bluuebunny/crossref_metadata_2025 huggingface dataset:
Detecting local ligand‐binding site similarity in nonhomologous proteins by surface patch comparison
Authors: Sael Lee , Kihara Daisuke
Published: December 2011

Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch‐Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch‐Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch‐Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket‐Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. Proteins 2012;. © 2011 Wiley Periodicals, Inc.
Why have no new herbicide modes of action appeared in recent years?
Authors: Duke Stephen O
Published: December 2011

Herbicides with new modes of action are badly needed to manage the evolution of resistance of weeds to existing herbicides. Yet no major new mode of action has been introduced to the market place for about 20 years. There are probably several reasons for this. New potential products may have remained dormant owing to concerns that glyphosate‐resistant (GR) crops have reduced the market for a new herbicide. The capture of a large fraction of the herbicide market by glyphosate with GR crops led to significantly diminished herbicide discovery efforts. Some of the reduced herbicide discovery research was also due to company consolidations and the availability of more generic herbicides. Another problem might be that the best herbicide molecular target sites may have already been discovered. However, target sites that are not utilized, for which there are inhibitors that are highly effective at killing plants, suggests that this is not true. Results of modern methods of target site discovery (e.g. gene knockout methods) are mostly not public, but there is no evidence of good herbicides with new target sites coming from these approaches. In summary, there are several reasons for a long dry period for new herbicide target sites; however, the relative magnitude of each is unclear. The economic stimulus to the herbicide industry caused by the evolution of herbicide‐resistant weeds, especially GR weeds, may result in one or more new modes of action becoming available in the not too distant future. Copyright © 2011 Society of Chemical Industry
Bioactivity‐guided Isolation of Cytotoxic Sesquiterpene Lactones of Gochnatia polymorpha ssp. floccosa
Authors: Strapasson Regiane L. B. , Cervi Armando C. , Carvalho João E. , Ruiz Ana Lúcia T. G. , Salvador Marcos J. , Stefanello Maria Élida A.
Published: December 2011

Phytochemical study of Gochnatia polymorpha (Less) Cabr. ssp. floccosa Cabr. trunk bark, guided by antiproliferative assays on 10 human cancer cell lines and the VERO cell line, yielded six known compounds identified as the triterpene bauerenyl acetate, the guaianolide 11α,13‐dihydrozaluzanin C and the dimeric guaianolides 10‐desoxygochnatiolide A, gochnatiolide A, 8‐hydroxi‐10‐desoxygochnatiolide A and 8‐hydroxigochnatiolide A. Extracts, fractions of extracts and isolated compounds were tested in vitro against a panel of human cancer cell lines, including U251 (glioma, CNS), UACC‐62 (melanoma), MCF‐7 (breast), NCI‐ADR/RES (drug‐resistant ovarian), 786.0 (kidney), NCI‐H460 (lung, no small cells), PC‐3 (prostate), OVCAR‐3 (ovarian), HT‐29 (colon), K562 (leukemia) and against the VERO no cancer cell line. Bauerenyl acetate was inactive, while 11α,13‐dihydrozaluzanin C showed weak activity against UACC62 and the VERO cell line. The most active compounds were 10‐desoxygochnatiolide A and gochnatiolide A, which inhibited the growth of kidney, melanoma, ovarian‐resistant and glioma cell lines with values of TGI (total growth inhibition) varying 0.21–1.09 µg/mL. This is the first report about cytotoxic activity of dimeric lactones against cell lines. Copyright © 2011 John Wiley & Sons, Ltd.
Kavalactone Metabolism in Rat Liver Microsomes
Authors: Fu Shuang , Rowe Anthony , Ramzan Iqbal
Published: December 2011

The specific CYP enzymes involved in kavalactone (KLT) metabolism and their kinetics have not been fully examined. This study used rat liver microsomes (RLM) to determine kavain (KA), methysticin (MTS) and desmethoxyyangonin (DMY) enzyme kinetic parameters, to elucidate the major CYP450 isoforms involved in KLT metabolism and to examine gender differences in KLT metabolism. Formation of the major KLT metabolites was first‐order, consistent with classic enzyme kinetics. In both male and female RLM, clotrimazole (CLO) was the most potent inhibitor of KA and MTS metabolism. This suggests CYP3A1/3A23 (females) and CYP3A2 (males) are the main isoenzymes involved in the metabolism of these KLTs in rats, while the roles of CYP1A2, ‐2 C6, ‐2 C9, ‐2E1 and ‐3A4 are limited. Desmethoxyyangonin metabolism was equally inhibited by cimetidine (CIM) and CLO in females, and CIM and nortriptyline in males. This implies that DMY metabolism involves CYP2C6 and CYP2C11 in males, and CPY2C12 in females. CYP3A1/3A23 may also be involved in females. Copyright © 2011 John Wiley & Sons, Ltd.
Time series predictor of Ku band rain attenuation over an Earth–space path at a tropical location
Authors: Das Dalia , Maitra Animesh
Published: December 2011

