bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant population processes in the course of forest succession in abandoned meadows. I. Variability and diversity of floristic compositions, and biological mechanisms of species turnover
Authors: Falińska Krystyna
Published: April 2013

Within Białowieża Forest the studies on the rate and nature of changes in meadow vegetation on the sites no longer mown were conducted for 15 years (1974-1988). The successional processes were analysed at various organizational levels by applying hierarchi­cal system of study areas, varying in size (Figs. 1, 2). Changes in plant landscape were studied on 15 ha, those in phytocoenoses - 4 × 1 ha, populations - 24 × 200 ml, and those in the individual development - 6 × 25 m2. Forest re-colonized abandoned meadows at a various rate through: a) gradual transformation of meadow phytocoenoses into tall­herb, and later brushwood communities, which went on for c. 15 years; b) formation of the mosaic of monospecific aggregations of a few, among 124, components of meadow communities, such aggregations persisted for 5-15 years; c) the development of tree biogroups (forest outpost) directly in the meadow sod. This diversity resulted from the habitat heterogeneity (microrelief, water level) and variety of colonization strategies among the species present prior to the succession. They vary in their role in the successional process and can: I) stimulate the changes in the structure of meadow phytocoenoses and lead to the formation of new communities (promotors), 2) limit species turnover due to their long-lived aggregations (inhibitors), 3) play no crucial role in the vegetation transformation (indifferents).
Materials to the Zygnemaceae of Poland. III. Spirogyra lagerheimii Wittrock 1889, a new species in Poland
Authors: Kadłubowska Joanna Z.
Published: April 2013

A species new in the Polish flora, Spirogyra lagerheimii Wittr, was found in the old riverbed of the Raba River in Mszana Dolna (Nowy Sącz Voivodship) and in a peat bog in Magdalenów (Piotrków Voivodship). Figures showing hitherto unknown scalariform conjugation, germinating zygotes, inflated vegetative cells in conjugating filaments are shown.
Young Children's Understandings of Length Measurement: Evaluating a Learning Trajectory
Authors: Szilágyi Janka , Clements Douglas H. , Sarama Julie
Published: April 2013

This study investigated the development of length measurement ideas in students from prekindergarten through 2nd grade. The main purpose was to evaluate and elaborate the developmental progression, or levels of thinking, of a hypothesized learning trajectory for length measurement to ensure that the sequence of levels of thinking is consistent with observed behaviors of most young children. The findings generally validate the developmental progression, including the tasks and the mental actions on objects that define each level, with several elaborations of the levels of thinking and minor modifications of the levels themselves.
A Review of Mathematics Education and Technology: Rethinking the Terrain: The 17th ICMI Study
Authors: Hegedus Stephen , Dalton Sara , Burke James
Published: April 2013

A review of Mathematics Education and Technology: Rethinking the Terrain, The 17th ICMI Study.
The Himalayas: Barrier and conduit for gene flow
Authors: Gayden Tenzin , Perez Annabel , Persad Patrice J. , Bukhari Areej , Chennakrishnaiah Shilpa , Simms Tanya , Maloney Trisha , Rodriguez Kristina , Herrera Rene J.
Published: April 2013

The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y‐chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian‐specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep‐rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y‐chromosome data indicate sex‐biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia. Am J Phys Anthropol 151:169–182, 2013. © 2013 Wiley Periodicals, Inc.
Infant mortality and intra‐household competition in the Northern Islands of Orkney, Scotland, 1855–2001
Authors: Sparks Corey S. , Wood James W. , Johnson Patricia L.
Published: April 2013

This study applies principles from the theory of household life cycles to the study of early childhood mortality in the population of the Northern Orkney Islands, Scotland. The primary hypothesis is that unfavorable household economic conditions resulting from changes in household demographic composition increase the risk of death for children under the age of 5 years because of limited resources and intra‐household competition. We apply Cox proportional hazards models to nearly 5,000 linked birth and death records from the Northern Orkney Islands, Scotland, from the period 1855 to 2001. The dependent variable is the child's risk of death before age 5. Findings suggest that children in households with unfavorable age compositions face higher risk of death. This elevated risk of death continues once heterogeneity among children, islands, and households is controlled. Results also show differential risk of death for male children, children of higher birth orders, and twin births. The analyses present evidence for intra‐household competition in this historic setting. The most convincing evidence of competition is found in the effects of household consumer/producer ratios and twinning on child mortality risks. Am J Phys Anthropol 151:191–201, 2013. © 2013 Wiley Periodicals, Inc.
Biocatalytic and Structural Properties of a Highly Engineered Halohydrin Dehalogenase
Authors: Schallmey Marcus , Floor Robert J. , Hauer Bernhard , Breuer Michael , Jekel Peter A. , Wijma Hein J. , Dijkstra Bauke W. , Janssen Dick B.
Published: April 2013

Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild‐type enzyme in the cyanolysis of ethyl (S)‐3,4‐epoxybutyrate, a conversion yielding ethyl (R)‐4‐cyano‐3‐hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild‐type enzyme, both for dehalogenation and for cyanolysis reactions. The 37‐fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild‐type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)‐3,4‐epoxybutyrate or with ethyl (R)‐4‐cyano‐3‐hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild‐type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.
A Redox‐Mediator‐Free Solar‐Driven Z‐Scheme Water‐Splitting System Consisting of Modified Ta3N5 as an Oxygen‐Evolution Photocatalyst
Authors: Ma Su Su Khine , Maeda Kazuhiko , Hisatomi Takashi , Tabata Masashi , Kudo Akihiko , Domen Kazunari
Published: April 2013

