bluuebunny/crossref_metadata_2025 huggingface dataset:
A nontrivial crossover in topological Hall effect regimes
Authors: Denisov K. S. , Rozhansky I. V. , Averkiev N. S. , Lähderanta E.
Published: December 2017

We propose a new theory of the topological Hall effect (THE) in systems with non-collinear magnetization textures such as magnetic skyrmions. We solve the problem of electron scattering on a magnetic skyrmion exactly, for an arbitrary strength of exchange interaction and the skyrmion size. We report the existence of different regimes of THE and resolve the apparent contradiction between the adiabatic Berry phase theoretical approach and the perturbation theory for THE. We traced how the topological charge Hall effect transforms into the spin Hall effect upon varying the exchange interaction strength or the skyrmion size. This transformation has a nontrivial character: it is accompanied by an oscillating behavior of both charge and spin Hall currents. This hallmark of THE allows one to identify the chirality driven contribution to Hall response in the experiments.
Insulin in motion: The A6-A11 disulfide bond allosterically modulates structural transitions required for insulin activity
Authors: van Lierop Bianca , Ong Shee Chee , Belgi Alessia , Delaine Carlie , Andrikopoulos Sofianos , Haworth Naomi L. , Menting John G. , Lawrence Michael C. , Robinson Andrea J. , Forbes Briony E.
Published: December 2017

The structural transitions required for insulin to activate its receptor and initiate regulation of glucose homeostasis are only partly understood. Here, using ring-closing metathesis, we substitute the A6-A11 disulfide bond of insulin with a rigid, non-reducible dicarba linkage, yielding two distinct stereo-isomers (cisandtrans). Remarkably, only thecisisomer displays full insulin potency, rapidly lowering blood glucose in mice (even under insulin-resistant conditions). It also posseses reduced mitogenic activityin vitro. Further biophysical, crystallographic and molecular-dynamics analyses reveal that the A6-A11 bond configuration directly affects the conformational flexibility of insulin A-chainN-terminal helix, dictating insulin’s ability to engage its receptor. We reveal that in native insulin, contraction of the Cα-Cαdistance of the flexible A6-A11 cystine allows the A-chainN-terminal helix to unwind to a conformation that allows receptor engagement. This motion is also permitted in thecisisomer, with its shorter Cα-Cαdistance, but prevented in the extendedtransanalogue. These findings thus illuminate for the first time the allosteric role of the A6-A11 bond in mediating the transition of the hormone to an active conformation, significantly advancing our understanding of insulin action and opening up new avenues for the design of improved therapeutic analogues.
Elevation of autophagy markers in Sjögren syndrome dry eye
Authors: Byun Yong-Soo , Lee Hyun Jung , Shin Soojung , Chung So-Hyang
Published: December 2017

Autophagy is known to be implicated in the pathogenesis of Sjögren syndrome (SS), but evidences are limited. We aimed to examine the levels of autophagy markers in tear film and conjunctival epithelial cells from SS dry eye patients, and analyze their correlations with clinical features. Patients with SS dry eye exhibited lower Schirmer values, lower tear breakup time, and higher ocular staining scores. In tears, ATG5 and LC3B-II/I levels were significantly higher in SS dry eye. ATG5 and LC3B-II mRNA in the conjunctiva were also elevated in SS dry eye compared with non-SS dry eye. The immunostaining of conjunctival epithelium showed a punctate pattern of ATG5 and LC3B-II in SS dry eye. These staining patterns were also observed in the lacrimal gland of SS animal models. ATG5 levels in tears and the conjunctival epithelium strongly correlated with ocular staining scores, and one month of topical corticosteroid treatment reduced both ATG5 and LC3B-II/I levels in tear film and the conjunctival epithelium of patients with SS dry eye. Our results suggest that autophagy is enhanced or dysregulated in SS and autophagy markers may be serve as both diagnostic and therapeutic biomarkers in SS dry eye.
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Authors: Desai Jigar S. , Sartor Ryan C. , Lawas Lovely Mae , Jagadish S. V. Krishna , Doherty Colleen J.
Published: December 2017

Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here: http://github.com/DohertyLab/ExRANGES. To install the package type: devtools::install_github(“DohertyLab/ExRANGES”).
Fisheries-independent surveys identify critical habitats for young scalloped hammerhead sharks (Sphyrna lewini) in the Rewa Delta, Fiji
Authors: Marie Amandine D. , Miller Cara , Cawich Celso , Piovano Susanna , Rico Ciro
Published: December 2017

Sharp declines in numerous shark populations around the world have generated considerable interest in better understanding and characterising their biology, ecology and critical habitats. The scalloped hammerhead shark (SHS,Sphyrna lewini) is subject to a multitude of natural and anthropogenic threats that are often exacerbated within the coastal embayments and estuaries used during SHS early life stages. In this study, we describe the temporal and spatial distribution, age class composition, and reproductive biology of SHS in the Rewa Delta (RD), Fiji. A total of 1054 SHS (including 796 tagged individuals; 101 of which were recaptured) were captured from September 2014 to March 2016 in the RD. A majority of the captures in this area were neonates and young-of-the-year (YOY) (99.8%). Significant seasonality in patterns of occurrence of both neonates and YOY individuals suggests a defined parturition period during the austral summer. Between the seven sampling sites in the RD we also found significant differences in SHS neonate catch per unit of effort, and average total length of individuals. According to the data, the RD is likely to represent an important nursery area for SHS up to one year of age.
Hypoxia-inducible factor 1α is Essential for Macrophage-mediated Erythroblast Proliferation in Acute Friend Retrovirus Infection
Authors: Schreiber Timm , Quinting Theresa , Dittmer Ulf , Fandrey Joachim , Sutter Kathrin
Published: December 2017

