bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloning and analysis of duplicated rfbM and rfbK genes involved in the formation of GDP-mannose in Escherichia coli O9:K30 and participation of rfb genes in the synthesis of the group I K30 capsular polysaccharide
Authors: Jayaratne P , Bronner D , MacLachlan P R , Dodgson C , Kido N , Whitfield C
Published: November 2016

The rfbO9 gene cluster, which is responsible for the synthesis of the lipopolysaccharide O9 antigen, was cloned from Escherichia coli O9:K30. The gnd gene, encoding 6-phosphogluconate dehydrogenase, was identified adjacent to the rfbO9 cluster, and by DNA sequence analysis the gene order gnd-rfbM-rfbK was established. This order differs from that described for other members of the family Enterobacteriaceae. Nucleotide sequence analysis was used to identify the rfbK and rfbM genes, encoding phosphomannomutase and GDP-mannose pyrophosphorylase, respectively. In members of the family Enterobacteriaceae, these enzymes act sequentially to form GDP-mannose, which serves as the activated sugar nucleotide precursor for mannose residues in cell surface polysaccharides. In the E. coli O9:K30 strain, a duplicated rfbM2-rfbK2 region was detected approximately 3 kbp downstream of rfbM1-rfbK1 and adjacent to the remaining genes of the rfbO9 cluster. The rfbM isogenes differed in upstream flanking DNA but were otherwise highly conserved. In contrast, the rfbK isogenes differed in downstream flanking DNA and in 3'-terminal regions, resulting in slight differences in the sizes of the predicted RfbK proteins. RfbMO9 and RfbKO9 are most closely related to CpsB and CpsG, respectively. These are isozymes of GDP-mannose pyrophosphorylase and phosphomannomutase, respectively, which are thought to be involved in the biosynthesis of the slime polysaccharide colanic acid in E. coli K-12 and Salmonella enterica serovar Typhimurium. An E. coli O-:K30 mutant, strain CWG44, lacks rfbM2-rfbK2 and has adjacent essential rfbO9 sequences deleted. The remaining chromosomal genes are therefore sufficient for GDP-mannose formation and K30 capsular polysaccharide synthesis. A mutant of E. coli CWG44, strain CWG152, was found to lack GDP-mannose pyrophosphorylase and lost the ability to synthesize K30 capsular polysaccharide. Wild-type capsular polysaccharide could be restored in CWG152, by transformation with plasmids containing either rfbM1 or rfbM2. Introduction of a complete rfbO9 gene cluster into CWG152 restored synthesis of both O9 and K30 polysaccharides. Consequently, rfbM is sufficient for the biosynthesis of GDP-mannose for both O antigen and capsular polysaccharide E. coli O9:K30. Analysis of a collection of serotype O8 and O9 isolates by Southern hybridization and PCR amplification experiments demonstrated extensive polymorphism in the rfbM-rfbK region.
Halotolerance of Methanobacterium thermoautotrophicum delta H and Marburg
Authors: Ciulla R , Clougherty C , Belay N , Krishnan S , Zhou C , Byrd D , Roberts M F
Published: November 2016

Methanobacterium thermoautotrophicum delta H and Marburg were adapted to grow in medium containing up to 0.65 M NaCl. From 0.01 to 0.5 M NaCl, there was a lag before cell growth which increased with increasing external NaCl. The effect of NaCl on methane production was not significant once the cells began to grow. Intracellular solutes were monitored by nuclear magnetic resonance (NMR) spectroscopy as a function of osmotic stress. In the delta H strain, the major intracellular small organic solutes, cyclic-2,3-diphosphoglycerate and glutamate, increased at most twofold between 0.01 and 0.4 M NaCl and decreased when the external NaCl was 0.5 M. M. thermoautotrophicum Marburg similarly showed a decrease in solute (cyclic-2,3-diphosphoglycerate, 1,3,4,6-tetracarboxyhexane, and L-alpha-glutamate) concentrations for cells grown in medium containing > 0.5 M NaCl. At 0.65 M NaCl, a new organic solute, which was visible in only trace amounts at the lower NaCl concentrations, became the dominant solute. Intracellular potassium in the delta H strain, detected by atomic absorption and 39K NMR, was roughly constant between 0.01 and 0.4 M and then decreased as the external NaCl increased further. The high intracellular K+ was balanced by the negative charges of the organic osmolytes. At the higher external salt concentrations, it is suggested that Na+ and possibly Cl- ions are internalized to provide osmotic balance. A striking difference of strain Marburg from strain delta H was that yeast extract facilitated growth in high-NaCl-containing medium. The yeast extract supplied only trace NMR-detectable solutes (e.g., betaine) but had a large effect on endogenous glutamate levels, which were significantly decreased. Exogenous choline and glycine, instead of yeast extract, also aided growth in NaCl-containing media. Both solutes were internalized with the choline converted to betaine; the contribution to osmotic balance of these species was 20 to 25% of the total small-molecule pool. These results indicate that M. thermoautotrophicum shows little changes in its internal solutes over a wide range of external NaCl. Furthermore, they illustrate the considerable differences in physiology in the delta H and Marburg strains of this organism.
Cloning, DNA sequence, and complementation analysis of the Salmonella typhimurium hemN gene encoding a putative oxygen-independent coproporphyrinogen III oxidase
Authors: Xu K , Elliott T
Published: November 2016

