bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of the tumour‐suppressor maspin in temporal bone carcinoma
Authors: Marioni Gino , Zanoletti Elisabetta , Stritoni Paola , Lionello Marco , Giacomelli Luciano , Gianatti Andrea , Cattaneo Laura , Blandamura Stella , Mazzoni Antonio , Martini Alessandro
Published: March 2013

Aims

Although it accounts for fewer than 0.2% of all head and neck tumours, temporal bone squamous cell carcinoma (SCC) is an aggressive malignancy with a poor prognosis in advanced cases. Novel therapeutic strategies should be developed focusing on specific targeted therapies. Maspin is a serpin showing tumour‐suppressing activity which has therapeutic potential. The present study is the first to investigate maspin expression in temporal bone SCCs, using a series of 29 cases.

Methods and results

Cytoplasmic maspin expression was significantly higher in the group of patients whose SCC did not recur than in the group experiencing recurrences (P = 0.029), and in G1–G2 SCCs than in G3 cases (P = 0.001). cT correlated with recurrence rate (P = 0.05), disease‐free survival (DFS) (P = 0.008) and disease‐specific survival (DSS) (P = 0.0043), and pT and pathological regional lymph node status correlated with recurrence rate (P = 0.008 and P = 0.03, respectively), DFS (P = 0.017 and P = 0.0049, respectively) and DSS (P = 0.008 and P = 0.0009, respectively).

Conclusions

Although further studies using larger series are required, our preliminary findings suggest that cytoplasmic maspin expression has promise as a prognostic indicator of disease recurrence in temporal bone SCC, and that reactivating maspin functions in association with apoptosis‐inducing or anti‐angiogenic chemotherapeutic agents might be an important goal in the treatment of temporal bone SCC.
An analysis of PLAG1 and HMGA2 rearrangements in salivary duct carcinoma and examination of the role of precursor lesions
Authors: Bahrami Armita , Perez‐Ordonez Bayardo , Dalton James D , Weinreb Ilan
Published: March 2013

Aims

Salivary duct carcinoma (SDC) often arises in pleomorphic adenoma (PA). Putative precursors, including low‐grade cribriform cystadenocarcinoma (LGCCC) and ductal carcinoma in‐situ (DCIS), are more controversial. Rearrangement of PLAG1 or HMGA2 is seen in 50–70% of PAs, but this has not been investigated in SDC. Using a large collection of SDCs from a single institution, we aimed to study these genes by fluorescence in‐situ hybridization (FISH), and to correlate the presence of precursor lesions/intraductal proliferations with gene alterations.

Methods and results

Forty‐four SDCs were stained for smooth muscle actin, CK14, and p63, and examined with PLAG1 and HMGA2 FISH. Eight cases were SDC ex‐PA; ten had a hyalinized nodule (HN), which is suspicious for PA; six arose in association with LGCCC; and twenty were ‘de‐novo’ SDCs. Ten cases had PLAG1 rearrangement/amplification (22.7%) and eight had HMGA2 (18.2%) rearrangement/amplification. The positive cases were four SDC ex‐PAs, eight SDCs with an HN, and five ‘de‐novo’ SDCs. Twenty‐three SDC ex‐PAs were present in total (52.3%). All six SDC ex‐LGCCCs were FISH‐negative. Myoepithelial staining surrounded all LGCCCs, and demonstrated DCIS in 17 cases. Eleven DCIS lesions were in SDC ex‐PAs or FISH‐positive ‘de‐novo’ SDCs. These cases represent ‘cancerization’ of ducts. Only six FISH‐negative ‘de‐novo’ SDCs showed DCIS.

Conclusions

A large proportion of SDCs arise in PAs (with or without residual evidence of a PA). A small proportion of SDCs arise in LGCCCs. Cases showing DCIS often represent cancerization.
TMPRSS2–ERG rearrangement in dominant anterior prostatic tumours: incidence and correlation with ERG immunohistochemistry
Authors: Gopalan Anuradha , Leversha Margaret A , Dudas Maria E , Maschino Alexandra C , Chang Jeremy , Al‐Ahmadie Hikmat A , Chen Ying‐Bei , Tickoo Satish K , Reuter Victor E , Fine Samson W
Published: March 2013

Aim

To study prostate cancer zonal differences in TMPRSS2–ERG gene rearrangement.

Methods and results

We examined 136 well‐characterized dominant anterior prostatic tumours, including 61 transition zone (TZ) and 75 anterior peripheral zone (PZ) lesions, defined using strict anatomical considerations. TMPRSS2–ERG FISH and ERG protein immunohistochemistry were performed on tissue microarrays. FISH results, available for 56 TZ and 71 anterior PZ samples, were correlated with ERG staining and TZ‐associated ‘clear cell’ histology. Fewer TZ cancers (four of 56; 7%) were rearranged than anterior PZ cancers (18 of 71; 25%) (P = 0.009); deletion was the sole mechanism of TZ cancer rearrangement. ERG protein overexpression was present in 4% (two of 56; both FISH+) and 30% (21 of 71; 17 FISH+) of TZ and anterior PZ tumours, respectively. ‘Clear cell’ histology was present in 21 of 56 (38%) TZ and eight of 71 (11%) anterior PZ tumours. Seven per cent of cancers with and 21% without this histology had rearrangement, regardless of zonal origin.

