bluuebunny/crossref_metadata_2025 huggingface dataset:
A new algorithm for context-based biomedical diagram similarity estimation
Authors: Xu Songhua , Sheng Jianqiang , Luo Xiaonan
Published: February 2013

Motivation: Diagrams embedded in the biomedical literature convey rich contents, which often concisely and intuitively highlight key thesis of a research article. Despite their vital importance and informative clues for biomedical literature navigation and retrieval; currently, we miss an effective computational method for automatically understanding and accessing these valuable resources.

Proposed Method: To address the aforementioned gap, we propose a novel context-based algorithm for estimating the similarity between a pair of biomedical diagrams. The main difference of the proposed algorithm with respect to the existing methods lies in the new algorithm’s incorporation of the semantic context associated with diagrams in their source documents into the diagram similarity estimation process. In addition, the new approach also performs a series of advanced image processing and text mining operations to comprehensively extract the semantic content graphically encoded inside diagram images.

Results: The new algorithm can be deployed as a reusable component providing a fundamental function for building many advanced, semantic-aware applications on biomedical diagram processing. As a case study, in our experiments, we demonstrate the advantage of the new algorithm for diagram retrieval. A set of biomedical diagram search and ranking experiments were conducted, where the performance of the new method was compared with that of five peer methods. The comparison results demonstrate the performance superiority of the new algorithm with all peer methods with statistical significance.

Contact:  songhua.xu@njit.edu, shengjianqiang@163.com or lnslxn@mail.sysu.edu.cn.
Coalescent simulation in continuous space
Authors: Kelleher Jerome , Barton Nicholas H. , Etheridge Alison M.
Published: February 2013

Coalescent simulation has become an indispensable tool in population genetics, and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalized version of this algorithm as a freely available Python module.

Availability: Package available at http://pypi.python.org/pypi/ercs

Contact:  jerome.kelleher@ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pain Intensity on the First Day after Surgery
Authors: Gerbershagen Hans J. , Aduckathil Sanjay , van Wijck Albert J. M. , Peelen Linda M. , Kalkman Cor J. , Meissner Winfried
Published: February 2013

Background:

Severe pain after surgery remains a major problem, occurring in 20–40% of patients. Despite numerous published studies, the degree of pain following many types of surgery in everyday clinical practice is unknown. To improve postoperative pain therapy and develop procedure-specific, optimized pain-treatment protocols, types of surgery that may result in severe postoperative pain in everyday practice must first be identified.

Methods:

This study considered 115,775 patients from 578 surgical wards in 105 German hospitals. A total of 70,764 patients met the inclusion criteria. On the first postoperative day, patients were asked to rate their worst pain intensity since surgery (numeric rating scale, 0–10). All surgical procedures were assigned to 529 well-defined groups. When a group contained fewer than 20 patients, the data were excluded from analysis. Finally, 50,523 patients from 179 surgical groups were compared.

Results:

The 40 procedures with the highest pain scores (median numeric rating scale, 6–7) included 22 orthopedic/trauma procedures on the extremities. Patients reported high pain scores after many “minor” surgical procedures, including appendectomy, cholecystectomy, hemorrhoidectomy, and tonsillectomy, which ranked among the 25 procedures with highest pain intensities. A number of “major” abdominal surgeries resulted in comparatively low pain scores, often because of sufficient epidural analgesia.

Conclusions:

Several common minor- to medium-level surgical procedures, including some with laparoscopic approaches, resulted in unexpectedly high levels of postoperative pain. To reduce the number of patients suffering from severe pain, patients undergoing so-called minor surgery should be monitored more closely, and postsurgical pain treatment needs to comply with existing procedure-specific pain-treatment recommendations.
Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state
Authors: Le Thomas Adrien , Rogers Alicia K. , Webster Alexandre , Marinov Georgi K. , Liao Susan E. , Perkins Edward M. , Hur Junho K. , Aravin Alexei A. , Tóth Katalin Fejes
Published: February 2013

In the metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression. We found that Drosophila Piwi is recruited to chromatin, colocalizing with RNA polymerase II (Pol II) on polytene chromosomes. Knockdown of Piwi in the germline increases expression of transposable elements that are targeted by piRNAs, whereas protein-coding genes remain largely unaffected. Derepression of transposons upon Piwi depletion correlates with increased occupancy of Pol II on their promoters. Expression of piRNAs that target a reporter construct results in a decrease in Pol II occupancy and an increase in repressive H3K9me3 marks and heterochromatin protein 1 (HP1) on the reporter locus. Our results indicate that Piwi identifies targets complementary to the associated piRNA and induces transcriptional repression by establishing a repressive chromatin state when correct targets are found.
Antimicrobial Effect of Bacteriocin KU24 Produced by Lactococcus lactis KU24 against Methicillin‐Resistant Staphylococcus aureus
Authors: Lee Na‐Kyoung , Jin Han Eun , Jun Han Kyoung , Paik Hyun‐Dong
Published: February 2013

