bluuebunny/crossref_metadata_2025 huggingface dataset:
Penetration depth of MgB2 measured using Josephson junctions and SQUIDs
Authors: Cunnane Daniel , Zhuang Chenggang , Chen Ke , Xi X. X. , Yong Jie , Lemberger T. R.
Published: February 2013

The penetration depth of MgB2 was measured using two methods of different mechanisms. The first method used MgB2 Josephson junctions and the magnetic field dependence of the junction critical current. The second method deduced the penetration depth from the inductance of a MgB2 microstrip used to modulate the voltage of a MgB2 DC SQUID. The two methods showed a consistent value of the low-temperature penetration depth for MgB2 to be about 40 nm. Both the small penetration depth value and its temperature dependence are in agreement with a microscopic theory for MgB2 in the clean limit.
Note: Electrochemical etching of silver tips in concentrated sulfuric acid
Authors: Hodgson P. A. , Wang Y. , Mohammad A. Awez , Kruse P.
Published: February 2013

Sharp metal tips have many uses, including in scanning probe microscopy. Silver is a particularly interesting metal for plasmonic enhancement, e.g., in tip-enhanced Raman spectroscopy, however few methods for the production of silver tips have been explored. A simple and reliable one step dc electrochemical method for the production of sharp silver tips in concentrated H2SO4 is presented. The optimal conditions are 10 V cell voltage and 99% sulfuric acid for tip radii below 100 nm. A LabView program was written to control the cut-off of the circuit to within a millisecond to avoid blunting the tips after drop-off.
A higher proportion of female lambs when ewes were fed oats and cottonseed meal prior to and following conception
Authors: Gulliver C. E. , Friend M. A. , King B. J. , Wilkins J. F. , Clayton E. H.
Published: February 2013

Diets high in omega-6 (n-6) fatty acids in mice have been associated with a higher proportion of female offspring, however, the specific effects of dietary fatty acids on the sex ratio of sheep has not previously been reported. The aim of the present study was to determine whether feeding ewes a diet differing in n-6 for 6 weeks before and 3 weeks following conception would increase the proportion of female lambs born. Merino × Border Leicester ewes (n = 296) were allocated to receive either a diet high in n-6 (70% oat grain, 8% cottonseed meal, High n-6 diet) or, a control diet low in n-6 (88% legume silage, Low n-6 diet), for 42 or 53 days before and 17 days after conception, using a stratified block randomisation procedure based on body condition score and liveweight. Following synchronisation, oestrus was detected daily during natural mating with rams. After mating, all ewes grazed improved pastures as one group until lambing. Plasma n-6 concentrations were greater (P < 0.001), the time to parturition was shorter (P < 0.001) and the proportion of female offspring was higher (58.2 vs 43.5%, P = 0.010) when ewes were fed the High n-6 diet compared with the Low n-6 diet. Further research is required to determine whether the observed differences in sex ratio were due to specific alterations in n-6 fatty acids, or other differences in the diets not specifically related to n-6 such as saturated fat or energy density.
Fluvial contributions of nutrient salts, dissolved trace elements and organic carbon to the sea by pristine temperate rivers (SW Europe)
Authors: Bernárdez P. , Ospina-Alvarez N. , Caetano M. , Prego R.
Published: February 2013

Environmental context We report the baseline levels of dissolved nutrients, organic matter and metals in the main temperate rivers draining the three Northern Galicia rias. Because the rivers are pristine, these rias are little affected by anthropogenic inputs, and their properties reflect the lithological characteristics of the rivers’ watersheds. Useful information in the development of European and global initiatives for assessing anthropogenic inputs to estuarine, coastal and open-sea environments has been provided. Abstract A summary of the water characteristics of the rivers Sor, Mera and Landro that drain into the Northern Galician Rias (NW Iberian Peninsula) is presented. The analysis was based on fortnightly monitoring during 2008, for major and minor chemical elements in the dissolved phase (Al, As, Cd, Co, Cu, Fe, Mn, Mo, Ni, Pb, U, V, Zn), nutrients (nitrate, nitrite, ammonium, phosphate, silicate), suspended particulate matter, chlorophyll-a and tracers of water quality chemistry (dissolved inorganic nitrogen and carbon). The data cover rivers not urban, agriculturally or industrially affected. Continental inputs of the material via rivers into the Northern Galician Rias were measured and annual fluxes of the dissolved chemical elements to the rias were calculated. In spite of the high variability in water flow, this study provides a good estimate of the overall amounts of nutrients and dissolved elements discharged to pristine ria systems.
Sensory adaptation as optimal resource allocation
Authors: Gepshtein Sergei , Lesmes Luis A. , Albright Thomas D.
Published: February 2013

