bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk factors for robotic gynecologic procedures requiring conversion to other surgical procedures
Authors: Unger Cecile A. , Lachiewicz Mark P. , Ridgeway Beri
Published: August 2016

Objective

To determine the incidence of, and risk factors for, conversion from robotic gynecologic procedures to other procedure types.

Methods

A retrospective cohort study included data from women who underwent any robotic gynecologic procedures between January 1, 2011 and December 31, 2012 at a tertiary care referral center in the USA. Demographic data, perioperative data, and surgeon experience (monthly case volume) data were retrieved; potential risk factors were compared between robotic procedures that were converted to other procedures and those completed as robotic procedures.

Results

There were 942 robotic procedures during the study period. Conversion from robotic to any other type of procedure was recorded for 47 (5.0%, 95% confidence interval 3.8–6.6) procedures and robotic‐to‐open‐surgery conversion occurred in 16 (1.7%, 95% confidence interval 1.0–2.7) procedures. Conversion from robotic surgery to another approach was associated with higher body mass index (P < 0.001), previous laparotomy (P = 0.042), and surgeons having a lower monthly robotic surgical case volume (P = 0.011). Asthma (P = 0.008), intra‐operative bowel injury (P < 0.001), intra‐operative vascular injury (P = 0.003), and single‐port robotic surgery (P = 0.034) were associated with increased odds of requiring conversion from robotic procedures.

Conclusion

The overall incidence of conversion from robotic surgery to laparotomy was low. Higher body mass index, previous laparotomy, history of asthma, using a single‐port approach, and surgeon case volume were associated with the risk of conversion.
-PURITY VERSUS LOG CANONICITY FOR POLYNOMIALS
Authors: HERNÁNDEZ DANIEL J.
Published: August 2016

In this article, we consider the conjectured relationship between$F$-purity and log canonicity for polynomials over$\mathbb{C}$. In particular, we show that log canonicity corresponds to dense$F$-pure type for all polynomials whose supporting monomials satisfy a certain nondegeneracy condition. We also show that log canonicity corresponds to dense$F$-pure type for very general polynomials over$\mathbb{C}$. Our methods rely on showing that the$F$-pure and log canonical thresholds agree for infinitely many primes, and we accomplish this by comparing these thresholds with the thresholds associated to their monomial term ideals.
On the measurement of occupancy in ecology and paleontology
Authors: Foote Michael
Published: August 2016

Occupancy statistics in ecology and paleontology are biased upward by the fact that we generally do not have solid data on species that exist but are not found. The magnitude of this bias increases as the average occupancy probability decreases and as the number of sites sampled decreases. A maximum-likelihood method is developed to estimate the underlying distribution of occupancy probabilities of all species based only on the sample of observed species with nonzero occupancy. The method is based on determining the probability that the number of occupied sites will take on any specific value for a given occupancy probability, integrated over the entire distribution of occupancy probabilities. If the shape of the underlying distribution is well modeled, the resulting occupancy estimates circumvent the bias inherent in failing to observe some species and the fact that this bias depends on the number of sites. For occupancy data on marine animal genera drawn from the Paleobiology Database, the underlying distribution is reasonably approximated as a right-truncated log-normal, but the methods developed can be extended to any distribution. Examples are presented to illustrate some observations that are robust and others that need to be revised in light of this bias correction. The method is compared to a recently developed, distribution-free approach to the same problem.
Genomic composition and dynamics amongMethanomicrobialespredict adaptation to contrasting environments
Authors: Browne Patrick , Tamaki Hideyuki , Kyrpides Nikos , Woyke Tanja , Goodwin Lynne , Imachi Hiroyuki , Bräuer Suzanna , Yavitt Joseph B , Liu Wen-Tso , Zinder Stephen , Cadillo-Quiroz Hinsby
Published: August 2016

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.
Sleep recalibrates homeostatic and associative synaptic plasticity in the human cortex
Authors: Kuhn Marion , Wolf Elias , Maier Jonathan G. , Mainberger Florian , Feige Bernd , Schmid Hanna , Bürklin Jan , Maywald Sarah , Mall Volker , Jung Nikolai H. , Reis Janine , Spiegelhalder Kai , Klöppel Stefan , Sterr Annette , Eckert Anne , Riemann Dieter , Normann Claus , Nissen Christoph
Published: August 2016

Sleep is ubiquitous in animals and humans, but its function remains to be further determined. The synaptic homeostasis hypothesis of sleep–wake regulation proposes a homeostatic increase in net synaptic strength and cortical excitability along with decreased inducibility of associative synaptic long-term potentiation (LTP) due to saturation after sleep deprivation. Here we use electrophysiological, behavioural and molecular indices to non-invasively study net synaptic strength and LTP-like plasticity in humans after sleep and sleep deprivation. We demonstrate indices of increased net synaptic strength (TMS intensity to elicit a predefined amplitude of motor-evoked potential and EEG theta activity) and decreased LTP-like plasticity (paired associative stimulation induced change in motor-evoked potential and memory formation) after sleep deprivation. Changes in plasma BDNF are identified as a potential mechanism. Our study indicates that sleep recalibrates homeostatic and associative synaptic plasticity, believed to be the neural basis for adaptive behaviour, in humans.
Global threats from invasive alien species in the twenty-first century and national response capacities
Authors: Early Regan , Bradley Bethany A. , Dukes Jeffrey S. , Lawler Joshua J. , Olden Julian D. , Blumenthal Dana M. , Gonzalez Patrick , Grosholz Edwin D. , Ibañez Ines , Miller Luke P. , Sorte Cascade J. B. , Tatem Andrew J.
Published: August 2016

