bluuebunny/crossref_metadata_2025 huggingface dataset:
An intertwined method for making low-rank, sum-of-product basis functions that makes it possible to compute vibrational spectra of molecules with more than 10 atoms
Authors: Thomas Phillip S. , Carrington Tucker
Published: May 2017

We propose a method for solving the vibrational Schrödinger equation with which one can compute spectra for molecules with more than ten atoms. It uses sum-of-product (SOP) basis functions stored in a canonical polyadic tensor format and generated by evaluating matrix-vector products. By doing a sequence of partial optimizations, in each of which the factors in a SOP basis function for a single coordinate are optimized, the rank of the basis functions is reduced as matrix-vector products are computed. This is better than using an alternating least squares method to reduce the rank, as is done in the reduced-rank block power method. Partial optimization is better because it speeds up the calculation by about an order of magnitude and allows one to significantly reduce the memory cost. We demonstrate the effectiveness of the new method by computing vibrational spectra of two molecules, ethylene oxide (C2H4O) and cyclopentadiene (C5H6), with 7 and 11 atoms, respectively.
Applying Bogomolny’s quantization method to generic classical systems
Authors: Kay Kenneth G.
Published: May 2017

The quantization method of Bogomolny [Nonlinearity 5, 805 (1992)] can potentially provide semiclassical estimates for energy levels of all bound states of arbitrary systems. This approach requires the formation of the transfer matrix TE as a function of energy E. Existing practical methods for calculating this matrix require a recalculation of many classical trajectories for each energy. This has hampered the application of Bogomolny’s method to generic systems that do not possess special classical scaling properties. Generalizing earlier work [H. Barak and K. G. Kay, Phys. Rev. E 88, 062926 (2013)], we develop initial value representation formulas for TE that overcome this problem. These expressions are obtained from a generalized Herman-Kluk formula for the propagator that allows one to easily derive a family of semiclassical integral approximations for the Green’s function that are, in turn, used to form the transfer matrix. Calculations for two-dimensional systems show that Bogomolny’s method with the present expressions for TE produces accurate semiclassical energy levels from small transfer matrices.
From a ℤ2 topological insulator to a square ribbon: Tuning quantum spin Hall states and conductivity
Authors: Zhang Zhiwei , Tian Yiteng , Fernando Gayanath W.
Published: May 2017

By introducing a new type of strained lattice, one dimensional arm-distorted ribbons, we demonstrate the possibility of opening a bandgap from the originally gapless graphene nanoribbons in the ℤ2 topological class. Typically, a gap opens up due to time-reversal/twofold rotational symmetry breaking; however, our approach leads to a bandgap at the edge of the Brillouin zone while preserving the above symmetries. The calculated gap opening is due to a properly scaled extra hopping interaction, compared to the Kane-Mele Hamiltonian where this hopping is omitted since it is a third neighbor interaction in graphene. For square ribbons with a variable number of legs, we discuss Rashba-related spin-dependent transport properties in the presence and absence of a magnetic flux. In such ribbons, opposite spins travel in opposite directions along the edges, while the spin current in the center leg turns out to be smaller by at least an order of magnitude. In addition, the spin difference between the left and right (say) edges shows plateaus as a function of the magnetic flux. We also discuss transport properties resulting from a non-spin-orbit coupled Hamiltonian which includes third neighbor hopping during a systematic transformation from honeycomb to square ribbons.
Behavioral synchronization induced by epidemic spread in complex networks
Authors: Sun Mengfeng , Lou Yijun , Duan Jinqiao , Fu Xinchu
Published: June 2017

During the spread of an epidemic, individuals in realistic networks may exhibit collective behaviors. In order to characterize this kind of phenomenon and explore the correlation between collective behaviors and epidemic spread, in this paper, we construct several mathematical models (including without delay, with a coupling delay, and with double delays) of epidemic synchronization by applying the adaptive feedback motivated by real observations. By using Lyapunov function methods, we obtain the conditions for local and global stability of these epidemic synchronization models. Then, we illustrate that quenched mean-field theory is more accurate than heterogeneous mean-field theory in the prediction of epidemic synchronization. Finally, some numerical simulations are performed to complement our theoretical results, which also reveal some unexpected phenomena, for example, the coupling delay and epidemic delay influence the speed of epidemic synchronization. This work makes further exploration on the relationship between epidemic dynamics and synchronization dynamics, in the hope of being helpful to the study of other dynamical phenomena in the process of epidemic spread.
Ultra-thin metasurface microwave flat lens for broadband applications
Authors: Azad Abul K. , Efimov Anatoly V. , Ghosh Shuprio , Singleton John , Taylor Antoinette J. , Chen Hou-Tong
Published: May 2017

