)$, as a directed graph whose vertex set is the set $I(R)$ and, for every two distinct vertices $I$ and $J$, there is an arc from $I$ to $J$, denoted by $I\longrightarrow J$, whenever $I+K=J$, for some ideal $K $ in $S$. Also, the Cayley sum graph $ \mathrm{Cay}^+ (I(R), S)$ is an undirected graph whose vertex set is the set $I(R)$ and two distinct vertices $I$ and $J$ are adjacent whenever $I+K=J$ or $J+K=I$, for some ideal $K $ in $ S$. In this paper, we study some basic properties of the graphs $\overrightarrow{\mathrm{Cay}}^+ (I(R),S)$ and $ \mathrm{Cay}^+ (I(R), S)$ such as connectivity, girth and clique number. Moreover, we investigate the planarity, outerplanarity and ring graph of $ \mathrm{Cay}^+ (I(R), S)$ and also we provide some characterization for rings $R$ whose Cayley sum graphs have genus one.
Analysis of high-molecular-weight glutenin subunits in five amphidiploids and their parental diploid speciesAegilops umbellulataandAegilops uniaristata
Authors: Dai Shoufen , Zhao Li , Xue Xiaofei , Jia Yanni , Liu Dengcai , Pu Zongjun , Zheng Youliang , Yan Zehong 
Published: June 2014

Amphidiploids serve as a bridge for transferring genes from wild species into wheat. In this study, five amphidiploids with AABBUU and AABBNN genomes were produced by spontaneous chromosome doubling of unreduced triploid F1gametes from crosses between diploidAegilops(A. umbellulataaccessions CIae 29 and PI 226500, andA. uniaristataaccession PI 554419) and tetraploidTriticum turgidum(ssp.durumcultivar Langdon and ssp.dicoccumaccessions PI 94 668 and PI 349045) species. The composition of high-molecular-weight glutenin subunits (HMW-GS) in these amphidiploids and in their parentalA. umbellulataandA. uniaristataspecies was analysed. As expected, the amphidiploids fromT. turgidumssp.dicoccumaccession PI 944668 or PI 349045 andA. umbellulataaccession CIae 29 or PI 226500 andA. uniaristataaccession PI 554419 showed the same HMW-GS patterns as those of theirAegilopsparents, because HMW-GS genes were all silenced in theT. turgidumssp.dicoccumparents. The amphidiploids from CIae 29 and Langdon inherited all of the HMW-GS genes from their parents except for the Uy type. Using 10 and 15% sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) and 10% urea/SDS–PAGE, 11 Ux and ten Uy types in 16 combinations were observed in 48A. umbellulataaccessions, and two Nx and two Ny types in two combinations were detected in sixA. uniaristataaccessions. These novel HMW-GS variants may provide new genetic resources for improving the quality of wheat.
From the field: Empowering women to improve family food security in Afghanistan
Authors: Wilcox Clair Sophia , Grutzmacher Stephanie , Ramsing Rebecca , Rockler Amanda , Balch Christie , Safi Marghuba , Hanson James 
Published: June 2014

AbstractKitchen gardens may improve family food security and nutrition. While these gardens are the domain of women in Afghanistan, women face unique challenges accessing training and resources to maximize small-scale agricultural output. The University of Maryland's Women in Agriculture Project builds capacity among female extension educators to work with vulnerable women to implement and maintain kitchen gardens. Extension educators use experiential methods to teach vegetable gardening, apiculture, small-scale poultry production, post-harvest handling and processing, nutrition and marketing through workshops, demonstration gardens and farmer field schools. This paper explores contextual factors related to women's food security and agricultural opportunities, describes key project activities and approaches and discusses project success and challenges, sustainability and implications for future programs.
Is ostension any more than attention?
Authors: Szufnarowska Joanna , Rohlfing Katharina J. , Fawcett Christine , Gredebäck Gustaf 
Published: June 2014

