bluuebunny/crossref_metadata_2025 huggingface dataset:
A New Race of Colletotrichum trifolii Identified on Alfalfa in Ohio
Authors: Ariss J. J. , Rhodes L. H.
Published: September 2007

Anthracnose of alfalfa (Medicago sativa L.), caused by the fungus Colletotrichum trifolii Bain & Essary, was identified as a potential problem of alfalfa in the United States in the late 1960s. Races 1 and 2 are known in the United States, and recently, race 4 was described in Australia (1). An additional race, race 3, had previously been reported in the United States, but isolates of this proposed race were not preserved and its status as a distinct race of C. trifolii is unclear. In June 2003, an isolate of C. trifolii was collected in Columbus, OH from a 4-year-old alfalfa stand of cv. 520. The isolate was obtained from typical anthracnose stem lesions. Stem sections with lesions were scraped with a sterile inoculation loop, and conidia were directly streaked onto acidified potato dextrose agar. Individual colonies were transferred to half-strength oatmeal agar. Morphological characters (conidia, acervuli, and setae) of this isolate, designated OH-WA-520, were consistent with those of other C. trifolii isolates and clearly distinguishable from C. destructivum or other Colletotrichum spp. that occur on alfalfa. The alfalfa differential cultivars Arc (resistant to race 1 and susceptible to race 2 of C. trifolii), Saranac AR (resistant to race 1 and race 2), and Saranac (susceptible to both races) were inoculated with conidia of isolate OH-WA-520 per the North American Alfalfa Improvement Conference standard protocol for determining anthracnose resistance (2). Isolate OH-WA-520 was avirulent on Arc but virulent on Saranac AR and Saranac. In each of three repetitions of the protocol, more than 65% of Arc plants survived, while less than 18% of Saranac and Saranac AR plants survived. These results indicate a physiological race inconsistent in reaction with C. trifolii race 1 or race 2, but similar in reaction to race 4 isolates previously described only from Australia (1). To our knowledge, this is the first report of a C. trifolii isolate virulent on Saranac AR but avirulent on Arc. This is also the first report of C. trifolii race 4 in the United States.

References: (1) J. M. Mackie et al. Aust. J. Agric. Res. 54:829, 2003. (2) N. R. O'Neill. Anthracnose resistance. Page D-1 in: Standard Tests to Characterize Alfalfa Cultivars. Online publication. North American Alfalfa Improvement Conference, Beltsville, MD, 1991.
Reoperation for sella haematoma after pituitary surgery
Authors: Atkinson John L. D. , Nippoldt Todd B. , Koeller Kelly K.
Published: September 2007

Objective  Although occasionally discussed as a general complication in large pituitary series, the incidence of reoperation for postoperative sella haematoma is unclear. We retrospectively reviewed a large pituitary surgical series to determine the incidence and associated factors of this complication.

Design  We reviewed all pituitary surgery at Mayo Rochester from January 1987 until January 2007. There were 2312 transsphenoidal procedures during this period.

Patients  All patients had proven pituitary pathology by computed tomography (CT) or magnetic resonance imaging and pituitary function studies.

Measurements  Reoperation for sella haematoma and perioperative clinical correlations were the only measurement tools. It is indeterminate how many patients had postoperative sella haematoma without visual loss because routine postoperative CT scanning was not performed.

Results  Three patients underwent reoperation for postoperative haematoma in the sella by three different endocrine neurosurgeons, and all three patients had progressive postoperative visual loss. All initial operations were for large macroadenomas; two had early postoperative hypertension that may have been a contributor; and one had markedly thickened bone felt to be the source of bleeding and deterioration 24 h later.

Conclusions  Reoperation for postoperative sellar haematoma is uncommon. However, postoperative progressive visual loss was clinically present in all three patients, and labile hypertension postoperatively may play a role.
Successful liver retransplantation for recurrent hepatopulmonary syndrome
Authors: Rajwal S. R. , Davison S. M. , Prasad R. , Brownlee K. , McClean P.
Published: September 2007

Abstract:  HPS is defined as arterial hypoxemia because of pulmonary vasodilation as a result of cirrhotic or non‐cirrhotic portal hypertension. This report describes a teenager with HPS because of primary sclerosing cholangitis/autoimmune hepatitis overlap syndrome requiring OLT. HPS resolved completely within three months of OLT, but recurred again at 12 months post‐OLT following liver dysfunction secondary to a biliary stricture. She underwent a second OLT successfully and remains well two yr and three months post‐second OLT. Recurrent HPS after OLT may occur because of graft dysfunction and as this novel case illustrates, retransplantation may lead to a successful outcome.
Nodular Lesions of the Tongue in Canine Leishmaniosis
Authors: Pinna Parpaglia M. L. , Vercelli A. , Cocco R. , Zobba R. , Manunta M. L.
Published: September 2007