We demonstrate a metasurface-based ultrathin flat lens operating at microwave frequencies. A series of subwavelength metallic split-ring resonators, which are sandwiched between two cross-polarized metallic gratings, are defined to obtain a radially symmetric parabolic phase distribution, covering relative phase differences ranging from 0 to 2.5π radians to create a lens. The tri-layer lens exhibits focusing/collimating of broadband microwaves from 7.0 to 10.0 GHz, with a gain enhancement of 17 dBi at a central wavelength 9.0 GHz while fed by a rectangular horn antenna. The measured focal length agrees reasonably well with design, achieving a 3 dB directionality <4.5° and confirming high-quality beam collimation along the propagation direction. The demonstrated metasurface flat lens enables light-weight, low-cost, and easily deployable flat transceivers for microwave communication, detection, and imaging applications.
Dual-frequency low-voltage subterahertz radial clinotron based on fan-shaped splitter
Authors: Chen Zaigao , Wang Jianguo , Wang Yue
Published: May 2017

To further improve the output power and tuning bandwidth of compact low-voltage subterahertz vacuum electron devices, a novel dual-frequency low-voltage subterahertz radial clinotron oscillator, in which two fan-shaped radial electron beams transmit inward along the axial direction and interact with two fan-shaped slow wave structures (SWSs) machined on the azimuthally symmetric planar plate individually, is studied in this paper. Compared to the clinotron where the planar SWS composed of the rectangular grooves is adopted, the dispersion curve of proposed fan-shaped radial SWSs is independent of radius and azimuthal coordinates. The particle-in-cell simulation results indicate that the designed clinotron can simultaneously produce the electromagnetic waves at 0.305 THz and 0.34 THz, the corresponding output powers are 9.1 W and 24 W, and the tuning range of bandwidth can be significantly broadened.
Temperature dependence of Rashba-Edelstein magnetoresistance in Bi/Ag/CoFeB trilayer structures
Authors: Nakayama Hiroyasu , An Hongyu , Nomura Akiyo , Kanno Yusuke , Haku Satoshi , Kuwahara Yusaku , Sakimura Hiroto , Ando Kazuya
Published: May 2017

We have investigated the recently discovered Rashba-Edelstein magnetoresistance (REMR) in Bi/Ag/CoFeB trilayer structures with different temperatures, Bi thicknesses, and magnetic fields via the angular-dependent magnetoresistance (ADMR) measurements. We found that the magnitude of the REMR shows a small variation with changing temperature, which is consistent with the previous work on the temperature evolution of the inverse Rashba-Edelstein effect. Furthermore, the ADMR measurements with different thicknesses of Bi layers and external magnetic fields revealed that the contribution from the field-dependent magnetoresistance is not negligibly small for thicker Bi films (≥10 nm) at low temperature.
Induced charge effects on electrokinetic entry flow
Authors: Prabhakaran Rama Aravind , Zhou Yilong , Zhao Cunlu , Hu Guoqing , Song Yongxin , Wang Junsheng , Yang Chun , Xuan Xiangchun
Published: June 2017

Electrokinetic flow, due to a nearly plug-like velocity profile, is the preferred mode for transport of fluids (by electroosmosis) and species (by electrophoresis if charged) in microfluidic devices. Thus far there have been numerous studies on electrokinetic flow within a variety of microchannel structures. However, the fluid and species behaviors at the interface of the inlet reservoir (i.e., the well that supplies the fluid and species) and microchannel are still largely unexplored. This work presents a fundamental investigation of the induced charge effects on electrokinetic entry flow due to the polarization of dielectric corners at the inlet reservoir-microchannel junction. We use small tracing particles suspended in a low ionic concentration fluid to visualize the electrokinetic flow pattern in the absence of Joule heating effects. Particles are found to get trapped and concentrated inside a pair of counter-rotating fluid circulations near the corners of the channel entrance. We also develop a depth-averaged numerical model to understand the induced charge on the corner surfaces and simulate the resultant induced charge electroosmosis (ICEO) in the horizontal plane of the microchannel. The particle streaklines predicted from this model are compared with the experimental images of tracing particles, which shows a significantly better agreement than those from a regular two-dimensional model. This study indicates the strong influences of the top/bottom walls on ICEO in shallow microchannels, which have been neglected in previous two-dimensional models.
Kinetic characteristics of ions in the gas discharge and on the target surface
Authors: Maiorov S. A. , Kodanova S. K. , Golyatina R. I. , Ramazanov T. S.
Published: June 2017

The drift velocities of ions in a constant homogeneous electric field are calculated using Monte Carlo simulations for noble-gas and some metal vapors. The ion mobility is analyzed as a function of the field strength and gas temperature. A general approximate formula for the dependence of the drift velocity on the reduced field and gas temperature is derived. The results of calculations of kinetic characteristics of ions crossing the surface of the target are presented. The authors focus on the angular and energy distributions of ions and differences between the distributions of the average volume and the average flow on the surface.
Reversibility of minor hysteresis loops in magnetocaloric Heusler alloys
Authors: Gottschall Tino , Stern-Taulats Enric , Mañosa Lluís , Planes Antoni , Skokov Konstantin P. , Gutfleisch Oliver
Published: June 2017

