bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature dependent double blueshift of photoluminescence peak position in MgZnO epitaxial layers
Authors: Karaliunas Mindaugas , Kuokstis Edmundas , Ting Shao-Ying , Huang Jeng-Jie , Yang C. C.
Published: September 2014

Temperature dependent photoluminescence (PL) of MgZnO epitaxial layers with high Mg content were studied to understand the effect of carrier localization on the PL dynamics, including the PL dependence on excitation power density and temperature. A double blueshift of the PL peak position with increase of measurement temperature was discovered. The blueshift took place at low as well as high temperature and could be attributed to the effect of carrier localization. It has been deduced that the randomly distributed carrier localization centers in the MgZnO films create two energy separated Gaussian-shape density-of-states tails in the vicinity of the fundamental band gap edge. Filling of these tail states by the thermally activated carriers with increase of temperature causes the temperature-induced double blueshift of the PL peak position. By analyzing the temperature dependent PL spectra, two parameters, σ and γ were extracted, which characterize the average energy depth distribution of the localizing potential field fluctuations. The value of these parameters were found to depend on the Mg content and crystalline structure of the MgZnO epitaxial layers.
Spin-dependent transport in antiferromagnetic tunnel junctions
Authors: Merodio P. , Kalitsov A. , Béa H. , Baltz V. , Chshiev M.
Published: September 2014

We investigate the behaviour of spin transfer torque (STT) and tunnelling magnetoresistance (TMR) in epitaxial antiferromagnetic-based tunnel junctions using tight binding calculations in the framework of the Keldysh formalism. We find that the STT out-of-plane component exhibits a staggered spatial distribution similar to its in-plane component. This behaviour is specific to the use of a tunnel barrier and significantly differs from the out-of-plane torques reported in previous works using a metallic spacer. Additionally, we show that unlike conventional ferromagnetic-based tunnel junctions, the TMR can increase with applied bias and reach values comparable to typical magnetoresistances found for usual spin valves.
Strain induced effects on electronic structure of semi-metallic and semiconducting tin nanowires
Authors: Ansari Lida , Fagas Giorgos , Greer James C.
Published: September 2014

Semimetal nanowires are known to undergo a semimetal to semiconductor transition as a consequence of quantum confinement as their diameters are decreased. Using density functional theory calculations, the electronic structure of tin nanowires (SnNWs) under uniaxial strain within a range of −4% to +4% is investigated. It is demonstrated that a [110]-oriented semi-metallic SnNW with a diameter of ∼4.2 nm can be made either more metallic or semiconducting by the application of tensile or compressive strain, respectively. On the contrary, a [100]-oriented semi-metallic SnNW with a slightly larger diameter of ∼4.5 nm remains semiconducting with the application of either compressive or tensile strain. Carrier effective masses are calculated from the band structures; it is shown that for semimetal SnNW along [110] orientation the conduction and valence bands display near linear dispersion under both compressive and tensile strains (<3%) which leads to very small effective masses of ∼0.007m0. We also show that strain energies and Young modulus vary with nanowire diameter and crystal orientation. The effect of alloying on the generation of tensile and compressive strains in SnNWs is also investigated.
Simultaneous chemical and electrical stimulation on lung cancer cells using a multichannel-dual-electric-field chip
Authors: Hou Hsien-San , Tsai Hsieh-Fu , Chiu Hsien-Tai , Cheng Ji-Yen
Published: September 2014

Electrotaxis has been identified as an important biological phenomenon in living organisms. Various types of cells respond to electrical stimuli by moving toward anode or cathode. However, the molecular mechanisms of cell migration under electric field still remain unclear. Many different microfluidic devices for electrotaxis studies have been reported in recent years. Yet, a device that allows rapid study of simultaneous chemical and electric-field (EF) effect on cells is not available. In this study, we report a multichannel-dual-electric-field (MDF) chip to investigate the concurrent effect of chemicals and EF on lung cancer cells. The chip provided 8 combinations of electrical/chemical stimulations in one experiment. The MDF chip is a poly-methylmethacrylate based microfluidic cell culture chip that integrates electrical stimulation and several chemically isolated channels. Alternatively, the chemically isolated channels can be filled with different types of cells in one experiment. The EF in these different channels was applied using one electrical power supply. Each chemically isolated channel has two segments possessing dual independent electric-fields, one with the applied electric-field strength (EFS) and the other with 0 EFS. In addition, a new design that includes on-chip salt bridges into the MDF chip provides better-controlled coexisting EF and chemical stimulation. Numerical simulation was conducted to verify the independency of the isolated channels and the dual EFS in the two segments of each channel. A highly metastasized lung cancer cell line, CL1-5 cell, was used to demonstrate the function of the chip. Our results showed that, after treating cells with phosphatidylinositide 3-kinases (PI3K) blocker (LY294002), both the migration speed and the directedness toward to anode were reduced for the electrically stimulated CL1-5 cells. However, suppressing Rho-associated coiled-coil kinase (ROCK) in the EF stimulated CL1-5 cells by Y27632, a ROCK inhibitor, only eliminated the directedness of electrotropism but showed no effect on the cell migration speed. The result suggests that ROCK, but not PI3K pathway, is more likely to be involved in directing the anodic migration of CL1-5 cells under electrical stimulation. Using the MDF chip, multiple combinations of chemical/EF stimulation was studied in one experiment. The dose dependency experiment of a chemical was also rapidly conducted. We expect the MDF chip will greatly shorten the experiment time and increase the accuracy of the electrotaxis studies.
Roughness analysis in strained silicon-on-insulator wires and films
Authors: Ureña Ferran , Olsen Sarah H. , Escobedo-Cousin Enrique , Minamisawa Renato A. , Raskin Jean-Pierre
Published: September 2014

