bluuebunny/crossref_metadata_2025 huggingface dataset:
A detailed study of Andromeda XIX, an extreme local analogue of ultradiffuse galaxies
Authors: Collins Michelle L M , Tollerud Erik J , Rich R Michael , Ibata Rodrigo A , Martin Nicolas F , Chapman Scott C , Gilbert Karoline M , Preston Janet
Published: November 2019

With a central surface brightness of μ0 = 29.3 mag arcsec−2, and half-light radius of $r_{\rm half}=3.1^{+0.9}_{-1.1}$ kpc, Andromeda XIX (And XIX) is an extremely diffuse satellite of Andromeda. We present spectra for ∼100 red giant branch stars in this galaxy, plus 16 stars in a nearby stellar stream. With this exquisite data set, we re-derive the properties of And XIX, measuring a systemic velocity of 〈vr〉 = −109.0 ± 1.6 km s−1 and a velocity dispersion of $\sigma _{vr} = 7.8^{+1.7}_{-1.5}$ km s−1 (higher than derived in our previous work). We marginally detect a velocity gradient along the major axis of $\frac{{\rm d} v}{{\rm d}\chi }= -2.1\pm 1.8~{\rm km\, s}^{-1}$ kpc−1. We find its mass-to-light ratio is higher than galaxies of comparable stellar mass (${}[M/L]_{\rm half} = 278^{+146}_{-198}\, \mathrm{M}_\odot /\mathrm{L}_\odot$), but its dynamics place it in a halo with a similar total mass to these galaxies. This could suggest that And XIX is a ‘puffed up’ dwarf galaxy, whose properties have been altered by tidal processes, similar to its Milky Way counterpart, Antlia II. For the nearby stream, we measure $v_r=-279.2\pm 3.7~{\rm km\, s}^{-1}$, and $\sigma _v=13.8^{+3.5}_{-2.6}~{\rm km\, s}^{-1}$. We measure its metallicity, and find it to be more metal rich than And XIX, implying that the two features are unrelated. Finally, And XIX’s dynamical and structural properties imply it is a local analogue to ultradiffuse galaxies (UDGs). Its complex dynamics suggest that the masses of distant UDGs measured from velocity dispersions alone should be carefully interpreted.
Superdiffusive stochastic Fermi acceleration in space and energy
Authors: Sioulas N , Isliker H , Vlahos L , Koumtzis A , Pisokas Th
Published: November 2019

We analyse the transport properties of charged particles (ions and electrons) interacting with randomly formed magnetic scatterers (e.g. large-scale local ‘magnetic fluctuations’ or ‘coherent magnetic irregularities’ usually present in strongly turbulent plasmas), using the energization processes proposed initially by Fermi in 1949. The scatterers are formed by large-scale local fluctuations (δB/B ≈ 1) and are randomly distributed inside the unstable magnetic topology. We construct a 3D grid on which a small fraction of randomly chosen grid points are acting as scatterers. In particular, we study how a large number of test particles are accelerated and transported inside a collection of scatterers in a finite volume. Our main results are: (1) The spatial mean-square displacement <(Δr)2 > inside the stochastic Fermi accelerator is superdiffusive, $\lt (\Delta r)^2\gt \sim t^{a_{r}},$ with ar ∼ 1.2–1.6, for the high-energy electrons with kinetic energy (W) larger than 1 MeV, and it is normal (ar = 1) for the heated low-energy (W < 10 keV) electrons. (2) The transport properties of the high-energy particles are closely related with the mean-free path that the particles travel in-between the scatterers (λsc). The smaller λsc is, the faster the electrons and ions escape from the acceleration volume. (3) The mean displacement in energy $\lt \Delta W\gt \sim t^{a_{W}}$ is strongly enhanced inside the acceleration volume (aW = 1.5–2.5) for the high-energy particles compared to the thermal low-energy particles (aW = 0.4), i.e. high-energy particles undergo an enhanced systematic gain in energy. (4) The mean-square displacement in energy  is superdiffusive for the high-energy particles and normal for the low-energy, heated particles.
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label
Authors: Heinz Marcel , Erlenbach Nicole , Stelzl Lukas S , Thierolf Grace , Kamble Nilesh R , Sigurdsson Snorri Th , Prisner Thomas F , Hummer Gerhard
Published: November 2019

Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
Fibroblast growth factor 23 and new-onset chronic kidney disease in the general population: the Prevention of Renal and Vascular Endstage Disease (PREVEND) study
Authors: De Jong Maarten A , Eisenga Michele F , van Ballegooijen Adriana J , Beulens Joline W J , Vervloet Marc G , Navis Gerjan , Gansevoort Ron T , Bakker Stephan J L , De Borst Martin H
Published: November 2019

Background

Fibroblast growth factor 23 (FGF23), a phosphate-regulating hormone that increases early in the course of chronic kidney disease (CKD), is associated with disease progression in patients with established CKD. Here we aimed to investigate the association between plasma FGF23 and new-onset CKD in the general population.