Bacteriocin KU24 produced by Lactococcus lactis KU24 exhibited an inhibitory effect against methicillin‐resistant Staphylococcus aureus (MRSA). Bacteriocin KU24 was inactivated by protease XIV, showing that it has a proteinaceous nature on S. aureus ATCC 33591. Also, bacteriocin KU24 exhibited a strong heat stability (121 °C for 15 min) and pH stability (pH 3 to 9). The mode of inhibition was determined for S. aureus ATCC 33591 by treatment of 0, 250, and 500 AU/mL of bacteriocin KU24. S. aureus ATCC 33591 was inhibited by added bacteriocin KU24, while control was increased. The cell membranes of S. aureus ATCC 33591 were damaged with treatment of 500 AU/mL of bacteriocin KU24. Also, bacteriocin KU24 inhibited the occurrence of mecA gene, the methicillin resistance gene in S. aureus ATCC 33591. Bacteriocin KU24 was purified by C18 Sep‐Pack column, cation exchange chromatography, and gel filtration chromatography, and molecular mass is approximately 6.5 kDa by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis. These results demonstrate that bacteriocin KU24 can be used as an alternative antimicrobial agent for the treatment of infection of MRSA in the food industry.
PNPLA3/adiponutrin functions in lipid droplet formation
Authors: Chamoun Zeina , Vacca Fabrizio , Parton Robert G. , Gruenberg Jean
Published: February 2013

Background Information

In animals, adipose tissue contains the main energy store as lipid droplets (LDs) composed of esterified cholesterol (CE) and triacylglycerol (TAG) enveloped in a mono‐layer of phospholipid and decorated by a coat of proteins. Upon increased energy demand, dedicated lipases hydrolyse TAG stepwise into free fatty acids that are released in circulation and made available to peripheral tissue. In case of aberrant caloric load, TAGs are deposited into non‐adipocyte tissues, primarily liver cells. For instance, non‐alcoholic fatty liver disease (NAFLD) is a common chronic disorder characterised by an excess of TAG in the liver of patients regardless of their susceptibility to obesity, diabetes or exposure to alcohol. Several independent linkage studies have associated NAFLD with a non‐synonymous variant of patatin‐like phospholipase domain‐containing 3 (PNPLA3/adiponutrin) encoding an isoleucine to methionine substitution at position 148 (I148M) (see Cohen et al., 2011 for review). However, the mechanism by which a variation in PNPLA3 gives susceptibility to NAFLD is not known, primarily because the physiological role of PNPLA3 still needs to be elucidated.

Results

We have identified PNPLA3 in a screen for genes upregulated by intracellular lipid accumulation. We investigated the sub‐cellular distribution and potential function of PNPLA3 in fibroblast‐like cells supplemented with lipids. We demonstrate that PNPLA3 is targetted to LDs in a process that requires an intact Brummer box domain, which is conserved in the patatin‐like phospholipase family. We show that increased levels of the NAFLD‐linked PNPLA3 isoform leads to larger LDs, whereas decreased levels of PNPLA3 had the opposite effect. Interestingly, however, PNPLA3 induced a reduction in LD size upon co‐expression with ABDH5/CGI‐58, an activator of the TAG lipase PNPLA2, which is the closest homolog of PNPLA3. By investigating LD populations according to their size and composition, we show that perturbing intracellular lipid trafficking drastically modifies LD nature.

Conclusions

Taken together, our results suggest that PNPLA3 exhibits a dual function in LD metabolism, and that it participates in the restoration of lipid homeostasis upon aberrant intracellular lipid accumulation.
Late anastomotic leakage in colorectal surgery: a significant problem
Authors: Morks A. N. , Ploeg R. J. , Sijbrand Hofker H. , Wiggers T. , Havenga K.
Published: February 2013

Aim

Reported incidence rates of colorectal anastomotic leakage (AL) vary between 2.5 and 20%. There is little information on late anastomotic leakage (LAL). The aim of this study was to determine the incidence of LAL after colorectal resection.

Method

All patients undergoing colorectal resection with primary anastomosis between January 2004 and October 2009 at the University Medical Center Groningen were included. LAL was defined as anastomotic leakage diagnosed more than 30 days after surgery.

Results

One hundred and forty‐one patients were analysed. Indications for surgery included both benign and malignant conditions. The incidence of early anastomotic leakage (EAL) within 30 days after surgery was 13%. The LAL rate was 6%. Eighty‐nine per cent of patients with EAL underwent relaparotomy compared with 44% for LAL (P = 0.02).

