bluuebunny/crossref_metadata_2025 huggingface dataset:
In silico bone mechanobiology: modeling a multifaceted biological system
Authors: Giorgi Mario , Verbruggen Stefaan W. , Lacroix Damien
Published: September 2016

Mechanobiology, the study of the influence of mechanical loads on biological processes through signaling to cells, is fundamental to the inherent ability of bone tissue to adapt its structure in response to mechanical stimulation. The immense contribution of computational modeling to the nascent field of bone mechanobiology is indisputable, having aided in the interpretation of experimental findings and identified new avenues of inquiry. Indeed, advances in computational modeling have spurred the development of this field, shedding new light on problems ranging from the mechanical response to loading by individual cells to tissue differentiation during events such as fracture healing. To date, in silico bone mechanobiology has generally taken a reductive approach in attempting to answer discrete biological research questions, with research in the field broadly separated into two streams: (1) mechanoregulation algorithms for predicting mechanobiological changes to bone tissue and (2) models investigating cell mechanobiology. Future models will likely take advantage of advances in computational power and techniques, allowing multiscale and multiphysics modeling to tie the many separate but related biological responses to loading together as part of a larger systems biology approach to shed further light on bone mechanobiology. Finally, although the ever‐increasing complexity of computational mechanobiology models will inevitably move the field toward patient‐specific models in the clinic, the determination of the context in which they can be used safely for clinical purpose will still require an extensive combination of computational and experimental techniques applied to in vitro and in vivo applications. WIREs Syst Biol Med 2016, 8:485–505. doi: 10.1002/wsbm.1356

This article is categorized under:

Analytical and Computational Methods > Computational Methods

Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models

Physiology > Physiology of Model Organisms
Lying behaviour and IgG-levels of newborn calves after feeding colostrum via tube and nipple bottle feeding
Authors: Bonk Stephanie , Nadalin Audrey , Heuwieser Wolfgang , Veira Douglas
Published: September 2016

Oesophageal tube feeding colostrum is used to ensure sufficient colostrum intake in newborn calves but the impact of tube feeding on animal behaviour is unclear. Therefore the objective of this study was to compare lying behaviour of tube-fed or bottle-fed dairy calves. Calves (n= 37) in 3 groups were offered 3·5 l colostrum 2 h after birth. Calves of the bottle group were fed with a nipple bottle. Calves of the placebo tubing group were tubed for 4 min but no colostrum was given and they were then fed with a nipple bottle. Calves of the tubing group received 3·5 l colostrum via tube feeding. Consumed amount of bottle and placebo tubing calves was recorded. If they refused some of the offered 3·5 l the rest was offered in a second feeding 2 h later. Lying behaviour was measured by data loggers fitted to right hind leg for 3 d. Blood samples were taken 24 h after birth for determination of IgG concentration. The voluntary colostrum intake differed significantly between bottle-fed and placebo tubed calves at first feeding. Considering both colostrum feedings, bottle-fed calves consumed 3·44 ± 0·14 l and placebo tubed calves consumed 3·20 ± 0·38 l colostrum. ImmunoglobulinG intake (255·6 ± 77·5 g IgG), serum IgG concentration 24 h after birth (22·8 ± 6·7 g/l) and total serum protein concentration (6·1 ± 0·6 g/dl) did not differ between groups. None of the calves had a failure of passive transfer. There was no effect of tubing on lying behaviour.
Modelling lactation curve for milk fat to protein ratio in Iranian buffaloes (Bubalus bubalis) using non-linear mixed models
Authors: Hossein-Zadeh Navid Ghavi
Published: September 2016

The aim of this study was to compare seven non-linear mathematical models (Brody, Wood, Dhanoa, Sikka, Nelder, Rook and Dijkstra) to examine their efficiency in describing the lactation curves for milk fat to protein ratio (FPR) in Iranian buffaloes. Data were 43 818 test-day records for FPR from the first three lactations of Iranian buffaloes which were collected on 523 dairy herds in the period from 1996 to 2012 by the Animal Breeding Center of Iran. Each model was fitted to monthly FPR records of buffaloes using the non-linear mixed model procedure (PROC NLMIXED) in SAS and the parameters were estimated. The models were tested for goodness of fit using Akaike's information criterion (AIC), Bayesian information criterion (BIC) and log maximum likelihood (−2 Log L). The Nelder and Sikka mixed models provided the best fit of lactation curve for FPR in the first and second lactations of Iranian buffaloes, respectively. However, Wood, Dhanoa and Sikka mixed models provided the best fit of lactation curve for FPR in the third parity buffaloes. Evaluation of first, second and third lactation features showed that all models, except for Dijkstra model in the third lactation, under-predicted test time at which daily FPR was minimum. On the other hand, minimum FPR was over-predicted by all equations. Evaluation of the different models used in this study indicated that non-linear mixed models were sufficient for fitting test-day FPR records of Iranian buffaloes.
Pre-calving feeding of rumen-protected rice bran to multiparous dairy cows improves recovery of calcaemia after calving
Authors: Martín-Tereso Javier , Martens Holger , Deiner Carolin , van Laar Harmen , den Hartog Leo A. , Verstegen Martin W A
Published: September 2016

