bluuebunny/crossref_metadata_2025 huggingface dataset:
Core structures analyses of (a+c)-edge dislocations in wurtzite GaN through atomistic simulations and Peierls–Nabarro model
Authors: Chen Cheng , Meng Fanchao , Song Jun
Published: May 2015

The core structures and slip characteristics of (a+c)-edge dislocations on pyramidal planes in wurtzite GaN were investigated employing molecular dynamics simulations. Multiple stable core configurations are identified for dislocations along the glide and shuffle planes. The corresponding generalized-stacking-fault energy (GSFE) curves for the glide and shuffle slips are calculated. The GSFE curves, combined with the Peierls–Nabarro model, demonstrate that the shuffle slip is favored over the glide slip given the markedly lower Peierls energy and stress of the shuffle slip. Our findings also indicate that in general slip motions for (a+c)-edge dislocations are only possible at elevated temperature, and the necessity of further studies of thermally activated processes to better understand the dynamics of (a+c) dislocations in GaN.
Self-similar impulsive capillary waves on a ligament
Authors: Duchemin L. , Le Dizès S. , Vincent L. , Villermaux E.
Published: May 2015

We study the short-time dynamics of a liquid ligament, held between two solid cylinders, when one is impulsively accelerated along its axis. A set of one-dimensional equations in the slender-slope approximation is used to describe the dynamics, including surface tension and viscous effects. An exact self-similar solution to the linearized equations is successfully compared to experiments made with millimetric ligaments. Another non-linear self-similar solution of the full set of equations is found numerically. Both the linear and non-linear solutions show that the axial depth at which the liquid is affected by the motion of the cylinder scales like t, a consequence of the imposed radial uniformity of the axial velocity at the cylinder surface, and differs from t2/3 known to prevail in surface-tension-driven flows. The non-linear solution presents the peculiar feature that there exists a maximum driving velocity U⋆ above which the solution disappears, a phenomenon probably related to the de-pinning of the contact line observed in experiments for large pulling velocities.
Interference of various active islanding detection methods with positive feedback in multi-inverter power system
Authors: Chen Kai , Wang Ying , Tian Shulin , Cheng Yuhua , Yin Chun
Published: May 2015

The islanding condition occurs when the utility is disconnected and the distributed generation (DG) continues to supply power for local load. This condition is not desirable which brings about the instability of voltage and frequency as well as the power quality degradation, thus presenting a great threaten to maintenance personnel. Considering equipment safety and personnel safety, unintentional islanding for DG operation will not be tolerated here. The study of interference of different islanding detection methods (IDMs) in multi-inverter situations as the potential method has attracted a lot of attention in relevant field. This paper discusses interaction and degradation of three active and positive feedback IDMs, including current-disturbing positive feedback, active frequency drift positive feedback, and Sandia frequency shift IDMs. Non-detection zones of multi-inverter systems in a load parameter space are used as analysis tool. Two 220 V–1 kW Simulink models are set up for the simulation tests and three scenarios with potential for interference and degradation of the system are simulated. Simulation results confirm that multi-inverter equipped with both current and frequency positive feedback disturbing exhibits more complicated phenomenon than the one equipped with single disturbing method.
Auger recombination rates in dilute-As GaNAs semiconductor
Authors: Tan Chee-Keong , Tansu Nelson
Published: May 2015

The evaluation of Auger recombination process for dilute-As GaNAs alloy is presented. Our analysis indicates the suppression of interband Auger recombination mechanism in dilute-As GaNAs alloy in the green spectral regime. The interband Auger coefficient in dilute-As GaNAs alloy is shown as two orders of magnitude lower than that of its corresponding intraband Auger rate. Our results confirm that the second conduction band has a negligible effect on the interband Auger process in dilute-As GaNAs alloy due to the non-resonant condition of the process. Our findings show the importance of dilute-As GaNAs as an alternative visible material with low Auger recombination rates.
Modelling Class Uncertainty in the Geodemographic Output Area Classification
Authors: Fisher Peter , Tate Nicholas J
Published: May 2015

Geodemographics is the study of people by where they live, and historically has relied in part on census information to provide essential variables. In 2005 the Office for National Statistics for England and Wales published a geodemographic classification of output areas (OAs; the smallest published areas of enumeration for the UK) of the 2001 UK Census. Uniquely among UK examples of such classifications not only are the classes to which each OA is assigned published for free with no restriction on use, but the difference between each OA and all class centroids are also made available. In this paper these differences (being Euclidian distances in the classification feature space) are used to introduce uncertainty by softening the classification using the methods derived from fuzzy c-means and the possibilistic c-means classifications. The former applies a probabilistic assumption that all fuzzy memberships for a particular OA sum to unity while the latter does not. This assumption (which is the same as that behind the published OA classification) may generate results which are potentially misleading because the fuzzy c-means method forces OAs into classes to which they may have relatively little similarity while minimising the importance of classes to which they may have a larger affinity. If the fuzzy memberships or possibilities were to be integrated with other socioeconomic variables which are also conceived as fuzzy sets for geodemographic applications (decision making for government resource allocation, site location modelling or marketing, for example), then the two results would produce different outcomes. It is suggested that the possibilistic c-means are the more useful although they do lead to the possibly confusing but analytically rich situation where one OA may have minimal affinity with any class, at the same time as others may have strong affinity with many classes.
DNA methylation reprogramming during oogenesis and interference by reproductive technologies: Studies in mouse and bovine models
Authors: Anckaert Ellen , Fair Trudee
Published: May 2015