Tantalum nitride (Ta3N5) modified with various O2‐evolution cocatalysts was employed as a photocatalyst for water oxidation under visible light (λ>420 nm) in an attempt to construct a redox‐mediator‐free Z‐scheme water‐splitting system. Ta3N5 was prepared by nitriding Ta2O5 powder under a flow of NH3 at 1023–1223 K. The activity of Ta3N5 for water oxidation from an aqueous AgNO3 solution as an electron acceptor without cocatalyst was dependent on the generation of a well‐crystallized Ta3N5 phase with a low density of anionic defects. Modification of Ta3N5 with nanoparticulate metal oxides as cocatalysts for O2 evolution improved water‐oxidation activity. Of the cocatalysts examined, cobalt oxide (CoOx) was found to be the most effective, improving the water‐oxidation efficiency of Ta3N5 by six to seven times. Further modification of CoOx/Ta3N5 with metallic Ir as an electron sink allowed one to achieve Z‐scheme water splitting under simulated sunlight through interparticle electron transfer without the need for a shuttle redox mediator in combination with Ru‐loaded SrTiO3 doped with Rh as a H2‐evolution photocatalyst.
Space Asymmetry as a Possible Global Feature
Authors: Shinitzky Meir
Published: April 2013

A series of reports in the literature indicated symmetry breaking in assemblies of chiral molecules of opposite handedness. These unexpected observations could be accounted for as being generated by the “parity violation” of the nuclear weak force, combined with an autocatalytic amplification process. However, in many such cases, in particular of chiral fluids, this putative mechanism is far from providing a reasonable explanation for such discrimination. In this article it is suggested that space may have deviated a priori from absolute symmetry, a possibility which complies with observations in atoms and molecules and may even be implicated in the asymmetrical configuration of spiral galaxies. Space asymmetry can be extrapolated to a difference between the relative statistical weights of the “right” versus the “left” directions with respect to Euclidian coordinates or, analogously, to a difference between the clockwise and anticlockwise orientations in polar coordinates. The difference in weights of these directions in space is estimated to be around 1%, based on the differences observed in density values of chiral fluids and chiral crystals of NaClO3. The implied asymmetry of time, as the conjugated fourth dimension, suggests a similar difference in magnitude of the time coordinate in a right‐handed versus left‐handed space, which is feasible for experimental verification. Chirality 25:308–311, 2013. © 2013 Wiley Periodicals, Inc.
The effect of nurse navigation on timeliness of breast cancer care at an academic comprehensive cancer center
Authors: Basu Mohua , Linebarger Jared , Gabram Sheryl G. A. , Patterson Sharla Gayle , Amin Miral , Ward Kevin C.
Published: April 2013

BACKGROUND

A patient navigation process is required for accreditation by the National Accreditation Program for Breast Centers (NAPBC). Patient navigation has previously been shown to improve timely diagnosis in patients with breast cancer. This study sought to assess the effect of nurse navigation on timeliness of care following the diagnosis of breast cancer by comparing patients who were treated in a comprehensive cancer center with and without the assistance of nurse navigation.

METHODS

Navigation services were initiated at an NAPBC‐accredited comprehensive breast center in July 2010. Two 9‐month study intervals were chosen for comparison of timeliness of care: October 2009 through June 2010 and October 2010 through June 2011. All patients with breast cancer diagnosed in the cancer center with stage 0 to III disease during the 2 study periods were identified by retrospective cancer registry review. Time from diagnosis to initial oncology consultation was measured in business days, excluding holidays and weekends.

RESULTS

Overall, 176 patients met inclusion criteria: 100 patients prior to and 76 patients following nurse navigation implementation. Nurse navigation was found to significantly shorten time to consultation for patients older than 60 years (B = −4.90, P = .0002). There was no change in timeliness for patients 31 to 60 years of age.

CONCLUSIONS

Short‐term analysis following navigation implementation showed decreased time to consultation for older patients, but not younger patients. Further studies are indicated to assess the long‐term effects and durability of this quality improvement initiative. Cancer 2013;119:2524–2531. © 2013 American Cancer Society.
Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22‐translocation
Authors: Panagopoulos Ioannis , Thorsen Jim , Gorunova Ludmila , Haugom Lisbeth , Bjerkehagen Bodil , Davidson Ben , Heim Sverre , Micci Francesca
Published: April 2013

