bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of cell-to-cell variability in divergent gene expression
Authors: Yan Chao , Wu Shuyang , Pocetti Christopher , Bai Lu 
Published: March 2016

AbstractCell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically ‘leak’ to the other, causing increased gene expression noise. We propose that the DGPs’ function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs.
The Coral Trait Database, a curated database of trait information for coral species from the global oceans
Authors: Madin Joshua S. , Anderson Kristen D. , Andreasen Magnus Heide , Bridge Tom C.L. , Cairns Stephen D. , Connolly Sean R. , Darling Emily S. , Diaz Marcela , Falster Daniel S. , Franklin Erik C. , Gates Ruth D. , Harmer Aaron M.T. , Hoogenboom Mia O. , Huang Danwei , Keith Sally A. , Kosnik Matthew A. , Kuo Chao-Yang , Lough Janice M. , Lovelock Catherine E. , Luiz Osmar , Martinelli Julieta , Mizerek Toni , Pandolfi John M. , Pochon Xavier , Pratchett Morgan S. , Putnam Hollie M. , Roberts T. Edward , Stat Michael , Wallace Carden C. , Widman Elizabeth , Baird Andrew H. 
Published: March 2016

AbstractTrait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.
Self-healing Characteristics of Collagen Coatings with Respect to Surface Abrasion
Authors: Kim Chang-Lae , Kim Dae-Eun 
Published: March 2016

AbstractA coating based on collagen with self-healing properties was developed for applications in mechanical components that are prone to abrasion due to contact with a counter surface. The inherent swelling behavior of collagen in water was exploited as the fundamental mechanism behind self-healing of a wear scar formed on the surface. The effects of freeze-drying process and water treatment of the collagen coatings on their mechanical and self-healing properties were analyzed. Water was also used as the medium to trigger the self-healing effect of the collagen coatings after the wear test. It was found that collagen coatings without freeze-drying did not demonstrate any self-healing effect whereas the coatings treated by freeze-drying process showed remarkable self-healing effect. Overall, collagen coatings that were freeze-dried and water treated showed the best friction and self-healing properties. Repeated self-healing ability of these coatings with respect to wear scar was also demonstrated. It was also confirmed that the self-healing property of the collagen coating was effective over a relatively wide range of temperature.
Cortical thickness in human V1 associated with central vision loss
Authors: Burge Wesley K. , Griffis Joseph C. , Nenert Rodolphe , Elkhetali Abdurahman , DeCarlo Dawn K. , ver Hoef Lawrence W. , Ross Lesley A. , Visscher Kristina M. 
Published: March 2016

AbstractBetter understanding of the extent and scope of visual cortex plasticity following central vision loss is essential both for clarifying the mechanisms of brain plasticity and for future development of interventions to retain or restore visual function. This study investigated structural differences in primary visual cortex between normally-sighted controls and participants with central vision loss due to macular degeneration (MD). Ten participants with MD and ten age-, gender-, and education-matched controls with normal vision were included. The thickness of primary visual cortex was assessed using T1-weighted anatomical scans, and central and peripheral cortical regions were carefully compared between well-characterized participants with MD and controls. Results suggest that, compared to controls, participants with MD had significantly thinner cortex in typically centrally-responsive primary visual cortex – the region of cortex that normally receives visual input from the damaged area of the retina. Conversely, peripherally-responsive primary visual cortex demonstrated significantly increased cortical thickness relative to controls. These results suggest that central vision loss may give rise to cortical thinning, while in the same group of people, compensatory recruitment of spared peripheral vision may give rise to cortical thickening. This work furthers our understanding of neural plasticity in the context of adult vision loss.
Hepatitis C virus NS5A protein cooperates with phosphatidylinositol 4-kinase IIIα to induce mitochondrial fragmentation
Authors: Siu Gavin Ka Yu , Zhou Fan , Yu Mei Kuen , Zhang Leiliang , Wang Tuanlao , Liang Yongheng , Chen Yangchao , Chan Hsiao Chang , Yu Sidney 
Published: March 2016

AbstractHepatitis C virus (HCV) has long been observed to take advantage of the host mitochondria to support viral replication and assembly. The HCV core protein has been implicated to fragment host mitochondria. In this report, we have discovered that the non-structural protein 5A (NS5A) plays an instructive role in attaching ER with mitochondria, causing mitochondrial fragmentation. Dynamin-related protein 1(Drp1), a host protein essential to mitochondrial membrane fission, does not play a role in NS5A-induced mitochondrial fragmentation. Instead, phosphatidylinositol 4-kinase IIIα (PI4KA), which has been demonstrated to bind to NS5A and is required to support HCV life cycle, is required for NS5A to induce mitochondrial fragmentation. Both NS5A and core are required by HCV to fragment the mitochondria, as inhibiting either of their respective downstream proteins, PI4KA or Drp1, resulted in lengthening of mitochondria tubules in HCVcc-infected cells. By fragmenting the mitochondria, NS5A renders the cells more resistant to mitochondria mediated apoptosis. This finding indicates previously-ignored contribution of NS5A in HCV-induced mitochondria dysfunction.
Different lasers in the treatment of benign prostatic hyperplasia: a network meta-analysis
Authors: Zhang Xingming , Shen Pengfei , He Qiying , Yin Xiaoxue , Chen Zhibin , Gui Haojun , Shu Kunpeng , Tang Qidun , Yang Yaojing , Pan Xiuyi , Wang Jia , Chen Ni , Zeng Hao 
Published: March 2016