Conclusions

TMPRSS2–ERG rearrangement occurs in dominant TZ and anterior PZ prostate cancers, with all rearranged TZ cancers in this cohort showing deletion. ERG immunohistochemistry demonstrated excellent sensitivity (86%) and specificity (96%) for TMPRSS2–ERG rearrangement. TMPRSS2–ERG fusion is rare in TZ tumours and present at a low frequency in tumours displaying ‘clear cell’ histology.
Worldwide transmission and seasonal variation of pandemic influenza A(H1N1)2009 virus activity during the 2009–2010 pandemic
Authors: Storms Aaron D. , Van Kerkhove Maria D. , Azziz‐Baumgartner Eduardo , Lee Wing‐Kei , Widdowson Marc‐Alain , Ferguson Neil M. , Mounts Anthony W.
Published: March 2013

Background

Seasonal influenza activity varies with geography and time of year.

Objective

To describe how pandemic influenza A(H1N1)2009 [A(H1N1)pdm09] activity varied during the 2009–2010 pandemic.

Methods

We analyzed influenza virological data compiled by the World Health Organization from June 2009–August 2010. We calculated weekly proportions of A(H1N1)pdm09‐positive specimens out of all A(H1N1)pdm09‐positive specimens detected during the study period for each country. We compared parameters of pandemic activity (e.g., peak A[H1N1]pdm09 weekly proportion [peak activity], number of weeks between the 5th and 95th percentiles of A(H1N1)pdm09 cumulative weekly proportion [duration of activity]) between countries in temperate and tropical–subtropical regions. We quantified the proportion of A(H1N1)pdm09 out of all influenza A specimens by country and correlated it with countries' central latitudes.

Results

We analyzed data from 80 countries (47 temperate, 33 tropical–subtropical). The median proportion of cases identified during the peak week was higher in temperate (0·12) than in tropical–subtropical (0·09) regions (P < 0·01). The median duration of activity was longer in tropical–subtropical (27 weeks) than in temperate countries (20 weeks) (P < 0·01). In most temperate countries (98%), peak pandemic activity occurred during the fall–winter period. There was a positive correlation between country central latitude and proportion of A(H1N1)pdm09 out of all influenza A specimens (r: 0·76; P < 0·01).

Conclusions

The transmission of A(H1N1)pdm09 exhibited similarities with seasonal influenza transmission in that activity varied between temperate and tropical–subtropical countries and by time of year. Our findings suggest the potential utility of accounting for these factors during future pandemic planning.
Using the palaeontological record of Microtus to test species distribution models and reveal responses to climate change
Authors: McGuire Jenny L. , Davis Edward Byrd
Published: March 2013

Aim

We used newly identified fossil specimens to reconstruct the Quaternary distributions of five Microtus species (Rodentia: Arvicolinae) from the Pacific coast of the United States. We used these distributions to test the hypothesis that when projected onto past, alternative climate surfaces, species distribution models (SDMs) created using only climate variables are concordant with the empirical data of fossil Microtus species occurrences.

Location

Specimens from 11 fossil localities in California, Oregon and Nevada were identified and evaluated.

Methods

Geometric morphometrics and discriminant analyses were used to identify fossil Microtus specimens. Using a maximum‐entropy modelling approach, the best model for all five species was selected using the Akaike information criterion. Nineteen bioclimate variables were used to create SDMs for the five Microtus species using both Community Climate System Model (CCSM) and Model for Interdisciplinary Research on Climate (MIROC) models.

Results

We confidently identified 144 Microtus fossils, including the first fossil specimens of Microtus oregoni and Microtus townsendii. SDMs reconstructed approximately half the extralimital fossil occurrences (i.e. those found outside the present‐day range). Those species with extralimital occurrences not reconstructed have niche models primarily influenced by precipitation variables. The two species whose extralimitals were well predicted occupy indistinguishable climatic niches.

Main conclusions

The ranges of Pacific coast Microtus species have undergone substantial regional contractions since the Last Glacial Maximum (LGM; 21 ka). Inconsistencies between LGM SDMs and Quaternary fossil ranges indicate potential problems with LGM precipitation reconstructions, although interspecific interactions are also likely to contribute to these differences. Overall, the study highlights the need for further, detailed, species‐level palaeodistributions to put recent observations in a broader temporal context and examine the effectiveness of SDMs coupled with climate models for predicting range dynamics under scenarios of climate change.
A COLLECTION OF SURVEYS ON MARKET EXPERIMENTS
Authors: Noussair Charles N. , Tucker Steven
Published: March 2013

This paper highlights the contributions in this special issue to the very large and rapidly growing research on experimental markets. It contains ten surveys of different streams of research in this area including asset markets, contests, environmental policy, frictions, general equilibrium, labor markets, multi‐unit auctions, oligopoly markets, and prediction markets.
Effects of reclining posture on velopharyngeal closing pressure during swallowing and phonation
Authors: Nakayama E. , Tohara H. , Hiraba H. , Sanpei R. , Wakasa H. , Ohno S. , Kumakura A. , Gora K. , Abe K. , Ueda K.
Published: March 2013

