bluuebunny/crossref_metadata_2025 huggingface dataset:
Ageing gracefully: physiology but not behaviour declines with age in a diving seabird
Authors: Elliott Kyle H. , Hare James F. , Le Vaillant Maryline , Gaston Anthony J. , Ropert‐Coudert Yan , Anderson W. Gary
Published: July 2014

A higher proportion of long‐lived animals die from senescence than short‐lived animals, yet many long‐lived homeotherms show few signs of physiological ageing in the wild. This may, however, differ in long‐lived diving homeotherms that frequently encounter hypoxic conditions and have very high metabolic rates.

To examine ageing within a long‐lived diving homeotherm, we studied resting metabolism and thyroid hormones (N = 43), blood oxygen stores (N = 93) and foraging behaviour (N = 230) of thick‐billed murres (Uria lomvia). Because murres dive exceptionally deep for their size and have a very high metabolism, we expected that ageing murres would show signs of physiological senescence. We paid particular attention to resting metabolism as we argue that these maintenance costs reflect those experienced during deep dives.

Blood oxygen stores (haematocrit), resting metabolic rate and thyroid hormone levels all declined significantly with age in incubating murres 3–30 years of age. In birds measured longitudinally 3 years apart, thyroid hormone levels and haematocrit were both significantly lower, suggesting progressive changes within individuals rather than selective disappearance of individuals with high metabolic rates. Within our longitudinal data set, we found no effect of age on dive depth, dive shape or behavioural aerobic dive limit.

A meta‐analysis of changes in resting metabolism with age across 15 animal species demonstrated that such declines are pervasive across most of the kingdom. The rate of decline was highest in species with high energy expenditure supporting a linkage between metabolism and senescence.

Physiological changes occurred in tandem with advancing age in murres, but offset each other such that there was no detectable decline in behavioural performance.
Oven, Microwave, and Combination Roasting of Peanuts: Comparison of Inactivation of Salmonella Surrogate Enterococcus faecium, Color, Volatiles, Flavor, and Lipid Oxidation
Authors: Smith Alicia L. , Perry Jennifer J. , Marshall Julie A. , Yousef Ahmed E. , Barringer Sheryl A.
Published: July 2014

Peanut safety and quality were evaluated for different roasting technologies. Shelled raw peanuts were roasted using an oven at 163 to 204 °C, microwave, or oven and microwave combinations. The lethal effect of these treatments was investigated on peanuts inoculated with the Salmonella surrogate, Enterococcus faecium and stored at room temperature for 1 h, 24 h, or 7 d before roasting. Roasted peanut color, odor activity values (OAVs), descriptive sensory panel analysis, free fatty acid, and peroxide values were determined. Color and OAVs were also analyzed on 2 commercial peanut butters. OAVs were calculated using volatile levels quantified with selected ion flow tube mass spectrometry and known odor thresholds. All treatments resulted in a minimum of 3 log reduction of inoculated bacterial population. Resistance to the process was not influenced by storage of inoculated peanuts prior to treatment. Roasting by different methods produced equivalent, commercially ideal L* color. Based on the OAVs, treatments had similar volatiles important to flavor compared to the commercial samples. Descriptive sensory analysis showed no significant difference between the roasting treatments for most of the sensory attributes. Lipid oxidation was not significantly different between the roasting methods, displaying no evidence that roasting time or temperature affected lipid oxidation, when ideal color was produced. These results suggest that oven, microwave, or combination roasting should be sufficient to mitigate the threat of Salmonella contamination and produce similar color, OAVs, sensory attributes, and lipid oxidation results.
Rphylip: anRinterface forPHYLIP
Authors: Revell Liam J. , Chamberlain Scott A.
Published: July 2014

The phylogeny methods software packagePHYLIPhas long been among the most widely used packages for phylogeny inference and phylogenetic comparative biology. Numerous methods available inPHYLIP, including several new phylogenetic comparative analyses of considerable importance, are not implemented in any other software.

Over the past decade, the popularity of the R statistical computing environment for many different types of phylogenetic analyses has soared, particularly in phylogenetic comparative biology. There are now numerous packages and methods developed for the R environment.

In this article, we present Rphylip, a new R interface for thePHYLIPpackage. Functions of Rphylip interface seamlessly with all of the major analysis functions of thePHYLIPpackage. This new interface will enable the much easier use ofPHYLIPprograms in an integrated R workflow.

In this study, we describe our motivation for developing Rphylip and present an illustration of how functions in the Rphylip package can be used for phylogenetic analysis in R.
Ultrasonic Assessment of Mucosal Thickness around Implants: Validity, Reproducibility, and Stability of Connective Tissue Grafts at the Buccal Aspect
Authors: Eghbali Aryan , De Bruyn Hugo , Cosyn Jan , Kerckaert Ingrid , Van Hoof Tom
Published: July 2014

Purpose

(1) To assess validity and reproducibility of mucosal thickness (MT) registration by means of an ultrasonic device and (2) to determine the MT stability of connective tissue grafts (CTGs) when applied at the buccal aspect of single implants demonstrating alveolar process deficiency.