Macrophages are the frontline of defence against foreign microorganisms, including bacteria, parasites, and viruses. During acute viral infection, macrophages must invade the inflamed tissue toward low oxygen concentrations, where genetic cellular responses depend on hypoxia-inducible factors (HIF). In the study reported here we investigated the role of HIF-1α in macrophage function during acute retroviral infection. Wild-type and myeloid cell–specificHIF-1αknockout mice were infected with Friend retrovirus (FV), and immune response was analysed 7 and 10 days after infection. FV infection led to increased spleen weight in wild-type and knockout mice, whereas a profound proliferation of erythroblasts was seen only in wild-type mice. The number of spleen-infiltrating macrophages was also significantly lower in knockout animals. Macrophage invasion after FV infection in wild-type mice led to elevated amounts of activated macrophage-stimulating 1 protein that resulted in massive proliferation of erythrocyte precursor cells. This proliferation was absent from knockout mice because of impaired invasion capabilities of HIF-1α–deficient macrophages. Our study elucidated a novel mechanism of FV-induced erythrocyte precursor cell proliferation.
Advanced Sulfur-Silicon Full Cell Architecture for Lithium Ion Batteries
Authors: Ye Rachel , Bell Jeffrey , Patino Daisy , Ahmed Kazi , Ozkan Mihri , Ozkan Cengiz S.
Published: December 2017

Lithium-ion batteries are crucial to the future of energy storage. However, the energy density of current lithium-ion batteries is insufficient for future applications. Sulfur cathodes and silicon anodes have garnered a lot of attention in the field due their high capacity potential. Although recent developments in sulfur and silicon electrodes show exciting results in half cell formats, neither electrode can act as a lithium source when put together into a full cell format. Current methods toward incorporating lithium in sulfur-silicon full cells involves prelithiating silicon or using lithium sulfide. These methods however, complicate material processing and creates safety hazards. Herein, we present a novel full cell battery architecture that bypasses the issues associated with current methods. This battery architecture gradually integrates controlled amounts of pure lithium into the system by allowing lithium the access to external circuit. A high specific energy density of 350 Wh/kg after 250 cycles at C/10 was achieved using this method. This work should pave the way for future researches into sulfur-silicon full cells.
Interaction of RNA-binding protein HuR and miR-466i regulates GM-CSF expression
Authors: Chen Jing , Adamiak William , Huang Ganlei , Atasoy Ulus , Rostami Abdolmohamad , Yu Shiguang
Published: December 2017

Granulocyte-macrophage colony-stimulating factor (GM-CSF) produced by T helper 17 (Th17) cells plays an essential role in autoimmune diseases. Transcriptional regulation of Th17 cell differentiation has been extensively studied, but post-transcriptional regulation of Th17 cell differentiation has remained less well characterized. The RNA-binding protein HuR functions to promote the stability of target mRNAs via binding the AU-rich elements of the 3′ untranslated region (3′UTR) of numerous pro-inflammatory cytokines including IL-4, IL-13, IL-17 and TNF-α. However, whether HuR regulates GM-CSF expression in Th17 cells has not been fully investigated. Here we showed that HuR conditional knockout (KO) Th17 cells have decreased GM-CSF mRNA in comparison with wild-type (WT) Th17 cells, and that HuR binds directly to GM-CSF mRNA 3′UTR. Interestingly, HuR deficiency increased the levels of certain microRNA expression in Th17 cells; for example, miR-466i functioned to mediate GM-CSF and IL-17 mRNA decay, which was confirmed by in vitro luciferase assay. Furthermore, we found that HuR promoted Mxi1 expression to inhibit certain miRNA expression. Taken together, these findings indicate that interaction of HuR and miR-466i orchestrates GM-CSF expression in Th17 cells.
Structure-driven CO2 selectivity and gas capacity of ionic clathrate hydrates
Authors: Hashimoto Hidenori , Yamaguchi Tsutomu , Ozeki Hiroyuki , Muromachi Sanehiro
Published: December 2017

Ionic clathrate hydrates can selectively capture small gas molecules such as CO2, N2, CH4 and H2. We investigated CO2 + N2 mixed gas separation properties of ionic clathrate hydrates formed with tetra-n-butylammonium bromide (TBAB), tetra-n-butylammonium chloride (TBAC), tetra-n-butylphosphonium bromide (TBPB) and tetra-n-butylphosphonium chloride (TBPC). The results showed that CO2 selectivity of TBAC hydrates was remarkably higher than those of the other hydrates despite less gas capacity of TBAC hydrates. The TBAB hydrates also showed irregularly high CO2 selectivity at a low pressure. X-ray diffraction and Raman spectroscopic analyses clarified that TBAC stably formed the tetragonal hydrate structure, and TBPB and TBPC formed the orthorhombic hydrate structure. The TBAB hydrates showed polymorphic phases which may consist of the both orthorhombic and tetragonal hydrate structures. These results showed that the tetragonal hydrate captured CO2 more efficiently than the orthorhombic hydrate, while the orthorhombic hydrate has the largest gas capacity among the basic four structures of ionic clathrate hydrates. The present study suggests new potential for improving gas capacity and selectivity of ionic clathrate hydrates by choosing suitable ionic guest substances for guest gas components.
Hypoxia-inducible factor prolyl-4-hydroxylase-1 is a convergent point in the reciprocal negative regulation of NF-κB and p53 signaling pathways
Authors: Ullah Karim , Rosendahl Ann-Helen , Izzi Valerio , Bergmann Ulrich , Pihlajaniemi Taina , Mäki Joni M. , Myllyharju Johanna
Published: December 2017

