bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation
Authors: Chara Osvaldo , Borges Augusto , Milhiet Pierre-Emmanuel , Nöllmann Marcelo , Cattoni Diego I. 
Published: March 2018

AbstractTransport of cellular cargo by molecular motors requires directionality to ensure proper biological functioning. During sporulation in Bacillus subtilis, directionality of chromosome transport is mediated by the interaction between the membrane-bound DNA translocase SpoIIIE and specific octameric sequences (SRS). Whether SRS regulate directionality by recruiting and orienting SpoIIIE or by simply catalyzing its translocation activity is still unclear. By using atomic force microscopy and single-round fast kinetics translocation assays we determined the localization and dynamics of diffusing and translocating SpoIIIE complexes on DNA with or without SRS. Our findings combined with mathematical modelling revealed that SpoIIIE directionality is not regulated by protein recruitment to SRS but rather by a fine-tuned balance among the rates governing SpoIIIE-DNA interactions and the probability of starting translocation modulated by SRS. Additionally, we found that SpoIIIE can start translocation from non-specific DNA, providing an alternative active search mechanism for SRS located beyond the exploratory length defined by 1D diffusion. These findings are relevant in vivo in the context of chromosome transport through an open channel, where SpoIIIE can rapidly explore DNA while directionality is modulated by the probability of translocation initiation upon interaction with SRS versus non-specific DNA.
Genetic markers for urine haptoglobin is associated with decline in renal function in type 2 diabetes in East Asians
Authors: Gurung Resham Lal , Dorajoo Rajkumar , Liu Sylvia , M Yiamunaa , Liu Jian-Jun , Wang Ling , Guo Lin , Yu Xueqing , Liu Jian-Jun , Lim Su Chi 
Published: March 2018

AbstractUrine haptoglobin (uHP) level prospectively predicts diabetic kidney disease (DKD) progression. Here, we aim to identify genetic determinants of uHP level and evaluate association with renal function in East Asians (EA) with type 2 diabetes (T2D). Genome-wide association study (GWAS) among 805 [236 Chinese (discovery) and 569 (57 Malay and 512 Chinese) (validation)] found that rs75444904/kgp16506790 variant was robustly associated with uHP level (MetaP = 1.21 × 10−60). rs75444904 correlates well with plasma HP protein levels and multimerization in EA but was not in perfect LD (r2 = 0.911 in Chinese, r2 = 0.536 in Malay) and is monomorphic in Europeans (1000 G data). Conditional probability analysis indicated weakening of effects but residual significant associations between rs75444904 and uHP when adjusted on HP structural variant (MetaP = 8.22 × 10−7). The rs75444904 variant was associated with DKD progression (OR = 1.77, P = 0.014) independent of traditional risk factors. In an additional validation-cohort of EA (410 end-stage renal disease (ESRD) cases and 1308 controls), rs75444904 was associated with ESRD (OR = 1.22, P = 0.036). Furthermore, increased risk of DKD progression (OR = 2.09, P = 0.007) with elevated uHP level through Mendelian randomisation analysis provide support for potential causal role of uHP in DKD progression in EA. However, further replication of our findings in larger study populations is warranted.
Modeling the effects of lipid peroxidation during ferroptosis on membrane properties
Authors: Agmon Eran , Solon Jérôme , Bassereau Patricia , Stockwell Brent R. 
Published: March 2018

AbstractFerroptosis is a form of regulated cell death characterized by the accumulation of lipid hydroperoxides. There has been significant research on the pathways leading to the accumulation of oxidized lipids, but the downstream effects and how lipid peroxides cause cell death during ferroptosis remain a major puzzle. We evaluated key features of ferroptosis in newly developed molecular dynamics models of lipid membranes to investigate the biophysical consequences of lipid peroxidation, and generated hypotheses about how lipid peroxides contribute to cell death during ferroptosis.
Resonance interaction energy between two entangled atoms in a photonic bandgap environment
Authors: Notararigo Valentina , Passante Roberto , Rizzuto Lucia 
Published: March 2018