In this case report, an atypical clinical presentation of leishmaniosis in a dog with multiple nodular lesions of the tongue is described. Haematological and biochemical analysis, serological test for Leishmania infantum antibodies and biopsy samples from several nodules of the tongue for histopathological examination were made. The final diagnosis of leishmaniosis was based upon the observation of amastigotes in the bioptic samples. It is recommended to consider leishmaniosis among the list of differentials of mucosal nodular lesions, at least in endemic areas.
Cell‐by‐cell reconstruction in reaggregates from neonatal gerbil retina begins from the inner retina and is promoted by retinal pigmented epithelium
Authors: Bytyqi Afrim H. , Bachmann Gesine , Rieke Matthias , Paraoanu Laura E. , Layer Paul G.
Published: September 2007

For future retinal tissue engineering, it is essential to understand formation of retinal tissue in a ‘cell‐by‐cell’ manner, as can be best studied in retinal reaggregates. In avians, complete laminar spheres can be produced, with ganglion cells internally and photoreceptors at the surface; a similar degree of retinal reconstruction has not been achieved for mammals. Here, we have studied self‐organizing potencies of retinal cells from neonatal gerbil retinae to form histotypic spheroids up to 15 days in culture (R‐spheres). Shortly after reaggregation, a first sign of tissue organization was detected by use of an amacrine cell (AC)‐specific calretinin (CR) antibody. These cells sorted out into small clusters and sent unipolar processes towards the centre of each cluster. Thereby, inner cell‐free spaces developed into inner plexiform layer (IPL)‐like areas with extended parallel CR+ fibres. Occasionally, IPL areas merged to combine an ‘inner half retina’, whereby ganglion cells (GCs) occupied the outer sphere surface. This tendency was much improved in the presence of supernatants from retinal pigmented cells (RPE‐spheres), e.g. cell organization and proliferation was much increased, and cell death shortened. As shown by several markers, a perfect outer ring was formed by GCs and displaced ACs, followed by a distinct IPL and 1–2 rows of ACs internally. The inner core of RPE spheres consisted of horizontal and possibly bipolar cells, while immunostaining and RT‐PCR analysis proved that photoreceptors were absent. This shows that (1) mammalian retinal histogenesis in reaggregates can be brought to a hitherto unknown high level, (2) retinal tissue self‐organizes from the level of the IPL, and (3) RPE factors promote formation of almost complete retinal spheres, however, their polarity was opposite to that found in respective avian spheroids.
Adult neural stem and progenitor cells modified to secrete GDNF can protect, migrate and integrate after intracerebral transplantation in rats with transient forebrain ischemia
Authors: Kameda M. , Shingo T. , Takahashi K. , Muraoka K. , Kurozumi K. , Yasuhara T. , Maruo T. , Tsuboi T. , Uozumi T. , Matsui T. , Miyoshi Y. , Hamada H. , Date I.
Published: September 2007

Adult neural stem and progenitor cells (NSPCs) are important autologous transplantation tools in regenerative medicine, as they can secrete factors that protect the ischemic brain. We investigated whether adult NSPCs genetically modified to secrete more glial cell line‐derived neurotrophic factor (GDNF) could protect against transient ischemia in rats. NSPCs were harvested from the subventricular zone of adult Wistar rats and cultured for 3 weeks in the presence of epidermal growth factor. The NSPCs were treated with fibre‐mutant Arg‐Gly‐Asp adenovirus containing the GDNF gene (NSPC‐GDNF) or enhanced green fluorescent protein (EGFP) gene (NSPC‐EGFP; control group). In one experiment, cultured cells were transplanted into the right ischemic boundary zone of Wistar rat brains. One week later, animals underwent 90 min of intraluminal right middle cerebral artery occlusion followed by magnetic resonance imaging and behavioural tests. The NSPC‐GDNF group had higher behavioural scores and lesser infarct volume than did controls at 1, 7 and 28 days postocclusion. In the second experiment, we transplanted NSPCs 3 h after ischemic insult. Compared to controls, rats receiving NSPC‐GDNF had decreased infarct volume and better behavioural assessments at 7 days post‐transplant. Animals were killed on day 7 and brains were collected for GDNF ELISA and morphological assessment. Compared to controls, more GDNF was secreted, more NSPC‐GDNF cells migrated toward the ischemic core and more NSPC‐GDNF cells expressed immature neuronal marker. Moreover, the NSPC‐GDNF group showed more effective inhibition of microglial invasion and apoptosis. These findings suggest that NSPC‐GDNF may be useful in treatment of cerebral ischemia.
Corticospinal control of antagonistic muscles in the cat
Authors: Ethier Christian , Brizzi Laurent , Giguère Dominic , Capaday Charles
Published: September 2007

