bluuebunny/crossref_metadata_2025 huggingface dataset:
Diffusive equilibration of N2, O2 and CO2 mixing ratios in a 1.5-million-years-old ice core
Authors: Bereiter B. , Fischer H. , Schwander J. , Stocker T. F.
Published: February 2014

Abstract. In the framework of the International Partnerships in Ice Core Sciences, one of the most important targets is to retrieve an Antarctic ice core that extends over the last 1.5 million years (i.e. an ice core that enters the climate era when glacial–interglacial cycles followed the obliquity cycles of the earth). In such an ice core the annual layers of the oldest ice would be thinned by a factor of about 100 and the climatic information of a 10 000 yr interval would be contained in less than 1 m of ice. The gas record in such an Antarctic ice core can potentially reveal the role of greenhouse gas forcing on these 40 000 yr cycles. However, besides the extreme thinning of the annual layers, also the long residence time of the trapped air in the ice and the relatively high ice temperatures near the bedrock favour diffusive exchanges. To investigate the changes in the O2 / N2 ratio, as well as the trapped CO2 concentrations, we modelled the diffusive exchange of the trapped gases O2, N2 and CO2 along the vertical axis. However, the boundary conditions of a potential drilling site are not yet well constrained and the uncertainties in the permeation coefficients of the air constituents in the ice are large. In our simulations, we have set the drill site ice thickness at 2700 m and the bedrock ice temperature at 5–10 K below the ice pressure melting point. Using these conditions and including all further uncertainties associated with the drill site and the permeation coefficients, the results suggest that in the oldest ice the precessional variations in the O2 / N2 ratio will be damped by 50–100%, whereas CO2 concentration changes associated with glacial–interglacial variations will likely be conserved (simulated damping 5%). If the precessional O2 / N2 signal will have disappeared completely in this future ice core, orbital tuning of the ice-core age scale will be limited.
Zeta Potential and Turbidimetry Analyzes for the Evaluation of Chitosan/Phytic Acid Complex Formation
Authors: Saïed Noura , Aider Mohammed
Published: February 2014

The aim of this work was to study the possible complex formation between chitosan and phytic acid. Zeta potential and turbidity measurements were used as a basis to confirm the possible complex between these two molecules. The obtained results showed that chitosan at a concentration of 0.1% (w/v) were soluble in 0.1% acetic acid solution. This concentration of the acetic acid was the lowest that allows chitosan to dissolve. A positive surface charge of chitosan was recorded in the pH interval from 1 to 7. The highest zeta potential values were obtained at pH < 5 and decreased significantly at pH 6 and 7. Regarding phytic acid, it was soluble in deionized water and acetic acid whatever the concentration of the acetic acid and in the entire pH range 2-10. Phytic acid had negative surface charge in deionized water and in 0.1% acetic acid, but was slightly positively charged in 5% acetic acid solution. The solubility of chitosan was decreased by the presence of phytic acid. The formation of chitosan/phytic acid complex as monitored by measuring the zeta potential does not allow us to conclude that the formation of this complex is possible.
Bacterial and viral indicators of fecal contamination in drinking water
Authors: Plummer Jeanine D. , Long Sharon C. , Charest Abigail J. , Roop Daniel O.
Published: February 2014

Coliform indicators are used as an index of waterborne disease risk. Coliforms respond differently to environmental stressors and engineered treatment processes than viral pathogens and thus are imperfect indicators. Bacteriophages, which are similar in structure and morphology to human enteric viruses, may be more highly correlated with the presence of viral pathogens. In this research, coliforms, Escherichia coli, male‐specific coliphages, and somatic coliphages were quantified in feces and in wastewater and drinking water samples collected in multiple regions and seasons. Physical and chemical water quality were also measured. Bacterial indicators varied with animal type in feces and varied with treatment stage in wastewater and drinking water. Samples analyzed for coliphages had a high number of nondetects (49% in fecal samples and up to 79% in drinking water samples), but coliphages can be analyzed in addition to bacteria to provide complementary information on fecal contamination in water and public health risk. In some cases, turbidity and organic carbon may provide a rapid indication of pollution that could trigger targeted microbiological monitoring.
High levels of anti‐Nef antibodies may prevent AIDS disease progression in vertically HIV‐1‐infected infants
Authors: Corró Guillermo , Crudeli Cintia Milena , Rocco Carlos Alberto , Marino Silvia Alejandra , Sen Luisa
Published: February 2014

Introduction

HIV‐1‐associated CD4+ T‐cell depletion is a consequence of uninfected cell death. Nef is one of the viral factors that trigger apoptosis on bystander cells, though the plasma Nef levels do not correlate with Th lymphocytes counts. The aim of our study was to evaluate whether anti‐Nef antibodies were involved in paediatric AIDS development and whether they can prevent the CD4+ T‐cell depletion in vertically infected children.

Methods

Two hundred and seventy three HIV‐1 vertically infected children seen at Garrahan Paediatric Hospital were randomly included in the study, adding 13 selected cases: seven LTNP (long‐term non‐progressors) and six RP (rapid progressors) children (ntotal=286). Specific anti‐HIV‐1‐Nef antibodies were titrated by indirect ELISA and compared between groups. The plasma blocking effect on Nef‐dependent cytotoxicity was evaluated in Jurkat cells using recombinant Nef as apoptotic stimulus and patient plasmas as blockers, measuring the apoptotic levels using Annexin‐V stain and flow cytometry.