Endometrial stromal sarcomas (ESS) are genetically heterogeneous uterine tumors in which a JAZF1‐SUZ12 chimeric gene resulting from the chromosomal translocation t(7;17)(p15;q21) as well as PHF1 rearrangements (in chromosomal band 6p21) with formation of JAZF1‐PHF1, EPC1‐PHF1, and MEAF6‐PHF1 chimeras have been described. Here, we investigated two ESS characterized cytogenetically by the presence of a der(22)t(X;22)(p11;q13). Whole transcriptome sequencing one of the tumors identified a ZC3H7‐BCOR chimeric transcript. Reverse transciptase‐PCR with the ZC3H7B forward and BCOR reverse primer combinations confirmed the presence of a ZC3H7‐BCOR chimeric transcript in both ESS carrying a der(22)t(X;22) but not in a control ESS with t(1;6) and the MEAF6‐PHF1 fusion. Sequencing of the amplified cDNA fragments showed that in both cases ESS exon 10 of ZC3H7B (from 22q13; accession number NM_017590 version 4) was fused to exon 8 of BCOR (from Xp11; accession number NM_001123385 version 1). Reciprocal multiple BCOR‐ZC3H7B cDNA fragments were amplified in only one case suggesting that ZC3H7B‐BCOR, on the der(22)t(X;22), is the pathogenetically important fusion gene. The putative ZC3H7B‐BCOR protein would contain the tetratricopeptide repeats and LD motif from ZC3H7B and the AF9 binding site (1093‐1233aa), the 3 ankyrin repeats (1410‐1509 aa), and the NSPC1 binding site of BCOR. Although the presence of these motifs suggests various functions of the chimeric protein, it is possible that its most important role may be in epigenetic regulation. Whether or not the (patho)genetic subsets JAZF1‐SUZ12, PHF1 rearrangements, and ZC3H7B‐BCOR correspond to any phenotypic, let alone clinically important, differences in ESS remain unknown. © 2013 Wiley Periodicals, Inc.
Frequent DNA methylation of MiR‐129‐2 and its potential clinical implication in hepatocellular carcinoma
Authors: Lu Chang‐Yi , Lin Kai‐Yuan , Tien Meng‐Tsung , Wu Cheng‐Tao , Uen Yih‐Huei , Tseng Tzu‐Ling
Published: April 2013

Hepatocellular carcinoma (HCC) is a highly malignant tumor with poor prognosis and high mortality due to a lack of effective medical treatment and apparent early stage symptoms. Understanding molecular mechanism of cancer development is crucial for HCC diagnosis, prognosis, and treatment. Recently, microRNAs have been shown to play an important role in carcinogenesis, being regulated by DNA methylation in several cases. In this study, a whole genome approach was used to identify methylation‐regulated miRNAs in HCC, finally focusing on miR‐129‐2. MiR‐129‐2 methylation and reduced expression were observed in all examined HCC cell lines but not in normal liver cells and tissues. In 39 (93%) of 42 HCC, the methylation levels of miR‐129‐2 were significantly increased in tumor tissues compared with adjacent normal tissues. Furthermore, miR‐129‐2 methylation was detectable in plasma samples from HCC patients, but not in plasma samples from healthy individuals or patients with liver cirrhosis. At a cut‐off value of −2.36 (log2 transformation of methylation level), it was possible to distinguish HCC from healthy and cirrhotic controls with sensitivity and specificity of 88% and 100%, respectively. This study indicates that miR‐129‐2 methylation is highly accurate in distinguishing HCC patients from cirrhosis patients and healthy individuals, implying its potential utility as an early diagnostic marker for HCC. © 2013 Wiley Periodicals, Inc.
A mechanism for sandbar straightening by oblique wave incidence
Authors: Garnier R. , Falqués A. , Calvete D. , Thiébot J. , Ribas F.
Published: April 2013

Breaker bars in the surf zone of sandy beaches generally evolve between straight bars parallel to the shore and meandering crescentic bars associated with intense (dangerous) currents flowing seaward through rip channels. Understanding the behavior of such systems is fundamental as they control the entire surf zone dynamics, the shape of the coastline, and the exchange of floating material with the shoreface. Although the mechanisms behind the meandering of an originally straight bar have been studied extensively, a clear physical explanation on the crescentic bar straightening was missing. Recent field observations have highlighted that this morphological reset can be due to wave obliquity. By using a two‐dimensional horizontal morphological model, we show that the bar straightening by oblique waves occurs because the rip current is both weakened in intensity and shifted downdrift from the channel deepest section. The technique employed is useful for the study of other types of bed forms.
Optimisation of antioxidant peptide preparation from corn gluten meal
Authors: Zhuang Hong , Tang Ning , Dong Shu‐ting , Sun Bin , Liu Jing‐bo
Published: April 2013

BACKGROUND

Corn gluten meal, containing approximately 600 g kg−1 protein, is a main by‐product of corn wet milling. The annual output of corn gluten meal in China is over 840 000 tons. However, it is difficult to utilise corn gluten meal in the food industry because of its low water solubility and amino acid imbalance. In the present study, corn gluten meal was hydrolysed by different proteases to produce hydrolysates with antioxidant activity in order to increase its value. The hydrolysis conditions were optimised by multiple linear regression and response surface methodology. Furthermore, the amino acid sequence of one corn peptide was determined.

RESULTS

The optimal conditions for alkaline protease hydrolysis were a pH of 9.5, an enzyme/substrate (E/S) ratio of 8 g per 100 g, a liquid/solid ratio of 25 mL g−1 and a time of 75 min, while the optimal conditions for flavourzyme hydrolysis were a pH of 7, an E/S ratio of 4.2 g per 100 g and a time of 66 min. After gel filtration chromatography, fraction F2 exhibited the highest antioxidant activities. The amino acid sequence of a purified peptide in fraction F2 was determined as Gly‐His‐Lys‐Pro‐Ser (507.2 Da).