The unavoidable existence of thermal hysteresis in magnetocaloric materials with a first-order phase transition is one of the central problems limiting their implementation in cooling devices. Using minor loops, however, allows achieving significant cyclic effects even in materials with relatively large hysteresis. Here, we compare thermometric measurements of the adiabatic temperature change ΔTad and calorimetric measurements of the isothermal entropy change ΔST when moving in minor hysteresis loops driven by magnetic fields. Under cycling in 2 T, the Ni-Mn-In-Co Heusler material provides a reversible magnetocaloric effect of ΔSTrev= 10.5 J kg–1 K−1 and ΔTadrev= 3.0 K. Even though the thermodynamic conditions and time scales are very different in adiabatic and isothermal minor loops, it turns out that after a suitable scaling, a self-consistent reversibility region in the entropy diagram is found. This region is larger than expected from basic thermodynamic considerations based on isofield measurements alone, which opens new opportunities in application.
Effect of angle of incidence on the performance of bulk heterojunction organic solar cells: A unified optoelectronic analytical framework
Authors: Rahman Md. Sadman Sakib , Alam Md. Kawsar
Published: June 2017

We analyze the performance of bulk heterojunction organic solar cells under oblique incidence of light. In this regard, we present an optoelectronic analytical model that describes the current-voltage characteristics of bulk heterojunction organic solar cells taking into account the effect of angle of incidence. A closed-form general expression is derived for the optical generation rate under oblique incidence employing transfer matrix formalism. The resulting expression is then incorporated in the classical drift-diffusion transport and continuity equations of charge carriers to derive a unified expression of voltage dependent current density combining optical and electrical parameters. Thus, the model is capable of determining the accurate optical absorption in the active layer for varying angles of incidence as well as predicting the corresponding wavelength dependent external quantum efficiency of the device. The results are verified by comparing with published numerical and experimental results. We show that the maximum efficiency might be achieved at an oblique angle of incidence rather than normal incidence for certain active layer thicknesses. We also report the optimum angles at which the maximum efficiency occurs and show that they are active layer thickness dependent.
Modeling of I-V characteristics in symmetric double-gate polysilicon thin-film transistors
Authors: Ma Xiaoyu , Chen Songlin , Deng Wanling , Huang Junkai
Published: June 2017

A new closed-form approximation for surface potential and drain current (DC) in symmetric double-gate polysilicon thin-film transistors (DG poly-Si TFTs) is proposed. The solution of the surface potential is single-piece and suitable for a wide range of gate voltages under different conditions. A comparison with numerical results shows that this scheme gives an accurate description of surface potential. The development of surface-potential-based compact model for I-V characteristics is achieved based on this calculation. Finally, the validity of the model is verified by comparisons with various experimental data. It is showing that the model is accurate over a wide range of operation regions.
Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase
Authors: Ho Thien-Hoang , Hong Myoung-Ki , Kim Seunghwan , Kim Jeong-Gu , Lee Jongha , Jung Kyoungho , Lee Inho , Choi Munyoung , Park Hyunjae , Lee Sanghee , Ahn Yeh-Jin , Kang Lin-Woo
Published: May 2017

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice, one of the most devastating rice diseases. We analysed the time-resolved transcriptional expression of aminoacyl-tRNA synthetase (aaRS) genes in Xoo cells treated with rice-leaf extract. Most aaRS genes showed decreased expression in the initial 30 min and recovered or increased expression in the later 30 min. The protein-synthetic machinery of bacterial cells is an important target for developing antibiotic agents; aaRSs play an essential role in peptide synthesis by attaching amino acids onto the corresponding tRNA. In bacteria, glutaminyl-tRNA (Gln-tRNAGln) is synthesised in two steps by glutamyl-tRNA synthetase (GluRS) and tRNA-dependent aminotransferase, the indirect biosynthetic mechanism of which is not present in eukaryotes. We determined the crystal structure of GluRS from Xoo (XoGluRS) at resolution of 3.0 Å, this being the first GluRS structure from a plant pathogen such as Xoo. The XoGluRS structure consists of five domains, which are conserved in other bacterial GluRS structures. In the bacterial GluRS structures, the Rossmann-fold catalytic domain and the stem-contact domain are most conserved in both sequence and structure. The anticodon-binding domain 1 is less conserved in sequence but overall structure is conserved. The connective-polypeptide domain and the anticodon-binding domain 2 show various conformations in structure. The XoGluRS structure could provide useful information to develop a new pesticide against Xoo and bacterial blight.
Tree-based techniques to predict soil units
Authors: Pinheiro H. S. K. , Owens P. R. , Anjos L. H. C. , Carvalho Júnior W. , Chagas C. S.
Published: May 2017