Dairy cows can have different degrees of hypocalcaemia around calving. Lowering dietary Ca availability before calving can prevent it. Rice bran, treated for lower rumen degradability of phytic acid can reduce dietary availability of Ca. During 3 periods of 3 weeks, 113 multiparous cows calved in a single close-up group, which was fed first a control diet, then 140 g/kg DM of rumen-protected rice bran, and at last the control diet again. Cows joined the group 3 weeks before expected calving date and left it at calving. Blood samples were taken weekly before parturition and 0, 6 and 12 h after calving, as well as 3 and 28 d in lactation. Serum was analysed for Ca, Mg, and P. Rice bran introduction produced a transient serum Ca decrease. Rice bran feeding reduced serum P and its withdrawal reduced serum Mg. Serum Ca at calving, nadir of serum Ca and serum Ca the first 3 d after calving was higher in cows calving during rice bran feeding. Serum P decreased less and recovered faster after calving when cows had been fed rice bran. Rumen-protected rice bran reduced dietary availability of Ca and induced adaptation of Ca metabolism resulting in improved Ca and P homoeostasis at calving.
Leucocyte expression of genes implicated in the plasminogen activation cascade is modulated by yoghurt peptides
Authors: Theodorou Georgios , Politis Ioannis
Published: September 2016

The urokinase-plasminogen activator (u-PA), its receptor (u-PAR) and the inhibitors of u-PA (PAI-1 and PAI-2) provide a multi-molecular system in leucocytes that exerts pleiotropic functions influencing the development of inflammatory and immune responses. The objective of the present study was to examine the ability of water soluble extracts (WSE) obtained from traditional Greek yoghurt made from bovine or ovine milk to modulate the expression of u-PA, u-PAR, PAI-1 and PAI-2 in ovine monocytes and neutrophils. WSE were obtained from 8 commercial traditional type Greek yoghurts made from ovine or bovine milk. WSE upregulated the expression of all 4 u-PA related genes in monocytes but the upregulation was much higher in the PAI-1 (10-fold) than in u-PA and u-PAR (3–4 fold) thus, shifting the system towards inhibition. In line with this observation, WSE reduced total and membrane-bound u-PA activity in monocytes. In neutrophils, WSE caused small (50–60%) but significant (P< 0·05) reductions in expression of u-PAR and PAI-2 but had no effect on expression of u-PA, PAI-1 and on total cell-associated and membrane-bound u-PA activity. WSE from yoghurts made from bovine or ovine milk were essentially equally effective in affecting the u-PA system except for the u-PAR gene in ovine neutrophils that was affected (reduced) by the ovine and not the bovine WSE. In conclusion, peptides present in WSE modulated the expression of u-PA related genes but the effect was much more prominent in monocytes than in neutrophils.
Separation and quantification of milk casein from different buffalo breeds
Authors: Li Shanshan , Li Ling , Zeng Qingkun , Liu Jianxin , Ren Daxi
Published: September 2016

Understanding the milk protein expression profile in different buffalo breeds plays an important role in improving hybrid selection and determining the effects on milk protein synthesis. The aim of this research is to compare the differences in milk protein content, composition and distribution between River buffalo and their crossbreeds for hybrid screening. Four groups of milk samples that included Nili-Ravi (N), Murrah (M), a Nili-Ravi-Murrah crossbreed (M-N), and a crossbreed of river buffalo with local swamp buffalo (C) were collected. The protein composition of the buffalo milk was determined by RP-HPLC. A gel-based proteomic approach consisting of two-dimensional gel electrophoresis coupled with mass spectrometry was utilised for the detailed protein characterisation of milk from different breeds. The results of this analysis showed that the river/swamp buffalo crossbreed (C) displayed the highest content of total protein (4·46%) and κ-casein (11·14%) but the lowest content of α-lactalbumin (6·79%). By selecting 23 different protein spots among the four types of milk that contained the most spots corresponding to κ-casein, β-casein and αs1-casein, correlations between the crossbreeds, protein polymorphism and phosphorylation could be made. The results of this study indicate that crossbreeding a swamp buffalo with a river buffalo has a notable effect on the protein content and composition that may be exploited for producing high-quality raw milk in food technology applications and dairy food production.
New Digital Maps Depict Alaska in Unprecedented Detail
Authors: Showstack Randy
Published: September 2016

The Obama administration plans to release high-resolution terrain models in 2017 for the entire Arctic.
Transition metal catalysis in the mitochondria of living cells
Authors: Tomás-Gamasa María , Martínez-Calvo Miguel , Couceiro José R. , Mascareñas José L.
Published: September 2016

The development of transition metal catalysts capable of promoting non-natural transformations within living cells can open significant new avenues in chemical and cell biology. Unfortunately, the complexity of the cell makes it extremely difficult to translate standard organometallic chemistry to living environments. Therefore, progress in this field has been very slow, and many challenges, including the possibility of localizing active metal catalysts into specific subcellular sites or organelles, remain to be addressed. Herein, we report a designed ruthenium complex that accumulates preferentially inside the mitochondria of mammalian cells, while keeping its ability to react with exogenous substrates in a bioorthogonal way. Importantly, we show that the subcellular catalytic activity can be used for the confined release of fluorophores, and even allows selective functional alterations in the mitochondria by the localized transformation of inert precursors into uncouplers of the membrane potential.
Type II enteropathy-associated T-cell lymphoma features a unique genomic profile with highly recurrent SETD2 alterations
Authors: Roberti Annalisa , Dobay Maria Pamela , Bisig Bettina , Vallois David , Boéchat Cloé , Lanitis Evripidis , Bouchindhomme Brigitte , Parrens Marie- Cécile , Bossard Céline , Quintanilla-Martinez Leticia , Missiaglia Edoardo , Gaulard Philippe , de Leval Laurence
Published: September 2016

Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole-exome sequencing of 15 EATL-II tumour-normal tissue pairs. The tumour suppressor gene SETD2 encoding a non-redundant H3K36-specific trimethyltransferase is altered in 14/15 cases (93%), mainly by loss-of-function mutations and/or loss of the corresponding locus (3p21.31). These alterations consistently correlate with defective H3K36 trimethylation. The JAK/STAT pathway comprises recurrent STAT5B (60%), JAK3 (46%) and SH2B3 (20%) mutations, including a STAT5B V712E activating variant. In addition, frequent mutations in TP53, BRAF and KRAS are observed. Conversely, in EATL-I, no SETD2, STAT5B or JAK3 mutations are found, and H3K36 trimethylation is preserved. This study describes SETD2 inactivation as EATL-II molecular hallmark, supports EATL-I and -II being two distinct entities, and defines potential new targets for therapeutic intervention.
NK cell development requires Tsc1-dependent negative regulation of IL-15-triggered mTORC1 activation
Authors: Yang Meixiang , Chen Shasha , Du Juan , He Junming , Wang Yuande , Li Zehua , Liu Guangao , Peng Wanwen , Zeng Xiaokang , Li Dan , Xu Panglian , Guo Wei , Chang Zai , Wang Song , Tian Zhigang , Dong Zhongjun
Published: September 2016

Activation of metabolic signalling by IL-15 is required for natural killer (NK) cell development. Here we show that Tsc1, a repressor of mTOR, is dispensable for the terminal maturation, survival and function of NK cells but is critical to restrict exhaustive proliferation of immature NK cells and activation downstream of IL-15 during NK cell development. Tsc1 is expressed in immature NK cells and is upregulated by IL-15. Haematopoietic-specific deletion of Tsc1 causes a marked decrease in the number of NK cells and compromises rejection of ‘missing-self’ haematopoietic tumours and allogeneic bone marrow. The residual Tsc1-null NK cells display activated, pro-apoptotic phenotype and elevated mTORC1 activity. Deletion of Raptor, a component of mTORC1, largely reverses these defects. Tsc1-deficient NK cells express increased levels of T-bet and downregulate Eomes and CD122, a subunit of IL-15 receptor. These results reveal a role for Tsc1-dependent inhibition of mTORC1 activation during immature NK cell development.
Vancomycin susceptibility in methicillin-resistant Staphylococcus aureus is mediated by YycHI activation of the WalRK essential two-component regulatory system
Authors: Cameron David R. , Jiang Jhih-Hang , Kostoulias Xenia , Foxwell Daniel J. , Peleg Anton Y.
Published: September 2016

The treatment of infections caused by methicillin-resistant Staphylococcus aureus is complicated by the emergence of strains with intermediate-level resistance to vancomycin (termed VISA). We have characterised a molecular pathway involved in the in vivo evolution of VISA mediated by the regulatory proteins YycH and YycI. In contrast to their function in other bacterial species, we report a positive role for these auxiliary proteins in regulation of the two-component regulator WalRK. Transcriptional profiling of yycH and yycI deletion mutants revealed downregulation of the ‘WalRK regulon’ including cell wall hydrolase genes atlA and sle1, with functional autolysis assays supporting these data by showing an impaired autolytic phenotype for each deletion strain. Using bacterial-two hybrid assays, we showed that YycH and YycI interact and that YycHI also interacts with the sensor kinase WalK, forming a ternary protein complex. Mutation to YycH or YycI associated with clinical VISA strains had a deleterious impact on the YycHI/WalK complex, suggesting that the interaction is important for the regulation of WalRK. Taken together, we have described a novel antibiotic resistance strategy for the human pathogen S. aureus, whereby YycHI mutations are selected for in vivo leading to reduced WalRK activation, impaired cell wall turnover and ultimately reduced vancomycin efficacy.
Coherence-Gated Sensorless Adaptive Optics Multiphoton Retinal Imaging
Authors: Cua Michelle , Wahl Daniel J. , Zhao Yuan , Lee Sujin , Bonora Stefano , Zawadzki Robert J. , Jian Yifan , Sarunic Marinko V.
Published: September 2016

Multiphoton microscopy enables imaging deep into scattering tissues. The efficient generation of non-linear optical effects is related to both the pulse duration (typically on the order of femtoseconds) and the size of the focused spot. Aberrations introduced by refractive index inhomogeneity in the sample distort the wavefront and enlarge the focal spot, which reduces the multiphoton signal. Traditional approaches to adaptive optics wavefront correction are not effective in thick or multi-layered scattering media. In this report, we present sensorless adaptive optics (SAO) using low-coherence interferometric detection of the excitation light for depth-resolved aberration correction of two-photon excited fluorescence (TPEF) in biological tissue. We demonstrate coherence-gated SAO TPEF using a transmissive multi-actuator adaptive lens for in vivo imaging in a mouse retina. This configuration has significant potential for reducing the laser power required for adaptive optics multiphoton imaging and for facilitating integration with existing systems.
miR-564 acts as a dual inhibitor of PI3K and MAPK signaling networks and inhibits proliferation and invasion in breast cancer
Authors: Mutlu Merve , Saatci Özge , Ansari Suhail A. , Yurdusev Emre , Shehwana Huma , Konu Özlen , Raza Umar , Şahin Özgür
Published: September 2016