Conclusion

The results indicate that corn gluten meal hydrolysates and/or its isolated peptides are potent antioxidants. © 2013 Society of Chemical Industry
α‐Linalool – a marker compound of forged/synthetic sweet basil (Ocimum basilicum L.) essential oils
Authors: Radulović Niko S , Blagojević Polina D , Miltojević Ana B
Published: April 2013

BACKGROUND

Ocimum basilicum L. (sweet basil) is known to occur as several chemotypes or cultivars that differ in their essential oil composition. The surprising discovery of 3,7‐dimethylocta‐1,7‐dien‐3‐ol, the rare α isomer of the well‐known monoterpene alcohol β‐linalool (3,7‐dimethylocta‐1,6‐dien‐3‐ol), in samples of Serbian basil oil provoked an investigation of the origin of α‐linalool in these samples. Three scenarios were considered, namely (a) the existence of a new natural chemotype, (b) an artefactual formation during the isolation procedure and (c) the case of a synthetic/forged oil.

RESULTS

Noteworthy amounts (15.1–16.9%) of pure α‐linalool were isolated from a commercial sample of basil oil, and detailed spectral analyses (MS, IR, 1H and 13C NMR) unequivocally confirmed its identity. The analysis by GC and GC/MS of an additional 20 samples of different O. basilicum oils commercially available on the Serbian market or isolated from plant material cultivated in Serbia resulted in the identification of 149 compounds. The obtained compositional data were compared using multivariate statistical analysis to reveal the possible existence of a new basil chemotype.

CONCLUSION

The results of the chemical and statistical analyses give more pro arguments for the synthetic/forged oil hypothesis and suggest that α‐linalool could be used as a marker compound of such O. basilicum oils. © 2013 Society of Chemical Industry
Functional Status Determines Postoperative Outcomes in Elderly Patients Undergoing Hepatic Resections
Authors: DE LA FUENTE SEBASTIAN G. , BENNETT KYLA M. , SCARBOROUGH JOHN E.
Published: April 2013

Background

With the aging population and increasing incidence of hepatic malignancies in elderly patients, establishing the safety of hepatic resections is crucial. The present study investigates early postoperative morbidity and mortality in elderly patients undergoing hepatic resection using a nationally validated database.

Methods

The National Surgical Quality Improvement Program Participant User Files (NSQIP‐PUF) for 2005–2009 were used for the retrospective analysis of all patients undergoing hepatic resection. The primary outcome measures were 30‐day postoperative mortality, overall complication rate, and serious complication rate. The primary predictor variable was patient age, which was treated as a dichotomous variable (age ≤70 years, age ≥70 years).

Results

Five thousand seven hundred six patients were included in the final analysis, 1,280 of which were ≥70 years of age. Thirty‐day postoperative mortality (≤70 years 1.9% vs. ≥70 years 4.5%, P < 0.0001), serious complications (≤70 years 15.2% vs. ≥ 70 years 18.4%, P < 0.006) and overall complications (≤70 years 23.1% vs. ≥70 years 26.6%, P < 0.01) were more common in the elderly group. Elderly patients had significantly more wound infections, pneumonia, prolonged ventilator support, unplanned re‐intubations, renal failure, strokes, myocardial infarction, cardiac arrests, and septic shock. The median length of hospitalization was also significantly longer in the elderly.

Conclusions

This study shows significantly higher complication rates and mortality following hepatic resections in elderly patients. These findings should be taken into account when considering hepatectomy in this population. J. Surg. Oncol. 2013;107:865–870. © 2013 Wiley Periodicals, Inc.
Limiting behavior of the stochastic sequential assignment problem
Authors: Baharian Golshid , Jacobson Sheldon H.
Published: April 2013

The stochastic sequential assignment problem (SSAP) considers how to allocate available distinct workers to sequentially arriving tasks with stochastic parameters such that the expected total reward obtained from the sequential assignments is maximized. Implementing the optimal assignment policy for the SSAP involves calculating a new set of breakpoints upon the arrival of each task (i.e., for every time period), which is impractical for large‐scale problems. This article studies two problems that are concerned with obtaining stationary policies, which achieve the optimal expected reward per task as the number of tasks approaches infinity. The first problem considers independent and identically distributed (IID) tasks with a known distribution function, whereas in the second problem tasks are derived from r different unobservable distributions governed by an ergodic Markov chain. The convergence rate of the expected reward per task to the optimal value is also obtained for both problems. © 2013 Wiley Periodicals, Inc. Naval Research Logistics, 2013
Biallelic DICER1 mutations occur in Wilms tumours
Authors: Wu MK , Sabbaghian N , Xu B , Addidou‐Kalucki S , Bernard C , Zou D , Reeve AE , Eccles MR , Cole C , Choong CS , Charles A , Tan TY , Iglesias DM , Goodyer PR , Foulkes WD
Published: April 2013