Results

Only 63.4% of the patients had specific anti‐Nef antibodies, and the levels of anti‐Nef antibodies found in the selected LTNPs plasmas were always significantly higher (p=1.55×10−4) than those in RPs or general HIV‐1+ paediatric populations. The LTNPs’ plasma had a strong inhibitory effect on Nef‐dependent cytotoxicity even at high dilutions, while RP plasmas had little or no effect on Nef‐induced apoptosis.

Discussion and conclusions

High anti‐Nef antibody levels are associated and predict slow or non‐progression to AIDS in vertically HIV‐1‐infected children. They could be an efficient tool in preventing Nef‐associated bystander effect, preserving CD4+ T‐cells and the immune function in the context of paediatric HIV‐1 infection.
Dual-Band Coherent Perfect Absorption/Thermal
Authors: Feng S.
Published: February 2014

Dual-band perfect absorption/thermal emission is shown to be a general property of an ultrathin bilayer consisting of a dielectric and a totally reflective layer if the permittivity of the dielectric can be described by Drude-Lorentz (DL) model.  The two bands coexist and reside on opposite sides of the Lorentzian resonant frequency where the material loss is small.  However, the perfect absorption mechanism for the two bands is distinguishably different.  One band is related to Fabry-Perot phenomenon and the surge of refractive index near the Lorentzian resonance.  This band is polarization insensitive.  The other band is associated with excitation of Brewster-type mode at the ϵ-near-zero (ENZ) wavelength and occurs only for p-polarized wave at oblique incidences.  This mode has a fast-wave non-radiative character and propagates along the ultrathin ENZ layer superimposed on the highly reflective surface.  Both bands exhibit wide-angle high emission with a small shift in their center frequencies which can be tuned by tuning the Lorentzian resonance.  The resonance-enhanced dual band absorption occurs in the ultrathin DL layer at the weakly absorbing wavelengths as a consequence of an interaction between the total transmission and the total reflection.  We demonstrate this phenomenon in a silicon carbide/copper bilayer.  The suggested structure may have applications in biological and chemical sensors, IR sensors, thermal emission controls, thermophotovoltaics, and photodetectors.
Local spring warming drives earlier river‐ice breakup in a large Arctic delta
Authors: Lesack Lance F. W. , Marsh Philip , Hicks Faye E. , Forbes Donald L.
Published: February 2014

Pan‐Arctic rivers strongly affect the Arctic Ocean and their vast lake‐rich deltas. Their discharges may be increasing because of an intensifying hydrological cycle driven by warming climate. We show that a previously unexplained trend toward earlier ice breakup in the Mackenzie River Delta is little affected by winter warming during the period of river‐ice growth and is unaffected by river discharge, but unexpectedly is strongly related to local spring warming during the period of river‐ice melt. These results are statistically linked to declining winter snowfall that was not expected because of an intensifying Arctic hydrological cycle. Earlier ice breakup is expected to cause declining water level peaks that will reduce off‐channel flows through the lake‐rich delta before river waters enter the ocean. Thus, local spring warming with unexpected snowfall declines, rather than warmer winters, can drive earlier ice breakup in large Arctic rivers and biogeochemical changes in their river‐ocean interface.
Power law scaling of topographic depressions and their hydrologic connectivity
Authors: Le Phong V. V. , Kumar Praveen
Published: February 2014

Topographic depressions, areas of no lateral surface flow, are ubiquitous characteristics of the land surface that control many ecosystem and biogeochemical processes. High density of depressions increases the surface storage capacity, whereas lower depression density increases runoff, thus influencing soil moisture states, hydrologic connectivity, and the climate‐soil‐vegetation interactions. With the widespread availability of high‐resolution lidar‐based digital elevation model (lDEM) data, it is now possible to identify and characterize the structure of the spatial distribution of topographic depressions for incorporation in ecohydrologic and biogeochemical studies. Here we use lDEM data to document the prevalence and patterns of topographic depressions across five different landscapes in the United States and quantitatively characterize the probability distribution of attributes, such as surface area, storage volume, and the distance to the nearest neighbor. Through the use of a depression identification algorithm, we show that these probability distributions of attributes follow scaling laws indicative of a structure in which a large fraction of land surface areas can consist of high number of topographic depressions of all sizes and can account for 4 to 21 mm of depression storage. This implies that the impacts of small‐scale topographic depressions in the landscapes on the redistribution of material fluxes, evaporation, and hydrologic connectivity are quite significant.
Application and testing of the L* neural network with the self‐consistent magnetic field model of RAM‐SCB
Authors: Yu Yiqun , Koller Josef , Jordanova Vania K. , Zaharia Sorin G. , Friedel Reinhard W. , Morley Steven K. , Chen Yue , Baker Daniel , Reeves Geoffrey D. , Spence Harlan E.
Published: February 2014

