bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities
Authors: Morrison-Whittle Peter , Goddard Matthew R 
Published: March 2015

AbstractWe have a limited understanding of the relative contributions of different processes that regulate microbial communities, which are crucial components of both natural and agricultural ecosystems. The contributions of selective and neutral processes in defining community composition are often confounded in field studies because as one moves through space, environments also change. Managed ecosystems provide an excellent opportunity to control for this and evaluate the relative strength of these processes by minimising differences between comparable niches separated at different geographic scales. We use next-generation sequencing to characterize the variance in fungal communities inhabiting adjacent fruit, soil and bark in comparable vineyards across 1000 kms in New Zealand. By compartmentalizing community variation, we reveal that niche explains at least four times more community variance than geographic location. We go beyond merely demonstrating that different communities are found in both different niches and locations by quantifying the forces that define these patterns. Overall, selection unsurprisingly predominantly shapes these microbial communities, but we show the balance of neutral processes also have a significant role in defining community assemblage in eukaryotic microbes.
Photonic crystals cause active colour change in chameleons
Authors: Teyssier Jérémie , Saenko Suzanne V. , van der Marel Dirk , Milinkovitch Michel C. 
Published: March 2015

AbstractMany chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection.
Analog time-reversed ultrasonically encoded light focusing inside scattering media with a 33,000× optical power gain
Authors: Ma Cheng , Xu Xiao , Wang Lihong V. 
Published: March 2015

AbstractRecent breakthrough in wavefront engineering shows great promises in controlling light propagation inside scattering media. At present, the digital approaches enjoy high gain, while their speeds are slow because of high data throughputs. In contrast, the analog approaches are intrinsically fast but suffer from poor efficiencies and small gains. Further improvements in both speed and gain are necessary to advance the existing technologies toward real-world applications. Here, we report analog time-reversal of acousto-optically tagged photons with a flux amplification of over 33,000 times (45 dB) at a target location inside scattering media. Such a substantial power gain enhancement is achieved when the temporal width of the time-reversed photon packet is squeezed below the carrier-recombination-limited hologram decay time in a photorefractive crystal. Despite a focusing energy gain below unity, the unprecedented power gain is expected to enable new optical imaging, sensing, manipulation and treatment applications.
Paliperidone and aripiprazole differentially affect the strength of calcium-secretion coupling in female pituitary lactotrophs
Authors: Kucka Marek , Tomić Melanija , Bjelobaba Ivana , Stojilkovic Stanko S. , Budimirovic Dejan B. 
Published: March 2015

AbstractHyperprolactinemia is a common adverse in vivo effect of antipsychotic medications that are used in the treatment of patients with schizophrenia. Here, we compared the effects of two atypical antipsychotics, paliperidone and aripiprazole, on cAMP/calcium signaling and prolactin release in female rat pituitary lactotrophs in vitro. Dopamine inhibited spontaneous cAMP/calcium signaling and prolactin release. In the presence of dopamine, paliperidone rescued cAMP/calcium signaling and prolactin release in a concentration-dependent manner, whereas aripiprazole was only partially effective. In the absence of dopamine, paliperidone stimulated cAMP/calcium signaling and prolactin release, whereas aripiprazole inhibited signaling and secretion more potently but less effectively than dopamine. Forskolin-stimulated cAMP production was facilitated by paliperidone and inhibited by aripiprazole, although the latter was not as effective as dopamine. None of the compounds affected prolactin transcript activity, intracellular prolactin accumulation, or growth hormone secretion. These data indicate that paliperidone has dual hyperprolactinemic actions in lactotrophs i) by preserving the coupling of spontaneous electrical activity and prolactin secretion in the presence of dopamine and ii) by inhibiting intrinsic dopamine receptor activity in the absence of dopamine, leading to enhanced calcium signaling and secretion. In contrast, aripiprazole acts on prolactin secretion by attenuating, but not abolishing, calcium-secretion coupling.
Metformin and salicylate synergistically activate liver AMPK, inhibit lipogenesis and improve insulin sensitivity
Authors: Ford Rebecca J. , Fullerton Morgan D. , Pinkosky Stephen L. , Day Emily A. , Scott John W. , Oakhill Jonathan S. , Bujak Adam L. , Smith Brennan K. , Crane Justin D. , Blümer Regje M. , Marcinko Katarina , Kemp Bruce E. , Gerstein Hertzel C. , Steinberg Gregory R. 
Published: March 2015