Invasive alien species (IAS) threaten human livelihoods and biodiversity globally. Increasing globalization facilitates IAS arrival, and environmental changes, including climate change, facilitate IAS establishment. Here we provide the first global, spatial analysis of the terrestrial threat from IAS in light of twenty-first century globalization and environmental change, and evaluate national capacities to prevent and manage species invasions. We find that one-sixth of the global land surface is highly vulnerable to invasion, including substantial areas in developing economies and biodiversity hotspots. The dominant invasion vectors differ between high-income countries (imports, particularly of plants and pets) and low-income countries (air travel). Uniting data on the causes of introduction and establishment can improve early-warning and eradication schemes. Most countries have limited capacity to act against invasions. In particular, we reveal a clear need for proactive invasion strategies in areas with high poverty levels, high biodiversity and low historical levels of invasion.
Chirality imprinting and direct asymmetric reaction screening using a stereodynamic Brønsted/Lewis acid receptor
Authors: Bentley Keith W. , Proano Daysi , Wolf Christian
Published: August 2016

Molecular recognition, activation and dynamic self-assembly with Brønsted and Lewis acids play a central role across the chemical sciences including catalysis, crystal engineering, supramolecular architectures and drug design. Despite this general advance, the utilization of the corresponding binding motifs for fast and robust quantitative chemosensing of chiral compounds in a complicate matrix has remained challenging. Here we show that a stereodynamic probe carrying complementary boronic acid and urea units achieves this goal with hydroxy carboxylic acids. Synergistic dual-site binding and instantaneous chirality imprinting result in characteristic ultraviolet and CD readouts that allow instantaneous determination of the absolute configuration, enantiomeric excess and concentration of the target compound even in complex mixtures. The robustness and practicality of this strategy for high-throughput screening purposes is demonstrated. Comprehensive sensing of only 0.5 mg of a crude reaction mixture of an asymmetric reduction eliminates cumbersome work-up protocols and minimizes analysis time, labour and waste production.
Hybrid bio-photo-electro-chemical cells for solar water splitting
Authors: Pinhassi Roy I. , Kallmann Dan , Saper Gadiel , Dotan Hen , Linkov Artyom , Kay Asaf , Liveanu Varda , Schuster Gadi , Adir Noam , Rothschild Avner
Published: August 2016

Photoelectrochemical water splitting uses solar power to decompose water to hydrogen and oxygen. Here we show how the photocatalytic activity of thylakoid membranes leads to overall water splitting in a bio-photo-electro-chemical (BPEC) cell via a simple process. Thylakoids extracted from spinach are introduced into a BPEC cell containing buffer solution with ferricyanide. Upon solar-simulated illumination, water oxidation takes place and electrons are shuttled by the ferri/ferrocyanide redox couple from the thylakoids to a transparent electrode serving as the anode, yielding a photocurrent density of 0.5 mA cm−2. Hydrogen evolution occurs at the cathode at a bias as low as 0.8 V. A tandem cell comprising the BPEC cell and a Si photovoltaic module achieves overall water splitting with solar to hydrogen efficiency of 0.3%. These results demonstrate the promise of combining natural photosynthetic membranes and man-made photovoltaic cells in order to convert solar power into hydrogen fuel.
Age-related cortical thickness trajectories in first episode psychosis patients presenting with early persistent negative symptoms
Authors: Makowski Carolina , Bodnar Michael , Malla Ashok K , Joober Ridha , Lepage Martin
Published: August 2016

Recent work has clearly established that early persistent negative symptoms (ePNS) can be observed following a first episode of psychosis (FEP), and can negatively affect functional outcome. There is also evidence for cortical changes associated with ePNS. Given that a FEP often occurs during a period of ongoing complex brain development and maturation, neuroanatomical changes may have a specific age-related component. The current study examines cortical thickness (CT) and trajectories with age using longitudinal structural imaging. Structural T1 volumes were acquired at three time points for ePNS (N=21), PNS due to secondary factors (N=31), non-PNS (N=45) patients, and controls (N=48). Images were processed using the CIVET pipeline. Linear mixed models were applied to test for the main effects of (a) group, (b) time, and interactions between (c) time and group membership, and (d) age and group membership. Compared with the non-PNS and secondary PNS patient groups, the ePNS group showed cortical thinning over time in temporal regions and a thickening with age primarily in prefrontal areas. Early PNS patients also had significantly different linear and quadratic age relationships with CT compared with other groups within cingulate, prefrontal, and temporal cortices. The current study demonstrates that FEP patients with ePNS show significantly different CT trajectories with age. Increased CT may be indicative of disruptions in cortical maturation processes within higher-order brain regions. Individuals with ePNS underline a unique subgroup of FEP patients that are differentiated at the clinical level and who exhibit distinct neurobiological patterns compared with their non-PNS peers.
Fast, vacancy-free climb of prismatic dislocation loops in bcc metals
Authors: Swinburne Thomas D. , Arakawa Kazuto , Mori Hirotaro , Yasuda Hidehiro , Isshiki Minoru , Mimura Kouji , Uchikoshi Masahito , Dudarev Sergei L.
Published: August 2016