Quantitative soil–landscape models offer a method for conducting soil surveys that use statistical tools to predict natural patterns in the occurrence of particular map units across a landscape. The aim of the present study was to predict soil units in a watershed with wide variation in landscape conditions. The approach relied on a modelling of soil-forming factors in order to understand the variability of the landscape components in the region. Models were generated for landscape attributes related to pedogenesis, specifically elevation, slope, curvature, compound topographic index, Euclidean distance from stream networks, landforms map, clay minerals index, iron oxide index and normalised difference vegetation index, along with an existing geology map. The soil classification was adapted from the World Reference Base System for Soil Resources, and the predominant soil taxonomic orders observed were Ferrasols, Acrisols, Gleysols, Cambisols, Fluvisols and Regosols. The algorithms used to predict the soil units were based on decision tree (DT) and random forest (RF) methods. The criteria used to evaluate the models’ performance were statistical indices, coherence between predicted units and the legacy map, as well as accuracy checks based on control samples. The best performing model was found to be the RF algorithm, with resulting statistical indices considered excellent (overall=0.966, kappa=0.962). The accuracy of the map as determined by control points was 67.89%, with a kappa value of 61.39%.
Resource partitioning among five sympatric species of freshwater turtles from the wet–dry tropics of northern Australia
Authors: Welsh Michael A. , Doody J. Sean , Georges Arthur
Published: May 2017

Context Resource partitioning of diet and microhabitat was examined for five sympatric species of freshwater turtles in the Daly River in the northern end of Northern Territory (Top End) in Australia. The Daly River supports a high diversity of freshwater turtles, making it the ideal place to study a freshwater turtle community. Aims To determine the dry-season diet and microhabitat use of Carettochelys insculpta, Elseya dentata, Chelodina oblonga, Emydura victoriae and Emydura subglobosa worrelli and examine intraspecific and interspecific niche overlap and ontogenetic dietary shift. Methods Gut contents were collected by stomach flushing, and microhabitat use was determined by recording where each turtle was first seen before capture. Diet and microhabitat use were compared using an index of relative importance. Niche overlap was measured with Horn’s overlap index. Key results Carettochelys insculpta is an opportunistic omnivore that feeds mostly on ribbonweed (Vallisneria spiralis) and aquatic snails. Elseya dentata is herbivorous, feeding primarily on aquatic algae. The diets of C. insculpta and E. dentata overlapped moderately, but the overall niche overlap was low because they occupied different microhabitats within the river. Chelodina oblonga fed very little, and may use the Daly River as a dry-season refuge. Emydura victoriae is molluscivorous, consuming more molluscs as it grows. This ontogenetic dietary shift was associated with megacephaly (extreme broadly expanded head that is too large to fit into the carapace) and expanded triturating surfaces. This specialisation allows adult E. victoriae to feed exclusively on molluscs and so their diet overlapped little with other species. Emydura subglobosa worrelli was omnivorous, consuming mostly freshwater sponge and apparently preferring more lentic water. Conclusions The freshwater turtles of the wet–dry tropics are usually reported as being heavily reliant on the seeds, fruits and leaves of riparian vegetation; however, the present study showed that the dry-season diet in perennial rivers is primarily of aquatic origin. Implications The study suggested that populations of C. insculpta, E. dentata and E. victoriae could be threatened by broad-scale development in northern Australia if there were substantive impacts on aquatic macrophytes and molluscs in the Daly River system.
Auxin steers root cell expansion via apoplastic pH regulation in
Arabidopsis thaliana
Authors: Barbez Elke , Dünser Kai , Gaidora Angelika , Lendl Thomas , Busch Wolfgang
Published: May 2017

Significance

Cellular growth in plants is constrained by cell walls; hence, loosening these structures is required for growth. The long-standing acid growth theory links auxin signaling, apoplastic pH homeostasis, and cellular expansion, providing a conceptual framework for cell expansion in plant shoots. Intriguingly, this model remains heavily debated for roots. Here, we present a fluorescent dye that allows for the correlation of cell size and apoplastic pH at a cellular resolution in
Arabidopsis thaliana
. This enabled us to elucidate a complex involvement of auxin in root apoplastic pH homeostasis, which is important for root cell expansion and gravitropic response. These findings shed light on the poorly understood acid growth mechanism in roots.
Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase
Authors: Neves Rui P. P. , Fernandes Pedro Alexandrino , Ramos Maria João
Published: May 2017

Significance

Protein disulfide isomerase (PDI) is a ubiquitous enzyme involved in disulfide bond formation during protein folding. It has been related to neurological diseases (Parkinson or Alzheimer’s) because of unfolded protein response phenomena. It also participates in the regulation of the glutathione redox buffer [glutathione/glutathione disulfide (GSH/GSSG)] in the endoplasmic reticulum, also important in protein folding. PDI catalyzes the nucleophilic attack of thiolates to disulfide bonds (thiol-disulfide exchange), enhancing the formation of correct disulfide links that drive protein folding and ensure protein function. This reaction is ubiquitous to disulfide-oxidoreductases across several organisms, and it shows a distinctive chemistry. We present the enzymatic mechanism of PDI in the GSH/GSSG buffer and discuss the chemistry of thiol-disulfide exchange.
Estimating the parameters of background selection and selective sweeps in
Drosophila
in the presence of gene conversion
Authors: Campos José Luis , Zhao Lei , Charlesworth Brian
Published: May 2017