Dysregulation of PI3K and MAPK pathways promotes uncontrolled cell proliferation, apoptotic inhibition and metastasis. Individual targeting of these pathways using kinase inhibitors has largely been insufficient due to the existence of cross-talks between these parallel cascades. MicroRNAs are small non-coding RNAs targeting several genes simultaneously and controlling cancer-related processes. To identify miRNAs repressing both PI3K and MAPK pathways in breast cancer, we re-analyzed our previous miRNA mimic screen data with reverse phase protein array (RPPA) output and identified miR-564 inhibiting both PI3K and MAPK pathways causing markedly decreased cell proliferation through G1 arrest. Moreover, ectopic expression of miR-564 blocks epithelial-mesenchymal transition (EMT) and reduces migration and invasion of aggressive breast cancer cells. Mechanistically, miR-564 directly targets a network of genes comprising AKT2, GNA12, GYS1 and SRF, thereby facilitating simultaneous repression of PI3K and MAPK pathways. Notably, combinatorial knockdown of these target genes using a cocktail of siRNAs mimics the phenotypes exerted upon miR-564 expression. Importantly, high miR-564 expression or low expression of target genes in combination is significantly correlated with better distant relapse-free survival of patients. Overall, miR-564 is a potential dual inhibitor of PI3K and MAPK pathways and may be an attractive target and prognostic marker for breast cancer.
Spin filtering and switching action in a diamond network with magnetic-nonmagnetic atomic distribution
Authors: Pal Biplab , Dutta Paramita
Published: September 2016

We propose a simple model quantum network consisting of diamond-shaped plaquettes with deterministic distribution of magnetic and non-magnetic atoms in presence of a uniform external magnetic flux in each plaquette and predict that such a simple model can be a prospective candidate for spin filter as well as flux driven spintronic switch. The orientations and the amplitudes of the substrate magnetic moments play a crucial role in the energy band engineering of the two spin channels which essentially gives us a control over the spin transmission leading to a spin filtering effect. The externally tunable magnetic flux plays an important role in inducing a switch on-switch off effect for both the spin states indicating the behavior like a spintronic switch. Even a correlated disorder configuration in the on-site potentials and in the magnetic moments may lead to disorder-induced spin filtering phenomenon where one of the spin channel gets entirely blocked leaving the other one transmitting over the entire allowed energy regime. All these features are established by evaluating the density of states and the two terminal transmission probabilities using the transfer-matrix formalism within a tight-binding framework. Experimental realization of our theoretical study may be helpful in designing new spintronic devices.
Increased phytotoxic O3 dose accelerates autumn senescence in an O3-sensitive beech forest even under the present-level O3
Authors: Kitao Mitsutoshi , Yasuda Yukio , Kominami Yuji , Yamanoi Katsumi , Komatsu Masabumi , Miyama Takafumi , Mizoguchi Yasuko , Kitaoka Satoshi , Yazaki Kenichi , Tobita Hiroyuki , Yoshimura Kenichi , Koike Takayoshi , Izuta Takeshi
Published: September 2016

Ground-level ozone (O3) concentrations are expected to increase over the 21st century, especially in East Asia. However, the impact of O3 has not been directly assessed at the forest level in this region. We performed O3 flux-based risk assessments of carbon sequestration capacity in an old cool temperate deciduous forest, consisting of O3-sensitive Japanese beech (Fagus crenata), and in a warm temperate deciduous and evergreen forest dominated by O3-tolerant Konara oak (Quercus serrata) based on long-term CO2 flux observations. On the basis of a practical approach for a continuous estimation of canopy-level stomatal conductance (Gs), higher phytotoxic ozone dose above a threshold of 0 uptake (POD0) with higher Gs was observed in the beech forest than that in the oak forest. Light-saturated gross primary production, as a measure of carbon sequestration capacity of forest ecosystem, declined earlier in the late growth season with increasing POD0, suggesting an earlier autumn senescence, especially in the O3-sensitive beech forest, but not in the O3-tolerant oak forest.
Joint estimation of preferential attachment and node fitness in growing complex networks
Authors: Pham Thong , Sheridan Paul , Shimodaira Hidetoshi
Published: September 2016

Complex network growth across diverse fields of science is hypothesized to be driven in the main by a combination of preferential attachment and node fitness processes. For measuring the respective influences of these processes, previous approaches make strong and untested assumptions on the functional forms of either the preferential attachment function or fitness function or both. We introduce a Bayesian statistical method called PAFit to estimate preferential attachment and node fitness without imposing such functional constraints that works by maximizing a log-likelihood function with suitably added regularization terms. We use PAFit to investigate the interplay between preferential attachment and node fitness processes in a Facebook wall-post network. While we uncover evidence for both preferential attachment and node fitness, thus validating the hypothesis that these processes together drive complex network evolution, we also find that node fitness plays the bigger role in determining the degree of a node. This is the first validation of its kind on real-world network data. But surprisingly the rate of preferential attachment is found to deviate from the conventional log-linear form when node fitness is taken into account. The proposed method is implemented in the R package PAFit.
Asymmetric competition over calling sites in two closely related treefrog species
Authors: Borzée Amaël , Kim Jun Young , Jang Yikweon
Published: September 2016