A channel model is proposed to predict the time series of Ku band rain attenuation during a rain event at a tropical location. The model is based on considering the Gaussian distribution of the conditional occurrence of rain attenuation with a particular value of the attenuation occurring before. The mean (μ) and standard deviation (σ) for the distribution are modeled with the experimental data. The measured attenuation at a particular time instant is used to obtain μ and σ and to predict the attenuation after certain interval. The channel model has tested well giving the predicted attenuation that agrees with the measured value with a mean error within 15% higher than 1 dB. Validity of the model is also tested with the first‐order and second‐order statistics of attenuation occurrence, on a long‐term basis. The method can also be applied even if attenuation measurements are missing for certain period of time with increased error. Copyright © 2011 John Wiley & Sons, Ltd.
A context‐aware approach to defend against unauthorized reading and relay attacks in RFID systems
Authors: Ma Di , Saxena Nitesh
Published: December 2011

Radio frequency identification (RFID) systems are becoming increasingly ubiquitous in both public and private domains. However, because of the inherent weaknesses of underlying wireless radio communications, RFID systems are plagued with a wide variety of security and privacy threats. A large number of these threats arise because of the tag's promiscuous response to any reader requests. This renders sensitive tag information easily subject to unauthorized reading. Promiscuous tag response also incites different forms of relay attacks whereby a malicious colluding pair, relaying messages between a tag and a reader, can successfully impersonate the tag without actually possessing it. Because of the increasing ubiquity of RFID devices, there is a pressing need for the development of security primitives and protocols to defeat unauthorized reading and relay attacks. However, currently deployed or proposed solutions often fail to satisfy the constraints and requirements of the underlying RFID applications in terms of (one or more of) efficiency, security, and usability. This paper proposes a novel research direction, one that utilizes sensing technologies, to tackle the problems of unauthorized reading and relay attacks with a goal of reconciling the requirements of efficiency, security, and usability. The premise of the proposed work is based on a current technological advancement that enables many RFID tags with low‐cost sensing capabilities. The on‐board tag sensors will be used to acquire useful contextual information about the tag's environment (or its owner, or the tag itself). For defense against unauthorized reading and relay attacks, such context information can be leveraged in two ways. First, contextual information can be used to design context‐aware selective unlocking mechanisms so that tags can selectively respond to reader interrogations and thus minimize the likelihood of unauthorized reading and “ghost‐and‐leech” relay attacks. Second, contextual information can be used as a basis for context‐aware secure transaction verification to defend against special types of relay attacks involving malicious readers. Copyright © 2011 John Wiley & Sons, Ltd.
Chinese High School Students' Academic Stress and Depressive Symptoms: Gender and School Climate as Moderators
Authors: Liu Yangyang , Lu Zuhong
Published: December 2011

In a sample of 368 Chinese high school students, the present study examined the different effects of Chinese high school students' academic stress on their depressive symptoms and the moderating effects of gender and students' perceptions of school climate on the relationships between their academic stress and depressive symptoms. Regression mixture model identified two different kinds of subgroups in the effects of students' academic stress on their depressive symptoms. One subgroup contained 90% of the students. In this subgroup, the students' perceptions of academic stress from lack of achievement positively predicted their depressive symptoms. For the other 10% of the students, academic stress did not significantly predict their depressive symptoms. Next, multinomial regression analysis revealed that girls or students who had high levels of achievement orientation were more likely to be in the first subgroup. The findings suggested that gender and students' perceptions of school climate could moderate the relationships between Chinese high school students' academic stress and their depressive symptoms. Copyright © 2011 John Wiley & Sons, Ltd.
Optimization of ethanol, citric acid, and α-amylase production from date wastes by strains of Saccharomyces cerevisiae, Aspergillus niger, and Candida guilliermondii
Authors: Acourene S , Ammouche A
Published: December 2011

The present study deals with submerged ethanol, citric acid, and α-amylase fermentation by Saccharomyces cerevisiae SDB, Aspergillus niger ANSS-B5, and Candida guilliermondii CGL-A10, using date wastes as the basal fermentation medium. The physical and chemical parameters influencing the production of these metabolites were optimized. As for the ethanol production, the optimum yield obtained was 136.00 ± 0.66 g/l under optimum conditions of an incubation period of 72 h, inoculum content of 4% (w/v), sugars concentration of 180.0 g/l, and ammonium phosphate concentration of 1.0 g/l. Concerning citric acid production, the cumulative effect of temperature (30°C), sugars concentration of 150.0 g/l, methanol concentration of 3.0%, initial pH of 3.5, ammonium nitrate concentration of 2.5 g/l, and potassium phosphate concentration of 2.5 g/l during the fermentation process of date wastes syrup did increase the citric acid production to 98.42 ± 1.41 g/l. For the production of α-amylase, the obtained result shows that the presence of starch strongly induces the production of α-amylase with a maximum at 5.0 g/l. Among the various nitrogen sources tested, urea at 5.0 g/l gave the maximum biomass and α-amylase estimated at 5.76 ± 0.56 g/l and 2,304.19 ± 31.08 μmol/l/min, respectively after 72 h incubation at 30°C, with an initial pH of 6.0 and potassium phosphate concentration of 6.0 g/l.
Fine tuning genomic evaluations in dairy cattle through SNP pre-selection with the Elastic-Net algorithm
Authors: CROISEAU PASCAL , LEGARRA ANDRÉS , GUILLAUME FRANÇOIS , FRITZ SÉBASTIEN , BAUR AURÉLIA , COLOMBANI CARINE , ROBERT-GRANIÉ CHRISTÈLE , BOICHARD DIDIER , DUCROCQ VINCENT
Published: December 2011