Materials and Methods

For the validity assessment, four human cadaver edentulous maxillae were used to determine MT at 100 different sites. Soft tissue thickness as recorded with the ultrasonic device was compared with MT as registered with Micro‐CT (UGent, Ghent, Belgium), taking the latter as gold standard. For the reproducibility assessment, 50 duplicate ultrasonic registrations were used. For the clinical part, 10 non‐smoking patients with a single implant were included. All demonstrated alveolar process deficiency and had been provided with a provisional screw‐retained crown at the time of inclusion. Following an intrasulcular incision at the buccal aspect, a CTG was inserted to thicken soft tissues. MT was assessed at t0 (before CTG), t1 (immediately after CTG), t2 (suture removal), t3 (permanent crown installation), and t4 (9 months after CTG).

Results

There was a strong correlation between ultrasonic and Micro‐CT measurements (r = 0.89, p < .001). However, the former significantly underrated MT by 0.13 mm (p = .030). There was a strong correlation between duplicate ultrasonic recordings (r = 0.99, p < .001). Seven females and three males were included in the clinical study with a mean age of 52. MT significantly increased by 0.92 mm between t0 and t1 (p = .005). Between t3 and t4, there was a slight, yet significant decrease of 0.15 mm (p = .047).

Conclusion

The ultrasonic device can be used as a non‐invasive, reliable, and reproducible method to evaluate MT. Using this technology around single implants demonstrated that CTG may substantially thicken the peri‐implant mucosa with acceptable stability over a 9‐month period.
Self‐rated health, nutritional intake and mortality in adult hospitalized patients
Authors: Lainscak Mitja , Farkas Jerneja , Frantal Sophie , Singer Pierre , Bauer Peter , Hiesmayr Michael , Schindler Karin
Published: July 2014

Background

In the general population, poor self‐rated health (SRH) is associated with malnutrition; however, these associations have not been studied in hospitalized patients. We aimed to evaluate SRH, indicators of nutrition, nutritional status and their association with in‐hospital mortality.

Materials and methods

The study is based on data from the nutritionDay, a multinational, multicentre European‐wide standardized 1‐day cross‐sectional survey of nutritional factors, food intake and in‐hospital mortality in hospitalized patients. A data set of surveys on SRH in 2010 and 2011 was used in the analysis.

Results

Complete sets of data were available for 28 106 patients (64 ± 18 years, 50% men, 7% terminally ill). In relation to body mass index, 7% were undernourished and 16% were obese. Fair/poor SRH was reported by 59% of patients and was associated with low food intake during the previous week or on survey day (P < 0·005). Thirty‐day in‐hospital mortality was 3%; in adjusted multivariate survival analysis, fair/poor SRH [hazard ratio (HR) 1·53, 95% confidence interval (CI) 1·14–2·05] and reduced food intake [nothing eaten (HR 2·13, 95% CI 1·46–3·11) or not allowed to eat on nutritionDay (HR 2·01, 95% CI 1·30–3·11)] predicted fatal outcome. At particularly high risk were patients who rated their health poor and had reduced food intake on the survey day or within the previous week with relative risks of 7·37 and 8·80, respectively.

Conclusions

We demonstrated high prevalence of poor SRH and insufficient food intake in hospitalized patients. This was associated, particularly in combination, with increased risk of in‐hospital mortality.
Strain rate concentration and dynamic stress concentration for double‐edge‐notched specimens subjected to high‐speed tensile loads
Authors: Noda N.‐A. , Ohtsuka H. , Zheng H. , Sano Y. , Ando M. , Shinozaki T. , Guan W.
Published: July 2014

Engineering plastics provide superior performance to ordinary plastics for wide range of the use. For polymer materials, dynamic stress and strain rate may be major factors to be considered when the strength is evaluated. Recently, high‐speed tensile test is being recognized as a standard testing method to confirm the strength under dynamic loads. In this study, therefore, high‐speed tensile test is analysed by the finite element method; then, the maximum dynamic stress and strain rate are discussed with varying the tensile speed and maximum forced displacement. The maximum strain rate increases with increasing the tensile speed u/t, but the strain rate concentration factor is found to be constant independent of tensile speed, which is defined as the maximum strain rate appearing at the notch root over the average nominal strain rate at the minimum section . It is found that the strain rate at the notch root depends on the dynamic stress rate at the notch root and independent of the notch root radius ρ. It is found that the difference between the static and dynamic maximum stress concentration (σyA,max − σyA,st) at the notch root is proportional to the tensile speed when u/t = 5000 mm/s. Strain rate concentration factors are also discussed with varying the notch depth and specimen length. Based on the elastic strain rate concentration factor, the master curve is obtained useful for understanding the impact fracture of polycarbonate for the wide range of temperature and impact speed.
Goniometric evaluation of both forelimbs and hind limbs in two species of Neotropical monkeys
Authors: Conceição Renato Tavares , Rahal Sheila Canevese , Melchert Alessandra , Bortoloni Zara , Teixeira Carlos Roberto , Imbeloni Aline Amaral , Monteiro Frederico Ozanan Barros
Published: July 2014

Background

The aim of this study was to evaluate the goniometric measurements of the forelimb and hind limb joints in two species of Neotropical primates maintained in captivity.

Methods

Eighteen intact monkeys organized into two groups were studied: Group 1–9 brown howlers (Alouatta fusca), and Group 2–9 tufted capuchins (Sapajus apella).