AbstractWe consider the resonance interaction energy between two identical entangled atoms, where one is in the excited state and the other in the ground state. They interact with the quantum electromagnetic field in the vacuum state and are placed in a photonic-bandgap environment with a dispersion relation quadratic near the gap edge and linear for low frequencies, while the atomic transition frequency is assumed to be inside the photonic gap and near its lower edge. This problem is strictly related to the coherent resonant energy transfer between atoms in external environments. The analysis involves both an isotropic three-dimensional model and the one-dimensional case. The resonance interaction asymptotically decays faster with distance compared to the free-space case, specifically as 1/r2 compared to the 1/r free-space dependence in the three-dimensional case, and as 1/r compared to the oscillatory dependence in free space for the one-dimensional case. Nonetheless, the interaction energy remains significant and much stronger than dispersion interactions between atoms. On the other hand, spontaneous emission is strongly suppressed by the environment and the correlated state is thus preserved by the spontaneous-decay decoherence effects. We conclude that our configuration is suitable for observing the elusive quantum resonance interaction between entangled atoms.
Lung Topology Characteristics in patients with Chronic Obstructive Pulmonary Disease
Authors: Belchi Francisco , Pirashvili Mariam , Conway Joy , Bennett Michael , Djukanovic Ratko , Brodzki Jacek 
Published: March 2018

AbstractQuantitative features that can currently be obtained from medical imaging do not provide a complete picture of Chronic Obstructive Pulmonary Disease (COPD). In this paper, we introduce a novel analytical tool based on persistent homology that extracts quantitative features from chest CT scans to describe the geometric structure of the airways inside the lungs. We show that these new radiomic features stratify COPD patients in agreement with the GOLD guidelines for COPD and can distinguish between inspiratory and expiratory scans. These CT measurements are very different to those currently in use and we demonstrate that they convey significant medical information. The results of this study are a proof of concept that topological methods can enhance the standard methodology to create a finer classification of COPD and increase the possibilities of more personalized treatment.
Ion implantation in nanodiamonds: size effect and energy dependence
Authors: Shiryaev Andrey A. , Hinks Jonathan A. , Marks Nigel A. , Greaves Graeme , Valencia Felipe J. , Donnelly Stephen E. , González Rafael I. , Kiwi Miguel , Trigub Alexander L. , Bringa Eduardo M. , Fogg Jason L. , Vlasov Igor I. 
Published: March 2018

AbstractNanoparticles are ubiquitous in nature and are increasingly important for technology. They are subject to bombardment by ionizing radiation in a diverse range of environments. In particular, nanodiamonds represent a variety of nanoparticles of significant fundamental and applied interest. Here we present a combined experimental and computational study of the behaviour of nanodiamonds under irradiation by xenon ions. Unexpectedly, we observed a pronounced size effect on the radiation resistance of the nanodiamonds: particles larger than 8 nm behave similarly to macroscopic diamond (i.e. characterized by high radiation resistance) whereas smaller particles can be completely destroyed by a single impact from an ion in a defined energy range. This latter observation is explained by extreme heating of the nanodiamonds by the penetrating ion. The obtained results are not limited to nanodiamonds, making them of interest for several fields, putting constraints on processes for the controlled modification of nanodiamonds, on the survival of dust in astrophysical environments, and on the behaviour of actinides released from nuclear waste into the environment.
Multi-Target Tracking of Human Spermatozoa in Phase-Contrast Microscopy Image Sequences using a Hybrid Dynamic Bayesian Network
Authors: Arasteh Abdollah , Vosoughi Vahdat Bijan , Salman Yazdi Reza 
Published: March 2018

AbstractMale infertility is mostly related to semen and spermatozoa, and any diagnosis or treatment requires the investigation of the motility patterns of spermatozoa. The movements of spermatozoa are fast and involve collision and occlusion with each other. In order to extract the motility patterns of spermatozoa, multi-target tracking (MTT) of spermatozoa is necessary. One of the most important steps of MTT is data association, in which the newly arrived observations are used to update the previous tracks. Dynamic Bayesian network (DBN) is a powerful tool for modeling and solving various types of problems such as tracking and classification. There can also be a hybrid-DBN (HDBN), in which both continuous and discrete nodes are present. HDBN has a suitable structure for modeling problems that have both discrete and continuous parameters like MTT. In this research, the data association for MTT of human spermatozoa has been studied. The proposed algorithm was tested over hundreds of manually extracted spermatozoa tracks and evaluated using several standard measures. The superior results of the proposed algorithm in comparison to the other well-known algorithms, show that it could be considered as an improved alternative to traditional computer assisted sperm analysis (CASA) algorithms.
Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies
Authors: Parada-Rojas C. H. , Quesada-Ocampo L. M. 
Published: March 2018