For genomic selection methods, the statistical challenge is to estimate the effect of each of the available single-nucleotide polymorphism (SNP). In a context where the number of SNPs (p) is much higher than the number of bulls (n), this task may lead to a poor estimation of these SNP effects if, as for genomic BLUP (gBLUP), all SNPs have a non-null effect. An alternative is to use approaches that have been developed specifically to solve the ‘p>>n’ problem. This is the case of variable selection methods and among them, we focus on the Elastic-Net (EN) algorithm that is a penalized regression approach. Performances of EN, gBLUP and pedigree-based BLUP were compared with data from three French dairy cattle breeds, giving very encouraging results for EN. We tried to push further the idea of improving SNP effect estimates by considering fewer of them. This variable selection strategy was considered both in the case of gBLUP and EN by adding an SNP pre-selection step based on quantitative trait locus (QTL) detection. Similar results were observed with or without a pre-selection step, in terms of correlations between direct genomic value (DGV) and observed daughter yield deviation in a validation data set. However, when applied to the EN algorithm, this strategy led to a substantial reduction of the number of SNPs included in the prediction equation. In a context where the number of genotyped animals and the number of SNPs gets larger and larger, SNP pre-selection strongly alleviates computing requirements and ensures that national evaluations can be completed within a reasonable time frame.
Pagodas and Prophets: Contesting Sacred Space and Power among Buddhist Karen in Karen State
Authors: Hayami Yoko
Published: December 2011

This paper analyzes multi-layered religious practices among local Buddhist Karen on the plains of Karen State in Burma, within the context of the larger socio-political dynamics of Burmese Buddhism. The purpose is threefold: first, to give ethnographic details of the hybrid nature of religious practices among Buddhist Pwo Karen, thereby demonstrating how sacred space and power are contested, despite the strong hand of the state; second, to challenge the assumed equation between non-Buddhist minorities on the one hand, and Buddhists as a lowland majority aligned to the state on the other; and third, to raise an alternative understanding to predominantly state-centered perspectives on Theravada Buddhism. Field-based observations on the young charismatic Phu Taki and his community, as well as on the practice of pagoda worship called Duwae that has hitherto been undocumented are presented. These are examined in relation to the changing religious policies of the regime, especially since the policies of “Myanmafication” of Buddhism by the reformist council began in 1980.
A multivariate approach to structural heterogeneity of retinal ganglion cells
Authors: PUSHCHIN I.I. , PODUGOLNIKOVA T.A. , KONDRASHEV S.L.
Published: December 2011

Knowing neuronal types is essential for understanding the structural and functional organization of the nervous system. It has long been recognized that neuronal types should be discovered and not defined. This can be done using cluster analysis (CA). Despite there being many studies using CA to classify neurons, only a few of them meet its formal prerequisites. In the present study, we provide an example of using CA in combination with other multivariate techniques for examining neuronal diversity. A special emphasis is put on formal prerequisites to the data and procedure. The data under scrutiny are a sample of ganglion cells projecting to the basal optic nucleus [accessory optic system-projecting ganglion cells (AOS GCs)] in the common frog. There is physiological evidence that these cells comprise at least two functional types but their structural heterogeneity has not been addressed. Cells were labeled with horseradish peroxidasein vivoand examined in whole-mounted retinae using light microscopy. A sample of well-stained cells was obtained and used to estimate 18 structural parameters. A variety of clustering algorithms were used to classify the cells. The joint polar distribution of dendrite mass was monomodal. CA did not reveal a statistically reliable cluster structure in the sample. The clusters were not cohesive and well isolated. ANOVA-on-Ranks revealed no significant between-cluster differences. Our formal conclusion is that functionally distinct frog AOS GCs do not differ in morphology or dendritic arbor orientation. The advantages and limitations of the adopted approach are discussed.
Evaluation of the relative performance of sea surface temperature measurements from different types of drifting and moored buoys using satellite‐derived reference products
Authors: Castro Sandra L. , Wick Gary A. , Emery William J.
Published: December 2011