DICER1 is an endoribonuclease central to the generation of microRNAs (miRNAs) and short interfering RNAs (siRNAs). Germline mutations in DICER1 have been associated with a pleiotropic tumour predisposition syndrome and Wilms tumour (WT) is a rare manifestation of this syndrome. Three WTs, each in a child with a deleterious germline DICER1 mutation, were screened for somatic DICER1 mutations and were found to bear specific mutations in either the RNase IIIa (n = 1) or the RNase IIIb domain (n = 2). In the two latter cases, we demonstrate that the germline and somatic DICER1 mutations were in trans, suggesting that the two‐hit hypothesis of tumour formation applies for these examples of WT. Among 191 apparently sporadic WTs, we identified five different missense or deletion somatic DICER1 mutations (2.6%) in four individual WTs; one tumour had two very likely deleterious somatic mutations in trans in the RNase IIIb domain (c.5438A>G and c.5452G>A). In vitro studies of two somatic single‐base substitutions (c.5429A>G and c.5438A>G) demonstrated exon 25 skipping from the transcript, a phenomenon not previously reported in DICER1. Further we show that DICER1 transcripts lacking exon 25 can be translated in vitro. This study has demonstrated that a subset of WTs exhibits two ‘hits’ in DICER1, suggesting that these mutations could be key events in the pathogenesis of these tumours. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase
Authors: Weikl Thomas R. , Boehr David D.
Published: April 2013

Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (DHFR) from Escherichia coli, which exhibits characteristic conformational changes of the active‐site loop during the catalytic step and during unbinding of the product. In this article, we present a general kinetic framework that can be used (1) to identify the ordering of events in the coupling of conformational changes, binding, and catalysis and (2) to determine the rates of the substeps of coupled processes from a combined analysis of nuclear magnetic resonance R2 relaxation dispersion experiments and traditional enzyme kinetics measurements. We apply this framework to E. coli DHFR and find that the conformational change during product unbinding follows a conformational‐selection mechanism, that is, the conformational change occurs predominantly prior to unbinding. The conformational change during the catalytic step, in contrast, is an induced change, that is, the change occurs after the chemical reaction. We propose that the reason for these conformational changes, which are absent in human and other vertebrate DHFRs, is robustness of the catalytic rate against large pH variations and changes to substrate/product concentrations in E. coli. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Relation between flexibility and positively selected HIV‐1 protease mutants against inhibitors
Authors: Braz Antônio S. K. , Tufanetto Patrícia , Perahia David , Scott Luis P. B.
Published: April 2013

The antiretroviral chemotherapy helps to reduce the mortality of HIVs infected patients. However, RNA dependant virus replication has a high mutation rate. Human immunodeficiency virus Type 1 protease plays an essential role in viral replication cycle. This protein is an important target for therapy with viral protein inhibitors. There are few works using normal mode analysis to investigate this problem from the structural changes viewpoint. The investigation of protein flexibility may be important for the study of processes associated with conformational changes and state transitions. The normal mode analysis allowed us to investigate structural changes in the protease (such as flexibility) in a straightforward way and try to associate these changes with the increase of fitness for each positively selected HIV‐1 mutant protease of patients treated with several protease inhibitors (saquinavir, indinavir, ritonavir, nelfinavir, lopinavir, fosamprenavir, atazanavir, darunavir, and tripanavir) in combination or separately. These positively selected mutations introduce significant flexibility in important regions such as the active site cavity and flaps. These mutations were also able to cause changes in accessible solvent area. This study showed that the majority of HIV‐1 protease mutants can be grouped into two main classes of protein flexibility behavior. We presented a new approach to study structural changes caused by positively selected mutations in a pathogen protein, for instance the HIV‐1 protease and their relationship with their resistance mechanism against known inhibitors. The method can be applied to any pharmaceutically relevant pathogen proteins and could be very useful to understand the effects of positively selected mutations in the context of structural changes. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Fucoidan Prevents High‐Fat Diet‐Induced Obesity in Animals by Suppression of Fat Accumulation
Authors: Kim Mi‐Ja , Jeon Joseph , Lee Jin‐Sil
Published: April 2013

This study examines the antiobesity effects of fucoidan in an animal model of diet‐induced obesity. Mice were fed a standard diet or high‐fat diet (HFD) for 5 weeks. After that, the mice were divided into four experimental groups, with 10 mice per group, including a standard diet group, HFD group, HFD containing 1% fucoidan (HFD + FUCO 1%) group and HFD containing 2% fucoidan (HFD + FUCO 2%) group. The fucoidan supplementation group had significantly decreased body‐weight gain, food efficiency ratio and relative liver and epididymal fat mass compared with the HFD group. The mice supplemented with fucoidan showed significantly reduced triglyceride, total cholesterol and low‐density lipoprotein levels in the plasma. Liver steatosis induced by the HFD improved in the fucoidan‐supplemented group. Furthermore, fucoidan affected the down‐regulation expression patterns of epididymal adipose tissue genes such as peroxisome proliferator‐activated receptor γ, adipose‐specific fatty acid binding protein and acetyl CoA carboxylase. Therefore, fucoidan may be considered for use in improving obesity. Copyright © 2013 John Wiley & Sons, Ltd.
A Mathematical Model of the Solid Flow Behavior in a Real Dimension Blast Furnace: Effects of the Solid Volume Fraction on the Velocity Profile
Authors: Safavi Nick Reza , Tilliander Anders , Jonsson Lage T. I. , Jönsson Pär G.
Published: April 2013