Coproporphyrinogen oxidation is a last step in heme biosynthesis. The biochemically characterized eukaryotic coproporphyrinogen III oxidases have an obligate requirement for molecular oxygen, and a similar enzyme is encoded by the hemF gene in Salmonella typhimurium. Anaerobic heme synthesis requires an oxygen-independent coproporphyrinogen oxidase, which is probably encoded by the hemN gene in S. typhimurium. The hemN gene has been cloned from an insertion mutant. The nucleotide sequence was obtained and used for PCR amplification of the wild-type gene. A single open reading frame was identified as the hemN gene on the basis of its interruption by the insertion mutation and plasmid complementation studies of hemF hemN double mutants. The predicted HemN protein has 38% amino acid sequence identity to a putative anaerobic Rhodobacter sphaeroides coproporphyrinogen oxidase. The hemN RNA 5' end and the inferred transcription initiation site were mapped by primer extension. The 52.8-kDa HemN protein is expressed from the second ATG codon of the hemN open reading frame. An open reading frame with an unknown function directly upstream of hemN has a striking amino acid sequence, including 11 acidic residues in a row.
Chromosomal alterations of Candida albicans are associated with the gain and loss of assimilating functions
Authors: Rustchenko E P , Howard D H , Sherman F
Published: November 2016

We have demonstrated that a normal laboratory strain of Candida albicans spontaneously produces mutants which acquire the ability to assimilate certain carbon sources that are not utilized by the parental strain. The examination of mutants acquiring the ability to utilize either sorbose or D-arabinose revealed a few additional phenotypic changes, including the gain and loss of the capacity to assimilate other carbon sources. The change of assimilation patterns resembled the polymorphic variation of assimilation patterns found among different wild-type strains of C. albicans. Most importantly, these sorbose- and D-arabinose-positive mutants were associated with chromosomal rearrangements, with each class of positive mutants having alterations of specific chromosomes. These findings demonstrated for the first time that chromosomal alterations in C. albicans are involved in genetic variation of fundamental functions of this asexual microorganism.
Glu-255 outside the predicted ChvE binding site in VirA is crucial for sugar enhancement of acetosyringone perception by Agrobacterium tumefaciens
Authors: Banta L M , Joerger R D , Howitz V R , Campbell A M , Binns A N
Published: November 2016

Transcriptional activation of the Agrobacterium tumefaciens vir regulon is regulated by phenolics such as acetosyringone (AS), certain monosaccharides, and acidic conditions produced by wounded plant cells. The transmembrane protein VirA acts as an environmental sensor, mediating signal transduction upon perception of these stimuli. Although the periplasmic domain of VirA is not absolutely required for AS-dependent vir gene induction, it is needed for interactions with the periplasmic sugar-binding protein ChvE that result in sugar-induced enhancement of phenolic sensitivity. In this report, we demonstrate that mutations within the periplasmic domain but outside the predicted ChvE binding region can drastically alter the sensitivity of VirA to As. Using site-directed mutagenesis, we have characterized the roles of three individual amino acids in sugar-dependent AS sensitivity and have correlated the induction phenotype with the tumorigenic capacity of strains expressing mutant versions of VirA. Substitution of leucine for Glu-255 abolishes sugar enhancement while replacement with aspartic acid results in a wild-type phenotype. This residue lies outside the predicted ChvE binding site and thus identifies a new region of the VirA periplasmic domain crucial for the enhancement of vir gene induction by carbohydrates. In the absence of inducing sugar, wild-type VirA protein appears to be subject to some form of inhibition that suppresses the maximal level of transcriptional activation; deletions within the periplasmic region relieve this suppression.
Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR
Authors: Ye R , Rehemtulla S N , Wong S L
Published: November 2016

Expression of the glucitol dehydrogenase gene (gutB) is suggested to be regulated both positively and negatively in Bacillus subtilis. A mutation in the gutR locus results in the constitutive expression of gutB. The exact nature of this mutation and the function of gutR are still unknown. Cloning and characterization of gutR indicated that this gene is located immediately upstream of gutB and is transcribed in the opposite direction relative to gutB. GutR is suggested to be a 95-kDa protein with a putative helix-turn-helix motif and a nucleotide binding domain at the N-terminal region. At the C-terminal region, a short sequence of GutR shows homology with two proteins, Cyc8 (glucose repression mediator protein) and GsiA (glucose starvation-inducible protein), known to be directly or indirectly involved in catabolite repression. Part of the C-terminal conserved sequence from these proteins shows all the features observed in the tetratricopeptide motif found in many eucaryotic proteins. To study the functional role of gutR, chromosomal gutR was insertionally inactivated. A total loss of glucitol inducibility was observed. Reintroduction of a functional gutR to the GutR-deficient strain through integration at the amyE locus restores the inducibility. Therefore, GutR serves as a regulatory factor to modulate glucitol induction. The nature of the gutR1 mutation was also determined. A single amino acid change (serine-289 to arginine-289) near the putative nucleotide binding motif B in GutR is responsible for the observed phenotype. Possible models for the action of GutR are discussed.
Correlation between polyploidy and auxotrophic segregation in the imperfect yeast Candida albicans
Authors: Suzuki T , Hitomi A , Magee P T , Sakaguchi S
Published: November 2016