Visual adaptation is expected to improve visual performance in the new environment. This expectation has been contradicted by evidence that adaptation sometimes decreases sensitivity for the adapting stimuli, and sometimes it changes sensitivity for stimuli very different from the adapting ones. We hypothesize that this pattern of results can be explained by a process that optimizes sensitivity for many stimuli, rather than changing sensitivity only for those stimuli whose statistics have changed. To test this hypothesis, we measured visual sensitivity across a broad range of spatiotemporal modulations of luminance, while varying the distribution of stimulus speeds. The manipulation of stimulus statistics caused a large-scale reorganization of visual sensitivity, forming the orderly pattern of sensitivity gains and losses. This pattern is predicted by a theory of distribution of receptive field characteristics in the visual system.
Contractible polyhedra in products of trees and absolute retracts in products of dendrites
Authors: Melikhov Sergey , Zaja̧c Justyna
Published: February 2013

We show that a compact

n
n

-polyhedron PL embeds in a product of

n
n

trees if and only if it collapses onto an

(
n
−
1
)

(n-1)

-polyhedron. If the

n
n

-polyhedron is contractible and

n
≠
3

n\ne 3

(or

n
=
3

n=3

and the Andrews–Curtis Conjecture holds), the product of trees may be assumed to collapse onto the image of the embedding.

In contrast, there exists a

2
2

-dimensional compact absolute retract

X
X

such that

X
×

I
k

X\times I^k

does not embed in any product of

2
+
k

2+k

dendrites for each

k
k

.
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields
Authors: Indio Valentina , Martelli Pier Luigi , Savojardo Castrense , Fariselli Piero , Casadio Rita
Published: February 2013

Motivation: Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins.

Results: We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low–false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available.

Availability: The TPpred datasets are available at http://biocomp.unibo.it/∼valentina/TPpred/. TPpred is available on request from the authors.

Contact:  gigi@biocomp.unibo.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Making automated multiple alignments of very large numbers of protein sequences
Authors: Sievers Fabian , Dineen David , Wilm Andreas , Higgins Desmond G.
Published: February 2013

Motivation: Recent developments in sequence alignment software have made possible multiple sequence alignments (MSAs) of >100000 sequences in reasonable times. At present, there are no systematic analyses concerning the scalability of the alignment quality as the number of aligned sequences is increased.

Results: We benchmarked a wide range of widely used MSA packages using a selection of protein families with some known structures and found that the accuracy of such alignments decreases markedly as the number of sequences grows. This is more or less true of all packages and protein families. The phenomenon is mostly due to the accumulation of alignment errors, rather than problems in guide-tree construction. This is partly alleviated by using iterative refinement or selectively adding sequences. The average accuracy of progressive methods by comparison with structure-based benchmarks can be improved by incorporating information derived from high-quality structural alignments of sequences with solved structures. This suggests that the availability of high quality curated alignments will have to complement algorithmic and/or software developments in the long-term.

Availability and implementation: Benchmark data used in this study are available at http://www.clustal.org/omega/homfam-20110613-25.tar.gz and http://www.clustal.org/omega/bali3fam-26.tar.gz.

Contact:  fabian.sievers@ucd.ie

Supplementary information:  Supplementary data are available at Bioinformatics online.
Rotavirus Vaccination in Central Europe
Authors: Mészner Zsófia , Anca Ioana , André Francis , Chlibek Roman , Čižman Milan , Grzesiowski Paweł , Mangarov Atanas , Pokorn Marko , Prymula Roman , Richter Darko , Salman Nuran , Šimurka Pavol , Tamm Eda , Tešović Goran , Urbancikova Ingrid , Usonis Vytautas , Zavadska Dace ,   Central European Vaccine Awareness Group (CEVAG)
Published: February 2013

Each year, rotavirus (RV) infection is the leading cause of acute gastroenteritis requiring hospitalisation and of nosocomially transmitted diseases in children younger than 5 years across Central European Vaccination Awareness Group (CEVAG) countries; however, inadequate surveillance systems and lack of routine RV testing still exist in most CEVAG countries, making it difficult to accurately assess the present burden of acute RV gastroenteritis in the younger population. Furthermore, routine immunisation of infants with RV vaccines has not been implemented, and no official and uniform recommendations exist in most of the countries in these territories. The present study provides CEVAG country‐specific estimates of the disease burden of RV gastroenteritis among the youngest population and presents evidence‐based advice on the use of RV vaccines in the region, while providing a framework for vaccination at the national level.
Pediatric Celiac Disease, Cryptogenic Hypertransaminasemia, and Autoimmune Hepatitis
Authors: Vajro Pietro , Paolella Giulia , Maggiore Giuseppe , Giordano Giuseppe
Published: February 2013

Objective:

The association between celiac disease (CD) and liver disease in pediatrics is widely recognized, but its prevalence is unknown. This study aims to conduct a systematic review and meta‐analysis to evaluate the prevalence of CD in children with cryptogenic persistent hypertransaminasemia (HTS) or autoimmune hepatitis (AIH), and vice versa.

Methods:

We searched MEDLINE/PubMed, the Cochrane Library, Web of Science, and MD Consult from 1977 to May 2012 for studies reporting either CD and HTS or AIH. Pooled prevalences with 95% confidence intervals (CI) and relative risk (RR) were calculated.