Hypoxia-inducible factor 1α (HIF1α) induces the expression of several hundred genes in hypoxia aiming at restoration of oxygen homeostasis. HIF prolyl-4-hydroxylases (HIF-P4Hs) regulate the stability of HIF1α in an oxygen-dependent manner. Hypoxia is a common feature in inflammation and cancer and the HIF pathway is closely linked with the inflammatory NF-κB and tumor suppressor p53 pathways. Here we show that genetic inactivation or chemical inhibition of HIF-P4H-1 leads to downregulation of proinflammatory genes, while proapoptotic genes are upregulated. HIF-P4H-1 inactivation reduces the inflammatory response under LPS stimulusin vitroand in an acute skin inflammation modelin vivo. Furthermore, HIF-P4H-1 inactivation increases p53 activity and stability and hydroxylation of proline 142 in p53 has an important role in this regulation. Altogether, our data suggest that HIF-P4H-1 inhibition may be a promising therapeutic candidate for inflammatory diseases and cancer, enhancing the reciprocal negative regulation of the NF-κB and p53 pathways.
Structural Dynamics of the MscL C-terminal Domain
Authors: Bavi Navid , Martinac Adam D. , Cortes D. Marien , Bavi Omid , Ridone Pietro , Nomura Takeshi , Hill Adam P. , Martinac Boris , Perozo Eduardo
Published: December 2017

The large conductance mechanosensitive channel (MscL), acts as an osmoprotective emergency valve in bacteria by opening a large, water-filled pore in response to changes in membrane tension. In its closed configuration, the last 36 residues at the C-terminus form a bundle of five α-helices co-linear with the five-fold axis of symmetry. Here, we examined the structural dynamics of the C-terminus of EcMscL using site-directed spin labelling electron paramagnetic resonance (SDSL EPR) spectroscopy. These experiments were complemented with computational modelling including molecular dynamics (MD) simulations and finite element (FE) modelling. Our results show that under physiological conditions, the C-terminus is indeed an α-helical bundle, located near the five-fold symmetry axis of the molecule. Both experiments and computational modelling demonstrate that only the top part of the C-terminal domain (from the residue A110 to E118) dissociates during the channel gating, while the rest of the C-terminus stays assembled. This result is consistent with the view that the C-terminus functions as a molecular sieve and stabilizer of the oligomeric MscL structure as previously suggested.
Structural abnormalities in islets from very young children with cystic fibrosis may contribute to cystic fibrosis-related diabetes
Authors: Bogdani Marika , Blackman Scott M. , Ridaura Cecilia , Bellocq Jean-Pierre , Powers Alvin C. , Aguilar-Bryan Lydia
Published: December 2017

Cystic fibrosis (CF)-related diabetes (CFRD) is thought to result from beta-cell injury due in part to pancreas exocrine damage and lipofibrosis. CFRD pancreata exhibit reduced islet density and altered cellular composition. To investigate a possible etiology, we tested the hypothesis that such changes are present in CF pancreata before the development of lipofibrosis. We evaluated pancreas and islet morphology in tissues from very young CF children (<4 years of age), and adult patients with CF and CFRD. The relative number of beta-cells in young CF tissues was reduced by 50% or more when compared to age-matched controls. Furthermore, young CF tissues displayed significantly smaller insulin-positive areas, lower proportion of beta-cells positive for the proliferation marker Ki67 or the ductal marker CK19 vs. control subjects, and islet inflammatory cell infiltrates, independently of the severity of the exocrine lesion and in the absence of amyloid deposits. CFRD pancreata exhibited greater islet injury with further reduction in islet density, decreased relative beta-cell number, and presence of amyloid deposits. Together, these results strongly suggest that an early deficiency in beta-cell number in infants with CF may contribute to the development of glucose intolerance in the CF pediatric population, and to CFRD, later in life.
A Novel EEG Based Spectral Analysis of Persistent Brain Function Alteration in Athletes with Concussion History
Authors: Munia Tamanna T. K. , Haider Ali , Schneider Charles , Romanick Mark , Fazel-Rezai Reza
Published: December 2017