In order to clarify the relationship between polyploidization and the capability of phenotypic switching in the imperfect yeast Candida albicans, two types of variants were isolated as segregants from a fusant, which produced a proportion of the cell population with a higher ploidy than the rest, either in a temperature-dependent or -independent manner, when incubated at low (28 degrees C) and high (37 degrees C) temperatures. In the case of the temperature-dependent type of variants, high-ploidy cells appeared at 37 degrees C but rarely at 28 degrees C. This phenotype was named Pldts (temperature-sensitive polyploidization), and the temperature-independent phenotype was called Pld-. The appearance of high-ploidy cells in the culture of the Pldts strain at 37 degrees C was accompanied by a significant increase in the frequency of auxotrophic variants; these variants probably occur as a result of segregation of auxotrophic markers from the heterozygous to the homozygous state. Both Pldts and Pld- phenotypes were recessive in a fusion with a Pld+ parent. An adenine auxotrophic marker (ade1) was introduced into a Pldts strain in a heterozygous state, and the individual high-ploidy cells of this strain, grown at 37 degrees C, were micromanipulated to form colonies, which consisted of red and white sectors appearing at high frequency on a pink background. When the ade1 auxotrophy was introduced into Pld- strains, frequently sectored colonies were produced. These results suggested an increased level of chromosome missegregation in both types of Pld mutants. Analyses by pulsed-field gel electrophoresis of Ade-segregants, derived from a micromanipulated high-ploidy cell of a Pld(ts) strain, suggested the occurrence of nonreciprocal recombination, some of which includes chromosome loss.
Length of the coupling sequence of Tn916
Authors: Rudy C K , Scott J R
Published: November 2016

The coupling sequences of conjugative transposons are short variable sequences derived from the DNA flanking the transposon insertion site. We show here that for Tn916 the left coupling sequence is 6 bases long. The right-hand end of the transposon can excise with either four or five T's, but integration occurs to restore the five T's at the transposon's right end.
A biochemical study of the intermediary carbon metabolism of Shewanella putrefaciens
Authors: Scott J H , Nealson K H
Published: November 2016

Cell extracts were used to determine the enzymes involved in the intermediary carbon metabolism of several strains of Shewanella putrefaciens. Enzymes of the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase) were detected, but those of the Embden-Meyerhof-Parnas pathway were not. While several tricarboxylic acid cycle enzymes were present under both aerobic and anaerobic conditions, two key enzymes (2-oxoglutarate dehydrogenase and pyruvate dehydrogenase) were greatly diminished under anaerobic conditions. Extracts of cell grown anaerobically on formate as the sole source of carbon and energy were positive for hydroxypyruvate reductase, the key enzyme of the serine pathway in other methylotrophs, while no hexulose synthase activity was seen.
Use of xylE fusions to demonstrate that lsi-1, a Neisseria gonorrhoeae lipooligosaccharide biosynthetic gene, and lsi-3 are not transcriptionally linked
Authors: Danaher R J , Petricoin E F , Stein D C
Published: November 2016

The Neisseria gonorrhoeae lipooligosaccharide biosynthetic gene lsi-1 is preceded by a 281-bp non-protein-encoding sequence, lsi-3, that contains two pairs of inverted repeats. Gonococcal chromosomal lsi-xylE gene fusions were generated to measure the effect of the secondary structure on transcriptional attenuation. The data obtained indicate that lsi-3 and lsi-1 are not transcriptionally linked and therefore that lsi-3 is not involved in the regulation of lsi-1.
Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli
Authors: Hale W B , van der Woude M W , Low D A
Published: November 2016

Seven GATC sites that are nonmethylated in logarithmic growth phase cells using glycerol as a carbon source were isolated from the Escherichia coli chromosome. Three of these GATC sites are located upstream of the operons gut, mtl, and ppiA, whereas DNA sequences adjacent to three other nonmethylated GATC sites are not homologous to previously identified genes. The seventh nonmethylated GATC site is located downstream of uspA. The protection of this site from DNA methylation requires leucine-responsive regulatory protein and is leucine responsive. The carbon source and the growth phase influenced the protection of the GATC site 5' of the ppiA gene. The other five sites were protected under all the environmental conditions examined.
Robust Extracellular pH Modulation by Candida albicans during Growth in Carboxylic Acids
Authors: Danhof Heather A. , Vylkova Slavena , Vesely Elisa M. , Ford Amy E. , Gonzalez-Garay Manuel , Lorenz Michael C.
Published: November 2016

