bluuebunny/crossref_metadata_2025_split huggingface dataset:
A molecular model for neurodevelopmental disorders
Authors: Gigek C O , Chen E S , Ota V K , Maussion G , Peng H , Vaillancourt K , Diallo A B , Lopez J P , Crapper L , Vasuta C , Chen G G , Ernst C 
Published: May 2015

AbstractGenes implicated in neurodevelopmental disorders (NDDs) important in cognition and behavior may have convergent function and several cellular pathways have been implicated, including protein translational control, chromatin modification, and synapse assembly and maintenance. Here, we test the convergent effects of methyl-CpG binding domain 5 (MBD5) and special AT-rich binding protein 2 (SATB2) reduced dosage in human neural stem cells (NSCs), two genes implicated in 2q23.1 and 2q33.1 deletion syndromes, respectively, to develop a generalized model for NDDs. We used short hairpin RNA stably incorporated into healthy neural stem cells to supress MBD5 and SATB2 expression, and massively parallel RNA sequencing, DNA methylation sequencing and microRNA arrays to test the hypothesis that a primary etiology of NDDs is the disruption of the balance of NSC proliferation and differentiation. We show that reduced dosage of either gene leads to significant overlap of gene-expression patterns, microRNA patterns and DNA methylation states with control NSCs in a differentiating state, suggesting that a unifying feature of 2q23.1 and 2q33.1 deletion syndrome may be a lack of regulation between proliferation and differentiation in NSCs, as we observed previously for TCF4 and EHMT1 suppression following a similar experimental paradigm. We propose a model of NDDs whereby the balance of NSC proliferation and differentiation is affected, but where the molecules that drive this effect are largely specific to disease-causing genetic variation. NDDs are diverse, complex and unique, but the optimal balance of factors that determine when and where neural stem cells differentiate may be a major feature underlying the diverse phenotypic spectrum of NDDs.
“When you see the lipstick kisses …” - military repatriation, public mourning and the politics of respect
Authors: Walklate Sandra , Mythen Gabe , McGarry Ross 
Published: May 2015

AbstractBetween 2007 and 2011, a small town in Wiltshire became indelibly associated with the repatriation of military personnel killed as a result of British involvement in the conflicts in Iraq and Afghanistan. This article offers some empirical insight into, and analysis of, what this process of bringing the dead back home meant for the people of Wootton Bassett, a town afforded “Royal” status for their role in this particular repatriation process. The data gathered affords a unique opportunity to offer some general reflections on the presence of death and the politics of respect evidenced during this time and the wider implications that these process have for making sense of the ineffable within contemporary society. We suggest that Royal Wootton Bassett has not only changed the way in which we “mark the sacrifice of war”, but also encourages us as social scientists to critically reflect on the extent to which the theories that we have enable us to make sense of contemporary practices of public mourning.
A natural experiment of social network formation and dynamics
Authors: Phan Tuan Q. , Airoldi Edoardo M. 
Published: May 2015

Significance
This paper presents an empirical analysis of the short- and long-term causal effects of a hurricane on social structure. Establishing causal relationships in social network formation and dynamics has historically been difficult because of the complexity of engineering social relations in a controlled environment, and the lack of time-resolved data about individuals' behavior. In addition, large-scale interventions of network structure are not feasible in practice. Here, we design an observational study that enables the estimation of causal effects by leveraging the locally well-defined impact of a hurricane. This aspect allows us to conceptualize the analysis of individuals’ behavior as a natural experiment, where the intervention is randomized by nature to locales, leaving only issues of balance to consider.
A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria
Authors: Nahum Joshua R. , Godfrey-Smith Peter , Harding Brittany N. , Marcus Joseph H. , Carlson-Stevermer Jared , Kerr Benjamin 
Published: May 2015

SignificanceThe “adaptive landscape” characterizes the relationship between genotype and fitness. As the landscape becomes more rugged, evolution can become more constrained. During the modern evolutionary synthesis, different views about the process of adaptation reflected different assumptions about landscape topography, which motivated the empirical assessment of adaptive landscapes in biological systems. Here, we describe how evolutionary patterns within experimental populations can yield information about landscape topography. Specifically, metapopulations ofEscherichia coliare evolved under different patterns of migration. We find bacteria reach higher fitness and accumulate more mutations under restricted migration than unrestricted migration, which is consistent with a rugged topography. In this way, experimental manipulation of population structure can provide insight into fundamental evolutionary constraints.
Body size affects the evolution of eyespots in caterpillars
Authors: Hossie Thomas John , Skelhorn John , Breinholt Jesse W. , Kawahara Akito Y. , Sherratt Thomas N. 
Published: May 2015