The use of assisted reproductive technology (ART) to overcome fertility problems has continued to increase since the birth of the first baby conceived by ART over 30 years ago. Similarly, embryo transfer is widely used as a mechanism to advance genetic gain in livestock. Despite repeated optimisation of ART treatments, pre- and postnatal outcomes remain compromised. Epigenetic mechanisms play a fundamental role in successful gametogenesis and development. The best studied of these is DNA methylation; the appropriate establishment of DNA methylation patterns in gametes and early embryos is essential for healthy development. Superovulation studies in the mouse indicate that specific ARTs are associated with normal imprinting establishment in oocytes, but abnormal imprinting maintenance in embryos. A similar limited impact of ART on oocytes has been reported in cattle, whereas the majority of embryo-focused studies have used cloned embryos, which do exhibit aberrant DNA methylation. The present review discusses the impact of ART on oocyte and embryo DNA methylation with regard to data available from mouse and bovine models.
Ephemeral plant indicators of livestock grazing in arid rangelands during wet conditions
Authors: Waudby Helen P. , Petit Sophie
Published: May 2015

Vegetation communities in arid rangeland systems are typically dominated by short-lived, ephemeral (annual) plants during periods of high rainfall. These conditions present a rare opportunity to examine herbivore–plant interactions and identify potential indicators of grazing intensity. The influence of cattle grazing on vegetation communities of arid cracking-clay gibber-gilgai systems in Australian rangelands was investigated during La Niña (wet) conditions, including 2010, which was the wettest year on record in the region. Seasonal annual plant diversity was assessed at three grazed and three less-grazed sites. Individual annual species’ responses to grazing intensity were examined among grazed and less-grazed sites (i.e. increasing or decreasing response). Additionally, rare (found at one site only) and restricted (found at grazed or less-grazed sites only) annual and perennial species were identified to elucidate their status as indicators. Prevailing La Niña conditions allowed the study of little-known, short-lived species, which constituted the bulk of species richness. Differences in grazing intensity were more clearly ascertained from examining individual species than plant diversity. Of 31 annual/short-lived species, 21 responded to grazing intensity. Although most species responded to grazing (n = 7 increasers and n = 14 decreasers), these responses did not necessarily reflect published accounts of their so-called palatability. Thirty other species were restricted to certain site types (grazed or less-grazed) and 20 were rare. The indicator species concept should be applied at appropriate scales, and more detailed information is needed on stock preferences for these ephemeral plants in these rangeland systems. Elucidating the effect of grazing on individual plant species’ phenology, and identifying indicators, is important for developing efficacious land management practices.
Evaluation of Creel Survey Methods to Estimate Recreational Harvest of Surf Smelt in Puget Sound, Washington
Authors: Lowry Dayv , Stick Kurt , Lindquist Adam , Cheng Yuk W.
Published: May 2015

Fisheries for Surf Smelt Hypomesus pretiosus in the inland marine waters of Washington State are currently managed under the assumption that annual recreational harvest is roughly similar to commercial harvest. Commercial harvest is monitored by submission of mandatory fish tickets that document sales to licensed vendors. Assessment of recreational effort and harvest is complicated by (1) the lack of a licensing requirement for fishers, (2) the fact that fishing occurs throughout the year but tends to peak during locally specific time windows, and (3) the ability of anglers to engage in the fishery from private shorelines in addition to public access points (e.g., boat ramps). To adequately estimate recreational harvest, a survey method must be developed that accounts for spatiotemporally diverse harvest patterns. Here, we report the results of a pilot study that combined access-point and roving, boat-based creel survey techniques to sample a known region of high recreational fishing pressure during the traditional fishing “season” for Surf Smelt. In addition to providing a statistically valid estimate of harvest at these locations, we described patterns of both fishing effort and catch across time, in association with various environmental variables, and at public access points and private beaches. We found that based on the site-specific estimates generated here and the number of high-use recreational fishing sites in Puget Sound, Surf Smelt harvest has the capacity to exceed the level that has been assumed for purposes of management. We conclude that combining access-point surveys and roving creel counts represents a logistically feasible and cost-effective method for estimating recreational harvest of Surf Smelt throughout Puget Sound or harvest in any other fishery with similarly complex spatiotemporal participation.