AbstractAccording to natural pedagogy theory, infants are sensitive to particular ostensive cues that communicate to them that they are being addressed and that they can expect to learn referential information. We demonstrate that 6-month-old infants follow others' gaze direction in situations that are highly attention-grabbing. This occurs irrespective of whether these situations include communicative intent and ostensive cues (a model looks directly into the child's eyes prior to shifting gaze to an object) or not (a model shivers while looking down prior to shifting gaze to an object). In contrast, in less attention-grabbing contexts in which the model simply looks down prior to shifting gaze to an object, no effect is found. These findings demonstrate that one of the central pillars of natural pedagogy is false. Sensitivity to gaze following in infancy is not restricted to contexts in which ostensive cues are conveyed.
MicroRNA-33b knock-in mice for an intron of sterol regulatory element-binding factor 1 (Srebf1) exhibit reduced HDL-C in vivo
Authors: Horie Takahiro , Nishino Tomohiro , Baba Osamu , Kuwabara Yasuhide , Nakao Tetsushi , Nishiga Masataka , Usami Shunsuke , Izuhara Masayasu , Nakazeki Fumiko , Ide Yuya , Koyama Satoshi , Sowa Naoya , Yahagi Naoya , Shimano Hitoshi , Nakamura Tomoyuki , Hasegawa Koji , Kume Noriaki , Yokode Masayuki , Kita Toru , Kimura Takeshi , Ono Koh 
Published: June 2014

AbstractMicroRNAs (miRs) are small non-protein-coding RNAs that bind to specific mRNAs and inhibit translation or promote mRNA degradation. Recent reports, including ours, indicated that miR-33a located within the intron of sterol regulatory element-binding protein (SREBP) 2 controls cholesterol homeostasis and can be a possible therapeutic target for treating atherosclerosis. Primates, but not rodents, express miR-33b from an intron of SREBF1. Therefore, humanized mice, in which a miR-33b transgene is inserted within a Srebf1 intron, are required to address its function in vivo. We successfully established miR-33b knock-in (KI) mice and found that protein levels of known miR-33a target genes, such as ABCA1, ABCG1 and SREBP-1, were reduced compared with those in wild-type mice. As a consequence, macrophages from the miR-33b KI mice had a reduced cholesterol efflux capacity via apoA-I and HDL-C. Moreover, HDL-C levels were reduced by almost 35% even in miR-33b KI hetero mice compared with the control mice. These results indicate that miR-33b may account for lower HDL-C levels in humans than those in mice and that miR-33b is possibly utilized for a feedback mechanism to regulate its host gene SREBF1. Our mice will also aid in elucidating the roles of miR-33a/b in different genetic disease models.
Synthesis, characterisation and antibacterial effects of sol–gel derived biphasic calcium phosphate nanopowders
Authors: Nazemi Zahra , Haghbin Nazarpak Masoumeh , Mehdikhani‐Nahrkhalaji Mehdi , Staji Hamid , Kalani Mohammad Mehdi 
Published: June 2014

Hydroxyapatite (HA) and β‐tricalcium phosphate (β‐TCP) represent the main types of calcium phosphates used for the reconstruction of bone defects in maxillofacial, dental, orthopaedic and drug delivery applications. The bioactivity and bioresorbability of biphasic calcium phosphate (BCP) ceramics can be controlled by varying the HA/β‐TCP ratio. In this reported work, BCP nanopowders were prepared by a simple sol–gel method, in which Ca(NO3)2 · 4H2O and P2O5 were used as precursors for calcium and phosphate, respectively. The different phase ratios of HA/β‐TCP were obtained by changing the sintering temperature. X‐ray diffraction, inductive coupled plasma‐atomic emission spectroscopy, scanning electron microscopy, transmission electron microscopy and Fourier transformer infrared spectrophotometer results have shown that increasing the sintering temperature could cause more decomposition of HA into β‐TCP. Moreover, the size of the prepared nanoparticles was measured between 10 and 500 nm. Finally, the antibacterial activity was studied using Escherichia coli (ATCC 25922) as the Gram‐negative bacteria. The antibacterial effect of the BCP sample with 50% HA–50%β‐TCP phase ratio was tested at concentrations of 100, 200 and 300 mg/ml. The results showed bacterial growth reduction at a concentration of 300 mg/ml, which makes it a good candidate for the treatment of bone defects.
Enhanced electroluminescence of all‐inorganic colloidal quantum dot light‐emitting diode by optimising the MoO3 intermediate layer
Authors: Tang Liyuan , Zhao Junliang , Zhang Xiaoli , Dai Haitao , Sun Xiaowei 
Published: June 2014