SignificanceEyespots are a widespread form of antipredator defense that have long captured the imagination of evolutionary biologists, geneticists, psychologists, and artists. These markings are particularly common within Lepidoptera, and eyespots on caterpillars have been shown to deter avian predators; however, why eyespots have evolved in particular caterpillar species, and why they are not even more widespread, remain unclear. Here we answer this question using a powerful three-pronged approach. Our phylogenetically controlled analysis of hawkmoths demonstrates that eyespots are typically restricted to large caterpillars, and our field and laboratory experiments provide an explanation for this. Eyespots are costly to small caterpillars because they enhance detectability without providing a protective advantage, but they are beneficial to large caterpillars because they deter predators.
Effect of warming temperatures on US wheat yields
Authors: Tack Jesse , Barkley Andrew , Nalley Lawton Lanier 
Published: May 2015

SignificanceThis study provides insights for wheat breeding efforts, public policy, and agricultural decision making related to climate change. Our findings provide opportunities for the international wheat breeding community to intensify research efforts to increase resistance to heat stress during focused developmental stages. These efforts could result in net positive warming effects since reduced exposure to freeze was found to be a yield-enhancing benefit of warming. Our results indicate that advancements in heat resistance could come at the expense of higher average yields, and that there is currently limited scope for producer adaptation through alternative variety selection. Our results also suggest that irrigation could help mitigate the effects of warming, which has implications for policies focused on the conservation of increasingly scarce water resources.
The two-domain tree of life is linked to a new root for the Archaea
Authors: Raymann Kasie , Brochier-Armanet Céline , Gribaldo Simonetta 
Published: May 2015

Significance
An archaeal origin for eukaryotes is an exciting recent finding. Nevertheless, it has been based largely on the reconstruction of universal trees. The use of an alternative strategy based on markers shared between Archaea and eukaryotes and Archaea and Bacteria bypasses potential problems linked to the analysis of the three domains simultaneously. Comparison of the phylogenies obtained by these two complementary sets of markers supports a sister relationship between eukaryotes and the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota lineage but also robustly indicates a root of the tree of Archaea that challenges the traditional topology of this domain. This sensibly changes our perspective of the ancient evolution of the Archaea, early life, and Earth.
Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens
Authors: Casson Cierra N. , Yu Janet , Reyes Valeria M. , Taschuk Frances O. , Yadav Anjana , Copenhaver Alan M. , Nguyen Hieu T. , Collman Ronald G. , Shin Sunny 
Published: May 2015

Significance
The innate immune system provides a first line of defense against invading pathogens. The inflammasome is an innate immune complex that activates inflammatory caspases upon infection, causing cell death and IL-1 cytokine release, which initiate defense against gram-negative bacterial pathogens but also mediate septic shock. Many inflammasome studies have been performed using cells from mice, but mice and humans differ in their complement of inflammatory caspases. Instead of caspase-11, humans encode the putative orthologs caspase-4 and caspase-5. Here, we show that caspase-4 plays a conserved role in inflammasome activation in response to virulent gram-negative pathogens in primary human macrophages. Our findings provide important insight into how inflammasomes are regulated in human cells.
Sigma-1 receptor regulates Tau phosphorylation and axon extension by shaping p35 turnover via myristic acid
Authors: Tsai Shang-Yi A. , Pokrass Michael J. , Klauer Neal R. , Nohara Hiroshi , Su Tsung-Ping 
Published: May 2015