Interspecific competition occurs when one species using a resource limits the use of that resource by another species. A dominance relationship between the species competing over a resource may result in asymmetric competition. Here, we tested the hypothesis that two sympatric treefrog species, the endangeredHyla suweonensisand the abundantH. japonica, compete with each other over calling sites. We observed the locations of calling individuals of the two treefrog species in rice paddies and tested whether removing one species affected the calling locations of the other species. Individuals of the two species were spatially isolated within rice paddies, withH. japonicaat the edges andH. suweonensisin the interior. MaleH. suweonensismoved towards the edges of rice paddies when maleH. japonicawere removed from the area, whereas maleH. japonicahardly moved when maleH. suweonensiswere removed. The results of both studies are consistent with asymmetric interspecific competition, in which the calling locations ofH. suweonensisare affected by the calling activity ofH. japonica. In addition,H. japonicawere found “sitting” on the substrate during call production, whereasH. suweonensiswere “holding” onto vegetation. The difference in calling posture may represent an adaptive response to asymmetric interspecific competition.
A universal design to realize a tunable perfect absorber from infrared to microwaves
Authors: Smaali Rafik , Omeis Fatima , Moreau Antoine , Taliercio Thierry , Centeno Emmanuel
Published: September 2016

We propose a design for an universal absorber, characterized by a resonance frequency that can be tuned from visible to microwave frequencies independently of the choice of the metal and the dielectrics involved. An almost perfect absorption up to 99.8% is demonstrated at resonance for all polarization states of light and for a very wide angular aperture. These properties originate from a magnetic Fabry-Perot mode that is confined in a dielectric spacer of λ/100 thickness by a metamaterial layer and a mirror. An extraordinary large funneling through nano-slits explains how light can be trapped in the structure. Simple scaling laws can be used as a recipe to design ultra-thin perfect absorbers whatever the materials and the desired resonance wavelength, making our design truly universal.
Stochastic assembly in a subtropical forest chronosequence: evidence from contrasting changes of species, phylogenetic and functional dissimilarity over succession
Authors: Mi Xiangcheng , Swenson Nathan G. , Jia Qi , Rao Mide , Feng Gang , Ren Haibao , Bebber Daniel P. , Ma Keping
Published: September 2016

Deterministic and stochastic processes jointly determine the community dynamics of forest succession. However, it has been widely held in previous studies that deterministic processes dominate forest succession. Furthermore, inference of mechanisms for community assembly may be misleading if based on a single axis of diversity alone. In this study, we evaluated the relative roles of deterministic and stochastic processes along a disturbance gradient by integrating species, functional, and phylogenetic beta diversity in a subtropical forest chronosequence in Southeastern China. We found a general pattern of increasing species turnover, but little-to-no change in phylogenetic and functional turnover over succession at two spatial scales. Meanwhile, the phylogenetic and functional beta diversity were not significantly different from random expectation. This result suggested a dominance of stochastic assembly, contrary to the general expectation that deterministic processes dominate forest succession. On the other hand, we found significant interactions of environment and disturbance and limited evidence for significant deviations of phylogenetic or functional turnover from random expectations for different size classes. This result provided weak evidence of deterministic processes over succession. Stochastic assembly of forest succession suggests that post-disturbance restoration may be largely unpredictable and difficult to control in subtropical forests.
Depinning of domain walls in permalloy nanowires with asymmetric notches
Authors: Gao Y. , You B. , Ruan X. Z. , Liu M. Y. , Yang H. L. , Zhan Q. F. , Li Z. , Lei N. , Zhao W. S. , Pan D. F. , Wan J. G. , Wu J. , Tu H. Q. , Wang J. , Zhang W. , Xu Y. B. , Du J.
Published: September 2016

Effective control of the domain wall (DW) motion along the magnetic nanowires is of great importance for fundamental research and potential application in spintronic devices. In this work, a series of permalloy nanowires with an asymmetric notch in the middle were fabricated with only varying the width (d) of the right arm from 200 nm to 1000 nm. The detailed pinning and depinning processes of DWs in these nanowires have been studied by using focused magneto-optic Kerr effect (FMOKE) magnetometer, magnetic force microscopy (MFM) and micromagnetic simulation. The experimental results unambiguously exhibit the presence of a DW pinned at the notch in a typical sample with d equal to 500 nm. At a certain range of 200 nm < d < 500 nm, both the experimental and simulated results show that the DW can maintain or change its chirality randomly during passing through the notch, resulting in two DW depinning fields. Those two depinning fields have opposite d dependences, which may be originated from different potential well/barrier generated by the asymmetric notch with varying d.
Nucleation and strain-stabilization during organic semiconductor thin film deposition
Authors: Li Yang , Wan Jing , Smilgies Detlef-M. , Bouffard Nicole , Sun Richard , Headrick Randall L.
Published: September 2016

The nucleation mechanisms during solution deposition of organic semiconductor thin films determine the grain morphology and may influence the crystalline packing in some cases. Here, in-situ optical spectromicroscopy in reflection mode is used to study the growth mechanisms and thermal stability of 6,13-bis(trisopropylsilylethynyl)-pentacene thin films. The results show that the films form in a supersaturated state before transforming to a solid film. Molecular aggregates corresponding to subcritical nuclei in the crystallization process are inferred from optical spectroscopy measurements of the supersaturated region. Strain-free solid films exhibit a temperature-dependent blue shift of optical absorption peaks due to a continuous thermally driven change of the crystalline packing. As crystalline films are cooled to ambient temperature they become strained although cracking of thicker films is observed, which allows the strain to partially relax. Below a critical thickness, cracking is not observed and grazing incidence X-ray diffraction measurements confirm that the thinnest films are constrained to the lattice constants corresponding to the temperature at which they were deposited. Optical spectroscopy results show that the transition temperature between Form I (room temperature phase) and Form II (high temperature phase) depends on the film thickness, and that Form I can also be strain-stabilized up to 135 °C.
G-actin guides p53 nuclear transport: potential contribution of monomeric actin in altered localization of mutant p53
Authors: Saha Taniya , Guha Deblina , Manna Argha , Panda Abir Kumar , Bhat Jyotsna , Chatterjee Subhrangsu , Sa Gaurisankar
Published: September 2016