Metformin is the mainstay therapy for type 2 diabetes (T2D) and many patients also take salicylate-based drugs [i.e., aspirin (ASA)] for cardioprotection. Metformin and salicylate both increase AMP-activated protein kinase (AMPK) activity but by distinct mechanisms, with metformin altering cellular adenylate charge (increasing AMP) and salicylate interacting directly at the AMPK β1 drug-binding site. AMPK activation by both drugs results in phosphorylation of ACC (acetyl-CoA carboxylase; P-ACC) and inhibition of acetyl-CoA carboxylase (ACC), the rate limiting enzyme controlling fatty acid synthesis (lipogenesis). We find doses of metformin and salicylate used clinically synergistically activate AMPK in vitro and in vivo, resulting in reduced liver lipogenesis, lower liver lipid levels and improved insulin sensitivity in mice. Synergism occurs in cell-free assays and is specific for the AMPK β1 subunit. These effects are also observed in primary human hepatocytes and patients with dysglycaemia exhibit additional improvements in a marker of insulin resistance (proinsulin) when treated with ASA and metformin compared with either drug alone. These data indicate that metformin–salicylate combination therapy may be efficacious for the treatment of non-alcoholic fatty liver disease (NAFLD) and T2D.
Basic fibroblast growth factor induces VEGF expression in chondrosarcoma cells and subsequently promotes endothelial progenitor cell-primed angiogenesis
Authors: Tzeng Huey-En , Chen Po-Chun , Lin Kai-Wei , Lin Chih-Yang , Tsai Chun-Hao , Han Shao-Min , Teng Chieh-Lin , Hwang Wen-Li , Wang Shih-Wei , Tang Chih-Hsin 
Published: March 2015

Chondrosarcoma, a common malignant tumour, develops in bone. Effective adjuvant therapy remains inadequate for treatment, meaning poor prognosis. It is imperative to explore novel remedies. Angiogenesis is a rate-limiting step in progression that explains neovessel formation for blood supply in the tumour microenvironment. Numerous studies indicate that EPCs (endothelial progenitor cells) promote angiogenesis and contribute to tumour growth. bFGF (basic fibroblast growth factor), a secreted cytokine, regulates biological activity, including angiogenesis, and correlates with tumorigenesis. However, the role of bFGF in angiogenesis-related tumour progression by recruiting EPCs in human chondrosarcoma is rarely discussed. In the present study, we found that bFGF induced VEGF (vascular endothelial growth factor) expression via the FGFR1 (fibroblast growth factor receptor 1)/c-Src/p38/NF-κB (nuclear factor κB) signalling pathway in chondrosarcoma cells, thereby triggering angiogenesis of endothelial progenitor cells. Our in vivo data revealed that tumour-secreted bFGF promotes angiogenesis in both mouse plug and chick CAM (chorioallantoic membrane) assays. Xenograft mouse model data, due to bFGF-regulated angiogenesis, showed the bFGF regulates angiogenesis-linked tumour growth. Finally, bFGF was highly expressed in chondrosarcoma patients compared with normal cartilage, positively correlating with VEGF expression and tumour stage. The present study reveals a novel therapeutic target for chondrosarcoma progression.
Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian
Authors: Yin Zongjun , Zhu Maoyan , Davidson Eric H. , Bottjer David J. , Zhao Fangchen , Tafforeau Paul 
Published: March 2015

SignificancePhylogenomic extrapolations indicate the last common ancestor of sponges and eumetazoans existed deep in the Cryogenian, perhaps 200 million years (Myr) before the Cambrian (541 Ma). This inference implies a long Precambrian history of animals phylogenetically allied with sponges. However, there is yet little unequivocal paleontological evidence of Precambrian sponges. Here, we present a newly discovered 600-Myr-old fossil preserved at cellular resolution, displaying multiple poriferan features. The animal was covered with a dense layer of flattened cells resembling sponge pinacocytes, displaying a hollow tubular structure with apparent water inflow and outflow orifices. Although requiring additional specimens of similar form for confirmation, this finding is consistent with phylogenomic inference, and implies the presence of eumetazoan ancestors by 60 Myr before the Cambrian.
The effects of reputational and social knowledge on cooperation
Authors: Gallo Edoardo , Yan Chang 
Published: March 2015