Sea surface temperature (SST) measurements from drifting and moored buoys have been used extensively to validate satellite SST products. Previous efforts explored overall uncertainties in the buoy measurements, but did not quantify differences in the performance of different buoy types. Here, drifting and moored buoys stratified into open‐ocean and coastal, were evaluated by manufacturer (drifters) and buoy program (moorings) to identify significant deviations in their suitability for satellite validation. Biases and standard deviations were computed for differences between the buoy SST measurements and two satellite references: the Advanced Microwave Scanning Radiometer SST product from Remote Sensing Systems and the U.S. Naval Oceanographic Office K10 analysis. No significant differences were found among the various drifting and tropical moored buoys, regardless of the manufacturer/program. The largest deviations were observed for the non‐tropical moored buoys possibly in part due to calibration differences. In general, coastal buoys exhibited greater standard deviations associated with increased physical variability within the coastal regions. Tropical moored buoys showed smaller standard deviations than for the drifters resulting from better quality measurements or reduced variability in the tropics. Large deviations between the coastal moorings and the SST references appeared linked to coastal currents with upwelling, rather than buoy performance. Coastal moorings provided sampling of small‐scale coastal variability, not resolved in satellite products, offering the potential for improving poorly parameterized coastal SSTs. Differences due to diurnal warming were largely eliminated by constraining collocations between the satellite and the buoy to ±1 h. Overall, most buoy types appear suitable for satellite SST validation.
The rates of sea salt sulfatization in the atmosphere and surface snow of inland Antarctica
Authors: Iizuka Yoshinori , Tsuchimoto Akira , Hoshina Yu , Sakurai Toshimitsu , Hansson Margareta , Karlin Torbjörn , Fujita Koji , Nakazawa Fumio , Motoyama Hideaki , Fujita Shuji
Published: December 2011

Most of the aerosol particles present in the surface snow and ice of inland Antarctica come from primary sea salt (sodium chloride) and marine biological activity (methansulfonic and sulfuric acids). Melted water from surface snow, firn, and Holocene ice contains mainly sodium, chloride, and sulfate ions. Although it is well known that sea salt aerosols react rapidly with sulfuric acid, a process known as sulfatization, it is not known when this process takes place. In this research we undertake to measure the proportion of sea salt aerosols that undergo sulfatization in the atmosphere and surface snow, as opposed to deeper ice, in order to understand the suitability of sea salt aerosols as a proxy for past climates in deep ice cores. We directly measure the sulfatization rates in recently fallen snow (0–4 m in depth) collected at the Dome Fuji station, using X‐ray dispersion spectroscopy to determine the constituent elements of soluble particles and computing the molar ratios of sodium chloride and sodium sulfate. We estimate that about 90% of the initial sea salt aerosols sulfatize as they are taken up by precipitation over Dome Fuji or in the snowpack within one year after being deposited on the ice sheet.
Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand
Authors: Gayevskiy Velimir , Goddard Matthew R
Published: December 2011

Yeasts are a diverse seemingly ubiquitous group of eukaryotic microbes, and many are naturally associated with fruits. Humans have harnessed yeasts since the dawn of civilisation to make wine, and thus it is surprising that we know little of the distribution of yeast communities naturally associated with fruits. Previous reports of yeast community diversity have been descriptive only. Here we present, we believe, the first robust test for the geographic delineation of yeast communities. Humans have relatively recently employed Saccharomyces cerevisiae as a model research organism, and have long harnessed its ancient adaption to ferment even in the presence of oxygen. However, as far as we are aware, there has not been a rigorous test for the presence of regional differences in natural S. cerevisiae populations before. We combined these community- and population-level questions and surveyed replicate vineyards and corresponding spontaneous ferments from different regions on New Zealand's (NZ's) North Island and analysed the resulting data with community ecology and population genetic tests. We show that there are distinct regional delineations of yeast communities, but the picture for S. cerevisiae is more complex: there is evidence for region-specific sub-populations but there are also reasonable levels of gene flow among these regions in NZ. We believe this is the first demonstration of regional delineations of yeast populations and communities worldwide.
Parent‐ and Adolescent‐Reported Barriers to Participation in an Adolescent Overweight and Obesity Intervention
Authors: Brennan Leah , Walkley Jeff , Wilks Ray
Published: December 2011

This study explored reported barriers to treatment completion in a sample of adolescents and their parents who either completed or did not complete family‐based cognitive behavioral lifestyle intervention for overweight and obese adolescents. The sample comprises 56 overweight or obese adolescents (52% female) aged 11.5–18.9 years (mean = 14.5, s.d. = 1.8) and a parent. 57% of families did not complete treatment and maintenance phases of the intervention. A telephone‐administered questionnaire assessing barriers to participation was completed by 96% of adolescents and 91% of parent completers and 100% of adolescents and 94% of parent noncompleters. Adolescents and parents most commonly reported barriers to participation related to research demands, treatment approach, program components/strategies, practical barriers, and other individual/family demands. Parents also noted adolescent effort, parent‐adolescent conflict, and adolescent unhappiness as barriers to participation. While both completers and noncompleters experienced barriers to participation, families who discontinued treatment reported experiencing more treatment barriers. Findings of the current study suggest that adolescents and parents may find it easier to participate in adolescent overweight and obesity interventions if research and out‐of‐session program demands are minimized, efforts are made to enhance adolescent motivation, and treatment is offered in a convenient location and scheduled around school holidays and other family demands. Results also suggest that targeting adolescent unhappiness, family stressors, and parent‐adolescent conflict in treatment may improve retention. Future research should explore the impact of these modifications on treatment completion and outcomes.
High‐Fat Diet Exacerbates Renal Dysfunction in SHR: Reversal by Induction of HO‐1–Adiponectin Axis
Authors: Cao Jian , Inoue Kazuyoshi , Sodhi Komal , Puri Nitin , Peterson Stephen J. , Rezzani Rita , Abraham Nader G.
Published: December 2011