Velopharyngeal closure plays an important role in preventing air pressure leakage during swallowing and phonation from oropharynx to nasopharynx. Levator veli palatini muscle activity is influenced by oral and nasal air pressure, volume of the swallow bolus and postural changes. However, it is unclear how velopharyngeal closing pressure is affected by reclining posture. The purpose of this study was to investigate the effects of reclining posture on velopharyngeal closing pressure during swallowing and phonation. Nine healthy male volunteers (age range, 27−34 years) participated in this study. Velopharyngeal closing pressure during a dry swallow, a 5‐mL liquid swallow, a 5‐mL honey‐thick liquid swallow and phonations of /P∧/ and /K∧/ were evaluated in an upright posture and at reclining postures of 60° and 30°. A manometer catheter was inserted transnasally onto the soft palate, and each trial was repeated three times. A solid‐state manometer catheter with an intra‐luminal transducer was used to evaluate the amplitude and duration of each trial, and data were statistically analysed. Average amplitudes during dry and liquid swallows were significantly lower in reclining postures compared with the upright posture, but the amplitude was not significantly different during the thick liquid swallow. Average durations were not affected by postural changes. The amplitudes during phonations were lower in reclining postures, but the differences were not significant. Velopharyngeal closure is significantly affected by reclining posture. This suggests that velopharyngeal closing pressure may be adjusted according to afferent inputs, such as reclining posture and bolus viscosity.
Patient satisfaction with mini‐implant stabilised full dentures. A 1‐year prospective study
Authors: Tomasi C. , Idmyr B.‐O. , Wennström J. L.
Published: March 2013

The purpose of this study was to evaluate patient‐centred outcomes with regard to function and comfort after placement of mini‐implants for stabilisation of complete dentures. The trial was designed as a prospective cohort of 12‐months duration and involved 21 subjects in the age of 50–90 years having a full denture in the maxilla or the mandible with poor stability during function. Flapless installation of 2–4 narrow‐body Dentatus Atlas® implants was performed and retention for the existing denture was obtained by the use of a silicone‐based soft lining material (Tuf‐Link®). Patients' judgement of perceived satisfaction with function and comfort of the dentures was recorded at baseline, 1‐ and 12‐months post‐treatment using 10‐centimetre visual analogue scales (VAS) and a questionnaire. Clinical examination of the conditions of the peri‐implant soft tissues was performed at 12 months. Nineteen of the 21 patients were available for the 12‐month follow‐up examination. The two drop‐out subjects lost all implants within 1 month and rejected retreatment. Further six subjects lost 1–2 implants, but were sucessfully retreated by insertion of new implants. Overall satisfaction, chewing and speaking comfort were all markedly improved from pre‐treatment median VAS scores of around 4–5 to median scores of 9·0–10 (10 = optimal) at the final examination. The prevalence of positive answers to questions regarding stability/function of the denture increased significantly to almost 100% for all questions. Treatment involving maxillary dentures and the use of short implants (7–10 mm) was associated with an increased risk of implant failure. The results indicate that placement of mini‐implants as retentive elements for full dentures with poor functional stability has a marked positive impact on the patients' perception of oral function and comfort as well as security in social life.
Molecular Analysis of ORF6, ORF7 and ORF8 of Beet yellows virus Iranian Isolate
Authors: Tabejamaat Zahra , Massah Amir , Ahoonmanesh Ali
Published: March 2013

Beet yellows virus (BYV), a member of the Closteroviridae family, is one of the most important sugar beet yellowing viruses. The nine ORFs of BYV genome encode different proteins required for BYV life cycle. We sequenced a part of the genome of BYV Iranian isolate consisting of ORF6, ORF7 and ORF8. The primer pair BYVA/Z was used for amplification of this region in RT‐PCR. The amplicon (1615 bp) was cloned and sequenced. Comparisons showed the amplified segment is corresponding to ORF6, ORF7 and ORF8 of BYV genome encoding coat protein, p20 and p21 proteins, respectively. The ORF7 of BYV Iranian isolate overlaps with ORF6 and ORF8 in four and 26 nucleotides at 5′ and 3′ ends, respectively. The ORF7 of Iranian isolate of BYV was sequenced completely. However, approximately 24 nt. from the beginning of ORF6 and 23 nt. from end of ORF8, including the stop codon, were not determined. ORF6, ORF7 and ORF8 showed the highest similarity at nucleotide (98.3, 99.4 and 99.2%) and amino acid (97.4, 98.9 and 100%) sequence levels, with BYV Ukrainian isolate. Phylogenetic analysis of the deduced amino acid sequences of ORF6, ORF7 and ORF8 revealed closer relationship of Iranian isolate of BYV with BYV Ukrainian isolate than other BYV isolates available at GenBank.
Growth conditions determine different melatonin levels in Lupinus albus L
Authors: Arnao Marino B. , Hernández‐Ruiz Josefa
Published: March 2013

Melatonin, an indoleamine, which has recently been assigned several roles in plant physiology as a growth promoter, as rooting agent, and as antioxidant in senescence delay and cytoprotection, seems to have a relevant function in plant stress situations. The presence of melatonin increases the resistance of lupin plant tissues (Lupinus albus L.) against natural or artificially induced adverse situations. In this work, we studied the response of lupin plants in controlled stress situations (drought‐, anaerobic‐, pH‐, and cold stress and using ZnSO4, NaCl, and H2O2 as chemical stressors) and measured the changes in endogenous melatonin levels in lupin plants. Also, the effect of abscisic acid, ethylene, and natural environmental conditions were evaluated. In general, nearly all stressful factors caused an increase in melatonin in the investigated organs. The chemical stress provoked by ZnSO4 or NaCl caused the most pronounced changes in the endogenous level of melatonin, followed by cold and drought stressors. In some cases, the level of melatonin increased 12‐fold with respect to the levels in control plants, indicating that melatonin biosynthesis is upregulated in common stress situations, in which it may serve as a signal molecule and/or as a direct antistress agent due to its well‐known antioxidative properties.
Melatonin improves insulin sensitivity independently of weight loss in old obese rats
Authors: Zanuto Ricardo , Siqueira‐Filho Mário A. , Caperuto Luciana C. , Bacurau Reury F. P. , Hirata Emiko , Peliciari‐Garcia Rodrigo A. , do Amaral Fernanda Gaspar , Marçal Anderson C. , Ribeiro Luciene M. , Camporez João P. G. , Carpinelli Ângelo Rafael , Bordin Silvana , Cipolla‐Neto José , Carvalho Carla R. O.
Published: March 2013