Significance
Neurodegeneration is tightly linked to tauopathy as a result of the overactivated cyclin-dependent kinase (cdk) 5 in the form of cdk5/p25. P35, another activator of cdk5, which is short-lived and myristoylated, is cleaved by calpain to the degradation-resistant activator p25. One way to tune down the aberrant, overreactive cdk/p25 is to reduce available p35. The sigma-1 receptor (Sig-1R) is an endoplasmic reticulum (ER) chaperone of unknown relation to tauopathy. Here we found that Sig-1Rs bind myristic acid and promote the degradation of p35. Further, the aberrant tau hyperphosphorylation and stunting of axon elongation in Sig-1R–KO neurons are mitigated by exogenously added myristic acid. Our results establish the role of ER Sig-1Rs in tauopathy and implicate the importance of myristic acid as a substance to fight against neurodegeneration.
Infection of phytoplankton by aerosolized marine viruses
Authors: Sharoni Shlomit , Trainic Miri , Schatz Daniella , Lehahn Yoav , Flores Michel J. , Bidle Kay D. , Ben-Dor Shifra , Rudich Yinon , Koren Ilan , Vardi Assaf 
Published: May 2015

Significance
Marine viruses constitute a major ecological and evolutionary driving force in marine ecosystems and are responsible for cycling of major nutrients; however, their dispersal mechanisms remain underexplored. By using one of the most established host–pathogen planktonic model systems we provide strong evidence that specific viruses of marine coccolithophores can be transmitted and stay infective as marine aerosols. Being transported by the wind, phytoplankton viruses can be conveyed long distances and transmit the infection to remote locations to which coccolithophore blooms can be extended. We show that this effective transmission mechanism that has been studied in human, animal, and plant diseases could play an important role in host–virus dynamics during phytoplankton blooms in the ocean.
Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes
Authors: Kuppusamy Kavitha T. , Jones Daniel C. , Sperber Henrik , Madan Anup , Fischer Karin A. , Rodriguez Marita L. , Pabon Lil , Zhu Wei-Zhong , Tulloch Nathaniel L. , Yang Xiulan , Sniadecki Nathan J. , Laflamme Michael A. , Ruzzo Walter L. , Murry Charles E. , Ruohola-Baker Hannele 
Published: May 2015

Significance
The adult human heart is incapable of significant regeneration after injury. Human embryonic stem cells (hESCs) have the capacity to generate an unlimited number of cardiomyocytes (CMs). However, hESC-derived CMs (hESC-CMs) are at a fetal state with respect to their functional and physiological characteristics, diminishing their utility for modeling adult-related heart disease and therapeutic screening. Thus, the potential for hESC-CMs may improve immensely in cardiac-related therapeutic applications if factors that drive their maturation are uncovered. In this study, we show that members of let-7 miRNA family control CM metabolism, cell size, and force contractility, making them one of the best factors identified to date in promoting maturity of stem cell derivatives.
Inositol phosphate pathway controls transcription of telomeric expression sites in trypanosomes
Authors: Cestari Igor , Stuart Ken 
Published: May 2015

Significance
African trypanosomes cause human and animal diseases and evade the host immune systems by periodically switching which variant surface glycoprotein (VSG) they express. The mechanisms that result in expression of one of the numerous VSG genes at a time and the switching of expression between different VSG genes are poorly understood. We show that specific steps in the inositol phosphate (IP) pathway control both monoallelic VSG gene transcription and the switching of VSG gene expression. The data indicate that the cellular amounts, locations, and molecular interactions of specific IP pathway enzymes and their metabolites control both processes. The results offer new drug targets and insights into the epigenetic control of gene expression by this biologically ubiquitous pathway.
Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota
Authors: Naito Mizue , Morton Joseph B. , Pawlowska Teresa E. 
Published: May 2015

Significance
Arbuscular mycorrhizal fungi (AMF) are soil fungi associated with the majority of land plants worldwide. They supply plants with mineral nutrients in exchange for photosynthates. Most AMF harbor endobacteria from the Mollicutes class. Exploring metagenomes of endobacterial populations in three AMF species, we discovered that these endobacteria have minimal genomes and are metabolically dependent on their fungal host. Despite vertical transmission, endobacterial genomes are uniquely plastic. In addition, the endobacteria contain multiple genes horizontally transferred from fungi. Many of these genes encode products thought to interact with fungal host proteins. Overall, the endobacterial genomes reveal a tightly knit network of interactions with the fungal host and highlight the importance of associations between bacteria and fungi.
Hydrological change in Southern Europe responding to increasing North Atlantic overturning during Greenland Stadial 1
Authors: Bartolomé Miguel , Moreno Ana , Sancho Carlos , Stoll Heather M. , Cacho Isabel , Spötl Christoph , Belmonte Ánchel , Edwards R. Lawrence , Cheng Hai , Hellstrom John C. 
Published: May 2015