Results:

Nine studies (2046 patients) were identified. Pooled prevalences of CD in children with mild, nonspecific cryptogenic persistent HTS and vice versa were 12.0% (95% CI 4.17–29.96) and 36.0% (95% CI 32.15–40.11), respectively. A gluten‐free diet normalized transaminase levels in 77% to 100% of patients with CD within 4 to 8 months. Pooled prevalences of CD in children with AIH and vice versa were 6.3% (95% CI 3.87–11.73) and 1.4% (95% CI 0.84–2.15), respectively. The RR of HTS in children with CD versus the general population, and of CD in children with HTS was 6.55 (95% CI 5.65–7.60) and 11.59 (95% CI 3.80–35.33), respectively. The corresponding RR of AIH in children with CD was 188.54 (95% CI 92.23–385.43). The RR of CD in children with AIH was 6.63 (95% CI 3.86–11.40).

Conclusions:

CD is associated with elevated transaminase levels in about one‐third of newly diagnosed children. Cryptogenic persistent HTS may signal gluten‐dependent nonspecific mild hepatitis (12.0% of cases) or more rarely (6.3%) severe CD‐related autoimmune hepatopathy. RRs confirm these trends in the considered associations.
Phylogenetic association of fluoroquinolone and cephalosporin resistance of D-O1-ST648 Escherichia coli carrying bla
CMY-2 from faecal samples of dogs in Japan
Authors: Sato Toyotaka , Yokota Shin-ichi , Okubo Torahiko , Usui Masaru , Fujii Nobuhiro , Tamura Yutaka
Published: February 2013

This study aimed to investigate the genetic association between fluoroquinolone (FQ) and/or cephalosporin (CEP) resistance in Escherichia coli isolates from dogs, and the risk to human health. We characterized E. coli clinical isolates, derived from faecal samples of dogs attending veterinary hospitals, using phylogenetic grouping, determination of virulence factor (VF) prevalence, multilocus sequence typing (MLST) and O serotyping. The D group was the dominant phylogenetic group among strains resistant to FQ and/or CEP. In contrast, the dominant group among susceptible strains was group B2. Group D strains showed a significantly higher prevalence of VFs than strains belonging to groups A and B1, and were resistant to significantly more antimicrobials than group B2 strains. The phylogenetic distribution of FQ–CEP-resistant E. coli groups (FQ–CEPRECs) and FQ-resistant groups was significantly correlated (r = 0.98), but FQ–CEPRECs and CEP-resistant E. coli groups were not correlated (r = 0.58). Data from PFGE, O serotype and MLST analyses indicated that the majority of FQ-resistant strains derived from a particular lineage of phylogenetic group D: serotype O1 and sequence type (ST) 648. Some D-O1-ST648 strains carried bla
CMY-2, showed multidrug resistance and possessed a higher prevalence of the VFs kspMT, ompT and PAI compared with other group D strains. Our data indicate that the emergence of FQ-CEP-resistant E. coli is based primarily on FQ-resistant E. coli. Moreover, as strains of the D-O1-ST648 lineage have been found in clinical isolates derived from humans at a relatively high frequency, our findings indicate that the spreading of D-O1-ST648 strains may cause serious difficulties in both veterinary and human clinical fields in the future.
Physical Modeling of Fold‐and‐Thrust Belt Evolution and Triangle Zone Development: Dabashan Foreland Belt (Northeast Sichuan basin, China) as an Example
Authors: Ruirui WANG , Yueqiao ZHANG , Guoai XIE
Published: February 2013

Triangle zones, generally found in foreland fold‐and‐thrust belts, serve as favorable objects of petroleum exploration. Taking the Dabashan foreland belt as an example, we studied the formation and development of triangle zones, and investigated the effect of décollements and the mechanical contrast of lithology by employing the method of physical modeling. Four experimental models were conducted in the work. The results showed that ‘sand wedges’ grew episodically, recorded by deformational length, height and slope angle. The height versus shortening rate presented an S‐shape curve, and uplifting occurred successively in the direction of the foreland belt. During the formation of the triangle zone, layer‐parallel shortening took place at the outset; deformation decoupling then occurred between the upper and lower brittle layers, divided by a middle‐embedded silicone polymers layer. The upper brittle layers deformed mainly by folding, while the lower sand layers by thrusting. As shortening continued, the geometry of a triangle zone was altered. We consider that the triangle zone in the Dabashan foreland belt was modified from an early one based on available seismic profiles and the experimental results. In addition, décollements and mechanical contrast impose significant influence on structural development, which can directly give rise to structural discrepancies. More décollements and obvious mechanical contrast between brittle layers can promote the coupling between the upper and lower brittle layers. Basal décollement controls the whole deformation and decreases the slope angle of the wedge, while roof décollement determines whether a triangle zone can be formed.
Groundwater Flow Simulation and its Application in Groundwater Resource Evaluation in the North China Plain, China
Authors: Jingli SHAO , Ling LI , Yali CUI , Zhaoji ZHANG
Published: February 2013