In aged rats, insulin signaling pathway (ISP) is impaired in tissues that play a pivotal role in glucose homeostasis, such as liver, skeletal muscle, and adipose tissue. Moreover, the aging process is also associated with obesity and reduction in melatonin synthesis from the pineal gland and other organs. The aim of the present work was to evaluate, in male old obese Wistar rats, the effect of melatonin supplementation in the ISP, analyzing the total protein amount and the phosphorylated status (immunoprecipitation and immunoblotting) of the insulin cascade components in the rat hypothalamus, liver, skeletal muscle, and periepididymal adipose tissue. Melatonin was administered in the drinking water for 8‐ and 12 wk during the night period. Food and water intake and fasting blood glucose remained unchanged. The insulin sensitivity presented a 2.1‐fold increase both after 8‐ and 12 wk of melatonin supplementation. Animals supplemented with melatonin for 12 wk also presented a reduction in body mass. The acute insulin‐induced phosphorylation of the analyzed ISP proteins increased 1.3‐ and 2.3‐fold after 8‐ and 12 wk of melatonin supplementation. The total protein content of the insulin receptor (IR) and the IR substrates (IRS‐1, 2) remained unchanged in all investigated tissues, except for the 2‐fold increase in the total amount of IRS‐1 in the periepididymal adipose tissue. Therefore, the known age‐related melatonin synthesis reduction may also be involved in the development of insulin resistance and the adequate supplementation could be an important alternative for the prevention of insulin signaling impairment in aged organisms.
Fresh and preserved green fodder modify effects of urinary acidifiers on urine pH of horses
Authors: Goren G. , Fritz J. , Dillitzer N. , Hipp B. , Kienzle E.
Published: March 2013

Hay stabilises urine pH in horses. It is unknown whether this is an effect of structure or of chemical composition. In this study, four ponies (230–384 kg body weight [BW]) were fed six different diets with either a structure or a composition similar to hay with and without acidifiers in a cross‐over experimental design in amounts to maintain body weight with the following main compounds: Fresh grass (GRASS), alfalfa hay (ALF), grass cobs (COBS), grass silage (SIL), straw (STR) or extruded straw (STRe) for 2 to 10 days. Urine pH was measured in all trials, blood pH, blood base excess and bicarbonate as well as mineral balance were determined in GRASS, ALF, STR and STRe. In the trials with straw and extruded straw, urine pH decreased significantly (STR control: 7.8 ± 0.23, acidifier: 5.2 ± 0.38) when acidifiers were added, whereas in all other diets that were based on fresh or preserved green fodder, pH did not decrease below 7. Blood pH was similarly affected by diet and acidifiers. Acidifiers had little effect on the pre‐prandial blood pH, only in diet STR there was a significant reduction in relation to control. Post‐prandial blood pH was significantly reduced by acidifiers in all diets. Blood bicarbonate and base excess showed corresponding effects. Faecal and renal mineral excretion and apparent mineral digestibility were not systematically affected by diet or acidifiers except for chloride. Chloride added as inorganic chloride salt had an even better apparent digestibility than chloride originating from feed. Because only green plant material stabilised acid base balance, chlorophyll and its metabolites are discussed as potential mediators of the effect of green fodder on acid base balance.
A redescription of morphologically similar species from the genus Euglena:E. laciniata, E. sanguinea, E. sociabilis, and E. splendens1
Authors: Karnkowska‐Ishikawa Anna , Milanowski Rafał , Triemer Richard E. , Zakryś Bożena
Published: March 2013

Euglena sanguinea (Ehrenberg 1831) was one of the first green euglenoid species described in the literature. At first, the species aroused the interest of researchers mainly due to the blood‐red color of its cells, which, as it later turned out, is not a constant feature. Complicated chloroplast morphology, labeled by Pringsheim as the “peculiar chromatophore system”, made the correct identification of the species difficult, which is the reason why, throughout the 20th century, new species resembling E. sanguinea were continually being named due to a lack of suitable diagnostic features to distinguish E. sanguinea. Interest in E. sanguinea has returned in recent years, following findings that the species can produce ichthyotoxins. This was followed by the need to classify E. sanguinea correctly, which was achieved through the verification of morphological and molecular data for all species similar to E. sanguinea. As the result of the analysis, the number of species sharing some morphological similarities with E. sanguinea could be reduced from 12, as described in the literature, to four, with established epitypes and updated diagnostic descriptions. The most important diagnostic features included: the presence of mucocysts (i.e., whether they were visible before and/or after staining), the number of chloroplasts, the size of the double‐sheathed pyrenoids, and the presence of the large paramylon grain in the vicinity of the stigma. Moreover, sequence analysis revealed the presence of unusually long SSU rDNA sequences in E. sanguinea. Previously, SSU rDNA sequences of such length were known to be present in primary osmotrophic euglenoids.
SRNAome parsing yields insights into tomato fruit ripening control
Authors: Zuo Jinhua , Fu Daqi , Zhu Yi , Qu Guiqin , Tian Huiqin , Zhai Baiqiang , Ju Zheng , Gao Chao , Wang Yunxiang , Luo Yunbo , Zhu Benzhong
Published: March 2013