Conclusion

One‐third of all anastomotic leakages were diagnosed more than 30 days after surgery. Of these, 44% underwent relaparotomy. Patients with leakage diagnosed within 30 days after surgery were more likely to undergo relaparotomy. LAL is a significant problem after colorectal surgery.
Effects of CXCL13 inhibition on lymphoid follicles in models of autoimmune disease
Authors: Finch Donna K. , Ettinger Rachel , Karnell Jodi L. , Herbst Ronald , Sleeman Matthew A.
Published: February 2013

The chemokine CXCL13 has a key role in secondary lymphoid tissue orchestration and lymphoid neogenesis. Transgenic mice deficient in CXCL13 or its receptor CXCR5 have severely impaired lymph node development, lack peritoneal B‐lymphocytes and are deficient in circulating antibodies to common bacterial antigens. However, total circulating numbers of B‐lymphocytes are slightly elevated and humoral responses to T‐dependent or blood‐borne antigens are relatively normal. Lymphoid neogenesis is an aberrant process that occurs in chronically inflamed tissue and provides a microenvironment supportive of pathogenic B‐cell survival and activation. Here, we describe the impact of therapeutic dosing of a CXCL13 antibody in a mouse model of arthritis, and detail the contribution CXCL13 makes to lymphoid follicle microenvironment, without affecting humoral immune responses.
Metaheuristics—the metaphor exposed
Authors: Sörensen Kenneth
Published: February 2013

In recent years, the field of combinatorial optimization has witnessed a true tsunami of “novel” metaheuristic methods, most of them based on a metaphor of some natural or man‐made process. The behavior of virtually any species of insects, the flow of water, musicians playing together – it seems that no idea is too far‐fetched to serve as inspiration to launch yet another metaheuristic. In this paper, we will argue that this line of research is threatening to lead the area of metaheuristics away from scientific rigor. We will examine the historical context that gave rise to the increasing use of metaphors as inspiration and justification for the development of new methods, discuss the reasons for the vulnerability of the metaheuristics field to this line of research, and point out its fallacies. At the same time, truly innovative research of high quality is being performed as well. We conclude the paper by discussing some of the properties of this research and by pointing out some of the most promising research avenues for the field of metaheuristics.
One‐piece zirconia oral implants: one‐year results from a prospective case series. 2. Three‐unit fixed dental prosthesis (FDP) reconstruction
Authors: Kohal Ralf‐Joachim , Patzelt Sebastian B. M. , Butz Frank , Sahlin Herman
Published: February 2013

Aim

To evaluate the clinical and radiological outcome of one‐piece zirconia oral implants for three‐unit fixed dental prosthesis (FDP) replacement after 1 year.

Materials

Twenty eight patients were recruited for the investigation and signed an informed consent. All patients were treated with a one‐stage implant surgery and a three‐unit immediate temporary restoration on two one‐piece zirconia implants. The implants were fabricated of yttria‐stabilized tetragonal zirconia (y‐TZP). The endosseous part of the implants was tapered with a porous surface. A total of 56 implants were inserted in the 28 patients. A total of 12 implants were placed in the upper jaws (six in the anterior area and six in the posterior area) and 44 in mandibles (all in the posterior area). At implant insertion and after 1 year, standardized radiographs were taken to evaluate the peri‐implant bone loss. To evaluate any influences from different baseline parameters on the marginal bone loss a univariate analysis was performed. Clinical soft tissue parameters probing depth (PD), clinical attachment level (CAL), modified bleeding index (mBI) and modified plaque index (mPI) were recorded. Implant cumulative survival rates were calculated using actuarial life table analysis. Changes in the clinical variables were assessed using the Wilcoxon Signed Ranks test (PD, CAL) and the Sign test (mBl, mPl). All significance tests were conducted at a 5% level of significance.

Results

After 1 year, one implant was lost resulting in a survival rate of 98.2%. The patient was excluded from further analysis. The marginal bone loss after 1 year amounted to 1.95 mm. In 40% of the patients a bone loss of at least 2 mm and in 28% of the patients a loss of more than 3 mm were observed. The PD decreased for implant and tooth sites over time, the values being significantly higher for implants than for teeth. Over 1 year, the CAL increased slightly around the implants and decreased around the teeth. At the 1‐year follow‐up, the CAL at the implant sites was statistically significantly higher than at the reference teeth. The mBI was significantly lower at implants than at teeth. The same result was found for the plaque index.

Conclusions

A high frequency of increased radiographic bone loss (>2 mm) after 1 year around the presented one‐piece zirconia implant system was found. The bone loss seems to be higher compared to the very limited availability of zirconia implant data. Therefore, within the limits of the present investigation, it may be concluded that the presented zirconia implant system possibly performs inferior to conventional titanium implants and to other zirconia implants regarding peri‐implant bone loss.
The preventative effects of a brief, early intervention for preschool‐aged children at risk for internalising: follow‐up into middle adolescence
Authors: Rapee Ronald M.
Published: February 2013

Background:  There are few evaluations of very early intervention for the prevention of internalising disorders and those that exist generally evaluate outcomes to a maximum of 12 months. The current study evaluated the very long term effects (11 years) of a brief internalising prevention program presented to parents of preschool aged children.