The opportunistic fungal pathogen
Candida albicans
thrives within diverse niches in the mammalian host. Among the adaptations that underlie this fitness is an ability to utilize a wide array of nutrients, especially sources of carbon that are disfavored by many other fungi; this contributes to its ability to survive interactions with the phagocytes that serve as key barriers against disseminated infections. We have reported that
C. albicans
generates ammonia as a byproduct of amino acid catabolism to neutralize the acidic phagolysosome and promote hyphal morphogenesis in a manner dependent on the Stp2 transcription factor. Here, we report that this species rapidly neutralizes acidic environments when utilizing carboxylic acids like pyruvate, α-ketoglutarate (αKG), or lactate as the primary carbon source. Unlike in cells growing in amino acid-rich medium, this does not result in ammonia release, does not induce hyphal differentiation, and is genetically distinct. While transcript profiling revealed significant similarities in gene expression in cells grown on either carboxylic or amino acids, genetic screens for mutants that fail to neutralize αKG medium identified a nonoverlapping set of genes, including
CWT1
, encoding a transcription factor responsive to cell wall and nitrosative stresses. Strains lacking
CWT1
exhibit retarded αKG-mediated neutralization
in vitro
, exist in a more acidic phagolysosome, and are more susceptible to macrophage killing, while double
cwt1Δ stp2Δ
mutants are more impaired than either single mutant. Together, our observations indicate that
C. albicans
has evolved multiple ways to modulate the pH of host-relevant environments to promote its fitness as a pathogen.

IMPORTANCE
The fungal pathogen
Candida albicans
is a ubiquitous and usually benign constituent of the human microbial ecosystem. In individuals with weakened immune systems, this organism can cause potentially life-threatening infections and is one of the most common causes of hospital-acquired infections. Understanding the interactions between
C. albicans
and immune phagocytic cells, such as macrophages and neutrophils, will define the mechanisms of pathogenesis in this species. One such adaptation is an ability to make use of nonstandard nutrients that we predict are plentiful in certain niches within the host, including within these phagocytic cells. We show here that the metabolism of certain organic acids enables
C. albicans
to neutralize acidic environments, such as those within macrophages. This phenomenon is distinct in several significant ways from previous reports of similar processes, indicating that
C. albicans
has evolved multiple mechanisms to combat the harmful acidity of phagocytic cells.
Adaptive Evolution of Phosphorus Metabolism in
Prochlorococcus
Authors: Casey John R. , Mardinoglu Adil , Nielsen Jens , Karl David M.
Published: November 2016

Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium
Prochlorococcus marinus
thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates.
Kwashiorkor: an unexpected complication to anorexia nervosa
Authors: Palm Camilla Viola Buskbjerg , Frølich Jacob Stampe , Snogdal Lena Sønder , Støving René Klinkby
Published: November 2016

We present the case of a woman aged 48 years, diagnosed with anorexia nervosa (AN) at the age of 12. She was admitted to a highly specialised eating disorder facility with distended abdomen, muscular atrophy, ulcerative dermatitis, electrolyte derangements and low serum albumin. Her weight was 53.1 kg, corresponding to a body mass index (BMI) of 17.9 kg/m2. After initial stabilisation, a therapeutic ascites puncture relieved the patient from 6500 mL of ascites. After 6 weeks of nutritional and diuretic treatment, the patient was discharged with a weight of 46.8 kg (BMI 15.7 kg/m2), without ascites and with healed ulcerations. The condition was consistent with kwashiorkor, a complication to malnutrition rarely seen in AN.
Successful recovery and allogeneic stem cell transplant following chemotherapy-induced severe cardiomyopathy: literature review of management and prognostic factors
Authors: Shahzad Muhammad Asim , Ishtiaq Rizwan , Zahid Umar , Anwer Faiz
Published: November 2016

Chemotherapy-induced cardiomyopathy is one of the major possible hazards that can result from potential cardiotoxic agents while treating cancer. Prognostic risk factors include the rate of drug administration, history of hypertension, female gender, extremes of age, previous history of mediastinal irradiation, cumulative dose and pre-existing heart disease. Close monitoring of the patients, timely diagnosis, use of well-known biomarkers including cardiac troponins, NT-ProBNP and imaging studies like 2D Echo or cardiac MRI are essential. Emerging biomarkers include carbonyl reductases (CBR1 and CBR3), aldo-keto reductases (AKR, type 1A1, 1C3, 7A2) and topoisomerase2β (Top2β). β blockers and ACE inhibitors have not only been shown to slow down the progression of cardiac dysfunction but also produce symptomatic improvement. Our case report describes a patient with acute myeloblastic leukaemia who developed severe cardiomyopathy acutely after starting the anthracycline-based regimen. Nevertheless, with timely intervention her symptoms improved and subsequently she successfully received allogeneic stem cell transplantation.
Case of Steven-Johnson Syndrome in a male with breast cancer secondary to docetaxel/cyclophosphamide therapy
Authors: Jarrett Benjamin , Ghazala Sehem , Chao Joseph , Chaudhary Sachin
Published: November 2016

The mortality rate for Stevens-Johnson syndrome (SJS) is estimated to be ∼12% and for toxic epidermal necrolysis (TEN) it is around 30%. It continues to be a severe life-threatening drug reaction. We present a 60-year-old Caucasian man with a medical history significant for breast cancer status post mastectomy and chemotherapy with docetaxel and cyclophosphamide who presented with severe mucositis and a progressing skin rash consistent with SJS. He was started on high-dose corticosteroids and IVIG but continued to have worsening mucosal ulcerations and severe bleeding from the oral, conjunctival and genital mucosa. He underwent several rounds of plasmapheresis and additional high-dose steroids with mild improvement in the mucocutaneous manifestations. He subsequently developed respiratory failure, which required mechanical ventilation, as well as disseminated intravascular coagulation, diffuse alveolar haemorrhage, withPneumocystis jiroveciipneumonia which led to his demise on hospital day 15.
Contact non-squeezing at large scale in ℝ2n × S1
Authors: Fraser Maia
Published: November 2016