The effects of the molybdenum trioxide (MoO3) intermediate layer on the performance of all‐inorganic colloidal quantum dot light‐emitting diodes (QD‐LEDs) with a structure of ITO/MoO3/NiO/QDs/ZnO/Al are explored. MoO3 layers with different thickness were inserted between the indium tin oxide and nickel oxide layer via a thermal evaporation process. The presented results show that an ultrathin (∼ 5 nm) MoO3 intermediate layer significantly enhanced the electroluminescence (EL) intensity of the QD‐LED, which was more than 100 times higher than the device without the MoO3 layer. It is suggested that the EL enhancement originates from the effectively facilitated injection of holes into quantum dots through the MoO3 intermediate layer.
Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens
Authors: Jin Chunyu , Yang Liuqing , Xie Min , Lin Chunru , Merkurjev Daria , Yang Joy C. , Tanasa Bogdan , Oh Soohwan , Zhang Jie , Ohgi Kenneth A. , Zhou Hongyan , Li Wenbo , Evans Christopher P. , Ding Sheng , Rosenfeld Michael G. 
Published: June 2014

Significance
The emergence of powerful new chemical library-screening approaches and the generation of new types of chemical structures makes novel methods available to link candidate chemicals to potential target genes, e.g., as in the interaction with and effects on chromatin-bound targets. Here we report a method that can provide the genome-wide location of a candidate drug. One such synthetic chemical, SD70—first identified in a screen for inhibitors of tumor translocation events—was resynthesized with a tag permitting a ChIP-sequencing–like analysis, referred to as “Chemical affinity capture and massively parallel DNA sequencing (Chem-seq).” As a consequence of finding its recruitment on androgen receptor-bound functional enhancers, we were able to demonstrate that SD70 could inhibit the prostate cancer cell transcriptional program, in part by inhibition of the demethylase KDM4C.
Characterization of the xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus)
Authors: Fujii Tatsuya , Inoue Hiroyuki , Ishikawa Kazuhiko 
Published: June 2014

Abstract
We cloned a putative Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) xlnR gene and isolated a xlnR disruptant strain. XlnR protein was localized in the nucleus. Xylanase production by the xlnR disruptant was lower than in the control strain at both the enzyme and transcriptional level. These data suggest that the XlnR protein regulates xylanase production in T. cellulolyticus.
Properness of associated minimal surfaces
Authors: Alarcón Antonio , López Francisco 
Published: June 2014

For any open Riemann surface

N

\mathcal {N}

and finite subset

Z

⊂

S

1

=
{
z
∈

C

|

|

z

|

=
1
}
,

\mathfrak {Z}\subset \mathbb {S}^1=\{z\in \mathbb {C}\,|\;|z|=1\},

there exist an infinite closed set

Z

N

⊂

S

1

\mathfrak {Z}_{\mathcal {N}} \subset \mathbb {S}^1

containing

Z

\mathfrak {Z}

and a null holomorphic curve

F
=
(

F
j

)

j
=
1
,
2
,
3

:

N

→

C

3

F=(F_j)_{j=1,2,3}:\mathcal {N}\to \mathbb {C}^3

such that the map
\[

Y

:

Z

N

×

N

→

R

2

,

Y

(

v

,
P
)
=

Re

(

v

(

F
1

,

F
2

)
(
P
)

)

,

\mathfrak {Y}:\mathfrak {Z}_{\mathcal {N}}\times \mathcal {N} \to \mathbb {R}^2,\quad \mathfrak {Y}(\mathfrak {v},P)=\textrm {Re}\big (\mathfrak {v} (F_1,F_2)(P)\big ),

\]
is proper.

In particular,

Re

(

v

F

)

:

N

→

R

3

\textrm {Re}\big (\mathfrak {v} F\big ):\mathcal {N} \to \mathbb {R}^3

is a proper conformal minimal immersion properly projecting into

R

2

≡

R

2

×
{
0
}
⊂

R

3

,

\mathbb {R}^2\equiv \mathbb {R}^2\times \{0\} \subset \mathbb {R}^3,

for all

v

∈

Z

N

.

\mathfrak {v} \in \mathfrak {Z}_{\mathcal {N}}.
Large scale analysis of signal reachability
Authors: Todor Andrei , Gabr Haitham , Dobra Alin , Kahveci Tamer 
Published: June 2014