Methods:  The original sample comprised 146 preschool‐aged children who scored high on measures of inhibited temperament. Half of the parents were given a brief educational program (six‐sessions) to assist them to help their children reduce anxiousness. Over 70% of the original sample (n = 103) was assessed for the current study, which occurred when the sample was approximately 15 years. They were assessed on current diagnoses of anxiety and depression, as well as symptoms of anxiety, depression, negative thoughts, and life interference.

Results:  Compared with controls, girls whose parents had been through the early intervention program showed significantly fewer internalising disorders, maternally reported anxiety symptoms and self‐reported life interference, and trends toward lower self‐reported anxiety symptoms and self reported thoughts of loss and failure. Boys showed few differences.

Conclusions:  A brief early intervention program delivered to parents of preschool‐aged children who are at risk for later internalising distress shows lasting benefits for girls into the high‐risk period of middle adolescence. Given the low costs associated with this program, these results show promise for strong public health benefits.
Population structure, spatial distribution and life‐history traits of blacktip reef sharks Carcharhinus melanopterus
Authors: Mourier J. , Mills S. C. , Planes S.
Published: February 2013

During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore‐reefs. Mean growth rate was c. 6 cm year−1. Males reached sexual maturity at 111 cm LT. This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species.
Antifungal Activity and Chemical Composition of Thyme, Peppermint and Citronella Oils in Vapor Phase against Avocado and Peach Postharvest Pathogens
Authors: Sellamuthu Periyar Selvam , Sivakumar Dharini , Soundy Puffy
Published: February 2013

The antifungal activity of three essential oils thyme: (Thymus vulgaris L), peppermint, (Mentha piperita L) and citronella (Cymbopogen nardus); against two avocado postharvest fungal pathogens: Colletotrichum gloeosporioides (anthracnose), Lasiodiplodia theobromae (stem‐end rot); and three peach pathogens: Monilinia fructicola (brown rot), Rhizopus stolonifer (Rhizopus rot) and Penicillium expensum (blue mould rot), was assayed using a disc volatilization method. In vitro study revealed that in the vapor phase, thyme oil at 5 μL/plate as opposed to peppermint and citronella oils completely inhibited the radial mycelia growth of all five pathogens. gas chromatograph/mass spectrometry analysis showed thymol (58.77%), menthol (46.45%) and R (+) citronellal (27.59%) as the major compounds in thyme, peppermint and citronella oils, respectively. Thyme oil vapor showed a fungicidal effect on C. gloeosporioides, L. theobromae and R. stolonifer at 5 μL/plate. Thyme oil vapor at 66.7 μL/L significantly reduced anthracnose and stem‐end rot in artificially wounded and infected fruit. Therefore, these results suggest that thyme oil vapors could be used as alternate natural fungicide to control the common postharvest diseases in avocado.

Practical Applications

Growers and suppliers of fresh produce are faced with the challenge of providing consumers with products that are attractive, free from disease, defects and toxic residues, and with longer shelf or storage life. The strict regulations enforced by the fresh produce‐importing countries regarding the minimum pesticide residue levels in the edible portion of the fresh produce, increasing resistance to synthetic fungicides by fungal pathogens, waste disposal of fungicides and growing concerns to lower the associated environmental footprint have necessitated the search for a natural novel fungicide to replace synthetic fungicide applications in the packing line as postharvest treatment. Consumer preference to organic fresh produce is increasingly becoming popular in developed countries. On the other hand, synthetic fungicide applications are expensive for small‐scale farmers from developing countries. Therefore, considering all the reasons mentioned earlier, the results of our study provide a novel practical tool using thyme oil vapors to reduce losses because of postharvest diseases in avocado, and thus ensuring safe food.
Unusual Occurrence of Staphylococcus warneri as Endophyte in Fresh Fruits along with Usual Bacillus spp
Authors: Phukon Madhurima , Sahu Priyanka , Srinath Rajaraman , Nithya Angamuthu , Babu Subramanian
Published: February 2013

In the present study, we obtained several bacterial isolates from direct plating (without enrichment) of the diluted extract of apples and oranges obtained from commercial market of major cities in Tamil Nadu, India. Based on the cultural growth characteristics in different selective media, the isolates were grouped into four groups. The 16S rRNA gene was amplified using universal primers. The expected amplified fragments were obtained in four isolates belonging to two culture groups and were sequenced. This resulted in the identification of Staphylococcus warneri and Bacillus pumilis in apples and B. flexus and B. subtilis in oranges. The different species of Bacillus are reported already as endophytes in plants and plant‐derived produce. However, the occurrence of S. warneri is unusual. The observation emphasizes the need to further our understanding of the changing ecology of bacteria, particularly human pathogenic Staphylococcus, which has adapted to inner tissues of fruits.