We expanded our previous work on L* neural networks that used empirical magnetic field models as the underlying models by applying and extending our technique to drift shells calculated from a physics‐based magnetic field model. While empirical magnetic field models represent an average, statistical magnetospheric state, the RAM‐SCB model, a first‐principles magnetically self‐consistent code, computes magnetic fields based on fundamental equations of plasma physics. Unlike the previous L* neural networks that include McIlwain L and mirror point magnetic field as part of the inputs, the new L* neural network only requires solar wind conditions and the Dst index, allowing for an easier preparation of input parameters. This new neural network is compared against those previously trained networks and validated by the tracing method in the International Radiation Belt Environment Modeling (IRBEM) library. The accuracy of all L* neural networks with different underlying magnetic field models is evaluated by applying the electron phase space density (PSD)‐matching technique derived from the Liouville's theorem to the Van Allen Probes observations. Results indicate that the uncertainty in the predicted L* is statistically (75%) below 0.7 with a median value mostly below 0.2 and the median absolute deviation around 0.15, regardless of the underlying magnetic field model. We found that such an uncertainty in the calculated L* value can shift the peak location of electron phase space density (PSD) profile by 0.2 RE radially but with its shape nearly preserved.
Semibrittle deformation and partial melting of perthitic K‐feldspar: An experimental study
Authors: Negrini Marianne , Stünitz Holger , Nasipuri Pritam , Menegon Luca , Morales Luiz F. G.
Published: February 2014

To investigate the relationships between deformation, cracking, and partial melting in the lower continental crust, axial compression and hydrostatic experiments were performed on K‐feldspar single crystals at temperatures of 700° and 900°C and confining pressures between 0.75 and 1.5 GPa. Sample deformation was carried out at a constant strain rate of ~ 10−6 s−1. The samples deformed at 700°C show typical brittle behavior with formation of conjugate fractures and peak stresses that increase with confining pressure. Samples deformed at 900°C show formation of shear fractures, peak stresses below the Goetze criterion, and inverse confining pressure dependence of peak stress, indicating that along the fractures deformation was not dominantly friction controlled. Microstructural and chemical analyses reveal the presence of melt (<6 vol %) of inhomogeneous composition along the shear zones and chemical compositional changes of gouge fragments. In a hydrostatic experiment performed at 900°C, no melt and no compositional changes were observed. These observations indicate that deformation of K‐feldspars at high pressures and temperatures is controlled by the simultaneous formation of brittle fractures and melt. The formation of melt is strongly accelerated and kinetically favored by cracking, as demonstrated by the absence of melting in the hydrostatic experiments. However, the melt along fractures does not dramatically weaken the samples, as the melt domains remain isolated during deformation. The fine‐grained gouge fragments formed along the fracture systems undergo chemical homogenization. The dominant deformation mechanism in the gouge is likely to be melt‐enhanced diffusion creep, which may also assist the chemical homogenization process.
A continuous record of intereruption velocity change at Mount St. Helens from coda wave interferometry
Authors: Hotovec‐Ellis A. J. , Gomberg J. , Vidale J. E. , Creager K. C.
Published: February 2014

In September 2004, Mount St. Helens volcano erupted after nearly 18 years of quiescence. However, it is unclear from the limited geophysical observations when or if the magma chamber replenished following the 1980–1986 eruptions in the years before the 2004–2008 extrusive eruption. We use coda wave interferometry with repeating earthquakes to measure small changes in the velocity structure of Mount St. Helens volcano that might indicate magmatic intrusion. By combining observations of relative velocity changes from many closely located earthquake sources, we solve for a continuous function of velocity changes with time. We find that seasonal effects dominate the relative velocity changes. Seismicity rates and repeating earthquake occurrence also vary seasonally; therefore, velocity changes and seismicity are likely modulated by snow loading, fluid saturation, and/or changes in groundwater level. We estimate hydrologic effects impart stress changes on the order of tens of kilopascals within the upper 4 km, resulting in annual velocity variations of 0.5 to 1%. The largest nonseasonal change is a decrease in velocity at the time of the deep Mw = 6.8 Nisqually earthquake. We find no systematic velocity changes during the most likely times of intrusions, consistent with a lack of observable surface deformation. We conclude that if replenishing intrusions occurred, they did not alter seismic velocities where this technique is sensitive due to either their small size or the finite compressibility of the magma chamber. We interpret the observed velocity changes and shallow seasonal seismicity as a response to small stress changes in a shallow, pressurized system.
Predicting time‐to‐failure in rock extrapolated from secondary creep
Authors: Hao Sheng‐Wang , Zhang Bao‐Ju , Tian Ji‐Feng , Elsworth Derek
Published: February 2014

Stress relaxation experiments are reported that culminate in energetic failure in rocks analogous to the loading cycle and subsequent localization or reactivation on brittle faults embedded in an elastic medium. Universally, rapid primary deformation arrests and transitions into a long secondary deformation phase that ultimately accelerates to catastrophic rupture. Primary deformation (u) conforms to Andrade's law as du/dt ~ (tc − t0)θ with a standard exponent of 2/3. In the long, and readily observable, secondary phase, the samples both deform and analogously shed load near linearly in time. This stress relaxation rate exhibits a robust power law dependency with time‐to‐rupture and exhibits the same 2/3 power law exponent observed in the primary phase. Similarly, the brittle strain energy released in the tertiary collapse scales with a normalized secondary stress relaxation rate. Together, these observations suggest a way to predict both the timing of rupture and its energetics from the observed stress (or strain) rate during the secondary relaxation stage.
Domes, pits, and small chaos on Europa produced by water sills
Authors: Michaut Chloé , Manga Michael
Published: February 2014