Vacancy-mediated climb models cannot account for the fast, direct coalescence of dislocation loops seen experimentally. An alternative mechanism, self climb, allows prismatic dislocation loops to move away from their glide surface via pipe diffusion around the loop perimeter, independent of any vacancy atmosphere. Despite the known importance of self climb, theoretical models require a typically unknown activation energy, hindering implementation in materials modeling. Here, extensive molecular statics calculations of pipe diffusion processes around irregular prismatic loops are used to map the energy landscape for self climb in iron and tungsten, finding a simple, material independent energy model after normalizing by the vacancy migration barrier. Kinetic Monte Carlo simulations yield a self climb activation energy of 2 (2.5) times the vacancy migration barrier for 1/2〈111〉 (〈100〉) dislocation loops. Dislocation dynamics simulations allowing self climb and glide show quantitative agreement with transmission electron microscopy observations of climbing prismatic loops in iron and tungsten, confirming that this novel form of vacancy-free climb is many orders of magnitude faster than what is predicted by traditional climb models. Self climb significantly influences the coarsening rate of defect networks, with important implications for post-irradiation annealing.
Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase
Authors: Chen Ji-Yun , Liu Liang , Cao Chun-Ling , Li Mei-Jun , Tan Kemin , Yang Xiaohan , Yun Cai-Hong
Published: August 2016

N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine Nε-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity.
Fear of Negative Evaluation Moderates the Effect of Subliminal Fear Priming on Rejection of Unfair Offers in the Ultimatum Game
Authors: Takagishi Haruto , Fujii Takayuki , Nishina Kuniyuki , Okada Hiroyuki
Published: August 2016

The purpose of this study was to examine whether the tendency to fear negative evaluation moderates the effect of fear emotion on the rejection of unfair offers in the ultimatum game (UG). A photograph of a fearful face or landscape was displayed subliminally (i.e., for 10 ms) before the proposer’s offer in the UG was presented to participants. We used the Fear of Negative Evaluation Scale (FNES) to measure participants’ anxiety regarding negative evaluations from others. Results showed a significant interaction between FNES and condition (fearful face vs. landscape) in relation to the rejection of an unfair offer. Furthermore, the mean rejection rate of an unfair offer was significantly higher in the fearful face condition relative to that in the landscape condition among participants whose FNES scores were higher than the median; however, this difference was not observed in participants whose FNES scores were lower than the median. These results suggest that fear of negative evaluation moderates the effect of subliminal fear priming on the rejection of unfair offers in the UG and that negative emotion induced by unconscious stimuli enhances rejection of these unfair offers.
Multitask learning improves prediction of cancer drug sensitivity
Authors: Yuan Han , Paskov Ivan , Paskov Hristo , González Alvaro J. , Leslie Christina S.
Published: August 2016

Precision oncology seeks to predict the best therapeutic option for individual patients based on the molecular characteristics of their tumors. To assess the preclinical feasibility of drug sensitivity prediction, several studies have measured drug responses for cytotoxic and targeted therapies across large collections of genomically and transcriptomically characterized cancer cell lines and trained predictive models using standard methods like elastic net regression. Here we use existing drug response data sets to demonstrate that multitask learning across drugs strongly improves the accuracy and interpretability of drug prediction models. Our method uses trace norm regularization with a highly efficient ADMM (alternating direction method of multipliers) optimization algorithm that readily scales to large data sets. We anticipate that our approach will enhance efforts to exploit growing drug response compendia in order to advance personalized therapy.
Identification of Multiple QTLs Linked to Neuropathology in the Engrailed-1 Heterozygous Mouse Model of Parkinson’s Disease
Authors: Kurowska Zuzanna , Jewett Michael , Brattås Per Ludvik , Jimenez-Ferrer Itzia , Kenéz Xuyian , Björklund Tomas , Nordström Ulrika , Brundin Patrik , Swanberg Maria
Published: August 2016