Practical Application

Identification and detection of human pathogenic bacteria like Staphylococcus in fresh fruits is applicable in creating awareness among the public about the route cause of foodborne illness because of consumption of unhealthful raw and unpasteurized juices. In addition, this study helps us to reevaluate the present production and handling practices of fruits. It also emphasizes the need for developing strategies based on a coordinated approach by the growers, distributors, retailers, importers and public health officials to eliminate or contain such human pathogenic bacteria in fresh fruits.
Stress analysis in human temporomandibular joint affected by anterior disc displacement during prolonged clenching
Authors: Abe S. , Kawano F. , Kohge K. , Kawaoka T. , Ueda K. , Hattori‐Hara E. , Mori H. , Kuroda S. , Tanaka E.
Published: February 2013

Parafunctional habits, such as prolonged clenching and bruxism, have been associated with dysfunctional overloading in the temporomandibular joint (TMJ). In this study, stress distributions in the TMJ were analysed during prolonged clenching, using three‐dimensional finite element (FE) models of the TMJ with and without disc displacement. The aim of this study was to investigate stress distribution of the cartilaginous tissues in the TMJ with and without disc displacement. Finite element models were developed on the basis of magnetic resonance images from two subjects with and without anterior disc displacement. Condylar movements recorded during a 5‐min clenching were used as the loading condition for stress analysis. In the asymptomatic model, the highest von Mises stresses were located in the lateral area (4·91 MPa) of the disc surfaces, and after 5‐min clenching, the higher stresses were still located at the lateral area (3·65 MPa). In all the cartilaginous tissues, 30–50% of stress reduction occurred during 5‐min clenching. In contrast, the von Mises stress in the cartilaginous tissues of the symptomatic model with disc displacement was markedly lower, compared with the asymptomatic model. However, in the condylar cartilage, stress relaxation during clenching was not recognised. Furthermore, relatively high stresses were observed in the retrodiscal tissues throughout clenching. The present results indicate that disc position could be involved in the stress distribution of the TMJ components during prolonged clenching.
Enigmatic occurrence of Permian plant roots in Lower Silurian rocks, Guizhou Province, China
Authors: Wang Yi , Edwards Dianne , Bassett Michael , Xu Hong‐He , Xiao Jiafei , Jiang Qing , Zhang Xiaole
Published: February 2013

Pinnatiramosus qianensis Geng, 1986, is a plant with a complex, extensive pinnate branching system and pitted tracheids, collected from marine Lower Silurian (Llandovery; c. 430 Ma) rocks in Guizhou Province, China. It challenges long‐held theories on the origin and early evolution of vascular plants in the Silurian and Devonian. However, there is a hypothesis that the fossils were not syngenetic with the entombing rock, but were the rooting systems of much younger plants, probably of Permian age. New sections and collections of P. qianensis have been subjected to detailed analyses, which indicate that P. qianensis belongs to an early Permian (c. 285 Ma) rooting system growing down into lower Silurian rocks.
The first specimen of the Middle Triassic Phalarodon atavus (Ichthyosauria: Mixosauridae) from South China, showing postcranial anatomy and peri‐Tethyan distribution
Authors: Liu Jun , Motani Ryosuke , Jiang Da‐Yong , Hu Shi‐Xue , Aitchison Jonathan C. , Rieppel Olivier , Benton Michael J. , Zhang Qi‐Yue , Zhou Chang‐Yong
Published: February 2013

Phalarodon atavus from the Germanic Muschelkalk Basin was previously represented only by cranial elements. Here we report a nearly complete and articulated specimen of P. atavus from the Middle Triassic Luoping Biota, Yunnan, South China. This is the first specimen of P. atavus from outside the Germanic Basin. This discovery demonstrates a peri‐Tethyan distribution of P. atavus. The new specimen is also the first one preserving the postcranial anatomy of this species, providing the opportunity to evaluate its sustained swimming ability. Inferences made on its functional morphology suggest that this species was probably adapted for active foraging. Tooth crown morphology suggests that P. atavus may have preferred externally soft prey.
Positive emotion modulates cognitive control: An event‐related potentials study
Authors: Xue Song , Cui Jingjing , Wang Kangcheng , Zhang Songyan , Qiu Jiang , Luo Yuejia
Published: February 2013

There is substantial evidence to indicate that negative emotion can modulate cognitive control processing. However, only a few studies have investigated this effect with positive emotion. Therefore, the present study explored the electrophysiological correlates of the impact of positive emotional stimuli on cognitive control, using event‐related potentials (ERPs). Sixteen healthy young adults completed a modified Simon task (Simon, 1969). Behavioral data indicated that reaction times were faster for positive emotional stimuli than for neutral emotional stimuli in the incongruent condition, but not in the congruent condition, which suggested that positive emotion expedited conflict resolution. TheERPdata showed that two negativeERPcomponents (N300–400 and N450–550) were associated with the positive emotional stimuli in the incongruent minus congruent condition. It is suggested that these components may respectively be related to the conflict monitoring (N300–400) and response selection (N450–550) stages of cognitive control processing. Overall, our results indicated that positive emotion could facilitate cognitive control processing. These results are in line with the neuropsychological theory, according to which, positive emotion could modulate cognitive control mediated by increased dopamine levels in frontal brain areas.
Phenotypic changes associated with RNA interference silencing of chalcone synthase in apple (Malus × domestica)
Authors: Dare Andrew P. , Tomes Sumathi , Jones Midori , McGhie Tony K. , Stevenson David E. , Johnson Ross A. , Greenwood David R. , Hellens Roger P.
Published: February 2013