We define a [Formula: see text]-equivariant version of the cylindrical contact homology used by Eliashberg–Kim–Polterovich [11] to prove contact non-squeezing for prequantized integer-capacity balls [Formula: see text], [Formula: see text] and we use it to extend their result to all [Formula: see text]. Specifically, we prove if [Formula: see text] there is no [Formula: see text], the group of compactly supported contactomorphisms of [Formula: see text] which squeezes [Formula: see text] into itself, i.e. maps the closure of [Formula: see text] into [Formula: see text]. A sheaf theoretic proof of non-existence of corresponding [Formula: see text], the identity component of [Formula: see text], is due to Chiu [7] it is not known if this is strictly weaker. Our construction has the advantage of retaining the contact homological viewpoint of Eliashberg–Kim–Polterovich and its potential for application in prequantizations of other Liouville manifolds. It makes use of the [Formula: see text]-action generated by a vertical [Formula: see text]-shift but can also be related, for prequantized balls, to the [Formula: see text]-equivariant contact homology developed by Milin [16] in her proof of orderability of lens spaces.
Traditional Chinese Medicine, Food Therapy, and Hypertension Control: A Narrative Review of Chinese Literature
Authors: Zou Ping
Published: November 2016

Despite the lack of English literature about Traditional Chinese Medicine (TCM) food therapy, there is abundant Chinese literature about the application of food therapy for hypertension control. This paper summarizes basic concepts of TCM, the principles of food therapy and its application for hypertension control according to Chinese literature. In TCM, food is conceptualized according to both nutritional and functional aspects, and can be used to treat illnesses. Four principles of TCM food therapy including light eating, balancing the “hot” and “cold” nature of food, the harmony of the five flavors of food, and consistency between dietary intake and different health conditions, can be used to facilitate hypertension control. Based on a statistical analysis of antihypertensive foods recommended in 20 books on the application of food therapy for hypertension control, the 38 most frequently recommended are celery, tomato, banana, hawthorn, garlic, onion, seaweed, apple, corn, green beans, persimmon, laver, kiwi, watermelon, eggplant, carrots, mushroom, peanut, soy products, sea cucumber, buckwheat, garland chrysanthemum, spinach, honey, dairy products, vinegar, black fungus, jellyfish, green onion, shepherd's purse, soybean, potato, pear, winter melon, bitter melon, oat, pea, and tea. Food therapy emphasizes the therapeutic effects of food, considering its nature, taste, and function on human balanced health, which leads to optimal blood pressure control. Current literature suggests that food therapy is effective in blood pressure control and can be incorporated into blood pressure self-management in the Chinese population.
Conceptual design studies for a CEPC detector
Authors: Chekanov S. V. , Demarteau M.
Published: November 2016

The physics potential of the Circular Electron Positron Collider (CEPC) can be significantly strengthened by two detectors with complementary designs. A promising detector approach based on the Silicon Detector (SiD) designed for the International Linear Collider (ILC) is presented. Several simplifications of this detector for the lower energies expected at the CEPC are proposed. A number of cost optimizations of this detector are illustrated using full detector simulations. We show that the proposed changes will enable one to reach the physics goals at the CEPC.
The quadruple deformation effects of 9Be in heavy-ion reactions
Authors: Seyyedi S. A.
Published: November 2016

The effects of the projectile deformation and orientation on the total potential characteristic have been studied for the reactions between weakly bound nucleus, 9Be, as the projectile and different targets. In this paper, the double-folding model is used to calculate the nuclear potentials and deformation of projectile included. It is shown that applying the deformation effects can modify the potential barrier height and depth in the interior regions of the potential. It is also shown that the gradient variation of the potential barrier height is linearly increased when the angle between the projectile and the target nuclei increases. The rate of the variation is constant in different reactions with 9Be. In order to study the possible effect of these deformation dependent potentials, application is made in the calculation of cross-sections of the different reactions. It is observed that the deformation and orientation are of important role in the dynamics of such reactions and improve the agreement with the experimental results.
EFFICIENT GENERATION OF HYPERBOLIC PATTERNS FROM A SINGLE ASYMMETRIC MOTIF
Authors: CHEN NING , CHUNG K. W.
Published: November 2016

We present an efficient method of constructing hyperbolic patterns based on an asymmetric motif designed in the central hyperbolic polygon. Since there is no rotational symmetry in each hyperbolic polygon, a subset of the hyperbolic group elements has to be selected carefully so that the central hyperbolic polygon is transformed to the other polygons once and only once. An efficient labeling procedure is proved by considering the group presentation and can be easily implemented using the computer. Illustrative hyperbolic patterns are constructed from given asymmetric motifs for the symmetry group [[Formula: see text], [Formula: see text]][Formula: see text] which consists of all compositions of an even number of reflections.
Frequency Analysis of the Orbit Responses of Active Magnetic Bearings in Touchdown Using Hilbert Transform
Authors: Lyu Mindong , Wang Zixi , Liu Tao , Jia Xiaohong , Wang Yuming
Published: November 2016