A mathematical model based on the continuum mechanic concept has been developed to describe the profile of solid particles in a blast furnace with respect to the in‐furnace conditions and characteristics, e.g., the shape and size of the deadman. The Navier‐Stokes differential equation for multi‐phase multi‐dimensional space has been used to describe the behavior of existing phases. The equation has been modified to make it possible to describe the dual nature of the solid phase in the system by applying the concept of the solid surface stress to characterize the inter‐granular surface interactions between particles. Since different phases co‐exist in a blast furnace, the volume fraction plays an important role in a blast furnace. Therefore, the influence of three different packing densities (0.68, 0.71, and 0.74, respectively) on the profile of the flow in the upper part of a furnace down to the tuyeres level has been studied. It is shown that an increase in the volume fraction of the solid phase lead to a decrease in magnitude of the velocity. The decrease in the magnitude of the velocity due to an increase in the solid volume fraction will increase the resident time of the particles inside a blast furnace. In addition, it is shown that the solid phase velocity magnitude decreases from the throat to the belly of the furnace for the studied conditions. However, after belly the velocity magnitude increases.
Clinical Implication of Cancer Adhesion in Papillary Thyroid Carcinoma: Clinicopathologic Characteristics and Prognosis Analyzed with Degree of Extrathyroidal Extension
Authors: Jung Seung Pil , Kim Minkuk , Choe Jun‐Ho , Kim Jee Soo , Nam Seok Jin , Kim Jung‐Han
Published: April 2013

Background

Macroscopic extrathyroidal extension (ETE) is a poor prognostic factor in papillary thyroid carcinoma (PTC). However, intraoperative inspection for ETE is often inaccurate and could lead the surgeon to misconstrue simple adhesion as gross ETE. Such confusion could result in more aggressive treatment than necessary. In the present study we investigated the frequency and clinical implication of simple adhesions.

Methods

We identified 858 patients who underwent total thyroidectomy for papillary thyroid carcinoma (PTC). Clinicopathologic features, prognosis, and stimulated serum thyroglobulin (Tg) levels were compared between four groups divided according to degree of ETE: no ETE (n = 335), simple adhesion (n = 16), microscopic ETE (n = 378), and macroscopic ETE (n = 129).

Results

In the total of 145 cases, which were recognized as gross ETE under intraoperative inspection, 16 cases (11.0 %) were diagnosed as cancer confined to the thyroid without ETE by definite histology. The simple adhesion group showed no statistical differences in postoperative stimulated Tg levels from the no ETE and microscopic ETE groups (p > 0.05). In contrast, the distribution of postoperative Tg levels in the macroscopic ETE group was significantly higher than in the other groups (p < 0.001). During the 54‐month median follow‐up period, the macroscopic ETE and microscopic ETE groups showed poorer relapse‐free survival than the no ETE and simple adhesion groups (p < 0.05).

Conclusions

The findings of the present study indicate that the discrepancy between intraoperative inspection and definite histology is not negligible when dense adhesions are present. When no tumor is found, the patient with inflammatory or fibrotic adhesions has a favorable prognosis.
Mammary gene expression and activity of antioxidant enzymes and oxidative indicators in the blood, milk, mammary tissue and ruminal fluid of dairy cows fed flax meal
Authors: Schogor Ana Luiza Bachmann , Palin Marie-France , dos Santos Geraldo Tadeu , Benchaar Chaouki , Lacasse Pierre , Petit Hélène V.
Published: April 2013

The effects of flax meal (FM) on the activity of antioxidant enzymes (superoxide dismutase (SOD), glutathione peroxidase (GPx) and catalase (CAT)) in the blood, mammary tissue and ruminal fluid, and oxidative stress indicators (thiobarbituric acid-reactive substances (TBARS) and 1,1-diphenyl-2-picrylhydrazyl-scavenging activity) in the milk, plasma and ruminal fluid of dairy cows were determined. The mRNA abundance of the antioxidant enzymes and oxidative stress-related genes was assessed in mammary tissue. A total of eight Holstein cows were used in a double 4 × 4 Latin square design. There were four treatments in the diet: control with no FM (CON) or 5 % FM (5FM), 10 % FM (10FM) and 15 % FM (15FM). There was an interaction between treatment and time for plasma GPx and CAT activities. Cows supplemented with FM had a linear reduction in TBARS at 2 h after feeding, and there was no treatment effect at 0, 4 and 6 h after feeding. TBARS production decreased in the milk of cows fed the 5FM and 10FM diets. There was a linear increase in nuclear factor (erythroid-derived 2)-like 2 (NFE2L2) mRNA abundance in mammary tissue with FM supplementation. A linear trend for increased mRNA abundance of the CAT gene was observed with higher concentrations of FM. The mRNA abundance of CAT, GPx1, GPx3, SOD1, SOD2, SOD3 and nuclear factor of κ light polypeptide gene enhancer in B-cells (NFKB) genes was not affected by the treatment. These findings suggest that FM supplementation can improve the oxidative status of Holstein cows as suggested by decreased TBARS production in ruminal fluid 2 h post-feeding and increased NFE2L2/nuclear factor-E2-related factor 2 (Nrf2) mRNA abundance in mammary tissue.
Why Do Closed-End Bond Funds Exist? An Additional Explanation for the Growth in Domestic Closed-End Bond Funds
Authors: Elton Edwin J. , Gruber Martin J. , Blake Christopher R. , Shachar Or
Published: April 2013