AbstractPhytophthora capsici is a devastating oomycete that affects solanaceous, cucurbitaceous, fabaceous, and other crops in the United States (US) and worldwide. The release of the P. capsici genome allows for design of robust markers for genetic studies. We identified and characterized microsatellites in the P. capsici transcriptome. A subset of 50 microsatellites were assayed in a diverse set of P. capsici isolates and evaluated for polymorphism. Polymorphic microsatellites were confirmed by fragment analysis, and 12 were used for population characterization of 50 P. capsici isolates from different states, hosts, and mating types. Analysis of genetic relationship among isolates revealed significant geographic structure by state. Our findings highlight the usefulness of these 12 microsatellites to characterize the population structure of P. capsici and potential transferability to closely-related Phytophthora spp. since markers are located in coding regions. Our markers will facilitate genetic characterization and complement phenotypic studies of P. capsici populations, which may assist in deployment of disease management strategies.
Increased Levels of Cardiac Troponin I in Subjects with Extremely Low B-type Natriuretic Peptide Levels
Authors: Sugawa Satoshi , Masuda Izuru , Kato Kiminori , Yoshimura Michihiro 
Published: March 2018

AbstractBecause of the lack of studies focused on the biological implications of extremely low B-type natriuretic peptide (BNP) levels, we investigated whether extremely low BNP levels could be harmful to the cardiovascular system due to compromised cardio-protection. By using cardiac troponin I (cTnI) as an indicator of cardiovascular disorder, we assessed whether cTnI was inversely associated with BNP in populations with low BNP levels. A total of 2,001 apparently healthy subjects older than 38 years were included in this study. We defined subgroups from this population by limiting the maximum BNP level with cut-off values ranging from 1 through 20 pg/mL and performed covariance structure analyses by comparing log(BNP) with log(cTnI) in each subgroup. The beta values between log(BNP) and log(cTnI) sharply decreased as the BNP cut-off was reduced from 20 pg/mL (beta = 0.04) to 1 pg/mL (beta = −0.29) and became significant when the BNP cut-off levels were lower than 4 pg/mL (p < 0.005). In subgroups with BNP levels lower than 4 pg/mL, elevation in cTnI level was inversely associated with BNP (p < 0.005), which suggests that insufficient BNP may play a pathogenic role in the occurrence of cardiovascular abnormalities.
Electrocaloric effect in cubic Hubbard nanoclusters
Authors: Szałowski Karol , Balcerzak Tadeusz 
Published: March 2018

AbstractIn the paper a computational study of the electrocaloric effect is presented for a cubic nanocluster consisting of 8 sites. The system of interest is described by means of an extended Hubbard model in external electric field at half filling of the energy levels. The thermodynamic description is obtained within canonical ensemble formalism on the basis of exact numerical diagonalization of the system Hamiltonian. In particular, the entropy and the specific heat are determined as a function of temperature and external electric field. The electrocaloric effect is described quantitatively by isothermal entropy change. The behaviour of this quantity is thoroughly analysed as a function of extended Hubbard model parameters, temperature and electric field variation magnitude. The existence of direct and inverse electrocaloric effect is predicted for some range of model parameters. A high sensitivity to Hubbard model parameters is shown, what paves the way towards controlling and tuning the effect. A non-linear, quadratic dependence of isothermal entropy change on electric field variation magnitude is demonstrated. The potential for applications of electrocaloric effect in strongly correlated nanoclusters is shown.
Modulation of the Neuregulin 1/ErbB system after skeletal muscle denervation and reinnervation
Authors: Morano Michela , Ronchi Giulia , Nicolò Valentina , Fornasari Benedetta Elena , Crosio Alessandro , Perroteau Isabelle , Geuna Stefano , Gambarotta Giovanna , Raimondo Stefania 
Published: March 2018