The purpose of this study is to establish a 3D groundwater flow modelling for evaluating groundwater resources of the North China Plain. First, the North China Plain was divided into three aquifers vertically through a characterization of hydrogeological conditions. Groundwater model software GMS was used for modeling to divide the area of simulation into a regular network of 164 rows and 148 lines. This model was verified through fitting of the observed and the simulated groundwater flow Gelds at deep and shallow layers and comparison between the observed and simulated hydrographs at 64 typical observation wells. Furthermore, water budget analysis was also performed during the simulation period (2002–2003). Results of the established groundwater flow model showed that the average annual groundwater recharge of the North China Plain during 1991 to 2003 was 256.68×108 m3/yr with safe yield of groundwater resources up to 213.49×108 m3/yr, in which safe yield of shallow groundwater and that of deep groundwater was up to 191.65×108 m3/yr and 22.64×108 m3/yr respectively. Finally, this model was integrated with proposal for groundwater withdrawal in the study area after commencement of water supply by South‐North Water Transfer Project, aiming to predict the changing trend of groundwater regime. As indicated by prediction results, South‐North Water Transfer Project, which is favorable for effective control of expansion and intensification of existing depression cone, would play a positive role in alleviation of short supply of groundwater in the North China Plain as well as maintenance and protection of groundwater.
Application of the Engineering‐Geological Conditions in Land‐Use Plans in the Petrvald Region (Czech Republic)
Authors: MARSCHALKO Marian , YILMAZ Işık , BEDNARIK Martin , KUBEČKA Karel , BOUCHAL Tomáš
Published: February 2013

The objective of this paper is to demonstrate necessity to inform relevant parties about engineering‐geological conditions for various practical purposes, especially including appropriate land‐use planning. However, the relationship between relevant geological information and the geological environment is vital for foundation engineering purposes, especially where demanding structures are involved. This information is most conveniently structured when accumulated information concerning engineering‐geological zones is utilized. This necessarily includes knowledge of rock workability and also of the pre‐Quaternary bedrock, and these characteristics were then related to the current built‐up area and future development according to the land‐use plans in a case study are from the Petrvald Region (Czech Republic). The geological environment of area has been severely influenced by anthropogenic effects of deep black coal mining. Results of this research showed that future development should be founded on spoil banks, dumps, and settling basins. According to the land‐use plan, this zone occupies 44.9% of the area of interest, and its materials predominantly emanate from mining in the Ostrava–Karvina Coal District. For future foundation structures planned there, it is imperative to consult detailed engineering‐geological study. However, attention to and reliance on this necessity is not reflected in the existing land‐use plan.
Avoiding fishy growth curves
Authors: Pardo Sebastián A. , Cooper Andrew B. , Dulvy Nicholas K.
Published: February 2013

Somatic growth is a fundamental property of living organisms, and is of particular importance for species with indeterminate growth that can change in size continuously throughout their life. For example, fishes can increase in size by 2–6 orders of magnitude during their lifetime, resulting in changes in production, consumption and function at the ecosystem scale. Within species, growth rates are traded off against other life‐history parameters, hence an accurate description of growth is essential to understand the comparative demography, productivity, fisheries yield and extinction risk of populations and species.

The growth trajectory of indeterminate growing sharks and rays (elasmobranchs) and bony fishes (teleosts) is usually modelled using a three‐parameter logarithmic function, the von Bertalanffy growth function (VBGF), to describe the total length of the average individual at any given age. Recently, however, a two‐parameter form has gained popularity. Rather than being estimated in the model fitting process, the third y‐intercept parameter (L0) of theVBGFhas been interpreted as being biologically equivalent to, and thus fixed as, the empirically estimated size at birth.

We tested the equivalence assumption thatL0is the same or similar to size at birth by comparing empirical estimates of size at birth available from the literature with estimates ofL0from published data from elasmobranchs, and found that even though there is an overlap of values, there is a high degree of variability between them.

We calculate the bias in the growth coefficient (k) of theVBGFby comparison between the two‐ and three‐parameter estimation methods. We show that slight deviations in fixedL0can cause considerable bias in growth estimates in the two‐parameterVBGFwhile providing no benefit even whenL0matches the true value. We show that the effect of this biased growth estimate has profound consequences for fisheries stock status.

We strongly recommend the use of the three‐parameterVBGFand discourage use of the two‐parameterVBGFbecause it results in substantially biased growth estimates even with slight variations in the value of fixedL0.
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
Authors: Zhan Aibin , Hulák Martin , Sylvester Francisco , Huang Xiaoting , Adebayo Abisola A. , Abbott Cathryn L. , Adamowicz Sarah J. , Heath Daniel D. , Cristescu Melania E. , MacIsaac Hugh J.
Published: February 2013

Concerns regarding the rapid loss of endemic biodiversity, and introduction and spread of non‐indigenous species, have focused attention on the need and ability to detect species present in communities at low abundance. However, detection of rare species poses immense technical challenges, especially for morphologically cryptic species, microscopic taxa and those beneath the water surface in aquatic ecosystems.

Next‐generation sequencing technology provides a robust tool to assess biodiversity, especially for detection of rare species. Here, we assess the sensitivity of 454 pyrosequencing for detection of rare species using known indicator species spiked into existing complex plankton samples. In addition, we develop universal small subunit ribosomal DNA primers for amplification of a wide range of taxa for detailed description of biodiversity in complex communities.