This paper provides a new explanation for why closed-end bond funds coexist along with otherwise identical open-end bond funds. Closed-end bond funds offer investors the opportunity to leverage their fixed income investment at very low borrowing rates and are attractive to investors for this reason. We find that differences in leverage are reflected in the discount on closed-end bond funds in a manner consistent with the advantage of leverage.
Space‐time coding with receive combiner bank for multiple‐input–multiple‐output system under multi‐user cochannel interference
Authors: Teng Wang Jui
Published: April 2013

Space‐time coding with receive combiner bank (STC‐RCB), in which a bank of receive combiners is added before the space‐time decoder for interference‐plus‐noise suppression, is proposed. Without loss of generality, the author consider space‐time block code (STBC) to be the representative of STC and study the performance for (STBC‐RCB). The author derive the output signal to interference‐plus‐noise ratio (SINR) (of the space‐time decoder) for STBC‐RCB under multi‐user cochannel interference. By regarding STBC as a special case of STBC‐RCB, the author also derive the output SINR for STBC under multi‐user cochannel interference. Simulation results show that the output SINR of STBC‐RCB can be much larger than that of STBC, also, they show that STBC‐RCB can adopt the appropriate receive combining strategy in the RCB to further improve the performance.
Optimisation of power allocation for asymmetric relay placement in multi‐hop relay systems
Authors: Dhaka Kalpana , Mallik Ranjan K. , Schober Robert
Published: April 2013

In this study, schemes for optimisation of power allocation (OPA) for asymmetric relay placement are presented for multi‐hop communication in a Rayleigh‐fading environment. For a decode‐and‐forward (DF) multi‐hop communication system, expressions are derived for optimised power allocation based on symbol error probability (SEP) and global channel state information (GCSI). The analysis for OPA based on GCSI is extended to a hybrid combination of amplify‐and‐forward (AF) and DF relays. Analysis is done for two kinds of modulation schemes: M‐ary phase‐shift keying with coherent detection and orthogonal M‐ary frequency‐shift keying with non‐coherent detection. Simulation results show that for a multi‐hop system with asymmetric relay placement, power optimisation schemes perform better than the conventional equal power allocation scheme. In addition, power optimisation based on GCSI shows substantially improved performance compared with power allocation based on end‐to‐end SEP. Further, performance comparison is shown for increase in number of relay nodes in an AF and DF multi‐hop system with and without power allocation. The performance of a DF system improves with increase in number of relay nodes whereas performance of an AF system degrades. Hybrid relaying provides an option to exercise switching between DF and AF so as to extract the maximum advantage of the two relaying schemes.
Electrical detection of spin reorientation transition in ferromagnetic La0.4Sm0.3Sr0.3MnO3
Authors: Aparnadevi M. , Mahendiran R.
Published: April 2013

Field-cooled magnetization of La0.4Sm0.3Sr0.3MnO3 samples shows an anomalous maximum at a temperature T* = 45 K within the ferromagnetic state, which is suggested to spin reorientation transition of the Mn sublattice aided by antiferromagnetic Sm(4f)-Mn(3d) interaction. While dc resistivity does not show any specific feature at T*, ac electrical impedance shows anomalous features at both T* and at the ferromagnetic transition temperature even in the absence of an external magnetic field. Our results indicate that ac electrical transport can be used to detect multiple magnetic phase transitions whose impact on the dc electrical transport is either weak or masked completely.
A mixed quantum-classical Liouville study of the population dynamics in a model photo-induced condensed phase electron transfer reaction
Authors: Rekik Najeh , Hsieh Chang-Yu , Freedman Holly , Hanna Gabriel
Published: April 2013

We apply two approximate solutions of the quantum-classical Liouville equation (QCLE) in the mapping representation to the simulation of the laser-induced response of a quantum subsystem coupled to a classical environment. These solutions, known as the Poisson Bracket Mapping Equation (PBME) and the Forward-Backward (FB) trajectory solutions, involve simple algorithms in which the dynamics of both the quantum and classical degrees of freedom are described in terms of continuous variables, as opposed to standard surface-hopping solutions in which the classical degrees of freedom hop between potential energy surfaces dictated by the discrete adiabatic state of the quantum subsystem. The validity of these QCLE-based solutions is tested on a non-trivial electron transfer model involving more than two quantum states, a time-dependent Hamiltonian, strong subsystem-bath coupling, and an initial energy shift between the donor and acceptor states that depends on the strength of the subsystem-bath coupling. In particular, we calculate the time-dependent population of the photoexcited donor state in response to an ultrafast, on-resonance pump pulse in a three-state model of an electron transfer complex that is coupled asymmetrically to a bath of harmonic oscillators through the optically dark acceptor state. Within this approach, the three-state electron transfer complex is treated quantum mechanically, while the bath oscillators are treated classically. When compared to the more accurate QCLE-based surface-hopping solution and to the numerically exact quantum results, we find that the PBME solution is not capable of qualitatively capturing the population dynamics, whereas the FB solution is. However, when the subsystem-bath coupling is decreased (which also decreases the initial energy shift between the donor and acceptor states) or the initial shift is removed altogether, both the PBME and FB results agree better with the QCLE-based surface-hopping results. These findings highlight the challenges posed by various conditions such as a time-dependent external field, the strength of the subsystem-bath coupling, and the degree of asymmetry on the accuracy of the PBME and FB algorithms.
Perpendicular magnetic tunnel junctions with synthetic antiferromagnetic pinned layers based on [Co/Pd] multilayers
Authors: Chang Yao-Jen , Canizo-Cabrera A. , Garcia-Vazquez Valentin , Chang Yang-Hua , Wu Te-ho
Published: April 2013