High‐dietary fat intake is a major risk factor for development of metabolic and cardiovascular‐renal dysfunction including obesity, coronary artery disease, hypertension, and chronic renal failure. We examined the effect of a high‐fat diet on renal function and morphology in spontaneously hypertensive rats (SHR), a phenotype designed to mimic metabolic syndrome. High‐fat diet induced increase (P < 0.05) in blood pressure, body weight, and renal lipid deposition in these rats. This increase in body weight was accompanied by elevations (P < 0.05) of blood glucose and low‐density lipoprotein (LDL) levels, a decrease (P < 0.05) in adiponectin and increases (P < 0.05) in plasma monocyte chemotactic protein‐1 (MCP‐1) along with renal macrophage infiltration. These pathophysiological perturbations were attenuated (P < 0.05) by heme oxygenase‐1 (HO‐1) induction by treatment with cobalt protoporphyrin (CoPP). Further effects of CoPP included increased (P < 0.05) renal expression of adiponectin along with enhancement (P < 0.05) of pAKT, pAMPK, and p‐eNOS in SHRs fed a high‐fat diet. Prevention of such beneficial effects of CoPP by the concurrent administration of the heme‐HO inhibitor stannous mesoporphyrin (SnMP) corroborates the role of HO system in mediating such effects. Taken together, our results demonstrate that high‐fat diet induces a metabolic syndrome‐like phenotype in hypertensive rats, which is amenable to rescue by increases in HO‐1‐ and adiponectin‐dependent pathways.
The human gene SLC25A17 encodes a peroxisomal transporter of coenzyme A, FAD and NAD+
Authors: Agrimi Gennaro , Russo Annamaria , Scarcia Pasquale , Palmieri Ferdinando
Published: December 2011

The essential cofactors CoA, FAD and NAD+ are synthesized outside the peroxisomes and therefore must be transported into the peroxisomal matrix where they are required for important processes. In the present study we have functionally identified and characterized SLC25A17 (solute carrier family 25 member 17), which is the only member of the mitochondrial carrier family that has previously been shown to be localized in the peroxisomal membrane. Recombinant and purified SLC25A17 was reconstituted into liposomes. Its transport properties and kinetic parameters demonstrate that SLC25A17 is a transporter of CoA, FAD, FMN and AMP, and to a lesser extent of NAD+, PAP (adenosine 3′,5′-diphosphate) and ADP. SLC25A17 functioned almost exclusively by a counter-exchange mechanism, was saturable and was inhibited by pyridoxal 5′-phosphate and other mitochondrial carrier inhibitors. It was expressed to various degrees in all of the human tissues examined. Its main function is probably to transport free CoA, FAD and NAD+ into peroxisomes in exchange for intraperoxisomally generated PAP, FMN and AMP. The present paper is the first report describing the identification and characterization of a transporter for multiple free cofactors in peroxisomes.
Improved photocurrent by using n-doped 2,3,8,9,14,15-hexachloro-5,6,11,12,17,18-hexaazatrinaphthylene as optical spacer layer in p-i-n type organic solar cells
Authors: Falkenberg Christiane , Leo Karl , Riede Moritz K.
Published: December 2011

We introduce 2,3,8,9,14,15-hexachloro-5,6,11,12,17,18-hexaazatrinaphthylene (HATNA-Cl6) as n-dopable electron transport material (ETM) for small molecule organic solar cells. Because of its large optical energy gap of 2.7 eV and its well suited energy level positions, the material can be implemented as a semitransparent spacer layer between the reflecting metal contact and the photoactive C60 acceptor layer in p-i-n type solar cells. By varying the ETM thickness, it is possible to shift the position of the photoactive area with respect to the interference maximum of the optical field distribution. Applying n-HATNA-Cl6 instead of the parasitically absorbing reference ETM n-C60 results in a considerably improved photocurrent density and accordingly in a higher efficiency. At dETM=100 nm the power conversion efficiency is more than doubled as it increases from (100 nm n-C60) = 0.5% to (100 nm n-HATNA-Cl6) = 1.1%.
Quantum breathers in Klein-Gordon lattice: Non-periodic boundary condition approach
Authors: Mandal Subhra Jyoti , Choudhary Kamal , Biswas Arindam , Bandyopadhyay A. K. , Bhattacharjee A. K. , Mandal D.
Published: December 2011

The presence of classical breathers and two-phonon bound state (TPBS) or quantum breather (QB) state through detailed quantum calculations have already been shown in technologically important ferroelectric materials, such as lithium niobate with antisite niobium charge defects concerning pinning transition, its control, and application. The latter was done in a periodic boundary condition with Bloch function in terms of significant variations of TPBS parameters against impurity, which is related to nonlinearity. In further extension of this work, in a non-periodic boundary condition and number-conserving approach, apart from various techniques available, only the temporal evolution of the number of quanta (i.e., phonons) in more sites is detailed in this present investigation for a generalized Klein-Gordon system with applications in ferroelectrics, metamaterials, and DNA. The critical time of redistribution of quanta that is proportional to the QB’s lifetime in these materials shows different types of behavior in the femtosecond range, which gives rise to the possibilities for making various devices.
Loss analysis of back-contact back-junction thin-film monocrystalline silicon solar cells
Authors: Haase F. , Eidelloth S. , Horbelt R. , Bothe K. , Garralaga Rojas E. , Brendel R.
Published: December 2011