AbstractNeuregulin 1 (NRG1) is a growth factor produced by both peripheral nerves and skeletal muscle. In muscle, it regulates neuromuscular junction gene expression, acetylcholine receptor number, muscle homeostasis and satellite cell survival. NRG1 signalling is mediated by the tyrosine kinase receptors ErbB3 and ErbB4 and their co-receptors ErbB1 and ErbB2. The NRG1/ErbB system is well studied in nerve tissue after injury, but little is known about this system in skeletal muscle after denervation/reinnervation processes. Here, we performed a detailed time-course expression analysis of several NRG1 isoforms and ErbB receptors in the rat superficial digitorum flexor muscle after three types of median nerve injuries of different severities. We found that ErbB receptor expression was correlated with the innervated state of the muscle, with upregulation of ErbB2 clearly associated with the denervation state. Interestingly, the NRG1 isoforms were differently regulated depending on the nerve injury type, leading to the hypothesis that both the NRG1α and NRG1β isoforms play a key role in the muscle reaction to injury. Indeed, in vitro experiments with C2C12 atrophic myotubes revealed that both NRG1α and NRG1β treatment influences the best-known atrophic pathways, suggesting that NRG1 might play an anti-atrophic role.
Use of implanted acoustic tags to assess platypus movement behaviour across spatial and temporal scales
Authors: Bino Gilad , Kingsford Richard T. , Grant Tom , Taylor Matthew D. , Vogelnest Larry 
Published: March 2018

AbstractThe platypus (Ornithorhynchus anatinus) is an evolutionarily distinct mammal, endemic to Australian freshwaters. Many aspects of its ecology and life-history, including detailed understanding of movements, are poorly known, hampered by its cryptic and mainly nocturnal habits and small numbers. We effectively trialled intraperitoneal implanted acoustic transmitters in nine platypuses in the Severn River (NSW), Australia, as a potential approach for studying movements in this challenging species. We tracked platypus movements over six months, at fine and broad spatial scales, using an array of acoustic sensors. Over six months (March-August 2016), four of five adult platypuses (two females\three males) maintained localized movements (average monthly maximums 0.37 km ± 0.03 sd), while one adult, one sub-adult, and one juvenile (males) moved further: average monthly maxima 1.2 km ± 2.0 sd, 0.9 km ± 0.6 sd, 4.5 km ± 5.9 sd, respectively. The longest recorded movement was by a male adult, covering 11.1 km in three days and travelling a maximum distance of about 13 km between records. Only one implanted animal was not detected immediately after release, indicative of transmission failure rather than an adverse event. High cumulative daily movements (daily 1.9 km ± 0.8 sd) indicated high metabolic requirements, with implications for previous estimates of platypus abundances and carrying capacities, essential for effective conservation. This novel approach offers new avenues to investigate relating to mating, nesting, and intraspecific competition behaviours and their temporal and spatial variation.
Repeatability and degree of territorial aggression differs among urban and rural great tits (Parus major)
Authors: Hardman Samuel I. , Dalesman Sarah 
Published: March 2018

AbstractAnimals in urban habitats face many novel selection pressures such as increased human population densities and human disturbance. This is predicted to favour bolder and more aggressive individuals together with greater flexibility in behaviour. Previous work has focussed primarily on studying these traits in captive birds and has shown increased aggression and reduced consistency between traits (behavioural syndromes) in birds from urban populations. However, personality (consistency within a behavioural trait) has not been well studied in the wild. Here we tested whether urban free-living male great tits show greater territorial aggression than rural counterparts. We also tested predictions that both behavioural syndromes and personality would show lower consistency in urban populations. We found that urban populations were more aggressive than rural populations and urban birds appeared to show lower levels of individual behavioural repeatability (personality) as predicted. However, we found no effect of urbanisation on behavioural syndromes (correlations between multiple behavioural traits). Our results indicate that urban environments may favour individuals which exhibit increased territorial aggression and greater within-trait flexibility which may be essential to success in holding urban territories. Determining how urban environments impact key fitness traits will be important in predicting how animals cope with ongoing urbanisation.
Urinary Biomarkers of Aminoglycoside-Induced Nephrotoxicity in Cystic Fibrosis: Kidney Injury Molecule-1 and Neutrophil Gelatinase-Associated Lipocalin
Authors: McWilliam Stephen J. , Antoine Daniel J. , Jorgensen Andrea L. , Smyth Rosalind L. , Pirmohamed Munir 
Published: March 2018