Small RNAs have emerged as critical regulators in the expression and function of eukaryotic genomes at the post‐transcriptional level. To elucidate the functions of microRNA (miRNAs) and endogenous small‐interfering RNAs (siRNAs) in tomato fruit ripening process, the deep sequencing and bioinformatics methods were combined to parse the small RNAs landscape in three fruit‐ripening stages (mature green, breaker and red‐ripe) on a whole genome. Two species‐specific miRNAs and two members of TAS3 family were identified, 590 putative phased small RNAs and 125 cis‐natural antisense (nat‐siRNAs) were also found in our results which enriched the tomato small RNAs repository and all of them showed differential expression patterns during fruit ripening. A large amount of the targets of the small RNAs were predicted to be involved in fruit ripening and ethylene pathway. Furthermore, the promoters of the conserved and novel miRNAs were found to contain the conserved motifs of TATA‐box and CT microsatellites which were also found in Arabidopsis and rice, and several species‐specific motifs were found in parallel.
C4 plants use fluctuating light less efficiently than do C3 plants: a study of growth, photosynthesis and carbon isotope discrimination
Authors: Kubásek Jiří , Urban Otmar , Šantrůček Jiří
Published: March 2013

Plants in the field are commonly exposed to fluctuating light intensity, caused by variable cloud cover, self‐shading of leaves in the canopy and/or leaf movement due to turbulence. In contrast to C3 plant species, only little is known about the effects of dynamic light (DL) on photosynthesis and growth in C4 plants. Two C4 and two C3 monocot and eudicot species were grown under steady light or DL conditions with equal sum of daily incident photon flux. We measured leaf gas exchange, plant growth and dry matter carbon isotope discrimination to infer CO2 bundle sheath leakiness in C4 plants. The growth of all species was reduced by DL, despite only small changes in steady‐state gas exchange characteristics, and this effect was more pronounced in C4 than C3 species due to lower assimilation at light transitions. This was partially attributed to increased bundle sheath leakiness in C4 plants under the simulated lightfleck conditions. We hypothesize that DL leads to imbalances in the coordination of C4 and C3 cycles and increasing leakiness, thereby decreasing the quantum efficiency of photosynthesis. In addition to their other constraints, the inability of C4 plants to efficiently utilize fluctuating light likely contributes to their absence in such environments as forest understoreys.
C‐Reactive Protein Triggers Calcium Signalling in Human Neutrophilic Granulocytes via FcγRIIa in an Allele‐Specific Way
Authors: Aas V. , Sand K. L. , Åsheim H.‐C. , Benestad H. B. , Iversen J.‐G.
Published: March 2013

C‐reactive protein (CRP) binds to Fcγ‐receptors, FcγRIIa (CD32) with high affinity and to FcγRIa (CD64) with low affinity. The binding to CD32 has been shown to be allele specific, that is, it binds to R/R131 but not to H/H131. Little is known about the cooperation of CRP and neutrophilic granulocytes (PMNs) in inflammatory reactions. The purpose of the present study was to examine CRP signalling in human PMNs, and whether this signalling is also allele specific. Cytosolic calcium of PMN was measured in a single‐cell digital imaging system. Receptor expression and polymorphism were studied by real‐time RT‐PCR, flow cytometry and standard PCR. C‐reactive protein induced cytosolic calcium signals in PMNs from homozygote R/R131donors, but not in PMNs from heterozygote R/H131 donors. However, after the heterozygote PMNs had been incubated with IFN‐γ (100 U/ml) for 2 h, both the proportion of cells responding and the size of the CRP‐induced calcium signals increased. IFN‐γ increased mRNA expression of CD64 about fivefold and surface protein expression of CD64 about fourfold. The calcium signal elicited by CRP was augmented by PMN adhesion to fibronectin, but almost totally abrogated by sphingosine kinase inhibitors. The signals were partly dependent on calcium influx. In conclusion, calcium signalling instigated by CRP in human PMN is FcγRIIa allele specific, as R/R131 responded to CRP, whereas R/H131 did not. However, increased expression of FcγRIa (CD64), stimulated by IFN‐γ, can augment calcium signalling by CRP in low‐responders. This suggests that the state of the PMNs, as well as the genetic origin, affect sensitivity for CRP.
Distinct Functions of Nuclear Distribution Proteins LIS1, Ndel1 and NudCL in Regulating Axonal Mitochondrial Transport
Authors: Shao Chong‐Yu , Zhu Jia , Xie Ya‐Jun , Wang Zheng , Wang Ya‐Nan , Wang Yin , Su Li‐Da , Zhou Liang , Zhou Tian‐Hua , Shen Ying
Published: March 2013

Neurons critically depend on the long‐distance transport of mitochondria. Motor proteins kinesin and dynein control anterograde and retrograde mitochondrial transport, respectively in axons. The regulatory molecules that link them to mitochondria need to be better characterized. Nuclear distribution (Nud) family proteins LIS1, Ndel1 and NudCL are critical components of cytoplasmic dynein complex. Roles of these Nud proteins in neuronal mitochondrial transport are unknown. Here we report distinct functions of LIS1, Ndel1 and NudCL on axonal mitochondrial transport in cultured hippocampal neurons. We found that LIS1 interacted with kinsein family protein KIF5b. Depletion of LIS1 enormously suppressed mitochondrial motility in both anterograde and retrograde directions. Inhibition of either Ndel1 or NudCL only partially reduced retrograde mitochondrial motility. However, knocking down both Ndel1 and NudCL almost blocked retrograde mitochondrial transport, suggesting these proteins may work together to regulate retrograde mitochondrial transport through linking dynein‐LIS1 complex. Taken together, our results uncover novel roles of LIS1, Ndel1 and NudCL in the transport of mitochondria in axons.
Admissible Finite-Time Stability and Stabilization of Uncertain Discrete Singular Systems
Authors: Xue Wenping , Mao Weijie
Published: March 2013