Motor symptoms in Parkinson’s disease are attributed to degeneration of midbrain dopaminergic neurons (DNs). Heterozygosity for Engrailed-1 (En1), one of the key factors for programming and maintenance of DNs, results in a parkinsonian phenotype featuring progressive degeneration of DNs in substantia nigra pars compacta (SNpc), decreased striatal dopamine levels and swellings of nigro-striatal axons in the SwissOF1-En1+/− mouse strain. In contrast, C57Bl/6-En1+/− mice do not display this neurodegenerative phenotype, suggesting that susceptibility to En1 heterozygosity is genetically regulated. Our goal was to identify quantitative trait loci (QTLs) that regulate the susceptibility to PD-like neurodegenerative changes in response to loss of one En1 allele. We intercrossed SwissOF1-En1+/− and C57Bl/6 mice to obtain F2 mice with mixed genomes and analyzed number of DNs in SNpc and striatal axonal swellings in 120 F2-En1+/− 17 week-old male mice. Linkage analyses revealed 8 QTLs linked to number of DNs (p = 2.4e-09, variance explained = 74%), 7 QTLs linked to load of axonal swellings (p = 1.7e-12, variance explained = 80%) and 8 QTLs linked to size of axonal swellings (p = 7.0e-11, variance explained = 74%). These loci should be of prime interest for studies of susceptibility to Parkinson’s disease-like damage in rodent disease models and considered in clinical association studies in PD.
COX7AR is a Stress-inducible Mitochondrial COX Subunit that Promotes Breast Cancer Malignancy
Authors: Zhang Kezhong , Wang Guohui , Zhang Xuebao , Hüttemann Philipp P. , Qiu Yining , Liu Jenney , Mitchell Allison , Lee Icksoo , Zhang Chao , Lee Jin-sook , Pecina Petr , Wu Guojun , Yang Zeng-quan , Hüttemann Maik , Grossman Lawrence I.
Published: August 2016

Cytochrome c oxidase (COX), the terminal enzyme of the mitochondrial respiratory chain, plays a key role in regulating mitochondrial energy production and cell survival. COX subunit VIIa polypeptide 2-like protein (COX7AR) is a novel COX subunit that was recently found to be involved in mitochondrial supercomplex assembly and mitochondrial respiration activity. Here, we report that COX7AR is expressed in high energy-demanding tissues, such as brain, heart, liver, and aggressive forms of human breast cancer cells. Under cellular stress that stimulates energy metabolism, COX7AR is induced and incorporated into the mitochondrial COX complex. Functionally, COX7AR promotes cellular energy production in human mammary epithelial cells. Gain- and loss-of-function analysis demonstrates that COX7AR is required for human breast cancer cells to maintain higher rates of proliferation, clone formation, and invasion. In summary, our study revealed that COX7AR is a stress-inducible mitochondrial COX subunit that facilitates human breast cancer malignancy. These findings have important implications in the understanding and treatment of human breast cancer and the diseases associated with mitochondrial energy metabolism.
Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System
Authors: Liu Long , Zhao Xing , Wang Qian , Sun Xiaoxian , Xia Lili , Wang Qianqian , Yang Biao , Zhang Yihui , Montgomery Sean , Meng He , Geng Tuoyu , Gong Daoqing
Published: August 2016

Goose can develop severe hepatic steatosis without overt injury, thus it may serve as a unique model for uncovering how steatosis-related injury is prevented. To identify the markedly prosteatotic and protective mechanisms, we performed an integrated analysis of liver transcriptomes and gut microbial metagenomes using samples collected from overfed and normally-fed geese at different time points. The results indicated that the fatty liver transcriptome, initially featuring a ‘metabolism’ pathway, was later joined by ‘cell growth and death’ and ‘immune diseases’ pathways. Gut microbiota played a synergistic role in the liver response as microbial and hepatic genes affected by overfeeding shared multiple pathways. Remarkably, the complement system, an inflammatory component, was comprehensively suppressed in fatty liver, which was partially due to increased blood lactic acid from enriched Lactobacillus. Data from in vitro studies suggested that lactic acid suppressed TNFα via the HNF1α/C5 pathway. In conclusion, gut microbes and their hosts respond to excess energy influx as an organic whole, severe steatosis and related tolerance of goose liver may be partially attributable to gut microbiotic products and suppressed complement system, and lactic acid from gut microbiota participates in the suppression of hepatic TNFα/inflammation through the HNF1α/C5 pathway.
Spontaneous separation of large-spin Fermi gas in the harmonic trap: a density functional study
Authors: Sun Zongli , Gu Qiang
Published: August 2016

The component separation of the trapped large-spin Fermi gas is studied within density functional theory. The ground state and ferromagnetic transition in the gas, with and without the spin mixing collision, are calculated. In the absence of spin mixing, two patterns of separation are observed as the interaction between atoms increases, whereas only one of them corresponds to a ferromagnetic transition. The phase diagram suggests that the pattern which the system chooses depends on the interaction strength in the collision channels. With the presence of spin mixing, the distribution of phase region changes because of the interplay between different collision channels. Specifically, the spin exchange benefits the FM transition, while it suppresses the component separation of CS-II pattern.
A rapid and versatile method for the isolation, purification and cryogenic storage of Schwann cells from adult rodent nerves
Authors: Andersen Natalia D. , Srinivas Shruthi , Piñero Gonzalo , Monje Paula V.
Published: August 2016