Pits, domes, and small chaos on Europa's surface are quasi‐circular features a few to a few tens of kilometers in diameter. We examine if injection of water sills into Europa's ice shell and their subsequent evolution can induce successive surface deformations similar to the morphologies of these features. We study the dynamics of water spreading within the elastic part of the ice shell and show that the mechanical properties of ice exert a strong control on the lateral extent of the sill. At shallow depths, water makes room for itself by lifting the overlying ice layer and water weight promotes lateral spreading of the sill. In contrast, a deep sill bends the underlying elastic layer and its weight does not affect its spreading. In that case, the sill lateral extent is limited by the fracture toughness of ice and the sill can thicken substantially. After emplacement, cooling of the sill warms the surrounding ice and thins the overlying elastic ice layer. As a result, preexisting stresses in the elastic part of the ice shell increase locally to the point that they may disrupt the ice above the sill (small chaos). Disruption of the surface also allows for partial isostatic compensation of water weight, leading to a topographic depression at the surface (pit), of the order of ~102 m. Complete water solidification finally causes expansion of the initial sill volume and results in an uplifted topography (dome) of ~102m.
Partitioning of evapotranspiration through oxygen isotopic measurements of water pools and fluxes in a temperate grassland
Authors: Hu Zhongmin , Wen Xuefa , Sun Xiaomin , Li Linghao , Yu Guirui , Lee Xuhui , Li Shenggong
Published: February 2014

Stable isotopic measurements of water provide a promising tool for partitioning of ecosystem evapotranspiration (ET). This approach, however, is still facing some challenges due to the uncertainties in estimating the isotopic compositions of ET and its components. In this study, a tunable diode laser analyzer was deployed for in situ measurements of the oxygen isotopic compositions of water vapor. Using these measurements together with samples of water in plant and soil pools, we partitioned ET via estimating the oxygen isotopic compositions of ET (δET) and that of its two components, i.e., plant transpiration (δT) and soil water evaporation (δE). A new δT model was developed in this study, which illustrated consistent estimations with the traditional model. Most of the variables and parameters in the new model can be measured directly with high accuracy, making its potential to be used at other sites high. Our results indicate that the ratio of plant transpiration to evapotranspiration (T/ET) illustrates a “U” shape diurnal pattern. Mean T/ET at 0630–1830 during the sampling days was 83%. Soil depth of 15 cm is a reasonable depth for soil water sampling for estimating δE at this site. We also investigated the uncertainties in estimating these three terms and their effects on partitioning. Overall, in terms of partitioning, the uncertainties are relatively small from δT and δE but quite large from δET. Quantifying and improving the precision of δET should be a priority in future endeavors of ET partitioning via the stable isotopic approach.
Controls on methane released through ebullition in peatlands affected by permafrost degradation
Authors: Klapstein Sara J. , Turetsky Merritt R. , McGuire A. David , Harden Jennifer W. , Czimczik Claudia I. , Xu Xiaomei , Chanton Jeffrey P. , Waddington James M.
Published: February 2014

Permafrost thaw in peat plateaus leads to the flooding of surface soils and the formation of collapse scar bogs, which have the potential to be large emitters of methane (CH4) from surface peat as well as deeper, previously frozen, permafrost carbon (C). We used a network of bubble traps, permanently installed 20 cm and 60 cm beneath the moss surface, to examine controls on ebullition from three collapse bogs in interior Alaska. Overall, ebullition was dominated by episodic events that were associated with changes in atmospheric pressure, and ebullition was mainly a surface process regulated by both seasonal ice dynamics and plant phenology. The majority (>90%) of ebullition occurred in surface peat layers, with little bubble production in deeper peat. During periods of peak plant biomass, bubbles contained acetate‐derived CH4 dominated (>90%) by modern C fixed from the atmosphere following permafrost thaw. Post‐senescence, the contribution of CH4 derived from thawing permafrost C was more variable and accounted for up to 22% (on average 7%), in the most recently thawed site. Thus, the formation of thermokarst features resulting from permafrost thaw in peatlands stimulates ebullition and CH4 release both by creating flooded surface conditions conducive to CH4 production and bubbling as well as by exposing thawing permafrost C to mineralization.
A global soil data set for earth system modeling
Authors: Shangguan Wei , Dai Yongjiu , Duan Qingyun , Liu Baoyuan , Yuan Hua
Published: February 2014

We developed a comprehensive, gridded Global Soil Dataset for use in Earth System Models (GSDE) and other applications. The GSDE provides soil information, such as soil particle‐size distribution, organic carbon, and nutrients, and quality control information in terms of confidence level at 30″ × 30″ horizontal resolution and for eight vertical layers to a depth of 2.3 m. The GSDE is based on the Soil Map of the World and various regional and national soil databases, including soil attribute data and soil maps. We used a standardized data structure and data processing procedures to harmonize the data collected from various sources. We then used a soil type linkage method (i.e., taxotransfer rules) and a polygon linkage method to derive the spatial distribution of the soil properties. To aggregate the attributes of different compositions of a mapping unit, we used three mapping approaches: the area‐weighting method, the dominant soil type method, and the dominant binned soil attribute method. The data set can also be aggregated to a lower resolution. In this paper, we only show the vertical and horizontal variations of sand, silt and clay contents, bulk density, and soil organic carbon as examples of the GSDE. The GSDE estimates of global soil organic carbon stock to the depths of 2.3, 1, and 0.3 m are 1922.7, 1455.4, and 720.1 Gt, respectively. This newly developed data set provides more accurate soil information and represents a step forward to advance earth system modeling.
New permafrost is forming around shrinking Arctic lakes, but will it last?
Authors: Briggs Martin A. , Walvoord Michelle A. , McKenzie Jeffrey M. , Voss Clifford I. , Day‐Lewis Frederick D. , Lane John W.
Published: February 2014