AbstractAminoglycosides are commonly used for the treatment of pulmonary exacerbations in patients with cystic fibrosis (CF). However, they are potentially nephrotoxic. This prospective observational cohort study aimed to investigate the potential validity of two urinary renal biomarkers, Kidney Injury Molecule-1 (KIM-1) and Neutrophil Gelatinase-associated Lipocalin (NGAL), in identifying aminoglycoside-induced nephrotoxicity in children with CF. Children and young adults up to 20 years of age with a confirmed diagnosis of CF were recruited from ten United Kingdom hospitals. Participants provided urine samples for measurement of KIM-1 and NGAL concentrations, at baseline, at regular outpatient appointments, and before, during and after exposure to clinically-indicated treatment with the aminoglycoside tobramycin. 37/158 patients recruited (23.4%) received at least one course of IV tobramycin during the study. The median peak fold-change during tobramycin exposure for KIM-1 was 2.28 (IQR 2.69) and 4.02 (IQR 7.29) for NGAL, in the absence of serum creatinine changes. Baseline KIM-1 was positively associated with cumulative courses of IV aminoglycosides (R2 = 0.11; β = 0.03; p < 0.0001). KIM-1, in particular, may be a useful, non-invasive, biomarker of acute and chronic proximal tubular injury associated with exposure to aminoglycosides in patients with CF, but its clinical utility needs to be further evaluated in prospective studies.
Mentha-Stabilized Silver Nanoparticles for High-Performance Colorimetric Detection of Al(III) in Aqueous Systems
Authors: Sharma Rekha , Dhillon Ankita , Kumar Dinesh 
Published: March 2018

AbstractThe present paper reports a facile and selective colorimetric method for the detection of potential environmental and health hazardous metal ions using green synthesized silver nanoparticles (AgNPs). Here the organic functional groups present in the plant extract (Mentha arvensis) are used as reductants and stabilizers in the synthesis of AgNPs. They also provide a suitable binding site to the (Al(III)) analyte in the detection mechanism. The leaf extract of Mentha arvensis was used to synthesize AgNPs at room-temperature and at 80 °C. The AgNPs synthesized at 80 °C exhibit excellent selective colorimetric detection of Al(III). The as-synthesized AgNPs have been characterized, and the synthesis, stabilization of NPs and detection mechanism has also been illustrated by using UV-vis, XPS, FTIR, TEM, EDX, SEM, AAS, and TGA analytical tools and techniques. The selectivity of detection probe was supported by the reaction between probe and metal ions followed first-order kinetics having the highest value of the regression coefficient (R2 = 0.99) for Al(III) and the analysis of thermodynamic parameters. The prepared sensor showed a lower limit of detection (LOD) of 1 nM (S/N = 3.2) in real water samples. The proposed method can be successfully utilized for the detection of Al(III) from both drinking and real water samples at the nanomolar level.
Structural prediction of host-guest structure in lithium at high pressure
Authors: Tsuppayakorn-aek Prutthipong , Luo Wei , Watcharatharapong Teeraphat , Ahuja Rajeev , Bovornratanaraks Thiti 
Published: March 2018

AbstractAb initio random structure searching (AIRSS) technique is used to identify the high-pressure phases of lithium (Li). We proposed the transition mechanism from the fcc to host-guest (HG) structures at finite temperature and high pressure. This complex structural phase transformation has been calculated using ab initio lattice dynamics with finite displacement method which confirms the dynamical harmonic stabilization of the HG structure. The electron distribution between the host-host atoms has also been investigated by electron localization function (ELF). The strongly localized electron of p bond has led to the stability of the HG structure. This remarkable result put the HG structure to be a common high-pressure structure among alkali metals.