We herein developed a protocol for the rapid procurement of adult nerve-derived Schwann cells (SCs) that was optimized to implement an immediate enzymatic dissociation of fresh nerve tissue while maintaining high cell viability, improving yields and minimizing fibroblast and myelin contamination. This protocol introduces: (1) an efficient method for enzymatic cell release immediately after removal of the epineurium and extensive teasing of the nerve fibers; (2) an adaptable drop-plating method for selective cell attachment, removal of myelin debris, and expansion of the initial SC population in chemically defined medium; (3) a magnetic-activated cell sorting purification protocol for rapid and effective fibroblast elimination; and (4) an optional step of cryopreservation for the storage of the excess of cells. Highly proliferative SC cultures devoid of myelin and fibroblast growth were obtained within three days of nerve processing. Characterization of the initial, expanded, and cryopreserved cell products confirmed maintenance of SC identity, viability and growth rates throughout the process. Most importantly, SCs retained their sensitivity to mitogens and potential for differentiation even after cryopreservation. To conclude, this easy-to-implement and clinically relevant protocol allows for the preparation of expandable homogeneous SC cultures while minimizing time, manipulation of the cells, and exposure to culture variables.
Characterisation of mouse epididymosomes reveals a complex profile of microRNAs and a potential mechanism for modification of the sperm epigenome
Authors: Reilly Jackson N. , McLaughlin Eileen A. , Stanger Simone J. , Anderson Amanda L. , Hutcheon Kate , Church Kiralee , Mihalas Bettina P. , Tyagi Sonika , Holt Janet E. , Eamens Andrew L. , Nixon Brett
Published: August 2016

Recent evidence has shown that the sperm epigenome is vulnerable to dynamic modifications arising from a variety of paternal environment exposures and that this legacy can serve as an important determinant of intergenerational inheritance. It has been postulated that such exchange is communicated to maturing spermatozoa via the transfer of small non-protein-coding RNAs (sRNAs) in a mechanism mediated by epididymosomes; small membrane bound vesicles released by the soma of the male reproductive tract (epididymis). Here we confirm that mouse epididymosomes encapsulate an impressive cargo of >350 microRNAs (miRNAs), a developmentally important sRNA class, the majority (~60%) of which are also represented by the miRNA signature of spermatozoa. This includes >50 miRNAs that were found exclusively in epididymal sperm and epididymosomes, but not in the surrounding soma. We also documented substantial changes in the epididymosome miRNA cargo, including significant fold changes in almost half of the miRNAs along the length of the epididymis. Finally, we provide the first direct evidence for the transfer of several prominent miRNA species between mouse epididymosomes and spermatozoa to afford novel insight into a mechanism of intercellular communication by which the sRNA payload of sperm can be selectively modified during their post-testicular maturation.
Characterizing Si:P quantum dot qubits with spin resonance techniques
Authors: Wang Yu , Chen Chin-Yi , Klimeck Gerhard , Simmons Michelle Y. , Rahman Rajib
Published: August 2016

Quantum dots patterned by atomically precise placement of phosphorus donors in single crystal silicon have long spin lifetimes, advantages in addressability, large exchange tunability, and are readily available few-electron systems. To be utilized as quantum bits, it is important to non-invasively characterise these donor quantum dots post fabrication and extract the number of bound electron and nuclear spins as well as their locations. Here, we propose a metrology technique based on electron spin resonance (ESR) measurements with the on-chip circuitry already needed for qubit manipulation to obtain atomic scale information about donor quantum dots and their spin configurations. Using atomistic tight-binding technique and Hartree self-consistent field approximation, we show that the ESR transition frequencies are directly related to the number of donors, electrons, and their locations through the electron-nuclear hyperfine interaction.
Rabbit hemorrhagic disease virus capsid, a versatile platform for foreign B-cell epitope display inducing protective humoral immune responses
Authors: Moreno Noelia , Mena Ignacio , Angulo Iván , Gómez Yolanda , Crisci Elisa , Montoya María , Castón José R. , Blanco Esther , Bárcena Juan
Published: August 2016

Virus-like particles (VLPs), comprised of viral structural proteins devoid of genetic material, are tunable nanoparticles that can be chemically or genetically engineered, to be used as platforms for multimeric display of foreign antigens. Here, we report the engineering of chimeric VLPs, derived from rabbit hemorrhagic disease virus (RHDV) for presentation of foreign B-cell antigens to the immune system. The RHDV capsid comprises 180 copies of a single capsid subunit (VP60). To evaluate the ability of chimeric RHDV VLPs to elicit protective humoral responses against foreign antigens, we tested two B-cell epitopes: a novel neutralizing B-cell epitope, derived from feline calicivirus capsid protein, and a well characterized B-cell epitope from the extracellular domain of influenza A virus M2 protein (M2e). We generated sets of chimeric RHDV VLPs by insertion of the foreign B-cell epitopes at three different locations within VP60 protein (which involved different levels of surface accessibility) and in different copy numbers per site. The immunogenic potential of the chimeric VLPs was analyzed in the mouse model. The results presented here indicated that chimeric RHDV VLPs elicit potent protective humoral responses against displayed foreign B-cell epitopes, demonstrated by both, in vitro neutralization and in vivo protection against a lethal challenge.
Glucose enhances indolic glucosinolate biosynthesis without reducing primary sulfur assimilation
Authors: Miao Huiying , Cai Congxi , Wei Jia , Huang Jirong , Chang Jiaqi , Qian Hongmei , Zhang Xin , Zhao Yanting , Sun Bo , Wang Bingliang , Wang Qiaomei
Published: August 2016

