bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global soil data set for earth system modeling
Authors: Shangguan Wei , Dai Yongjiu , Duan Qingyun , Liu Baoyuan , Yuan Hua 
Published: February 2014

AbstractWe 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

AbstractWidespread 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

AbstractWe 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

AbstractSnow 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

Abstract

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

AbstractFlow 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

Abstract

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

Abstract

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

AbstractVitelline 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

SummaryThis 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.
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

ABSTRACTObjectivesGlutathione 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.MethodsThese 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.ResultsOur 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.ConclusionsThis 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.
The effects of storage time and temperature on recovery of salivary secretory immunoglobulin A
Authors: Presser Elise , Simuyandi Michelo , Brown Joe 
Published: February 2014

ABSTRACTObjectivesThis study aimed to determine the optimal storage temperature to minimise degradation of salivary s‐IgA for field‐based surveillance applications in resource‐limited settings.MethodsSaliva samples from 40 Zambian adults were stored at +25°C, +4°C, −20°C, and −80°C and each tested by ELISA for salivary s‐IgA concentration at 0, 1, 2, 7, and 15 days. Differences were determined among concentrations over time and temperature compared with baseline values. Kruskal‐Wallis tests were applied to analyse variance. Single and multivariate regression analyses estimated the influence of storage time and temperature on recoverable s‐IgA.ResultsResults revealed a statistically significant decrease in salivary s‐IgA concentration as storage time increased and as temperature decreased. Degradation during storage time was most pronounced at lower temperatures.Conclusionss‐IgA is stable at ambient temperatures in Zambia for at least 15 days, suggesting no need for cold chain handling before analysis in field‐based surveillance applications. Am. J. Hum. Biol. 26:417–420, 2014. © 2014 Wiley Periodicals, Inc.
Prediction of outcome of radiofrequency ablation of the inferior turbinates
Authors: Sahin‐Yilmaz Asli , Oysu Çağatay , Devecioglu Ibrahim , Demir Kadri , Corey Jacquelynne P. 
Published: February 2014

BackgroundRadiofrequency ablation (RFA) of the turbinates is used commonly for nasal obstruction; however, there is no consensus on patient selection for this surgery.MethodsIn a prospective clinical study, 53 adult subjects with bilateral turbinate hypertrophy were evaluated subjectively and objectively with anterior rhinomanometry at baseline and at 1, 3, and 6 months post‐RFA of turbinates.ResultsRFA of the turbinates resulted in a significant decrease in predecongestant and postdecongestant visual analogue scale (VAS) scores and resistance measurements at postoperative months 1, 3, and 6 (p < 0.001 for all). Preoperative baseline subjective response to the decongestant showed a positive correlation with postoperative first month subjective and objective outcome (p < 0.05). Preoperative baseline objective response to the decongestant showed a highly significant correlation with postoperative 1‐month, 3‐month, and 6‐month objective outcomes of surgery (p < 0.05 for all).ConclusionObjective measures do not correlate with long‐term subjective satisfaction even when the nose is objectively patent in subjects who underwent inferior turbinate RFA. The patients’ long‐term subjective benefit from RFA surgery cannot be estimated after a rhinomanometry with topical decongestion is performed. Performing a rhinomanometry with topical decongestion may help only to estimate the patients’ objective benefit from RFA surgery.
Copper(II)‐Catalyzed Silylation of Activated Alkynes in Water: Diastereodivergent Access to E‐ or Z‐β‐Silyl‐α,β‐Unsaturated Carbonyl and Carboxyl Compounds
Authors: Calderone Joseph A. , Santos Webster L. 
Published: February 2014

AbstractCopper(II)‐catalyzed silylation of substituted alkynylcarbonyl compounds was investigated. Through the activation of Me2PhSiBpin in water at room temperature and open atmosphere, vinylsilanes conjugated to carbonyl groups are synthesized in high yield. A surprising diastereodivergent access to olefin geometry was discovered using a silyl conjugate addition strategy: aldehydes and ketones were Z selective while esters and amides were exclusively transformed into the E products.
Ozonated Graphene Oxide Film as a Proton‐Exchange Membrane
Authors: Gao Wei , Wu Gang , Janicke Michael T. , Cullen David A. , Mukundan Rangachary , Baldwin Jon K. , Brosha Eric L. , Galande Charudatta , Ajayan Pulickel M. , More Karren L. , Dattelbaum Andrew M. , Zelenay Piotr 
Published: February 2014

AbstractGraphene oxide (GO) contains several chemical functional groups that are attached to the graphite basal plane and can be manipulated to tailor GO for specific applications. It is now revealed that the reaction of GO with ozone results in a high level of oxidation, which leads to significantly improved ionic (protonic) conductivity of the GO. Freestanding ozonated GO films were synthesized and used as efficient polymer electrolyte fuel cell membranes. The increase in protonic conductivity of the ozonated GO originates from enhanced proton hopping, which is due to the higher content of oxygenated functional groups in the basal planes and edges of ozonated GO as well as the morphology changes in GO that are caused by ozonation. The results of this study demonstrate that the modification of dispersed GO presents a powerful opportunity for optimizing a nanoscale material for proton‐exchange membranes.