Results

Significant differences were observed in the maximum flexion of the shoulder, elbow, carpus, stifle, and tarsus (G1>G2); maximum extension and abduction of the shoulder (G1G2) and adduction (G1G2). The ROM was significantly different in all joints: shoulder (G1<G2), elbow (G1G2), hip (G1>G2), stifle (G1<G2), and tarsus (G1<G2).

Conclusions

A. fusca and S. apella maintained in captivity have significant differences in the goniometric measurements of both forelimb and hind limb joints, primarily in maximum flexion and ROM.
Renal Sympathetic Denervation for Treatment of Resistant Hypertension: Egyptian Experience
Authors: HAMZA MOHAMED , KHAMIS HAZEM
Published: July 2014

Background

Among the Egyptian population with essential hypertension, a minority are under control (systolic pressure <140 mmHg and diastolic pressure <90 mmHg), despite the use of multiple antihypertensive medications. In this article, we describe our experience with percutaneous treatment using renal artery radiofrequency (RF) ablation.

Objectives

To evaluate the feasibility, efficacy, and safety of catheter‐based radiofrequency renal sympathetic denervation for treatment of resistant hypertension in Egyptian patients.

Methods

Patients with essential hypertension unresponsive to at least 3 types of antihypertensive medical therapy (baseline office systolic blood pressure ≥160 mmHg) (n = 55) were enrolled between February 2012 and June 2013 and received percutaneous RF ablation. Patients were followed up for 6 months after treatment to detect any change in office‐based measurement of blood pressure. Urine and blood samples were taken to evaluate the effects on renal function.

Results

A reduction of mean office blood pressure was seen from 174/103 ± 9/5 mmHg at baseline to 150/91 ± 8/5 mmHg at 6 months follow‐up (P = 0.001). Also, we noted a significant decrease in plasma renin activity (3.66 ± 0.64 vs. 3.37 ± 0.47 ng/mL per hour; P = 0.003), and there were no periprocedural complications, no adverse events, and no change in renal function during the follow‐up period. Also, no change was noted in the number of medications after 6 months (3.95 ± 1.64 vs. 3.67 ± 0.72; P = 0.27).

Conclusion

In this observational study, catheter‐based renal denervation causes sustained blood pressure reduction in patients with resistant hypertension, without serious adverse events. (J Interven Cardiol 2014;27:423–427)
Tactile sensory and pain thresholds in the face and tongue of subjects asymptomatic for oro‐facial pain and headache
Authors: Okayasu I. , Komiyama O. , Ayuse T. , De Laat A.
Published: July 2014

The aim of this study was to examine the tactile sensory and pain thresholds in the face, tongue, hand and finger of subjects asymptomatic for pain. Sixteen healthy volunteers (eight men and eight women, mean age 35·7 years, range 27–41) participated. Using Semmes–Weinstein monofilaments, the tactile detection threshold (TDT) and the filament‐prick pain detection threshold (FPT) were measured at five sites: on the cheek skin (CS), tongue tip (TT), palm side of the thenar skin (TS), dorsum of the hand (DH) and the finger tip (FT). The difference between the tactile sensory and pain threshold (FPT–TDT) was also calculated. Both for the TDT and FPT, TT and DH had the lowest and highest values, respectively. As for the FPT–TDT, there were no significant differences among the measurement sites. As the difference between FPT and TDT (FPT–TDT) is known to be an important consideration in interpreting QST (quantitative sensory testing) data and can be altered by neuropathology, taking the FPT–TDT as a new parameter in addition to the TDT and FPT separately would be useful for case–control studies on oro‐facial pain patients with trigeminal neuralgia, atypical facial pain/atypical odontalgia and burning mouth syndrome/glossodynia.
Occurrence of Alternaria japonica on Seeds of Wild and Cultivated Rocket
Authors: Gilardi Giovanna , Demarchi Stefano , Ortu Giuseppe , Gullino Maria Lodovica , Garibaldi Angelo
Published: July 2014

In vitro evaluation was carried out on seed samples of wild and cultivated rocket cultivars, most frequently grown in Italy, and obtained from farms affected by the leaf spot caused by Alternaria japonica in Piedmont and Lombardy during the fall of 2010. Twelve seed samples were collected and assayed for the presence of A. japonica. The pathogen was isolated only from not disinfected seeds. Among the two seed samples of cultivated rocket (Eruca vesicaria), only one was infected by A. japonica at a level of one infected seed out of 800. Four out of ten samples of wild (Diplotaxis tenuifolia) rocket seeds were contaminated by A. japonica with the highest level of infection detected in a single sample of 3 out of 800. All tested isolates of A. japonica obtained from seeds were pathogenic on both wild and cultivated rocket.
Concurrent imaging of chlorophyll fluorescence, Chlorophyll a content and green fluorescent proteins‐like proteins of symbiotic cnidarians
Authors: Leal Miguel Costa , Jesus Bruno , Ezequiel João , Calado Ricardo , Rocha Rui Jorge Miranda , Cartaxana Paulo , Serôdio João
Published: July 2014