Significance
This study presents robust evidence of two hydrological phases within the Greenland Stadial 1 (GS-1) cold event (12.8−11.7 ka B.P.) in Southern Europe. We present a well-dated high-resolution speleothem record (Seso Cave, Central Pyrenees) where temperature and hydrological signals are independently reconstructed. Detailed interpretation of stable isotopes and trace elements allow characterizing a first dry period followed, after 12,500 y before 2000 A.D., by more humid conditions. Our findings point to the resumption of the Atlantic overturning circulation as the main mechanism behind the hydrological response in Europe during this mid–GS-1 transition. The second phase, cold in Greenland but humid in Western Europe, represents a new paradigm in the well-established model of dry, cold stadials during the last glacial period.
Prolonged daily light exposure increases body fat mass through attenuation of brown adipose tissue activity
Authors: Kooijman Sander , van den Berg Rosa , Ramkisoensing Ashna , Boon Mariëtte R. , Kuipers Eline N. , Loef Marieke , Zonneveld Tom C. M. , Lucassen Eliane A. , Sips Hetty C. M. , Chatzispyrou Iliana A. , Houtkooper Riekelt H. , Meijer Johanna H. , Coomans Claudia P. , Biermasz Nienke R. , Rensen Patrick C. N. 
Published: May 2015

Significance
Increased light exposure has been associated with obesity in both humans and mice. In this article, we elucidate a mechanistic basis of this association by performing studies in mice. We report that prolonging daily light exposure increases adiposity by decreasing energy expenditure rather than increasing food intake or locomotor activity. This was caused by a light-exposure period-dependent attenuation of the noradrenergic activation of brown adipose tissue that has recently been shown to contribute substantially to energy expenditure by converting fatty acids and glucose into heat. Therefore, we conclude that impaired brown adipose tissue activity may mediate the relationship between increased light exposure and adiposity.
Regulation of AMPA receptor phosphorylation by the neuropeptide PACAP38
Authors: Toda Alyssa M. A. , Huganir Richard L. 
Published: May 2015

Significance
AMPA receptors (AMPARs) conduct the majority of excitatory synaptic transmission in the brain. Through changes in AMPAR synaptic localization or conductance the strength of a synapse can be altered. It is hypothesized that such changes underlie complex behaviors such as learning and memory. AMPAR phosphorylation is one signaling event used to alter receptor targeting and conductance. We demonstrate the neuropeptide PACAP38 stimulates AMPAR GluA1 subunit phosphorylation at S845 and dephosphorylation at T840. Investigation of PACAP38-dependent changes in AMPAR phosphorylation will help us to better understand the factors involved in regulating AMPAR function.
Protective effects of Nitraria retusa extract and its constituent isorhamnetin against amyloid β-induced cytotoxicity and amyloid β aggregation
Authors: Iida Akihisa , Usui Takeo , Zar Kalai Feten , Han Junkyu , Isoda Hiroko , Nagumo Yoko 
Published: May 2015

Abstract
Nitraria retusa is a halophyte species that is distributed in North Africa and used as a traditional medicinal plant. In this study, N. retusa ethanol extract and its constituent isorhamnetin (IRA) protected against amyloid β (Aβ)-induced cytotoxicity in human neuroblastoma SH-SY5Y cells. An in vitro Aβ aggregation assay suggested that IRA destabilizes Aβ fibrils.
Profilin 2 promotes migration, invasion, and stemness of HT29 human colorectal cancer stem cells
Authors: Kim Min-Jung , Lee Yoo-Sun , Han Gi-Yeon , Lee Han-Na , Ahn Chiyoung , Kim Chan-Wha 
Published: May 2015

Abstract
We investigated the role of profilin 2 in the stemness, migration, and invasion of HT29 cancer stem cells (CSCs). Increased and decreased levels of profilin 2 significantly enhanced and suppressed the self-renewal, migration, and invasion ability of HT29 CSCs, respectively. Moreover, profilin 2 directly regulated the expression of stemness markers (CD133, SOX2, and β-catenin) and epithelial mesenchymal transition (EMT) markers (E-cadherin and snail). CD133 and β-catenin were up-regulated by overexpression of profilin 2 and down-regulated by depletion of profilin 2. SOX2 was decreased by profilin 2 depletion. E-cadherin was not influenced by profilin 2- overexpression but increased by profilin 2- knockdown. The expression of snail was suppressed by profilin 2- knockdown. We speculated that stemness and the EMT are closely linked through profilin 2-related pathways. Therefore, this study indicates that profilin 2 affects the metastatic potential and stemness of colorectal CSCs by regulating EMT- and stemness-related proteins.
Construction of Soliton-Cnoidal Wave Interaction Solution for the (2+1)-Dimensional Breaking Soliton Equation*
Authors: Cheng Wen-Guang , Li Biao , Chen Yong 
Published: May 2015