Methods

We included 5253 individuals without CKD who participated in the Prevention of Renal and Vascular Endstage Disease study, a prospective, population-based cohort. Multi-variable Cox regression was used to study the association of plasma C-terminal FGF23 with new-onset CKD, defined as a combined endpoint of estimated glomerular filtration rate (eGFR) <60 mL/min/ 1.73 m2, urinary 24-h albumin excretion (UAE) >30 mg/24 h or both, or with all-cause mortality.

Results

The median baseline FGF23 was 68 [interquartile range (IQR) 56–85] RU/mL, eGFR was 95 ± 13 mL/min/1.73 m2 and UAE was 7.8 (IQR 5.8–11.5)  mg/24 h. After follow-up of 7.5 (IQR 7.2–8.0)  years, 586 participants developed CKD and 214 participants died. A higher FGF23 level was associated with new-onset CKD, independent of risk factors for kidney disease and parameters of bone and mineral homoeostasis {fully adjusted hazard ratio (HR) 1.25 [95% confidence interval (CI) 1.10–1.44] per doubling of FGF23; P = 0.001}. In secondary analyses, FGF23 was independently associated with new-onset eGFR <60 mL/min/1.73 m2 [adjusted HR 1.28 (95% CI 1.00–1.62); P = 0.048] or with UAE >30 mg/24 h [adjusted HR 1.24 (95% CI 1.06–1.45); P = 0.01] individually. A higher FGF23 level was also associated with an increased risk of all-cause mortality [fully adjusted HR 1.30 (95% CI 1.03–1.63); P = 0.03].

Conclusions

High FGF23 levels are associated with an increased risk of new-onset CKD and all-cause mortality in this prospective population-based cohort, independent of established CKD risk factors.
The association of microhematuria with mesangial hypercellularity, endocapillary hypercellularity, crescent score and renal outcomes in immunoglobulin A nephropathy
Authors: Bobart Shane A , Alexander Mariam P , Shawwa Khaled , Vaughan Lisa E , Ghamrawi Ranine , Sethi Sanjeev , Cornell Lynn , Glassock Richard J , Fervenza Fernando C , Zand Ladan
Published: November 2019

Background

Microhematuria is common in immunoglobulin A nephropathy (IgAN). However, current prognostication is based on proteinuria and mesangial hypercellularity, endocapillary hypercellularity, segmental sclerosis, tubulointerstitial fibrosis and crescent (MEST-C) scores.

Methods

In this retrospective study, we evaluated whether MEST-C score components are associated with the presence of microhematuria at biopsy and whether the degree of microhematuria during follow-up is associated with change in estimated glomerular filtration rate (eGFR), after adjusting for clinical and histological parameters. We identified 125 patients with biopsy-proven IgAN and MEST-C scoring who were not on immunosuppressive therapy at biopsy. Microhematuria was defined as ≥3 red blood cells (RBCs)/high-power field (hpf).

Results

Of the 125 patients, 97 had microhematuria at baseline and were more likely to have M1, E1 and C ≥ 1 lesions (P < 0.05 for all) compared with patients without microhematuria. Of the 125 patients, 72 had follow-up data available. An increase in the degree of microhematuria was significantly associated with an eGFR decline of −0.81 mL/min/1.73 m2 [95% confidence interval (CI) −1.44 to −0.19, P = 0.01], after adjusting for follow-up time, proteinuria and T score. Severe microhematuria (≥21 RBCs/hpf) was associated with an even larger decline in eGFR (−3.99 mL/min/1.73 m2; 95% CI −6.9411 to −1.0552, P = 0.008), after similar adjustments.

Conclusion

Degree of microhematuria during follow-up is an independent predictor of eGFR decline after adjusting for clinical and histological parameters. Therefore, monitoring the degree of microhematuria as well as proteinuria is important when evaluating patients with IgAN. Additional studies using improvement in microhematuria as a primary surrogate outcome are needed.
Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis
Authors: Leškov� Alexandra , Zvar�k Milan , Araya Takao , Giehl Ricardo F H
Published: November 2019

Contamination of soils with heavy metals, such as nickel (Ni), is a major environmental concern due to increasing pollution from industrial activities, burning of fossil fuels, incorrect disposal of sewage sludge, excessive manure application and the use of fertilizers and pesticides in agriculture. Excess Ni induces leaf chlorosis and inhibits plant growth, but the mechanisms underlying growth inhibition remain largely unknown. A detailed analysis of root development in Arabidopsis thaliana in the presence of Ni revealed that this heavy metal induces gravitropic defects and locally inhibits root growth by suppressing cell elongation without significantly disrupting the integrity of the stem cell niche. The analysis of auxin-responsive reporters revealed that excess Ni inhibits shootward auxin distribution. Furthermore, we found that PIN2 is very sensitive to Ni, as the presence of this heavy metal rapidly reduced PIN2 levels in roots. A transcriptome analysis also showed that Ni affects the expression of many genes associated with plant cell walls and that Ni-induced transcriptional changes are largely independent of iron (Fe). In addition, we raised evidence that excess Ni increases the accumulation of reactive oxygen species and disturbs the integrity and orientation of microtubules. Together, our results highlight which processes are primarily targeted by Ni to alter root growth and development.
Homogeneous Spinor Flow
Authors: Freibert Marco , Schiemanowski Lothar , Weiss Hartmut
Published: November 2019