Widespread lake shrinkage in cold regions has been linked to climate warming and permafrost thaw. Permafrost aggradation, however, has been observed within the margins of recently receded lakes, in seeming contradiction of climate warming. Here permafrost aggradation dynamics are examined at Twelvemile Lake, a retreating lake in interior Alaska. Observations reveal patches of recently formed permafrost within the dried lake margin, colocated with discrete bands of willow shrub. We test ecological succession, which alters shading, infiltration, and heat transport, as the driver of aggradation using numerical simulation of variably saturated groundwater flow and heat transport with phase change (i.e., freeze‐thaw). Simulations support permafrost development under current climatic conditions, but only when net effects of vegetation on soil conditions are incorporated, thus pointing to the role of ecological succession. Furthermore, model results indicate that permafrost aggradation is transitory with further climate warming, as new permafrost thaws within seven decades.
Shallow cumulus rooted in photosynthesis
Authors: Vilà‐Guerau de Arellano Jordi , Ouwersloot Huug G. , Baldocchi Dennis , Jacobs Cor M. J.
Published: February 2014

We study the interactions between plant evapotranspiration, controlled by photosynthesis (C3 and C4 grasses), and moist thermals responsible for the formation of shallow cumulus clouds (SCu). Our findings are based on a series of systematic numerical experiments at fine spatial and temporal scales using large eddy simulations explicitly coupled to a plant‐physiology model. The shading provided by SCu leads to strong spatial variability in photosynthesis and the surface energy balance. This in turn results in SCu characterized by less extreme and less skewed values of liquid water path. The larger water use efficiency of C4 grass leads to two opposite effects that influence boundary layer clouds: more vigorous and deeper thermals due to the larger buoyancy surface flux (positive effect) characterized by less moisture content (negative). We find that under these midlatitude and well‐watered soil conditions, SCu are characterized by a larger cloud cover and liquid water path over C4 grass fields.
Comparison of surface albedo feedback in climate models and observations
Authors: Crook J. A. , Forster P. M.
Published: February 2014

Snow and ice albedo feedback plays an important role in the greater warming of the Arctic compared to the tropics. Previous work has estimated the observed Northern Hemisphere cryosphere feedback, but there have been no estimates of surface albedo feedback from observations globally. Here we compare the zonal mean surface albedo feedback from satellite data sets with that from eleven ocean‐atmosphere coupled climate models for both climate change and the seasonal cycle. Differences between observed data sets make it difficult to constrain models. Nevertheless, we find that climate change Northern Hemisphere extratropical feedback is considerably higher for observations (potentially 3.1 ± 1.3 W m−2 K−1) than models (0.4–1.2 W m−2 K−1), whereas the seasonal cycle feedback is similar in observations and models, casting doubt on the ability of the seasonal cycle to accurately predict the climate change feedback. Observed Antarctic sea ice feedback is strongly positive in the seasonal cycle and similar to models.
Azotobacter
Cysts
Authors: Segura Daniel , Núñez Cinthia , Espín Guadalupe
Published: February 2014

Azotobacter
is a genus of Gram‐negative, organotrophic, nitrogen‐fixing soil bacteria. These bacteria undergo a differentiation process to form cysts, which are dormant cells resistant to deleterious conditions. A cyst consists of a contracted oval cell, called central body, covered with a two‐layer capsule. Although the process of encystment has been known for many years and many physiological and morphological studies were published decades ago, the biosynthetic pathways of the major components of the cyst and how they are regulated remained largely unknown. More recent work has elucidated the biosynthesis and genetics of some of these components, like alginate, polyhydroxybutyrate and the phenolic lipids alkylresorcinols and alkylpyrones and also the regulators controlling their biosynthesis and the changes occurring during encystment, such as the loss of flagella. Among these regulators are the alternative sigma factors AlgU and RpoS, the global regulatory systems Gac/Rsm and the transcriptional regulators AlgR, ArpR and CydR.

Key Concepts:

The encysting process results in a dormant cell more resistant to adverse conditions than the vegetative cell.

During the encysting process, a coordinated array of metabolic and morphological changes take place to produce a dormant cell.

The central body of the cyst is surrounded by a protective two‐layered capsule, which is composed of carbohydrates, proteins and lipids.

The exopolysaccharide alginate constitutes a structural part of the cyst envelope and is essential for desiccation resistance.