We recently suggested that movement‐related inter‐joint muscle synergies are recruited by selected excitation and selected release from inhibition of cortical points. Here we asked whether a similar cortical mechanism operates in the functional linking of antagonistic muscles. To this end experiments were done on ketamine‐anesthetized cats. Intracortical microstimulation (ICMS) and intramuscular electromyographic recordings were used to find and characterize wrist, elbow and shoulder antagonistic motor cortical points. Simultaneous ICMS applied at two cortical points, each evoking activity in one of a pair of antagonistic muscles, produced co‐contraction of antagonistic muscle pairs. However, we found an obvious asymmetry in the strength of reciprocal inhibition; it was always significantly stronger on physiological extensors than flexors. Following intravenous injection of a single bolus of strychnine, a cortical point at which only a physiological flexor was previously activated also elicited simultaneous activation of its antagonist. This demonstrates that antagonistic corticospinal neurons are closely grouped, or intermingled. To test whether releasing a cortical point from inhibition allows it to be functionally linked with an antagonistic cortical point, one of three GABAA receptor antagonists, bicuculline, gabazine or picrotoxin, was injected iontophoretically at one cortical point while stimulation was applied to an antagonistic cortical point. This coupling always resulted in co‐contraction of the represented antagonistic muscles. Thus, antagonistic motor cortical points are linked by excitatory intracortical connections held in check by local GABAergic inhibition, with reciprocal inhibition occurring at the spinal level. Importantly, the asymmetry of cortically mediated reciprocal inhibition would appear significantly to bias muscle maps obtained by ICMS in favor of physiological flexors.
Is intrapartum asphyxia preventable?
Authors: Becher J‐C , Stenson BJ , Lyon AJ
Published: September 2007

The contribution of intrapartum events to asphyxia‐related mortality and morbidity and the degree to which it may be prevented are controversial. We examined trends in asphyxia‐related mortality and morbidity in a single large regional perinatal centre. Between 1994 and 2005, the rate of asphyxia fell from 2.86/1000 births in 1994 to 0.91/1000 births in 2005 (P < 0.001). Hypoxic‐ischaemic encephalopathy of all grades fell from 2.41 to 0.77/1000 live births (P < 0.001). This substantial and steady fall in the rate of asphyxia‐related mortality and morbidity over a 12‐year period suggests that a significant proportion of cases of intrapartum asphyxia may be preventable.
Pleurotaenium trabecula, a desmid of wetland biofilms: the extracellular matrix and adhesion mechanisms1
Authors: Domozych David S. , Elliott Leah , Kiemle Sarah N. , Gretz Michael R.
Published: September 2007

Pleurotaenium trabecula(Ehren.) Nägeli is a placoderm desmid that commonly occurs in wetland biofilms of the southeastern Adirondacks (NY, USA). It often displays a distinctive habit whereby the cell remains attached to the substrate via the polar end of one semicell, while the remainder of the cell is suspended in the water column. In this study, we examined the extracellular matrix (ECM) of this alga to elucidate its adhesion mechanisms and postadhesion behavior. The ECM consists of the following: (i) an extracellular polymeric substance (EPS), which includes polyanionic and sulfated polysaccharides; (ii) a thin pectin‐containing primary cell wall, which is quickly sloughed off after postcytokinetic semicell expansion; and (iii) a thick secondary cell wall that is perforated with a distinct pore complex. Each pore of this complex possesses an external network of densely aggregated fibrils. Selective solubilization and immunolabeling studies suggest that these fibrillar aggregates or “adhesion centers” (i.e., ACs) contain arabinogalactan protein and are involved in initial adhesion of the cell to a substrate. We propose that postinitial adhesion behavior entails localized secretion of EPS derived from a large pool of EPS‐containing vesicles situated in the peripheral cytoplasm. As the EPS absorbs water, hygroscopic pressure breaks the connections between the ACs on the cell wall and substrate and allows a portion of a cell to lift up into the water column.
Comparative study of the life cycles of Alexandrium tamutum and Alexandrium minutum (Gonyaulacales, Dinophyceae) in culture1
Authors: Figueroa Rosa Isabel , Garcés Esther , Bravo Isabel
Published: September 2007

The microalgal genus Alexandrium includes species known to produce paralytic shellfish poisoning (PSP). Due to the importance of discriminating between HAB‐forming species, we compared the undescribed life‐cycle pattern of Alexandrium tamutum Montresor, Beran et U. John and of its toxic relative Alexandrium minutum Halim. Sexual stages, asexual and sexual division, mating type, and nuclear morphology were studied in both species. Sexual cysts are known to be morphologically identical. However, the relative size of the U‐shaped nucleus may be used to differentiate between the cysts of these species since DNA packaging in the resting cysts was lower in A. tamutum than in A. minutum, species in which the planozygote nucleus was reduced to half its volume prior to encystment. The dormancy period of the cysts was <20 d for A. tamutum, but longer than 1 month for A. minutum. In both species, cyst appearance needed to be explained by the existence of more than two sexual types (+/–), which indicates a complex heterothallic mating type. However, planozygotes of both species may divide instead of encysting. This characteristic was used for nutritional and heritage studies. Isolated planozygotes of both species encysted in larger percentages in medium deficient in both nitrates and phosphates (L/15) than in medium without phosphates added (L‐P), a medium in which most planozygotes neither divide nor encyst. Parental strains of A. minutum with and without the ventral pore formed planozygotes and, later, offspring with the ventral pore, although apparently smaller than usual. A synchronization–flow cytometry method for discriminating diploids formed by sexual fusion (planozygotes) from cells with 2C DNA content resulting from self‐duplication of DNA (dividing cells) was described. The results indicated that the maximum percentage of A. minutum planozygotes (20%) was achieved only 3 to 5 d after crossing the parental strains, and that light might not be needed for the sexual fusion and formation of planozygotes.
Comparative responses of phytoplankton during chemical recovery in atmospherically and experimentally acidified lakes1
Authors: Graham Mark D. , Vinebrooke Rolf D. , Keller Bill , Heneberry Jocelyne , Nicholls Kenneth H. , Findlay David L.
Published: September 2007