We have identified in apple (Malus × domestica) three chalcone synthase (CHS) genes. In order to understand the functional redundancy of this gene family RNA interference knockout lines were generated where all three of these genes were down‐regulated. These lines had no detectable anthocyanins and radically reduced concentrations of dihydrochalcones and flavonoids. Surprisingly, down‐regulation of CHS also led to major changes in plant development, resulting in plants with shortened internode lengths, smaller leaves and a greatly reduced growth rate. Microscopic analysis revealed that these phenotypic changes extended down to the cellular level, with CHS‐silenced lines showing aberrant cellular organisation in the leaves. Fruit collected from one CHS‐silenced line was smaller than the ‘Royal Gala’ controls, lacked flavonoids in the skin and flesh and also had changes in cell morphology. Auxin transport experiments showed increased rates of auxin transport in a CHS‐silenced line compared with the ‘Royal Gala’ control. As flavonoids are well known to be key modulators of auxin transport, we hypothesise that the removal of almost all flavonoids from the plant by CHS silencing creates a vastly altered environment for auxin transport to occur and results in the observed changes in growth and development.
Evolution of microtubule organizing centers across the tree of eukaryotes
Authors: Yubuki Naoji , Leander Brian S.
Published: February 2013

The architecture of eukaryotic cells is underpinned by complex arrrays of microtubules that stem from an organizing center, referred to as the MTOC. With few exceptions, MTOCs consist of two basal bodies that anchor flagellar axonemes and different configurations of microtubular roots. Variations in the structure of this cytoskeletal system, also referred to as the ‘flagellar apparatus’, reflect phylogenetic relationships and provide compelling evidence for inferring the overall tree of eukaryotes. However, reconstructions and subsequent comparisons of the flagellar apparatus are challenging, because these studies require sophisticated microscopy, spatial reasoning and detailed terminology. In an attempt to understand the unifying features of MTOCs and broad patterns of cytoskeletal homology across the tree of eukaryotes, we present a comprehensive overview of the eukaryotic flagellar apparatus within a modern molecular phylogenetic context. Specifically, we used the known cytoskeletal diversity within major groups of eukaryotes to infer the unifying features (ancestral states) for the flagellar apparatus in the Plantae, Opisthokonta, Amoebozoa, Stramenopiles, Alveolata, Rhizaria, Excavata, Cryptophyta, Haptophyta, Apusozoa, Breviata and Collodictyonidae. We then mapped these data onto the tree of eukaryotes in order to trace broad patterns of trait changes during the evolutionary history of the flagellar apparatus. This synthesis suggests that: (i) the most recent ancestor of all eukaryotes already had a complex flagellar apparatus, (ii) homologous traits associated with the flagellar apparatus have a punctate distribution across the tree of eukaryotes, and (iii) streamlining (trait losses) of the ancestral flagellar apparatus occurred several times independently in eukaryotes.
The Arabidopsis U–box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility
Authors: Wang Hai , Lu Yuqing , Jiang Tiantian , Berg Howard , Li Cong , Xia Yiji
Published: February 2013

Pollen formation is a complex developmental process that has been extensively investigated to unravel underlying fundamental developmental mechanisms and for genetic manipulation of the male‐sterility trait for hybrid crop production. Here we describe identification of AtPUB4, a U–box/ARM repeat‐containing E3 ubiquitin ligase, as a novel player in male fertility in Arabidopsis. Loss of AtPUB4 function causes hypertrophic growth of the tapetum layer. The Atpub4 mutation also leads to incomplete degeneration of the tapetal cells and strikingly abnormal exine structures of pollen grains. As a result, although the Atpub4 mutant produces viable pollen, the pollen grains adhere to each other and to the remnants of incompletely degenerated tapetal cells, and do not properly disperse from dehisced anthers for successful pollination. We found that the male‐sterility phenotype caused by the Atpub4 mutation is temperature‐dependent: the mutant plants are sterile when grown at 22°C but are partially fertile at 16°C. Our study also indicates that the AtPUB4‐mediated pathway acts in parallel with the brassinosteroid pathway in controlling developmental fates of the tapetal cells to ensure male fertility.
A Simple Thermal Resistance Model for Open Cell Metal Foams
Authors: Kamath Pradeep. M. , Balaji C. , Venkateshan S. P.
Published: February 2013