AbstractIn this paper, the truncated Painlevé analysis and the consistent tanh expansion (CTE) method are developed for the (2+1)-dimensional breaking soliton equation. As a result, the soliton-cnoidal wave interaction solution of the equation is explicitly given, which is difficult to be found by other traditional methods. When the value of the Jacobi elliptic function modulus m = 1, the soliton-cnoidal wave interaction solution reduces back to the two-soliton solution. The method can also be extended to other types of nonlinear evolution equations in mathematical physics.
An Alternative Adiabatic Quantum Algorithm for the Hamiltonian Cycle Problem
Authors: Zhang Da-Jian , Tong Dian-Min , Lu Yao , Long Gui-Lu 
Published: May 2015

Abstract
We put forward an alternative quantum algorithm for finding Hamiltonian cycles in any N-vertex graph based on adiabatic quantum computing. With a von Neumann measurement on the final state, one may determine whether there is a Hamiltonian cycle in the graph and pick out a cycle if there is any. Although the proposed algorithm provides a quadratic speedup, it gives an alternative algorithm based on adiabatic quantum computation, which is of interest because of its inherent robustness.
Vector Meson Mass in Finite Density and Temperature Lattice QCD*
Authors: Wang Rui , Chen Ying , Gong Ming , Liu Chuan , Liu Yu-Bin , Liu Zhao-Feng , Ma Jian-Ping , Meng Xiang-Fei , Zhang Jian-Bo 
Published: May 2015

Abstract
Vector meson mass values are studied at finite chemical potential and temperature in lattice QCD with lattice size of 24 × 122 × 6 using two flavors of staggered quarks. The investigation focuses on the change of the vector meson mass in the critical region close to Tc with two different types of chemical potentials switched on: the isoscalar chemical potential μs and its isovector counterpart μv. It is found that the vector meson mass increases in the QGP phase with both chemical potentials and decreases with μs in the confinement phase.
Asymmetric Coupling in Two-Lane Asymmetric Simple Exclusion Processes with Unequal Injection Rates: Effect of Different Hoping Rates*
Authors: Xiao Song , Chen Xiao-Yu , Liu Yan-Na 
Published: May 2015

Abstract
This paper investigates the effect of both unequal injection rates and different hopping rates on two-lane asymmetric simple exclusion processes (ASEPs) with asymmetric coupling. When the hopping rates of both lanes are different, the system includes six steady phases, however, when the hopping rates of both lanes are same, the seventh phase (MC, MC) will exist in the system. Interestingly, with different hopping rates of both lanes, the densities of the system cannot be influenced by the non-zero vertical transition rate. Our theoretical arguments are in well agreement with extensively performed Monte Carlo simulations.
Molecular Dynamics Studies on Ballistic Thermal Resistance of Graphene Nano-Junctions*
Authors: Yao Wen-Jun , Cao Bing-Yang 
Published: May 2015

Abstract
Ballistic thermal resistance of graphene nano-junctions is investigated using non-equilibrium molecular dynamics simulation. The simulation system is consisted of two symmetrical trapezoidal or rectangular graphene nano-ribbons (GNRs) and a connecting nanoscale constriction in between. From the simulated temperature profile, a big temperature jump resulted from the constriction is found, which is proportional to the heat current and corresponds to a local ballistic thermal resistance. Fixing the constriction width and the length of GNRs, this ballistic thermal resistance is independent of the width of the GNRs bottom layer, i.e., the convex angle. But interestingly, this thermal resistance has obvious size effect. It is inversely proportional to the constriction width and will disappear with the constriction being wider. Moreover, based on the phonon dynamics theory, a theoretical model of the ballistic thermal resistance in two-dimensional nano-systems is developed, which gives a good explanation on microcosmic level and agrees well with the simulation result quantitatively and qualitatively.