Twenty lakes recovering from a century of atmospheric acid deposition over Northeastern Ontario were resurveyed for phytoplankton following a 20‐year period and were compared with a 23‐year study of an experimentally acidified lake, L302S (Experimental Lakes Area, ON, Canada). Phytoplankton species significantly tracked abiotic changes during both acidification and chemical recovery in all lakes based on concordance testing. However, ordination analyses showed that many phytoplankton communities had not returned to their preacidification state. Significant explanatory variables of taxonomic responses were pH, dissolved organic carbon (DOC), and inorganic nutrients (N, P), based on canonical correspondence analysis (CCA). Increases in DOC and pH influenced a significant taxonomic shift from acid‐tolerant dinoflagellates to a diverse assemblage of cyanobacteria, chlorophytes, and diatoms. Declining nitrogen levels defined a secondary environmental gradient, which was characterized by a decrease in filamentous green algal abundance. L302S remained remote in ordination space from the more chronically and heavily polluted lakes in Northeastern Ontario, indicating that experimental acidification provided a conservative estimate of the true damage to atmospherically polluted lakes. However, L302S did increasingly resemble lakes in Northeastern Ontario, suggesting that experimental acidification simulated the impacts of moderate levels of atmospheric pollution. Our findings demonstrate the importance of ecological history in understanding the responses by boreal lake ecosystems to environmental change.
Group size in a gregarious tortoise beetle: patterns of oviposition vs. larval behaviour
Authors: Costa Juan F. , Cosio Walter , Gianoli Ernesto
Published: September 2007

In laboratory and garden experiments, we tested for the existence of adaptive patterns of oviposition and larval behaviour regarding group size in the gregarious tortoise beetle Chelymorpha varians Blanchard (Coleoptera: Chrysomelidae: Cassidinae) on its host plant Calystegia sepium L. (Convolvulaceae). Specifically, we addressed the following questions: (i) Which is the more frequent egg cluster size? (ii) Does cluster size fully predict larval group size? (iii) Are newborn larvae attracted or repelled to conspecific groupings? and (iv) Which is the group size associated with enhanced larval development and adult mass? We found that the mean cluster size was 21.4 eggs. Egg hatch time was significantly shorter in larger clusters. A regression analysis of larval group size against cluster size showed non‐significant results. Thus, original cluster size did not totally determine the larval group size. The mean larval group size was 17.1. Choice tests in an experimental arena showed that larvae clearly preferred leaves of a host plant rather than moistened papers, and that larvae preferred a small group of conspecifics (four larvae per leaf) over larger groups (12 or 20 larvae). Empty leaves of the host plant showed an intermediate level of preference. Development time and beetle performance (adult mass) were affected by larval group size. Larvae in the smallest group (one per leaf) took four more days to attain adulthood than larvae in the larger groups (12 and 20 larvae). Adult C. varians reared in the 12‐larvae group were significantly larger than those reared at the other densities. Comparison of patterns across experimental groups, excluding the 12‐larvae group, showed a tendency for a greater final mass with slower developmental rate.
Day care in relation to respiratory‐tract and gastrointestinal infections in a German birth cohort study
Authors: Zutavern Anne , Rzehak Peter , Brockow Inken , Schaaf Beate , Bollrath Christina , Von Berg Andrea , Link Elke , Kraemer Ursula , Borte Michael , Herbarth Olf , Wichmann H‐Erich , Heinrich Joachim ,   for the LISA Study Group
Published: September 2007

Aim: To describe day care attendance in Germany today (in former East and former West Germany). To investigate longitudinally whether children attending day care centres have an increased risk of acquiring common cold, bronchitis, pneumonia, otitis media or diarrhea.

Methods: Questionnaire information was collected when the children in the cohort were 6, 12, 18, 24 months, and 4 and 6 years old. Day care within the first and first 2 years of life was investigated longitudinally with GEE (generalised estimating equations) methods in relation to common cold, bronchitis, pneumonia, otitis media and diarrhea within the first 6 years of life.

Results: Day care centre attendance is more common in former East than in former West Germany; this difference is evident even 10–12 years after German reunification. Children attending a day care centre were more likely to have common cold, bronchitis, pneumonia, otitis media and diarrhea within the first 2–3 years of life. With the exception of common cold, from year 4 onwards these associations were not statistically significant anymore and even reversed for some of the infections.

Conclusions: Children attending day care centres were at an increased risk of respiratory and gastrointestinal infections within the first years of life. However, around school age these differences disappeared or even partly reversed.
Bed‐sharing in the first four months of life: a risk factor for sudden infant death
Authors: Ruys Jan H , De Jonge Guus A , Brand Ronald , Engelberts Adèle C , Semmekrot Ben A
Published: September 2007

Aim: To investigate the risk of sudden infant death in the Netherlands during bed‐sharing in the first half year of life and the protective effect of breastfeeding on it.

Methods: During a 10‐year period between September 1996 and September 2006 nationwide, 213 cot deaths were investigated.