Strained silicon is used to enhance performance in state-of-the-art CMOS. Under device operating conditions, the effect of strain is to reduce the carrier scattering at the channel by a smoother semiconductor surface. This has never been completely understood. This paper gives first evidence of the variation in surface roughness under realistic strained conditions. At the nanoscale, the SiO2/Si interface roughness is dependent on the scale of observation (self-affinity). To date, there is no experimental study of the SiO2/Si interface roughness scaling with strain. This work presents the effect of uniaxial and biaxial strains on the surface roughness of strained silicon-on-insulator films and wires using atomic force microscopy. Levels of strain ranging from 0% to 2.3%, encompassing those used in present CMOS devices have been investigated. It is shown that the silicon surface is affected by uniaxial and biaxial strains differently. Three surface roughness parameters have been analyzed: root mean square roughness, correlation length, and the Hurst exponent, which is used to describe the scaling behavior of a self-affine surface. The results show that the root mean square roughness decreases (up to ∼40%) with increasing tensile strain, whereas the correlation length increases (up to ∼63 nm/%) with increasing tensile strain. The Hurst exponent also varies with strain and with the undulation wavelength regime (between ∼0.8 and 0.2). This dependency explains why some models used to determine the carrier mobility from experiments fit the data better with a Gaussian form, whereas other models fit the data better with an exponential form.
Flexible interference ablation using fibers to split and deliver laser pulses for direct plasmonic nanopatterning
Authors: Lin Yuanhai , Zhang Xinping
Published: September 2014

Optical fibers are used to achieve a flexible interference ablation scheme, where the bundled end of fibers functions as a beam splitter and the fibers are used to deliver 5-ns ultraviolet laser pulses at 355 nm. The divergent beams from the free ends of fibers are overlapped onto the film of colloidal gold nanoparticles. A single-pulse single-shot exposure process leads to removal of the gold nanoparticles within the bright interference fringes. Gold nanogratings are produced on glass substrates coated with indium tin oxide after an annealing process at 400 °C. Fano coupling between plasmon and waveguide resonance modes was observed.
Deep hole injection assisted by large V-shape pits in InGaN/GaN multiple-quantum-wells blue light-emitting diodes
Authors: Li Yufeng , Yun Feng , Su Xilin , Liu Shuo , Ding Wen , Hou Xun
Published: September 2014

We investigated the hole injection mechanism in InGaN/GaN blue light-emitting diodes by growing monolithic dual-wavelength multiple-quantum-wells and measuring the electroluminescence spectra at different current densities under room temperature. By analyzing the spectral competition from quantum wells at different vertical locations, the hole injection depth was quantitatively measured. During the epitaxial growth, large size V-shape pits with 200–330 nm diameter were intentionally formed in the active region by controlling the growth condition. It was found that such defect has a significant influence on the hole injection depth. With large V-shape pits and reduced quantum barrier thickness, the hole can be injected beyond 8 pairs of quantum well/quantum barrier. And less “droop” effect at large current density were observed. A carrier transport model with the presence of large V-shape pits is established.
Group index oscillations in photonic crystal waveguides
Authors: Sarkissian Raymond , O'Brien John
Published: September 2014

This work studies the phase contributions of a photonic crystal waveguide resonator. When studying the transmission spectrum of such resonators oscillations of group index are observed that can not be described by typical models conventionally used for analysis. We develop a simple mathematical tool capable of describing these oscillations. Furthermore, we carry out experiments on a Si photonic crystal waveguide resonator and apply that tool extracting phase contributions of the photonic crystal waveguide terminations.
Oncostatin M and leukaemia inhibitory factor trigger signal transducer and activator of transcription 3 and extracellular signal-regulated kinase 1/2 pathways but result in heterogeneous cellular responses in trophoblast cells
Authors: Chaiwangyen Wittaya , Ospina-Prieto Stephanie , Morales-Prieto Diana M. , Pereira de Sousa Francisco Lazaro , Pastuschek Jana , Fitzgerald Justine S. , Schleussner Ekkehard , Markert Udo R.
Published: September 2014