The neurocognitive sequelae of a sport-related concussion and its management are poorly defined. Detecting deficits are vital in making a decision about the treatment plan as it can persist one year or more following a brain injury. The reliability of traditional cognitive assessment tools is debatable, and thus attention has turned to assessments based on electroencephalogram (EEG) to evaluate subtle post-concussive alterations. In this study, we calculated neurocognitive deficits combining EEG analysis with three standard post-concussive assessment tools. Data were collected for all testing modalities from 21 adolescent athletes (seven concussive and fourteen healthy) in three different trials. For EEG assessment, along with linear frequency-based features, we introduced a set of time-frequency (Hjorth Parameters) and nonlinear features (approximate entropy and Hurst exponent) for the first time to explore post-concussive deficits. Besides traditional frequency-band analysis, we also presented a new individual frequency-based approach for EEG assessment. While EEG analysis exhibited significant discrepancies between the groups, none of the cognitive assessment resulted in significant deficits. Therefore, the evidence from the study highlights that our proposed EEG analysis and markers are more efficient at deciphering post-concussion residual neurocognitive deficits and thus has a potential clinical utility of proper concussion assessment and management.
Indium phosphide metasurface with enhanced nonlinear absorption
Authors: Slovick Brian , Zipp Lucas , Krishnamurthy Srini
Published: December 2017

We solve the nonlinear Maxwell equations in an InP-based dielectric metamaterial, considering both two-photon absorption and photo-induced free-carrier absorption. We obtain the intensity-dependent reflection, absorption, and effective permittivity and permeability of the metamaterial. Our results show that nonlinear absorption dampens both the electric and magnetic Mie resonance, although the magnetic resonance is more affected because it occurs at longer wavelengths where the free-carrier absorption cross section is larger. Owing to field concentration in the metamaterial at resonance, the threshold intensity for nonlinear absorption is reduced by a factor of about 30 compared to a homogeneous layer of the same thickness. Our results have implications on the use of dielectric metamaterials for nonlinear applications such as higher harmonic generation, optical limiting, and ultrafast modulation.
Long-term maintenance of peripheral blood derived human NK cells in a novel human IL-15- transgenic NOG mouse
Authors: Katano Ikumi , Nishime Chiyoko , Ito Ryoji , Kamisako Tsutomu , Mizusawa Takuma , Ka Yuyo , Ogura Tomoyuki , Suemizu Hiroshi , Kawakami Yutaka , Ito Mamoru , Takahashi Takeshi
Published: December 2017

We generated a novel mouse strain expressing transgenic human interleukin-15 (IL-15) using the severe immunodeficient NOD/Shi-scid-IL-2Rγnull(NOG) mouse genetic background (NOG-IL-15 Tg). Human natural killer (NK) cells, purified from the peripheral blood (hu-PB-NK) of normal healthy donors, proliferated when transferred into NOG-IL-15 Tg mice. In addition, the cell number increased, and the hu-PB-NK cells persisted for 3 months without signs of xenogeneic graft versus host diseases (xGVHD). Thesein vivo-expanded hu-PB-NK cells maintained the original expression patterns of various surface antigens, including NK receptors and killer cell immunoglobulin-like receptor (KIR) molecules. They also contained significant amounts of granzyme A and perforin. Inoculation of K562 leukemia cells into hu-PB-NK-transplanted NOG-IL-15 Tg mice resulted in significant suppression of tumor growth compared with non-transplanted mice. Furthermore, NOG-IL-15 Tg mice allowed for engraftment ofin vitro-expanded NK cells prepared for clinical cell therapy. These cells exerted antibody-dependent cell-mediated cytotoxicity (ADCC) on Her2-positive gastric cancer cells in the presence of therapeutic anti-Her2 antibody, and subsequently suppressed tumor growth. Our results collectively suggest that the NOG-IL-15 Tg mice are a useful model for studying human NK biology and evaluating human NK cell-mediatedin vivocytotoxicity.
Elemental preference and atomic scale site recognition in a Co-Al-W-base superalloy
Authors: Chen Yanhui , Xue Fei , Mao Shengcheng , Long Haibo , Zhang Bin , Deng Qingsong , Chen Bin , Liu Yinong , Maguire Pierce , Zhang Hongzhou , Han Xiaodong , Feng Qiang
Published: December 2017

Using state-of-the-art atomic scale super energy dispersive X-ray spectroscopy and high angle annular dark field imaging this study reveals the elemental partitioning preference between the γ′ and γ phases in a Co-Al-W-Ti-Ta superalloy and the site preference of its alloying elements in the ordered L12 γ′ phase. A semi-quantitative analysis of atomic column compositions in the ordered L12 γ′ structure is provided. Co atoms were found to occupy the {1/2, 1/2, 0} face-center positions whereas Al, W, Ti and Ta atoms prefer to occupy the {0, 0, 0} cube corner positions in the L12 γ phase. These findings agree well with predictions from first principles simulations in the literature.
Enhanced electronic-transport modulation in single-crystalline VO2 nanowire-based solid-state field-effect transistors
Authors: Wei Tingting , Kanki Teruo , Chikanari Masashi , Uemura Takafumi , Sekitani Tsuyoshi , Tanaka Hidekazu
Published: December 2017

Field-effect transistors using correlated electron materials with an electronic phase transition pave a new avenue to realize steep slope switching, to overcome device size limitations and to investigate fundamental science. Here, we present a new finding in gate-bias-induced electronic transport switching in a correlated electron material, i.e., a VO2 nanowire channel through a hybrid gate, which showed an enhancement in the resistive modulation efficiency accompanied by expansion of metallic nano-domains in an insulating matrix by applying gate biases near the metal-insulator transition temperature. Our results offer an understanding of the innate ability of coexistence state of metallic and insulating domains in correlated materials through carrier tuning and serve as a valuable reference for further research into the development of correlated materials and their devices.
Embryonic lethality and defective male germ cell development in mice lacking UTF1
Authors: Kasowitz Seth D. , Luo Mengcheng , Ma Jun , Leu N. Adrian , Wang P. Jeremy
Published: December 2017