Research on photosynthetic cnidarians has been mainly focused on the symbiosis established between the cnidarian host and its dinoflagellates endosymbionts from genus Symbiodinium. Despite the potential of imaging techniques for assessing the spatial distribution of key parameters of cnidarian photobiology, such as photochemical activity, chlorophyll a content or green fluorescent proteins (GFPs), to our best knowledge, no study has ever attempted to simultaneous map these three features. In this study, we developed a modified imaging pulse amplitude fluorometer by applying excitation light of different wavelengths and selectively detecting short spectral bands through bandpass filters. The imaging system was used to sequentially excite and quantify chlorophyll variable fluorescence (maximum quantum yield of photosystem II, Fv/Fm), Chl a content (normalized difference vegetation index) and relative content of GFPs. The spatial distribution of these photophysiological parameters was mapped both horizontally, across the surface of the soft corals Sarcophyton cf. glaucum and Sinularia flexibilis and the zoanthid Protopalythoa sp., and vertically, throughout a vertical section of S. cf. glaucum. Results showed bleached areas within each individual coral colony and registered photophysiological changes with S. cf. glaucum tissue depth. Analysis of Protopalythoa sp. polyps’ expansion revealed differential surface patterns of NDVI and GFP concentration, and a negative relation between these latter parameters within each polyp. This novel non‐invasive approach allowed a high‐resolution characterization of the spatial relationship between these key parameters through the analysis of image information on a pixel‐by‐pixel basis, which has great potential for investigating the physiological state of symbiotic associations.
Macrobenthos relative to the oxygen minimum zone on the East Indian margin, Bay of Bengal
Authors: Raman Akkur V. , Damodaran Rayaroth , Levin Lisa A. , Ganesh Thiruchitrambalam , Rao Yannamani K. V. , Nanduri Sateesh , Madhusoodhanan Rakhesh
Published: July 2014

The Bay of Bengal remains one of the least studied of the world's oxygen minimum zones (OMZs). Here we offer a detailed investigation of the macrobenthos relative to oxygen minimum zone [OMZ – DO (dissolved oxygen), concentration <0.5 ml·1−1] at 110 stations off the North East Indian margin (160 and 200 N) featuring coastal, shelf and slope settings (10–1004 m). Macrobenthos (>0.5 mm) composition, abundance and diversity were studied in relation to variations in depth, dissolved oxygen, sediment texture and organic carbon. Using multivariate procedures powered by SIMPROF analysis we identified distinct OMZ core sites (depth 150–280 m; DO 0.37 ml·1−1) that exhibited dense populations of surface‐feeding polychaetes (mean 2188 ind. m−2) represented by spionids and cossurids (96%). Molluscs and crustaceans were poorly represented except for ampeliscid amphipods. The lower OMZ sites (DO > 0.55 ml·l−1) supported a different assemblage of polychaetes (cirratulids, amphinomids, eunicids, orbinids, paraonids), crustaceans and molluscs, albeit with low population densities (mean 343 ind. m−2). Species richness [E(S100)], diversity (Margalef d; H’) and evenness (J’) were lower and dominance was higher within the OMZ core region. Multiple regression analysis showed that a combination of sand, clay, organic carbon, and dissolved oxygen explained 62–78% of the observed variance in macrobenthos species richness and diversity: E(S100) and H’. For polychaetes, clay and oxygen proved important. At low oxygen sites (DO <1 ml·l−1), depth accounted for most variance. Residual analysis (after removing depth effects) revealed that dissolved oxygen and sediment organic matter influenced 50–62% of residual variation in E(S100), H’ and d for total macrofauna. Of this, oxygen alone influenced up to ~50–62%. When only polychaetes were evaluated, oxygen and organic matter explained up to 58–63%. For low oxygen sites, organic matter alone had the explanatory power when dominance among polychaetes was considered. Overall, macrobenthic patterns in the Bay of Bengal were consistent with those reported for other upwelling margins. However, the compression of faunal gradients at shallower depths was most similar to the Chile/Peru margin, and different from the Arabian Sea, where the depth range of the OMZ is two times greater. The Bay of Bengal patterns may take on added significance as OMZs shoal globally.
Long‐term nutrient enrichment alters nematode trophic structure and body size in a Spartina alterniflora salt marsh
Authors: Mitwally Hanan M. , Fleeger John W.
Published: July 2014

The effects of long‐term experimental nutrient enrichment on nematode trophic guilds and morphometrics were examined in intertidal saltmarsh creeks of Plum Island Estuary, Massachusetts, USA. Nematodes from the marsh‐edge Spartina alterniflora habitat in a reference creek (n = 3300) were sampled annually and compared with nematodes (n = 3100) from a creek in which nitrate and phosphate loading rates were increased approximately 10–15× for 6 years. Trophic guilds in both creeks were dominated by epistrate (diatom) feeders and predators, and natural temporal variability across years was high. However, after 4 years of nutrient enrichment, a shift in the nutrient‐enriched creek was detected from a dominance of epistrate feeders to an increased proportion of predators, even though neither the benthic microalgae biomass nor the total density of nematodes was affected by fertilization. Nematodes also became longer, and longer relative to their diameter over time with nutrient enrichment because of the shift in trophic structure as short‐stout epistrate feeders were replaced with longer, more slender predators. These changes may have been directly related to nutrient enrichment effects on benthic algae or indirectly to the many other effects of enrichments on ecosystem structure or function. Our research indicates that nutrient enrichment alters the nematode community and this alternation may directly or indirectly affect the response of benthic algae to nutrient enrichment and as well as other ecosystem services.
Prominent intraspecific genetic divergence within Anopheles gambiae sibling species triggered by habitat discontinuities across a riverine landscape
Authors: Caputo B. , Nwakanma D. , Caputo F. P. , Jawara M. , Oriero E. C. , Hamid‐Adiamoh M. , Dia I. , Konate L. , Petrarca V. , Pinto J. , Conway D. J. , Della Torre A.
Published: July 2014