Significance

The level of DNA sequence variation at a site in the genome is affected by selection acting on genetically linked sites. We have developed models of selection at linked sites to explain the observed negative relation between the level of nearly neutral variability in
Drosophila
genes and their protein sequence divergence from a related species. We use fits of these models to polymorphism and divergence data to show that selective sweeps are the main determinants of this pattern. We obtain estimates of the strengths of selection on advantageous mutations and the proportions of new mutations that are selectively advantageous. Gene conversion, a major source of genetic recombination within genes, has a large effect on these parameter estimates.
Visual cortex entrains to sign language
Authors: Brookshire Geoffrey , Lu Jenny , Nusbaum Howard C. , Goldin-Meadow Susan , Casasanto Daniel
Published: May 2017

Significance

Language comprehension is thought to rely on a combination of specialized and general-purpose neural mechanisms. When people listen to speech, low-frequency oscillations in cerebral cortex (

<

8 Hz) become entrained to quasirhythmic fluctuations in volume. Entrainment of auditory cortex to speech rhythms has been well documented, but its functional significance has remained unclear. By showing similar entrainment of visual cortex to sign language, we establish that this phase-locking is not due to specific properties of auditory cortex or of oral speech perception. Rather, low-frequency entrainment is a generalized cortical strategy for boosting perceptual sensitivity to informational peaks in time-varying signals.
Follistatin is critical for mouse uterine receptivity and decidualization
Authors: Fullerton Paul T. , Monsivais Diana , Kommagani Ramakrishna , Matzuk Martin M.
Published: May 2017

Significance

An estimated 50% of in vitro fertilization attempts fail to achieve implantation, making implantation one of the most significant challenges in the assisted reproductive technologies (ART) clinic. Unfortunately, no effective treatments or biomarkers are available for the receptivity of the uterus to embryo implantation. Understanding the molecular mechanisms underlying implantation will enable future advances in ART to improve success rates and reduce the emotional, physical, and financial toll that ART failure takes on patients. We generated conditional knockout of follistatin in the uterus and demonstrated that follistatin plays a critical role in establishing uterine receptivity. Our results contribute to the understanding of the molecular mechanisms underlying uterine receptivity and offer a useful animal model for studying implantation and decidualization failure.
Spontaneous formation of aligned DNA nanowires by capillarity-induced skin folding
Authors: Nagashima So , Ha Hyun Dong , Kim Do Hyun , Košmrlj Andrej , Stone Howard A. , Moon Myoung-Woon
Published: May 2017

Significance

Developing a method that is capable of manipulating the size, geometry, and alignment of DNA nanowires would expand their uses in fabricating functional materials and performing genetic analysis. Here, we present an approach that yields arrays of size-controllable straight or undulated DNA nanowires. This approach uses a template composed of a thin skin that dynamically changes its surface morphology in response to water. In particular, we exploit capillary forces of water containing DNA molecules to induce a wrinkle-to-fold transition of the template surface in an unconventional way, which in turn stretches and confines the molecules in the folded regions without any external forces and consequently forms the nanowires. This approach could make possible new fabrication opportunities for functional materials.
Three classes of oxygen-dependent cyclase involved in chlorophyll and bacteriochlorophyll biosynthesis
Authors: Chen Guangyu E. , Canniffe Daniel P. , Hunter C. Neil
Published: May 2017

Significance

(Bacterio)chlorophylls harvest and convert the solar energy that powers the biosphere. The absorption properties of these pigments are determined in part by formation of the isocyclic ring, which confers their characteristic green color. This last remaining uncharacterized biosynthetic step has remained enigmatic for more than 60 y, and only a single subunit of the O
2
-dependent cyclase, AcsF, has been identified. Here we demonstrate that Ycf54 is a bona fide subunit of this enzyme in oxygenic phototrophs; identify a new cyclase subunit, BciE, in Alphaproteobacteria; and confirm that the AcsF found in other classes of bacterial phototrophs is the principal form of the cyclase, requiring neither Ycf54 nor BciE for activity.
AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production
Authors: Schäper Simon , Steinchen Wieland , Krol Elizaveta , Altegoer Florian , Skotnicka Dorota , Søgaard-Andersen Lotte , Bange Gert , Becker Anke
Published: May 2017