The germ cell lineage is specified early in embryogenesis and undergoes complex developmental programs to generate gametes. Here, we conducted genetic studies to investigate the role ofUtf1(Undifferentiated embryonic cell transcription factor 1) in mouse germ cell development.Utf1is expressed in pluripotent embryonic stem (ES) cells and regulates ES cell differentiation. In a proteomics screen, we identified UTF1 among 38 proteins including DNMT3L and DND1 that associate with chromatin in embryonic testes. We find that UTF1 is expressed in embryonic and newborn gonocytes and in a subset of early spermatogonia. Ubiquitous inactivation ofUtf1causes embryonic lethality in mice with a hybrid genetic background. Male mice with a germline-specific deletion ofUtf1resulting fromPrdm1-Cre mediated recombination are born with significantly fewer gonocytes and exhibit defective spermatogenesis and reduced sperm count as young adults. These defects are ameliorated in older animals. These results demonstrate that UTF1 is required for embryonic development and regulates male germ cell development.
Impact of self-esteem and sex on stress reactions
Authors: Kogler Lydia , Seidel Eva-Maria , Metzler Hannah , Thaler Hanna , Boubela Roland N. , Pruessner Jens C. , Kryspin-Exner Ilse , Gur Ruben C. , Windischberger Christian , Moser Ewald , Habel Ute , Derntl Birgit
Published: December 2017

Positive self-evaluation is a major psychological resource modulating stress coping behavior. Sex differences have been reported in self-esteem as well as stress reactions, but so far their interactions have not been investigated. Therefore, we investigated sex-specific associations of self-esteem and stress reaction on behavioral, hormonal and neural levels. We applied a commonly used fMRI-stress task in 80 healthy participants. Men compared to women showed higher activation during stress in hippocampus, precuneus, superior temporal gyrus (STG) and insula. Furthermore, men outperformed women in the stress task and had higher cortisol and testosterone levels than women after stress. Self-esteem had an impact on precuneus, insula and STG activation during stress across the whole group. During stress, men recruit regions associated with emotion and stress regulation, self-referential processing and cognitive control more strongly than women. Self-esteem affects stress processing, however in a sex-independent fashion: participants with lower self-esteem show higher activation of regions involved in emotion and stress regulation, self-referential processing and cognitive control. Taken together, our data suggest that men are more engaged during the applied stress task. Across women and men, lower self-esteem increases the effort in emotion and stress processing and cognitive control, possibly leading to self-related thoughts in stressful situations.
The chemokines CXCL12 and CXCL14 differentially regulate connective tissue markers during limb development
Authors: Nassari Sonya , Blavet Cédrine , Bonnin Marie-Ange , Stricker Sigmar , Duprez Delphine , Fournier-Thibault Claire
Published: December 2017

Connective tissues (CT) support and connect organs together. Understanding the formation of CT is important, as CT deregulation leads to fibrosis. The identification of CT specific markers has contributed to a better understanding of CT function during development. In developing limbs, Osr1 transcription factor is involved in the differentiation of irregular CT while the transcription factor Scx labels tendon. In this study, we show that the CXCL12 and CXCL14 chemokines display distinct expression pattern in limb CT during chick development. CXCL12 positively regulates the expression of OSR1 and COL3A1, a collagen subtype of irregular CT, while CXCL14 activates the expression of the tendon marker SCX. We provide evidence that the CXCL12 effect on irregular CT involves CXCR4 receptor and vessels. In addition, the expression of CXCL12, CXCL14 and OSR genes is suppressed by the anti-fibrotic BMP signal. Finally, mechanical forces, known to be involved in adult fibrosis, control the expression of chemokines, CT-associated transcription factors and collagens during limb development. Such unexpected roles of CXCL12 and CXCL14 chemokines during CT differentiation can contribute to a better understanding of the fibrosis mechanisms in adult pathological conditions.
Morphophysiological mechanism of rice yield increase in response to optimized nitrogen management
Authors: Zhou Wei , Lv Tengfei , Yang Zhiping , Wang Tao , Fu Yong , Chen Yong , Hu Binhua , Ren Wanjun
Published: December 2017

The yield-increasing mechanism of an optimized nitrogen fertilizer application (OFA) in rice was reported in this work through a three-year test. Results showed that the number of branches and spikelets increased, panicle length, the diameter and vascular bundle number of panicle-neck internode improved with OFA. Under the condition of OFA, high effective leaf areas, especially for the flag and the second upper leaf areas, increased, the net photosynthetic rate of the upper three leaves promoted, so the photosynthetic productivity went up by a large margin; moreover, the content of soluble protein and chlorophyll of leaf also increased, and the content of soluble sugar and malondialdehyde (MDA) decreased, as a result in slowing down the senescence speed in leaves, and increasing the photosynthetic time. Gene expression level, including MOC1, LAX1, SP1, GS1;1, were up-regulated obviously in different panicle initiation stage under OFA condition, which conduced to the increase in the secondary branches and spikelets. So we concluded that the changes in organ formation and panicle structure, together with the responses in physiological and molecular made the photosynthetic area, rate and time all increased with OFA, which provided the matter basis for the big panicle development, consequently, got a higher yield.
RNAStructuromeDB: A genome-wide database for RNA structural inference
Authors: Andrews Ryan J. , Baber Levi , Moss Walter N.
Published: December 2017

RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database (https://structurome.bb.iastate.edu), a comprehensive repository of RNA secondary structural information that spans the entire human genome. Here, we compile folding information for every base pair of the genome that may be transcribed: coding, noncoding, and intergenic regions, as well as repetitive elements, telomeres, etc. This was done by fragmenting the GRCh38 reference genome into 154,414,320 overlapping sequence fragments and, for each fragment, calculating a set of metrics based on the sequence’s folding properties. These data will facilitate a wide array of investigations: e.g. discovery of structured regulatory elements in differential gene expression data or noncoding RNA discovery, as well as allow genome-scale analyses of RNA folding.
Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong
Authors: Chow Viola C. Y. , Kwong Thomas N. Y. , So Erica W. M. , Ho Yolanda I. I. , Wong Sunny H. , Lai Raymond W. M. , Chan Raphael C. Y.
Published: December 2017

Incidence of Clostridium difficile infection (CDI) is rapidly increasing and it poses a major health burden globally. However, data regarding the epidemiology of CDI in Asia are limited. We aimed to characterize the antimicrobial susceptibility patterns of common ribotypes of toxigenic C. difficile in Hong Kong. Fifty-three PCR ribotypes were identified among 284 toxigenic C. difficile clinical isolates. The five most prevalent ribotypes were 002 (13%), 017 (12%), 014 (10%), 012 (9.2%), and 020 (9.5%). All tested C. difficile strains remained susceptible to metronidazole, vancomycin, meropenem and piperacillin/tazobactam, but highly resistant to cephalosporins. Of the fluoroquinolones, highest resistance to ciprofloxacin was observed (99%), followed by levofloxacin (43%) and moxifloxacin (23%). The two newly emerged PCR ribotypes, 017 and 002, demonstrated high levels of co-resistance towards clindamycin, tetracycline, erythromycin and moxifloxacin. PCR ribotypes 017 and 002 with multi-drug resistance are rapidly emerging and continuous surveillance is important to monitor the epidemiology of C. difficile to prevent outbreaks of CDI.
Exploring biased attention towards body-related stimuli and its relationship with body awareness
Authors: Salvato Gerardo , De Maio Gabriele , Bottini Gabriella
Published: December 2017

Stimuli of great social relevance exogenously capture attention. Here we explored the impact of body-related stimuli on endogenous attention. Additionally, we investigate the influence of internal states on biased attention towards this class of stimuli. Participants were presented with a body, face, or chair cue to hold in memory (Memory task) or to merely attend (Priming task) and, subsequently, they were asked to find a circle in an unrelated visual search task. In the valid condition, the circle was flanked by the cue. In the invalid condition, the pre-cued picture re-appeared flanking the distracter. In the neutral condition, the cue item did not re-appear in the search display. We found that although bodies and faces benefited from a general faster visual processing compared to chairs, holding them in memory did not produce any additional advantage on attention compared to when they are merely attended. Furthermore, face cues generated larger orienting effect compared to body and chairs cues in both Memory and Priming task. Importantly, results showed that individual sensitivity to internal bodily responses predicted the magnitude of the memory-based orienting of attention to bodies, shedding new light on the relationship between body awareness and visuo-spatial attention.
Poly(methyl vinyl ether-alt-maleic acid) and ethyl monoester as building polymers for drug-loadable electrospun nanofibers
Authors: Mira Amalia , Mateo C. Reyes , Mallavia Ricardo , Falco Alberto
Published: December 2017

New biomaterials are sought for the development of bioengineered nanostructures. In the present study, electrospun nanofibers have been synthesized by using poly(methyl vinyl ether-alt-maleic acid) and poly(methyl vinyl ether-alt-maleic ethyl monoester) (PMVEMA-Ac and PMVEMA-ES, respectively) as building polymers for the first time. To further functionalize these materials, nanofibers of PMVEMA-Ac and PMVEMA-ES containing a conjugated polyelectrolyte (HTMA-PFP, blue emitter, and HTMA-PFNT, red emitter) were achieved with both forms maintaining a high solid state fluorescence yield without altered morphology. Also, 5-aminolevulinic acid (5-ALA) was incorporated within these nanofibers, where it remained chemically stable. In all cases, nanofiber diameters were less than 150 nm as determined by scanning and transmission electron microscopy, and encapsulation efficiency of 5-ALA was 97 ± 1% as measured by high-performance liquid chromatography. Both polymeric matrices showed rapid release kinetics in vertical cells (Franz cells) and followed Higuchi kinetics. In addition, no toxicity of nanofibers, in the absence of light, was found in HaCaT and SW480 cell lines. Finally, it was shown that loaded 5-ALA was functional, as it was internalized by cells in nanofiber-treated cultures and served as a substrate for the generation of protoporphyrin IX, suggesting these pharmaceutical vehicles are suitable for photodynamic therapy applications.
Effect of high pressure treatment and short term storage on changes in main volatile compounds of Chinese liquor
Authors: Xu Menglong , Zhu Songming , Ramaswamy Hosahalli S. , Yu Yong
Published: December 2017