Several regulators of gene expression control the differentiation process, leading to production of cyst.
Cell Cycle Analysis by Flow Cytometry
Authors: Darzynkiewicz Zbigniew , Zhao Hong
Published: February 2014

Flow cytometry, the methodology that provides a way to measure physical and chemical attributes of individual cells rapidly and with high accuracy, is widely used in cell cycle analysis. The most common assays are: univariate analysis of cellulardeoxyribonucleic acid (DNA)content discloses frequencies of cells in G0/1, S and G2/M phases; bivariate analysis of DNA versusribonucleic acid (RNA)content reveals frequencies of G0, G1, S and G2M cells, of DNA content versus histone H3 phosphorylated on Ser10 defines frequencies of G0/1, S, G2and M cells. Detection of cells that incorporated DNA precursor, such as 5‐bromo‐2′‐deoxyuridine (BrdU) or 5‐ethynyl‐2′‐deoxyuridine (EdU) identifies cells that replicated DNA. Immunocytochemical detection of cyclin D1, cyclin E, Cyclin A and cyclin B1 concurrent with DNA content reveals the proteins that are essential for driving the cell through the cell cycle. The stathmokinetic approach makes it possible to assess the kinetics of progression through the cell cycle.

Key Concepts:

Cellular DNA content identifies cell position in the cell cycle.

Fractional cellular DNA content (‘sub‐G1’ cells) is a marker of apoptotic cells.

Low cellular RNA content is a biomarker of G0(quiescent) cells.

Incorporation of BrdU or EdU identifies DNA replication cells.

Phosphorylation of histone H3 on Ser10 is a marker of mitotic cells.

Detection of cyclin proteins is a marker of cell progression machinery.

Stathmokinetic approach based on cell arrest in metaphase makes it possible to assess the entry of cells to mitosis (‘mitotic rate’, ‘cell birth rate’) and reveals kinetics of cell progression through the cycle.
Protein Stability
Authors: Pace C Nick , Grimsley Gerald R , Scholtz J Martin , Shaw Kevin L
Published: February 2014

Proteins must fold to a globular conformation to carry out the most important tasks in living organisms. The folded, biologically active conformation of a protein is only marginally more stable than the unfolded, inactive conformations. Thus, making proteins more stable is important in medicine and basic research. The major destabilising force that must be overcome is conformational entropy. The major stabilising forces are the hydrophobic effect and hydrogen bonding. The ionisable side chains of amino acid residues may also contribute favourably to protein stability through attractive charge–charge interactions, ion pair formation or the formation of hydrogen bonds when such groups are buried in the protein interior. Replacing a nonproline or nonglycine residue in a β‐turn can also significantly increase protein stability.

Key Concepts:

Under physiological conditions, a folded protein is ∼20 to 60 kJ mol
–1
more stable than unfolded forms.

The major destabilising force to protein folding is conformational entropy, which contributes ∼7 kJ mol
−1
per residue.

The major stabilising forces are the hydrophobic effect, where the burying of each –CH
2
– contributes ∼−5 kJ mol
−1
, and hydrogen bonding, especially buried intramolecular hydrogen bonds, which may contribute ∼−7 kJ mol
−1
per bond.

The ionisable side chains of amino acid residues may contribute favourably to protein stability through attractive charge–charge interactions, ion pair formation and hydrogen bonding when the ionisable group is buried in the protein interior. Replacing a nonproline or nonglycine residue in a β‐turn may increase protein stability.
Prospects for Prenatal Gene Therapy
Authors: Coutelle Charles
Published: February 2014

Somatic prenatal gene therapy (PGT) aims at treatment/prevention of progressive tissue/organ damage in early‐manifesting life‐threatening and otherwise incurable genetic diseases. Preclinical investigations applying different vectors and transgenes on several animal models including nonhuman primates have shown PGT to provide better access to target cells and their progenitors, induce tolerance to vector/transgenic protein and reduce the required amount of vector in comparison to postnatal gene therapy. Human application of PGT is now technically possible, however, safety issues regarding potential adverse effects on fetal development, oncogenesis‐induction and germline transmission as well as ethical considerations concerning risk–benefit assessment and alternative reproductive choices have so far prohibited human trials. Increasing the safety profile, for example, by use of novel vector systems and long‐time primate safety/efficiency studies, may prospectively validate PGT for selected human applications. High standards regarding information given to prospective patients (informed consent) and to the public on the aims, benefits and remaining risks will play an important role in any future clinical application of PGT.

Key Concepts:

Somatic gene therapy addresses genetic diseases of the treated individual at the level of the molecular defect.

Prenatal gene therapy of early onset genetic disease prevents irreparable damage to tissues and organs and induces postnatal tolerance to therapeutic transgenic proteins.

Prenatal gene delivery can reach proliferating precursor cell compartments more effectively than postnatal gene therapy.

Different animal models including models of human genetic disease are required to establish optimal vectors and routes for gene delivery including those applicable in humans, to demonstrate the therapeutic efficiency of the delivered gene therapy, and to monitor and investigate the occurrence of potential adverse effects.

In utero
gene therapy could provide an alternative to termination of pregnancy or acceptance of an affected child after prenatal diagnosis of a genetically affected fetus, or to
in vitro
fertilisation followed by embryo selection in families with preconceptional knowledge of a specific genetic risk.

Current options to avoid birth of a genetically affected child (termination of pregnancy, preimplantation diagnosis/embryo selection) impose very high demands on the outcome of human prenatal gene therapy with respect to its level of safety and effectiveness.