Received January 9, 2014; accepted January 13, 2015
Dispersal Patterns of Coastal Largemouth Bass in Response to Tournament Displacement
Authors: Brown Daniel T. , Rice James A. , Suski Cory D. , Derek Aday D.
Published: May 2015

Tournament displacement, stockpiling near release points, and handling stress are major concerns for managers of sport fisheries in the southeastern USA. We examined the effects of transport distance and tournament handling stress on dispersal of 40 Largemouth Bass Micropterus salmoides via telemetry from May 2012 to September 2013 in the Albemarle Sound system of eastern North Carolina. Largemouth Bass were captured from four tributaries of Albemarle Sound and transported 16.5–45 km to a central release point before being acoustically tagged and released. Movement data from an array of passive receivers was used to calculate rates of dispersal from the release point, emigration from the study area and return to capture location over time. Blood cortisol concentration, collected from our tagged Largemouth Bass and those captured in an actual tournament, was used to determine the effect of stress on potential postrelease movement and survival. Our findings indicate little evidence of long-term stockpiling (i.e., fish remaining close to release point; Richardson-Heft et al. 2000); 57% of displaced Largemouth Bass dispersed more than 500 m from the release point within 7 d and 87% within 21 d postrelease. Half of those that emigrated from Edenton Bay returned to their capture location. However, no Largemouth Bass displaced 35–45 km returned to their capture locations, suggesting that long-distance displacement inhibits return. Fishing (2.8%) and nonharvest mortality (0.5%) were low throughout this study except for peaks observed during late spring (42.9%) and early summer (25.1%) of 2013. Mean cortisol concentrations were similar in Largemouth Bass collected during our simulated tournament (126.7 ng/mL) and an actual tournament (118.4 ng/mL). However, cortisol concentrations were unrelated to survival, postrelease dispersal, or return of tagged individuals to their capture location. Largemouth Bass appear to be able to cope with current tournament practices; however, restrictions on displacement distance may increase return rates.

Received August 26, 2014; accepted January 14, 2015
Characteristics and Spatial Segregation of Sympatric Saugers and Walleyes in the Ottawa River, Canada
Authors: Haxton Tim
Published: May 2015

Few comparative studies exist on the sympatric populations of Saugers Sander canadensis and Walleyes S. vitreus, especially in northern rivers. Depth-stratified, standardized index netting surveys were conducted in the Ottawa River, Canada—a large, fragmented northern river. The objectives of this study were to (1) determine whether Saugers and Walleyes were spatially segregated within river reaches; (2) assess whether relative abundances of the two species were correlated within river reaches and ascertain factors affecting their relative abundances; (3) determine whether life history characteristics in this northern river were within the variation reported for each species; and (4) evaluate whether there was synchrony in year-class strength between the two species and identify the factors affecting year-class strength. Saugers and Walleyes were spatially segregated, specifically by depth. Probability of capture was greatest in the 20–35-m depth stratum for Saugers and in the 6–12-m depth stratum for Walleyes. Relative abundances of Saugers and Walleyes were correlated and were positively related to reach characteristics (i.e., mean and maximum depth, reach length, and river kilometers upstream from the confluence) but negatively related to thermal conditions (i.e., growing degree-days, water temperature at preferred depths, and human population in proximity to the river). Life history characteristics were within the literature-reported ranges except for Saugers, which were older with a smaller length at 50% maturity. Year-class strengths of Saugers and Walleyes were synchronous at the reach and river levels and were positively correlated with mean annual temperature but negatively correlated with mean annual river flow. Saugers and Walleyes can coexist within large water bodies. Recruitment synchrony suggests that spawning management efforts could benefit both species, which could be advantageous when managing the Sauger, a lesser studied species. However, life history differences advocate that harvest regulations (e.g., size limits) must be species specific in order to be effective.

Received June 13, 2013; accepted January 27, 2015
English secondary students’ thinking about the status of scientific theories: consistent, comprehensive, coherent and extensively evidenced explanations of aspects of the natural world – or just ‘an idea someone has’
Authors: Taber Keith S. , Billingsley Berry , Riga Fran , Newdick Helen
Published: May 2015

Teaching about the nature of science (NOS) is seen as a priority for science education in many national contexts. The present paper focuses on one central issue in learning about NOS: understanding the nature and status of scientific theories. A key challenge in teaching about NOS is to persuade students that scientific knowledge is generally robust and reliable, yet also in principle always open to challenge and modification. Theories play a central role, as they are a form of conjectural knowledge that over time may be abandoned, replaced, modified, yet sometimes become well established as current best scientific understanding. The present paper reports on findings from interviews with 13–14 year olds in England where target knowledge presents theories as ‘consistent, comprehensive, coherent and extensively evidenced explanations of aspects of the natural world’. Student thinking reflected a two‐tier typology of scientific knowledge in which largely unsupported imaginative ideas (‘theories’) became transformed into fairly definitive knowledge (such as laws) through relatively straightforward testing. These results are considered in relation to research into intellectual development which indicates that effective teaching in this area requires careful scaffolding of student learning, but has potential to contribute to supporting intellectual development across the curriculum.
A General Equilibrium Theory of Contracts in Community Supported Agriculture
Authors: Sproul Thomas W. , Kropp Jaclyn D.
Published: May 2015

Community Supported Agriculture (CSA) contracts allow consumers to buy claims on a farm's future production. In turn, the consumer provides working capital to the farm during the growing season. CSA contracts also provide risk management for farmers with limited access to Federal crop insurance by transferring part of the farm's risk to the consumer. We derive a theory of CSA contract pricing for the two most prevalent types of CSA contracts: yield contracts, in which consumers receive a percentage of the farm's production, and weight contracts, in which consumers receive fixed quantities. We develop a two‐period model in which expected utility maximizing producers and consumers engage in CSA contracting in the first period based on anticipation of yields and spot prices in the second period. Using the model, we generate several testable hypotheses to be explored in future research. Additionally, we present an overview of the data necessary to test the propositions and potential challenges that might arise in related empirical work.
Involvement of the cytoplasmic cysteine-238 of CD40 in its up-regulation of CD23 expression and its enhancement of TLR4-triggered responses
Authors: Nadiri Amal , Jundi Malek , El Akoum Souhad , Hassan Ghada S. , Yacoub Daniel , Mourad Walid
Published: May 2015