p53 preserves genomic integrity by restricting anomaly at the gene level. Till date, limited information is available for cytosol to nuclear shuttling of p53; except microtubule-based trafficking route, which utilizes minus-end directed motor dynein. The present study suggests that monomeric actin (G-actin) guides p53 traffic towards the nucleus. Histidine-tag pull-down assay using purified p53(1–393)-His and G-actin confirms direct physical association between p53 and monomeric G-actin. Co-immunoprecipitation data supports the same. Confocal imaging explores intense perinuclear colocalization between p53 and G-actin. To address atomistic details of the complex, constraint-based docked model of p53:G-actin complex was generated based on crystal structures. MD simulation reveals that p53 DNA-binding domain arrests very well the G-actin protein. Docking benchmark studies have been carried out for a known crystal structure, 1YCS (complex between p53DBD and BP2), which validates the docking protocol we adopted. Co-immunoprecipitation study using “hot-spot” p53 mutants suggested reduced G-actin association with cancer-associated p53 conformational mutants (R175H and R249S). Considering these findings, we hypothesized that point mutation in p53 structure, which diminishes p53:G-actin complexation results in mutant p53 altered subcellular localization. Our model suggests p53Arg249 form polar-contact with Arg357 of G-actin, which upon mutation, destabilizes p53:G-actin interaction and results in cytoplasmic retention of p53R249S.
Spin orbit torques and Dzyaloshinskii-Moriya interaction in dual-interfaced Co-Ni multilayers
Authors: Yu Jiawei , Qiu Xuepeng , Wu Yang , Yoon Jungbum , Deorani Praveen , Besbas Jean Mourad , Manchon Aurelien , Yang Hyunsoo
Published: September 2016

We study the spin orbit torque (SOT) and Dzyaloshinskii-Moriya interaction (DMI) in the dual-interfaced Co-Ni perpendicular multilayers. Through the combination of top and bottom layer materials (Pt, Ta, MgO and Cu), SOT and DMI are efficiently manipulated due to an enhancement or cancellation of the top and bottom contributions. However, SOT is found to originate mostly from the bulk of a heavy metal (HM), while DMI is more of interfacial origin. In addition, we find that the direction of the domain wall (DW) motion can be either along or against the electron flow depending on the DW tilting angle when there is a large DMI. Such an abnormal DW motion induces a large assist field required for hysteretic magnetization reversal. Our results provide insight into the role of DMI in SOT driven magnetization switching, and demonstrate the feasibility of achieving desirable SOT and DMI for spintronic devices.
Infrared Spectroscopic Evidences of Strong Electronic Correlations in (Sr1−xLax)3Ir2O7
Authors: Ahn Gihyeon , Song S. J. , Hogan T. , Wilson S. D. , Moon S. J.
Published: September 2016

We report on infrared spectroscopic studies of the electronic response of the (Sr1−xLax)3Ir2O7 system. Our experiments revealed hallmarks of strong electronic correlations in the evolution of the electronic response across the filling-controlled insulator-metal transition. We observed a collapse of the Jeff = 1/2 Mott gap accompanying the transfer of the spectral weight from the high-energy region to the gap region with electron doping. The intraband conductivity at the metallic side of the transition was found to consist of coherent Drude-like and incoherent responses. The sum rule and the extended Drude model analyses further indicated a large mass enhancement. Our results demonstrate a critical role of the electronic correlations in the charge dynamics of the (Sr1−xLax)3Ir2O7 system.
A novel molecular synchrotron for cold collision and EDM experiments
Authors: Hou Shunyong , Wei Bin , Deng Lianzhong , Yin Jianping
Published: September 2016

Limited by the construction demands, the state-of-the-art molecular synchrotrons consist of only 40 segments that hardly make a good circle. Imperfections in the circular structure will lead to the appearance of unstable velocity regions (i.e. stopbands), where molecules of certain forward velocity will be lost from the structure. In this paper, we propose a stopband-free molecular synchrotron. It contains 1570 ring electrodes, which nearly make a perfect circle, capable of confining both light and heavy polar molecules in the low-field-seeking states. Molecular packets can be conveniently manipulated with this synchrotron by various means, like acceleration, deceleration or even trapping. Trajectory calculations are carried out using a pulsed 88SrF molecular beam with a forward velocity of 50 m/s. The results show that the molecular beam can make more than 500 round trips inside the synchrotron with a 1/e lifetime of 6.2 s. The synchrotron can find potential applications in low-energy collision and reaction experiments or in the field of precision measurements, such as the searches for electric dipole moment of elementary particles.
Low-Temperature Synthesis of Bismuth Chalcohalides: Candidate Photovoltaic Materialswith Easily, Continuously Controllable Band gap
Authors: Kunioku Hironobu , Higashi Masanobu , Abe Ryu
Published: September 2016