The Anopheles gambiae complex of mosquitoes includes malaria vectors at different stages of speciation, whose study enables a better understanding of how adaptation to divergent environmental conditions leads to evolution of reproductive isolation. We investigated the population genetic structure of closely related sympatric taxa that have recently been proposed as separate species (An. coluzzii and An. gambiae), sampled from diverse habitats along the Gambia river in West Africa. We characterized putatively neutral microsatellite loci as well as chromosomal inversion polymorphisms known to be associated with ecological adaptation. The results revealed strong ecologically associated population subdivisions within both species. Microsatellite loci on chromosome‐3L revealed clear differentiation between coastal and inland populations, which in An. coluzzii is reinforced by a unusual inversion polymorphism pattern, supporting the hypothesis of genetic divergence driven by adaptation to the coastal habitat. A strong reduction of gene flow was observed between An. gambiae populations west and east of an extensively rice‐cultivated region apparently colonized exclusively by An. coluzzii. Notably, this ‘intraspecific’ differentiation is higher than that observed between the two species and involves also the centromeric region of chromosome‐X which has previously been considered a marker of speciation within this complex, possibly suggesting that the two populations may be at an advanced stage of differentiation triggered by human‐made habitat fragmentation. These results confirm ongoing ecological speciation within these most important Afro‐tropical malaria vectors and raise new questions on the possible effect of this process in malaria transmission.
Transport dynamics of mass failures along weakly cohesive clinoform foresets
Authors: Abeyta Antoinette , Paola Chris
Published: July 2014

This study addresses the initiation mechanisms of mass failures on clinoform foresets. Previous studies have created mass flows by releasing dense water–sediment mixtures into standing water, thus imposing the initial conditions for the mass failures rather than allowing them to form on their own. Para‐meters such as the density, composition and initial momentum of the failures are pre‐determined, precluding observation of the factors that set them initially. This study uses a new experimental method that allows a range of mass failures to self‐generate. Building a clinoform using a cohesive mixture of walnut‐shell sand and kaolinite allows the foreset to build up and fail episodically, generating mass failures. Slopes undergo a series of morphological changes prior to failure, creating a concave shape that becomes exaggerated as deposition continues. This morphology leaves the slope in a metastable state. Once the slope is destabilised, failure is initiated. This study investigates the effect of clinoform progradation rates on failure size and frequency by conducting experiments over a range of water and sediment discharge rates. Neither failure size nor failure frequency changes with discharge rate; instead, increases in sediment supply are taken up by changes in the partitioning of sediment between the steep upper foreset and the more gradual delta‐front apron (toeset) below. Sediment is delivered to the delta‐front apron by a form of semi‐continuous slow creep along the foreset. This slow creep is a failure mode that has not received sufficient attention in the submarine mass‐flow literature. The independence of failure size and frequency from sediment supply rate suggests that the presence of mass‐failure deposits does not provide information on the rate of sediment delivery. If these relations hold at field scales, this would imply that individual mass failures are relatively insensitive to changes in water and sediment supply.
A glutathione responsive rice glyoxalase II, OsGLYII‐2, functions in salinity adaptation by maintaining better photosynthesis efficiency and anti‐oxidant pool
Authors: Ghosh Ajit , Pareek Ashwani , Sopory Sudhir K. , Singla‐Pareek Sneh L.
Published: July 2014

Glyoxalase II (GLY II), the second enzyme of glyoxalase pathway that detoxifies cytotoxic metabolite methylglyoxal (MG), belongs to the superfamily of metallo‐β‐lactamases. Here, detailed analysis of one of the uncharacterized rice glyoxalase II family members, OsGLYII‐2 was conducted in terms of its metal content, enzyme kinetics and stress tolerance potential. Functional complementation of yeast GLY II mutant (∆GLO2) and enzyme kinetics data suggested that OsGLYII‐2 possesses characteristic GLY II activity using S‐lactoylglutathione (SLG) as the substrate. Further, Inductively Coupled Plasma Atomic Emission spectroscopy and modelled structure revealed that OsGLYII‐2 contains a binuclear Zn/Fe centre in its active site and chelation studies indicated that these are essential for its activity. Interestingly, reconstitution of chelated enzyme with Zn2+, and/or Fe2+ could not reactivate the enzyme, while addition of Co2+ was able to do so. End product inhibition study provides insight into the kinetics of GLY II enzyme and assigns hitherto unknown function to reduced glutathione (GSH). Ectopic expression of OsGLYII‐2 in Escherichia coli and tobacco provides improved tolerance against salinity and dicarbonyl stress indicating towards its role in abiotic stress tolerance. Maintained levels of MG and GSH as well as better photosynthesis rate and reduced oxidative damage in transgenic plants under stress conditions seems to be the possible mechanism facilitating enhanced stress tolerance.
Sexual risk behaviour and donor deferral in Europe
Authors: Offergeld R. , Kamp C. , Heiden M. , Norda R. , Behr‐Gross M.‐E.
Published: July 2014