Significance

Cyclic dimeric GMP (c-di-GMP) has emerged as ubiquitous bacterial second messenger, regulating multiple cellular functions, such as cell cycle, virulence, and biofilm formation. However, our knowledge on the molecular inventory, diversity, and function of c-di-GMP receptors, and the molecular evolution of c-di-GMP–responsive proteins is still incomplete. We have identified a class of c-di-GMP–responsive transcription factors, strikingly illustrating how a classical transcription factor has acquired the ability to sense this signaling molecule. The mode of c-di-GMP binding to the AraC-like transcription factor CuxR is highly reminiscent to that of the PilZ domain, the prototypic c-di-GMP receptor. PilZ and CuxR provide an example of convergent evolution in which c-di-GMP binding sites of similar topology have evolved independently in two distinct protein families.
Increased nitrous oxide emissions from Arctic peatlands after permafrost thaw
Authors: Voigt Carolina , Marushchak Maija E. , Lamprecht Richard E. , Jackowicz-Korczyński Marcin , Lindgren Amelie , Mastepanov Mikhail , Granlund Lars , Christensen Torben R. , Tahvanainen Teemu , Martikainen Pertti J. , Biasi Christina
Published: May 2017

Significance

The Arctic is warming rapidly, causing permafrost soils to thaw. Vast stocks of nitrogen (>67 billion tons) in the permafrost, accumulated thousands of years ago, could now become available for decomposition, leading to the release of nitrous oxide (N
2
O) to the atmosphere. N
2
O is a strong greenhouse gas, almost 300 times more powerful than CO
2
for warming the climate. Although carbon dynamics in the Arctic are well studied, the fact that Arctic soils store enormous amounts of nitrogen has received little attention so far. We report that the Arctic may become a substantial source of N
2
O when the permafrost thaws, and that N
2
O emissions could occur from surfaces covering almost one-fourth of the entire Arctic.
Synchrony affects Taylor’s law in theory and data
Authors: Reuman Daniel C. , Zhao Lei , Sheppard Lawrence W. , Reid Philip C. , Cohen Joel E.
Published: May 2017

Significance

Two widely confirmed patterns in ecology are Taylor’s law (TL), which states that the variance of population density is approximately a power of mean population density, and population synchrony, the tendency of species’ population sizes in different areas to be correlated through time. TL has been applied in many areas, including fisheries management, conservation, agriculture, finance, physics, and meteorology. Synchrony of populations increases the likelihood of large-scale pest or disease outbreaks and shortages of resources. We show that changed synchrony modifies and can invalidate TL. Widespread recent changes in synchrony, possibly resulting from climate change, may broadly affect TL and its applications.
Cortical neurons multiplex reward-related signals along with sensory and motor information
Authors: Ramakrishnan Arjun , Byun Yoon Woo , Rand Kyle , Pedersen Christian E. , Lebedev Mikhail A. , Nicolelis Miguel A. L.
Published: May 2017

Significance

The ability to learn highly skilled movements may depend on the dopamine-related plasticity occurring in motor cortex, because the density of dopamine receptors—the reward sensor—increases in this area from rodents to primates. We hypothesized that primary motor (M1) and somatosensory (S1) neurons would encode rewards during operant conditioned motor behaviors. Rhesus monkeys were implanted with cortical multielectrode implants and trained to perform arm-reaching tasks with different reward schedules. Consistent with our hypothesis, M1 and S1 neurons represented reward anticipation and delivery and a mismatch between the quantities of anticipated and actual rewards. These same neurons also represented arm movement parameters. We suggest that this multiplexing of motor and reinforcement information by cortical neurons underlies motor learning.
Peripheral modifications of [Ψ[CH
2
NH]Tpg
4
]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics
Authors: Okano Akinori , Isley Nicholas A. , Boger Dale L.
Published: May 2017

Significance

In a quest for antibiotics that may display durable clinical lifetimes, analogs of the glycopeptide antibiotics, including vancomycin, have been designed that not only directly overcome the molecular basis of existing vancomycin resistance but also contain two added peripheral modifications that endow them with two additional independent mechanisms of actions not found in the parent antibiotics. It is shown that such peripherally and binding pocket-modified vancomycin analogs display little propensity for acquired resistance by vancomycin-resistant Enterococci and that both their antimicrobial potency and durability against such challenges follow trends (three > two > one mechanisms of action) that are now predictable.
A mechanism for lipid binding to apoE and the role of intrinsically disordered regions coupled to domain–domain interactions
Authors: Frieden Carl , Wang Hanliu , Ho Chris M. W.
Published: May 2017

Significance

Alzheimer’s disease is the most common cause of dementia. It is irreversible, devastating, and costly. Apolipoprotein E4 (ApoE4), a protein whose function in the brain is to transport cholesterol-laden lipid, is a major risk factor for the development of late-onset Alzheimer’s disease relative to the common apoE3 isoform. The two proteins differ by only a single amino acid. There has been no detailed mechanism explaining how apoE functions. Here, we propose a mechanism for lipid binding that involves simple domain–domain movement coupled to the role of intrinsically disordered regions of the protein. This mechanism may lead to the development of small molecular weight compounds that interfere with the role apoE4 plays in the development of Alzheimer’s disease.
Personhood Status of the Human Zygote, Embryo, Fetus
Authors: Miklavcic John Janez , Flaman Paul
Published: May 2017

The fields of biology, medicine, and embryology have described the developmental milestones of humans throughout gestation in great detail. It is less clear as to when humans are recognized as people, persons, or beings with rights that are protected by legislation. The practice of law is irrevocably intertwined with that of ethical conduct; and the time at which a human life is considered a person has implications that extend to health care, legislation on abortion, and autonomy of individuals. This article reviews the economical position that fertilization is the moment that personhood of the conceptus begins. Alternate positions proposing that personhood begins at other possible times after fertilization are presented and contrasted to the economical hypothesis.