CD40, a member of the tumor necrosis factor receptor superfamily, plays a key role in both adaptive and innate immunity. Engagement of CD40 with its natural trimeric ligand or with cross-linked antibodies results in disulfide-linked CD40 (dl-CD40) homodimer formation, a process mediated by the cysteine-238 residues of the cytoplasmic tail of CD40. The present study was designed to elucidate the biological relevance of cysteine-238-mediated dl-CD40 homodimers to the expression of CD23 on B cells and to investigate its possible involvement in the innate response. Our results indicate that cysteine-238-mediated dl-CD40 homodimerization is required for CD40-induced activation of PI3-kinase/Akt signaling and the subsequent CD23 expression, as inhibition of dl-CD40 homodimer formation through a point mutation-approach specifically impairs these responses. Interestingly, cysteine-238-mediated dl-CD40 homodimers are also shown to play a crucial role in Toll-like receptor 4-induced CD23 expression, further validating the importance of this system in bridging innate and adaptive immune responses. This process also necessitates the activation of the PI3-kinase/Akt cascade. Thus, our results highlight new roles for CD40 and cysteine-238-mediated CD40 homodimers in cell biology and identify a potential new target for therapeutic strategies against CD40-associated chronic inflammatory diseases.
Common marmoset CD117
+
hematopoietic cells possess multipotency
Authors: Shimada Shin , Nunomura Satoshi , Mori Shuya , Suemizu Hiroshi , Itoh Toshio , Takabayashi Shuji , Okada Yoshinori , Yahata Takashi , Shiina Takashi , Katoh Hideki , Suzuki Ryuji , Tani Kenzaburo , Ando Kiyoshi , Yagita Hideo , Habu Sonoko , Sasaki Erika , Kametani Yoshie
Published: May 2015

Analysis of the hematopoiesis of non-human primates is important to clarify the evolution of primate-specific hematopoiesis and immune regulation. However, the engraftment and development of the primate hematopoietic system are well-documented only in humans and are not clear in non-human primates. Callithrix jacchus (common marmoset, CM) is a New World monkey with a high rate of pregnancy and small size that lives in closed colonies. As stem cell factor (SCF) is an essential molecule for hematopoietic stem cell development in mice and humans, we focused on CD117, the SCF receptor, and examined whether CD117-expressing cells possess the hematopoietic stem/progenitor cell characteristics of newborn marmoset-derived hematopoietic cells that can develop into T cells and B cells. When CD117 + cell fractions of the bone marrow were transplanted into immunodeficient NOD (non-obese diabetic)/Shi-scid, common γc-null (NOG) mice, these cells engrafted efficiently in the bone marrow and spleens of the NOG mice. The CD117 + cells developed into myeloid lineage cells, CD20 + B cells and CD3 + T cells, which could express CM cytokines in vivo . The development of B cells did not precede that of T cells. The development of CD8 + T cells was dominant in NOG mice. The engraftment was comparable for both CD117 + CD34 + cells and CD117 + CD34 − cells. These results suggest that the CD117 + cell fraction can differentiate into all three cell lineages, and the development of marmoset immunity in the xenogeneic environment follows diverse developmental pathways compared with human immunity.
Automating the generation of lexical patterns for processing free text in clinical documents
Authors: Meng Frank , Morioka Craig
Published: May 2015

Objective Many tasks in natural language processing utilize lexical pattern-matching techniques, including information extraction (IE), negation identification, and syntactic parsing. However, it is generally difficult to derive patterns that achieve acceptable levels of recall while also remaining highly precise.

Materials and Methods We present a multiple sequence alignment (MSA)-based technique that automatically generates patterns, thereby leveraging language usage to determine the context of words that influence a given target. MSAs capture the commonalities among word sequences and are able to reveal areas of linguistic stability and variation. In this way, MSAs provide a systemic approach to generating lexical patterns that are generalizable, which will both increase recall levels and maintain high levels of precision.

Results The MSA-generated patterns exhibited consistent F1-, F.5-, and F2- scores compared to two baseline techniques for IE across four different tasks. Both baseline techniques performed well for some tasks and less well for others, but MSA was found to consistently perform at a high level for all four tasks.

Discussion The performance of MSA on the four extraction tasks indicates the method’s versatility. The results show that the MSA-based patterns are able to handle the extraction of individual data elements as well as relations between two concepts without the need for large amounts of manual intervention.