One of the most controversial policies in blood transfusion worldwide is the permanent deferral from donating blood of men with sexual contacts to other men (MSM). This policy was implemented for safety reasons as sex between men is known to be a high risk factor for acquiring severe infectious diseases transmissible by blood transfusion. Sexual contacts among heterosexual persons may hold similar risks but a clear‐cut discrimination between different individual risks is impossible. Nevertheless, the current blood donor deferral periods defined by European Union (EU) legislation depend on a distinction of different grades of risk with respect to sexual behaviour. Under the aegis of the Steering Committee on Blood Transfusion (CD‐P‐TS) of the Council of Europe (CoE), an international working group evaluated epidemiological and behavioural data, modelling studies on residual risk and spread of infections, and studies on adherence to donor selection criteria. The aim was to distinguish sexual behaviour of different risk categories. It was concluded, that existing data confirm that MSM and commercial sex workers (CSW) are groups at high risk. Any further grading lacks a scientific data base. Modelling studies indicate that adherence to deferral policies is of major relevance suggesting that good donor adherence may outweigh the small negative effects on blood safety postulated for changing from permanent to temporary deferral periods for high risk sexual behaviours. The fact that a considerable percentage of donors are MSM – despite the permanent deferral policy – demonstrates the need to increase donor understanding and adherence.
Influence of intramuscular heat stimulation on modulation of nociception: complex role of central opioid receptors in descending facilitation and inhibition
Authors: You Hao‐Jun , Lei Jing , Ye Gang , Fan Xiao‐Li , Li Qiang
Published: July 2014

Key points

Due to a lower triggering threshold of descending facilitation, driving of the descending inhibition alone without irritation of descending facilitation is critically challenged in the modulation of pain.

We test the hypothesis and provide the novel finding that intramuscular non‐painful heat stimulation may bypass the lower triggering thresholds of descending facilitation, and initiate the descending inhibition alone, which gives us a promising avenue to treat pain.

We further reveal distinct roles of μ/δ/κ‐opioid receptors in the function of the thalamic ‘nociceptive discriminators’, the thalamic mediodorsal and ventromedial nuclei, in descending facilitatory and inhibitory controls of nociception.

The present study helps us understand the mechanisms of the triggering and strengthening of endogenous descending inhibition via non‐painful heat stimulation, i.e. moxibustion, in effective relief of pain.

It has been reported that the threshold to activate ‘silent’ or inactive descending facilitation of nociception is lower than that of descending inhibition. Thus, the development of pain therapy to effectively drive descending inhibition alone, without the confounding influences of facilitation is a challenge. To address this issue we investigated the effects of intramuscular stimulation with a heating‐needle on spinal nociception, assessed by measuring nociceptive paw withdrawal reflex in rats. Additionally, involvement of the thalamic ‘nociceptive discriminators’ (thalamic mediodorsal (MD) and ventromedial (VM) nuclei), and opioid‐mediated mechanisms were further explored. Descending facilitation and inhibition were elicited by 46°C noxious heating‐needle stimulation, and were regulated by thalamic MD and VM nuclei, respectively. In contrast, innocuous heating‐needle stimulation at a temperature of 43°C elicited descending inhibition modulated by the thalamic VM nucleus alone. Microinjection of μ/δ/κ‐opioid receptor antagonists β‐funaltrexamine hydrochloride/naltrindole/nor‐binaltorphimine, into the VM nucleus attenuated the 46°C intramuscular heating‐needle stimulation‐evoked descending inhibition, whereas treatment of the MD nucleus with β‐funaltrexamine hydrochloride significantly decreased the descending facilitation. By contrast, descending inhibition evoked by 43°C heating‐needle stimulation was only depressed by naltrindole, as opposed to μ‐ and κ‐opioid receptor antagonists, which failed to influence descending inhibition. The present study reveals distinct roles of μ‐opioid receptors in the function of thalamic MD and VM nuclei, which exert facilitatory and inhibitory actions on nociception. Furthermore, innocuous, but not noxious, intramuscular heating‐needle stimulation targeting δ‐opioid receptors is suggested to be a promising avenue for the effective inhibition of pain.
Moving source localization with a single hydrophone using multipath time delays in the deep ocean
Authors: Duan Rui , Yang Kunde , Ma Yuanliang , Yang Qiulong , Li Hui
Published: July 2014

Localizing a source of radial movement at moderate range using a single hydrophone can be achieved in the reliable acoustic path by tracking the time delays between the direct and surface-reflected arrivals (D-SR time delays). The problem is defined as a joint estimation of the depth, initial range, and speed of the source, which are the state parameters for the extended Kalman filter (EKF). The D-SR time delays extracted from the autocorrelation functions are the measurements for the EKF. Experimental results using pseudorandom signals show that accurate localization results are achieved by offline iteration of the EKF.
Mind the midzone
Authors: Hadders Michael A. , Lens Susanne M.A.
Published: July 2014

Is the separation of chromosomes during cell division monitored by a checkpoint?