The problems of admissible finite-time stability (AFTS) and admissible finite-time stabilization for a class of uncertain discrete singular systems are addressed in this study. The definition of AFTS is first given. Second, a sufficient condition for the AFTS of the nominal unforced system is established, which is further extended to the uncertain case. Then, a sufficient condition is proposed for the design of a state feedback controller such that the closed-loop system is admissibly finite-time stable for all admissible uncertainties. Both the AFTS and the controller design conditions are presented in terms of linear matrix inequalities (LMIs) with a fixed parameter. Finally, two numerical examples are provided to illustrate the effectiveness of the developed theory.
On Exponential Flocking to the Virtual Leader in Network of Agents With Double-Integrator Dynamics
Authors: Tavafoghi Jahromi Hamidreza , Haeri Mohammad
Published: March 2013

This paper considers flocking to the virtual leader in network of agents with double-integrator. A locally linear algorithm is employed which guarantees exponential flocking to the virtual leader. A lower bound for flocking rate is calculated which is independent of the initial conditions. Simulations are provided to validate the result and it is shown that the calculated rate is not over bound the actual convergence rate. The effect of coefficients of algorithm is investigated and it is shown that the similar results can be inferred from the calculated formula for the convergence rate.
Minimum Maneuver Time Calculation Using Convex Optimization
Authors: Timings Julian P. , Cole David J.
Published: March 2013

The problem of calculating the minimum lap or maneuver time of a nonlinear vehicle, which is linearized at each time step, is formulated as a convex optimization problem. The formulation provides an alternative to previously used quasi-steady-state analysis or nonlinear optimization. Key steps are: the use of model predictive control; expressing the minimum time problem as one of maximizing distance traveled along the track centerline; and linearizing the track and vehicle trajectories by expressing them as small displacements from a fixed reference. A consequence of linearizing the vehicle dynamics is that nonoptimal steering control action can be generated, but attention to the constraints and the cost function minimizes the effect. Optimal control actions and vehicle responses for a 90 deg bend are presented and compared to the nonconvex nonlinear programming solution.
Piecewise Polynomial Control Parameterization in the Direct Solution of Optimal Control Problems
Authors: Fabien Brian C.
Published: March 2013

This paper describes an algorithm for the direct solution of a class of optimal control problems. The algorithm is based on approximating the unknown control inputs via a finite dimensional parameterization. Specific control approximations that are implemented include (i) piecewise constant, (ii) piecewise linear, or (iii) piecewise cubic polynomials. The cubic approximation presented here is believed to be new. Another novel feature of the algorithm is that the state equations are approximated using single step Runge–Kutta methods on a fixed mesh. The parameterized optimal control problem is solved using a sequential quadratic programming technique. The paper presents examples to illustrate the convergence behavior of the various control parameterization schemes.
Robust Joint Position Feedback Control of Robot Manipulators
Authors: Hsiao Tesheng , Weng Mao-Chiao
Published: March 2013

Most manipulator motion controllers require joint velocity feedback. Whenever joint velocities are not measurable, they are estimated from the joint positions. However, velocity estimates tend to be inaccurate under low-speed motion or low sensor resolution conditions. Moreover, velocity estimators may either be susceptible to model uncertainties or introduce additional dynamics (e.g., phase lag) to the control loop. Consequently, direct substitution of velocity estimates into the controller results in the deterioration of the control performance and robustness margin. Therefore, this paper proposes a robust position-feedback motion controller which gets rid of the problems of uncompensated dynamics and model uncertainties introduced by velocity estimators. Furthermore, a globally asymptotically stable system, which is robust with respective to model parameter variations, is guaranteed. Theoretical analysis and experimental verifications are carried out. The results demonstrate that the proposed controller is robust and outperforms the conventional computed torque plus proportional integral differential (PID) controller.
Mountain Pine Beetles Colonizing Historical and Naïve Host Trees Are Associated with a Bacterial Community Highly Enriched in Genes Contributing to Terpene Metabolism
Authors: Adams Aaron S. , Aylward Frank O. , Adams Sandye M. , Erbilgin Nadir , Aukema Brian H. , Currie Cameron R. , Suen Garret , Raffa Kenneth F.
Published: March 2013

The mountain pine beetle,
Dendroctonus ponderosae
, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of
D. ponderosae
to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with
D. ponderosae
beetles and their galleries from their historical host,
Pinus contorta
, and their more recent host, hybrid
P. contorta-Pinus banksiana
. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera
Pseudomonas
,
Rahnella
,
Serratia
, and
Burkholderia
, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.
Development of a Reverse Transcription-Quantitative PCR Assay for Detection of Salivirus/Klassevirus
Authors: Haramoto Eiji , Kitajima Masaaki , Otagiri Mikie
Published: March 2013