Significance
Cooperation is essential for societies to prosper. Recent experiments show that cooperation emerges in dynamic networks in which subjects can select their connections. However, these studies fixed the amount of reputation information available and did not display the network to subjects. Here, we systematically vary the knowledge available to subjects about reputation and the network to investigate experimentally their roles in determining cooperation in dynamic networks. Common knowledge about everyone’s reputation is the main driver of cooperation leading to dense and clustered networks. The addition of common knowledge about the network affects the distribution of cooperative activity: cooperators form a separate community and achieve a higher payoff from within-community interactions than members of the less cooperative community.
MiR-2 family regulates insect metamorphosis by controlling the juvenile hormone signaling pathway
Authors: Lozano Jesus , Montañez Raúl , Belles Xavier 
Published: March 2015

SignificanceMicroRNAs are short, single-stranded RNAs that bind to target mRNAs and block their translation. Five years ago we observed in the cockroachBlattella germanicathat general depletion of microRNAs prevents metamorphosis. This observation led to two key questions: Which microRNAs are involved in this action, and which target do they act on? The results reported herein show that the microRNAs involved are those of an miR-2 family (miR-2, miR-13a, and miR-13b), and the target is the transcription factor Krüppel homolog 1, a master repressor of insect metamorphosis. The data presented indicate that miR-2 microRNAs rapidly clear Krüppel homolog 1 transcripts in the last nymphal instar, a process that is crucial for proper metamorphosis. This reveals the elegant mechanism of an miRNA family leading metamorphosis to its correct conclusion.
Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean
Authors: Schroeder Hannes , Ávila-Arcos María C. , Malaspinas Anna-Sapfo , Poznik G. David , Sandoval-Velasco Marcela , Carpenter Meredith L. , Moreno-Mayar José Víctor , Sikora Martin , Johnson Philip L. F. , Allentoft Morten Erik , Samaniego José Alfredo , Haviser Jay B. , Dee Michael W. , Stafford Thomas W. , Salas Antonio , Orlando Ludovic , Willerslev Eske , Bustamante Carlos D. , Gilbert M. Thomas P. 
Published: March 2015

Significance
The transatlantic slave trade resulted in the forced movement of over 12 million Africans to the Americas. Although many coastal shipping points are known, they do not necessarily reflect the slaves’ actual ethnic or geographic origins. We obtained genome-wide data from 17th-century remains of three enslaved individuals who died on the Caribbean island of Saint Martin and use them to identify their genetic origins in Africa, with far greater precision than previously thought possible. The study demonstrates that genomic data can be used to trace the genetic ancestry of long-dead individuals, a finding that has important implications for archeology, especially in cases where historical information is missing.
Quantitative modeling of transcription factor binding specificities using DNA shape
Authors: Zhou Tianyin , Shen Ning , Yang Lin , Abe Namiko , Horton John , Mann Richard S. , Bussemaker Harmen J. , Gordân Raluca , Rohs Remo 
Published: March 2015

Significance
Genomes provide an abundance of putative binding sites for each transcription factor (TF). However, only small subsets of these potential targets are functional. TFs of the same protein family bind to target sites that are very similar but not identical. This distinction allows closely related TFs to regulate different genes and thus execute distinct functions. Because the nucleotide sequence of the core motif is often not sufficient for identifying a genomic target, we refined the description of TF binding sites by introducing a combination of DNA sequence and shape features, which consistently improved the modeling of in vitro TF−DNA binding specificities. Although additional factors affect TF binding in vivo, shape-augmented models reveal binding specificity mechanisms that are not apparent from sequence alone.
Reduced fitness in progeny from old parents in a natural population
Authors: Schroeder Julia , Nakagawa Shinichi , Rees Mark , Mannarelli Maria-Elena , Burke Terry 
Published: March 2015

Significance
As parents age, gamete quality declines. If this decline affects the next generation, it could influence the evolution of longevity. Older parents often produce offspring of low fitness in the laboratory. Our long-term data from a natural bird population shows, for the first time to our knowledge, a transgenerational reduction in fitness of the next generation associated with parental age. We use a 10-year cross-fostering experiment to exclude environmental explanations. Our results challenge the currently favored hypothesis in evolutionary biology and behavioral ecology that old age signals high quality in mating partners. Our results imply a substantial cost of reproducing with older, rather than younger, partners. The results inform increasing concern about delayed reproduction in medicine, sociology, and conservation biology.
Computational protein design enables a novel one-carbon assimilation pathway
Authors: Siegel Justin B. , Smith Amanda Lee , Poust Sean , Wargacki Adam J. , Bar-Even Arren , Louw Catherine , Shen Betty W. , Eiben Christopher B. , Tran Huu M. , Noor Elad , Gallaher Jasmine L. , Bale Jacob , Yoshikuni Yasuo , Gelb Michael H. , Keasling Jay D. , Stoddard Barry L. , Lidstrom Mary E. , Baker David 
Published: March 2015