Conclusion We presented an MSA-based framework for generating lexical patterns that showed consistently high levels of both performance and recall over four different extraction tasks when compared to baseline methods.
Hemagglutination Inhibition Antibody Titers as a Correlate of Protection Against Seasonal A/H3N2 Influenza Disease
Authors: Benoit Anne , Beran Jiri , Devaster Jeanne-Marie , Esen Meral , Launay Odile , Leroux-Roels Geert , McElhaney Janet E. , Oostvogels Lidia , van Essen Gerrit A. , Gaglani Manjusha , Jackson Lisa A. , Vesikari Timo , Legrand Catherine , Tibaldi Fabian , Innis Bruce L. , Dewé Walthère
Published: May 2015

Background.  To investigate the relationship between hemagglutinin-inhibition (HI) antibody levels to the risk of influenza disease, we conducted a correlate of protection analysis using pooled data from previously published randomized trials.

Methods.  Data on the occurrence of laboratory-confirmed influenza and HI levels pre- and postvaccination were analyzed from 4 datasets: 3 datasets included subjects aged <65 years who received inactivated trivalent influenza vaccine (TIV) or placebo, and 1 dataset included subjects aged ≥65 years who received AS03-adjuvanted TIV (AS03-TIV) or TIV. A logistic model was used to evaluate the relationship between the postvaccination titer of A/H3N2 HI antibodies and occurrence of A/H3N2 disease. We then built a receiver-operating characteristic curve to ide.jpegy a potential cutoff titer between protection and no protection.

Results.  The baseline odds ratio of A/H3N2 disease was higher for subjects aged ≥65 years than <65 years and higher in seasons of strong epidemic intensity than moderate or low intensity. Including age and epidemic intensity as covariates, a 4-fold increase in titer was associated with a 2-fold decrease in the risk of A/H3N2 disease.

Conclusions.  The modeling exercise confirmed a relationship between A/H3N2 disease and HI responses, but it did not allow an evaluation of the predictive power of the HI response.
Evaluation of Methods to Quantify Populations of Rhizoctonia in Soil
Authors: Spurlock T. N. , Rothrock C. S. , Monfort W. S.
Published: May 2015

The best method to quantitatively determine populations of Rhizoctonia in soil from soybean fields undergoing rice and soybean rotations was determined for use in a large-scale spatial study to be done over multiple fields and years. The methods evaluated were the toothpick-baiting method, the multiple-pellet soil sampler, and the pour-plate method using elutriated organic matter from soil or surface residue. The toothpick-baiting method was calibrated using the multiple-pellet soil sampler and determined to assay an approximate soil volume of 15.43 cm3. The radius of isolation with the toothpick-baiting technique was approximately 1 cm. In 2009 and 2010, the toothpick method was determined to be the most reliable method for assaying soils, with the most isolates across space and greater recovery of Rhizoctonia solani AG1-IA, R. solani AG11, and R. oryzae, the major Rhizoctonia spp. in these fields, when quantified as propagules per volume of soil or organic matter. In 2011, the recovery of these three groups of Rhizoctonia did not differ statistically when the toothpick-baiting method was compared with the multiple-pellet soil sampler after the volume of soil assayed by the pellet sampler was increased to be similar to that of the toothpick method. However, the labor involved in assaying a similar volume of soil with the multiple-pellet soil sampler was limiting for a large-scale spatial study. The toothpick-baiting method was preferred over the other methods because it was determined to be thorough, inexpensive, nondestructive, and rapid. Additionally, the use of the toothpick-baiting method allows for the determination of the depth of inoculum of isolated fungi for intact soil cores. The mean depth of activity of R. solani AG1-IA, R. solani AG11, and R. oryzae was 1.15, 1.55, and 1.47 cm respectively.
Protective versus Conventional Ventilation for Surgery
Authors: Serpa Neto Ary , Hemmes Sabrine N. T. , Barbas Carmen S. V. , Beiderlinden Martin , Biehl Michelle , Binnekade Jan M. , Canet Jaume , Fernandez-Bustamante Ana , Futier Emmanuel , Gajic Ognjen , Hedenstierna Göran , Hollmann Markus W. , Jaber Samir , Kozian Alf , Licker Marc , Lin Wen-Qian , Maslow Andrew D. , Memtsoudis Stavros G. , Reis Miranda Dinis , Moine Pierre , Ng Thomas , Paparella Domenico , Putensen Christian , Ranieri Marco , Scavonetto Federica , Schilling Thomas , Schmid Werner , Selmo Gabriele , Severgnini Paolo , Sprung Juraj , Sundar Sugantha , Talmor Daniel , Treschan Tanja , Unzueta Carmen , Weingarten Toby N. , Wolthuis Esther K. , Wrigge Hermann , Gama de Abreu Marcelo , Pelosi Paolo , Schultz Marcus J. ,   for the PROVE Network Investigators
Published: May 2015

AbstractAbstract

This individual patient meta-analysis of 2,127 patients ventilated under general anesthesia for surgery from 15 randomized controlled trials shows that intraoperative ventilation with low tidal volume protects against postoperative pulmonary complications, but further trials are necessary to define the role of intraoperative higher positive end–expiratory pressure to prevent postoperative pulmonary complications after major abdominal surgery.

Background:

Recent studies show that intraoperative mechanical ventilation using low tidal volumes (V
T) can prevent postoperative pulmonary complications (PPCs). The aim of this individual patient data meta-analysis is to evaluate the individual associations between V
T size and positive end–expiratory pressure (PEEP) level and occurrence of PPC.