We study the spinor flow on homogeneous spin manifolds. After providing the general setup we discuss the homogeneous spinor flow in dimension three and on almost abelian Lie groups in detail. As a further example, the flag manifold in dimension six is treated.
High-Content Image-Based Single-Cell Phenotypic Analysis for the Testicular Toxicity Prediction Induced by Bisphenol A and Its Analogs Bisphenol S, Bisphenol AF, and Tetrabromobisphenol A in a Three-Dimensional Testicular Cell Co-culture Model
Authors: Yin Lei , Siracusa Jacob Steven , Measel Emily , Guan Xueling , Edenfield Clayton , Liang Shenxuan , Yu Xiaozhong
Published: November 2019

Emerging data indicate that structural analogs of bisphenol A (BPA) such as bisphenol S (BPS), tetrabromobisphenol A (TBBPA), and bisphenol AF (BPAF) have been introduced into the market as substitutes for BPA. Our previous study compared in vitro testicular toxicity using murine C18-4 spermatogonial cells and found that BPAF and TBBPA exhibited higher spermatogonial toxicities as compared with BPA and BPS. Recently, we developed a novel in vitro three-dimensional (3D) testicular cell co-culture model, enabling the classification of reproductive toxic substances. In this study, we applied the testicular cell co-culture model and employed a high-content image (HCA)-based single-cell analysis to further compare the testicular toxicities of BPA and its analogs. We also developed a machine learning (ML)-based HCA pipeline to examine the complex phenotypic changes associated with testicular toxicities. We found dose- and time-dependent changes in a wide spectrum of adverse endpoints, including nuclear morphology, DNA synthesis, DNA damage, and cytoskeletal structure in a single-cell-based analysis. The co-cultured testicular cells were more sensitive than the C18 spermatogonial cells in response to BPA and its analogs. Unlike conventional population-averaged assays, single-cell-based assays not only showed the levels of the averaged population, but also revealed changes in the sub-population. Machine learning-based phenotypic analysis revealed that treatment of BPA and its analogs resulted in the loss of spatial cytoskeletal structure, and an accumulation of M phase cells in a dose- and time-dependent manner. Furthermore, treatment of BPAF-induced multinucleated cells, which were associated with altered DNA damage response and impaired cellular F-actin filaments. Overall, we demonstrated a new and effective means to evaluate multiple toxic endpoints in the testicular co-culture model through the combination of ML and high-content image-based single-cell analysis. This approach provided an in-depth analysis of the multi-dimensional HCA data and provided an unbiased quantitative analysis of the phenotypes of interest.
Purchase Patterns, Socioeconomic Status, and Political Inclination
Authors: Dong Xiaowen , Jahani Eaman , Morales Alfredo J , Bozkaya Burçin , Lepri Bruno , Pentland Alex ´Sandy'
Published: November 2019

This paper analyzes millions of credit card transaction records during several months for tens of thousands of individuals from two different countries. The study shows that, purchase patterns are strongly correlated with important societal indices such as socioeconomic status and political inclination. The results suggest the possibility of understanding and predicting the evolution of such societal indices from purchase behavioral patterns, potentially at high temporal and spatial resolutions.
Root-Secreted Spermine Binds to Bacillus amyloliquefaciens SQR9 Histidine Kinase KinD and Modulates Biofilm Formation
Authors: Liu Yunpeng , Feng Haichao , Chen Lin , Zhang Huihui , Dong Xiaoyan , Xiong Qin , Zhang Ruifu
Published: November 2019

The signal molecules in root exudates that are sensed by plant growth–promoting rhizobacteria (PGPR) are critical to regulate their root colonization. Phosphorylated Spo0A is an important global transcriptional regulator that controls colonization and sporulation in Bacillus species. In this study, we found that deletion of kinD from PGPR strain Bacillus amyloliquefaciens SQR9, encoding an original phosphate donor of Spo0A, resulted in reduced biofilm formation in root exudates compared with the wild-type strain, indicating that KinD is responsible for sensing root exudates. Ligands of B. amyloliquefaciens SQR9 KinD in cucumber root exudates were determined by both the nontargeted ligand fishing method and the targeted surface plasmon resonance detection method. In total, we screened 80 compounds in root exudates for binding to KinD and found that spermine and guanosine could bind to KinD with dissociation constant values of 213 and 51 μΜ, respectively. In addition, calcium l-threonate, N-acetyl-l-aspartic acid, sodium decanoic acid, and parabanic acid could also bind weakly to KinD. The three-dimensional binding models were then constructed to demonstrate the interactions between the root-secreted signals and KinD. It was observed that exogenous spermine reduced the wrinkles of biofilm when kinD was deleted, indicating that KinD might be involved in sensing root-secreted spermine and stabilizing biofilm in response to this negative effector. This study provided a new insight of interaction between a rhizobacterial sensor and root-secreted signals.
Characteristics and Rapid Diagnosis of Pectobacterium carotovorum ssp. Associated With Bacterial Soft Rot of Vegetables in China
Authors: Li Xiaoying , Fu Lu , Chen Changlong , Sun Wangwang , Tian Yu , Xie Hua
Published: November 2019