A universality test of newly designed primers for the hypervariable V4 region of the nuclear small subunit ribosomal DNA (V4‐nSSU) using a plankton sample collected from Hamilton Harbor showed that 454 pyrosequencing based on this universal primer pair can recover a wide range of taxa, including animals, plants (algae), fungi, blue‐green algae and protists.

A sensitivity test showed that 454 pyrosequencing based on newly designed universal V4‐nSSU primers was extremely sensitive for detection of very rare species. Pyrosequencing was able to recover spiked indicator species with biomass percentage as low as approximately 2·3 × 10−5% when 24 artificially assembled samples were tagged and sequenced in one PicoTiter plate (i.e. sequencing depth of an equivalent of 1/24 PicoTiter plate). In addition, spiked rare species were sometimes recovered as singletons (i.e. Operational Taxonomic Units represented by a single sequence), suggesting that at least some singletons are informative for recovering unique lineages in ‘rare biospheres’.

The method established here allows biologists to better investigate the composition of aquatic communities, especially for detection of rare taxa. Despite a small‐scale pyrosequencing effort, we demonstrate the extreme sensitivity of pyrosequencing using rare species spiked into plankton samples. We propose that the method is a powerful tool for detection of rare native and/or alien species.
Glacier thermal regime linked to processes of annual moraine formation at Midtdalsbreen, southern Norway
Authors: Reinardy Benedict T. I. , Leighton Iain , Marx Peter J.
Published: February 2013

Glacier thermal regime is shown to have a significant influence on the formation of ice‐marginal moraines. Annual moraines at the margin of Midtdalsbreen are asymmetrical and contain sorted fine sediment and diamicton layers dipping gently up‐glacier. The sorted fine sediments include sands and gravels that were initially deposited fluvially directly in front of the glacier. Clast‐form data indicate that the diamictons have a mixed subglacial and fluvial origin. Winter cold is able to penetrate through the thin (<10 m) ice margin and freeze these sediments to the glacier sole. During winter, sediment becomes elevated along the wedge‐shaped advancing glacier snout before melting out and being deposited as asymmetrical ridges. These annual moraines have a limited preservation potential of ∼40 years, and this is reflected in the evolution of landforms across the glacier foreland. Despite changing climatic conditions since the Little Ice Age and particularly within the last 10 years when frontal retreat has significantly speeded up, glacier dynamics have remained relatively constant with moraines deposited via basal freeze‐on, which requires stable glacier geometry. While the annual moraines on the eastern side of Midtdalsbreen indicate a slow steady retreat, the western foreland contains contrasting ice‐stagnation topography, highlighting the importance of local forcing factors such as shielding, aspect and debris cover in addition to changing climate. This study indicates that, even in temperate glacial environments, restricted or localised areas of cold‐based ice can have a significant impact on the geomorphic imprint of the glacier system and may actually be more widespread within both modern and ancient glacial environments than previously thought.
The impact of policy measures and coaching on the availability and accessibility of early child care: A longitudinal study
Authors: Vandenbroeck Michel , Geens Naomi , Berten Hans
Published: February 2013

We conducted a study of changes in the availability, accessibility and enrolment of children from low‐income, single‐parent and ethnic minority families in early child care centres. The study was carried out in Brussels which offers unique possibilities to study accessibility in a context in which quality and costs are controlled across centres. A survey on access policies in 89 day care centres, and on 150 mothers regarding their search process, was complemented by two focus groups attended by centre directors. The results were compared with data from a similar study we conducted in 2005. The results show that while inequality in availability has remained, centre directors' awareness of social priority criteria has changed, resulting in a significant increase in the enrolment of children from single‐parent and ethnic minority families, and – to a lesser extent – an increase in the enrolment of children from low‐income families. The results support the hypothesis that policy measures, combined with support, can influence inequalities in enrolment rates.
Differential protease activity augments polyphagy in Helicoverpa armigera
Authors: Chikate Y. R. , Tamhane V. A. , Joshi R. S. , Gupta V. S. , Giri A. P.
Published: February 2013

Helicoverpa armigera (Lepidoptera: Noctuidae) and other polyphagous agricultural pests are extending their plant host range and emerging as serious agents in restraining crop productivity. Dynamic regulation, coupled with a diversity of digestive and detoxifying enzymes, play a crucial role in the adaptation of polyphagous insects. To investigate the functional intricacy of serine proteases in the development and polyphagy of H. armigera, we profiled the expression of eight trypsin‐like and four chymotrypsin‐like phylogenetically diverse mRNAs from different life stages of H. armigera reared on nutritionally distinct host plants. These analyses revealed diet‐ and stage‐specific protease expression patterns. The trypsins expressed showed structural variations, which might result in differential substrate specificity and interaction with inhibitors. Protease profiles in the presence of inhibitors and their mass spectrometric analyses revealed insight into their differential activity. These findings emphasize the differential expression of serine proteases and their consequences for digestive physiology in promoting polyphagy in H. armigera.
Significance of hepatitis B virus core‐related antigen and covalently closed circular DNA levels as markers of hepatitis B virus re‐infection after liver transplantation
Authors: Matsuzaki Toshihisa , Tatsuki Ichikawa , Otani Masashi , Akiyama Motohisa , Ozawa Eisuke , Miuma Satoshi , Miyaaki Hisamitsu , Taura Naota , Hayashi Tomayoshi , Okudaira Sadayuki , Takatsuki Mitsuhisa , Isomoto Hajime , Takeshima Fuminao , Eguchi Susumu , Nakao Kazuhiko
Published: February 2013