We investigate power losses in back-contact back-junction monocrystalline thin-film silicon solar cells fabricated using the porous silicon layer transfer process. Our loss analysis combines two-dimensional finite element modeling and resistance network simulations. The input parameters of the finite element modeling are determined experimentally by measuring saturation current densities and sheet resistances on test samples prepared identically to the solar cells. Characteristic solar cell parameters such as short circuit current, open circuit voltage, fill factor, and efficiency of measured and network simulated current voltage characteristics investigated in this study match within an uncertainty of 5%. Free energy loss analysis serves as comparison of all losses in units of power per area at the maximum power point. The largest loss is bulk recombination due to a carrier lifetime of 2 μs in the epitaxial Si layer. Further significant losses result from recombination at the base contacts characterized by a diode saturation current density of 50 000 fA cm−2 as well as resistive losses due to lateral majority carrier current flows within the solar cell base and contact resistance losses.
Hybrid W-shaped graphene nanoribbons: Distinct electronic and transport properties
Authors: Kou Liangzhi , Tang Chun , Chen Changfeng , Guo Wanlin
Published: December 2011

We present a first-principles study of electronic and transport properties of a novel W-shaped graphene nanoribbon (W-GNR) structure that comprises hybrid GNR segments with alternating armchair and zigzag edges. Such hybrid W-GNRs exhibit semiconducting characteristics with distinct properties that stem from a unique combination of the features of the armchair and zigzag constituents. When the ribbon is narrow, the interplay of the two GNR components leads to much reduced variation in band gap. The spin-polarized edge states of the zigzag GNR engender an electric-field-driven half-metallicity. Moreover, spin-dependent density of states at the band edge produces asymmetric spin transmission coefficients, yielding unequal spin currents under a large bias voltage. These findings suggest that these new W-GNRs hold great promise for applications in nanoscale spintronic devices.
Structural and electrical characterization of silicided Ni/Au contacts formed at low temperature (<300 °C) on p-type [001] silicon
Authors: Alberti A. , Badalà P. , Pellegrino G. , Santangelo A.
Published: December 2011

Silicided Ni/Au contacts with very low contact resistance were realized on p-type [001] silicon at low temperature by ex-situ or, alternatively, by in situ annealing processes. During the ex-situ annealing, performed at 200  °C for 10 s, a uniformly thin (14 nm) Ni2Si layer was formed having an extremely flat interface with silicon thanks to the trans-rotational structure of the silicide. During the in situ annealing, promoted by a sputter etch processing (T < 300  °C), a 44 nm-thick silicide layer was formed as a mixture of trans-rotational NiSi and epitaxial NiSi2, domains. In both cases, using a low thermal budget has guaranteed a limited consumption of silicon during the reaction process and a good adhesion with the substrate avoiding gold contaminations. As a consequence of the presence of trans-rotational domains, wherein a pseudo-epitaxial relationship between the silicide and the silicon lattices is established, an ohmic behavior was observed in a wide range of substrate doping (3.5 × 1018 ÷ 3 × 1019 B/cm3) for both annealing processes (in situ and ex-situ). On the other hand, conventional TiNiAu and CrNiAu contacts showed, in the same range of B doping concentration, a rectifying behavior with systematically higher specific contact resistance values (Rc) compared to those of the Ni silicided contacts.
Domain wall conductivity in oxygen deficient multiferroic YMnO3 single crystals
Authors: Du Y. , Wang X. L. , Chen D. P. , Dou S. X. , Cheng Z. X. , Higgins M. , Wallace G. , Wang J. Y.
Published: December 2011

The transport properties of domain walls in oxygen deficient multiferroic YMnO3 single crystals have been probed using conductive atomic force microscopy and piezoresponse force microscopy. Domain walls exhibit significantly enhanced conductance after being poled in electric fields, possibly induced by oxygen vacancy ordering at domain walls. The electronic conduction can be understood by the Schottky emission and Fowler-Nordheim tunnelling mechanisms. Our results show that the domain wall conductance can be modulated through band structure engineering by manipulating ordered oxygen vacancies in the poling fields.
Putting Space in Place: Philosophical Topography and Relational Geography
Authors: Malpas Jeff
Published: December 2011

Space is a concept that is central to geographical thinking. Yet, relatively little attention has been given to exploration of the concept of space as such, and this is so outside of geography no less than within it. Beginning with an examination of the ‘relational’ view of space that now seems dominant in geography as well as many other areas of the social sciences (and which is often presented as an elucidation of space itself), this paper explores the concept of space as it stands in connection with time and place, making particular use of the notions of boundedness, extendedness, and emergence while also shedding light on the idea of relationality. The aim is to outline a different mode of theorizing space than is to be found in much of contemporary geography and social theory—one that also draws geographical thinking into the domain of ‘philosophical topography’.
DNA methyltransferase 3a limits the expression of interleukin-13 in T helper 2 cells and allergic airway inflammation
Authors: Yu Qing , Zhou Baohua , Zhang Yanlu , Nguyen Evelyn T. , Du Jianguang , Glosson Nicole L. , Kaplan Mark H.
Published: December 2011