Pectobacterium carotovorum, a causal agent of vegetable soft rot, contains three valid subspecies: P. carotovorum subsp. carotovorum (Pcc), P. carotovorum subsp. brasiliensis (Pcb), and P. carotovorum subsp. odoriferum (Pco). Using 16S rDNA sequencing and genus-specific PCR, we identified 72 P. carotovorum strains from Chinese cabbage, bok choy, and celery and assessed their pathogenicity on Chinese cabbage petioles and potato tubers. Based on phylogenetic analysis of pmrA sequences and confirmation by subspecies-specific PCR, the strains were divided into 18 Pcc, 29 Pco, and 25 Pcb. Several characteristic features were also assessed and supported the distinctiveness of the Pco strains. All P. carotovorum strains caused soft rot symptoms on Chinese cabbage and potato, but the Pco strains exhibited the greatest severity. We developed a conventional PCR and a quantitative PCR (qPCR) assay for the identification of Pco based on its specific srlE gene encoding sorbitol-specific phosphotransferase. These two methods could specifically amplify the expected products of 674 and 108 bp, respectively, from all of the Pco strains. The assays demonstrated high sensitivity and could detect as little as 1 and 100 pg/µl of bacterial genomic DNA, respectively. Both assays could also detect the pathogens directly from plant tissues infected with as little as 2.5 × 10−2 CFU/mg of Pco, even before external symptoms appeared. These assays constitute effective tools for disease diagnosis and the rapid identification of soft rot pathogens.
Activity‐dependent cleavage of dyskinesia‐related proline‐rich transmembrane protein 2 (PRRT2) by calpain in mouse primary cortical neurons
Authors: Hatta Daisuke , Shirotani Keiro , Hori Yuma , Kurotaki Naohiro , Iwata Nobuhisa
Published: November 2019

Mutations of PRRT2 (proline‐rich transmembrane protein 2) cause several neurological disorders, represented by paroxysmal kinesigenic dyskinesia (PKD), which is characterized by attacks of involuntary movements triggered by sudden voluntary movements. PRRT2 is reported to suppress neuronal excitation, but it is unclear how the function of PRRT2 is modulated during neuronal excitation. We found that PRRT2 is processed to a 12 kDa carboxy‐terminal fragment (12K‐CTF) by calpain, a calcium‐activated cysteine protease, in a neuronal activity‐dependent manner, predominantly via NMDA receptors or voltage‐gated calcium channels. Furthermore, we clarified that 12K‐CTF is generated by sequential cleavages at Q220 and S244. The amino‐terminal fragment (NTF) of PRRT2, which corresponds to PKD‐related truncated mutants, is not detected, probably due to rapid cleavage at multiple positions. Given that 12K‐CTF lacks most of the proline‐rich domain, this cleavage might be involved in the activity‐dependent enhancement of neuronal excitation perhaps through transient retraction of PRRT2's function. Therefore, PRRT2 might serve as a buffer for neuronal excitation, and lack of this function in PKD patients might cause neuronal hyperexcitability in their motor circuits.
Flight capacity increases then declines from the core to the margins of an invasive species' range
Authors: Merwin Andrew C.
Published: November 2019

Individuals that disperse farther than other individuals are more likely to be on the frontlines of spreading populations and may be more likely to mate with one another as a consequence of their spatial proximity. Over generations, this process—known as spatial sorting—can produce patterns of increasing dispersal ability from a population's core towards the spreading front. By contrast, when the spread of a population is limited by the availability of suitable habitat, theory predicts that range boundaries can select against more dispersive phenotypes and produce patterns of decreasing dispersal capacity towards population margins. In a common garden study of invasive kudzu bugs (Megacopta cribraria)—which are limited by the availability of hostplants in their southern and western margins—I show that midrange individuals fly 49% farther than individuals in the core and 37% farther than individuals at margins. This result highlights that other processes, such as maternal effects or selection at range boundaries, may create more complicated patterns of dispersal ability across landscapes than predicted by models of spatial sorting alone.
Parasite-induced plasticity in host social behaviour depends on sex and susceptibility
Authors: Stephenson Jessica F.
Published: November 2019