Changes in main volatile compounds of Chinese liquor after high pressure (HP) treatment and following short term storage were investigated. 400 MPa-15 min & 400 MPa-30 min were applied to young liquor. Results from gas chromatography (GC) analysis revealed decreasing trends in alcohols, aldehydes and ethyl acetate immediately after HP treatments, which was in consistent with those in natural aging process; but no significant change was found in acids. However, differences in main volatile compounds between young liquor and pressurized liquors disappeared after two to six months of storage. Principal component analysis (PCA) performed well in presenting overall differences among all liquor groups, which verified our previous findings in GC analysis. This research broadened the knowledge of HP processing on distilled alcoholic beverages and provided an alternative technique for liquor quality modification.
Alternate partial root-zone drip irrigation improves water– and nitrogen– use efficiencies of sweet-waxy maize with nitrogen fertigation
Authors: Fu Fengbei , Li Fusheng , Kang Shaozhong
Published: December 2017

Alternate partial root–zone drip irrigation (ADI) or fertigation has favorable effect on crop water- and nitrogen- use efficiencies (WUE and NUE). However, the advantage of combined application of ADI and nitrogen fertigation on crop WUE and NUE remains unclear. A pot experiment was conducted to investigate the impact of three irrigation methods (CDI conventional drip irrigation (both halves of pot irrigated), ADI (both halves of pot alternatively irrigated) and FDI fixed partial root–zone drip irrigation (fixed half of pot irrigated)) and five nitrogen treatments (F0 no N supplied, F1-F4 0.2, 0.18, 0.16 and 0.14 g N per kg soil via fertigation) on sweet-waxy maize. Compared with CDI, ADI reduced water consumption by 19.9%, but increased water use efficiency based on dry seed yield (WUEs) by 32.3%, and also enhanced nitrogen apparent recovery fraction (Nrf) and nitrogen agronomic efficiency (NAE). F1-F4 augmented dry mass accumulation, dry seed yield and total nitrogen uptake if compared to F0. Moreover, F2-ADI had higher shoot and total dry masses, WUEs, total nitrogen uptake, Nrf and NAE. Thus ADI increased nitrogen uptake, WUE and NUE of sweet-waxy maize with nitrogen fertigation of 0.18 g N per kg soil in this study.
Polymorphisms in JMJD1C are associated with pubertal onset in boys and reproductive function in men
Authors: Mørup Nina , Busch Alexander Siegfried , Bang Anne Kirstine , Nordkap Loa , Nielsen John E. , Rajpert-De Meyts Ewa , Juul Anders , Jørgensen Niels , Almstrup Kristian
Published: December 2017

JMJD1C, a member of the Jumonji-domain containing histone demethylases protein family, has been associated with levels of sex-hormone binding globulin (SHBG) and testosterone in men, and knock-out rodent models show age-dependent infertility. The objective of this study was to investigate whether single nucleotide polymorphisms (SNPs) nearby JMJD1C are associated with pubertal onset in boys and with male reproduction. 671 peri-pubertal boys, 1,027 young men, 315 fertile men, and 252 infertile men were genotyped for two JMJD1C SNPs (rs7910927 and rs10822184). rs7910927 and rs10822184 showed high linkage. Boys with the rs7910927 TT genotype entered puberty 3.6 months earlier than their peers (p = 2.5 × 10−2). In young men, the number of T alleles was associated with decreased levels of SHBG, follicle-stimulating hormone (FSH), testosterone, and testosterone x luteinizing hormone, as well as increased levels of Inhibin B, Inhibin B/FSH ratio, and testis size. No significant associations with semen parameters were observed and the genotype distribution was comparable among fertile and infertile men. In conclusion, genetic variation in the vicinity of JMJD1C had a surprisingly large impact on the age at pubertal onset in boys as well as levels of reproductive hormones and testis size in men, emphasizing the relationship between JMJD1C and reproductive functions.
Interplay between geo-population factors and hierarchy of cities in multilayer urban networks
Authors: Makarov Vladimir V. , Hramov Alexander E. , Kirsanov Daniil V. , Maksimenko Vladimir A. , Goremyko Mikhail V. , Ivanov Alexey V. , Yashkov Ivan A. , Boccaletti Stefano
Published: December 2017

Only taking into consideration the interplay between processes occurring at different levels of a country can provide the complete social and geopolitical plot of its urban system. We study the interaction of the administrative structure and the geographical connectivity between cities with the help of a multiplex network approach. We found that a spatially-distributed geo-network imposes its own ranking to the hierarchical administrative network, while the latter redistributes the shortest paths between nodes in the geographical layer. Using both real demographic data of population censuses of the Republic of Kazakhstan and theoretical models, we show that in a country-scale urban network and for each specific city, the geographical neighbouring with highly populated areas is more important than its political setting. Furthermore, the structure of political subordination is instead crucial for the wealth of transportation network and communication between populated regions of the country.
Specific binding of a polymer chain to a sequence of surface receptors
Authors: Bell Samuel , Terentjev Eugene M.
Published: December 2017