Leukaemia inhibitory factor (LIF) and oncostatin M (OSM) are pleiotropic cytokines present at the implantation site that are important for the normal development of human pregnancy. These cytokines share the cell membrane receptor subunit gp130, resulting in similar functions. The aim of this study was to compare the response to LIF and OSM in several trophoblast models with particular regard to intracellular mechanisms and invasion. Four trophoblast cell lines with different characteristics were used: HTR-8/SVneo, JEG-3, ACH-3P and AC1-M59 cells. Cells were incubated with LIF, OSM (both at 10 ng mL–1) and the signal transducer and activator of transcription (STAT) 3 inhibitor S3I-201 (200 µM). Expression and phosphorylation of STAT3 (tyr705) and extracellular regulated kinase (ERK) 1/2 (thr202/204) and the STAT3 DNA-binding capacity were analysed by Western blotting and DNA-binding assays, respectively. Cell viability and invasiveness were assessed by the methylthiazole tetrazolium salt (MTS) and Matrigel assays. Enzymatic activity of matrix metalloproteinase (MMP)-2 and MMP-9 was investigated by zymography. OSM and LIF triggered phosphorylation of STAT3 and ERK1/2, followed by a significant increase in STAT3 DNA-binding activity in all tested cell lines. Stimulation with LIF but not OSM significantly enhanced invasion of ACH-3P and JEG-3 cells, but not HTR-8/SVneo or AC1-M59 cells. Similarly, STAT3 inhibition significantly decreased the invasiveness of only ACH-3P and JEG-3 cells concomitant with decreases in secreted MMP-2 and MMP-9. OSM shares with LIF the capacity to activate ERK1/2 and STAT3 pathways in all cell lines tested, but their resulting effects are dependent on cell type. This suggests that LIF and OSM may partially substitute for each other in case of deficiencies or therapeutic interventions.
MicroRNA-223 coordinates cholesterol homeostasis
Authors: Vickers Kasey C. , Landstreet Stuart R. , Levin Michael G. , Shoucri Bassem M. , Toth Cynthia L. , Taylor Robert C. , Palmisano Brian T. , Tabet Fatiha , Cui Huanhuan L. , Rye Kerry-Anne , Sethupathy Praveen , Remaley Alan T.
Published: September 2014

Significance

Results from this study represent a breakthrough in our understanding of posttranscriptional control of cholesterol metabolism and how microRNAs (miRNAs) are at the heart of cholesterol regulatory circuitry and homeostasis. Although cells are adept at maintaining proper cholesterol levels, it was unknown how cells posttranscriptionally coordinate cholesterol uptake, efflux, and synthesis. MicroRNA-223 (miR-223) transcription and expression are maintained by cholesterol, and, as a feedback network, miR-223 inhibits cholesterol biosynthesis and uptake and increases cholesterol efflux. This study clearly demonstrates the extensive role that miRNAs play in coordinating metabolic adaptation to disease and general homeostasis. This work highlights a unique regulatory control point for cholesterol homeostasis and illustrates how important the study of miRNAs is to the greater understanding of dyslipidemia and cardiovascular disease.
Platelet mechanosensing of substrate stiffness during clot formation mediates adhesion, spreading, and activation
Authors: Qiu Yongzhi , Brown Ashley C. , Myers David R. , Sakurai Yumiko , Mannino Robert G. , Tran Reginald , Ahn Byungwook , Hardy Elaissa T. , Kee Matthew F. , Kumar Sanjay , Bao Gang , Barker Thomas H. , Lam Wilbur A.
Published: September 2014

Significance

Platelets are cell fragments in the blood that initiate clot formation at the site of bleeding. Although the biological aspects of this process have been well characterized, whether platelets can detect and physiologically respond to the mechanical aspects of its local environment is unclear. Here, we show that platelets sense the stiffness of the underlying clot substrate, and increasing substrate stiffness increases platelet adhesion and spreading. Importantly, adhesion on stiffer substrates leads to higher levels of platelet activation. Mechanistically, we determined that Rac1, actin, and myosin activity mediate this process. This newfound capability of how platelets adjust their degree of activation based on the mechanical properties of their environment provides new insight into how clots are formed.
Cell fate regulation by gelsolin in human gynecologic cancers
Authors: Abedini Mohammad R. , Wang Pei-Wen , Huang Yu-Fang , Cao Mingju , Chou Cheng-Yang , Shieh Dar-Bin , Tsang Benjamin K.
Published: September 2014

Significance

We tested the hypothesis that gelsolin (GSN) plays an important role in gynecological chemoresistance through the following: We provided strong evidence in support of GSN as an important etiologic factor in chemoresistance in vitro. We also determined the mechanism by which GSN exerts its prosurvival action. Our findings also suggest that the application of C-terminal GSN may represent a new therapeutic strategy for chemoresistant gynecologic cancer. We have also validated our in vitro findings with a clinical investigation that determines the relationship between GSN expression and
cis
-Diammine dichloroplatinium (II) sensitivity in human ovarian tumor. These findings agree with the notion that GSN plays a key role in the regulation of gynecological cell fate as reflected in chemoresistance.
Unique semantic space in the brain of each beholder predicts perceived similarity
Authors: Charest Ian , Kievit Rogier A. , Schmitz Taylor W. , Deca Diana , Kriegeskorte Nikolaus
Published: September 2014