Understanding the effects of parasites on host behaviour, of host behaviour on parasite infection, and the reciprocal interactions between these processes is vital to improving our understanding of animal behaviour and disease dynamics. However, behaviour and parasite infection are both highly variable within and between individual hosts, and how this variation affects behaviour–parasite feedbacks is poorly understood. For example, it is unclear how an individual's behaviour before infection might change once it becomes infected, or as the infection progresses, and how these changes depend on the host's parasite susceptibility. Here, using the guppy,Poecilia reticulata, and a directly transmitted ectoparasite,Gyrodactylus turnbulli, I show that parasite-induced behavioural plasticity depends on host sex and susceptibility. Among females, time spent shoaling (sociality), a behaviour that increases parasite transmission, did not depend on infection status (infected/not) or susceptibility. By contrast, male sociality in the absence of infection was negatively correlated with susceptibility, suggesting that the most susceptible males use behaviour to avoid infection. However, in late infection, when parasite transmission is most likely, male sociality and susceptibility became positively correlated, suggesting that susceptible males modify their behaviour upon infection potentially to increase transmission and mating opportunities. I discuss the implications of these patterns for disease dynamics.
Oxygen supply limits the heat tolerance of avian embryos
Authors: Vimmerstedt Jon C. , Padilla Pérez Dylan J. , Angilletta Michael J. , VandenBrooks John M.
Published: November 2019

Physiologists have primarily focused on two potential explanations for heat stress in animals—the classic model of molecular stability and an alternative model of oxygen limitation. Although the classic model has widespread support, the oxygen-supply model applies to many aquatic animals and some terrestrial ones. In particular, the embryonic stage of terrestrial animals seems most susceptible to oxygen limitation because embryos acquire oxygen from the atmosphere by diffusion rather than ventilation. We report experiments confirming the two conditions of the oxygen-supply model in Japanese quail embryos,Coturnix coturnix. Hypoxia (12% O2) greatly reduced the chance of survival at 47.5°C, and hyperoxia greatly improved the chance of survival at 48.5°C. This finding expands the scope of the oxygen-supply model to a terrestrial, endothermic species, suggesting that oxygen supply generally limits the heat tolerance of embryos.
How localized force spreads on elastic contour feathers
Authors: Bhar Kinjal , Chang Brian , Virot Emmanuel , Straker Lorian , Kang Hosung , Paris Romain , Clanet Christophe , Jung Sunghwan
Published: November 2019

Birds can experience localized forces against their bodies due to impact against solid objects (like a branch or another bird) or water (during plunge-dives or landings). In this study, we hypothesize that densely packed contour feathers around the bird body would spread localized impact force while diving and maintaining plumage integrity. To test the hypothesis, we performed experiments with individual feathers and elastic beams, and developed a theoretical model to determine the response of feathers during the dive. First, we used a micro computed tomography scanner to characterize the internal structure of the contour feather from a northern gannet and calculate Young’s modulus of feathers sampled from different parts of the body. This value was found to be of the order of 109Pa for feathers from chest and belly. Second, we model the feathers as elastic beams taking into account their pre-curvature and non-uniform cross-section. Results from our experiments with polycarbonate beams suggest that the interaction of feathers on the skin patch redistributes the force, thereby reducing the impact on any particular area of the skin. Finally, a theoretical model of multiple overlaying feathers is proposed to quantify the spreading of impact force on the skin of the bird body which shows that the pressure on the skin at the impact point can be reduced by as much as three times the pressure if feathers had been absent.
Helical fibrillar microstructure of tendon using serial block-face scanning electron microscopy and a mechanical model for interfibrillar load transfer
Authors: Safa Babak N. , Peloquin John M. , Natriello Jessica R. , Caplan Jeffrey L. , Elliott Dawn M.
Published: November 2019

Tendon's hierarchical structure allows for load transfer between its fibrillar elements at multiple length scales. Tendon microstructure is particularly important, because it includes the cells and their surrounding collagen fibrils, where mechanical interactions can have potentially important physiological and pathological contributions. However, the three-dimensional (3D) microstructure and the mechanisms of load transfer in that length scale are not known. It has been postulated that interfibrillar matrix shear or direct load transfer via the fusion/branching of small fibrils are responsible for load transfer, but the significance of these mechanisms is still unclear. Alternatively, the helical fibrils that occur at the microstructural scale in tendon may also mediate load transfer; however, these structures are not well studied due to the lack of a three-dimensional visualization of tendon microstructure. In this study, we used serial block-face scanning electron microscopy to investigate the 3D microstructure of fibrils in rat tail tendon. We found that tendon fibrils have a complex architecture with many helically wrapped fibrils. We studied the mechanical implications of these helical structures using finite-element modelling and found that frictional contact between helical fibrils can induce load transfer even in the absence of matrix bonding or fibril fusion/branching. This study is significant in that it provides a three-dimensional view of the tendon microstructure and suggests friction between helically wrapped fibrils as a mechanism for load transfer, which is an important aspect of tendon biomechanics.
Three-dimensional myocardial strain correlates with murine left ventricular remodelling severity post-infarction
Authors: Soepriatna Arvin H. , Yeh A. Kevin , Clifford Abigail D. , Bezci Semih E. , O'Connell Grace D. , Goergen Craig J.
Published: November 2019