Significance
This paper describes the development of a computationally designed enzyme that is the cornerstone of a novel metabolic pathway. This enzyme, formolase, performs a carboligation reaction, directly fixing one-carbon units into three-carbon units that feed into central metabolism. By combining formolase with several naturally occurring enzymes, we created a new carbon fixation pathway, the formolase pathway, which assimilates one-carbon units via formate. Unlike native carbon fixation pathways, this pathway is linear, not oxygen sensitive, and consists of a small number of thermodynamically favorable steps. We demonstrate in vitro pathway function as a proof of principle of how protein design in a pathway context can lead to new efficient metabolic pathways.
Facilitation of fear extinction by novelty depends on dopamine acting on D1-subtype dopamine receptors in hippocampus
Authors: Menezes Jefferson , Alves Niége , Borges Sidnei , Roehrs Rafael , de Carvalho Myskiw Jociane , Furini Cristiane Regina Guerino , Izquierdo Ivan , Mello-Carpes Pâmela B. 
Published: March 2015

Significance
A brief exposure to a novel environment was recently shown to enhance the extinction of contextual fear probably through a protein synthesis-dependent process of synaptic tagging and capture in the hippocampus. Here we report that this finding can be generalized to the extinction of another fear-motivated task, one-trial inhibitory avoidance. This generalization is important because extinction is used in exposure therapy to treat posttraumatic stress disorder in humans, and this may derive from various forms of fear-related stress. In addition, here we show that the effect of novelty on fear extinction is dependent on dopamine D1 but not D5 receptors in the hippocampus. These findings could be applicable to the exposure therapy of fear memory disorders.
Human Ebola virus infection results in substantial immune activation
Authors: McElroy Anita K. , Akondy Rama S. , Davis Carl W. , Ellebedy Ali H. , Mehta Aneesh K. , Kraft Colleen S. , Lyon G. Marshall , Ribner Bruce S. , Varkey Jay , Sidney John , Sette Alessandro , Campbell Shelley , Ströher Ute , Damon Inger , Nichol Stuart T. , Spiropoulou Christina F. , Ahmed Rafi 
Published: March 2015

Significance
In 2014, Ebola virus became a household term. The ongoing outbreak in West Africa is the largest Ebola virus outbreak ever recorded, with over 20,000 cases and over 8,000 deaths to date. Very little is known about the human cellular immune response to Ebola virus infection, and this lack of knowledge has hindered development of effective therapies and vaccines. In this study, we characterize the human immune response to Ebola virus infection in four patients. We define the kinetics of T- and B-cell activation, and determine which viral proteins are targets of the Ebola virus-specific T-cell response in humans.
Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions
Authors: Ji Xiong , Dadon Daniel B. , Abraham Brian J. , Lee Tong Ihn , Jaenisch Rudolf , Bradner James E. , Young Richard A. 
Published: March 2015

Significance
More than a thousand proteins are thought to contribute to mammalian chromatin and its regulation, but our understanding of the genomic occupancy and function of most of these proteins is limited. We have used a chromatin proteomic profiling approach to produce a catalogue of proteins associated with genomic regions whose chromatin is marked by specific modified histones. A substantial number of the newly identified proteins are associated with human disease. Future chromatin proteomic profiling studies should prove valuable for identifying additional chromatin-associated proteins in a broad spectrum of cell types.
Identification and characterization of the diuretic hormone 31 receptor in the silkwormBombyx mori
Authors: Iga Masatoshi , Kataoka Hiroshi 
Published: March 2015

AbstractThe receptor for diuretic hormone 31 (DH31R) was identified in the silkworm Bombyx mori. A heterologous expression system revealed that an orphan G-protein coupled receptor, BNGR-B1, responded to DH31 and upregulated the intracellular cAMP level. DH31R (BNGR-B1) was predominantly expressed in the anterior silk gland, midgut, and ovary, whereas DH31 was predominantly expressed in the central nervous system and midgut.
Orthogonal polynomials with respect to a family of Sobolev inner products on the unit circle
Authors: Ranga A. 
Published: March 2015

The principal objective here is to look at some algebraic properties of the orthogonal polynomials