Although bismuth chalcohalides, such as BiSI and BiSeI, have been recently attractingconsiderable attention as photovoltaic materials, the methods available tosynthesize them are quite limited thus far. In this study, a novel, facile method tosynthesize these chalcohalides, includingBiSBr1−xIx solid solutions,at low temperatures was developed via the substitution of anions fromO2− to S2− (orSe2−) using bismuth oxyhalide precursors. Completephase transition was readily observed upon treatment of BiOI particles withH2S or H2Se at surprisingly low temperatures of less than150 °C and short reaction times of less than1 h, producing BiSI and BiSeI particles, respectively. This method wasalso applied for synthesizingBiSBr1−xIx, where continuouschanges in their band gaps were observed depending on the ratio between iodine andbromine. The composition of all elements (except oxygen) in the chalcohalides thusproduced was almost identical to that of the oxyhalide precursors, attributed to thesuppressed volatilization of halogens at such low temperatures. All chalcohalidesloaded on FTO clearly exhibited an anodic photocurrent in an acetonitrile solutioncontaining I−, attributed to their n-type nature, e.g.,the BiSI electrode exhibited high IPCE (64% at 700 nm,+0.2 V vs. Ag/AgCl).
Transition between segregation and aggregation: the role of environmental constraints
Authors: Nicolis Stamatios C. , Halloy José , Deneubourg Jean-Louis
Published: September 2016

Interactions between sub-groups (species, strains) have been reported in many species among many taxae. We propose a generic model based on earlier experiments accounting for both conspecific (or between individuals of the same strains) and heterospecific (or between strains) interactions. The model predicts different collective behaviours without any change of individuals’ algorithm as some key generic parameters such as the carrying capacity, the number of individuals involved and the strength of inter-attraction between sub-groups are varied. A key result is the possibility for sub-groups to segregate between patches and for transition between different patterns, even in absence of active agonistic behaviour. The model can be viewed as a network of feedbacks that is independent of the signals or cues involved in mixed groups interactions. Its predictions are therefore applicable to a wide spectrum of situations including social insects (inter castes interaction) and provides insights on possible mechanisms that can be at work.
Contribution of the respiratory network to rhythm and motor output revealed by modulation of GIRK channels, somatostatin and neurokinin-1 receptors
Authors: Montandon Gaspard , Liu Hattie , Horner Richard L.
Published: September 2016

Breathing is generated by a respiratory network in the brainstem. At its core, a population of neurons expressing neurokinin-1 receptors (NK1R) and the peptide somatostatin (SST) form the preBötzinger Complex (preBötC), a site essential for the generation of breathing. PreBötC interneurons generate rhythm and follower neurons shape motor outputs by activating upper airway respiratory muscles. Since NK1R-expressing preBötC neurons are preferentially inhibited by μ-opioid receptors via activation of GIRK channels, NK1R stimulation may also involve GIRK channels. Hence, we identify the contribution of GIRK channels to rhythm, motor output and respiratory modulation by NK1Rs and SST. In adult rats, GIRK channels were identified in NK1R-expressing preBötC cells. Their activation decreased breathing rate and genioglossus muscle activity, an important upper airway muscle. NK1R activation increased rhythmic breathing and genioglossus muscle activity in wild-type mice, but not in mice lacking GIRK2 subunits (GIRK2−/−). Conversely, SST decreased rhythmic breathing via SST2 receptors, reduced genioglossus muscle activity likely through SST4 receptors, but did not involve GIRK channels. In summary, NK1R stimulation of rhythm and motor output involved GIRK channels, whereas SST inhibited rhythm and motor output via two SST receptor subtypes, therefore revealing separate circuits mediating rhythm and motor output.
Synergistic effect of N-decorated and Mn2+ doped ZnO nanofibers with enhanced photocatalytic activity
Authors: Wang Yuting , Cheng Jing , Yu Suye , Alcocer Enric Juan , Shahid Muhammad , Wang Ziyuan , Pan Wei
Published: September 2016

Here we report a high efficiency photocatalyst, i.e., Mn2+-doped and N-decorated ZnO nanofibers (NFs) enriched with vacancy defects, fabricated via electrospinning and a subsequent controlled annealing process. This nanocatalyst exhibits excellent visible-light photocatalytic activity and an apparent quantum efficiency up to 12.77%, which is 50 times higher than that of pure ZnO. It also demonstrates good stability and durability in repeated photocatalytic degradation experiments. A comprehensive structural analysis shows that high density of oxygen vacancies and nitrogen are introduced into the nanofibers surface. Hence, the significant enhanced visible photocatalytic properties for Mn-ZnO NFs are due to the synergetic effects of both Mn2+ doping and N decorated. Further investigations exhibit that the Mn2+-doping facilitates the formation of N-decorated and surface defects when annealing in N2 atmosphere. N doping induce the huge band gap decrease and thus significantly enhance the absorption of ZnO nanofibers in the range of visible-light. Overall, this paper provides a new approach to fabricate visible-light nanocatalysts using both doping and annealing under anoxic ambient.
Modulating memristive performance of hexagonal WO3 nanowire by water-oxidized hydrogen ion implantation
Authors: Zhou Yong , Peng Yuehua , Yin Yanling , Zhou Fang , Liu Chang , Ling Jing , Lei Le , Zhou Weichang , Tang Dongsheng
Published: September 2016