Significance

Everyone is different. Understanding the unique way an individual perceives the world is a fundamental goal of psychology and brain science. Using novel methods for analyzing functional MRI (fMRI) data, we show that each person viewing a set of objects represents the objects uniquely in his or her brain. Moreover, given an individual’s measured brain-activity patterns, idiosyncrasies in his or her perception of the similarities among the objects can be predicted. Prediction accuracy is modest using current technology. However, our results demonstrate that fMRI has the power to reveal individually unique representations of particular objects in the human brain. The novel method might help us understand the biological substrate of individual experience in mental health and disease.
Left–right dissociation of hippocampal memory processes in mice
Authors: Shipton Olivia A. , El-Gaby Mohamady , Apergis-Schoute John , Deisseroth Karl , Bannerman David M. , Paulsen Ole , Kohl Michael M.
Published: September 2014

Significance

The hippocampus is implicated in memory and spatial navigation. In rodents, in which this bilateral brain structure has been studied extensively, the left and right hippocampi have generally been considered functionally equivalent. However, recent work has revealed unexpected asymmetries in the molecular and morphological characteristics of neuronal connections according to brain hemisphere. To investigate whether this left–right difference has implications for hippocampal function, we acutely inhibited activity in an area-specific and genetically-defined population of hippocampal neurons during various behavioral tasks. We found that silencing the CA3 area of the left hippocampus impaired associative spatial long-term memory, whereas the equivalent manipulation in the right hippocampus did not. Thus, our data show that hippocampal long-term memory processing is lateralized in mice.
A mechanistic framework for noncell autonomous stem cell induction in
Arabidopsis
Authors: Daum Gabor , Medzihradszky Anna , Suzaki Takuya , Lohmann Jan U.
Published: September 2014

Significance

Cell–cell communication is a prerequisite of multicellular development and noncell autonomous stem cell induction has been conserved during evolution. Cytoplasmic bridges, called plasmodesmata, which facilitate the exchange of molecules between neighboring cells, are a striking innovation for cell–cell signaling in plants. Here, we show that plasmodesmata function is required for the activity of shoot apical stem cells in
Arabidopsis
and provide evidence that the stem cell inducing transcription factor WUSCHEL moves from the niche into the stem cells via this route. WUSCHEL movement is functionally relevant and mediated by multiple protein domains. Because parts of the protein that restrict movement are required for homodimerization, the formation of WUSCHEL dimers might contribute to the regulation of stem cell activity in
Arabidopsis
.
Precisely modulated pathogenicity island interference with late phage gene transcription
Authors: Ram Geeta , Chen John , Ross Hope F. , Novick Richard P.
Published: September 2014

Significance

Highly mobile staphylococcal pathogenicity islands (SaPIs) are the only source of toxic shock toxin and certain other superantigens, especially enterotoxin B. To promote their survival and spread, the SaPIs parasitize and interfere with certain bacteriophages. Unlike the interference of the clustered regularly interspaced short palindromic repeats (CRISPRs), the interference of SaPIs is never complete, allowing horizontal gene transfer and adaptation. We report a novel SaPI-determined interference mechanism that targets a phage gene essential for both phage and SaPI. Because SaPI is not self-destructive, it must modulate this inhibition to ensure production of its own infectious particles, as well as those of the phage, and it does so by means of a novel SaPI protein that binds to the inhibitor.
Epigenetic dysregulation by nickel through repressive chromatin domain disruption
Authors: Jose Cynthia C. , Xu Beisi , Jagannathan Lakshmanan , Trac Candi , Mallela Ramya K. , Hattori Takamitsu , Lai Darson , Koide Shohei , Schones Dustin E. , Cuddapah Suresh
Published: September 2014

Significance

Histone modifications associated with gene silencing typically mark large contiguous regions of the genome forming repressive chromatin domain structures. Since the repressive domains exist in close proximity to active regions, maintenance of domain structure is critically important. This study shows that nickel, a nonmutagenic carcinogen, can disrupt histone H3 lysine 9 dimethylation (H3K9me2) domain structures genome-wide, resulting in spreading of H3K9me2 marks into the active regions, which is associated with gene silencing. Our results suggest inhibition of DNA binding of the insulator protein CCCTC-binding factor (CTCF) at the H3K9me2 domain boundaries as a potential reason for H3K9me2 domain disruption. These findings have major implications in understanding chromatin dynamics and the consequences of chromatin domain disruption during pathogenesis.
Application of desorption electrospray ionization mass spectrometry imaging in breast cancer margin analysis
Authors: Calligaris David , Caragacianu Diana , Liu Xiaohui , Norton Isaiah , Thompson Christopher J. , Richardson Andrea L. , Golshan Mehra , Easterling Michael L. , Santagata Sandro , Dillon Deborah A. , Jolesz Ferenc A. , Agar Nathalie Y. R.
Published: September 2014

Significance

This study is the first demonstration, to our knowledge, of the application of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) for discrimination of breast cancer and delineation of tumor margins. Using DESI-MSI, it is possible to discriminate between cancerous and adjacent normal tissue on the basis of the detection and specific spatial distributions of different lipid species. This study proves the feasibility of classifying cancerous and normal breast tissues using ambient ionization MSI. It will allow the surgeon to access to this information in real time so as to make accurate intraoperative decisions quickly. It will result in improved cosmesis and decrease the need for multiple operations for margin reexcision.
Beclin-1 deficiency in the murine ovary results in the reduction of progesterone production to promote preterm labor
Authors: Gawriluk Thomas R. , Ko CheMyong , Hong Xiaoman , Christenson Lane K. , Rucker Edmund B.
Published: September 2014