Results and discussion: Of 138 cot deaths of less than 6 months of age, 36 (26%) bed‐shared. In a reference group of 1628 babies from infant welfare centres only 9.4% were bed‐sharing in the night prior to the interview.

After correction for smoking of one or both parents the odds ratio for cot death during bed‐sharing with parents decreased with age from 9.1 (CI 4.2–19.4) at 1 month, to 4.0 (CI 2.3–6.7) at 2 months, to 1.7 (CI 0.9–3.4) at 3 months and to 1.3 (CI 1.0–1.6) at 4 through 5 months of age. The excess risk (OR > 1) associated with bed‐sharing is itself not significantly influenced by the presence or absence of breastfeeding.

Conclusion: Bed‐sharing is a serious risk factor for sudden infant death for all babies of less than 4 months of age. From 4 months onwards bed‐sharing did not contribute significantly to the risk of cot death anymore in our study.
Nurses promote openness regarding the genetic origins after gamete donation
Authors: Sydsjö G , Lampic C , Sunnerud S , Svanberg A Skoog
Published: September 2007

Aim: To study attitudes and knowledge concerning different aspects of sperm and oocyte donation among paediatric nurses at child health care centres (CHCs) in Sweden.

Method: A study‐specific questionnaire, to be completed anonymously, was sent to 188 nurses, 141 of whom (75%) responded.

Results: The majority of the respondents (62%) stated that they had no professional experience of families created with the help of a donor. A majority (53%) stated that they had good knowledge of the procedure followed in sperm donation, whereas 43% stated that they had good knowledge of the procedure of oocyte donation. More than 80% agreed that the parents should be honest with their child with regard to the child's genetic origin. Among the respondents who were in favour of disclosure, the preferred age for informing the child varied between 0 to 19 years (mean 7.2, SD 5.7).

Conclusion: We conclude that the nurses working in CHCs need guidance and information about gamete donation in order to be able to support parents in the disclosure of information to their children and also how to inform or withhold information to significant others in their surrounding milieu.
Cry features in siblings of SIDS
Authors: Robb Michael P , Crowell David H , Dunn‐Rankin Peter , Tinsley Cynthia
Published: September 2007

Aim: To examine the acoustic features of crying demonstrated by infants whose older sibling died of sudden infant death syndrome (SIDS) and compare these features to a nonrisk group of infants.

Methods: Pain‐induced crying episodes were collected from a group of healthy term (HT) infants and siblings of SIDS infants. One complete crying episode was obtained from each infant and analyzed acoustically with regard to durational and spectral features.

Results: The cries of SIDS siblings were found to be significantly higher in pitch and reflected hyperadductory vocal fold vibratory behaviour compared to the HT group. There were no group differences with regard to durational features of crying.

Conclusions: The laryngeal behaviour of infant crying, as inferred via acoustic analyses, differs between HT infants and siblings of SIDS infants. Accordingly, acoustic features of infant crying may serve as an additional diagnostic marker in the identification of children who may be at risk for SIDS.
Novel Drug Resistance Pattern Associated with the Mutations K70G and M184V in Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Authors: Bradshaw D. , Malik S. , Booth C. , Van Houtte M. , Pattery T. , Waters A. , Ainsworth J. , Geretti A. M.
Published: September 2007

We describe an unusual pathway of human immunodeficiency virus type 1 reverse transcriptase resistance during therapy with tenofovir-emtricitabine, characterized initially by the mutations K70E and M184V and later by K70G and M184V, with the two mutations coexisting on the same viral genome. Phenotypic resistance to lamivudine, emtricitabine, abacavir, didanosine, and tenofovir was observed, whereas susceptibility to zidovudine and stavudine was preserved.
Intrinsic Novobiocin Resistance in
Staphylococcus saprophyticus
Authors: Vickers Anna A. , Chopra Ian , O'Neill Alex J.
Published: September 2007

Intrinsic novobiocin resistance in
Staphylococcus saprophyticus
was associated with expression of a novobiocin-resistant form of the drug target protein (GyrB). Site-directed mutagenesis established that resistance depends upon the presence of two specific amino acid residues in GyrB: a glycine at position 85 and a lysine at position 140.
RNAIII-Inhibiting Peptide Affects Biofilm Formation in a Rat Model of Staphylococcal Ureteral Stent Infection
Authors: Cirioni Oscar , Ghiselli Roberto , Minardi Daniele , Orlando Fiorenza , Mocchegiani Federico , Silvestri Carmela , Muzzonigro Giovanni , Saba Vittorio , Scalise Giorgio , Balaban Naomi , Giacometti Andrea
Published: September 2007

Ureteral stents coated with the quorum-sensing inhibitor RNAIII-inhibiting peptide (RIP) were implanted in rat bladders and shown to suppress
Staphylococcus aureus
formation on the stent and in urine and was especially effective when combined with teicoplanin. Coating ureteral stents with RIP thus increases the efficacy of teicoplanin in preventing ureteral stent-associated staphylococcal infections.
Tissue Engineering Laboratory in Malaysia
Authors: Hj. Idrus Ruszymah , Saim Aminuddin
Published: September 2007

The article is about the tissue engineering laboratory in Malaysia. It touches on six areas of bioengineering, namely: skin, cartilage, bone, respiratory epithelium, stem cells and biomaterials.
Bioengineering as a Career
Authors: Ng Kee Woei
Published: September 2007