The effect of glucose as a signaling molecule on induction of aliphatic glucosinolate biosynthesis was reported in our former study. Here, we further investigated the regulatory mechanism of indolic glucosinolate biosynthesis by glucose in Arabidopsis. Glucose exerted a positive influence on indolic glucosinolate biosynthesis, which was demonstrated by induced accumulation of indolic glucosinolates and enhanced expression of related genes upon glucose treatment. Genetic analysis revealed that MYB34 and MYB51 were crucial in maintaining the basal indolic glucosinolate accumulation, with MYB34 being pivotal in response to glucose signaling. The increased accumulation of indolic glucosinolates and mRNA levels of MYB34, MYB51 and MYB122 caused by glucose were inhibited in the gin2-1 mutant, suggesting an important role of HXK1 in glucose-mediated induction of indolic glucosinolate biosynthesis. In contrast to what was known on the function of ABI5 in glucose-mediated aliphatic glucosinolate biosynthesis, ABI5 was not required for glucose-induced indolic glucosinolate accumulation. In addition, our results also indicated that glucose-induced glucosinolate accumulation was due to enhanced sulfur assimilation instead of directed sulfur partitioning into glucosinolate biosynthesis. Thus, our data provide new insights into molecular mechanisms underlying glucose-regulated glucosinolate biosynthesis.
High-fat diet disrupts metabolism in two generations of rats in a parent-of-origin specific manner
Authors: Chambers T. J. G. , Morgan M. D. , Heger A. H. , Sharpe R. M. , Drake A. J.
Published: August 2016

Experimental and epidemiological evidence demonstrate that ancestral diet might contribute towards offspring health. This suggests that nutrition may be able to modify genetic or epigenetic information carried by germ cells (GCs). To examine if a parental high fat diet (HFD) influences metabolic health in two generations of offspring, GC-eGFP Sprague Dawley rats were weaned onto HFD (45% fat) or Control Diet (CD; 10% fat). At 19 weeks, founders (F0) were bred with controls, establishing the F1 generation. HFD resulted in 9.7% and 14.7% increased weight gain in male and female F0 respectively. F1 offspring of HFD mothers and F1 daughters of HFD-fed fathers had increased weight gain compared to controls. F1 rats were bred with controls at 19 weeks to generate F2 offspring. F2 male offspring derived from HFD-fed maternal grandfathers exhibited increased adiposity, plasma leptin and luteinising hormone to testosterone ratio. Despite transmission via the founding male germline, we did not find significant changes in the F0 intra-testicular GC transcriptome. Thus, HFD consumption by maternal grandfathers results in a disrupted metabolic and reproductive hormone phenotype in grandsons in the absence of detectable changes in the intra-testicular GC transcriptome.
Molecular vibrational trapping revisited: a case study with D2+
Authors: Badankó Péter , Halász Gábor J. , Vibók Ágnes
Published: August 2016

The present theoretical study is concerned with the vibrational trapping or bond hardening, which is a well-known phenomenon predicted by a dressed state representation of small molecules like "Equation missing" and "Equation missing"in an intense laser field. This phenomenon is associated with a condition where the energy of the light induced, vibrational level coincides with one of the vibrational levels on the field-free potential curve, which at the same time maximizes the wave function overlap between these two levels. One-dimensional numerical simulations were performed to investigate this phenomenon in a more quantitative way than has been done previously by calculating the photodissociation probability of "Equation missing" for a wide range of photon energy. The obtained results undoubtedly show that the nodal structure of the field-free vibrational wave functions plays a decisive role in the vibrational trapping, in addition to the current understanding of this phenomenon.
High throughput cytotoxicity screening of anti-HER2 immunotoxins conjugated with antibody fragments from phage-displayed synthetic antibody libraries
Authors: Hou Shin-Chen , Chen Hong-Sen , Lin Hung-Wei , Chao Wei-Ting , Chen Yao-Sheng , Fu Chi-Yu , Yu Chung-Ming , Huang Kai-Fa , Wang Andrew H.-J. , Yang An-Suei
Published: August 2016

Immunotoxins are an important class of antibody-based therapeutics. The potency of the immunotoxins depends on the antibody fragments as the guiding modules targeting designated molecules on cell surfaces. Phage-displayed synthetic antibody scFv libraries provide abundant antibody fragment candidates as targeting modules for the immunoconjugates, but the discovery of optimally functional immunoconjugates is limited by the scFv-payload conjugation procedure. In this work, cytotoxicity screening of non-covalently assembled immunotoxins was developed in high throughput format to discover highly functional synthetic antibody fragments for delivering toxin payloads. The principles governing the efficiency of the antibodies as targeting modules have been elucidated from large volume of cytotoxicity data: (a) epitope and paratope of the antibody-based targeting module are major determinants for the potency of the immunotoxins; (b) immunotoxins with bivalent antibody-based targeting modules are generally superior in cytotoxic potency to those with corresponding monovalent targeting module; and (c) the potency of the immunotoxins is positively correlated with the densities of the cell surface antigen. These findings suggest that screening against the target cells with a large pool of antibodies from synthetic antibody libraries without the limitations of natural antibody responses can lead to optimal potency and minimal off-target toxicity of the immunoconjugates.
Drone exposure to the systemic insecticide Fipronil indirectly impairs queen reproductive potential
Authors: Kairo Guillaume , Provost Bertille , Tchamitchian Sylvie , Ben Abdelkader Faten , Bonnet Marc , Cousin Marianne , Sénéchal Jacques , Benet Pauline , Kretzschmar André , Belzunces Luc P. , Brunet Jean-Luc
Published: August 2016