Touchdown bearing (TDB) is one of the key elements in active magnetic bearings (AMBs). When the magnetic bearing fails or is exposed to an overload, touchdown events will occur. According to ISO 14839, three typical orbit responses (pendulum vibration, combined rub and bouncing, and full rub) can be detected in touchdown events. The magnitude of the dynamic forces between the rotor and TDBs has been considered as an indicator to identify these orbit responses. However, the contact forces may not be easy to measure with precision. The instantaneous frequency of the rotor vibration is another significant difference between them. In this paper, a performance analysis model has been established that considers the dynamic and thermal effects in touchdown events. Simulations under different working conditions have been conducted and a recommendation for safety working conditions of the AMB system has been developed. The instantaneous frequency of the rotor vibration has been computed using Hilbert transform and the frequency characteristics of the three orbit responses have been analyzed and discussed. The results reveal that the instantaneous frequency of the pendulum vibration is almost fixed. The instantaneous frequency of the combined rub and bouncing fluctuates vehemently in most cases. The instantaneous frequency of the backward whirl shows periodic regularity.
A note on the generalized hypercenter of a finite group
Authors: Murashka V. I.
Published: November 2016

Let [Formula: see text] be a formation, [Formula: see text] be a partition of the set of all primes into mutually disjoint subsets and [Formula: see text] be the formation of all [Formula: see text]-groups from [Formula: see text]. We found under what conditions the intersection of normalizers of all [Formula: see text]-maximal subgroups for all [Formula: see text] coincides with the [Formula: see text]-hypercenter of a finite group. As corollaries we obtained well-known results of R. Baer about the hypercenter of a finite group.
Preparation, Characterization, Electrical and Magnetic Properties of Mn-Doped Dilute Magnetic Semiconductors
Authors: Malik Samiksha , Mohite Komal , Naik Pranav , Tangsali R. B.
Published: November 2016

Nanoparticle dilute magnetic semiconductors (DMS) are becoming increasingly important due to their possible applications in spintronics, an emerging field where the conduction process in the materials is a spin-based process. Nanoparticles of Mn-doped ZnO (DMS) material with general formula Zn[Formula: see text]MnxO ([Formula: see text]) were prepared by opting single stage combustion synthesis process. The samples characterized, exhibited formation of monophasic nanoparticles of the sample with average particle size ranging between 17 nm to 23 nm. The calculations of energy bandgap made from UV absorption spectra showed variation of the bandgap from 2.18 eV to 2.32 eV. The magnetic measurements (VSM) made on the samples confirmed formation of a single diamagnetic (Zn[Formula: see text]Mn[Formula: see text]) and two namely (Zn[Formula: see text]Mn[Formula: see text]) (Zn[Formula: see text]Mn[Formula: see text]) paramagnetic samples. It is interesting to see that all the three magnetic profiles exhibit hysteresis type behavior both in diamagnetic form and paramagnetic form. The resistivity of the samples was of the order of 10[Formula: see text] Ohm-cm ([Formula: see text]-cm) at lower temperatures. Temperature-dependent resistivity curves exhibited peaking behavior for all the three samples which is very interesting. Temperature-dependent thermo-power profiles give an indication of [Formula: see text]-type semiconductor behavior with significantly deep and broad minima around 100[Formula: see text] which becomes sharper for sample with higher Mn concentration.
Simulation and Analysis of Strain Sensitivity of CNT-Based Strain Sensors
Authors: Sapra Gaurav , Vig Renu , Sharma Manu
Published: November 2016

Carbon nanotubes (CNT) is turning out to be a replacement to all the existing traditional sensors due to their high gauge factor, multidirectional sensing capability, high flexibility, low mass density, high dynamic range and high sensitivity to strains at nano and macro- scales. The strain sensitivity of CNT-based strain sensors depends on number of parameters; quality and quantity of CNT used, type of polymer used, deposition and dispersion technique adopted and also on environmental conditions. Due to all these parameters, the piezoresistive behavior of CNT is diversified and it needs to be explored. This paper theoretically analyses the strain sensitivity of CNT-based strain sensors. The strain sensitivity response of CNT strain sensor is a result of change in total resistance of CNT network with respect to applied strain. The total resistance of CNT network consists of intrinsic resistance and inter-tube resistance. It has been found that the change in intrinsic resistance under strain is due to the variation of bandgap of individual, which depends on the chirality of the tube and it varies exponentially with strain. The inter-tube resistance of CNT network changes nonlinearly due to change in distance between neighboring CNTs with respect to applied strain. As the distance [Formula: see text] between CNTs increases due to applied strain, tunneling resistance [Formula: see text] increases nonlinearly in exponential manner. When the concentration of CNTs in composite is close to percolation threshold, then the change of inter-tube resistances is more dominant than intrinsic resistance. At percolation threshold, the total resistance of CNT networks changes nonlinearly and this effect of nonlinearity is due to tunneling effect. The strain sensitivity of CNT-based strain sensors also varies nonlinearly with the change in temperature. For the change of temperature from [Formula: see text]C to 50[Formula: see text]C, there is more than 100% change in strain sensitivity of CNT/polymer composite strain sensor. This change is mainly due to the infiltration of polymer into CNTs.
Synthesis of Mesoporous Titania–Silica Monolith Composites — A Comprehensive Study on their Photocatalytic Degradation of Acid Blue 113 Dye Under UV Light
Authors: Thejaswini Thurlapathi VL , Prabhakaran Deivasigamani
Published: November 2016