Methods:

Randomized controlled trials comparing protective ventilation (low V
T with or without high levels of PEEP) and conventional ventilation (high V
T with low PEEP) in patients undergoing general surgery. The primary outcome was development of PPC. Predefined prognostic factors were tested using multivariate logistic regression.

Results:

Fifteen randomized controlled trials were included (2,127 patients). There were 97 cases of PPC in 1,118 patients (8.7%) assigned to protective ventilation and 148 cases in 1,009 patients (14.7%) assigned to conventional ventilation (adjusted relative risk, 0.64; 95% CI, 0.46 to 0.88; P < 0.01). There were 85 cases of PPC in 957 patients (8.9%) assigned to ventilation with low V
T and high PEEP levels and 63 cases in 525 patients (12%) assigned to ventilation with low V
T and low PEEP levels (adjusted relative risk, 0.93; 95% CI, 0.64 to 1.37; P = 0.72). A dose–response relationship was found between the appearance of PPC and V
T size (R
2 = 0.39) but not between the appearance of PPC and PEEP level (R
2 = 0.08).

Conclusions:

These data support the beneficial effects of ventilation with use of low V
T in patients undergoing surgery. Further trials are necessary to define the role of intraoperative higher PEEP to prevent PPC during nonopen abdominal surgery.
Interference lithographic nanopatterning of plant and bacterial light-harvesting complexes on gold substrates
Authors: Patole Samson , Vasilev Cvetelin , El-Zubir Osama , Wang Lin , Johnson Matthew P. , Cadby Ashley J. , Leggett Graham J. , Hunter C. Neil
Published: May 2015

We describe a facile approach for nanopatterning of photosynthetic light-harvesting complexes over macroscopic areas, and use optical spectroscopy to demonstrate retention of native properties by both site-specifically and non-specifically attached photosynthetic membrane proteins. A Lloyd's mirror dual-beam interferometer was used to expose self-assembled monolayers of amine-terminated alkylthiolates on gold to laser irradiation. Following exposure, photo-oxidized adsorbates were replaced by oligo(ethylene glycol) terminated thiols, and the remaining intact amine-functionalized regions were used for attachment of the major light-harvesting chlorophyll–protein complex from plants, LHCII. These amine patterns could be derivatized with nitrilotriacetic acid (NTA), so that polyhistidine-tagged bacteriochlorophyll–protein complexes from phototrophic bacteria could be attached with a defined surface orientation. By varying parameters such as the angle between the interfering beams and the laser irradiation dose, it was possible to vary the period and widths of NTA and amine-functionalized lines on the surfaces; periods varied from 1200 to 240 nm and linewidths as small as 60 nm (
λ
/4) were achieved. This level of control over the surface chemistry was reflected in the surface topology of the protein nanostructures imaged by atomic force microscopy; fluorescence imaging and spectral measurements demonstrated that the surface-attached proteins had retained their native functionality.
Climbing with adhesion: from bioinspiration to biounderstanding
Authors: Cutkosky Mark R.
Published: May 2015

Bioinspiration is an increasingly popular design paradigm, especially as robots venture out of the laboratory and into the world. Animals are adept at coping with the variability that the world imposes. With advances in scientific tools for understanding biological structures in detail, we are increasingly able to identify design features that account for animals' robust performance. In parallel, advances in fabrication methods and materials are allowing us to engineer artificial structures with similar properties. The resulting robots become useful platforms for testing hypotheses about which principles are most important. Taking gecko-inspired climbing as an example, we show that the process of extracting principles from animals and adapting them to robots provides insights for both robotics and biology.
Bioinspiration: something for everyone
Authors: Whitesides George M.
Published: May 2015

‘Bioinspiration’—using phenomena in biology to stimulate research in non-biological science and technology—is a strategy that suggests new areas for research. Beyond its potential to nucleate new ideas, bioinspiration has two other interesting characteristics. It can suggest subjects in research that are relatively simple technically; it can also lead to areas in which results can lead to useful function more directly than some of the more familiar areas now fashionable in chemistry. Bioinspired research thus has the potential to be accessible to laboratories that have limited resources, to offer routes to new and useful function, and to bridge differences in technical and cultural interactions of different geographical regions.
Bioinspired genotype–phenotype linkages: mimicking cellular compartmentalization for the engineering of functional proteins
Authors: van Vliet Liisa D. , Colin Pierre-Yves , Hollfelder Florian
Published: May 2015

The idea of compartmentalization of genotype and phenotype in cells is key for enabling Darwinian evolution. This contribution describes bioinspired systems that use
in vitro
compartments—water-in-oil droplets and gel-shell beads—for the directed evolution of functional proteins. Technologies based on these principles promise to provide easier access to protein-based therapeutics, reagents for processes involving enzyme catalysis, parts for synthetic biology and materials with biological components.
Bioinspired membrane-based systems for a physical approach of cell organization and dynamics: usefulness and limitations
Authors: Lagny Thibaut J. , Bassereau Patricia
Published: May 2015