Ethical considerations regarding the assessment and communication of the risks and benefits of prenatal gene therapy and its perception by affected families, the medical profession and the general public will play an important part in decisions on the clinical application of this novel therapeutic approach.
Vitelline Macular Dystrophy
Authors: Priya Doss C George , Kumar Aditi S , Narayan Vaishnavi
Published: February 2014

Vitelline macular dystrophy (also known as Best disease) is a progressive, chronic disease of the macula (central retina) at the back of the eye. Best disease is characterised by the development of a lesion in the retinal pigment epithelium and emerging as one of the leading causes of blindness in both juvenile and adult cases. This disease has an autosomal dominant pattern of inheritance with varied penetrance and expressivity. Diagnosis of this disease is delayed due to the fact that the individual may be asymptomatic for several years and the disease can be identified only after visual acuity reduces, during which the disease could have progressed to later stages. Mutations observed in the BEST1 and PRPH2 genes are involved in development of the disease. In this article, a review of the history, genetics and pathophysiology, diagnosis and treatment is outlined for further understanding of this disease.

Key Concepts:

Macular dystrophy is a rare, genetic condition of the eye, wherein the macula, which is the central part of the retina, is damaged due to successive buildup of eye pigments within the epithelial cells of the retina. There are two main types of this disease: Best disease, which is seen in juvenile cases, and adult‐onset macular dystrophy.

Best disease is also known as early‐onset or juvenile vitelliform macular dystrophy. It is an autosomal dominant disorder characterised by the accumulation of specific eye pigment material in the subretinal space, which leads to the formation of a lesion on the macula.

Adult‐onset vitelliform macular dystrophy is a disease of the retina wherein central vision loss occurs in the fourth or fifth decade of life. It is an autosomal dominant disorder. It is a dystrophy of the retinal pigment epithelium causing lesions on the macula.

VMD2gene, also known as theBEST1gene, codes for a protein called bestrophin. This protein functions as a chloride ion channel in the eye and its dysfunction leads to buildup of pigments and eventual loss of central vision.

PRPH2gene codes for a protein called peripherin. This protein is essential for light sensing in the retina. Mutations in this gene lead to central vision loss.
New efficient adaptive fast transversal filtering (FTF)‐type algorithms for mono and stereophonic acoustic echo cancelation
Authors: Djendi Mohamed
Published: February 2014

This paper addresses the field of stereophonic acoustic echo cancelation (SAEC) by adaptive filtering algorithms. Recently, simplified versions of the fast transversal filter (SFTF)‐type algorithm has been proposed. In this paper, we propose two major contributions. In the first contribution, we propose two new FTF‐type algorithms with low complexity and good convergence speed characteristics. These two proposed algorithms are mainly on the basis of a forward prediction scheme to estimate the so called dual Kalman gain, which is inherent in the filtering part update. This computation complexity is achieved by the introduction of new relations for the computation of the likelihood variables that are simple and lead to further simplifications on the prediction part of the two proposed algorithms. In the second contribution, we propose to adapt then apply these four new SFTF‐type algorithms, (the two proposed algorithms in this paper and their original versions) in the SAEC applications. A fair comparison of the proposed algorithms with the original SFTF and the normalized least mean square algorithms, in mono and SAEC applications, is presented. Copyright © 2014 John Wiley & Sons, Ltd.
Charge Generation at Polymer/Metal Oxide Interface: from Molecular Scale Dynamics to Mesoscopic Effects
Authors: Kandada Ajay Ram Srimath , Guarnera Simone , Tassone Francesco , Lanzani Guglielmo , Petrozza Annamaria
Published: February 2014

The correlation between molecular scale morphology and charge generation across hybrid photovoltaic interfaces made of metal oxides (ZnO and TiO2) and a prototypical electron donor polymer, P3HT, is investigated. Device characterization and UV‐NIR transient absorption spectroscopy are used to demonstrate that the local disorder of the polymer chains on the surface of the metal–oxide film provides better electron injection efficiencies than the crystalline phases, though the latter are essential for energy and charge transport. An unambiguous spectroscopic tool is also demonstrated to probe the occupation of the conduction band of ZnO following the electron injection from the polymer through the ultrafast tracking of the Burstein‐Moss effect.
25th Anniversary Article: Microstructure Dependent Bias Stability of Organic Transistors
Authors: Lee Wi Hyoung , Choi Hyun Ho , Kim Do Hwan , Cho Kilwon
Published: February 2014

Recent studies of the bias‐stress‐driven electrical instability of organic field‐effect transistors (OFETs) are reviewed. OFETs are operated under continuous gate and source/drain biases and these bias stresses degrade device performance. The principles underlying this bias instability are discussed, particularly the mechanisms of charge trapping. There are three main charge‐trapping sites: the semiconductor, the dielectric, and the semiconductor‐dielectric interface. The charge‐trapping phenomena in these three regions are analyzed with special attention to the microstructural dependence of bias instability. Finally, possibilities for future research in this field are presented. This critical review aims to enhance our insight into bias‐stress‐induced charge trapping in OFETs with the aim of minimizing operational instability.
One‐Step Fabrication of Unique Mesoporous NiO Hollow Sphere Film on FTO for High‐Performance P‐Type Dye‐Sensitized Solar Cells
Authors: Yang Hong Bin , Liu Bin , Khoo Si Yun , Zhu Lin Nan , Guo Chun Xian , Dong Yong Qiang , Li Chang Ming
Published: February 2014