The inverse correlation between DNA methylation and lineage-specific gene expression during T helper cell development is well documented. However, the specific functions of the de novo methyltransferases Dnmt3a and Dnmt3b in cytokine gene regulation have not been defined. We demonstrate that the expression of Dnmt3a and Dnmt3b are induced to a greater extent in T helper 2 (Th2) cells than in T helper 1 cells during polarization. Using conditional mutant mice, we determined that Dnmt3a, but not Dnmt3b, regulated expression of T helper cell cytokine genes, with theIl13gene most prominently affected.Dnmt3adeficiency was accompanied by decreases in DNA methylation and changes in the H3K27 acetylation/methylation status at theIl13locus. Dnmt3a-dependent regulation ofIl13also occurred in vivo becauseDnmt3afl/flCd4cremice exhibited increased lung inflammation in a murine asthma model, compared with littermate controls. Based on these observations, we conclude that Dnmt3a is required for controlling normalIl13gene expression and functions as a rate-limiting factor to restrict T helper 2-mediated inflammation.
Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states
Authors: Ferguson Matthew L. , Le Coq Dominique , Jules Matthieu , Aymerich Stéphane , Radulescu Ovidiu , Declerck Nathalie , Royer Catherine A.
Published: December 2011

Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two
Bacillus subtilis
promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for the glycolytic promoter. Noise pattern parameters of the two antagonistic promoters controlling the nutrient switch were differentially affected on glycolytic and gluconeogenic carbon sources, discriminating between the different mechanisms that control their activity. Our stochastic model for the transcription events reproduced the observed noise patterns and identified the critical parameters responsible for the differences in expression profiles of the promoters. The model also resolved apparent contradictions between in vitro operator affinity and in vivo repressor activity at these promoters. Finally, our results demonstrate that negative feedback is not noise-reducing in the case of strong transcriptional bursting.
Conformational properties of cardiolipin-bound cytochrome
c
Authors: Hanske Jonas , Toffey Jason R. , Morenz Anna M. , Bonilla Amber J. , Schiavoni Katherine H. , Pletneva Ekaterina V.
Published: December 2011

Interactions of cytochrome
c
(cyt
c
) with cardiolipin (CL) are important for both electron transfer and apoptotic functions of this protein. A sluggish peroxidase in its native state, when bound to CL, cyt
c
catalyzes CL peroxidation, which contributes to the protein apoptotic release. The heterogeneous CL-bound cyt
c
ensemble is difficult to characterize with traditional structural methods and ensemble-averaged probes. We have employed time-resolved FRET measurements to evaluate structural properties of the CL-bound protein in four dansyl (Dns)-labeled variants of horse heart cyt
c
. The Dns decay curves and extracted Dns-to-heme distance distributions
P
(
r
) reveal a conformational diversity of the CL-bound cyt
c
ensemble with distinct populations of the polypeptide structures that vary in their degree of protein unfolding. A fraction of the ensemble is substantially unfolded, with Dns-to-heme distances resembling those in the guanidine hydrochloride-denatured state. These largely open cyt
c
structures likely dominate the peroxidase activity of the CL-bound cyt
c
ensemble. Site variations in
P
(
r
) distributions uncover structural features of the CL-bound cyt
c
, rationalize previous findings, and implicate the prime role of electrostatic interactions, particularly with the protein
C
terminus, in the CL-induced unfolding.
Cellulose synthase interactive protein 1 (CSI1) links microtubules and cellulose synthase complexes
Authors: Li Shundai , Lei Lei , Somerville Chris R. , Gu Ying
Published: December 2011

Cellulose synthase (CESA) complexes can be observed by live-cell imaging to move with trajectories that parallel the underlying cortical microtubules. Here we report that CESA interactive protein 1 (CSI1) is a microtubule-associated protein that bridges CESA complexes and cortical microtubules. Simultaneous in vivo imaging of CSI1, CESA complexes, and microtubules demonstrates that the association of CESA complexes and cortical microtubules is dependent on CSI1. CSI1 directly binds to microtubules as demonstrated by in vitro microtubule-binding assay.
The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations
Authors: Yan Kelley S. , Chia Luis A. , Li Xingnan , Ootani Akifumi , Su James , Lee Josephine Y. , Su Nan , Luo Yuling , Heilshorn Sarah C. , Amieva Manuel R. , Sangiorgi Eugenio , Capecchi Mario R. , Kuo Calvin J.
Published: December 2011