Ψ
n

(
b
,
s
,
t
)

\Psi _n^{(b,s,t)}

with respect to the Sobolev inner product on the unit circle
\[

⟨
f
,
g

⟩

S

(
b
,
s
,
t
)

=
(
1
−
t
)

⟨
f
,
g

⟩

μ

(
b
)

+
t

f
(
1
)

¯

g
(
1
)
+
s

⟨

f

′

,

g

′

⟩

μ

(
b
+
1
)

,

\langle f,g\rangle _{S^{(b,s,t)}} = (1-t)\, \langle f,g\rangle _{\mu ^{(b)}} + t\, \overline {f(1)}\,g(1) + s\, \langle f^{\prime },g^{\prime }\rangle _{\mu ^{(b+1)}},

\]
where

⟨
f
,
g

⟩

μ

(
b
)

=

τ
(
b
)

2
π

∫

0

2
π

f
(

e

i
θ

)

¯

g
(

e

i
θ

)

(

e

π
−
θ

)

I

m
(
b
)

(

sin

2

⁡
(
θ

/

2
)

)

R

e
(
b
)

d
θ
.

\langle f,g\rangle _{\mu ^{(b)}} = \frac {\tau (b)}{2\pi } \int _{0}^{2\pi }\overline {f(e^{i\theta })} \,g(e^{i\theta })\,(e^{\pi -\theta })^{\mathcal {I}m(b)} (\sin ^{2}(\theta /2))^{\mathcal {R}e(b)} d\theta .

Here,

R

e
(
b
)
>
−
1

/

2

\mathcal {R}e(b) > -1/2

,

0
≤
t
>
1

0 \leq t > 1

,

s
>
0

s > 0

and

τ
(
b
)

\tau (b)

is taken to be such that

⟨
1
,
1

⟩

μ

(
b
)

=
1

\langle 1,1\rangle _{\mu ^{(b)}} = 1

. We show that, for example, the monic Sobolev orthogonal polynomials

Ψ
n

(
b
,
s
,
t
)

\Psi _n^{(b,s,t)}

satisfy the recurrence

Ψ
n

(
b
,
s
,
t
)

(
z
)
−

β
n

(
b
,
s
,
t
)

Ψ

n
−
1

(
b
,
s
,
t
)

(
z
)
=

Φ
n

(
b
,
t
)

(
z
)
,

\Psi _n^{(b,s,t)}(z) - \beta _n^{(b,s,t)} \Psi _{n-1}^{(b,s,t)}(z) = \Phi _n^{(b,t)}(z),

n
≥
1

n \geq 1

, where

Φ
n

(
b
,
t
)

\Phi _n^{(b,t)}

are the monic orthogonal polynomials with respect to the inner product

⟨
f
,
g

⟩

μ

(
b
,
t
)

=
(
1
−
t
)

⟨
f
,
g

⟩

μ

(
b
)

+
t

f
(
1
)

¯

g
(
1
)

\langle f,g\rangle _{\mu ^{(b,t)}} = (1-t)\, \langle f,g\rangle _{\mu ^{(b)}} + t\, \overline {f(1)}\,g(1)

. Some related bounds and asymptotic properties are also given.
Reducing the search space for causal genetic variants with VASP
Authors: Field Matthew A. , Cho Vicky , Cook Matthew C. , Enders Anselm , Vinuesa Carola G. , Whittle Belinda , Andrews T. Daniel , Goodnow Chris C. 
Published: March 2015

Abstract
Motivation: Increasingly, cost-effective high-throughput DNA sequencing technologies are being utilized to sequence human pedigrees to elucidate the genetic cause of a wide variety of human diseases. While numerous tools exist for variant prioritization within a single genome, the ability to concurrently analyze variants within pedigrees remains a challenge, especially should there be no prior indication of the underlying genetic cause of the disease. Here, we present a tool, variant analysis of sequenced pedigrees (VASP), a flexible data integration environment capable of producing a summary of pedigree variation, providing relevant information such as compound heterozygosity, genome phasing and disease inheritance patterns. Designed to aggregate data across a sequenced pedigree, VASP allows both powerful filtering and custom prioritization of both single nucleotide variants (SNVs) and small indels. Hence, clinical and research users with prior knowledge of a disease are able to dramatically reduce the variant search space based on a wide variety of custom prioritization criteria.
Availability and implementation: Source code available for academic non-commercial research purposes at https://github.com/mattmattmattmatt/VASP.
Contact: matt.field@anu.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.