Heart failure continues to be a common and deadly sequela of myocardial infarction (MI). Despite strong evidence suggesting the importance of myocardial mechanics in cardiac remodelling, many MI studies still rely on two-dimensional analyses to estimate global left ventricular (LV) function. Here, we integrated four-dimensional ultrasound with three-dimensional strain mapping to longitudinally characterize LV mechanics within and around infarcts in order to study the post-MI remodelling process. To induce infarcts with varying severities, we separated 15 mice into three equal-sized groups: (i) sham, (ii) 30 min ischaemia–reperfusion, and (iii) permanent ligation of the left coronary artery. Four-dimensional ultrasound from a high-frequency small animal system was used to monitor changes in LV geometry, function and strain over 28 days. We reconstructed three-dimensional myocardial strain maps and showed that strain profiles at the infarct border followed a sigmoidal behaviour. We also identified that mice with mild remodelling had significantly higher strains in the infarcted myocardium than those with severe injury. Finally, we developed a new approach to non-invasively estimate infarct size from strain maps, which correlated well with histological results. Taken together, the presented work provides a thorough approach to quantify regional strain, an important component when assessing post-MI remodelling.
Experimental study on repair of fractured rock mass by microbial induction technology
Authors: Gao Rugao , Luo Yilin , Deng Hongwei
Published: November 2019

The surrounding rock mass is often required to have good strength and impermeability in underground engineering. Some grouting methods, such as the chemical grouting method and the cement grouting pressure pump method, are often applied to reform underground environment and improve the engineering performance of rock mass. However, the application of some traditional grouting materials would destroy the original environment in which the project is located. This paper focuses on the repairing effect of
Bacillus pasteurii
composites in fractured rocks. The repairing effect of microbial materials on fractured sandstone is analysed through nuclear magnetic resonance (NMR) and unconfined compression-shearing equipment. The result shows that the longer the repairing time is, the better the effect will be. After 42 days of repairing, the porosity of fractured sandstone decreases by 36.41%, the impermeability increases by 94.62%, and the compressive strength increases by 30.52%. Through the study of reaction mechanisms, this technology has the advantages of mild reaction conditions, no pollution and good environmental compatibility. The application of this technology to the maintenance of geotechnical engineering can provide new ideas for the research and development of new environmental grouting materials and underground space reconstruction technology.
Fauna of the Kemp Caldera and its upper bathyal hydrothermal vents (South Sandwich Arc, Antarctica)
Authors: Linse Katrin , Copley Jonathan T. , Connelly Douglas P. , Larter Robert D. , Pearce David A. , Polunin Nick V. C. , Rogers Alex D. , Chen Chong , Clarke Andrew , Glover Adrian G. , Graham Alastair G. C. , Huvenne Veerle A. I. , Marsh Leigh , Reid William D. K. , Roterman C. Nicolai , Sweeting Christopher J. , Zwirglmaier Katrin , Tyler Paul A.
Published: November 2019

Faunal assemblages at hydrothermal vents associated with island-arc volcanism are less well known than those at vents on mid-ocean ridges and back-arc spreading centres. This study characterizes chemosynthetic biotopes at active hydrothermal vents discovered at the Kemp Caldera in the South Sandwich Arc. The caldera hosts sulfur and anhydrite vent chimneys in 1375–1487 m depth, which emit sulfide-rich fluids with temperatures up to 212°C, and the microbial community of water samples in the buoyant plume rising from the vents was dominated by sulfur-oxidizing Gammaproteobacteria. A total of 12 macro- and megafaunal taxa depending on hydrothermal activity were collected in these biotopes, of which seven species were known from the East Scotia Ridge (ESR) vents and three species from vents outside the Southern Ocean. Faunal assemblages were dominated by large vesicomyid clams, actinostolid anemones,
Sericosura
sea spiders and lepetodrilid and cocculinid limpets, but several taxa abundant at nearby ESR hydrothermal vents were rare such as the stalked barnacle
Neolepas scotiaensis
. Multivariate analysis of fauna at Kemp Caldera and vents in neighbouring areas indicated that the Kemp Caldera is most similar to vent fields in the previously established Southern Ocean vent biogeographic province, showing that the species composition at island-arc hydrothermal vents can be distinct from nearby seafloor-spreading systems.
δ
13
C and
δ
15
N isotope values of megafaunal species analysed from the Kemp Caldera were similar to those of the same or related species at other vent fields, but none of the fauna sampled at Kemp Caldera had
δ
13
C values, indicating nutritional dependence on Epsilonproteobacteria, unlike fauna at other island-arc hydrothermal vents.
Predicting the fate of eDNA in the environment and implications for studying biodiversity
Authors: Harrison Jori B. , Sunday Jennifer M. , Rogers Sean M.
Published: November 2019

Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
A molecular war: convergent and ontogenetic evidence for adaptive host manipulation in related parasites infecting divergent hosts
Authors: Herbison Ryan , Evans Steven , Doherty Jean-François , Algie Michael , Kleffmann Torsten , Poulin Robert
Published: November 2019