The small intestine epithelium undergoes rapid and continuous regeneration supported by crypt intestinal stem cells (ISCs). Bmi1 and Lgr5 have been independently identified to mark long-lived multipotent ISCs by lineage tracing in mice; however, the functional distinctions between these two populations remain undefined. Here, we demonstrate that Bmi1 and Lgr5 mark two functionally distinct ISCs in vivo. Lgr5 marks mitotically active ISCs that exhibit exquisite sensitivity to canonical Wnt modulation, contribute robustly to homeostatic regeneration, and are quantitatively ablated by irradiation. In contrast, Bmi1 marks quiescent ISCs that are insensitive to Wnt perturbations, contribute weakly to homeostatic regeneration, and are resistant to high-dose radiation injury. After irradiation, however, the normally quiescent Bmi1
+
ISCs dramatically proliferate to clonally repopulate multiple contiguous crypts and villi. Clonogenic culture of isolated single Bmi1
+
ISCs yields long-lived self-renewing spheroids of intestinal epithelium that produce Lgr5-expressing cells, thereby establishing a lineage relationship between these two populations in vitro. Taken together, these data provide direct evidence that Bmi1 marks quiescent, injury-inducible reserve ISCs that exhibit striking functional distinctions from Lgr5
+
ISCs and support a model whereby distinct ISC populations facilitate homeostatic vs. injury-induced regeneration.
The Politics of Zoroastrian Philanthropy and the Case of Qasr-e Firuzeh
Authors: Stewart Sarah
Published: December 2011

In Iran and India religious philanthropy has been a feature of Zoroastrian piety as well as providing the means by which both communities have prospered throughout their respective histories. In Iran an elaborate structure for the regulation of charitable donations was already in place during the Sasanian period and laid the foundation for the laws governing pious foundations, awqāf, after the Islamic conquest. The increased interaction between Iranian Zoroastrians and Parsis from the mid-nineteenth century onwards led to the expansion of the Tehran Zoroastrian community and the rise of a wealthy merchant class which in turn enabled philanthropic activity to flourish. This development will be discussed here with reference to a particular vaqf, that of the first ārāmgāh or Zoroastrian cemetery to be established in Tehran in the early twentieth century. The case of Qasr-e Firuzeh spans three successive governments in Iran and gives an insight into the management of a charitable endowment within different political contexts.
Recent change of vegetation growth trend in China
Authors: Peng Shushi , Chen Anping , Xu Liang , Cao Chunxiang , Fang Jingyun , Myneni Ranga B , Pinzon Jorge E , Tucker Compton J , Piao Shilong
Published: December 2011

Using satellite-derived normalized difference vegetation index (NDVI) data, several previous studies have indicated that vegetation growth significantly increased in most areas of China during the period 1982–99. In this letter, we extended the study period to 2010. We found that at the national scale the growing season (April–October) NDVI significantly increased by 0.0007 yr−1 from 1982 to 2010, but the increasing trend in NDVI over the last decade decreased in comparison to that of the 1982–99 period. The trends in NDVI show significant seasonal and spatial variances. The increasing trend in April and May (AM) NDVI (0.0013 yr−1) is larger than those in June, July and August (JJA) (0.0003 yr−1) and September and October (SO) (0.0008 yr−1). This relatively small increasing trend of JJA NDVI during 1982–2010 compared with that during 1982–99 (0.0012 yr−1) (Piao et al 2003 J. Geophys. Res.—Atmos.
108 4401) implies a change in the JJA vegetation growth trend, which significantly turned from increasing (0.0039 yr−1) to slightly decreasing ( − 0.0002 yr−1) in 1988. Regarding the spatial pattern of changes in NDVI, the growing season NDVI increased (over 0.0020 yr−1) from 1982 to 2010 in southern China, while its change was close to zero in northern China, as a result of a significant changing trend reversal that occurred in the 1990s and early 2000s. In northern China, the growing season NDVI significantly increased before the 1990s as a result of warming and enhanced precipitation, but decreased after the 1990s due to drought stress strengthened by warming and reduced precipitation. Our results also show that the responses of vegetation growth to climate change vary across different seasons and ecosystems.
G(o) activation is required for both appetitive and aversive memory acquisition in Drosophila
Authors: Madalan Adrian , Yang Xiao , Ferris Jacob , Zhang Shixing , Roman Gregg
Published: December 2011

Heterotrimeric G(o) is an abundant brain protein required for negatively reinforced short-term associative olfactory memory in Drosophila. G(o) is the only known substrate of the S1 subunit of pertussis toxin (PTX) in fly, and acute expression of PTX within the mushroom body neurons (MB) induces a reversible deficit in associative olfactory memory. We demonstrate here that the induction of PTX within the α/β and γ lobe MB neurons leads to impaired memory acquisition without affecting memory stability. The induction of PTX within these MB neurons also leads to a significant defect in an optimized positively reinforced short-term memory paradigm; however, this PTX-induced learning deficit is noticeably less severe than found with the negatively reinforced paradigm. Both negatively and positively reinforced memory phenotypes are rescued by the constitutive expression of G(o)α transgenes bearing the Cys351Ile mutation. Since this mutation renders the G(o) molecule insensitive to PTX, the results isolate the effect of PTX on both forms of olfactory associative learning to the inhibition of the G(o) activation.
Paraformaldehyde Fixation of Drosophila Testes
Authors: Bonaccorsi Silvia , Giansanti Maria G. , Cenci Giovanni , Gatti Maurizio
Published: December 2011

This protocol describes paraformaldehyde fixation of Drosophila testes. The procedure preserves F-actin-containing structures because it does not involve the use of methanol. Thus, it is particularly suitable for contractile ring and fusome visualization. However, it does not preserve cell morphology and microtubules as efficiently as methanol–acetone fixation and does not permit clear detection of the Y loops.