Significance

The success of mammalian reproduction is contingent upon the production of hormones within the female to not only promote germ cell development, but to establish and maintain pregnancy. We demonstrate that abrogating autophagy, a cellular process to maintain energy stores, can lead to reproductive defects that prevent a successful pregnancy in mice. Females that lack the crucial autophagy gene
Beclin1
(
Becn1
) in the progesterone-producing cells of the ovary demonstrate reduced circulating progesterone and a preterm birth phenotype concurrent with the loss of litters, which is rescued by the administration of exogenous progesterone. Because progesterone is a necessary hormone for mammalian pregnancy, these data suggest that autophagy may play a role in steroidogenesis and, thus, in successful human reproduction.
Hematopoietic RIPK1 deficiency results in bone marrow failure caused by apoptosis and RIPK3-mediated necroptosis
Authors: Roderick Justine E. , Hermance Nicole , Zelic Matija , Simmons Matthew J. , Polykratis Apostolos , Pasparakis Manolis , Kelliher Michelle A.
Published: September 2014

Significance

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is involved in TNF signaling and interacts with the related RIPK3 to regulate cell death and inflammation. RIPK1 has kinase-independent prosurvival and kinase-dependent prodeath functions. To identify the lineages that depend on RIPK1 for survival, we generated conditional
Ripk1
mice. Acute
Ripk1
deletion results in rapid death of the animal caused by extensive cell death in the intestinal and hematopoietic lineages. A hematopoietic RIPK1 deficiency stimulates proinflammatory cytokine/chemokine production and cell death, resulting in bone marrow failure. Hematopoietic failure is partially rescued by a RIPK3 deficiency, indicating that RIPK1-deficient hematopoietic cells undergo RIPK3-mediated necroptosis. These findings show that in the hematopoietic lineage RIPK1 suppresses RIPK3 activity and suggest that RIPK-dependent necroptosis may contribute to human bone marrow failure syndromes.
Epitaxial growth of large-gap quantum spin Hall insulator on semiconductor surface
Authors: Zhou Miao , Ming Wenmei , Liu Zheng , Wang Zhengfei , Li Ping , Liu Feng
Published: September 2014

Significance

Quantum phase of matter is of great scientific and technological interest. The quantum spin Hall (QSH) insulator is a newly discovered two-dimensional material that exhibits topological edge state residing inside bulk energy gap, so that its edge is metallic with quantized conductance and its bulk is insulating. For its potential applications in spintronics and quantum computing, a large energy gap is desirable, e.g., for room-temperature application. So far, large-gap QSH insulators have been predicted only in freestanding films. Here we demonstrate the formation of a large-gap QSH state on a semiconductor substrate through epitaxial growth of heavy metal atoms on halogenated Si surface. Our findings not only reveal a new formation mechanism of large-gap QSH insulator, but may also pave the way for its experimental realization.
The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C
Authors: Hwang Peter M. , Cai Fangze , Pineda-Sanabria Sandra E. , Corson David C. , Sykes Brian D.
Published: September 2014

Significance

Protein–protein interactions typically involve some degree of induced fit, producing complementary surfaces that account for high affinity and specificity. However, there are increasingly more examples of intrinsically disordered regions (IDRs) that exert important biologic effects despite never attaining a rigid structure. Here we show how a particularly disordered region of cardiac troponin I impacts the overall global conformation and function of its binding partner, cardiac troponin C. This newly described role for an IDR is accomplished through electrostatic interactions, which are particularly suited to IDRs. The regulation of electrostatic interactions in IDRs through phosphorylation is an emerging concept in cellular signaling, and troponin I is now another important example, one known by cardiac physiologists for 40 y.
Object and spatial mnemonic interference differentially engage lateral and medial entorhinal cortex in humans
Authors: Reagh Zachariah M. , Yassa Michael A.
Published: September 2014

Significance

Episodic memories are complex records of experience, consisting of “what” happened as well as “where” and “when” it happened. Animal studies have demonstrated distinct brain networks supporting memory for information about what experience occurred and information about where the experience occurred. However, such dissociations have been elusive in humans. Using a memory interference task that pits object (i.e., what) vs. spatial (i.e., where) memories against each other and high-resolution fMRI, we report evidence for two parallel but interacting networks in the human hippocampus and its input regions, supporting prior work in animals. We propose a conceptual model of how object and spatial interference are reduced in the regions providing input to the hippocampus, allowing rich, distinct memories to be built.
Statistical learning of recurring sound patterns encodes auditory objects in songbird forebrain
Authors: Lu Kai , Vicario David S.
Published: September 2014