This paper considers a biologically relevant question of a Gaussian chain (such as an unfolded protein) binding to a sequence of receptors with matching multiple ligands distributed along the chain. Using the characteristic time for a tethered ligand to bind to a surface receptor, we study the case of multiple binding to a linear sequence of receptors on the surface. The tethered binding time is determined by the entropic barrier for the chain to be stretched sufficiently to reach the distant receptor target, and a restriction on chain conformations near the substrate. Adsorption (multiple-site binding) is shown to be dominated by a simple zipper sequence, only occasionally accelerated by loop formation. However, when the number of receptors increases, a competing rate-limiting process takes over: the center of mass of the remaining free chain has to drift down the line of receptors, which takes longer when the receptors are close and the entropic pulling force is low. As a result, the time for the complete chain adsorption is minimised by a certain optimal number of receptors, depending on the distance to be traversed by the free end, and the chain length.
Detection and measure of genuine tripartite entanglement with partial transposition and realignment of density matrices
Authors: Li Ming , Wang Jing , Shen Shuqian , Chen Zhihua , Fei Shao-Ming
Published: December 2017

It is challenging task to detect and measure genuine multipartite entanglement. We investigate the problem by considering the average based positive partial transposition(PPT) criterion and the realignment criterion. Sufficient conditions for detecting genuine tripartite entanglement are presented. We also derive lower bounds for the genuine tripartite entanglement concurrence with respect to the conditions. While the PPT criterion and the realignment criterion are powerful for detecting bipartite entanglement and for providing lower bounds of bipartite concurrences, our results give an effective operational way to detect and measure the genuine tripartite entanglement.
Binding Modes of Teixobactin to Lipid II: Molecular Dynamics Study
Authors: Liu Yang , Liu Yaxin , Chan-Park Mary B. , Mu Yuguang
Published: December 2017

Teixobactin (TXB) is a newly discovered antibiotic targeting the bacterial cell wall precursor Lipid II (LII). In the present work, four binding modes of TXB on LII were identified by a contact-map based clustering method. The highly flexible binary complex ensemble was generated by parallel tempering metadynamics simulation in a well-tempered ensemble (PTMetaD-WTE). In agreement with experimental findings, the pyrophosphate group and the attached first sugar subunit of LII are found to be the minimal motif for stable TXB binding. Three of the four binding modes involve the ring structure of TXB and have relatively higher binding affinities, indicating the importance of the ring motif of TXB in LII recognition. TXB-LII complexes with a ratio of 2:1 are also predicted with configurations such that the ring motif of two TXB molecules bound to the pyrophosphate-MurNAc moiety and the glutamic acid residue of one LII, respectively. Our findings disclose that the ring motif of TXB is critical to LII binding and novel antibiotics can be designed based on its mimetics.
Smoking and alcohol drinking in relation to the risk of esophageal squamous cell carcinoma: A population-based case-control study in China
Authors: Yang Xiaorong , Chen Xingdong , Zhuang Maoqiang , Yuan Ziyu , Nie Shuping , Lu Ming , Jin Li , Ye Weimin
Published: December 2017

Previous results regarding the associations between esophageal squamous-cell carcinoma (ESCC) risk and smoking/alcohol drinking in high-risk areas are inconsistent. We performed a large population-based case-control study from 2010 to 2013 in a high-incidence area of China, and enrolled 1353 ESCC cases and 1961 controls. Data regarding smoking and alcohol drinking were collected via face-to-face interviews using a structured questionnaire. Odd ratios (ORs) with 95% confidence intervals (CIs) were estimated using unconditional logistic regression models. After adjusting for alcohol drinking and other potential confounders, male heavy smokers (i.e., those who started smoked more than 20 cigarettes per day or 40 pack-years, or started smoking early), showed a moderately increased risk for ESCC; however, current smoking was not associated with an increased risk. Alcohol drinking among males significantly increased the risk for ESCC (OR = 2.20, 95%CI:1.79~2.70). We observed increasing excess ESCC risks with decreasing age at behavior initiation as well as with increasing duration and intensity of alcohol intake, which were particularly evident among current smokers. In contrast, neither smoking nor alcohol drinking was not associated with ESCC risk among females. In conclusion, alcohol drinking shows a monotonic dose-response relationship with ESCC risk among men, and this relationship is particularly evident among smokers.
Prediction of cassava protein interactome based on interolog method
Authors: Thanasomboon Ratana , Kalapanulak Saowalak , Netrphan Supatcharee , Saithong Treenut
Published: December 2017

Cassava is a starchy root crop whose role in food security becomes more significant nowadays. Together with the industrial uses for versatile purposes, demand for cassava starch is continuously growing. However, in-depth study to uncover the mystery of cellular regulation, especially the interaction between proteins, is lacking. To reduce the knowledge gap in protein-protein interaction (PPI), genome-scale PPI network of cassava was constructed using interolog-based method (MePPI-In, available at http://bml.sbi.kmutt.ac.th/ppi). The network was constructed from the information of seven template plants. The MePPI-In included 90,173 interactions from 7,209 proteins. At least, 39 percent of the total predictions were found with supports from gene/protein expression data, while further co-expression analysis yielded 16 highly promising PPIs. In addition, domain-domain interaction information was employed to increase reliability of the network and guide the search for more groups of promising PPIs. Moreover, the topology and functional content of MePPI-In was similar to the networks of Arabidopsis and rice. The potential contribution of MePPI-In for various applications, such as protein-complex formation and prediction of protein function, was discussed and exemplified. The insights provided by our MePPI-In would hopefully enable us to pursue precise trait improvement in cassava.