[Also see Report by

Afonso
et al.

]
Walter Gehring (1939–2014)
Authors: Levine Michael
Published: July 2014

A brief reflection on the life and lab of a preeminent developmental biologist
Researchers aim for an electrical memory prosthesis
Authors: Underwood Emily
Published: July 2014

DARPA-funded effort to develop implants for traumatic brain injuries draws skepticism.
Harvest of genome data for wheat growers
Authors: Pennisi Elizabeth
Published: July 2014

DNA survey orders genes, edging closer to the deciphering of this complex crop.
Using Transcriptional Control To Increase Titers of Secreted Heterologous Proteins by the Type III Secretion System
Authors: Metcalf Kevin J. , Finnerty Casey , Azam Anum , Valdivia Elias , Tullman-Ercek Danielle
Published: July 2014

The type III secretion system (T3SS) encoded at the
Salmonella
pathogenicity island 1 (SPI-1) locus secretes protein directly from the cytosol to the culture media in a concerted, one-step process, bypassing the periplasm. While this approach is attractive for heterologous protein production, product titers are too low for many applications. In addition, the expression of the SPI-1 gene cluster is subject to native regulation, which requires culturing conditions that are not ideal for high-density growth. We used transcriptional control to increase the amount of protein that is secreted into the extracellular space by the T3SS of
Salmonella enterica
. The controlled expression of the gene encoding SPI-1 transcription factor HilA circumvents the requirement of endogenous induction conditions and allows for synthetic induction of the secretion system. This strategy increases the number of cells that express SPI-1 genes, as measured by promoter activity. In addition, protein secretion titer is sensitive to the time of addition and the concentration of inducer for the protein to be secreted and SPI-1 gene cluster. Overexpression of
hilA
increases secreted protein titer by >10-fold and enables recovery of up to 28 ± 9 mg/liter of secreted protein from an 8-h culture. We also demonstrate that the protein beta-lactamase is able to adopt an active conformation after secretion, and the increase in secreted titer from
hilA
overexpression also correlates to increased enzyme activity in the culture supernatant.
A Novel Agarolytic β-Galactosidase Acts on Agarooligosaccharides for Complete Hydrolysis of Agarose into Monomers
Authors: Lee Chan Hyoung , Kim Hee Taek , Yun Eun Ju , Lee Ah Reum , Kim Sa Rang , Kim Jae-Han , Choi In-Geol , Kim Kyoung Heon
Published: July 2014

Marine red macroalgae have emerged to be renewable biomass for the production of chemicals and biofuels, because carbohydrates that form the major component of red macroalgae can be hydrolyzed into fermentable sugars. The main carbohydrate in red algae is agarose, and it is composed of
d
-galactose and 3,6-anhydro-
l
-galactose (AHG), which are alternately bonded by β1-4 and α1-3 linkages. In this study, a novel β-galactosidase that can act on agarooligosaccharides (AOSs) to release galactose was discovered in a marine bacterium (
Vibrio
sp. strain EJY3); the enzyme is annotated as
Vibrio
sp. EJY3 agarolytic β-galactosidase (
Vej
ABG). Unlike the
lacZ
-encoded β-galactosidase from
Escherichia coli
,
Vej
ABG does not hydrolyze common substrates like lactose and can act only on the galactose moiety at the nonreducing end of AOS. The optimum pH and temperature of
Vej
ABG on an agarotriose substrate were 7 and 35°C, respectively. Its catalytic efficiency with agarotriose was also similar to that with agaropentaose or agaroheptaose. Since agarotriose lingers as the unreacted residual oligomer in the currently available saccharification system using β-agarases and acid prehydrolysis, the agarotriose-hydrolyzing capability of this novel β-galactosidase offers an enormous advantage in the saccharification of agarose or agar in red macroalgae for its use as a biomass feedstock for fermentable sugar production.
Dead or Alive: Molecular Assessment of Microbial Viability
Authors: Cangelosi Gerard A. , Meschke John S.
Published: July 2014

Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.
The Contribution of Candida albicans Vacuolar ATPase Subunit V
1
B, Encoded by
VMA2
, to Stress Response, Autophagy, and Virulence Is Independent of Environmental pH
Authors: Rane Hallie S. , Bernardo Stella M. , Hayek Summer R. , Binder Jessica L. , Parra Karlett J. , Lee Samuel A.
Published: July 2014