AbstractAll available surgical treatments for benign prostatic hyperplasia (BPH) have their individual advantages or disadvantages. However, the lack of head-to-head studies comparing different surgeries makes it unavailable to conduct direct analysis. To compare the efficacy and safety among different lasers and transurethral resection of prostate (TURP) for BPH, randomized controlled trials were searched in MEDLINE, EMBASE, Cochrane library, WHO International Clinical Trial Registration Platform and Clinical Trial.gov by 2015.5; and the effectiveness-, perioperation- and complication-related outcomes were assessed by network meta-analysis. 36 studies involving 3831 patients were included. Holmium laser through resection and enucleation had the best efficacy in maximum flow rate. Thulium laser through vapo-resection was superior in improving international prostate symptom score and holmium laser through enucleation was the best for post-voiding residual volume improvement. Diode laser through vaporization was the rapidest in removing postoperative indwelling catheter, while TURP was the longest. TURP required the longest hospitalization and thulium laser through vapo-resection was relatively shorter. Holmium and thulium lasers seem to be relatively better in surgical efficacy and safety, so that these two lasers might be preferred in selection of optimal laser surgery. Actually, more large-scale and high quality head-to-head RCTs are suggested to validate the conclusions.
Thermally activated charge transport in microbial protein nanowires
Authors: Lampa-Pastirk Sanela , Veazey Joshua P. , Walsh Kathleen A. , Feliciano Gustavo T. , Steidl Rebecca J. , Tessmer Stuart H. , Reguera Gemma 
Published: March 2016

AbstractThe bacterium Geobacter sulfurreducens requires the expression of conductive protein filaments or pili to respire extracellular electron acceptors such as iron oxides and uranium and to wire electroactive biofilms, but the contribution of the protein fiber to charge transport has remained elusive. Here we demonstrate efficient long-range charge transport along individual pili purified free of metal and redox organic cofactors at rates high enough to satisfy the respiratory rates of the cell. Carrier characteristics were within the orders reported for organic semiconductors (mobility) and inorganic nanowires (concentration), and resistivity was within the lower ranges reported for moderately doped silicon nanowires. However, the pilus conductance and the carrier mobility decreased when one of the tyrosines of the predicted axial multistep hopping path was replaced with an alanine. Furthermore, low temperature scanning tunneling microscopy demonstrated the thermal dependence of the differential conductance at the low voltages that operate in biological systems. The results thus provide evidence for thermally activated multistep hopping as the mechanism that allows Geobacter pili to function as protein nanowires between the cell and extracellular electron acceptors.
Residual matrix from different separation techniques impacts exosome biological activity
Authors: Paolini Lucia , Zendrini Andrea , Noto Giuseppe Di , Busatto Sara , Lottini Elisabetta , Radeghieri Annalisa , Dossi Alessandra , Caneschi Andrea , Ricotta Doris , Bergese Paolo 
Published: March 2016

AbstractExosomes are gaining a prominent role in research due to their intriguing biology and several therapeutic opportunities. However, their accurate purification from body fluids and detailed physicochemical characterization remain open issues. We isolated exosomes from serum of patients with Multiple Myeloma by four of the most popular purification methods and assessed the presence of residual contaminants in the preparations through an ad hoc combination of biochemical and biophysical techniques - including Western Blot, colloidal nanoplasmonics, atomic force microscopy (AFM) and scanning helium ion microscopy (HIM). The preparations obtained by iodixanol and sucrose gradients were highly pure. To the contrary, those achieved with limited processing (serial centrifugation or one step precipitation kit) resulted contaminated by a residual matrix, embedding the exosomes. The contaminated preparations showed lower ability to induce NfkB nuclear translocation in endothelial cells with respect to the pure ones, probably because the matrix prevents the interaction and fusion of the exosomes with the cell membrane. These findings suggest that exosome preparation purity must be carefully assessed since it may interfere with exosome biological activity. Contaminants can be reliably probed only by an integrated characterization approach aimed at both the molecular and the colloidal length scales.
Enhancing the Temporal Complexity of Distributed Brain Networks with Patterned Cerebellar Stimulation
Authors: Farzan Faranak , Pascual-Leone Alvaro , Schmahmann Jeremy D. , Halko Mark 
Published: March 2016