Mermithids (phylum Nematoda) and hairworms (phylum Nematomorpha) somehow drive their arthropod hosts into water, which is essential for the worms' survival after egression. The mechanisms behind this behavioural change have been investigated in hairworms, but not in mermithids. Establishing a similar mechanistic basis for host behavioural change between these two distantly related parasitic groups would provide strong convergent evidence for adaptive manipulation and insight into how these parasites modify and/or create behaviour. Here, we search for this convergence, and also contrast changes in physiology between hosts infected with immature and mature mermithids to provide the first ontogenetic evidence for adaptive manipulation by disentangling host response and pathology from the parasite's apparent manipulative effects. We used SWATH-mass spectrometry on brains ofForficula auricularia(earwig) andBellorchestia quoyana(sandhopper), infected with the mermithidsMermis nigrescensandThaumamermis zealandica, respectively, at both immature and mature stages of infection, to quantify proteomic changes resulting from mermithid infection. Across both hosts (and hairworm-infected hosts, from earlier studies), the general function of dysregulated proteins was conserved. Proteins involved in energy generation/mobilization were dysregulated, corroborating reports of erratic/hyperactive behaviour in infected hosts. Dysregulated proteins involved in axon/dendrite and synapse modulation were also common to all hosts, suggesting neuronal manipulation is involved in inducing positive hydrotaxis. Furthermore, downregulation of CamKII and associated proteins suggest manipulation of memory also contributes to the behavioural shift.
Genotypic variation in parasite avoidance behaviour and other mechanistic, nonlinear components of transmission
Authors: Strauss Alexander T. , Hite Jessica L. , Civitello David J. , Shocket Marta S. , Cáceres Carla E. , Hall Spencer R.
Published: November 2019

Traditional epidemiological models assume that transmission increases proportionally to the density of parasites. However, empirical data frequently contradict this assumption. General yet mechanistic models can explain why transmission depends nonlinearly on parasite density and thereby identify potential defensive strategies of hosts. For example, hosts could decrease their exposure rates at higher parasite densities (via behavioural avoidance)ordecrease their per-parasite susceptibility when encountering more parasites (e.g. via stronger immune responses). To illustrate, we fitted mechanistic transmission models to 19 genotypes ofDaphnia dentiferahosts over gradients of the trophically acquired parasite,Metschnikowia bicuspidata. Exposure rate (foraging,F) frequently decreased with parasite density (Z), and per-parasite susceptibility (U) frequently decreased with parasite encounters (F×Z). Consequently, infection rates (F×U×Z) often peaked at intermediate parasite densities. Moreover, host genotypes varied substantially in these responses. Exposure rates remained constant for some genotypes but decreased sensitively with parasite density for others (up to 78%). Furthermore, genotypes with more sensitive foraging/exposure also foraged faster in the absence of parasites (suggesting ‘fast and sensitive’ versus ‘slow and steady’ strategies). These relationships suggest that high densities of parasites can inhibit transmission by decreasing exposure rates and/or per-parasite susceptibility, and identify several intriguing axes for the evolution of host defence.
A regional-scale assessment of using metabolic scaling theory to predict ecosystem properties
Authors: McCarthy James K. , Dwyer John M. , Mokany Karel
Published: November 2019

Metabolic scaling theory (MST) is one of ecology's most high-profile general models and can be used to link size distributions and productivity in forest systems. Much of MST's foundation is based on size distributions following a power law function with a scaling exponent of −2, a property assumed to be consistent in steady-state ecosystems. We tested the theory's generality by comparing actual size distributions with those predicted using MST parameters assumed to be general. We then used environmental variables and functional traits to explain deviation from theoretical expectations. Finally, we compared values of relative productivity predicted using MST with a remote-sensed measure of productivity. We found that fire-prone heath communities deviated from MST-predicted size distributions, whereas fire-sensitive rainforests largely agreed with the theory. Scaling exponents ranged from −1.4 to −5.3. Deviation from the power law assumption was best explained by specific leaf area, which varies along fire frequency and moisture gradients. While MST may hold in low-disturbance systems, we show that it cannot be applied under many environmental contexts. The theory should remain general, but understanding the factors driving deviation from MST and subsequent refinements is required if it is to be applied robustly across larger scales.
Influence of electromagnetic radiation emitted by daily-use electronic devices on the Eyemate® system
Authors: Invernizzi Azzurra , Haykal Shereif , Lo Faro Valeria , Pennisi Vincenzo , Choritz Lars
Published: November 2019

Purpose

Eyemate® is a system for the continual monitoring of intraocular pressure (IOP), comprised of an intraocular sensor, and a hand-held reader device. The eyemate®-IO sensor is surgically implanted in the eye during cataract surgery. Once implanted, the sensor communicates telemetrically with the hand-held device to activate and record IOP measurements. The aim of this study was to assess the possible influence of electromagnetic radiation emitted by daily-use electronic devices on the eyemate® IOP measurements.

Methods

The eyemate®-IO sensor was placed in a plastic bag, immersed in a sterile sodium chloride solution at 0.9% and placed in a water bath at 37°C. The antenna, connected to a laptop for recording the data, was positioned at a fixed distance of 1 cm from the sensor. Approximately two hours of “quasi-continuous” measurements was recorded for the baseline and for cordless phone, smart-phone and laptop. Repeated measures ANOVA was used to compare any possible differences between the baseline and the tested devices.