A species that requires sexual reproduction but cannot reproduce is doomed to extinction. The important increasing loss of species emphasizes the ecological significance of elucidating the effects of environmental stressors, such as pesticides, on reproduction. Despite its special reproductive behavior, the honey bee was selected as a relevant and integrative environmental model because of its constant and diverse exposure to many stressors due to foraging activity. The widely used insecticide Fipronil, the use of which is controversial because of its adverse effects on honey bees, was chosen to expose captive drones in hives via syrup contaminated at 0.1 μg/L and gathered by foragers. Such environmental exposure led to decreased spermatozoa concentration and sperm viability coupled with an increased sperm metabolic rate, resulting in drone fertility impairment. Subsequently, unexposed queens inseminated with such sperm exhibited fewer spermatozoa with lower viability in their spermatheca, leaving no doubt about the detrimental consequences for the reproductive potential of queens, which are key for colony sustainability. These findings suggest that pesticides could contribute to declining honey bee populations through fertility impairment, as exemplified by Fipronil. More broadly, reproductive disorders should be taken into consideration when investigating the decline of other species.
Cinnamomi Cortex (Cinnamomum verum) Suppresses Testosterone-induced Benign Prostatic Hyperplasia by Regulating 5α-reductase
Authors: Choi Hyun-Myung , Jung Yunu , Park Jinbong , Kim Hye-Lin , Youn Dong-Hyun , Kang JongWook , Jeong Mi-Young , Lee Jong-Hyun , Yang Woong Mo , Lee Seok-Geun , Ahn Kwang Seok , Um Jae-Young
Published: August 2016

Cinnamomi cortex (dried bark of Cinnamomum verum) is an important drug in Traditional Korean Medicine used to improve blood circulation and Yang Qi. Benign prostatic hyperplasia (BPH) is a common chronic disease in aging men. This study was conducted to determine the effect of Cinnamomi cortex water extract (CC) on BPH. BPH was induced by a pre-4-week daily injection of testosterone propionate (TP). Six weeks of further injection with (a) vehicle, (b) TP, (c) TP + CC, (d) TP + finasteride (Fi) was carried on. As a result, the prostate weight and prostatic index of the CC treatment group were reduced. Histological changes including epithelial thickness and lumen area were recovered as normal by CC treatment. The protein expressions of prostate specific antigen, estrogen receptor α (ERα), androgen receptor (AR), 5α-reductase (5AR), and steroid receptor coactivator 1 were suppressed by treatment of CC. Immunohistochemical assays supported the western blot results, as the expressions of AR and ERα were down-regulated by CC treatment as well. Further in vitro experiments showed CC was able to inhibit proliferation of RWPE-1 cells by suppressing 5AR and AR. These results all together suggest CC as a potential treatment for BPH.
TGF-β/BAMBI pathway dysfunction contributes to peripheral Th17/Treg imbalance in chronic obstructive pulmonary disease
Authors: Zhang Jian-Chu , Chen Gang , Chen Long , Meng Zhao-Ji , Xiong Xian-Zhi , Liu Hong-Ju , Jin Yang , Tao Xiao-Nan , Wu Jiang-Hua , Sun Sheng-Wen
Published: August 2016

BMP and activin membrane-bound inhibitor (BAMBI) is postulated to inhibit or modulate transforming growth factor β (TGF-β) signaling. Furthermore, strong upregulation of BAMBI expression following in vitro infection of chronic obstructive pulmonary disease (COPD) lung tissue has been demonstrated. In this study, we investigated whether TGF-β/BAMBI pathway is associated with COPD. Blood samples were obtained from 27 healthy controls (HC), 24 healthy smokers (HS) and 29 COPD patients. Elevated Th17/Treg ratios and increased levels of BAMBI protein and mRNA (in plasma and CD4+ T cells respectively), were observed in COPD compared with HC and HS. BAMBI expression was first observed on human CD4+ T cells, with a typical membrane-bound pattern. The enhanced plasma BAMBI levels in COPD positively correlated with the increased plasma TGF-β1 levels and Th17/Treg ratio. Together, an impaired TGF-β/BAMBI pathway may promote the inflammation leading to Th17/Treg imbalance, which is a new mechanism in smokers who develop COPD.
The Hippo-Salvador signaling pathway regulates renal tubulointerstitial fibrosis
Authors: Seo Eunjeong , Kim Wan-Young , Hur Jeongmi , Kim Hanbyul , Nam Sun Ah , Choi Arum , Kim Yu-Mi , Park Sang Hee , Chung Chaeuk , Kim Jin , Min Soohong , Myung Seung-Jae , Lim Dae-Sik , Kim Yong Kyun
Published: August 2016