We fabricated MgO-based perpendicular magnetic tunnel junctions (p-MTJ) with Ta/CoFeB magnetic electrodes. Synthetic antiferromagnetic (SAF) pinned layers with perpendicular magnetic anisotropy (PMA) were included into the p-MTJs by using two Co/Pd multilayers (MLs) separated by a thin Ru spacer layer. The MTJs stack has the structure bottom contact/free layer CoFeB (1.0)/MgO (1)/pinned layer CoFeB (1.0)/Ta spacer layer/SAF/Ru cap layer/top contact (the units in parenthesis are in nanometers). The SAF was optimized by changing the repetition period n in one of the Co/Pd multilayers and the Ru thickness in order to obtain PMA with antiferromagnetic (AFM) coupling. The Ru spacer values were 0.7, 0.75, 0.8, 0.85, and 0.9 nm. The magnetic studies show that all magnetic films, including the Ta/CoFeB layers, are perpendicularly magnetized. The two Co/Pd MLs are AFM coupled for n > 2. Controlling the Ru thickness, the interlayer exchange coupling strength Jiec can be tailored. Jiec vs. Ru thickness exhibits a simple exponential decay. The electrical properties of the full p-MTJ with SAF show a low resistance-area (RA) product of 44.7 Ω μm2 and a tunnel magnetoresistance (TMR) ratio of 10.2%.
Size-dependent scaling of exchange bias in NiFe2O4/NiO nanogranular systems synthesized by a phase separation method
Authors: Tian Z. M. , Huang S. , Qiu Y. , Yuan S. L. , Wu Y. Y. , Li L.
Published: April 2013

Exchange bias (EB) effect has been studied in a series of nanogranular systems of ferrimagnetic (FiM) NiFe2O4 nanoparticles embedded into antiferromagnetic (AFM) NiO matrix, synthesized by a phase pprecipitation method from diluted Ni(1−x)FexO3 (x = 0.09) oxides. For these systems, the crystalline size (DNFO) of NiFe2O4 ranging from ∼3 nm to ∼55 nm has been obtained with thermal treated at different temperatures from 550 °C to 1000 °C. Magnetization measurement shows that both exchange bias field (HEB) and vertical magnetization shifts (MShift) can be exhibited below 250 K after field cooling procedure. The HEB and MShift decrease monotonically with crystalline size, and their behavior strongly depend on the crystalline size of NiFe2O4 nanoparticles. Linear relationship between HEB and MShift is observed for systems with smaller sizes (DNFO ≤ 8 nm), reveals a straightforward correlation between them. This phenomenon is ascribed to the interfacial exchange coupling between FiM NiFe2O4 clusters and spin-glass-like (SGL) phases, where the frozen uncompensated spins in SGL phases play critical role of inducing EB effect. As DNFO is above 12 nm, the dependence of HEB on MShift deviates from the linear relationship, which is discussed in terms of the superimposed contribution from the exchange coupling between FiM NiFe2O4 core with the SGL phase, and the exchange coupling between FiM NiFe2O4 core and AFM NiO phases at the interfaces.
Nanostructured magnesium oxide biosensing platform for cholera detection
Authors: Patel Manoj K. , Azahar Ali Md. , Agrawal Ved V. , Ansari Z. A. , Ansari S. G. , Malhotra B. D.
Published: April 2013

We report fabrication of highly crystalline nanostructured magnesium oxide (NanoMgO, size >30 nm) film electrophoretically deposited onto indium-tin-oxide (ITO) glass substrate for Vibrio cholerae detection. The single stranded deoxyribonucleic acid (ssDNA) probe, consisting of 23 bases (O1 gene sequence) immobilized onto NanoMgO/ITO electrode surface, has been characterized using electrochemical, Fourier Transform-Infra Red, and UltraViolet-visible spectroscopic techniques. The hybridization studies of ssDNA/NanoMgO/ITO bioelectrode with fragmented target DNA conducted using differential pulse voltammetry reveal sensitivity as 16.80 nA/ng/cm2, response time of 3 s, linearity as 100–500 ng/μL, and stability of about 120 days.
Optical Faraday rotation with graphene
Authors: Martinez J. C. , Jalil M. B. A. , Tan S. G.
Published: April 2013

Plane polarized electromagnetic waves propagating through a dielectric medium parallel to a magnetic field undergo Faraday rotation (FR) of their polarization. “Giant” Faraday rotation by as much as 0.1 rad was recently observed for terahertz waves with graphene over a SiC substrate. We show that for the (more technologically useful) optical frequency range, the same effect may be achieved with interband transitions between Landau levels formed by application of real or pseudo-magnetic fields induced by strain. At some resonant condition, the FR angle shows a sharp transition and sign reversal, which may be used to rotate the polarizations of the sodium doublet D-lines so as to be perpendicular to each other.