Being at the periphery of each cell compartment and enclosing the entire cell while interacting with a large part of cell components, cell membranes participate in most of the cell's vital functions. Biologists have worked for a long time on deciphering how membranes are organized, how they contribute to trafficking, motility, cytokinesis, cell–cell communication, information transport, etc., using top-down approaches and always more advanced techniques. In contrast, physicists have developed bottom-up approaches and minimal model membrane systems of growing complexity in order to build up general models that explain how cell membranes work and how they interact with proteins, e.g. the cytoskeleton. We review the different model membrane systems that are currently available, and how they can help deciphering cell functioning, but also list their limitations. Model membrane systems are also used in synthetic biology and can have potential applications beyond basic research. We discuss the possible synergy between the development of complex
in vitro
membrane systems in a biological context and for technological applications. Questions that could also be discussed are: what can we still do with synthetic systems, where do we stop building up and which are the alternative solutions?
Risungbinella pyongyangensis gen. nov., sp. nov., a mesophilic member of the family Thermoactinomycetaceae isolated from an agricultural soil sample
Authors: Kim MyongChol , Kim TongRyul , Ri SongYong , Jiang Fan , Chang Xulu , Liu Ying , Ren Lvzhi , Qiu Xia , Deng Sangsang , Fang Chengxiang , Zheng Congyi , Peng Fang
Published: May 2015

A mesophilic strain, designed MC 210T, was isolated from an agricultural soil sample from Pyongyang, Democratic People's Republic of Korea, and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew well on PYI medium, and no diffusible pigments were produced. The optimum temperature for growth was 37 °C. The aerial mycelium was well developed, but not fragmented. The strain was Gram-reaction-positive and non-motile and formed endospores on the aerial mycelium. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MC 210T belongs to the family Thermoactinomycetaceae. Strain MC 210T showed 16S rRNA gene sequence similarities of 92.90 and 92.54  % to the type strains of Geothermomicrobium terrae and Shimazuella kribbensis, respectively. The cell wall of strain MC 210T contained meso-diaminopimelic acid, glutamic acid and alanine as the diagnostic amino acids, and whole-cell hydrolysates contained glucose, arabinose and galactose. Strain MC 210T contained anteiso-C13 : 0, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, C16 : 0 and iso-C13 : 0 as the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown aminophospholipids, an unknown aminolipid, three unknown phospholipids and five unknown polar lipids. The predominant menaquinone was MK-7.The G+C content of the genomic DNA was 42.1 mol%. On the basis of our phylogenetic, physiological and chemotaxonomic data, strain MC 210T is considered to represent a novel genus and species, for which we propose the name Risungbinella pyongyangensis gen. nov., sp. nov., in the family Thermoactinomycetaceae. The type strain of Risungbinella pyongyangensis is MC 210T (CCTCC AA 2013021T = NRRL B-59118T).
Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants
Authors: Kim Tae-Su , Han Ji-Hye , Joung Yochan , Kim Seung Bum
Published: May 2015

Two Gram-staining-positive, aerobic, endospore-forming, motile bacteria, strains DT7-4T and DLE-12T, were isolated from roots of evening primrose (Oenothera biennis) and day lily (Hemerocallis fulva), respectively, and subjected to taxonomic characterization. Analysis of 16S rRNA gene sequences indicated that the two strains fell into two distinct phylogenetic clusters belonging to the genus Paenibacillus. Strain DT7-4T was most closely related to Paenibacillus phyllosphaerae PALXIL04T and Paenibacillus taihuensis THMBG22T, with 96.3 % 16S rRNA gene sequence similarity to each, and strain DLE-12T was most closely related to Paenibacillus ginsengarvi Gsoil 139T and Paenibacillus hodogayensis SGT, with 96.6 and 93.3  % sequence similarity, respectively. Both isolates contained anteiso-C15 : 0 as the dominant fatty acid, meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and MK-7 as the respiratory menaquinone. The cellular polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified polar lipids. The DNA G+C contents of strains DT7-4T and DLE-12T were 50.1 ± 0.7 and 55.2 ± 0.5 mol%, respectively. The chemotaxonomic properties of both isolates were typical of members of the genus Paenibacillus. However, our biochemical and phylogenetic analyses distinguished each isolate from related species. Based on our polyphasic taxonomic analysis, strains DT7-4T and DLE-12T should be recognized as representatives of novel species of Paenibacillus, for which the names Paenibacillus oenotherae sp. nov. (type strain DT7-4T = KCTC 33186T = JCM 19573T) and Paenibacillus hemerocallicola sp. nov. (type strain DLE-12T = KCTC 33185T = JCM 19572T) are proposed.
Reclassification of Bacillus invictae as a later heterotypic synonym of Bacillus altitudinis
Authors: Liu Yang , Lai Qiliang , Du Juan , Shao Zongze
Published: May 2015