This paper presents a methodology for obtaining the convective heat transfer coefficient from the wall of a heated aluminium plate, placed in a vertical channel filled with open cell metal foams. For accomplishing this, a thermal resistance model from literature for metal foams is suitably modified to account for contact resistance. The contact resistance is then evaluated using the experimental results. A correlation for the estimation of the contact resistance as a function of the pertinent parameters, based on the above approach is developed. The model is first validated with experimental results in literature for the asymptotic case of negligible contact resistance. A parametric study of the effect of different foam parameters on the heat transfer is reported with and without the presence of contact resistance. The significance of the effect of contact resistance in the mixed convection and forced convection regimes is discussed. The procedure to employ the present methodology in an actual case is demonstrated and verified with additional, independent experimental data.
The Onset of Double-Diffusive Convection in a Vertical Cylinder With Vertical Throughflow
Authors: Nield D. A. , Kuznetsov A. V.
Published: February 2013

The effect of vertical throughflow on the onset of convection, induced by an applied vertical temperature gradient in a vertical cylinder is studied analytically using linear stability theory. This problem is important to hydrologists to investigate under what conditions convection is taking place in a well or borehole. The effect of double diffusion is included. Both nonoscillatory and oscillatory situations are studied.
Design of a New Portable Cryostorage Device
Authors: Breeden F. , LaFountain J. , Laurent M. , Robert J. , Devireddy R. V.
Published: February 2013

The currently available cryostorage systems are cumbersome to operate and offer little in the way of sample storage flexibility and user-friendliness. The aim is to redesign and fabricate a user-friendly portable storage system with monitoring capabilities for storage of cryopreserved biological samples for use in a small research laboratory setting. The proposed system consists of two concentric cylinders, between which a vacuum layer provides a thermal barrier and is similar to existing systems. More importantly, to improve sample accessibility and sample retrieval time, a new suspended tower design was developed while an instrumentation backpack provides housing for the monitoring systems. The new suspended tower design for holding the frozen biological samples is designed to hold traditional cryovials (1.5 ml and/or 1.2 ml or 1.5 × 10−6 m3 and/or 1.2 × 10−6 m3) and can also be modified to hold larger T-flasks, if required. The instrumentation consists of a capacitance based liquid level sensor, level monitor, and transmitter. The designed system is capable of holding ∼430 cryovials and holds ∼50 l (0.05 m3) of liquid nitrogen and requires refilling approximately every four to five weeks.
A Fuel Cell/Battery Hybrid Vehicle Modeling and Power Management/Regenerative Braking Controller Design
Authors: Naderi P. , Azizianfard M.
Published: February 2013

Here, a hybrid vehicle structure comprising fuel cell/battery and a PMDC electrical machine has been proposed, in which an intelligent controller is to perform power management and regenerative braking tasks. Instead of a gasoline engine, an electric machine fulfills the power demand from the vehicle during driving and braking modes. In addition, regenerative braking is possible in the proposed structure. The fuel cell is connected to a battery (DC bus) via a DC/DC converter which can control the fuel cell power/current with a switching strategy. A Nero–Fuzzy controller has been devised in order for taking the power demand as one of its controlling signals and making decision with respect to the power management issue. Duty cycle of the DC/DC converter is computed by the driving controller and applied with a certain switching frequency. Along with the power demand, braking pedal displacement, and the battery state of charge act as controlling signals, which allow the power management controller to perform pertinent analysis for power sharing decision between both the power sources. A threshold zone has been considered for braking pedal, according to which a regenerative torque is produced by the electrical machine. Finally, the simulation results have been considered from different point of views and evaluated, which shows a tenable achievement. Particularly, a series of driving maneuvers were applied to the vehicle, and the results show that the proposed structure has a promising performance as a civic automobile with zero emissions.
Computational Fluid Dynamics Evaluation of Equivalency in Hemodynamic Alterations Between Driver, Integrity, and Similar Stents Implanted Into an Idealized Coronary Artery
Authors: Gundert Timothy J. , Dholakia Ronak J. , McMahon Dennis , LaDisa John F.
Published: February 2013

We tested the hypothesis that a slight modification in fabrication from the Driver to the Integrity stent (Medtronic) results in nearly equivalent distributions of wall shear stress (WSS) and mean exposure time (MET), reflective of flow stagnation, and that these differences are considerably less than the Multi-Link Vision (Abbott Vascular) or BX Velocity (Cordis) bare metal stents when evaluated by computational fluid dynamics (CFD). Arteries were modeled as idealized straight rigid vessels without lesions. Two vessel diameters (2.25 and 3.0 mm) were studied for each stent and 2.75 mm diameter Integrity stents were also modeled to quantify the impact from best- and worst-case orientations of the stent struts relative to the primary blood flow direction. All stents were 18 mm in length and over-deployed by 10%. The results indicated that, regardless of diameter, the BX Velocity stents had the greatest percentage of the vessel exposed to adverse WSS followed by the Vision, Integrity, and Driver stents. In general, when strut thickness and stent:lumen ratio are similar, the orientation of struts is a determining factor for deleterious flow patterns. For a given stent, the number of struts was a larger determinant of adverse WSS and MET than strut orientation, suggesting that favorable blood flow patterns can be achieved by limiting struts to those providing adequate scaffolding. In conclusion, the Driver and Integrity stents both limit their number of linkages to those which provide adequate scaffolding while also maintaining similar strut thickness and stent:lumen ratios. The Integrity stent also imparts a slight helical velocity component. The modest difference in the fabrication approach between the Driver and Integrity stents is, therefore, not hemodynamically substantial in this idealized analysis, particularly relative to potentially adverse flow conditions introduced by the other stents modeled. This data was used in conjunction with associated regulatory filings and submitted to the FDA as part of the documents facilitating the recent approval for sale of the Resolute Integrity stent in the United States.
Structural and electrical characterization of InN, InGaN, and p-InGaN grown by metal-modulated epitaxy
Authors: Moseley Michael , Gunning Brendan , Lowder Jonathan , Alan Doolittle W. , Namkoong Gon
Published: February 2013