In a two-terminal Au/hexagonal WO3 nanowire/Au device, ions drifting or carriers self-trapping under external electrical field will modulate the Schottky barriers between the nanowire and electrodes, and then result in memristive effect. When there are water molecules adsorbed on the surface of WO3 nanowire, hydrogen ions will generate near the positively-charged electrode and transport in the condensed water film, which will enhance the memristive performance characterized by analogic resistive switching remarkably. When the bias voltage is swept repeatedly under high relative humidity level, hydrogen ions will accumulate on the surface and then implant into the lattice of the WO3 nanowire, which leads to a transition from semiconducting WO3 nanowire to metallic HxWO3 nanowire. This insulator-metal transition can be realized more easily after enough electron-hole pairs being excited by laser illumination. The concentration of hydrogen ions in HxWO3 nanowire will decrease when the device is exposed to oxygen atmosphere or the bias voltage is swept in atmosphere with low relative humidity. By modulating the concentration of hydrogen ions, conductive hydrogen tungsten bronze filament might form or rupture near electrodes when the polarity of applied voltage changes, which will endow the device with memristive performance characterized by digital resistive switching.
The efficacy and safety of liraglutide added to metformin in patients with diabetes: a meta-analysis of randomized controlled trials
Authors: Gu Jianqiu , Meng Xin , Guo Yan , Wang Lei , Zheng Hongzhi , Liu Yixuan , Wu Bingshu , Wang Difei
Published: September 2016

Liraglutide, a glucagon-like peptide (GLP-1) receptor agonist, has showed favorable effects in the glycaemic control and weight reduction in patients with type 2 diabetes mellitus (T2DM). The meta-analysis was to compare the efficacy and safety of liraglutide added to metformin with other treatments in patients with T2DM. A systematic literature search on PubMed, Embase, Web of Science and the Cochrane library databases were performed. Eligible studies were randomized controlled trials (RCTs) of patients with T2DM who received the combination treatment of liraglutide and metformin. Pooled estimates were performed using a fixed-effects model or random-effects model. A total of nine RCTs met the inclusion criteria. Compared with control (placebo, sitagliptin, glimepiride, dulaglutide, insulin glargine, and NPH), liraglutide in combination with metformin resulted in significant reductions in HbA1c, bodyweight, FPG, and PPG, and similar reductions in SBP, and DBP. Moreover, liraglutide combined with metformin did not increase the risk of hypoglycemia, but induced a higher incidence of gastrointestinal disorders. In conclusion, this meta-analysis confirmed the use of liraglutide as add-on to metformin appeared to be effective and safe for patients with T2DM. However, considering the potential limitations in this study, more large-scale, well-conducted RCTs are needed to identify our findings.
A Molecularly Complete Planar Bacterial Outer Membrane Platform
Authors: Hsia Chih-Yun , Chen Linxiao , Singh Rohit R. , DeLisa Matthew P. , Daniel Susan
Published: September 2016

The bacterial outer membrane (OM) is a barrier containing membrane proteins and liposaccharides that fulfill crucial functions for Gram-negative bacteria. With the advent of drug-resistant bacteria, it is necessary to understand the functional role of this membrane and its constituents to enable novel drug designs. Here we report a simple method to form an OM-like supported bilayer (OM-SB), which incorporates native lipids and membrane proteins of gram-negative bacteria from outer membrane vesicles (OMVs). We characterize the formation of OM-SBs using quartz crystal microbalance with dissipation (QCM-D) and fluorescence microscopy. We show that the orientation of proteins in the OM-SB matches the native bacterial membrane, preserving the characteristic asymmetry of these membranes. As a demonstration of the utility of the OM-SB platform, we quantitatively measure antibiotic interactions between OM-SBs and polymyxin B, a cationic peptide used to treat Gram-negative infections. This data enriches understanding of the antibacterial mechanism of polymyxin B, including disruption kinetics and changes in membrane mechanical properties. Combining OM-SBs with microfluidics will enable higher throughput screening of antibiotics. With a broader view, we envision that a molecularly complete membrane-scaffold could be useful for cell-free applications employing engineered membrane proteins in bacterial membranes for myriad technological purposes.
Identification of SET Domain-Containing Proteins in Gossypium raimondii and Their Response to High Temperature Stress
Authors: Huang Yong , Mo Yijia , Chen Pengyun , Yuan Xiaoling , Meng Funing , Zhu Shengwei , Liu Zhi
Published: September 2016

SET (Su(var), E(z), and Trithorax) domain-containing proteins play an important role in plant development and stress responses through modifying lysine methylation status of histone. Gossypium raimondii may be the putative contributor of the D-subgenome of economical crops allotetraploid G. hirsutum and G. barbadense and therefore can potentially provide resistance genes. In this study, we identified 52 SET domain-containing genes from G. raimondii genome. Based on conserved sequences, these genes are grouped into seven classes and are predicted to catalyze the methylation of different substrates: GrKMT1 for H3K9me, GrKMT2 and GrKMT7 for H3K4me, GrKMT3 for H3K36me, GrKMT6 for H3K27me, but GrRBCMT and GrS-ET for nonhistones substrate-specific methylation. Seven pairs of GrKMT and GrRBCMT homologous genes are found to be duplicated, possibly one originating from tandem duplication and five from a large scale or whole genome duplication event. The gene structure, domain organization and expression patterns analyses suggest that these genes’ functions are diversified. A few of GrKMTs and GrRBCMTs, especially for GrKMT1A;1a, GrKMT3;3 and GrKMT6B;1 were affected by high temperature (HT) stress, demonstrating dramatically changed expression patterns. The characterization of SET domain-containing genes in G. raimondii provides useful clues for further revealing epigenetic regulation under HT and function diversification during evolution.