The present work deals with the synthesis of bi-continuous macro and mesoporous crack-free titania–silica monoliths, with well-defined structural dimensions and high surface area. The work also highlights their potential photocatalytic environmental applications. The highly ordered titania–silica monoliths are synthesized through direct surface template method using organic precursors of silica and titania in the presence of surface directing agents such as pluronic P123 and PEG, under acetic acid medium. The monoliths are synthesized with different Ti/Si ratios to obtain monolithic designs that exhibit better photocatalytic activity for dye degradation. The titania–silica monoliths are characterized using XRD, SEM, EDAX, FT-IR, TG–DTA and BET analysis. The photocatalytic activity of the synthesized monoliths is tested on the photodegradation of a textile dye (acid blue 113). It is observed that the monolith with 7:3 ratio of Ti/Si showed significant photocatalysis behavior in the presence of UV light. The influence of various physico-chemical properties such as, solution pH, photocatalyst dosage, light intensity, dye concentration, effect of oxidants, etc. are analyzed and optimized using a customized photoreactor set-up. Under optimized conditions, the monoliths exhibited superior degradation kinetics, with the dye dissipation complete within 10[Formula: see text]min of photolysis. The mesoporous catalysts are recoverable and reusable up to four cycles of repeated usage.
Fabrication and Characterization of Polyvinylidene Fluoride Microfilms for Microfluidic Applications
Authors: Rao Yammani Venkat Subba , Raghavan Aravinda Narayanan , Viswanathan Meenakshi
Published: November 2016

The ability to create patterns of piezo responsive material on smooth substrate is an important method to develop efficient microfluidic mixers. This paper reports the fabrication of Poly vinylidene fluoride microfilms using spin-coating on smooth glass surface. The suitable crystalline phases, surface morphology and microstructural properties of the PVDF films have been investigated. We found that films of average thickness 10[Formula: see text][Formula: see text]m, had average roughness of 0.13[Formula: see text][Formula: see text]m. These PVDF films are useful in microfluidic mixer applications.
Accurate estimation of electrostatic binding energy with Poisson-Boltzmann equation solver DelPhi program
Authors: Li Anbang , Gao Kaifu
Published: November 2016

Poisson–Boltzmann (PB) model is a widely used implicit solvent approximation in biophysical modeling because of its ability to provide accurate and reliable PB electrostatic salvation free energies ([Formula: see text] as well as electrostatic binding free energy ([Formula: see text] estimations. However, a recent study has warned that the 0.5[Formula: see text]Å grid spacing which is normally adopted can produce unacceptable errors in [Formula: see text] estimation with the solvent excluded surface (SES) (Harris RC, Boschitsch AH and Fenley MO, Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation, J Chem Theory Comput 19: 3677–3685, 2013). In this work, we investigate the grid dependence of the widely used PB solver DelPhi v6.2 with molecular surface (MS) for estimating both electrostatic solvation free energies and electrostatic binding free energies. Our results indicate that, for the molecular complex and components the absolute errors of [Formula: see text] are smaller than that of [Formula: see text], and grid spacing of 0.8[Formula: see text]Å with DelPhi program ensures the accuracy and reliability of [Formula: see text]; however, the accuracy of [Formula: see text] largely relies on the order of magnitude of [Formula: see text] itself rather than that of [Formula: see text] or [Formula: see text]. Our findings suggest that grid spacing of 0.5[Formula: see text]Å is enough to produce accurate [Formula: see text] for molecules whose [Formula: see text] are large, but finer grids are needed when [Formula: see text] is very small.
α-Amino Thiophene on Si(100)2 × 1: Adsorption and transition states investigated by van der Waals corrected DFT and CI-NEB
Authors: Carbone Marilena
Published: November 2016

The adsorption of [Formula: see text]-AminoTiophene on Si(100)2[Formula: see text][Formula: see text][Formula: see text]1 was investigated by van der Waals corrected DFT and climbing image nudged-elastic band, in view of potential applications in silicon-based technologies. The overall scenario indicates that dissociative states are more favorable than the molecular ones, the one occurring through N–C bond breakage and Si–N and Si–C bond formation, having the largest adsorption energy (2.71[Formula: see text]eV). Furthermore, this configuration is also kinetically easily accessible, being connecting to one of the physisorbed states (Phys1) by a nearly barrierless transition. Also the molecular states are relatively easily kinetically accessible, with transition barriers from the corresponding physisorbed states in the 0.05–0.30[Formula: see text]eV range. At variance with this, the transitions to the dissociative state characterized by N–H bond breakage and Si–N and Si–H bond formation (N–H Diss) either from physisorbed or from molecular states are all significantly higher, i.e. in the 0.63–2.70[Formula: see text]eV range. Finally, the effects of the coverage on the adsorption energy were evaluated for the N–H Diss configuration and indicating a gain, whose extent depends both on the coverage and on the surface arrangement, i.e. whether cis or trans. The trend is different if the vdW forces are excluded.
An Improved Specified Finite Particle Method and Its Application to Transient Heat Conduction
Authors: Wang Lu , Xu Fei , Yang Yang
Published: November 2016