Background and Aim

Currently, hepatitis B virus (HBV) re‐infection after liver transplantation (LT) can be almost completely suppressed by the administration of HBV reverse transcriptase inhibitors and hepatitis B immunoglobulins. However, after transplantation, there is no indicator of HBV replication because tests for the serum hepatitis B surface antigen and HBV‐DNA are both negative. Therefore, the criteria for reducing and discontinuing these precautions are unclear. In this study, we examined the serum HBV core‐related antigen (HBcrAg) and intrahepatic covalently closed circular DNA (cccDNA) in order to determine if these could be useful markers for HBV re‐infection.

Methods

Thirty‐one patients underwent LT for HBV‐related liver disease at Nagasaki University Hospital from 2001 to 2010. Of these, 20 cases were followed up for more than 1 year (median follow‐up period, 903 days). We measured serum HBcrAg and intrahepatic cccDNA levels in liver tissue. In addition, in nine cases, we assessed the serial changes of HBcrAg and intrahepatic cccDNA levels from preoperative periods to stable periods.

Results

We examined serum HBcrAg and intrahepatic cccDNA levels in 20 patients (35 samples). HBcrAg and cccDNA levels were significantly correlated with each other (r = 0.616, P < 0.001). From a clinical aspect, the fibrosis stage was significantly lower in both HBcrAg‐ and cccDNA‐negative patients than in HBcrAg‐ or cccDNA‐positive patients.

Conclusions

HBcrAg and cccDNA were useful as HBV re‐infection markers after LT. Keeping patients' HBcrAg and cccDNA negative after LT might contribute to long‐term graft survival.
Ejaculation Profiles of Men Following Radiation Therapy for Prostate Cancer
Authors: Sullivan John F. , Stember Doron S. , Deveci Serkan , Akin-Olugbade Yemi , Mulhall John P.
Published: February 2013

Objectives

Radical prostatectomy (RP) is associated with anejaculation, which for some men is a source of bother and sexual dissatisfaction. Clinical experience has shown us some men after pelvic radiation therapy (RT) also experience anejaculation. This analysis was conducted to define the ejaculation profiles of men after RT for prostate cancer (PCa).

Methods

As a routine part of the sexual health evaluation for post-RT patients, men provided information regarding their ejaculatory function and orgasm. Analysis was conducted of a sexual medicine database reviewing demographic data, PCa factors, erectile, ejaculatory, and orgasmic function. Men with prior history of RP, cryotherapy, focal therapies, and androgen deprivation therapy (ADT) were excluded. Patients completed the International Index of Erectile Function (IIEF) questionnaire at follow-up visits commencing with the first posttreatment visit and specific attention was paid to the IIEF orgasm domain.

Results

Three hundred and sixty-four consecutive patients were included. Two hundred and fifty-two patients had external beam, and 112 patients had brachytherapy (BT). Mean age was 64 ± 11 (42–78) years and mean follow-up after RT was 6 ± 4.5 years. Mean prostate size at time of RT was 42 ± 21 g. Of the entire population, 72% lost the ability to ejaculate in an antegrade fashion after prostate RT by their last visit. The proportion experiencing anejaculation at 1, 3, and 5 years after RT was 16%, 69%, and 89%, respectively. For men with at least two IIEF questionnaires completed, the orgasm domain scores decreased dramatically over the follow-up period; orgasm domain scores (0–10): <12 months post-RT 7.4, 13–24 months 5.4, 25–36 months 3.2, >36 months 2.8 (P < 0.01). Multivariable analysis identified several factors predictive of failure to ejaculate: older age, ADT, RT dose > 100 Gy, and smaller prostates at the time of RT.

Conclusions

The vast majority of men after prostate RT will experience anejaculation and should be counseled accordingly prior to undergoing therapy. We have identified predictive factors.
Hospital mortality over time in patients with specific complications of cirrhosis
Authors: Vergara Mercedes , Clèries Montse , Vela Emili , Bustins Montserrat , Miquel Mireia , Campo Rafael
Published: February 2013

Hospital mortality secondary to cirrhosis is high.

Aim

To evaluate hospital mortality in patients admitted for specific complications of cirrhosis over time.

Material and methods

Registry‐data from Administrative Inpatient Dataset of acute care hospitals were collected at discharge from 2003 to 2010. Inclusion criteria were as follows: hospital admissions where one of the diagnoses was cirrhosis and the reason for admission was a specific complication of cirrhosis (ascites, encephalopathy, hepatorenal syndrome and haemorrhage from varices, bacterial spontaneous peritonitis). Analysis of variance was used for comparisons of quantitative variables and Chi‐square for qualitative variables. Logistic regression was performed to identify the risk factors associated with hospital mortality; the Hosmer and Lemeshow test was applied to evaluate calibration and the ROC curve for discrimination respectively.