AbstractGrowing evidence suggests that sensory, motor, cognitive and affective processes map onto specific, distributed neural networks. Cerebellar subregions are part of these networks, but how the cerebellum is involved in this wide range of brain functions remains poorly understood. It is postulated that the cerebellum contributes a basic role in brain functions, helping to shape the complexity of brain temporal dynamics. We therefore hypothesized that stimulating cerebellar nodes integrated in different networks should have the same impact on the temporal complexity of cortical signals. In healthy humans, we applied intermittent theta burst stimulation (iTBS) to the vermis lobule VII or right lateral cerebellar Crus I/II, subregions that prominently couple to the dorsal-attention/fronto-parietal and default-mode networks, respectively. Cerebellar iTBS increased the complexity of brain signals across multiple time scales in a network-specific manner identified through electroencephalography (EEG). We also demonstrated a region-specific shift in power of cortical oscillations towards higher frequencies consistent with the natural frequencies of targeted cortical areas. Our findings provide a novel mechanism and evidence by which the cerebellum contributes to multiple brain functions: specific cerebellar subregions control the temporal dynamics of the networks they are engaged in.
Shear-coupled grain boundary migration assisted by unusual atomic shuffling
Authors: Niu Liang-Liang , Zhang Ying , Shu Xiaolin , Gao Fei , Jin Shuo , Zhou Hong-Bo , Lu Guang-Hong 
Published: March 2016

AbstractShear-coupled grain boundary (GB) migration can be an efficacious mechanism to accommodate plastic deformation when the grain size of polycrystalline materials goes small. Nevertheless, how this kind of GB motion comes into play at the atomic level has not been fully revealed. Here, we have investigated the shear-coupled migration (SCM) of typical [100] group symmetrical tilt GBs in bcc W using atomistic simulations. Depending on GB character, the SCM is found to proceed via dislocation slipping in the 〈100〉 or 〈110〉 mode with striking shear strength difference between them. We demonstrate that there exists an unusual atomic shuffling along the tilt axis, which greatly assists SCM to operate in the easier 〈110〉 mode instead of the 〈100〉 one. The present results highlight the significant role of GB character in the atomistic SCM process and contribute to the future design and fabrication of high-performance materials in GB engineering.
Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582
Authors: Florea Michael , Reeve Benjamin , Abbott James , Freemont Paul S. , Ellis Tom 
Published: March 2016

AbstractBacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.
Hydrothermal synthesis and electrochemical performance of walnut‐like CoS2 hierarchical structures
Authors: Liu Fusheng , Zhao Hongxiao , Jia Huimin , Zhu Congxu , Li Jing , Zheng Zhi 
Published: March 2016

Walnut‐like CoS2 hierarchical structures were synthesised by a simple hydrothermal method. The crystalline phase and morphology of the products were characterised with X‐ray diffraction and scanning electron microscope, respectively. The results showed that CoS2 prepared by hydrothermal method were hierarchical walnut‐like materials consist of nanoparticles. As an anode material of Li ion batteries (LIBs), reversible capacity of these CoS2 materials reached 132.8 mAh/g after 100 cycles. Due to outstanding electrochemical performance, CoS2 materials can be exploited as a practical anode material for LIBs.
A single membrane-bound enzyme catalyzes the conversion of 2,5-diketo-d-gluconate to 4-keto-d-arabonate in d-glucose oxidative fermentation by Gluconobacter oxydans NBRC 3292
Authors: Tazoe Masaaki , Oishi Hiromi , Kobayashi Setsuko , Hoshino Tatsuo 
Published: March 2016

Abstract
4-Keto-d-arabonate synthase (4KAS), which converts 2,5-diketo-d-gluconate (DKGA) to 4-keto-d-arabonate (4KA) in d-glucose oxidative fermentation by some acetic acid bacteria, was solubilized from the Gluconobacter oxydans NBRC 3292 cytoplasmic membrane, and purified in an electrophoretically homogenous state. A single membrane-bound enzyme was found to catalyze the conversion from DKGA to 4KA. The 92-kDa 4KAS was a homodimeric protein not requiring O2 or a cofactor for the conversion, but was stimulated by Mn2+. N-terminal amino acid sequencing of 4KAS, followed by gene homology search indicated a 1,197-bp open reading frame (ORF), corresponding to the GLS_c04240 locus, GenBank accession No. CP004373, encoding a 398-amino acid protein with a calculated molecular weight of 42,818 Da. An Escherichia coli transformant with the 4kas plasmid exhibited 4KAS activity. Furthermore, overexpressed recombinant 4KAS was purified in an electrophoretically homogenous state and had the same molecular size as the natural enzyme.
Special functions, integral equations and a Riemann-Hilbert problem
Authors: Wong R. , Zhao Yu-Qiu 
Published: March 2016