The article is written by a post-graduate student who touches on his experience on choosing bioengineering as a career.
Integrated Test Solutions for a System DesignEnvironment
Authors: Kornegay Kevin T. , Brodersen Robert W.
Published: September 2007

While the performance, density, and complexity of application‐specific systems increase at a rapid pace, equivalent
advances are not being made in making them more easily testable, diagnosable, and maintainable. Even though
testability bus standards, like JTAG Boundary Scan, have been developed to help eliminate these costs, there
exists a need for efficient hardware and software tools to support them. Hence, a testability design and hardware
support environment for application‐specific systems is described which provides a designer with a set of hardware
modules and circuitry, that support these standards and software tools for automatic incorporation of testability
hardware, as well as automatic test vector and test program generation.
Cluster Partitioning Techniques for Data PathSynthesis
Authors: Chen Chien-In Henry , Sobelman Gerald
Published: September 2007

New, efficient algorithms for the automated synthesis of buses in data path design are presented. Modifications
to the technique of Generalized Clique Partitioning (GCP) are discussed which lead to better designs and reduced
computation time in large synthesis problems. The new approach, Weighted Cluster Partitioning (WCP), eliminates
the need for backtracking. The algorithm guides the process of bus formation by assigning a higher weight to
those interconnection units that should be combined first. The operation of the WCP algorithm is clearly demonstrated
using a detailed example.

A modified priority ordering in the selection of the candidate pair is also discussed which can improve the
performance of GCP and WCP. We demonstrate that GCP II performs better than GCP, while WCP II consistently
produces the best results of all these algorithms on a set of large synthesis examples.
Formulation of Macroscopic TransportModels for Numerical Simulationof Semiconductor Devices
Authors: Kan Edwin C. , Yu Zhiping , Dutton Robert W. , Chen Datong , Ravaioli Umberto
Published: September 2007

According to different assumptions in deriving carrier and energy flux equations, macroscopic semiconductor
transport models from the moments of the Boltzmann transport equation (BTE) can be divided into two main
categories: the hydrodynamic (HD) model which basically follows Bløtekjer′s approach [1, 2], and the Energy
Transport (ET) model which originates from Strattton′s approximation [3, 4]. The formulation, discretization,
parametrization and numerical properties of the HD and ET models are carefully examined and compared. The
well‐known spurious velocity spike of the HD model in simple nin structures can then be understood from its
formulation and parametrization of the thermoelectric current components. Recent progress in treating negative
differential resistances with the ET model and extending the model to thermoelectric simulation is summarized.
Finally, we propose a new model denoted by DUET (Dual ET)which accounts for all thermoelectric effects in
most modern devices and demonstrates very good numerical properties. The new advances in applicability and
computational efficiency of the ET model, as well as its easy implementation by modifying the conventional
drift‐diffusion (DD) model, indicate its attractiveness for numerical simulation of advanced semiconductor
devices
Mixed‐RKDG Finite Element Methodsfor the 2‐D Hydrodynamic Modelfor Semiconductor Device Simulation
Authors: Chen Zhangxin , Cockburn Bernardo , Jerome Joseph W. , Shu Chi-Wang
Published: September 2007

In this paper we introduce a new method for numerically solving the equations of the hydrodynamic model for
semiconductor devices in two space dimensions. The method combines a standard mixed finite element method,
used to obtain directly an approximation to the electric field, with the so‐called Runge‐Kutta Discontinuous
Galerkin (RKDG) method, originally devised for numerically solving multi‐dimensional hyperbolic systems of
conservation laws, which is applied here to the convective part of the equations. Numerical simulations showing
the performance of the new method are displayed, and the results compared with those obtained by using
Essentially Nonoscillatory (ENO) finite difference schemes. From the perspective of device modeling, these
methods are robust, since they are capable of encompassing broad parameter ranges, including those for which
shock formation is possible. The simulations presented here are for Gallium Arsenide at room temperature, but
we have tested them much more generally with considerable success.
Decomposition of Sequential Behavior UsingInterface Specification and Complementation
Authors: Rath Kamlesh , Choppella Venkatesh , Johnson Steven D.
Published: September 2007

Decomposition of system behavior along functional boundaries into interacting sequential components is a key step in
top‐down system design. In this paper, we present sequential decomposition, a method for factoring sequential components
from a system specification based on interface specifications of the components. The resulting components can be
independently synthesized, or realized using off‐the‐shelf components. We introduce interface specification language (ISL),
based on finite‐state machine semantics, to specify the input/output behavior of synchronous sub‐systems. A component is
factored from a system by embedding an implementation of the complement of its interface into the system description. The
composition of a machine with its complement is shown to be isomorphic to the machine, and the composition of a machine
with an implementation of its component is shown to be a safe interaction. We apply sequential decomposition to a
non‐trivial example, a special‐purpose computer with Scheme programming language primitives as its instructions.
RT Component Sets for High‐Level Design Applications
Authors: Dutt Nikil D. , Jha Pradip K.
Published: September 2007