Results

A total of 12,671 hospital admissions were analysed; 67.7% were men. Mean hospitalization stay was 10.9 (SD 9.2) days and the most frequent causes were encephalopathy (44.2%) and ascites (30.9%). Global hospital mortality was 11.6%. Logistic regression showed that once all factors had been adjusted, hepatorenal syndrome conveyed the highest risk for death (49.2%; OR = 8.1(95%CI:6.6–9.9). Risk of death was also increased by associated comorbidities and older age. Hospital mortality in the period 2006–2010 was 27% inferior to the period 2003–2005. The area under the ROC curve (AUROC) was 0.77 (95%CI 0.76–0.78).

Conclusions

Hospital mortality as a result of specific complications of cirrhosis is high, but has been declining in recent years.
Mixed adenoneuroendocrine carcinoma of the gallbladder with squamous cell carcinomatous and osteosarcomatous differentiation: Report of a case
Authors: Shintaku Masayuki , Kataoka Kozo , Kawabata Kenji
Published: February 2013

An extremely rare case of mixed adenoneuroendocrine carcinoma (MANEC) of the gallbladder is reported, in which the tumor showed diverse differentiation toward neuroendocrine tumor (grade 2), tubular adenocarcinoma, squamous cell carcinoma, and, in addition, osteosarcoma. The patient was an 80‐year‐old man, who underwent cholecystectomy because of a large polypoid tumor filling the gallbladder lumen. The tumor consisted of an intimate admixture of neuroendocrine tumor (grade 2) and tubular adenocarcinoma, and, in many areas, cell nests of neuroendocrine tumor appeared to bud off from tubular structures of the adenocarcinoma, in a manner resembling the ‘ductulo‐insular complex’ seen in nesidioblastosis of the pancreas. Small areas of squamous cell carcinoma were also found. The stroma consisted of a dense proliferation of atypical spindle cells showing focal osteosarcomatous differentiation, and an apparent transition from an epithelial tissue component to atypical spindle cells was observed. Immunohistochemically, neuroendocrine cells were positive for synaptophysin, chromogranin A, and serotonin, and the sarcomatoid stroma was partly immunoreactive for cytokeratin. The present case is the first example of MANEC of the gallbladder with simultaneous squamous cell carcinomatous and osteosarcomatous differentiation. ‘Neometaplasia’ of carcinoma cells in diverse directions was considered the most plausible explanation for the formation of this multifaceted neoplasm.
Cancer‐initiating cell marker‐positive cells generate metastatic tumors that recapitulate the histology of the primary tumors
Authors: Nishijima Nobuhiko , Ishii Genichiro , Nagai Kanji , Atsumi Naho , Aokage Keiju , Tokunaga Yuichi , Ichinokawa Hideomi , Ohe Yuichiro , Ochiai Atsushi
Published: February 2013

Cancer‐initiating cell (CIC) hypothesis suggests that CICs may be responsible for the generation of tumors that recapitulate the histology of the primary tumor at distant sites. We investigated the distribution of CIC markers (podoplanin (PDPN), CD44, and p63) positive cells of lung squamous cell carcinoma (SqCC) within primary and matched lymph node (LN) metastatic tumors to confirm this hypothesis (n = 113). In 61 cases, the PDPN‐positive cells were localized in more peripheral areas of the tumor nests than the CD44‐ and p63‐positive cells. This distribution pattern corresponded to a ‘hierarchical distribution (HD)’ reported previously. Among the cases with HD‐(+) primary tumors (n = 61), the number showing HD‐(+) LN metastatic tumors was 31 (51%), while among the cases with HD‐(−) primary tumors (n = 52), the number showing HD‐(+) LN metastatic tumors was 7 (13%) (p < 0.01). Primary and matched pulmonary metastatic (PM) tumors were also analyzed (n = 31), and a significant relationship of the HD pattern between them was also detected (p = 0.01). These results indicate that PDPN‐positive cells might reflect the most immature cells in the differentiation process of metastatic SqCC and might generate metastatic tumors that recapitulate the histologic heterogeneity of the primary tumor.
Optimal Crop Choice, Irrigation Allocation, and the Impact of Contract Farming
Authors: Huh Woonghee Tim , Lall Upmanu
Published: February 2013

The changing climate and concerns over food security are prompting a new look at the supply chain reliability of products derived from agriculture, and the potential role of contract farming as a mechanism to address climate and price risk while contributing toward crop diversification and water use efficiency is also emerging. In this study, the decision problem of a farmer associated with allocating his land among different crops with varying water requirements is considered, given that a subset of the crops may be associated with a forward contract that is being offered by a buyer. The problem includes a decision to acquire a certain amount of irrigation water capacity prior to the season and to allocate this capacity as irrigation water to be applied during the season to each of the crops selected. Rainfall in the growing season and the market price of each crop at the end of the season are considered to be random variables. Two stochastic programming models are developed to consider facets of this problem and to understand how contracts that reduce market price uncertainty from the problem may change the farmer's decision. The structural properties of these models are discussed, and selected implications are illustrated through an application to data from the Ganganagar district in Rajasthan, India.
A Note on Optimal Selling to Asymmetric Retailers
Authors: Kostamis Dimitris
Published: February 2013