The aim of this study was to reclarify the taxonomic status of strain Bacillus invictae Bi.FFUP1
T by performing comparative analyses with the other four type strains within the Bacillus pumilus group. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains B. invictae Bi.FFUP1
T ( = DSMZ 26896T = MCCC 1A07089T), B. altitudinis 41KF2bT ( = DSMZ 21631T = MCCC 1A06452T), B. safensis FO-36bT ( = DSMZ 19292T = MCCC 1A6451T), B. pumilus ATCC 7061T ( = DSMZ 27T = MCCC 1A06453T) and B. xiamenensis HYC-10T ( = MCCC 1A00008T) were, respectively, 82.90  % and 98.10  %, which are greater than the thresholds for bacterial species delineation, suggesting that they should belong to the same species, while the dDDH and ANI values between strain B. invictae DSMZ 26896T and the other three type strains within the B. pumilus group were below the respective thresholds of 70  % and 95  %. Meanwhile, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT shared 98.7  % gyrB gene sequence similarity based on resequencing, whereas strain B. invictae DSMZ 26896T shared low similarities ( < 95  %) with the other three type strains. In addition, in comparison with those from the other three type strains, phenotypic data of B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, including API 20NE, API ZYM, Biolog GN2 and API 50CHB tests, showed slight differences. The data from these combined genotypic and phenotypic analyses suggest that Bacillus invictae Branquinho et al. 2014 should be regarded as a later heterotypic synonym of Bacillus altitudinis
Shivaji et al. 2006.
Changes of biochemical components and physiological activities of coffee beans according to different roasting conditions
Authors: Nam Sanghae , Kang Suji
Published: May 2015

Four different kinds of coffee beans (CS, Colombia supremo; EY, Ethiopia yirgacheffee; IM, Indonesia mandheling; and IMM, India monsooned malabar) were roasted at 200 and 250°C for 10, 15, and 20 min. To determine the optimum roasting conditions, various components of the coffee beans such as pyrazines produced during the roasting, and their antioxidant and antidiabetic effects were analyzed. The different roasting condition did not affect on the concentration of caffeine. However, the amount of 5-caffeoylquinic acid and the total phenolics decreased significantly, at a greater temperature and a longer roasting time. The greatest amount of pyrazines was produced from the IMM however, the amount of pyrazines decreased rapidly at 250°C according to increasing in roasting time. The DPPH free radical scavenging activity was mostly 80% more effective than that of BHT and α-tocopherol activities at the same concentration. In the case of the FRAP assay, the reducing power of the coffee slightly decreased at a greater temperature pand longer time. While the inhibitory effect on α-glucosidase was negligible, the activity decreased by more than 80% when the coffee beans were roasted at 250°C for 20 min. The inhibitory effect on α-amylase showed similar results. Taken together, the optimum roasting conditions were determined to be 200°C and 15 min, which provided the best physiological activity and nutty and chocolatey aromas from the pyrazine of coffee.
Quality characteristics of dumpling shell with sea tangle powder
Authors: Park In-Duck
Published: May 2015

This study investigated the effects of sea tangle powder (SP) on the physicochemical and sensory characteristics of dumpling shells. Various dumpling shell samples were prepared with wheat flour containing different amounts of SP. The characteristics of the dumpling shell samples were investigated based on their viscosity, cooking properties, color values, and texture properties. Their sensory characteristics were evaluated by using seven scores. According to the amylograph data, the composite SP-wheat flour samples showed an increased gelatinization temperature with an increasing SP content, whereas the initial viscosity at 95°C was decreased after 15 minutes. The increase of SP amount decreased the values of L and b whereas the a value increased. With regard to the textural characteristics, the dumpling shells with an increased amount of SP showed increased hardness, cohesiveness, and adhesiveness, whereas the SP addition reduced the springiness of the dumpling shell. The dumpling shell with the addition of 3% SP showed the highest overall acceptability in the sensory evaluation.
Quality characteristics of dumpling shell added with dropwort powder
Authors: Park Geum-Soon , Kim Ji-Young
Published: May 2015

We investigated quality changes in dumpling shells by addition of various concentrations of dropwort powder. Dumpling shells were added with 0, 1, 3, 5, and 7%. dropwort powder respectively. Their water-binding capacity, weight, volume, and turbidity increased after cooking. As the added dropwort powder increased, their DPPH radical scavenging activity significantly increased (p<0.001). In addition, their L and a values decreased whereas their b value increased. In terms of the textural characteristics, the hardness and springiness increased and the cohesiveness and brittleness of the cooked dumpling shells significantly increased with an increasing content of dropwort powder. The savory taste, moisture, and chewiness of the dumpling shells prepared with the addition of 3% dropwort powder were preferred. Overall, the sensory evaluation showed that the sensory characteristics of the dumpling shells were best with the addition of 3% dropwort powder.
Quality characteristics of sponge cake with buckwheat powder
Authors: Lee Seon-Ho , Bae Jong-Ho
Published: May 2015

This study investigated the quality characteristics of sponge cake by introduction of buckwheat powder (BP). Cake batter was prepared by substituting wheat flour with an equivalent amount of BP based on weight. Sponge cakes were prepared with different amounts of BP (0, 10, 20, and 30%, respectively). Their physicochemical and sensory properties were tested. The specific gravity was not affected by the addition of BP (10~30%) (p<0.05). The lightness (L value) and yellowness (b value) of the crumb significantly decreased with the increase in the BP contents (p<0.05), whereas the redness (a value) increased (p<0.05). As the increase in the amount of BP addition, the hardness, cake volume (mL), baking loss rate (%), and specific volume (mL/g) significantly decreased (p<0.05). On the contrary, the cake weight increased. In the sensory evaluation, no significant differences in terms of color, taste, texture, flavor, and overall acceptance were observed among the different amout of BP addition (0~20%) (p<0.05). Overall, the sponge cake prepared with the addition of 20% BP was recommended to use due to its advantages in functional property.