Significance

Human infants and adults can extract statistical regularities from a continuous sound stream even when passively exposed. This type of unreinforced learning is important for language acquisition and auditory perception. We exposed songbirds, a well-developed model for studying perception and production of learned vocal signals, to sound streams and then recorded neural activity from the auditory forebrain. Responses demonstrated neuronal recognition of complex recurring patterns present in the stream, even for patterns made of nonadjacent sounds. These results show that passive exposure can create and differentiate representations of recently heard sounds in the neuronal population. Because auditory information about the world is received serially over time, recognition of complex auditory objects may depend on this type of ongoing memory process.
Neuronal mechanism for acute mechanosensitivity in tactile-foraging waterfowl
Authors: Schneider Eve R. , Mastrotto Marco , Laursen Willem J. , Schulz Vincent P. , Goodman Jena B. , Funk Owen H. , Gallagher Patrick G. , Gracheva Elena O. , Bagriantsev Sviatoslav N.
Published: September 2014

Significance

Like vision, audition, and olfaction, mechanosensation is a fundamental way in which animals interact with the environment, but it remains the least well understood at the cellular and molecular levels. Here, we explored evolutionary changes that contribute to the enhancement of mechanosensitivity in tactile-foraging ducks. We found that the somatosensory neurons that innervate the duck bill can detect physical force much more efficiently than analogous cells in other species, such as mice. Furthermore, ducks exhibit an increase in the number of neurons dedicated to this task in their sensory ganglia and a decrease in the number of neurons that detect temperature. Our findings provide an explanation for the acute mechanosensitivity of the duck bill at the level of somatosensory neurons.
Discontinuity in the responses of ecosystem processes and multifunctionality to altered soil community composition
Authors: Bradford Mark A. , Wood Stephen A. , Bardgett Richard D. , Black Helaina I. J. , Bonkowski Michael , Eggers Till , Grayston Susan J. , Kandeler Ellen , Manning Peter , Setälä Heikki , Jones T. Hefin
Published: September 2014

Significance

Ecosystem functioning is more strongly affected by biodiversity loss when multiple functions are considered because different species affect different functions. To quantify these biodiversity-functioning relationships, the emerging multifunctionality framework advocates calculation of indices that aggregate responses of individual functions. Data aggregation, however, is notorious for providing misleading information by obscuring true relationships between explanatory and response variables. We test the ability of common multifunctionality indices to reveal effects on key ecosystem functions of changes in soil communities. The multifunctionality indices all decrease with soil animal loss, but the responses of individual functions diverge markedly from these aggregated metrics. Application of the multifunctionality framework for landscape provision of multiple ecosystem services should therefore emphasize understanding relationships between communities and individual functions.
Range of cell-wall alterations enhance saccharification in
Brachypodium distachyon
mutants
Authors: Marriott Poppy E. , Sibout Richard , Lapierre Catherine , Fangel Jonatan U. , Willats William G. T. , Hofte Herman , Gómez Leonardo D. , McQueen-Mason Simon J.
Published: September 2014

Significance

Bioethanol produced from waste biomass from crops has the potential to provide a sustainable alternative to petroleum-based transportation fuel that does not compete with human food supply. The main obstacle to this approach is the resistance of this biomass to digestion. Thus, expensive energetic pretreatment and high enzyme inputs are needed to increase digestion. In this study, we screened a population of randomly mutated plants for digestibility with the aim of identifying novel factors that impact on this trait. We found a number of mutants with high digestibility and no impairments in growth or fitness. These mutants show a range of alterations in cell-wall composition, and we have mapped and characterized the mutant with the highest increase in digestibility.
Discrete elements for 3D microfluidics
Authors: Bhargava Krisna C. , Thompson Bryant , Malmstadt Noah
Published: September 2014

Significance

Microfluidic systems promise to improve the analysis and synthesis of materials, biological or otherwise, by lowering the required volume of fluid samples, offering a tightly controlled fluid-handling environment, and simultaneously integrating various chemical processes. To build these systems, designers depend on microfabrication techniques that restrict them to arranging their designs in two dimensions and completely fabricating their design in a single step. This study introduces modular, reconfigurable components containing fluidic and sensor elements adaptable to many different microfluidic circuits. These elements can be assembled to allow for 3D routing of channels. This assembly approach allows for the application of network analysis techniques like those used in classical electronic circuit design, facilitating the straightforward design of predictable flow systems.
Insulin and insulin-like growth factor 1 receptors are required for normal expression of imprinted genes
Authors: Boucher Jeremie , Charalambous Marika , Zarse Kim , Mori Marcelo A. , Kleinridders Andre , Ristow Michael , Ferguson-Smith Anne C. , Kahn C. Ronald
Published: September 2014

Significance

Imprinted genes are normally selectively expressed, depending on the parent from whom the gene is inherited. These genes play important roles in control of growth and metabolism. We find that the loss of insulin and insulin-like growth factor 1 (IGF1) receptors in cells induces a major decrease in expression of multiple imprinted genes, regardless of whether they would be maternally or paternally expressed. This deregulation is associated with changes in methylation of DNA, but is not due to classical imprinting control. Our results demonstrate a previously unrecognized function of insulin and IGF1 receptors independent of these hormones and provide a new pathway by which insulin and IGF1 receptors may regulate growth and metabolism during early development and thereafter.
Learning bundles of stimuli renders stimulus order as a cue, not a confound
Authors: Qian Ting , Aslin Richard N.
Published: September 2014