Abstract
Motivation: Major disorders, such as leukemia, have been shown to alter the transcription of genes. Understanding how gene regulation is affected by such aberrations is of utmost importance. One promising strategy toward this objective is to compute whether signals can reach to the transcription factors through the transcription regulatory network (TRN). Due to the uncertainty of the regulatory interactions, this is a #P-complete problem and thus solving it for very large TRNs remains to be a challenge.
Results: We develop a novel and scalable method to compute the probability that a signal originating at any given set of source genes can arrive at any given set of target genes (i.e., transcription factors) when the topology of the underlying signaling network is uncertain. Our method tackles this problem for large networks while providing a provably accurate result. Our method follows a divide-and-conquer strategy. We break down the given network into a sequence of non-overlapping subnetworks such that reachability can be computed autonomously and sequentially on each subnetwork. We represent each interaction using a small polynomial. The product of these polynomials express different scenarios when a signal can or cannot reach to target genes from the source genes. We introduce polynomial collapsing operators for each subnetwork. These operators reduce the size of the resulting polynomial and thus the computational complexity dramatically. We show that our method scales to entire human regulatory networks in only seconds, while the existing methods fail beyond a few tens of genes and interactions. We demonstrate that our method can successfully characterize key reachability characteristics of the entire transcriptions regulatory networks of patients affected by eight different subtypes of leukemia, as well as those from healthy control samples.
Availability: All the datasets and code used in this article are available at bioinformatics.cise.ufl.edu/PReach/scalable.htm.
Contact: atodor@cise.ufl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
Authors: Cao Mengfei , Pietras Christopher M. , Feng Xian , Doroschak Kathryn J. , Schaffner Thomas , Park Jisoo , Zhang Hao , Cowen Lenore J. , Hescott Benjamin J. 
Published: June 2014

Abstract
Motivation: It has long been hypothesized that incorporating models of network noise as well as edge directions and known pathway information into the representation of protein–protein interaction (PPI) networks might improve their utility for functional inference. However, a simple way to do this has not been obvious. We find that diffusion state distance (DSD), our recent diffusion-based metric for measuring dissimilarity in PPI networks, has natural extensions that incorporate confidence, directions and can even express coherent pathways by calculating DSD on an augmented graph.
Results: We define three incremental versions of DSD which we term cDSD, caDSD and capDSD, where the capDSD matrix incorporates confidence, known directed edges, and pathways into the measure of how similar each pair of nodes is according to the structure of the PPI network. We test four popular function prediction methods (majority vote, weighted majority vote, multi-way cut and functional flow) using these different matrices on the Baker’s yeast PPI network in cross-validation. The best performing method is weighted majority vote using capDSD. We then test the performance of our augmented DSD methods on an integrated heterogeneous set of protein association edges from the STRING database. The superior performance of capDSD in this context confirms that treating the pathways as probabilistic units is more powerful than simply incorporating pathway edges independently into the network.
Availability: All source code for calculating the confidences, for extracting pathway information from KEGG XML files, and for calculating the cDSD, caDSD and capDSD matrices are available from http://dsd.cs.tufts.edu/capdsd
Contact: lenore.cowen@tufts.edu or benjamin.hescott@tufts.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated detection and tracking of many cells by using 4D live-cell imaging data
Authors: Tokunaga Terumasa , Hirose Osamu , Kawaguchi Shotaro , Toyoshima Yu , Teramoto Takayuki , Ikebata Hisaki , Kuge Sayuri , Ishihara Takeshi , Iino Yuichi , Yoshida Ryo 
Published: June 2014

Abstract
Motivation: Automated fluorescence microscopes produce massive amounts of images observing cells, often in four dimensions of space and time. This study addresses two tasks of time-lapse imaging analyses; detection and tracking of the many imaged cells, and it is especially intended for 4D live-cell imaging of neuronal nuclei of Caenorhabditis elegans. The cells of interest appear as slightly deformed ellipsoidal forms. They are densely distributed, and move rapidly in a series of 3D images. Thus, existing tracking methods often fail because more than one tracker will follow the same target or a tracker transits from one to other of different targets during rapid moves.
Results: The present method begins by performing the kernel density estimation in order to convert each 3D image into a smooth, continuous function. The cell bodies in the image are assumed to lie in the regions near the multiple local maxima of the density function. The tasks of detecting and tracking the cells are then addressed with two hill-climbing algorithms. The positions of the trackers are initialized by applying the cell-detection method to an image in the first frame. The tracking method keeps attacking them to near the local maxima in each subsequent image. To prevent the tracker from following multiple cells, we use a Markov random field (MRF) to model the spatial and temporal covariation of the cells and to maximize the image forces and the MRF-induced constraint on the trackers. The tracking procedure is demonstrated with dynamic 3D images that each contain &gt;100 neurons of C.elegans.
Availability: http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014
Supplementary information: Supplementary data are available at http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014
Contact: yoshidar@ism.ac.jp