The system‐level design process typically involves refining a design specification down to
the point where each of the system′s components is described as a block diagram or netlist
of abstract Register‐Transfer (RT) level components. In this paper, we motivate the need for
such a standard RT component set, and describe a library environment that supports automatic
model generation, design reuse, and synthesis with technology‐specific estimators. We
demonstrate the efficacy of the standard RT‐component set approach with experiments performed
on the HLSW92 benchmarks. Our preliminary results indicate only a small overhead
of about 10% in using these standard, generic components. We then describe an automatic
model generation and technology projection scheme that uses fast (on‐line) estimators for
predicting the area and delay of generic RT components tuned to a particular technology
library with an accuracy of 10%. These model generators and estimators have been integrated
with a high‐level synthesis system at U.C. Irvine.
Macro‐Cell Placement for Custom‐Chip Design Using Self‐Organizing Fuzzy Technique
Authors: Chang Ray-I , Hsiao Pei-Yung
Published: September 2007

In this paper, a new optimization technique called SOFT(self-organizing fuzzy technique)
is proposed to solve the macro‐cell placement problem. In SOFT, different criteria are
simultaneously accounted by a novel fuzzy gain function which models expert knowledge
to control the optimization process. The presented procedure is an adaptation of
Kohonen′s self-organization algorithm which is well suited for implementation on
massively parallel architecture for fast computing. The MCNC benchmark examples are
presented to verify the performance and feasibility of SOFT. Comparisons are made
with the Hopfield network, SOAP and TimberWolf MC5.6. Experiments show that the
proposed method yields an average of 17% improvement in total wire length compared
with previous methods. Large size problems with 225 and 1024 arbitrarily‐sized macrocells
are also presented.
Weak Limits of the Quantum Hydrodynamic Model
Authors: Pietra Paola , Pohl Carsten
Published: September 2007

A numerical study of the dispersive limit of the quantum hydrodynamic equations for
semiconductors is presented. The solution may develop high frequency oscillations
when the scaled Planck constant is small. Numerical evidence is given of the fact that in
such cases the solution does not converge to the solution of the formal limit equations.
Lower‐Power and Min‐Crosstalk Channel Routing for Deep‐Submicron Layout Design
Authors: Nam S. H. , Cho J. D. , Wagner D.
Published: September 2007

Consider a set of nets given by horizontal segments S  =  {s1,  s2,  …,  sn} and a set of tracks T  = {t1, t2, …, tk} in a channel, then a track assignment consists in an assignment
of the nets to the tracks such that no two nets assigned to the same track overlap. One
important goal is to find a track assignment with the minimum number of tracks such
that the signal interference between nets assigned to neighboring tracks is minimized.
This problem is called crosstalk minimization. For a given track assignment with k
tracks, crosstalk can be reduced by finding another track assignment for S with k tracks (i.e., by permuting tracks). However, considering all possible permutations requires
exponential time. For general cost function for crosstalk measure, the problem is NPhard.
Several heuristic approaches were previously presented. In this paper, we consider
special instances of the crosstalk‐minimization problem where the cost function depends
only on the length of the segments that runs in parallel and all pairs of segments intersect.
An algorithm solving this problem in O(n log n) time is presented. An extension
applied to the instances with more general function of switching activity and mixed
signal sensitivity to reduce crosstalk and power consumption is also presented.
Hierarchy Restructuring for Hierarchical LVS Comparison
Authors: Kim Wonjong , Shin Hyunchul
Published: September 2007

A new hierarchical layout vs. schematic (LVS) comparison system for layout verification
has been developed. The schematic hierarchy is restructured to remove ambiguities for
consistent hierarchical matching. Then the circuit hierarchy is reconstructed from the
layout netlist by using a modified SubGemini algorithm recursively in bottom‐up fashion.
For efficiency, simple gates are found by using a fast rule‐based pattern matching
algorithm during preprocessing. Experimental results show that our hierarchical netlist
comparison technique is effective and efficient in CPU time and in memory usage,
especially when the circuit is large and hierarchically structured.
Discrete Transparent Boundary Conditions for GeneralSchrödinger‐type Equations
Authors: Ehrhardt Matthias
Published: September 2007

Transparent boundary conditions (TBCs) for general Schrödinger‐type equations on a
bounded domain can be derived explicitly under the assumption that the given potential
V is constant on the exterior of that domain. In 1D these boundary conditions are non‐local
in time (of memory type).

Existing discretizations of these TBCs have accuracy problems and render the overall
Crank–Nicolson finite difference method only conditionally stable. In this paper a
novel discrete TBC is derived directly from the discrete whole‐space problem that yields
an unconditionally stable scheme. Numerical examples illustrate the superiority of the
discrete TBC over other existing consistent discretizations of the differential TBCs.