I consider a channel with one manufacturer selling the same product to two retailers engaged in imperfect competition. The retailers are asymmetric because one has a lower marginal selling cost (or a higher demand potential) than the other. I design the manufacturer's optimal selling mechanism, whereby the manufacturer must offer the same contract options to both retailers. I fully characterize the manufacturer's optimal selling mechanism for varying degrees of retailer asymmetry and competition intensity. I find that under certain conditions, the manufacturer is better off selling a larger quantity through the high‐cost (or low‐demand potential) retailer. I also show how the optimal mechanism can be implemented using a menu of two‐part tariffs with quantity controls.
Equine alopecia areata: a retrospective clinical descriptive study at the University of California, Davis (1980–2011)
Authors: Hoolahan Danielle E. , White Stephen D. , Outerbridge Catherine A. , Shearer Patrick L. , Affolter Verena K.
Published: February 2013

Background

Alopecia areata (AA) causes hair loss due to inflammatory changes within and around hair bulbs and lower portions of the hair follicles. Documentation of AA in horses is limited to a few case reports.

Hypothesis/Objectives

The aim of this retrospective study was to characterize equine AA by describing patterns in age, sex, breed and lesion distribution in a series of cases. An attempt was made to characterize the long‐term course of the disease by surveying owners of affected horses.

Animals

Computerized records from 1 January 1980 to 1 July 2011 yielded 15 horses.

Methods

Descriptive statistics were calculated for age at presentation, breed, sex, dermatological signs, season when diagnosed and any recurrence of AA. The breed and sex distribution of horses with AA was compared with the equine hospital population during the study period.

Results

The prevalence of AA was 0.017%. Appaloosas and quarter horses were the most commonly recorded breeds. The median age was 9 years, with an age range from 3 to 15 years. Alopecia was the primary dermatological abnormality in all horses and commonly affected the mane, tail and face. More than half of the horses presented for other medical conditions. Five of seven (71.4%) owners who returned completed surveys reported a seasonal pattern to the disease, which usually worsened in spring and summer.

Conclusions and clinical importance

Alopecia areata is a rare disease in horses, and is typically cosmetic in nature. To the authors' knowledge, this is the first study investigating the epidemiology of equine AA.
Part-Load Operation of a Piloted FLOX® Combustion System
Authors: Roediger Tim , Lammel Oliver , Aigner Manfred , Beck Christian , Krebs Werner
Published: February 2013

A large operational envelope is a key requirement for modern gas turbines. Fuel staging is used here to improve the part load performance of an enhanced FLOX® type combustor. A swirl-stabilized pilot stage is integrated in the FLOX® burner and the results of high pressure lab-scale experiments at system relevant conditions are presented. The operational envelope of the piloted system could be extended by approximately 10%. Pressure scaling and variations of air preheat temperature and jet velocity describe fundamental characteristics of the piloted system. OH* chemiluminescence imaging is used to investigate flame shapes and the effect of the interacting flames. Emissions and pressure pulsations define limits, and optimum operation conditions of the combustor and show the influence of part load relevant parameters.
Complete Genome Sequence of the Industrial Strain Gluconobacter oxydans H24
Authors: Ge Xin , Zhao Yan , Hou Wei , Zhang Weicai , Chen Weiwei , Wang Jianhua , Zhao Nan , Lin Jian , Wang Wenxi , Chen Mengxia , Wang Qingge , Jiao Yinghui , Yuan Zhigang , Xiong Xianghua
Published: February 2013

Gluconobacter oxydans
is characterized by its ability to incompletely oxidize carbohydrates and alcohols. The high yields of its oxidation products and complete secretion into the medium make it important for industrial use. We report the finished genome sequence of
Gluconobacter oxydans
H24, an industrial strain with high
l
-sorbose productivity.
A mixed methods protocol to investigate medication adherence in patients with rheumatoid arthritis of White British and South Asian origin
Authors: Kumar Kanta , Raza Karim , Nightingale Peter , Horne Rob , Shaw Karen , Greenfield Sheila , Gill Paramjit
Published: February 2013

Background

Low adherence to medicines is an important issue as up to 40% of patients with chronic diseases do not take their medications as prescribed. This leads to suboptimal clinical benefit. In the context of rheumatoid arthritis, there is a dearth of data on adherence to disease-modifying antirheumatic drugs among minority ethnic groups. This study aims to assess the relationship between adherence to medicines and biopsychosocial variables in patients with rheumatoid arthritis of South Asian and White British origin.

Methods/analysis

A mixed methods approach will be used, encompassing a cross-sectional survey of 176 patients collecting demographic and clinical data, including information on adherence behaviour collected using a series of questionnaires. This will be followed by indepth qualitative interviews.

Ethics and dissemination

This study has been approved by the South Birmingham (10/H1207/89) and Coventry and Warwickshire (12/WM/0041) Research Ethics Committees. The authors will disseminate the findings in peer-reviewed publications.