Significance

The effects of stimulus order on human cognition have been previously reported in various cognitive tasks, and the prevalent explanations have been that sensitivity to stimulus order is due to either constraints on cognitive resources (e.g., working memory) or misconceptions about probability axioms. Our work suggests a fundamentally different interpretation: Humans are sensitive to order because it serves as an important cue. This interpretation is philosophically consistent with the burgeoning literature on rational cognition, where human behavior has been shown to (at least approximately) match the statistically optimal solution of a task. We propose that redefining the role of stimulus order as a cue may provide a more general perspective for understanding human cognition.
Dominance of misfolded intermediates in the dynamics of α-helix folding
Authors: Lin Milo M. , Shorokhov Dmitry , Zewail Ahmed H.
Published: September 2014

Significance

Proteins fill the vast majority of infrastructural and functional roles at the biological nanoscale. Despite their structural variability, most proteins contain α-helix motifs. Aptly described as molecular zippers, α-helices form by first aligning numerous degrees of freedom to stabilize a helical nucleus, after which the helix can presumably rapidly grow. Here, we show that helix zipping in polyalanine can get “caught” by nonhelical contacts that block growth, and that these misfolded intermediates can dominate the folding process, leading to zipping times that are an order of magnitude longer than expected based on unimpeded growth. The dominance of intermediate misfolded structures and their influence on folding dynamics have implications for protein aggregation, which is of significance in diseases such as Alzheimer’s.
FBH1 affects warm temperature responses in the
Arabidopsis
circadian clock
Authors: Nagel Dawn H. , Pruneda-Paz Jose L. , Kay Steve A.
Published: September 2014

Significance

The circadian clock integrates external signals such as temperature with internal temporal processes to generate robust rhythms. However, the regulatory mechanism by which the clock integrates and responds to external temperature changes and the likely targets modulating this regulation are largely unknown. Leveraging data from a large-scale functional genomics screen, we identified a basic helix-loop-helix transcription factor that alters the clock response to warm temperature signals. We functionally characterized the regulation of this transcription factor on a central component of the circadian clock in
Arabidopsis
. The results of this study contribute to our understanding of how the complex regulatory machinery interacts with environmental signals.
Encoding order and developmental dyslexia: A family of skills predicting different orthographic components
Authors: Romani Cristina , Tsouknida Effie , Olson Andrew
Published: September 2014

We investigated order encoding in developmental dyslexia using a task that presented nonalphanumeric visual characters either simultaneously or sequentially—to tap spatial and temporal order encoding, respectively—and asked participants to reproduce their order. Dyslexic participants performed poorly in the sequential condition, but normally in the simultaneous condition, except for positions most susceptible to interference. These results are novel in demonstrating a selective difficulty with temporal order encoding in a dyslexic group. We also tested the associations between our order reconstruction tasks and: (a) lexical learning and phonological tasks; and (b) different reading and spelling tasks. Correlations were extensive when the whole group of participants was considered together. When dyslexics and controls were considered separately, different patterns of association emerged between orthographic tasks on the one side and tasks tapping order encoding, phonological processing, and written learning on the other. These results indicate that different skills support different aspects of orthographic processing and are impaired to different degrees in individuals with dyslexia. Therefore, developmental dyslexia is not caused by a single impairment, but by a family of deficits loosely related to difficulties with order. Understanding the contribution of these different deficits will be crucial to deepen our understanding of this disorder.
Arrest is a regulator of fiber-specific alternative splicing in the indirect flight muscles of Drosophila
Authors: Oas Sandy T. , Bryantsev Anton L. , Cripps Richard M.
Published: September 2014

Drosophila melanogaster flight muscles are distinct from other skeletal muscles, such as jump muscles, and express several uniquely spliced muscle-associated transcripts. We sought to identify factors mediating splicing differences between the flight and jump muscle fiber types. We found that the ribonucleic acid–binding protein Arrest (Aret) is expressed in flight muscles: in founder cells, Aret accumulates in a novel intranuclear compartment that we termed the Bruno body, and after the onset of muscle differentiation, Aret disperses in the nucleus. Down-regulation of the aret gene led to ultrastructural changes and functional impairment of flight muscles, and transcripts of structural genes expressed in the flight muscles became spliced in a manner characteristic of jump muscles. Aret also potently promoted flight muscle splicing patterns when ectopically expressed in jump muscles or tissue culture cells. Genetically, aret is located downstream of exd (extradenticle), hth (homothorax), and salm (spalt major), transcription factors that control fiber identity. Our observations provide insight into a transcriptional and splicing regulatory network for muscle fiber specification.
The Glassey conjecture on asymptotically flat manifolds
Authors: Wang Chengbo
Published: September 2014

We verify the

3
3

-dimensional Glassey conjecture on asymptotically flat manifolds

(

R

1
+
3

,

g

)

(\mathbb {R}^{1+3},\mathfrak {g})

, where the metric

g

\mathfrak {g}

is a certain small space-time perturbation of the flat metric, as well as the nontrapping asymptotically Euclidean manifolds. Moreover, for radial asymptotically flat manifolds

(

R

1
+
n

,

g

)

(\mathbb {R}^{1+n},\mathfrak {g})

with

n
≥
3

n\ge 3

, we verify the Glassey conjecture in the radial case. High dimensional wave equations with higher regularity are also discussed. The main idea is to exploit local energy and KSS estimates with variable coefficients, together with the weighted Sobolev estimates including trace estimates.
Comprehensive large-scale assessment of intrinsic protein disorder
Authors: Walsh Ian , Giollo Manuel , Di Domenico Tomás , Ferrari Carlo , Zimmermann Olav , Tosatto Silvio C. E.
Published: September 2014

Motivation: Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started to collect disorder annotations from multiple experimental structures.