We consider a pair of special functions,

u
β

u_\beta

and

v
β

v_\beta

, defined respectively as the solutions to the integral equations

u
(
x
)
=
1
+

∫
0
∞

K
(
t
)
u
(
t
)
d
t

t
+
x

and

v
(
x
)
=
1
−

∫
0
∞

K
(
t
)
v
(
t
)
d
t

t
+
x

,

x
∈
[
0
,
∞
)
,

\begin{equation*} u(x)=1+\int ^\infty _0 \frac {K(t) u(t) dt}{t+x} ~~\mbox {and}~~v(x)=1-\int ^\infty _0 \frac { K(t) v(t) dt}{t+x},~~x\in [0, \infty ),\end{equation*}

where

K
(
t
)
=

1
π

exp
⁡

(
−

t
β

sin
⁡

π
β

2

)

sin
⁡

(

t
β

cos
⁡

π
β

2

)

K(t)= \frac {1} \pi \exp \left (- t^\beta \sin \frac {\pi \beta } 2\right )\sin \left ( t^\beta \cos \frac {\pi \beta } 2 \right )

for

β
∈
(
0
,
1
)

\beta \in (0, 1)

. In this note, we establish the existence and uniqueness of

u
β

u_\beta

and

v
β

v_\beta

which are bounded and continuous in

[
0
,
+
∞
)

[0, +\infty )

. Also, we show that a solution to a model Riemann-Hilbert problem in Kriecherbauer and McLaughlin [Int.Math.Res.Not.,1999] can be constructed explicitly in terms of these functions. A preliminary asymptotic study is carried out on the Stokes phenomena of these functions by making use of their connection formulas.

Several open questions are also proposed for a thorough investigation of the analytic and asymptotic properties of the functions

u
β

u_\beta

and

v
β

v_\beta

, and a related new special function

G
β

G_\beta

.
Handle with Care
Authors: Gross Kali Nicole 
Published: March 2016

Abstract
Chapter 1 begins with the discovery of a man’s disembodied torso next to a pound in Eddington, Pennsylvania—a town just outside of Philadelphia. It then traces the investigation by exploring the fascination, anxiety, and difficulty that arise as citizens and investigators alike grapple with shifting notions of race particularly as the torso’s complexion is such that few can definitively identify its race. This chapter also examines how that racial ambiguity shapes the investigation. In doing so, it delves into efforts to redefine and reform white supremacy in absence of enslavement and amid increased ethnic European immigration and it explores the role that the race-science of the period plays therein.
A Most Revolting Deed
Authors: Gross Kali Nicole 
Published: March 2016

Abstract
Chapter 6 concludes the story by revealing the trial outcomes and the ultimate sentences that George Wilson and Hannah Mary Tabbs served. It also discusses the advent of plea deals versus jury verdicts and discusses the efficacy of Tabbs’s courtroom manuevers. This chapter also offers a little history into what happened to both Wilson and Tabbs after they served their respective sentences. It also concludes with observations about Tabbs’s use of lies, omission, and racial deference during the course of the investigation and court proceedings. It argues that she embraced the nihilism of the era and found ways to exploit black people’s alienation from the criminal justice system.
Toward a Science of Emerging Media
Authors: Smith Barry 
Published: March 2016

Abstract
If media studies are to become established as a genuine science, then it needs to be determined what the subject matter of this science is to be. The chapter proposes a specification of this subject matter as consisting of: (1) the new sorts of digital entities that have been added to social reality through the invention of the digital computer, and (2) the new sorts of interactions involving human beings that such entities make possible. The chapter supports this proposal by examining examples of some of the ways in which the digital products of emerging media differ from entities of other sorts. The chapter then draws consequences from this examination to demonstrate how these products mark out a new realm within the larger domain of social ontology.
New Media, Old Concerns: Heidegger Revisited
Authors: Kondor Zsuzsanna 
Published: March 2016

Abstract
According to Heidegger, the new, ready-to-hand instruments that technology can provide are, significantly, tools that create a framework within which humans’ relations to their environment change unnoticed. Heidegger touches on some of his era’s new media, such as radio and telephony, and an earlier invention, the typewriter. His analyses suggest that technological inventions have a distortive potential as they conceal the primordial relation to certain phenomena and activities. At the same time, however, he considers these processes to be unavoidable: at the very beginning, philosophical reasoning has gone astray. This chapter investigates new media against the background of Heidegger’s philosophical inquiry. It is beyond question that today’s new media are capable of transforming everyday and scientific practices, and, accordingly, entail the alteration of beliefs, expectations, and biases. The crucial question is whether new media can help us re-establish our primordial (now forgotten) relation to our environment.