As an application of these boundary conditions to wave propagation problems in
underwater acoustics results for the so‐called standard and wide angle “parabolic”
equation (SPE, WAPE) models are presented.
An Integrated Approach to Data Path Synthesis for Behavioral‐level Power Optimization
Authors: Park Chaeryung , Kim Taewhan , Liu C. L.
Published: September 2007

This paper presents an integrated approach to data path synthesis which solves three
important design problems: scheduling, allocation, and hardware partitioning with
power minimization as a key design objective. Based on the rules of thumbs introduced
in prior work on synthesis for low power we derive an integer programming formulation
for solving the problems. We then, based on the formulation, develop an efficient
algorithm which performs scheduling, allocation and hardware partitioning simultaneously
so that the effects of them on power consumption are exploited more fully and
effectively. Our experimentation results show that the algorithm is quite effective,
producing designs with significant savings in power consumption.
Salt-Induced Nephropathy in Obese Spontaneously Hypertensive Rats Via Paradoxical Activation of the Mineralocorticoid Receptor
Authors: Nagase Miki , Matsui Hiromitsu , Shibata Shigeru , Gotoda Takanari , Fujita Toshiro
Published: September 2007

Aldosterone is implicated in the pathogenesis of proteinuria and chronic kidney disease. We previously demonstrated the contribution of elevated serum aldosterone in the early nephropathy of SHR/NDmcr-cp (SHR/cp), a rat model of metabolic syndrome. In the present study, we investigated the effect of salt loading on renal damage in SHR/cps and explored the underlying mechanisms. SHR/cps fed a high-sodium diet for 4 weeks developed severe hypertension, massive proteinuria, and advanced renal lesions. High salt also worsened glomerular podocyte impairment. Surprisingly, selective mineralocorticoid receptor (MR) antagonist eplerenone dramatically ameliorated the salt-induced proteinuria and renal injury in SHR/cps. Although salt loading reduced circulating aldosterone, it increased nuclear MR and expression of aldosterone effector kinase Sgk1 in the kidney. Gene expressions of transforming growth factor-β1 and plasminogen activator inhibitor-1 were also enhanced in the kidneys of salt-loaded SHR/cps, and eplerenone completely inhibited these injury markers. To clarify the discrepancy between decreased aldosterone and enhanced MR signaling by salt, we further investigated the role of oxidative stress, a putative key factor mediating salt-induced tissue damage. Interestingly, antioxidant Tempol attenuated the salt-evoked MR upregulation and Sgk1 induction and alleviated proteinuria and renal histological abnormalities, suggesting the involvement of oxidative stress in salt-induced MR activation. MR activation by salt was not attributed to increased serum corticosterone or reduced 11β-hydroxysteroid dehydrogenase type 2 activity. In conclusion, sodium loading exacerbated proteinuria and renal injury in metabolic syndrome rats. Salt reduced circulating aldosterone but caused renal MR activation at least partially via induction of oxidative stress, and eplerenone effectively improved the nephropathy.
Re-Writing the History of Media Art: From Personal Cinema to Artistic Collaboration
Authors: Kluszczynski Ryszard W.
Published: September 2007

The author reinterprets the artistic phenomena that composed historical avant-garde art. His method of interpretation is an intertextual strategy that approaches the historical artifacts through recent phenomena. The first case study is of structural film; its most important attributes appear to be artistic strategies questioning the structural/material integrity, durability and permanence of the film work. The second case study is of the avant-garde strategy of collective work, reinterpreted through the open-source work and interactive art of today. The author identifies three steps in the development of the 20th-century concept of joint creative work: avant-garde general strategies of artistic collaboration; avant-garde film works oriented toward creative collectivism; and collaborative artistic practices that manifest themselves in non-hierarchical strategies of contemporary interactive art.
Leukemia-associated antigen-specific T-cell responses following combined PR1 and WT1 peptide vaccination in patients with myeloid malignancies
Authors: Rezvani Katayoun , Yong Agnes S. M. , Mielke Stephan , Savani Bipin N. , Musse Laura , Superata Jeanine , Jafarpour Behnam , Boss Carol , Barrett A. John
Published: September 2007

We describe the safety and immunogenicity of a combined vaccine of 2 leukemia-associated antigenic peptides, PR1 and WT1. Eight patients with myeloid malignancies received one subcutaneous dose each of PR1 and WT1 vaccines in Montanide adjuvant, with granulocyte-macrophage colony-stimulating factor. Patients were reviewed weekly for 4 weeks to monitor toxicity and immunologic responses. Toxicity was limited to grades 1 to 2. Using peptide/HLA-A*0201 tetramers and intracellular interferon-γ staining, CD8+ T cells against PR1 or WT1 were detected in 8 of 8 patients after a single vaccination. To monitor the kinetics of vaccine-induced CD8+ T-cell responses and disease regression after vaccination, absolute PR1 and WT1+CD8+ T-cell numbers and WT1 expression were studied weekly after vaccination. Responses occurred as early as 1 week after vaccination. After vaccination, the emergence of PR1 or WT1+CD8+ T cells was associated with a decrease in WT1 mRNA expression as a marker of minimal residual disease, suggesting a vaccine-driven antileukemia effect. Conversely, loss of response was associated with reappearance of WT1 transcripts (P < .01). This is the first demonstration that a combined PR1 and WT1 vaccine is immunogenic. These results support further studies of combination immunization strategies in leukemia patients. This study is registered at http://clinicaltrials.gov as NCT00313638.
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Authors: Faith Jeremiah J , Olson Andrew J , Gardner Timothy S , Sachidanandam Ravi
Published: September 2007

Background

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal.

Results

lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales.

Conclusion

lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.