Candida albicans
vacuoles are central to many critical biological processes, including filamentation and
in vivo
virulence. The V-ATPase proton pump is a multisubunit complex responsible for organellar acidification and is essential for vacuolar biogenesis and function. To study the function of the V
1
B subunit of
C. albicans
V-ATPase, we constructed a tetracycline-regulatable
VMA2
mutant, tetR-
VMA2
. Inhibition of
VMA2
expression resulted in the inability to grow at alkaline pH and altered resistance to calcium, cold temperature, antifungal drugs, and growth on nonfermentable carbon sources. Furthermore, V-ATPase was unable to fully assemble at the vacuolar membrane and was impaired in proton transport and ATPase-specific activity.
VMA2
repression led to vacuolar alkalinization in addition to abnormal vacuolar morphology and biogenesis. Key virulence-related traits, including filamentation and secretion of degradative enzymes, were markedly inhibited. These results are consistent with previous studies of
C. albicans
V-ATPase; however, differential contributions of the V-ATPase V
o
and V
1
subunits to filamentation and secretion are observed. We also make the novel observation that inhibition of
C. albicans
V-ATPase results in increased susceptibility to osmotic stress. Notably, V-ATPase inhibition under conditions of nitrogen starvation results in defects in autophagy. Lastly, we show the first evidence that V-ATPase contributes to virulence in an acidic
in vivo
system by demonstrating that the tetR-
VMA2
mutant is avirulent in a
Caenorhabditis elegans
infection model. This study illustrates the fundamental requirement of V-ATPase for numerous key virulence-related traits in
C. albicans
and demonstrates that the contribution of V-ATPase to virulence is independent of host pH.
Adeno-Associated Virus Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles of Human Diploid Fibroblasts Analyzed by Third-Generation PacBio DNA Sequencing
Authors: Hüser Daniela , Gogol-Döring Andreas , Chen Wei , Heilbronn Regine
Published: July 2014

Genome-wide analysis of adeno-associated virus (AAV) type 2 integration in HeLa cells has shown that wild-type AAV integrates at numerous genomic sites, including AAVS1 on chromosome 19q13.42. Multiple GAGY/C repeats, resembling consensus AAV Rep-binding sites are preferred, whereas
rep
-deficient AAV vectors (rAAV) regularly show a random integration profile. This study is the first study to analyze wild-type AAV integration in diploid human fibroblasts. Applying high-throughput third-generation PacBio-based DNA sequencing, integration profiles of wild-type AAV and rAAV are compared side by side. Bioinformatic analysis reveals that both wild-type AAV and rAAV prefer open chromatin regions. Although genomic features of AAV integration largely reproduce previous findings, the pattern of integration hot spots differs from that described in HeLa cells before. DNase-Seq data for human fibroblasts and for HeLa cells reveal variant chromatin accessibility at preferred AAV integration hot spots that correlates with variant hot spot preferences. DNase-Seq patterns of these sites in human tissues, including liver, muscle, heart, brain, skin, and embryonic stem cells further underline variant chromatin accessibility. In summary, AAV integration is dependent on cell-type-specific, variant chromatin accessibility leading to random integration profiles for rAAV, whereas wild-type AAV integration sites cluster near GAGY/C repeats.

IMPORTANCE
Adeno-associated virus type 2 (AAV) is assumed to establish latency by chromosomal integration of its DNA. This is the first genome-wide analysis of wild-type AAV2 integration in diploid human cells and the first to compare wild-type to recombinant AAV vector integration side by side under identical experimental conditions. Major determinants of wild-type AAV integration represent open chromatin regions with accessible consensus AAV Rep-binding sites. The variant chromatin accessibility of different human tissues or cell types will have impact on vector targeting to be considered during gene therapy.
A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research
Authors: Choquet Rémy , Maaroufi Meriem , de Carrara Albane , Messiaen Claude , Luigi Emmanuel , Landais Paul
Published: July 2014

Background Although rare disease patients make up approximately 6–8% of all patients in Europe, it is often difficult to find the necessary expertise for diagnosis and care and the patient numbers needed for rare disease research. The second French National Plan for Rare Diseases highlighted the necessity for better care coordination and epidemiology for rare diseases. A clinical data standard for normalization and exchange of rare disease patient data was proposed. The original methodology used to build the French national minimum data set (F-MDS-RD) common to the 131 expert rare disease centers is presented.

Methods To encourage consensus at a national level for homogeneous data collection at the point of care for rare disease patients, we first identified four national expert groups. We reviewed the scientific literature for rare disease common data elements (CDEs) in order to build the first version of the F-MDS-RD. The French rare disease expert centers validated the data elements (DEs). The resulting F-MDS-RD was reviewed and approved by the National Plan Strategic Committee. It was then represented in an HL7 electronic format to maximize interoperability with electronic health records.

Results The F-MDS-RD is composed of 58 DEs in six categories: patient, family history, encounter, condition, medication, and questionnaire. It is HL7 compatible and can use various ontologies for diagnosis or sign encoding. The F-MDS-RD was aligned with other CDE initiatives for rare diseases, thus facilitating potential interconnections between rare disease registries.

Conclusions The French F-MDS-RD was defined through national consensus. It can foster better care coordination and facilitate determining rare disease patients’ eligibility for research studies, trials, or cohorts. Since other countries will need to develop their own standards for rare disease data collection, they might benefit from the methods presented here.
A very rare cause of chronic foot pain in a child: metatarsal tubercular osteomyelitis
Authors: Prakash Jatin , Agnihotri Akhil , Jaiswal Yashwardhan , Mehtani Anil
Published: July 2014

Pure tubercular osteomyelitis without joint involvement is rare and easily missed. Moreover the lesion is common in spine and large joints like hip and knee. The involvement of isolated metatarsal has been described rarely, only as few sporadic case reports. We present one such case of isolated first metatarsal involvement in an 8-year-old child who presented with chronic pain in left foot for over 6 months. The X-rays suggested a lytic lesion and lesion was confirmed on histopathology and acid-fast bacteria staining. The patient was treated with multidrug antitubercular chemotherapy. The results were excellent with complete healing of the lesion.