P‐type dye sensitized solar cells (p‐DSCs) deliver much lower overall efficiency than their inverse model, n‐DSCs. However, they have fundamental and practical significance, in particular, their tandem structured solar cells with both p‐ and n‐photoelectrodes could offer great potential to significantly improve the efficiency of existing solar cells. A facile and environmentally friendly method is developed to directly one‐step grow hollow NiO spherical structures on fluorine‐doped tin oxide (FTO) substrate, in which a Ni2+ and polymer complex spherical structure is self‐constructed through a controlled solvent evaporation process, followed by calcination‐converting to a unique NiO hollow sphere film. The prepared material is further used as a photocathode in p‐type dye sensitized solar cells, resulting in 41% increase of an open‐circuit voltage and 18% enhancement of power conversion efficiency than NiO nanoparticles photocathode. The improved performance can be ascribed to suppressed charge recombination at the photocathode/electrolyte interface. This template‐free approach could be universally used to fabricate other nanostructured hollow spheres for a wide range of energy conversion applications such as electrochemical capacitors, chemical sensors, and electrochromic devices.
High‐Performance, High‐Index‐Contrast Chalcogenide Glass Photonics on Silicon and Unconventional Non‐planar Substrates
Authors: Zou Yi , Zhang Danning , Lin Hongtao , Li Lan , Moreel Loise , Zhou Jie , Du Qingyang , Ogbuu Okechukwu , Danto Sylvain , Musgraves J. David , Richardson Kathleen , Dobson Kevin D. , Birkmire Robert , Hu Juejun
Published: February 2014

This paper reports a versatile technique for the fabrication of high‐index‐contrast photonic structures on both silicon and plastic substrates. The fabrication technique combines low‐temperature chalcogenide glass film deposition and resist‐free single‐step thermal nanoimprint to process low‐loss, sub‐micron single‐mode waveguides with a smooth surface finish using simple contact photolithography. Using this approach, the first chalcogenide glass microring resonators are fabricated by thermal nanoimprinting. The devices exhibit an ultra‐high quality factor of 4 × 105 near 1550 nm wavelengths, which represents the highest value reported in chalcogenide glass microring resonators. Furthermore, sub‐micrometer nanoimprinting of chalcogenide glass films on non‐planar plastic substrates is demonstrated, which establishes the method as a facile route for the monolithic fabrication of high‐index‐contrast devices on a wide array of unconventional substrates.
Advanced Monte Carlo simulations of the adsorption of chiral alcohols in a homochiral metal‐organic framework
Authors: Qiao Zhiwei , Torres‐Knoop Ariana , Dubbeldam David , Fairen‐Jimenez David , Zhou Jian , Snurr Randall Q.
Published: February 2014

Grand canonical Monte Carlo (GCMC) simulations with configurational biasing were used to study the enantioselective adsorption of four alkanols in a homochiral metal‐organic framework, known as hybrid organic‐inorganic zeolite analogue HOIZA‐1. Conventional GCMC simulations are not able to converge satisfactorily for this system due to the tight fit of the chiral alcohols in the narrow pores. However, parallel tempering and parallel mole‐fraction GCMC simulations overcome this problem. The simulations show that the enantioselective adsorption of the different (R,S)‐alkanols is due to the specific geometry of the chiral molecules relative to the pore size and shape. © 2014 American Institute of Chemical Engineers AIChE J, 60: 2324–2334, 2014
Functional variability of glutathione S‐transferases in basque populations
Authors: Iorio Andrea , Piacentini Sara , Polimanti Renato , De Angelis Flavio , Calderon Rosario , Fuciarelli Maria
Published: February 2014

Objectives

Glutathione S‐transferases (GSTs) are enzymes involved in Phase II reactions. They play a key role in cellular detoxification. Various studies have shown that genes coding for the GST are highly polymorphic and some of these variants are directly associated with a decrease of enzyme activity making individuals more susceptible to different clinical phenotypes. The aim of this study is to investigate the genetic variability of GST genes among human populations. We have focused our attention on the polymorphic variants of the GSTA1, GSTM1, GSTO1, GSTO2, GSTP1, GSTT1, and GSTT2B genes.

Methods

These polymorphisms were analyzed in a whole sample of 151 individuals: 112 autochthonous Navarrese Basques, and 39 non‐autochthonous Navarrese Basques. DNA extraction from plasma was performed by using the phenol:chloroform:isoamylic alcohol method. Genotyping of the gene polymorphisms was performed by PCR Multiplex and the PCR‐RFLP method. We applied correspondence analysis and built frequency‐maps to compare the genetic structure in worldwide populations.

Results

Our results were compared with data available on the Human Genome Diversity Project (HGDP) and on the 1,000 Genomes Project to obtain information on the functional variability of GSTs in Basques. Our data indicated that Basque communities showed a higher differentiation of certain functional GST variants (i.e., GSTM1‐positive/null genotype, GSTP1*I105V, and GSTT2B*1/0) than other European and Mediterranean populations.

Conclusions

This might account for epidemiological differences in the predisposition to diseases and drug response among Basques and could be used to design and interpret genetic association studies for this particular population. Am. J. Hum. Biol. 26:361–366, 2014. © 2014 Wiley Periodicals, Inc.