Results: MobiDB annotates disorder for UniProt sequences, allowing us to conduct the first large-scale assessment of fast disorder predictors on 25 833 different sequences with X-ray crystallographic structures. In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations. (i) The predictors cluster according to their disorder definition, with a consensus giving more confidence. (ii) Previous assessments appear over-reliant on data annotated at the PDB chain level and performance is lower on entire UniProt sequences. (iii) Long disordered regions are harder to predict. (iv) Depending on the structural and functional types of the proteins, differences in prediction performance of up to 10% are observed.

Availability: The datasets are available from Web site at URL: http://mobidb.bio.unipd.it/lsd .

Contact:  silvio.tosatto@unipd.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Stars as resonant absorbers of gravitational waves
Authors: McKernan B. , Ford K. E. S. , Kocsis B. , Haiman Z.
Published: September 2014

Quadrupole oscillation modes in stars can resonate with incident gravitational waves (GWs), and grow non-linear at the expense of GW energy. Stars near massive black hole binaries (MBHBs) can act as GW-charged batteries, discharging radiatively. Mass-loss from these stars can prompt MBHB accretion at near-Eddington rates. GW opacity is independent of amplitude, so distant resonating stars can eclipse GW sources. Absorption by the Sun of GWs from Galactic white dwarf binaries may be detectable with second-generation space-based GW detectors as a shadow within a complex diffraction pattern.
Neuropsychological Functioning and Health‐Related Quality of Life
Authors: Sorensen Lisa G. , Neighbors Katie , Zhang Song , Limbers Christine A. , Varni James W. , Ng Vicky L. , Squires Robert H. , Alonso Estella M. ,   Pediatric Acute Liver Failure Study Group
Published: September 2014

Objectives:

Pediatric acute liver failure (PALF) is a rare but serious event, with poorly understood functional outcomes. The goal was to determine the prevalence of reduced neuropsychological functioning and health‐related quality of life (HRQOL) following PALF.

Methods:

This multicenter study examined neuropsychological functioning and HRQOL 1 to 6 (median 3.8) years after PALF. Participants ages 6 to 16 (median 9.9) years were recruited from the PALF registry and administered measures of intelligence, visual spatial/visual motor coordination, attention, executive function, depression, and adaptive skills. HRQOL and fatigue were assessed using the Pediatric Quality of Life Inventory 4.0 Generic Core Scales (PedsQL 4.0) and PedsQL Multidimensional Fatigue Scale.

Results:

A total of 36 patients participated; 50% were boys and 67% were white. Median age at PALF was 5.6 years. A history of grade 3 or 4 hepatic encephalopathy was reported in 5/36 (14%) participants and 23/36 (64%) received a liver transplant. Visual spatial ability was significantly better than norms (P = 0.009), but motor coordination was worse (P = 0.04). Teachers (P = 0.04 to P < 0.0001) and parents (P = 0.005) reported more executive deficits versus norms, and participants had worse attention (P = 0.02). Participants did not differ significantly from norms on IQ, depression, or adaptive functioning. All of the child self‐report PedsQL Generic Core and fatigue scales were significantly lower than a matched healthy sample (P = 0.001 to P < 0.0001) and parent proxy report was lower on the fatigue scales (P = 0.001 to P < 0.0001).

Conclusions:

Long‐term PALF survivors demonstrate average IQ and visual spatial ability, but greater than expected impairments in motor skills, attention, executive function, HRQOL, and fatigue.
Structures of pyruvate kinases display evolutionarily divergent allosteric strategies
Authors: Morgan Hugh P. , Zhong Wenhe , McNae Iain W. , Michels Paul A. M. , Fothergill-Gilmore Linda A. , Walkinshaw Malcolm D.
Published: September 2014

The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of
Trypanosoma cruzi
pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (
k
cat
/
S
0.5
). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists
T. cruzi
,
T. brucei
and
Leishmania mexicana
shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (
k
cat
/
S
0.5
) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.
Hydrodynamics of periodic breathers
Authors: Chabchoub A. , Kibler B. , Dudley J. M. , Akhmediev N.
Published: September 2014

We report the first experimental observation of periodic breathers in water waves. One of them is Kuznetsov–Ma soliton and another one is Akhmediev breather. Each of them is a localized solution of the nonlinear Schrödinger equation (NLS) on a constant background. The difference is in localization which is either in time or in space. The experiments conducted in a water wave flume show results that are in good agreement with the NLS theory. Basic features of the breathers that include the maximal amplitudes and spectra are consistent with the theoretical predictions.