This article is an original work critically analyzing the various arguments for human personhood at fertilization and thereafter. The various positions on human personhood are compared and contrasted herein. The time of the human lifespan at which personhood is conferred has important implications for health care, legislation, and personal autonomy.
The quest for legitimacy in independent Kosovo: the unfulfilled promise of diversity and minority rights
Authors: Landau Dana M.
Published: May 2017

When Kosovo declared its independence in 2008, it did so not as a nation-state, but as a “state of communities,” self-defining as multiethnic, diverse, and committed to extensive rights for minorities. In this paper, this choice is understood as a response to a dual legitimation problem. Kosovo experienced both an external legitimation challenge, regarding its contested statehood internationally, and an internal one, vis-à-vis its Serb minority. The focus on diversity and minority rights was expected to confer legitimacy on the state both externally and internally. International state-builders and the domestic political elite in post-conflict Kosovo both pursued this strategy. However, it inadvertently created an additional internal legitimation challenge, this time from within Kosovo's majority Albanian population. This dynamic is illustrated by the opposition movement “Lëvizja Vetëvendosje” (Self-Determination Movement), which rejects the framing of Kosovo as first and foremost a multiethnic state. The movement's counter-narrative represents an additional internal legitimation challenge to the new state. This paper thus finds that internationally endorsed “diversity management” through minority rights did not deliver as a panacea for the legitimacy dilemmas of the post-conflict polity. On the contrary, the “state of communities” continues to be contested by both majority and minority groups in Kosovo.
Use of Wind Fetch and Shoreline Relief to Predict Nearshore Substrate Composition in a North Temperate Lake
Authors: Schall Benjamin J. , Cross Timothy K. , Katzenmeyer Eric , Zentner Douglas L.
Published: May 2017

Spawning habitat assessments often focus on substrate composition, but few studies have predicted shoal substrates by using environmental factors. We developed a model for predicting shoal substrates in Belle Lake, Minnesota, using wind fetch and shoreline relief characteristics. Percent composition of four substrate classes (silt, sand, gravel, and rock), water depth estimated at 1 m from shore (shoal slope), effective wind fetch measured using a GIS model, and riparian bank height derived from LIDAR imaging were determined at 50 transects. Classification and regression tree (CART) analysis grouped substrates into categories, and general additive modeling described the effects of three predictor variables on the percent composition of substrate classes. The CART analysis correctly grouped 39 of 50 transects into four categories, and misclassifications primarily resulted from the movement of sand. Effective fetch most influenced silt (low fetch) and rock (high fetch) substrate classes, shoal slope was predictive of rock, and riparian height was useful in distinguishing sand from gravel. These results demonstrate the utility of a single empirical model for determining shoal substrate composition. Fisheries managers can use this technique to determine potential fish spawning locations and identify potential areas for habitat restoration or protection projects.

Received December 5, 2016; accepted May 5, 2017 Published online July 19, 2017
HUGIn: Hi-C Unifying Genomic Interrogator
Authors: Martin Joshua S , Xu Zheng , Reiner Alex P , Mohlke Karen L , Sullivan Patrick , Ren Bing , Hu Ming , Li Yun
Published: May 2017

Motivation

High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability.

Results

We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTL results and functional genomics data.

Availability and implementation

HUGIn is available at http://yunliweb.its.unc.edu/HUGIn

Supplementary information

Supplementary data are available at Bioinformatics online.
Food quality and safety in Singapore: microbiology aspects
Authors: Zwe Ye Htut , Yuk Hyun Gyun
Published: June 2017

BACKGROUND

Singapore’s status as a first world island city-state which relies chiefly on food imports to meet the demand for consumption presents unique challenges in terms of microbial food safety and quality. Despite the efforts of the Ministry of Health in Singapore, in conjunction with the Agri-Food & Veterinary Authority of Singapore and the National Environment Agency actively collaborate together to promote safety in Singapore, foodborne diseases are still a major public health issue.