A broadly reactive and highly sensitive reverse transcription-quantitative PCR assay to detect salivirus/klassevirus was developed. By means of the developed assay, salivirus/klassevirus was detected in 13 (93%) raw sewage, 4 (29%) secondary-treated sewage, and 9 (16%) river water samples, with a maximum concentration of 9.7 × 10
6
copies/liter.
Biochemical Diversity of Carboxyl Esterases and Lipases from Lake Arreo (Spain): a Metagenomic Approach
Authors: Mart�nez-Mart�nez M�nica , Alcaide Mar�a , Tchigvintsev Anatoli , Reva Oleg , Polaina Julio , Bargiela Rafael , Guazzaroni Mar�a-Eugenia , Chicote �lvaro , Canet Albert , Valero Francisco , Rico Eguizabal Eugenio , Guerrero Mar�a del Carmen , Yakunin Alexander F. , Ferrer Manuel
Published: March 2013

The esterases and lipases from the α/β hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity, and activities. Here, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of Lake Arreo, an evaporite karstic lake in Spain (42�46′N, 2�59′W; altitude, 655 m). Together with oligonucleotide usage patterns and BLASTP analysis, our study of esterases/lipases mined from Lake Arreo suggests that its sediment contains moderately halophilic and cold-adapted proteobacteria containing DNA fragments of distantly related plasmids or chromosomal genomic islands of plasmid and phage origins. This metagenome encodes esterases/lipases with broad substrate profiles (tested over a set of 101 structurally diverse esters) and habitat-specific characteristics, as they exhibit maximal activity at alkaline pH (8.0 to 8.5) and temperature of 16 to 40�C, and they are stimulated (1.5 to 2.2 times) by chloride ions (0.1 to 1.2 M), reflecting an adaptation to environmental conditions. Our work provides further insights into the potential significance of the Lake Arreo esterases/lipases for biotechnology processes (i.e., production of enantiomers and sugar esters), because these enzymes are salt tolerant and are active at low temperatures and against a broad range of substrates. As an example, the ability of a single protein to hydrolyze triacylglycerols, (non)halogenated alkyl and aryl esters, cinnamoyl and carbohydrate esters, lactones, and chiral epoxides to a similar extent was demonstrated.
Detection of Escherichia coli O104 in the Feces of Feedlot Cattle by a Multiplex PCR Assay Designed To Target Major Genetic Traits of the Virulent Hybrid Strain Responsible for the 2011 German Outbreak
Authors: Paddock Z. D. , Bai J. , Shi X. , Renter D. G. , Nagaraja T. G.
Published: March 2013

A multiplex PCR was designed to detect
Escherichia coli
O104:H4, a hybrid pathotype of Shiga toxigenic and enteroaggregative
E. coli
, in cattle feces. A total of 248 fecal samples were tested, and 20.6% were positive for serogroup O104. The O104 isolates did not carry genes characteristic of the virulent hybrid strain.
Culture-Independent Analysis of Aerosol Microbiology in a Metropolitan Subway System
Authors: Robertson Charles E. , Baumgartner Laura K. , Harris J. Kirk , Peterson Kristen L. , Stevens Mark J. , Frank Daniel N. , Pace Norman R.
Published: March 2013

The goal of this study was to determine the composition and diversity of microorganisms associated with bioaerosols in a heavily trafficked metropolitan subway environment. We collected bioaerosols by fluid impingement on several New York City subway platforms and associated sites in three sampling sessions over a 1.5-year period. The types and quantities of aerosolized microorganisms were determined by culture-independent phylogenetic analysis of small-subunit rRNA gene sequences by using both Sanger (universal) and pyrosequencing (bacterial) technologies. Overall, the subway bacterial composition was relatively simple; only 26 taxonomic families made up ∼75% of the sequences determined. The microbiology was more or less similar throughout the system and with time and was most similar to outdoor air, consistent with highly efficient air mixing in the system. Identifiable bacterial sequences indicated that the subway aerosol assemblage was composed of a mixture of genera and species characteristic of soil, environmental water, and human skin commensal bacteria. Eukaryotic diversity was mainly fungal, dominated by organisms of types associated with wood rot. Human skin bacterial species (at 99% rRNA sequence identity) included the
Staphylococcus
spp.
Staphylococcus epidermidis
(the most abundant and prevalent commensal of the human integument),
S. hominis
,
S. cohnii
,
S. caprae
, and
S. haemolyticus
, all well-documented human commensal bacteria. We encountered no organisms of public health concern. This study is the most extensive culture-independent survey of subway microbiota so far and puts in place pre-event information required for any bioterrorism surveillance activities or monitoring of the microbiological impact of recent subway flooding events.
Repetitive, Marker-Free, Site-Specific Integration as a Novel Tool for Multiple Chromosomal Integration of DNA
Authors: Petersen Kia Vest , Martinussen Jan , Jensen Peter Ruhdal , Solem Christian
Published: March 2013

We present a tool for repetitive, marker-free, site-specific integration in
Lactococcus lactis
, in which a nonreplicating plasmid vector (pKV6) carrying a phage attachment site (
attP
) can be integrated into a bacterial attachment site (
attB
). The novelty of the tool described here is the inclusion of a minimal bacterial attachment site (

attB
min

), two mutated
loxP
sequences (
lox66
and
lox71
) allowing for removal of undesirable vector elements (antibiotic resistance marker), and a counterselection marker (
oroP
) for selection of
loxP
recombination on the pKV6 vector. When transformed into
L. lactis
expressing the phage TP901-1 integrase, pKV6 integrates with high frequency into the chromosome, where it is flanked by
attL
and
attR
hybrid attachment sites. After expression of Cre recombinase from a plasmid that is not able to replicate in
L. lactis
,
loxP
recombinants can be selected for by using 5-fluoroorotic acid. The introduced