Renal tubulointerstitial fibrosis (TIF) is the final pathway of various renal injuries that result in chronic kidney disease. The mammalian Hippo-Salvador signaling pathway has been implicated in the regulation of cell proliferation, cell death, tissue regeneration, and tumorigenesis. Here, we report that the Hippo-Salvador pathway plays a role in disease development in patients with TIF and in a mouse model of TIF. Mice with tubular epithelial cell (TEC)-specific deletions of Sav1 (Salvador homolog 1) exhibited aggravated renal TIF, enhanced epithelial-mesenchymal transition-like phenotypic changes, apoptosis, and proliferation after unilateral ureteral obstruction (UUO). Moreover, Sav1 depletion in TECs increased transforming growth factor (TGF)-β and activated β-catenin expression after UUO, which likely accounts for the abovementioned enhanced TEC fibrotic phenotype. In addition, TAZ (transcriptional coactivator with PDZ-binding motif), a major downstream effector of the Hippo pathway, was significantly activated in Sav1-knockout mice in vivo. An in vitro study showed that TAZ directly regulates TGF-β and TGF-β receptor II expression. Collectively, our data indicate that the Hippo-Salvador pathway plays a role in the pathogenesis of TIF and that regulating this pathway may be a therapeutic strategy for reducing TIF.
Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance
Authors: Barber-Zucker Shiran , Uebe René , Davidov Geula , Navon Yotam , Sherf Dror , Chill Jordan H. , Kass Itamar , Bitton Ronit , Schüler Dirk , Zarivach Raz
Published: August 2016

Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human.
Onco-lncRNA HOTAIR and its functional genetic variants in papillary thyroid carcinoma
Authors: Zhu Hui , Lv Zheng , An Changming , Shi Meng , Pan Wenting , Zhou Liqing , Yang Wenjun , Yang Ming
Published: August 2016

The role of long noncoding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) and its functional single nucleotide polymorphisms (SNPs) in papillary thyroid carcinoma (PTC) is still largely unclear. Therefore, we investigated the involvement of lncRNA HOTAIR and its three haplotype-tagging SNPs (htSNPs) in PTC. There was higher expression of HOTAIR in PTC tissues compared to normal tissues. A series of gain-loss assays demonstrated that HOTAIR acts as a PTC oncogene via promoting tumorigenic properties of PTC cells. Additionally, the functional HOTAIR rs920778 genetic variant was a PTC susceptibility SNP. Subjects with the HOTAIR rs920778 TT genotype had an odds ratio (OR) of 1.88, 1.25 and 1.61 (P = 6.0 × 10−6, P = 0.028 and P = 3.2 × 10−5) for developing PTC in Shandong, Jiangsu and Jilin case-control sets compared with subjects with the CC genotype. This statistically significant associations were only found between the rs920778 genetic polymorphism and PTC risk in females but not in males. The allele-specific regulation on HOTAIR expression by the rs920778 SNP was confirmed both in vitro and in vivo. Our results demonstrate that functional SNPs influencing lncRNA regulation may explain a part of PTC genetic basis.
Synthesis of Vertically Standing MoS2 Triangles on SiC
Authors: Lan Feifei , Lai Zhanping , Xu Yongkuan , Cheng Hongjuan , Wang Zaien , Qi Chengjun , Chen Jianli , Zhang Song
Published: August 2016

Layered material MoS2 has been attracting much attention due to its excellent electronical properties and catalytic property. Here we report the synthesis of vertically standing MoS2 triangles on silicon carbon(SiC), through a rapid sulfidation process. Such edge-terminated films are metastable structures of MoS2, which may find applications in FinFETs and catalytic reactions. We have confirmed the catalytic property in a hydrogen evolution reaction(HER). The Tafel slope is about 54mV/decade.
Concentric Circular Grating Generated by the Patterning Trapping of Nanoparticles in an Optofluidic Chip
Authors: Dai Hailang , Cao Zhuangqi , Wang Yuxing , Li Honggen , Sang Minghuang , Yuan Wen , Chen Fan , Chen Xianfeng
Published: August 2016

Due to the field enhancement effect of the hollow-core metal-cladded optical waveguide chip, massive nanoparticles in a solvent are effectively trapped via exciting ultrahigh order modes. A concentric ring structure of the trapped nanoparticles is obtained since the excited modes are omnidirectional at small incident angle. During the process of solvent evaporation, the nanoparticles remain well trapped since the excitation condition of the optical modes is still valid and a concentric circular grating consisting of deposited nanoparticles can be produced by this approach. Experiments via scanning electron microscopy, atomic force microscopy and diffraction of a probe laser confirmed the above hypothesis. This technique provides an alternative strategy to enable effective trapping of dielectric particles with low-intensity nonfocused illumination and a better understanding of the correlation between the guided modes in an optical waveguide and the nanoparticles in a solvent.