OBJECTIVE

The aim of the review was to summarize the various foodborne diseases reported in Singapore in the past few years as well as to give an account of all the currently available microbiological findings indicating safety and quality of poultry, vegetables, fruits, and seafood sold in Singapore.
Values Guide Us in Times of Uncertainty: DACA and Graduate Medical Education
Authors: Poll-Hunter Norma I. , Young Geoffrey H. , Shick Matthew
Published: May 2017

With a new administration and Congress, there is uncertainty surrounding the future of the Deferred Action for Childhood Arrivals (DACA) program. In light of this uncertainty, medical schools have tried to better understand how they can support trainees with DACA. In their article in this issue, Nakae and colleagues describe the issues often encountered by medical students with DACA as they prepare for residency and by the program directors who receive their applications. They offer recommendations for best practices to support these trainees. The authors of this Invited Commentary expand on these important considerations, based on their experiences at a national level. They argue that the core values in academic medicine should drive decision making, the student voice is critical, teamwork is essential, and wellness deserves attention. Academic medicine is part of a larger movement with partners across the health professions and higher education focused on advancing the values of access and opportunity for all. The authors of this Invited Commentary argue that remaining steadfast and committed to the core values in medicine will allow the academic medicine community to successfully navigate these uncertain times.
Collaborative Clinical Reasoning—A Systematic Review of Empirical Studies
Authors: Kiesewetter Jan , Fischer Frank , Fischer Martin R.
Published: May 2017

Introduction:

Health care delivery involves multiple health professions, and increasingly, diagnostic and therapeutic decisions are made through interprofessional teamwork. We define collaborative clinical reasoning (CCR) as the process in which two or more health care team members negotiate diagnostic, therapeutic, or prognostic issues of an individual patient resulting in an illness or treatment plan (and to reduce uncertainty). In a systematic review, we aimed to answer the following research question: Which empirically observable factors are considered crucial influences on performance in CCR in current empirical research?

Methods:

A systematic literature review was conducted. We included empirical studies taking place in a hospital setting, with a clear focus on CCR and published between January 1990 and September 2014. The studies were only included when at least one physician was part of the team. Nine articles were included in the review.

Results:

The factors crucially influencing the CCR performance (ie, diagnosis or treatment plan of patients) are (1) the initial distribution of information over team members, (2) clinical experience of physicians within a team, (3) information exchange within a team, and (4) individual retrieval of information from the team or information representation.

Discussion:

Despite the sparse empirical evidence on CCR, four factors influencing performance were extracted from the literature. Overall, there is little evidence though how each of these factors actually influences CCR performance. Thus, we need more empirical studies to better understand and foster CCR performance.
SymptomCare@Home
Authors: Beck Susan L. , Eaton Linda H. , Echeverria Christina , Mooney Kathi H.
Published: May 2017

SymptomCare@Home, an integrated symptom monitoring and management system, was designed as part of randomized clinical trials to help patients with cancer who receive chemotherapy in ambulatory clinics and often experience significant symptoms at home. An iterative design process was informed by chronic disease management theory and features of assessment and clinical decision support systems used in other diseases. Key stakeholders participated in the design process: nurse scientists, clinical experts, bioinformatics experts, and computer programmers. Especially important was input from end users, patients, and nurse practitioners participating in a series of studies testing the system. The system includes both a patient and clinician interface and fully integrates two electronic subsystems: a telephone computer-linked interactive voice response system and a Web-based Decision Support–Symptom Management System. Key features include (1) daily symptom monitoring, (2) self-management coaching, (3) alerting, and (4) nurse practitioner follow-up. The nurse practitioner is distinctively positioned to provide assessment, education, support, and pharmacologic and nonpharmacologic interventions to intensify management of poorly controlled symptoms at home. SymptomCare@Home is a model for providing telehealth. The system facilitates using evidence-based guidelines as part of a comprehensive symptom management approach. The design process and system features can be applied to other diseases and conditions.
OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY FEATURES OF CHOROIDAL NEOVASCULARIZATION ASSOCIATED WITH CHOROIDAL NEVUS
Authors: Pellegrini Marco , Corvi Federico , Say Emil A. T. , Shields Carol L. , Staurenghi Giovanni
Published: May 2017

Purpose:

To describe the imaging features of choroidal neovascularization (CNV) associated with choroidal nevus using optical coherence tomography angiography (OCT-A) imaging.

Methods:

Retrospective observational case series. Patients with CNV secondary to choroidal nevus underwent full imaging examination including fundus photography, fluorescein angiography, indocyanine green angiography, spectral domain OCT, and OCT-A. The OCT-A features were analyzed and correlated with conventional angiography findings and spectral domain OCT.

Results:

There were 11 eyes from 11 patients (6 men and 5 women, mean age of 65 ± 20.4 years) included in the analysis. Fluorescein angiography and indocyanine green angiography disclosed CNV in 90% and 83%, respectively. Optical coherence tomography angiography displayed CNV network in 11 eyes (100%) and the pattern was classified as “sea-fan” in 8 (73%) and “long filamentous linear vessels” in 3 (27%) eyes. Distinct from CNV, intrinsic vasculature within the nevus was observed in six eyes (55%), corresponding to those with chronic retinal pigment epithelium changes.

Conclusion:

Optical coherence tomography angiography is a useful imaging technique to disclose CNV associated with choroidal nevus. Despite the presence of intraretinal or subretinal fluid and hemorrhage, OCT-A revealed the CNV in all cases, results noninferior to indocyanine green angiography. This imaging modality can be useful for analysis of long-standing nevi with related exudation.