InN, high indium content InGaN, and Mg-doped InGaN were grown by metal modulated epitaxy (MME). Transient reflection high-energy electron diffraction intensities were analyzed during the growth of InN and found to be similar to that previously reported for GaN and AlN. The x-ray diffraction rocking curve and background electron concentration of InN grown by MME were found to be respectable in comparison to recent reports in literature. InGaN alloys grown by MME were also investigated, and a method for detecting indium surface segregation was demonstrated. It was found that the shutter modulation scheme could be modified to prevent phase separation by indium surface segregation, and a range of single-phase InGaN samples with indium contents throughout the miscibility gap were grown. Using the discovered method of suppressing phase separation, several p-InxGa1 − xN samples were grown with indium contents from x = 0 to 0.22. A maximum hole concentration of 2.4 × 1019 cm−3 was detected by Hall effect characterization, demonstrating feasibility of these p-InGaN layers for use in several device applications.
A new respiratory gating device to improve 4D PET/CT
Authors: Didierlaurent David , Ribes Sophie , Caselles Olivier , Jaudet Cyril , Cazalet Jean‐Marc , Batatia Hadj , Courbon Frédéric
Published: February 2013

Purpose:

Respiratory motion creates artifacts in positon emission tomography with computed tomography (PET/CT) images especially for lung tumors, and can alter diagnosis. To account for motion effects, respiratory gating techniques have been developed. However, the lack of measures strongly correlated with tumor motion limits their accuracy. The authors developed a real‐time pneumotachograph device (SPI) allowing to sort PET and CT images depending on lung volumes.

Methods:

The performance of this innovative respiratory tracking system was characterized and compared to a standard system. Our experimental setup consisted in a movable platform and a thorax phantom with six fillable spheres simulating lung tumors. The accuracy of SPI to detect inhalation peaks was also determined on volunteers. A comparison with the real‐time position management (RPM) device, that relies on abdominal height measurement, was then investigated.

Results:

Experiments showed a high accuracy of the measured signal compared to the input signal (R = 0.88 to 0.99), and of the detection of the inhalation peaks (error of 0.1 +/− 5.8 ms) necessary for prospective binning mode. Activity recovery coefficient was improved (until +39%) and the smearing effect was reduced (until 2.74 times lower) with SPI compared to ungated PET/CT acquisition. The spatial distribution of activity in spheres was similar for 4D PET gated with SPI and RPM. Significant improvement of the binning stability and matching between PET and CT were highlighted for irregular breathing patterns with SPI.

Conclusions:

SPI is an innovative device that provides better binning performance than the current gating device on phantom experiments. Future works will focus on patients where the authors expect a significant improvement of specificity and sensitivity of PET/CT examinations.
A study on investigating the delivery parameter error effect on the variation of patient quality assurance during RapidArc treatment
Authors: Peng Jiayuan , Zhang Zhen , Zhou Lijun , Zhao Jinfang , Wang Jiazhou , Kong Lin , Hu Weigang
Published: February 2013

Purpose:

The purpose of this study is to evaluate delivery parameter errors (DPEs) and their impact on clinical dose variation with the Varian RapidArc technique.

Methods:

The dynalog files of 16 head‐and‐neck patients were retrospectively analyzed to characterize three RapidArc DPEs: dose MU, gantry angle, and MLC gap errors. A total of 64 reconstructed plans were created by creating four variants of each of the original 16 plans (three with the DPEs applied individually and one with the three DPEs combined). These reconstructed plans were compared to the original plans to evaluate the impact of the DPEs on the clinical dose distribution.

Results:

The mean dose MU, gantry angle, and MLC gap error for all patients were 0.00 ± 0.00 MU, −0.36 ± 0.03°, and 0.00 ± 0.01 mm, respectively. The DPEs had no obvious dosimetric impact on any of the studied dosimetric endpoints except the parotid dose. The gantry angle error, MLC gap error, and combined DPEs changed the parotid Dmean (mean dose) and parotid V30 (volume receiving at least 30 Gy) by 1%–2%.

Conclusions:

It is feasible to use dose distributions reconstructed from dynalog file data as a quality assurance tool. The dose MU, gantry angle, and MLC errors have only minor effects on the accuracy of the delivered dose.