attB
min

site can subsequently be used for a second round of integration. To examine if
attP
recombination was specific to the
attB
site, integration was performed in strains containing the
attB
,
attL
, and
attR
sites or the
attL
and
attR
sites only. Only
attP-attB
recombination was observed when all three sites were present. In the absence of the
attB
site, a low frequency of
attP-attL
recombination was observed. To demonstrate the functionality of the system, the xylose utilization genes (
xylABR
and
xylT
) from
L. lactis
strain KF147 were integrated into the chromosome of
L. lactis
strain MG1363 in two steps.
Enzymatic Synthesis of Novel Phloretin Glucosides
Authors: Pandey Ramesh Prasad , Li Tai Feng , Kim Eun-Hee , Yamaguchi Tokutaro , Park Yong Il , Kim Joong Su , Sohng Jae Kyung
Published: March 2013

A UDP-glycosyltransferase from
Bacillus licheniformis
was exploited for the glycosylation of phloretin. The
in vitro
glycosylation reaction confirmed the production of five phloretin glucosides, including three novel glucosides. Consequently, we demonstrated the application of the same glycosyltransferase for the efficient whole-cell biocatalysis of phloretin in engineered
Escherichia coli
.
Prevalence and Genetic Characterization of Toxoplasma gondii in Bats in Myanmar
Authors: Sun Hongchao , Wang Yiyin , Zhang Yingguang , Ge Wei , Zhang Fuqiang , He Biao , Li Zuosheng , Fan Quanshui , Wang Wei , Tu Changchun , Li Jiping , Liu Quan
Published: March 2013

We detected
Toxoplasma gondii
in 29.3% (95% confidence interval [CI], 25.5% to 33.1%) of 550 insectivorous bats collected in Myanmar. The genotyping of these positive samples revealed they were closely related to or belong to clonal type I, which is highly virulent in mice, showing that these bats are potential reservoirs for
T. gondii
transmission.
Effects of Bartonella spp. on Flea Feeding and Reproductive Performance
Authors: Morick Danny , Krasnov Boris R. , Khokhlova Irina S. , Gutiérrez Ricardo , Fielden Laura J. , Gottlieb Yuval , Harrus Shimon
Published: March 2013

Numerous pathogens are transmitted from one host to another by hematophagous insect vectors. The interactions between a vector-borne organism and its vector vary in many ways, most of which are yet to be explored and identified. These interactions may play a role in the dynamics of the infection cycle. One way to evaluate these interactions is by studying the effects of the tested organism on the vector. In this study, we tested the effects of infection with
Bartonella
species on fitness-related variables of fleas by using
Bartonella
sp. strain OE 1-1,
Xenopsylla ramesis
fleas, and
Meriones crassus
jirds as a model system. Feeding parameters, including blood meal size and metabolic rate during digestion, as well as reproductive parameters, including fecundity, fertility, and life span, were compared between fleas experimentally infected with
Bartonella
and uninfected fleas. In addition, the developmental time, sex ratio, and body size of F
1
offspring fleas were compared between the two groups. Most tested parameters did not differ between infected and uninfected fleas. However, F
1
males produced by
Bartonella-
positive females were significantly smaller than F
1
males produced by
Bartonella
-negative female fleas. The findings in this study suggest that bartonellae are well adapted to their flea vectors, and by minimally affecting their fitness they have evolved to better spread themselves in the natural environment.
Effect of Soil Slope on the Appearance of Mycobacterium avium subsp. paratuberculosis in Water Running off Grassland Soil after Application of Contaminated Slurry
Authors: Salgado M. , Alfaro M. , Salazar F. , Troncoso E. , Mitchell R. M. , Ramirez L. , Naguil A. , Zamorano P. , Collins M. T.
Published: March 2013

The study assessed the effect of soil slope on
Mycobacterium avium
subsp.
paratuberculosis
transport into rainwater runoff from agricultural soil after application of
M. avium
subsp.
paratuberculosis
-contaminated slurry. Under field conditions, 24 plots of undisturbed loamy soil 1 by 2 m
2
were placed on platforms. Twelve plots were used for water runoff: 6 plots at a 3% slope and 6 plots at a 15% slope. Half of the plots of each slope were treated with
M. avium
subsp.
paratuberculosis
-contaminated slurry, and half were not treated. Using the same experimental design, 12 plots were established for soil sampling on a monthly basis using the same spiked slurry application and soil slopes. Runoff following natural rainfall was collected and analyzed for
M. avium
subsp.
paratuberculosis
, coliforms, and turbidity.
M. avium
subsp.
paratuberculosis
was detected in runoff from all plots treated with contaminated slurry and one control plot. A higher slope (15%) increased the likelihood of
M. avium
subsp.
paratuberculosis
detection but did not affect the likelihood of finding coliforms. Daily rainfall increased the likelihood that runoff would have coliforms and the coliform concentration, but it decreased the
M. avium
subsp.
paratuberculosis
concentration in the runoff. When there was no runoff, rain was associated with increased
M. avium
subsp.
paratuberculosis
concentrations. Coliform counts in runoff were related to runoff turbidity.
M. avium
subsp.
paratuberculosis
presence/absence, however, was related to turbidity. Study duration decreased bacterial detection and concentration. These findings demonstrate the high likelihood that
M. avium
subsp.
paratuberculosis
in slurry spread on pastures will contaminate water runoff, particularly during seasons with high rainfall.
M. avium
subsp.
paratuberculosis
contamination of water has potential consequences for both animal and human health.