Compared with the traditional Smoothed Particle Hydrodynamics (SPH), Finite Particle Method (FPM) has higher accuracy for boundary region. However, there are still two inherent defects which are the time consuming and the numerical instability in FPM. In this paper, a high-order algorithm based on the Taylor series expansion and the matrix theory is proposed and the corresponding particles selected mode is discussed. It is validated that the algorithm has higher-order accuracy than the previous low-order improvement algorithm for FPM. Further, transient heat conduction examples have been discussed to verify the feasibility and effectiveness of the new algorithm.
Atomic Understanding of the Swelling and Phase Transition of Polyacrylamide Hydrogel
Authors: Xu Shuai , Wang Ying , Hu Jianying , Liu Zishun
Published: November 2016

A polymer network can imbibe copious amounts of solvent (water) and swell, and the resulting state is known as a hydrogel. In this study, we have made the modification for the all-atom consistent valence force field (CVFF) to investigate the swelling property of polyacrylamide (PAM) hydrogel by molecular dynamics simulation. We have built 21 hydrogel models with different solvent contents and calculate the average chemical potential and diffusion coefficient of solvent molecules in PAM hydrogel. We find that when the mass fraction of solvent is about 90%, PAM hydrogel reaches its free swelling limitation and loses the motivation of absorbing solvent. Furthermore, it is also found that PAM hydrogel has a phase transition phenomenon when the values of solvent chemical potential are between [Formula: see text][Formula: see text]kcal/mol and [Formula: see text][Formula: see text]kcal/mol. This study will provide insight into the basic parameters which are widely used in continuum mechanics analysis of hydrogels from atomic point of view and help researchers to improve the continuum mechanics model for neutral hydrogel.
A general framework for the benchmark pricing in a fully collateralized market
Authors: Fujii Masaaki , Takahashi Akihiko
Published: November 2016

Collateralization with daily margining has become a new standard in the post-crisis market. Although there appeared vast literature on a so-called multi-curve framework, a complete picture of a multi-currency setup with cross-currency basis can be rarely found since our initial attempts. This work gives its extension regarding a general framework of interest rates in a fully collateralized market. It gives a new formulation of the currency funding spread which is better suited for the general dependence. In the last half, it develops a discretization of the HJM framework with a fixed tenor structure, which makes it implementable as a traditional Market Model.
Optimal pairs trading with time-varying volatility
Authors: Li Thomas Nanfeng , Tourin Agnès
Published: November 2016

In this paper, we propose a pairs trading model that incorporates a time-varying volatility of the constant elasticity of variance type. Our approach is based on stochastic control techniques; given a fixed time horizon and a portfolio of two cointegrated assets, we define the trading strategies as the portfolio weights maximizing the expected power utility from terminal wealth. We compute the optimal pairs strategies by using a finite difference method. Finally, we illustrate our results by conducting tests on historical market data at daily frequency. The parameters are estimated by the generalized method of moments.
Loss of glutaredoxin 3 impedes mammary lobuloalveolar development during pregnancy and lactation
Authors: Pham Khanh , Dong Jie , Jiang Xiqian , Qu Ying , Yu Han , Yang Yisheng , Olea Walter , Marini Juan C. , Chan Lawrence , Wang Jin , Wehrens Xander H. T. , Cui Xiaojiang , Li Yi , Hadsell Darryl L. , Cheng Ninghui
Published: November 2016

Mammalian glutaredoxin 3 (Grx3) has been shown to be important for regulating cellular redox homeostasis in the cell. Our previous studies indicate that Grx3 is significantly overexpressed in various human cancers including breast cancer and demonstrate that Grx3 controls cancer cell growth and invasion by regulating reactive oxygen species (ROS) and NF-κB signaling pathways. However, it remains to be determined whether Grx3 is required for normal mammary gland development and how it contributes to epithelial cell proliferation and differentiation in vivo. In the present study, we examined Grx3 expression in different cell types within the developing mouse mammary gland (MG) and found enhanced expression of Grx3 at pregnancy and lactation stages. To assess the physiological role of Grx3 in MG, we generated the mutant mice in which Grx3 was deleted specifically in mammary epithelial cells (MECs). Although the reduction of Grx3 expression had only minimal effects on mammary ductal development in virgin mice, it did reduce alveolar density during pregnancy and lactation. The impairment of lobuloalveolar development was associated with high levels of ROS accumulation and reduced expression of milk protein genes. In addition, proliferative gene expression was significantly suppressed with proliferation defects occurring in knockout MECs during alveolar development compared with wild-type controls. Therefore, our findings suggest that Grx3 is a key regulator of ROS in vivo and is involved in pregnancy-dependent mammary gland development and secretory activation through modulating cellular ROS.