Results

For baseline measurements, the sensor maintained a steady-state. The same behavior was observed with the devices measurements during active and inactive states.

Conclusion

We found no evidence of signal drifts or fluctuations associated with the tested devices, thus showing a lack of electromagnetic interference with data transmission. Patients who already have the eyemate®-IO sensor implanted, or those considering it, can be informed that the electromagnetic radiation emitted by their daily-use electronic devices does not interfere with IOP measurements made by the eyemate®-IO sensor.
Within Visit Test-Retest Reliability of EEG Profiles in Children with Autism Spectrum Disorder and Typical Development
Authors: Levin April R. , Naples Adam J. , Scheffler Aaron Wolfe , Webb Sara J. , Shic Frederick , Sugar Catherine A. , Murias Michael , Bernier Raphael A. , Chawarska Katarzyna , Dawson Geraldine , Faja Susan , Jeste Shafali , Nelson Charles A. , McPartland James C. , Şentürk Damla ,   the Autism Biomarkers Consortium for Clinical Trials
Published: November 2019

Biomarker development is currently a high priority in neurodevelopmental disorder research. For many types of biomarkers (particularly biomarkers of diagnosis), reliability over short time periods is critically important. In the field of autism spectrum disorder (ASD), resting electroencephalography (EEG) power spectral densities (PSD) are well-studied for their potential as biomarkers. Classically, such data have been decomposed into pre-specified frequency bands (e.g., delta, theta, alpha, beta, and gamma). Recent technical advances, such as the Fitting Oscillations and One-Over-F (FOOOF) algorithm, allow for targeted characterization of the features that naturally emerge within an EEG PSD, permitting a more detailed characterization of the frequency band-agnostic shape of each individual’s EEG PSD. Here, using two resting EEGs collected a median of 6 days apart from 22 children with ASD and 25 typically developing (TD) controls during the Feasibility Visit of the Autism Biomarkers Consortium for Clinical Trials, we estimate within visit test-retest reliability based on characterization of the PSD shape in two ways: (1) Using the FOOOF algorithm we estimate six parameters (offset, slope, number of peaks, and amplitude, center frequency and bandwidth of the largest alpha peak) that characterize the shape of the EEG PSD; and (2) using nonparametric functional data analyses, we decompose the shape of the EEG PSD into a reduced set of basis functions that characterize individual power spectrum shapes. We show that individuals exhibit idiosyncratic PSD signatures that are stable over recording sessions using both characterizations. Our data show that EEG activity from a brief two-minute recording provides an efficient window into understanding brain activity at the single-subject level with desirable psychometric characteristics that persist across different analytical decomposition methods. This is a necessary step towards analytical validation of biomarkers based on the EEG PSD, and provides insights into parameters of the PSD that offer short-term reliability (and thus promise as potential biomarkers of trait or diagnosis) versus those that are more variable over the short term (and thus may index state or other rapidly dynamic measures of brain function). Future research should address longer-term stability of the PSD, for purposes such as monitoring development or response to treatment.
Non-affine displacements encode collective conformational fluctuations in proteins
Authors: Prakashchand Dube Dheeraj , Ahalawat Navjeet , Bandyopadhyay Satyabrata , Sengupta Surajit , Mondal Jagannath
Published: November 2019

Identifying subtle conformational fluctuations underlying the dynamics of bio macro-molecules is crucial for resolving their free energy landscape. We show that a collective variable, originally proposed for crystalline solids, is able to filter out essential macro-molecular motions more efficiently than other approaches. While homogenous or ‘affine’ deformations of the biopolymer are trivial, biopolymer conformations are complicated by the occurrence of in-homogenous or ‘non-affine’ displacements of atoms relative to their positions in the native structure. We show that these displacements encode functionally relevant conformations of macromolecule and, in combination with a formalism based upon time-structured independent component analysis, quantitatively resolve the free energy landscape of a number of macromolecules of hierarchical complexity. The kinetics of conformational transitions among the basins can now be mapped within the framework of a Markov state model. The non-affine modes, obtained by projecting out homogenous fluctuations from the local displacements, are found to be responsible for local structural changes required for transitioning between pairs of macro states.
Nα-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles inSaccharomyces cerevisiae
Authors: Friedrich Ulrike A. , Zedan Mostafa , Hessling Bernd , Fenzl Kai , Gillet Ludovic , Barry Joseph , Knop Michael , Kramer Günter , Bukau Bernd
Published: November 2019

Summary

N-terminal (Nt)-acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt-acetyltransferases (Nat) with differing specificities. Nt-acetylation has been implicated in protein quality control but its broad biological significance remains elusive. We investigated the roles of the two major Nats ofS. cerevisiae, NatA and NatB, by performing transcriptome, translatome and proteome profiling ofnatAΔ andnatBΔ mutants. Our results do not support a general role of Nt-acetylation in protein degradation but reveal an unexpected range of Nat-specific phenotypes. NatA is implicated in systemic adaptation control, asnatAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, asnatBΔ mutants accumulate protein aggregates, induce stress responses and display reduced fitness in absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.